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  • Articles  (172)
  • Bacteria
  • Dissolved organic carbon
  • Springer  (166)
  • American Geophysical Union  (6)
  • Molecular Diversity Preservation International
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  • 1
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Druffel, E. R. M., Griffin, S., Wang, N., Garcia, N. G., McNichol, A. P., Key, R. M., & Walker, B. D. Dissolved organic radiocarbon in the central Pacific Ocean. Geophysical Research Letters, 46(10), (2019):5396-5403, doi:10.1029/2019GL083149.
    Description: We report marine dissolved organic carbon (DOC) concentrations, and DOC ∆14C and δ13C values in seawater collected from the central Pacific. Surface ∆14C values are low in equatorial and polar regions where upwelling occurs and high in subtropical regions dominated by downwelling. A core feature of these data is that 14C aging of DOC (682 ± 86 14C years) and dissolved inorganic carbon (643 ± 40 14C years) in Antarctic Bottom Water between 54.0°S and 53.5°N are similar. These estimates of aging are minimum values due to mixing with deep waters. We also observe minimum ∆14C values (−550‰ to −570‰) between the depths of 2,000 and 3,500 m in the North Pacific, though the source of the low values cannot be determined at this time.
    Description: We thank Jennifer Walker, Xiaomei Xu, and Dachun Zhang for their help with the stable carbon isotope measurements; John Southon and staff of the Keck Carbon Cycle AMS Laboratory for their assistance and advice; the support of chief scientists Samantha Siedlecki, Molly Baringer, Alison Macdonald, and Sabine Mecking; the guidance of Jim Swift and Dennis Hansell for shared ship time; and Sarah Bercovici for collecting water on the GoA cruise. We appreciate the comments of Christian Lewis and Niels Hauksson on this manuscript. This work was supported by NSF (OCE‐141458941 to E. R. M. D. and OCE‐0824864, OCE‐1558654, and Cooperative Agreement OCE1239667 to R. M. K. and A. P. M.), the Fred Kavli Foundation, the Keck Carbon Cycle AMS Laboratory, and the NSF/NOAA‐funded GO‐SHIP Program. This research was undertaken, in part, thanks to funding from the Canada Research Chairs program (to B. D. W.) and an American Chemical Society Petroleum Research Fund New Directions grant (55430‐ND2 to E. R. M. D. and B. D. W.). Data from the P16N cruises are available in Table S2 in the Supporting Information and at the Repeat Hydrography Data Center at the CCHDO website (http://cdiac.esd.ornl.gov/oceans/index.html) using the expo codes 3RO20150329, 3RO20150410, and 3RO20150525. There are no real or perceived financial conflicts of interests for any author.
    Description: 2019-11-02
    Keywords: Dissolved organic carbon ; Radiocarbon ; Pacific Ocean ; Dissolved inorganic carbon ; Deep ocean circulation ; AABW
    Repository Name: Woods Hole Open Access Server
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  • 2
    Publication Date: 2022-10-26
    Description: Author Posting. © American Geophysical Union, 2021. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Global Biogeochemical Cycles 35(4), (2021): e2020GB006895, https://doi.org/10.1029/2020GB006895.
    Description: The Amazon River drains a diverse tropical landscape greater than 6 million km2, culminating in the world's largest export of freshwater and dissolved constituents to the ocean. Here, we present dissolved organic carbon (DOC), organic and inorganic nitrogen (DON, DIN), orthophosphate (PO43−), and major and trace ion concentrations and fluxes from the Amazon River using 26 samples collected over three annual hydrographs. Concentrations and fluxes were predominantly controlled by the annual wet season flood pulse. Average DOC, DON, DIN, and PO43− fluxes (±1 s.d.) were 25.5 (±1.0), 1.14 (±0.05), 0.82 (±0.03), and 0.063 (±0.003) Tg yr−1, respectively. Chromophoric dissolved organic matter absorption (at 350 nm) was strongly correlated with DOC concentrations, resulting in a flux of 74.8 × 106 m−2 yr−1. DOC and DON concentrations positively correlated with discharge while nitrate + nitrite concentrations negatively correlated, suggesting mobilization and dilution responses, respectively. Ammonium, PO43−, and silica concentrations displayed chemostatic responses to discharge. Major and trace ion concentrations displayed clockwise hysteresis (except for chloride, sodium, and rubidium) and exhibited either dilution or chemostatic responses. The sources of weathered cations also displayed seasonality, with the highest proportion of carbonate- and silicate-derived cations occurring during peak and baseflow, respectively. Finally, our seasonally resolved weathering model resulted in an average CO2 consumption yield of (3.55 ± 0.11) × 105 mol CO2 km−2 yr−1. These results represent an updated and temporally refined quantification of dissolved fluxes that highlight the strong seasonality of export from the world's largest river and set a robust baseline against which to gauge future change.
