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  1. Article ; Online: Chemolithoautotrophic denitrification intensifies nitrogen loss in the Eastern Arabian Sea Shelf waters during sulphidic events

    Pratihary, Anil / Lavik, Gaute / Naqvi, S.W.A. / Shirodkar, Gayatri / Sarakāra, Amita / Marchant, Hannah / Ohde, Thomas / Shenoy, Damodar / Kurian, Siby / Uskaikar, Hema / Kuypers, Marcel M.M.

    Progress in Oceanography. 2023 Sept., Oct., v. 217 p.103075-

    2023  

    Abstract: The Eastern Arabian Sea Shelf i.e. Western Indian Continental Shelf (WICS) – a known biogeochemical hotspot is characterized by monsoonal upwelling, seasonal O₂ deficiency, extremely high N₂O build-up and sulphidic events. The frequency and duration of ... ...

    Abstract The Eastern Arabian Sea Shelf i.e. Western Indian Continental Shelf (WICS) – a known biogeochemical hotspot is characterized by monsoonal upwelling, seasonal O₂ deficiency, extremely high N₂O build-up and sulphidic events. The frequency and duration of the sulphidic events have increased over the last two decades, but their impact on the pelagic N cycling, N budget, and N₂O dynamics is poorly constrained. Thus, to address these problems and assess their implications on WICS biogeochemistry, we carried out physico-chemical measurements, ¹⁵N-labeled incubations and bag incubations on five transects over the shelf during the sulphidic event (September-October) of 2011. We observed very high rates of sulphide-driven chemolithotrophic denitrification (1885–5825 nM N₂ d⁻¹) in the sulphidic, nitrate-depleted waters, and its potential occurrence in the sulphide-free, nitrate-replete waters (460–3137 nM N₂ d⁻¹), along with high transient N₂O production, and comparably low rates of anammox (0–119 nM N₂ d⁻¹) and DNRA (0–45 nM N d⁻¹). Despite the predominant cloud cover during the monsoon season, we could for the first time show the satellite image of a large colloidal sulphur (S⁰) plume associated with the sulphidic event off Western India providing further evidence of extensive sulphide oxidation coupled to denitrification. Sulphide-driven denitrification (mean rate = 2697 nM N₂ d⁻¹) appeared to be the dominant N loss process during the anoxic regime (September-October) replacing the chemoorganotrophic (i.e. heterotrophic) denitrification (342 nM N₂ d⁻¹) that predominates during the preceding suboxic regime (July-August). Overall, the highest sulphide-driven denitrification rate over the WICS was found to be the second highest among the anoxic coastal systems of the world. Furthermore, simultaneous consumption of NOₓ⁻ and S²⁻ at a ratio close to the theoretical value in the anaerobic incubations of chemocline waters indicated that the sulphide-driven denitrifiers were fixing carbon. The estimated dark C production (0.21 g C m⁻² d⁻¹) due to chemolithoautotrophic denitrification was 18% of the photoautotrophic production and accounted for 15% of the total column productivity. Based on our conservative estimates, the chemolithoautotrophic denitrification was responsible for the removal of 0.4 Tg of fixed N and 0.57 Tg of sulphide, and fixation of 0.1 Tg of carbon annually in the shelf waters. Thus, the sulphidic event impacted the biogeochemistry and ecology, and modulated the N loss pathways and rates over the WICS. With the expansion and intensification of OMZs induced by global climate change, and the spreading of dead zones due to increasing anthropogenic activities, chemolithoautotrophic denitrification is likely to become increasingly significant in oceanic N cycle and impact the N budgets of shallow marine systems particularly.
    Keywords anaerobic ammonium oxidation ; carbon ; climate change ; cloud cover ; continental shelf ; denitrification ; denitrifying microorganisms ; ecology ; monsoon season ; nitrogen ; nitrogen cycle ; nitrogen fixation ; oceanography ; oxidation ; remote sensing ; sulfides ; sulfur ; Arabian Sea ; India ; Anoxia ; Sulphide ; Nitrous oxide ; Chemoautotrophy ; Shelf
    Language English
    Dates of publication 2023-09
    Publishing place Elsevier Ltd
    Document type Article ; Online
    ISSN 0079-6611
    DOI 10.1016/j.pocean.2023.103075
    Database NAL-Catalogue (AGRICOLA)

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  2. Article ; Online: Recent advances in marine N-cycle studies using

    Marchant, Hannah K / Mohr, Wiebke / Kuypers, Marcel Mm

    Current opinion in biotechnology

    2016  Volume 41, Page(s) 53–59

    Abstract: ... ...

