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  • Frontiers Media  (145)
  • 2020-2023  (145)
  • 1
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    Bio-GO-SHIP: the time is right to establish global repeat sections of ocean biology (2022)
    Frontiers Media
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Clayton, S., Alexander, H., Graff, J. R., Poulton, N. J., Thompson, L. R., Benway, H., Boss, E., & Martiny, A. Bio-GO-SHIP: the time is right to establish global repeat sections of ocean biology. Frontiers in Marine Science, 8, (2022): 767443, https://doi.org/10.3389/fmars.2021.767443.
    Description: In this article, we present Bio-GO-SHIP, a new ocean observing program that will incorporate sustained and consistent global biological ocean observations into the Global Ocean Ship-based Hydrographic Investigations Program (GO-SHIP). The goal of Bio-GO-SHIP is to produce systematic and consistent biological observations during global ocean repeat hydrographic surveys, with a particular focus on the planktonic ecosystem. Ocean plankton are an essential component of the earth climate system, form the base of the oceanic food web and thereby play an important role in influencing food security and contributing to the Blue Economy. Despite its importance, ocean biology is largely under-sampled in time and space compared to physical and chemical properties. This lack of information hampers our ability to understand the role of plankton in regulating biogeochemical processes and fueling higher trophic levels, now and in future ocean conditions. Traditionally, many of the methods used to quantify biological and ecosystem essential ocean variables (EOVs), measures that provide valuable information on the ecosystem, have been expensive and labor- and time-intensive, limiting their large-scale deployment. In the last two decades, new technologies have been developed and matured, making it possible to greatly expand our biological ocean observing capacity. These technologies, including cell imaging, bio-optical sensors and 'omic tools, can be combined to provide overlapping measurements of key biological and ecosystem EOVs. New developments in data management and open sharing can facilitate meaningful synthesis and integration with concurrent physical and chemical data. Here we outline how Bio-GO-SHIP leverages these technological advances to greatly expand our knowledge and understanding of the constituents and function of the global ocean plankton ecosystem.
    Description: The Bio-GO-SHIP pilot program was funded under the National Oceanographic Partnership Program as an inter-agency partnership between NOAA and NASA, with the US Integrated Ocean Observing System and NOAA's Global Ocean Monitoring and Observing program (HA, SC, JG, AM, and NP). HA was supported by a WHOI Independent Research and Development award. AM was supported by funding from NSF OCE-1848576 and 1948842 and NASA 80NSSC21K1654. JG was funded by NASA from grants 80NSSC17K0568 and NNX15AAF30G. LT was supported by award NA06OAR4320264 06111039 to the Northern Gulf Institute by NOAA's Office of Oceanic and Atmospheric Research, U.S. Department of Commerce.
    Keywords: Biological oceanography ; Plankton ecosystems ; Ocean observing ; Repeat hydrography ; GO-SHIP program
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  • 2
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    Dark reduction drives evasion of mercury from the ocean (2022)
    Frontiers Media
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lamborg, C. H., Hansel, C. M., Bowman, K. L., Voelker, B. M., Marsico, R. M., Oldham, V. E., Swarr, G. J., Zhang, T., & Ganguli, P. M. Dark reduction drives evasion of mercury from the ocean. Frontiers in Environmental Chemistry, 2, (2021): 659085, https://doi.org/10.3389/fenvc.2021.659085.
    Description: Much of the surface water of the ocean is supersaturated in elemental mercury (Hg0) with respect to the atmosphere, leading to sea-to-air transfer or evasion. This flux is large, and nearly balances inputs from the atmosphere, rivers and hydrothermal vents. While the photochemical production of Hg0 from ionic and methylated mercury is reasonably well-studied and can produce Hg0 at fairly high rates, there is also abundant Hg0 in aphotic waters, indicating that other important formation pathways exist. Here, we present results of gross reduction rate measurements, depth profiles and diel cycling studies to argue that dark reduction of Hg2+ is also capable of sustaining Hg0 concentrations in the open ocean mixed layer. In locations where vertical mixing is deep enough relative to the vertical penetration of UV-B and photosynthetically active radiation (the principal forms of light involved in abiotic and biotic Hg photoreduction), dark reduction will contribute the majority of Hg0 produced in the surface ocean mixed layer. Our measurements and modeling suggest that these conditions are met nearly everywhere except at high latitudes during local summer. Furthermore, the residence time of Hg0 in the mixed layer with respect to evasion is longer than that of redox, a situation that allows dark reduction-oxidation to effectively set the steady-state ratio of Hg0 to Hg2+ in surface waters. The nature of these dark redox reactions in the ocean was not resolved by this study, but our experiments suggest a likely mechanism or mechanisms involving enzymes and/or important redox agents such as reactive oxygen species and manganese (III).
    Description: This work was supported by NSF Grant OCE-1355720 (to CH, CL, and BV).
    Keywords: Mercury ; Evasion ; Elemental ; Dark ; Ocean ; Reactive oxygen species ; Manganese ; Global model
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  • 3
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    The helium and carbon isotope characteristics of the Andean Convergent Margin (2022)
    Frontiers Media
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Barry, P. H., De Moor, J. M., Chiodi, A., Aguilera, F., Hudak, M. R., Bekaert, D. V., Turner, S. J., Curtice, J., Seltzer, A. M., Jessen, G. L., Osses, E., Blamey, J. M., Amenabar, M. J., Selci, M., Cascone, M., Bastianoni, A., Nakagawa, M., Filipovich, R., Bustos, E., Schrenk, M. O. , Buongiorno, J., Ramírez, C. J., Rogers, T. J., Lloyd, K. G. & Giovannelli, D. The helium and carbon isotope characteristics of the Andean Convergent Margin. Frontiers in Earth Science, 10, (2022): 897267, https://doi.org/10.3389/feart.2022.897267.
    Description: Subduction zones represent the interface between Earth’s interior (crust and mantle) and exterior (atmosphere and oceans), where carbon and other volatile elements are actively cycled between Earth reservoirs by plate tectonics. Helium is a sensitive tracer of volatile sources and can be used to deconvolute mantle and crustal sources in arcs; however it is not thought to be recycled into the mantle by subduction processes. In contrast, carbon is readily recycled, mostly in the form of carbon-rich sediments, and can thus be used to understand volatile delivery via subduction. Further, carbon is chemically-reactive and isotope fractionation can be used to determine the main processes controlling volatile movements within arc systems. Here, we report helium isotope and abundance data for 42 deeply-sourced fluid and gas samples from the Central Volcanic Zone (CVZ) and Southern Volcanic Zone (SVZ) of the Andean Convergent Margin (ACM). Data are used to assess the influence of subduction parameters (e.g., crustal thickness, subduction inputs, and convergence rate) on the composition of volatiles in surface volcanic fluid and gas emissions. He isotopes from the CVZ backarc range from 0.1 to 2.6 RA (n = 23), with the highest values in the Puna and the lowest in the Sub-Andean foreland fold-and-thrust belt. Atmosphere-corrected He isotopes from the SVZ range from 0.7 to 5.0 RA (n = 19). Taken together, these data reveal a clear southeastward increase in 3He/4He, with the highest values (in the SVZ) falling below the nominal range associated with pure upper mantle helium (8 ± 1 RA), approaching the mean He isotope value for arc gases of (5.4 ± 1.9 RA). Notably, the lowest values are found in the CVZ, suggesting more significant crustal inputs (i.e., assimilation of 4He) to the helium budget. The crustal thickness in the CVZ (up to 70 km) is significantly larger than in the SVZ, where it is just ∼40 km. We suggest that crustal thickness exerts a primary control on the extent of fluid-crust interaction, as helium and other volatiles rise through the upper plate in the ACM. We also report carbon isotopes from (n = 11) sites in the CVZ, where δ13C varies between −15.3‰ and −1.2‰ [vs. Vienna Pee Dee Belemnite (VPDB)] and CO2/3He values that vary by over two orders of magnitude (6.9 × 108–1.7 × 1011). In the SVZ, carbon isotope ratios are also reported from (n = 13) sites and vary between −17.2‰ and −4.1‰. CO2/3He values vary by over four orders of magnitude (4.7 × 107–1.7 × 1012). Low δ13C and CO2/3He values are consistent with CO2 removal (e.g., calcite precipitation and gas dissolution) in shallow hydrothermal systems. Carbon isotope fractionation modeling suggests that calcite precipitation occurs at temperatures coincident with the upper temperature limit for life (122°C), suggesting that biology may play a role in C-He systematics of arc-related volcanic fluid and gas emissions.
    Description: This work was principally supported by the NSF-FRES award 2121637 to PB, KL, and JM. Field work was also supported by award G-2016-7206 from the Alfred P. Sloan Foundation and the Deep Carbon Observatory to PB, KL, DG, and JM. Additional support came from The National Fund for Scientific and Technological Development of Chile (FONDECYT) Grant 11191138 (The National Research and Development Agency of Chile, ANID Chile), and COPAS COASTAL ANID FB210021 to GJ. DG was partially supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program Grant Agreement No. 948972—COEVOLVE—ERC-2020-STG.
    Keywords: Helium ; Carbon ; SVZ ; CVZ ; Andes (Argentina and Chile)
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  • 4
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    Interactions between a marine heatwave and tropical cyclone Amphan in the Bay of Bengal in 2020 (2022)
    Frontiers Media
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Rathore, S., Goyal, R., Jangir, B., Ummenhofer, C., Feng, M., & Mishra, M. Interactions between a marine heatwave and tropical cyclone Amphan in the Bay of Bengal in 2020. Frontiers in Climate, 4, (2022): 861477, https://doi.org/10.3389/fclim.2022.861477.
    Description: Interactions are diagnosed between a marine heatwave (MHW) event and tropical super cyclone Amphan in the Bay of Bengal. In May 2020, an MHW developed in the Bay of Bengal driven by coupled ocean-atmosphere processes which included shoaling of the mixed layer depth due to reduced wind speed, increased net surface shortwave radiation flux into the ocean, increased upper ocean stratification, and increased sub-surface warming. Ocean temperature, rather than salinity, dominated the stratification that contributed to the MHW development and the subsurface ocean warming that also increased tropical cyclone heat potential. The presence of this strong MHW with sea surface temperature anomalies 〉2.5°C in the western Bay of Bengal coincided with the cyclone track and facilitated the rapid intensification of tropical cyclone Amphan to a super cyclone in just 24 h. This rapid intensification of a short-lived tropical cyclone, with a lifespan of 5 days over the ocean, is unprecedented in the Bay of Bengal during the pre-monsoon period (March-May). As the cyclone approached landfall in northern India, the wind-induced mixing deepened the mixed layer, cooled the ocean's surface, and reduced sub-surface warming in the bay, resulting in the demise of the MHW. This study provides new perspectives on the interactions between MHWs and tropical cyclones that could aid in improving the current understanding of compound extreme events that have severe socio-economic consequences in affected countries.
    Description: CU acknowledges support from the James E. and Barbara V. Moltz Fellowship for Climate-Related Research and the Independent Research & Development Program at WHOI. MF was supported by the Centre for Southern Hemisphere Oceans Research (CSHOR), which is a joint initiative between the Qingdao National Laboratory for Marine Science and Technology (QNLM), CSIRO, University of New South Wales, and the University of Tasmania.
    Keywords: Compound extreme events ; Marine heatwave ; Tropical cyclone ; Amphan ; Fani ; Super cyclone ; Rapid intensification ; Extremely severe cyclone
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  • 5
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    Marine Heatwaves and their depth structures on the Northeast U.S. continental shelf (2022)
    Frontiers Media
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Großelindemann, H., Ryan, S., Ummenhofer, C., Martin, T., & Biastoch, A. Marine Heatwaves and their depth structures on the Northeast U.S. continental shelf. Frontiers in Climate, 4, (2022): 857937, https://doi.org/10.3389/fclim.2022.857937.
    Description: Marine Heatwaves (MHWs) are ocean extreme events, characterized by anomalously high temperatures, which can have significant ecological impacts. The Northeast U.S. continental shelf is of great economical importance as it is home to a highly productive ecosystem. Local warming rates exceed the global average and the region experienced multiple MHWs in the last decade with severe consequences for regional fisheries. Due to the lack of subsurface observations, the depth-extent of MHWs is not well-known, which hampers the assessment of impacts on pelagic and benthic ecosystems. This study utilizes a global ocean circulation model with a high-resolution (1/20°) nest in the Atlantic to investigate the depth structure of MHWs and associated drivers on the Northeast U.S. continental shelf. It is shown that MHWs exhibit varying spatial extents, with some only occurring at depth. The highest intensities are found around 100 m depth with temperatures exceeding the climatological mean by up to 7°C, while surface intensities are typically smaller (around 3°C). Distinct vertical structures are associated with different spatial MHW patterns and drivers. Investigation of the co-variability of temperature and salinity reveals that over 80% of MHWs at depth (〉50 m) coincide with extreme salinity anomalies. Two case studies provide insight into opposing MHW patterns at the surface and at depth, being forced by anomalous air-sea heat fluxes and Gulf Stream warm core ring interaction, respectively. The results highlight the importance of local ocean dynamics and the need to realistically represent them in climate models.
    Description: This work was supported by a DAAD RISE Worldwide fellowship (to HG), a Feodor-Lynen Fellowship by the Alexander von Humboldt Foundation and the WHOI Postdoctoral Scholar program (to SR), and the James E. and Barbara V. Moltz Fellowship for Climate-Related Research (to CU). Franziska Schwarzkopf performed the integration of the OGCM simulations, which was performed on the Earth System Modeling Project (ESM) partition of the supercomputer JUWELS at the Jülich Supercomputing Centre (JSC).
    Keywords: Marine heatwaves ; Northeast U.S. continental shelf ; Ecosystem impacts ; Subsurface marine heatwaves ; Gulf Stream warm core rings
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  • 6
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    Ancient metabolisms of a thermophilic subseafloor bacterium (2022)
    Frontiers Media
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Smith, A. R., Mueller, R., Fisk, M. R., & Colwell, F. S. Ancient metabolisms of a thermophilic subseafloor bacterium. Frontiers in Microbiology, 12, (2021): 764631, https://doi.org/10.3389/fmicb.2021.764631.
    Description: The ancient origins of metabolism may be rooted deep in oceanic crust, and these early metabolisms may have persisted in the habitable thermal anoxic aquifer where conditions remain similar to those when they first appeared. The Wood–Ljungdahl pathway for acetogenesis is a key early biosynthetic pathway with the potential to influence ocean chemistry and productivity, but its contemporary role in oceanic crust is not well established. Here, we describe the genome of a novel acetogen from a thermal suboceanic aquifer olivine biofilm in the basaltic crust of the Juan de Fuca Ridge (JdFR) whose genome suggests it may utilize an ancient chemosynthetic lifestyle. This organism encodes the genes for the complete canonical Wood–Ljungdahl pathway, but is potentially unable to use sulfate and certain organic carbon sources such as lipids and carbohydrates to supplement its energy requirements, unlike other known acetogens. Instead, this organism may use peptides and amino acids for energy or as organic carbon sources. Additionally, genes involved in surface adhesion, the import of metallic cations found in Fe-bearing minerals, and use of molecular hydrogen, a product of serpentinization reactions between water and olivine, are prevalent within the genome. These adaptations are likely a reflection of local environmental micro-niches, where cells are adapted to life in biofilms using ancient chemosynthetic metabolisms dependent on H2 and iron minerals. Since this organism is phylogenetically distinct from a related acetogenic group of Clostridiales, we propose it as a new species, Candidatus Acetocimmeria pyornia.
    Description: Metagenome sequencing was made possible by the Deep Carbon Observatory Census of Deep Life supported by the Alfred P. Sloan Foundation and was performed at the Marine Biological Laboratory (Woods Hole, MA, United States). This work was funded by NASA grant NNX08AO22G and a graduate fellowship from the NSF Center for Dark Energy Biosphere Investigations. The flow cells were funded under J0972A from the U.S. Science Support Program of Joint Oceanographic Institutions.
    Keywords: Metabolism ; Carbon fixation ; Acetogenesis ; Bacteria ; Seafloor ; Hydrogen ; Amino acid ; Clostridia
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  • 7
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    Pathways to justice, equity, diversity, and inclusion in marine science and conservation (2022)
    Frontiers Media
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Johri, S., Carnevale, M., Porter, L., Zivian, A., Kourantidou, M., Meyer, E. L., Seevers, J., & Skubel, R. A. Pathways to justice, equity, diversity, and inclusion in marine science and conservation. Frontiers in Marine Science, 8, (2021): 696180, https://doi.org/10.3389/fmars.2021.696180.
    Description: Marine conservation sciences have traditionally been, and remain, non-diverse work environments with many barriers to justice, equity, diversity, and inclusion (JEDI). These barriers disproportionately affect entry of early career scientists and practitioners and limit the success of marine conservation professionals from under-represented, marginalized, and overburdened groups. These groups specifically include women, LGBTQ+, Black, Indigenous, and people of color (BIPOC). However, the issues also arise from the global North/South and East/West divide with under-representation of scientists from the South and East in the global marine conservation and science arena. Persisting inequities in conservation, along with a lack of inclusiveness and diversity, also limit opportunities for innovation, cross-cultural knowledge exchange, and effective implementation of conservation and management policies. As part of its mandate to increase diversity and promote inclusion of underrepresented groups, the Diversity and Inclusion committee of the Society for Conservation Biology-Marine Section (SCB Marine) organized a JEDI focus group at the Sixth International Marine Conservation Congress (IMCC6) which was held virtually. The focus group included a portion of the global cohort of IMCC6 attendees who identified issues affecting JEDI in marine conservation and explored pathways to address those issues. Therefore, the barriers and pathways identified here focus on issues pertinent to participants’ global regions and experiences. Several barriers to just, equitable, diverse, and inclusive conservation science and practice were identified. Examples included limited participation of under-represented minorities (URM) in research networks, editorial biases against URM, limited professional development and engagement opportunities for URM and non-English speakers, barriers to inclusion of women, LGBTQ+, and sensory impaired individuals, and financial barriers to inclusion of URM in all aspects of marine conservation and research. In the current policy brief, we explore these barriers, assess how they limit progress in marine conservation research and practice, and seek to identify initiatives for improvements. We expect the initiatives discussed here to advances practices rooted in principles of JEDI, within SCB Marine and, the broader conservation community. The recommendations and perspectives herein broadly apply to conservation science and practice, and are critical to effective and sustainable conservation and management outcomes.
    Description: The Society for Conservation – Marine Section provided partial funding to support publication costs of this manuscript.
    Keywords: Equity ; Diversity ; Inclusion ; Conferences ; Peer-review ; Bias ; Marine ; Conservation
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  • 8
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    Unique habitat for benthic foraminifera in subtidal blue holes on carbonate platforms (2022)
    Frontiers Media
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Little, S. N., van Hengstum, P. J., Beddows, P. A., Donnelly, J. P., Winkler, T. S., & Albury, N. A. . Unique habitat for benthic foraminifera in subtidal blue holes on carbonate platforms. Frontiers in Ecology and Evolution, 9, (2021): 794728, https://doi.org/10.3389/fevo.2021.794728.
    Description: Dissolution of carbonate platforms, like The Bahamas, throughout Quaternary sea-level oscillations have created mature karst landscapes that can include sinkholes and off-shore blue holes. These karst features are flooded by saline oceanic waters and meteoric-influenced groundwaters, which creates unique groundwater environments and ecosystems. Little is known about the modern benthic meiofauna, like foraminifera, in these environments or how internal hydrographic characteristics of salinity, dissolved oxygen, or pH may influence benthic habitat viability. Here we compare the total benthic foraminiferal distributions in sediment-water interface samples collected from 〈2 m water depth on the carbonate tidal flats, and the two subtidal blue holes Freshwater River Blue Hole and Meredith’s Blue Hole, on the leeward margin of Great Abaco Island, The Bahamas. All samples are dominated by miliolid foraminifera (i.e., Quinqueloculina and Triloculina), yet notable differences emerge in the secondary taxa between these two environments that allows identification of two assemblages: a Carbonate Tidal Flats Assemblage (CTFA) vs. a Blue Hole Assemblage (BHA). The CTFA includes abundant common shallow-water lagoon foraminifera (e.g., Peneroplis, Rosalina, Rotorbis), while the BHA has higher proportions of foraminifera that are known to tolerate stressful environmental conditions of brackish and dysoxic waters elsewhere (e.g., Pseudoeponides, Cribroelphidium, Ammonia). We also observe how the hydrographic differences between subtidal blue holes can promote different benthic habitats for foraminifera, and this is observed through differences in both agglutinated and hyaline fauna. The unique hydrographic conditions in subtidal blue holes make them great laboratories for assessing the response of benthic foraminiferal communities to extreme environmental conditions (e.g., low pH, dysoxia).
    Description: The financial support for this work was provided by grants from the National Science Foundation to PvH (EAR-1833117) and JD (EAR-1702946).
    Keywords: The Bahamas ; Groundwater ; Benthic foraminifera ; Blue holes ; Karst landscapes ; Environmental stress
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  • 9
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    A code of conduct is imperative for ocean carbon dioxide removal research (2022)
    Frontiers Media
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Loomis, R., Cooley, S. R., Collins, J. R., Engler, S., & Suatoni, L. A code of conduct is imperative for ocean carbon dioxide removal research. Frontiers in Marine Science, 9, (2022): 872800, https://doi.org/10.3389/fmars.2022.872800.
    Description: As the impacts of rising temperatures mount and the global transition to clean energy advances only gradually, scientists and policymakers are looking towards carbon dioxide removal (CDR) methods to prevent the worst impacts of climate change. Attention has increasingly focused on ocean CDR techniques, which enhance or restore marine systems to sequester carbon. Ocean CDR research presents the risk of uncertain impacts to human and environmental welfare, yet there are no domestic regulations aimed at ensuring the safety and efficacy of this research. A code of conduct that establishes principles of responsible research, fairness, and equity is needed in this field. This article presents fifteen key components of an ocean CDR research code of conduct.
    Description: JC acknowledges funding support from Bezos Earth Fund.
    Keywords: Carbon dioxide removal ; Ocean ; Policy ; Research governance ; Geoengineering
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  • 10
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    How warm Gulf Stream water sustains a cold underwater waterfall (2022)
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    Publication Date: 2022-11-10
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Semper, S., Glessmer, M., Våge, K., & Pickart, R. How warm Gulf Stream water sustains a cold underwater waterfall. Frontiers for Young Minds, 10, (2022): 765740, https://doi.org/10.3389/frym.2022.765740.
    Description: The most famous ocean current, the Gulf Stream, is part of a large system of currents that brings warm water from Florida to Europe. It is a main reason for northwestern Europe’s mild climate. What happens to the warm water that flows northward, since it cannot just pile up? It turns out that the characteristics of the water change: in winter, the ocean warms the cold air above it, and the water becomes colder. Cold seawater, which is heavier than warm seawater, sinks down to greater depths. But what happens to the cold water that disappears from the surface? While on a research ship, we discovered a new ocean current that solves this riddle. The current brings the cold water to an underwater mountain ridge. The water spills over the ridge as an underwater waterfall before it continues its journey, deep in the ocean, back toward the equator.
    Description: Support for this work was provided by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 101022251 (SS), the Trond Mohn Foundation Grant BFS2016REK01 (SS and KV), and the U.S. National Science Foundation Grants OCE-1558742 and OCE-1259618 (RP).
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  • 11
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    Fractionation of 226Ra and Ba in the upper North Pacific Ocean (2022)
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    Publication Date: 2022-11-10
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in van Beek, P., François, R., Honda, M., Charette, M., Reyss, J.-L., Ganeshram, R., Monnin, C., & Honjo, S. Fractionation of 226Ra and Ba in the upper North Pacific Ocean. Frontiers in Marine Science, 9, (2022): 859117, https://doi.org/10.3389/fmars.2022.859117.
    Description: Investigations conducted during the GEOSECS program concluded that radium-226 (T1/2 = 1602 y) and barium are tightly correlated in waters above 2500 m in the Atlantic, Pacific and Antarctic Oceans, with a fairly uniform 226Ra/Ba ratio of 2.3 ± 0.2 dpm µmol-1 (4.6 nmol 226Ra/mol Ba). Here, we report new 226Ra and Ba data obtained at three different stations in the Pacific Ocean: stations K1 and K3 in the North-West Pacific and station old Hale Aloha, off Hawaii Island. The relationship between 226Ra and Ba found at these stations is broadly consistent with that reported during the GEOSECS program. At the three investigated stations, however, we find that the 226Ra/Ba ratios are significantly lower in the upper 500 m of the water column than at greater depths, a pattern that was overlooked during the GEOSECS program, either because of the precision of the measurements or because of the relatively low sampling resolution in the upper 500 m. Although not always apparent in individual GEOSECS profiles, this trend was noted before from the non-zero intercept of the linear regression when plotting the global data set of Ba versus 226Ra seawater concentration and was attributed, at least in part, to the predominance of surface input from rivers for Ba versus bottom input from sediments for 226Ra. Similarly, low 226Ra/Ba ratios in the upper 500 m have been reported in other oceanic basins (e.g. Atlantic Ocean). Parallel to the low 226Ra/Ba ratios in seawater, higher 226Ra/Ba ratios were found in suspended particles collected in the upper 500 m. This suggests that fractionation between the two elements may contribute to the lower 226Ra/Ba ratios found in the upper 500 m, with 226Ra being preferentially removed from surface water, possibly as a result of mass fractionation during celestite formation by acantharians and/or barite precipitation, since both chemical elements have similar ionic radius and the same configuration of valence electrons. This finding has implications for dating of marine carbonates by 226Ra, which requires a constant initial 226Ra/Ba ratio incorporated in the shells and for using 226Ra as an abyssal circulation and mixing tracer.
    Description: This work was supported by a Lavoisier fellowship attributed by the French Ministry of Foreign Affairs to PB in year 2002 and by the Woods Hole Oceanographic Institution (WHOI). This work was completed at the University of Edinburgh in 2003, while PB was a postdoctoral fellow there, with a Marie Curie fellowship from the European Union. The European Union is thus also thanked. MC acknowledges support from the National Science Foundation, Chemical Oceanography program.
    Keywords: Radium ; Barium ; Seawater ; Ratio ; Fractionation ; Dating ; Ocean circulation ; Suspended particles
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  • 12
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    Ammonium and sulfate assimilation is widespread in benthic foraminifera (2022)
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    Publication Date: 2022-11-15
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in LeKieffre, C., Jauffrais, T., Bernhard, J., Filipsson, H., Schmidt, C., Roberge, H., Maire, O., Panieri, G., Geslin, E., & Meibom, A. Ammonium and sulfate assimilation is widespread in benthic foraminifera. Frontiers in Marine Science, 9, (2022): 861945, https://doi.org/10.3389/fmars.2022.861945.
    Description: Nitrogen and sulfur are key elements in the biogeochemical cycles of marine ecosystems to which benthic foraminifera contribute significantly. Yet, cell-specific assimilation of ammonium, nitrate and sulfate by these protists is poorly characterized and understood across their wide range of species-specific trophic strategies. For example, detailed knowledge about ammonium and sulfate assimilation pathways is lacking and although some benthic foraminifera are known to maintain intracellular pools of nitrate and/or to denitrify, the potential use of nitrate-derived nitrogen for anabolic processes has not been systematically studied. In the present study, NanoSIMS isotopic imaging correlated with transmission electron microscopy was used to trace the incorporation of isotopically labeled inorganic nitrogen (ammonium or nitrate) and sulfate into the biomass of twelve benthic foraminiferal species from different marine environments. On timescales of twenty hours, no detectable 15N-enrichments from nitrate assimilation were observed in species known to perform denitrification, indicating that, while denitrifying foraminifera store intra-cellular nitrate, they do not use nitrate-derived nitrogen to build their biomass. Assimilation of both ammonium and sulfate, with corresponding 15N and 34S-enrichments, were observed in all species investigated (with some individual exceptions for sulfate). Assimilation of ammonium and sulfate thus can be considered widespread among benthic foraminifera. These metabolic capacities may help to underpin the ability of benthic foraminifera to colonize highly diverse marine habitats.
    Description: This work was supported by the Swiss National Science Foundation (grant no. 200021_149333), and a postdoctoral fellowship allowed to CL by the University Loire-Bretagne. SBB sampling was funded by US National Science Foundation grant BIO IOS 1557430 to JMB, who also acknowledges NASA grant #80NSSC21K0478 for partial support. HF acknowledges funding from the Swedish Research Council VR (grant number 2017-04190). Svalbard sampling was supported by the Research Council of Norway through CAGE (Center for Excellence in Arctic Gas Hydrate Environment and Climate, project number 223259) and NORCRUST (project number 255150) to GP and the fellowship MOPGA (Make Our Planet Great Again) by CAMPUS France to CS.
    Keywords: Marine protists ; Coastal environments ; Biogeochemical cycles ; NanoSIMS ; Nitrogen ; Sulfur
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    Recommendations for plankton measurements on OceanSITES moorings with relevance to other observing sites (2022)
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    Publication Date: 2022-12-06
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Boss, E., Waite, A., Karstensen, J., Trull, T., Muller-Karger, F., Sosik, H., Uitz, J., Acinas, S., Fennel, K., Berman-Frank, I., Thomalla, S., Yamazaki, H., Batten, S., Gregori, G., Richardson, A., & Wanninkhof, R. Recommendations for plankton measurements on OceanSITES moorings with relevance to other observing sites. Frontiers in Marine Science, 9, (2022): 929436, https://doi.org/10.3389/fmars.2022.929436.
    Description: Measuring plankton and associated variables as part of ocean time-series stations has the potential to revolutionize our understanding of ocean biology and ecology and their ties to ocean biogeochemistry. It will open temporal scales (e.g., resolving diel cycles) not typically sampled as a function of depth. In this review we motivate the addition of biological measurements to time-series sites by detailing science questions they could help address, reviewing existing technology that could be deployed, and providing examples of time-series sites already deploying some of those technologies. We consider here the opportunities that exist through global coordination within the OceanSITES network for long-term (climate) time series station in the open ocean. Especially with respect to data management, global solutions are needed as these are critical to maximize the utility of such data. We conclude by providing recommendations for an implementation plan.
    Description: This work was partially supported from funding to SCOR WG 154 (P-OBS) provided by national committees of the Scientific Committee on Oceanic Research (SCOR) and from a grant to SCOR from the U.S. National Science Foundation (OCE-1840868). FM-K acknowledges the support provided for participation by the Marine Biodiversity Observation Network (MBON) sponsored by NASA, NOAA, ONR, BOEM. HS acknowledges support from the Simons Foundation.
