GLORIA

GEOMAR Library Ocean Research Information Access

X
feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
  • 1
    facet.materialart.
    Unknown
    Unchanged nitrate and nitrite isotope fractionation during heterotrophic and Fe(II)-mixotrophic denitrification suggest a non-enzymatic link between denitrification and Fe(II) oxidation (2023)
    Frontiers Media
    Details
    Publication Date: 2023-03-08
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Visser, A.-N., Wankel, S., Frey, C., Kappler, A., & Lehmann, M. Unchanged nitrate and nitrite isotope fractionation during heterotrophic and Fe(II)-mixotrophic denitrification suggest a non-enzymatic link between denitrification and Fe(II) oxidation. Frontiers in Microbiology, 13, (2022): 927475, https://doi.org/10.3389/fmicb.2022.927475.
    Description: Natural-abundance measurements of nitrate and nitrite (NOx) isotope ratios (δ15N and δ18O) can be a valuable tool to study the biogeochemical fate of NOx species in the environment. A prerequisite for using NOx isotopes in this regard is an understanding of the mechanistic details of isotope fractionation (15ε, 18ε) associated with the biotic and abiotic NOx transformation processes involved (e.g., denitrification). However, possible impacts on isotope fractionation resulting from changing growth conditions during denitrification, different carbon substrates, or simply the presence of compounds that may be involved in NOx reduction as co-substrates [e.g., Fe(II)] remain uncertain. Here we investigated whether the type of organic substrate, i.e., short-chained organic acids, and the presence/absence of Fe(II) (mixotrophic vs. heterotrophic growth conditions) affect N and O isotope fractionation dynamics during nitrate (NO3–) and nitrite (NO2–) reduction in laboratory experiments with three strains of putative nitrate-dependent Fe(II)-oxidizing bacteria and one canonical denitrifier. Our results revealed that 15ε and 18ε values obtained for heterotrophic (15ε-NO3–: 17.6 ± 2.8‰, 18ε-NO3–:18.1 ± 2.5‰; 15ε-NO2–: 14.4 ± 3.2‰) vs. mixotrophic (15ε-NO3–: 20.2 ± 1.4‰, 18ε-NO3–: 19.5 ± 1.5‰; 15ε-NO2–: 16.1 ± 1.4‰) growth conditions are very similar and fall within the range previously reported for classical heterotrophic denitrification. Moreover, availability of different short-chain organic acids (succinate vs. acetate), while slightly affecting the NOx reduction dynamics, did not produce distinct differences in N and O isotope effects. N isotope fractionation in abiotic controls, although exhibiting fluctuating results, even expressed transient inverse isotope dynamics (15ε-NO2–: –12.4 ± 1.3 ‰). These findings imply that neither the mechanisms ordaining cellular uptake of short-chain organic acids nor the presence of Fe(II) seem to systematically impact the overall N and O isotope effect during NOx reduction. The similar isotope effects detected during mixotrophic and heterotrophic NOx reduction, as well as the results obtained from the abiotic controls, may not only imply that the enzymatic control of NOx reduction in putative NDFeOx bacteria is decoupled from Fe(II) oxidation, but also that Fe(II) oxidation is indirectly driven by biologically (i.e., via organic compounds) or abiotically (catalysis via reactive surfaces) mediated processes co-occurring during heterotrophic denitrification.
    Description: This study was supported by the German Research Foundation (DFG)-funded RTG 1708 “Molecular Principles of Bacterial Survival Strategies.” Work performed under the supervision of ML was supported by the University of Basel funds.
    Keywords: Denitrification ; Nitrate/nitrite isotopes ; Iron oxidation ; Isotope fractionation ; Carbon substrate
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 2
    facet.materialart.
    Unknown
    Oxygen isotopes (delta O-18) trace photochemical hydrocarbon oxidation at the sea surface (2019)
    American Geophysical Union
    Details
    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
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 3
    facet.materialart.
    Unknown
    Spectroscopic insights into ferromanganese crust formation and diagenesis (2021)
    American Geophysical Union
    Details
    Publication Date: 2022-10-26
    Description: 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.
    Description: 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.
    Description: 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.
    Description: 2021-04-26
    Keywords: Diagenesis ; Ferromanganese crust ; Manganese oxide minerals ; X‐ray absorption spectroscopy
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 4
    facet.materialart.