    Abstract 15
    MeSH term(s) Isotope Labeling/methods ; Nitrogen/metabolism ; Nitrogen Cycle/physiology ; Nitrogen Isotopes/analysis ; Seawater/chemistry
    Chemical Substances Nitrogen Isotopes ; Nitrogen (N762921K75)
    Language English
    Publishing date 2016-10
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1052045-4
    ISSN 1879-0429 ; 0958-1669
    ISSN (online) 1879-0429
    ISSN 0958-1669
    DOI 10.1016/j.copbio.2016.04.019
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Biofilms on glacial surfaces: hotspots for biological activity.

    Smith, Heidi J / Schmit, Amber / Foster, Rachel / Littman, Sten / Kuypers, Marcel Mm / Foreman, Christine M

    NPJ biofilms and microbiomes

    2016  Volume 2, Page(s) 16008

    Abstract: Glaciers are important constituents in the Earth's hydrological and carbon cycles, with predicted warming leading to increases in glacial melt and the transport of nutrients to adjacent and downstream aquatic ecosystems. Microbial activity on glacial ... ...

    Abstract Glaciers are important constituents in the Earth's hydrological and carbon cycles, with predicted warming leading to increases in glacial melt and the transport of nutrients to adjacent and downstream aquatic ecosystems. Microbial activity on glacial surfaces has been linked to the biological darkening of cryoconite particles, affecting albedo and increased melt. This phenomenon, however, has only been demonstrated for alpine glaciers and the Greenland Ice Sheet, excluding Antarctica. In this study, we show via confocal laser scanning microscopy that microbial communities on glacial surfaces in Antarctica persist in biofilms. Overall, ~35% of the cryoconite sediment surfaces were covered by biofilm. Nanoscale scale secondary ion mass spectrometry measured significant enrichment of
    Language English
    Publishing date 2016
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2817021-0
    ISSN 2055-5008
    ISSN 2055-5008
    DOI 10.1038/npjbiofilms.2016.8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Purple sulfur bacteria fix N2 via molybdenum-nitrogenase in a low molybdenum Proterozoic ocean analogue

    Philippi, Miriam / Kitzinger, Katharina / Berg, Jasmine S. / Tschitschko, Bernhard / Kidane, Abiel T. / Littmann, Sten / Marchant, Hannah K. / Storelli, Nicola / Winkel, Lenny H.E. / Schubert, Carsten J. / Mohr, Wiebke / Kuypers, Marcel M.M.

    Nature Communications, 12 (1)

    2021  

    Abstract: Biological N2 fixation was key to the expansion of life on early Earth. The N2-fixing microorganisms and the nitrogenase type used in the Proterozoic are unknown, although it has been proposed that the canonical molybdenum-nitrogenase was not used due to ...

    Abstract Biological N2 fixation was key to the expansion of life on early Earth. The N2-fixing microorganisms and the nitrogenase type used in the Proterozoic are unknown, although it has been proposed that the canonical molybdenum-nitrogenase was not used due to low molybdenum availability. We investigate N2 fixation in Lake Cadagno, an analogue system to the sulfidic Proterozoic continental margins, using a combination of biogeochemical, molecular and single cell techniques. In Lake Cadagno, purple sulfur bacteria (PSB) are responsible for high N2 fixation rates, to our knowledge providing the first direct evidence for PSB in situ N2 fixation. Surprisingly, no alternative nitrogenases are detectable, and N2 fixation is exclusively catalyzed by molybdenum-nitrogenase. Our results show that molybdenum-nitrogenase is functional at low molybdenum conditions in situ and that in contrast to previous beliefs, PSB may have driven N2 fixation in the Proterozoic ocean.

    ISSN:2041-1723
    Keywords Element cycles ; Environmental microbiology ; Environmental sciences ; Stable isotope analysis
    Subject code 333
    Language English
    Publishing date 2021-08-06
    Publisher Nature Publishing Group
    Publishing country ch
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article: Dark aerobic sulfide oxidation by anoxygenic phototrophs in anoxic waters

    Berg, Jasmine S / Pjevac, Petra / Sommer, Tobias / Buckner, Caroline R.T / Philippi, Miriam / Hach, Philipp F / Liebeke, Manuel / Holtappels, Moritz / Danza, Francesco / Tonolla, Mauro / Sengupta, Anupam / Schubert, Carsten J / Milucka, Jana / Kuypers, Marcel M.M

    Environmental microbiology. 2019 May, v. 21, no. 5

    2019  

    Abstract: Anoxygenic phototrophic sulfide oxidation by green and purple sulfur bacteria (PSB) plays a key role in sulfide removal from anoxic shallow sediments and stratified waters. Although some PSB can also oxidize sulfide with nitrate and oxygen, little is ... ...