    Keywords: Plankton ; Ocean ; Measurements ; Sensors ; OceanSITES ; Ocean biology
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  • 14
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    Microbial ecosystem responses to alkalinity enhancement in the North Atlantic Subtropical Gyre (2022)
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    Publication Date: 2022-12-22
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Subhas, A., Marx, L., Reynolds, S., Flohr, A., Mawji, E., Brown, P., & Cael, B. Microbial ecosystem responses to alkalinity enhancement in the North Atlantic Subtropical Gyre. Frontiers in Climate, 4, (2022): 784997, https://doi.org/10.3389./fclim.2022.784997
    Description: In addition to reducing carbon dioxide (CO2) emissions, actively removing CO2 from the atmosphere is widely considered necessary to keep global warming well below 2°C. Ocean Alkalinity Enhancement (OAE) describes a suite of such CO2 removal processes that all involve enhancing the buffering capacity of seawater. In theory, OAE both stores carbon and offsets ocean acidification. In practice, the response of the marine biogeochemical system to OAE must be demonstrably negligible, or at least manageable, before it can be deployed at scale. We tested the OAE response of two natural seawater mixed layer microbial communities in the North Atlantic Subtropical Gyre, one at the Western gyre boundary, and one in the middle of the gyre. We conducted 4-day microcosm incubation experiments at sea, spiked with three increasing amounts of alkaline sodium salts and a 13C-bicarbonate tracer at constant pCO2. We then measured a suite of dissolved and particulate parameters to constrain the chemical and biological response to these additions. Microbial communities demonstrated occasionally measurable, but mostly negligible, responses to alkalinity enhancement. Neither site showed a significant increase in biologically produced CaCO3, even at extreme alkalinity loadings of +2,000 μmol kg−1. At the gyre boundary, alkalinity enhancement did not significantly impact net primary production rates. In contrast, net primary production in the central gyre decreased by ~30% in response to alkalinity enhancement. The central gyre incubations demonstrated a shift toward smaller particle size classes, suggesting that OAE may impact community composition and/or aggregation/disaggregation processes. In terms of chemical effects, we identify equilibration of seawater pCO2, inorganic CaCO3 precipitation, and immediate effects during mixing of alkaline solutions with seawater, as important considerations for developing experimental OAE methodologies, and for practical OAE deployment. These initial results underscore the importance of performing more studies of OAE in diverse marine environments, and the need to investigate the coupling between OAE, inorganic processes, and microbial community composition.
    Description: AS was supported through WHOI internal and Assistant Scientist Startup funding. LM and SR were supported by the University of Portsmouth Ph.D. scheme and the UK NERC National Capability programme CLASS (Climate Linked Atlantic Sector Science) ECR Fellowship. BC, AF, EM, and PB were supported by the UK NERC National Capability programme CLASS, grant number NE/R015953/1.
    Keywords: Climate—change ; Ocean alkalinity enhancement ; Biogeochemistry ; North Atlantic ; Carbon flux
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  • 15
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    The microbiological drivers of temporally dynamic Dimethylsulfoniopropionate cycling processes in Australian coastal shelf waters (2022)
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    Publication Date: 2022-10-31
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in O’Brien, J., McParland, E. L., Bramucci, A. R., Ostrowski, M., Siboni, N., Ingleton, T., Brown, M. V., Levine, N. M., Laverock, B., Petrou, K., & Seymour, J. The microbiological drivers of temporally dynamic Dimethylsulfoniopropionate cycling processes in Australian coastal shelf waters. Frontiers in Microbiology, 13, (2022): 894026, https://doi.org/10.3389/fmicb.2022.894026.
    Description: The organic sulfur compounds dimethylsulfoniopropionate (DMSP) and dimethyl sulfoxide (DMSO) play major roles in the marine microbial food web and have substantial climatic importance as sources and sinks of dimethyl sulfide (DMS). Seasonal shifts in the abundance and diversity of the phytoplankton and bacteria that cycle DMSP are likely to impact marine DMS (O) (P) concentrations, but the dynamic nature of these microbial interactions is still poorly resolved. Here, we examined the relationships between microbial community dynamics with DMS (O) (P) concentrations during a 2-year oceanographic time series conducted on the east Australian coast. Heterogenous temporal patterns were apparent in chlorophyll a (chl a) and DMSP concentrations, but the relationship between these parameters varied over time, suggesting the phytoplankton and bacterial community composition were affecting the net DMSP concentrations through differential DMSP production and degradation. Significant increases in DMSP were regularly measured in spring blooms dominated by predicted high DMSP-producing lineages of phytoplankton (Heterocapsa, Prorocentrum, Alexandrium, and Micromonas), while spring blooms that were dominated by predicted low DMSP-producing phytoplankton (Thalassiosira) demonstrated negligible increases in DMSP concentrations. During elevated DMSP concentrations, a significant increase in the relative abundance of the key copiotrophic bacterial lineage Rhodobacterales was accompanied by a three-fold increase in the gene, encoding the first step of DMSP demethylation (dmdA). Significant temporal shifts in DMS concentrations were measured and were significantly correlated with both fractions (0.2–2 μm and 〉2 μm) of microbial DMSP lyase activity. Seasonal increases of the bacterial DMSP biosynthesis gene (dsyB) and the bacterial DMS oxidation gene (tmm) occurred during the spring-summer and coincided with peaks in DMSP and DMSO concentration, respectively. These findings, along with significant positive relationships between dsyB gene abundance and DMSP, and tmm gene abundance with DMSO, reinforce the significant role planktonic bacteria play in producing DMSP and DMSO in ocean surface waters. Our results highlight the highly dynamic nature and myriad of microbial interactions that govern sulfur cycling in coastal shelf waters and further underpin the importance of microbial ecology in mediating important marine biogeochemical processes.
    Description: This research was supported by the Australian Research Council Grants FT130100218 and DP180100838 awarded to JS and DP140101045 awarded to JS and KP, as well as an Australian Government Research Training Program Scholarship awarded to JO’B.
    Keywords: DMSP ; DMS ; DLA ; Phytoplankton ; Bacteria ; qPCR ; 16S rRNA gene ; 18S rRNA gene
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  • 16
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    Landscape genomics provides evidence of ecotypic adaptation and a barrier to gene flow at treeline for the arctic foundation species Eriophorum vaginatum0 (2022)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Stunz, E., Fetcher, N., Lavretsky, P., Mohl, J., Tang, J., & Moody, M. Landscape genomics provides evidence of ecotypic adaptation and a barrier to gene flow at treeline for the arctic foundation species Eriophorum vaginatum. Frontiers in Plant Science, 13, (2022): 860439, https://doi.org/10.3389/fpls.2022.860439.
    Description: Global climate change has resulted in geographic range shifts of flora and fauna at a global scale. Extreme environments, like the Arctic, are seeing some of the most pronounced changes. This region covers 14% of the Earth’s land area, and while many arctic species are widespread, understanding ecotypic variation at the genomic level will be important for elucidating how range shifts will affect ecological processes. Tussock cottongrass (Eriophorum vaginatum L.) is a foundation species of the moist acidic tundra, whose potential decline due to competition from shrubs may affect ecosystem stability in the Arctic. We used double-digest Restriction Site-Associated DNA sequencing to identify genomic variation in 273 individuals of E. vaginatum from 17 sites along a latitudinal gradient in north central Alaska. These sites have been part of 30 + years of ecological research and are inclusive of a region that was part of the Beringian refugium. The data analyses included genomic population structure, demographic models, and genotype by environment association. Genome-wide SNP investigation revealed environmentally associated variation and population structure across the sampled range of E. vaginatum, including a genetic break between populations north and south of treeline. This structure is likely the result of subrefugial isolation, contemporary isolation by resistance, and adaptation. Forty-five candidate loci were identified with genotype-environment association (GEA) analyses, with most identified genes related to abiotic stress. Our results support a hypothesis of limited gene flow based on spatial and environmental factors for E. vaginatum, which in combination with life history traits could limit range expansion of southern ecotypes northward as the tundra warms. This has implications for lower competitive attributes of northern plants of this foundation species likely resulting in changes in ecosystem productivity.
    Description: This research was made possible by funding provided by NSF/PLR-1417645 to MM. The Botanical Society of America Graduate Student Research Award and the Dodson Research Grant from the Graduate School of the University of Texas at El Paso provided assistance to ES. The grant 5U54MD007592 from the National Institute on Minority Health and Health Disparities (NIMHD), a component of the National Institutes of Health (NIH) provided bioinformatics resources and support of JM.
    Keywords: Arctic ; Climate change ; Eriophorum vaginatum ; Landscape genomics ; Environmental niche modeling ; Genotype-environment association analyses ; Refugia
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    The lesser Pacific Striped Octopus, Octopus chierchiae: an emerging laboratory model (2022)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Grearson, A. G., Dugan, A., Sakmar, T., Sivitilli, D. M., Gire, D. H., Caldwell, R. L., Niell, C. M., Doelen, G., Wang, Z. Y., & Grasse, B. The lesser Pacific Striped Octopus, Octopus chierchiae: an emerging laboratory model. Frontiers in Marine Science, 8, (2021): 753483, https://doi.org/10.3389/fmars.2021.753483.
    Description: Cephalopods have the potential to become useful experimental models in various fields of science, particularly in neuroscience, physiology, and behavior. Their complex nervous systems, intricate color- and texture-changing body patterns, and problem-solving abilities have attracted the attention of the biological research community, while the high growth rates and short life cycles of some species render them suitable for laboratory culture. Octopus chierchiae is a small octopus native to the central Pacific coast of North America whose predictable reproduction, short time to maturity, small adult size, and ability to lay multiple egg clutches (iteroparity) make this species ideally suited to laboratory culture. Here we describe novel methods for multigenerational culture of O. chierchiae, with emphasis on enclosure designs, feeding regimes, and breeding management. O. chierchiae bred in the laboratory grow from a 3.5 mm mantle length at hatching to an adult mantle length of approximately 20–30 mm in 250–300 days, with 15 and 14% survivorship to over 400 days of age in first and second generations, respectively. O. chierchiae sexually matures at around 6 months of age and, unlike most octopus species, can lay multiple clutches of large, direct-developing eggs every ∼30–90 days. Based on these results, we propose that O. chierchiae possesses both the practical and biological features needed for a model octopus that can be cultured repeatedly to address a wide range of biological questions.
    Description: The cephalopod program at the Marine Biological Laboratory (MBL) was supported by NSF 1827509 and NSF 1723141 grants. CN received funding from HFSP RGP0042. DG and DS received funding and research support from the University of Washington Friday Harbor Laboratories. ZYW was supported by funds from the Whitman Center at the MBL.
    Keywords: Iteroparity ; Cephalopod ; Model organism ; Aquaculture ; Reproduction – mollusk ; Developmental biology ; Neurobiology
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    How much marsh restoration is enough to deliver wave attenuation coastal protection benefits? (2022)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Castagno, K., Ganju, N., Beck, M., Bowden, A., & Scyphers, S. How much marsh restoration is enough to deliver wave attenuation coastal protection benefits? Frontiers in Marine Science, 8, (2022): 756670, https://doi.org/10.3389/fmars.2021.756670.
    Description: As coastal communities grow more vulnerable to sea-level rise and increased storminess, communities have turned to nature-based solutions to bolster coastal resilience and protection. Marshes have significant wave attenuation properties and can play an important role in coastal protection for many communities. Many restoration projects seek to maximize this ecosystem service but how much marsh restoration is enough to deliver measurable coastal protection benefits is still unknown. This question is critical to guiding assessments of cost effectiveness and for funding, implementation, and optimizing of marsh restoration for risk reduction projects. This study uses SWAN model simulations to determine empirical relationships between wave attenuation and marsh vegetation. The model runs consider several different common marsh morphologies (including systems with channels, ponds, and fringing mudflats), vegetation placement, and simulated storm intensity. Up to a 95% reduction in wave energy is seen at as low as 50% vegetation cover. Although these empirical relationships between vegetative cover and wave attenuation provide essential insight for marsh restoration, it is also important to factor in lifespan estimates of restored marshes when making overall restoration decisions. The results of this study are important for coastal practitioners and managers seeking performance goals and metrics for marsh restoration, enhancement, and creation.
    Keywords: Salt marsh ; Restoration ; Coastal protection ; UVVR ; Cost effectiveness ; Vegetation ; Numerical model ; Modeling
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    Modeling nitrous oxide emissions from large-scale intensive cropping systems in the southern Amazon (2022)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Costa Jr, C., Galford, G. L., Coe, M. T., Macedo, M., Jankowski, K., O’Connell, C., & Neill, C. Modeling nitrous oxide emissions from large-scale intensive cropping systems in the southern Amazon. Frontiers in Sustainable Food Systems, 5, (2021): 701416. https://doi.org/10.3389/fsufs.2021.701416.
    Description: Nitrogen (N) fertilizer use is rapidly intensifying on tropical croplands and has the potential to increase emissions of the greenhouse gas, nitrous oxide (N2O). Since about 2005 Mato Grosso (MT), Brazil has shifted from single-cropped soybeans to double-cropping soybeans with maize, and now produces 1.5% of the world's maize. This production shift required an increase in N fertilization, but the effects on N2O emissions are poorly known. We calibrated the process-oriented biogeochemical DeNitrification-DeComposition (DNDC) model to simulate N2O emissions and crop production from soybean and soybean-maize cropping systems in MT. After model validation with field measurements and adjustments for hydrological properties of tropical soils, regional simulations suggested N2O emissions from soybean-maize cropland increased almost fourfold during 2001–2010, from 1.1 ± 1.1 to 4.1 ± 3.2 Gg 1014 N-N2O. Model sensitivity tests showed that emissions were spatially and seasonably variable and especially sensitive to soil bulk density and carbon content. Meeting future demand for maize using current soybean area in MT might require either (a) intensifying 3.0 million ha of existing single soybean to soybean-maize or (b) increasing N fertilization to ~180 kg N ha−1 on existing 2.3 million ha of soybean-maize area. The latter strategy would release ~35% more N2O than the first. Our modifications of the DNDC model will improve estimates of N2O emissions from agricultural production in MT and other tropical areas, but narrowing model uncertainty will depend on more detailed field measurements and spatial data on soil and cropping management.
    Description: This work was supported by National Science Foundation (NSF#1257944) and CNPq-Ciências Sem Fronteiras Post-Doctoral Fellowship (249380/2013-7).
    Keywords: GHG emission ; Agriculture ; Nitrogen fertilization management ; Amazon ; Food system
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    Modeling marsh dynamics using a 3-D coupled wave-flow-sediment model (2022)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kalra, T. S., Ganju, N. K., Aretxabaleta, A. L., Carr, J. A., Defne, Z., & Moriarty, J. M. Modeling marsh dynamics using a 3-D coupled wave-flow-sediment model. Frontiers in Marine Science, 8, (2021): 740921, https://doi.org/10.3389/fmars.2021.740921.
    Description: Salt marshes are dynamic biogeomorphic systems that respond to external physical factors, including tides, sediment transport, and waves, as well as internal processes such as autochthonous soil formation. Predicting the fate of marshes requires a modeling framework that accounts for these processes in a coupled fashion. In this study, we implement two new marsh dynamic processes in the 3-D COAWST (coupled-ocean-atmosphere-wave sediment transport) model. The processes added are the erosion of the marsh edge scarp caused by lateral wave thrust from surface waves and vertical accretion driven by biomass production on the marsh platform. The sediment released from the marsh during edge erosion causes a change in bathymetry, thereby modifying the wave-energy reaching the marsh edge. Marsh vertical accretion due to biomass production is considered for a single vegetation species and is determined by the hydroperiod parameters (tidal datums) and the elevation of the marsh cells. Tidal datums are stored at user-defined intervals as a hindcast (on the order of days) and used to update the vertical growth formulation. Idealized domains are utilized to verify the lateral wave thrust formulation and show the dynamics of lateral wave erosion leading to horizontal retreat of marsh edge. The simulations of Reedy and Dinner Creeks within the Barnegat Bay estuary system demonstrate the model capability to account for both lateral wave erosion and vertical accretion due to biomass production in a realistic marsh complex. The simulations show that vertical accretion is dominated by organic deposition in the marsh interior, whereas deposition of mineral estuarine sediments occurs predominantly along the channel edges. The ability of the model to capture the fate of the sediment can be extended to model to simulate the impacts of future storms and relative sea-level rise (RSLR) scenarios on salt-marsh ecomorphodynamics.
    Description: This work was supported by USGS Coastal and Marine Hazards and Resources Program.
    Keywords: Marsh morphology ; Sediment transport ; Numerical model ; COAWST model ; Marsh accretion
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  • 21
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    Recent nitrogen storage and accumulation rates in mangrove soils exceed historic rates in the urbanized San Juan Bay Estuary (Puerto Rico, United States) (2022)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Wigand, C., Oczkowski, A. J., Branoff, B. L., Eagle, M., Hanson, A., Martin, R. M., Balogh, S., Miller, K. M., Huertas, E., Loffredo, J., & Watson, E. B. Recent nitrogen storage and accumulation rates in mangrove soils exceed historic rates in the urbanized San Juan Bay Estuary (Puerto Rico, United States). Frontiers in Forests and Global Change, 4, (2021): 765896, https://doi.org/10.3389/ffgc.2021.765896.
    Description: Tropical mangrove forests have been described as “coastal kidneys,” promoting sediment deposition and filtering contaminants, including excess nutrients. Coastal areas throughout the world are experiencing increased human activities, resulting in altered geomorphology, hydrology, and nutrient inputs. To effectively manage and sustain coastal mangroves, it is important to understand nitrogen (N) storage and accumulation in systems where human activities are causing rapid changes in N inputs and cycling. We examined N storage and accumulation rates in recent (1970 – 2016) and historic (1930 – 1970) decades in the context of urbanization in the San Juan Bay Estuary (SJBE, Puerto Rico), using mangrove soil cores that were radiometrically dated. Local anthropogenic stressors can alter N storage rates in peri-urban mangrove systems either directly by increasing N soil fertility or indirectly by altering hydrology (e.g., dredging, filling, and canalization). Nitrogen accumulation rates were greater in recent decades than historic decades at Piñones Forest and Martin Peña East. Martin Peña East was characterized by high urbanization, and Piñones, by the least urbanization in the SJBE. The mangrove forest at Martin Peña East fringed a poorly drained canal and often received raw sewage inputs, with N accumulation rates ranging from 17.7 to 37.9 g m–2 y–1 in recent decades. The Piñones Forest was isolated and had low flushing, possibly exacerbated by river damming, with N accumulation rates ranging from 18.6 to 24.2 g m–2 y–1 in recent decades. Nearly all (96.3%) of the estuary-wide mangrove N (9.4 Mg ha–1) was stored in the soils with 7.1 Mg ha–1 sequestered during 1970–2017 (0–18 cm) and 2.3 Mg ha–1 during 1930–1970 (19–28 cm). Estuary-wide mangrove soil N accumulation rates were over twice as great in recent decades (0.18 ± 0.002 Mg ha–1y–1) than historically (0.08 ± 0.001 Mg ha–1y–1). Nitrogen accumulation rates in SJBE mangrove soils in recent times were twofold larger than the rate of human-consumed food N that is exported as wastewater (0.08 Mg ha–1 y–1), suggesting the potential for mangroves to sequester human-derived N. Conservation and effective management of mangrove forests and their surrounding watersheds in the Anthropocene are important for maintaining water quality in coastal communities throughout tropical regions.
    Description: Some funding was provided by the United States Geological Coastal and Marine Hazards and Resources Program.
    Keywords: Nitrogen storage ; Nitrogen accumulation ; Mangrove forest ; Wastewater ; Anthropogenic stressors ; Peri-urban mangrove ; Urbanization
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    Synuclein regulates synaptic vesicle clustering and docking at a vertebrate synapse (2022)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Fouke, K. E., Wegman, M. E., Weber, S. A., Brady, E. B., Roman-Vendrell, C., & Morgan, J. R. Synuclein regulates synaptic vesicle clustering and docking at a vertebrate synapse. Frontiers in Cell and Developmental Biology, 9, (2021): 774650, https://doi.org/10.3389/fcell.2021.774650.
    Description: Neurotransmission relies critically on the exocytotic release of neurotransmitters from small synaptic vesicles (SVs) at the active zone. Therefore, it is essential for neurons to maintain an adequate pool of SVs clustered at synapses in order to sustain efficient neurotransmission. It is well established that the phosphoprotein synapsin 1 regulates SV clustering at synapses. Here, we demonstrate that synuclein, another SV-associated protein and synapsin binding partner, also modulates SV clustering at a vertebrate synapse. When acutely introduced to unstimulated lamprey reticulospinal synapses, a pan-synuclein antibody raised against the N-terminal domain of α-synuclein induced a significant loss of SVs at the synapse. Both docked SVs and the distal reserve pool of SVs were depleted, resulting in a loss of total membrane at synapses. In contrast, antibodies against two other abundant SV-associated proteins, synaptic vesicle glycoprotein 2 (SV2) and vesicle-associated membrane protein (VAMP/synaptobrevin), had no effect on the size or distribution of SV clusters. Synuclein perturbation caused a dose-dependent reduction in the number of SVs at synapses. Interestingly, the large SV clusters appeared to disperse into smaller SV clusters, as well as individual SVs. Thus, synuclein regulates clustering of SVs at resting synapses, as well as docking of SVs at the active zone. These findings reveal new roles for synuclein at the synapse and provide critical insights into diseases associated with α-synuclein dysfunction, such as Parkinson’s disease.
    Description: Funding support for this project was provided by the National Institutes of Health NINDS/NIA R01 NS078165 (to JM); University of Chicago Jeff Metcalf Fellowship Grant (to SW).
    Keywords: Exocytosis ; Endocytosis ; Synapsin ; Lamprey ; Liquid phase separation ; VAMP2
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  • 23
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    Survival and axonal outgrowth of the Mauthner cell following spinal cord crush does not drive post-injury startle responses (2022)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zottoli, S. J., Faber, D. S., Hering, J., Dannhauer, A. C., & Northen, S. Survival and axonal outgrowth of the Mauthner cell following spinal cord crush does not drive post-injury startle responses. Frontiers in Cell and Developmental Biology, 9, (2021): 744191, https://doi.org/10.3389/fcell.2021.744191.
    Description: A pair of Mauthner cells (M-cells) can be found in the hindbrain of most teleost fish, as well as amphibians and lamprey. The axons of these reticulospinal neurons cross the midline and synapse on interneurons and motoneurons as they descend the length of the spinal cord. The M-cell initiates fast C-type startle responses (fast C-starts) in goldfish and zebrafish triggered by abrupt acoustic/vibratory stimuli. Starting about 70 days after whole spinal cord crush, less robust startle responses with longer latencies manifest in adult goldfish, Carassius auratus. The morphological and electrophysiological identifiability of the M-cell provides a unique opportunity to study cellular responses to spinal cord injury and the relation of axonal regrowth to a defined behavior. After spinal cord crush at the spinomedullary junction about one-third of the damaged M-axons of adult goldfish send at least one sprout past the wound site between 56 and 85 days postoperatively. These caudally projecting sprouts follow a more lateral trajectory relative to their position in the fasciculus longitudinalis medialis of control fish. Other sprouts, some from the same axon, follow aberrant pathways that include rostral projections, reversal of direction, midline crossings, neuromas, and projection out the first ventral root. Stimulating M-axons in goldfish that had post-injury startle behavior between 198 and 468 days postoperatively resulted in no or minimal EMG activity in trunk and tail musculature as compared to control fish. Although M-cells can survive for at least 468 day (∼1.3 years) after spinal cord crush, maintain regrowth, and elicit putative trunk EMG responses, the cell does not appear to play a substantive role in the emergence of acoustic/vibratory-triggered responses. We speculate that aberrant pathway choice of this neuron may limit its role in the recovery of behavior and discuss structural and functional properties of alternative candidate neurons that may render them more supportive of post-injury startle behavior.
    Description: Support for this research came in part from NSF grant (BNS 8809445), NIH grant (2-P01-NS24707-09), and HHMI and Essel Foundation grants to Williams College.
    Keywords: Spinal cord regeneration ; Functional recovery ; Startle responses ; Mauthner cells ; Adult goldfish
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    Editorial: microbial communities and metabolisms involved in the degradation of cellular and extracellular organic biopolymers (2022)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ruff, S. E. Editorial: microbial communities and metabolisms involved in the degradation of cellular and extracellular organic biopolymers. Frontiers in Microbiology, 12, (2022): 802619, https://doi.org/10.3389/fmicb.2021.802619.
    Description: Most organic matter on Earth occurs in the form of macromolecules and complex biopolymers, which include the building blocks of every organism. Plant, animal, fungal, and microbial cells largely consist of macromolecules belonging to four compound classes: proteins, polysaccharides, nucleic acids, and lipids (Figure 1). The percentage of these compounds per dry weight can vary greatly between lineages, but also between individuals of the same species or developmental stages of the same organism. Living and lysing cells release a substantial quantity and variety of macromolecules to the environment. These compounds often contain nitrogen, phosphorus, and sulfur, in addition to carbon, and are thus ideal food sources for heterotrophic organisms. Although the degradation of biopolymers and macromolecules has received considerable attention, many knowledge gaps remain, particularly in very complex ecosystems such as soils and sediments.
    Keywords: Macromolecule ; Necromass ; Heterotrophic microorganism ; Protein ; Polysaccharide ; Carbohydrate ; Nucleic acid ; Lipid
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    Common environmental pollutants negatively affect development and regeneration in the sea anemone Nematostella vectensis holobiont (2022)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Klein, S., Frazier, V., Readdean, T., Lucas, E., Diaz-Jimenez, E. P., Sogin, M., Ruff, E. S., & Echeverri, K. Common environmental pollutants negatively affect development and regeneration in the sea anemone Nematostella vectensis holobiont. Frontiers in Ecology and Evolution, 9, (2021): 786037, https://doi.org/10.3389/fevo.2021.786037.
    Description: The anthozoan sea anemone Nematostella vectensis belongs to the phylum of cnidarians which also includes jellyfish and corals. Nematostella are native to United States East Coast marsh lands, where they constantly adapt to changes in salinity, temperature, oxygen concentration and pH. Its natural ability to continually acclimate to changing environments coupled with its genetic tractability render Nematostella a powerful model organism in which to study the effects of common pollutants on the natural development of these animals. Potassium nitrate, commonly used in fertilizers, and Phthalates, a component of plastics are frequent environmental stressors found in coastal and marsh waters. Here we present data showing how early exposure to these pollutants lead to dramatic defects in development of the embryos and eventual mortality possibly due to defects in feeding ability. Additionally, we examined the microbiome of the animals and identified shifts in the microbial community that correlated with the type of water that was used to grow the animals, and with their exposure to pollutants.
    Description: This work was funded by a Pilot Program award to ER and KE from the Microbiome Center at the University of Chicago. The microbiome sequencing was funded by a grant from the McDonnell Initiative to ER. KE was supported by a grant from NICHD R01 HD092451, start-up funds from the MBL and funding from the Owens Family Foundation. ER was supported by start-up funds from the MBL and MLS receives support from the Unger G. Vetlesen Foundation.
    Keywords: Nematostella ; Growth ; Microbiome ; Stressors ; Development
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    Activating transcription factor 3 (ATF3) is a highly conserved pro-regenerative transcription factor in the vertebrate nervous system (2022)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Katz, H. R., Arcese, A. A., Bloom, O., & Morgan, J. R. Activating transcription factor 3 (ATF3) is a highly conserved pro-regenerative transcription factor in the vertebrate nervous system. Frontiers in Cell and Developmental Biology, 10, (2022): 824036, https://doi.org/10.3389/fcell.2022.824036.
    Description: The vertebrate nervous system exhibits dramatic variability in regenerative capacity across species and neuronal populations. For example, while the mammalian central nervous system (CNS) is limited in its regenerative capacity, the CNS of many other vertebrates readily regenerates after injury, as does the peripheral nervous system (PNS) of mammals. Comparing molecular responses across species and tissues can therefore provide valuable insights into both conserved and distinct mechanisms of successful regeneration. One gene that is emerging as a conserved pro-regenerative factor across vertebrates is activating transcription factor 3 (ATF3), which has long been associated with tissue trauma. A growing number of studies indicate that ATF3 may actively promote neuronal axon regrowth and regeneration in species ranging from lampreys to mammals. Here, we review data on the structural and functional conservation of ATF3 protein across species. Comparing RNA expression data across species that exhibit different abilities to regenerate their nervous system following traumatic nerve injury reveals that ATF3 is consistently induced in neurons within the first few days after injury. Genetic deletion or knockdown of ATF3 expression has been shown in mouse and zebrafish, respectively, to reduce axon regeneration, while inducing ATF3 promotes axon sprouting, regrowth, or regeneration. Thus, we propose that ATF3 may be an evolutionarily conserved regulator of neuronal regeneration. Identifying downstream effectors of ATF3 will be a critical next step in understanding the molecular basis of vertebrate CNS regeneration.
    Description: This work was supported by: a Morton Cure Paralysis Fund Research Grant (to HK); a NIH/NINDS R03 Research Grant (No. 1R03NS078519) and the New York State Spinal Cord Injury Research Board (to OB); and the Marine Biological Laboratory Eugene Bell Center Endowment, Rowe Endowment for Regenerative Biology, and Charles Evans Research Development award (to JM).
    Keywords: Regeneration ; Spinal cord injury ; Zebrafish ; Lamprey ; Dorsal root ganglia (DRG) neurons
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    The transcriptional response of soil bacteria to long-term warming and short-term seasonal fluctuations in a terrestrial forest (2022)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Chowdhury, P. R., Golas, S. M., Alteio, L., Stevens, J. T. E., Billings, A. F., Blanchard, J. L., Melillo, J. M., & DeAngelis, K. M. The transcriptional response of soil bacteria to long-term warming and short-term seasonal fluctuations in a terrestrial forest. Frontiers in Microbiology, 12, (2021): 666558, https://doi.org/10.3389/fmicb.2021.666558.
    Description: Terrestrial ecosystems are an important carbon store, and this carbon is vulnerable to microbial degradation with climate warming. After 30 years of experimental warming, carbon stocks in a temperate mixed deciduous forest were observed to be reduced by 30% in the heated plots relative to the controls. In addition, soil respiration was seasonal, as was the warming treatment effect. We therefore hypothesized that long-term warming will have higher expressions of genes related to carbohydrate and lipid metabolism due to increased utilization of recalcitrant carbon pools compared to controls. Because of the seasonal effect of soil respiration and the warming treatment, we further hypothesized that these patterns will be seasonal. We used RNA sequencing to show how the microbial community responds to long-term warming (~30 years) in Harvard Forest, MA. Total RNA was extracted from mineral and organic soil types from two treatment plots (+5°C heated and ambient control), at two time points (June and October) and sequenced using Illumina NextSeq technology. Treatment had a larger effect size on KEGG annotated transcripts than on CAZymes, while soil types more strongly affected CAZymes than KEGG annotated transcripts, though effect sizes overall were small. Although, warming showed a small effect on overall CAZymes expression, several carbohydrate-associated enzymes showed increased expression in heated soils (~68% of all differentially expressed transcripts). Further, exploratory analysis using an unconstrained method showed increased abundances of enzymes related to polysaccharide and lipid metabolism and decomposition in heated soils. Compared to long-term warming, we detected a relatively small effect of seasonal variation on community gene expression. Together, these results indicate that the higher carbohydrate degrading potential of bacteria in heated plots can possibly accelerate a self-reinforcing carbon cycle-temperature feedback in a warming climate.
    Description: Funding for this study was provided by the Department of Energy Terrestrial Ecosystem Sciences program under contract number DE-SC0010740. Sites for sample collection were maintained with funding in part from the National Science Foundation (NSF) Long-Term Ecological Research (DEB 1237491) and the NSF Long-Term Research in Environmental Biology (DEB 1456528) programs.
    Keywords: Meta-transcriptomes ; Microbial ; Terrestrial ; Carbon cycle ; Global warming
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    Improved wetland soil organic carbon stocks of the conterminous U.S. through data harmonization (2022)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Uhran, B., Windham-Myers, L., Bliss, N., Nahlik, A. M., Sundquist, E., & Stagg, C. L. Improved wetland soil organic carbon stocks of the conterminous U.S. through data harmonization. Frontiers in Soil Science, 1, (2021): 706701, https://doi.org/10.3389/fsoil.2021.706701.
