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  • 1
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    PANGAEA
    In:  Supplement to: Uhlig, Christiane; Kirkpatrick, John B; d'Hondt, Steven L; Loose, Brice (2018): Methane-oxidizing seawater microbial communities from an Arctic shelf. Biogeosciences, 15, 3311-3329, https://doi.org/10.5194/bg-15-3311-2018
    Publication Date: 2024-01-06
    Description: Arctic seawater was collected at two sites close to Utqiagvik, North Slope, Alaska on 7, 9, 11 and 15 April 2016 in the Beaufort Sea. Site "Elson Lagoon" (EL) was located North of Utqiagvik (7.4.2016, 71.334° N, -156.363° W), covered with 1.5 m thick sea ice and shallow with approximately 1.5 m depth. Water was collected from a depth of 1.5 m in a narrow layer of water between the sea ice and the sediment. Site "Ice Mass Balance Buoy" (IMB) was located 1 km offshore of Utqiagvik (7.4.2016, 71.373° N, -156.548° W, and 9.4.2016 - 15.4.2016, 71.372° N, -156.540° W). This site was characterized by 1 m thick fast ice cover and a water depth of approximately 7 m. Water was collected at five depths from 1 to 6.5 m. Sea ice was collected at station IMB on 11 and 15 April 2016 in the Beaufort Sea (71.372° N, -156.540° W) using a Kovacs Mark II ice corer (Kovacs, Roseburg, Oregon, USA). The ice cores were sectioned into 15 cm and split lengthwise. The core sections were sealed into custom-made gas-tight tubes for determination of methane concentration and isotope ratios. In the laboratory, the gas-tight tubes were flushed with ultrapure nitrogen for several gas volumes. Due to technical limitations, ice core 1 (IC1) was melted within a week at 5°C, while ice core 2 (IC2) was melted within a day, while frequently being mixed, at room temperature. Seawater temperature and salinity were recorded with an YSI Professional Plus probe (YSI, Ohio, USA) and a YSI 600 OMS V2 sonde (YSI, Ohio, USA). Water was collected using either a peristaltic pump (Masterflex Environmental Sampler, Cole Parmer, Illinois, USA) or submersible pump (Cyclone, Proactive Environmental Products, Florida, USA) from different water depths. Methane concentration and isotope ratios were determined with a Picarro G2201-i cavity ring-down spectrometer (Picarro, Santa Clara, California, USA) coupled to a Small Sample Isotope Module (SSIM) (Picarro, Santa Clara, California, USA), in a headspace approach. Nutrient concentrations were determined using a QuickChem QC8500 automated ion analyzer (Lachat, Loveland, Colorado, USA). The total number of prokaryotic cells was counted on a BD Influx^TM^ flow cytometer with BD FACS^TM^ software. Formol-fixed samples were stained with SYBR Green I (Invitrogen, Molecular Probes, Eugene, Oregon, USA) before analysis.
    Keywords: Elson_Lagoon; MULT; Multiple investigations; Utqiagvik_IMB-1; Utqiagvik_IMB-2; Utqiagvik_IMB-3; Utqiagvik_IMB-4
    Type: Dataset
    Format: application/zip, 2 datasets
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  • 2
    Publication Date: 2024-01-06
    Keywords: Core; Date/Time of event; Depth, bottom/max; DEPTH, ice/snow; Depth, top/min; Event label; Latitude of event; Longitude of event; Methane; Methane, standard deviation; MULT; Multiple investigations; Prokaryotes; Prokaryotes, standard deviation; Salinity; Sample amount; Sample ID; Temperature, water; Utqiagvik_IMB-2; Utqiagvik_IMB-4; δ13C, methane; δ13C, methane, standard deviation
    Type: Dataset
    Format: text/tab-separated-values, 146 data points
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  • 3
    Publication Date: 2024-01-06
    Keywords: Date/Time of event; DEPTH, water; Elson_Lagoon; Event label; Latitude of event; Longitude of event; Methane; Methane, standard deviation; MULT; Multiple investigations; Nitrate; Nitrite; Phosphate; Prokaryotes; Prokaryotes, standard deviation; Salinity; Sample amount; Sample ID; Temperature, water; Utqiagvik_IMB-1; Utqiagvik_IMB-2; Utqiagvik_IMB-3; Utqiagvik_IMB-4; δ13C, methane; δ13C, methane, standard deviation
    Type: Dataset
    Format: text/tab-separated-values, 184 data points
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  • 4
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    COPERNICUS GESELLSCHAFT MBH
    In:  EPIC3Biogeosciences, COPERNICUS GESELLSCHAFT MBH, 15, pp. 3311-3329, ISSN: 1726-4170
    Publication Date: 2018-11-08
