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Research Highlights, A Membrane-Bounded Genome in a Bacterium Discovered from Deep Subsurface

Geological Survey of Japan

Life Science and Biotechnology

A Membrane-Bounded Genome in a Bacterium Discovered from Deep Subsurface

KATAYAMA Taiki, YOSHIOKA Hideyoshi
Research Institute for Geo-Resources and Environment
Masaru K. Nobu, KUSADA Hiroyuki, MENG Xian-Ying,
KAMAGATA Yoichi, TAMAKI Hideyuki
Bioproduction Research Institute

Released: December 14, 2020

A prokaryote with a membrane surrounding its genomic DNA

A "phylum" level as-yet-uncultivated bacterial group that extensively inhabits subsurface environments around the world and which has the potential to contribute to the global carbon cycle, such as methane production, was successfully cultured for the first time in the world. Furthermore, the amazing discovery was made that even though this bacterium is a prokaryote, it has a membrane surrounding its genomic DNA. This discovery is an achievement which may result in a redefinition of prokaryote, and will lead to a deeper understanding of methane production mechanisms and biological evolution in subsurface environments.

photo: Genomic DNA localized in RT761 strain cell

Genomic DNA localized in RT761 strain cell
(A) A dividing cell. The white line indicates the outline of the cell corresponding to the position of the cell membrane.
(B) The cell in (A) with the membrane composed of lipids (red: the red line indicates the outline) and the genomic DNA (blue) stained.

Elucidation of subsurface microbial ecology

Understanding microbial activity in subsurface environments will lead to, for example, efficient use of natural gas resources and accurate estimation of gas reserves. It can also contribute to preservation of the global environment and the safe and efficient use of global resources. This research successfully isolated and cultured a previously unknown bacterium involved in the production of natural gas and methane from paleo-sea water and sediment samples in the Minami-Kanto gas field.

Illustration: Atribacter laminatus RT761, the novel bacterium in a new phylum Atribacterota

A prokaryote with a membrane inside the cell

A new species of bacteria classified as a new phylum, the RT761 strain, was cultured and isolated over a period of five years. Unlike common prokaryotes, a "membrane" inside the cell surrounds the genomic DNA of this bacterium. It was also proved that the RT761 strain is a new bacterial species at the "phylum" level, the highest taxonomic rank of prokaryotes. Therefore, Atribacterota was proposed as the new phylum representing this strain, and the new species Atribacter laminatus was proposed as the scientific name for the RT761 strain, and this nomenclature was formally validated.

Elucidation of role and evolutionary process in subsurface environments

The findings will be used to clarify the details of the activity of Atribacterota phylum bacteria in deep subsurface environments, including the role played in the methane production process. Efforts will also be made to elucidate the evolutionary path by which the Atribacterota phylum, which branched early in bacterial evolution, came to have a unique cell structure.

Contact for inquiries related to this theme

Geomicrobiology Research Group, Research Institute for Geo-Resources and Environment

KATAYAMA Taiki, Senior Researcher

AIST Tsukuba Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567 Japan

E-mail: geore-web-ml*aist.go.jp (Please convert “*” to “@”)

Web: https://unit.aist.go.jp/georesenv/geomicrob/index_en.html

Microbial and Genetic Resources Research Group, Bioproduction Research Institute

Masaru K. Nobu, Researcher

TAMAKI Hideyuki, Group Leader

AIST Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 Japan

E-mail: bpri-webmaster-ml*aist.go.jp (Please convert “*” to “@”)

Web: https://unit.aist.go.jp/bpri/index_e.html

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