    Description: Wetland soil stocks are important global repositories of carbon (C) but are difficult to quantify and model due to varying sampling protocols, and geomorphic/spatio-temporal discontinuity. Merging scales of soil-survey spatial extents with wetland-specific point-based data offers an explicit, empirical and updatable improvement for regional and continental scale soil C stock assessments. Agency-collected and community-contributed soil datasets were compared for representativeness and bias, with the goal of producing a harmonized national map of wetland soil C stocks with error quantification for wetland areas of the conterminous United States (CONUS) identified by the USGS National Landcover Change Dataset. This allowed an empirical predictive model of SOC density to be applied across the entire CONUS using relational %OC distribution alone. A broken-stick quantile-regression model identified %OC with its relatively high analytical confidence as a key predictor of SOC density in soil segments; soils 〈6% OC (hereafter, mineral wetland soils, 85% of the dataset) had a strong linear relationship of %OC to SOC density (RMSE = 0.0059, ~4% mean RMSE) and soils 〉6% OC (organic wetland soils, 15% of the dataset) had virtually no predictive relationship of %OC to SOC density (RMSE = 0.0348 g C cm−3, ~56% mean RMSE). Disaggregation by vegetation type or region did not alter the breakpoint significantly (6% OC) and did not improve model accuracies for inland and tidal wetlands. Similarly, SOC stocks in tidal wetlands were related to %OC, but without a mappable product for disaggregation to improve accuracy by soil class, region or depth. Our layered harmonized CONUS wetland soil maps revised wetland SOC stock estimates downward by 24% (9.5 vs. 12.5Pg C) with the overestimation being entirely an issue of inland organic wetland soils (35% lower than SSURGO-derived SOC stocks). Further, SSURGO underestimated soil carbon stocks at depth, as modeled wetland SOC stocks for organic-rich soils showed significant preservation downcore in the NWCA dataset (〈3% loss between 0 and 30 cm and 30 and 100 cm depths) in contrast to mineral-rich soils (37% downcore stock loss). Future CONUS wetland soil C assessments will benefit from focused attention on improved organic wetland soil measurements, land history, and spatial representativeness.
    Description: This project was funded through the U.S. Geological Survey's Land Carbon Program and a grant to ES through the U.S. Geological Survey's Community for Data Integration Program for generating cross-agency assessments.
    Keywords: Soil organic carbon ; Soil carbon density ; Wetland ; Organic matter ; Soil profile ; Soil carbon stock vulnerability
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    Modulation of G(q)/PLC-mediated signaling by acute lithium exposure (2022)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sanchez Trivino, C. A., Landinez, M. P., Duran, S., Gomez, M. del P., & Nasi, E. Modulation of G(q)/PLC-mediated signaling by acute lithium exposure. Frontiers in Cellular Neuroscience, 16, (2022): 838939, https://doi.org/10.3389/fncel.2022.838939.
    Description: Although lithium has long been one of the most widely used pharmacological agents in psychiatry, its mechanisms of action at the cellular and molecular levels remain poorly understood. One of the targets of Li+ is the phosphoinositide pathway, but whereas the impact of Li+ on inositol lipid metabolism is well documented, information on physiological effects at the cellular level is lacking. We examined in two mammalian cell lines the effect of acute Li+ exposure on the mobilization of internal Ca2+ and phospholipase C (PLC)-dependent membrane conductances. We first corroborated by Western blots and immunofluorescence in HEK293 cells the presence of key signaling elements of a muscarinic PLC pathway (M1AchR, Gq, PLC-β1, and IP3Rs). Stimulation with carbachol evoked a dose-dependent mobilization of Ca, as determined with fluorescent indicators. This was due to release from internal stores and proved susceptible to the PLC antagonist U73122. Li+ exposure reproducibly potentiated the Ca response in a concentration-dependent manner extending to the low millimolar range. To broaden those observations to a neuronal context and probe potential Li modulation of electrical signaling, we next examined the cell line SHsy5y. We replicated the potentiating effects of Li on the mobilization of internal Ca, and, after characterizing the basic properties of the electrical response to cholinergic stimulation, we also demonstrated an equally robust upregulation of muscarinic membrane currents. Finally, by directly stimulating the signaling pathway at different links downstream of the receptor, the site of action of the observed Li effects could be narrowed down to the G protein and its interaction with PLC-β. These observations document a modulation of Gq/PLC/IP3-mediated signaling by acute exposure to lithium, reflected in distinct physiological changes in cellular responses.
    Description: This work was supported by DIB-Universidad Nacional de Colombia, grant Hermes No. 41821.
    Keywords: Lithium ; Phospholipase C ; Gq ; Calcium ; SHSY5Y ; HEK-293
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    Editorial: seagrasses under times of change (2022)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Winters, G., Teichberg, M., Reuter, H., Viana, I. G., & Willette, D. A. Editorial: seagrasses under times of change. Frontiers in Plant Science, 13, (2022): 870478, https://doi.org/10.3389/fpls.2022.870478.
    Description: Awareness of the ecological importance of seagrasses is growing due to recent attention to their role in carbon sequestration as a potential blue carbon sink (Fourqurean et al., 2012; Bedulli et al.), as well as their role in nutrient cycling (Romero et al., 2006), sediment stabilization (James et al., 2019), pathogen filtration (Lamb et al., 2017), and the formation of essential habitats for economically important marine species (Jackson et al., 2001; Jones et al.). Despite their importance and the increasing public and scientific awareness of seagrasses, simultaneous global (e.g., ocean warming, increase in frequency and severity of extreme events, introduction and spread of invasive species) and local (e.g., physical disturbances, eutrophication, and sedimentation) anthropogenic stressors continue to be the main causes behind the ongoing global decline of seagrass meadows (Orth et al., 2006; Waycott et al., 2009).
    Description: This research was partially funded through the BMBF project SEANARIOS (Seagrass scenarios under thermal and nutrient stress: FKZ 03F0826A) to HR and MT. MT was partially funded through the DFG project SEAMAC (Seagrass and macroalgal community dynamics and performance under environmental change; TE 1046/3-1). IV was supported by a postdoctoral research grant Juan de la Cierva-Incorporación (IJC2019-040554-I) and from MCIN/AEI /10.13039/501100011033 (Spain).
    Keywords: Seagrasses ; Climate change ; Eutrophication ; Responses of seagrasses to single and combined stressors ; Spatial-temporal modeling
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    Eukaryotic parasites are integral to a productive microbial food web in oxygen-depleted waters (2022)
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2022]. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Suter, E. A., Pachiadaki, M., Taylor, G. T., & Edgcomb, V. P. Eukaryotic parasites are integral to a productive microbial food web in oxygen-depleted waters. Frontiers in Microbiology, 12, (2022): 764605, https://doi.org/10.3389/fmicb.2021.764605.
    Description: Oxygen-depleted water columns (ODWCs) host a diverse community of eukaryotic protists that change dramatically in composition over the oxic-anoxic gradient. In the permanently anoxic Cariaco Basin, peaks in eukaryotic diversity occurred in layers where dark microbial activity (chemoautotrophy and heterotrophy) were highest, suggesting a link between prokaryotic activity and trophic associations with protists. Using 18S rRNA gene sequencing, parasites and especially the obligate parasitic clade, Syndiniales, appear to be particularly abundant, suggesting parasitism is an important, but overlooked interaction in ODWC food webs. Syndiniales were also associated with certain prokaryotic groups that are often found in ODWCs, including Marinimicrobia and Marine Group II archaea, evocative of feedbacks between parasitic infection events, release of organic matter, and prokaryotic assimilative activity. In a network analysis that included all three domains of life, bacterial and archaeal taxa were putative bottleneck and hub species, while a large proportion of edges were connected to eukaryotic nodes. Inclusion of parasites resulted in a more complex network with longer path lengths between members. Together, these results suggest that protists, and especially protistan parasites, play an important role in maintaining microbial food web complexity, particularly in ODWCs, where protist diversity and microbial productivity are high, but energy resources are limited relative to euphotic waters.
    Description: This work was supported by the National Science Foundation (NSF) grants (OCE-1336082 to VE and OCE-1335436 and OCE-1259110 to GT). The Cyverse infrastructure and resources are supported by the NSF under Award Numbers DBI-0735191, DBI-1265383, and DBI-1743442 (www.cyverse.org). Support was also provided by the Faculty Scholarship and Academic Advancement Committee at Molloy College.
    Keywords: 18S (SSU) rRNA gene ; Oxygen-depleted environment ; Oxygen minimum zone (OMZ) ; Protist ; Syndiniales ; Parasite ; Eukaryotes ; Network analysis
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    Oceanic crustal fluid single cell genomics complements metagenomic and metatranscriptomic surveys with orders of magnitude less sample volume (2022)
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in D’Angelo, T., Goordial, J., Poulton, N., Seyler, L., Huber, J., Stepanauskas, R., & Orcutt, B. Oceanic crustal fluid single cell genomics complements metagenomic and metatranscriptomic surveys with orders of magnitude less sample volume. Frontiers in Microbiology, 12, (2022): 738231, https://doi.org/10.3389/fmicb.2021.738231.
    Description: Fluids circulating through oceanic crust play important roles in global biogeochemical cycling mediated by their microbial inhabitants, but studying these sites is challenged by sampling logistics and low biomass. Borehole observatories installed at the North Pond study site on the western flank of the Mid-Atlantic Ridge have enabled investigation of the microbial biosphere in cold, oxygenated basaltic oceanic crust. Here we test a methodology that applies redox-sensitive fluorescent molecules for flow cytometric sorting of cells for single cell genomic sequencing from small volumes of low biomass (approximately 103 cells ml–1) crustal fluid. We compare the resulting genomic data to a recently published paired metagenomic and metatranscriptomic analysis from the same site. Even with low coverage genome sequencing, sorting cells from less than one milliliter of crustal fluid results in similar interpretation of dominant taxa and functional profiles as compared to ‘omics analysis that typically filter orders of magnitude more fluid volume. The diverse community dominated by Gammaproteobacteria, Bacteroidetes, Desulfobacterota, Alphaproteobacteria, and Zetaproteobacteria, had evidence of autotrophy and heterotrophy, a variety of nitrogen and sulfur cycling metabolisms, and motility. Together, results indicate fluorescence activated cell sorting methodology is a powerful addition to the toolbox for the study of low biomass systems or at sites where only small sample volumes are available for analysis.
    Description: The borehole observatories that form the backbone of this project were funded by the Integrated Ocean Drilling Program (IODP, now the International Ocean Discovery Program), the United States National Science Foundation (NSF), and the Gordon and Betty Moore Foundation (grant GBMF1609). Cruise AT39-01 was funded by the NSF (OCE-1634025 to C. Geoff Wheat). Analyses were funded by the NSF (OCE-1536623 to BO; OIA-1826734 to RS, NP, and BO; and OCE-16435208 and OCE-1745589 to JH), the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) Science and Technology Center (via subawards from OIA-0939564 to BO and JH), and the NASA Exobiology program (80NSSC19K0466 to BO). This is C-DEBI publication 571.
    Keywords: Deep biosphere ; Oceanic crust ; Crustal fluid ; Single cell genomics ; Metatranscriptomics ; IODP ; CORKS ; North Pond
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    New opportunities and untapped scientific potential in the abyssal ocean (2022)
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Marlow, J., Anderson, R., Reysenbach, A.-L., Seewald, J., Shank, T., Teske, A., Wanless, V., & Soule, S. New opportunities and untapped scientific potential in the abyssal ocean. Frontiers in Marine Science, 8, (2022): 798943, https://doi.org/10.3389./fmars.2021.798943
    Description: The abyssal ocean covers more than half of the Earth’s surface, yet remains understudied and underappreciated. In this Perspectives article, we mark the occasion of the Deep Submergence Vehicle Alvin’s increased depth range (from 4500 to 6500 m) to highlight the scientific potential of the abyssal seafloor. From a geologic perspective, ultra-slow spreading mid-ocean ridges, Petit Spot volcanism, transform faults, and subduction zones put the full life cycle of oceanic crust on display in the abyss, revealing constructive and destructive forces over wide ranges in time and space. Geochemically, the abyssal pressure regime influences the solubility of constituents such as silica and carbonate, and extremely high-temperature fluid-rock reactions in the shallow subsurface lead to distinctive and potentially unique geochemical profiles. Microbial residents range from low-abundance, low-energy communities on the abyssal plains to fast growing thermophiles at hydrothermal vents. Given its spatial extent and position as an intermediate zone between coastal and deep hadal settings, the abyss represents a lynchpin in global-scale processes such as nutrient and energy flux, population structure, and biogeographic diversity. Taken together, the abyssal ocean contributes critical ecosystem services while facing acute and diffuse anthropogenic threats from deep-sea mining, pollution, and climate change.
    Description: We would like to thank the National Science Foundation for their support through grants NSF 2009117 and 2129431 to SAS.
    Keywords: Abyssal ocean ; Geochemistry ; Microbiology ; Geology ; Ecology
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    Shale heavy metal isotope records of low environmental O2 between two Archean Oxidation Events (2022)
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ostrander, C. M., Kendall, B., Gordon, G. W., Nielsen, S. G., Zheng, W., & Anbar, A. D. Shale heavy metal isotope records of low environmental O2 between two Archean Oxidation Events. Frontiers in Earth Science, 10, (2022): 833609, https://doi.org/10.3389/feart.2022.833609.
    Description: Evidence of molecular oxygen (O2) accumulation at Earth’s surface during the Archean (4.0–2.5 billion years ago, or Ga) seems to increase in its abundance and compelling nature toward the end of the eon, during the runup to the Great Oxidation Event. Yet, many details of this late-Archean O2 story remain under-constrained, such as the extent, tempo, and location of O2 accumulation. Here, we present a detailed Fe, Tl, and U isotope study of shales from a continuous sedimentary sequence deposited between ∼2.6 and ∼2.5 Ga and recovered from the Pilbara Craton of Western Australia (the Wittenoom and Mt. Sylvia formations preserved in drill core ABDP9). We find a progressive decrease in bulk-shale Fe isotope compositions moving up core (as low as δ56Fe = –0.78 ± 0.08‰; 2SD) accompanied by invariant authigenic Tl isotope compositions (average ε205TlA = –2.0 ± 0.6; 2SD) and bulk-shale U isotope compositions (average δ238U = –0.30 ± 0.05‰; 2SD) that are both not appreciably different from crustal rocks or bulk silicate Earth. While there are multiple possible interpretations of the decreasing δ56Fe values, many, to include the most compelling, invoke strictly anaerobic processes. The invariant and near-crustal ε205TlA and δ238U values point even more strongly to this interpretation, requiring reducing to only mildly oxidizing conditions over ten-million-year timescales in the late-Archean. For the atmosphere, our results permit either homogenous and low O2 partial pressures (between 10−6.3 and 10−6 present atmospheric level) or heterogeneous and spatially restricted O2 accumulation nearest the sites of O2 production. For the ocean, our results permit minimal penetration of O2 in marine sediments over large areas of the seafloor, at most sufficient for the burial of Fe oxide minerals but insufficient for the burial of Mn oxide minerals. The persistently low background O2 levels implied by our dataset between ∼2.6 and ∼2.5 Ga contrast with the timeframes immediately before and after, where strong evidence is presented for transient Archean Oxidation Events. Viewed in this broader context, our data support the emerging narrative that Earth’s initial oxygenation was a dynamic process that unfolded in fits-and-starts over many hundreds-of-millions of years.
    Description: This work was supported financially by the NSF Frontiers in Earth System Dynamics program award NSF EAR-1338810 (AA), a Woods Hole Oceanographic Institution Postdoctoral Scholarship (CO), a NSERC Discovery Grant (RGPIN-435930) and the Canada Research Chair program (BK), and a NASA Exobiology award 80NSSC20K0615 (SN).
    Keywords: Archean ; Thallium ; Iron ; Uranium ; Isotopes ; Oxygen
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    Bacterioplankton diversity and distribution in relation to phytoplankton community structure in the Ross Sea surface waters (2022)
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cordone, A., D’Errico, G., Magliulo, M., Bolinesi, F., Selci, M., Basili, M., de Marco, R., Saggiomo, M., Rivaro, P., Giovannelli, D., & Mangoni, O. Bacterioplankton diversity and distribution in relation to phytoplankton community structure in the Ross Sea surface waters. Frontiers in Microbiology, 13, (2022): 722900, https://doi.org/10.3389/fmicb.2022.722900.
    Description: Primary productivity in the Ross Sea region is characterized by intense phytoplankton blooms whose temporal and spatial distribution are driven by changes in environmental conditions as well as interactions with the bacterioplankton community. However, the number of studies reporting the simultaneous diversity of the phytoplankton and bacterioplankton in Antarctic waters are limited. Here, we report data on the bacterial diversity in relation to phytoplankton community structure in the surface waters of the Ross Sea during the Austral summer 2017. Our results show partially overlapping bacterioplankton communities between the stations located in the Terra Nova Bay (TNB) coastal waters and the Ross Sea Open Waters (RSOWs), with a dominance of members belonging to the bacterial phyla Bacteroidetes and Proteobacteria. In the TNB coastal area, microbial communities were characterized by a higher abundance of sequences related to heterotrophic bacterial genera such as Polaribacter spp., together with higher phytoplankton biomass and higher relative abundance of diatoms. On the contrary, the phytoplankton biomass in the RSOW were lower, with relatively higher contribution of haptophytes and a higher abundance of sequences related to oligotrophic and mixothrophic bacterial groups like the Oligotrophic Marine Gammaproteobacteria (OMG) group and SAR11. We show that the rate of diversity change between the two locations is influenced by both abiotic (salinity and the nitrogen to phosphorus ratio) and biotic (phytoplankton community structure) factors. Our data provide new insight into the coexistence of the bacterioplankton and phytoplankton in Antarctic waters, suggesting that specific rather than random interaction contribute to the organic matter cycling in the Southern Ocean.
    Description: Samples were collected in the framework of Plankton biodiversity and functioning of the Ross Sea ecosystems in a changing Southern Ocean [P-ROSE – (PNRA16_00239)], and CDW Effects on glacial mElting and on Bulk of Fe in the Western Ross sea [CELEBeR – (PNRA16_00207)] projects – Italian National Antarctic Program – funded by the Ministry of Education, University and Research (MIUR), awarded to OM and PR, respectively. MM was supported by an Earth-Life Science Institute (Tokyo, Japan) visiting fellowship. This work was partially supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 948972) to DG.
    Keywords: Bacterial diversity ; Bacterioplankton ; Phytoplankton ; Ross Sea ; Antarctica
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    Making use of relicts: brisingid seastars aggregate on hydrothermally inactive sulfide chimneys near black smokers (2022)
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Woods, D., Cheadle, M., John, B., German, C., & Van Dover, C. Making use of relicts: brisingid seastars aggregate on hydrothermally inactive sulfide chimneys near black smokers. Frontiers in Marine Science, 9, (2022): 774628, https://doi.org/10.3389/fmars.2022.774628.
    Description: When hydrothermal activity ceases at black-smoker chimneys on mid-ocean ridges, populations of associated invertebrates hosting chemoautotrophic endosymbionts decline and then disappear, but the chimneys can persist on the seabed as relicts. Suspension-feeding brisingid seastars colonize hydrothermally inactive (relict) chimneys on the East Pacific Rise (EPR), though their distribution relative to available hard substrata and proximity to hydrothermal activity is poorly documented. In this study, brisingid abundance on sulfide and basalt substrata was assessed along an ∼3,700 m ROV Jason II transect at the summit of Pito Seamount (SE Pacific; ∼2,275 m). Brisingids were non-randomly distributed, with highest densities (up to ∼300 m–2) on relict sulfides chimneys near active black smokers. Brisingids were relatively uncommon on basalt substrata, and absent on black smokers. We infer that both relict sulfide structures and proximity to black smokers play key roles in the maintenance of dense brisingid populations on Pito Seamount and in similar environments on the EPR. Our observations suggest that experimental introduction of “artificial” relict chimneys providing microtopographic relief could test whether such an approach might mitigate potential impacts of mineral extraction on populations of suspension-feeding invertebrates.
    Description: his project was partially supported by the Global Ocean Biodiversity Initiative through the International Climate Initiative (IKI; grant no. 16_IV_049_Global_A_Global Ocean Biodiversity Initiative GOBI). The Federal Ministry for the Environment, Nature Conservation, and Nuclear Safety (BMU) supports IKI on the basis of a decision adopted by the German Bundestag. DW was supported by Duke University funds to CV. CG’s participation was funded through WHOI’s Deep Ocean Exploration Institute. The AT37-08 cruise was funded by NSF OCE-1459462 (MC and BJ) and OCE-1459387 (J Gee, Scripps Institution of Oceanography).
    Keywords: Brisingid seastar ; East Pacific Rise (EPR) ; Hydrothermal vent ; Pito Seamount ; Nautile Hydrothermal Field ; Deep-sea mining (DSM) ; Black smoker ; Hydrothermally inactive sulfide
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    Physical characteristics and evolution of a long-lasting mesoscale cyclonic eddy in the Straits of Florida (2022)
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    Publication Date: 2022-10-20
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zhang, Y., Hu, C., Kourafalou, V., Liu, Y., McGillicuddy, D., Barnes, B., & Hummon, J. Physical characteristics and evolution of a long-lasting mesoscale cyclonic eddy in the Straits of Florida. Frontiers in Marine Science, 9, (2022): 779450, https://doi.org/10.3389/fmars.2022.779450.
    Description: Ocean eddies along the Loop Current (LC)/Florida Current (FC) front have been studied for decades, yet studies of the entire evolution of individual eddies are rare. Here, satellite altimetry and ocean color observations, Argo profiling float records and shipborne acoustic Doppler current profiler (ADCP) measurements, together with high-resolution simulations from the global Hybrid Coordinate Ocean Model (HYCOM) are used to investigate the physical and biochemical properties, 3-dimensional (3-D) structure, and evolution of a long-lasting cyclonic eddy (CE) in the Straits of Florida (SoF) along the LC/FC front during April–August 2017. An Angular Momentum Eddy Detection Algorithm (AMEDA) is used to detect and track the CE during its evolution process. The long-lasting CE is found to form along the eastern edge of the LC on April 9th, and remained quasi-stationary for about 3 months (April 23 to July 15) off the Dry Tortugas (DT) until becoming much smaller due to its interaction with the FC and topography. This frontal eddy is named a Tortugas Eddy (TE) and is characterized with higher Chlorophyll (Chl) and lower temperature than surrounding waters, with a mean diameter of ∼100 km and a penetrating depth of ∼800 m. The mechanisms that contributed to the growth and evolution of this long-lasting TE are also explored, which reveal the significant role of oceanic internal instability.
    Description: This work was supported by the NASA student fellowship program “Future Investigators in NASA Earth and Space Science and Technology” (FINESST, 80NSSC19K1358), the National Academies of Sciences, Engineering and Medicine (NASEM) UGOS-1 (2000009918), the NOAA IOOS SECOORA Program [IOOS.21(097)USF.BW.OBS.1], and the NOAA RESTORE Science Program (NA17NOS4510099).
    Keywords: Satellite altimetry ; Ocean color ; Argo profiling float ; ADCP ; Global HYCOM ; Cyclonic eddy ; Straits of Florida ; Dry Tortugas
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    Improving resource management for unattended observation of the marginal ice zone using autonomous underwater gliders (2022)
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    Publication Date: 2022-10-20
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Duguid, Z., & Camilli, R. Improving resource management for unattended observation of the marginal ice zone using autonomous underwater gliders. Frontiers in Robotics and AI, 7, (2020): 579256, https://doi.org/10.3389/frobt.2020.579256.
    Description: We present control policies for use with a modified autonomous underwater glider that are intended to enable remote launch/recovery and long-range unattended survey of the Arctic's marginal ice zone (MIZ). This region of the Arctic is poorly characterized but critical to the dynamics of ice advance and retreat. Due to the high cost of operating support vessels in the Arctic, the proposed glider architecture minimizes external infrastructure requirements for navigation and mission updates to brief and infrequent satellite updates on the order of once per day. This is possible through intelligent power management in combination with hybrid propulsion, adaptive velocity control, and dynamic depth band selection based on real-time environmental state estimation. We examine the energy savings, range improvements, decreased communication requirements, and temporal consistency that can be attained with the proposed glider architecture and control policies based on preliminary field data, and we discuss a future MIZ survey mission concept in the Arctic. Although the sensing and control policies presented here focus on under ice missions with an unattended underwater glider, they are hardware independent and are transferable to other robotic vehicle classes, including in aerial and space domains.
    Description: Support for this research was provided through NASA PSTAR Grant #NNX16AL08G and the National Science Foundation Navigating the New Arctic grant #1839063.
    Keywords: Autonomous underwater glider ; Under-ice ; Long-range ; Onboard acoustic sensing ; Environment state estimation ; Marginal ice zone ; Adaptive control ; Energy efficiency
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    Impacts of coastal infrastructure on shoreline response to major hurricanes in southwest Louisiana (2022)
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    Publication Date: 2022-10-20
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cadigan, J., Bekkaye, J., Jafari, N., Zhu, L., Booth, A., Chen, Q., Raubenheimer, B., Harris, B., O’Connor, C., Lane, R., Kemp, G., Day, J., Day, J., & Ulloa, H. Impacts of coastal infrastructure on shoreline response to major hurricanes in southwest Louisiana. Frontiers in Built Environment, 8, (2022): 885215. https://doi.org/10.3389/fbuil.2022.885215.
    Description: The Rockefeller Wildlife Refuge, located along the Chenier Plain in Southwest Louisiana, was the location of the sequential landfall of two major hurricanes in the 2020 hurricane season. To protect the rapidly retreating coastline along the Refuge, a system of breakwaters was constructed, which was partially completed by the 2020 hurricane season. Multi-institutional, multi-disciplinary rapid response deployments of wave gauges, piezometers, geotechnical measurements, vegetation sampling, and drone surveys were conducted before and after Hurricanes Laura and Delta along two transects in the Refuge; one protected by a breakwater system and one which was the natural, unprotected shoreline. Geomorphological changes were similar on both transects after Hurricane Laura, while after Delta there was higher inland sediment deposition on the natural shoreline. Floodwaters drained from the transect with breakwater protection more slowly than the natural shoreline, though topography profiles are similar, indicating a potential dampening or complex hydrodynamic interactions between the sediment—wetland—breakwater system. In addition, observations of a fluidized mud deposit in Rollover Bayou in the Refuge are presented and discussed in context of the maintenance of wetland elevation and stability in the sediment starved Chenier Plain.
    Description: Funding for the study has been partially provided by the National Science Foundation through grants NSF 2139882, 2139883, 1829136, 1848650, and 1939275, as well as through the United States Army Corps of Engineers Regional Sediment Management program. Student support provided through the National Science Foundation Graduate Research Fellowship Program and the Louisiana Coastal Science Assistantship Program.
    Keywords: Hurricane impact ; Wave attenuation and erosion control ; Storm surge ; Chenier plain ; Breakwater ; Field measured data ; Natural infrastructure ; Shoreline retreat
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    A review of the opportunities and challenges for using remote sensing for management of surface-canopy forming kelps (2022)
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    Publication Date: 2022-10-20
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cavanaugh, K. C., Bell, T., Costa, M., Eddy, N. E., Gendall, L., Gleason, M. G., Hessing-Lewis, M., Martone, R., McPherson, M., Pontier, O., Reshitnyk, L., Beas-Luna, R., Carr, M., Caselle, J. E., Cavanaugh, K. C., Miller, R. F., Hamilton, S., Heady, W. N., Hirsh, H. K., Hohman R., Lee L. C., Lorda J., Ray J., Reed D. C., Saccomanno V. R., Schroeder, S. B. A review of the opportunities and challenges for using remote sensing for management of surface-canopy forming kelps. Frontiers in Marine Science, 8, (2021): 753531, https://doi.org/10.3389/fmars.2021.753531.
    Description: Surface-canopy forming kelps provide the foundation for ecosystems that are ecologically, culturally, and economically important. However, these kelp forests are naturally dynamic systems that are also threatened by a range of global and local pressures. As a result, there is a need for tools that enable managers to reliably track changes in their distribution, abundance, and health in a timely manner. Remote sensing data availability has increased dramatically in recent years and this data represents a valuable tool for monitoring surface-canopy forming kelps. However, the choice of remote sensing data and analytic approach must be properly matched to management objectives and tailored to the physical and biological characteristics of the region of interest. This review identifies remote sensing datasets and analyses best suited to address different management needs and environmental settings using case studies from the west coast of North America. We highlight the importance of integrating different datasets and approaches to facilitate comparisons across regions and promote coordination of management strategies.
    Description: Funding was provided by the Nature Conservancy (Grant No. 02042019-5719), the U.S. National Science Foundation (Grant No. OCE 1831937), and the U.S. Department of Energy ARPA-E (Grant No. DE-AR0000922).
    Keywords: Kelp forest ; Remote sensing ; North America ; Coastal management ; Kelp management ; Bull kelp ; Giant kelp
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    Underwater sound propagation modeling in a complex shallow water environment (2022)
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    Publication Date: 2022-10-20
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Oliveira, T. C. A., Lin, Y.-T., & Porter, M. B. Underwater sound propagation modeling in a complex shallow water environment. Frontiers in Marine Science, 8, (2021): 751327, https://doi.org/10.3389/fmars.2021.751327.
    Description: Three-dimensional (3D) effects can profoundly influence underwater sound propagation in shallow-water environments, hence, affecting the underwater soundscape. Various geological features and coastal oceanographic processes can cause horizontal reflection, refraction, and diffraction of underwater sound. In this work, the ability of a parabolic equation (PE) model to simulate sound propagation in the extremely complicated shallow water environment of Long Island Sound (United States east coast) is investigated. First, the 2D and 3D versions of the PE model are compared with state-of-the-art normal mode and beam tracing models for two idealized cases representing the local environment in the Sound: (i) a 2D 50-m flat bottom and (ii) a 3D shallow water wedge. After that, the PE model is utilized to model sound propagation in three realistic local scenarios in the Sound. Frequencies of 500 and 1500 Hz are considered in all the simulations. In general, transmission loss (TL) results provided by the PE, normal mode and beam tracing models tend to agree with each other. Differences found emerge with (1) increasing the bathymetry complexity, (2) expanding the propagation range, and (3) approaching the limits of model applicability. The TL results from 3D PE simulations indicate that sound propagating along sand bars can experience significant 3D effects. Indeed, for the complex shallow bathymetry found in some areas of Long Island Sound, it is challenging for the models to track the interference effects in the sound pattern. Results emphasize that when choosing an underwater sound propagation model for practical applications in a complex shallow-water environment, a compromise will be made between the numerical model accuracy, computational time, and validity.
    Description: TO thanks FCT/MCTES for the financial support to CESAM (UIDP/50017/2020 + UIDB/50017/2020), through national funds. The funding support from the Office of Naval Research for Y-TL via the grant N00014-21-1-2416 was also acknowledged. MP was supported by the Office of Naval Research under contracts N68335-17-C-0553 and N00014-18-C-7007.
