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  • 1
    Publication Date: 2022-10-26
    Description: Author Posting. © American Geophysical Union, 2019. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 46(12), (2019): 6745-6754, doi:10.1029/2019GL082867.
    Description: Although photochemical oxidation is an environmental process that drives organic carbon (OC) cycling, its quantitative detection remains analytically challenging. Here, we use samples from the Deepwater Horizon oil spill to test the hypothesis that the stable oxygen isotope composition of oil (δ18OOil) is a sensitive marker for photochemical oxidation. In less than one‐week, δ18OOil increased from −0.6 to 7.2‰, a shift representing ~25% of the δ18OOC dynamic range observed in nature. By accounting for different oxygen sources (H2O or O2) and kinetic isotopic fractionation of photochemically incorporated O2, which was −9‰ for a wide range of OC sources, a mass balance was established for the surface oil's elemental oxygen content and δ18O. This δ18O‐based approach provides novel insights into the sources and pathways of hydrocarbon photo‐oxidation, thereby improving our understanding of the fate and transport of petroleum hydrocarbons in sunlit waters, and our capacity to respond effectively to future spills.
    Description: We thank Robert Ricker and Greg Baker (NOAA) for helping secure the oil residues, James Payne (Payne Environmental Consultants, Inc.) for collecting many of the surface oil residues, Joy Matthews (UC Davis) for exceptional assistance in preparing and analyzing the oil residues for oxygen content and isotopes, Hank Levi and Art Gatenby at CSC Scientific Company for assistance with the water content measurements, Robyn Comny (US EPA) for providing the Alaska North Slope oil, and Rose Cory (UMich) for discussions about our findings. Special thanks to John Hayes who provided constructive feedback on a preliminary version of this dataset prior to his passing in February of 2017. We thank Alex Sessions (CalTech) for his constructive feedback during the review process. This work was supported, in part, by National Science Foundation grants RAPID OCE‐1043976 (CMR), OCE‐1333148 (CMR), OCE‐1333026 (CMS), OCE‐1333162 (DLV), OCE‐1841092 (CPW), NASA NESSF NNX15AR62H (KMS), the Gulf of Mexico Research Initiative grants ‐ 015, SA 16‐30, and DEEP‐C consortium, a fellowship through the Hansewissenschaftskolleg (Institute for Advanced Studies) to SDW, and assistant scientist salary support from the Frank and Lisina Hoch Endowed Fund (CPW).
    Description: 2019-11-30
    Keywords: Petroleum hydrocarbons ; Photochemical oxidation ; Deepwater Horizon ; Stable oxygen isotopes ; Organic carbon
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 2
    Publication Date: 2022-10-21
    Description: The Hunting Bubbles Cruise took place in August-September 2018 on the R/V Falkor (cruise ID 180824). Ship time was provided by the Schmidt Ocean Institute. This cruise investigated transport of methane from seeps located on the Cascadia Margin. Data archived at the WHOAS repository supplements additional data from this cruise available at the R2R rolling deck to repository and at MGDS: Marine Geoscience Data System.
    Keywords: Methane ; Bubbles ; Seeps
    Repository Name: Woods Hole Open Access Server
    Type: Dataset
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  • 3
    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 Long, M. H., Sutherland, K., Wankel, S. D., Burdige, D. J., & Zimmerman, R. C. Ebullition of oxygen from seagrasses under supersaturated conditions. Limnology and Oceanography, (2019), doi:10.1002/lno.11299.
