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  • 1
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    Archaeal lipid concentration and isotopic data in sediments from expeditions M84/1 and POS450 (2021)
    PANGAEA
    Details
    Publication Date: 2023-02-24
    Description: Archaea occupy an important niche in the global carbon cycle and their lipids are widely used as indicators of environmental conditions in both paleoenvironmental and modern biogeochemical studies. The principal sources of archaeal lipids in marine sediments are benthic archaea, fossil remnants of planktonic archaea, and allochthonous sources such as soils. However, the relative contributions of these sources to the sedimentary lipid pool have not been comprehensively constrained, complicating a mechanistic understanding of archaeal lipid proxies. In order to provide insights into the relative contributions of these sources and identify signals derived from the sedimentary activity, we performed a systematic survey of concentrations and stable carbon isotopic compositions of both core and intact archaeal lipids The sample set consisted of 44 sediment horizons from the Mediterranean and adjacent basins and represented diverse sources of organic matter and depositional conditions.
    Keywords: Archaea; Butanetriol dibiphytanyl glycerol tetraethers; DARCLIFE; Deep subsurface Archaea: carbon cycle, life strategies, and role in sedimentary ecosystems; Geochemical zones; Glycerol dibiphytanyl glycerol tetraethers; in situ production; Intact polar lipids; marine sediments; stable carbon isotopes; Terrestrial input
    Type: Dataset
    Format: application/zip, 2 datasets
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  • 2
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    Planktonic archaeal phosphorus affinity and apportionment (PAPAA) (2020)
    PANGAEA
    Details
    Publication Date: 2023-07-07
    Description: Complete cell count, nutrient concentration, and radiotracer data for culture incubations and results presented in the manuscript "Carbon recycling efficiency and phosphate turnover by marine nitrifying archaea". This includes measurement of the following parameters for up to nine time points in cultures of N. maritimus strains NAOA6 and SCM1: For each culture incubation, the time points where C and P uptake rates were considered to be first-order are identified by a value of 1 in the column "Linear Y/N". Columns headed by "SD" provide the standard deviation of the value listed in the column to the immediate left.
    Keywords: Affinity for phosphate, standard deviation; AOA; Archaea; Archaea, standard deviation; Bicarbonate/Phophate uptake ratio; Bicarbonate uptake; Bicarbonate uptake rate; Bicarbonate uptake rate, standard deviation; Bicarbonate uptake rate per cell; Bicarbonate uptake rate per cell, standard deviation; Calculated; Category; C fixation; DATE/TIME; Linearity; Measured; nitrification; Nitrification rate; Nitrification rate, standard deviation; Nitrification rate per cell; Nitrification rate per cell, standard deviation; Nitrite; Nitrite, standard deviation; P assimilation; Phosphate; Phosphate turnover time; Phosphate turnover time, standard deviation; Phosphate uptake; Phosphate uptake, standard deviation; Phosphate uptake rate; Phosphate uptake rate per cell; Phosphate uptake rate per cell, standard deviation; P limitation; Specific phosphate affinity; Specific phosphate affinity, standard deviation; Strain; Time, incubation; Time point, descriptive; Volume
    Type: Dataset
    Format: text/tab-separated-values, 2787 data points
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  • 3
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    Archaeal lipid carbon isotopic data in sediments from expeditions M84/1 and POS450 (2021)
    PANGAEA
    Details
    Publication Date: 2024-02-02