    Keywords: Underwater soundscape ; 3D PE ; Bellhop3D ; Kraken3D ; Long Island Sound ; Sand bars
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    Best practice data standards for discrete chemical oceanographic observations (2022)
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Jiang, L.-Q., Pierrot, D., Wanninkhof, R., Feely, R. A., Tilbrook, B., Alin, S., Barbero, L., Byrne, R. H., Carter, B. R., Dickson, A. G., Gattuso, J.-P., Greeley, D., Hoppema, M., Humphreys, M. P., Karstensen, J., Lange, N., Lauvset, S. K., Lewis, E. R., Olsen, A., Pérez, F. F., Sabine, C., Sharp, J. D., Tanhua, T., Trull, T. W., Velo, A., Allegra, A. J., Barker, P., Burger, E., Cai, W-J., Chen, C-T. A., Cross, J., Garcia, H., Hernandez-Ayon J. M., Hu, X., Kozyr, A., Langdon, C., Lee., K, Salisbury, J., Wang, Z. A., & Xue, L. Best practice data standards for discrete chemical oceanographic observations. Frontiers in Marine Science, 8, (2022): 705638, https://doi.org/10.3389/fmars.2021.705638.
    Description: Effective data management plays a key role in oceanographic research as cruise-based data, collected from different laboratories and expeditions, are commonly compiled to investigate regional to global oceanographic processes. Here we describe new and updated best practice data standards for discrete chemical oceanographic observations, specifically those dealing with column header abbreviations, quality control flags, missing value indicators, and standardized calculation of certain properties. These data standards have been developed with the goals of improving the current practices of the scientific community and promoting their international usage. These guidelines are intended to standardize data files for data sharing and submission into permanent archives. They will facilitate future quality control and synthesis efforts and lead to better data interpretation. In turn, this will promote research in ocean biogeochemistry, such as studies of carbon cycling and ocean acidification, on regional to global scales. These best practice standards are not mandatory. Agencies, institutes, universities, or research vessels can continue using different data standards if it is important for them to maintain historical consistency. However, it is hoped that they will be adopted as widely as possible to facilitate consistency and to achieve the goals stated above.
    Description: Funding for L-QJ and AK was from NOAA Ocean Acidification Program (OAP, Project ID: 21047) and NOAA National Centers for Environmental Information (NCEI) through NOAA grant NA19NES4320002 [Cooperative Institute for Satellite Earth System Studies (CISESS)] at the University of Maryland/ESSIC. BT was in part supported by the Australia’s Integrated Marine Observing System (IMOS), enabled through the National Collaborative Research Infrastructure Strategy (NCRIS). AD was supported in part by the United States National Science Foundation. AV and FP were supported by BOCATS2 Project (PID2019-104279GB-C21/AEI/10.13039/501100011033) funded by the Spanish Research Agency and contributing to WATER:iOS CSIC interdisciplinary thematic platform. MH was partly funded by the European Union’s Horizon 2020 Research and Innovation Program under grant agreement N°821001 (SO-CHIC).
    Keywords: Data standard for chemical oceanography ; Discrete chemical oceanographic observations ; Column header abbreviations ; WOCE WHP exchange formats ; Quality control flags ; Content vs. concentration ; CO2SYS ; TEOS-10
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    Linkages among dissolved organic matter export, dissolved metabolites, and associated microbial community structure response in the northwestern Sargasso Sea on a seasonal scale (2022)
    Frontiers Media
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Liu, S., Longnecker, K., Kujawinski, E., Vergin, K., Bolaños, L., Giovannoni, S., Parsons, R., Opalk, K., Halewood, E., Hansell, D., Johnson, R., Curry, R., & Carlson, C. Linkages among dissolved organic matter export, dissolved metabolites, and associated microbial community structure response in the northwestern Sargasso Sea on a seasonal scale. Frontiers in Microbiology, 13, (2022): 833252, https://doi.org/10.3389/fmicb.2022.833252.
    Description: Deep convective mixing of dissolved and suspended organic matter from the surface to depth can represent an important export pathway of the biological carbon pump. The seasonally oligotrophic Sargasso Sea experiences annual winter convective mixing to as deep as 300 m, providing a unique model system to examine dissolved organic matter (DOM) export and its subsequent compositional transformation by microbial oxidation. We analyzed biogeochemical and microbial parameters collected from the northwestern Sargasso Sea, including bulk dissolved organic carbon (DOC), total dissolved amino acids (TDAA), dissolved metabolites, bacterial abundance and production, and bacterial community structure, to assess the fate and compositional transformation of DOM by microbes on a seasonal time-scale in 2016–2017. DOM dynamics at the Bermuda Atlantic Time-series Study site followed a general annual trend of DOC accumulation in the surface during stratified periods followed by downward flux during winter convective mixing. Changes in the amino acid concentrations and compositions provide useful indices of diagenetic alteration of DOM. TDAA concentrations and degradation indices increased in the mesopelagic zone during mixing, indicating the export of a relatively less diagenetically altered (i.e., more labile) DOM. During periods of deep mixing, a unique subset of dissolved metabolites, such as amino acids, vitamins, and benzoic acids, was produced or lost. DOM export and compositional change were accompanied by mesopelagic bacterial growth and response of specific bacterial lineages in the SAR11, SAR202, and SAR86 clades, Acidimicrobiales, and Flavobacteria, during and shortly following deep mixing. Complementary DOM biogeochemistry and microbial measurements revealed seasonal changes in DOM composition and diagenetic state, highlighting microbial alteration of the quantity and quality of DOM in the ocean.
    Description: This project was funded by the Simons Foundation International’s BIOS-SCOPE program and US National Science Foundation (NSF OCE-1756105 for BATS cruises).
    Keywords: Dissolved organic matter ; Amino acids ; Metabolites ; Bacterioplankton ; Sargasso Sea ; Seasonal ; Mixing
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    Integrating Multidisciplinary Observations in Vent Environments (IMOVE): decadal progress in deep-sea observatories at hydrothermal vents (2022)
    Frontiers Media
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Matabos, M., Barreyre, T., Juniper, S., Cannat, M., Kelley, D., Alfaro-Lucas, J., Chavagnac, V., Colaço, A., Escartin, J., Escobar, E., Fornari, D., Hasenclever, J., Huber, J., Laës-Huon, A., Lantéri, N., Levin, L., Mihaly, S., Mittelstaedt, E., Pradillon, F., Lantéri, N., Levin, L. A., Mihaly, S., Mittelstaedt, E., Pradillon, F., Sarradin, P-M., Sarrazin, J., Tomasi, B., Venkatesan, R., & Vic, C. Integrating Multidisciplinary Observations in Vent Environments (IMOVE): decadal progress in deep-sea observatories at hydrothermal vents. Frontiers in Marine Science, 9, (2022): 866422, https://doi.org/10.3389/fmars.2022.866422.
    Description: The unique ecosystems and biodiversity associated with mid-ocean ridge (MOR) hydrothermal vent systems contrast sharply with surrounding deep-sea habitats, however both may be increasingly threatened by anthropogenic activity (e.g., mining activities at massive sulphide deposits). Climate change can alter the deep-sea through increased bottom temperatures, loss of oxygen, and modifications to deep water circulation. Despite the potential of these profound impacts, the mechanisms enabling these systems and their ecosystems to persist, function and respond to oceanic, crustal, and anthropogenic forces remain poorly understood. This is due primarily to technological challenges and difficulties in accessing, observing and monitoring the deep-sea. In this context, the development of deep-sea observatories in the 2000s focused on understanding the coupling between sub-surface flow and oceanic and crustal conditions, and how they influence biological processes. Deep-sea observatories provide long-term, multidisciplinary time-series data comprising repeated observations and sampling at temporal resolutions from seconds to decades, through a combination of cabled, wireless, remotely controlled, and autonomous measurement systems. The three existing vent observatories are located on the Juan de Fuca and Mid-Atlantic Ridges (Ocean Observing Initiative, Ocean Networks Canada and the European Multidisciplinary Seafloor and water column Observatory). These observatories promote stewardship by defining effective environmental monitoring including characterizing biological and environmental baseline states, discriminating changes from natural variations versus those from anthropogenic activities, and assessing degradation, resilience and recovery after disturbance. This highlights the potential of observatories as valuable tools for environmental impact assessment (EIA) in the context of climate change and other anthropogenic activities, primarily ocean mining. This paper provides a synthesis on scientific advancements enabled by the three observatories this last decade, and recommendations to support future studies through international collaboration and coordination. The proposed recommendations include: i) establishing common global scientific questions and identification of Essential Ocean Variables (EOVs) specific to MORs, ii) guidance towards the effective use of observatories to support and inform policies that can impact society, iii) strategies for observatory infrastructure development that will help standardize sensors, data formats and capabilities, and iv) future technology needs and common sampling approaches to answer today’s most urgent and timely questions.
    Description: The first workshop in Bergen was additionally funded by the K.G. Jebsen Centre for Deep Sea Research and the University of Bergen. The second workshop was supported by ISblue project, Interdisciplinary graduate school for the blue planet (ANR-17-EURE-0015) and co-funded by a grant from the French government under the program “Investissements d’Avenir”. Additional funding was provided by Ifremer, and the départment du Finistère. The operation and maintenance of the EMSO-Azores observatory is funded by the by the EMSO-FR Research Infrastructure (MESR), which is managed by an Ifremer-CNRS collaboration. The operation and maintenance of the Endeavour observatory is funded by the Canada Foundation for Innovation’s Major Science Infrastructure program and the Department of Fisheries and Oceans (Canada). The operation and maintenance of the Axial Seamount observatory is funded by the National Science Foundation as part of the Ocean Observatories Initiative Regional Cabled Array. MM, JS and PMS acknowledge funding from the EU Horizon 2020 iAtlantic project (Grant Agreement No. 818123). AC was supported by the Operational Program AZORES 2020, through the Fund 01-0145-FEDER-1279 000140 “MarAZ Researchers: Consolidate a body of researchers in Marine Sciences in the Azores” of the European Union. She was also supported by FCT – Foundation for Science and Technology, I.P., under the project UIDB/05634/2020 and UIDP/05634/2020 and through the Regional Government of the Azores through the initiative to support the Research Centers of the University of the Azores and through the project M1.1.A/REEQ.CIENTÍFICO UI&D/2021/010.
    Keywords: Essential ocean variables (EOVs) ; Essential biological variables (EBVs) ; Mid-ocean ridge (MOR) ; Sensors, seabed platforms ; Vent fluid dynamics ; Vent communities dynamics
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    Marine microeukaryotem metatranscriptomics: sample processing and bioinformatic workflow recommendations for ecological applications (2022)
    Frontiers Media
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cohen, N., Alexander, H., Krinos, A., Hu, S., & Lampe, R. Marine microeukaryotem metatranscriptomics: sample processing and bioinformatic workflow recommendations for ecological applications. Frontiers in Marine Science, 9, (2022): 867007, https://doi.org/10.3389/fmars.2022.867007.
    Description: Microeukaryotes (protists) serve fundamental roles in the marine environment as contributors to biogeochemical nutrient cycling and ecosystem function. Their activities can be inferred through metatranscriptomic investigations, which provide a detailed view into cellular processes, chemical-biological interactions in the environment, and ecological relationships among taxonomic groups. Established workflows have been individually put forth describing biomass collection at sea, laboratory RNA extraction protocols, and bioinformatic processing and computational approaches. Here, we present a compilation of current practices and lessons learned in carrying out metatranscriptomics of marine pelagic protistan communities, highlighting effective strategies and tools used by practitioners over the past decade. We anticipate that these guidelines will serve as a roadmap for new marine scientists beginning in the realms of molecular biology and/or bioinformatics, and will equip readers with foundational principles needed to delve into protistan metatranscriptomics.
    Description: We acknowledge funding support from the University of Georgia Skidaway Institute of Oceanography (to NRC), National Science Foundation (NSF) (OCE-1948025 to HA), and Department of Energy Computational Science Graduate Fellowship (DE-SC0020347 to AIK). SKH participation was supported through NSF OCE-1947776.
    Keywords: Metatranscriptomics ; Phytoplankton ; Biological oceanography ; Microbial ecology ; Bioinformatics
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    Pathway-centric analysis of microbial metabolic potential and expression along nutrient and energy gradients in the western Atlantic Ocean (2022)
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cavaco, M. A., Bhatia, M. P., Hawley, A. K., Torres-Beltran, M., Johnson, W. M., Longnecker, K., Konwar, K., Kujawinski, E. B., & Hallam, S. J. Pathway-centric analysis of microbial metabolic potential and expression along nutrient and energy gradients in the western Atlantic Ocean. Frontiers in Marine Science, 9, (2022): 867310, https://doi.org/10.3389/fmars.2022.867310.
    Description: Microbial communities play integral roles in driving nutrient and energy transformations in the ocean, collectively contributing to fundamental biogeochemical cycles. Although it is well known that these communities are stratified within the water column, there remains limited knowledge of how metabolic pathways are distributed and expressed. Here, we investigate pathway distribution and expression patterns from surface (5 m) to deep dark ocean (4000 m) at three stations along a 2765 km transect in the western South Atlantic Ocean. This study is based on new data, consisting of 43 samples for 16S rRNA gene sequencing, 20 samples for metagenomics and 19 samples for metatranscriptomics. Consistent with previous observations, we observed vertical zonation of microbial community structure largely partitioned between light and dark ocean waters. The metabolic pathways inferred from genomic sequence information and gene expression stratified with depth. For example, expression of photosynthetic pathways increased in sunlit waters. Conversely, expression of pathways related to carbon conversion processes, particularly those involving recalcitrant and organic carbon degradation pathways (i.e., oxidation of formaldehyde) increased in dark ocean waters. We also observed correlations between indicator taxa for specific depths with the selective expression of metabolic pathways. For example, SAR202, prevalent in deep waters, was strongly correlated with expression of the methanol oxidation pathway. From a biogeographic perspective, microbial communities along the transect encoded similar metabolic potential with some latitudinal stratification in gene expression. For example, at a station influenced by input from the Amazon River, expression of pathways related to oxidative stress was increased. Finally, when pairing distinct correlations between specific particulate metabolites (e.g., DMSP, AMP and MTA) and both the taxonomic microbial community and metatranscriptomic pathways across depth and space, we were able to observe how changes in the marine metabolite pool may be influenced by microbial function and vice versa. Taken together, these results indicate that marine microbial communities encode a core repertoire of widely distributed metabolic pathways that are differentially regulated along nutrient and energy gradients. Such pathway distribution patterns are consistent with robustness in microbial food webs and indicate a high degree of functional redundancy.
    Description: This work was funded by the NSF Division of Ocean Sciences (Grant no. OCE-1154320 to EK and KL) and a small (“Microbial controls on marine organic carbon cycling”) and large (“Marine microbial communities from the Southern Atlantic Ocean transect to study dissolved organic matter and carbon cycling”) community sequencing grants from the Joint Genome Institute (US Department of Energy, Walnut Creek, CA) to SH and MB. MB was supported by an NSERC post-doctoral fellowship and a CIFAR Global Scholars fellowship. MC was supported by a Campus Alberta Innovates Program (CAIP) chair to MB.
    Keywords: Marine microbiology ; Metagenomics ; Metatranscriptomics ; Metabolites ; Atlantic Ocean ; Biogeochemistry ; Metabolic pathways ; Functional redundancy
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    Submarine shallow-water fluid emissions and their geomicrobiological imprint: a global overview (2022)
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    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Caramanna, G., Sievert, S. M., & Buehring, S. I. Submarine shallow-water fluid emissions and their geomicrobiological imprint: a global overview. Frontiers in Marine Science, 8, (2021): 727199, https://doi.org/10.3389/fmars.2021.727199.
    Description: Submarine fluids emissions in the form of geothermal vents are widespread in a variety of geological settings ranging from volcanic to tectonically active areas. This overview aims to describe representative examples of submarine vents in shallow-water areas around the globe. The areas described include: Iceland, Azores, Mediterranean Sea (Italy and Greece), Caribbean, Baja California, Japan, Papua, New Zealand, Taiwan. Common and divergent characteristics in terms of origin and geochemistry of the emitted fluids and their impact on the indigenous organisms and the surrounding environment have been identified. In the hottest vents seawater concentration is common as well as some water vapor phase separation. Carbon dioxide is the most common gas often associated with compounds of sulfur and methane. In several vents precipitation of minerals can be identified in the surrounding sediments. The analyses of the microbial communities often revealed putative chemoautotrophs, with Campylobacteria abundantly present at many vents where reduced sulfur compounds are available. The techniques that can be used for the detection and quantification of underwater vents are also described, including geophysical and geochemical tools. Finally, the main geobiological effects due to the presence of the hydrothermal activity and the induced changes in water chemistry are assessed.
    Description: SMS was supported by the United States National Science Foundation (OCE-1124272) and the WHOI Investment in Science Fund and SIB by the Deutsche Forschungsgemeinschaft (Emmy Noether grant BU 2606/1).
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    Birds of a feather eat plastic together: high levels of plastic ingestion in Great Shearwater adults and juveniles across their annual migratory cycle (2022)
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    Publication Date: 2022-05-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Robuck, A. R., Hudak, C. A., Agvent, L., Emery, G., Ryan, P. G., Perold, V., Powers, K. D., Pedersen, J., Thompson, M. A., Suca, J. J., Moore, M. J., Harms, C. A., Bugoni, L., Shield, G., Glass, T., Wiley, D. N., & Lohmann, R. Birds of a feather eat plastic together: high levels of plastic ingestion in Great Shearwater adults and juveniles across their annual migratory cycle. Frontiers in Marine Science, 8, (2022): 719721, https://doi.org/10.3389/fmars.2021.719721.
    Description: Limited work to date has examined plastic ingestion in highly migratory seabirds like Great Shearwaters (Ardenna gravis) across their entire migratory range. We examined 217 Great Shearwaters obtained from 2008–2019 at multiple locations spanning their yearly migration cycle across the Northwest and South Atlantic to assess accumulation of ingested plastic as well as trends over time and between locations. A total of 2328 plastic fragments were documented in the ventriculus portion of the gastrointestinal tract, with an average of 9 plastic fragments per bird. The mass, count, and frequency of plastic occurrence (FO) varied by location, with higher plastic burdens but lower FO in South Atlantic adults and chicks from the breeding colonies. No fragments of the same size or morphology were found in the primary forage fish prey, the Sand Lance (Ammodytes spp., n = 202) that supports Great Shearwaters in Massachusetts Bay, United States, suggesting the birds directly ingest the bulk of their plastic loads rather than accumulating via trophic transfer. Fourier-transform infrared spectroscopy indicated that low- and high-density polyethylene were the most common polymers ingested, within all years and locations. Individuals from the South Atlantic contained a higher proportion of larger plastic items and fragments compared to analogous life stages in the NW Atlantic, possibly due to increased use of remote, pelagic areas subject to reduced inputs of smaller, more diverse, and potentially less buoyant plastics found adjacent to coastal margins. Different signatures of polymer type, size, and category between similar life stages at different locations suggests rapid turnover of ingested plastics commensurate with migratory stage and location, though more empirical evidence is needed to ground-truth this hypothesis. This work is the first to comprehensively measure the accumulation of ingested plastics by Great Shearwaters over the last decade and across multiple locations spanning their yearly trans-equatorial migration cycle and underscores their utility as sentinels of plastic pollution in Atlantic ecosystems.
    Description: This project was supported by the NOAA Fisheries National Seabird Program and the Volgenau Foundation. AR acknowledges support from the National Oceanic and Atmospheric Administration Dr. Nancy Foster Scholarship Program (NOAA Award Number NA17NOS4290028), the Robert and Patricia Switzer Foundation, the STEEP Superfund Research Program (NIEHS Award Number P42ES027706), and the Oak Ridge Institute for Science and Education (ORISE) program. LB was funded by INCT-Mar COI and PQ Grant No. 311409/2018-0, both by the Brazilian National Research Council (CNPq). JS was funded by the National Science Foundation Graduate Research Fellowship program.
    Keywords: Ardenna gravis ; migration ; pollution ; shearwaters ; marine debris ; microplastic ; nurdles ; bycatch
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    High larval concentrations and onshore transport of barnacle cyprids associated with thermal stratification (2022)
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    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Yamhure, G. M., Reyns, N., & Pineda, J. High larval concentrations and onshore transport of barnacle cyprids associated with thermal stratification. Frontiers in Marine Science, 8, (2021): 748389, https://doi.org/10.3389/fmars.2021.748389.
    Description: To better understand the hydrodynamic and hydrographic conditions experienced by larvae in the nearshore (within 1 km of shore), and the role that larval behavior plays in mediating shoreward transport to adult benthic habitats, we examined the vertical distribution and concentration of barnacle cyprids in a shallow, nearshore region in southern California, United States. We collected high-resolution physical measurements of currents and temperature at 3 stations (8, 5, and 4 m depths), and high-frequency measurements of barnacle larvae at a 4 m deep station ∼300 m from shore. Larvae were sampled from distinct 1 m depth intervals between the surface and the bottom (0–1 m, 1–2 m, 2–3 m, 3 m-bottom), each hour for overnight periods that ranged between 13 to 24 h in five cruises during the summers of 2017 and 2018. Barnacle cyprids of Chthamalus fissus predominated in all samples. Thermal stratification decreased closer to shore, but when the nearshore-most station remained stratified (Δ°C m–1 ≥ 0.1), C. fissus cyprid concentrations were high to extremely abundant (exceeding 200 and 4,000 individuals m–3, respectively). There were significant positive correlations between thermal stratification and the log-transformed C. fissus concentration at cruise-to-cruise scales, and between stratification and vertical variability in the high-frequency cross-shore currents at 2-day scales. Additionally, estimated larval transport was relatively high and shoreward when nearshore thermal stratification was greatest. Significant, albeit small, diel differences in cyprid distributions were also observed, with the proportion of cyprids increasing near the surface at night, and concentrations greater during the day than at night. Collectively, these results suggest that thermal stratification increases larval supply to the nearshore, and may enhance onshore larval transport to augment chances of successful settlement and recruitment to the intertidal adult habitat.
    Description: This study was funded by the National Science Foundation under grants OCE-1357290, OCE-1357327, OCE-1630459, and OCE-1630474.
    Keywords: larval vertical distribution ; thermocline ; larval transport ; Chthamalus fissus ; diel cycles ; nearshore
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    Functional analyses of peripheral auditory system adaptations for echolocation in air vs. water (2022)
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    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ketten, D. R., Simmons, J. A., Riquimaroux, H., & Simmons, A. M. Functional analyses of peripheral auditory system adaptations for echolocation in air vs. water. Frontiers in Ecology and Evolution, 09, (2021): 661216, https://doi.org/10.3389/fevo.2021.661216.
    Description: The similarity of acoustic tasks performed by odontocete (toothed whale) and microchiropteran (insectivorous bat) biosonar suggests they may have common ultrasonic signal reception and processing mechanisms. However, there are also significant media and prey dependent differences, notably speed of sound and wavelengths in air vs. water, that may be reflected in adaptations in their auditory systems and peak spectra of out-going signals for similarly sized prey. We examined the anatomy of the peripheral auditory system of two species of FM bat (big brown bat Eptesicus fuscus; Japanese house bat Pipistrellus abramus) and two toothed whales (harbor porpoise Phocoena phocoena; bottlenose dolphin Tursiops truncatus) using ultra high resolution (11–100 micron) isotropic voxel computed tomography (helical and microCT). Significant differences were found for oval and round window location, cochlear length, basilar membrane gradients, neural distributions, cochlear spiral morphometry and curvature, and basilar membrane suspension distributions. Length correlates with body mass, not hearing ranges. High and low frequency hearing range cut-offs correlate with basilar membrane thickness/width ratios and the cochlear radius of curvature. These features are predictive of high and low frequency hearing limits in all ears examined. The ears of the harbor porpoise, the highest frequency echolocator in the study, had significantly greater stiffness, higher basal basilar membrane ratios, and bilateral bony support for 60% of the basilar membrane length. The porpoise’s basilar membrane includes a “foveal” region with “stretched” frequency representation and relatively constant membrane thickness/width ratio values similar to those reported for some bat species. Both species of bats and the harbor porpoise displayed unusual stapedial input locations and low ratios of cochlear radii, specializations that may enhance higher ultrasonic frequency signal resolution and deter low frequency cochlear propagation.
    Description: MicroCT scanning, data analyses, and manuscript preparation were assisted by funding to DK from the Joint Industry Program (contract JIP22 III-16-08 – 55205300) and fellowships from the Hanse-Wissenschaftskolleg ICBM Fellowship and the Helmholtz International Fellow research programs. Big brown bat data collection and analysis were supported by an Office of Naval Research grant N00014-14-1-05880 to JS and an Office of Naval Research MURI grant N00014-17-1-2736 to JS and AS. Specimen collection, histology processing, and helical scanning related to the data reported in this study were supported through multiple grants and contracts since 2010 to DK from NIH, N45/LMRS-United States Navy Environmental Division (EnvDiv), Office of Naval Research, and ONR Global.
    Keywords: biosonar ; cochlea ; basilar membrane ; stapes ; inner ear ; echolocation ; bat ; dolphin
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    Designing coastal adaptation strategies to tackle sea level rise (2022)
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    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bongarts Lebbe, T., Rey-Valette, H., Chaumillon, E., Camus, G., Almar, R., Cazenave, A., Claudet, J., Rocle, N., Meur-Ferec, C., Viard, F., Mercier, D., Dupuy, C., Menard, F., Rossel, B. A., Mullineaux, L., Sicre, M.-A., Zivian, A., Gaill, F., & Euzen, A. Designing coastal adaptation strategies to tackle sea level rise. Frontiers in Marine Science, 8, (2021): 740602, https://doi.org/10.3389/fmars.2021.740602.
    Description: Faced with sea level rise and the intensification of extreme events, human populations living on the coasts are developing responses to address local situations. A synthesis of the literature on responses to coastal adaptation allows us to highlight different adaptation strategies. Here, we analyze these strategies according to the complexity of their implementation, both institutionally and technically. First, we distinguish two opposing paradigms – fighting against rising sea levels or adapting to new climatic conditions; and second, we observe the level of integrated management of the strategies. This typology allows a distinction between four archetypes with the most commonly associated governance modalities for each. We then underline the need for hybrid approaches and adaptation trajectories over time to take into account local socio-cultural, geographical, and climatic conditions as well as to integrate stakeholders in the design and implementation of responses. We show that dynamic and participatory policies can foster collective learning processes and enable the evolution of social values and behaviors. Finally, adaptation policies rely on knowledge and participatory engagement, multi-scalar governance, policy monitoring, and territorial solidarity. These conditions are especially relevant for densely populated areas that will be confronted with sea level rise, thus for coastal cities in particular.
    Description: This work was conducted as part of the project SEA’TIES led by the Ocean & Climate Platform. SEA’TIES is funded by the Prince Albert II Foundation (No. 3112), Veolia Foundation (No. 20EB2004), and Fondation de France, Monaco. It was coordinated by the CNRS, in the framework of the RTPi (International Multidisciplinary Thematic Network) which drives the scientific component of the SEA’TIES project.
    Keywords: climate change ; sea level rise ; adaptation ; governance ; nature-based solutions ; multidisciplinary approach ; vulnerability ; coastal cities
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    Impact of shifting subpolar front on phytoplankton dynamics in the western margin of East/Japan Sea (2022)
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    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kim, D., Ji, R., Park, H. J., Feng, Z., Jang, J., Lee, C. l, Kang, Y.-H., & Kang, C.-K. Impact of shifting subpolar front on phytoplankton dynamics in the western margin of East/Japan Sea. Frontiers in Marine Science, 8, (2021): 790703, https://doi.org/10.3389/fmars.2021.790703.
    Description: A subpolar front (SPF) generated between the East Korea Warm Current (EKWC) and the North Korea Cold Current (NKCC) in the western margin of the East/Japan Sea has shifted northward in recent decades. This study investigated the biomass and composition of the phytoplankton assemblage in relation to hydrological and biogeochemical features in the shallow shelf and slope off the Korean coast from January to June in 2016 and 2017, to determine the mechanistic effects of SPF on spring–summer phytoplankton bloom dynamics. Monthly average depth-integrated chlorophyll a (Chl a) levels and the contribution of phytoplankton classes revealed bimodal diatom blooms in early spring and summer in the frontal zone. Canonical correspondence analysis showed that the distribution of high Chl a was associated with cold, low-salinity NKCC water in March 2016. No Chl a peak was observed in March 2017 when the warm saline EKWC water mass invaded. These results suggest that the NKCC intrusion acts as a forcing mechanism leading to enhanced phytoplankton biomass in the frontal zone. In contrast, positive correlations of Chl a concentration with water density and nutrient concentrations suggest that summer blooms were fed by the subsurface chlorophyll maximum (SCM) driven by shoaling of the pycnocline and nitracline. Varying water-column stratification determined the thickness of the SCM layer, driving year-to-year variability in the magnitude of diatom blooms. These findings further suggest that seasonal/interannual variability in the timing of algal blooms affects regional trophodynamics and hence could be an important factor in explaining ecosystem changes in this region.
    Description: This research was supported by “Long-term change of structure and function in marine ecosystems of Korea” and “Walleye pollock stock management based on marine information and communication technology” funded by the Ministry of Oceans and Fisheries, South Korea.
    Keywords: phytoplankton ; diatom bloom ; photosynthetic pigments ; subpolar front ; Ulleung Basin ; East/Japan Sea ; trophodynamics ; ocean currents
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    COI metabarcoding of zooplankton species diversity for time-series monitoring of the NW Atlantic continental shelf (2022)
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    Publication Date: 2022-08-04
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bucklin, A., Batta-Lona, P., Questel, J., Wiebe, P., Richardson, D., Copley, N., & O’Brien, T. COI metabarcoding of zooplankton species diversity for time-series monitoring of the NW Atlantic continental shelf. Frontiers in Marine Science, 9, (2022): 867893, https://doi.org/10.3389/fmars.2022.867893.
    Description: Marine zooplankton are rapid-responders and useful indicators of environmental variability and climate change impacts on pelagic ecosystems on time scales ranging from seasons to years to decades. The systematic complexity and taxonomic diversity of the zooplankton assemblage has presented significant challenges for routine morphological (microscopic) identification of species in samples collected during ecosystem monitoring and fisheries management surveys. Metabarcoding using the mitochondrial Cytochrome Oxidase I (COI) gene region has shown promise for detecting and identifying species of some – but not all – taxonomic groups in samples of marine zooplankton. This study examined species diversity of zooplankton on the Northwest Atlantic Continental Shelf using 27 samples collected in 2002-2012 from the Gulf of Maine, Georges Bank, and Mid-Atlantic Bight during Ecosystem Monitoring (EcoMon) Surveys by the NOAA NMFS Northeast Fisheries Science Center. COI metabarcodes were identified using the MetaZooGene Barcode Atlas and Database (https://metazoogene.org/MZGdb) specific to the North Atlantic Ocean. A total of 181 species across 23 taxonomic groups were detected, including a number of sibling and cryptic species that were not discriminated by morphological taxonomic analysis of EcoMon samples. In all, 67 species of 15 taxonomic groups had ≥ 50 COI sequences; 23 species had 〉1,000 COI sequences. Comparative analysis of molecular and morphological data showed significant correlations between COI sequence numbers and microscopic counts for 5 of 6 taxonomic groups and for 5 of 7 species with 〉1,000 COI sequences for which both types of data were available. Multivariate statistical analysis showed clustering of samples within each region based on both COI sequence numbers and EcoMon counts, although differences among the three regions were not statistically significant. The results demonstrate the power and potential of COI metabarcoding for identification of species of metazoan zooplankton in the context of ecosystem monitoring.
