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Clades of huge phages from across Earth's ecosystems

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:83 パーセンタイル:99.63(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.


Assessment of the potential for criticality in the far field of a used nuclear fuel repository

Atz, M.*; Salazar, A.*; 平野 史生; Fratoni, M.*; Ahn, J.*

Annals of Nuclear Energy, 124, p.28 - 38, 2019/02

 被引用回数:0 パーセンタイル:0.01(Nuclear Science & Technology)



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. M.*; 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

 被引用回数:16 パーセンタイル:86.93(Multidisciplinary Sciences)

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$$_{2}$$ and other terminal electron acceptors. The type C heme-copper oxygen reductase found in Melainabacteria BJ4A may be adapted to low O$$_{2}$$ 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$$_{2}$$, thus are adapted to low O$$_{2}$$ levels. These contemporary lineages have representatives with fermentative H$$_{2}$$-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$$_{2}$$ metabolism were central metabolic features.


Radiocesium interaction with clay minerals; Theory and simulation advances Post-Fukushima

奥村 雅彦; Kerisit, S.*; Bourg, I. C.*; Lammers, L. N.*; 池田 隆司*; Sassi, M.*; Rosso, K. M.*; 町田 昌彦

Journal of Environmental Radioactivity, 189, p.135 - 145, 2018/09

 被引用回数:31 パーセンタイル:90.13(Environmental Sciences)



Uncertainty analysis of far-field precipitation from used nuclear fuel

Salazar, A.*; Fratoni, M.*; Ahn, J.*; 平野 史生

Proceedings of 2017 International High-Level Radioactive Waste Management Conference (IHLRWM 2017) (CD-ROM), p.600 - 607, 2017/04

The safety assessment of a geological repository for used nuclear fuel must ensure that future generations are shielded from radiation from fission products, in particular those released by re-criticality events. An investigation is required to understand whether or not criticality can actually be achieved. In fulfilling this end, this study assesses the uncertainty in the composition and total mass of precipitates forming in the far-field due to variation in transport parameters. The Latin Hypercube Sampling technique is employed to generate an accurate, random distribution of variables employed in the transport model and to assess the uncertainty of attaining a critical mass. The average characteristics of the damaged fuel from the Fukushima Daiichi reactor cores is used as the reference waste form. Results are compared to the minimum critical masses of previous studies to assess the criticality safety margin.


Material composition effects on far-field deposition minimum critical mass

Atz, M.*; Liu, X.*; Fratoni, M.*; Ahn, J.*; 平野 史生

Proceedings of 2017 International High-Level Radioactive Waste Management Conference (IHLRWM 2017) (CD-ROM), p.608 - 614, 2017/04

After nuclear waste is buried in a repository, hydrogeological processes can dissolve, transport, separate, and rearrange radionuclides inside or outside the repository. If fissile material becomes separated from neutron absorbers and precipitates in a far-field geologic formation, a critical mass may be formed. The scope of this study is to assess the impact of the spent fuel composition and host rock type on the risk of criticality in the far field. In particular, this study performs neutronics analysis in order to determine the minimum theoretical mass of fissile material needed to achieve criticality in a water-saturated far-field deposition under conservative conditions. Understanding of the effects of composition of spent fuels and host rock types enable discussion of the likelihood of far field criticality from LWR used fuel. In addition, this work makes recommendations on repository design and LWR fuel cycle management so as to minimize the risk of far-field criticality.


Effects of random geometry on post-closure repository criticality safety

Liu, X.*; Fratoni, M.*; Ahn, J.*; 平野 史生

Proceedings of 2017 International High-Level Radioactive Waste Management Conference (IHLRWM 2017) (CD-ROM), p.595 - 599, 2017/04

The present work aims to study the effect of random geometry on the long-term criticality safety. Preliminary considerations on uranium depositions in randomly fractured rocks have been obtained through an approximated analytical solution to calculate spherical fuel lumps with random locations. With stochastic and heterogeneous conditions applied, the present work examines the conservatives of the neutronic models for repository criticality safety assessment, and provides deeper understandings of the system. The major finding is that, when parameters are chosen to optimized the criticality, effective multiplication factor for systems with the random geometries can be well-bounded by the average case.


Potential for microbial H$$_{2}$$ 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


 被引用回数:56 パーセンタイル:96.62(Ecology)



A New view of the tree of life

Hug, L. A.*; Baker, B. J.*; Anantharaman, K.*; Brown, C. T.*; Probst, A. J.*; Castelle, C. J.*; Butterfield, C. N.*; Hernsdorf, A. W.*; 天野 由記; 伊勢 孝太郎; et al.

