Heterotrophic bacteria exhibit a wide range of rates of extracellular production and decay of hydrogen peroxide

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bond, R. J., Hansel, C. M., & Voelker, B. M. Heterotrophic bacteria exhibit a wide range of rates of extracellular production and decay of hydrogen peroxide. Frontiers in Marine Science, 7, (2020): 72, doi:10.3389/fmars.2020.00072.Bacteria have been implicated as both a source and sink of hydrogen peroxide (H2O2), a reactive oxygen species which can both impact microbial growth and participate in the geochemical cycling of trace metals and carbon in natural waters. In this study, simultaneous H2O2 production and decay by twelve species of heterotrophic bacteria were evaluated in both batch and flow-through incubations. While wide species-to-species variability of cell-normalized H2O2 decay rate coefficients [2 × 10–8 to 5 × 10–6 hr–1 (cell mL–1)–1] was observed, these rate coefficients were relatively consistent for a given bacterial species. By contrast, observed production rates (below detection limit to 3 × 102 amol cell–1 hr–1) were more variable even for the same species. Variations based on incubation conditions in some bacterial strains suggest that external conditions may impact extracellular H2O2 levels either through increased extracellular production or leakage of intracellular H2O2. Comparison of H2O2 production rates to previously determined superoxide (O2–) production rates suggests that O2– and H2O2 production are not necessarily linked. Rates measured in this study indicate that bacteria could account for a majority of H2O2 decay observed in aqueous systems but likely only make a modest contribution to dark H2O2 production.This research was supported by NSF grant OCE-1131734/1246174 to BV and CH

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

© 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

The spatial and temporal variability of Mn speciation in the coastal Northwest Atlantic Ocean

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 Journal of Geophysical Research-Oceans 125(1),(2020): e2019JC015167, doi:10.1029/2019JC015167.Manganese (Mn) is distributed widely throughout the global ocean, where it cycles between three oxidation states that each play important biogeochemical roles. The speciation of Mn in seawater was previously operationally defined on filtration, with soluble Mn presumed to be Mn(II) and solid‐phase Mn as Mn(III/IV) oxides. Recent findings of abundant soluble Mn(III) complexes (Mn(III)‐L) highlights the need to reexamine the redox cycling of Mn, as these complexes can donate or accept electrons. To better understand the complex cycling of Mn in coastal waters, the distribution of Mn species at four Northwest Atlantic sites with different characteristics was examined. Diurnal influences on Mn speciation were investigated within a productive site. At all sites, Mn(III)‐L complexes dominated, particularly in surface waters, and Mn oxides were low in abundance in surface waters but high in bottom waters. Despite intrasite similarities, Mn speciation was highly variable between our stations, emphasizing the diverse processes that impact Mn redox. Diel Mn measurements revealed that the cycling of Mn is also highly variable over time, even on time scales as short as hours. We observed a change of over 100 nM total Mn over 17 hrs and find that speciation changed drastically. These changes could include contributions from biological, light‐mediated, and/or abiotic mechanisms but more likely point to the importance of lateral mixing at coastal sites. This exploration demonstrates the spatial and temporal variability of the Mn redox cycle and indicates that single timepoint vertical profiling is not sufficient when describing the geochemistry of dynamic coastal systems.This work was funded by grants from the Chemical Oceanography program of the National Science Foundation (OCE‐1355720 to CMH and CHL). Véronique Oldham thanks Woods Hole Oceanographic Institution for the receipt of the WHOI Postdoctoral Scholarship. Thanks also to Kevin Sutherland, Jen Karolweski, Gabriella Farfan, Kalina Grabb, Kaitlin Bowman, Alison Agather, and Lindsey Starr for the shipboard sampling assistance, as well as the captain and crew of the R/V Endeavor who made the sampling for this research possible. All data presented in the manuscript are available through the Biological and Chemical Oceanography Data Management Office (BCO‐DMO) under Project 756930 at the following link (https://www.bco‐dmo.org/project/756930).2020-06-2

Coupled x-ray fluorescence and x-ray absorption spectroscopy for microscale imaging and identification of sulfur species within tissues and skeletons of scleractinian corals

Author Posting. © The Author(s), 2018. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Analytical Chemistry 90 (2018): 12559–12566, doi:10.1021/acs.analchem.8b02638.Identifying and mapping the wide range of sulfur species within complex matrices presents a challenge for under-standing the distribution of these important biomolecules within environmental and biological systems. Here, we present a coupled micro X-ray fluorescence (μXRF) and X-ray absorption near edge structure (XANES) spectroscopy method for determining the presence of specific sulfur species in coral tissues and skeletons at high spatial resolution. By using multiple energy stacks and principal component analysis of a large spectral database, we were able to more accurately identify sulfur species components and distinguish different species and distributions of sulfur formerly unresolved by previous studies. Specifically, coral tissues were domi-nated by more reduced sulfur species, such as glutathione disulfide, cysteine and sulfoxide, as well as organic sulfate as represented by chondroitin sulfate. Sulfoxide distributions were visually correlated with the presence of zooxanthellae endosymbionts. Coral skeletons were composed primarily of carbonate-associated sulfate (CAS), along with minor contributions from organic sulfate and a separate inorganic sulfate likely in the form of adsorbed sulfate. This coupled XRF-XANES approach allows for a more accurate and informative view of sulfur within biological systems in situ, and holds great promise for pairing with other techniques to allow for a more encompassing understanding of elemental distributions within the environment.We thank Ray Dalio for funding the Micronesian expedition and K. Hughen,This material is based upon work supported by the Na-tional Science Foundation Graduate Research Fellowship under Grant No. 1122374 and a Ford Foundation Dissertation Fellowship for Gabriela Farfan

