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  • Biogeochemistry  (7)
  • Antarctic bacterioplankton
  • Frontiers Media  (7)
  • American Institute of Physics (AIP)
  • Nature Publishing Group
  • 1
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    Pathway-centric analysis of microbial metabolic potential and expression along nutrient and energy gradients in the western Atlantic Ocean (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 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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  • 2
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    Microbial ecosystem responses to alkalinity enhancement in the North Atlantic Subtropical Gyre (2022)
    Frontiers Media
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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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  • 3
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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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  • 4
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    Soil warming accelerates biogeochemical silica cycling in a temperate forest. (2019)
    Frontiers Media
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gewirtzman, J., Tang, J., Melillo, J. M., Werner, W. J., Kurtz, A. C., Fulweiler, R. W., & Carey, J. C. Soil warming accelerates biogeochemical silica cycling in a temperate forest. Frontiers in Plant Science, 10, (2019): 1097, doi:10.3389/fpls.2019.01097.
    Description: Biological cycling of silica plays an important role in terrestrial primary production. Soil warming stemming from climate change can alter the cycling of elements, such as carbon and nitrogen, in forested ecosystems. However, the effects of soil warming on the biogeochemical cycle of silica in forested ecosystems remain unexplored. Here we examine long-term forest silica cycling under ambient and warmed conditions over a 15-year period of experimental soil warming at Harvard Forest (Petersham, MA). Specifically, we measured silica concentrations in organic and mineral soils, and in the foliage and litter of two dominant species (Acer rubrum and Quercus rubra), in a large (30 × 30 m) heated plot and an adjacent control plot (30 × 30 m). In 2016, we also examined effects of heating on dissolved silica in the soil solution, and conducted a litter decomposition experiment using four tree species (Acer rubrum, Quercus rubra, Betula lenta, Tsuga canadensis) to examine effects of warming on the release of biogenic silica (BSi) from plants to soils. We find that tree foliage maintained constant silica concentrations in the control and warmed plots, which, coupled with productivity enhancements under warming, led to an increase in total plant silica uptake. We also find that warming drove an acceleration in the release of silica from decaying litter in three of the four species we examined, and a substantial increase in the silica dissolved in soil solution. However, we observe no changes in soil BSi stocks with warming. Together, our data indicate that warming increases the magnitude of silica uptake by vegetation and accelerates the internal cycling of silica in in temperate forests, with possible, and yet unresolved, effects on the delivery of silica from terrestrial to marine systems.
    Description: This research was supported by the National Science Foundation (NSF PLR-1417763 to JT), the Geological Society of America (Stephen G. Pollock Undergraduate Research Grant to JG), the Institute at Brown for Environment and Society, and the Marine Biological Laboratory. Sample analysis and Fulweiler’s involvement were supported by Boston University and a Bullard Fellowship from Harvard University. The soil warming experiment was supported by the National Science Foundation (DEB-0620443) and Department of Energy (DE-FC02-06-ER641577 and DE-SC0005421).
    Keywords: Silica ; Climate change ; Soil ; Warming ; Phytoliths ; Plants ; Biogeochemistry
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  • 5
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    The tropical Atlantic observing system (2019)
    Frontiers Media
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Foltz, G. R., Brandt, P., Richter, I., Rodriguez-Fonsecao, B., Hernandez, F., Dengler, M., Rodrigues, R. R., Schmidt, J. O., Yu, L., Lefevre, N., Da Cunha, L. C., Mcphaden, M. J., Araujo, M., Karstensen, J., Hahn, J., Martin-Rey, M., Patricola, C. M., Poli, P., Zuidema, P., Hummels, R., Perez, R. C., Hatje, V., Luebbecke, J. F., Palo, I., Lumpkin, R., Bourles, B., Asuquo, F. E., Lehodey, P., Conchon, A., Chang, P., Dandin, P., Schmid, C., Sutton, A., Giordani, H., Xue, Y., Illig, S., Losada, T., Grodsky, S. A., Gasparinss, F., Lees, T., Mohino, E., Nobre, P., Wanninkhof, R., Keenlyside, N., Garcon, V., Sanchez-Gomez, E., Nnamchi, H. C., Drevillon, M., Storto, A., Remy, E., Lazar, A., Speich, S., Goes, M., Dorrington, T., Johns, W. E., Moum, J. N., Robinson, C., Perruches, C., de Souza, R. B., Gaye, A. T., Lopez-Paragess, J., Monerie, P., Castellanos, P., Benson, N. U., Hounkonnou, M. N., Trotte Duha, J., Laxenairess, R., & Reul, N. The tropical Atlantic observing system. Frontiers in Marine Science, 6(206), (2019), doi:10.3389/fmars.2019.00206.