    Description: This work was supported by a grant from the Harbourton Foundation to R. G. M. Spencer and R. M. Holmes. T. W. Drake was supported by ETH Zurich core funding to J. Six. R. G. M. Spencer was additionally supported by NSF OCE-1333157.
    Description: 2021-09-15
    Keywords: Amazon river ; Dissolved organic carbon ; Fluxes ; Weathering ; Geochemistry
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  • 3
    Publication Date: 2022-10-26
    Description: Author Posting. © American Geophysical Union, 2021. 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 48(10), (2021): e2021GL092904, https://doi.org/10.1029/2021GL092904.
    Description: We report marine dissolved organic carbon (DOC) concentrations, and DOC Δ14C and δ13C values in seawater collected from the Southern Ocean and eastern Pacific GOSHIP cruise P18 in 2016/2017. The aging of 14C in DOC in circumpolar deep water northward from 69°S to 20°N was similar to that measured in dissolved inorganic carbon in the same samples, indicating that the transport of deep waters northward is the primary control of 14C in DIC and DOC. Low DOC ∆14C and δ13C measurements between 1,200 and 3,400 m depth may be evidence of a source of DOC produced in nearby hydrothermal ridge systems (East Pacific Rise).
    Description: This work was supported by NSF (OCE-1458941 and OCE-1951073 to Ellen R. M. Druffel), Fred Kavli Foundation, Keck Carbon Cycle AMS Laboratory, NSF/NOAA funded GO-SHIP Program, Canada Research Chairs program (to Brett D. Walker) and American Chemical Society Petroleum Research Fund New Directions (55,430-ND2 to Ellen R. M. Druffel and Brett D. Walker).
    Description: 2021-11-24
    Keywords: 13C ; Carbon cycle ; Circumpolar deep water ; Dissolved inorganic carbon ; Dissolved organic carbon ; Radiocarbon
    Repository Name: Woods Hole Open Access Server
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  • 4
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Dragone, N. B., Diaz, M. A., Hogg, I., Lyons, W. B., Jackson, W. A., Wall, D. H., Adams, B. J., & Fierer, N. Exploring the boundaries of microbial habitability in soil. Journal of Geophysical Research: Biogeosciences, 126(6), (2021): e2020JG006052, https://doi.org/10.1029/2020JG006052.
    Description: Microbes are widely assumed to be capable of colonizing even the most challenging terrestrial surface environments on Earth given enough time. We would not expect to find surface soils uninhabited by microbes as soils typically harbor diverse microbial communities and viable microbes have been detected in soils exposed to even the most inhospitable conditions. However, if uninhabited soils do exist, we might expect to find them in Antarctica. We analyzed 204 ice-free soils collected from across a remote valley in the Transantarctic Mountains (84–85°S, 174–177°W) and were able to identify a potential limit of microbial habitability. While most of the soils we tested contained diverse microbial communities, with fungi being particularly ubiquitous, microbes could not be detected in many of the driest, higher elevation soils—results that were confirmed using cultivation-dependent, cultivation-independent, and metabolic assays. While we cannot confirm that this subset of soils is completely sterile and devoid of microbial life, our results suggest that microbial life is severely restricted in the coldest, driest, and saltiest Antarctic soils. Constant exposure to these conditions for thousands of years has limited microbial communities so that their presence and activity is below detectable limits using a variety of standard methods. Such soils are unlikely to be unique to the studied region with this work supporting previous hypotheses that microbial habitability is constrained by near-continuous exposure to cold, dry, and salty conditions, establishing the environmental conditions that limit microbial life in terrestrial surface soils.
    Description: This work was supported by grants from the U.S. National Science Foundation (ANT 1341629 to B. J. Adams, N. Fierer, W. Berry Lyons, and D. H. Wall and OPP 1637708 to B. J. Adams) with additional support provided to N. B. Dragone from University Colorado Department of Ecology and Evolutionary Biology.
    Keywords: Antarctica ; Soils ; Bacteria ; Fungi ; Extremophiles ; Astrobiology
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  • 5
    Publication Date: 2022-10-26
    Description: Author Posting. © American Geophysical Union, 2021. 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: Biogeosciences 126(7), (2021): e2020JG005977, https://doi.org/10.1029/2020JG005977.