    Keywords: Analyses of biphytanyl (BP) moieties; Analyses of phytanyl (Phy) moieties; Archaea; Archaeal intact polar lipids, δ13C; Butanetriol dibiphytanyl glycerol tetraethers; Core lipids, δ13C; DARCLIFE; DARCSEAS II; Deep subsurface Archaea: carbon cycle, life strategies, and role in sedimentary ecosystems; Depth, bottom/max; DEPTH, sediment/rock; Depth, top/min; Event label; GC; GeoB15103-1; GeoB15103-2; GeoB15103-3; GeoB15104-1; GeoB15104-2; GeoB15105-2; GeoB15105-4; GeoB17302-5; GeoB17306-1; GeoB17306-2; GeoB17307-5; GeoB17307-8; GeoB17308-1; GeoB17308-4; Geochemical zones; Glycerol dibiphytanyl glycerol tetraethers; Gravity corer; in situ production; Intact polar lipids; M84/1; M84/1_119-1; M84/1_120-1; M84/1_121-1; M84/1_122-1; M84/1_123-1; M84/1_127-1; M84/1_129-1; marine sediments; Meteor (1986); MUC; MultiCorer; POS450; POS450_576-5; POS450_582-1; POS450_583-5; POS450_584-1; POS450_585-3; POS450_586-1; POS450_587-1; Poseidon; stable carbon isotopes; Terrestrial input; Western Mediterranean Sea
    Type: Dataset
    Format: text/tab-separated-values, 417 data points
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  • 4
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    Archaeal lipid concentration data in sediments from expeditions M84/1 and POS450 (2021)
    PANGAEA
    Details
    Publication Date: 2024-02-02
    Keywords: 2Me-Acyclic glycerol dibiphytanyl glycerol tetraether; 2Me-Monocyclic glycerol dibiphytanyl glycerol tetraether; Acyclic glycerol dibiphytanyl glycerol tetraether; Archaea; Archaeol; Butanetriol dibiphytanyl glycerol tetraether, 0; Butanetriol dibiphytanyl glycerol tetraether, 0a; Butanetriol dibiphytanyl glycerol tetraether, 1; Butanetriol dibiphytanyl glycerol tetraether, 1a; Butanetriol dibiphytanyl glycerol tetraether, 1b; Butanetriol dibiphytanyl glycerol tetraether, 2; Butanetriol dibiphytanyl glycerol tetraether, 2a; Butanetriol dibiphytanyl glycerol tetraethers; Crenarchaeol; Crenarchaeol regio-isomer; DARCLIFE; DARCSEAS II; Deep subsurface Archaea: carbon cycle, life strategies, and role in sedimentary ecosystems; Depth, bottom/max; DEPTH, sediment/rock; Depth, top/min; Dicyclic glycerol dibiphytanyl glycerol tetraether; Dicyclic glycerol dibiphytanyl glycerol tetraether, 2a; Diglycosidic archaeol; Diglycosyl acyclic glycerol dibiphytanyl glycerol tetraether; Diglycosyl butanetriol dibiphytanyl glycerol tetraether, 0; Diglycosyl crenarchaeol; Diglycosyl crenarchaeol regio-isomer; Diglycosyl dicyclic glycerol dibiphytanyl glycerol tetraether; Diglycosyl monocyclic glycerol dibiphytanyl glycerol tetraether; Diglycosyl monohydroxylated acyclic glycerol dibiphytanyl glycerol tetraether; Diglycosyl monohydroxylated dicyclic glycerol dibiphytanyl glycerol tetraether; Diglycosyl monohydroxylated monocyclic glycerol dibiphytanyl glycerol tetraether; Diglycosyl pentanetriol dibiphytanyl glycerol tetraether, 0; Diglycosyl tetracyclic glycerol dibiphytanyl glycerol tetraether; Diglycosyl tricyclic glycerol dibiphytanyl glycerol tetraether; Dihydroxylated acyclic glycerol dibiphytanyl glycerol tetraethers; Dihydroxylated glycerol dibiphytanyl glycerol tetraethers, 0a; Event label; GC; GeoB15103-1; GeoB15103-2; GeoB15103-3; GeoB15104-1; GeoB15104-2; GeoB15105-2; GeoB15105-4; GeoB17302-5; GeoB17306-1; GeoB17306-2; GeoB17307-5; GeoB17307-8; GeoB17308-1; GeoB17308-4; Geochemical zones; Glycerol dibiphytanol diether, 0; Glycerol dibiphytanol diether, 1; Glycerol dibiphytanol diether, 1a; Glycerol dibiphytanol diether, 2; Glycerol dibiphytanol diether, 2a; Glycerol dibiphytanol diether, 3; Glycerol dibiphytanol diether, 3a; Glycerol dibiphytanol diether, 4; Glycerol dibiphytanol diether, 4a; Glycerol dibiphytanol diether, 5; Glycerol dibiphytanol diether, 5a; Glycerol dibiphytanyl glycerol tetraether; Glycerol dibiphytanyl glycerol tetraether, 1a; Glycerol dibiphytanyl glycerol tetraethers; Gravity corer; Hexosephosphohexose acyclic glycerol dibiphytanyl glycerol tetraether; Hexosephosphohexose crenarchaeol; Hexosephosphohexose dicyclic glycerol dibiphytanyl glycerol tetraether; Hexosephosphohexose monocyclic glycerol dibiphytanyl glycerol tetraether; Hexosephosphohexose tetracyclic glycerol dibiphytanyl glycerol tetraether; Hexosephosphohexose tricyclic glycerol dibiphytanyl glycerol tetraether; Hydroxyarchaeols; Hydroxylated acyclic glycerol dibiphytanyl glycerol tetraether; Hydroxylated acyclic glycerol dibiphytanyl glycerol tetraether, 0a; Hydroxylated dicyclic glycerol dibiphytanyl glycerol tetraether; Hydroxylated dicyclic glycerol dibiphytanyl glycerol tetraether, 2a; Hydroxylated glycerol dibiphytanol diether, 