    Description: he tropical Atlantic is home to multiple coupled climate variations covering a wide range of timescales and impacting societally relevant phenomena such as continental rainfall, Atlantic hurricane activity, oceanic biological productivity, and atmospheric circulation in the equatorial Pacific. The tropical Atlantic also connects the southern and northern branches of the Atlantic meridional overturning circulation and receives freshwater input from some of the world’s largest rivers. To address these diverse, unique, and interconnected research challenges, a rich network of ocean observations has developed, building on the backbone of the Prediction and Research Moored Array in the Tropical Atlantic (PIRATA). This network has evolved naturally over time and out of necessity in order to address the most important outstanding scientific questions and to improve predictions of tropical Atlantic severe weather and global climate variability and change. The tropical Atlantic observing system is motivated by goals to understand and better predict phenomena such as tropical Atlantic interannual to decadal variability and climate change; multidecadal variability and its links to the meridional overturning circulation; air-sea fluxes of CO2 and their implications for the fate of anthropogenic CO2; the Amazon River plume and its interactions with biogeochemistry, vertical mixing, and hurricanes; the highly productive eastern boundary and equatorial upwelling systems; and oceanic oxygen minimum zones, their impacts on biogeochemical cycles and marine ecosystems, and their feedbacks to climate. Past success of the tropical Atlantic observing system is the result of an international commitment to sustained observations and scientific cooperation, a willingness to evolve with changing research and monitoring needs, and a desire to share data openly with the scientific community and operational centers. The observing system must continue to evolve in order to meet an expanding set of research priorities and operational challenges. This paper discusses the tropical Atlantic observing system, including emerging scientific questions that demand sustained ocean observations, the potential for further integration of the observing system, and the requirements for sustaining and enhancing the tropical Atlantic observing system.
    Description: MM-R received funding from the MORDICUS grant under contract ANR-13-SENV-0002-01 and the MSCA-IF-EF-ST FESTIVAL (H2020-EU project 797236). GF, MG, RLu, RP, RW, and CS were supported by NOAA/OAR through base funds to AOML and the Ocean Observing and Monitoring Division (OOMD; fund reference 100007298). This is NOAA/PMEL contribution #4918. PB, MDe, JH, RH, and JL are grateful for continuing support from the GEOMAR Helmholtz Centre for Ocean Research Kiel. German participation is further supported by different programs funded by the Deutsche Forschungsgemeinschaft, the Deutsche Bundesministerium für Bildung und Forschung (BMBF), and the European Union. The EU-PREFACE project funded by the EU FP7/2007–2013 programme (Grant No. 603521) contributed to results synthesized here. LCC was supported by the UERJ/Prociencia-2018 research grant. JOS received funding from the Cluster of Excellence Future Ocean (EXC80-DFG), the EU-PREFACE project (Grant No. 603521) and the BMBF-AWA project (Grant No. 01DG12073C).
    Keywords: Tropical Atlantic Ocean ; Observing system ; Weather ; Climate ; Hurricanes ; Biogeochemistry ; Ecosystems ; Coupled model bias
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  • 6
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    Advancing observation of ocean biogeochemistry, biology, and ecosystems with cost-effective in situ sensing technologies (2019)
    Frontiers Media
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    Publication Date: 2022-10-20
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Wang, Z. A., Moustahfid, H., Mueller, A., V., Michel, A. P. M., Mowlem, M., Glazer, B. T., Mooney, T. A., Michaels, W., McQuillan, J. S., Robidart, J. C., Churchill, J., Sourisseau, M., Daniel, A., Schaap, A., Monk, S., Friedman, K., & Brehmer, P. Advancing observation of ocean biogeochemistry, biology, and ecosystems with cost-effective in situ sensing technologies. Frontiers in Marine Science, 6, (2019): 519, doi:10.3389/fmars.2019.00519.
