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  • 1
    Electronic Resource
    Electronic Resource
    A conspicuous nickel protein in microbial mats that oxidize methane anaerobically (2003)
    [s.l.] : Macmillian Magazines Ltd.
    Nature 426 (2003), S. 878-881 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Anaerobic oxidation of methane (AOM) in marine sediments is an important microbial process in the global carbon cycle and in control of greenhouse gas emission. The responsible organisms supposedly reverse the reactions of methanogenesis, but cultures providing biochemical proof of this have ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nature02207
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    Paper (German National Licenses)
    Fulltext
  • 2
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    Bacterial sulfur cycling shapes microbial communities in surface sediments of an ultramafic hydrothermal vent field (2011)
    Wiley
    In:  Environmental Microbiology, 13 (10). pp. 2633-2648.
    Details
    Publication Date: 2018-09-12
    Description: The ultramafic-hosted Logatchev hydrothermal field (LHF) is characterized by vent fluids, which are enriched in dissolved hydrogen and methane compared with fluids from basalt-hosted systems. Thick sediment layers in LHF are partly covered by characteristic white mats. In this study, these sediments were investigated in order to determine biogeochemical processes and key organisms relevant for primary production. Temperature profiling at two mat-covered sites showed a conductive heating of the sediments. Elemental sulfur was detected in the overlying mat and metal-sulfides in the upper sediment layer. Micro-profiles revealed an intensive hydrogen sulfide flux from deeper sediment layers. Fluorescence in situ hybridization showed that filamentous and vibrioid, Arcobacter-related Epsilonproteobacteria dominated the overlying mats. This is in contrast to sulfidic sediments in basalt-hosted fields where mats of similar appearance are composed of large sulfur-oxidizing Gammaproteobacteria. Epsilonproteobacteria (7-21%) and Deltaproteobacteria (20-21%) were highly abundant in the surface sediment layer. The physiology of the closest cultivated relatives, revealed by comparative 16S rRNA sequence analysis, was characterized by the capability to metabolize sulfur components. High sulfate reduction rates as well as sulfide depleted in (34)S further confirmed the importance of the biogeochemical sulfur cycle. In contrast, methane was found to be of minor relevance for microbial life in mat-covered surface sediments. Our data indicate that in conductively heated surface sediments microbial sulfur cycling is the driving force for bacterial biomass production although ultramafichosted systems are characterized by fluids with high levels of dissolved methane and hydrogen
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1111/j.1462-2920.2011.02530.x
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 3
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    Microbial metal-sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses (2019)
    Wiley / Society for Applied Microbiology and Blackwell Publishing Ltd,
    In:  Environmental Microbiology, 21 (2). pp. 682-701.
    Details
    Publication Date: 2022-01-31
    Description: Metal-sulfides are wide-spread in marine benthic habitats. At deep-sea hydrothermal vents, they occur as massive sulfide chimneys formed by mineral precipitation upon mixing of reduced vent fluids with cold oxygenated sea water. Although microorganisms inhabiting actively venting chimneys and utilizing compounds supplied by the venting fluids are well studied, only little is known about microorganisms inhabiting inactive chimneys. In this study, we combined 16S rRNA gene-based community profiling of sulfide chimneys from the Manus Basin (SW Pacific) with radiometric dating, metagenome (n = 4) and metaproteome (n = 1) analyses. Our results shed light on potential lifestyles of yet poorly characterized bacterial clades colonizing inactive chimneys. These include sulfate-reducing Nitrospirae and sulfide-oxidizing Gammaproteobacteria dominating most of the inactive chimney communities. Our phylogenetic analysis attributed the gammaproteobacterial clades to the recently described Woeseiaceae family and the SSr-clade found in marine sediments around the world. Metaproteomic data identified these Gammaproteobacteria as autotrophic sulfide-oxidizers potentially facilitating metal-sulfide dissolution via extracellular electron transfer. Considering the wide distribution of these gammaproteobacterial clades in marine environments such as hydrothermal vents and sediments, microbially accelerated neutrophilic mineral oxidation might be a globally relevant process in benthic element cycling and a considerable energy source for carbon fixation in marine benthic habitats
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1111/1462-2920.14514
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 4
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    Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments (2016)