    Description: This publication resulted in part from support provided by the Scientific Committee on Oceanic Research (SCOR). Funds were also contributed by the U.S. National Science Foundation (Grant OCE-1840868) and by national SCOR committees.
    Keywords: zooplankton ; metabarcoding ; cytochrome oxidase I ; species diversity ; ecosystem monitoring ; Northwest Atlantic continental shelf
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    Microbial hydrocarbon degradation in Guaymas Basin—exploring the roles and potential interactions of fungi and sulfate-reducing bacteria (2022)
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    Publication Date: 2022-07-13
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Edgcomb, V., Teske, A., & Mara, P. Microbial hydrocarbon degradation in Guaymas Basin—exploring the roles and potential interactions of fungi and sulfate-reducing bacteria. Frontiers in Microbiology, 13, (2022): 831828, https://doi.org/10.3389/fmicb.2022.831828.
    Description: Hydrocarbons are degraded by specialized types of bacteria, archaea, and fungi. Their occurrence in marine hydrocarbon seeps and sediments prompted a study of their role and their potential interactions, using the hydrocarbon-rich hydrothermal sediments of Guaymas Basin in the Gulf of California as a model system. This sedimented vent site is characterized by localized hydrothermal circulation that introduces seawater sulfate into methane- and hydrocarbon-rich sediments, and thus selects for diverse hydrocarbon-degrading communities of which methane, alkane- and aromatics-oxidizing sulfate-reducing bacteria and archaea have been especially well-studied. Current molecular and cultivation surveys are detecting diverse fungi in Guaymas Basin hydrothermal sediments, and draw attention to possible fungal-bacterial interactions. In this Hypothesis and Theory article, we report on background, recent results and outcomes, and underlying hypotheses that guide current experiments on this topic in the Edgcomb and Teske labs in 2021, and that we will revisit during our ongoing investigations of bacterial, archaeal, and fungal communities in the deep sedimentary subsurface of Guaymas Basin.
    Description: This project was supported by collaborative NSF Biological Oceanography grants OCE-1829903 and OCE-1829680 “Hydrothermal fungi in the Guaymas Basin Hydrocarbon Ecosystem” to VE and AT, and collaborative NSF Biological Oceanography grants OCE-2046799 and OCE-2048489 “IODP-enabled Insights into Fungi and Their Metabolic Interactions with Other Microorganisms in Deep Subsurface Hydrothermal Sediments” to VE and AT. PM was supported by OCE-2046799 and OCE-1829903. Sampling in Guaymas Basin was supported by collaborative NSF Biological Oceanography grant 1357238 “Collaborative Research: Microbial carbon cycling and its interaction with sulfur and nitrogen transformations in Guaymas Basin hydrothermal sediments” to AT.
    Keywords: hydrocarbon ; fungi ; sulfate-reducing bacteria ; microbial interaction ; Guaymas Basin
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    Diversity of microbial eukaryotes along the West Antarctic Peninsula in austral spring (2022)
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    Publication Date: 2022-09-22
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Grattepanche, J.-D., Jeffrey, W., Gast, R., & Sanders, R. Diversity of microbial eukaryotes along the West Antarctic Peninsula in austral spring. Frontiers in Microbiology, 13, (2022): 844856, https://doi.org/10.3389/fmicb.2022.844856.
    Description: During a cruise from October to November 2019, along the West Antarctic Peninsula, between 64.32 and 68.37°S, we assessed the diversity and composition of the active microbial eukaryotic community within three size fractions: micro- (〉 20 μm), nano- (20–5 μm), and pico-size fractions (5–0.2 μm). The communities and the environmental parameters displayed latitudinal gradients, and we observed a strong similarity in the microbial eukaryotic communities as well as the environmental parameters between the sub-surface and the deep chlorophyll maximum (DCM) depths. Chlorophyll concentrations were low, and the mixed layer was shallow for most of the 17 stations sampled. The richness of the microplankton was higher in Marguerite Bay (our southernmost stations), compared to more northern stations, while the diversity for the nano- and pico-plankton was relatively stable across latitude. The microplankton communities were dominated by autotrophs, mostly diatoms, while mixotrophs (phototrophs-consuming bacteria and kleptoplastidic ciliates, mostly alveolates, and cryptophytes) were the most abundant and active members of the nano- and picoplankton communities. While phototrophy was the dominant trophic mode, heterotrophy (mixotrophy, phagotrophy, and parasitism) tended to increase southward. The samples from Marguerite Bay showed a distinct community with a high diversity of nanoplankton predators, including spirotrich ciliates, and dinoflagellates, while cryptophytes were observed elsewhere. Some lineages were significantly related—either positively or negatively—to ice coverage (e.g., positive for Pelagophyceae, negative for Spirotrichea) and temperature (e.g., positive for Cryptophyceae, negative for Spirotrichea). This suggests that climate changes will have a strong impact on the microbial eukaryotic community.
    Description: This work was supported by the National Science Foundation (Grant Nos. ANT 1744767 to RS, ANT 1744663 to RG, and ANT 1744638 to WJ). This research was based, in part, upon sequencing conducted using the Rhode Island Genomics and Sequencing Center, which was supported in part by the National Science Foundation (MRI Grant No. DBI-0215393 and EPSCoR Grant Nos. 0554548 and EPS-1004057), the US Department of Agriculture (Grant Nos. 2002-34438-12688 and 2003-34438-13111), and the University of Rhode Island. This research includes calculations carried out on Temple University HPC resources supported in part by the National Science Foundation through major research instrumentation (Grant No. 1625061) and by the US Army Research Laboratory under (Contract No. W911NF-16-2-0189).
    Keywords: picoplankton ; nanoplankton ; microplankton ; Antarctic protists ; high-throughput sequencing ; RNA community
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    Sounding the call for a global library of underwater biological sounds (2022)
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    Publication Date: 2022-06-09
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Parsons, M., Lin, T.-H., Mooney, T., Erbe, C., Juanes, F., Lammers, M., Li, S., Linke, S., Looby, A., Nedelec, S., Van Opzeeland, I., Radford, C., Rice, A., Sayigh, L., Stanley, J., Urban, E., & Di Iorio, L. Sounding the call for a global library of underwater biological sounds. Frontiers in Ecology and Evolution, 10, (2022): 810156, https://doi.org/10.3389/fevo.2022.810156.
    Description: Aquatic environments encompass the world’s most extensive habitats, rich with sounds produced by a diversity of animals. Passive acoustic monitoring (PAM) is an increasingly accessible remote sensing technology that uses hydrophones to listen to the underwater world and represents an unprecedented, non-invasive method to monitor underwater environments. This information can assist in the delineation of biologically important areas via detection of sound-producing species or characterization of ecosystem type and condition, inferred from the acoustic properties of the local soundscape. At a time when worldwide biodiversity is in significant decline and underwater soundscapes are being altered as a result of anthropogenic impacts, there is a need to document, quantify, and understand biotic sound sources–potentially before they disappear. A significant step toward these goals is the development of a web-based, open-access platform that provides: (1) a reference library of known and unknown biological sound sources (by integrating and expanding existing libraries around the world); (2) a data repository portal for annotated and unannotated audio recordings of single sources and of soundscapes; (3) a training platform for artificial intelligence algorithms for signal detection and classification; and (4) a citizen science-based application for public users. Although individually, these resources are often met on regional and taxa-specific scales, many are not sustained and, collectively, an enduring global database with an integrated platform has not been realized. We discuss the benefits such a program can provide, previous calls for global data-sharing and reference libraries, and the challenges that need to be overcome to bring together bio- and ecoacousticians, bioinformaticians, propagation experts, web engineers, and signal processing specialists (e.g., artificial intelligence) with the necessary support and funding to build a sustainable and scalable platform that could address the needs of all contributors and stakeholders into the future.
    Description: Support for the initial author group to meet, discuss, and build consensus on the issues within this manuscript was provided by the Scientific Committee on Oceanic Research, Monmouth University Urban Coast Institute, and Rockefeller Program for the Human Environment. The U.S. National Science Foundation supported the publication of this article through Grant OCE-1840868 to the Scientific Committee on Oceanic Research.
    Keywords: soundscape ; bioacoustics database ; artificial intelligence ; biodiversity ; passive acoustic monitoring ; ecological informatics
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    Two decades of full-depth current velocity observations from a moored observatory in the central equatorial Atlantic at 0°N, 23°W (2022)
    Frontiers Media
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    Publication Date: 2022-11-04
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Tuchen, F., Brandt, P., Hahn, J., Hummels, R., Krahmann, G., Bourlès, B., Provost, C., McPhaden, M., & Toole, J. Two decades of full-depth current velocity observations from a moored observatory in the central equatorial Atlantic at 0°N, 23°W. Frontiers in Marine Science, 9, (2022): 910979, https://doi.org/10.3389/fmars.2022.910979.
    Description: Regional climate variability in the tropical Atlantic, from interannual to decadal time scales, is inevitably connected to changes in the strength and position of the individual components of the tropical current system with impacts on societally relevant climate hazards such as anomalous rainfall or droughts over the surrounding continents (Bourlès et al., 2019; Foltz et al., 2019). Furthermore, the lateral supply of dissolved oxygen in the tropical Atlantic upper-ocean is closely linked to the zonal current bands (Brandt et al., 2008; Brandt et al., 2012; Burmeister et al., 2020) and especially to the Equatorial Undercurrent (EUC) and its long-term variations with potential implications for regional marine ecosystems (Brandt et al., 2021). The eastward flowing EUC is located between 70 to 200 m depth and forms one of the strongest tropical currents with maximum velocities of up to 1 m s-1 and maximum variability on seasonal time scales (Brandt et al., 2014; Johns et al., 2014). In the intermediate to deep equatorial Atlantic, variability on longer time scales is mainly governed by alternating, vertically-stacked, zonal currents (equatorial deep jets (EDJs); Johnson and Zhang, 2003). At a fixed location, the phases of these jets are propagating downward with time, implying that parts of their energy must propagate upward towards the surface (Brandt et al., 2011). In fact, a pronounced interannual cycle of about 4.5 years, that is associated with EDJs, is projected onto surface parameters such as sea surface temperature or precipitation (Brandt et al., 2011) further demonstrating the importance of understanding equatorial circulation variability and its role in tropical climate variability.
    Description: This study was funded by EU H2020 under grant agreement 817578 TRIATLAS project, by the Deutsche Forschungsgemeinschaft as part of the Sonderforschungsbereich754 “Climate–Biogeochemistry Interactions in the Tropical Ocean” and through several research cruises with RV Meteor, RV Maria S. Merian, RV L'Atalante, and RV Sonne and by the Deutsche Bundesministerium für Bildung und Forschung (BMBF) as part of the projects RACE (03F06518) and by the European Union 7th Framework Programme (FP7) under Grant Agreement 603521. Moored velocity observations were acquired in cooperation with the PIRATA project supported by NOAA (USA), IRD and Meteo-France (France), INPE (Brazil) and the Brazil Navy. This research was performed while FPT held an NRC Research Associateship Award at NOAA’s Atlantic Oceanographic and Meteorological Laboratory. FPT, PB, JH, RH, and GK are grateful for continuing support from GEOMAR Helmholtz Centre for Ocean Research Kiel. MM acknowledges the support of NOAA; PMEL contribution no. 5359. JT's contributions to this study were supported by the U.S. National Science Foundation.
    Keywords: Ocean observations ; Physical oceanography ; Equatorial Atlantic circulation ; Ocean currents ; Moored observations ; Climate variability
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    A warm and a cold spot in Cape Cod waters amid the recent New England Shelf Warming (2022)
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    Publication Date: 2022-11-04
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Yu, L., & Yang, K. A warm and a cold spot in Cape Cod waters amid the recent New England Shelf Warming. Frontiers in Marine Science, 9, (2022): 922046, https://doi.org/10.3389/fmars.2022.922046.
    Description: Despite the widely recognized warming of the New England Continental Shelf (NES), climate patterns of the shelf’s economically and ecologically important coastal environments remain less examined. Here we use a satellite sea-surface temperature (SST) analysis gridded on 0.05°C spatial resolution to show, for the first time, the existence of a warm and a cold spot in the environs of Cape Cod, Massachusetts amid the NES warming of the past 15 years. The warm spot refers to an increasing warming trend in shallow waters of Nantucket Sound sheltered by the islands of Martha’s Vineyard and Nantucket. The summer SST maxima have increased by 3.1±1.0°C (p〈0.1), about three times faster than the warming elsewhere on the NES, and the summer season has lengthened by 20 ± 7 days (p〈0.1). The cold spot refers to an increasing cooling trend over Nantucket Shoals, an area of shallow sandy shelf that extends south and southeast from Nantucket Island and also known for strong tidal mixing. The strong cooling trend during June–August reduced the SST maxima by -2.5±1.2°C (p〈0.1) and shortened the warm season by -32 ± 11 days (p〈0.1). Away from the Cape Cod waters, the broad warming on the shelf is attributable to a forward shifted annual cycle. The shift is most significant in August–November, during which the summer temperatures lingered longer into the fall, producing a pronounced warming and delaying the onset of the fall season by 13 ± 6 days (p〈0.1). The three different patterns of SST phenology trends displayed by the respective warm spot, the cold spot, and the broad shelf highlight the highly dynamically diverse responses of coastal waters under climate warming. Finally, the study showed that spatial resolution of SST datasets affects the characterization of the spatial heterogeneity in the nearshore SSTs. The widely used Optimum Interpolation SST (OISST) on 0.25°C resolution was examined. Although the two SST datasets agree well with the measurements from the moored buoys at four locations, OISST does not have the cold spot and shows a higher rate of warming on the shelf.
    Description: This study is supported by NOAA Global Ocean Monitoring and Observation (GOMO) Program, grand number NA19OAR4320074.
    Keywords: New England continental shelf warming ; Cape Cod ; Phenology change of sea surface temperature ; Fine-resolution satellite observations ; Coastal warm spot ; Coastal cold spot
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    Drivers of marine heatwaves in the Northwest Atlantic: the role of air-sea interaction during onset and decline (2021)
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Schlegel, R. W., Oliver, E. C. J., & Chen, K. Drivers of marine heatwaves in the Northwest Atlantic: the role of air-sea interaction during onset and decline. Frontiers in Marine Science, 8, (2021): 627970, https://doi.org/10.3389/fmars.2021.627970
    Description: Marine heatwaves (MHWs) are increasing in duration and intensity at a global scale and are projected to continue to increase due to the anthropogenic warming of the climate. Because MHWs may have drastic impacts on fisheries and other marine goods and services, there is a growing interest in understanding the predictability and developing practical predictions of these events. A necessary step toward prediction is to develop a better understanding of the drivers and processes responsible for the development of MHWs. Prior research has shown that air–sea heat flux and ocean advection across sharp thermal gradients are common physical processes governing these anomalous events. In this study we apply various statistical analyses and employ the self-organizing map (SOM) technique to determine specifically which of the many candidate physical processes, informed by a theoretical mixed-layer heat budget, have the most pronounced effect on the onset and/or decline of MHWs on the Northwest Atlantic continental shelf. It was found that latent heat flux is the most common driver of the onset of MHWs. Mixed layer depth (MLD) also strongly modulates the onset of MHWs. During the decay of MHWs, atmospheric forcing does not explain the evolution of the MHWs well, suggesting that oceanic processes are important in the decay of MHWs. The SOM analysis revealed three primary synoptic scale patterns during MHWs: low-pressure cyclonic Autumn-Winter systems, high-pressure anti-cyclonic Spring-Summer blocking, and mild but long-lasting Summer blocking. Our results show that nearly half of past MHWs on the Northwest Atlantic shelf are initiated by positive heat flux anomaly into the ocean, but less than one fifth of MHWs decay due to this process, suggesting that oceanic processes, e.g., advection and mixing are the primary driver for the decay of most MHWs.
    Description: RS was supported by the Ocean Frontier Institute International Postdoctoral Fellowship hosted jointly by Dalhousie University and Woods Hole Oceanographic Institution, through an award from the Canada First Research Excellence Fund. EO was funded through the National Sciences and Engineering Research Council of Canada Discovery Grant RGPIN-2018-05255 and Marine Environmental Observation, Prediction, and Response Network Early Career Faculty Grant 1-02-02-059.1. KC was supported by National Oceanic and Atmospheric Administration Climate Program Office Modeling, Analysis, Predictions, and Projections (MAPP) program under grant NA19OAR4320074 and Climate Variability and Predictability (CVP) program under grant NA20OAR4310398.
    Keywords: Marine heatwaves ; Air-sea heat flux ; Drivers ; Northwest Atlantic ; SST ; Physical oceanography
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    Comparison of oyster aquaculture methods and their potential to from coastal ecosystems (2021)
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Mara, P., Edgcomb, V. P., Sehein, T. R., Beaudoin, D., Martinsen, C., Lovely, C., Belcher, B., Cox, R., Curran, M., Farnan, C., Giannini, P., Lott, S., Paquette, K., Pinckney, A., Schafer, N., Surgeon-Rogers, T., & Rogers, D. R. Comparison of oyster aquaculture methods and their potential to from coastal ecosystems. Frontiers in Marine Science, 8,(2021): 633314, https://doi.org/10.3389/fmars.2021.633314.
    Description: Coastal ecosystems are impacted by excessive nutrient inputs that cause degradation of water quality and impairments of ecosystem functioning. Regulatory and management efforts to enhance nutrient export from coastal ecosystems include sustainable oyster aquaculture that removes nitrogen in the form of oyster biomass and increases particulate export to underlying sediments where increased organic material may enhance microbial denitrification. To better understand the impacts of oyster aquaculture on nitrogen removal, we examined bacterial processes in sediments underlying three of the most common aquaculture methods that vary in the proximity of oysters to the sediments. Sediment samples underlying sites managed with these different aquaculture methods were examined using the 16S rRNA gene to assess microbial community structure, gene expression analyses to examine nitrogen and sulfur cycling genes, and nitrogen gas flux measurements. All sites were located in the same hydrodynamic setting within Waquoit Bay, MA during 2018 and 2019. Although sediments under the different oyster farming practices showed similar communities, ordination analysis revealed discrete community groups formed along the sampling season. Measured N2 fluxes and expression of key genes involved in denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA) increased during mid-summer and into fall in both years primarily under bottom cages. While all three oyster growing methods enhanced nitrogen removal relative to the control site, gene expression data indicate that the nitrogen retaining process of DNRA is particularly enhanced after end of July under bottom cages, and to a lesser extent, under suspended and floating bags. The choice of gear can also potentially increase processes that induce nitrogen retention in the form of ammonia in the underlying sediments over time, thus causing deviations from predicted nitrogen removal. If nitrogen removal is a primary objective, monitoring for these shifts is essential for making decisions about siting and size of aquaculture sites from year to year.
    Description: This work was supported by the National Oceanic and Atmospheric Administration and National Estuarine Research Reserve System Science Collaborative, award NAI4NOS4190145 (subaward 3004686666) to DR and VE.
    Keywords: Nitrogen removal ; Oyster cultures ; Denitrification ; Anammox ; DNRA
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    Assessing the skill of a high-resolution marine biophysical model using geostatistical analysis of mesoscale ocean chlorophyll variability from field observations and remote sensing (2021)
    Frontiers Media
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creaive Commons Attribution License. The definitive version was published in Eveleth, R., Glover, D. M., Long, M. C., Lima, I. D., Chase, A. P., & Doney, S. C. . Assessing the skill of a high-resolution marine biophysical model using geostatistical analysis of mesoscale ocean chlorophyll variability from field observations and remote sensing. Frontiers in Marine Science, 8, (2021): 612764, https://doi.org/10.3389/fmars.2021.612764.
    Description: High-resolution ocean biophysical models are now routinely being conducted at basin and global-scale, opening opportunities to deepen our understanding of the mechanistic coupling of physical and biological processes at the mesoscale. Prior to using these models to test scientific questions, we need to assess their skill. While progress has been made in validating the mean field, little work has been done to evaluate skill of the simulated mesoscale variability. Here we use geostatistical 2-D variograms to quantify the magnitude and spatial scale of chlorophyll a patchiness in a 1/10th-degree eddy-resolving coupled Community Earth System Model simulation. We compare results from satellite remote sensing and ship underway observations in the North Atlantic Ocean, where there is a large seasonal phytoplankton bloom. The coefficients of variation, i.e., the arithmetic standard deviation divided by the mean, from the two observational data sets are approximately invariant across a large range of mean chlorophyll a values from oligotrophic and winter to subpolar bloom conditions. This relationship between the chlorophyll a mesoscale variability and the mean field appears to reflect an emergent property of marine biophysics, and the high-resolution simulation does poorly in capturing this skill metric, with the model underestimating observed variability under low chlorophyll a conditions such as in the subtropics.
    Description: This work was supported in part by the National Aeronautics and Space Administration (NASA) as part of the North Atlantic Aerosol and Marine Ecosystems Study (NAAMES; NASA grant 80NSSC18K0018). The CESM project is supported by the National Science Foundation and the Office of Science (BER) of the United States Department of Energy. Computing resources were provided by the Climate Simulation Laboratory at NCAR’s Computational and Information Systems Laboratory (CISL), sponsored by the National Science Foundation and other agencies. This research was enabled by CISL compute and storage resources.
    Keywords: Geostatistical analysis ; North Atlantic Ocean ; Community Earth System Model ; Model validataion ; Chlorophyll
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    Element-selective targeting of nutrient metabolites in environmental samples by inductively coupled plasma mass spectrometry and electrospray ionization mass spectrometry (2021)
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Li, J., Boiteau, R. M., Babcock-Adams, L., Acker, M., Song, Z., McIlvin, M. R., & Repeta, D. J. Element-selective targeting of nutrient metabolites in environmental samples by inductively coupled plasma mass spectrometry and electrospray ionization mass spectrometry. Frontiers in Marine Science, 8, (2021): 630494, https://doi.org/10.3389/fmars.2021.630494.
    Description: Metabolites that incorporate elements other than carbon, nitrogen, hydrogen and oxygen can be selectively detected by inductively coupled mass spectrometry (ICPMS). When used in parallel with chromatographic separations and conventional electrospray ionization mass spectrometry (ESIMS), ICPMS allows the analyst to quickly find, characterize and identify target metabolites that carry nutrient elements (P, S, trace metals; “nutrient metabolites”), which are of particular interest to investigations of microbial biogeochemical cycles. This approach has been applied to the study of siderophores and other trace metal organic ligands in the ocean. The original method used mass search algorithms that relied on the ratio of stable isotopologues of iron, copper and nickel to assign mass spectra collected by ESIMS to metabolites carrying these elements detected by ICPMS. However, while isotopologue-based mass assignment algorithms were highly successful in characterizing metabolites that incorporate some trace metals, they do not realize the whole potential of the ICPMS/ESIMS approach as they cannot be used to assign the molecular ions of metabolites with monoisotopic elements or elements for which the ratio of stable isotopes is not known. Here we report a revised ICPMS/ESIMS method that incorporates a number of changes to the configuration of instrument hardware that improves sensitivity of the method by a factor of 4–5, and allows for more accurate quantitation of metabolites. We also describe a new suite of mass search algorithms that can find and characterize metabolites that carry monoisotopic elements. We used the new method to identify siderophores in a laboratory culture of Vibrio cyclitrophicus and a seawater sample collected in the North Pacific Ocean, and to assign molecular ions to monoisotopic cobalt and iodine nutrient metabolites in extracts of a laboratory culture of the marine cyanobacterium Prochorococcus MIT9215.
    Description: This work was generously supported by the National Science Foundation grant OCE-1829761 to RB and OCE-1356747 and -1736280 to DR. DR also received generous support from the Simons Foundation Life Sciences Project Award 49476.
    Keywords: LC-MS ; Algorithm ; Environmental metabolomics ; Trace metal ; Siderophores
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    Impacts of multiple stressors on a benthic foraminiferal community: a long-term experiment assessing response to ocean acidification, hypoxia and warming (2021)
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bernhard, J. M., Wit, J. C., Starczak, V. R., Beaudoin, D. J., Phalen, W. G., & McCorkle, D. C. Impacts of multiple stressors on a benthic foraminiferal community: a long-term experiment assessing response to ocean acidification, hypoxia and warming. Frontiers in Marine Science, 8, (2021): 643339, https://doi.org/10.3389/fmars.2021.643339.
    Description: Ocean chemistry is changing as a result of human activities. Atmospheric carbon dioxide (CO2) concentrations are increasing, causing an increase in oceanic pCO2 that drives a decrease in oceanic pH, a process called ocean acidification (OA). Higher CO2 concentrations are also linked to rising global temperatures that can result in more stratified surface waters, reducing the exchange between surface and deep waters; this stronger stratification, along with nutrient pollution, contributes to an expansion of oxygen-depleted zones (so called hypoxia or deoxygenation). Determining the response of marine organisms to environmental changes is important for assessments of future ecosystem functioning. While many studies have assessed the impact of individual or paired stressors, fewer studies have assessed the combined impact of pCO2, O2, and temperature. A long-term experiment (∼10 months) with different treatments of these three stressors was conducted to determine their sole or combined impact on the abundance and survival of a benthic foraminiferal community collected from a continental-shelf site. Foraminifera are well suited to such study because of their small size, relatively rapid growth, varied mineralogies and physiologies. Inoculation materials were collected from a ∼77-m deep site south of Woods Hole, MA. Very fine sediments (〈53 μm) were used as inoculum, to allow the entire community to respond. Thirty-eight morphologically identified taxa grew during the experiment. Multivariate statistical analysis indicates that hypoxia was the major driving factor distinguishing the yields, while warming was secondary. Species responses were not consistent, with different species being most abundant in different treatments. Some taxa grew in all of the triple-stressor samples. Results from the experiment suggest that foraminiferal species’ responses will vary considerably, with some being negatively impacted by predicted environmental changes, while other taxa will tolerate, and perhaps even benefit, from deoxygenation, warming and OA.
    Description: This work was supported by the US NSF SEES-OA grant OCE-1219948 to JB and the Investment in Science Program at WHOI. DM also received support from the NSF Independent Research and Development Program.
    Keywords: Deoxygenation ; Ocean acidification ; Benthic communities ; Benthic foraminifera ; Climate change ; Propagule bank ; Global warming
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    Variable species responses to experimental stony coral tissue loss disease (SCTLD) exposure (2021)
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Meiling, S. S., Muller, E. M., Lasseigne, D., Rossin, A., Veglia, A. J., MacKnight, N., Dimos, B., Huntley, N., Correa, A. M. S., Smith, T. B., Holstein, D. M., Mydlarz, L. D., Apprill, A., & Brandt, M. E. Variable species responses to experimental stony coral tissue loss disease (SCTLD) exposure. Frontiers in Marine Science, 8, (2021): 670829, https://doi.org/10.3389/fmars.2021.670829.
    Description: Stony coral tissue loss disease (SCTLD) was initially documented in Florida in 2014 and outbreaks with similar characteristics have since appeared in disparate areas throughout the northern Caribbean, causing significant declines in coral communities. SCTLD is characterized by focal or multifocal lesions of denuded skeleton caused by rapid tissue loss and affects at least 22 reef-building species of Caribbean corals. A tissue-loss disease consistent with the case definition of SCTLD was first observed in the U.S. Virgin Islands (USVI) in January of 2019 off the south shore of St. Thomas at Flat Cay. The objective of the present study was to characterize species susceptibility to the disease present in St. Thomas in a controlled laboratory transmission experiment. Fragments of six species of corals (Colpophyllia natans, Montastraea cavernosa, Orbicella annularis, Porites astreoides, Pseudodiploria strigosa, and Siderastrea siderea) were simultaneously incubated with (but did not physically contact) SCTLD-affected colonies of Diploria labyrinthiformis and monitored for lesion appearance over an 8 day experimental period. Paired fragments from each corresponding coral genotype were equivalently exposed to apparently healthy colonies of D. labyrinthiformis to serve as controls; none of these fragments developed lesions throughout the experiment. When tissue-loss lesions appeared and progressed in a disease treatment, the affected coral fragment, and its corresponding control genet, were removed and preserved for future analysis. Based on measures including disease prevalence and incidence, relative risk of lesion development, and lesion progression rates, O. annularis, C. natans, and S. siderea showed the greatest susceptibility to SCTLD in the USVI. These species exhibited earlier average development of lesions, higher relative risk of lesion development, greater lesion prevalence, and faster lesion progression rates compared with the other species, some of which are considered to be more susceptible based on field observations (e.g., P. strigosa). The average transmission rate in the present study was comparable to tank studies in Florida, even though disease donor species differed. Our findings suggest that the tissue loss disease affecting reefs of the USVI has a similar epizootiology to that observed in other regions, particularly Florida.
    Description: This work was supported by the National Science Foundation (Biological Oceanography) award number 1928753 to MB and TS, 1928609 to AC, 1928817 to EM, 19228771 to LM, 1927277 to DH, and 1928761 to AA as well as by VI EPSCoR (NSF #0814417 and NSF #1946412).
    Keywords: Stony coral tissue loss disease ; Coral disease ; Transmission experiment ; Susceptibility ; Lesion progression rate ; Caribbean ; United States Virgin Islands ; Histopathology
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    International Quality-Controlled Ocean Database (IQuOD) v0.1: the temperature uncertainty specification (2021)
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cowley, R., Killick, R. E., Boyer, T., Gouretski, V., Reseghetti, F., Kizu, S., Palmer, M. D., Cheng, L., Storto, A., Le Menn, M., Simoncelli, S., Macdonald, A. M., & Domingues, C. M. International Quality-Controlled Ocean Database (IQuOD) v0.1: the temperature uncertainty specification. Frontiers in Marine Science, 8, (2021): 689695, https://doi.org/10.3389/fmars.2021.689695.
    Description: Ocean temperature observations are crucial for a host of climate research and forecasting activities, such as climate monitoring, ocean reanalysis and state estimation, seasonal-to-decadal forecasts, and ocean forecasting. For all of these applications, it is crucial to understand the uncertainty attached to each of the observations, accounting for changes in instrument technology and observing practices over time. Here, we describe the rationale behind the uncertainty specification provided for all in situ ocean temperature observations in the International Quality-controlled Ocean Database (IQuOD) v0.1, a value-added data product served alongside the World Ocean Database (WOD). We collected information from manufacturer specifications and other publications, providing the end user with uncertainty estimates based mainly on instrument type, along with extant auxiliary information such as calibration and collection method. The provision of a consistent set of observation uncertainties will provide a more complete understanding of historical ocean observations used to examine the changing environment. Moving forward, IQuOD will continue to work with the ocean observation, data assimilation and ocean climate communities to further refine uncertainty quantification. We encourage submissions of metadata and information about historical practices to the IQuOD project and WOD.
    Description: This work was supported by the Scientific Committee on Oceanic Research (SCOR) Working Group 148, funded by national SCOR committees and a grant to SCOR from the U.S. National Science Foundation (Grant OCE-1546580); and the Intergovernmental Oceanographic Commission of UNESCO/International Oceanographic Data and Information Exchange (IOC/IODE) IQuOD Steering Group. RC was supported through funding from the Earth Systems and Climate Change Hub of the Australian Government's National Environmental Science Program. RK and MP were supported by the Met Office Hadley Centre Climate Programme funded by BEIS and Defra. CD was supported by the Australian Research Council (Discovery Grant DP160103130), ARC Centre of Excellence for Climate Extremes (CE170100023) and by the Natural Environment Research Council (TICTOC, NE/P019293/1). AM's contribution was supported by National Science Foundation grant OCE#-1923387 and National Oceanographic and Atmospheric Administration grant #NA16OAR4310172.
