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  • 1
    facet.materialart.
    Unknown
    PANGAEA
    In:  Supplement to: Löscher, Carolin R; Großkopf, Tobias; Desai, Falguni; Gill, Diana; Schunck, Harald; Croot, Peter L; Schlosser, Christian; Neulinger, Sven C; Pinnow, Nicole; Lavik, Gaute; Kuypers, Marcel MM; LaRoche, Julie; Schmitz, Ruth A (2014): Facets of diazotrophy in the oxygen minimum zone waters off Peru. The ISME Journal, https://doi.org/10.1038/ismej.2014.71
    Publication Date: 2023-10-28
    Description: Nitrogen fixation, the biological reduction of dinitrogen gas (N2) to ammonium (NH4+), is quantitatively the most important external source of new nitrogen (N) to the open ocean. Classically, the ecological niche of oceanic N2 fixers (diazotrophs) is ascribed to tropical oligotrophic surface waters, often depleted in fixed N, with a diazotrophic community dominated by cyanobacteria. Although this applies for large areas of the ocean, biogeochemical models and phylogenetic studies suggest that the oceanic diazotrophic niche may be much broader than previously considered, resulting in major implications for the global N-budget. Here, we report on the composition, distribution and abundance of nifH, the functional gene marker for N2 fixation. Our results show the presence of eight clades of diazotrophs in the oxygen minimum zone (OMZ) off Peru. Although proteobacterial clades dominated overall, two clusters affiliated to spirochaeta and archaea were identified. N2 fixation was detected within OMZ waters and was stimulated by the addition of organic carbon sources supporting the view that non-phototrophic diazotrophs were actively fixing dinitrogen. The observed co-occurrence of key functional genes for N2 fixation, nitrification, anammox and denitrification suggests that a close spatial coupling of N-input and N-loss processes exists in the OMZ off Peru. The wide distribution of diazotrophs throughout the water column adds to the emerging view that the habitat of marine diazotrophs can be extended to low oxygen/high nitrate areas. Furthermore, our statistical analysis suggests that NO2- and PO43- are the major factors affecting diazotrophic distribution throughout the OMZ. In view of the predicted increase in ocean deoxygenation resulting from global warming, our findings indicate that the importance of OMZs as niches for N2 fixation may increase in the futur
    Keywords: Climate - Biogeochemistry Interactions in the Tropical Ocean; SFB754
    Type: Dataset
    Format: application/zip, 3 datasets
    Location Call Number Expected Availability
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  • 2
    Publication Date: 2023-10-28
    Keywords: Bacterial nitrogen fixation, cluster; Bacterial nitrogen fixation, cluster, standard deviation; Bacterial nitrogen fixation, total; Climate - Biogeochemistry Interactions in the Tropical Ocean; CTD/Rosette; CTD-RO; Date/Time of event; DEPTH, water; Event label; Latitude of event; Longitude of event; M77/3; M77/3-CTD109; M77/3-CTD110; M77/3-CTD13; M77/3-CTD14; M77/3-CTD15; M77/3-CTD17; M77/3-CTD19; M77/3-CTD21; M77/3-CTD24; M77/3-CTD25; M77/3-CTD4; M77/3-CTD55; M77/3-CTD57; M77/3-CTD58; M77/3-CTD59; M77/3-CTD6; M77/3-CTD60; M77/3-CTD62; M77/3-CTD63; M77/3-CTD67; M77/3-CTD7; M77/3-CTD70; M77/3-CTD71; Meteor (1986); Sample code/label; SFB754; Standard deviation; Station label
    Type: Dataset
    Format: text/tab-separated-values, 5138 data points
    Location Call Number Expected Availability
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  • 3
    Publication Date: 2023-10-28