    In:  EPIC3The ISME Journal, 10(8), pp. 1939-1953, ISSN: 1751-7362
    Details
    Publication Date: 2017-02-01
    Description: Marine sediments are the largest carbon sink on earth. Nearly half of dark carbon fixation in the oceans occurs in coastal sediments, but the microorganisms responsible are largely unknown. By integrating the 16S rRNA approach, single-cell genomics, metagenomics and transcriptomics with (14)C-carbon assimilation experiments, we show that uncultured Gammaproteobacteria account for 70-86% of dark carbon fixation in coastal sediments. First, we surveyed the bacterial 16S rRNA gene diversity of 13 tidal and sublittoral sediments across Europe and Australia to identify ubiquitous core groups of Gammaproteobacteria mainly affiliating with sulfur-oxidizing bacteria. These also accounted for a substantial fraction of the microbial community in anoxic, 490-cm-deep subsurface sediments. We then quantified dark carbon fixation by scintillography of specific microbial populations extracted and flow-sorted from sediments that were short-term incubated with (14)C-bicarbonate. We identified three distinct gammaproteobacterial clades covering diversity ranges on family to order level (the Acidiferrobacter, JTB255 and SSr clades) that made up 〉50% of dark carbon fixation in a tidal sediment. Consistent with these activity measurements, environmental transcripts of sulfur oxidation and carbon fixation genes mainly affiliated with those of sulfur-oxidizing Gammaproteobacteria. The co-localization of key genes of sulfur and hydrogen oxidation pathways and their expression in genomes of uncultured Gammaproteobacteria illustrates an unknown metabolic plasticity for sulfur oxidizers in marine sediments. Given their global distribution and high abundance, we propose that a stable assemblage of metabolically flexible Gammaproteobacteria drives important parts of marine carbon and sulfur cycles.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev , info:eu-repo/semantics/article
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    PAPER (OA)
  • 5
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    Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria) (2020)
    In:  EPIC3The ISME Journal, 14(1), pp. 104-122, ISSN: 1751-7362
    Details
    Publication Date: 2021-09-25
    Description: Most autotrophs use the Calvin–Benson–Bassham (CBB) cycle for carbon fixation. In contrast, all currently described autotrophs from the Campylobacterota (previously Epsilonproteobacteria) use the reductive tricarboxylic acid cycle (rTCA) instead. We discovered campylobacterotal epibionts (“Candidatus Thiobarba”) of deep-sea mussels that have acquired a complete CBB cycle and may have lost most key genes of the rTCA cycle. Intriguingly, the phylogenies of campylobacterotal CBB cycle genes suggest they were acquired in multiple transfers from Gammaproteobacteria closely related to sulfur-oxidizing endosymbionts associated with the mussels, as well as from Betaproteobacteria. We hypothesize that “Ca. Thiobarba” switched from the rTCA cycle to a fully functional CBB cycle during its evolution, by acquiring genes from multiple sources, including co-occurring symbionts. We also found key CBB cycle genes in free-living Campylobacterota, suggesting that the CBB cycle may be more widespread in this phylum than previously known. Metatranscriptomics and metaproteomics confirmed high expression of CBB cycle genes in mussel-associated “Ca. Thiobarba”. Direct stable isotope fingerprinting showed that “Ca. Thiobarba” has typical CBB signatures, suggesting that it uses this cycle for carbon fixation. Our discovery calls into question current assumptions about the distribution of carbon fixation pathways in microbial lineages, and the interpretation of stable isotope measurements in the environment.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
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  • 6
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    Bacterial communities in temperate and polar coastal sands are seasonally stable (2021)
    Nature Publishing Group
    In:  EPIC3ISME Communications, Nature Publishing Group, 1(1), pp. 1-11
    Details
    Publication Date: 2021-10-20
    Description: Coastal sands are biocatalytic filters for dissolved and particulate organic matter of marine and terrestrial origin, thus, acting as centers of organic matter transformation. At high temporal resolution, we accessed the variability of benthic bacterial communities over two annual cycles at Helgoland (North Sea), and compared it with seasonality of communities in Isfjorden (Svalbard, 78°N) sediments, where primary production does not occur during winter. Benthic community structure remained stable in both, temperate and polar sediments on the level of cell counts and 16S rRNA-based taxonomy. Actinobacteriota of uncultured Actinomarinales and Microtrichales were a major group, with 8 ± 1% of total reads (Helgoland) and 31 ± 6% (Svalbard). Their high activity (frequency of dividing cells 28%) and in situ cell numbers of 〉10% of total microbes in Svalbard sediments, suggest Actinomarinales and Microtrichales as key heterotrophs for carbon mineralization. Even though Helgoland and Svalbard sampling sites showed no phytodetritus-driven changes of the benthic bacterial community structure, they harbored significantly different communities (p 〈 0.0001, r = 0.963). The temporal stability of benthic bacterial communities is in stark contrast to the dynamic succession typical of coastal waters, suggesting that pelagic and benthic bacterial communities respond to phytoplankton productivity very differently.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