    Abstract Anoxygenic phototrophic sulfide oxidation by green and purple sulfur bacteria (PSB) plays a key role in sulfide removal from anoxic shallow sediments and stratified waters. Although some PSB can also oxidize sulfide with nitrate and oxygen, little is known about the prevalence of this chemolithotrophic lifestyle in the environment. In this study, we investigated the role of these phototrophs in light‐independent sulfide removal in the chemocline of Lake Cadagno. Our temporally resolved, high‐resolution chemical profiles indicated that dark sulfide oxidation was coupled to high oxygen consumption rates of ~9 μM O2·h−1. Single‐cell analyses of lake water incubated with 13CO2 in the dark revealed that Chromatium okenii was to a large extent responsible for aerobic sulfide oxidation and it accounted for up to 40% of total dark carbon fixation. The genome of Chr. okenii reconstructed from the Lake Cadagno metagenome confirms its capacity for microaerophilic growth and provides further insights into its metabolic capabilities. Moreover, our genomic and single‐cell data indicated that other PSB grow microaerobically in these apparently anoxic waters. Altogether, our observations suggest that aerobic respiration may not only play an underappreciated role in anoxic environments but also that organisms typically considered strict anaerobes may be involved.
    Keywords Chromatium okenii ; aerobiosis ; anaerobes ; anaerobic conditions ; autotrophs ; carbon dioxide fixation ; genome ; lakes ; lifestyle ; metagenomics ; nitrates ; oxidation ; oxygen ; oxygen consumption ; sediments
    Language English
    Dates of publication 2019-05
    Size p. 1611-1626.
    Publishing place John Wiley & Sons, Inc.
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 2020213-1
    ISSN 1462-2920 ; 1462-2912
    ISSN (online) 1462-2920
    ISSN 1462-2912
    DOI 10.1111/1462-2920.14543
    Database NAL-Catalogue (AGRICOLA)

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  6. Article: Epifluorescence, SEM, TEM and nanoSIMS image analysis of the cold phenotype of Clostridium psychrophilum at subzero temperatures

    Perfumo, Amedea / Elsaesser, Andreas / Littmann, Sten / Foster, Rachel A / Kuypers, Marcel M.M / Cockell, Charles S / Kminek, Gerhard

    FEMS microbiology ecology. 2014 Dec., v. 90, no. 3

    2014  

    Abstract: We have applied an image‐based approach combining epifluorescence microscopy, electron microscopy and nanoscale secondary ion mass spectrometry (nanoSIMS) with stable isotope probing to examine directly the characteristic cellular features involved in ... ...

    Abstract We have applied an image‐based approach combining epifluorescence microscopy, electron microscopy and nanoscale secondary ion mass spectrometry (nanoSIMS) with stable isotope probing to examine directly the characteristic cellular features involved in the expression of the cold phenotype in the Antarctic bacterium Clostridium psychrophilum exposed to a temperature range from +5 to −15 °C under anoxic conditions. We observed dramatic morphological changes depending on temperature. At temperatures below −10 °C, cell division was inhibited and consequently filamentous growth predominated. Bacterial cells appeared surrounded by a remarkably thick cell wall and a capsule formed of long exopolysaccharide fibres. Moreover, bacteria were entirely embedded within a dense extracellular matrix, suggesting a role both in cryo‐protection and in the cycling of nutrients and genetic material. Strings of extracellular DNA, transient cell membrane permeability and release of membrane vesicles were observed that suggest that evolution via transfer of genetic material may be especially active under frozen conditions. While at −5 °C, the bacterial population was metabolically healthy, at temperatures below −10 °C, most cells showed no sign of active metabolism or the metabolic flux was extremely slowed down; instead of being consumed, carbon was accumulated and stored in intracellular granules as in preparation for a long‐term survival.
    Keywords Clostridium ; DNA ; anaerobic conditions ; bacteria ; carbon ; cell division ; cell walls ; cold ; cytoplasmic granules ; evolution ; exopolysaccharides ; extracellular matrix ; fluorescence microscopy ; image analysis ; mass spectrometry ; membrane permeability ; metabolism ; nutrients ; phenotype ; scanning electron microscopy ; stable isotopes ; temperature ; transmission electron microscopy ; Antarctic region
    Language English
    Dates of publication 2014-12
    Size p. 869-882.
    Publishing place Published by Elsevier Science Publishers on behalf of the Federation of European Microbiological Societies
    Document type Article
    ZDB-ID 283722-5
    ISSN 1574-6941 ; 0168-6496
    ISSN (online) 1574-6941
    ISSN 0168-6496
    DOI 10.1111/1574-6941.12443
    Database NAL-Catalogue (AGRICOLA)

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  7. Article ; Online: Crenothrix are major methane consumers in stratified lakes.