    Keywords: XBT ; Ocean temperature profiles ; Ocean data assimilation ; Ocean climate ; Accuracy ; Uncertainty ; Bias correction
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    A blueprint for an inclusive, global deep-sea ocean decade field program (2021)
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Howell, K. L., Hilario, A., Allcock, A. L., Bailey, D. M., Baker, M., Clark, M. R., Colaco, A., Copley, J., Cordes, E. E., Danovaro, R., Dissanayake, A., Escobar, E., Esquete, P., Gallagher, A. J., Gates, A. R., Gaudron, S. M., German, C. R., Gjerde, K. M., Higgs, N. D., Le Bris, N., Levin, L. A., Manea, E., McClain, C., Menot, L., Mestre, N. C., Metaxas, A., Milligan, R. J., Muthumbi, A. W. N., Narayanaswamy, B. E., Ramalho, S. P., Ramirez-Llodra, E., Robson, L. M., Rogers, A. D., Sellanes, J., Sigwart, J. D., Sink, K., Snelgrove, P. V. R., Stefanoudis, P., V., Sumida, P. Y., Taylor, M. L., Thurber, A. R., Vieira, R. P., Watanabe, H. K., Woodall, L. C., & Xavier, J. R. A blueprint for an inclusive, global deep-sea ocean decade field program. Frontiers in Marine Science, 7, (2020): 584861, doi:10.3389/fmars.2020.584861.
    Description: The ocean plays a crucial role in the functioning of the Earth System and in the provision of vital goods and services. The United Nations (UN) declared 2021–2030 as the UN Decade of Ocean Science for Sustainable Development. The Roadmap for the Ocean Decade aims to achieve six critical societal outcomes (SOs) by 2030, through the pursuit of four objectives (Os). It specifically recognizes the scarcity of biological data for deep-sea biomes, and challenges the global scientific community to conduct research to advance understanding of deep-sea ecosystems to inform sustainable management. In this paper, we map four key scientific questions identified by the academic community to the Ocean Decade SOs: (i) What is the diversity of life in the deep ocean? (ii) How are populations and habitats connected? (iii) What is the role of living organisms in ecosystem function and service provision? and (iv) How do species, communities, and ecosystems respond to disturbance? We then consider the design of a global-scale program to address these questions by reviewing key drivers of ecological pattern and process. We recommend using the following criteria to stratify a global survey design: biogeographic region, depth, horizontal distance, substrate type, high and low climate hazard, fished/unfished, near/far from sources of pollution, licensed/protected from industry activities. We consider both spatial and temporal surveys, and emphasize new biological data collection that prioritizes southern and polar latitudes, deeper (〉 2000 m) depths, and midwater environments. We provide guidance on observational, experimental, and monitoring needs for different benthic and pelagic ecosystems. We then review recent efforts to standardize biological data and specimen collection and archiving, making “sampling design to knowledge application” recommendations in the context of a new global program. We also review and comment on needs, and recommend actions, to develop capacity in deep-sea research; and the role of inclusivity - from accessing indigenous and local knowledge to the sharing of technologies - as part of such a global program. We discuss the concept of a new global deep-sea biological research program ‘Challenger 150,’ highlighting what it could deliver for the Ocean Decade and UN Sustainable Development Goal 14.
    Description: Development of this paper was supported by funding from the Scientific Committee on Oceanic Research (SCOR) awarded to KH and AH as working group 159 co-chairs. KH, BN, and KS are supported by the UKRI funded One Ocean Hub NE/S008950/1. AH work is supported by the CESAM (UIDP/50017/2020 + 1432 UIDB/50017/2020) that is funded by Fundação para a Ciência e a Tecnologia (FCT)/MCTES through national funds. AA is supported by Science Foundation Ireland and the Marine Institute under the Investigators Program Grant Number SFI/15/IA/3100 co-funded under the European Regional Development Fund 2014–2020. AC is supported through the FunAzores -ACORES 01-0145-FEDER-000123 grant and by FCT through strategic project UID/05634/2020 and FCT and Direção-Geral de Politica do Mar (DGPM) through the project Mining2/2017/005. PE is funded by national funds (OE), through FCT in the scope of the framework contract foreseen in the numbers 4, 5 and 6 of the article 23, of the Decree-Law 57/2016, of August 29, changed by Law 57/2017, of July 19. SG research is supported by CNRS funds. CG is supported by an Independent Study Award and the Investment in Science Fund at WHOI. KG gratefully acknowledges support from Synchronicity Earth. LL is funded by the NOAA Office of Ocean Exploration and Research (NA19OAR0110305) and the US National Science Foundation (OCE 1634172). NM is supported by FCT and DGPM, through the project Mining2/2017/001 and the FCT grants CEECIND/00526/2017, UIDB/00350/2020 + UIDP/00350/2020. SR is funded by the FCTgrant CEECIND/00758/2017. JS is supported by ANID FONDECYT #1181153 and ANID Millennium Science Initiative Program #NC120030. JX research is funded by the European Union’s Horizon 2020 research and innovation program through the SponGES project (grant agreement no. 679849) and further supported by national funds through FCT within the scope of UIDB/04423/2020 and UIDP/04423/2020. The Natural Sciences and Engineering Council of Canada supports AM and PVRS. MB and the Deep-Ocean Stewardship Initiative are supported by Arcadia - A charitable fund of Lisbet Rausing and Peter Baldwin. BN work is supported by the NERC funded Arctic PRIZE NE/P006302/1.
    Keywords: Deep sea ; Blue economy ; Ocean Decade ; Biodivercity ; Essential ocean variables
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    Genomic and physiological characterization of Bacilli isolated from salt-pans with plant growth promoting features (2021)
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Petrillo, C., Castaldi, S., Lanzilli, M., Selci, M., Cordone, A., Giovannelli, D., & Isticato, R. Genomic and physiological characterization of Bacilli isolated from salt-pans with plant growth promoting features. Frontiers in Microbiology, 12, (2021): 715678, https://doi.org/10.3389/fmicb.2021.715678.
    Description: Massive application of chemical fertilizers and pesticides has been the main strategy used to cope with the rising crop demands in the last decades. The indiscriminate use of chemicals while providing a temporary solution to food demand has led to a decrease in crop productivity and an increase in the environmental impact of modern agriculture. A sustainable alternative to the use of agrochemicals is the use of microorganisms naturally capable of enhancing plant growth and protecting crops from pests known as Plant-Growth-Promoting Bacteria (PGPB). Aim of the present study was to isolate and characterize PGPB from salt-pans sand samples with activities associated to plant fitness increase. To survive high salinity, salt-tolerant microbes produce a broad range of compounds with heterogeneous biological activities that are potentially beneficial for plant growth. A total of 20 halophilic spore-forming bacteria have been screened in vitro for phyto-beneficial traits and compared with other two members of Bacillus genus recently isolated from the rhizosphere of the same collection site and characterized as potential biocontrol agents. Whole-genome analysis on seven selected strains confirmed the presence of numerous gene clusters with PGP and biocontrol functions and of novel secondary-metabolite biosynthetic genes, which could exert beneficial impacts on plant growth and protection. The predicted biocontrol potential was confirmed in dual culture assays against several phytopathogenic fungi and bacteria. Interestingly, the presence of predicted gene clusters with known biocontrol functions in some of the isolates was not predictive of the in vitro results, supporting the need of combining laboratory assays and genome mining in PGPB identification for future applications.
    Keywords: Spore-forming bacteria ; Biocontrol agents ; Halophiles ; Plant-growth-promoting bacteria ; Genome mining ; Bacilli
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    Mechanisms of manganese(II) oxidation by filamentous ascomycete fungi vary with species and time as a function of secretome composition (2021)
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zeiner, C. A., Purvine, S. O., Zink, E., Wu, S., Pasa-Tolic, L., Chaput, D. L., Santelli, C. M., & Hansel, C. M. Mechanisms of manganese(II) oxidation by filamentous ascomycete fungi vary with species and time as a function of secretome composition. Frontiers in Microbiology, 12, (2021): 610497, https://doi.org/10.3389/fmicb.2021.610497.
    Description: Manganese (Mn) oxides are among the strongest oxidants and sorbents in the environment, and Mn(II) oxidation to Mn(III/IV) (hydr)oxides includes both abiotic and microbially-mediated processes. While white-rot Basidiomycete fungi oxidize Mn(II) using laccases and manganese peroxidases in association with lignocellulose degradation, the mechanisms by which filamentous Ascomycete fungi oxidize Mn(II) and a physiological role for Mn(II) oxidation in these organisms remain poorly understood. Here we use a combination of chemical and in-gel assays and bulk mass spectrometry to demonstrate secretome-based Mn(II) oxidation in three phylogenetically diverse Ascomycetes that is mechanistically distinct from hyphal-associated Mn(II) oxidation on solid substrates. We show that Mn(II) oxidative capacity of these fungi is dictated by species-specific secreted enzymes and varies with secretome age, and we reveal the presence of both Cu-based and FAD-based Mn(II) oxidation mechanisms in all 3 species, demonstrating mechanistic redundancy. Specifically, we identify candidate Mn(II)-oxidizing enzymes as tyrosinase and glyoxal oxidase in Stagonospora sp. SRC1lsM3a, bilirubin oxidase in Stagonospora sp. and Paraconiothyrium sporulosum AP3s5-JAC2a, and GMC oxidoreductase in all 3 species, including Pyrenochaeta sp. DS3sAY3a. The diversity of the candidate Mn(II)-oxidizing enzymes identified in this study suggests that the ability of fungal secretomes to oxidize Mn(II) may be more widespread than previously thought.
    Description: This work was supported by the National Science Foundation, grant numbers EAR-1249489 and CBET-1336496, both awarded to CH, by a JGI-EMSL Collaborative Science Initiative grant (proposal number 48100) awarded to CH and CS, and by the University of St. Thomas. Personal support for CZ was also provided by Harvard University and by a Ford Foundation Predoctoral Fellowship administered by the National Academies. A portion of this research was performed under the Facilities Integrating Collaborations for User Science (FICUS) program and used resources at the DOE Joint Genome Institute and the Environmental Molecular Sciences Laboratory (grid.436923.9), which are DOE Office of Science User Facilities. Both facilities are sponsored by the Biological and Environmental Research Program and operated under Contract Nos. DE-AC02-05CH11231 (JGI) and DE-AC05-76RL01830 (EMSL). Part of this research was performed at the Bauer Core Facility of the FAS Center for Systems Biology at Harvard University. A portion of the bioinformatics analysis was performed at Harvard’s FAS Research Computing facility.
    Keywords: Manganese oxides ; Filamentous fungi ; Geomicrobiology ; Proteomics ; Biomineralization ; Secretome
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    Ratio of electron donor to acceptor influences metabolic specialization and denitrification dynamics in Pseudomonas aeruginosa in a mixed carbon medium (2021)
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zhang, I. H., Mullen, S., Ciccarese, D., Dumit, D., Martocello, D. E., Toyofuku, M., Nomura, N., Smriga, S., & Babbin, A. R. Ratio of electron donor to acceptor influences metabolic specialization and denitrification dynamics in Pseudomonas aeruginosa in a mixed carbon medium. Frontiers in Microbiology, 12, (2021): 711073, https://doi.org/10.3389/fmicb.2021.711073.
    Description: Denitrifying microbes sequentially reduce nitrate (NO3–) to nitrite (NO2–), NO, N2O, and N2 through enzymes encoded by nar, nir, nor, and nos. Some denitrifiers maintain the whole four-gene pathway, but others possess partial pathways. Partial denitrifiers may evolve through metabolic specialization whereas complete denitrifiers may adapt toward greater metabolic flexibility in nitrogen oxide (NOx–) utilization. Both exist within natural environments, but we lack an understanding of selective pressures driving the evolution toward each lifestyle. Here we investigate differences in growth rate, growth yield, denitrification dynamics, and the extent of intermediate metabolite accumulation under varying nutrient conditions between the model complete denitrifier Pseudomonas aeruginosa and a community of engineered specialists with deletions in the denitrification genes nar or nir. Our results in a mixed carbon medium indicate a growth rate vs. yield tradeoff between complete and partial denitrifiers, which varies with total nutrient availability and ratios of organic carbon to NOx–. We found that the cultures of both complete and partial denitrifiers accumulated nitrite and that the metabolic lifestyle coupled with nutrient conditions are responsible for the extent of nitrite accumulation.
    Description: Funding for this work was provided by Simons Foundation award 622065 and an MIT Environmental Solutions Initiative seed grant to AB. Additional support was received by the MIT Ferry Fund.
    Keywords: Pseudomonas aeruginosa ; Denitrification ; Rate-yield tradeoff ; Specialization ; Nitrite
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    Extracellular reef metabolites across the protected Jardines de la Reina, Cuba Reef System (2021)
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Weber, L., Armenteros, M., Soule, M. K., Longnecker, K., Kujawinski, E. B., & Apprill, A. Extracellular reef metabolites across the protected Jardines de la Reina, Cuba Reef System. Frontiers in Marine Science, 7, (2020): 582161, https://doi.org/10.3389/fmars.2020.582161.
    Description: Coral reef ecosystems are incredibly diverse marine biomes that rely on nutrient cycling by microorganisms to sustain high productivity in generally oligotrophic regions of the ocean. Understanding the composition of extracellular reef metabolites in seawater, the small organic molecules that serve as the currency for microorganisms, may provide insight into benthic-pelagic coupling as well as the complexity of nutrient cycling in coral reef ecosystems. Jardines de la Reina (JR), Cuba is an ideal environment to examine extracellular metabolites across protected and high-quality reefs. Here, we used liquid chromatography mass spectrometry (LC-MS) to quantify specific known metabolites of interest (targeted metabolomics approach) and to survey trends in metabolite feature composition (untargeted metabolomics approach) from surface and reef depth (6 – 14 m) seawater overlying nine forereef sites in JR. We found that untargeted metabolite feature composition was surprisingly similar between reef depth and surface seawater, corresponding with other biogeochemical and physicochemical measurements and suggesting that environmental conditions were largely homogenous across forereefs within JR. Additionally, we quantified 32 of 53 detected metabolites using the targeted approach, including amino acids, nucleosides, vitamins, and other metabolic intermediates. Two of the quantified metabolites, riboflavin and xanthosine, displayed interesting trends by depth. Riboflavin concentrations were higher in reef depth compared to surface seawater, suggesting that riboflavin may be produced by reef organisms at depth and degraded in the surface through photochemical oxidation. Xanthosine concentrations were significantly higher in surface reef seawater. 5′-methylthioadenosine (MTA) concentrations increased significantly within the central region of the archipelago, displaying biogeographic patterns that warrant further investigation. Here we lay the groundwork for future investigations of variations in metabolite composition across reefs, sources and sinks of reef metabolites, and changes in metabolites over environmental, temporal, and reef health gradients.
    Description: This work was supported by the Dalio Foundation (now “OceanX”) and the National Science Foundation (OCE-1736288) (award to Amy Apprill). The mass spectrometry samples were analyzed at the WHOI FT-MS Users’ Facility with instrumentation funded by the National Science Foundation (grant OCE-1058448 to EK and MK) and the Simons Foundation (Award ID #509042, EK). Lastly, a portion of the publication fees was supported by the Massachusetts Institute of Technology (MIT) Open Access Article Publication Subvention fund from MIT Libraries.
    Keywords: Metabolomics ; Coral reefs ; Microorganisms ; Ecology ; DOM cycling
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    The osmolyte ties that bind: genomic insights into synthesis and breakdown of organic osmolytes in marine microbes (2021)
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in McParland, E. L., Alexander, H., & Johnson, W. M. The osmolyte ties that bind: genomic insights into synthesis and breakdown of organic osmolytes in marine microbes. Frontiers in Marine Science, 8, (2021): 689306, https://doi.org/10.3389/fmars.2021.689306.
    Description: The production and consumption of organic matter by marine organisms plays a central role in the marine carbon cycle. Labile organic compounds (metabolites) are the major currency of energetic demands and organismal interaction, but these compounds remain elusive because of their rapid turnover and concomitant minuscule concentrations in the dissolved organic matter pool. Organic osmolytes are a group of small metabolites synthesized at high intracellular concentrations (mM) to regulate cellular osmolarity and have the potential to be released as abundant dissolved substrates. Osmolytes may represent an essential currency of exchange among heterotrophic prokaryotes and primary and secondary producers in marine food webs. For example, the well-known metabolite dimethylsulfoniopropionate (DMSP) is used as an osmolyte by some phytoplankton and can be subsequently metabolized by 60% of the marine bacterial community, supplying up to 13% of the bacterial carbon demand and 100% of the bacterial sulfur demand. While marine osmolytes have been studied for decades, our understanding of their cycling and significance within microbial communities is still far from comprehensive. Here, we surveyed the genes responsible for synthesis, breakdown, and transport of 14 key osmolytes. We systematically searched for these genes across marine bacterial genomes (n = 897) and protistan transcriptomes (n = 652) using homologous protein profiles to investigate the potential for osmolyte metabolisms. Using the pattern of gene presence and absence, we infer the metabolic potential of surveyed microbes to interact with each osmolyte. Specifically, we identify: (1) complete pathways for osmolyte synthesis in both prokaryotic and eukaryotic marine microbes, (2) microbes capable of transporting osmolytes but lacking complete synthesis and/or breakdown pathways, and (3) osmolytes whose synthesis and/or breakdown appears to be specialized and is limited to a subset of organisms. The analysis clearly demonstrates that the marine microbial loop has the genetic potential to actively recycle osmolytes and that this abundant group of small metabolites may function as a significant source of nutrients through exchange among diverse microbial groups that significantly contribute to the cycling of labile carbon.
    Description: EM was supported by the Postdoctoral Scholar Program at Woods Hole Oceanographic Institution. WJ was supported by a Research Initiative Award from the College of Arts and Sciences at the University of North Carolina Wilmington. HA was supported by a Independent Research and Development Award from the Woods Hole Oceanographic Institution.
    Keywords: Osmolytes ; Glycine betaine ; Mannitol ; Transporters ; Biosynthesis ; Metatranscriptomics
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    Effects of excess brain-derived human alpha-synuclein on synaptic vesicle trafficking (2021)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Roman-Vendrell, C., Medeiros, A. T., Sanderson, J. B., Jiang, H., Bartels, T., & Morgan, J. R. Effects of excess brain-derived human alpha-synuclein on synaptic vesicle trafficking. Frontiers in Neuroscience, 15, (2021): 639414, https://doi.org/10.3389./fnins.2021.639414
    Description: α-Synuclein is a presynaptic protein that regulates synaptic vesicle trafficking under physiological conditions. However, in several neurodegenerative diseases, including Parkinson’s disease, dementia with Lewy bodies, and multiple system atrophy, α-synuclein accumulates throughout the neuron, including at synapses, leading to altered synaptic function, neurotoxicity, and motor, cognitive, and autonomic dysfunction. Neurons typically contain both monomeric and multimeric forms of α-synuclein, and it is generally accepted that disrupting the balance between them promotes aggregation and neurotoxicity. However, it remains unclear how distinct molecular species of α-synuclein affect synapses where α-synuclein is normally expressed. Using the lamprey reticulospinal synapse model, we previously showed that acute introduction of excess recombinant monomeric or dimeric α-synuclein impaired distinct stages of clathrin-mediated synaptic vesicle endocytosis, leading to a loss of synaptic vesicles. Here, we expand this knowledge by investigating the effects of native, physiological α-synuclein isolated from the brain of a neuropathologically normal human subject, which comprised predominantly helically folded multimeric α-synuclein with a minor component of monomeric α-synuclein. After acute introduction of excess brain-derived human α-synuclein, there was a moderate reduction in the synaptic vesicle cluster and an increase in the number of large, atypical vesicles called “cisternae.” In addition, brain-derived α-synuclein increased synaptic vesicle and cisternae sizes and induced atypical fusion/fission events at the active zone. In contrast to monomeric or dimeric α-synuclein, the brain-derived multimeric α-synuclein did not appear to alter clathrin-mediated synaptic vesicle endocytosis. Taken together, these data suggest that excess brain-derived human α-synuclein impairs intracellular vesicle trafficking and further corroborate the idea that different molecular species of α-synuclein produce distinct trafficking defects at synapses. These findings provide insights into the mechanisms by which excess α-synuclein contributes to synaptic deficits and disease phenotypes.
    Description: This work was supported by the NIH (NINDS/NIA R01NS078165 and R01NS078165-S1 to JM; NINDS U54-NS110435, R01-NS109209, and R21-NS107950 to TB); research funds from the Marine Biological Laboratory (to JM); grants from the UK Dementia Research Institute (DRI), which receives its funding from DRI Ltd., the UK Medical Research Council and Alzheimer’s Society, and Alzheimer’s Research UK (to TB); the Michael J. Fox Foundation (Ken Griffin Imaging Award to TB); a Parkinson’s Disease Foundation Stanley Fahn Award (PF-JFA-1884 to TB); the Eisai Pharmaceutical postdoctoral program to TB; and the Chan Zuckerberg Collaborative Pairs Initiative (to TB).
    Keywords: Clathrin mediated endocytosis ; Electron microscopy ; Endosome ; Lamprey ; Reticulospinal synapse
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    Quantifying slopes as a driver of forest to marsh conversion using geospatial techniques: application to Chesapeake Bay coastal-plain, United States (2021)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Molino, G. D., Defne, Z., Aretxabaleta, A. L., Ganju, N. K., & Carr, J. A. Quantifying slopes as a driver of forest to marsh conversion using geospatial techniques: application to Chesapeake Bay coastal-plain, United States. Frontiers in Environmental Science, 9, (2021): 616319, https://doi.org/10.3389/fenvs.2021.616319.
    Description: Coastal salt marshes, which provide valuable ecosystem services such as flood mitigation and carbon sequestration, are threatened by rising sea level. In response, these ecosystems migrate landward, converting available upland into salt marsh. In the coastal-plain surrounding Chesapeake Bay, United States, conversion of coastal forest to salt marsh is well-documented and may offset salt marsh loss due to sea level rise, sediment deficits, and wave erosion. Land slope at the marsh-forest boundary is an important factor determining migration likelihood, however, the standard method of using field measurements to assess slope across the marsh-forest boundary is impractical on the scale of an estuary. Therefore, we developed a general slope quantification method that uses high resolution elevation data and a repurposed shoreline analysis tool to determine slope along the marsh-forest boundary for the entire Chesapeake Bay coastal-plain and find that less than 3% of transects have a slope value less than 1%; these low slope environments offer more favorable conditions for forest to marsh conversion. Then, we combine the bay-wide slope and elevation data with inundation modeling from Hurricane Isabel to determine likelihood of coastal forest conversion to salt marsh. This method can be applied to local and estuary-scale research to support management decisions regarding which upland forested areas are more critical to preserve as available space for marsh migration.
    Description: Funding for this study was provided by the United States Geological Survey’s Coastal/Marine Hazards and Resources Program and Ecosystems Mission Area.
    Keywords: Salt marsh ; Coastal forest ; Sea level rise ; Chesapeake Bay ; Marsh migration
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    The possession of coccoliths fails to deter microzooplankton grazers (2021)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Mayers, K. M. J., Poulton, A. J., Bidle, K., Thamatrakoln, K., Schieler, B., Giering, S. L. C., Wells, S. R., Tarran, G. A., Mayor, D., Johnson, M., Riebesell, U., Larsen, A., Vardi, A., & Harvey, E. L. The possession of coccoliths fails to deter microzooplankton grazers. Frontiers in Marine Science, 7, (2020): 562020, doi:10.3389/fmars.2020.569896.
    Description: Phytoplankton play a central role in the regulation of global carbon and nutrient cycles, forming the basis of the marine food webs. A group of biogeochemically important phytoplankton, the coccolithophores, produce calcium carbonate scales that have been hypothesized to deter or reduce grazing by microzooplankton. Here, a meta-analysis of mesocosm-based experiments demonstrates that calcification of the cosmopolitan coccolithophore, Emiliania huxleyi, fails to deter microzooplankton grazing. The median grazing to growth ratio for E. huxleyi (0.56 ± 0.40) was not significantly different among non-calcified nano- or picoeukaryotes (0.71 ± 0.31 and 0.55 ± 0.34, respectively). Additionally, the environmental concentration of E. huxleyi did not drive preferential grazing of non-calcified groups. These results strongly suggest that the possession of coccoliths does not provide E. huxleyi effective protection from microzooplankton grazing. Such indiscriminate consumption has implications for the dissolution and fate of CaCO3 in the ocean, and the evolution of coccoliths.
    Description: Mesocosm experiments in 2015 were supported by the Kiel Excellence Cluster “The Future Ocean” (CP1540) and the Leibniz Award to UR, in 2017 the MESOHUX experiment was supported by NSF (OCE-1559179) to KT and KB, NSF (OCE-1537951 and OCE-1459200) to KB, NSF (OCE-1459190, 1657808, and DBI-1624593) to EH, and in 2018 by AQUACOSM (EU H2020-INFRAIA-project No 731065). KM was supported by a NERC Doctoral Training Partnership (DTP) studentship as part of the Southampton Partnership for Innovative Training of Future Investigators Researching the Environment (SPITFIRE, grant number NE/L002531/1) and Research Council of Norway project (#280414) MIXsTRUCT.
    Keywords: coccolithophore ; phytoplankton ; microzooplankton ; biomineralisation ; predation ; evolution
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    Defined tau phosphospecies differentially inhibit fast axonal transport through activation of two independent signaling pathways (2021)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Morris, S. L., Tsai, M., Aloe, S., Bechberger, K., Konig, S., Morfini, G., & Brady, S. T. Defined tau phosphospecies differentially inhibit fast axonal transport through activation of two independent signaling pathways. Frontiers in Molecular Neuroscience, 13, (2021): 610037, https://doi.org/10.3389/fnmol.2020.610037.
    Description: Tau protein is subject to phosphorylation by multiple kinases at more than 80 different sites. Some of these sites are associated with tau pathology and neurodegeneration, but other sites are modified in normal tau as well as in pathological tau. Although phosphorylation of tau at residues in the microtubule-binding repeats is thought to reduce tau association with microtubules, the functional consequences of other sites are poorly understood. The AT8 antibody recognizes a complex phosphoepitope site on tau that is detectable in a healthy brain but significantly increased in Alzheimer’s disease (AD) and other tauopathies. Previous studies showed that phosphorylation of tau at the AT8 site leads to exposure of an N-terminal sequence that promotes activation of a protein phosphatase 1 (PP1)/glycogen synthase 3 (GSK3) signaling pathway, which inhibits kinesin-1-based anterograde fast axonal transport (FAT). This finding suggests that phosphorylation may control tau conformation and function. However, the AT8 includes three distinct phosphorylated amino acids that may be differentially phosphorylated in normal and disease conditions. To evaluate the effects of specific phosphorylation sites in the AT8 epitope, recombinant, pseudophosphorylated tau proteins were perfused into the isolated squid axoplasm preparation to determine their effects on axonal signaling pathways and FAT. Results from these studies suggest a mechanism where specific phosphorylation events differentially impact tau conformation, promoting activation of independent signaling pathways that differentially affect FAT. Implications of findings here to our understanding of tau function in health and disease conditions are discussed.
    Description: This research was funded by NIH grants R21NS096642 (GM); 1R01NS118177-01A1 (GM), R01 NS082730 (SB), a Zenith Award from the Alzheimer’s Association (SB), and a grant from the Tau Consortium/Rainwater Foundation (SB).
    Keywords: Tau phosphorylation ; Fast axonal transport ; Signal transduction ; GSK3 ; JNK ; PP1
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    Atmospheric and oceanographic forcing impact particle flux composition and carbon sequestration in the eastern Mediterranean Sea: a three-year time-series study in the deep Ierapetra Basin (2021)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Pedrosa-Pamies, R., Parinos, C., Sanchez-Vidal, A., Calafat, A., Canals, M., Velaoras, D., Mihalopoulos, N., Kanakidou, M., Lampadariou, N., & Gogou, A. Atmospheric and oceanographic forcing impact particle flux composition and carbon sequestration in the eastern Mediterranean Sea: a three-year time-series study in the deep Ierapetra Basin. Frontiers in Earth Science, 9, (2021): 591948, https://doi.org/10.3389/feart.2021.591948.
    Description: Sinking particles are a critical conduit for the export of organic material from surface waters to the deep ocean. Despite their importance in oceanic carbon cycling, little is known about the biotic composition and seasonal variability of sinking particles reaching abyssal depths. Herein, sinking particle flux data, collected in the deep Ierapetra Basin for a three-year period (June 2010 to June 2013), have been examined at the light of atmospheric and oceanographic parameters and main mass components (lithogenic, opal, carbonates, nitrogen, and organic carbon), stable isotopes of particulate organic carbon (POC) and source-specific lipid biomarkers. Our aim is to improve the current understanding of the dynamics of particle fluxes and the linkages between atmospheric dynamics and ocean biogeochemistry shaping the export of organic matter in the deep Eastern Mediterranean Sea. Overall, particle fluxes showed seasonality and interannual variability over the studied period. POC fluxes peaked in spring April–May 2012 (12.2 mg m−2 d−1) related with extreme atmospheric forcing. Summer export was approximately fourfold higher than mean wintertime, fall and springtime (except for the episodic event of spring 2012), fueling efficient organic carbon sequestration. Lipid biomarkers indicate a high relative contribution of natural and anthropogenic, marine- and land-derived POC during both spring (April–May) and summer (June–July) reaching the deep-sea floor. Moreover, our results highlight that both seasonal and episodic pulses are crucial for POC export, while the coupling of extreme weather events and atmospheric deposition can trigger the influx of both marine labile carbon and anthropogenic compounds to the deep Levantine Sea. Finally, the comparison of time series data of sinking particulate flux with the corresponding biogeochemical parameters data previously reported for surface sediment samples from the deep-sea shed light on the benthic–pelagic coupling in the study area. Thus, this study underscores that accounting the seasonal and episodic pulses of organic carbon into the deep sea is critical in modeling the depth and intensity of natural and anthropogenic POC sequestration, and for a better understanding of the global carbon cycle.
    Description: This research was supported by the REDECO (CTM2008-04973-E/MAR) and PERSEUS (GA 287600) projects. We further acknowledge support by the projects PANACEA—‘PANhellenic infrastructure for Atmospheric Composition and climatE chAnge’ (MIS 5021516) and ENIRISST—‘Intelligent Research Infrastructure for Shipping, Supply Chain, Transport and Logistics’ (MIS 5027930), which are implemented under the Action “Reinforcement of the Research and Innovation Infrastructure,” funded by the Operational Program “Competitiveness, Entrepreneurship and Innovation” (NSRF 2014-2020) and co-financed by Greece and EU; and by the Action “National Νetwork on Climate Change and its Impacts - Climpact” which is implemented under the sub-project 3 of the project “Infrastructure of national research networks in the fields of Precision Medicine, Quantum Technology and Climate Change,” funded by the Public Investment Program of Greece, General Secretary of Research and Technology/Ministry of Development and Investments.” Researchers from GRC Geociències Marines benefited from a Grups de Recerca Consolidats grant (2017 SGR 315) by Generalitat de Catalunya autonomous government.
