News/Press Release

February 4, 2025
Japan Atomic Energy Agency (JAEA)
University of California Berkeley
University of Wisconsin-Madison
The University of Tokyo

Diverse microbiome functions, limited temporal variation and substantial genomic conservation in deep underground research laboratories
— Estimation of long-term stability of subsurface environments based on microbial communities —

[Summary of announcement]
  • Recent research has revealed that life exists in abundance deep underground. Although life that exists there is very tiny creatures, i.e. "microorganisms", a large part of the mechanism of subsurface microorganisms is yet to be discovered.
  • This research utilized underground research laboratories, which target at two different types of rock beds, namely, granites and sedimentary rocks. We monitored subsurface microorganisms for several years by means of metagenomic analysis for the first time in the world and comprehensively analyzed microbial communities and metabolic reactions. As a result, it was discovered that unknown microorganisms exist both in granite and sedimentary rocks in abundance and that they have representative metabolic reactions in common, although their rock types differ significantly.
  • It was revealed that about one-third of microbial genomes in sedimentary rocks are almost identical, although the sampling depths for groundwater were different. Moreover, we detected closely related species overlaps between the Japanese URLs and underground locations in the USA.
  • We attribute the genomic homogeneity within the Horonobe URL in part to consistent and stable geochemical and physical environments. The finding of biological stability is important for assessment of long-term confinement of geological disposal.
Figure: Conceptual diagram of the groundwater flow in the Horonobe area and microbiomes living in that area
[Information on article]
Name of journal: Environmental Microbiome
Title of article: Diverse microbiome functions, limited temporal variation and substantial genomic conservation within sedimentary and granite rock deep underground research laboratories
Names of authors (and their organizations): Yuki Amano1,5, Rohan Sachdeva2, Daniel Gittins2, Karthik Anantharaman3, Shufei Lei4, Luis E. Valentin‑Alvarado2, Spencer Diamond2, Hikari Beppu1, Teruki Iwatsuki5, Akihito Mochizuki5, Kazuya Miyakawa5, Eiichi Ishii5, Hiroaki Murakami5, Alexander L. Jaffe6, Cindy Castelle2, Adi Lavy4, Yohey Suzuki7 and Jillian F. Banfield2,4
1
Nuclear Fuel Cycle Engineering Laboratories, Japan Atomic Energy Agency
2
Innovative Genomics Institute, University of California, Berkeley
3
Department of Bacteriology, University of Wisconsin-Madison
4
Department of Earth and Planetary Science, University of California Berkeley,
5
Horonobe Underground Research Center, Japan Atomic Energy Agency
6
Department of Plant and Microbial Biology, University of California, Berkeley
7
Department of Earth and Planetary Science, The University of Tokyo)
DOI: https://doi.org/10.1186/s40793-024-00649-3