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

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

https://doi.org/10.1186/s40793-024-00649-3

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.

Microbiome analysis of the restricted bacteria in radioactive element-containing water at the Fukushima Daiichi Nuclear Power Station

藁科 友朗*; 佐藤 朝子*; 比内 浩; Shaikhutdinov, N.*; Shagimardanova, E.*; 森 宙史*; 玉木 聡志*; 斎藤 元文*; 眞田 幸尚; 佐々木 祥人; et al.

Applied and Environmental Microbiology, 90(4), p.e02113-23_1 - e02113-23_23, 2024/04

https://doi.org/10.1128/aem.02113-23

A major incident occurred at the Fukushima Daiichi Nuclear Power Station following the tsunami triggered by the Tohoku-Pacific Ocean Earthquake in March 2011, whereby seawater entered the torus room in the basement of the reactor building. Here, we identify and analyze the bacterial communities in the torus room water and several environmental samples. Samples of the torus room water (1 10 BqCs/L) were collected by the Tokyo Electric Power Company Holdings from two sampling points between 30 cm and 1 m from the bottom of the room (TW1) and the bottom layer (TW2). A structural analysis of the bacterial communities based on 16S rRNA amplicon sequencing revealed that the predominant bacterial genera in TW1 and TW2 were similar. TW1 primarily contained the genus Limnobacter, a thiosulfate-oxidizing bacterium. -Irradiation tests on Limnobacter thiooxidans, the most closely related phylogenetically found in TW1, indicated that its radiation resistance was similar to ordinary bacteria. TW2 predominantly contained the genus Brevirhabdus, a manganese- oxidizing bacterium. Although bacterial diversity in the torus room water was lower than seawater near Fukushima, 70% of identified genera were associated with metal corrosion. Latent environment allocation - an analytical technique that estimates habitat distributions and co-detection analyses - revealed that the microbial communities in the torus room water originated from a distinct blend of natural marine microbial and artificial bacterial communities typical of biofilms, sludge, and wastewater. Understanding the specific bacteria linked to metal corrosion in damaged plants is important for advancing decommissioning efforts.

Degradation of nuclear fuel debris analog by siderophore-releasing microorganisms

大貫 敏彦*; 中瀬 正彦*; Liu, J.; 土津田 雄馬; 佐藤 志彦; 北垣 徹; 香西 直文

Journal of Nuclear Science and Technology, 61(3), p.384 - 396, 2023/07

https://doi.org/10.1080/00223131.2023.2231951

We investigated the effect of siderophore-releasing microorganism (SB) on fuel debris. Fuel debris analogue pellet samples (FDAPSs) and powder samples containing CeO (an alternative to UO)-ZrO solid solution, and metallic iron were fabricated. FDAPSs were contacted with SB on a membrane filter placed on agar medium for 50 days. By the addition of SB, Fe-containing degradation products were detected on the filter, and on the agar medium, revealing that some fraction of Fe ions were dissolved and precipitated on FDAPSs, and the rest became detached from FDAPSs, and migrated through the filter. Although Zr were detected in small amounts on the Fe area, the dissolution of Zr may be limited. These results clarify that the presence of RB accelerates the degradation of fuel debris in which Fe metal regions are preferentially degraded, and some fraction of Fe were detached and migrated from the fuel debris.

廃炉における微生物腐食の課題

若井 暁*; 平野 伸一*; 上野 文義; 岡本 章玄*

材料と環境, 70(12), p.491 - 496, 2021/12

https://doi.org/10.3323/jcorr.70.491

福島第一原子力発電所は、2011年3月11日に発生した地震に関連する東日本大震災の影響により廃炉が進められている。事故以前から腐食に関する対策は十分に取られ、事故後も速やかに対策が立てられ、適切に管理することで大きな腐食事故事例は発生していない。一方で、事故当時に行われた海水注入や連続的に建屋内に入り込んでいる地下水との接触によって微生物の影響が継続的に発生している。この様な観点と最新の微生物腐食研究の知見から、福島第一原子力発電所で起こりうる微生物腐食リスクについて整理する。

Function of microbes on chemical species transformation of radionuclides

大貫 敏彦*; 尾崎 卓郎*; 香西 直文; 宇都宮 聡*

Behavior of Radionuclides in the Environment I; Function of Particles in Aquatic System, p.67 - 92, 2020/00

https//doi.org/10.1007/978-981-15-0679-6

バクテリアや酵母等の微生物の細胞はアクチノイドを細胞表面に吸着する能力が高く、細胞から分泌されるリン酸イオンはアクチノイドのリン酸塩を作るなど、放射性核種の物理化学状態に微生物が影響することが実験的に知られている。本章では、ソビエト連邦の核技術施設で発生した放射性廃棄物の投棄場所であったカラチャイ湖周辺の地下水に含まれるアクチノイドの移行における微生物の役割を議論する。

Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria

Matheus Carnevali, P. B.*; Schulz, F.*; Castelle, C. J.*; Kantor, R. S.*; Shih, P.*; Sharon, I.*; Santini, J.*; Olm, M. R.*; 天野 由記; Thomas, B. C.*; et al.