Profiling microbial communities in manganese remediation systems treating coal mine drainage

Author Posting. © American Society for Microbiology, 2015. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 81 (2015): 2189-2198, doi:10.1128/AEM.03643-14.Water discharging from abandoned coal mines can contain extremely high manganese levels. Removing this metal is an ongoing challenge. Passive Mn(II) removal beds (MRBs) contain microorganisms that oxidize soluble Mn(II) to insoluble Mn(III/IV) minerals, but system performance is unpredictable. Using amplicon pyrosequencing, we profiled the bacterial, fungal, algal and archaeal communities in four variably-performing MRBs in Pennsylvania to determine whether they differed among MRBs and from surrounding soil, and to establish the relative abundance of known Mn(II)-oxidizers. Archaea were not detected; PCRs with archaeal primers returned only non-target bacterial sequences. Fungal taxonomic profiles differed starkly between sites that remove the majority of influent Mn and those that do not, with the former dominated by Ascomycota (mostly Dothideomycetes) and the latter by Basidiomycota (almost entirely Agaricomycetes). Taxonomic profiles for the other groups did not differ significantly between MRBs, but OTU-based analyses showed significant clustering by MRB with all four groups (p<0.05). Soil samples clustered separately from MRBs in all groups except fungi, whose soil samples clustered loosely with their respective MRB. Known Mn(II) oxidizers accounted for a minor proportion of bacterial sequences (up to 0.20%) but a greater proportion of fungal sequences (up to 14.78%). MRB communities are more diverse than previously thought, and more organisms may be capable of Mn(II) oxidation than are currently known.This project was funded by Smithsonian Scholarly Studies and Next-Generation Sequencing grants to C.M.S., by a Smithsonian Postdoctoral Fellowship to D.L.C., and by the National Science Foundation, grant numbers EAR-1249489 (awarded to C.M.H.) and CBET-1336496 (awarded to C.M.H. and C.M.S.)

Species-level variability in extracellular production rates of reactive oxygen species by diatoms

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Chemistry 4 (2016): 5, doi:10.3389/fchem.2016.00005.Biological production and decay of the reactive oxygen species (ROS) hydrogen peroxide (H2O2) and superoxide (O−2) likely have significant effects on the cycling of trace metals and carbon in marine systems. In this study, extracellular production rates of H2O2 and O−2 were determined for five species of marine diatoms in the presence and absence of light. Production of both ROS was measured in parallel by suspending cells on filters and measuring the ROS downstream using chemiluminescence probes. In addition, the ability of these organisms to break down O−2 and H2O2 was examined by measuring recovery of O−2 and H2O2 added to the influent medium. O−2 production rates ranged from undetectable to 7.3 × 10−16 mol cell−1 h−1, while H2O2 production rates ranged from undetectable to 3.4 × 10−16 mol cell−1 h−1. Results suggest that extracellular ROS production occurs through a variety of pathways even amongst organisms of the same genus. Thalassiosira spp. produced more O−2 in light than dark, even when the organisms were killed, indicating that O−2 is produced via a passive photochemical process on the cell surface. The ratio of H2O2 to O−2 production rates was consistent with production of H2O2 solely through dismutation of O−2 for T. oceanica, while T. pseudonana made much more H2O2 than O−2. T. weissflogii only produced H2O2 when stressed or killed. P. tricornutum cells did not make cell-associated ROS, but did secrete H2O2-producing substances into the growth medium. In all organisms, recovery rates for killed cultures (94–100% H2O2; 10–80% O−2) were consistently higher than those for live cultures (65–95% H2O2; 10–50% O−2). While recovery rates for killed cultures in H2O2 indicate that nearly all H2O2 was degraded by active cell processes, O−2 decay appeared to occur via a combination of active and passive processes. Overall, this study shows that the rates and pathways for ROS production and decay vary greatly among diatom species, even between those that are closely related, and as a function of light conditions.This research was supported by NSF grant OCE-1131734/1246174 to BV and CH

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

Contrasting Effects of Al Substitution on Microbial Reduction of Fe(III) (Hydr)oxides

Aluminum, one of the most abundant elements in soils and sediments, is commonly found co-precipitated with Fe in natural Fe(III) (hydr)oxides; yet, little is known about how Al substitution impacts bacterial Fe(III) reduction. Accordingly, we investigated the reduction of Al substituted (0–13 mol% Al) goethite, lepidocrocite, and ferrihydrite by the model dissimilatory Fe(III)-reducing bacterium (DIRB), Shewanella putrefaciens CN32. Here we reveal that the impact of Al on microbial reduction varies with Fe(III) (hydr)oxide type. No significant difference in Fe(III) reduction was observed for either goethite or lepidocrocite as a function of Al substitution. In contrast, Fe(III) reduction rates significantly decreased with increasing Al substitution of ferrihydrite, with reduction rates of 13% Al-ferrihydrite more than 50% lower than pure ferrihydrite. Although Al substitution changed the minerals’ surface area, particle size, structural disorder, and abiotic dissolution rates, we did not observe a direct correlation between any of these physiochemical properties and the trends in bacterial Fe(III) reduction. Based on projected Al-dependent Fe(III) reduction rates, reduction rates of ferrihydrite fall below those of lepidocrocite and goethite at substitution levels equal to or greater than 18 mol% Al. Given the prevalence of Al substitution in natural Fe(III) (hydr)oxides, our results bring into question the conventional assumptions about Fe (hydr)oxide bioavailability and suggest a more prominent role of natural lepidocrocite and goethite phases in impacting DIRB activity in soils and sediments.Engineering and Applied Science