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  • 1
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    Nature Computational Science
    Nature Research
    Online: 1(1).2021 –
    Details
    Publisher: Nature Research
    Electronic ISSN: 2662-8457
    Topics: Computer Science
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    JOURNAL
  • 2
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    Nature Reviews Methods Primers
    Nature Research
    Online: 1(1).2021 –
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    Publisher: Nature Research
    Electronic ISSN: 2662-8449
    Topics: Technology
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    JOURNAL
  • 3
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    Chytrid fungi distribution and co-occurrence with diatoms correlate with sea ice melt in the Arctic (2020)
    Nature Research
    In:  EPIC3Nature Communications Biology, Nature Research, (3), pp. 183
    Details
    Publication Date: 2020-05-04
    Description: Global warming is rapidly altering physicochemical attributes of Arctic waters. These changes are predicted to alter microbial networks, potentially perturbing wider community functions including parasite infections and saprotrophic recycling of biogeochemical compounds. Specifically, the interaction between autotrophic phytoplankton and heterotrophic fungi e.g. chytrids (fungi with swimming tails) requires further analysis. Here, we investigate the diversity and distribution patterns of fungi in relation to abiotic variables during one record sea ice minimum in 2012 and explore co-occurrence of chytrids with diatoms, key primary producers in these changing environments. We show that chytrid fungi are primarily encountered at sites influenced by sea ice melt. Furthermore, chytrid representation positively correlates with sea ice-associated diatoms such as Fragilariopsis or Nitzschia. Our findings identify a potential future scenario where chytrid representation within these communities increases as a consequence of ice retreat, further altering community structure through perturbation of parasitic or saprotrophic interaction networks
    Repository Name: EPIC Alfred Wegener Institut
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  • 4
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    Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes (2020)
    Nature Research
    In:  EPIC3Communications Biology, Nature Research, 3(119), ISSN: 23993642
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    Publication Date: 2020-08-13
    Description: The genome encodes the metabolic and functional capabilities of an organism and should be a major determinant of its ecological niche. Yet, it is unknown if the niche can be predicted directly from the genome. Here, we conduct metagenomic binning on 123 water samples spanning major environmental gradients of the Baltic Sea. The resulting 1961 metagenome-assembled genomes represent 352 species-level clusters that correspond to 1/3 of the metagenome sequences of the prokaryotic size-fraction. By using machine-learning, the placement of a genome cluster along various niche gradients (salinity level, depth, size-fraction) could be predicted based solely on its functional genes. The same approach predicted the genomes’ placement in a virtual niche-space that captures the highest variation in distribution patterns. The predictions generally outperformed those inferred from phylogenetic information. Our study demonstrates a strong link between genome and ecological niche and provides a conceptual framework for predictive ecology based on genomic data.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev , info:eu-repo/semantics/article
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  • 5
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    Diverse interactions and ecosystem engineering can stabilize community assembly (2020)
    Nature Research
    In:  EPIC3nature communications, Nature Research, 11(3307), ISSN: 2041-1723
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    Publication Date: 2020-08-13
    Description: The complexity of an ecological community can be distilled into a network, where diverse interactions connect species in a web of dependencies. Species interact directly with each other and indirectly through environmental effects, however to our knowledge the role of these ecosystem engineers has not been considered in ecological network models. Here we explore the dynamics of ecosystem assembly, where species colonization and extinction depends on the constraints imposed by trophic, service, and engineering dependencies. We show that our assembly model reproduces many key features of ecological systems, such as the role of generalists during assembly, realistic maximum trophic levels, and increased nestedness with mutualistic interactions. We find that ecosystem engineering has large and nonlinear effects on extinction rates. While small numbers of engineers reduce stability by increasing primary extinctions, larger numbers of engineers increase stability by reducing primary extinctions and extinction cascade magnitude. Our results suggest that ecological engineers may enhance community diversity while increasing persistence by facilitating colonization and limiting competitive exclusion.
    Repository Name: EPIC Alfred Wegener Institut
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  • 6
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    Thresholds for ecological responses to global change do not emerge from empirical data (2020)
    Nature Research
    In:  EPIC3Nature Ecology and Evolution, Nature Research, ISSN: 2397-334X
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    Publication Date: 2020-09-21
    Description: To understand ecosystem responses to anthropogenic global change, a prevailing framework is the definition of threshold levels of pressure, above which response magnitudes and their variances increase disproportionately. However, we lack systematic quantitative evidence as to whether empirical data allow definition of such thresholds. Here, we summarize 36 meta-analyses measuring more than 4,600 global change impacts on natural communities. We find that threshold transgressions were rarely detectable, either within or across meta-analyses. Instead, ecological responses were characterized mostly by progressively increasing magnitude and variance when pressure increased. Sensitivity analyses with modelled data revealed that minor variances in the response are sufficient to preclude the detection of thresholds from data, even if they are present. The simulations reinforced our contention that global change biology needs to abandon the general expectation that system properties allow defining thresholds as a way to manage nature under global change. Rather, highly variable responses, even under weak pressures, suggest that ‘safe-operating spaces’ are unlikely to be quantifiable.
    Repository Name: EPIC Alfred Wegener Institut
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  • 7
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    Past megadroughts in central Europe were longer, more severe and less warm than modern droughts (2021)
    Nature Research
    In:  EPIC3Communications Earth & Environment, Nature Research, 2(1), pp. 61, ISSN: 2662-4435
    Details
    Publication Date: 2021-07-01
    Description: Megadroughts are notable manifestations of the American Southwest, but not so much of the European climate. By using long-term hydrological and meteorological observations, as well as paleoclimate reconstructions, here we show that central Europe has experienced much longer and severe droughts during the Spörer Minimum (~AD 1400–1480) and Dalton Minimum (~AD 1770–1840), than the ones observed during the 21st century. These two megadroughts appear to be linked with a cold state of the North Atlantic Ocean and enhanced winter atmospheric blocking activity over the British Isles and western part of Europe, concurrent with reduced solar forcing and explosive volcanism. Moreover, we show that the recent drought events (e.g., 2003, 2015, and 2018), are within the range of natural variability and they are not unprecedented over the last millennium.
    Repository Name: EPIC Alfred Wegener Institut
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  • 8
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    Fires prime terrestrial organic carbon for riverine export to the global oceans (2020)
    Nature Research
    In:  EPIC3nature communications, Nature Research, 11(2791), ISSN: 2041-1723
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    Publication Date: 2020-08-13
    Description: Black carbon (BC) is a recalcitrant form of organic carbon (OC) produced by landscape fires. BC is an important component of the global carbon cycle because, compared to unburned biogenic OC, it is selectively conserved in terrestrial and oceanic pools. Here we show that the dissolved BC (DBC) content of dissolved OC (DOC) is twice greater in major (sub)tropical and high-latitude rivers than in major temperate rivers, with further significant differences between biomes. We estimate that rivers export 18 ± 4 Tg DBC year−1 globally and that, including particulate BC fluxes, total riverine export amounts to 43 ± 15 Tg BC year−1 (12 ± 5% of the OC flux). While rivers export ~1% of the OC sequestered by terrestrial vegetation, our estimates suggest that 34 ± 26% of the BC produced by landscape fires has an oceanic fate. Biogeochemical models require modification to account for the unique dynamics of BC and to predict the response of recalcitrant OC export to changing environmental conditions.
    Repository Name: EPIC Alfred Wegener Institut
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  • 9
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    Long-term cyclic persistence in an experimental predator–prey system (2019)
    Nature Research
    In:  EPIC3Nature, Nature Research, 577, pp. 226-230, ISSN: 1476-4687
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    Publication Date: 2020-09-21
    Description: Predator–prey cycles rank among the most fundamental concepts in ecology, are predicted by the simplest ecological models and enable, theoretically, the indefinite persistence of predator and prey1,2,3,4. However, it remains an open question for how long cyclic dynamics can be self-sustained in real communities. Field observations have been restricted to a few cycle periods5,6,7,8 and experimental studies indicate that oscillations may be short-lived without external stabilizing factors9,10,11,12,13,14,15,16,17,18,19. Here we performed microcosm experiments with a planktonic predator–prey system and repeatedly observed oscillatory time series of unprecedented length that persisted for up to around 50 cycles or approximately 300 predator generations. The dominant type of dynamics was characterized by regular, coherent oscillations with a nearly constant predator–prey phase difference. Despite constant experimental conditions, we also observed shorter episodes of irregular, non-coherent oscillations without any significant phase relationship. However, the predator–prey system showed a strong tendency to return to the dominant dynamical regime with a defined phase relationship. A mathematical model suggests that stochasticity is probably responsible for the reversible shift from coherent to non-coherent oscillations, a notion that was supported by experiments with external forcing by pulsed nutrient supply. Our findings empirically demonstrate the potential for infinite persistence of predator and prey populations in a cyclic dynamic regime that shows resilience in the presence of stochastic events.
    Repository Name: EPIC Alfred Wegener Institut
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  • 10
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    Mapping the bacterial metabolic niche space (2020)
    Nature Research
    In:  EPIC3nature communications, Nature Research, 11(4887), ISSN: 2041-1723
    Details
    Publication Date: 2020-10-15
    Description: The rise in the availability of bacterial genomes defines a need for synthesis: abstracting from individual taxa, to see larger patterns of bacterial lifestyles across systems. A key concept for such synthesis in ecology is the niche, the set of capabilities that enables a population’s persistence and defines its impact on the environment. The set of possible niches forms the niche space, a conceptual space delineating ways in which persistence in a system is possible. Here we use manifold learning to map the space of metabolic networks representing thousands of bacterial genera. The results suggest a metabolic niche space comprising a collection of discrete clusters and branching manifolds, which constitute strategies spanning life in different habitats and hosts. We further demonstrate that communities from similar ecosystem types map to characteristic regions of this functional coordinate system, permitting coarse-graining of microbiomes in terms of ecological niches that may be filled.
    Repository Name: EPIC Alfred Wegener Institut
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  • 11
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    Krill vs salps: dominance shift from krill to salps is associated with higher dissolved N:P ratios (2020)
    Nature Research
    In:  EPIC3Scientific Reports, Nature Research, 10(5911), ISSN: 2045-2322
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    Publication Date: 2020-08-13
    Description: Pronounced atmospheric and oceanic warming along the West Antarctic Peninsula (WAP) has resulted in abundance shifts in populations of Antarctic krill and Salpa thompsoni determined by changes in the timing of sea-ice advance, the duration of sea-ice cover and food availability. Krill and salps represent the most important macrozooplankton grazers at the WAP, but differ profoundly in their feeding biology, population dynamics and stoichiometry of excretion products with potential consequences for the relative availability of dissolved nitrogen and phosphorus. Alternation of the dissolved nutrient pool due to shifts in krill and salp densities have been hypothesized but never explicitly tested by using observational data. We therefore used the Palmer LTER dataset in order to investigate whether the dominance of either grazer is related with the observed dissolved nitrogen:phosphorus (N:P) ratios at the WAP. Across the whole sampling grid, the dominance of salps over krill was significantly correlated to higher concentrations of both N and P as well as a higher N:P ratios. Using actual long-term data, our study shows for the first time that changes in key grazer dominance may have consequences for the dynamics of dissolved nitrogen and phosphorus at the WAP.
    Repository Name: EPIC Alfred Wegener Institut
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  • 12
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    Inter-annual decrease in pulse rate and peak frequency of Southeast Pacific blue whale song types (2020)
    Nature Research
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Malige, F., Patris, J., Buchan, S. J., Stafford, K. M., Shabangu, F., Findlay, K., Hucke-Gaete, R., Neira, S., Clark, C. W., & Glotin, H. Inter-annual decrease in pulse rate and peak frequency of Southeast Pacific blue whale song types. Scientific Reports, 10(1), (2020): 8121, doi:10.1038/s41598-020-64613-0.
    Description: A decrease in the frequency of two southeast Pacific blue whale song types was examined over decades, using acoustic data from several different sources in the eastern Pacific Ocean ranging between the Equator and Chilean Patagonia. The pulse rate of the song units as well as their peak frequency were measured using two different methods (summed auto-correlation and Fourier transform). The sources of error associated with each measurement were assessed. There was a linear decline in both parameters for the more common song type (southeast Pacific song type n.2) between 1997 to 2017. An abbreviated analysis, also showed a frequency decline in the scarcer southeast Pacific song type n.1 between 1970 to 2014, revealing that both song types are declining at similar rates. We discussed the use of measuring both pulse rate and peak frequency to examine the frequency decline. Finally, a comparison of the rates of frequency decline with other song types reported in the literature and a discussion on the reasons of the frequency shift are presented.
    Description: The authors thank the help of Explorasub diving center (Chile), Agrupación turística Chañaral de Aceituno (Chile), ONG Eutropia (Chile), Valparaiso university (Chile), the international institutions and research programs CTBTO, IWC, BRILAM STIC AmSud 17-STIC-01. S.J.B. thanks support from the Center for Oceanographic Research COPAS Sur-Austral, CONICYT PIA PFB31, Biology Department of Woods Hole Oceanographic Institution, the Office of Naval Research Global (awards N62909-16-2214 and N00014-17-2606), and a grant to the Centro de Estudios Avanzados en Zonas Ãridas (CEAZA) “Programa Regional CONICYT R16A10003”. We thank SABIOD MI CNRS, EADM MaDICS CNRS and ANR-18-CE40-0014 SMILES supporting this research. We are grateful to colleagues at DCLDE 2018 and SOLAMAC 2018 conferences for useful comments on the preliminary version of this work. In this work we used only the free and open-source softwares Latex, Audacity and OCTAVE.
    Repository Name: Woods Hole Open Access Server
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  • 13
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    Representing the function and sensitivity of coastal interfaces in earth system models (2020)
    Nature Research
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ward, N. D., Megonigal, J. P., Bond-Lamberty, B., Bailey, V. L., Butman, D., Canuel, E. A., Diefenderfer, H., Ganju, N. K., Goni, M. A., Graham, E. B., Hopkinson, C. S., Khangaonkar, T., Langley, J. A., McDowell, N. G., Myers-Pigg, A. N., Neumann, R. B., Osburn, C. L., Price, R. M., Rowland, J., Sengupta, A., Simard, M., Thornton, P. E., Tzortziou, M., Vargas, R., Weisenhorn, P. B., & Windham-Myers, L. Representing the function and sensitivity of coastal interfaces in earth system models. Nature Communications, 11(1), (2020): 2458, doi:10.1038/s41467-020-16236-2.
    Description: Between the land and ocean, diverse coastal ecosystems transform, store, and transport material. Across these interfaces, the dynamic exchange of energy and matter is driven by hydrological and hydrodynamic processes such as river and groundwater discharge, tides, waves, and storms. These dynamics regulate ecosystem functions and Earth’s climate, yet global models lack representation of coastal processes and related feedbacks, impeding their predictions of coastal and global responses to change. Here, we assess existing coastal monitoring networks and regional models, existing challenges in these efforts, and recommend a path towards development of global models that more robustly reflect the coastal interface.
    Description: Funding for this work was provided by Pacific Northwest National Laboratory (PNNL) Laboratory Directed Research & Development (LDRD) as part of the Predicting Ecosystem Resilience through Multiscale Integrative Science (PREMIS) Initiative. PNNL is operated by Battelle for the U.S. Department of Energy under Contract DE-AC05-76RL01830. Additional support to J.P.M. was provided by the NSF-LTREB program (DEB-0950080, DEB-1457100, DEB-1557009), DOE-TES Program (DE-SC0008339), and the Smithsonian Institution. This manuscript was motivated by discussions held by co-authors during a three-day workshop at PNNL in Richland, WA: The System for Terrestrial Aquatic Research (STAR) Workshop: Terrestrial-Aquatic Research in Coastal Systems. The authors thank PNNL artist Nathan Johnson for preparing the figures in this manuscript and Terry Clark, Dr. Charlette Geffen, and Dr. Nancy Hess for their aid in organizing the STAR workshop. The authors thank all workshop participants not listed as authors for their valuable insight: Lihini Aluwihare (contributed to biogeochemistry discussions and development of concept for Fig. 3), Gautam Bisht (contributed to modeling discussion), Emmett Duffy (contributed to observational network discussions), Yilin Fang (contributed to modeling discussion), Jeremy Jones (contributed to biogeochemistry discussions), Roser Matamala (contributed to biogeochemistry discussions), James Morris (contributed to biogeochemistry discussions), Robert Twilley (contributed to biogeochemistry discussions), and Jesse Vance (contributed to observational network discussions). A full report on the workshop discussions can be found at https://www.pnnl.gov/publications/star-workshop-terrestrial-aquatic-research-coastal-systems.
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  • 14
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    Polystyrene nanoplastics disrupt glucose metabolism and cortisol levels with a possible link to behavioural changes in larval zebrafish (2019)
    Nature Research
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Brun, N. R., van Hage, P., Hunting, E. R., Haramis, A. G., Vink, S. C., Vijver, M. G., Schaaf, M. J. M., & Tudorache, C. Polystyrene nanoplastics disrupt glucose metabolism and cortisol levels with a possible link to behavioural changes in larval zebrafish. Communications Biology, 2, (2019): 382, doi:10.1038/s42003-019-0629-6.
    Description: Plastic nanoparticles originating from weathering plastic waste are emerging contaminants in aquatic environments, with unknown modes of action in aquatic organisms. Recent studies suggest that internalised nanoplastics may disrupt processes related to energy metabolism. Such disruption can be crucial for organisms during development and may ultimately lead to changes in behaviour. Here, we investigated the link between polystyrene nanoplastic (PSNP)-induced signalling events and behavioural changes. Larval zebrafish exhibited PSNP accumulation in the pancreas, which coincided with a decreased glucose level. By using hyperglycemic and glucocorticoid receptor (Gr) mutant larvae, we demonstrate that the PSNP-induced disruption in glucose homoeostasis coincided with increased cortisol secretion and hyperactivity in challenge phases. Our work sheds new light on a potential mechanism underlying nanoplastics toxicity in fish, suggesting that the adverse effect of PSNPs are at least in part mediated by Gr activation in response to disrupted glucose homeostasis, ultimately leading to aberrant locomotor activity.
    Description: We thank Natalia Novik and Laurie Mans for technical assistance during glucose assay and in situ hybridisation, respectively, Rubén Marín-Juez for providing the ins riboprobe, and John J. Stegeman for his helpful comments on the manuscript. The research described in this work was supported by the Dutch research council NWO (MGV; 864.13.010).
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  • 15
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    Seawater temperature and buffering capacity modulate coral calcifying pH (2019)
    Nature Research
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Guo, W. Seawater temperature and buffering capacity modulate coral calcifying pH. Scientific Reports, 9(1), (2019):1189, doi:10.1038/s41598-018-36817-y.
    Description: Scleractinian corals promote the precipitation of their carbonate skeleton by elevating the pH and dissolved inorganic carbon (DIC) concentration of their calcifying fluid above that of seawater. The fact corals actively regulate their calcifying fluid chemistry implies the potential for acclimation to ocean acidification. However, the extent to which corals can adjust their regulation mechanism in the face of decreasing ocean pH has not been rigorously tested. Here I present a numerical model simulating pH and DIC up-regulation by corals, and use it to determine the relative importance of physiological regulation versus seawater conditions in controlling coral calcifying fluid chemistry. I show that external seawater temperature and buffering capacity exert the first-order control on the extent of pH elevation in the calcifying fluid and explain most of the observed inter- and intra-species variability. Conversely, physiological regulation, represented by the interplay between enzymatic proton pumping, carbon influx and the exchange of calcifying fluid with external seawater, contributes to some variability but remain relatively constant as seawater conditions change. The model quantitatively reproduces variations of calcifying fluid pH in natural Porites colonies, and predicts an average 0.16 unit decrease in Porites calcifying fluid pH, i.e., ~43% increase in H+ concentration, by the end of this century as a combined result of projected ocean warming and acidification, highlighting the susceptibility of coral calcification to future changes in ocean conditions. In addition, my findings support the development of coral-based seawater pH proxies, but suggest the influences of physicochemical and biological factors other than seawater pH must be considered.
    Description: This work was supported by the U.S. National Science Foundation Award ANT-1246387 and by the Woods Hole Oceanographic Institution through the Ocean Life Institute, Investment in Science Fund and an Early Career Award.
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  • 16
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    Amplified seasonal cycle in hydroclimate over the Amazon river basin and its plume region (2020)
    Nature Research
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Liang, Y., Lo, M., Lan, C., Seo, H., Ummenhofer, C. C., Yeager, S., Wu, R., & Steffen, J. D. Amplified seasonal cycle in hydroclimate over the Amazon river basin and its plume region. Nature Communications, 11(1), (2020): 4390, doi:10.1038/s41467-020-18187-0.
    Description: The Amazon river basin receives ~2000 mm of precipitation annually and contributes ~17% of global river freshwater input to the oceans; its hydroclimatic variations can exert profound impacts on the marine ecosystem in the Amazon plume region (APR) and have potential far-reaching influences on hydroclimate over the tropical Atlantic. Here, we show that an amplified seasonal cycle of Amazonia precipitation, represented by the annual difference between maximum and minimum values, during the period 1979–2018, leads to enhanced seasonalities in both Amazon river discharge and APR ocean salinity. An atmospheric moisture budget analysis shows that these enhanced seasonal cycles are associated with similar amplifications in the atmospheric vertical and horizontal moisture advections. Hierarchical sensitivity experiments using global climate models quantify the relationships of these enhanced seasonalities. The results suggest that an intensified hydroclimatological cycle may develop in the Amazonia atmosphere-land-ocean coupled system, favouring more extreme terrestrial and marine conditions.
    Description: M.-H.L., C.-W.L., and R.-J.W. are supported by the Ministry of Science and Technology in Taiwan under grant 106-2111-M-002-010-MY4. H.S. and J.D.S. are grateful for support from NOAA NA19OAR4310376 and NA17OAR4310255. C.C.U. acknowledges support from the U.S. National Science Foundation under grant OCE-1663704. The National Center for Atmospheric Research (NCAR) is a major facility sponsored by the US National Science Foundation (NSF) under Cooperative Agreement No. 1852977. We thank Dr. Young-Oh Kwon at Woods Hole Oceanographic Institution and Dr. Who Kim at NCAR for discussions about the ocean model experiment design. We thank Dr. Mehnaz Rashid at National Taiwan University and Wen-Yin Wu at the University of Texas at Austin in helping generate the high-resolution Amazon river mask. We also thank Dr. Gael Forget at Massachusetts Institue of Technology for comments on using ECCO and other ocean-state estimate products.
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  • 17
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    Ocean acidification disrupts the orientation of postlarval Caribbean spiny lobsters (2020)
    Nature Research
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gravinese, P. M., Page, H. N., Butler, C. B., Spadaro, A. J., Hewett, C., Considine, M., Lankes, D., & Fisher, S. Ocean acidification disrupts the orientation of postlarval Caribbean spiny lobsters. Scientific Reports, 10(1), (2020): 18092, doi:10.1038/s41598-020-75021-9.
    Description: Anthropogenic inputs into coastal ecosystems are causing more frequent environmental fluctuations and reducing seawater pH. One such ecosystem is Florida Bay, an important nursery for the Caribbean spiny lobster, Panulirus argus. Although adult crustaceans are often resilient to reduced seawater pH, earlier ontogenetic stages can be physiologically limited in their tolerance to ocean acidification on shorter time scales. We used a Y-maze chamber to test whether reduced-pH seawater altered the orientation of spiny lobster pueruli toward chemical cues produced by Laurencia spp. macroalgae, a known settlement cue for the species. We tested the hypothesis that pueruli conditioned in reduced-pH seawater would be less responsive to Laurencia spp. chemical cues than pueruli in ambient-pH seawater by comparing the proportion of individuals that moved to the cue side of the chamber with the proportion that moved to the side with no cue. We also recorded the amount of time (sec) before a response was observed. Pueruli conditioned in reduced-pH seawater were less responsive and failed to select the Laurencia cue. Our results suggest that episodic acidification of coastal waters might limit the ability of pueruli to locate settlement habitats, increasing postsettlement mortality.
    Description: We thank the Steinwachs Family Foundation, which provided funding that supported Gravinese’s postdoctoral fellowship at Mote Marine Laboratory and Aquarium. We also acknowledge the partial support provided by the St. Petersburg College Titan Achievement minigrant program. Page was supported by a Mote Marine Laboratory and Aquarium Postdoctoral Research Fellowship. Postlarval spiny lobsters were collected with a state-issued Special Activity License (SAL-17-1868G-SR). We also thank those who helped with animal collection throughout this work including in-kind support provided by E. Muller and the Mote CAOS facility, as well as E. Bartels and C. Walter of the Coral Reef Monitoring and Assessment Program at Mote Marine Laboratory and Aquarium, as well as other field personnel including: L. Toth, S. Perry, T. Parker, A. Fine, L. Humphrey, and many undergraduate interns. We also thank L. Toth, E. Ross, B. Sharp, C. Crowley, J. Butler, and B. Crowder for editorial comments.
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  • 18
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    Sources and upstream pathways of the densest overflow water in the Nordic Seas (2020)
    Nature Research
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Huang, J., Pickart, R. S., Huang, R. X., Lin, P., Brakstad, A., & Xu, F. Sources and upstream pathways of the densest overflow water in the Nordic Seas. Nature Communications, 11(1), (2020): 5389, doi:10.1038/s41467-020-19050-y.
