Diverse microbiome functions, limited temporal variation and substantial genomic conservation within sedimentary and granite rock deep underground research laboratories

堆積岩及び花崗岩の地下研究施設における多様な微生物代謝機能、限られた経時変化、高いゲノム保存性

天野 由記   ; Sachdeva, R.*; Gittins, D.*; Anantharaman, K.*; Lei, S.*; Valentin-Alvarado, L. E.*; Diamond, S.*; 別部 光里*; 岩月 輝希  ; 望月 陽人  ; 宮川 和也   ; 石井 英一   ; 村上 裕晃  ; Jaffe, A. L.*; Castelle, C. J.*; Lavy, A.*; 鈴木 庸平*; Banfield, J. F.*

Amano, Yuki; Sachdeva, R.*; Gittins, D.*; Anantharaman, K.*; Lei, S.*; Valentin-Alvarado, L. E.*; Diamond, S.*; Beppu, Hikari*; Iwatsuki, Teruki; Mochizuki, Akihito; Miyakawa, Kazuya; Ishii, Eiichi; Murakami, Hiroaki; Jaffe, A. L.*; Castelle, C. J.*; Lavy, A.*; Suzuki, Yohei*; Banfield, J. F.*

Underground research laboratories (URLs) provide a window on the deep biosphere and enable investigation of potential microbial impacts on nuclear waste, CO and H 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. 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 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-rich Horonobe URL. We detected near-identical genotypes for approximately one third of all genomically defined organisms at multiple depths within the Horonobe URL. This cannot be explained by inactivity, as in situ growth was detected for some bacteria, albeit at slow rates. Given the current low hydraulic conductivity and groundwater compositional heterogeneity, ongoing inter-site strain dispersal seems unlikely. Alternatively, the Horonobe URL microbiome homogeneity may be explained by higher groundwater mobility during the last glacial period. Genotypically-defined species closely related to those detected in the URLs were identified in three other subsurface environments in the USA. Thus, dispersal rates between widely separated underground sites may be fast enough relative to mutation rates to have precluded substantial divergence in species composition. Species overlaps between subsurface locations on different continents constrain expectations regarding the scale of global subsurface biodiversity. Overall, microbiome and geochemical stability over the study period has important implications for underground storage applications.