    Description: Gas ebullition from aquatic systems to the atmosphere represents a potentially important fraction of primary production that goes unquantified by measurements of dissolved gas concentrations. Although gas ebullition from photosynthetic surfaces has often been observed, it is rarely quantified. The resulting underestimation of photosynthetic activity may significantly bias the determination of ecosystem trophic status and estimated rates of biogeochemical cycling from in situ measures of dissolved oxygen. Here, we quantified gas ebullition rates in Zostera marina meadows in Virginia, U.S.A. using simple funnel traps and analyzed the oxygen concentration and isotopic composition of the captured gas. Maximum hourly rates of oxygen ebullition (3.0 mmol oxygen m−2 h−1) were observed during the coincidence of high irradiance and low tides, particularly in the afternoon when oxygen and temperature maxima occurred. The daily ebullition fluxes (up to 11 mmol oxygen m−2 d−1) were roughly equivalent to net primary production rates determined from dissolved oxygen measurements indicating that bubble ebullition can represent a major component of primary production that is not commonly included in ecosystem‐scale estimates. Oxygen content comprised 20–40% of the captured bubble gas volume and correlated negatively with its δ18O values, consistent with a predominance of mixing between the higher δ18O of atmospheric oxygen in equilibrium with seawater and the lower δ18O of oxygen derived from photosynthesis. Thus, future studies interested in the metabolism of highly productive, shallow water ecosystems, and particularly those measuring in situ oxygen flux, should not ignore the bubble formation and ebullition processes described here.
    Description: Two anonymous reviewers provided thoughtful contributions that improved this manuscript. We thank Miraflor Santos, Victoria Hill, David Ruble, Jeremy Bleakney, and Brian Collister for assistance in the field and the staff of the Anheuser‐Busch Coastal Research Center for logistical support. This work was supported by NSF OCE grants 1633951 (to MHL) and 1635403 (to RCZ and DJB), NASA Fellowship NESSF NNX15AR62H (to KS), and a fellowship from the Hansewissenschaftskolleg (Institute for Advanced Studies; to SDW).
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 4
    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 ISME Journal (2019), doi:10.1038/s41396-019-0373-4.
    Description: The benthos in estuarine environments often experiences periods of regularly occurring hypoxic and anoxic conditions, dramatically impacting biogeochemical cycles. How oxygen depletion affects the growth of specific uncultivated microbial populations within these diverse benthic communities, however, remains poorly understood. Here, we applied H218O quantitative stable isotope probing (qSIP) in order to quantify the growth of diverse, uncultured bacterial populations in response to low oxygen concentrations in estuarine sediments. Over the course of 7- and 28-day incubations with redox conditions spanning from hypoxia to euxinia (sulfidic), 18O labeling of bacterial populations exhibited different patterns consistent with micro-aerophilic, anaerobic, facultative anaerobic, and aerotolerant anaerobic growth. 18O-labeled populations displaying anaerobic growth had a significantly non-random phylogenetic distribution, exhibited by numerous clades currently lacking cultured representatives within the Planctomycetes, Actinobacteria, Latescibacteria, Verrucomicrobia, and Acidobacteria. Genes encoding the beta-subunit of the dissimilatory sulfate reductase (dsrB) became 18O labeled only during euxinic conditions. Sequencing of these 18O-labeled dsrB genes showed that Acidobacteria were the dominant group of growing sulfate-reducing bacteria, highlighting their importance for sulfur cycling in estuarine sediments. Our findings provide the first experimental constraints on the redox conditions underlying increased growth in several groups of “microbial dark matter”, validating hypotheses put forth by earlier metagenomic studies.
    Description: This work was supported by a grant OR 417/1-1 from the Deutsche Forschungsgemeinschaft, and a Junior Researcher Fund grant from LMU Munich to WDO. This work was performed in part, through the Master’s Program in Geobiology and Paleontology (MGAP) at LMU Munich.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 5
    Publication Date: 2022-06-10
    Description: Author Posting. © American Geophysical Union, 2018. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Isotopic constraints on nitrogen transformation rates in the deep sedimentary marine biosphere. Global Biogeochemical Cycles, 32, (2018):1688–1702., doi: 10.1029/2018GB005948.
    Description: Little is known about the nature of microbial community activity contributing to the cycling of nitrogen in organic-poor sediments underlying the expansive oligotrophic ocean gyres. Here we use pore water concentrations and stable N and O isotope measurements of nitrate and nitrite to constrain rates of nitrogen cycling processes over a 34-m profile from the deep North Atlantic spanning fully oxic to anoxic conditions. Using a 1-D reaction-diffusion model to predict the distribution of nitrogen cycling rates, results converge on two distinct scenarios: (1) an exceptionally high degree of coupling between nitrite oxidation and nitrate reduction near the top of the anoxic zone or (2) an unusually large N isotope effect (~60‰) for nitrate reduction that is decoupled from the corresponding O isotope effect, which is possibly explained by enzyme-level interconversion between nitrite and nitrate.
