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  • 1
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    Hydrogen consumption by gills of Bathymodiolus spp. collected at the Comfortless cove and Lilliput hydrothermal vent fields in May 2006 (2013)
    PANGAEA
    Details
    Publication Date: 2024-02-02
    Description: The discovery of deep-sea hydrothermal vents in 1977 revolutionized our understanding of the energy sources that fuel primary productivity on Earth. Hydrothermal vent ecosystems are dominated by animals that live in symbiosis with chemosynthetic bacteria. So far, only two energy sources have been shown to power chemosynthetic symbioses: reduced sulphur compounds and methane. Using metagenome sequencing, single-gene fluorescence in situ hybridization, immunohistochemistry, shipboard incubations and in situ mass spectrometry, we show here that the symbionts of the hydrothermal vent mussel Bathymodiolus from the Mid-Atlantic Ridge use hydrogen to power primary production. In addition, we show that the symbionts of Bathymodiolus mussels from Pacific vents have hupL, the key gene for hydrogen oxidation. Furthermore, the symbionts of other vent animals such as the tubeworm Riftia pachyptila and the shrimp Rimicaris exoculata also have hupL. We propose that the ability to use hydrogen as an energy source is widespread in hydrothermal vent symbioses, particularly at sites where hydrogen is abundant.
    Keywords: Comment; DERIDGE; Event label; From Mantle to Ocean: Energy-, Material- and Life-cycles at Spreading Axes; Hydrogen; Hydrogen concentration; Hydrogen consumption rate; Hydrogen consumption rate per weight; M68/1; M68/1-20-ROV; M68/1-24-ROV; M68/1-39-ROV; M68/1-70-ROV; MARSUED3; Meteor (1986); Remote operated vehicle; ROV; Sample ID; Time in minutes; Tissue piece, number of; Wet mass
    Type: Dataset
    Format: text/tab-separated-values, 1582 data points
    Location Call Number Limitation Availability
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    DATA PANGAEA
  • 2
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    Results of H2-consumption experiments during METEOR cruise M64/2 (2011)
    PANGAEA
    Details
    Publication Date: 2024-04-13
    Description: The discovery of deep-sea hydrothermal vents in 1977 revolutionized our understanding of the energy sources that fuel primary productivity on Earth. Hydrothermal vent ecosystems are dominated by animals that live in symbiosis with chemosynthetic bacteria. So far, only two energy sources have been shown to power chemosynthetic symbioses: reduced sulphur compounds and methane. Using metagenome sequencing, single-gene fluorescence in situ hybridization, immunohistochemistry, shipboard incubations and in situ mass spectrometry, we show here that the symbionts of the hydrothermal vent mussel Bathymodiolus from the Mid-Atlantic Ridge use hydrogen to power primary production. In addition, we show that the symbionts of Bathymodiolus mussels from Pacific vents have hupL, the key gene for hydrogen oxidation. Furthermore, the symbionts of other vent animals such as the tubeworm Riftia pachyptila and the shrimp Rimicaris exoculata also have hupL. We propose that the ability to use hydrogen as an energy source is widespread in hydrothermal vent symbioses, particularly at sites where hydrogen is abundant.
    Keywords: Comment; DERIDGE; Event label; From Mantle to Ocean: Energy-, Material- and Life-cycles at Spreading Axes; Hydrogen; Hydrogen concentration; Hydrogen consumption rate; Hydrogen consumption rate per weight; HYDROMAR2; M64/2; M64/2-244-ROV; M64/2-263-ROV; M64/2-266-ROV; M64/2-281-ROV; Meteor (1986); Mid-Atlantic Ridge at 10-15°N; Remote operated vehicle; ROV; Sample ID; Time in minutes; Wet mass
    Type: Dataset
    Format: text/tab-separated-values, 986 data points
    Location Call Number Limitation Availability
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    DATA PANGAEA
  • 3
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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
    Location Call Number Limitation Availability
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    DATA PANGAEA
  • 4
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    FISH analysis on samples of the Menez Gwen hydrothermal field (2016)
    PANGAEA
    Details
    Publication Date: 2024-04-13
    Keywords: Alphaproteobacteria, targeted with ALF968 oligonucleotides FISH-probe; Archaea, targed with ARCH915 oligonucleotide FISH-probe; Bacteria, targed with EUB338(I-III) oligonucleotide FISH-probe; Bacteria, targed with the ALV735/ALV735 oligonucleotide FISH-probe; Center for Marine Environmental Sciences; CTD/Rosette; CTD-RO; DEPTH, water; Event label; Gammaproteobacteria, targed with the EPSY549/EPS914 oligonucleotide FISH-probe; Gammaproteobacteria, targed with the SUP05_1241 oligonucleotide FISH-probe; Gammaproteobacteria, targeted with Gam42a oligonucleotide FISH-probe; LATITUDE; LONGITUDE; M82/3; M82/3_716-1; M82/3_718-1; M82/3_726-1; M82/3_727-1; M82/3_729-1; M82/3_736-1; M82/3_743-1; M82/3_750-1; M82/3_756-1; M82/3_761-1; MARUM; Meteor (1986); Prokaryotic cell abundance; Remote operated vehicle; ROV; Sample ID; SAR11
