Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea View Full Text


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Article Info

DATE

2016-02-15

AUTHORS

Brett J. Baker, Jimmy H. Saw, Anders E. Lind, Cassandre Sara Lazar, Kai-Uwe Hinrichs, Andreas P. Teske, Thijs J. G. Ettema

ABSTRACT

The subsurface biosphere is largely unexplored and contains a broad diversity of uncultured microbes1. Despite being one of the few prokaryotic lineages that is cosmopolitan in both the terrestrial and marine subsurface2–4, the physiological and ecological roles of SAGMEG (South-African Gold Mine Miscellaneous Euryarchaeal Group) Archaea are unknown. Here, we report the metabolic capabilities of this enigmatic group as inferred from genomic reconstructions. Four high-quality (63–90% complete) genomes were obtained from White Oak River estuary and Yellowstone National Park hot spring sediment metagenomes. Phylogenomic analyses place SAGMEG Archaea as a deeply rooting sister clade of the Thermococci, leading us to propose the name Hadesarchaea for this new Archaeal class. With an estimated genome size of around 1.5 Mbp, the genomes of Hadesarchaea are distinctly streamlined, yet metabolically versatile. They share several physiological mechanisms with strict anaerobic Euryarchaeota. Several metabolic characteristics make them successful in the subsurface, including genes involved in CO and H2 oxidation (or H2 production), with potential coupling to nitrite reduction to ammonia (DNRA). This first glimpse into the metabolic capabilities of these cosmopolitan Archaea suggests they are mediating key geochemical processes and are specialized for survival in the subsurface biosphere. More... »

PAGES

16002

References to SciGraph publications

  • 2007-11-08. Uncultured archaea in deep marine subsurface sediments: have we caught them all? in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2009-08-21. Community-wide analysis of microbial genome sequence signatures in GENOME BIOLOGY
  • 2013-05-14. Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage in NATURE COMMUNICATIONS
  • 1990-07. Nitrate respiration, denitrification, and utilization of nitrogen sources by aerobic carbon monoxide-oxidizing bacteria in ARCHIVES OF MICROBIOLOGY
  • 2005-07. Deep sub-seafloor prokaryotes stimulated at interfaces over geological time in NATURE
  • 2008-07-17. A comparison of methods for total community DNA preservation and extraction from various thermal environments in JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
  • 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
  • 1995-02-01. Enzymes and coenzymes of the carbon monoxide dehydrogenase pathway for autotrophic CO2 fixation in Archaeoglobus lithotrophicus and the lack of carbon monoxide dehydrogenase in the heterotrophic A. profundus in ARCHIVES OF MICROBIOLOGY
  • 2015-09-01. A metagenomic window into carbon metabolism at 3 km depth in Precambrian continental crust in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2010-03-08. Prodigal: prokaryotic gene recognition and translation initiation site identification in BMC BIOINFORMATICS
  • 2015-04-13. Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria in MICROBIOME
  • 2011-03-09. Anaerobic transformation of carbon monoxide by microbial communities of Kamchatka hot springs in EXTREMOPHILES
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nmicrobiol.2016.2

    DOI

    http://dx.doi.org/10.1038/nmicrobiol.2016.2

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1009322467

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/27572167


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