    Description: Overflow water from the Nordic Seas comprises the deepest limb of the Atlantic Meridional Overturning Circulation, yet questions remain as to where it is ventilated and how it reaches the Greenland-Scotland Ridge. Here we use historical hydrographic data from 2005-2015, together with satellite altimeter data, to elucidate the source regions of the Denmark Strait and Faroe Bank Channel overflows and the pathways feeding these respective sills. A recently-developed metric is used to calculate how similar two water parcels are, based on potential density and potential spicity. This reveals that the interior of the Greenland Sea gyre is the primary wintertime source of the densest portion of both overflows. After subducting, the water progresses southward along several ridge systems towards the Greenland-Scotland Ridge. Kinematic evidence supports the inferred pathways. Extending the calculation back to the 1980s reveals that the ventilation occurred previously along the periphery of the Greenland Sea gyre.
    Description: Funding for the study was provided by the US National Science Foundation under grants OCE-1558742 (J.H., R.P.) and OCE-1259618 (P.L.); the Bergen Research Foundation under grant BFS2016REK01 (A.B.); and the National Natural Science Foundation of China No. 41576018 (F.X.) and 41606020 (F.X.).
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    The role of suction thrust in the metachronal paddles of swimming invertebrates (2020)
    Nature Research
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Colin, S. P., Costello, J. H., Sutherland, K. R., Gemmell, B. J., Dabiri, J. O., & Du Clos, K. T. The role of suction thrust in the metachronal paddles of swimming invertebrates. Scientific Reports, 10(1), (2020): 17790, doi:10.1038/s41598-020-74745-y.
    Description: An abundance of swimming animals have converged upon a common swimming strategy using multiple propulsors coordinated as metachronal waves. The shared kinematics suggest that even morphologically and systematically diverse animals use similar fluid dynamic relationships to generate swimming thrust. We quantified the kinematics and hydrodynamics of a diverse group of small swimming animals who use multiple propulsors, e.g. limbs or ctenes, which move with antiplectic metachronal waves to generate thrust. Here we show that even at these relatively small scales the bending movements of limbs and ctenes conform to the patterns observed for much larger swimming animals. We show that, like other swimming animals, the propulsors of these metachronal swimmers rely on generating negative pressure along their surfaces to generate forward thrust (i.e., suction thrust). Relying on negative pressure, as opposed to high pushing pressure, facilitates metachronal waves and enables these swimmers to exploit readily produced hydrodynamic structures. Understanding the role of negative pressure fields in metachronal swimmers may provide clues about the hydrodynamic traits shared by swimming and flying animals.
    Description: This work was funded by National Science Foundation (NSF OCE 1829913 to SPC), the Alfred P. Sloan Foundation (to BJG) and the Gordon and Betty Moore Foundation (8835 to KRS). The work was also supported by the Roger Williams Foundation to Promote Scholarship and Teaching.
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    Copepod manipulation of oil droplet size distribution (2019)
    Nature Research
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Uttieri, M., Nihongi, A., Hinow, P., Motschman, J., Jiang, H., Alcaraz, M., & Strickler, J. R. (2019). Copepod manipulation of oil droplet size distribution AU uttieri, M nihongi, A hinow, P motschman, J jiang, H alcaraz, M strickler, JR. Scientific Reports, 9, 547 , doi:10.1038/s41598-018-37020-9.
    Description: Oil spills are one of the most dangerous sources of pollution in aquatic ecosystems. Owing to their pivotal position in the food web, pelagic copepods can provide crucial intermediary transferring oil between trophic levels. In this study we show that the calanoid Paracartia grani can actively modify the size-spectrum of oil droplets. Direct manipulation through the movement of the feeding appendages and egestion work in concert, splitting larger droplets (Ø = 16 µm) into smaller ones (Ø = 4–8 µm). The copepod-driven change in droplet size distribution can increase the availability of oil droplets to organisms feeding on smaller particles, sustaining the transfer of petrochemical compounds among different compartments. These results raise the curtain on complex small-scale interactions which can promote the understanding of oil spills fate in aquatic ecosystems.
    Description: This research was made possible by a grant from The Gulf of Mexico Research Initiative. Data are publicly available through the Gulf of Mexico Research Initiative Information & Data Cooperative (GRIIDC) at https://data.gulfresearchinitiative.org (doi: 10.7266/N7H70CV7). MU was sponsored by the MOKA project (Modelling and Observation of zooplanKtonic orgAnisms; ID: RBFR10VF6M) financed by the Italian Ministry of Education, University and Research, and by SZN internal grant. PH was supported by the Simons Foundation grant “Collaboration on Mathematical Biology” (278436). JM was the financed by the Support for Undergraduate Research Fellows (SURF) and the Center for International Education (CIE), University of Wisconsin-Milwaukee. HJ was supported by NSF grant no. OCE-1433979. MA was funded by the Spanish research project TOPCOP (CTM2011–23480, from the Spanish Ministry of Education and Science, and 2009SGR-1283 from the Catalan Government). MU thanks Mark Pottek for the design of the MOKA project cartoon, and UWM for hospitality during a research stay in January 2017 supported by Simons Foundation (grant to PH). The authors have no competing interests. No ethical considerations apply. All symbols provided in Fig. 2 courtesy of the Integration and Application Network, University of Maryland Center for Environmental Science (ian.umces.edu/symbols/).
    Keywords: Ecosystem ecology ; Marine biology
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    CRISPR/Cas9 mediated mutation of the mtnr1a melatonin receptor gene causes rod photoreceptor degeneration in developing Xenopus tropicalis (2020)
    Nature Research
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Wiechmann, A. F., Martin, T. A., & Horb, M. E. CRISPR/Cas9 mediated mutation of the mtnr1a melatonin receptor gene causes rod photoreceptor degeneration in developing Xenopus tropicalis. Scientific Reports, 10(1), (2020): 13757, doi:10.1038/s41598-020-70735-2.
    Description: Nighttime surges in melatonin levels activate melatonin receptors, which synchronize cellular activities with the natural light/dark cycle. Melatonin receptors are expressed in several cell types in the retina, including the photon-sensitive rods and cones. Previous studies suggest that long-term photoreceptor survival and retinal health is in part reliant on melatonin orchestration of circadian homeostatic activities. This scenario would accordingly envisage that disruption of melatonin receptor signaling is detrimental to photoreceptor health. Using in vivo CRISPR/Cas9 genomic editing, we discovered that a small deletion mutation of the Mel1a melatonin receptor (mtnr1a) gene causes a loss of rod photoreceptors in retinas of developing Xenopus tropicalis heterozygous, but not homozygous mutant tadpoles. Cones were relatively spared from degeneration, and the rod loss phenotype was not obvious after metamorphosis. Localization of Mel1a receptor protein appeared to be about the same in wild type and mutant retinas, suggesting that the mutant protein is expressed at some level in mutant retinal cells. The severe impact on early rod photoreceptor viability may signify a previously underestimated critical role in circadian influences on long-term retinal health and preservation of sight. These data offer evidence that disturbance of homeostatic, circadian signaling, conveyed through a mutated melatonin receptor, is incompatible with rod photoreceptor survival.
    Description: The National Xenopus Resource (NXR) Genome Editing Workshop conducted at the Marine Biological Laboratory (MBL) contributed to the early development of this project (A.F.W. & M.E.H). We thank Dr. Marcin Wlizla, Sean McNamara, Rosie Falco, and Dr. Will Ratzen of the NXR and MBL for their advice and assistance with the F0 founders. We thank Cynthia Bulmer of the NIH Diabetes CoBRE (P20GM104934) Core Histology Facility at the University of Oklahoma Health Sciences Center (OUHSC) for preparing the histology specimens. We thank Dr. David Sherry of OUHSC for critically reading the initial version of the manuscript and his helpful advice during this study.
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    Compounding impact of severe weather events fuels marine heatwave in the coastal ocean (2020)
    Nature Research
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Dzwonkowski, B., Coogan, J., Fournier, S., Lockridge, G., Park, K., & Lee, T. Compounding impact of severe weather events fuels marine heatwave in the coastal ocean. Nature Communications, 11(1), (2020): 4623, doi:10.1038/s41467-020-18339-2.
    Description: Exposure to extreme events is a major concern in coastal regions where growing human populations and stressed natural ecosystems are at significant risk to such phenomena. However, the complex sequence of processes that transform an event from notable to extreme can be challenging to identify and hence, limit forecast abilities. Here, we show an extreme heat content event (i.e., a marine heatwave) in coastal waters of the northern Gulf of Mexico resulted from compounding effects of a tropical storm followed by an atmospheric heatwave. This newly identified process of generating extreme ocean temperatures occurred prior to landfall of Hurricane Michael during October of 2018 and, as critical contributor to storm intensity, likely contributed to the subsequent extreme hurricane. This pattern of compounding processes will also exacerbate other environmental problems in temperature-sensitive ecosystems (e.g., coral bleaching, hypoxia) and is expected to have expanding impacts under global warming predictions.
    Description: This work would not have been possible without the help of the Tech Support Group at the Dauphin Island Sea Lab. A portion of this work was conducted at the Jet Propulsion Laboratory, California Institute of Technology, under contract with NASA. This research was made possible by the NOAA RESTORE Science Program (NA17NOS4510101 and NA19NOS4510194) and NOAA NGI NMFS Regional Collaboration Network (18-NGI3-61).
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    Rapid microbial diversification of dissolved organic matter in oceanic surface waters leads to carbon sequestration (2020)
    Nature Research
    In:  EPIC3Scientific Reports, Nature Research, 10(13025), ISSN: 2045-2322
    Details
    Publication Date: 2021-12-15
    Description: The pool of dissolved organic matter (DOM) in the deep ocean represents one of the largest carbon sinks on the planet. In recent years, studies have shown that most of this pool is recalcitrant, because individual compounds are present at low concentrations and because certain compounds seem resistant to microbial degradation. The formation of the diverse and recalcitrant deep ocean DOM pool has been attributed to repeated and successive processing of DOM by microorganisms over time scales of weeks to years. Little is known however, about the transformation and cycling that labile DOM undergoes in the first hours upon its release from phytoplankton. Here we provide direct experimental evidence showing that within hours of labile DOM release, its breakdown and recombination with ambient DOM leads to the formation of a diverse array of new molecules in oligotrophic North Atlantic surface waters. Furthermore, our results reveal a preferential breakdown of N and P containing molecules versus those containing only carbon. Hence, we show the preferential breakdown and molecular diversification are the crucial first steps in the eventual formation of carbon rich DOM that is resistant to microbial remineralization.
    Repository Name: EPIC Alfred Wegener Institut
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    Ocean mass, sterodynamic effects, and vertical land motion largely explain US coast relative sea level rise (2023)
    Nature Research
    Details
    Publication Date: 2023-03-08
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Harvey, T., Hamlington, B. D., Frederikse, T., Nerem, R. S., Piecuch, C. G., Hammond, W. C., Blewitt, G., Thompson, P. R., Bekaert, D. P. S., Landerer, F. W., Reager, J. T., Kopp, R. E., Chandanpurkar, H., Fenty, I., Trossman, D. S., Walker, J. S., & Boening, C. W. Ocean mass, sterodynamic effects, and vertical land motion largely explain US coast relative sea level rise. Communications Earth & Environment, 2(1), (2021): 233, https://doi.org/10.1038/s43247-021-00300-w.
    Description: Regional sea-level changes are caused by several physical processes that vary both in space and time. As a result of these processes, large regional departures from the long-term rate of global mean sea-level rise can occur. Identifying and understanding these processes at particular locations is the first step toward generating reliable projections and assisting in improved decision making. Here we quantify to what degree contemporary ocean mass change, sterodynamic effects, and vertical land motion influence sea-level rise observed by tide-gauge locations around the contiguous U.S. from 1993 to 2018. We are able to explain tide gauge-observed relative sea-level trends at 47 of 55 sampled locations. Locations where we cannot explain observed trends are potentially indicative of shortcomings in our coastal sea-level observational network or estimates of uncertainty.
    Description: The research was carried out in part at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration. C.G.P. was supported by NASA grant 80NSSC20K1241. B.D.H., T.C.H., and T.F. were supported by NASA JPL Task 105393.281945.02.25.04.59. R.E.K. and J.S.W. were supported by U.S. National Aeronautics and Space Administration (grants 80NSSC17K0698, 80NSSC20K1724 and JPL task 105393.509496.02.08.13.31) and U.S. National Science Foundation (grant ICER-1663807). P.R.T. acknowledges financial support from the NOAA Global Ocean Monitoring and Observing program in support of the University of Hawaii Sea Level Center (NA11NMF4320128). The ECCO project is funded by the NASA Physical Oceanography; Modeling, Analysis, and Prediction; and Cryosphere Programs.
    Keywords: Climate sciences ; Ocean sciences ; Solid Earth sciences
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    Increased typhoon activity in the Pacific deep tropics driven by Little Ice Age circulation changes (2020)
    Nature Research
    Details
    Publication Date: 2022-10-26
    Description: Author Posting. © The Author(s), 2020. This is the author's version of the work. It is posted here by permission of Nature Research for personal use, not for redistribution. The definitive version was published in Bramante, J. F., Ford, M. R., Kench, P. S., Ashton, A. D., Toomey, M. R., Sullivan, R. M., Karnauskas, K. B., Ummenhofer, C. C., & Donnelly, J. P. (2020). Increased typhoon activity in the Pacific deep tropics driven by Little Ice Age circulation changes. Nature Geoscience, 13, 806–811. doi:10.1038/s41561-020-00656-2.
    Description: The instrumental record reveals that tropical cyclone activity is sensitive to oceanic and atmospheric variability on inter-annual and decadal scales. However, our understanding of the influence of climate on tropical cyclone behaviour is restricted by the short historical record and the sparseness of prehistorical reconstructions, particularly in the western North Pacific, where coastal communities suffer loss of life and livelihood from typhoons annually. Here, to explore past regional typhoon dynamics, we reconstruct three millennia of deep tropical North Pacific cyclogenesis. Combined with existing records, our reconstruction demonstrates that low-baseline typhoon activity prior to 1350 ce was followed by an interval of frequent storms during the Little Ice Age. This pattern, concurrent with hydroclimate proxy variability, suggests a centennial-scale link between Pacific hydroclimate and tropical cyclone climatology. An ensemble of global climate models demonstrates a migration of the Pacific Walker circulation and variability in two Pacific climate modes during the Little Ice Age, which probably contributed to enhanced tropical cyclone activity in the tropical western North Pacific. In the next century, projected changes to the Pacific Walker circulation and expansion of the tropics will invert these Little Ice Age hydroclimate trends, potentially reducing typhoon activity in the deep tropical Pacific.
    Description: This work was supported by the Strategic Environmental Research and Development Program (SERDP RC-2336). C.C.U. acknowledges support from NSF under AGS-1602455. We thank student intern D. Carter for extensive labwork on core LTD3. We acknowledge the WCRP’s Working Group on Coupled Modelling, which is responsible for CMIP, and we thank the climate modelling groups for producing and making available their model output. CMIP5 model output was provided by the WHOI CMIP5 Community Storage Server via their website: http://cmip5.whoi.edu/. Any use of trade, firm or product names is for descriptive purposes only and does not imply endorsement by the US Government.
    Description: 2021-05-16
    Keywords: Tropical cyclones ; Little Ice Age ; Last millennium ; Paleoclimate
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    Iron mobilization during lactation reduces oxygen stores in a diving mammal (2022)
    Nature Research
    Details
    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 Shero, M. R., Kirkham, A. L., Costa, D. P., & Burns, J. M. Iron mobilization during lactation reduces oxygen stores in a diving mammal. Nature Communications, 13(1), (2022): 4322, https://doi.org/10.1038/s41467-022-31863-7.
    Description: The profound impacts that maternal provisioning of finite energy resources has on offspring survival have been extensively studied across mammals. This study shows that in addition to calories, high hemoprotein concentrations in diving mammals necessitates exceptional female-to-pup iron transfer. Numerous indices of iron mobilization (ferritin, serum iron, total-iron-binding-capacity, transferrin saturation) were significantly elevated during lactation in adult female Weddell seals (Leptonychotes weddellii), but not in skip-breeders. Iron was mobilized from endogenous stores for incorporation into the Weddell seal’s milk at concentrations up to 100× higher than terrestrial mammals. Such high rates of iron offload to offspring drew from the female’s own heme stores and led to compromised physiologic dive capacities (hemoglobin, myoglobin, and total body oxygen stores) after weaning their pups, which was further reflected in shorter dive durations. We demonstrate that lactational iron transfer shapes physiologic dive thresholds, identifying a cost of reproduction to a marine mammal.
    Description: This research was conducted with support from NSF ANT-0838892 to DPC; ANT-0838937 and ANT-1246463 to JMB (which also supported ALK and MRS); and The Investment in Science Fund at WHOI to MRS.
    Keywords: Animal physiology ; Ecophysiology ; Homeostasis
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    Sources of dehydration fluids underneath the Kamchatka arc (2022)
    Nature Research
    Details
    Publication Date: 2022-11-18
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Shu, Y., Nielsen, S. G., Le Roux, V., Wörner, G., Blusztajn, J., & Auro, M. Sources of dehydration fluids underneath the Kamchatka arc. Nature Communications, 13(1), (2022): 4467, https://doi.org/10.1038/s41467-022-32211-5.
    Description: Fluids mediate the transport of subducted slab material and play a crucial role in the generation of arc magmas. However, the source of subduction-derived fluids remains debated. The Kamchatka arc is an ideal subduction zone to identify the source of fluids because the arc magmas are comparably mafic, their source appears to be essentially free of subducted sediment-derived components, and subducted Hawaii-Emperor Seamount Chain (HESC) is thought to contribute a substantial fluid flux to the Kamchatka magmas. Here we show that Tl isotope ratios are unique tracers of HESC contribution to Kamchatka arc magma sources. In conjunction with trace element ratios and literature data, we trace the progressive dehydration and melting of subducted HESC across the Kamchatka arc. In succession, serpentine (〈100 km depth), lawsonite (100–250 km depth) and phengite (〉250 km depth) break down and produce fluids that contribute to arc magmatism at the Eastern Volcanic Front (EVF), Central Kamchatka Depression (CKD), and Sredinny Ridge (SR), respectively. However, given the Tl-poor nature of serpentine and lawsonite fluids, simultaneous melting of subducted HESC is required to explain the HESC-like Tl isotope signatures observed in EVF and CKD lavas. In the absence of eclogitic crust melting processes in this region of the Kamchatka arc, we propose that progressive dehydration and melting of a HESC-dominated mélange offers the most compelling interpretation of the combined isotope and trace element data.
    Description: This study was financially supported by grants from the National Natural Science Foundation of China (NSFC) (Grant No. 41903008) and Chinese Postdoctoral Science Foundation (Grant No. 2019M660153) to Y.S., NSF (Grant No. EAR-1829546) to S.G.N. and NSF (Grant No. EAR-1855302) to V.L.R.
    Keywords: Geochemistry ; Marine chemistry
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    Rapid 20th century warming reverses 900-year cooling in the Gulf of Maine (2023)
    Nature Research
    Details
    Publication Date: 2023-02-25
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Whitney, N. M., Wanamaker, A. D., Ummenhofer, C. C., Johnson, B. J., Cresswell-Clay, N., & Kreutz, K. J. Rapid 20th century warming reverses 900-year cooling in the Gulf of Maine. Communications Earth & Environment, 3(1), (2022): 179, https://doi.org/10.1038/s43247-022-00504-8.
    Description: The Gulf of Maine, located in the western North Atlantic, has undergone recent, rapid ocean warming but the lack of long-term, instrumental records hampers the ability to put these significant hydrographic changes into context. Here we present multiple 300-year long geochemical records (oxygen, nitrogen, and previously published radiocarbon isotopes) measured in absolutely-dated Arctica islandica shells from the western Gulf of Maine. These records, in combination with climate model simulations, suggest that the Gulf of Maine underwent a long-term cooling over most of the last 1000 years, driven primarily by volcanic forcing and North Atlantic ocean dynamics. This cooling trend was reversed by warming beginning in the late 1800s, likely due to increased atmospheric greenhouse gas concentrations and changes in western North Atlantic circulation. The climate model simulations suggest that the warming over the last century was more rapid than almost any other 100-year period in the last 1000 years in the region.
    Description: Funding for this research was provided by the following sources: Bruce Bowen Fellowship (N.M.W.), Geological Society of America Graduate Student Research Grant (N.M.W.), James E. and Barbara V. Moltz Fellowship for Climate-Related Research at WHOI (C.C.U.), Maine Marine Research Fund (B.J.J.), National Oceanic and Atmospheric Administration Climate and Global Change Postdoctoral Fellowship (N.M.W.), National Science Foundation grant OCE 1003438 and MGG 2028197 (A.D.W.), National Science Foundation grant OCE 1003423 (K.J.K.), National Science Foundation grant OCE 0929900 (B.J.J.). We thank the CESM1(CAM5) Last Millennium Ensemble Community Project for providing the climate model simulations, which were performed using the supercomputing resources provided by NSF/CISL/Yellowstone.
    Keywords: Climate and Earth system modelling ; Marine chemistry ; Palaeoceanography ; Physical oceanography
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    Consistently dated Atlantic sediment cores over the last 40 thousand years (2019)
    Nature Research
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Waelbroeck, C., Lougheed, B. C., Riveiros, N. V., Missiaen, L., Pedro, J., Dokken, T., Hajdas, I., Wacker, L., Abbott, P., Dumoulin, J., Thil, F., Eynaud, F., Rossignol, L., Fersi, W., Albuquerque, A. L., Arz, H., Austin, W. E. N., Came, R., Carlson, A. E., Collins, J. A., Dennielou, B., Desprat, S., Dickson, A., Elliot, M., Farmer, C., Giraudeau, J., Gottschalk, J., Henderiks, J., Hughen, K., Jung, S., Knutz, P., Lebreiro, S., Lund, D. C., Lynch-Stieglitz, J., Malaize, B., Marchitto, T., Martinez-Mendez, G., Mollenhauer, G., Naughton, F., Nave, S., Nuernberg, D., Oppo, D., Peck, V., Peeters, F. J. C., Penaud, A., Portilho-Ramos, R. d. C., Repschlaeger, J., Roberts, J., Ruehlemann, C., Salgueiro, E., Goni, M. F. S., Schonfeld, J., Scussolini, P., Skinner, L. C., Skonieczny, C., Thornalley, D., Toucanne, S., Van Rooij, D., Vidal, L., Voelker, A. H. L., Wary, M., Weldeab, S., & Ziegler, M. Consistently dated Atlantic sediment cores over the last 40 thousand years. Scientific Data, 6, (2019): 165, doi:10.1038/s41597-019-0173-8.
    Description: Rapid changes in ocean circulation and climate have been observed in marine-sediment and ice cores over the last glacial period and deglaciation, highlighting the non-linear character of the climate system and underlining the possibility of rapid climate shifts in response to anthropogenic greenhouse gas forcing. To date, these rapid changes in climate and ocean circulation are still not fully explained. One obstacle hindering progress in our understanding of the interactions between past ocean circulation and climate changes is the difficulty of accurately dating marine cores. Here, we present a set of 92 marine sediment cores from the Atlantic Ocean for which we have established age-depth models that are consistent with the Greenland GICC05 ice core chronology, and computed the associated dating uncertainties, using a new deposition modeling technique. This is the first set of consistently dated marine sediment cores enabling paleoclimate scientists to evaluate leads/lags between circulation and climate changes over vast regions of the Atlantic Ocean. Moreover, this data set is of direct use in paleoclimate modeling studies.
    Description: The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Program (FP7/2007-2013 Grant agreement n° 339108). New 14C dates for cores EW9209-1JPC and V29-202 were funded by NSF OCE grants to DWO. FN, ES and AV acknowledge FCT funding support through project UID/Multi/04326/2019. We thank T. Garlan and P. Guyomard for having given us access to cores from the Service Hydrographique et Océanographique de la Marine. We acknowledge N. Smialkowski for help with formatting the data into text files, and L. Mauclair, L. Leroy and G. Isguder for the picking of numerous foraminifer samples for radiocarbon dating. We are grateful to S. Obrochta, E. Cortijo, E. Michel, F. Bassinot, J.C. Duplessy, and L. Labeyrie for advice and fruitful discussions. This paper is LSCE contribution 6572.
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    Oscillations in the near-field feeding current of a calanoid copepod are useful for particle sensing (2020)
    Nature Research
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Giuffre, C., Hinow, P., Jiang, H., & Strickler, J. R. Oscillations in the near-field feeding current of a calanoid copepod are useful for particle sensing. Scientific Reports, 9(1), (2019): 17742, doi: 10.1038/s41598-019-54264-1.