0; Hydroxylated glycerol dibiphytanol diether, 0a; Hydroxylated glycerol dibiphytanol diether, 1; Hydroxylated glycerol dibiphytanol diether, 1a; Hydroxylated glycerol dibiphytanol diether, 2; Hydroxylated glycerol dibiphytanol diether, 2a; Hydroxylated monocyclic glycerol dibiphytanyl glycerol tetraether; Hydroxylated monocyclic glycerol dibiphytanyl glycerol tetraether, 1a; in situ production; Intact polar lipids; M84/1; M84/1_119-1; M84/1_120-1; M84/1_121-1; M84/1_122-1; M84/1_123-1; M84/1_127-1; M84/1_129-1; marine sediments; Meteor (1986); Methoxy acyclic glycerol dibiphytanyl glycerol tetraether; Methoxy archaeol; Methoxy dicyclic glycerol dibiphytanyl glycerol tetraether; Methoxy dicyclic glycerol dibiphytanyl glycerol tetraether, 2a; Methoxy monocyclic glycerol dibiphytanyl glycerol tetraether; Methoxy monocyclic glycerol dibiphytanyl glycerol tetraether, 1a; Methylated acyclic glycerol dibiphytanyl glycerol tetraether; Monocyclic glycerol dibiphytanyl glycerol tetraether; Monoglycosidic archaeol; Monoglycosyl acyclic glycerol dibiphytanyl glycerol tetraether; Monoglycosyl butanetriol dibiphytanyl glycerol tetraether, 0; Monoglycosyl crenarchaeol; Monoglycosyl crenarchaeol regio-isomer; Monoglycosyl dicyclic glycerol dibiphytanyl glycerol tetraether; Monoglycosyl monocyclic glycerol dibiphytanyl glycerol tetraether; Monoglycosyl monohydroxylated acyclic glycerol dibiphytanyl glycerol tetraether; Monoglycosyl monohydroxylated dicyclic glycerol dibiphytanyl glycerol tetraether; Monoglycosyl monohydroxylated monocyclic glycerol dibiphytanyl glycerol tetraether; Monoglycosyl pentanetriol dibiphytanyl glycerol tetraether, 0; Monoglycosyl tetracyclic glycerol dibiphytanyl glycerol tetraether; Monoglycosyl tricyclic glycerol dibiphytanyl glycerol tetraether; MUC; MultiCorer; Pentanetriol dibiphytanyl glycerol tetraether, 0; Pentanetriol dibiphytanyl glycerol tetraether, 1; POS450; POS450_576-5; POS450_582-1; POS450_583-5; POS450_584-1; POS450_585-3; POS450_586-1; POS450_587-1; Poseidon; stable carbon isotopes; Terrestrial input; Tetracyclic glycerol dibiphytanyl glycerol tetraether; Tetracyclic glycerol dibiphytanyl glycerol tetraether, 4a; Tricyclic glycerol dibiphytanyl glycerol tetraether; Tricyclic glycerol dibiphytanyl glycerol tetraether, 3a; Triglycosyl acyclic glycerol dibiphytanyl glycerol tetraether; Triglycosyl crenarchaeol; Triglycosyl dicyclic glycerol dibiphytanyl glycerol tetraether; Triglycosyl monocyclic glycerol dibiphytanyl glycerol tetraether; Triglycosyl monohydroxylated acyclic glycerol dibiphytanyl glycerol tetraether; Triglycosyl monohydroxylated dicyclic glycerol dibiphytanyl glycerol tetraether; Triglycosyl monohydroxylated monocyclic glycerol dibiphytanyl glycerol tetraether; Triglycosyl tetracyclic glycerol dibiphytanyl glycerol tetraether; Triglycosyl tricyclic glycerol dibiphytanyl glycerol tetraether; Western Mediterranean Sea
    Type: Dataset
    Format: text/tab-separated-values, 4443 data points
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  • 5
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    Absolute concentrations of BDGTs and PDGTs in sediments from expeditions M84/1 and POS450 (2019)
    PANGAEA
    In:  Supplement to: Coffinet, Sarah; Meador, Travis B; Mühlena, Lukas; Becker, Kevin W; Schröder, Jan Martin; Zhu, Qing-Zeng; Lipp, Julius S; Heuer, Verena B; Crump, Matthew P; Hinrichs, Kai-Uwe (2019): Structural elucidation and environmental distributions of butanetriol and pentanetriol dialkyl glycerol tetraethers (BDGTs and PDGTs). Biogeosciences, 17, 317-330, https://doi.org/10.5194/bg-17-317-2020
    Details
    Publication Date: 2024-02-02