    Type: Dataset
    Format: text/tab-separated-values, 109 data points
    Location Call Number Limitation Availability
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    DATA PANGAEA
  • 5
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    Hydrogen consumption in vent files of the equatorial Atlantic (2013)
    PANGAEA
    In:  Supplement to: Petersen, Jillian M; Zielinski, Frank U; Pape, Thomas; Seifert, Richard; Moraru, Cristina; Amann, Rudolf; Hourdez, Stéphane; Girguis, Peter R; Wankel, Scott D; Barbe, Valerie; Pelletier, Eric; Fink, Dennis; Borowski, Christian; Bach, Wolfgang; Dubilier, Nicole (2011): Hydrogen is an energy source for hydrothermal vent symbioses. Nature, 476, 176-180, https://doi.org/10.1038/nature10325
    Details
    Publication Date: 2024-04-13
    Description: The discovery of deep-sea hydrothermal vents in 1977 revolutionized our understanding of the energy sources that fuel primary productivity on Earth. Hydrothermal vent ecosystems are dominated by animals that live in symbiosis with chemosynthetic bacteria. So far, only two energy sources have been shown to power chemosynthetic symbioses: reduced sulphur compounds and methane. Using metagenome sequencing, single-gene fluorescence in situ hybridization, immunohistochemistry, shipboard incubations and in situ mass spectrometry, we show here that the symbionts of the hydrothermal vent mussel Bathymodiolus from the Mid-Atlantic Ridge use hydrogen to power primary production. In addition, we show that the symbionts of Bathymodiolus mussels from Pacific vents have hupL, the key gene for hydrogen oxidation. Furthermore, the symbionts of other vent animals such as the tubeworm Riftia pachyptila and the shrimp Rimicaris exoculata also have hupL. We propose that the ability to use hydrogen as an energy source is widespread in hydrothermal vent symbioses, particularly at sites where hydrogen is abundant.
    Keywords: DERIDGE; From Mantle to Ocean: Energy-, Material- and Life-cycles at Spreading Axes; HYDROMAR2; M64/2; M64/2-244-ROV; M64/2-263-ROV; M64/2-266-ROV; M64/2-281-ROV; M68/1; M68/1-20-ROV; M68/1-24-ROV; M68/1-39-ROV; M68/1-70-ROV; MARSUED3; Meteor (1986); Mid-Atlantic Ridge at 10-15°N; Remote operated vehicle; ROV
    Type: Dataset
    Format: application/zip, 2 datasets
    Location Call Number Limitation Availability
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    DATA PANGAEA
  • 6
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    Biochemical characterization of vent fluids and the microbial community (2016)
    PANGAEA
    In:  Supplement to: Meier, Dimitri V; Bach, Wolfgang; Girguis, Peter R; Gruber-Vodicka, Harald R; Reeves, Eoghan P; Richter, Michael; Vidoudez, Charles; Amann, Rudolf; Meyerdierks, Anke (2016): Heterotrophic Proteobacteria in the vicinity of diffuse hydrothermal venting. Environmental Microbiology, 18(12), 4348-4368, https://doi.org/10.1111/1462-2920.13304
    Details
    Publication Date: 2024-04-13
    Description: In this study, microbial communities in hydrothermal fluids from four different venting areas (White Flames, Cage Site, Woody and Babylon) within the Menez Gwen hydrothermal field (Mid-Atlantic Ridge) were analyzed. Samples were taken along mixing gradients, including diffuse fluid discharge points, their immediate surroundings, and the buoyant parts of hydrothermal plumes, selected based on visible venting, temperature readings and gas concentrations as indicated by in situ mass spectrometry (ISMS) spectra. High throughput 16S rRNA gene amplicon sequences obtained by Illumina paired-end sequencing using the primer combination Bakt_341F and Bakt_805R were analyzed. Total cell counts were determined and fluorescence in situ hybridization was conducted using probes specific for Archaea and Bacteria as well as for different bacterial subgroups. Additionally, three metagenomes were sequenced (Illumina MiSeq paired-end shotgun), assembled, binned, compared and analyzed for key metabolic pathways. Molecular analyses were combined with geochemical analyses and thermodynamic calculations. The study revealed that close to diffuse venting orifices dominated by chemolithoautotrophic Epsilonproteobacteria, in areas where environmental conditions still supported chemolithoautotrophic processes, microbial communities enriched for versatile heterotrophic Alpha- and Gammaproteobacteria were present. The potential for alkane degradation could be shown for several genera and yet uncultured clades. It was proposed that hotspots of chemolithoautotrophic life support a "belt" of heterotrophic bacteria significantly different from the dominating oligotrophic microbiota of the deep sea.
