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  • 1
    Electronic Resource
    Electronic Resource
    Bicarbonate uptake by marine Crenarchaeota (2003)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 219 (2003), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Biphytanyl membrane lipids and 16S rRNA sequences derived from marine Crenarchaeota were detected in shallow North Sea surface water in February 2002. To investigate the carbon fixation mechanism of these uncultivated archaea in situ 13C bicarbonate tracer experiments were performed with this water in the absence of light. About 70% of the detected 13C incorporation into lipids (including fatty acids and sterols) is accounted for by the crenarchaeotal biphytanyl membrane lipids. This finding indicates that marine Crenarchaeota can utilize bicarbonate or CO2 derived thereof in the absence of light and are chemoautotrophic organisms.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/S0378-1097(03)00060-0
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    Paper (German National Licenses)
    Fulltext
  • 2
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    TEX86 values and temperature estimation for sediment trap samples
    PANGAEA
    In:  Supplement to: Wuchter, Cornelia; Schouten, Stefan; Wakeham, Stuart G; Sinninghe Damsté, Jaap S (2006): Archaeal tetraether membrane lipid fluxes in the northeastern Pacific and the Arabian Sea: Implications for TEX86 aleothermometry. Paleoceanography, 21(4), PA4208, https://doi.org/10.1029/2006PA001279
    Details
    Publication Date: 2023-05-12
    Description: The newly introduced temperature proxy, the tetraether index of archaeal lipids with 86 carbon atoms (TEX86), is based on the number of cyclopentane moieties in the glycerol dialkyl glycerol tetraether (GDGT) lipids of marine Crenarchaeota. The composition of sedimentary GDGTs used for TEX86 paleothermometry is thought to reflect sea surface temperature (SST). However, marine Crenarchaeota occur ubiquitously in the world oceans over the entire depth range and not just in surface waters. We analyzed the GDGT distribution in settling particulate organic matter collected in sediment traps from the northeastern Pacific Ocean and the Arabian Sea to investigate the seasonal and spatial distribution of the fluxes of crenarchaeotal GDGTs and the origin of the TEX86 signal transported to the sediment. In both settings the TEX86 measured at all trap deployment depths reflects SST. In the Arabian Sea, analysis of an annual time series showed that the SST estimate based on TEX86 in the shallowest trap at 500 m followed the in situ SST with a 1 to 3 week time delay, likely caused by the relatively low settling speed of sinking particles. This revealed that the GDGT signal that reaches deeper water is derived from the upper water column rather than in situ production of GDGTs. The GDGT temperature signal in deeper traps at 1500 m and 3000 m did not show a seasonal cyclicity observed in the 500 m trap but rather reflected the annual mean SST. This is probably due to a homogenization of the TEX86 SST signal carried by particles as they ultimately reach the interior of the ocean. Our data confirm the use of TEX86 as a temperature proxy of surface ocean waters.
    Keywords: Arabian Sea; MS-3; MUC; MultiCorer; Northeast Pacific; Trap, sediment; TRAPS; VERTEX_5A; VERTEX_5C
    Type: Dataset
    Format: application/zip, 2 datasets
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    DATA PANGAEA
  • 3
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    (Table 2) TEX86 values and temperature estimation for two sediment traps from the northeastern Pacific Ocean
    PANGAEA
    Details
    Publication Date: 2023-05-12
    Keywords: Calculated, TEX86; Comment; DEPTH, water; Event label; Northeast Pacific; Temperature, water; Temperature, water, interpolated; Tetraether index of 86 carbon atoms; Trap, sediment; TRAPS; VERTEX_5A; VERTEX_5C
    Type: Dataset
    Format: text/tab-separated-values, 31 data points
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    DATA PANGAEA
  • 4
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    (Table 3) TEX86 values and temperature estimation for sediment traps MS-3
    PANGAEA
    Details
    Publication Date: 2023-05-12
    Keywords: Arabian Sea; Calculated, TEX86; DATE/TIME; Date/time end; Day of the year; DEPTH, water; MS-3; MUC; MultiCorer; Temperature, water, interpolated; Tetraether index of 86 carbon atoms
    Type: Dataset
    Format: text/tab-separated-values, 315 data points
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    DATA PANGAEA
  • 5
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    Climate oscillations reflected within the microbiome of Arabian Sea sediments (2017)
    Nature Publishing Group
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 6040, doi:10.1038/s41598-017-05590-9.
