Asgard archaea capable of anaerobic hydrocarbon cycling View Full Text


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Article Info

DATE

2019-04-23

AUTHORS

Kiley W. Seitz, Nina Dombrowski, Laura Eme, Anja Spang, Jonathan Lombard, Jessica R. Sieber, Andreas P. Teske, Thijs J. G. Ettema, Brett J. Baker

ABSTRACT

Large reservoirs of natural gas in the oceanic subsurface sustain complex communities of anaerobic microbes, including archaeal lineages with potential to mediate oxidation of hydrocarbons such as methane and butane. Here we describe a previously unknown archaeal phylum, Helarchaeota, belonging to the Asgard superphylum and with the potential for hydrocarbon oxidation. We reconstruct Helarchaeota genomes from metagenomic data derived from hydrothermal deep-sea sediments in the hydrocarbon-rich Guaymas Basin. The genomes encode methyl-CoM reductase-like enzymes that are similar to those found in butane-oxidizing archaea, as well as several enzymes potentially involved in alkyl-CoA oxidation and the Wood-Ljungdahl pathway. We suggest that members of the Helarchaeota have the potential to activate and subsequently anaerobically oxidize hydrothermally generated short-chain hydrocarbons. More... »

PAGES

1822

References to SciGraph publications

  • 2014-08-14. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences in NATURE REVIEWS MICROBIOLOGY
  • 2016-09-27. HydDB: A web tool for hydrogenase classification and analysis in SCIENTIFIC REPORTS
  • 2009-08-21. Community-wide analysis of microbial genome sequence signatures in GENOME BIOLOGY
  • 2014-09-14. Binning metagenomic contigs by coverage and composition in NATURE METHODS
  • 2017-11-10. Archaea and the origin of eukaryotes in NATURE REVIEWS MICROBIOLOGY
  • 2019-04-01. Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism in NATURE MICROBIOLOGY
  • 2008-06-30. Methanogenic archaea: ecologically relevant differences in energy conservation in NATURE REVIEWS MICROBIOLOGY
  • 2010-03-08. Prodigal: prokaryotic gene recognition and translation initiation site identification in BMC BIOINFORMATICS
  • 2016-10-03. Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota in NATURE MICROBIOLOGY
  • 2016-10-17. Thermophilic archaea activate butane via alkyl-coenzyme M formation in NATURE
  • 2010-07-13. BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments in BMC ECOLOGY AND EVOLUTION
  • 2009-08. Electron transfer in syntrophic communities of anaerobic bacteria and archaea in NATURE REVIEWS MICROBIOLOGY
  • 2015-05-06. Complex archaea that bridge the gap between prokaryotes and eukaryotes in NATURE
  • 2016-10-24. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system in NATURE COMMUNICATIONS
  • 2017-08-23. Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments in MICROBIOME
  • 2010-08-18. Hidden Markov model speed heuristic and iterative HMM search procedure in BMC BIOINFORMATICS
  • 2018-05-28. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy in NATURE MICROBIOLOGY
  • 2015-10-21. Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria in NATURE
  • 2017-01-11. Asgard archaea illuminate the origin of eukaryotic cellular complexity in NATURE
  • 2016-01-29. Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2018-11-27. Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments in NATURE COMMUNICATIONS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41467-019-09364-x

    DOI

    http://dx.doi.org/10.1038/s41467-019-09364-x

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1113639340

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/31015394


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    RDF/XML is a standard XML format for linked data.

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