    Keywords: Center for Marine Environmental Sciences; MARUM
    Type: Dataset
    Format: application/zip, 2 datasets
    Location Call Number Limitation Availability
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    DATA PANGAEA
  • 7
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    (Table 1) Main environmental parameters of hydrothermal fields (2016)
    PANGAEA
    Details
    Publication Date: 2024-04-13
    Keywords: Carbon dioxide; Center for Marine Environmental Sciences; Comment; CTD/Rosette; CTD-RO; DEPTH, water; Event label; Filter; Hydrogen; Hydrogen sulfide; LATITUDE; LONGITUDE; M82/3; M82/3_716-1; M82/3_718-1; M82/3_726-1; M82/3_727-1; M82/3_729-1; M82/3_736-1; M82/3_743-1; M82/3_750-1; M82/3_756-1; M82/3_761-1; MARUM; Meteor (1986); Methane; Name; Oxygen; pH; Remote operated vehicle; ROV; Sample code/label; Sample ID; Sulfate; Temperature, water
    Type: Dataset
    Format: text/tab-separated-values, 328 data points
    Location Call Number Limitation Availability
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    DATA PANGAEA
  • 8
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    Genetic tool development in marine protists: emerging model organisms for experimental cell biology (2020)
    Nature Research
    Details
    Publication Date: 2023-02-08
    Description: Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species, which do not represent eukaryotic diversity or environmentally relevant taxa. Here, we report on the development of genetic tools in a range of protists primarily from marine environments. We present evidence for foreign DNA delivery and expression in 13 species never before transformed and for advancement of tools for eight other species, as well as potential reasons for why transformation of yet another 17 species tested was not achieved. Our resource in genetic manipulation will provide insights into the ancestral eukaryotic lifeforms, general eukaryote cell biology, protein diversification and the evolution of cellular pathways.
    Type: Article , PeerReviewed
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    Format: other
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 9
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    Roadmap for naming uncultivated Archaea and Bacteria (2020)
    Details
    Publication Date: 2023-02-08
    Description: The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ‘type material’, thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.
    Type: Article , PeerReviewed
    Format: text
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 10
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    Links from mantle to microbe at the Lau Integrated Study Site : insights from a back-arc spreading center (2012)
    The Oceanography Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © The Oceanography Society, 2012. This article is posted here by permission of The Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 25, no. 1 (2012): 62–77, doi:10.5670/oceanog.2012.04.
    Description: The Lau Integrated Study Site (ISS) has provided unique opportunities for study of ridge processes because of its back-arc setting in the southwestern Pacific. Its location allows study of a biogeographical province distinct from those of eastern Pacific and mid-Atlantic ridges, and crustal compositions along the ridge lie outside the range of mid-ocean ridge crustal compositions. The Lau ISS is located above a subduction zone, at an oblique angle. The underlying mantle receives water and other elements derived from the downgoing lithospheric slab, with an increase in slab influence from north to south. Water lowers the mantle melting temperature and leads to greater melt production where the water flux is greater, and to distinctive regional-scale gradients along the ridge. There are deeper faulted axial valleys with basaltic volcanism in the north and inflated axial highs with andesites in the south. Differences in igneous rock composition and release of magmatic volatiles affect compositions of vent fluids and deposits. Differences in vent fluid compositions and small-scale diffuse-flow regimes correlate with regional-scale patterns in microbial and megafaunal distributions. The interdisciplinary research effort at the Lau ISS has successfully identified linkages between subsurface processes and deep-sea biological communities, from mantle to microbe to megafauna.
    Description: Support was provided by National Science Foundation grants OCE-1038135 to MKT, OCE-0732369 and OCE-0240985 to CRF, OCE-0732369 and OCE-0838107 to PRG, OCE-0242618 to CHL, OCE-0242902 and OCE-0752256 to PJM, OCE-0728391 and OCE-0937404 to A-LR, and a GRFP to RB.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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    PAPER (OA)
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