    Keywords: Bacterial nitrogen fixation, cluster; Bacterial nitrogen fixation, cluster, standard deviation; Bacterial nitrogen fixation, total; Climate - Biogeochemistry Interactions in the Tropical Ocean; CTD/Rosette; CTD-RO; Date/Time of event; DEPTH, water; Event label; Latitude of event; Longitude of event; M77/4; M77/4_143; M77/4_152; M77/4_160; M77/4-CTD14; M77/4-CTD18; M77/4-CTD23; M77/4-CTD24; M77/4-CTD29; M77/4-CTD34; M77/4-CTD38; M77/4-CTD39; M77/4-CTD40; M77/4-CTD58; M77/4-CTD68; M77/4-CTD73; M77/4-CTD75; M77/4-CTD79; M77/4-CTD81; M77/4-CTD82; M77/4-CTD90; Meteor (1986); Sample code/label; SFB754; Standard deviation; Station label
    Type: Dataset
    Format: text/tab-separated-values, 1674 data points
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  • 4
    Publication Date: 2023-10-28
    Keywords: Archael_amoA, standard deviation; Archael_amoA distribution; Climate - Biogeochemistry Interactions in the Tropical Ocean; CTD/Rosette; CTD-RO; Date/Time of event; DEPTH, water; Event label; Functional gene beta amoA; Functional gene beta amoA, standard deviation; Functional gene hzo; Functional gene hzo, standard deviation; Functional gene nirS; Functional gene nirS, standard deviation; Functional gene nrfA; Functional gene nrfA, standard deviation; Latitude of event; Longitude of event; M77/3; M77/3-CTD109; M77/3-CTD110; M77/3-CTD13; M77/3-CTD14; M77/3-CTD15; M77/3-CTD17; M77/3-CTD19; M77/3-CTD21; M77/3-CTD23; M77/3-CTD24; M77/3-CTD25; M77/3-CTD4; M77/3-CTD55; M77/3-CTD57; M77/3-CTD58; M77/3-CTD59; M77/3-CTD6; M77/3-CTD60; M77/3-CTD62; M77/3-CTD63; M77/3-CTD67; M77/3-CTD7; M77/3-CTD70; M77/3-CTD71; Meteor (1986); Sample code/label; SFB754; Station label
    Type: Dataset
    Format: text/tab-separated-values, 3820 data points
    Location Call Number Expected Availability
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  • 5
    facet.materialart.
    Unknown
    PANGAEA
    In:  IFM-GEOMAR Leibniz-Institute of Marine Sciences, Kiel University
    Publication Date: 2024-05-22
    Keywords: Ammonium; Archael_amoA distribution; Bacterial nitrogen fixation, Chrocosphaera; Bacterial nitrogen fixation, Cyanothese; Bacterial nitrogen fixation, filamentous; Bacterial nitrogen fixation, GammaAO; Bacterial nitrogen fixation, total; Bacterial nitrogen fixation, UCYN-A; Bottle number; Climate - Biogeochemistry Interactions in the Tropical Ocean; CTD; CTD/Rosette; CTD-RO; Date/Time of event; DEPTH, water; Event label; Fluorescence-based quantitative real-time PCR (qPCR); Freon-12 (dichlorodifluoromethane); Latitude of event; Longitude of event; Maria S. Merian; MSM10/1; MSM10/1-CTD1; MSM10/1-CTD10; MSM10/1-CTD100; MSM10/1-CTD101; MSM10/1-CTD102; MSM10/1-CTD103; MSM10/1-CTD104; MSM10/1-CTD105; MSM10/1-CTD106; MSM10/1-CTD107; MSM10/1-CTD108; MSM10/1-CTD109; MSM10/1-CTD11; MSM10/1-CTD110; MSM10/1-CTD111; MSM10/1-CTD112; MSM10/1-CTD113; MSM10/1-CTD114; MSM10/1-CTD115; MSM10/1-CTD116; MSM10/1-CTD117; MSM10/1-CTD118; MSM10/1-CTD119; MSM10/1-CTD12; MSM10/1-CTD120; MSM10/1-CTD121; MSM10/1-CTD122; MSM10/1-CTD123; MSM10/1-CTD124; MSM10/1-CTD125; MSM10/1-CTD126; MSM10/1-CTD127; MSM10/1-CTD128; MSM10/1-CTD129; MSM10/1-CTD13; MSM10/1-CTD130; MSM10/1-CTD131; MSM10/1-CTD132; MSM10/1-CTD133; MSM10/1-CTD134; MSM10/1-CTD135; MSM10/1-CTD136; MSM10/1-CTD137; MSM10/1-CTD138; MSM10/1-CTD139; MSM10/1-CTD14; MSM10/1-CTD140; MSM10/1-CTD141; MSM10/1-CTD142; MSM10/1-CTD143; MSM10/1-CTD144; MSM10/1-CTD145; MSM10/1-CTD146; MSM10/1-CTD147; MSM10/1-CTD148; MSM10/1-CTD149; MSM10/1-CTD15; MSM10/1-CTD150; MSM10/1-CTD151; MSM10/1-CTD152; MSM10/1-CTD153; MSM10/1-CTD154; MSM10/1-CTD155; MSM10/1-CTD156; MSM10/1-CTD157; MSM10/1-CTD158; MSM10/1-CTD159; MSM10/1-CTD16; MSM10/1-CTD160