    Description: Calanoid copepods are small crustaceans that constitute a major element of aquatic ecosystems. Key to their success is their feeding apparatus consisting of sensor-studded mouth appendages that are in constant motion. These appendages generate a feeding current to enhance the encounter probability with food items. Additionally, sensing enables the organism to determine the position and quality of food particles, and to alter the near-field flow to capture and manipulate the particles for ingestion or rejection. Here we observe a freely swimming copepod Leptodiaptomus sicilis in multiple perspectives together with suspended particles that allow us to analyse the flow field created by the animal. We observe a highly periodic motion of the mouth appendages that is mirrored in oscillations of nearby tracer particles. We propose that the phase shift between the fluid and the particle velocities is sufficient for mechanical detection of the particles entrained in the feeding current. Moreover, we propose that an immersed algal cell may benefit from the excitation by increased uptake of dissolved inorganic compounds.
    Description: We acknowledge funding from the Simons Foundation (grant #278436 to PH) during two visits of HJ to Milwaukee. HJ was also supported by NSF grant OCE-1559062. We thank Dr. Russell Cuhel (School of Freshwater Sciences, University of Wisconsin - Milwaukee) for collecting the animals from Lake Michigan and four unknown readers for valuable comments.
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    Helium, inorganic and organic carbon isotopes of fluids and gases across the Costa Rica convergent margin (2020)
    Nature Research
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Barry, P. H., Nakagawa, M., Giovannelli, D., de Moor, J. M., Schrenk, M., Seltzer, A. M., Manini, E., Fattorini, D., di Carlo, M., Regoli, F., Fullerton, K., & Lloyd, K. G. Helium, inorganic and organic carbon isotopes of fluids and gases across the Costa Rica convergent margin. Scientific Data, 6(1), (2019): 284, doi: 10.1038/s41597-019-0302-4.
    Description: In 2017, fluid and gas samples were collected across the Costa Rican Arc. He and Ne isotopes, C isotopes as well as total organic and inorganic carbon concentrations were measured. The samples (n = 24) from 2017 are accompanied by (n = 17) samples collected in 2008, 2010 and 2012. He-isotopes ranged from arc-like (6.8 RA) to crustal (0.5 RA). Measured dissolved inorganic carbon (DIC) δ13CVPDB values varied from 3.55 to −21.57‰, with dissolved organic carbon (DOC) following the trends of DIC. Gas phase CO2 only occurs within ~20 km of the arc; δ13CVPDB values varied from −0.84 to −5.23‰. Onsite, pH, conductivity, temperature and dissolved oxygen (DO) were measured; pH ranged from 0.9–10.0, conductivity from 200–91,900 μS/cm, temperatures from 23–89 °C and DO from 2–84%. Data were used to develop a model which suggests that ~91 ± 4.0% of carbon released from the slab/mantle beneath the Costa Rican forearc is sequestered within the crust by calcite deposition with an additional 3.3 ± 1.3% incorporated into autotrophic biomass.
    Description: This work was principally supported by a grant (G-2016-7206) from the Alfred P. Sloan Foundation and the Deep Carbon Observatory to P.H.B. In addition, P.H.B. was supported by NSF grant 1144559 during a portion of this project. D.G. was supported by an NSF grant (MCB 15–17567) and an ELSI Origins Network (EON) research Fellowship, which is supported by a grant from the John Templeton Foundation. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the John Templeton Foundation. DG was also partially supported a Deep Life Modeling and Visualization Fellowship, which is supported by the Deep Carbon Observatory. This work was further supported in party by JSPS KAKENHI grants (JP17K14412, JP17H06105, JP17H02989) awarded to M.N., NSF OCE-1431598 and NASA Exobiology NNX16AL59G awarded to K.G.L. J.M.d.M. gratefully acknowledges funding from Universidad Nacional Costa Rica, the World Bank, and the Costa Rican Ley Transitorio 8933 used to acquire a laser carbon isotope system in collaboration with R. Sánchez-Murillo and G. Esquivel-Hernandez. M.N. produced the most data. We thank Patricia Barcala Dominguez for assistance with figure illustration. We thank Bruce Deck, Marten Wahlen and Keith Blackmon for analytical assistance at SIO. Finally, we acknowledge D. Hummer, T. Lopez, C.A. Pratt, Y. Alpízar Segura, A. Battaglia, P. Beaudry, G. Bini, M. Cascante, G. d’Errico, K. Fullerton, E. Gazel, G. González, S. A. Halldórsson, K. Iacovino, T. Ilanko, J.T. Kulongoski, M. Martínez, H. Miller, S. Ono, S. Patwardhan, C.J. Ramírez, F. Smedile, S. Turner, C. Vetriani, M. Yücel, C.J. Ballentine, T.P. Fischer, and D.R. Hilton, who were instrumental in proposal writing, sample collection, sample analysis and data analysis.
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    Mn oxide formation by phototrophs: spatial and temporal patterns, with evidence of an enzymatic superoxide-mediated pathway (2020)
    Nature Research
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Chaput, D. L., Fowler, A. J., Seo, O., Duhn, K., Hansel, C. M., & Santelli, C. M. Mn oxide formation by phototrophs: spatial and temporal patterns, with evidence of an enzymatic superoxide-mediated pathway. Scientific Reports, 9(1), (2019): 18244, doi: 10.1038/s41598-019-54403-8.
    Description: Manganese (Mn) oxide minerals influence the availability of organic carbon, nutrients and metals in the environment. Oxidation of Mn(II) to Mn(III/IV) oxides is largely promoted by the direct and indirect activity of microorganisms. Studies of biogenic Mn(II) oxidation have focused on bacteria and fungi, with phototrophic organisms (phototrophs) being generally overlooked. Here, we isolated phototrophs from Mn removal beds in Pennsylvania, USA, including fourteen Chlorophyta (green algae), three Bacillariophyta (diatoms) and one cyanobacterium, all of which consistently formed Mn(III/IV) oxides. Isolates produced cell-specific oxides (coating some cells but not others), diffuse biofilm oxides, and internal diatom-specific Mn-rich nodules. Phototrophic Mn(II) oxidation had been previously attributed to abiotic oxidation mediated by photosynthesis-driven pH increases, but we found a decoupling of Mn oxide formation and pH alteration in several cases. Furthermore, cell-free filtrates of some isolates produced Mn oxides at specific time points, but this activity was not induced by Mn(II). Manganese oxide formation in cell-free filtrates occurred via reaction with the oxygen radical superoxide produced by soluble extracellular proteins. Given the known widespread ability of phototrophs to produce superoxide, the contribution of phototrophs to Mn(II) oxidation in the environment may be greater and more nuanced than previously thought.
    Description: This work was funded by a Smithsonian Scholarly Studies grant to CMS, by a Smithsonian Postdoctoral Fellowship to DLC, by the National Science Foundation, grant number CBET-1336496, to CMH and CMS, and by MnDRIVE Environment at the University of Minnesota to CMS. We thank Margaret Dunn and Cliff Denholm, Stream Restoration Inc., for assistance and access to field sites, Carolyn Zeiner (WHOI/Harvard) for useful discussions and advice regarding ROS experiments, as well as Jeff Post, Tim Rose and Tim Gooding (Smithsonian NMNH) for assistance with the SEM/EDS work. Portions of the laboratory work were conducted in and with the support of the L.A.B. facilities at the National Museum of Natural History, Smithsonian Institution.
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    Nanoparticle-biological interactions in a marine benthic foraminifer (2020)
    Nature Research
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ciacci, C., Grimmelpont, M. V., Corsi, I., Bergami, E., Curzi, D., Burini, D., Bouchet, V. M. P., Ambrogini, P., Gobbi, P., Ujiié, Y., Ishitani, Y., Coccioni, R., Bernhard, J. M., & Frontalini, F. Nanoparticle-biological interactions in a marine benthic foraminifer. Scientific Reports, (91), (2019): 19441, doi:10.1038/s41598-019-56037-2.
    Description: The adverse effects of engineered nanomaterials (ENM) in marine environments have recently attracted great attention although their effects on marine benthic organisms such as foraminifera are still largely overlooked. Here we document the effects of three negatively charged ENM, different in size and composition, titanium dioxide (TiO2), polystyrene (PS) and silicon dioxide (SiO2), on a microbial eukaryote (the benthic foraminifera Ammonia parkinsoniana) using multiple approaches. This research clearly shows the presence, within the foraminiferal cytoplasm, of metallic (Ti) and organic (PS) ENM that promote physiological stress. Specifically, marked increases in the accumulation of neutral lipids and enhanced reactive oxygen species production occurred in ENM-treated specimens regardless of ENM type. This study indicates that ENM represent ecotoxicological risks for this microbial eukaryote and presents a new model for the neglected marine benthos by which to assess natural exposure scenarios.
    Description: The authors are very grateful to two anonymous reviewers for their thoughtful and valuable comments that have greatly improved our contribution. NP characterization by DLS was conducted at the facilities of the Department of Biotechnologies, Chemistry and Pharmacy of the University of Siena (Italy). The authors acknowledge Prof. Andrea M. Atrei for the support in DLS analysis. Margot V. Grimmelpont’s stay at Urbino University was supported by an ERASMUS + fellowship.
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    Limited and localized magmatism in the Central Atlantic Magmatic Province (2020)
    Nature Research
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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 Marzen, R. E., Shillington, D. J., Lizarralde, D., Knapp, J. H., Heffner, D. M., Davis, J. K., & Harder, S. H. Limited and localized magmatism in the Central Atlantic Magmatic Province. Nature Communications, 11(1), (2020): 3397, doi:10.1038/s41467-020-17193-6.
    Description: The Central Atlantic Magmatic Province (CAMP) is the most aerially extensive magmatic event in Earth’s history, but many questions remain about its origin, volume, and distribution. Despite many observations of CAMP magmatism near Earth’s surface, few constraints exist on CAMP intrusions at depth. Here we present detailed constraints on crustal and upper mantle structure from wide-angle seismic data across the Triassic South Georgia Rift that formed shortly before CAMP. Lower crustal magmatism is concentrated where synrift sedimentary fill is thickest and the crust is thinnest, suggesting that lithospheric thinning influenced the locus and volume of magmatism. The limited distribution of lower crustal intrusions implies modest total CAMP volumes of 85,000 to 169,000 km3 beneath the South Georgia Rift, consistent with moderately elevated mantle potential temperatures (〈1500 °C). These results suggest that CAMP magmatism in the South Georgia Rift is caused by syn-rift decompression melting of a warm, enriched mantle.
    Description: This project was funded by an NSF GRFP fellowship DGE 16-44869 and a grant from the National Science Foundation’s Division of Earth Sciences (NSF-EAR) EarthScope program through the collaborative awards EAR-1144534/−1144829/−1144391. Data collection was made possible with help from IRIS PASSCAL, the University of Texas El Paso Seismic Source Facility, the teams of students who deployed and recovered geophones, and the support of landowners and county and state officials. We thank Alistair Harding for the VMTomo code, Nathan Miller for the PyVM toolbox, and William Wilcock for maintaining the Upicker package to pick arrivals.
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    Microbial diversity drives carbon use efficiency in a model soil (2020)
    Nature Research
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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 Domeignoz-Horta, L. A., Pold, G., Liu, X. A., Frey, S. D., Melillo, J. M., & DeAngelis, K. M. Microbial diversity drives carbon use efficiency in a model soil. Nature Communications, 11(1), (2020): 3684, doi:10.1038/s41467-020-17502-z.
    Description: Empirical evidence for the response of soil carbon cycling to the combined effects of warming, drought and diversity loss is scarce. Microbial carbon use efficiency (CUE) plays a central role in regulating the flow of carbon through soil, yet how biotic and abiotic factors interact to drive it remains unclear. Here, we combine distinct community inocula (a biotic factor) with different temperature and moisture conditions (abiotic factors) to manipulate microbial diversity and community structure within a model soil. While community composition and diversity are the strongest predictors of CUE, abiotic factors modulated the relationship between diversity and CUE, with CUE being positively correlated with bacterial diversity only under high moisture. Altogether these results indicate that the diversity × ecosystem-function relationship can be impaired under non-favorable conditions in soils, and that to understand changes in soil C cycling we need to account for the multiple facets of global changes.
    Description: Funding for this project was provided by the Department of Energy grant DE-SC0016590 to K.M.D. and S.D.F., and an American Association of University Women Dissertation fellowship to G.P. We would also like to thank Stuart Grandy and Kevin Geyer for the fruitful discussions and Mary Waters, Courtney Bly and Ana Horta for their help with samples processing.
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    Deep high-temperature hydrothermal circulation in a detachment faulting system on the ultra-slow spreading ridge (2020)
    Nature Research
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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 Tao, C., Seyfried, W. E., Jr., Lowell, R. P., Liu, Y., Liang, J., Guo, Z., Ding, K., Zhang, H., Liu, J., Qiu, L., Egorov, I., Liao, S., Zhao, M., Zhou, J., Deng, X., Li, H., Wang, H., Cai, W., Zhang, G., Zhou, H., Lin, J., & Li, W. Deep high-temperature hydrothermal circulation in a detachment faulting system on the ultra-slow spreading ridge. Nature Communications, 11(1), (2020): 1300, doi:10.1038/s41467-020-15062-w.
    Description: Coupled magmatic and tectonic activity plays an important role in high-temperature hydrothermal circulation at mid-ocean ridges. The circulation patterns for such systems have been elucidated by microearthquakes and geochemical data over a broad spectrum of spreading rates, but such data have not been generally available for ultra-slow spreading ridges. Here we report new geophysical and fluid geochemical data for high-temperature active hydrothermal venting at Dragon Horn area (49.7°E) on the Southwest Indian Ridge. Twin detachment faults penetrating to the depth of 13 ± 2 km below the seafloor were identified based on the microearthquakes. The geochemical composition of the hydrothermal fluids suggests a long reaction path involving both mafic and ultramafic lithologies. Combined with numerical simulations, our results demonstrate that these hydrothermal fluids could circulate ~ 6 km deeper than the Moho boundary and to much greater depths than those at Trans-Atlantic Geotraverse and Logachev-1 hydrothermal fields on the Mid-Atlantic Ridge.
    Description: This work was supported by National Key R&D Program of China under contract no. 2018YFC0309901, 2017YFC0306603, 2017YFC0306803, and 2017YFC0306203, COMRA Major Project under contract No. DY135-S1-01-01 and No. DY135-S1-01-06.
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    Dual clumped isotope thermometry resolves kinetic biases in carbonate formation temperatures (2020)
    Nature Research
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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 Bajnai, D., Guo, W., Spötl, C., Coplen, T. B., Methner, K., Löffler, N., Krsnik, E., Gischler, E., Hansen, M., Henkel, D., Price, G. D., Raddatz, J., Scholz, D., & Fiebig, J. Dual clumped isotope thermometry resolves kinetic biases in carbonate formation temperatures. Nature Communications, 11(1), (2020): 4005, doi:10.1038/s41467-020-17501-0.
    Description: Surface temperature is a fundamental parameter of Earth’s climate. Its evolution through time is commonly reconstructed using the oxygen isotope and the clumped isotope compositions of carbonate archives. However, reaction kinetics involved in the precipitation of carbonates can introduce inaccuracies in the derived temperatures. Here, we show that dual clumped isotope analyses, i.e., simultaneous ∆47 and ∆48 measurements on the single carbonate phase, can identify the origin and quantify the extent of these kinetic biases. Our results verify theoretical predictions and evidence that the isotopic disequilibrium commonly observed in speleothems and scleractinian coral skeletons is inherited from the dissolved inorganic carbon pool of their parent solutions. Further, we show that dual clumped isotope thermometry can achieve reliable palaeotemperature reconstructions, devoid of kinetic bias. Analysis of a belemnite rostrum implies that it precipitated near isotopic equilibrium and confirms the warmer-than-present temperatures during the Early Cretaceous at southern high latitudes.
    Description: This work became possible through DFG grant “INST 161/871-1” and the Investment in Science Fund at Woods Hole Oceanographic Institution. The authors would like to thank Sven Hofmann and Manuel Schumann for their assistance in the joint Goethe University – Senckenberg BiK-F Stable Isotope Facility at the Institute of Geosciences, Goethe University Frankfurt. K.M. acknowledges funding through “DFG ME 4955/1-1”, E.K. through “DFG MU 2845/6-1”, D.S. through “DFG SCHO 1274/8-1” and “DFG SCHO 1274/11-1”, and M.H. through “DFG HA 8694/1-1”. C.S. acknowledges funding from the University of Innsbruck. A review of the manuscript by David Evans on behalf of the USGS is acknowledged.
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    Historically unprecedented Northern Gulf of Mexico hurricane activity from 650 to 1250 CE (2020)
    Nature Research
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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 Rodysill, J. R., Donnelly, J. P., Sullivan, R., Lane, P. D., Toomey, M., Woodruff, J. D., Hawkes, A. D., MacDonald, D., d'Entremont, N., McKeon, K., Wallace, E., & van Hengstum, P. J. Historically unprecedented Northern Gulf of Mexico hurricane activity from 650 to 1250 CE. Scientific Reports, 10(1), (2020): 19092. doi:10.1038/s41598-020-75874-0.
    Description: Hurricane Michael (2018) was the first Category 5 storm on record to make landfall on the Florida panhandle since at least 1851 CE (Common Era), and it resulted in the loss of 59 lives and $25 billion in damages across the southeastern U.S. This event placed a spotlight on recent intense (exceeding Category 4 or 5 on the Saffir-Simpson Hurricane Wind Scale) hurricane landfalls, prompting questions about the natural range in variability of hurricane activity that the instrumental record is too short to address. Of particular interest is determining whether the frequency of recent intense hurricane landfalls in the northern Gulf of Mexico (GOM) is within or outside the natural range of intense hurricane activity prior to 1851 CE. In this study, we identify intense hurricane landfalls in northwest Florida during the past 2000 years based on coarse anomaly event detection from two coastal lacustrine sediment archives. We identified a historically unprecedented period of heightened storm activity common to four Florida panhandle localities from 650 to 1250 CE and a shift to a relatively quiescent storm climate in the GOM spanning the past six centuries. Our study provides long-term context for events like Hurricane Michael and suggests that the observational period 1851 CE to present may underrepresent the natural range in landfalling hurricane activity.
    Description: Funding for this project was provided by the Strategic Environmental Research and Development Program (SERDP) grant and NSF awards 0903020, 1902463, and 1854980 awarded to Jeffrey Donnelly, and the USGS Land Change Science Program.
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    Octopus arms exhibit exceptional flexibility (2020)
    Nature Research
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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 Kennedy, E. B. L., Buresch, K. C., Boinapally, P., & Hanlon, R. T. Octopus arms exhibit exceptional flexibility. Scientific Reports, 10(1), (2020): 20872. doi:10.1038/s41598-020-77873-7.
    Description: The octopus arm is often referred to as one of the most flexible limbs in nature, yet this assumption requires detailed inspection given that this has not been measured comprehensively for all portions of each arm. We investigated the diversity of arm deformations in Octopus bimaculoides with a frame-by-frame observational analysis of laboratory video footage in which animals were challenged with different tasks. Diverse movements in these hydrostatic arms are produced by some combination of four basic deformations: bending (orally, aborally; inward, outward), torsion (clockwise, counter-clockwise), elongation, and shortening. More than 16,500 arm deformations were observed in 120 min of video. Results showed that all eight arms were capable of all four types of deformation along their lengths and in all directions. Arms function primarily to bring the sucker-lined oral surface in contact with target surfaces. Bending was the most common deformation observed, although the proximal third of the arms performed relatively less bending and more shortening and elongation as compared with other arm regions. These findings demonstrate the exceptional flexibility of the octopus arm and provide a basis for investigating motor control of the entire arm, which may aid the future development of soft robotics.
    Description: We gratefully acknowledge funding from Grant N00014-19-1-2445 from the Office of Naval Research, Tom McKenna and Marc Steinberg, Program Managers. We also thank the staff of the Marine Resources Center at MBL for assistance with water quality measurements, seawater system maintenance, and collection of food items for octopuses.
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    Maximizing CRISPR/Cas9 phenotype penetrance applying predictive modeling of editing outcomes in Xenopus and zebrafish embryos (2020)
    Nature Research
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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 Naert, T., Tulkens, D., Edwards, N. A., Carron, M., Shaidani, N. I., Wlizla, M., Boel, A., Demuynck, S., Horb, M. E., Coucke, P., Willaert, A., Zorn, A. M., & Vleminckx, K. Maximizing CRISPR/Cas9 phenotype penetrance applying predictive modeling of editing outcomes in Xenopus and zebrafish embryos. Scientific Reports, 10(1), (2020): 14662, doi:10.1038/s41598-020-71412-0.
    Description: CRISPR/Cas9 genome editing has revolutionized functional genomics in vertebrates. However, CRISPR/Cas9 edited F0 animals too often demonstrate variable phenotypic penetrance due to the mosaic nature of editing outcomes after double strand break (DSB) repair. Even with high efficiency levels of genome editing, phenotypes may be obscured by proportional presence of in-frame mutations that still produce functional protein. Recently, studies in cell culture systems have shown that the nature of CRISPR/Cas9-mediated mutations can be dependent on local sequence context and can be predicted by computational methods. Here, we demonstrate that similar approaches can be used to forecast CRISPR/Cas9 gene editing outcomes in Xenopus tropicalis, Xenopus laevis, and zebrafish. We show that a publicly available neural network previously trained in mouse embryonic stem cell cultures (InDelphi-mESC) is able to accurately predict CRISPR/Cas9 gene editing outcomes in early vertebrate embryos. Our observations can have direct implications for experiment design, allowing the selection of guide RNAs with predicted repair outcome signatures enriched towards frameshift mutations, allowing maximization of CRISPR/Cas9 phenotype penetrance in the F0 generation.
    Description: Research in the Vleminckx laboratory is supported by the Research Foundation—Flanders (FWO-Vlaanderen) (Grants G0A1515N and G029413N), by the Belgian Science Policy (Interuniversity Attraction Poles—IAP7/07) and by the Concerted Research Actions from Ghent University (BOF15/GOA/011). Further support was obtained by the Hercules Foundation, Flanders (Grant AUGE/11/14) and the Desmoid Tumor Research Foundation and the Desmoid Tumour Foundation Canada. T.N. is funded by “Kom op tegen Kanker” (Stand up to Cancer), the Flemish cancer society and previously held PhD fellowship with VLAIO-HERMES during the course of this work. D.T. and M. C. hold a PhD fellowship from the Research Foundation-Flanders (FWO-Vlaanderen). The Zorn Lab is supported by Funding from NIH National Institute of Child Health and Human Development (NICHD) P01 HD093363. A.W. and A.B. are supported by the Ghent University (Universiteit Gent) Methusalem grant BOFMET2015000401 to Anne De Paepe. The National Xenopus Resource and Horb lab is supported by funding from the National Institutes of Health (P40 OD010997 and R01 HD084409).
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    Chaotic genetic structure and past demographic expansion of the invasive gastropod Tritia neritea in its native range, the Mediterranean Sea (2021)
    Nature Research
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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 Boissin, E., Neglia, V., Baksay, S., Micu, D., Bat, L., Topaloglu, B., Todorova, V., Panayotova, M., Kruschel, C., Milchakova, N., Voutsinas, E., Beqiraj, S., Nasto, I., Aglieri, G., Taviani, M., Zane, L., & Planes, S. Chaotic genetic structure and past demographic expansion of the invasive gastropod Tritia neritea in its native range, the Mediterranean Sea. Scientific Reports, 10(1), (2020): 21624. doi:10.1038/s41598-020-77742-3.
    Description: To better predict population evolution of invasive species in introduced areas it is critical to identify and understand the mechanisms driving genetic diversity and structure in their native range. Here, we combined analyses of the mitochondrial COI gene and 11 microsatellite markers to investigate both past demographic history and contemporaneous genetic structure in the native area of the gastropod Tritia neritea, using Bayesian skyline plots (BSP), multivariate analyses and Bayesian clustering. The BSP framework revealed population expansions, dated after the last glacial maximum. The haplotype network revealed a strong geographic clustering. Multivariate analyses and Bayesian clustering highlighted the strong genetic structure at all scales, between the Black Sea and the Adriatic Sea, but also within basins. Within basins, a random pattern of genetic patchiness was observed, suggesting a superimposition of processes involving natural biological effects (no larval phase and thus limited larval dispersal) and putative anthropogenic transport of specimens. Contrary to the introduced area, no isolation-by-distance patterns were recovered in the Mediterranean or the Black Seas, highlighting different mechanisms at play on both native and introduced areas, triggering unknown consequences for species’ evolutionary trajectories. These results of Tritia neritea populations on its native range highlight a mixture of ancient and recent processes, with the effects of paleoclimates and life history traits likely tangled with the effects of human-mediated dispersal.
    Description: This project was funded by the European FP7 CoCoNet project (Ocean.2011-4, grant agreement #287844) and we are grateful to the whole CoCoNET consortium. We are grateful to the following people for their critical help with logistics and field work ‘Antheus srl (Lecce, Italy)’; S Bevilacqua, G Guarnieri, S Fraschetti and T Terlizzi (University of Salento, Italy); L Angeletti and M Sigovini (ISMAR, Italy); D Shamrey (IBSS, Sevastopol); A Anastasopoulou, MA Pancucci-Papadopoulou and S Reizopoulou (HCMR, Greece) and E Hajdëri (Catholic University ‘Our Lady of Good Counsel’, Tirana). Thank you to J Almany for English corrections. This is ISMAR-CNR scientific contribution n1987. E Boissin was supported by a European Marie Curie postdoctoral fellowship MC-CIG-618480.