    Description: Samples analyzed for this study were collected during the final expedition of the RV Knorr, KN223. The expedition would not have been possible without the captain and crew of the RV Knorr and the efforts of the shipboard science party. We would like to acknowledge Robert Pockalny for planning and facilitating the expedition. Inorganic geochemistry sample collection, processing, and analysis were performed shipboard by Arthur Spivack,Dennis Graham, Chloe Anderson, Emily Estes, Kira Homola, Claire McKinley, Theodore Present, and Justine Sauvage. Coring capabilities were provided by the Oregon State University and Woods Hole Oceanographic Institute Coring Facilities, directed and funded by the U. S. National Science Foundation (NSF) Ship Facilities Program. The cored materials and discrete samples from the expedition are curated and stored by the Marine Geological Samples Laboratory at the University of Rhode Island, codirected by Rebecca Robinson and Katherine Kelly and funded by the NSF Ocean Sciences Division. The nutrient and isotope data from pore waters in this study will be available at The Biological and Chemical Data Management Office (https://www.bcodmo.org/project/567401). This project was partially funded by an NSF CDEBI postdoctoral fellowship to C. Buchwald. Portions of this material are based upon work supported while R. W. M. was serving at the National Science Foundation.
    Description: 2019-04-18
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 6
    Publication Date: 2022-05-26
    Description: Author Posting. © American Geophysical Union, 2019. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 46(12), (2019): 6786-6795, doi:10.1029/2019GL082075.
    Description: Denitrification in the anoxic sediments of the Santa Barbara Basin has been well documented in the historic and modern record, but the regulation of and frequency with which denitrification occurs in the overlying water column are less understood. Since 2004, the magnitude and speciation of redox active nitrogen species in bottom waters have changed markedly. Most notable are periods of decreased nitrate and increased nitrite concentrations. Here we examine these changes in nitrogen cycling as recorded by the stable isotopes of dissolved nitrate from 2010–2016. When compared to previous studies, our data identify an increase in water column denitrification in the bottom waters of the basin. Observations from inside the basin as well as data from the wider California Current Ecosystem implicate a long‐term trend of decreasing oxygen concentrations as the driver for these observed changes, with ramifications for local benthic communities and regional nitrogen loss.
    Description: We thank CalCOFI and Shonna Dovel for sample collection and two anonymous reviewers for improving the manuscript. Thanks also to Daniel Sigman for useful discussions, and Zoe Sandwith and Jen Karolewski for help with sample analysis. Data sets presented here were supported in part by CCE‐LTER augmented funding (NSF grant OCE‐1026607). Additional funding came from the Edna Bailey Sussman Foundation and the San Diego Foundation Blasker Environment grant. All data can be accessed at http://calcofi.org and https://oceaninformatics.ucsd.edu/datazoo/catalogs/ccelter/datasets. SDW acknowledges the support of a fellowship through the Hanse‐Wissenschaftskolleg (Institute for Advanced Studies).
    Description: 2019-12-11
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 7
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).. The definitive version was published in Vuillemin, A., Wankel, S. D., Coskun, Ö. K., Magritsch, T., Vargas, S., Estes, E. R., Spivack, A. J., Smith, D. C., Pockalny, R., Murray, R. W., D'Hondt, S., & Orsi, W. D. Archaea dominate oxic subseafloor communities over multimillion-year time scales. Science Advances, 5(6), (2019): eaaw4108, doi: 10.1126/sciadv.aaw4108.