    Keywords: Sinking particle fluxes ; Carbon cycle ; Lipid biomarkers ; Atmospheric forcing ; Eastern mediterranean sea ; Surface sediment ; Deep ocean ; Particulate organic carbon
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    NLRP3 inflammasome assembly in neutrophils is supported by PAD4 and promotes NETosis under sterile conditions (2021)
    Frontiers Media
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Muenzer, P., Negro, R., Fukui, S., di Meglio, L., Aymonnier, K., Chu, L., Cherpokova, D., Gutch, S., Sorvillo, N., Shi, L., Magupalli, V. G., Weber, A. N. R., Scharf, R. E., Waterman, C. M., Wu, H., & Wagner, D. D. NLRP3 inflammasome assembly in neutrophils is supported by PAD4 and promotes NETosis under sterile conditions. Frontiers in Immunology, 12, (2021): 683803, https://doi.org/10.3389/fimmu.2021.683803.
    Description: Neutrophil extracellular trap formation (NETosis) and the NLR family pyrin domain containing 3 (NLRP3) inflammasome assembly are associated with a similar spectrum of human disorders. While NETosis is known to be regulated by peptidylarginine deiminase 4 (PAD4), the role of the NLRP3 inflammasome in NETosis was not addressed. Here, we establish that under sterile conditions the cannonical NLRP3 inflammasome participates in NETosis. We show apoptosis-associated speck-like protein containing a CARD (ASC) speck assembly and caspase-1 cleavage in stimulated mouse neutrophils without LPS priming. PAD4 was needed for optimal NLRP3 inflammasome assembly by regulating NLRP3 and ASC protein levels post-transcriptionally. Genetic ablation of NLRP3 signaling resulted in impaired NET formation, because NLRP3 supported both nuclear envelope and plasma membrane rupture. Pharmacological inhibition of NLRP3 in either mouse or human neutrophils also diminished NETosis. Finally, NLRP3 deficiency resulted in a lower density of NETs in thrombi produced by a stenosis-induced mouse model of deep vein thrombosis. Altogether, our results indicate a PAD4-dependent formation of the NLRP3 inflammasome in neutrophils and implicate NLRP3 in NETosis under noninfectious conditions in vitro and in vivo.
    Description: This work was supported by a grant from National Heart, Lung, and Blood Institute of the National Institutes of Health (grant R35 HL135765) and a Steven Berzin family support to DDW, an Individual Erwin Deutsch fellowship by the German, Austrian and Swiss Society of Thrombosis and Hemostasis Research to RES, a Whitman fellowship (MBL) to DDW, and an Individual Marie Skłodowska-Curie Actions fellowship by the European Commission (796365 - COAGULANT) to PM. ANRW was funded by the Deutsche Forschungsgemeinschaft (TRR156/2 –246807620) and a research grant (We-4195/15-19). CMW was supported by the Division of Intramural Research, NHLBI, NIH.
    Keywords: Neutrophils ; NETs ; NLRP3 inflammasome ; MCC950 ; Deep vein thrombosis ; PAD4
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    Stochastic dispersal rather than deterministic selection explains the spatio-temporal distribution of soil bacteria in a temperate grassland (2021)
    Frontiers Media
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Richter-Heitmann, T., Hofner, B., Krah, F., Sikorski, J., Wuest, P. K., Bunk, B., Huang, S., Regan, K. M., Berner, D., Boeddinghaus, R. S., Marhan, S., Prati, D., Kandeler, E., Overmann, J., & Friedrich, M. W. Stochastic dispersal rather than deterministic selection explains the spatio-temporal distribution of soil bacteria in a temperate grassland. Frontiers in Microbiology, 11, (2020): 1391, https://doi.org/10.3389/fmicb.2020.01391.
    Description: Spatial and temporal processes shaping microbial communities are inseparably linked but rarely studied together. By Illumina 16S rRNA sequencing, we monitored soil bacteria in 360 stations on a 100 square meter plot distributed across six intra-annual samplings in a rarely managed, temperate grassland. Using a multi-tiered approach, we tested the extent to which stochastic or deterministic processes influenced the composition of local communities. A combination of phylogenetic turnover analysis and null modeling demonstrated that either homogenization by unlimited stochastic dispersal or scenarios, in which neither stochastic processes nor deterministic forces dominated, explained local assembly processes. Thus, the majority of all sampled communities (82%) was rather homogeneous with no significant changes in abundance-weighted composition. However, we detected strong and uniform taxonomic shifts within just nine samples in early summer. Thus, community snapshots sampled from single points in time or space do not necessarily reflect a representative community state. The potential for change despite the overall homogeneity was further demonstrated when the focus shifted to the rare biosphere. Rare OTU turnover, rather than nestedness, characterized abundance-independent β-diversity. Accordingly, boosted generalized additive models encompassing spatial, temporal and environmental variables revealed strong and highly diverse effects of space on OTU abundance, even within the same genus. This pure spatial effect increased with decreasing OTU abundance and frequency, whereas soil moisture – the most important environmental variable – had an opposite effect by impacting abundant OTUs more than the rare ones. These results indicate that – despite considerable oscillation in space and time – the abundant and resident OTUs provide a community backbone that supports much higher β-diversity of a dynamic rare biosphere. Our findings reveal complex interactions among space, time, and environmental filters within bacterial communities in a long-established temperate grassland.
    Description: The work has been funded by the DFG Priority Program 1374 “Infrastructure-Biodiversity-Exploratories” (Grants KA 1590/8-2, FR 1151/5-2, and OV 20/21-1). Field work permits were issued by the responsible state environmental office of Baden-Württemberg (according to § 72 BbgNatSchG).
    Keywords: Spatio-temporal analysis ; Soil bacteria communities ; Community assembly ; Variable selection ; Generalized additive model
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    Tau: a signaling hub protein (2021)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Mueller, R. L., Combs, B., Alhadidy, M. M., Brady, S. T., Morfini, G. A., & Kanaan, N. M. Tau: a signaling hub protein. Frontiers in Molecular Neuroscience, 14, (2021): 647054, https://doi.org/10.3389/fnmol.2021.647054.
    Description: Over four decades ago, in vitro experiments showed that tau protein interacts with and stabilizes microtubules in a phosphorylation-dependent manner. This observation fueled the widespread hypotheses that these properties extend to living neurons and that reduced stability of microtubules represents a major disease-driving event induced by pathological forms of tau in Alzheimer’s disease and other tauopathies. Accordingly, most research efforts to date have addressed this protein as a substrate, focusing on evaluating how specific mutations, phosphorylation, and other post-translational modifications impact its microtubule-binding and stabilizing properties. In contrast, fewer efforts were made to illuminate potential mechanisms linking physiological and disease-related forms of tau to the normal and pathological regulation of kinases and phosphatases. Here, we discuss published work indicating that, through interactions with various kinases and phosphatases, tau may normally act as a scaffolding protein to regulate phosphorylation-based signaling pathways. Expanding on this concept, we also review experimental evidence linking disease-related tau species to the misregulation of these pathways. Collectively, the available evidence supports the participation of tau in multiple cellular processes sustaining neuronal and glial function through various mechanisms involving the scaffolding and regulation of selected kinases and phosphatases at discrete subcellular compartments. The notion that the repertoire of tau functions includes a role as a signaling hub should widen our interpretation of experimental results and increase our understanding of tau biology in normal and disease conditions.
    Description: This work was supported by NIH grants (R01AG067762 and R01AG044372 to NK, R01NS082730 to NK and SB, R01NS118177 and R21NS120126 to GM, R01NS023868 and R01NS041170 to SB), a gift from Neurodegenerative Research Inc. (GM), a Zenith Award from the Alzheimer’s Association (SB), a grant from the Secchia Family Foundation (NK), NIH/National Institute on Aging (NIA) funded Michigan Alzheimer’s Disease Research Center 5P30AG053760 (BC), the Office of the Assistant Secretary of Defense for Health Affairs through the Peer-Reviewed Alzheimer’s Research Program (Award No. W81XWH-20-1-0174 to BC), and an Alzheimer’s Association Research Grant 20-682085 (BC).
    Keywords: Tauopathy ; Kinase ; Phosphatase ; Scaffold protein ; Axon ; Synpase ; Nucleus ; Oligodendrocyte
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    A long-term geothermal observatory across subseafloor gas hydrates, IODP Hole U1364A, Cascadia accretionary prism (2021)
    Frontiers Media
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in WHOI Becker, K., Davis, E. E., Heesemann, M., Collins, J. A., & McGuire, J. J. A long-term geothermal observatory across subseafloor gas hydrates, IODP Hole U1364A, Cascadia accretionary prism. Frontiers in Earth Science, 8, (2020): 568566, https://doi.org/10.3389/feart.2020.568566
    Description: We report 4 years of temperature profiles collected from May 2014 to May 2018 in Integrated Ocean Drilling Program Hole U1364A in the frontal accretionary prism of the Cascadia subduction zone. The temperature data extend to depths of nearly 300 m below seafloor (mbsf), spanning the gas hydrate stability zone at the location and a clear bottom-simulating reflector (BSR) at ∼230 mbsf. When the hole was drilled in 2010, a pressure-monitoring Advanced CORK (ACORK) observatory was installed, sealed at the bottom by a bridge plug and cement below 302 mbsf. In May 2014, a temperature profile was collected by lowering a probe down the hole from the ROV ROPOS. From July 2016 through May 2018, temperature data were collected during a nearly two-year deployment of a 24-thermistor cable installed to 268 m below seafloor (mbsf). The cable and a seismic-tilt instrument package also deployed in 2016 were connected to the Ocean Networks Canada (ONC) NEPTUNE cabled observatory in June of 2017, after which the thermistor temperatures were logged by Ocean Networks Canada at one-minute intervals until failure of the main ethernet switch in the integrated seafloor control unit in May 2018. The thermistor array had been designed with concentrated vertical spacing around the bottom-simulating reflector and two pressure-monitoring screens at 203 and 244 mbsf, with wider thermistor spacing elsewhere to document the geothermal state up to seafloor. The 4 years of data show a generally linear temperature gradient of 0.055°C/m consistent with a heat flux of 61–64 mW/m2. The data show no indications of thermal transients. A slight departure from a linear gradient provides an approximate limit of ∼10−10 m/s for any possible slow upward advection of pore fluids. In-situ temperatures are ∼15.8°C at the BSR position, consistent with methane hydrate stability at that depth and pressure.
    Description: KB was supported by NSF grant OCE-1259718 for construction and deployment of the thermistor cable in the hole. Construction of the seismic-strain-tilt instrumentation was supported by a Keck Foundation grant to WHOI, and deployment and recovery of the integrated sensor string was supported by NSF grant OCE-1259243 to JM and JC. Support for the pressure-monitoring instrumentation and 2014 CTD profile was provided by the Geological Survey of Canada and Ocean Networks Canada.
    Keywords: Heat flux ; Geothermal gradient ; Gas hydrates ; Bottom-simulating reflector ; Pore-fluid advection ; Borehole observatory ; Integrated Ocean Drilling Program
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    Migratory zooplankton excreta and its influence on prokaryotic communities (2021)
    Frontiers Media
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Maas, A. E., Liu, S., Bolanos, L. M., Widner, B., Parsons, R., Kujawinski, E. B., Blanco-Bercial, L., & Carlson, C. A. Migratory zooplankton excreta and its influence on prokaryotic communities. Frontiers in Marine Science, 7, (2020): 573268, doi:10.3389/fmars.2020.573268.
    Description: Particulate organic matter (POM) (fecal pellets) from zooplankton has been demonstrated to be an important nutrient source for the pelagic prokaryotic community. Significantly less is known about the chemical composition of the dissolved organic matter (DOM) produced by these eukaryotes and its influence on pelagic ecosystem structure. Zooplankton migrators, which daily transport surface-derived compounds to depth, may act as important vectors of limiting nutrients for mesopelagic microbial communities. In this role, zooplankton may increase the DOM remineralization rate by heterotrophic prokaryotes through the creation of nutrient rich “hot spots” that could potentially increase niche diversity. To explore these interactions, we collected the migratory copepod Pleuromamma xiphias from the northwestern Sargasso Sea and sampled its excreta after 12–16 h of incubation. We measured bulk dissolved organic carbon (DOC), dissolved free amino acids (DFAA) via high performance liquid chromatography and dissolved targeted metabolites via quantitative mass spectrometry (UPLC-ESI-MSMS) to quantify organic zooplankton excreta production and characterize its composition. We observed production of labile DOM, including amino acids, vitamins, and nucleosides. Additionally, we harvested a portion of the excreta and subsequently used it as the growth medium for mesopelagic (200 m) bacterioplankton dilution cultures. In zooplankton excreta treatments we observed a four-fold increase in bacterioplankton cell densities that reached stationary growth phase after five days of dark incubation. Analyses of 16S rRNA gene amplicons suggested a shift from oligotrophs typical of open ocean and mesopelagic prokaryotic communities to more copiotrophic bacterial lineages in the presence of zooplankton excreta. These results support the hypothesis that zooplankton and prokaryotes are engaged in complex and indirect ecological interactions, broadening our understanding of the microbial loop.
    Description: Funding for this research was provided by Simons Foundation International as part of the BIOS-SCOPE project to AM, LB-B, CC, and EK.
    Keywords: DOC ; Dissolved metabolites ; Diel vertical migration ; Biogeochemistry ; Copepod
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    Quantifying Po-210/Pb-210 disequilibrium in seawater: a comparison of two precipitation methods with differing results (2021)
    Frontiers Media
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Roca-Marti, M., Puigcorbe, V., Castrillejo, M., Casacuberta, N., Garcia-Orellana, J., Kirk Cochran, J., & Masque, P. Quantifying Po-210/Pb-210 disequilibrium in seawater: a comparison of two precipitation methods with differing results. Frontiers in Marine Science, 8, (2021): 684484, https://doi.org/10.3389/fmars.2021.684484.
    Description: The disequilibrium between lead-210 (210Pb) and polonium-210 (210Po) is increasingly used in oceanography to quantify particulate organic carbon (POC) export from the upper ocean. This proxy is based on the deficits of 210Po typically observed in the upper water column due to the preferential removal of 210Po relative to 210Pb by sinking particles. Yet, a number of studies have reported unexpected large 210Po deficits in the deep ocean indicating scavenging of 210Po despite its radioactive mean life of ∼ 200 days. Two precipitation methods, Fe(OH)3 and Co-APDC, are typically used to concentrate Pb and Po from seawater samples, and deep 210Po deficits raise the question whether this feature is biogeochemically consistent or there is a methodological issue. Here, we present a compilation of 210Pb and 210Po studies that suggests that 210Po deficits at depths 〉300 m are more often observed in studies where Fe(OH)3 is used to precipitate Pb and Po from seawater, than in those using Co-APDC (in 68 versus 33% of the profiles analyzed for each method, respectively). In order to test whether 210Po/210Pb disequilibrium can be partly related to a methodological artifact, we directly compared the total activities of 210Pb and 210Po in four duplicate ocean depth-profiles determined by using Fe(OH)3 and Co-APDC on unfiltered seawater samples. While both methods produced the same 210Pb activities, results from the Co-APDC method showed equilibrium between 210Pb and 210Po below 100 m, whereas the Fe(OH)3 method resulted in activities of 210Po significantly lower than 210Pb throughout the entire water column. These results show that 210Po deficits in deep waters, but also in the upper ocean, may be greater when calculated using a commonly used Fe(OH)3 protocol. This finding has potential implications for the use of the 210Po/210Pb pair as a tracer of particle export in the oceans because 210Po (and thus POC) fluxes calculated using Fe(OH)3 on unfiltered seawater samples may be overestimated. Recommendations for future research are provided based on the possible reasons for the discrepancy in 210Po activities between both analytical methods.
    Description: MR-M was supported by an Endeavour Research Fellowship (6054) from the Australian Government, the Woods Hole Oceanographic Institution’s Ocean Twilight Zone study, and the Ocean Frontier Institute. VP received funding from the Edith Cowan University under the Early Career Researcher Grant Scheme (G1003456) and the Collaboration Enhancement Scheme (G1003362). MC is currently funded by an ETH Zurich Postdoctoral Fellowship Program (17-2 FEL-30), co-funded by the Marie Curie Actions for People COFUND Program. Support to JKC was provided by the National Science Foundation grant OCE-1736591. The authors acknowledge the financial support from the Spanish Ministry of Science, Innovation and Universities through the “María de Maeztu” program for Units of Excellence (CEX2019-000940-M), the Australian Research Council LIEF Project (LE170100219), and the Generalitat de Catalunya (MERS; 2017 SGR-1588).
    Keywords: Marine chemistry ; Radiochemistry ; Polonium isotopes ; Precipitation methods ; Co-APDC ; Fe(OH)3 ; 210Po/210Pb disequilibrium
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    Using a Ladder of Seeps with computer decision processes to explore for and evaluate cold seeps on the Costa Rica active margin (2021)
    Frontiers Media
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    Publication Date: 2022-10-20
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Vrolijk, P., Summa, L., Ayton, B., Nomikou, P., Huepers, A., Kinnaman, F., Sylva, S., Valentine, D., & Camilli, R. Using a Ladder of Seeps with computer decision processes to explore for and evaluate cold seeps on the Costa Rica active margin. Frontiers in Earth Science, 9, (2021): 601019, https://doi.org/10.3389/feart.2021.601019.
    Description: Natural seeps occur at the seafloor as loci of fluid flow where the flux of chemical compounds into the ocean supports unique biologic communities and provides access to proxy samples of deep subsurface processes. Cold seeps accomplish this with minimal heat flux. While individual expertize is applied to locate seeps, such knowledge is nowhere consolidated in the literature, nor are there explicit approaches for identifying specific seep types to address discrete scientific questions. Moreover, autonomous exploration for seeps lacks any clear framework for efficient seep identification and classification. To address these shortcomings, we developed a Ladder of Seeps applied within new decision-assistance algorithms (Spock) to assist in seep exploration on the Costa Rica margin during the R/V Falkor 181210 cruise in December, 2018. This Ladder of Seeps [derived from analogous astrobiology criteria proposed by Neveu et al. (2018)] was used to help guide human and computer decision processes for ROV mission planning. The Ladder of Seeps provides a methodical query structure to identify what information is required to confirm a seep either: 1) supports seafloor life under extreme conditions, 2) supports that community with active seepage (possible fluid sample), or 3) taps fluids that reflect deep, subsurface geologic processes, but the top rung may be modified to address other scientific questions. Moreover, this framework allows us to identify higher likelihood seep targets based on existing incomplete or easily acquired data, including MBES (Multi-beam echo sounder) water column data. The Ladder of Seeps framework is based on information about the instruments used to collect seep information (e.g., are seeps detectable by the instrument with little chance of false positives?) and contextual criteria about the environment in which the data are collected (e.g., temporal variability of seep flux). Finally, the assembled data are considered in light of a Last-Resort interpretation, which is only satisfied once all other plausible data interpretations are excluded by observation. When coupled with decision-making algorithms that incorporate expert opinion with data acquired during the Costa Rica experiment, the Ladder of Seeps proved useful for identifying seeps with deep-sourced fluids, as evidenced by results of geochemistry analyses performed following the expedition.
    Description: Support for this research was provided through NASA PSTAR Grant #NNX16AL08G and National Science Foundation Navigating the New Arctic grant #1839063. Use of the R/V Falkor and ROV SuBastian were provided through a grant from the Schmidt Ocean Institute. The AUG Nemesis and the Aurora in-situ mass spectrometer was provided through in-kind support from Teledyne Webb Research and Navistry Corp, respectively.
    Keywords: Seep ; Autonomous exploration ; Costa Rica ; Geochemistry ; Water column data ; Temporal variability ; Decision-making algorithm
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    Observations of shallow methane bubble emissions from Cascadia Margin (2021)
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    Publication Date: 2022-10-20
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Michel, A. P. M., Preston, V. L., Fauria, K. E., & Nicholson, D. P. Observations of shallow methane bubble emissions from Cascadia Margin. Frontiers in Earth Science, 9, (2021): 613234, https://doi.org/10.3389/feart.2021.613234.
    Description: Open questions exist about whether methane emitted from active seafloor seeps reaches the surface ocean to be subsequently ventilated to the atmosphere. Water depth variability, coupled with the transient nature of methane bubble plumes, adds complexity to examining these questions. Little data exist which trace methane transport from release at a seep into the water column. Here, we demonstrate a coupled technological approach for examining methane transport, combining multibeam sonar, a field-portable laser-based spectrometer, and the ChemYak, a robotic surface kayak, at two shallow (〈75 m depth) seep sites on the Cascadia Margin. We demonstrate the presence of elevated methane (above the methane equilibration concentration with the atmosphere) throughout the water column. We observe areas of elevated dissolved methane at the surface, suggesting that at these shallow seep sites, methane is reaching the air-sea interface and is being emitted to the atmosphere.
    Description: Funding for VP was provided by an NDSEG Fellowship. Funding for KF was provided by a WHOI Postdoctoral Scholar Fellowship. Ship time on the R/V Falkor was provided by the Schmidt Ocean Institute (FK180824).
    Keywords: Methane ; Bubbles ; Cascadia Margin ; Laser spectrometer ; Ocean sensing ; Surface vehicle ; Multibeam sonar ; Seeps
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    Exploring the use of environmental DNA (eDNA) to detect animal taxa in the Mesopelagic Zone (2021)
    Frontiers Media
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    Publication Date: 2022-10-20
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Govindarajan, A. F., Francolini, R. D., Jech, J. M., Lavery, A. C., Llopiz, J. K., Wiebe, P. H., & Zhang, W. Exploring the use of environmental DNA (eDNA) to detect animal taxa in the Mesopelagic Zone. Frontiers in Ecology and Evolution, 9, (2021): 574877, https://doi.org/10.3389/fevo.2021.574877.
    Description: Animal biodiversity in the ocean’s vast mesopelagic zone is relatively poorly studied due to technological and logistical challenges. Environmental DNA (eDNA) analyses show great promise for efficiently characterizing biodiversity and could provide new insight into the presence of mesopelagic species, including those that are missed by traditional net sampling. Here, we explore the utility of eDNA for identifying animal taxa. We describe the results from an August 2018 cruise in Slope Water off the northeast United States. Samples for eDNA analysis were collected using Niskin bottles during five CTD casts. Sampling depths along each cast were selected based on the presence of biomass as indicated by the shipboard Simrad EK60 echosounder. Metabarcoding of the 18S V9 gene region was used to assess taxonomic diversity. eDNA metabarcoding results were compared with those from net-collected (MOCNESS) plankton samples. We found that the MOCNESS sampling recovered more animal taxa, but the number of taxa detected per liter of water sampled was significantly higher in the eDNA samples. eDNA was especially useful for detecting delicate gelatinous animals which are undersampled by nets. We also detected eDNA changes in community composition with depth, but not with sample collection time (day vs. night). We provide recommendations for applying eDNA-based methods in the mesopelagic including the need for studies enabling interpretation of eDNA signals and improvement of barcode reference databases.
    Description: This research was part of the Woods Hole Oceanographic Institution’s Ocean Twilight Zone Project, funded as part of The Audacious Project housed at TED. Funding for the NOAA Ship Henry B Bigelow was provided by NOAA’s Office of Marine and Aviation Operations (OMAO).
    Keywords: Environmental DNA ; Mesopelagic ; Biodiversity ; Metabarcoding ; Zooplankton
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    Editorial: small scale spatial and temporal patterns in particles, plankton, and other organisms (2021)
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    Publication Date: 2022-10-20
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nayak, A. R., Jiang, H., Byron, M. L., Sullivan, J. M., McFarland, M. N., & Murphy, D. W. Editorial: small scale spatial and temporal patterns in particles, plankton, and other organisms. Frontiers in Marine Science, 8, (2021): 669530, https://doi.org/10.3389./fmars.2021.669530
    Description: Scientists have long known that small-scale interactions of aquatic particles, plankton, and other organisms with their immediate environment play an important role in diverse research areas, including marine ecology, ocean optics, and climate change (Guasto et al., 2012; Prairie et al., 2012). Typically, the distribution of particles and other organisms in the water column tends to be quite “patchy,” i.e., non-homogeneous, both spatially and temporally (Durham and Stocker, 2012). Patchiness can manifest itself through well-known phenomena such as harmful algal blooms (HABs), phytoplankton and zooplankton “thin layers,” deep scattering layers, and schooling of marine organisms such as krill and fish. This non-homogeneous distribution can significantly influence predator-prey encounters and outcomes, export fluxes, marine ecosystem health, and biological productivity (Sullivan et al., 2010; Durham et al., 2013). Thus, there is a continuing need to study and characterize the small-scale biological-physical interactions between particles/organisms and their local environment, as well as the scaled-up effects of these small-scale interactions on larger-scale dynamics. These studies are also directly linked to broader research topics listed as part of the future “grand challenges” in marine ecosystem ecology, as outlined in Borja et al. (2020).
    Description: AN was supported through a National Academy of Sciences, Engineering, and Medicine (NASEM) Gulf Research Program (GRP) Early Career Research Fellowship and a faculty start-up grant at Florida Atlantic University. HJ was supported by US National Science Foundation awards (OCE-1559062 and IOS-1353937). MB was supported by a faculty start-up grant at Penn State University. AN, JS, and MM were supported by US National Science Foundation awards (OCE-1634053 and OCE-1657332). DM was supported by the US National Science Foundation (CBET-1846925).
    Keywords: Marine particles ; Plankton ; Spatial patterns ; Ocean microscale biophysics ; Small-scale processes ; Oceanic instrumentation
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    Microbial communities under distinct thermal and geochemical regimes in axial and off-axis sediments of Guaymas Basin (2021)
    Frontiers Media
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Teske, A., Wegener, G., Chanton, J. P., White, D., MacGregor, B., Hoer, D., de Beer, D., Zhuang, G., Saxton, M. A., Joye, S. B., Lizarralde, D., Soule, S. A., & Ruff, S. E. Microbial communities under distinct thermal and geochemical regimes in axial and off-axis sediments of Guaymas Basin. Frontiers in Microbiology, 12, (2021): 633649, https://doi.org/10.3389/fmicb.2021.633649.
    Description: Cold seeps and hydrothermal vents are seafloor habitats fueled by subsurface energy sources. Both habitat types coexist in Guaymas Basin in the Gulf of California, providing an opportunity to compare microbial communities with distinct physiologies adapted to different thermal regimes. Hydrothermally active sites in the southern Guaymas Basin axial valley, and cold seep sites at Octopus Mound, a carbonate mound with abundant methanotrophic cold seep fauna at the Central Seep location on the northern off-axis flanking regions, show consistent geochemical and microbial differences between hot, temperate, cold seep, and background sites. The changing microbial actors include autotrophic and heterotrophic bacterial and archaeal lineages that catalyze sulfur, nitrogen, and methane cycling, organic matter degradation, and hydrocarbon oxidation. Thermal, biogeochemical, and microbiological characteristics of the sampling locations indicate that sediment thermal regime and seep-derived or hydrothermal energy sources structure the microbial communities at the sediment surface.
    Description: Research on Guaymas Basin in the Teske lab is supported by NSF Molecular and cellular Biology grant 1817381 “Collaborative Research: Next generation physiology: a systems-level understanding of microbes driving carbon cycling in marine sediments”. Sampling in Guaymas Basin was supported by collaborative NSF Biological Oceanography grants 1357238 and 1357360 “Collaborative Research: Microbial carbon cycling and its interaction with sulfur and nitrogen transformations in Guaymas Basin hydrothermal sediments” to AT and SJ, respectively. SER was supported by an AITF/Eyes High Postdoctoral Fellowship and start-up funds provided by the Marine Biological Laboratory.
    Keywords: Cold seep ; Hydrothermal sediment ; Porewater profiles ; Bacteria, archaea ; Guaymas Basin
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    Equitable allocations in northern fisheries: bridging the divide for Labrador Inuit (2021)
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kourantidou, M., Hoagland, P., Dale, A., & Bailey, M. Equitable allocations in northern fisheries: bridging the divide for Labrador Inuit. Frontiers in Marine Science, 8, (2021): 590213, https://doi.org/10.3389/fmars.2021.590213.
    Description: Canada has undertaken commitments to recognize the rights of Indigenous Peoples in fisheries through policies and agreements, including Integrated Fishery Management Plans, the Reconciliation Strategy, and Land Claim Agreements (LCAs). In addition to recognizing rights, these commitments were intended to respect geographic adjacency principles, to enhance the economic viability of Indigenous communities, and to be reflective of community dependence on marine resources. We examined the determinants of quota allocations in commercial fisheries involving Nunatsiavut, Northern Labrador, the first self-governing region for the Inuit peoples in Canada. It has been argued that current fishery allocations for Nunatsiavut Inuit have not satisfied federal commitments to recognize Indigenous rights. Indicators that measure equity in commercial allocations for the turbot or Greenland halibut (Reinhardtius hippoglossoides) and northern shrimp (Pandalus borealis) fisheries were identified and assessed. In these two cases, historical allocations continue to predominate for allocations based upon equity or other social or economic considerations. We illustrate equity-enhancing changes in the quota distribution under scenarios of different levels of inequality aversion, and we make qualitative assessments of the effects of these allocations to Nunatsiavut for socioeconomic welfare. This approach could benefit fisheries governance in Northern Labrador, where federal commitments to equity objectives continue to be endorsed but have not yet been integrated fully into quota allocations.
    Description: This research was undertaken with funding from the Canada First Research Excellence Fund through the Ocean Frontier Institute (MK and MB) and the Johnson Endowment of the Woods Hole Oceanographic Institution’s (WHOI) Marine Policy Center (PH).
    Keywords: Fisheries ; Allocations ; Equity ; Indigenous rights ; Access
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    Pathways, volume transport, and seasonal variability of the lower deep limb of the Pacific Meridional Overturning Circulation at the Yap-Mariana Junction (2021)
    Frontiers Media
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Wang, J., Wang, F., Lu, Y., Ma, Q., Pratt, L. J., & Zhang, Z. Pathways, volume transport, and seasonal variability of the lower deep limb of the Pacific Meridional Overturning Circulation at the Yap-Mariana Junction. Frontiers in Marine Science, 8, (2021): 672199, https://doi.org/10.3389/fmars.2021.672199.
    Description: The lower deep branch of the Pacific Meridional Overturning Circulation (L-PMOC) is responsible for the deep-water transport from Antarctic to the North Pacific and is a key ingredient in the regulation of global climate through its influence on the storage and residence time of heat and carbon. At the Pacific Yap-Mariana Junction (YMJ), a major gateway for deep-water flowing into the Western Pacific Ocean, we deployed five moorings from 2018 to 2019 in the Eastern, Southern, and Northern Channels in order to explore the pathways and variability of L-PMOC. We have identified three main patterns for L-PMOC pathways. In Pattern 1, the L-PMOC intrudes into the YMJ from the East Mariana Basin (EMB) through the Eastern Channel and then flows northward into the West Mariana Basin (WMB) through the Northern Channel and southward into the West Caroline Basin (WCB) through the Southern Channel. In Pattern 2, the L-PMOC intrudes into the YMJ from both the WCB and the EMB and then flows into the WMB. In Pattern 3, the L-PMOC comes from the WCB and then flows into the EMB and WMB. The volume transports of L-PMOC through the Eastern, Southern, and Northern Channels all exhibit seasonality. During November–April (May–October), the flow pathway conforms to Pattern 1 (Patterns 2 and 3), and the mean and standard deviation of L-PMOC transports are −4.44 ± 1.26 (−0.30 ± 1.47), −0.96 ± 1.13 (1.75 ± 1.49), and 1.49 ± 1.31 (1.07 ± 1.10) Sv in the Eastern, Southern, and Northern Channels, respectively. Further analysis of numerical ocean modeling results demonstrates that L-PMOC transport at the YMJ is forced by a deep pressure gradient between two adjacent basins, which is mainly determined by the sea surface height (SSH) and water masses in the upper 2,000-m layer. The seasonal variability of L-PMOC transport is attributed to local Ekman pumping and westward-propagating Rossby waves. The L-PMOC transport greater than 3,500 m is closely linked to the wind forcing and the upper ocean processes.