; MSM10/1-CTD161; MSM10/1-CTD162; MSM10/1-CTD163; MSM10/1-CTD164; MSM10/1-CTD165; MSM10/1-CTD166; MSM10/1-CTD167; MSM10/1-CTD168; MSM10/1-CTD169; MSM10/1-CTD17; MSM10/1-CTD170; MSM10/1-CTD171; MSM10/1-CTD172; MSM10/1-CTD173; MSM10/1-CTD174; MSM10/1-CTD175; MSM10/1-CTD176; MSM10/1-CTD177; MSM10/1-CTD179; MSM10/1-CTD18; MSM10/1-CTD180; MSM10/1-CTD181; MSM10/1-CTD182; MSM10/1-CTD183; MSM10/1-CTD184; MSM10/1-CTD185; MSM10/1-CTD186; MSM10/1-CTD187; MSM10/1-CTD188; MSM10/1-CTD189; MSM10/1-CTD19; MSM10/1-CTD190; MSM10/1-CTD191; MSM10/1-CTD192; MSM10/1-CTD193; MSM10/1-CTD194; MSM10/1-CTD195; MSM10/1-CTD196; MSM10/1-CTD197; MSM10/1-CTD198; MSM10/1-CTD199; MSM10/1-CTD2; MSM10/1-CTD20; MSM10/1-CTD200; MSM10/1-CTD201; MSM10/1-CTD202; MSM10/1-CTD203; MSM10/1-CTD204; MSM10/1-CTD205; MSM10/1-CTD206; MSM10/1-CTD207; MSM10/1-CTD208; MSM10/1-CTD209; MSM10/1-CTD21; MSM10/1-CTD210; MSM10/1-CTD211; MSM10/1-CTD212; MSM10/1-CTD213; MSM10/1-CTD214; MSM10/1-CTD215; MSM10/1-CTD216; MSM10/1-CTD217; MSM10/1-CTD218; MSM10/1-CTD219; MSM10/1-CTD22; MSM10/1-CTD220; MSM10/1-CTD221; MSM10/1-CTD222; MSM10/1-CTD223; MSM10/1-CTD224; MSM10/1-CTD225; MSM10/1-CTD226; MSM10/1-CTD227; MSM10/1-CTD228; MSM10/1-CTD229; MSM10/1-CTD23; MSM10/1-CTD24; MSM10/1-CTD25; MSM10/1-CTD26; MSM10/1-CTD27; MSM10/1-CTD28; MSM10/1-CTD29; MSM10/1-CTD3; MSM10/1-CTD30; MSM10/1-CTD31; MSM10/1-CTD32; MSM10/1-CTD33; MSM10/1-CTD34; MSM10/1-CTD35; MSM10/1-CTD36; MSM10/1-CTD37; MSM10/1-CTD38; MSM10/1-CTD39; MSM10/1-CTD4; MSM10/1-CTD40; MSM10/1-CTD41; MSM10/1-CTD42; MSM10/1-CTD43; MSM10/1-CTD44; MSM10/1-CTD45; MSM10/1-CTD46; MSM10/1-CTD47; MSM10/1-CTD48; MSM10/1-CTD49; MSM10/1-CTD5; MSM10/1-CTD50; MSM10/1-CTD51; MSM10/1-CTD52; MSM10/1-CTD53; MSM10/1-CTD54; MSM10/1-CTD55; MSM10/1-CTD56; MSM10/1-CTD57; MSM10/1-CTD58; MSM10/1-CTD59; MSM10/1-CTD6; MSM10/1-CTD60; MSM10/1-CTD61; MSM10/1-CTD62; MSM10/1-CTD63; MSM10/1-CTD64; MSM10/1-CTD65; MSM10/1-CTD66; MSM10/1-CTD67; MSM10/1-CTD68; MSM10/1-CTD69; MSM10/1-CTD7; MSM10/1-CTD70; MSM10/1-CTD71; MSM10/1-CTD72; MSM10/1-CTD73; MSM10/1-CTD74; MSM10/1-CTD75; MSM10/1-CTD76; MSM10/1-CTD77; MSM10/1-CTD78; MSM10/1-CTD79; MSM10/1-CTD8; MSM10/1-CTD80; MSM10/1-CTD81; MSM10/1-CTD82; MSM10/1-CTD83; MSM10/1-CTD84; MSM10/1-CTD85; MSM10/1-CTD86; MSM10/1-CTD87; MSM10/1-CTD88; MSM10/1-CTD89; MSM10/1-CTD9; MSM10/1-CTD90; MSM10/1-CTD91; MSM10/1-CTD92; MSM10/1-CTD93; MSM10/1-CTD94; MSM10/1-CTD95; MSM10/1-CTD96; MSM10/1-CTD97; MSM10/1-CTD98; MSM10/1-CTD99; Nitrate; Nitrite; Oxygen; Phosphate; Pressure, water; Salinity; Sample code/label; SFB754; Silicate; Sulfur hexafluoride, SF6; Temperature, water; Trifluoromethyl sulfur pentafluoride
    Type: Dataset
    Format: text/tab-separated-values, 36613 data points
    Location Call Number Expected Availability
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  • 6
    Publication Date: 2012-01-01
    Electronic ISSN: 1664-302X
    Topics: Biology
    Published by Frontiers Media
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  • 7
  • 8
    Publication Date: 2005-01-01
    Print ISSN: 0749-503X
    Electronic ISSN: 1097-0061
    Topics: Biology
    Published by Wiley
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  • 9
    Publication Date: 2016-01-08