    Description: Ammonia-oxidizing archaea (AOA) dominate microbial communities throughout oxic subseafloor sediment deposited over millions of years in the North Atlantic Ocean. Rates of nitrification correlated with the abundance of these dominant AOA populations, whose metabolism is characterized by ammonia oxidation, mixotrophic utilization of organic nitrogen, deamination, and the energetically efficient chemolithoautotrophic hydroxypropionate/hydroxybutyrate carbon fixation cycle. These AOA thus have the potential to couple mixotrophic and chemolithoautotrophic metabolism via mixotrophic deamination of organic nitrogen, followed by oxidation of the regenerated ammonia for additional energy to fuel carbon fixation. This metabolic feature likely reduces energy loss and improves AOA fitness under energy-starved, oxic conditions, thereby allowing them to outcompete other taxa for millions of years.
    Description: This work was supported primarily by the Deutsche Forschungsgemeinschaft (DFG) project OR 417/1-1 granted to W.D.O. Preliminary work was supported by the Center for Dark Energy Biosphere Investigations project OCE-0939564 also granted to W.D.O. Publication of the manuscript was supported by the LMU Mentoring Program. The expedition was funded by the US National Science Foundation through grant NSF-OCE-1433150 to A.J.S, S.D., and R.P. R.W.M. led the expedition. This is a contribution of the Deep Carbon Observatory (DCO). S.D.W. acknowledges partial support from NASA Exobiology (NNX15AM04G). This is Center for Dark Energy Biosphere Investigations (C-DEBI) publication number 463. Portions of this material are based on work supported while R.W.M. was serving at the National Science Foundation. A portion of this work was performed as part of the LMU Masters Program “Geobiology and Paleobiology” (MGAP).
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 8
    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 Sutherland, K. M., Coe, A., Gast, R. J., Plummer, S., Suffridge, C. P., Diaz, J. M., Bowman, J. S., Wankel, S. D., & Hansel, C. M. Extracellular superoxide production by key microbes in the global ocean. Limnology and Oceanography, (2019), doi:10.1002/lno.11247.
    Description: Bacteria and eukaryotes produce the reactive oxygen species superoxide both within and outside the cell. Although superoxide is typically associated with the detrimental and sometimes fatal effects of oxidative stress, it has also been shown to be involved in a range of essential biochemical processes, including cell signaling, growth, differentiation, and defense. Light‐independent extracellular superoxide production has been shown to be widespread among many marine heterotrophs and phytoplankton, but the extent to which this trait is relevant to marine microbial physiology and ecology throughout the global ocean is unknown. Here, we investigate the dark extracellular superoxide production of five groups of organisms that are geographically widespread and represent some of the most abundant organisms in the global ocean. These include Prochlorococcus, Synechococcus, Pelagibacter, Phaeocystis, and Geminigera. Cell‐normalized net extracellular superoxide production rates ranged seven orders of magnitude, from undetectable to 14,830 amol cell−1 h−1, with the cyanobacterium Prochlorococcus being the lowest producer and the cryptophyte Geminigera being the most prolific producer. Extracellular superoxide production exhibited a strong inverse relationship with cell number, pointing to a potential role in cell signaling. We demonstrate that rapid, cell‐number–dependent changes in the net superoxide production rate by Synechococcus and Pelagibacter arose primarily from changes in gross production of extracellular superoxide, not decay. These results expand the relevance of dark extracellular superoxide production to key marine microbes of the global ocean, suggesting that superoxide production in marine waters is regulated by a diverse suite of marine organisms in both dark and sunlit waters.
    Description: The authors would like to acknowledge their funding sources including NASA NESSF NNX15AR62H (K.M.S.), NASA Exobiology grant NNX15AM04G to S.D.W. and C.M.H., NSF‐OCE grant 1355720 to C.M.H., NSF‐OPP 1641019 (J.S.B), and Simons Foundation SCOPE Award ID 329108 (Sallie W. Chisholm). The authors would also like to thank the Harvey lab (Skidaway Institute of Oceanography) for use of their flow cytometer in this study. We thank Stephen Giovannoni and Sallie Chisholm for providing bacteria strains and laboratory facilities. Additional thanks to Marianne Acker, Rogier Braakman, and Aldo Arellano for assistance in lab and helpful conversations.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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