    Description: Increasing Arctic temperatures are thawing permafrost soils and liberating ancient organic matter, but the fate of this material remains unclear. Thawing of permafrost releases dissolved organic matter (DOM) into fluvial networks. Unfortunately, tracking this material in Arctic rivers such as the Kolyma River in Siberia has proven challenging due to its high biodegradability. Here, we evaluate late summer abruptly thawed yedoma permafrost dissolved organic carbon (DOC) inputs from Duvannyi Yar. We implemented ultrahigh-resolution mass spectrometry alongside ramped pyrolysis oxidation (RPO) and isotopic analyses. These approaches offer insight into DOM chemical composition and DOC radiocarbon values of thermochemical components for a permafrost thaw stream, the Kolyma River, and their biodegraded counterparts (n = 4). The highly aliphatic molecular formula found in undegraded permafrost DOM contrasted with the comparatively aliphatic-poor formula of Kolyma River DOM, represented by an 8.9% and 2.6% relative abundance, respectively, suggesting minimal inputs of undegraded permafrost DOM in the river. RPO radiocarbon fractions of Kolyma River DOC exhibited no “hidden” aged component indicative of permafrost influence. Thermostability analyses suggested that there was limited biodegraded permafrost DOC in the Kolyma River, in part determined by the formation of high-activation energy (thermally stable) biodegradation components in permafrost DOM that were lacking in the Kolyma River. A mixing model based on thermostability and radiocarbon allowed us to estimate a maximum input of between 0.8% and 7.7% of this Pleistocene-aged permafrost to the Kolyma River DOC. Ultimately, our findings highlight that export of modern terrestrial DOC currently overwhelms any permafrost DOC inputs in the Kolyma River.
    Description: This work was funded by NSF grants ANT-1203885 and PLR-1500169 to R.G.M.S. The work was also supported by the National Science Foundation Division of Chemistry through DMR-1644779 and the State of Florida.
    Description: 2022-01-09
    Keywords: Permafrost ; Dissolved organic carbon ; Dissolved organic matter ; FT-ICR MS ; Ramped pyrolysis oxidation ; Arctic
    Repository Name: Woods Hole Open Access Server
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  • 6
    Publication Date: 2022-05-26
    Description: © The Authors 2009. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License. The definitive version was published in Functional & Integrative Genomics 10 (2010): 97-110, doi:10.1007/s10142-009-0142-y.
    Description: Bacteria of the genus Shewanella can thrive in different environments and demonstrate significant variability in their metabolic and ecophysiological capabilities including cold and salt tolerance. Genomic characteristics underlying this variability across species are largely unknown. In this study, we address the problem by a comparison of the physiological, metabolic, and genomic characteristics of 19 sequenced Shewanella species. We have employed two novel approaches based on association of a phenotypic trait with the number of the trait-specific protein families (Pfam domains) and on the conservation of synteny (order in the genome) of the trait-related genes. Our first approach is top-down and involves experimental evaluation and quantification of the species’ cold tolerance followed by identification of the correlated Pfam domains and genes with a conserved synteny. The second, a bottom-up approach, predicts novel phenotypes of the species by calculating profiles of each Pfam domain among their genomes and following pair-wise correlation of the profiles and their network clustering. Using the first approach, we find a link between cold and salt tolerance of the species and the presence in the genome of a Na+/H+ antiporter gene cluster. Other cold-tolerance-related genes include peptidases, chemotaxis sensory transducer proteins, a cysteine exporter, and helicases. Using the bottom-up approach, we found several novel phenotypes in the newly sequenced Shewanella species, including degradation of aromatic compounds by an aerobic hybrid pathway in Shewanella woodyi, degradation of ethanolamine by Shewanella benthica, and propanediol degradation by Shewanella putrefaciens CN32 and Shewanella sp. W3-18-1.
    Description: This research was supported by the U.S. Department of Energy (DOE) Office of Biological and Environmental Research under the Genomics: GTL Program via the Shewanella Federation consortium.
    Keywords: Phenotypic trait ; Bacteria ; Molecular mechanisms of cold tolerance ; Shewanella ; Protein families
    Repository Name: Woods Hole Open Access Server
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  • 7
    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2012. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Global Biogeochemical Cycles 26 (2012): GB0E02, doi:10.1029/2012GB004299.
    Description: While much of the dissolved organic carbon (DOC) within rivers is destined for mineralization to CO2, a substantial fraction of riverine bicarbonate (HCO3−) flux represents a CO2 sink, as a result of weathering processes that sequester CO2 as HCO3−. We explored landscape-level controls on DOC and HCO3− flux in subcatchments of the boreal, with a specific focus on the effect of permafrost on riverine dissolved C flux. To do this, we undertook a multivariate analysis that partitioned the variance attributable to known, key regulators of dissolved C flux (runoff, lithology, and vegetation) prior to examining the effect of permafrost, using riverine biogeochemistry data from a suite of subcatchments drawn from the Mackenzie, Yukon, East, and West Siberian regions of the circumboreal. Across the diverse catchments that we study, controls on HCO3− flux were near-universal: runoff and an increased carbonate rock contribution to weathering (assessed as riverwater Ca:Na) increased HCO3− yields, while increasing permafrost extent was associated with decreases in HCO3−. In contrast, permafrost had contrasting and region-specific effects on DOC yield, even after the variation caused by other key drivers of its flux had been accounted for. We used ionic ratios and SO4 yields to calculate the potential range of CO2 sequestered via weathering across these boreal subcatchments, and show that decreasing permafrost extent is associated with increases in weathering-mediated CO2 fixation across broad spatial scales, an effect that could counterbalance some of the organic C mineralization that is predicted with declining permafrost.