    Description: This study was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (grant XDA22000000), the National Natural Science Foundation of China (grants 91958204 and 41776022), the Key Research Program of Frontier Sciences, CAS (grant QYZDB-SSW-SYS034), and the International Partnership Program of CAS (grant 133137KYSB20180056). FW thanks the support from the National Natural Science Foundation of China (grants 41730534 and 41421005). QM thanks the support by the National Natural Science Foundation of China (grant 42006003).
    Keywords: PMOC ; Mooring observations ; Seasonal variability ; Pathways ; Transport ; Yap-Mariana Junction ; Ekman pumping ; Rossby waves
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    Anthropogenic sound exposure-induced stress in captive dolphins and implications for cetacean health (2021)
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    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Yang, W.-C., Chen, C.-F., Chuah, Y.-C., Zhuang, C.-R., Chen, I.-H., Mooney, T. A., Stott, J., Blanchard, M., Jen, I.-F., & Chou, L.-S. Anthropogenic sound exposure-induced stress in captive dolphins and implications for cetacean health. Frontiers in Marine Science, 8,(2021): 606736, https://doi.org/10.3389/fmars.2021.606736.
    Description: Many cetaceans are exposed to increasing pressure caused by anthropogenic activities in their marine environment. Anthropogenic sound has been recognized as a possible stressor for cetaceans that may have impacts on health. However, the relationship between stress, hormones, and cytokines secretion in cetaceans is complex and not fully understood. Moreover, the effects of stress are often inconsistent because the character, intensity, and duration of the stressors are variable. For a better understanding of how anthropogenic sounds affect the psychophysiology of cetaceans, the present study compared the changes of cortisol concentration and cytokine gene transcriptions in blood samples and behaviors of captive bottlenose dolphins (Tursiops truncatus) after sound exposures. The sound stimuli were 800 Hz pure-tone multiple impulsive sound for 30 min at three different sound levels (estimated mean received SPL: 0, 120, and 140 dB re 1 μPa) that likely cause no permanent and temporary hearing threshold shift in dolphins. Six cytokine genes (IL-2Rα, IL-4, IL-10, IL-12, TNF-α, and IFN-γ) were selected for analysis. Cortisol levels and IL-10 gene transcription increased and IFNγ/IL-10 ratio was lower after a 30-min high-level sound exposure, indicating the sound stimuli used in this study could be a stressor for cetaceans, although only minor behavior changes were observed. This study may shed light on the potential impact of pile driving-like sounds on the endocrine and immune systems in cetaceans and provide imperative information regarding sound exposure for free-ranging cetaceans.
    Description: This work was supported by the Ministry of Science and Technology in Taiwan (MOST 108-2313-B-002-021 and MOST 109-2628-B-002-028).
    Keywords: sound ; cortisol ; cytokine ; behavior ; dolphins ; stress
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    Regional variation in winter foraging strategies by Weddell Seals in Eastern Antarctica and the Ross Sea (2021)
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    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Harcourt, R., Hindell, M. A., McMahon, C. R., Goetz, K. T., Charrassin, J.-B., Heerah, K., Holser, R., Jonsen, I. D., Shero, M. R., Hoenner, X., Foster, R., Lenting, B., Tarszisz, E., & Pinkerton, M. H. Regional variation in winter foraging strategies by Weddell Seals in Eastern Antarctica and the Ross Sea. Frontiers in Marine Science, 8, (2021): 720335, https://doi.org/10.3389/fmars.2021.720335.
    Description: The relative importance of intrinsic and extrinsic determinants of animal foraging is often difficult to quantify. The most southerly breeding mammal, the Weddell seal, remains in the Antarctic pack-ice year-round. We compared Weddell seals tagged at three geographically and hydrographically distinct locations in East Antarctica (Prydz Bay, Terre Adélie, and the Ross Sea) to quantify the role of individual variability and habitat structure in winter foraging behaviour. Most Weddell seals remained in relatively small areas close to the coast throughout the winter, but some dispersed widely. Individual utilisation distributions (UDi, a measure of the total area used by an individual seal) ranged from 125 to 20,825 km2. This variability was not due to size or sex but may be due to other intrinsic states for example reproductive condition or personality. The type of foraging (benthic vs. pelagic) varied from 56.6 ± 14.9% benthic dives in Prydz Bay through 42.1 ± 9.4% Terre Adélie to only 25.1 ± 8.7% in the Ross Sea reflecting regional hydrographic structure. The probability of benthic diving was less likely the deeper the ocean. Ocean topography was also influential at the population level; seals from Terre Adélie, with its relatively narrow continental shelf, had a core (50%) UD of only 200 km2, considerably smaller than the Ross Sea (1650 km2) and Prydz Bay (1700 km2). Sea ice concentration had little influence on the time the seals spent in shallow coastal waters, but in deeper offshore water they used areas of higher ice concentration. Marine Protected Areas (MPAs) in the Ross Sea encompass all the observed Weddell seal habitat, and future MPAs that include the Antarctic continental shelf are likely to effectively protect key Weddell seal habitat.
    Description: Field support was provided in the Ross Sea by Malcolm O’Toole, Rupert Woods, and Antarctica New Zealand and in Prydz Bay by Malcolm O’Toole, Andrew Doube, Iain Field, and the Australian Antarctic Division. The tagging study in Terre Adélie had logistical support from IPEV (Institut Paul Emile Victor) and the French Polar Institute. New Zealand funding was provided by the Ministry for Business, Innovation and Employment Endeavour Fund C01 × 1710: “RAMPing-up protection of the Ross Sea”. The 2014 field event was funded by NZARI (NZ Antarctic Research Institute) and Fisheries New Zealand (respectively), with Regina Eisert as CI, and tags and some field personnel funded by IMOS. The IMOS deployments in Prydz Bay were supported logistically by the Australian Antarctic Division through the Australian Antarctic Science Grant Scheme (AAS Projects 2794 & 4329). The tagging study in Terre Adélie was supported by the Program Terre-Océan-Surface Continentale-Atmosphère from Centre National d’Etudes Spatiales (TOSCA-CNES). The ARGOS seal tracking and dive data were sourced and are available from the Integrated Marine Observing System (IMOS), NIWA, and LOCEAN. IMOS is a national collaborative research infrastructure, supported by the Australian Government. It is operated by a consortium of institutions as an unincorporated joint venture, with the University of Tasmania as lead agent.
    Keywords: marine protected areas ; Antarctica ; marine ecosystems ; bathymetry ; ecosystem monitoring ; Weddell seals
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    A decade of incorporating social sciences in the Integrated Marine Biosphere Research Project (IMBeR): much done, much to do? (2021)
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    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in van Putten, I., Kelly, R., Cavanagh, R. D., Murphy, E. J., Breckwoldt, A., Brodie, S., Cvitanovic, C., Dickey-Collas, M., Maddison, L., Melbourne-Thomas, J., Arrizabalaga, H., Azetsu-Scott, K., Beckley, L. E., Bellerby, R., Constable, A. J., Cowie, G., Evans, K., Glaser, M., Hall, J., Hobday, A. J., Johnston, N. M., Llopiz, J. K., Mueter, F., Muller-Karger, F. E., Weng, K. C., Wolf-Gladrow, D., Xavier, J. C. A decade of incorporating social sciences in the Integrated Marine Biosphere Research Project (IMBeR): much done, much to do? Frontiers in Marine Science, 8, (2021): 662350, https://doi.org/10.3389/fmars.2021.662350.
    Description: Successful management and mitigation of marine challenges depends on cooperation and knowledge sharing which often occurs across culturally diverse geographic regions. Global ocean science collaboration is therefore essential for developing global solutions. Building effective global research networks that can enable collaboration also need to ensure inter- and transdisciplinary research approaches to tackle complex marine socio-ecological challenges. To understand the contribution of interdisciplinary global research networks to solving these complex challenges, we use the Integrated Marine Biosphere Research (IMBeR) project as a case study. We investigated the diversity and characteristics of 1,827 scientists from 11 global regions who were attendees at different IMBeR global science engagement opportunities since 2009. We also determined the role of social science engagement in natural science based regional programmes (using key informants) and identified the potential for enhanced collaboration in the future. Event attendees were predominantly from western Europe, North America, and East Asia. But overall, in the global network, there was growing participation by females, students and early career researchers, and social scientists, thus assisting in moving toward interdisciplinarity in IMBeR research. The mainly natural science oriented regional programmes showed mixed success in engaging and collaborating with social scientists. This was mostly attributed to the largely natural science (i.e., biological, physical) goals and agendas of the programmes, and the lack of institutional support and push to initiate connections with social science. Recognising that social science research may not be relevant to all the aims and activities of all regional programmes, all researchers however, recognised the (potential) benefits of interdisciplinarity, which included broadening scientists’ understanding and perspectives, developing connections and interlinkages, and making science more useful. Pathways to achieve progress in regional programmes fell into four groups: specific funding, events to come together, within-programme-reflections, and social science champions. Future research programmes should have a strategic plan to be truly interdisciplinary, engaging natural and social sciences, as well as aiding early career professionals to actively engage in such programmes.
    Description: This publication resulted in part from support from the U.S. National Science Foundation (Grant OCE-1840868) to the Scientific Committee on Oceanic Research (SCOR).
    Keywords: marine science ; research networks ; disciplines ; global ; regional programmes
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    Kelp in the Eastern Canadian Arctic: current and future predictions of habitat suitability and cover (2021)
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    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Goldsmit, J., Schlegel, R. W., Filbee-Dexter, K., MacGregor, K. A., Johnson, L. E., Mundy, C. J., Savoie, A. M., McKindsey, C. W., Howland, K. L., & Archambault, P. Kelp in the Eastern Canadian Arctic: current and future predictions of habitat suitability and cover. Frontiers in Marine Science, 18, (2021): 742209. https://doi.org/10.3389/fmars.2021.742209
    Description: Climate change is transforming marine ecosystems through the expansion and contraction of species’ ranges. Sea ice loss and warming temperatures are expected to expand habitat availability for macroalgae along long stretches of Arctic coastlines. To better understand the current distribution of kelp forests in the Eastern Canadian Arctic, kelps were sampled along the coasts for species identifications and percent cover. The sampling effort was supplemented with occurrence records from global biodiversity databases, searches in the literature, and museum records. Environmental information and occurrence records were used to develop ensemble models for predicting habitat suitability and a Random Forest model to predict kelp cover for the dominant kelp species in the region – Agarum clathratum, Alaria esculenta, and Laminariaceae species (Laminaria solidungula and Saccharina latissima). Ice thickness, sea temperature and salinity explained the highest percentage of kelp distribution. Both modeling approaches showed that the current extent of arctic kelps is potentially much greater than the available records suggest. These modeling approaches were projected into the future using predicted environmental data for 2050 and 2100 based on the most extreme emission scenario (RCP 8.5). The models agreed that predicted distribution of kelp in the Eastern Canadian Arctic is likely to expand to more northern locations under future emissions scenarios, with the exception of the endemic arctic kelp L. solidungula, which is more likely to lose a significant proportion of suitable habitat. However, there were differences among species regarding predicted cover for both current and future projections. Notwithstanding model-specific variation, it is evident that kelps are widespread throughout the area and likely contribute significantly to the functioning of current Arctic ecosystems. Our results emphasize the importance of kelp in Arctic ecosystems and the underestimation of their potential distribution there.
    Description: This work was supported by ArcticNet (P101 ArcticKelp), Fisheries and Oceans Canada Arctic Climate Change Adaptation Strategy, Arctic Science and Aquatic Invasive Species Monitoring and Research Funds, the Natural Sciences and Engineering Research Council (NSERC), NRCan Polar Continental Shelf Program Support, Canadian Aquatic Invasive Species Network (CAISN), the Nunavut Marine Region Wildlife Management Board (NWMB), Quebec-Ocean, and the Ocean Frontier Institute through an award from the Canada First Research Excellence Fund, the Marine Environmental Observation, Prediction and Response Network of Centres of Excellence’s (MEOPAR-NCE) Southampton Island Marine Ecosystem Project, and the Belmont Forum–BiodivERsA’s De-icing of Arctic Coasts: critical or new opportunities for marine biodiversity and Ecosystem Services (ACCES). KF-D was supported by the Australian Research Council (DE190100692).
    Keywords: Laminariales ; polar ; ensemble model ; species distribution model (SDM) ; climate change ; shallow subtidal benthic
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    Marine genetic resources in areas beyond national jurisdiction: promoting marine scientific research and enabling equitable benefit sharing (2021)
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    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Rogers, A. D., Baco, A., Escobar-Briones, E., Gjerde, K., Gobin, J., Jaspars, M., Levin, L., Linse, K., Rabone, M., Ramirez-Llodra, E., Sellanes, J., Shank, T. M., Sink, K., Snelgrove, P. V. R., Taylor, M. L., Wagner, D., & Harden-Davies, H. Marine genetic resources in areas beyond national jurisdiction: promoting marine scientific research and enabling equitable benefit sharing. Frontiers in Marine Science, 8, (2021): 667274, https://doi.org/10.3389/fmars.2021.667274.
    Description: Growing human activity in areas beyond national jurisdiction (ABNJ) is driving increasing impacts on the biodiversity of this vast area of the ocean. As a result, the United Nations General Assembly committed to convening a series of intergovernmental conferences (IGCs) to develop an international legally-binding instrument (ILBI) for the conservation and sustainable use of marine biological diversity of ABNJ [the biodiversity beyond national jurisdiction (BBNJ) agreement] under the United Nations Convention on the Law of the Sea. The BBNJ agreement includes consideration of marine genetic resources (MGR) in ABNJ, including how to share benefits and promote marine scientific research whilst building capacity of developing states in science and technology. Three IGCs have been completed to date with the fourth delayed by the Covid pandemic. This delay has allowed a series of informal dialogues to take place between state parties, which have highlighted a number of areas related to MGR and benefit sharing that require technical guidance from ocean experts. These include: guiding principles on the access and use of MGR from ABNJ; the sharing of knowledge arising from research on MGR in ABNJ; and capacity building and technology transfer for developing states. In this paper, we explain what MGR are, the methods required to collect, study and archive them, including data arising from scientific investigation. We also explore the practical requirements of access by developing countries to scientific cruises, including the sharing of data, as well as participation in research and development on shore whilst promoting rather than hindering marine scientific research. We outline existing infrastructure and shared resources that facilitate access, research, development, and benefit sharing of MGR from ABNJ; and discuss existing gaps. We examine international capacity development and technology transfer schemes that might facilitate or complement non-monetary benefit sharing activities. We end the paper by highlighting what the ILBI can achieve in terms of access, utilization, and benefit sharing of MGR and how we might future-proof the BBNJ Agreement with respect to developments in science and technology.
    Description: We would like to thank the Governments of The Kingdom of Belgium, The Principality of Monaco and Costa Rica, as well as The Prince Albert II Monaco Foundation, The Norwegian Nobel Institute, The Nobel Institute, The High Seas Alliance, The Pew Charitable Trusts, Ocean Unite and REV Ocean for supporting the High Seas Treaty Dialogues which have allowed informal discussions between States representatives on the Biodiversity Beyond National Jurisdiction agreement.
    Keywords: high seas ; marine genetic resources ; access and benefit sharing ; UNCLOS ; developing states
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    Rapid adaptation to temperature via a potential genomic island of divergence in the invasive green crab, Carcinus maenas (2021)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Tepolt, C. K., & Palumbi, S. R. Rapid adaptation to temperature via a potential genomic island of divergence in the invasive green crab, Carcinus maenas. Frontiers in Ecology and Evolution, 8, (2020): 580701, doi:10.3389/fevo.2020.580701.
    Description: Widespread species often adapt easily to novel conditions – both those found in new habitats and those generated by climate change. However, rapid adaptation may be hindered in the marine realm, where long-distance dispersal and consequently high gene flow are predicted to limit potential for local adaptation. Here, we use a highly dispersive invasive marine crab to test the nature and speed of adaptation to temperature in the sea. Using single nucleotide polymorphisms (SNPs) generated from cardiac transcriptome sequencing, we characterized six populations of the European green crab (Carcinus maenas) located across parallel thermal gradients in their native and invasive ranges. We compared SNP frequencies with local temperatures and previously generated data on cardiac heat and cold tolerance to identify candidate markers associated with population-level differences in thermal physiology. Of 10,790 SNPs, 104 were identified as frequency outliers, a signal that was strongly driven by association with temperature and/or cold tolerance. Seventy-two of these outlier markers, representing 28 different genes, were in a cluster of SNPs identified as a potential inversion polymorphism using linkage disequilibrium network analysis. This SNP cluster was unique in the data set, which was otherwise characterized by low levels of linkage disequilibrium, and markers in this cluster showed a significant enrichment of coding substitutions relative to the full SNP set. These 72 outlier SNPs appear to be transmitted as a unit, and represent a putative genomic island of divergence which varied in frequency with organismal cold tolerance. This relationship was strikingly similar across both native and invasive populations, all of which showed a very strong correlation with cold tolerance (R2 = 0.96 over all six populations). Notably, three of these populations have diverged recently (〈100 years) and show little to no neutral divergence, suggesting that this genomic region may be responding to temperature on a relatively short time scale. This relationship indicates adaptation to temperature based on the action of a putative genomic island of divergence, perhaps partially explaining the extraordinary invasive ability of this species.
    Description: CT was supported on this project by a National Defense Science and Engineering Grant, a Stanford Graduate Fellowship, a Stanford Center for Computational, Evolutionary, and Human Genomics Fellowship, and the Penzance Endowed Fund in Support of Assistant Scientists at WHOI. The sampling and sequencing of the data used in this analysis was funded by the Partnership for the Interdisciplinary Study of Coastal Oceans, the Myers Trust, the Explorer’s Club Exploration Fund, the Lerner Gray Memorial Fund of the American Museum of Natural History, the Vice Provost for Graduate Education at Stanford, the Eugene C. and Aileen E. Haderlie Memorial Fund, and a National Science Foundation Doctoral Dissertation Improvement Grant (1210057).
    Keywords: rapid adaptation ; supergene ; thermal adaptation ; gene flow ; invasive species ; balanced polymorphism ; chromosomal inversion
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    Horizontal and vertical movement patterns and habitat use of juvenile porbeagles (Lamna nasus) in the Western North Atlantic (2021)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Skomal, G., Marshall, H., Galuardi, B., Natanson, L., Braun, C. D., & Bernal, D. Horizontal and vertical movement patterns and habitat use of juvenile porbeagles (Lamna nasus) in the Western North Atlantic. Frontiers in Marine Science, 8,(2021): 624158, https://doi.org/10.3389/fmars.2021.624158.
    Description: The porbeagle (Lamna nasus) is a large, highly migratory endothermic shark broadly distributed in the higher latitudes of the Atlantic, South Pacific, and Indian Oceans. In the North Atlantic, the porbeagle has a long history of fisheries exploitation and current assessments indicate that this stock is severely overfished. Although much is known of the life history of this species, there is little fisheries-independent information about habitat preferences and ecology. To examine migratory routes, vertical behavior, and environmental associations in the western North Atlantic, we deployed pop-up satellite archival transmitting tags on 20 porbeagles in late November, 2006. The sharks, ten males and ten females ranging from 128 to 154 cm fork length, were tagged and released from a commercial longline fishing vessel on the northwestern edge of Georges Bank, about 150 km east of Cape Cod, MA. The tags were programmed to release in March (n = 7), July (n = 7), and November (n = 6) of 2007, and 17 (85%) successfully reported. Based on known and derived geopositions, the porbeagles exhibited broad seasonally-dependent horizontal and vertical movements ranging from minimum linear distances of 937 to 3,310 km and from the surface to 1,300 m, respectively. All of the sharks remained in the western North Atlantic from the Gulf of Maine, the Scotian Shelf, on George's Bank, and in the deep, oceanic waters off the continental shelf along the edge of, and within, the Gulf Stream. In general, the population appears to be shelf-oriented during the summer and early fall with more expansive offshore radiation in the winter and spring. Although sharks moved through temperatures ranging from 2 to 26°C, the bulk of their time (97%) was spent in 6-20°C. In the summer months, most of the sharks were associated with the continental shelf moving between the surface and the bottom and remaining 〈 200 m deep. In the late fall and winter months, the porbeagles moved into pelagic habitat and exhibited two behavioral patterns linked with the thermal features of the Gulf Stream: “non-divers” (n = 7) largely remained at epipelagic depths and “divers” (n = 10) made frequent dives into and remained at mesopelagic depths (200–1000 m). These data demonstrate that juvenile porbeagles are physiologically capable of exploiting the cool temperate waters of the western North Atlantic as well as the mesopelagic depths of the Gulf Stream, possibly allowing exploitation of prey not available to other predators.
    Description: This research was funded by the Large Pelagics Research Center (Grant 06-125).
    Keywords: porbeagle movements ; diving behavior ; Western North Atlantic Ocean ; Gulf Stream ; endothermy
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  • 97
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    Identifying priorities for the protection of deep Mediterranean Sea ecosystems through an integrated approach (2021)
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    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Fanelli, E., Bianchelli, S., Foglini, F., Canals, M., Castellan, G., Guell-Bujons, Q., Galil, B., Goren, M., Evans, J., Fabri, M.-C., Vaz, S., Ciuffardi, T., Schembri, P. J., Angeletti, L., Taviani, M., & Danovaro, R. Identifying priorities for the protection of deep Mediterranean Sea ecosystems through an integrated approach. Frontiers in Marine Science, 8, (2021): 698890, https://doi.org/10.3389/fmars.2021.698890.
    Description: Benthic habitats of the deep Mediterranean Sea and the biodiversity they host are increasingly jeopardized by increasing human pressures, both direct and indirect, which encompass fisheries, chemical and acoustic pollution, littering, oil and gas exploration and production and marine infrastructures (i.e., cable and pipeline laying), and bioprospecting. To this, is added the pervasive and growing effects of human-induced perturbations of the climate system. International frameworks provide foundations for the protection of deep-sea ecosystems, but the lack of standardized criteria for the identification of areas deserving protection, insufficient legislative instruments and poor implementation hinder an efficient set up in practical terms. Here, we discuss the international legal frameworks and management measures in relation to the status of habitats and key species in the deep Mediterranean Basin. By comparing the results of a multi-criteria decision analysis (MCDA) and of expert evaluation (EE), we identify priority deep-sea areas for conservation and select five criteria for the designation of future protected areas in the deep Mediterranean Sea. Our results indicate that areas (1) with high ecological relevance (e.g., hosting endemic and locally endangered species and rare habitats),(2) ensuring shelf-slope connectivity (e.g., submarine canyons), and (3) subject to current and foreseeable intense anthropogenic impacts, should be prioritized for conservation. The results presented here provide an ecosystem-based conservation strategy for designating priority areas for protection in the deep Mediterranean Sea.
    Description: This study was supported by the DG ENV project IDEM (Implementation of the MSFD to the Deep Mediterranean Sea; contract EU No. 11.0661/2017/750680/SUB/EN V.C2). MC and QG-B acknowledge support from Generalitat de Catalunya autonomous government through its funding scheme to excellence research groups (Grant 2017 SGR 315).
    Keywords: biodiversity hotspots ; deep-sea ecosystems ; multicriteria decision analysis ; expert evaluation ; marine protected areas ; Marine Strategy Framework Directive ; Mediterranean Sea ; protection guidelines
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  • 98
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    Explaining regeneration: cells and limbs as complex living systems, learning from history (2021)
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    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in MacCord, K., & Maienschein, J. Explaining regeneration: cells and limbs as complex living systems, learning from history. Frontiers in Cell and Developmental Biology, 9, (2021): 734315, https://doi.org/10.3389/fcell.2021.734315.
    Description: Regeneration has been investigated since Aristotle, giving rise to many ways of explaining what this process is and how it works. Current research focuses on gene expression and cell signaling of regeneration within individual model organisms. We tend to look to model organisms on the reasoning that because of evolution, information gained from other species must in some respect be generalizable. However, for all that we have uncovered about how regeneration works within individual organisms, we have yet to translate what we have gleaned into achieving the goal of regenerative medicine: to harness and enhance our own regenerative abilities. Turning to history may provide a crucial perspective in advancing us toward this goal. History gives perspective, allowing us to reflect on how our predecessors did their work and what assumptions they made, thus also revealing limitations. History, then, may show us how we can move from our current reductionist thinking focused on particular selected model organisms toward generalizations about this crucial process that operates across complex living systems and move closer to repairing our own damaged bodies.
    Description: This article was a product of the McDonnell Initiative at the Marine Biological Laboratory. The McDonnell Initiative began with support from two generous grants from the James S. McDonnell Foundation, along with substantive input from the Foundation Director, Susan Fitzpatrick (“Integrating the Life Sciences with the History and Philosophy of Science” JSMF Grant No. 220020480 and “Transforming Discovery: Historians, Philosophers, and Life Scientists Exploring Regeneration” JSMF Grant No. 220020480.01).
    Keywords: regeneration ; complex living systems ; Morgan ; generalizability ; reductionism ; model organisms ; blastema
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  • 99
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    Compound-specific stable isotope analysis of amino acids in pelagic shark vertebrae reveals baseline, trophic, and physiological effects on bulk protein isotope records (2021)
    Frontiers Media
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    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Magozzi, S., Thorrold, S. R., Houghton, L., Bendall, V. A., Hetherington, S., Mucientes, G., Natanson, L. J., Queiroz, N., Santos, M. N., & Trueman, C. N. Compound-specific stable isotope analysis of amino acids in pelagic shark vertebrae reveals baseline, trophic, and physiological effects on bulk protein isotope records. Frontiers in Marine Science, 8, (2021): 673016, https://doi.org/10.3389/fmars.2021.673016.
    Description: Variations in stable carbon and nitrogen isotope compositions in incremental tissues of pelagic sharks can be used to infer aspects of their spatial and trophic ecology across life-histories. Interpretations from bulk tissue isotopic compositions are complicated, however, because multiple processes influence these values, including variations in primary producer isotope ratios and consumer diets and physiological processing of metabolites. Here we challenge inferences about shark tropho-spatial ecology drawn from bulk tissue isotope data using data for amino acids. Stable isotope compositions of individual amino acids can partition the isotopic variance in bulk tissue into components associated with primary production on the one hand, and diet and physiology on the other. The carbon framework of essential amino acids (EAAs) can be synthesised de novo only by plants, fungi and bacteria and must be acquired by consumers through the diet. Consequently, the carbon isotopic composition of EAAs in consumers reflects that of primary producers in the location of feeding, whereas that of non-essential amino acids (non-EAAs) is additionally influenced by trophic fractionation and isotope dynamics of metabolic processing. We determined isotope chronologies from vertebrae of individual blue sharks and porbeagles from the North Atlantic. We measured carbon and nitrogen isotope compositions in bulk collagen and carbon isotope compositions of amino acids. Despite variability among individuals, common ontogenetic patterns in bulk isotope compositions were seen in both species. However, while life-history movement inferences from bulk analyses for blue sharks were supported by carbon isotope data from essential amino acids, inferences for porbeagles were not, implying that the observed trends in bulk protein isotope compositions in porbeagles have a trophic or physiological explanation, or are suprious effects. We explored variations in carbon isotope compositions of non-essential amino acids, searching for systematic variations that might imply ontogenetic changes in physiological processing, but patterns were highly variable and did not explain variance in bulk protein δ13C values. Isotopic effects associated with metabolite processing may overwhelm spatial influences that are weak or inconsistently developed in bulk tissue isotope values, but interpreting mechanisms underpinning isotopic variation in patterns in non-essential amino acids remains challenging.
    Description: The internship of SM at the Woods Hole Oceanographic Institution was funded by the School of Ocean and Earth Science at University of Southampton. Stable isotope analyses were paid by CT and ST research budgets and SM Ph.D. and placement funding.
    Keywords: carbon ; essential amino acids ; non-essential amino acids ; migration ; diet ; routing ; blue sharks (Prionace glauca) ; porbeagles (Lamna nasus)
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    How do marine mammals manage and usually avoid gas emboli formation and gas embolic pathology? critical clues from studies of wild dolphins (2021)
    Frontiers Media
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Fahlman, A., Moore, M. J., & Wells, R. S. How do marine mammals manage and usually avoid gas emboli formation and gas embolic pathology? critical clues from studies of wild dolphins. Frontiers in Marine Science, 8, (2021): 598633, https://doi.org/10.3389/fmars.2021.598633.
    Description: Decompression theory has been mainly based on studies on terrestrial mammals, and may not translate well to marine mammals. However, evidence that marine mammals experience gas bubbles during diving is growing, causing concern that these bubbles may cause gas emboli pathology (GEP) under unusual circumstances. Marine mammal management, and usual avoidance, of gas emboli and GEP, or the bends, became a topic of intense scientific interest after sonar-exposed, mass-stranded deep-diving whales were observed with gas bubbles. Theoretical models, based on our current understanding of diving physiology in cetaceans, predict that the tissue and blood N2 levels in the bottlenose dolphin (Tursiops truncatus) are at levels that would result in severe DCS symptoms in similar sized terrestrial mammals. However, the dolphins appear to have physiological or behavioral mechanisms to avoid excessive blood N2 levels, or may be more resistant to circulating bubbles through immunological/biochemical adaptations. Studies on behavior, anatomy and physiology of marine mammals have enhanced our understanding of the mechanisms that are thought to prevent excessive uptake of N2. This has led to the selective gas exchange hypothesis, which provides a mechanism how stress-induced behavioral change may cause failure of the normal physiology, which results in excessive uptake of N2, and in extreme cases may cause formation of symptomatic gas emboli. Studies on cardiorespiratory function have been integral to the development of this hypothesis, with work initially being conducted on excised tissues and cadavers, followed by studies on anesthetized animals or trained animals under human care. These studies enabled research on free-ranging common bottlenose dolphins in Sarasota Bay, FL, and off Bermuda, and have included work on the metabolic and cardiorespiratory physiology of both shallow- and deep-diving dolphins and have been integral to better understand how cetaceans can dive to extreme depths, for long durations.
    Description: Many of the studies that have resulted in the data in this review, and that have been integral to develop the selective gas exchange hypothesis have been funded by the Office of Naval Research (ONR Awards # N000141010159, N000141613088, N000141410563, N000140811220, and ONR YIP Award # N000141410563), and Dolphin Quest. The authors declare that Dolphin Quest was not involved in the study design, collection, analysis, interpretation of data, the writing of this article or the decision to submit it for publication.
    Keywords: diving physiology ; lung function ; dive response ; plasticity ; cardiac output ; selective gas exchange hypothesis ; gasembolic pathology ; decompression sickness
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