    Unknown
    Spatial heterogeneity in particle-associated, light-independent superoxide production within productive coastal waters (2021)
    American Geophysical Union
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sutherland, K. M., Grabb, K. C., Karolewski, J. S., Plummer, S., Farfan, G. A., Wankel, S. D., Diaz, J. M., Lamborg, C. H., & Hansel, C. M. Spatial heterogeneity in particle-associated, light-independent superoxide production within productive coastal waters. Journal of Geophysical Research: Oceans, 125(10), (2020): e2020JC016747, https://doi.org/10.1029/2020JC016747.
    Description: In the marine environment, the reactive oxygen species (ROS) superoxide is produced through a diverse array of light‐dependent and light‐independent reactions, the latter of which is thought to be primarily controlled by microorganisms. Marine superoxide production influences organic matter remineralization, metal redox cycling, and dissolved oxygen concentrations, yet the relative contributions of different sources to total superoxide production remain poorly constrained. Here we investigate the production, steady‐state concentration, and particle‐associated nature of light‐independent superoxide in productive waters off the northeast coast of North America. We find exceptionally high levels of light‐independent superoxide in the marine water column, with concentrations ranging from 10 pM to in excess of 2,000 pM. The highest superoxide concentrations were particle associated in surface seawater and in aphotic seawater collected meters off the seafloor. Filtration of seawater overlying the continental shelf lowered the light‐independent, steady‐state superoxide concentration by an average of 84%. We identify eukaryotic phytoplankton as the dominant particle‐associated source of superoxide to these coastal waters. We contrast these measurements with those collected at an off‐shelf station, where superoxide concentrations did not exceed 100 pM, and particles account for an average of 40% of the steady‐state superoxide concentration. This study demonstrates the primary role of particles in the production of superoxide in seawater overlying the continental shelf and highlights the importance of light‐independent, dissolved‐phase reactions in marine ROS production.
    Description: This work was funded by grants from the Chemical Oceanography program of the National Science Foundation (OCE‐1355720 to C. M. H. and C. H. L.), NASA Earth and Space Science Fellowship (Grant NNX15AR62H to K. M. S.), Agouron Institute Postdoctoral Fellowship (K. M. S.), NSF GRFPs (2016230268 to K. C. G. and 2017250547 to S. P.), and a Sloan Research Fellowship (J. M. D.). The Guava flow cytometer was purchased through an NSF equipment improvement grant (1624593).
    Keywords: reactive oxygen species ; Extracellular superoxide ; Light‐independent ROS
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 5
    facet.materialart.
    Unknown
    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).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 6
    facet.materialart.
    Unknown
    Microbial activity in the marine deep biosphere : progress and prospects (2014)
    Frontiers Media
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 4 (2013): 189, doi:10.3389/fmicb.2013.00189.
    Description: The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists—all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these “extreme” environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) “theme team” on microbial activity (www.darkenergybiosphere.org).
    Description: Funding for the meeting was provided by C-DEBI, a US National Science Foundation (NSF)-funded Science and Technology Center (OCE-0939564). Funding for this publication was provided, in part, by NSF (OCE-1233226 to BNO).
    Keywords: Deep biosphere ; IODP ; Biogeochemistry ; Sediment ; Oceanic crust ; C-DEBI ; Subsurface microbiology
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 7
    facet.materialart.
    Unknown
    Isotopic constraints on nitrogen transformation rates in the deep sedimentary marine biosphere (2019)
    American Geophysical Union
    Details
    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
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 8
    facet.materialart.
    Unknown
    Recent increases in water column denitrification in the seasonally suboxic bottom waters of the Santa Barbara Basin (2019)
    American Geophysical Union
    Details
    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
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 9
    facet.materialart.
    Unknown
    Enriched iron(III)-reducing bacterial communities are shaped by carbon substrate and iron oxide mineralogy (2014)
    Frontiers Media
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 3 (2012): 404, doi:10.3389/fmicb.2012.00404.
    Description: 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.
    Description: 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.
    Keywords: Fe ; Iron oxides ; Iron reduction ; Sulfate reduction ; Cultivation ; Niche differentiation
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    PAPER (OA)
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...