Dark biological superoxide production as a significant flux and sink of marine dissolved oxygen

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sutherland, K. M., Wankel, S. D., & Hansel, C. M. Dark biological superoxide production as a significant flux and sink of marine dissolved oxygen. Proceedings of the National Academy of Sciences of the United States of America, 117(7), (2020): 3433-3439, doi:10.1073/pnas.1912313117.The balance between sources and sinks of molecular oxygen in the oceans has greatly impacted the composition of Earth’s atmosphere since the evolution of oxygenic photosynthesis, thereby exerting key influence on Earth’s climate and the redox state of (sub)surface Earth. The canonical source and sink terms of the marine oxygen budget include photosynthesis, respiration, photorespiration, the Mehler reaction, and other smaller terms. However, recent advances in understanding cryptic oxygen cycling, namely the ubiquitous one-electron reduction of O2 to superoxide by microorganisms outside the cell, remains unexplored as a potential player in global oxygen dynamics. Here we show that dark extracellular superoxide production by marine microbes represents a previously unconsidered global oxygen flux and sink comparable in magnitude to other key terms. We estimate that extracellular superoxide production represents a gross oxygen sink comprising about a third of marine gross oxygen production, and a net oxygen sink amounting to 15 to 50% of that. We further demonstrate that this total marine dark extracellular superoxide flux is consistent with concentrations of superoxide in marine environments. These findings underscore prolific marine sources of reactive oxygen species and a complex and dynamic oxygen cycle in which oxygen consumption and corresponding carbon oxidation are not necessarily confined to cell membranes or exclusively related to respiration. This revised model of the marine oxygen cycle will ultimately allow for greater reconciliation among estimates of primary production and respiration and a greater mechanistic understanding of redox cycling in the ocean.This work was supported by NASA Earth and Space Science Fellowship NNX15AR62H to K.M.S., NASA Exobiology grant NNX15AM04G to S.D.W. and C.M.H., and NSF Division of Ocean Sciences grant 1355720 to C.M.H. This research was further supported in part by Hanse-Wissenschaftskolleg Institute of Advanced Study fellowships to C.M.H. and S.D.W. We thank Danielle Hicks for assistance with figures and Community Earth Systems Model (CESM) Large Ensemble Project for the availability and use of its data product. The CESM project is primarily supported by the NSF

Enriched Iron(III)-Reducing Bacterial Communities are Shaped by Carbon Substrate and Iron Oxide Mineralogy

Iron (Fe) oxides exist in a spectrum of structures in the environment, with ferrihydrite widely considered the most bioavailable phase. Yet, ferrihydrite is unstable and rapidly transforms to more crystalline Fe(III) oxides (e.g., goethite, hematite), which are poorly reduced by model dissimilatory Fe(III)-reducing microorganisms. This begs the question, what processes and microbial groups are responsible for reduction of crystalline Fe(III) oxides within sedimentary environments? Further, how do changes in Fe mineralogy shape oxide-hosted microbial populations? To address these questions, we conducted a large-scale cultivation effort using various Fe(III) oxides (ferrihydrite, goethite, hematite) and carbon substrates (glucose, lactate, acetate) along a dilution gradient to enrich for microbial populations capable of reducing Fe oxides spanning a wide range of crystallinities and reduction potentials. While carbon source was the most important variable shaping community composition within Fe(III)-reducing enrichments, both Fe oxide type and sediment dilution also had a substantial influence. For instance, with acetate as the carbon source, only ferrihydrite enrichments displayed a significant amount of Fe(III) reduction and the well-known dissimilatory metal reducer Geobacter sp. was the dominant organism enriched. In contrast, when glucose and lactate were provided, all three Fe oxides were reduced and reduction coincided with the presence of fermentative (e.g., Enterobacter spp.) and sulfate-reducing bacteria (e.g., Desulfovibrio spp.). Thus, changes in Fe oxide structure and resource availability may shift Fe(III)-reducing communities between dominantly metal-respiring to fermenting and/or sulfate-reducing organisms which are capable of reducing more recalcitrant Fe phases. These findings highlight the need for further targeted investigations into the composition and activity of speciation-directed metal-reducing populations within natural environments.Engineering and Applied Science

Enriched iron(III)-reducing bacterial communities are shaped by carbon substrate and iron oxide mineralogy

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 3 (2012): 404, doi:10.3389/fmicb.2012.00404.Iron (Fe) oxides exist in a spectrum of structures in the environment, with ferrihydrite widely considered the most bioavailable phase. Yet, ferrihydrite is unstable and rapidly transforms to more crystalline Fe(III) oxides (e.g., goethite, hematite), which are poorly reduced by model dissimilatory Fe(III)-reducing microorganisms. This begs the question, what processes and microbial groups are responsible for reduction of crystalline Fe(III) oxides within sedimentary environments? Further, how do changes in Fe mineralogy shape oxide-hosted microbial populations? To address these questions, we conducted a large-scale cultivation effort using various Fe(III) oxides (ferrihydrite, goethite, hematite) and carbon substrates (glucose, lactate, acetate) along a dilution gradient to enrich for microbial populations capable of reducing Fe oxides spanning a wide range of crystallinities and reduction potentials. While carbon source was the most important variable shaping community composition within Fe(III)-reducing enrichments, both Fe oxide type and sediment dilution also had a substantial influence. For instance, with acetate as the carbon source, only ferrihydrite enrichments displayed a significant amount of Fe(III) reduction and the well-known dissimilatory metal reducer Geobacter sp. was the dominant organism enriched. In contrast, when glucose and lactate were provided, all three Fe oxides were reduced and reduction coincided with the presence of fermentative (e.g., Enterobacter spp.) and sulfate-reducing bacteria (e.g., Desulfovibrio spp.). Thus, changes in Fe oxide structure and resource availability may shift Fe(III)-reducing communities between dominantly metal-respiring to fermenting and/or sulfate-reducing organisms which are capable of reducing more recalcitrant Fe phases. These findings highlight the need for further targeted investigations into the composition and activity of speciation-directed metal-reducing populations within natural environments.This work was supported by a National Science Foundation Graduate Research Fellowship under grant no. DGE-0946799 and DGE-1144152 awarded to Christopher J. Lentini

