1887

Abstract

An anaerobic, mesophilic, syntrophic, archaeon strain MK-D1, was isolated as a pure co-culture with sp. strain MK-MG from deep-sea methane seep sediment. This organism is, to our knowledge, the first cultured representative of ‘Asgard’ archaea, an archaeal group closely related to eukaryotes. Here, we describe the detailed physiology and phylogeny of MK-D1 and propose gen. nov., sp. nov. to accommodate this strain. Cells were non-motile, small cocci, approximately 300–750 nm in diameter and produced membrane vesicles, chains of blebs and membrane-based protrusions. MK-D1 grew at 4–30 °C with optimum growth at 20 °C. The strain grew chemoorganotrophically with amino acids, peptides and yeast extract with obligate dependence on syntrophy with H-/formate-utilizing organisms. MK-D1 showed the fastest growth and highest maximum cell yield when grown with yeast extract as the substrate: approximately 3 months to full growth, reaching up to 6.7×10 16S rRNA gene copies ml. MK-D1 had a circular 4.32 Mb chromosome with a DNA G+C content of 31.1 mol%. The results of phylogenetic analyses of the 16S rRNA gene and conserved marker proteins indicated that the strain is affiliated with ‘Asgard’ archaea and more specifically DHVC1/DSAG/MBG-B and ‘Lokiarchaeota’/‘Lokiarchaeia’. On the basis of the results of 16S rRNA gene sequence analysis, the most closely related isolated relatives were 3507LT (76.09 %) and RMAS (77.45 %) and the closest relative in enrichment culture was ‘Lokiarchaeum ossiferum’ (95.39 %). The type strain of the type species is MK-D1 (JCM 39240 and JAMSTEC no. 115508). We propose the associated family, order, class, phylum, and kingdom as fam. nov., ord. nov., class. nov., phyl. nov., and regn. nov., respectively. These are in accordance with ICNP Rules 8 and 22 for nomenclature, Rule 30(3)(b) for validation and maintenance of the type strain, and Rule 31a for description as a member of an unambiguous syntrophic association.

Funding
This study was supported by the:
  • Core Research for Evolutional Science and Technology (Award JPMJCR19S5)
    • Principle Award Recipient: MakotoMiyata
  • Gordon and Betty Moore Foundation (Award GBMF9743)
    • Principle Award Recipient: MasaruK. Nobu
  • Japan Society for the Promotion of Science (Award JP19H05689)
    • Principle Award Recipient: MoriyaOhkuma
  • Japan Society for the Promotion of Science (Award JP22H04985)
    • Principle Award Recipient: HiroyukiImachi
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2024-07-05
2024-07-15
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