    Oswald, Kirsten / Graf, Jon S / Littmann, Sten / Tienken, Daniela / Brand, Andreas / Wehrli, Bernhard / Albertsen, Mads / Daims, Holger / Wagner, Michael / Kuypers, Marcel Mm / Schubert, Carsten J / Milucka, Jana

    The ISME journal

    2017  Volume 11, Issue 9, Page(s) 2124–2140

    Abstract: Methane-oxidizing bacteria represent a major biological sink for methane and are thus Earth's natural protection against this potent greenhouse gas. Here we show that in two stratified freshwater lakes a substantial part of upward-diffusing methane was ... ...

    Abstract Methane-oxidizing bacteria represent a major biological sink for methane and are thus Earth's natural protection against this potent greenhouse gas. Here we show that in two stratified freshwater lakes a substantial part of upward-diffusing methane was oxidized by filamentous gamma-proteobacteria related to Crenothrix polyspora. These filamentous bacteria have been known as contaminants of drinking water supplies since 1870, but their role in the environmental methane removal has remained unclear. While oxidizing methane, these organisms were assigned an 'unusual' methane monooxygenase (MMO), which was only distantly related to 'classical' MMO of gamma-proteobacterial methanotrophs. We now correct this assignment and show that Crenothrix encode a typical gamma-proteobacterial PmoA. Stable isotope labeling in combination swith single-cell imaging mass spectrometry revealed methane-dependent growth of the lacustrine Crenothrix with oxygen as well as under oxygen-deficient conditions. Crenothrix genomes encoded pathways for the respiration of oxygen as well as for the reduction of nitrate to N
    Language English
    Publishing date 2017-09
    Publishing country England
    Document type Journal Article
    ZDB-ID 2406536-5
    ISSN 1751-7370 ; 1751-7362
    ISSN (online) 1751-7370
    ISSN 1751-7362
    DOI 10.1038/ismej.2017.77
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Chemical microenvironments and single-cell carbon and nitrogen uptake in field-collected colonies of Trichodesmium under different pCO

    Eichner, Meri J / Klawonn, Isabell / Wilson, Samuel T / Littmann, Sten / Whitehouse, Martin J / Church, Matthew J / Kuypers, Marcel Mm / Karl, David M / Ploug, Helle

    The ISME journal

    2017  Volume 11, Issue 6, Page(s) 1305–1317

    Abstract: Gradients of oxygen ( ... ...

    Abstract Gradients of oxygen (O
    MeSH term(s) Carbon/metabolism ; Carbon Cycle/physiology ; Carbon Dioxide/pharmacology ; Hydrogen-Ion Concentration ; Light ; Nitrogen/metabolism ; Nitrogen Fixation/physiology ; Oxygen/metabolism ; Photosynthesis ; Trichodesmium/metabolism
    Chemical Substances Carbon Dioxide (142M471B3J) ; Carbon (7440-44-0) ; Nitrogen (N762921K75) ; Oxygen (S88TT14065)
    Language English
    Publishing date 2017-04-11
    Publishing country England
    Document type Journal Article
    ZDB-ID 2406536-5
    ISSN 1751-7370 ; 1751-7362
    ISSN (online) 1751-7370
    ISSN 1751-7362
    DOI 10.1038/ismej.2017.15
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: GeneFISH - an in situ technique for linking gene presence and cell identity in environmental microorganisms

    Moraru, Cristina / Lam, Phyllis / Fuchs, Bernhard M / Kuypers, Marcel M.M / Amann, Rudolf

    Environmental microbiology. 2010 Nov., v. 12, no. 11

    2010  

    Abstract: Our knowledge concerning the metabolic potentials of as yet to be cultured microorganisms has increased tremendously with the advance of sequencing technologies and the consequent discoveries of novel genes. On the other hand, it is often difficult to ... ...

