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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.
archaea host diverse and interacting extrachromosomal elementsShi, L.-D.*; West-Roberts, J.*; Schoelmerich, M. C.*; Penev, P. I.*; Chen, L.-X.*; 天野 由記; Lei, S.*; Sachdeva, R.*; Banfield, J. F.*
Nature Microbiology (Internet), 9(9), p.2422 - 2433, 2024/09
被引用回数：0 パーセンタイル：0.00(Microbiology)Methane emissions that contribute to climate change can be mitigated by anaerobic methane-oxidizing archaea such as . Some have huge extrachromosomal genetic elements (ECEs) called Borgs that may modulate their activity, yet the broader diversity of ECEs is little studied. Here, we report small enigmatic linear ECEs, circular viruses and unclassified ECEs, that we predict replicate within . The linear ECEs have features such as inverted terminal repeats, pervasive tandem repeats, and coding patterns that are strongly reminiscent of Borgs, but they are only 52 kb to 145 kb in length. They share proteins with Borgs and . Thus, we refer to them as mini-Borgs. Mini-Borgs are genetically diverse and we assign them to at least five family-level groups. We also identify eight novel families of viruses, some of which encode multiheme cytochromes, and unclassified circular ECEs that encode TnpB genes. A population-heterogeneous CRISPR array is encoded in close proximity to TnpB and has spacers that target other ECEs including previously reported plasmids. The diverse groups of ECEs exchange genetic information with each other and with , likely impacting the activity and evolution of these environmentally important archaea.
neutron diffractionZhou, Y.*; Song, W.*; Zhang, F.*; Wu, Y.*; Lei, Z.*; Jiao, M.*; Zhang, X.*; Dong, J.*; Zhang, Y.*; Yang, M.*; et al.
Journal of Alloys and Compounds, 971, p.172635_1 - 172635_7, 2024/01
被引用回数：1 パーセンタイル：16.17(Chemistry, Physical)The grain orientation-dependent lattice strain evolution of a (TiZrHfNb)
refractory high-entropy alloy (HEA) during tensile loading has been investigated using neutron diffraction. The equivalent strain-hardening rate of each of the primary 
-oriented grain families was found to be relatively low, manifesting the macroscopically weak work-hardening ability of such a body-centered cubic (BCC)-structured HEA. This finding is indicative of a dislocation planar slip mode that is confined in a few single-slip planes and leads to in-plane softening by high pile-up stresses.
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：275 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.
PdZhou, H. B.*; Zhou, X. H.*; Zhang, Y. H.*; Zheng, Y.*; Liu, M. L.*; Zhang, N. T.*; Chen, L.*; Wang, S. T.*; Li, G. S.*; Wang, H. X.*; et al.
European Physical Journal A, 47(9), p.107_1 - 107_7, 2011/09
被引用回数：6 パーセンタイル：41.10(Physics, Nuclear)Pd原子核の高スピン状態を、タンデム加速器及び多重
線検出装置GEMINI-IIを用いて、インビーム線核分光法で調べた。既知の
バンド, 1/2
[550]バンドをより高スピン状態まで拡張した。発見されたバンド交差は
陽子の整列によるものであると解釈した。Pdの回転バンドの性質を周辺の核、及びcranked shell modelと比較・議論した。
[503] band of 
PtLi, G. S.*; Zhou, X. H.*; Zhang, Y. H.*; Zheng, Y.*; Liu, M. L.*; Hua, W.*; Zhou, H. B.*; Ding, B.*; Wang, H. X.*; Lei, X. G.*; et al.
Journal of Physics G; Nuclear and Particle Physics, 38(9), p.095105_1 - 095105_9, 2011/09
被引用回数：1 パーセンタイル：11.49(Physics, Nuclear)Ptの高スピン状態をタンデム加速器と多重線検出装置GEMINI-IIを用いて調べた。低スピン指標逆転現象が7/2[503]バンドで観測された。この現象は、中性子が7/2[503]軌道から7/2[514]軌道に移ることによって起こるという解釈は、DonauとFrauendorfの反古典的近似による計算結果によって支持された。
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.*
no journal, ,
Underground research laboratories (URLs) provide a window on the deep biosphere and enable investigation of potential microbial impacts on geological disposal, 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. 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 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. 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.