    Description: Funding for this work was provided through NSF-OPP-0229302 and NSF-OPP-0732985. Additional support to S.E.T. was provided by an NSERC Postdoctoral Fellowship.
    Description: 2013-02-21
    Keywords: Arctic ; Bicarbonate ; Dissolved organic carbon ; Permafrost
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Journal of industrial microbiology and biotechnology 8 (1991), S. 201-207 
    ISSN: 1476-5535
    Keywords: Diffusion chamber ; Cadmium-sensitive ; Cadmium-resitant ; Sediment ; Bacteria ; Cadmium-sorption
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary Sorption of cadmium by sediment bacteria and freshwater sediment was investigated using diffusion chambers to simulate the water-sediment interface. Diffusion chambers were constructed to provide two compartments separated by a dialysis membrane. Diffusion of cadmium across the membrane was monitored after pure cultures of sediment bacteria or lake sediments were added to the sediment side of a diffusion chamber. Cellular accumulation of cadmium by cadmium-sensitive and cadmium-resistant bacteria removed between 20% and 80% of the dissolved cadmium from the simulated water column and pore water. Cellular accumulation of cadmium was greatest for cadmium-sensitive isolates that were tested. Sediment with an intact microbial community sequestered 80% of the cadmium added to sediment, whereas autoclaved sediment retained 97% of the metal that was added. Addition of glucose to cadmium-amended sediment decreased retention of cadmium by untreated and autoclaved sediments, resulting in elevated concentrations of dissolved cadmium in the simulated water column.
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    Journal of industrial microbiology and biotechnology 8 (1991), S. 223-227 
    ISSN: 1476-5535
    Keywords: Deionized water ; Ultra-pure water ; Ozone ; Ultra-violet sterilization ; Oligotroph ; Bacteria ; R2A medium
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary Presently, tryptic soy agar (TSA) medium is used in the semiconductor industry to determine the concentration of viable oligotrophic bacteria in ultra-pure water systems. Deionized water from an ultra-pure water pilot plant was evaluated for bacterial growth at specific locations, using a non-selective medium (R2A) designed to detect injured heterotrophic as well as oligotrophic bacteria. Results were compared to those obtained using Tryptic Soy Agar. Statistically greater numbers of bacteria were observed when R2A was used as the growth medium. Total viable bacterial numbers were compared both before and after each treatment step of the recirculating loop to determine their effectiveness in removing bacteria. The reduction in bacterial numbers for the reverse osmosis unit, the ion exchange bed, and the ultraviolet sterilizer were 97.4%, 31.3%, and 72.8%, respectively, using TSA medium, and 98.4%, 78.4%, and 35.8% using R2A medium. The number of viable bacteria increased by 60.7% based on TSA medium and 15.7% based on R2A medium after passage of the water through an in-line 0.2-μm pore size nylon filter, probably because of the growth of bacteria on the filter. Our results suggest that R2A medium may give a better representation of the microbial water quality in ultra-pure water systems and therefore a better idea of the effectiveness of the various treatment processes in the control of bacteria.
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    Journal of industrial microbiology and biotechnology 5 (1990), S. 79-84 
    ISSN: 1476-5535
    Keywords: Bacteria ; Soil ; Conjugation ; Gene transfer ; Plasmids ; Survival
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary Experiments conducted in microcosms containing loam soil samples inoculated with eitherE. coli orPseudomonas spp. donor and recipient cells showed that bacterial cells survived and conjugated over a 24-h incubation period.E. coli transconjugants were detected 6 h after donor and recipient strains were introduced into sterile soil samples. In non-sterile soil samples, transconjugants were detected between 8 and 24 h incubation.Pseudomonas transconjugants were recovered from sterile soil samples between 6 and 12 h after their introduction and as early as 2 h in non-sterile soil. The results show that genetic interactions occur in non-sterile soil in relatively short periods of time at relatively high transfer frequencies (10−3 to 10−4). Studies on genetic interactions in soil are becoming necessary in risk assessment/environmental impact studies prior to the release of genetically engineered or modified organisms into uncontained environments.
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