    Description: Advancing our understanding of ocean biogeochemistry, biology, and ecosystems relies on the ability to make observations both in the ocean and at the critical boundaries between the ocean and other earth systems at relevant spatial and temporal scales. After decades of advancement in ocean observing technologies, one of the key remaining challenges is how to cost-effectively make measurements at the increased resolution necessary for illuminating complex system processes and rapidly evolving changes. In recent years, biogeochemical in situ sensors have been emerging that are threefold or more lower in cost than established technologies; the cost reduction for many biological in situ sensors has also been significant, although the absolute costs are still relatively high. Cost savings in these advancements has been driven by miniaturization, new methods of packaging, and lower-cost mass-produced components such as electronics and materials. Recently, field projects have demonstrated the potential for science-quality data collection via large-scale deployments using cost-effective sensors and deployment strategies. In the coming decade, it is envisioned that ocean biogeochemistry and biology observations will be revolutionized by continued innovation in sensors with increasingly low price points and the scale-up of deployments of these in situ sensor technologies. The goal of this study is therefore to: (1) provide a review of existing sensor technologies that are already achieving cost-effectiveness compared with traditional instrumentation, (2) present case studies of cost-effective in situ deployments that can provide insight into methods for bridging observational gaps, (3) identify key challenge areas where progress in cost reduction is lagging, and (4) present a number of potentially transformative directions for future ocean biogeochemical and biological studies using cost-effective technologies and deployment strategies.
    Description: The unpublished work related to iTag and mini-DO sensor was supported by the US National Science Foundation (NSF) (DBI-145559). The US NSF (OCE-1233654), the US National Institute of Standards and Technology (NIST) (60NANB10D024), and the NOAA Sea Grant (2017-R/RCM-51) supported the development of the CHANOS sensor. Part of this work was supported by the European Commission via the STEMM-CCS, AtlantOS, SenseOCEAN, TriAtlas, and Preface projects under the European Union’s Horizon 2020 research and innovation program (Grant Nos. 603521, 654462, 633211, 614141, and 817578), as well as the AWA project (IRD and BMBF; 01DG12073E), and the Blue Belt Initiative (BBI). The work on the LOC nutrients and carbonate sensors was supported by the Autonuts and CarCASS projects, part of the UK Natural Environment Research Council capital program OCEANIDS (NE/P020798/1 and NE/P02081X/1). The work on zooplankton and chlorophyll sensors was co-supported by the ROEC program (Reseau d’Observation en Environnement Côtier 2015–2020) and the European Regional Development Fund (ERDF).
    Keywords: In situ ; Sensor ; OceanObs ; Ocean technology ; EOVs ; Biogeochemistry ; Biology ; Cost effective
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  • 7
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    Microbial activity in the marine deep biosphere : progress and prospects (2014)
    Frontiers Media
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 4 (2013): 189, doi:10.3389/fmicb.2013.00189.
    Description: The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists—all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these “extreme” environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) “theme team” on microbial activity (www.darkenergybiosphere.org).
    Description: Funding for the meeting was provided by C-DEBI, a US National Science Foundation (NSF)-funded Science and Technology Center (OCE-0939564). Funding for this publication was provided, in part, by NSF (OCE-1233226 to BNO).
    Keywords: Deep biosphere ; IODP ; Biogeochemistry ; Sediment ; Oceanic crust ; C-DEBI ; Subsurface microbiology
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  • 8
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    A metagenomic assessment of winter and summer bacterioplankton from Antarctica Peninsula coastal surface waters (2012)
    Nature Publishing Group
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in The ISME Journal 6 (2012): 1901-1915, doi:10.1038/ismej.2012.31.
    Description: Antarctic surface oceans are well-studied during summer when irradiance levels are high, sea ice is melting and primary productivity is at a maximum. Coincident with this timing, the bacterioplankton respond with significant increases in secondary productivity. Little is known about bacterioplankton in winter when darkness and sea-ice cover inhibit photoautotrophic primary production. We report here an environmental genomic and small subunit ribosomal RNA (SSU rRNA) analysis of winter and summer Antarctic Peninsula coastal seawater bacterioplankton. Intense inter-seasonal differences were reflected through shifts in community composition and functional capacities encoded in winter and summer environmental genomes with significantly higher phylogenetic and functional diversity in winter. In general, inferred metabolisms of summer bacterioplankton were characterized by chemoheterotrophy, photoheterotrophy and aerobic anoxygenic photosynthesis while the winter community included the capacity for bacterial and archaeal chemolithoautotrophy. Chemolithoautotrophic pathways were dominant in winter and were similar to those recently reported in global ‘dark ocean’ mesopelagic waters. If chemolithoautotrophy is widespread in the Southern Ocean in winter, this process may be a previously unaccounted carbon sink and may help account for the unexplained anomalies in surface inorganic nitrogen content.
    Description: CSR was supported by an NSF Postdoctoral Fellowship in Biological Informatics (DBI-0532893). The research was supported by National Science Foundation awards: ANT 0632389 (to AEM and JJG), and ANT 0632278 and 0217282 (to HWD), all from the Antarctic Organisms and Ecosystems Program.
    Keywords: Antarctic bacterioplankton ; Metagenomics ; Chemolithoautotrophy
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