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  • 7
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    Seasonal grain-size measurements of surface sediments off Svalbard (2021)
    PANGAEA
    Details
    Publication Date: 2024-04-13
    Description: All sediment samples were obtained from four stations close to the coast and within 1 km distance to each other (station 5: 78.11°N 14.35°E; station 6: 78.10°N 14.38°E; station 7: 78.10°N 14.38°E; station 23: 78.10°N 14.39°E) in Isfjorden, Svalbard, Arctic Ocean. The sampling was performed with a Van Veen grab deployed from R/V Farm. Six repeated sediment sampling campaigns took place between December 2017 and September 2019 (for further details see Miksch et al. 2020) Particle-size measurements were performed in the Particle-Size Laboratory at MARUM, University of Bremen with a Beckman Coulter Laser Diffraction Particle Size Analyzer LS 13320. Prior to the measurements, the samples were boiled with approximately 0.3 g tetra-sodium diphosphate decahydrate (Na~4~P~2~O~7~ * 10H~2~O, 3 min) to destroy aggregates. Sample preparation and measurements were carried out with deionized, degassed and filtered water (filter mesh size: 0.2 µm) to reduce the potential influence of gas bubbles or particles within the water. The obtained results provide the particle-size distribution of a sample from 0.04 to 2000 μm divided in 116 size classes. The calculation of the particle sizes relies on the Fraunhofer diffraction theory and the Polarization Intensity Differential Scattering (PIDS) for particles from 0.4 to 2000 µm and from 0.04 to 0.4 µm, respectively. The reproducibility is checked regularly by replicate analyses of three internal glass-bead standards and is found to be better than ±0.7 µm for the mean and ±0.6 µm for the median particle size (1 sigma). The average standard deviation integrated over all size classes is better than ±4 vol% (note that the standard deviation of the individual size classes is not distributed uniformly). All provided statistic values are based on a geometric statistic.
    Keywords: Isfjorden; Seasonal grain-size distribution; Svalbard
    Type: Dataset
    Format: application/zip, 2 datasets
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    DATA PANGAEA
  • 8
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    Document with supplementary information (2012)
    PANGAEA
    In:  Supplement to: Schauer, Regina; Røy, Hans; Augustin, Nico; Gennerich, Hans-Hermann; Peters, Marc; Wenzhöfer, Frank; Amann, Rudolf; Meyerdierks, Anke (2011): Bacterial sulfur cycling shapes microbial communities in surface sediments of an ultramafic hydrothermal vent field. Environmental Microbiology, 13(10), 2633-2648, https://doi.org/10.1111/j.1462-2920.2011.02530.x
    Details
    Publication Date: 2024-04-13
    Description: The ultramafic-hosted Logatchev hydrothermal field (LHF) is characterized by vent fluids, which are enriched in dissolved hydrogen and methane compared with fluids from basalt-hosted systems. Thick sediment layers in LHF are partly covered by characteristic white mats. In this study, these sediments were investigated in order to determine biogeochemical processes and key organisms relevant for primary production. Temperature profiling at two mat-covered sites showed a conductive heating of the sediments. Elemental sulfur was detected in the overlying mat and metal-sulfides in the upper sediment layer. Microprofiles revealed an intensive hydrogen sulfide flux from deeper sediment layers. Fluorescence in situ hybridization showed that filamentous and vibrioid, Arcobacter-related Epsilonproteobacteria dominated the overlying mats. This is in contrast to sulfidic sediments in basalt-hosted fields where mats of similar appearance are composed of large sulfur-oxidizing Gammaproteobacteria. Epsilonproteobacteria (7- 21%) and Deltaproteobacteria (20-21%) were highly abundant in the surface sediment layer. The physiology of the closest cultivated relatives, revealed by comparative 16S rRNA sequence analysis, was characterized by the capability to metabolize sulfur com- ponents. High sulfate reduction rates as well as sulfide depleted in 34S further confirmed the importance of the biogeochemical sulfur cycle. In contrast, methane was found to be of minor relevance for microbial life in mat-covered surface sediments. Our data indicate that in conductively heated surface sediments microbial sulfur cycling is the driving force for bacterial biomass production although ultramafic- hosted systems are characterized by fluids with high levels of dissolved methane and hydrogen.