    Description: Iron (Fe) is an essential micronutrient for many processes in all living cells. Dissolved Fe (dFe) concentrations in the ocean are of the order of a few nM, and Fe is often a factor limiting primary production. Bioavailability of Fe in aquatic environments is believed to be primarily controlled through chelation by Fe-binding ligands. Marine microbes have evolved different mechanisms to cope with the scarcity of bioavailable dFe. Gradients in dFe concentrations and diversity of the Fe-ligand pool from coastal to open ocean waters have presumably imposed selection pressures that should be reflected in the genomes of microbial communities inhabiting the pelagic realm. We applied a hidden Markov model (HMM)-based search for proteins related to cellular iron metabolism, and in particular those involved in Fe uptake mechanisms in 164 microbial genomes belonging to diverse taxa and occupying different aquatic niches. A multivariate statistical approach demonstrated that in phototrophic organisms, there is a clear influence of the ecological niche on the diversity of Fe uptake systems. Extending the analyses to the metagenome database from the Global Ocean Sampling expedition, we demonstrated that the Fe uptake and homeostasis mechanisms differed significantly across marine niches defined by temperatures and dFe concentrations, and that this difference was linked to the distribution of microbial taxa in these niches. Using the dN/dS ratios (which signify the rate of non-synonymous mutations) of the nucleotide sequences, we identified that genes encoding for TonB, Ferritin, Ferric reductase, IdiA, ZupT, and Fe(2+) transport proteins FeoA and FeoB were evolving at a faster rate (positive selection pressure) while genes encoding ferrisiderophore, heme and Vitamin B12 uptake systems, siderophore biosynthesis, and IsiA and IsiB were under purifying selection pressure (evolving slowly).
    Type: Article , PeerReviewed
    Format: text
    Format: other
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  • 10
    Publication Date: 2017-03-09
    Description: Nitrogen fixation, the biological reduction of dinitrogen gas (N2) to ammonium (NH4+), is quantitatively the most important external source of new nitrogen (N) to the open ocean. Classically, the ecological niche of oceanic N2 fixers (diazotrophs) is ascribed to tropical oligotrophic surface waters, often depleted in fixed N, with a diazotrophic community dominated by cyanobacteria. Although this applies for large areas of the ocean, biogeochemical models and phylogenetic studies suggest that the oceanic diazotrophic niche may be much broader than previously considered, resulting in major implications for the global N-budget. Here, we report on the composition, distribution and abundance of nifH, the functional gene marker for N2 fixation. Our results show the presence of eight clades of diazotrophs in the oxygen minimum zone (OMZ) off Peru. Although proteobacterial clades dominated overall, two clusters affiliated to spirochaeta and archaea were identified. N2 fixation was detected within OMZ waters and was stimulated by the addition of organic carbon sources supporting the view that non-phototrophic diazotrophs were actively fixing dinitrogen. The observed co-occurrence of key functional genes for N2 fixation, nitrification, anammox and denitrification suggests that a close spatial coupling of N-input and N-loss processes exists in the OMZ off Peru. The wide distribution of diazotrophs throughout the water column adds to the emerging view that the habitat of marine diazotrophs can be extended to low oxygen/high nitrate areas. Furthermore, our statistical analysis suggests that NO2− and PO43− are the major factors affecting diazotrophic distribution throughout the OMZ. In view of the predicted increase in ocean deoxygenation resulting from global warming, our findings indicate that the importance of OMZs as niches for N2 fixation may increase in the futur
    Type: Article , PeerReviewed
    Format: text
    Format: text
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