    Description: Selection of microorganisms in marine sediment is shaped by energy-yielding electron acceptors for respiration that are depleted in vertical succession. However, some taxa have been reported to reflect past depositional conditions suggesting they have experienced weak selection after burial. In sediments underlying the Arabian Sea oxygen minimum zone (OMZ), we performed the first metagenomic profiling of sedimentary DNA at centennial-scale resolution in the context of a multi-proxy paleoclimate reconstruction. While vertical distributions of sulfate reducing bacteria and methanogens indicate energy-based selection typical of anoxic marine sediments, 5–15% of taxa per sample exhibit depth-independent stratigraphies indicative of paleoenvironmental selection over relatively short geological timescales. Despite being vertically separated, indicator taxa deposited under OMZ conditions were more similar to one another than those deposited in bioturbated intervals under intervening higher oxygen. The genomic potential for denitrification also correlated with palaeo-OMZ proxies, independent of sediment depth and available nitrate and nitrite. However, metagenomes revealed mixed acid and Entner-Dourdoroff fermentation pathways encoded by many of the same denitrifier groups. Fermentation thus may explain the subsistence of these facultatively anaerobic microbes whose stratigraphy follows changing paleoceanographic conditions. At least for certain taxa, our analysis provides evidence of their paleoenvironmental selection over the last glacial-interglacial cycle.
    Description: his work was primarily supported by NSF MGG Grant #1357017 to MJLC, VG, and LG, and the KAUST-WHOI Special Academic Partnership Program OCRF-SP-WHOI-2013 (grants 7000000463 to XI and 7000000464 to MJLC). Additional financial support was provided via a C-DEBI grant #OCE-0939564 to WDO.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 6
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    Archaeal nitrification in the ocean (2008)
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © National Academy of Sciences, 2006. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 103 (2006): 12317-12322, doi:10.1073/pnas.0600756103.
    Description: Marine Crenarchaeota are the most abundant single group of prokaryotes in the ocean but their physiology and role in marine biogeochemical cycles are unknown. Recently, a member of this clade was isolated from a sea aquarium and shown to be capable of nitrification, tentatively suggesting that they may play a role in the oceanic nitrogen cycle. We enriched a crenarchaeote from North Sea water and show that it oxidizes ammonium to nitrite. A time series study in the North Sea revealed that the abundance of the gene encoding for the archaeal ammonia monooxygenase alfa subunit (amoA) is correlated with the decline in ammonium concentrations and with the abundance of Crenarcheota. Remarkably, the archaeal amoA abundance was 1-2 orders of magnitude higher than those of bacterial nitrifiers which are commonly thought to mediate the oxidation of ammonium to nitrite in marine environments. Analysis of Atlantic waters of the upper 1000 m, where most of the ammonium regeneration and oxidation takes place, showed that crenarchaeotal amoA copy numbers are also one to three orders of magnitude higher than those of bacterial amoA. Our data thus suggest a major role for Archaea in oceanic nitrification.
    Description: This study was partially supported by grants to JSSD and MJLC (VENI) from the Netherlands Organisation for Scientific Research (NWO).
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
    Format: application/pdf
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  • 7
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    Neoglacial climate anomalies and the Harappan metamorphosis (2018)
    Copernicus Publications on behalf of the European Geosciences Union
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Climate of the Past 14 (2018): 1669-1686, doi:10.5194/cp-14-1669-2018.