    Type: Dataset
    Format: application/pdf, 990.6 kBytes
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    DATA PANGAEA
  • 9
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    Environmental parameters of deep-sea hydrothermal vents from the Manus Basin (2017)
    PANGAEA
    In:  Supplement to: Meier, Dimitri V; Pjevac, Petra; Bach, Wolfgang; Hourdez, Stéphane; Girguis, Peter R; Vidoudez, Charles; Amann, Rudolf; Meyerdierks, Anke (2017): Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents. The ISME Journal, 11(7), 1545-1558, https://doi.org/10.1038/ismej.2017.37
    Details
    Publication Date: 2024-04-13
    Description: Thirtythree diffuse fluid and water column samples and 23 samples from surfaces of chimneys, rocks and fauna were subjected to a combined analyses of 16S rRNA gene sequences, metagenomes and real-time in situ measured geochemical parameters to study distribution and niche-partitioning of sulfur-oxidizing bacteria (SOB) in deep-sea hydrothermal environments of the Manus Basin, a back-arc fast-spreading center located between New Britain and New Ireland in the Bismarck Sea. High throughput 16S rRNA gene amplicon sequences obtained by Illumina paired-end sequencing using the primer combination Bakt_341F and Bakt_805R for all samples were analyzed as well as full-length 16S rRNA genes using a Pacific Biosciences RSII sequencer. Additionally, 5 metagenomes were sequenced (Illumina HiSeq 2500, paired-end shotgun), assembled, binned, and re-binned, resulting in 11 Sulfurovum-related, 5 Sulfurimonas-related and 12 SUP05-clade bins. These bins were analyzed with respect to genomic variability among hydrothermal vent SOB and especially with respect to the differentiation of their sulfur oxidation genes. Correlating distribution patterns to real-time geochemical data, tentative niches could be assigned to key hydrothermal SOB clades: Sulfurovum Epsilonproteobacteria were mainly found attached to surfaces exposed to diffuse venting, while the SUP05-clade dominated the bacterioplankton in highly diluted mixtures of vent fluids and seawater. The high diversity within Sulfurimonas- and Sulfurovum-related Epsilonproteobacteria observed in this study was proposed to be derived from the high variation of environmental parameters such as oxygen and sulfide concentrations across small spatial and temporal scales.
    Keywords: BAMBUS; Bismarck Sea; Carbon, inorganic, dissolved; Center for Marine Environmental Sciences; CTD/Rosette; CTD-RO; DEPTH, water; Event label; Hydrogen sulfide; LATITUDE; LONGITUDE; MARUM; Methane; Oxygen; pH; Remote operated vehicle; ROV; Sample code/label; Sample ID; Sample material; SO216; SO216-1-1; SO216-12-1; SO216-14-1; SO216-19-1; SO216-21-1; SO216-23-1; SO216-25-1; SO216-27-1; SO216-29-1; SO216-31-1; SO216-35-1; SO216-37-1; SO216-39-1; SO216-41-1; SO216-43-1; SO216-45-1; SO216-47-1; SO216-49-1; SO216-53-1; SO216-7-1; Sonne; Temperature, water; Δ G hydrogen sulfide
    Type: Dataset
    Format: text/tab-separated-values, 336 data points
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    DATA PANGAEA
  • 10
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    Niche differentiation of sulfur-oxidizing bacteria (SUP05) in submarine hydrothermal plumes (2021)
    PANGAEA
    Details
    Publication Date: 2024-04-13
    Description: Chemistry and microbial cell numbers of two bathy- (Brothers volcano; BrV-cone and northwest caldera; NWC) and a mesopelagic (Macauley volcano; McV) plumes on the Kermadec intra-oceanic arc in the South Pacific Ocean. The microbial cell numbers were determined using Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). Chemical measurements of DFe, DOC, TDN, PO4, NOx and SPE-DOC in the plumes are given.
    Keywords: Analysis; Archaea, targed with ARCH915 oligonucleotide FISH-probe; Bacteria, targed with EUB338(I-III) oligonucleotide FISH-probe; Candidatus Thioglobus; Carbon, organic, dissolved; Carbon, organic, dissolved, extracted; Catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH); Colorimetric analysis; CTD, SEA-BIRD SBE 9 plus; CTD/Rosette; CTD-RO; Date/Time of event; DEPTH, water; Event label; Gammaproteobacteria, targed with the SUP05_1241 oligonucleotide FISH-probe; Gammaproteobacteria, targeted with Gam42a oligonucleotide FISH-probe; High Resolution Sector Field Inductively Coupled Plasma Mass Spectrometry; High temperature catalytic combustion; HR-SF-ICP-MS; Hydrogen sulfide; HYDROTHERMADEC; intraoceanic arc; Iron, dissolved; Latitude of event; Location; Longitude of event; metabolic flexibility; Metagenome; metatranscriptome; microbial ecology; Modeled; Nitrogen, total dissolved; Nitrogen oxide; Origin; Oxygen; pH; Phosphate; Prokaryotic cell abundance; Sample ID; SO253; SO253_10-1; SO253_1-1; SO253_4-1; SO253_49-1; SO253_54-1; SO253_79-1; Solid-phase extracted (Dittmer etal, 2008); Sonne_2; South Pacific Ocean; SPE; Temperature, water; Turbidity (Nephelometric turbidity unit); Type; volcanic arc
    Type: Dataset
    Format: text/tab-separated-values, 526 data points
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    DATA PANGAEA
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