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Genomic conservation in diverse, distinct but functionally similar microbiomes in deep subsurface sedimentary and granitic environments

地下深部の堆積岩と花崗岩環境下での多様で特異的だが代謝機能は類似したマイクロバイオームにおけるゲノムの保存性

天野 由記   ; Sachdeva, R.*; Gittins, D.*; Anantharaman, K.*; Lei, S.*; 別部 光里*; 望月 陽人  ; Thomas, B. C.*; 鈴木 庸平*; Banfield, J. F.*

Amano, Yuki; Sachdeva, R.*; Gittins, D.*; Anantharaman, K.*; Lei, S.*; Beppu, Hikari*; Mochizuki, Akihito; Thomas, B. C.*; Suzuki, Yohei*; Banfield, J. F.*

Underground research laboratories (URLs) provide a window on the deep biosphere and enable investigation of potential microbial impacts on geological disposal, CO$$_{2}$$ and H$$_{2}$$ stored in the subsurface. We carried out the first multi-year study of groundwater microbiomes sampled from defined intervals between 140 and 400 m below the surface of the Horonobe and Mizunami URLs, Japan. We reconstructed draft genomes for $$<$$90% of all organisms detected over a four-year period. The Horonobe and Mizunami microbiomes are dissimilar, likely because the Mizunami URL is hosted in granitic rock and the Horonobe URL in sedimentary rock. Despite this, hydrogen metabolism, rubisco-based CO$$_{2}$$ fixation, reduction of nitrogen compounds and sulfate reduction are well represented functions in microbiomes from both URLs, although methane metabolism is more prevalent at the organic- and CO$$_{2}$$ -rich Horonobe URL. High fluid flow zones and proximity to subsurface tunnels apparently impact microbial community composition. We detected near-identical genotypes for approximately one third of genomically defined organisms at multiple depths within the Horonobe URL. Sequencing data indicate that at least some of the bacteria are growing, albeit slowly. Genotypically-defined species closely related to those detected in the URLs were identified in three other subsurface environments in the USA. Thus, dispersal rates may be fast enough relative to mutation rates to have limited substantial species divergence. Hydraulic and isotopic measurements predict inter-site movement of groundwater over thousands of years, but it is uncertain whether the permeability is sufficient for transport of microbial cells. Alternatively, Horonobe URL microbiome homogeneity may be explained by dispersal during last glacial period.

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