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    Role of C4 carbon fixation in Ulva prolifera, the macroalga responsible for the world's largest green tides (2020)
    Nature Research
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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 Liu, D., Ma, Q., Valiela, I., Anderson, D. M., Keesing, J. K., Gao, K., Zhen, Y., Sun, X., & Wang, Y. Role of C4 carbon fixation in Ulva prolifera, the macroalga responsible for the world's largest green tides. Communications Biology, 3(1), (2020): 494, doi:10.1038/s42003-020-01225-4.
    Description: Most marine algae preferentially assimilate CO2 via the Calvin-Benson Cycle (C3) and catalyze HCO3− dehydration via carbonic anhydrase (CA) as a CO2-compensatory mechanism, but certain species utilize the Hatch-Slack Cycle (C4) to enhance photosynthesis. The occurrence and importance of the C4 pathway remains uncertain, however. Here, we demonstrate that carbon fixation in Ulva prolifera, a species responsible for massive green tides, involves a combination of C3 and C4 pathways, and a CA-supported HCO3− mechanism. Analysis of CA and key C3 and C4 enzymes, and subsequent analysis of δ13C photosynthetic products showed that the species assimilates CO2 predominately via the C3 pathway, uses HCO3− via the CA mechanism at low CO2 levels, and takes advantage of high irradiance using the C4 pathway. This active and multi-faceted carbon acquisition strategy is advantageous for the formation of massive blooms, as thick floating mats are subject to intense surface irradiance and CO2 limitation.
    Description: This work was supported by the State Key Project of Research and Development Plan, Ministry of Science and Technology of the Peopleʼs Republic of China (2016YFC1402106). Support for D.M.A. provided by the Woods Hole Oceanographic Institution—Ocean University of China Cooperative Research Initiative. We thank Dr. Juntian Xu, Jing Ma, Ying Li, and Chenglong Ji for assisting culture experiments and sample analysis.
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    The hierarchical assembly of septins revealed by high-speed AFM (2020)
    Nature Research
    Details
    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 Jiao, F., Cannon, K. S., Lin, Y. C., Gladfelter, A. S., & Scheuring, S. The hierarchical assembly of septins revealed by high-speed AFM. Nature Communications, 11(1), (2020): 5062, doi:10.1038/s41467-020-18778-x.
    Description: Septins are GTP-binding proteins involved in diverse cellular processes including division and membrane remodeling. Septins form linear, palindromic heteromeric complexes that can assemble in filaments and higher-order structures. Structural studies revealed various septin architectures, but questions concerning assembly-dynamics and -pathways persist. Here we used high-speed atomic force microscopy (HS-AFM) and kinetic modeling which allowed us to determine that septin filament assembly was a diffusion-driven process, while formation of higher-order structures was complex and involved self-templating. Slightly acidic pH and increased monovalent ion concentrations favor filament-assembly, -alignment and -pairing. Filament-alignment and -pairing further favored diffusion-driven assembly. Pairing is mediated by the septin N-termini face, and may occur symmetrically or staggered, likely important for the formation of higher-order structures of different shapes. Multilayered structures are templated by the morphology of the underlying layers. The septin C-termini face, namely the C-terminal extension of Cdc12, may be involved in membrane binding.
    Description: We thank J. Thorner for the generous gift of the CTE mutant plasmids. K.S.C. was supported in part by a grant from NIGMS under award T32 GM119999 and A.S.G., F.J. and S.S. were supported by NIH RO1 GM130934.
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    Revising evidence of hurricane strikes on Abaco Island (the Bahamas) over the last 700 years (2020)
    Nature Research
    Details
    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 Winkler, T. S., van Hengstum, P. J., Donnelly, J. P., Wallace, E. J., Sullivan, R. M., MacDonald, D., & Albury, N. A. Revising evidence of hurricane strikes on Abaco Island (the Bahamas) over the last 700 years. Scientific Reports, 10(1), (2020): 16556, doi:10.1038/s41598-020-73132-x.
    Description: The northern Bahamas have experienced more frequent intense-hurricane impacts than almost anywhere else in the Atlantic since 1850 CE. In 2019, category 5 (Saffir-Simpson scale) Hurricane Dorian demonstrated the destructive potential of these natural hazards. Problematically, determining whether high hurricane activity levels remained constant through time is difficult given the short observational record (〈 170 years). We present a 700-year long, near-annually resolved stratigraphic record of hurricane passage near Thatchpoint Blue Hole (TPBH) on Abaco Island, The Bahamas. Using longer sediment cores (888 cm) and more reliable age-control, this study revises and temporally expands a previous study from TPBH that underestimated the sedimentation rate. TPBH records at least 13 ≥ category 2 hurricanes per century between 1500 to 1670 CE, which exceeds the 9 ≥ category 2 hurricanes per century within 50 km of TPBH since 1850 CE. The eastern United States also experienced frequent hurricanes from 1500 to 1670 CE, but frequency was depressed elsewhere in the Atlantic Ocean. This suggests that spatial heterogeneity in Atlantic hurricane activity since 1850 CE could have persisted throughout the last millennium. This heterogeneity is impacted by climatic and stochastic forcing, but additional high-resolution paleo-hurricane reconstructions are required to assess the mechanisms that impact regional variability.
    Description: Field support was provided by Jody Albury and the staff of Friends of the Environment in Marsh Harbour, The Bahamas, and technical support was provided was provided by M. Horgan and S. Molodtsov. Funding for this project was provided by NSF Awards OCE-1356509, OCE-1356708, OCE-1854917, OCE-1903616, and ICER-1854980. The open access publishing fees for this article have been covered by the Texas A&M University Open Access to Knowledge Fund (OAKFund), supported by the University Libraries.
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  • 45
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    Groundwater discharge impacts marine isotope budgets of Li, Mg, Ca, Sr, and Ba (2021)
    Nature Research
    Details
    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 Mayfield, K. K., Eisenhauer, A., Santiago Ramos, D. P., Higgins, J. A., Horner, T. J., Auro, M., Magna, T., Moosdorf, N., Charette, M. A., Gonneea, M. E., Brady, C. E., Komar, N., Peucker-Ehrenbrink, B., & Paytan, A. Groundwater discharge impacts marine isotope budgets of Li, Mg, Ca, Sr, and Ba. Nature Communications, 12(1), (2021): 148-020-20248-3, doi:10.1038/s41467-020-20248-3.
    Description: Groundwater-derived solute fluxes to the ocean have long been assumed static and subordinate to riverine fluxes, if not neglected entirely, in marine isotope budgets. Here we present concentration and isotope data for Li, Mg, Ca, Sr, and Ba in coastal groundwaters to constrain the importance of groundwater discharge in mediating the magnitude and isotopic composition of terrestrially derived solute fluxes to the ocean. Data were extrapolated globally using three independent volumetric estimates of groundwater discharge to coastal waters, from which we estimate that groundwater-derived solute fluxes represent, at a minimum, 5% of riverine fluxes for Li, Mg, Ca, Sr, and Ba. The isotopic compositions of the groundwater-derived Mg, Ca, and Sr fluxes are distinct from global riverine averages, while Li and Ba fluxes are isotopically indistinguishable from rivers. These differences reflect a strong dependence on coastal lithology that should be considered a priority for parameterization in Earth-system models.
    Description: We thank A. Beck, H. Dulai, I. Santos, C. Benitez-Nelson, W. Moore, A. Martin, and H. Windom for sample access. We also thank A. Kolevica, A. Heuser, H. Pryer, J. Middleton, R. Franks, F. Lon, N. Slater, and O. Šebek for their laboratory and analytical assistance. This material is based upon research supported by the National Science Foundation Graduate Research Fellowship Program and an internship provided through the U.S. Geological Survey Graduate Research Internship Program (GRIP). This research was also supported by grants from: the German Academic Exchange Service (DAAD), Northern California chapter of the Achievement Rewards for College Scientists Foundation, International Association of GeoChemistry, Geological Society of America, Northern California Geological Society, Myers Trust, Friends of Long Marine Lab, and UC MEXUS (to K.K.M.). We acknowledge funding from EU-ITN Horizon project 643084 (to A.E. and T.M.) and NSF grant Award Number 1259440 (to A.P.). We also acknowledge funding from NSF grant award number OCE-1736949 (to T.J.H.). Any use of trade, firm or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
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  • 46
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    Lipid metabolism in Calanus finmarchicus is sensitive to variations in predation risk and food availability (2021)
    Nature Research
    Details
    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 Skottene, E., Tarrant, A. M., Altin, D., Olsen, R. E., Choquet, M., & Kvile, K. O. Lipid metabolism in Calanus finmarchicus is sensitive to variations in predation risk and food availability. Scientific Reports, 10(1),(2020): 22322, https://doi.org/10.1038/s41598-020-79165-6.
    Description: Late developmental stages of the marine copepods in the genus Calanus can spend extended periods in a dormant stage (diapause) that is preceded by the accumulation of large lipid stores. We assessed how lipid metabolism during development from the C4 stage to adult is altered in response to predation risk and varying food availability, to ultimately understand more of the metabolic processes during development in Calanus copepods. We used RNA sequencing to assess if perceived predation risk in combination with varied food availability affects expression of genes associated with lipid metabolism and diapause preparation in C. finmarchicus. The lipid metabolism response to predation risk differed depending on food availability, time and life stage. Predation risk caused upregulation of lipid catabolism with high food, and downregulation with low food. Under low food conditions, predation risk disrupted lipid accumulation. The copepods showed no clear signs of diapause preparation, supporting earlier observations of the importance of multiple environmental cues in inducing diapause in C. finmarchicus. This study demonstrates that lipid metabolism is a sensitive endpoint for the interacting environmental effects of predation pressure and food availability. As diapause may be controlled by lipid accumulation, our findings may contribute towards understanding processes that can ultimately influence diapause timing.
    Description: ES was funded by the Department of Biology, Norwegian University of Science and Technology. Support for AMT was provided by the National Science Foundation (NSF) OPP-1746087. KØK was funded by VISTA—a basic research program in collaboration between The Norwegian Academy of Science and Letters, and Equinor. The RNA seq work was provided by the Genomics Core Facility (GCF). GCF is funded by the Faculty of Medicine and Health Sciences at NTNU and Central Norway Regional Health Authority. The authors thank Lotte Thommesen for help conducting the experiment, Mari-Ann Østensen for performing RNA extraction with ES and preparing cDNA libraries for Illumina RNAseq, and the EMBRC-ERIC Laboratory for Low Level Trophic Interactions at NTNU SeaLab for access to the Calanus finmarchicus culture.
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    The Angola Gyre is a hotspot of dinitrogen fixation in the South Atlantic Ocean (2022)
    Nature Research
    Details
    Publication Date: 2022-10-14
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Marshall, T., Granger, J., Casciotti, K. L., Dahnke, K., Emeis, K.-C., Marconi, D., McIlvin, M. R., Noble, A. E., Saito, M. A., Sigman, D. M., & Fawcett, S. E. The Angola Gyre is a hotspot of dinitrogen fixation in the South Atlantic Ocean. Communications Earth & Environment, 3(1), (2022): 151, https://doi.org/10.1038/s43247-022-00474-x.
    Description: Biological dinitrogen fixation is the major source of new nitrogen to marine systems and thus essential to the ocean’s biological pump. Constraining the distribution and global rate of dinitrogen fixation has proven challenging owing largely to uncertainty surrounding the controls thereon. Existing South Atlantic dinitrogen fixation rate estimates vary five-fold, with models attributing most dinitrogen fixation to the western basin. From hydrographic properties and nitrate isotope ratios, we show that the Angola Gyre in the eastern tropical South Atlantic supports the fixation of 1.4–5.4 Tg N.a−1, 28-108% of the existing (highly uncertain) estimates for the basin. Our observations contradict model diagnoses, revealing a substantial input of newly-fixed nitrogen to the tropical eastern basin and no dinitrogen fixation west of 7.5˚W. We propose that dinitrogen fixation in the South Atlantic occurs in hotspots controlled by the overlapping biogeography of excess phosphorus relative to nitrogen and bioavailable iron from margin sediments. Similar conditions may promote dinitrogen fixation in analogous ocean regions. Our analysis suggests that local iron availability causes the phosphorus-driven coupling of oceanic dinitrogen fixation to nitrogen loss to vary on a regional basis.
    Description: This work was supported by the South African National Research Foundation (114673 and 130826 to T.M., 115335, 116142 and 129320 to S.E.F.); the US National Science Foundation (CAREER award, OCE-1554474 to J.G., OCE-1736652 to D.M.S. and K.L.C., OCE-05-26277 to K.L.C.); the German Federal Agency for Education and Research (DAAD-SPACES 57371082 to T.M.); the Royal Society (FLAIR fellowship to S.E.F.); and the University of Cape Town (T.M., J.G., S.E.F.). The authors also recognize the support of the South African Department of Science and Innovation’s Biogeochemistry Research Infrastructure Platform (BIOGRIP).
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    A deep Tasman outflow of Pacific waters during the last glacial period (2022)
    Nature Research
    Details
    Publication Date: 2022-10-12
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Struve, T., Wilson, D., Hines, S., Adkins, J., & van de Flierdt, T. A deep Tasman outflow of Pacific waters during the last glacial period. Nature Communications, 13(1), (2022): 3763, https://doi.org/10.1038/s41467-022-31116-7.
    Description: The interoceanic exchange of water masses is modulated by flow through key oceanic choke points in the Drake Passage, the Indonesian Seas, south of Africa, and south of Tasmania. Here, we use the neodymium isotope signature (εNd) of cold-water coral skeletons from intermediate depths (1460‒1689 m) to trace circulation changes south of Tasmania during the last glacial period. The key feature of our dataset is a long-term trend towards radiogenic εNd values of ~−4.6 during the Last Glacial Maximum and Heinrich Stadial 1, which are clearly distinct from contemporaneous Southern Ocean εNd of ~−7. When combined with previously published radiocarbon data from the same corals, our results indicate that a unique radiogenic and young water mass was present during this time. This scenario can be explained by a more vigorous Pacific overturning circulation that supported a deeper outflow of Pacific waters, including North Pacific Intermediate Water, through the Tasman Sea.
    Description: The authors acknowledge financial support from the Grantham Institute of Climate Change and the Environment (T.v.d.F. and T.S.), the Ministry for Science and Culture of the State of Lower Saxony (T.S.), Marie Curie Reintegration grant IRG 230828 (T.v.d.F.), Leverhulme Trust grant RPG-398 (T.v.d.F.), Natural Environment Research Council grants NE/F016751/1 (T.v.d.F.), NE/N001141/1 (T.v.d.F. and D.J.W.), and NE/T011440/1 (D.J.W.), and National Science Foundation grant OCE-1503129 (J.F.A. and S.K.V.H.). Open Access funding is enabled by the DFG open access publication fund and the Carl von Ossietzky University Oldenburg.
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    Isotopic evidence for the formation of the moon in a canonical giant impact (2021)
    Nature Research
    Details
    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 Nielsen, S. G., Bekaert, D. V., & Auro, M. Isotopic evidence for the formation of the moon in a canonical giant impact. Nature Communications, 12(1), (2021): 1817, https://doi.org/10.1038/s41467-021-22155-7.
    Description: Isotopic measurements of lunar and terrestrial rocks have revealed that, unlike any other body in the solar system, the Moon is indistinguishable from the Earth for nearly every isotopic system. This observation, however, contradicts predictions by the standard model for the origin of the Moon, the canonical giant impact. Here we show that the vanadium isotopic composition of the Moon is offset from that of the bulk silicate Earth by 0.18 ± 0.04 parts per thousand towards the chondritic value. This offset most likely results from isotope fractionation on proto-Earth during the main stage of terrestrial core formation (pre-giant impact), followed by a canonical giant impact where ~80% of the Moon originates from the impactor of chondritic composition. Our data refute the possibility of post-giant impact equilibration between the Earth and Moon, and implies that the impactor and proto-Earth mainly accreted from a common isotopic reservoir in the inner solar system.
    Description: This study was funded by NASA Emerging Worlds grant NNX16AD36G to S.G.N. We thank NASA-JSC, Tony Irving, and Thorsten Kleine for access to meteorite and Apollo mission samples. US Antarctic meteorite samples are recovered by the Antarctic Search for Meteorites (ANSMET) program, which has been funded by NSF and NASA, and characterized and curated by the Astromaterials Curation Office at NASA Johnson Space Center and the Department of Mineral Sciences of the Smithsonian Institution. J. Blusztajn is thanked for help with mass spectrometry support at WHOI.
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    Possible limitations of dolphin echolocation: a simulation study based on a cross-modal matching experiment (2021)
    Nature Research
    Details
    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 Wei, C., Hoffmann-Kuhnt, M., Au, W. W. L., Ho, A. Z. H., Matrai, E., Feng, W., Ketten, D. R., & Zhang, Y. Possible limitations of dolphin echolocation: a simulation study based on a cross-modal matching experiment. Scientific Reports, 11(1), (2021): 6689, https://doi.org/10.1038/s41598-021-85063-2.
    Description: Dolphins use their biosonar to discriminate objects with different features through the returning echoes. Cross-modal matching experiments were conducted with a resident bottlenose dolphin (Tursiops aduncus). Four types of objects composed of different materials (water-filled PVC pipes, air-filled PVC pipes, foam ball arrays, and PVC pipes wrapped in closed-cell foam) were used in the experiments, respectively. The size and position of the objects remained the same in each case. The data collected in the experiment showed that the dolphin’s matching accuracy was significantly different across the cases. To gain insight into the underlying mechanism in the experiments, we used finite element methods to construct two-dimensional target detection models of an echolocating dolphin in the vertical plane, based on computed tomography scan data. The acoustic processes of the click’s interaction with the objects and the surrounding media in the four cases were simulated and compared. The simulation results provide some possible explanations for why the dolphin performed differently when discriminating the objects that only differed in material composition in the previous matching experiments.
    Description: One of the authors, Wei. C is supported by a Forrest Research Foundation Fellowship. Support for D. Ketten for this effort was provided by the Joint Industry Programme and by the Helmholtz Foundation. This work was also supported by the Hawaii Institute of Marine Biology (HIMB) contribution No. 1630 and School of Ocean and Earth Science and Technology (SOEST) contribution No. 9452.
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    Postnatal structural development of mammalian basilar membrane provides anatomical basis for the maturation of tonotopic maps and frequency tuning (2021)
    Nature Research
    Details
    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 Tani, T., Koike-Tani, M., Tran, M. T., Shribak, M., & Levic, S. Postnatal structural development of mammalian basilar membrane provides anatomical basis for the maturation of tonotopic maps and frequency tuning. Scientific Reports, 11(1), (2021): 7581, https://doi.org/10.1038/s41598-021-87150-w.
    Description: The basilar membrane (BM) of the mammalian cochlea constitutes a spiraling acellular ribbon that is intimately attached to the organ of Corti. Its graded stiffness, increasing from apex to the base of the cochlea provides the mechanical basis for sound frequency analysis. Despite its central role in auditory signal transduction, virtually nothing is known about the BM’s structural development. Using polarized light microscopy, the present study characterized the architectural transformations of freshly dissected BM at time points during postnatal development and maturation. The results indicate that the BM structural elements increase progressively in size, becoming radially aligned and more tightly packed with maturation and reach the adult structural signature by postnatal day 20 (P20). The findings provide insight into structural details and developmental changes of the mammalian BM, suggesting that BM is a dynamic structure that changes throughout the life of an animal.
    Description: This work was supported by Medical Research Council grant MR/ N004299/1 (to SL), University of Sussex Research Innovation Funds (to SL), Brighton and Sussex Medical School research funds (to SL), National Institute of General Medical Sciences, NIH grant R01 GM101701 (to MS), NIH R01 GM100160 (to TT) and KAKENHI JP18K19962 (to TT).
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    A warm jet in a cold ocean (2021)
    Nature Research
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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 MacKinnon, J. A., Simmons, H. L., Hargrove, J., Thomson, J., Peacock, T., Alford, M. H., Barton, B., Boury, S., Brenner, S. D., Couto, N., Danielson, S. L., Fine, E. C., Graber, H. C., Guthrie, J., Hopkins, J. E., Jayne, S. R., Jeon, C., Klenz, T., Lee, C. M., Lenn, Y-D., Lucas, A. J., Lund, B., Mahaffey, C., Norman, L., Rainville, L., Smith, M. M., Thomas, L. N., Torres-Valdés, S., & Wood, K. R. A warm jet in a cold ocean. Nature Communications, 12(1), (2021): 2418, https://doi.org/10.1038/s41467-021-22505-5.
    Description: Unprecedented quantities of heat are entering the Pacific sector of the Arctic Ocean through Bering Strait, particularly during summer months. Though some heat is lost to the atmosphere during autumn cooling, a significant fraction of the incoming warm, salty water subducts (dives beneath) below a cooler fresher layer of near-surface water, subsequently extending hundreds of kilometers into the Beaufort Gyre. Upward turbulent mixing of these sub-surface pockets of heat is likely accelerating sea ice melt in the region. This Pacific-origin water brings both heat and unique biogeochemical properties, contributing to a changing Arctic ecosystem. However, our ability to understand or forecast the role of this incoming water mass has been hampered by lack of understanding of the physical processes controlling subduction and evolution of this this warm water. Crucially, the processes seen here occur at small horizontal scales not resolved by regional forecast models or climate simulations; new parameterizations must be developed that accurately represent the physics. Here we present novel high resolution observations showing the detailed process of subduction and initial evolution of warm Pacific-origin water in the southern Beaufort Gyre.
    Description: Support for this work was provided by the US Office of Naval Research Stratified Ocean Dynamics of the Arctic program (grant numbers N000141512903, N000141612378, N000141612377, N000141612379, N0001416123450, N000141612360, N000141612349, N000141812007, N000141812475, and N000141912514). Additional support for biogeochemistry sampling was provided by UK (NERC) and Germany (BMBF) through the Changing Arctic Ocean Program’s ARISE (NE/P006035/1, NE/P006000/2), PEANUTS (NE/R01275X/1, NE/R012547/2, and BMBF 03F0804) projects and the UK-France PhD program DGA/Dstl. Float deployments and hydrographic data compilations were supported in part by North Pacific Research Board grants A91-99a and A91-00a. The deployment of autonomous ocean profilers was supported by ONR, NOAA Research, and the Joint Institute for the Study of the Atmosphere and Ocean (JISAO) under NOAA Cooperative Agreement NA15OAR4320063.
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    Corals regulate the distribution and abundance of Symbiodiniaceae and biomolecules in response to changing water depth and sea surface temperature (2021)
    Nature Research
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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 Sivaguru, M., Todorov, L. G., Fouke, C. E., Munro, C. M. O., Fouke, K. W., Fouke, K. E., Baughman, M. E., & Fouke, B. W. Corals regulate the distribution and abundance of Symbiodiniaceae and biomolecules in response to changing water depth and sea surface temperature. Scientific Reports, 11(1), (2021): 2230, https://doi.org/10.1038/s41598-021-81520-0.
    Description: The Scleractinian corals Orbicella annularis and O. faveolata have survived by acclimatizing to environmental changes in water depth and sea surface temperature (SST). However, the complex physiological mechanisms by which this is achieved remain only partially understood, limiting the accurate prediction of coral response to future climate change. This study quantitatively tracks spatial and temporal changes in Symbiodiniaceae and biomolecule (chromatophores, calmodulin, carbonic anhydrase and mucus) abundance that are essential to the processes of acclimatization and biomineralization. Decalcified tissues from intact healthy Orbicella biopsies, collected across water depths and seasonal SST changes on Curaçao, were analyzed with novel autofluorescence and immunofluorescence histology techniques that included the use of custom antibodies. O. annularis at 5 m water depth exhibited decreased Symbiodiniaceae and increased chromatophore abundances, while O. faveolata at 12 m water depth exhibited inverse relationships. Analysis of seasonal acclimatization of the O. faveolata holobiont in this study, combined with previous reports, suggests that biomolecules are differentially modulated during transition from cooler to warmer SST. Warmer SST was also accompanied by decreased mucus production and decreased Symbiodiniaceae abundance, which is compensated by increased photosynthetic activity enhanced calcification. These interacting processes have facilitated the remarkable resiliency of the corals through geological time.
    Description: Financial support for this work was provided by the Office of Naval Research (N00014-00-1-0609), the Illinois Carl R. Woese Institute for Genomic Biology Undergraduate Summer Research Fellowship, the Illinois Carl R. Woese Institute for Genomic Biology Mark Tracy Fellowship for Translational Research, and the Illinois Department of Molecular and Cellular Biology Jenner Family Summer Research Fellowship and the Edward and Barbara Weil Research Fund provided to the University of Illinois Urbana-Champaign.
    Keywords: Autofluorescence ; Two-photon microscopy ; X-ray Micro CT ; Water Depth ; Bathymetry ; Sea surface temperature ; Symbiodiniaceae symbiont ; chromatophores ; calmodulin ; carbonic anhydrase ; mucus ; Scleractinian corals ; Orbicella annularis ; Orbicella faveolata
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    Rapid ecosystem-scale consequences of acute deoxygenation on a Caribbean coral reef (2021)
    Nature Research
    Details
    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 Johnson, M. D., Scott, J. J., Leray, M., Lucey, N., Bravo, L. M. R., Wied, W. L., & Altieri, A. H. Rapid ecosystem-scale consequences of acute deoxygenation on a Caribbean coral reef. Nature Communications, 12(1), (2021): 4522, https://doi.org/10.1038/s41467-021-24777-3.