Quantifying population-specific growth in benthic bacterial communities under low oxygen using H218O

© 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.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.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

Isotopic constraints on nitrogen transformation rates in the deep sedimentary marine biosphere

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.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.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.2019-04-1

Spectroscopic insights into ferromanganese crust formation and diagenesis

Author Posting. © American Geophysical Union, 2020. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry, Geophysics, Geosystems 21(11), (2020): e2020GC009074, doi:10.1029/2020GC009074.Marine ferromanganese deposits, often called the scavengers of the sea, adsorb and coprecipitate with a wide range of metals of great interest for paleo‐environmental reconstructions and economic geology. The long (up to ∼75 Ma), near‐continuous record of seawater chemistry afforded by ferromanganese deposits offers much historical information about the global ocean and surface earth including crustal processes, mantle processes, ocean circulation, and biogeochemical cycles. The extent to which the ferromanganese deposits hosting these geochemical proxies undergo diagenesis on the seafloor, however, remains an important and challenging factor in assessing the fidelity of such records. In this study, we employ multiple X‐ray techniques including micro–X‐ray fluorescence, bulk and micro–X‐ray absorption spectroscopy, and X‐ray powder diffraction to probe the structural, compositional, redox, and mineral changes within a single ferromanganese crust. These techniques illuminate a complex two‐dimensional structure characterized by crust growth controlled by the availability of manganese (Mn), a dynamic range in Mn oxidation state from +3.4 to +4.0, changes in Mn mineralogy over time, and recrystallization in the lower phosphatized portions of the crust. Iron (Fe) similarly demonstrates spatial complexity with respect to concentration and mineralogy, but lacks the dynamic range of oxidation state seen for Mn. Micrometer‐scale measurements of metal abundances reveal complex element associations between trace elements and the two major oxide phases, which are not typically resolvable via bulk analytical methods. These findings provide evidence of post‐depositional processes altering chemistry and mineralogy, and provide important geochemical context for the interpretation of element and isotopic records in ferromanganese crusts.This research is supported by NASA Exobiology NNX15AM046 to Scott D. Wankel and Colleen M. Hansel, NASA NESSF NNX15AR62H to Kevin M. Sutherland, and WHOI Ocean Exploration Institute to Colleen M. Hansel. The Stanford Synchrotron Radiation Lightsource was utilized in this study. Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE‐AC02‐76SF00515.2021-04-2

Ebullition of Oxygen From Seagrasses Under Supersaturated Conditions

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

Nitrite oxidation exceeds reduction and fixed nitrogen loss in anoxic Pacific waters

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Babbin, A. R., Buchwald, C., Morel, F. M. M., Wankel, S. D., & Ward, B. B. Nitrite oxidation exceeds reduction and fixed nitrogen loss in anoxic Pacific waters. Marine Chemistry, 224, (2020): 103814, doi:10.1016/j.marchem.2020.103814.The diversity of nitrogen-based dissimilatory metabolisms in anoxic waters continues to increase with additional studies to the marine oxygen deficient zones (ODZs). Although the microbial oxidation of nitrite (NO2–) has been known for over a century, studies of the pathways and microbes involved have generally proceeded under the assumption that nitrite oxidation to nitrate requires dioxygen (O2). Anaerobic NO2– oxidation until now has been conclusively shown only for anammox bacteria, albeit only as a limited sink for NO2– in their metabolism compared to the NO2– reduced to N2. Here, using direct experimental techniques optimized for replicating in situ anoxic conditions, we show that NO2– oxidation is substantial, widespread, and consistent across the ODZs of the eastern tropical Pacific Ocean. Regardless of the specific oxidant, NO2– oxidation rates are up to an order of magnitude larger than simultaneous N2 production rates for which these zones are known, and cannot be explained by anammox rates alone. Higher rates of NO2– oxidation over reduction in anoxic waters are paradoxical but help to explain how anammox rates can be enhanced over denitrification in shallow anoxic waters (σθ < 26.4) at the edge of the ODZs but not within the ODZ core. Furthermore, nitrite oxidation may be the key to reconciliation of the perceived imbalance of the global fixed nitrogen loss budget.This work was funded by National Science Foundation grants OCE–1029951 to B.B.W, BIO–1402109 to A.R.B., and OCE-1260373 to S.D.W. Additional financial support to A.R.B. was provided by Simons Foundation grant 622065 and the generous contributions of Dr. Bruce L. Heflinger

Recent increases in water column denitrification in the seasonally suboxic bottom waters of the Santa Barbara Basin

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.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.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).2019-12-1