    Description: Climate exerted constraints on the growth and decline of past human societies but our knowledge of temporal and spatial climatic patterns is often too restricted to address causal connections. At a global scale, the inter-hemispheric thermal balance provides an emergent framework for understanding regional Holocene climate variability. As the thermal balance adjusted to gradual changes in the seasonality of insolation, the Intertropical Convergence Zone migrated southward accompanied by a weakening of the Indian summer monsoon. Superimposed on this trend, anomalies such as the Little Ice Age point to asymmetric changes in the extratropics of either hemisphere. Here we present a reconstruction of the Indian winter monsoon in the Arabian Sea for the last 6000 years based on paleobiological records in sediments from the continental margin of Pakistan at two levels of ecological complexity: sedimentary ancient DNA reflecting water column environmental states and planktonic foraminifers sensitive to winter conditions. We show that strong winter monsoons between ca. 4500 and 3000 years ago occurred during a period characterized by a series of weak interhemispheric temperature contrast intervals, which we identify as the early neoglacial anomalies (ENA). The strong winter monsoons during ENA were accompanied by changes in wind and precipitation patterns that are particularly evident across the eastern Northern Hemisphere and tropics. This coordinated climate reorganization may have helped trigger the metamorphosis of the urban Harappan civilization into a rural society through a push–pull migration from summer flood-deficient river valleys to the Himalayan piedmont plains with augmented winter rains. The decline in the winter monsoon between 3300 and 3000 years ago at the end of ENA could have played a role in the demise of the rural late Harappans during that time as the first Iron Age culture established itself on the Ghaggar-Hakra interfluve. Finally, we speculate that time-transgressive land cover changes due to aridification of the tropics may have led to a generalized instability of the global climate during ENA at the transition from the warmer Holocene thermal maximum to the cooler Neoglacial.
    Description: This work was supported by the NSF OCE grant no. 0634731 and internal WHOI funds to Liviu Giosan, NSF MGG grant no. 1357017 to Marco J. L. Coolen, Valier Galy and Liviu Giosan; and a C-DEBI grant no. OCE-0939564 to William D. Orsi.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 8
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    Microbial diversity and methanogenic activity of Antrim Shale formation waters from recently fractured wells (2014)
    Frontiers Media
    Details
    Publication Date: 2022-05-25
    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): 367, doi:10.3389/fmicb.2013.00367.
    Description: The Antrim Shale in the Michigan Basin is one of the most productive shale gas formations in the U.S., but optimal resource recovery strategies must rely on a thorough understanding of the complex biogeochemical, microbial, and physical interdependencies in this and similar systems. We used Illumina MiSeq 16S rDNA sequencing to analyze the diversity and relative abundance of prokaryotic communities present in Antrim shale formation water of three closely spaced recently fractured gas-producing wells. In addition, the well waters were incubated with a suite of fermentative and methanogenic substrates in an effort to stimulate microbial methane generation. The three wells exhibited substantial differences in their community structure that may arise from their different drilling and fracturing histories. Bacterial sequences greatly outnumbered those of archaea and shared highest similarity to previously described cultures of mesophiles and moderate halophiles within the Firmicutes, Bacteroidetes, and δ- and ε-Proteobacteria. The majority of archaeal sequences shared highest sequence similarity to uncultured euryarchaeotal environmental clones. Some sequences closely related to cultured methylotrophic and hydrogenotrophic methanogens were also present in the initial well water. Incubation with methanol and trimethylamine stimulated methylotrophic methanogens and resulted in the largest increase in methane production in the formation waters, while fermentation triggered by the addition of yeast extract and formate indirectly stimulated hydrogenotrophic methanogens. The addition of sterile powdered shale as a complex natural substrate stimulated the rate of methane production without affecting total methane yields. Depletion of methane indicative of anaerobic methane oxidation (AMO) was observed over the course of incubation with some substrates. This process could constitute a substantial loss of methane in the shale formation.
    Description: Tracy J. Mincer was supported for this project from NSF CHE-OCE Award # 1131415.
    Keywords: Antrim gas shale ; Biogenic gas ; Formation water ; Fermenting bacteria ; Methanogens
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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