    Description: Loss of oxygen in the global ocean is accelerating due to climate change and eutrophication, but how acute deoxygenation events affect tropical marine ecosystems remains poorly understood. Here we integrate analyses of coral reef benthic communities with microbial community sequencing to show how a deoxygenation event rapidly altered benthic community composition and microbial assemblages in a shallow tropical reef ecosystem. Conditions associated with the event precipitated coral bleaching and mass mortality, causing a 50% loss of live coral and a shift in the benthic community that persisted a year later. Conversely, the unique taxonomic and functional profile of hypoxia-associated microbes rapidly reverted to a normoxic assemblage one month after the event. The decoupling of ecological trajectories among these major functional groups following an acute event emphasizes the need to incorporate deoxygenation as an emerging stressor into coral reef research and management plans to combat escalating threats to reef persistence.
    Description: M.D.J. was funded by postdoctoral fellow awards from the Smithsonian Institution’s Marine Global Earth Observatory (MarineGEO) and the Smithsonian Tropical Research Institute (STRI); M.L. and N.L. were funded by postdoctoral support from the STRI Office of Fellowships. J.J.S. was funded by a grant from the Gordon and Betty Moore Foundation awarded to STRI and UC Davis (doi:10.37807/GBMF5603). L.M.R.B., W.L.W., and A.H.A. were supported by MarineGEO, a private funder, and STRI funds to A.H.A. Many of the computations were conducted on the Smithsonian High-Performance Cluster (SI/HPC), Smithsonian Institution (doi:10.25572/SIHPC). We thank Rachel Collin for facilities support at the Bocas del Toro Research Station, Plinio Gondola and the research station staff for logistical support, Roman Barco for insight into the functional analyses, Sherly Castro for informative feedback, and Mike Fox for assistance with community analyses. Research permits were provided by the Autoridad Nacional del Ambiente de Panamá. This paper is the result of research funded by the National Oceanic and Atmospheric Administration’s National Centers for Coastal Ocean Science Competitive Research Program under award NA18NOS4780170 to A.H.A. and M.D.J. through the University of Florida. This is contribution 257 from the Coastal Hypoxia Research Program and 86 from the Smithsonian’s MarineGEO and Tennenbaum Marine Observatories Network.
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    An intermittent detachment faulting system with a large sulfide deposit revealed by multi-scale magnetic surveys (2021)
    Nature Research
    Details
    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 Wu, T., Tivey, M. A., Tao, C., Zhang, J., Zhou, F., & Liu, Y. An intermittent detachment faulting system with a large sulfide deposit revealed by multi-scale magnetic surveys. Nature Communications, 12(1), (2021): 5642, https://doi.org/10.1038/s41467-021-25880-1.
    Description: Magmatic and tectonic processes can contribute to discontinuous crustal accretion and play an important role in hydrothermal circulation at ultraslow-spreading ridges, however, it is difficult to accurately describe the processes without an age framework to constrain crustal evolution. Here we report on a multi-scale magnetic survey that provides constraints on the fine-scale evolution of a detachment faulting system that hosts hydrothermal activity at 49.7°E on the Southwest Indian Ridge. Reconstruction of the multi-stage detachment faulting history shows a previous episode of detachment faulting took place 0.76~1.48 My BP, while the present fault has been active for the past ~0.33 My and is just in the prime of life. This fault sustains hydrothermal circulation that has the potential for developing a large sulfide deposit. High resolution multiscale magnetics allows us to constrain the relative balance between periods of detachment faulting and magmatism to better describe accretionary processes on an ultraslow spreading ridge.
    Description: This work was supported by National Key R&D Program of China under contract no. 2018YFC0309901, National Natural Science Foundation of China (41906065), National Key R&D Program of China (2017YFC0306803) and COMRA Major Project under contract no. DY135-S1-01-06 and no. DY135-S1-01-01.
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    Asynchronous release sites align with NMDA receptors in mouse hippocampal synapses (2021)
    Nature Research
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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 Li, S., Raychaudhuri, S., Lee, S. A., Brockmann, M. M., Wang, J., Kusick, G., Prater, C., Syed, S., Falahati, H., Ramos, R., Bartol, T. M., Hosy, E., & Watanabe, S. Asynchronous release sites align with NMDA receptors in mouse hippocampal synapses. Nature Communications, 12(1), (2021): 677, https://doi.org/10.1038/s41467-021-21004-x.
    Description: Neurotransmitter is released synchronously and asynchronously following an action potential. Our recent study indicates that the release sites of these two phases are segregated within an active zone, with asynchronous release sites enriched near the center in mouse hippocampal synapses. Here we demonstrate that synchronous and asynchronous release sites are aligned with AMPA receptor and NMDA receptor clusters, respectively. Computational simulations indicate that this spatial and temporal arrangement of release can lead to maximal membrane depolarization through AMPA receptors, alleviating the pore-blocking magnesium leading to greater activation of NMDA receptors. Together, these results suggest that release sites are likely organized to activate NMDA receptors efficiently.
    Description: e also thank the Marine Biological Laboratory and their Neurobiology course for supporting the initial set of experiments (course supported by National Institutes of Health grant R25NS063307). S.W. and this work were supported by start-up funds from the Johns Hopkins University School of Medicine, Johns Hopkins Discovery funds, and the National Science Foundation (1727260), the National Institutes of Health (1DP2 NS111133-01 and 1R01 NS105810-01A1) awarded to S.W. S.W. is an Alfred P. Sloan fellow, McKnight Foundation Scholar, and Klingenstein and Simons Foundation scholar. G.K. was supported by a grant from the National Institutes of Health to the Biochemistry, Cellular and Molecular Biology Program of the Johns Hopkins University School of Medicine (T32 GM007445) and is a National Science Foundation Graduate Research Fellow (2016217537). E.H. and T.M.B. are supported by CRCNS-NIH-ANR grant AMPAR-T. The EM ICE high-pressure freezer was purchased partly with funds from an equipment grant from the National Institutes of Health (S10RR026445) awarded to Scot C Kuo.
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    Shifting seasonality of cyclones and western boundary current interactions in Bay of Bengal as observed during Amphan and Fani (2022)
    Nature Research
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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 Sil, S., Gangopadhyay, A., Gawarkiewicz, G., & Pramanik, S. Shifting seasonality of cyclones and western boundary current interactions in Bay of Bengal as observed during Amphan and Fani. Scientific Reports, 11(1), (2021): 22052 https://doi.org/10.1038/s41598-021-01607-6.
    Description: In recent years, the seasonal patterns of Tropical Cyclones (TC) in the Bay of Bengal have been shifting. While tropical depressions have been common in March–May (spring), they typically have been relatively weaker than the TCs during October–December. Here we show that the spatial pattern of recent warming trends during the last two decades in the southwestern Bay has allowed for stronger springtime pre-monsoon cyclones such as Amphan (May 2020, Super Cyclone) and Fani (April–May 2019, Extremely Severe Cyclone). The tracks of the pre-monsoon cyclones shifted westward, concurrent with an increasing rate of warming. This shift allowed both Fani and Amphan tracks to cross the northeastward warm Western Boundary Current (WBC) and associated warm anti-cyclonic eddies, while the weaker Viyaru (April 2013, Cyclonic Storm) did not interact with the WBC. A quantitative model linking the available along-track heat potential to cyclone’s intensity is developed to understand the impact of the WBC on cyclone intensification. The influence of the warming WBC and associated anti-cyclonic eddies will likely result in much stronger springtime TCs becoming relatively common in the future.
    Description: The authors gratefully acknowledge the financial and infrastructural support from the Indian Institute of Technology Bhubaneswar to carry out this research. SS acknowledges the financial assistance from Science and Engineering Research Board (SERB), Government of India (Grant No. CRG/2019/005842). All the figures are prepared using MATLAB. AG and SS appreciate the support of SERB's VAJRA Faculty Scheme (VJR/2018/000108) for the initiation of this collaborative work between SMAST and IITBBS. AG also acknowledges partial support from NSF (OCE 1851242) in completing this manuscript. GG was supported by a Grant from the Office of Naval Research as part of the Task Force Ocean initiative.
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    Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod (2021)
    Nature Research
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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 Lenz, P. H., Roncalli, V., Cieslak, M. C., Tarrant, A. M., Castelfranco, A. M., & Hartline, D. K. Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod. Communications Biology, 4(1), (2021): 426, https://doi.org/10.1038/s42003-021-01946-0.
    Description: Many arthropods undergo a seasonal dormancy termed “diapause” to optimize timing of reproduction in highly seasonal environments. In the North Atlantic, the copepod Calanus finmarchicus completes one to three generations annually with some individuals maturing into adults, while others interrupt their development to enter diapause. It is unknown which, why and when individuals enter the diapause program. Transcriptomic data from copepods on known programs were analyzed using dimensionality reduction of gene expression and functional analyses to identify program-specific genes and biological processes. These analyses elucidated physiological differences and established protocols that distinguish between programs. Differences in gene expression were associated with maturation of individuals on the reproductive program, while those on the diapause program showed little change over time. Only two of six filters effectively separated copepods by developmental program. The first one included all genes annotated to RNA metabolism and this was confirmed using differential gene expression analysis. The second filter identified 54 differentially expressed genes that were consistently up-regulated in individuals on the diapause program in comparison with those on the reproductive program. Annotated to oogenesis, RNA metabolism and fatty acid biosynthesis, these genes are both indicators for diapause preparation and good candidates for functional studies.
    Description: This work was supported by National Science Foundation Grants (NSF) OCE-1459235 and OCE-1756767 to P.H.L., D.K.H. and AE Christie and OPP-1746087 to A.M.T.
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    The chemical defensome of five model teleost fish (2021)
    Nature Research
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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 Eide, M., Zhang, X., Karlsen, O. A., Goldstone, J., Stegeman, J., Jonassen, I., & Goksoyr, A. The chemical defensome of five model teleost fish. Scientific Reports, 11(1), (2021): 10546, https://doi.org/10.1038/s41598-021-89948-0.
    Description: How an organism copes with chemicals is largely determined by the genes and proteins that collectively function to defend against, detoxify and eliminate chemical stressors. This integrative network includes receptors and transcription factors, biotransformation enzymes, transporters, antioxidants, and metal- and heat-responsive genes, and is collectively known as the chemical defensome. Teleost fish is the largest group of vertebrate species and can provide valuable insights into the evolution and functional diversity of defensome genes. We have previously shown that the xenosensing pregnane x receptor (pxr, nr1i2) is lost in many teleost species, including Atlantic cod (Gadus morhua) and three-spined stickleback (Gasterosteus aculeatus), but it is not known if compensatory mechanisms or signaling pathways have evolved in its absence. In this study, we compared the genes comprising the chemical defensome of five fish species that span the teleosteii evolutionary branch often used as model species in toxicological studies and environmental monitoring programs: zebrafish (Danio rerio), medaka (Oryzias latipes), Atlantic killifish (Fundulus heteroclitus), Atlantic cod, and three-spined stickleback. Genome mining revealed evolved differences in the number and composition of defensome genes that can have implication for how these species sense and respond to environmental pollutants, but we did not observe any candidates of compensatory mechanisms or pathways in cod and stickleback in the absence of pxr. The results indicate that knowledge regarding the diversity and function of the defensome will be important for toxicological testing and risk assessment studies.
    Description: The work was supported by the Norwegian Research Council as part of the iCOD and iCOD 2.0 projects (Grant Nos. 192441/I30 and 244654/E40), and the dCod 1.0 project (Grant No. 248840) which is part of Centre for Digital Life Norway. The American collaborators were funded by the National Institute of Health (USA) NIH P42ES007381 (Boston University Superfund Center to JJS and JVG), NIH R21HD073805 (JVG) and NHI R01ES029917 (JVG) grants. The Ocean Outlook exchange program funded the trans-Atlantic collaboration.
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    Nutrient content and stoichiometry of pelagic Sargassum reflects increasing nitrogen availability in the Atlantic Basin (2021)
    Nature Research
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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 Lapointe, B. E., Brewton, R. A., Herren, L. W., Wang, M., Hu, C., McGillicuddy, D. J., Lindell, S., Hernandez, F. J., & Morton, P. L. Nutrient content and stoichiometry of pelagic Sargassum reflects increasing nitrogen availability in the Atlantic Basin. Nature Communications, 12(1), (2021): 3060, https://doi.org/10.1038/s41467-021-23135-7.
    Description: The pelagic brown macroalgae Sargassum spp. have grown for centuries in oligotrophic waters of the North Atlantic Ocean supported by natural nutrient sources, such as excretions from associated fishes and invertebrates, upwelling, and N2 fixation. Using a unique historical baseline, we show that since the 1980s the tissue %N of Sargassum spp. has increased by 35%, while %P has decreased by 44%, resulting in a 111% increase in the N:P ratio (13:1 to 28:1) and increased P limitation. The highest %N and δ15N values occurred in coastal waters influenced by N-rich terrestrial runoff, while lower C:N and C:P ratios occurred in winter and spring during peak river discharges. These findings suggest that increased N availability is supporting blooms of Sargassum and turning a critical nursery habitat into harmful algal blooms with catastrophic impacts on coastal ecosystems, economies, and human health.
    Description: This work was funded by the US NASA Ocean Biology and Biogeochemistry Program (80NSSC20M0264, NNX16AR74G) and Ecological Forecast Program (NNX17AF57G), NOAA RESTORE Science Program (NA17NOS4510099), National Science Foundation (NSF-OCE 85–15492 and OCE 88–12055), “Save Our Seas” Specialty License Plate funds, granted through the Harbor Branch Oceanographic Institute Foundation, Ft. Pierce, FL, and a Red Wright Fellowship from the Bermuda Biological Station. A portion of this work was performed at the National High Magnetic Field Laboratory, which is supported by National Science Foundation Cooperative Agreement No. DMR-1644779 and the State of Florida. D.J.M. gratefully acknowledges the Holger W. Jannasch and Columbus O’Donnell Iselin Shared Chairs for Excellence in Oceanography, as well as support from the Mill Reef Fund.
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    Large-scale shift in the structure of a kelp forest ecosystem co-occurs with an epizootic and marine heatwave (2021)
    Nature Research
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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 McPherson, M. L., Finger, D. J., I., Houskeeper, H. F., Bell, T. W., Carr, M. H., Rogers-Bennett, L., & Kudela, R. M. Large-scale shift in the structure of a kelp forest ecosystem co-occurs with an epizootic and marine heatwave. Communications Biology, 4(1), (2021): 298, https://doi.org/10.1038/s42003-021-01827-6.
    Description: Climate change is responsible for increased frequency, intensity, and duration of extreme events, such as marine heatwaves (MHWs). Within eastern boundary current systems, MHWs have profound impacts on temperature-nutrient dynamics that drive primary productivity. Bull kelp (Nereocystis luetkeana) forests, a vital nearshore habitat, experienced unprecedented losses along 350 km of coastline in northern California beginning in 2014 and continuing through 2019. These losses have had devastating consequences to northern California communities, economies, and fisheries. Using a suite of in situ and satellite-derived data, we demonstrate that the abrupt ecosystem shift initiated by a multi-year MHW was preceded by declines in keystone predator population densities. We show strong evidence that northern California kelp forests, while temporally dynamic, were historically resilient to fluctuating environmental conditions, even in the absence of key top predators, but that a series of coupled environmental and biological shifts between 2014 and 2016 resulted in the formation of a persistent, altered ecosystem state with low primary productivity. Based on our findings, we recommend the implementation of ecosystem-based and adaptive management strategies, such as (1) monitoring the status of key ecosystem attributes: kelp distribution and abundance, and densities of sea urchins and their predators, (2) developing management responses to threshold levels of these attributes, and (3) creating quantitative restoration suitability indices for informing kelp restoration efforts.
    Description: M.H.C. received support from the National Science Foundation (OCE‐1538582).
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    Hydraulic transmissivity inferred from ice-sheet relaxation following Greenland supraglacial lake drainages (2021)
    Nature Research
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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 Lai, C.-Y., Stevens, L. A., Chase, D. L., Creyts, T. T., Behn, M. D., Das, S. B., & Stone, H. A. Hydraulic transmissivity inferred from ice-sheet relaxation following Greenland supraglacial lake drainages. Nature Communications, 12(1), (2021): 3955, https://doi.org/10.1038/s41467-021-24186-6.
    Description: Surface meltwater reaching the base of the Greenland Ice Sheet transits through drainage networks, modulating the flow of the ice sheet. Dye and gas-tracing studies conducted in the western margin sector of the ice sheet have directly observed drainage efficiency to evolve seasonally along the drainage pathway. However, the local evolution of drainage systems further inland, where ice thicknesses exceed 1000 m, remains largely unknown. Here, we infer drainage system transmissivity based on surface uplift relaxation following rapid lake drainage events. Combining field observations of five lake drainage events with a mathematical model and laboratory experiments, we show that the surface uplift decreases exponentially with time, as the water in the blister formed beneath the drained lake permeates through the subglacial drainage system. This deflation obeys a universal relaxation law with a timescale that reveals hydraulic transmissivity and indicates a two-order-of-magnitude increase in subglacial transmissivity (from 0.8 ± 0.3 mm3 to 215 ± 90.2 mm3) as the melt season progresses, suggesting significant changes in basal hydrology beneath the lakes driven by seasonal meltwater input.
    Description: C.-Y.L. and L.A.S thank Lamont-Doherty Earth Observatory for funding through the Lamont Postdoctoral Fellowships. D.L.C acknowledges support from the National Science Foundation (NSF) Graduate Research Fellowship. T.T.C. was supported by NSF’s Office of Polar Programs (NSF-OPP) through OPP-1643970, the National Aeronautics and Space Administration (NASA) through NNX16AJ95G, and a grant from the Vetlesen Foundation. S.B.D. and M.D.B. acknowledge funding from NSF-OPP and NASA’s Cryospheric Sciences Program through OPP-1838410, ARC-1023364, ARC-0520077, and NNX10AI30G. H.A.S. thanks the High Meadows Environmental Institute and the Carbon Mitigation Initiative at Princeton University. This publication was supported by the Princeton University Library Open Access Fund.
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    Decline in plankton diversity and carbon flux with reduced sea ice extent along the Western Antarctic Peninsula (2021)
    Nature Research
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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 Lin, Y., Moreno, C., Marchetti, A., Ducklow, H., Schofield, O., Delage, E., Meredith, M., Li, Z., Eveillard, D., Chaffron, S., & Cassar, N. Decline in plankton diversity and carbon flux with reduced sea ice extent along the Western Antarctic Peninsula. Nature Communications, 12(1), (2021): 4948, https://doi.org/10.1038/s41467-021-25235-w.
    Description: Since the middle of the past century, the Western Antarctic Peninsula has warmed rapidly with a significant loss of sea ice but the impacts on plankton biodiversity and carbon cycling remain an open question. Here, using a 5-year dataset of eukaryotic plankton DNA metabarcoding, we assess changes in biodiversity and net community production in this region. Our results show that sea-ice extent is a dominant factor influencing eukaryotic plankton community composition, biodiversity, and net community production. Species richness and evenness decline with an increase in sea surface temperature (SST). In regions with low SST and shallow mixed layers, the community was dominated by a diverse assemblage of diatoms and dinoflagellates. Conversely, less diverse plankton assemblages were observed in waters with higher SST and/or deep mixed layers when sea ice extent was lower. A genetic programming machine-learning model explained up to 80% of the net community production variability at the Western Antarctic Peninsula. Among the biological explanatory variables, the sea-ice environment associated plankton assemblage is the best predictor of net community production. We conclude that eukaryotic plankton diversity and carbon cycling at the Western Antarctic Peninsula are strongly linked to sea-ice conditions.
    Description: This work is supported by NSF OPP-1643534 to N.C., NSF OPP-1341479 to A.M., and NSF PLR-1440435 to H.D. and O.S. (Palmer LTER).
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    Real-time polarization microscopy of fibrillar collagen in histopathology (2021)
    Nature Research
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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 Keikhosravi, A., Shribak, M., Conklin, M. W., Liu, Y., Li, B., Loeffler, A., Levenson, R. M., & Eliceiri, K. W. Real-time polarization microscopy of fibrillar collagen in histopathology. Scientific Reports, 11(1), (2021): 19063, https://doi.org/10.1038/s41598-021-98600-w.
    Description: Over the past two decades, fibrillar collagen reorganization parameters such as the amount of collagen deposition, fiber angle and alignment have been widely explored in numerous studies. These parameters are now widely accepted as stromal biomarkers and linked to disease progression and survival time in several cancer types. Despite all these advances, there has not been a significant effort to make it possible for clinicians to explore these biomarkers without adding steps to the clinical workflow or by requiring high-cost imaging systems. In this paper, we evaluate previously described polychromatic polarization microscope (PPM) to visualize collagen fibers with an optically generated color representation of fiber orientation and alignment when inspecting the sample by a regular microscope with minor modifications. This system does not require stained slides, but is compatible with histological stains such as H&E. Consequently, it can be easily accommodated as part of regular pathology review of tissue slides, while providing clinically useful insight into stromal composition.
    Description: This work was supported by NIH R01 CA238191 (KWE), NIH P41GM135019 (KWE), NIH R01 GM101701 (MS), funding from the Morgridge Institute for Research (KWE), the Semiconductor Research Corporation (SRC) (KWE), and the William T. Golden Endowment (MS).
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    Developmental exposure to non-dioxin-like polychlorinated biphenyls promotes sensory deficits and disrupts dopaminergic and GABAergic signaling in zebrafish (2021)
    Nature Research
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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 Brun, N. R., Panlilio, J. M., Zhang, K., Zhao, Y., Ivashkin, E., Stegeman, J. J., & Goldstone, J. Developmental exposure to non-dioxin-like polychlorinated biphenyls promotes sensory deficits and disrupts dopaminergic and GABAergic signaling in zebrafish. Communications Biology, 4(1), (2021): 1129, https://doi.org/10.1038/s42003-021-02626-9.
    Description: The most abundant polychlorinated biphenyl (PCB) congeners found in the environment and in humans are neurotoxic. This is of particular concern for early life stages because the exposure of the more vulnerable developing nervous system to neurotoxic chemicals can result in neurobehavioral disorders. In this study, we uncover currently unknown links between PCB target mechanisms and neurobehavioral deficits using zebrafish as a vertebrate model. We investigated the effects of the abundant non-dioxin-like (NDL) congener PCB153 on neuronal morphology and synaptic transmission linked to the proper execution of a sensorimotor response. Zebrafish that were exposed during development to concentrations similar to those found in human cord blood and PCB contaminated sites showed a delay in startle response. Morphological and biochemical data demonstrate that even though PCB153-induced swelling of afferent sensory neurons, the disruption of dopaminergic and GABAergic signaling appears to contribute to PCB-induced motor deficits. A similar delay was observed for other NDL congeners but not for the potent dioxin-like congener PCB126. The effects on important and broadly conserved signaling mechanisms in vertebrates suggest that NDL PCBs may contribute to neurodevelopmental abnormalities in humans and increased selection pressures in vertebrate wildlife.
    Description: This work was supported by the Swiss National Science Foundation P2EZP2_165200 (NRB), the Boston University Superfund Research Program NIH 5P42ES007381 (J.J.S. and J.V.G.), the Woods Hole Center for Oceans and Human Health (NIH: P01ES021923 and P01ES028938; NSF: OCE-1314642 and OCE-1840381) (N.R.B., J.M.P., and J.J.S.), and the National Natural Science Foundation of China 22006099 (K.Z. and Y.Z.) and the Shanghai Pujiang Program 19PJ1404900 (K.Z. and Y.Z.).
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    Placozoan fiber cells: mediators of innate immunity and participants in wound healing (2022)
    Nature Research
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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 Mayorova, T. D., Hammar, K., Jung, J. H., Aronova, M. A., Zhang, G., Winters, C. A., Reese, T. S., & Smith, C. L. Placozoan fiber cells: mediators of innate immunity and participants in wound healing. Scientific Reports, 11(1), (2021): 23343, https://doi.org/10.1038/s41598-021-02735-9.
    Description: Placozoa is a phylum of non-bilaterian marine animals. These small, flat organisms adhere to the substrate via their densely ciliated ventral epithelium, which mediates mucociliary locomotion and nutrient uptake. They have only six morphological cell types, including one, fiber cells, for which functional data is lacking. Fiber cells are non-epithelial cells with multiple processes. We used electron and light microscopic approaches to unravel the roles of fiber cells in Trichoplax adhaerens, a representative member of the phylum. Three-dimensional reconstructions of serial sections of Trichoplax showed that each fiber cell is in contact with several other cells. Examination of fiber cells in thin sections and observations of live dissociated fiber cells demonstrated that they phagocytose cell debris and bacteria. In situ hybridization confirmed that fiber cells express genes involved in phagocytic activity. Fiber cells also are involved in wound healing as evidenced from microsurgery experiments. Based on these observations we conclude that fiber cells are multi-purpose macrophage-like cells. Macrophage-like cells have been described in Porifera, Ctenophora, and Cnidaria and are widespread among Bilateria, but our study is the first to show that Placozoa possesses this cell type. The phylogenetic distribution of macrophage-like cells suggests that they appeared early in metazoan evolution.
