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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; et al.
Environmental Microbiome (Internet), 19, p.105_1 - 105_17, 2024/12
被引用回数：0 パーセンタイル：0.00(Genetics & Heredity)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.
Al-Shayeb, B.*; Sachdeva, R.*; Chen, L.-X.*; Ward, F.*; Munk, P.*; Devoto, A.*; Castelle, C. J.*; Olm, M. R.*; Bouma-Gregson, K.*; 天野 由記; et al.
Nature, 578(7795), p.425 - 431, 2020/02
被引用回数：291 パーセンタイル：99.46(Multidisciplinary Sciences)Phage typically have small genomes and depend on their bacterial hosts for replication. We generated metagenomic datasets from many diverse ecosystems and reconstructed hundreds of huge phage genomes, between 200 kbp and 716 kbp in length. Thirty four genomes were manually curated to completion, including the largest phage genomes yet reported. Expanded genetic repertoires include diverse and new CRISPR-Cas systems, tRNAs, tRNA synthetases, tRNA modification enzymes, initiation and elongation factors and ribosomal proteins. Phage CRISPR have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. Some phage repurpose bacterial systems for phage-defense to eliminate competing phage. We phylogenetically define seven major clades of huge phage from human and other animal microbiomes, oceans, lakes, sediments, soils and the built environment. We conclude that large gene inventories reflect a conserved biological strategy, observed across a broad bacterial host range and resulting in the distribution of huge phage across Earth's ecosystems.
天野 由記; Diamond, S.*; Lavy, A.*; Anantharaman, K.*; 宮川 和也; 岩月 輝希; 別部 光里*; 鈴木 庸平*; Thomas, B. C.*; Banfield, J. F.*
no journal, ,
We investigated the microbiology two Japanese subsurface research sites and compared the major groups of organisms lacking cultivated representatives found from other subsurface sites, including a Colorado aquifer and deep aquifers underlying the Crystal Geyser. We analyzed metagenomic data 19 samples from the Horonobe site and 7 from the Mizunami site. DNA sequences from each sample were assembled independently and scaffolds encoding the ribosomal protein S3 sequence were identified. 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, ANME-2D 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, 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. Given the importance of the subsurface as a potential host environment for storage of nuclear waste, finding some commonality would indicate the general relevance of information from one site for prediction of the characteristics of other sites.