    Description: Marine microbial communities can consume dissolved methane before it can escape to the atmosphere and contribute to global warming. Seawater over the shallow Arctic shelf is characterized by excess methane compared to atmospheric equilibrium. This methane originates in sediment, permafrost, and hydrate. Particularly high concentrations are found beneath sea ice. We studied the structure and methane oxidation potential of the microbial communities from seawater collected close to Utqiagvik, Alaska, in April 2016. The in situ methane concentrations were 16.3 ± 7.2 nmol L−1, approximately 4.8 times oversaturated relative to atmospheric equilibrium. The group of methane-oxidizing bacteria (MOB) in the natural seawater and incubated seawater was 〉 97 % dominated by Methylococcales (γ-Proteobacteria). Incubations of seawater under a range of methane concentrations led to loss of diversity in the bacterial community. The abundance of MOB was low with maximal fractions of 2.5 % at 200 times elevated methane concentration, while sequence reads of non-MOB methylotrophs were 4 times more abundant than MOB in most incubations. The abundances of MOB as well as non-MOB methylotroph sequences correlated tightly with the rate constant (kox) for methane oxidation, indicating that non-MOB methylotrophs might be coupled to MOB and involved in community methane oxidation. In sea ice, where methane concentrations of 82 ± 35.8 nmol / kg were found, Methylobacterium (α-Proteobacteria) was the dominant MOB with a relative abundance of 80 %. Total MOB abundances were very low in sea ice, with maximal fractions found at the ice–snow interface (0.1 %), while non-MOB methylotrophs were present in abundances similar to natural seawater communities. The dissimilarities in MOB taxa, methane concentrations, and stable isotope ratios between the sea ice and water column point toward different methane dynamics in the two environments.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 5
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    In:  EPIC3ASLO Ocean Sciences Meeting, Hawaii, USA, 2017-02-26-2017-03-03
    Publication Date: 2017-09-20
    Description: In the shallow marginal seas of the Arctic seawater methane concentrations are frequently in excess of atmospheric saturation, partly caused by reduced sea-air-exchange around sea ice cover. These same regions can host rich ice-attached and water column microbial communities, including methane-oxidizing bacteria. How much methane accumulating beneath seasonal sea ice is oxidized by bacteria and how much escapes to the atmosphere? To determine methane oxidation rates, we incubated seawater from beneath sea ice, collected close to Point Barrow, Alaska under a variety of methane concentrations. Methane concentrations and stable isotope ratios were monitored using a Picarro trace gas analyzer, equipped with a Small Sample Isotope Module (SSIM). High oxidation rates were observed in the presence of high methane concentrations, while at lower concentrations the methane budget was zero or slightly positive. Trends in the mass balance were accompanied by a respective trend in stable isotope ratios, indicating that biological processes are responsible for these changes. Increasing cell densities hint to microbial uptake of the methane and a shift towards methanotrophs in the community. While the low concentration experiments elucidate methane cycling at in situ concentrations, the high amended experiments show the potential of the communities to mitigate events of high methane release from the seabed or while the methane is caught under the sea ice cover. With a decreased sea ice cover or earlier ice breakup it is possible that more methane will be vented to the atmosphere due to decreased residence time in the water column and thus accessibility to the methanotrophic community.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Conference , notRev
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  • 6
    Publication Date: 2022-05-26
    Description: Author Posting. © American Geophysical Union, 2010. 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 24 (2010): GB4001, doi:10.1029/2009GB003651.
    Description: Net community production (NCP) and gross primary production (GPP) are two key metrics for quantifying the biological carbon cycle. In this study, we present a detailed characterization of NCP and GPP in the western equatorial Pacific during August and September 2006. We use continuous measurements of dissolved gases (O2 and Ar) in the surface water in order to quantify NCP at subkilometer scale resolution. We constrain GPP in discrete samples using the triple isotopic composition of O2. We find the average NCP in the western equatorial Pacific is 5.9 ± 0.9 mmol O2 m−2 d−1 (equivalent to 1.5 ± 0.2 mol C m−2 yr−1 with error estimates reflecting 1σ confidence levels) and the average GPP is 121 ± 34 mmol O2 m−2 d−1 (equivalent to 32 ± 9 mol C m−2 yr−1). The measurements reveal significant spatial variability on length scales as small as 50 km. The NCP/GPP ratio is 5.7% ± 1.8%. We also present results for NCP and GPP in the coastal area off Papua New Guinea and for GPP in the central Pacific along the equator.