    Description: Open Access funding provided by the National Institutes of Health (NIH).
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    Orphan cytochrome P450 20a1 CRISPR/Cas9 mutants and neurobehavioral phenotypes in zebrafish (2022)
    Nature Research
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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 Brun, N. R., Salanga, M. C., Mora-Zamorano, F. X., Lamb, D. C., Goldstone, J. V., & Stegeman, J. J. Orphan cytochrome P450 20a1 CRISPR/Cas9 mutants and neurobehavioral phenotypes in zebrafish. Scientific Reports, 11(1), (2021): 23892, https://doi.org/10.1038/s41598-021-03068-3.
    Description: Orphan cytochrome P450 (CYP) enzymes are those for which biological substrates and function(s) are unknown. Cytochrome P450 20A1 (CYP20A1) is the last human orphan P450 enzyme, and orthologs occur as single genes in every vertebrate genome sequenced to date. The occurrence of high levels of CYP20A1 transcripts in human substantia nigra and hippocampus and abundant maternal transcripts in zebrafish eggs strongly suggest roles both in the brain and during early embryonic development. Patients with chromosome 2 microdeletions including CYP20A1 show hyperactivity and bouts of anxiety, among other conditions. Here, we created zebrafish cyp20a1 mutants using CRISPR/Cas9, providing vertebrate models with which to study the role of CYP20A1 in behavior and other neurodevelopmental functions. The homozygous cyp20a1 null mutants exhibited significant behavioral differences from wild-type zebrafish, both in larval and adult animals. Larval cyp20a1-/- mutants exhibited a strong increase in light-simulated movement (i.e., light–dark assay), which was interpreted as hyperactivity. Further, the larvae exhibited mild hypoactivity during the adaptation period of the optomotor assays. Adult cyp20a1 null fish showed a pronounced delay in adapting to new environments, which is consistent with an anxiety paradigm. Taken together with our earlier morpholino cyp20a1 knockdown results, the results described herein suggest that the orphan CYP20A1 has a neurophysiological role.
    Description: These studies were supported in part by the Boston University Superfund Research Program NIH 5P42ES007381 (MCS, NRB, FXM, JVG, JJS), the Woods Hole Center for Oceans and Human Health (NIH: P01ES021923 and P01ES028938; NSF: OCE-1314642 and OCE-1840381; NRB and JJS), and EBI/EMBL Medakatox NIEHS R01ES029917 (JVG). DCL was funded by a UK-US Fulbright Scholarship.
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    Substantial oxygen consumption by aerobic nitrite oxidation in oceanic oxygen minimum zones (2022)
    Nature Research
    Details
    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 Beman, J. M., Vargas, S. M., Wilson, J. M., Perez-Coronel, E., Karolewski, J. S., Vazquez, S., Yu, A., Cairo, A. E., White, M. E., Koester, I., Aluwihare, L. I., & Wankel, S. D. Substantial oxygen consumption by aerobic nitrite oxidation in oceanic oxygen minimum zones. Nature Communications, 12(1), (2021): 7043, https://doi.org/10.1038/s41467-021-27381-7.
    Description: Oceanic oxygen minimum zones (OMZs) are globally significant sites of biogeochemical cycling where microorganisms deplete dissolved oxygen (DO) to concentrations 〈20 µM. Amid intense competition for DO in these metabolically challenging environments, aerobic nitrite oxidation may consume significant amounts of DO and help maintain low DO concentrations, but this remains unquantified. Using parallel measurements of oxygen consumption rates and 15N-nitrite oxidation rates applied to both water column profiles and oxygen manipulation experiments, we show that the contribution of nitrite oxidation to overall DO consumption systematically increases as DO declines below 2 µM. Nitrite oxidation can account for all DO consumption only under DO concentrations 〈393 nM found in and below the secondary chlorophyll maximum. These patterns are consistent across sampling stations and experiments, reflecting coupling between nitrate reduction and nitrite-oxidizing Nitrospina with high oxygen affinity (based on isotopic and omic data). Collectively our results demonstrate that nitrite oxidation plays a pivotal role in the maintenance and biogeochemical dynamics of OMZs.
    Description: This work was supported by NSF CAREER Grant OCE-1555375 to J.M.B. Metagenome sequencing was supported by the UCMEXUS-CONACyT Collaborative Grants Program (joint awards to J.M.B. and José García Maldonado).
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    Coral reef biofilm bacterial diversity and successional trajectories are structured by reef benthic organisms and shift under chronic nutrient enrichment (2022)
    Nature Research
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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 Remple, K. L., Silbiger, N. J., Quinlan, Z. A., Fox, M. D., Kelly, L. W., Donahue, M. J., & Nelson, C. E. Coral reef biofilm bacterial diversity and successional trajectories are structured by reef benthic organisms and shift under chronic nutrient enrichment. Npj Biofilms and Microbiomes, 7(1), (2021): 84, https://doi.org/10.1038/s41522-021-00252-1.
    Description: Work on marine biofilms has primarily focused on host-associated habitats for their roles in larval recruitment and disease dynamics; little is known about the factors regulating the composition of reef environmental biofilms. To contrast the roles of succession, benthic communities and nutrients in structuring marine biofilms, we surveyed bacteria communities in biofilms through a six-week succession in aquaria containing macroalgae, coral, or reef sand factorially crossed with three levels of continuous nutrient enrichment. Our findings demonstrate how biofilm successional trajectories diverge from temporal dynamics of the bacterioplankton and how biofilms are structured by the surrounding benthic organisms and nutrient enrichment. We identify a suite of biofilm-associated bacteria linked with the orthogonal influences of corals, algae and nutrients and distinct from the overlying water. Our results provide a comprehensive characterization of marine biofilm successional dynamics and contextualize the impact of widespread changes in reef community composition and nutrient pollution on biofilm community structure.
    Description: This work was supported through grants from the National Science Foundation for Biological Oceanography (1923877 to C.E.N. and M.J.D., 1949033 to C.E.N. and 2118687 to L.W.K., and 1924281 to N.J.S.) and the National Fish and Wildlife Foundation (grant no. 44447 to C.E.N.). This paper is funded in part by the National Oceanic and Atmospheric Administration, Project A/AS-1, which is sponsored by the University of Hawaii Sea Grant College Program, SOEST, under Institutional Grant No. NA18OAR4170076 from NOAA Office of Sea Grant, Department of Commerce. This is CSUN marine biology contribution #365, UH Sea Grant contribution UNIHI-SEAGRANT-JC-21-06, and UH SOEST contribution 11435.
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    Attachment of zebra and quagga mussel adhesive plaques to diverse substrates (2022)
    Nature Research
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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 James, B. D., Kimmins, K. M., Nguyen, M.-T., Lausch, A. J., & Sone, E. D. Attachment of zebra and quagga mussel adhesive plaques to diverse substrates. Scientific Reports, 11(1), (2021): 23998, https://doi.org/10.1038/s41598-021-03227-6.
    Description: Like marine mussels, freshwater zebra and quagga mussels adhere via the byssus, a proteinaceous attachment apparatus. Attachment to various surfaces allows these invasive mussels to rapidly spread, however the adhesion mechanism is not fully understood. While marine mussel adhesion mechanics has been studied at the individual byssal-strand level, freshwater mussel adhesion has only been characterized through whole-mussel detachment, without direct interspecies comparisons on different substrates. Here, adhesive strength of individual quagga and zebra mussel byssal plaques were measured on smooth substrates with varying hydrophobicity—glass, PVC, and PDMS. With increased hydrophobicity of substrates, adhesive failures occurred more frequently, and mussel adhesion strength decreased. A new failure mode termed 'footprint failure' was identified, where failure appeared to be adhesive macroscopically, but a microscopic residue remained on the surface. Zebra mussels adhered stronger and more frequently on PDMS than quagga mussels. While their adhesion strengths were similar on PVC, there were differences in the failure mode and the plaque-substrate interface ultrastructure. Comparisons with previous marine mussel studies demonstrated that freshwater mussels adhere with comparable strength despite known differences in protein composition. An improved understanding of freshwater mussel adhesion mechanics may help explain spreading dynamics and will be important in developing effective antifouling surfaces.
    Description: This work was supported by Discovery grant (#342455) to EDS from the National Sciences and Engineering Research Council (NSERC) of Canada (RGPIN-2019-06210).
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    Differential susceptibility of reef-building corals to deoxygenation reveals remarkable hypoxia tolerance (2022)
    Nature Research
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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 Johnson, M. D., Swaminathan, S. D., Nixon, E. N., Paul, V. J., & Altieri, A. H. Differential susceptibility of reef-building corals to deoxygenation reveals remarkable hypoxia tolerance. Scientific Reports, 11(1), (2021): 23168, https://doi.org/10.1038/s41598-021-01078-9.
    Description: Ocean deoxygenation threatens the persistence of coastal ecosystems worldwide. Despite an increasing awareness that coastal deoxygenation impacts tropical habitats, there remains a paucity of empirical data on the effects of oxygen limitation on reef-building corals. To address this knowledge gap, we conducted laboratory experiments with ecologically important Caribbean corals Acropora cervicornis and Orbicella faveolata. We tested the effects of continuous exposure to conditions ranging from extreme deoxygenation to normoxia (~ 1.0 to 6.25 mg L−1 dissolved oxygen) on coral bleaching, photophysiology, and survival. Coral species demonstrated markedly different temporal resistance to deoxygenation, and within a species there were minimal genotype-specific treatment effects. Acropora cervicornis suffered tissue loss and mortality within a day of exposure to severe deoxygenation (~ 1.0 mg L−1), whereas O. faveolata remained unaffected after 11 days of continuous exposure to 1.0 mg L−1. Intermediate deoxygenation treatments (~ 2.25 mg L−1, ~ 4.25 mg L−1) elicited minimal responses in both species, indicating a low oxygen threshold for coral mortality and coral resilience to oxygen concentrations that are lethal for other marine organisms. These findings demonstrate the potential for variability in species-specific hypoxia thresholds, which has important implications for our ability to predict how coral reefs may be affected as ocean deoxygenation intensifies. With deoxygenation emerging as a critical threat to tropical habitats, there is an urgent need to incorporate deoxygenation into coral reef research, management, and action plans to facilitate better stewardship of coral reefs in an era of rapid environmental change.
    Description: This research was funded by an award from the National Oceanic and Atmospheric Administration’s National Centers for Coastal Ocean Science Competitive Research Program to AA, MJ, and VP (NA18NOS4780170) through the University of Florida. MJ was funded by postdoctoral fellow awards from the Smithsonian Institution's Marine Global Earth Observatory (MarineGEO), the Smithsonian Marine Station, and Woods Hole Oceanographic Institution. This material is based on work supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-1842473. This is contribution 259 from the Coastal Hypoxia Research Program, 93 from the Smithsonian’s MarineGEO and Tennenbaum Marine Observatories Network, and 1167 from the Smithsonian Marine Station at Fort Pierce.
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    Rapid microbial methanogenesis during CO2 storage in hydrocarbon reservoirs (2022)
    Nature Research
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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 Tyne, R. L., Barry, P. H., Lawson, M., Byrne, D. J., Warr, O., Xie, H., Hillegonds, D. J., Formolo, M., Summers, Z. M., Skinner, B., Eiler, J. M., & Ballentine, C. J. Rapid microbial methanogenesis during CO2 storage in hydrocarbon reservoirs. Nature, 600(7890), (2021): 670-674, https://doi.org/10.1038/s41586-021-04153-3.
    Description: Carbon capture and storage (CCS) is a key technology to mitigate the environmental impact of carbon dioxide (CO2) emissions. An understanding of the potential trapping and storage mechanisms is required to provide confidence in safe and secure CO2 geological sequestration1,2. Depleted hydrocarbon reservoirs have substantial CO2 storage potential1,3, and numerous hydrocarbon reservoirs have undergone CO2 injection as a means of enhanced oil recovery (CO2-EOR), providing an opportunity to evaluate the (bio)geochemical behaviour of injected carbon. Here we present noble gas, stable isotope, clumped isotope and gene-sequencing analyses from a CO2-EOR project in the Olla Field (Louisiana, USA). We show that microbial methanogenesis converted as much as 13–19% of the injected CO2 to methane (CH4) and up to an additional 74% of CO2 was dissolved in the groundwater. We calculate an in situ microbial methanogenesis rate from within a natural system of 73–109 millimoles of CH4 per cubic metre (standard temperature and pressure) per year for the Olla Field. Similar geochemical trends in both injected and natural CO2 fields suggest that microbial methanogenesis may be an important subsurface sink of CO2 globally. For CO2 sequestration sites within the environmental window for microbial methanogenesis, conversion to CH4 should be considered in site selection.
    Description: R.L.T. was supported by a Natural Environment Research Council studentship (grant reference NE/L002612/1). C.J.B. and P.H.B. acknowledge A. Regberg and B. Meurer for their support of the project and help with sample collection. C.J.B. was part supported by an Earth4D CIFAR fellowship. P.H.B. was supported by NSF awards 1923915 and 2015789. O.W. was supported by Natural Sciences and Engineering Research Council of Canada Discovery and Accelerator grants awarded to the Sherwood Lollar research group and acknowledges B. Sherwood Lollar’s support for the project. Z.M.S. acknowledges J. Biddle and G. Christman for their help in generating the microbial data.
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    Origin of spatial variation in US East Coast sea-level trends during 1900-2017 (2019)
    Nature Research
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © The Authors, 2018. This is the author's version of the work. It is posted here by permission of Nature Research for personal use, not for redistribution. The definitive version was published in Piecuch, C. G., Huybers, P., Hay, C. C., Kemp, A. C., Little, C. M., Mitrovica, J. X., Ponte, R. M., & Tingley, M. P. (2018). Origin of spatial variation in US east coast sea-level trends during 1900-2017. Nature, 564(7736), 400-404, doi:10.1038/s41586-018-0787-6.
    Description: Identifying the causes of historical trends in relative sea level—the height of the sea surface relative to Earth’s crust—is a prerequisite for predicting future changes. Rates of change along the U.S. East Coast during the last century were spatially variable, and relative sea level rose faster along the Mid-Atlantic Bight than the South Atlantic Bight and Gulf of Maine. Past studies suggest that Earth’s ongoing response to the last deglaciation1–5, surface redistribution of ice and water 5–9, and changes in ocean circulation9–13 contributed importantly to this large-scale spatial pattern. Here we analyze instrumental data14, 15 and proxy reconstructions4, 12 using probabilistic methods16–18 to show that vertical motions of Earth’s crust exerted the dominant control on regional spatial differences in relative sea level trends along the U.S. East Coast during 1900–2017, explaining a majority of the large-scale spatial variance. Rates of coastal subsidence caused by ongoing relaxation of the peripheral forebulge associated with the last deglaciation are strongest near North Carolina,Maryland, and Virginia. Such structure indicates that Earth’s elastic lithosphere is thicker than has been assumed in other models19–22. We also find a significant coastal gradient in relative sea level trends over this period that is unrelated to deglaciation, and suggests contributions from twentieth-century redistribution of ice and water. Our results indicate that the majority of large-scale spatial variation in longterm rates of relative sea level rise on the U.S. East Coast was due to geological processes that will persist at similar rates for centuries into the future.
    Description: Funding came from Woods Hole Oceanographic Institution’s Investment in Science Fund; Harvard University; NSF awards 1558939, 1558966, and 1458921; and NASA awards NNH16CT01C, NNX17AE17G, and 80NSSC17K0698. We acknowledge helpful conversations with S. Adhikari, B.D. Hamlington, F.W. Landerer, S.J. Lentz, and P.R. Thompson. Comments from three anonymous referees and the editor, Michael White, are greatly appreciated.
    Description: 2019-06-18
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    The contribution of water radiolysis to marine sedimentary life (2021)
    Nature Research
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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 Sauvage, J. F., Flinders, A., Spivack, A. J., Pockalny, R., Dunlea, A. G., Anderson, C. H., Smith, D. C., Murray, R. W., & D'Hondt, S. The contribution of water radiolysis to marine sedimentary life. Nature Communications, 12(1), (2021): 1297, https://doi.org/10.1038/s41467-021-21218-z.
    Description: Water radiolysis continuously produces H2 and oxidized chemicals in wet sediment and rock. Radiolytic H2 has been identified as the primary electron donor (food) for microorganisms in continental aquifers kilometers below Earth’s surface. Radiolytic products may also be significant for sustaining life in subseafloor sediment and subsurface environments of other planets. However, the extent to which most subsurface ecosystems rely on radiolytic products has been poorly constrained, due to incomplete understanding of radiolytic chemical yields in natural environments. Here we show that all common marine sediment types catalyse radiolytic H2 production, amplifying yields by up to 27X relative to pure water. In electron equivalents, the global rate of radiolytic H2 production in marine sediment appears to be 1-2% of the global organic flux to the seafloor. However, most organic matter is consumed at or near the seafloor, whereas radiolytic H2 is produced at all sediment depths. Comparison of radiolytic H2 consumption rates to organic oxidation rates suggests that water radiolysis is the principal source of biologically accessible energy for microbial communities in marine sediment older than a few million years. Where water permeates similarly catalytic material on other worlds, life may also be sustained by water radiolysis.
    Description: This project was funded by the US National Science Foundation (through grant NSF-OCE-1130735 and the Center for Deep Dark Energy Biosphere Investigations [C-DEBI; grant NSF-OCE-0939564]); the National Aeronautics and Space Administration (grant NNX12AD65G); the U.S. Science Support Program, IODP; and a Schlanger Ocean Drilling Fellowship to J.F.S. This is a contribution to the Deep Carbon Observatory (DCO). It is C-DEBI publication 553.
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    Large subglacial source of mercury from the southwestern margin of the Greenland Ice Sheet (2021)
    Nature Research
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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 Hawkings, J. R., Linhoff, B. S., Wadham, J. L., Stibal, M., Lamborg, C. H., Carling, G. T., Lamarche-Gagnon, G., Kohler, T. J., Ward, R., Hendry, K. R., Falteisek, L., Kellerman, A. M., Cameron, K. A., Hatton, J. E., Tingey, S., Holt, A. D., Vinsova, P., Hofer, S., Bulinova, M., Větrovský, T., Meire, L., Spencer, R. G. M. Large subglacial source of mercury from the southwestern margin of the Greenland Ice Sheet. Nature Geoscience, 14, (2021): 496-502, https://doi.org/10.1038/s41561-021-00753-w.
    Description: The Greenland Ice Sheet is currently not accounted for in Arctic mercury budgets, despite large and increasing annual runoff to the ocean and the socio-economic concerns of high mercury levels in Arctic organisms. Here we present concentrations of mercury in meltwaters from three glacial catchments on the southwestern margin of the Greenland Ice Sheet and evaluate the export of mercury to downstream fjords based on samples collected during summer ablation seasons. We show that concentrations of dissolved mercury are among the highest recorded in natural waters and mercury yields from these glacial catchments (521–3,300 mmol km−2 year−1) are two orders of magnitude higher than from Arctic rivers (4–20 mmol km−2 year−1). Fluxes of dissolved mercury from the southwestern region of Greenland are estimated to be globally significant (15.4–212 kmol year−1), accounting for about 10% of the estimated global riverine flux, and include export of bioaccumulating methylmercury (0.31–1.97 kmol year−1). High dissolved mercury concentrations (~20 pM inorganic mercury and ~2 pM methylmercury) were found to persist across salinity gradients of fjords. Mean particulate mercury concentrations were among the highest recorded in the literature (~51,000 pM), and dissolved mercury concentrations in runoff exceed reported surface snow and ice values. These results suggest a geological source of mercury at the ice sheet bed. The high concentrations of mercury and its large export to the downstream fjords have important implications for Arctic ecosystems, highlighting an urgent need to better understand mercury dynamics in ice sheet runoff under global warming.
    Description: This research is part of a European Commission Horizon 2020 Marie Skłodowska-Curie Actions fellowship ICICLES (grant agreement #793962) to J.R.H. Greenland terrestrial research campaigns were funded by a UK NERC standard grant (NE/I008845/1) and a Leverhulme Trust Research Grant (RPG-2016-439) to J.L.W., with additional support provided by a Royal Society Wolfson Merit Award to J.L.W. Additional funding came from Czech Science Foundation grants (GACR; 15-17346Y and 18-12630S) to M.S. Fjord fieldwork was supported by European Research Council grant ICY-LAB (grant agreement 678371) and Royal Society Enhancement Award (grant RGF\EA\181036) to K.R.H. L.M. was funded by research programme VENI (0.16.Veni.192.150, NWO). T.J.K. was supported by Charles University Research Centre program no. 204069. The authors thank the captain and crew of the RV Kisaq and staff at the Greenland Institute of Natural Resources for assistance during fjord fieldwork, and all those involved with fieldwork at Leverett Camp during the 2012 and 2015 field campaigns. M. Cooper is thanked for providing the geological overview file for Extended Data Fig. 1a, and K. Mankoff for help in generating the modelled GrIS discharge datasets. The authors also thank G. White in the geochemistry group at the National High Magnetic Field Geochemistry Laboratory, which is supported by NSF DMR-1644779 and the State of Florida, for analytical support.
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    Subpolar North Atlantic western boundary density anomalies and the Meridional Overturning Circulation (2021)
    Nature Research
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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 Li, F., Lozier, M. S., Bacon, S., Bower, A. S., Cunningham, S. A., de Jong, M. F., DeYoung, B., Fraser, N., Fried, N., Han, G., Holliday, N. P., Holte, J., Houpert, L., Inall, M. E., Johns, W. E., Jones, S., Johnson, C., Karstensen, J., Le Bras, I. A., P. Lherminier, X. Lin, H. Mercier, M. Oltmanns, A. Pacini, T. Petit, R. S. Pickart, D. Rayner, F. Straneo, V. Thierry, M. Visbeck, I. Yashayaev & Zhou, C. Subpolar North Atlantic western boundary density anomalies and the Meridional Overturning Circulation. Nature Communications, 12(1), (2021): 3002, https://doi.org/10.1038/s41467-021-23350-2.
    Description: Changes in the Atlantic Meridional Overturning Circulation, which have the potential to drive societally-important climate impacts, have traditionally been linked to the strength of deep water formation in the subpolar North Atlantic. Yet there is neither clear observational evidence nor agreement among models about how changes in deep water formation influence overturning. Here, we use data from a trans-basin mooring array (OSNAP—Overturning in the Subpolar North Atlantic Program) to show that winter convection during 2014–2018 in the interior basin had minimal impact on density changes in the deep western boundary currents in the subpolar basins. Contrary to previous modeling studies, we find no discernable relationship between western boundary changes and subpolar overturning variability over the observational time scales. Our results require a reconsideration of the notion of deep western boundary changes representing overturning characteristics, with implications for constraining the source of overturning variability within and downstream of the subpolar region.
    Description: We acknowledge funding from the Physical Oceanography Program of the U.S. National Science Foundation (OCE-1259398, OCE-1756231, OCE-1948335); the U.K. Natural Environment Research Council (NERC) National Capability programs the Extended Ellett Line and CLASS (NE/R015953/1), and NERC grants UK-OSNAP (NE/K010875/1, NE/K010875/2, NE/K010700/1) and U.K. OSNAP Decade (NE/T00858X/1, NE/T008938/1). Additional support was received from the European Union 7th Framework Program (FP7 2007-2013) under grant 308299 (NACLIM), the Horizon 2020 research and innovation program under grants 727852 (Blue-Action), 862626 (EuroSea). We also acknowledge support from the Royal Netherlands Institute for Sea Research, the Surface Water and Ocean Topography-Canada (SWOT-C), Canadian Space Agency, the Aquatic Climate Change Adaptation Services Program (ACCASP), Fisheries and Oceans Canada, an Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant, and from the China’s national key research and development projects (2016YFA0601803), the National Natural Science Foundation of China (41925025) and the Fundamental Research Funds for the Central Universities (201424001). Support for the 53°N array by the RACE program of the German Ministry BMBF is acknowledged, as is the contribution from Fisheries and Oceans Canada’s Atlantic Zone Monitoring Program.
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    The cytochrome P450 (CYP) superfamily in cnidarians (2021)
    Nature Research
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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 Pankov, K., McArthur, A. G., Gold, D. A., Nelson, D. R., Goldstone, J., & Wilson, J. Y. The cytochrome P450 (CYP) superfamily in cnidarians. Scientific Reports, 11(1), (2021): 9834, https://doi.org/10.1038/s41598-021-88700-y.
    Description: The cytochrome P450 (CYP) superfamily is a diverse and important enzyme family, playing a central role in chemical defense and in synthesis and metabolism of major biological signaling molecules. The CYPomes of four cnidarian genomes (Hydra vulgaris, Acropora digitifera, Aurelia aurita, Nematostella vectensis) were annotated; phylogenetic analyses determined the evolutionary relationships amongst the sequences and with existing metazoan CYPs. 155 functional CYPs were identified and 90 fragments. Genes were from 24 new CYP families and several new subfamilies; genes were in 9 of the 12 established metazoan CYP clans. All species had large expansions of clan 2 diversity, with H. vulgaris having reduced diversity for both clan 3 and mitochondrial clan. We identified potential candidates for xenobiotic metabolism and steroidogenesis. That each genome contained multiple, novel CYP families may reflect the large evolutionary distance within the cnidarians, unique physiology in the cnidarian classes, and/or different ecology of the individual species.
