We’re sorry, but GBIF doesn’t work properly without JavaScript enabled.
Our website has detected that you are using an outdated insecure browser that will prevent you from using the site. We suggest you upgrade to a modern browser.
{{nav.loginGreeting}}
  • Get data
      • Occurrences
      • GBIF API
      • Species
      • Datasets
      • Occurrence snapshots
      • Hosted portals
      • Trends
  • How-to
    • Share data

      • Quick-start guide
      • Dataset classes
      • Data hosting
      • Standards
      • Become a publisher
      • Data quality
      • Data papers
    • Use data

      • Featured data use
      • Citation guidelines
      • GBIF citations
      • Citation widget
  • Tools
    • Publishing

      • IPT
      • Data validator
      • Scientific Collections
      • Suggest a dataset
      • New data model ⭐️
    • Data access and use

      • Hosted portals
      • Data processing
      • Derived datasets
      • rgbif
      • pygbif
      • MAXENT
      • Tools catalogue
    • GBIF labs

      • Species matching
      • Name parser
      • Sequence ID
      • Relative observation trends
      • GBIF data blog
  • Community
    • Network

      • Participant network
      • Nodes
      • Publishers
      • Network contacts
      • Community forum
      • alliance for biodiversity knowledge
    • Volunteers

      • Mentors
      • Ambassadors
      • Translators
      • Citizen scientists
    • Activities

      • Capacity enhancement
      • Programmes & projects
      • Training and learning resources
      • Data Use Club
      • Living Atlases
  • About
    • Inside GBIF

      • What is GBIF?
      • Become a member
      • Governance
      • Implementation plan
      • Work Programme
      • Funders
      • Partnerships
      • Release notes
      • Contacts
    • News & outreach

      • News
      • Newsletters and lists
      • Events
      • Ebbe Nielsen Challenge
      • Graduate Researchers Award
      • Science Review
      • Data use
  • User profile

Specialists instead of generalists oxidize alkanes in anoxic marine hydrocarbon seep sediments

Dataset homepage

Citation

MGnify (2019). Specialists instead of generalists oxidize alkanes in anoxic marine hydrocarbon seep sediments. Sampling event dataset https://doi.org/10.15468/73vrme accessed via GBIF.org on 2023-02-07.

Description

The anaerobic oxidation of non-methane hydrocarbons mediated by sulfate-reducing bacteria (SRB) is a major process of organic matter degradation at marine hydrocarbon seeps. Several SRB have been successfully cultured, however, knowledge about in situ active organisms is still very limited. Here, we identified alkane-degrading key players from two contrasting seeps at the Mediterranean Amon Mud Volcano (Amon MV) and Guaymas Basin in the Gulf of California using complementary stable-isotope probing (SIP) techniques. Anoxic sediments were incubated with 13C-labeled butane or dodecane under close to in situ conditions. DNA- and RNA-based SIP in combination with 454-pyrosequencing (PYRO-SIP) allowed the identification of four phylogenetically distinct deltaproteobacterial groups of alkane-oxidizing SRB within the family Desulfobacteraceae. We named the groups degrading short-chain alkanes ‘SCA-SRB1' and ‘SCA-SRB2' and those degrading long-chain alkanes ‘LCA-SRB1' and ‘LCA-SRB2'. CARD-FISH with newly developed specific probes revealed a high relative in situ abundance of SCA-SRB1 and SCA-SRB2 with 2% of the total community, while groups LCA-SRB1 and LCA-SRB2 were below 1% of total cells. Protein-based SIP (Protein-SIP), which enables to trace stable isotopes from substrate to protein, confirmed alkane-degrading key players of the family Desulfobacteraceae. In addition, Protein-SIP indicated additional carbon sources for 13C biosynthesis besides alkanes, and gave insights into possible metabolic pathways: (1-methylalkyl)succinylation as initial step of butane degradation and the oxidative Wood–Ljungdahl pathway as terminal point of alkane degradation.

Sampling Description

Sampling

The anaerobic oxidation of non-methane hydrocarbons mediated by sulfate-reducing bacteria (SRB) is a major process of organic matter degradation at marine hydrocarbon seeps. Several SRB have been successfully cultured, however, knowledge about in situ active organisms is still very limited. Here, we identified alkane-degrading key players from two contrasting seeps at the Mediterranean Amon Mud Volcano (Amon MV) and Guaymas Basin in the Gulf of California using complementary stable-isotope probing (SIP) techniques. Anoxic sediments were incubated with 13C-labeled butane or dodecane under close to in situ conditions. DNA- and RNA-based SIP in combination with 454-pyrosequencing (PYRO-SIP) allowed the identification of four phylogenetically distinct deltaproteobacterial groups of alkane-oxidizing SRB within the family Desulfobacteraceae. We named the groups degrading short-chain alkanes ‘SCA-SRB1' and ‘SCA-SRB2' and those degrading long-chain alkanes ‘LCA-SRB1' and ‘LCA-SRB2'. CARD-FISH with newly developed specific probes revealed a high relative in situ abundance of SCA-SRB1 and SCA-SRB2 with 2% of the total community, while groups LCA-SRB1 and LCA-SRB2 were below 1% of total cells. Protein-based SIP (Protein-SIP), which enables to trace stable isotopes from substrate to protein, confirmed alkane-degrading key players of the family Desulfobacteraceae. In addition, Protein-SIP indicated additional carbon sources for 13C biosynthesis besides alkanes, and gave insights into possible metabolic pathways: (1-methylalkyl)succinylation as initial step of butane degradation and the oxidative Wood–Ljungdahl pathway as terminal point of alkane degradation.

Method steps

  1. Pipeline used: https://www.ebi.ac.uk/metagenomics/pipelines/4.1

Taxonomic Coverages

Geographic Coverages

Bibliographic Citations

  1. Kleindienst S, Herbst FA, Stagars M, von Netzer F, von Bergen M, Seifert J, Peplies J, Amann R, Musat F, Lueders T, Knittel K. 2014. Diverse sulfate-reducing bacteria of the Desulfosarcina/Desulfococcus clade are the key alkane degraders at marine seeps. ISME J vol. 8 - DOI:10.1038/ismej.2014.51

Contacts

originator
MPI BREMEN
metadata author
MPI BREMEN
administrative point of contact
MPI BREMEN
What is GBIF? API FAQ Newsletter Privacy Terms and agreements Citation Code of Conduct Acknowledgements
Contact GBIF Secretariat Universitetsparken 15 DK-2100 Copenhagen Ø Denmark