Isolation of an archaeon at the prokaryote–eukaryote interface

Hiroyuki Imachi (), Masaru K. Nobu (), Nozomi Nakahara, Yuki Morono, Miyuki Ogawara, Yoshihiro Takaki, Yoshinori Takano, Katsuyuki Uematsu, Tetsuro Ikuta, Motoo Ito, Yohei Matsui, Masayuki Miyazaki, Kazuyoshi Murata, Yumi Saito, Sanae Sakai, Chihong Song, Eiji Tasumi, Yuko Yamanaka, Takashi Yamaguchi, Yoichi Kamagata, Hideyuki Tamaki and Ken Takai
Additional contact information
Hiroyuki Imachi: Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
Masaru K. Nobu: National Institute of Advanced Industrial Science and Technology (AIST)
Nozomi Nakahara: Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
Yuki Morono: Kochi Institute for Core Sample Research, X-star, JAMSTEC
Miyuki Ogawara: Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
Yoshihiro Takaki: Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
Yoshinori Takano: Research Institute for Marine Resources Utilization, JAMSTEC
Katsuyuki Uematsu: Marine Work Japan
Tetsuro Ikuta: Research Institute for Global Change, JAMSTEC
Motoo Ito: Kochi Institute for Core Sample Research, X-star, JAMSTEC
Yohei Matsui: Research Institute for Marine Resources Utilization, JAMSTEC
Masayuki Miyazaki: Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
Kazuyoshi Murata: National Institute for Physiological Sciences
Yumi Saito: Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
Sanae Sakai: Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
Chihong Song: National Institute for Physiological Sciences
Eiji Tasumi: Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
Yuko Yamanaka: Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
Takashi Yamaguchi: Nagaoka University of Technology
Yoichi Kamagata: National Institute of Advanced Industrial Science and Technology (AIST)
Hideyuki Tamaki: National Institute of Advanced Industrial Science and Technology (AIST)
Ken Takai: Japan Agency for Marine-Earth Science and Technology (JAMSTEC)

Nature, 2020, vol. 577, issue 7791, 519-525

Abstract: Abstract The origin of eukaryotes remains unclear1–4. Current data suggest that eukaryotes may have emerged from an archaeal lineage known as ‘Asgard’ archaea5,6. Despite the eukaryote-like genomic features that are found in these archaea, the evolutionary transition from archaea to eukaryotes remains unclear, owing to the lack of cultured representatives and corresponding physiological insights. Here we report the decade-long isolation of an Asgard archaeon related to Lokiarchaeota from deep marine sediment. The archaeon—‘Candidatus Prometheoarchaeum syntrophicum’ strain MK-D1—is an anaerobic, extremely slow-growing, small coccus (around 550 nm in diameter) that degrades amino acids through syntrophy. Although eukaryote-like intracellular complexes have been proposed for Asgard archaea6, the isolate has no visible organelle-like structure. Instead, Ca. P. syntrophicum is morphologically complex and has unique protrusions that are long and often branching. On the basis of the available data obtained from cultivation and genomics, and reasoned interpretations of the existing literature, we propose a hypothetical model for eukaryogenesis, termed the entangle–engulf–endogenize (also known as E3) model.

Date: 2020
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DOI: 10.1038/s41586-019-1916-6

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