‘ARMAN’ archaea depend on association with euryarchaeal host in culture and in situ

Olga V. Golyshina (), Stepan V. Toshchakov, Kira S. Makarova, Sergey N. Gavrilov, Aleksei A. Korzhenkov, Violetta La Cono, Erika Arcadi, Taras Y. Nechitaylo, Manuel Ferrer, Ilya V. Kublanov, Yuri I. Wolf, Michail M. Yakimov and Peter N. Golyshin
Additional contact information
Olga V. Golyshina: Bangor University
Stepan V. Toshchakov: Immanuel Kant Baltic Federal University
Kira S. Makarova: National Center for Biotechnology Information, National Library of Medicine—National Institutes of Health
Sergey N. Gavrilov: Winogradsky Institute of Microbiology, Research Center for Biotechnology Russian Academy of Sciences
Aleksei A. Korzhenkov: Immanuel Kant Baltic Federal University
Violetta La Cono: Institute for Coastal Marine Environment, CNR
Erika Arcadi: Institute for Coastal Marine Environment, CNR
Taras Y. Nechitaylo: Max Planck Institute for Chemical Ecology
Manuel Ferrer: Institute of Catalysis CSIC
Ilya V. Kublanov: Immanuel Kant Baltic Federal University
Yuri I. Wolf: National Center for Biotechnology Information, National Library of Medicine—National Institutes of Health
Michail M. Yakimov: Immanuel Kant Baltic Federal University
Peter N. Golyshin: Bangor University

Nature Communications, 2017, vol. 8, issue 1, 1-12

Abstract: Abstract Intriguing, yet uncultured ‘ARMAN’-like archaea are metabolically dependent on other members of the microbial community. It remains uncertain though which hosts they rely upon, and, because of the lack of complete genomes, to what extent. Here, we report the co-culturing of ARMAN-2-related organism, Mia14, with Cuniculiplasma divulgatum PM4 during the isolation of this strain from acidic streamer in Parys Mountain (Isle of Anglesey, UK). Mia14 is highly enriched in the binary culture (ca. 10% genomic reads) and its ungapped 0.95 Mbp genome points at severe voids in central metabolic pathways, indicating dependence on the host, C. divulgatum PM4. Analysis of C. divulgatum isolates from different sites and shotgun sequence data of Parys Mountain samples suggests an extensive genetic exchange between Mia14 and hosts in situ. Within the subset of organisms with high-quality genomic assemblies representing the ‘DPANN’ superphylum, the Mia14 lineage has had the largest gene flux, with dozens of genes gained that are implicated in the host interaction.

Date: 2017
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DOI: 10.1038/s41467-017-00104-7

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