    Abstract Our knowledge concerning the metabolic potentials of as yet to be cultured microorganisms has increased tremendously with the advance of sequencing technologies and the consequent discoveries of novel genes. On the other hand, it is often difficult to reliably assign a particular gene to a phylogenetic clade, because these sequences are usually found on genomic fragments that carry no direct marker of cell identity, such as rRNA genes. Therefore, the aim of the present study was to develop geneFISH - a protocol for linking gene presence with cell identity in environmental samples, the signals of which can be visualized at a single cell level. This protocol combines rRNA‐targeted catalysed reporter deposition - fluorescence in situ hybridization and in situ gene detection. To test the protocol, it was applied to seawater samples from the Benguela upwelling system. For gene detection, a polynucleotide probe mix was used, which was designed based on crenarchaeotal amoA clone libraries prepared from each seawater sample. Each probe in the mix was selected to bind to targets with up to 5% mismatches. To determine the hybridization parameters, the Tm of probes, targets and hybrids was estimated based on theoretical calculations and in vitro measurements. It was shown that at least 30%, but potentially the majority of the Crenarchaeota present in these samples harboured the amoA gene and were therefore likely to be catalysing the oxidation of ammonia.
    Keywords Crenarchaeota ; ammonia ; clones ; fluorescence in situ hybridization ; genes ; hybrids ; microorganisms ; oxidation ; ribosomal RNA ; seawater
    Language English
    Dates of publication 2010-11
    Size p. 3057-3073.
    Publishing place Blackwell Publishing Ltd
    Document type Article
    ZDB-ID 2020213-1
    ISSN 1462-2920 ; 1462-2912
    ISSN (online) 1462-2920
    ISSN 1462-2912
    DOI 10.1111/j.1462-2920.2010.02281.x
    Database NAL-Catalogue (AGRICOLA)

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  10. Book ; Online: Geochemistry and P and Fe fractionation in anoxic sediments, supplementary data to: Kraal, Peter; Slomp, Caroline P; Forster, Astrid; Kuypers, Marcel MM; Sluijs, Appy (2009): Pyrite oxidation during sample storage determines phosphorus fractionation in carbonate-poor anoxic sediments. Geochimica et Cosmochimica Acta, 73(11), 3277-3290

    Kraal, Peter / Forster, Astrid / Kuypers, Marcel MM / Slomp, Caroline P / Sluijs, Appy

    2009  

    Abstract: We investigated the phosphorus (P) and iron (Fe) fractionation in four cores with anoxic sediments, deposited during the mid-Cretaceous oceanic anoxic event 2 (~94 Ma) and the Paleocene-Eocene thermal maximum (?55 Ma), that were exposed to oxygen after ... ...

    Abstract We investigated the phosphorus (P) and iron (Fe) fractionation in four cores with anoxic sediments, deposited during the mid-Cretaceous oceanic anoxic event 2 (~94 Ma) and the Paleocene-Eocene thermal maximum (?55 Ma), that were exposed to oxygen after core recovery. Surprisingly, P associated with iron oxyhydroxides (Fe-bound P) was a major P phase in these laminated sediments deposited under euxinic conditions. A significant fraction of total Fe was present as (poorly) crystalline ferric Fe. This fraction increased with increasing storage time of the investigated cores. In carbonate-poor samples, Fe-bound P accounted for up to 99% of total P and its abundance correlated with pyrite contents. In samples with higher CaCO3 contents (>5 wt% in the investigated samples), P was mostly present in authigenic Ca-P minerals, irrespective of pyrite contents. We conclude that the P fractionation in anoxic, carbonate-poor, sediments is strongly affected by pyrite oxidation that occurs when these sediments are exposed to oxygen. Pyrite oxidation produces sulfuric acid and iron oxyhydroxides. The abundance of poorly crystalline Fe oxyhydroxides provides further evidence that these were indeed formed through recent (post-recovery) oxidation rather than in situ tens of millions of years ago. The acid dissolves apatite and the released phosphate is subsequently bound in the freshly formed iron oxyhydroxides. Pyrite oxidation thus leads to a conversion of authigenic Ca-P to Fe-bound P. In more calcareous samples, CaCO3 can act as an effective buffer against acidic dissolution of Ca-P minerals. The results indicate that shielding of sediments from atmospheric oxygen is vital to preserve the in situ P fractionation and to enable a valid reconstruction of marine phosphorus cycling based on sediment records.
    Language English
    Dates of publication 2009-9999
    Size Online-Ressource
    Publisher PANGAEA - Data Publisher for Earth & Environmental Science
    Publishing place Bremen/Bremerhaven
    Document type Book ; Online
    Note This dataset is supplement to doi:10.1016/j.gca.2009.02.026
    DOI 10.1594/PANGAEA.783338
    Database Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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