    Description: Butanetriol and pentanetriol dialkyl glycerol tetraethers (BDGTs and PDGTs) are membrane lipids recently discovered in sedimentary environments and in the methanogenic archaeon Methanomassiliicoccus luminyensis. They possess an unusual structure, which challenges fundamental assumptions in lipid biochemistry. Indeed, they bear a butanetriol or a pentanetriol backbone instead of a glycerol at one end of their core structure. In this study, we unambiguously located the additional methyl group of the BDGT compound on the C3 carbon of the lipid backbone via high-field two-dimensional NMR experiments. We further systematically explored the abundance, distribution and isotopic composition of BDGTs and PDGTs as both intact polar and core lipid forms in marine sediments collected in contrasting environments of the Mediterranean Sea and Black Sea. In addition, relatively 13C-depleted BDGTs from the Rhone delta and from the Black Sea are in agreement with a probable methanogenic source for these lipids. In line with this interpretation, high proportions of intact polar BDGTs and PDGTs were detected in the deeper methane-laden sedimentary layers. However, relatively 13C enriched BDGTs and contrasting headgroup distribution patterns of BDGTs and PDGTs in sediments of the Eastern Mediterranean Sea imply that additional archaeal groups also produce these unique lipids.
    Keywords: Acyclic butanetriol dialkyl glycerol tetraethers in core lipids, per unit mass organic carbon; Center for Marine Environmental Sciences; DARCLIFE; DARCSEAS II; Deep subsurface Archaea: carbon cycle, life strategies, and role in sedimentary ecosystems; Depth, bottom/max; DEPTH, sediment/rock; Depth, top/min; Dicyclic butanetriol dialkyl glycerol tetraethers in core lipids, per unit mass organic carbon; Diglycosidic butanetriol dialkyl glycerol tetraethers, per unit mass organic carbon; Diglycosidic pentanetriol dialkyl glycerol tetraethers, per unit mass organic carbon; Event label; GC; GeoB15103-1; GeoB15103-2; GeoB15103-3; GeoB15104-1; GeoB15104-2; GeoB15105-2; GeoB15105-4; GeoB17302-5; GeoB17304-3; GeoB17306-1; GeoB17306-2; GeoB17307-5; GeoB17307-8; GeoB17308-1; GeoB17308-4; Gravity corer; Identification; M84/1; M84/1_119-1; M84/1_120-1; M84/1_121-1; M84/1_122-1; M84/1_123-1; M84/1_127-1; M84/1_129-1; MARUM; Meteor (1986); Monocyclic butanetriol dialkyl glycerol tetraethers in core lipids, per unit mass organic carbon; Monoglycosidic butanetriol dialkyl glycerol tetraethers, per unit mass organic carbon; Monoglycosidic pentanetriol dialkyl glycerol tetraethers, per unit mass organic carbon; MUC; MultiCorer; Pentanetriol dialkyl glycerol tetraethers in core lipids, per unit mass organic carbon; POS450; POS450_576-5; POS450_580-3; POS450_582-1; POS450_583-5; POS450_584-1; POS450_585-3; POS450_586-1; POS450_587-1; Poseidon; Proposed International Geo Sample Number; Western Mediterranean Sea
    Type: Dataset
    Format: text/tab-separated-values, 455 data points
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  • 6
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    Polar membrane lipids and elemental composition of Thermococcus kodakarensis cells according to growth stage and phosphorus supply (2014)
    PANGAEA
    In:  Supplement to: Meador, Travis B; Gagen, Emma; Loscar, Michael E; Goldhammer, Tobias; Yoshinaga, Marcos Yukio; Wendt, Jenny; Thomm, Michael; Hinrichs, Kai-Uwe (2014): Thermococcus kodakarensis modulates its polar membrane lipids and elemental composition according to growth stage and phosphate availability. Frontiers in Microbiology, 5, 1-13, https://doi.org/10.3389/fmicb.2014.00010
    Details
    Publication Date: 2024-03-07
    Description: We observed significant changes in the elemental and intact polar lipid (IPL) composition of the archaeon Thermococcus kodakarensis (KOD1) in response to growth stage and phosphorus supply. Reducing the amount of organic supplements and phosphate in growth media resulted in significant decreases in cell size and cellular quotas of carbon (C), nitrogen (N), and phosphorus (P), which coincided with significant increases in cellular IPL quota and IPLs comprising multiple P atoms and hexose moieties. Relatively more cellular P was stored as IPLs in P-limited cells (2-8%) compared to control cells (〈0.8%). We also identified a specific IPL biomarker containing a phosphatidyl-N-acetylhexoseamine headgroup that was relatively enriched during rapid cell division. These observations serve as empirical evidence of IPL adaptations in Archaea that will help to interpret the distribution of these biomarkers in natural systems. The reported cell quotas of C, N, and P represent the first such data for a specific archaeon and suggest that thermophiles are C-rich compared to the cell carbon-to-volume relationship reported for planktonic bacteria.