Nature Communications (Internet), 10, p.463_1 - 463_15, 2019/01

https://doi.org/10.1038/s41467-018-08246-y

The metabolic platform in which microbial aerobic respiration evolved is tightly linked to the origins of Cyanobacteria (Oxyphotobacteria). Melainabacteria and Sericytochromatia, close phylogenetic neighbores to Oxyphotobacteria comprise both fermentative and aerobic representatives, or clades that are capablee of both. Here, we predict the metabolisms of Margulisbacteria from two distinct environments and Saganbacteria, and compare them to genomes of organisms from the related lineages. Melainabacteria BJ4A obtained from Mizunami site are potentially able to use O and other terminal electron acceptors. The type C heme-copper oxygen reductase found in Melainabacteria BJ4A may be adapted to low O levels, as expected for microaerophilic or anoxic environments such as the subsurface. Notably, Melainabacteria BJ4A seems to have a branched electron transport chain, with one branch leading to a cytochrome d ubiquinol oxidoreductase and the other one leading to the type C heme-copper oxygen reductase. Both these enzymes have high affinity for O, thus are adapted to low O levels. These contemporary lineages have representatives with fermentative H-based metabolism, lineages capable of aerobic or anaerobic respiration, and lineages with both. Our findings support the idea that the ancestor of these lineages was an anaerobe in which fermentation and H metabolism were central metabolic features.

Removal of soluble strontium via incorporation into biogenic carbonate minerals by halophilic bacterium Bacillus sp. strain TK2d in a highly saline solution

堀池 巧*; 土津田 雄馬*; 中野 友里子*; 落合 朝須美*; 宇都宮 聡*; 大貫 敏彦; 山下 光雄*

Applied and Environmental Microbiology, 83(20), p.e00855-17_1 - e00855-17_11, 2017/10

https://doi.org/10.1128/AEM.00855-17

福島第一原子力発電所事故により、放射性ストロンチウムの一部が海洋に漏出した。塩濃度が高い条件では一般的な吸着剤によるSrの除去効率が低いので、本研究では生物起源鉱物による塩水中からの水溶性Srの除去を検討した。海底堆積物から単離したバチルス属細菌のTK2k株は、塩水中のSrの99%以上を除去した。Srはまず細胞表面に吸着し、その後細胞外に形成した炭酸塩鉱物に取り込まれることを明らかにした。

Potential for microbial H and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments

Hernsdorf, A. W.*; 天野 由記; 宮川 和也; 伊勢 孝太郎; 鈴木 庸平*; Anantharaman, K.*; Probst, A. J.*; Burstein, D.*; Thomas, B. C.*; Banfield, J. F.*

ISME Journal, 11, p.1915 - 1929, 2017/03

AA2016-0002.pdf:2.21MB

https://doi.org/10.1038/ismej.2017.39

地層処分システムにおける微生物影響の可能性を評価するために、北海道の幌延深地層研究センター地下施設を利用して、堆積岩地下の生態系における微生物群集構造と代謝機能について調査を行った。全体として、微生物生態系は多様な系統群からなる微生物種で構成されており、その多くはこれまで培養されていない生物門に属していることが示された。大部分の微生物種は、酸化型[NiFe]ヒドロゲナーゼあるいはフェレドキシンをベースとする代謝経路を可能にする電子分岐型[FeFe]ヒドロゲナーゼを介して水素代謝をおこなうことが明らかになった。水素代謝と関連して、多くの微生物が炭素,窒素,鉄および硫黄を代謝することが推定された。特に、ANME-2dというメタン酸化を行う古細菌として知られている未培養微生物が、鉄関連の代謝反応を行う可能性が示唆された。得られた結果から、幌延堆積岩環境における微生物群集の生態学的概念モデルを推定した。

Deep microbial life in high-quality granitic groundwater from geochemically and geographically distinct underground boreholes

伊能 康平*; 今野 祐多*; 幸塚 麻里子*; 廣田 明成*; 東郷 洋子*; 福田 朱里*; 小松 大介*; 角皆 潤*; 田辺 章文*; 山本 智*; et al.

Environmental Microbiology Reports (Internet), 8(2), p.285 - 294, 2016/04

https://doi.org/10.1111/1758-2229.12379

瑞浪超深地層研究所の深度300mの花崗岩中の地下水を対象として、ボーリング孔を利用した微生物特性の調査を行った。ボーリング孔から得られた地下水は、当初、好気性の水素酸化に関わるHydrogenophaga spp.が優勢種であったが、3年後にはNitrospirae門の微生物が優勢種となった。後者の微生物種は系統学的に深部地下水や陸域の温泉水において観察される種であり、この地域の土着の微生物種と考えられた。

Screening of cesium-accumulating mutant of radioresistant bacterium by ion beam breeding technology

佐藤 勝也; 上田 涼史郎*; 長谷 純宏; 鳴海 一成*; 大野 豊

JAEA-Review 2015-022, JAEA Takasaki Annual Report 2014, P. 100, 2016/02

https://doi.org/10.11484/jaea-review-2015-022

Bioremediation uses biological organisms to solve an environmental problem. However, microorganisms are sometimes not enough effective to achieve efficient recovery. Therefore, enhancing the functionality of microorganisms is needed to promote the active use of bioremediation. This study began with the purpose of development of Cs-accumulating bacteria by ion beam breeding technology. Previously, we suggested that is the most suitable species for the development of high Cs-accumulating bacteria by ion beam breeding technology. Candidates of Cs-accumulating mutant were screened from the mutagenized cells by ion beam breeding technology on the basis of the luminescent intensity and the cell area as indicators of intracellular Cs level and cell growth, respectively. As a result, we obtained 33 candidates, whose Cs-accumulating abilities were over 2-fold higher than that of the wild-type, from the population of mutagenized cells.