    Description: This study was supported by grants from the Natural Science Engineering Research Council of Canada in the form of a Discovery Grant (RGPIN-328204-2011 and RGPIN-05767-2016) to J.Y.W. A.G.M. held a Cisco Research Chair in Bioinformatics, supported by Cisco Systems Canada, Inc. K.V.P. was supported by a Natural Sciences and Engineering Research Council of Canada (NSERC) Undergraduate Student Research Award (USRA). Computer resources were supplied by the McMaster Service Lab and Repository computing cluster, funded in part by grants to A.G.M. from the Canadian Foundation for Innovation (34531 to A.G.M.).
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    Linking deeply-sourced volatile emissions to plateau growth dynamics in southeastern Tibetan Plateau (2021)
    Nature Research
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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 Zhang, M., Guo, Z., Xu, S., Barry, P. H., Sano, Y., Zhang, L., Halldorsson, S. A., Chen, A.-T., Cheng, Z., Liu, C.-Q., Li, S.-L., Lang, Y.-C., Zheng, G., Li, Z., Li, L., & Li, Y. Linking deeply-sourced volatile emissions to plateau growth dynamics in southeastern Tibetan Plateau. Nature Communications, 12(1), (2021): 4157, https://doi.org/10.1038/s41467-021-24415-y.
    Description: The episodic growth of high-elevation orogenic plateaux is controlled by a series of geodynamic processes. However, determining the underlying mechanisms that drive plateau growth dynamics over geological history and constraining the depths at which growth originates, remains challenging. Here we present He-CO2-N2 systematics of hydrothermal fluids that reveal the existence of a lithospheric-scale fault system in the southeastern Tibetan Plateau, whereby multi-stage plateau growth occurred in the geological past and continues to the present. He isotopes provide unambiguous evidence for the involvement of mantle-scale dynamics in lateral expansion and localized surface uplift of the Tibetan Plateau. The excellent correlation between 3He/4He values and strain rates, along the strike of Indian indentation into Asia, suggests non-uniform distribution of stresses between the plateau boundary and interior, which modulate southeastward growth of the Tibetan Plateau within the context of India-Asia convergence. Our results demonstrate that deeply-sourced volatile geochemistry can be used to constrain deep dynamic processes involved in orogenic plateau growth.
    Description: This work was supported by China Seismic Experimental Site (CSES) (2019CSES0104), the Strategic Priority Research Program (B) of Chinese Academy of Sciences (XDB26000000), the National Key Research and Development Program of China (2020YFA0607700), the National Natural Science Foundation of China (41930642, 41602341, 41772355, and 41702361), the Second Tibetan Plateau Scientific Expedition and Research Program (STEP) (2019QZKK0702), and the United Laboratory of High-Pressure Physics and Earthquake Science (2019HPPES02). P.H.B. was supported by the US National Science Foundation EAR Grant 1144559 during a portion of this work.
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    Understanding physical drivers of the 2015/16 marine heatwaves in the Northwest Atlantic (2021)
    Nature Research
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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 Perez, E., Ryan, S., Andres, M., Gawarkiewicz, G., Ummenhofer, C. C., Bane, J., & Haines, S. Understanding physical drivers of the 2015/16 marine heatwaves in the Northwest Atlantic. Scientific Reports, 11(1), (2021): 17623, https://doi.org/10.1038/s41598-021-97012-0.
    Description: The Northwest Atlantic, which has exhibited evidence of accelerated warming compared to the global ocean, also experienced several notable marine heatwaves (MHWs) over the last decade. We analyze spatiotemporal patterns of surface and subsurface temperature structure across the Northwest Atlantic continental shelf and slope to assess the influences of atmospheric and oceanic processes on ocean temperatures. Here we focus on MHWs from 2015/16 and examine their physical drivers using observational and reanalysis products. We find that a combination of jet stream latitudinal position and ocean advection, mainly due to warm core rings shed by the Gulf Stream, plays a role in MHW development. While both atmospheric and oceanic drivers can lead to MHWs they have different temperature signatures with each affecting the vertical structure differently and horizontal spatial patterns of a MHW. Northwest Atlantic MHWs have significant socio-economic impacts and affect commercially important species such as squid and lobster.
    Description: The work was supported by a Woods Hole Oceanographic Institution Summer Student Fellowship (to E.P.) through the National Science Foundation (NSF) REU under grant OCE-1852460, a Feodor-Lynen Fellowship by the Alexander von Humboldt Foundation and the WHOI Postdoctoral Scholar program (to S.R.), NSF grants OCE-1924041 (to M.A.) and OCE-1851261 (to G.G.) and OCE-1558920 (to J.B. and H. Seim at the Univ. of North Carolina), ONR grant N-14-19-1-2646 (to G.G.), and the James E. and Barbara V. Moltz Fellowship for Climate-Related Research (to C.C.U.).
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    A genetically encoded tool for reconstituting synthetic modulatory neurotransmission and reconnect neural circuits in vivo (2021)
    Nature Research
    Details
    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 Hawk, J. D., Wisdom, E. M., Sengupta, T., Kashlan, Z. D., & Colon-Ramos, D. A. A genetically encoded tool for reconstituting synthetic modulatory neurotransmission and reconnect neural circuits in vivo. Nature Communications, 12(1), (2021): 4795, https://doi.org/10.1038/s41467-021-24690-9.
    Description: Chemogenetic and optogenetic tools have transformed the field of neuroscience by facilitating the examination and manipulation of existing circuits. Yet, the field lacks tools that enable rational rewiring of circuits via the creation or modification of synaptic relationships. Here we report the development of HySyn, a system designed to reconnect neural circuits in vivo by reconstituting synthetic modulatory neurotransmission. We demonstrate that genetically targeted expression of the two HySyn components, a Hydra-derived neuropeptide and its receptor, creates de novo neuromodulatory transmission in a mammalian neuronal tissue culture model and functionally rewires a behavioral circuit in vivo in the nematode Caenorhabditis elegans. HySyn can interface with existing optogenetic, chemogenetic and pharmacological approaches to functionally probe synaptic transmission, dissect neuropeptide signaling, or achieve targeted modulation of specific neural circuits and behaviors.
    Description: This work was initiated in the Grass Laboratory at the Marine Biological Laboratories (MBL) with funding through a Grass Fellowship awarded to J.D.H. Thanks to Richard Goodman (OHSU) for encouragement during the conceptualization of the fellowship application, and the 2019 Grass Fellows, Mel Coleman (Grass Director), and Christophe Dupré (Associate Director) for advice and support during the summer fellowship. We thank the MBL Division of Education and participants in the Vendor Equipment Loan Program. Special thanks to Sutter Instruments, who generously provided all electrophysiology equipment and substantial on-site assistance, and Zeiss, who provided on-site assistance at MBL. We thank Zhao-Wen Wang and Ping Liu (UConn) for guidance and training in patch-clamp electrophysiology, as well as providing Neuro2a cells. We thank Rob Steele (UCI) for supplying Hydra, as well as advice and inspiration on Hydra biology. We thank members of the Colón-Ramos lab and Hari Shroff (NIH) for thoughtful comments on the manuscript. We thank Michael Koelle and Andrew Olson (Yale University) for advice and reagents regarding serotonin rewiring experiments. We also thank Steve Flavell (MIT) for ideas and reagents regarding the experiments associated with del-7. We thank Life Science Editors for editing assistance. D.A.C.-R. is an MBL Fellow. Research in the D.A.C.-R. lab was supported by NIH R01NS076558, DP1NS111778, and by an HHMI Scholar Award.
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    Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization (2022)
    Nature Research
    Details
    Publication Date: 2022-08-03
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Schmidbaur, H., Kawaguchi, A., Clarence, T., Fu, X., Hoang, O. P., Zimmermann, B., Ritschard, E. A., Weissenbacher, A., Foster, J. S., Nyholm, S., Bates, P. A., Albertin, C. B., Tanaka, E., & Simakov, O. Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization. Nature Communications, 13(1), (2022): 2172, https://doi.org/10.1038/s41467-022-29694-7.
    Description: Coleoid cephalopods (squid, cuttlefish, octopus) have the largest nervous system among invertebrates that together with many lineage-specific morphological traits enables complex behaviors. The genomic basis underlying these innovations remains unknown. Using comparative and functional genomics in the model squid Euprymna scolopes, we reveal the unique genomic, topological, and regulatory organization of cephalopod genomes. We show that coleoid cephalopod genomes have been extensively restructured compared to other animals, leading to the emergence of hundreds of tightly linked and evolutionary unique gene clusters (microsyntenies). Such novel microsyntenies correspond to topological compartments with a distinct regulatory structure and contribute to complex expression patterns. In particular, we identify a set of microsyntenies associated with cephalopod innovations (MACIs) broadly enriched in cephalopod nervous system expression. We posit that the emergence of MACIs was instrumental to cephalopod nervous system evolution and propose that microsyntenic profiling will be central to understanding cephalopod innovations.
    Description: H.S., O.P.H., E.R., and O.S. were supported by the Austrian Science Fund (FWF) grant P30686-B29. O.S. was supported by Whitman Center Early Career Fellowship (Frank R. Lillie Quasi-Endowment Fund, L. & A. Colwin Summer Research Fellowship, Bell Research Award in Tissue Engineering). H.S. was supported by the short-term grant abroad (KWA) of the University of Vienna. H.S. and O.S. were supported by the University of Chicago/Vienna Strategic Partnership Programme Mobility Grant. A.K. was supported by the JSPS Postdoctoral Fellowship for Overseas Researchers program from Japan. C.B.A. was supported by the Hibbitt Early Career Fellowship. Eggs and paralarvae of E. scolopes were generated in part by support by the NASA Space Biology 80NSSC18K1465 awarded to J.S.F. S.V.N. was supported by the National Science Foundation IOS-1557914. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC0001003), the UK Medical Research Council (FC001003), and the Wellcome Trust (FC001003).
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    Turbulence-induced bubble nucleation in hydrothermal fluids beneath Yellowstone Lake (2022)
    Nature Research
    Details
    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 Caudron, C., Vandemeulebrouck, J., & Sohn, R. A. Turbulence-induced bubble nucleation in hydrothermal fluids beneath Yellowstone Lake. Communications Earth & Environment, 3(1), (2022): 103, https://doi.org/10.1038/s43247-022-00417-6.
    Description: Volcanic systems generate large amounts of gas, and understanding gas fluxes is a fundamental aspect of volcanology and hazard mitigation. Volcanic gases can be challenging to measure, but acoustic methods hold promise in underwater environments because gas bubbles are powerful sound sources. We deployed an acoustic system to study the nature of gas discharge at a large (~30 MW) thermal field on the floor of Yellowstone Lake, which has experienced numerous hydrothermal explosions since the last glaciation (~13.4 ka). We find that small (〈10 Pa) turbulent flow instabilities trigger the nucleation of CO2 bubbles in the saturated fluids. The observation of CO2 bubbles nucleating in hydrothermal fluids due to small pressure perturbations informs our understanding of hydrothermal explosions in Yellowstone Lake, and demonstrates that acoustic data in underwater environments can provide insight into the stability of gas-rich systems, as well as gas fluxes.
    Description: This research was supported by the National Science Foundation grant EAR-1516361 to R.A.S. All work in Yellowstone National Park was completed under an authorized research permit (YELL-2018-SCI-7018). We also acknowledge the IRGA 2021 Volquan project (funded by Université Grenoble Alpes) and Thomas Jefferson Fund Face Foundation (project TJF20_009 ‘Quantifying underwater volcano degassing using novel seismo-acoustic approaches’).
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    Fluid flow stimulates chemoautotrophy in hydrothermally influenced coastal sediments (2022)
    Nature Research
    Details
    Publication Date: 2022-08-15
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sievert, S. M., Buehring, S., Gulmann, L. K., Hinrichs, K.-U., Ristova, P. P., & Gomez-Saez, G. Fluid flow stimulates chemoautotrophy in hydrothermally influenced coastal sediments. Communications Earth & Environment, 3(1), (2022): 96, https://doi.org/10.1038/s43247-022-00426-5.
    Description: Hydrothermalism in coastal sediments strongly impacts biogeochemical processes and supports chemoautotrophy. Yet, the effect of fluid flow on microbial community composition and rates of chemoautotrophic production is unknown because rate measurements under natural conditions are difficult, impeding an assessment of the importance of these systems. Here, in situ incubations controlling fluid flow along a transect of three geochemically distinct locations at a shallow-water hydrothermal system off Milos (Greece) show that Campylobacteria dominated chemoautotrophy in the presence of fluid flow. Based on injected 13C-labelled dissolved inorganic carbon and its incorporation into fatty acids, we constrained carbon fixation to be as high as 12 µmol C cm−3 d−1, corresponding to areal rates up to 10-times higher than previously reported for coastal sediments, and showed the importance of fluid flow for supplying the necessary substrates to support chemoautotrophy. Without flow, rates were substantially lower and microbial community composition markedly shifted. Our results highlight the importance of fluid flow in shaping the composition and activity of microbial communities of shallow-water hydrothermal vents, identifying them as hotspots of microbial productivity.
    Description: Open Access funding enabled and organized by Projekt DEAL.
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    Arctic drainage of Laurentide Ice Sheet meltwater throughout the past 14,700 years (2022)
    Nature Research
    Details
    Publication Date: 2022-08-15
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sufke, F., Gutjahr, M., Keigwin, L. D., Reilly, B., Giosan, L., & Lippold, J. Arctic drainage of Laurentide Ice Sheet meltwater throughout the past 14,700 years. Communications Earth & Environment, 3(1), (2022): 98, https://doi.org/10.1038/s43247-022-00428-3.
    Description: During the last deglaciation substantial volumes of meltwater from the decaying Laurentide Ice Sheet were supplied to the Arctic, Gulf of Mexico and North Atlantic along different drainage routes, sometimes as catastrophic flood events. These events are suggested to have impacted global climate, for example initiating the Younger Dryas cold period. Here we analyze the authigenic Pb isotopic composition of sediments in front of the Arctic Mackenzie Delta, a sensitive tracer for elevated freshwater runoff of the retreating Laurentide Ice Sheet. Our data reveal continuous meltwater supply to the Arctic along the Mackenzie River since the onset of the Bølling–Allerød. The strongest Lake Agassiz outflow event is observed at the end of the Bølling–Allerød close to the onset of the Younger Dryas. In context of deglacial North American runoff records from the southern and eastern outlets, our findings provide a detailed reconstruction of the deglacial drainage chronology of the disintegrating Laurentide Ice Sheet.
    Description: Open Access funding enabled and organized by Projekt DEAL.
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    Genome and transcriptome mechanisms driving cephalopod evolution (2022)
    Nature Research
    Details
    Publication Date: 2022-08-19
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Albertin, C. B., Medina-Ruiz, S., Mitros, T., Schmidbaur, H., Sanchez, G., Wang, Z. Y., Grimwood, J., Rosenthal, J. J. C., Ragsdale, C. W., Simakov, O., & Rokhsar, D. S. Genome and transcriptome mechanisms driving cephalopod evolution. Nature Communications, 13(1), (2022): 2427, https://doi.org/10.1038/s41467-022-29748-w.
    Description: Cephalopods are known for their large nervous systems, complex behaviors and morphological innovations. To investigate the genomic underpinnings of these features, we assembled the chromosomes of the Boston market squid, Doryteuthis (Loligo) pealeii, and the California two-spot octopus, Octopus bimaculoides, and compared them with those of the Hawaiian bobtail squid, Euprymna scolopes. The genomes of the soft-bodied (coleoid) cephalopods are highly rearranged relative to other extant molluscs, indicating an intense, early burst of genome restructuring. The coleoid genomes feature multi-megabase, tandem arrays of genes associated with brain development and cephalopod-specific innovations. We find that a known coleoid hallmark, extensive A-to-I mRNA editing, displays two fundamentally distinct patterns: one exclusive to the nervous system and concentrated in genic sequences, the other widespread and directed toward repetitive elements. We conclude that coleoid novelty is mediated in part by substantial genome reorganization, gene family expansion, and tissue-dependent mRNA editing.
    Description: We thank the Marine Resources Center and the Cephalopod program at the Marine Biological Laboratory for supplying D. pealeii, R. Hanlon for the image in Fig. 1a, R. Hanlon and S. Senft for help with tissue dissection, Dr. Chuck Winkler for supplying O. bimaculoides, B. Burford and W. Gilly for assistance with D. opalescens collection, and the Vienna Zoo (Tiergarten Schönbrunn), particularly R. Halbauer, A. Weissenbacher, and the aquarist team for E. scolopes husbandry. Computation was done using the Life Science Cluster at the University of Vienna. This project began with generous funding from the Grass Foundation, administered by the MBL through J.J.R. It was also supported by Austrian Science fund FWF (P30686-B29) to H.S. and O.S., the Whitman Center Early Career Fellowship to O.S., the Okinawa Institute of Science and Technology Molecular Genetics Unit, Chan-Zuckerberg BioHub, and the Marthella Foskett Brown Chair in Computational Biology to D.S.R, NSF grant (IOS-1354898) to C.W.R, and the Hibbitt Early Career Fellowship to C.B.A. Sequencing at the University of Chicago Functional Genomics Facility was partially supported by the NIH (5UL1TR002389-02 and UL1 TR000430).
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    A Maluku Sea intermediate western boundary current connecting Pacific Ocean circulation to the Indonesian Throughflow (2022)
    Nature Research
    Details
    Publication Date: 2022-08-19
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Yuan, D., Yin, X., Li, X., Corvianawatie, C., Wang, Z., Li, Y., Yang, Y., Hu, X., Wang, J., Tan, S., Surinati, D., Purwandana, A., Wardana, A., Ismail, M., Budiman, A., Bayhaqi, A., Avianto, P., Santoso, P., Kusmanto, E., Dirhamsyah, Arifin, Z., & Pratt, L. A Maluku Sea intermediate western boundary current connecting Pacific Ocean circulation to the Indonesian Throughflow. Nature Communications, 13(1), (2022): 2093, https://doi.org/10.1038/s41467-022-29617-6.
    Description: The Indonesian Throughflow plays an important role in the global ocean circulation and climate. Existing studies of the Indonesian Throughflow have focused on the Makassar Strait and the exit straits, where the upper thermocline currents carry North Pacific waters to the Indian Ocean. Here we show, using mooring observations, that a previous unknown intermediate western boundary current (with the core at ~1000 m depth) exists in the Maluku Sea, which transports intermediate waters (primarily the Antarctic Intermediate Water) from the Pacific into the Seram-Banda Seas through the Lifamatola Passage above the bottom overflow. Our results suggest the importance of the western boundary current in global ocean intermediate circulation and overturn. We anticipate that our study is the beginning of more extensive investigations of the intermediate circulation of the Indo-Pacific ocean in global overturn, which shall improve our understanding of ocean heat and CO2 storages significantly.
    Description: This study is supported by NSFC (D.Y., Z.W., Y.L., Y.Y., S.T., J.W., and X.L.: 41720104008; D.Y., J.W., Y.L., X.L., Y.Y., S.T., X.H., and X.Y.: 91858204), the National Key Research and Development Program of China (D.Y. and X.L.: 2020YFA0608800), CAS (D.Y., Z.W., J.W., and Y.L.: XDB42000000), projects. Affiliations 1 and 2 share the first position. D.Y. is supported by QMSNL (2018SDKJ0104-02), and Shandong Provincial (U1606402) and the “Kunpeng Outstanding Scholar Program” of the FIO/NMR of China, J.W. supported by NSFC (41776011), Z.W. by NSFC (41876025).
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    Robust but weak winter atmospheric circulation response to future Arctic sea ice loss (2022)
    Nature Research
    In:  EPIC3Nature Communications, Nature Research, 13, pp. 727, ISSN: 2041-1723
    Details
    Publication Date: 2022-06-29
    Description: The possibility that Arctic sea ice loss weakens mid-latitude westerlies, promoting more severe cold winters, has sparked more than a decade of scientific debate, with apparent support from observations but inconclusive modelling evidence. Here we show that sixteen models contributing to the Polar Amplification Model Intercomparison Project simulate a weakening of mid-latitude westerlies in response to projected Arctic sea ice loss. We develop an emergent constraint based on eddy feedback, which is 1.2 to 3 times too weak in the models, suggesting that the real-world weakening lies towards the higher end of the model simulations. Still, the modelled response to Arctic sea ice loss is weak: the North Atlantic Oscillation response is similar in magnitude and offsets the projected response to increased greenhouse gases, but would only account for around 10% of variations in individual years. We further find that relationships between Arctic sea ice and atmospheric circulation have weakened recently in observations and are no longer inconsistent with those in models.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed , info:eu-repo/semantics/article
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    Deletion in chromosome 6 spanning alpha-synuclein and multimerin1 loci in the Rab27a/b double knockout mouse (2022)
    Nature Research
    Details
    Publication Date: 2022-09-23
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Pattanayak, R., Underwood, R., Crowley, M. R., Crossman, D. K., Morgan, J. R., & Yacoubian, T. A. Deletion in chromosome 6 spanning alpha-synuclein and multimerin1 loci in the Rab27a/b double knockout mouse. Scientific Reports, 12(1), (2022): 9837, https://doi.org/10.1038/s41598-022-13557-8.
    Description: We report an incidental 358.5 kb deletion spanning the region encoding for alpha-synuclein (αsyn) and multimerin1 (Mmrn1) in the Rab27a/Rab27b double knockout (DKO) mouse line previously developed by Tolmachova and colleagues in 2007. Western blot and RT-PCR studies revealed lack of αsyn expression at either the mRNA or protein level in Rab27a/b DKO mice. PCR of genomic DNA from Rab27a/b DKO mice demonstrated at least partial deletion of the Snca locus using primers targeted to exon 4 and exon 6. Most genes located in proximity to the Snca locus, including Atoh1, Atoh2, Gm5570, Gm4410, Gm43894, and Grid2, were shown not to be deleted by PCR except for Mmrn1. Using whole genomic sequencing, the complete deletion was mapped to chromosome 6 (60,678,870–61,037,354), a slightly smaller deletion region than that previously reported in the C57BL/6J substrain maintained by Envigo. Electron microscopy of cortex from these mice demonstrates abnormally enlarged synaptic terminals with reduced synaptic vesicle density, suggesting potential interplay between Rab27 isoforms and αsyn, which are all highly expressed at the synaptic terminal. Given this deletion involving several genes, the Rab27a/b DKO mouse line should be used with caution or with appropriate back-crossing to other C57BL/6J mouse substrain lines without this deletion.
    Description: This study was supported by NIH [R56NS115767 (TAY), RF1NS115767-01A1 (TAY), P50NS108675 (TAY), and NINDS/NIA RF1NS078165 (JRM)].
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    Characteristics and evolution of sill-driven off-axis hydrothermalism in Guaymas Basin - the Ringvent site (2019)
    Nature Research
    Details
    Publication Date: 2022-06-06
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Teske, A., McKay, L. J., Ravelo, A. C., Aiello, I., Mortera, C., Núñez-Useche, F., Canet, C., Chanton, J. P., Brunner, B., Hensen, C., Ramírez, G. A., Sibert, R. J., Turner, T., White, D., Chambers, C. R., Buckley, A., Joye, S. B., Soule, S. A., & Lizarralde, D. Characteristics and evolution of sill-driven off-axis hydrothermalism in Guaymas Basin - the Ringvent site. Scientific Reports, 9(1), (2019): 13847, doi:10.1038/s41598-019-50200-5.
    Description: The Guaymas Basin spreading center, at 2000 m depth in the Gulf of California, is overlain by a thick sedimentary cover. Across the basin, localized temperature anomalies, with active methane venting and seep fauna exist in response to magma emplacement into sediments. These sites evolve over thousands of years as magma freezes into doleritic sills and the system cools. Although several cool sites resembling cold seeps have been characterized, the hydrothermally active stage of an off-axis site was lacking good examples. Here, we present a multidisciplinary characterization of Ringvent, an ~1 km wide circular mound where hydrothermal activity persists ~28 km northwest of the spreading center. Ringvent provides a new type of intermediate-stage hydrothermal system where off-axis hydrothermal activity has attenuated since its formation, but remains evident in thermal anomalies, hydrothermal biota coexisting with seep fauna, and porewater biogeochemical signatures indicative of hydrothermal circulation. Due to their broad potential distribution, small size and limited life span, such sites are hard to find and characterize, but they provide critical missing links to understand the complex evolution of hydrothermal systems.
    Description: This work was funded by NSF OCE grant 1449604 “Rapid Proposal: Guaymas Basin site survey cruise for IODP proposal 833” to Andreas Teske; NSF C-DEBI grant “Characterizing subseafloor life and environments in Guaymas Basin” to Andreas Teske, Ivano Aiello and Ana Christina Ravelo; and 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 Andreas Teske and Samantha B. Joye, respectively. We thank the Alvin and Sentry teams for a stellar performance during Guaymas Basin cruise AT37-06, and the science crew of RV El Puma for their dedication, skill, and “can-do” collaborative spirit during the 2014 Guaymas coring campaign. Sequencing of bacterial and archaeal communities was supported by the Deep Carbon Observatory, and performed at the Marine Biological Laboratory in Woods Hole, MA.
