Deep-sea hydrothermal vent metagenome-assembled genomes provide insight into the phylum Nanoarchaeota

Environ Microbiol Rep. 2019 Apr;11(2):262-270. doi: 10.1111/1758-2229.12740.


Ectosymbiotic Nanoarchaeota live on the surface of diverse archaeal hosts. Despite being broadly distributed in global geothermal systems, only three Nanoarchaeota have been successfully co-cultivated with their hosts, and until now no nanoarchaeotal cultures or genomes have been described from deep-sea hydrothermal vents. We recovered three nanoarchaeotal metagenome-assembled genomes (MAGs) from deep-sea hydrothermal vent sites at the Eastern Lau Spreading Center (M10-121), Guaymas Basin (Gua-46) and the Mid-Cayman Rise (MC-1). Based on average amino acid identity analysis, M10-121 is a novel species in the candidate genus Nanoclepta, while the other two MAGs represent novel genera in the Nanoarchaeota. Like previously sequenced Nanoarchaeota, each MAG encodes at least one split protein-coding gene. The MAGs also contain a mosaic of key nanoarchaeotal features, including CRISPR repeat regions and marker genes for gluconeogenesis and archaeal flagella. MC-1 also encodes the pentose bisphosphate pathway, which may allow the nanoarchaeote to bypass several steps in glycolysis and produce ATP.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Archaea / classification
  • Archaea / genetics
  • Archaeal Proteins / genetics
  • Archaeal Proteins / metabolism
  • DNA, Archaeal / genetics
  • Genome, Archaeal / genetics*
  • Hydrothermal Vents / microbiology*
  • Metagenomics
  • Nanoarchaeota / classification
  • Nanoarchaeota / genetics*
  • Phylogeny
  • RNA, Ribosomal, 16S / genetics
  • Sequence Analysis, DNA


  • Archaeal Proteins
  • DNA, Archaeal
  • RNA, Ribosomal, 16S