    Description: This work was supported by the NSF Chemical Oceanography and the Office of Polar Programs, by the NOAA climate and global change program (fellowship to RHRS), and by Princeton University (Hess fellowship to RHRS).
    Keywords: Production ; Triple oxygen isotopes ; Equatorial pacific
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 7
    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
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  • 8
    Publication Date: 2022-05-26
    Description: © The International Society for Microbial Ecology, 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ISME Journal 10 (2016): 979–989, doi:10.1038/ismej.2015.175.
    Description: We investigated compositional relationships between bacterial communities in the water column and those in deep-sea sediment at three environmentally distinct Pacific sites (two in the Equatorial Pacific and one in the North Pacific Gyre). Through pyrosequencing of the v4–v6 hypervariable regions of the 16S ribosomal RNA gene, we characterized 450 104 pyrotags representing 29 814 operational taxonomic units (OTUs, 97% similarity). Hierarchical clustering and non-metric multidimensional scaling partition the samples into four broad groups, regardless of geographic location: a photic-zone community, a subphotic community, a shallow sedimentary community and a subseafloor sedimentary community (greater than or equal to1.5 meters below seafloor). Abundance-weighted community compositions of water-column samples exhibit a similar trend with depth at all sites, with successive epipelagic, mesopelagic, bathypelagic and abyssopelagic communities. Taxonomic richness is generally highest in the water-column O2 minimum zone and lowest in the subseafloor sediment. OTUs represented by abundant tags in the subseafloor sediment are often present but represented by few tags in the water column, and represented by moderately abundant tags in the shallow sediment. In contrast, OTUs represented by abundant tags in the water are generally absent from the subseafloor sediment. These results are consistent with (i) dispersal of marine sedimentary bacteria via the ocean, and (ii) selection of the subseafloor sedimentary community from within the community present in shallow sediment.
    Description: This study was funded by the Biological Oceanography Program of the US National Science Foundation (grant OCE-0752336) and by the NSF-funded Center for Dark Energy Biosphere Investigations (grant NSF-OCE-0939564).
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 9
    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Applied and Environmental Microbiology 82 (2016): 4994-4999, doi:10.1128/AEM.00809-16.
    Description: Subseafloor sediment hosts a large, taxonomically rich and metabolically diverse microbial ecosystem. However, the factors that control microbial diversity in subseafloor sediment have rarely been explored. Here we show that bacterial richness varies with organic degradation rate and sediment age. At three open-ocean sites (in the Bering Sea and equatorial Pacific) and one continental margin site (Indian Ocean), richness decreases exponentially with increasing sediment depth. The rate of decrease in richness with depth varies from site to site. The vertical succession of predominant terminal electron acceptors correlates to abundance-weighted community composition, but does not drive the vertical decrease in richness. Vertical patterns of richness at the open-ocean sites closely match organic degradation rates; both properties are highest near the seafloor and decline together as sediment depth increases. This relationship suggests that (i) total catabolic activity and/or electron donor diversity exerts a primary influence on bacterial richness in marine sediment, and (ii) many bacterial taxa that are poorly adapted for subseafloor sedimentary conditions are degraded in the geologically young sediment where respiration rates are high. Richness consistently takes a few hundred thousand years to decline from near-seafloor values to much lower values in deep anoxic subseafloor sediment, regardless of sedimentation rate, predominant terminal electron acceptor, or oceanographic context.
    Description: This work, including the efforts of Mitchell L. Sogin and Steven D’Hondt, was funded by Sloan Foundation (Census of Deep Life). This work, including the efforts of Steven D’Hondt, was funded by U.S. Science Support Program for IODP. This work, including the efforts of Steven D’Hondt, was funded by National Science Foundation (NSF) (OCE- 0752336 and OCE-0939564). The work of E. A. Walsh, J. B. Kirkpatrick, R. Pockalny, and J. Sauvage was funded by the grants to S. D’Hondt.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 10
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