    Keywords: Archaeol, per cell; Carbon, organic, total, per cell; Dry mass; Glycerol dialkyl glycerol tetraether, per cell; Growth phase; Incubation duration; Nitrogen, total, per cell; Phosphorus, total, per cell; Replicate; Thermococcus kodakarensis; Treatment
    Type: Dataset
    Format: text/tab-separated-values, 458 data points
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  • 7
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    Biogeochemical relationships between ultrafiltered dissolved organic matter and picoplankton activity in the Eastern Mediterranean Sea (2010)
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 57 (2010): 1460-1477, doi:10.1016/j.dsr2.2010.02.015.
    Description: We targeted the warm, subsurface waters of the Eastern Mediterranean Sea (EMS) to investigate processes that are linked to the chemical composition and cycling of dissolved organic carbon (DOC) in seawater. The apparent respiration of semi-labile DOC accounted for 27 ± 18% of oxygen consumption in EMS mesopelagic and bathypelagic waters; this value is higher than that observed in the bathypelagic open ocean, so the chemical signals that accompany remineralization of DOC may thus be more pronounced in this region. Ultrafiltered dissolved organic matter (UDOM) collected from four deep basins at depths ranging from 2 to 4350 m exhibited bulk chemical (1H-NMR) and molecular level (amino acid and monosaccharide) abundances, composition, and spatial distribution that were similar to previous reports, except for a sample collected in the deep waters of the N. Aegean Sea that had been isolated for over a decade. The amino acid component of UDOM was tightly correlated with apparent oxygen utilization and prokaryotic activity, indicating its relationship with remineralization processes that occur over a large range of timescales. Principal component analyses of relative mole percentages of monomers revealed that oxygen consumption and prokaryotic activity were correlated with variability in amino acid distributions but not well correlated with monosaccharide distributions. Taken together, this study elucidates key relationships between the chemical composition of DOM and heterotrophic metabolism.
    Description: TBM and AG acknowledge funding from the Hellenic GSRT/European Union (non-EU Grant No180) and SESAME Project (European Commission's Sixth Framework Program, EC Contract No GOCE-036949). TY was supported by the Japanese Society for the Promotion of Science (JSPS) Postdoctoral Fellowship for research abroad and DDC received a fellowship of the University of Groningen. Microbial laboratory work and molecular analyses were supported by a grant of the Earth and Life Science Division of the Dutch Science Foundation (ARCHIMEDES project, 835.20.023) to GJH. DJR and TBM were supported by grants from the Gordon and Betty Moore Foundation and from the C-MORE organization of NSF.
    Keywords: DOM ; Biogeochemical cycles ; Ultrafiltration ; AOU ; Microbial loop
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
    Format: application/pdf
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  • 8
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    Substrate-dependent incorporation of carbon and hydrogen for lipid biosynthesis by Methanosarcina barkeri (2020)
    Wiley Online Library
    In:  EPIC3Environmental Microbiology Reports, Wiley Online Library, 12(5), pp. 555-567
    Details
    Publication Date: 2021-10-20
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
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  • 9
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    Substrate‐dependent incorporation of carbon and hydrogen for lipid biosynthesis by Methanosarcina barkeri (2020)
    Wiley
    Details
    Publication Date: 2020-09-22
    Electronic ISSN: 1758-2229
    Topics: Biology
    Published by Wiley
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  • 10
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    Thermococcus kodakarensis modulates its polar membrane lipids and elemental composition according to growth stage and phosphate availability (2014)
    Frontiers Media
    Details
    Publication Date: 2014-01-01
    Electronic ISSN: 1664-302X
    Topics: Biology
    Published by Frontiers Media
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