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    An integrative re-evaluation of Typhlatya shrimp within the karst aquifer of the Yucatan Peninsula, Mexico (2022)
    Nature Research
    Details
    Publication Date: 2022-07-20
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ballou, L., Brankovits, D., Chavez-Solis, E. M., Diaz, J. M. C., Gonzalez, B. C., Rohret, S., Salinas, A., Liu, A., Simoes, N., Alvarez, F., Miglietta, M. P., Iliffe, T. M., & Borda, E. An integrative re-evaluation of Typhlatya shrimp within the karst aquifer of the Yucatan Peninsula, Mexico. Scientific Reports, 12(1), (2022): 5302, https://doi.org/10.1038/s41598-022-08779-9.
    Description: The Yucatán Peninsula, Mexico is a carbonate platform well-known for extensive karst networks of densely stratified aquifer ecosystems. This aquifer supports diverse anchialine fauna, including species of the globally distributed anchialine shrimp genus Typhlatya (Atyidae). Four species (T. campecheae, T. pearsei, T. dzilamensis and T. mitchelli) are endemic to the Peninsula, of which three are federally listed in Mexico. This first integrative evaluation (i.e., molecular, morphological, broad geographic and type locality sampling, and environmental data) of Yucatán Typhlatya reveals considerable species identity conflict in prior phylogenetic assessments, broad species ranges, syntopy within cave systems and five genetic lineages (of which two are new to science). Despite sampling from the type locality of endangered T. campecheae, specimens (and molecular data) were indistinguishable from vulnerable T. pearsei. Ancestral/divergence reconstructions support convergent evolution of a low-salinity ancestor for a post-Paleogene arc Yucatán + Cuba Typhlatya clade within the anchialine Atyidae clade. A secondary adaptation for the coastal-restricted euryhaline (2–37 psu), Typhlatya dzilamensis (unknown conservation status) was identified, while remaining species lineages were low-salinity (〈 5 psu) adapted and found within the meteoric lens of inland and coastal caves. This study demonstrates the need for integrative/interdisciplinary approaches when conducting biodiversity assessments in complex and poorly studied aquifers.
    Description: Financial support for this study was provided by Texas A&M-CONACYT (TI, FA), TI, FA), PAPIIT IN208519 (DGAPA-UNAM) (FA), CONACYT Ciencia Básica A1-S-32846 (FA), Texas A&M University San Antonio (TAMUSA) Start-up Funds (EB), TAMUSA Research Council Grant (EB), TAMUSA Summer Faculty Grant and Fellowship (EB). NSF-REU/OCE: 1560242 supported AL and EB, and TAMU-Louis Stokes Alliance for Minority Participation (HRD: 1612776) supported SR, LS. This work was also supported by the NSF Graduate Research Fellowship Program (M1703014) and the Cave Conservancy Foundation (LB). Typhlatya sampling was sanctioned under collection permits SEMARNAT/SGPA/DGVS 05263/14, 004471/18, 05996/19.
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    Tropical origins of the record-breaking 2020 summer rainfall extremes in East Asia (2022)
    Nature Research
    Details
    Publication Date: 2022-07-21
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kim, S., Park, J.-H., & Kug, J.-S. Tropical origins of the record-breaking 2020 summer rainfall extremes in East Asia. Scientific Reports, 12(1), (2022): 5366, https://doi.org/10.1038/s41598-022-09297-4.
    Description: The East Asian countries have experienced heavy rainfalls in boreal summer 2020. Here, we investigate the dynamical processes driving the rainfall extremes in East Asia during July and August. The Indian Ocean basin warming in June can be responsible for the anticyclonic anomalies in the western North Pacific (WNP), which modulate the zonally-elongated rainfalls in East Asia during July through an atmospheric Rossby wave train. In August, the East Asian rainfall increase is also related to the anticyclonic anomalies in the subtropical WNP, although it is located further north. The north tropical Atlantic warming in June partly contributes to the subtropical WNP rainfall decrease in August through a subtropical teleconnection. Then the subtropical WNP rainfall decrease drives the local anticyclonic anomalies that cause the rainfall increase in East Asia during August. The tropical Indian Ocean anomalously warmed in June and the subtropical WNP rainfall decreased in August 2020, which played a role in modulating the WNP anticyclonic anomalies. Therefore, the record-breaking rainfall extremes in East Asia that occurred during summer 2020 can be explained by the teleconnections associated with the tropical origins among the Indian, Pacific, and Atlantic Oceans and their interbasin interactions.
    Description: This work is supported by the National Research Foundation of Korea (NRF-2018R1A5A1024958 & NRF-2021M3I6A1086808).
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    Adaptive responses of marine diatoms to zinc scarcity and ecological implications (2022)
    Nature Research
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    Publication Date: 2022-07-21
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kellogg, R., Moosburner, M., Cohen, N., Hawco, N., McIlvin, M., Moran, D., DiTullio, G., Subhas, A., Allen, A., & Saito, M. Adaptive responses of marine diatoms to zinc scarcity and ecological implications. Nature Communications, 13(1), (2022): 1995, https://doi.org/10.1038/s41467-022-29603-y.
    Description: Scarce dissolved surface ocean concentrations of the essential algal micronutrient zinc suggest that Zn may influence the growth of phytoplankton such as diatoms, which are major contributors to marine primary productivity. However, the specific mechanisms by which diatoms acclimate to Zn deficiency are poorly understood. Using global proteomic analysis, we identified two proteins (ZCRP-A/B, Zn/Co Responsive Protein A/B) among four diatom species that became abundant under Zn/Co limitation. Characterization using reverse genetic techniques and homology data suggests putative Zn/Co chaperone and membrane-bound transport complex component roles for ZCRP-A (a COG0523 domain protein) and ZCRP-B, respectively. Metaproteomic detection of ZCRPs along a Pacific Ocean transect revealed increased abundances at the surface (〈200 m) where dZn and dCo were scarcest, implying Zn nutritional stress in marine algae is more prevalent than previously recognized. These results demonstrate multiple adaptive responses to Zn scarcity in marine diatoms that are deployed in low Zn regions of the Pacific Ocean.
    Description: This work was funded by the National Science Foundation (OCE-1736599 and OCE-1657766), NIH (R01GM135709), Gordon and Betty Moore Foundation (GBMF3782) to M.A.S., and Simons Foundation award 544236 to N.R.C. This work was further supported by the National Science Foundation (NSF-OCE-1756884 and NSF-MCB-1818390), United States Department of Energy (DE-SC0018344), and Gordon and Betty Moore Foundation grants GBMF3828 and GBMF5006 to A.E.A.
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    Drawing the borders of the mesophotic zone of the Mediterranean Sea using satellite data (2022)
    Nature Research
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    Publication Date: 2022-07-15
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Castellan, G., Angeletti, L., Montagna, P., & Taviani, M. Drawing the borders of the mesophotic zone of the Mediterranean Sea using satellite data. Scientific Reports, 12(1), (2022): 5585, https://doi.org/10.1038/s41598-022-09413-4.
    Description: The 30–150 m bathymetric range is commonly adopted in the literature to constrain the mesophotic zone. However, such depth interval varies depending on sunlight penetration, which is primarily a function of solar radiation incidence and water clarity. This is especially obvious in the Mediterranean Sea with its peculiar biophysical properties. Integrating information on light regime in the estimation of the bathymetric range of the mesophotic zone would provide a more robust definition, orienting conservation actions targeting its ecosystems. We present a first assessment of the spatial and vertical extension of the mesophotic zone in the Mediterranean Sea based upon light penetration, comparing our prediction with literature data. Our study also represents a baseline to monitor future variations in the bathymetric interval associated with the mesophotic zone in the Mediterranean Sea in relation to global changes.
    Description: This is ISMAR-CNR Bologna scientific contribution n. 2061. This work was supported by the “Convenzione MATTMCNR per i Programmi di Monitoraggio per la Direttiva sulla Strategia Marina (MSFD, Art. 11, Dir. 2008/56/CE)”, the H2020 Project RELIANCE (Grant agreement no: 101017501), the DG Environment programme IDEM (Grant agreement no. 11.0661/2017/750680/SUB/EN V.C2) and MIUR-PRIN 2017 GLIDE 2017FREXZY. This contribution is supported by Ph.D. program in Cultural and Natural Heritage of the University of Bologna (GC).
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    Ice viscosity is more sensitive to stress than commonly assumed (2022)
    Nature Research
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    Publication Date: 2022-07-15
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Millstein, J. D., Minchew, B. M., & Pegler, S. S. Ice viscosity is more sensitive to stress than commonly assumed. Communications Earth & Environment, 3(1), (2022): 57, https://doi.org/10.1038/s43247-022-00385-x.
    Description: Accurate representation of the viscous flow of ice is fundamental to understanding glacier dynamics and projecting sea-level rise. Ice viscosity is often described by a simple but largely untested and uncalibrated constitutive relation, Glen’s Flow Law, wherein the rate of deformation is proportional to stress raised to the power n. The value n = 3 is commonly prescribed in ice-flow models, though observations and experiments support a range of values across stresses and temperatures found on Earth. Here, we leverage recent remotely-sensed observations of Antarctic ice shelves to show that Glen’s Flow Law approximates the viscous flow of ice with n = 4.1 ± 0.4 in fast-flowing areas. The viscosity and flow rate of ice are therefore more sensitive to changes in stress than most ice-flow models allow. By calibrating the governing equation of ice deformation, our result is a pathway towards improving projections of future glacier change.
    Description: .D.M. was partially funded through an NSF Graduate Research Fellowship. J.D.M. and B.M.M. where partially funded through NSF-NERC award 1853918. B.M.M. received additional funding through NSF-NERC award 1739031.
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    Microbiomes in the Challenger Deep slope and bottom-axis sediments (2022)
    Nature Research
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    Publication Date: 2022-07-15
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zhou, Y.-L., Mara, P., Cui, G.-J., Edgcomb, V., & Wang, Y. Microbiomes in the Challenger Deep slope and bottom-axis sediments. Nature Communications, 13(1), (2022): 1515, https://doi.org/10.1038/s41467-022-29144-4.
    Description: Hadal trenches are the deepest and most remote regions of the ocean. The 11-kilometer deep Challenger Deep is the least explored due to the technical challenges of sampling hadal depths. It receives organic matter and heavy metals from the overlying water column that accumulate differently across its V-shaped topography. Here, we collected sediments across the slope and bottom-axis of the Challenger Deep that enable insights into its in situ microbial communities. Analyses of 586 metagenome-assembled genomes retrieved from 37 metagenomes show distinct diversity and metabolic capacities between bottom-axis and slope sites. 26% of prokaryotic 16S rDNA reads in metagenomes were novel, with novelty increasing with water and sediment depths. These predominantly heterotrophic microbes can recycle macromolecules and utilize simple and complex hydrocarbons as carbon sources. Metagenome and metatranscriptome data support reduction and biotransformation of arsenate for energy gain in sediments that present a two-fold greater accumulation of arsenic compared to non-hadal sites. Complete pathways for anaerobic ammonia oxidation are predominantly identified in genomes recovered from bottom-axis sediments compared to slope sites. Our results expand knowledge of microbially-mediated elemental cycling in hadal sediments, and reveal differences in distribution of processes involved in nitrogen loss across the trench.
    Description: This study was supported by the Strategic Priority Research Program B of the Chinese Academy of Sciences (No. XDB06010201 to Y.W.).
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    Evaluation of sxtA and rDNA qPCR assays through monitoring of an inshore bloom of Alexandrium catenella Group 1 (2019)
    Nature Research
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Murray, S. A., Ruvindy, R., Kohli, G. S., Anderson, D. M., & Brosnahan, M. L. Evaluation of sxtA and rDNA qPCR assays through monitoring of an inshore bloom of Alexandrium catenella Group 1. Scientific Reports, 9(1), (2019): 14532, doi:10.1038/s41598-019-51074-3.
    Description: Alexandrium catenella (formerly A. tamarense Group 1, or A. fundyense) is the leading cause of Paralytic Shellfish Poisoning in North and South America, Europe, Africa, Australia and Asia. The quantification of A.catenella via sxtA, a gene involved in Paralytic Shellfish Toxin synthesis, may be a promising approach, but has not been evaluated in situ on blooms of A. catenella, in which cell abundances may vary from not detectable to in the order of 106 cells L−1. In this study, we compared sxtA assay performance to a qPCR assay targeted to a species-specific region of ribosomal DNA (rDNA) and an established fluorescent in situ hybridization (FISH) microscopy method. Passing-Bablok regression analyses revealed the sxtA assay to overestimate abundances when 〈5 cell equivalents A. catenella DNA were analysed, but otherwise was closer to microscopy estimates than the rDNA assay, which overestimated abundance across the full range of concentrations analysed, indicative of a copy number difference between the bloom population and a culture used for assay calibration a priori. In contrast, the sxtA assay performed more consistently, indicating less copy number variation. The sxtA assay was generally reliable, fast and effective in quantifying A. catenella and was predictive of PST contamination of shellfish.
    Description: We thank the Australian Research Council for Funding (FT120100704). We thank Chowdhury Sarowar for the toxicity measurements, at the Sydney Institute of Marine Science. Support to MB and DA was provided by MIT Sea Grant (NA14OAR4170077) and the Woods Hole Center for Oceans and Human Health (National Science Foundation award OCE-1840381 and National Institute of Environmental Health Sciences award 1-P01-ES028938–01). We are grateful for assistance from David Kulis, Claire Mullen, and Isaac Rosenthal for assistance in the collection and processing of Salt Pond samples.
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    Decadal predictability of North Atlantic blocking and the NAO (2020)
    Nature Research
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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 Athanasiadis, P. J., Yeager, S., Kwon, Y. O., Bellucci, A., Smith, D. W., & Tibaldi, S. Decadal predictability of North Atlantic blocking and the NAO. Npj Climate and Atmospheric Science, 3(1), (2020): 20, doi:10.1038/s41612-020-0120-6.
    Description: Can multi-annual variations in the frequency of North Atlantic atmospheric blocking and mid-latitude circulation regimes be skilfully predicted? Recent advances in seasonal forecasting have shown that mid-latitude climate variability does exhibit significant predictability. However, atmospheric predictability has generally been found to be quite limited on multi-annual timescales. New decadal prediction experiments from NCAR are found to exhibit remarkable skill in reproducing the observed multi-annual variations of wintertime blocking frequency over the North Atlantic and of the North Atlantic Oscillation (NAO) itself. This is partly due to the large ensemble size that allows the predictable component of the atmospheric variability to emerge from the background chaotic component. The predictable atmospheric anomalies represent a forced response to oceanic low-frequency variability that strongly resembles the Atlantic Multi-decadal Variability (AMV), correctly reproduced in the decadal hindcasts thanks to realistic ocean initialization and ocean dynamics. The occurrence of blocking in certain areas of the Euro-Atlantic domain determines the concurrent circulation regime and the phase of known teleconnections, such as the NAO, consequently affecting the stormtrack and the frequency and intensity of extreme weather events. Therefore, skilfully predicting the decadal fluctuations of blocking frequency and the NAO may be used in statistical predictions of near-term climate anomalies, and it provides a strong indication that impactful climate anomalies may also be predictable with improved dynamical models.
    Description: This study received support by the Blue-Action project (European Union’s Horizon 2020 research and innovation program, #727852). A.B. was supported by the H2020 EUCP (grant no. GA 776613) project. S.Y. acknowledges the support of National Science Foundation (NSF) grants OPP-1737377 and OCE-1243015. NCAR is a major facility sponsored by NSF under Cooperative Agreement No. 1852977. The CESM-DPLE was generated using computational resources provided by the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract DE-AC02-05CH11231, as well as by an Accelerated Scientific Discovery grant for Cheyenne (https://doi.org/10.5065/D6RX99HX) that was awarded by NCAR’s Computational and Information Systems Laboratory. Y.-O.K. was supported by the DOE Regional and Global Model Analysis Program (DE-SC0019492), and the NSF Arctic Natural Science Program (OPP-1736738) and Climate and Large-scale Dynamics Program (AGS-1355339).
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    Baleen whale acoustic presence and behaviour at a Mid-Atlantic migratory habitat, the Azores Archipelago (2020)
    Nature Research
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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 Romagosa, M., Baumgartner, M., Cascão, I., Lammers, M. O., Marques, T. A., Santos, R. S., & Silva, M. A. Baleen whale acoustic presence and behaviour at a Mid-Atlantic migratory habitat, the Azores Archipelago. Scientific Reports, 10(1), (2020): 4766, doi: 10.1038/s41598-020-61849-8.
    Description: The identification of important areas during the annual life cycle of migratory animals, such as baleen whales, is vital for their conservation. In boreal springtime, fin and blue whales feed in the Azores on their way to northern latitudes while sei whales migrate through the archipelago with only occasional feeding. Little is known about their autumn or winter presence or their acoustic behaviour in temperate migratory habitats. This study used a 5-year acoustic data set collected by autonomous recorders in the Azores that were processed and analysed using an automated call detection and classification system. Fin and blue whales were acoustically present in the archipelago from autumn to spring with marked seasonal differences in the use of different call types. Diel patterns of calling activity were only found for fin whales with more calls during the day than night. Sei whales showed a bimodal distribution of acoustic presence in spring and autumn, corresponding to their expected migration patterns. Diel differences in sei whale calling varied with season and location. This work highlights the importance of the Azores as a migratory and wintering habitat for three species of baleen whales and provides novel information on their acoustic behaviour in a mid-Atlantic region.
    Description: This work was supported by Fundação para a Ciência e Tecnologia (FCT), Azores 2020 Operational Programme and Fundo Regional da Ciência e Tecnologia (FRCT) through research projects TRACE (PTDC/MAR/74071/2006), MAPCET (M2.1.2/F/012/2011) and AWARENESS (PTDC/BIA-BMA/30514/201), co-funded by FEDER, COMPETE, QREN, POPH, ERDF, ESF, the Lisbon Regional Operational Programme, and the Portuguese Ministry for Science and Education. Funding for publication fees was provided by Project AWARENESS (PTDC/BIA-BMA/30514/201). Okeanos R&D Centre is supported by FCT, through the strategic fund (UIDB/05634/2020). MR was supported by a DRCT doctoral grant (M3.1.a/F/028/2015) and MAS by an FCT-Investigator contract (IF/00943/2013). TAM thanks partial support by CEAUL (funded by FCT - Fundação para a Ciência e a Tecnologia, Portugal, through the project UID/MAT/00006/2013). We are grateful to Rui Prieto, Sérgio Gómez, Norberto Serpa, skilled skippers and crew that participated in the preparation and deployment of EARs at DOP/IMAR and to Ken Sexton and Michael Richlen for their roles in manufacturing the EARs. We are also grateful to Dr. Helena Silva for her feedback on statistical analysis.
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    Cover crops and chicken grazing in a winter fallow field improve soil carbon and nitrogen contents and decrease methane emissions (2020)
    Nature Research
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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 Zheng, H., Zhou, L., Wei, J., Tang, Q., Zou, Y., Tang, J., & Xu, H. Cover crops and chicken grazing in a winter fallow field improve soil carbon and nitrogen contents and decrease methane emissions. Scientific Reports, 10(1), (2020): 12607, doi:10.1038/s41598-020-69407-y.
    Description: Using symbiotic farming methods [cover crops and chicken grazing (+ C)] in a winter fallow field, we found that the soil organic matter and total nitrogen of the + C treatment were 5.2% and 26.6% higher, respectively, than those of a treatment with cover crops and no chicken grazing (− C). The annual rice grain yield of the + C treatment was 3.8% higher than that of the − C treatment and 12.3% higher than that of the bare fallow field (CK), while the annual CH4 emissions of the + C treatment were 26.9% lower than those of the − C treatment and 10.6% lower than those of the CK treatment. The 100-year global warming potential of the + C treatment was 6.2% lower than that of the − C treatment. Therefore, the use of winter cover crops and chicken grazing in a winter fallow field was effective at reducing CH4 emissions and significantly improving soil nutrients and rice yield.
    Description: This study was supported by the Earmarked Fund for China Agriculture Research System (CARS-01-26), the China-UK joint Red Soil Critical Zone project from the National Natural Science Foundation of China (Grant No. 41571130053), and Hunan “A Hundred Scholars” Program.
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    Genetic tool development in marine protists: emerging model organisms for experimental cell biology (2020)
    Nature Research
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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 Faktorova, D., Nisbet, R. E. R., Robledo, J. A. F., Casacuberta, E., Sudek, L., Allen, A. E., Ares, M., Jr., Areste, C., Balestreri, C., Barbrook, A. C., Beardslee, P., Bender, S., Booth, D. S., Bouget, F., Bowler, C., Breglia, S. A., Brownlee, C., Burger, G., Cerutti, H., Cesaroni, R., Chiurillo, M. A., Clemente, T., Coles, D. B., Collier, J. L., Cooney, E. C., Coyne, K., Docampo, R., Dupont, C. L., Edgcomb, V., Einarsson, E., Elustondo, P. A., Federici, F., Freire-Beneitez, V., Freyria, N. J., Fukuda, K., Garcia, P. A., Girguis, P. R., Gomaa, F., Gornik, S. G., Guo, J., Hampl, V., Hanawa, Y., Haro-Contreras, E. R., Hehenberger, E., Highfield, A., Hirakawa, Y., Hopes, A., Howe, C. J., Hu, I., Ibanez, J., Irwin, N. A. T., Ishii, Y., Janowicz, N. E., Jones, A. C., Kachale, A., Fujimura-Kamada, K., Kaur, B., Kaye, J. Z., Kazana, E., Keeling, P. J., King, N., Klobutcher, L. A., Lander, N., Lassadi, I., Li, Z., Lin, S., Lozano, J., Luan, F., Maruyama, S., Matute, T., Miceli, C., Minagawa, J., Moosburner, M., Najle, S. R., Nanjappa, D., Nimmo, I. C., Noble, L., Vanclova, A. M. G. N., Nowacki, M., Nunez, I., Pain, A., Piersanti, A., Pucciarelli, S., Pyrih, J., Rest, J. S., Rius, M., Robertson, D., Ruaud, A., Ruiz-Trillo, I., Sigg, M. A., Silver, P. A., Slamovits, C. H., Smith, G. J., Sprecher, B. N., Stern, R., Swart, E. C., Tsaousis, A. D., Tsypin, L., Turkewitz, A., Turnsek, J., Valach, M., Verge, V., von Dassow, P., von der Haar, T., Waller, R. F., Wang, L., Wen, X., Wheeler, G., Woods, A., Zhang, H., Mock, T., Worden, A. Z., & Lukes, J. Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nature Methods, 17, (2020): 481-494, doi:10.1038/s41592-020-0796-x.
    Description: Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species, which do not represent eukaryotic diversity or environmentally relevant taxa. Here, we report on the development of genetic tools in a range of protists primarily from marine environments. We present evidence for foreign DNA delivery and expression in 13 species never before transformed and for advancement of tools for eight other species, as well as potential reasons for why transformation of yet another 17 species tested was not achieved. Our resource in genetic manipulation will provide insights into the ancestral eukaryotic lifeforms, general eukaryote cell biology, protein diversification and the evolution of cellular pathways.
    Description: We thank M. Salisbury and D. Lacono, C. Poirier, M. Hamilton, C. Eckmann, H. Igel, C. Yung and K. Hoadley for assistance; V.K. Nagarajan, M. Accerbi and P.J. Green who carried out Agrobacterium studies in Heterosigma akashiwo, and N. Kraeva, C. Bianchi and V. Yurchenko for the help with designing the p57-V5+NeoR construct. We are also grateful to the protocols.io team (L. Teytelman and A. Broellochs) for their support. This collaborative effort was supported by the Gordon and Betty Moore Foundation EMS Program of the Marine Microbiology Initiative (grant nos. GBMF4972 and 4972.01 to F.-Y.B.; GBMF4970 and 4970.01 to M.A. and A.Z.W.; GBMF3788 to A.Z.W.; GBMF 4968 and 4968.01 to H.C.; GBMF4984 to V.H.; GBMF4974 and 4974.01 to C. Brownlee; GBMF4964 to Y. Hirakawa; GBMF4961 to T. Mock; GBMF4958 to P.S.; GBMF4957 to A.T.; GBMF4960 to G.J.S.; GBMF4979 to K.C.; GBMF4982 and 4982.01 to J.L.C.; GBMF4964 to P.J.K.; GBMF4981 to P.v.D.; GBMF5006 to A.E.A.; GBMF4986 to C.M.; GBMF4962 to J.A.F.R.; GBMF4980 and 4980.01 to S.L.; GBMF 4977 and 4977.01 to R.F.W.; GBMF4962.01 to C.H.S.; GBMF4985 to J.M.; GBMF4976 and 4976.01 to C.H.; GBMF4963 and 4963.01 to V.E.; GBMF5007 to C.L.D.; GBMF4983 and 4983.01 to J.L.; GBMF4975 and 4975.01 to A.D.T.; GBMF4973 and 4973.01 to I.R.-T. and GBMF4965 to N.K.), by The Leverhulme Trust (RPG-2017-364) to T. Mock and A. Hopes, and by ERD funds (16_019/0000759) from the Czech Ministry of Education to J.L.
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