Vast metabolic and phylogenetic diversity shared across deep subsurface environments

Although the structure of microbial communities in the deep subsurface remains relatively little known, recent research has revealed large groups of novel bacteria and archaea in these environments. Here, we investigate the microbiology of two Japanese subsurface Underground Research Laboratories (URL) and compared to those found from other subsurface sites, including a shallow Rifle, Colorado aquifer and deep aquifers underlying the Crystal Geyser, Utah.

Samples were collected from Horonobe between 140 m and 250 m below the surface (relatively organic rich, saline groundwater) and from Mizunamifrom 200 to 400 m below the surface (organic-poor, low ionic strength groundwater). Total DNA was extracted and sequenced from each sample, and subsequently assembled independently. A phylogenetic census of organisms and their abundance was carried out by identifying a non-redundant set of scaffolds encoding the ribosomal protein S3 sequence.

The major characteristic of the microbiology of the Mizumani site that distinguished it from the Horonobe site is local very high abundances of Nitrospirae, Parcubacteria , Ignavibacteria, and Micrarchaeota. In contrast, the Horonobe site has locations that are highly enriched in Altarchiales, Syntrophobacteriales, Atribacteria, ANME-2D and Methanogens. Beyond reshaping the Tree of Life (Hug et al. 2016), the societal importance of these discoveries remains little known. However, given the huge inventory of new groups of proteins and pathways in the genomes of these organisms, it is reasonable to anticipate major discoveries will hold relevance, for example, in terms of pharmaceutical discovery. One clear example that illustrates the potential value of sequences from subsurface organisms is the discovery of new minimal CRISPR-Cas systems of direct relevance for genome editing. Given the importance of the subsurface as a potential host environment for disposal of nuclear waste, finding some commonality would indicate the general relevance of information from one site for prediction of the characteristics of other sites.

Hug et al., (2016) Nature Microbiology, 1, 16048.

This study was partly performed as a part of "The project for validating assessment methodology in geological disposal system" funded by the Ministry of Economy, Trade and Industry of Japan.