Nature Microbiology (Internet), 1(5), p.16048_1 - 16048_6, 2016/05

 被引用回数:842 パーセンタイル:99.98(Microbiology)



Conditions for criticality by uranium deposition in water-saturated geological formations

Liu, X.*; Ahn, J.*; 平野 史生

Journal of Nuclear Science and Technology, 52(3), p.416 - 425, 2015/03

 被引用回数:1 パーセンタイル:12.03(Nuclear Science & Technology)

The present study focuses on neutronic analysis to determine the criticality conditions for uranium depositions in geological formations resulting from geological disposal of damaged fuels from Fukushima Daiichi reactors. MCNP models are used to evaluate the neutron multiplication factor ($$k_{eff}$$) and critical mass for various combinations of host rock and geometries. It has been observed that the $$k_{eff}$$ of the deposition become greater with (1) smaller concentrations of neutron-absorbing materials in the host rock, (2) larger porosity of the host rock, (3) heterogeneous geometry of the deposition, and (4) greater mass of uranium in the deposition. The present study has revealed that the planar fracture geometry applied in the previous criticality safety assessment for geological disposal would not necessarily yield conservative results against the homogeneous uranium deposition.


Repository criticality analysis for damaged fuels; Geometry effect in the modeling of uranium and plutonium deposition in geological formations

Liu, X.*; Ahn, J.*; 平野 史生

Proceedings of 14th International High-Level Radioactive Waste Management Conference (IHLRWMC 2013) (CD-ROM), p.527 - 534, 2013/04



Development of geologic repository models for design and decision making

村上 冶子*; Ahn, J.*

Proceedings of 16th Pacific Basin Nuclear Conference (PBNC-16) (CD-ROM), 6 Pages, 2008/10

This paper presents a new radionuclide transport model for performance assessment and design of a geologic repository for high-level radioactive wastes. The model applies compartmentalization and a Markov-chain approach. A model space consists of an array of compartments, among which radionuclide transport is described by a transition probability matrix. While the model is similar to Eulerian methods, the advantages of this approach are considered in flexibility in including various types of transport processes by probabilistic interpretation. We demonstrate this model approach with a hypothetical repository assumed in porous rock formation. A three-dimensional, non-uniform groundwater flow field is generated numerically by the finite element method. The transition probability matrix is constructed based on the velocity field and hydraulic dispersion coefficients. The results show that this transport model can effectively show differences in repository performance due to the change of hydraulic properties in the domain for differing repository configurations and material degradation.



池上 哲雄; Ahn, J.*

JAEA-Research 2006-045, 17 Pages, 2006/07


地層処分との関係において、分離変換の対象核種と分離変換の程度に関する目標設定に資することを目的に、従来の高レベル廃棄物そのものの潜在的放射性毒性に代わり、処分場での長寿命核種の移行挙動を考慮した新たな指標である「環境影響」を導入して、PWRサイクル及びFBRサイクルについて評価を行った。評価にあたって必要となる長寿命核種の廃棄物固化体への初期装荷量は廃棄物処理(conditioning)モデルを用いて求めた。環境影響を評価すると同時に、処分場内での核種移行挙動にかかわる各種パラメータの不確かさが環境影響に及ぼす影響も評価した。その結果、分離変換の目標は次のように設定できると考えられる。(1)PWRサイクルの場合:本評価で想定した廃棄物への移行率:U:0.604%, Pu:0.297%に加え、$$^{237}$$Np, $$^{243}$$Am, ($$^{241}$$Pu)の移行率を1%以下に抑える。(2)FBRサイクルの場合:全アクチニドに対するサイクルシステムとしての回収率99.9%は適切な設定である。


Release of Radionuclides from Multiple Conisters in a High Level Waste Repository

Ahn, J.*; Rob, D. A.*; Kuo, S.*; Cha, P.L.*

PNC TY1952 98-001, 37 Pages, 1998/07





立岩 尚之; 芳賀 芳範; 松田 達磨*; 山本 悦嗣; Fisk, Z.

no journal, , 



Molecular modeling of adsorption sites in micaceous clay minerals

奥村 雅彦; 中村 博樹; 町田 昌彦

no journal, , 



Sulfur and hydrogen metabolism linked to CO$$_{2}$$ fixation by abundant Nitrospirae in the deep subsurface

天野 由記; Anantharaman, K.*; Tomas, B. C.*; Olm, M.*; Burstein, D.*; Castelle, C. J.*; 別部 光里*; 宮川 和也; 岩月 輝希; 鈴木 庸平*; et al.

no journal, , 

The bacterial phylum Nitrospirae is phylogenetically diverse. There are relatively few isolated representatives available for laboratory study and the physiology, functions and distributions of these bacteria across environments remain largely unknown. To understand the ecological role of Nitrospirae in the deep subsurface, we analyzed metagenomically-derived near complete genomes from groundwaters associated with granite and sedimentary rock where Nitrospirae are very abundant. The bacteria are autotrophs that fix CO$$_{2}$$ via the Wood-Ljungdahl pathway and reductive TCA cycles. The genomes encode versatile energy-generating pathways that involve sulfate reduction, hydrogen oxidation and nitrite reduction. Phylogenetic analyses indicate that the organisms are most similar to the isolated magnetotactic bacterium, Candidatus Magnetobacterium bavaricum, with only 89-91% 16S rRNA gene sequence identity. These Nitrospirae bacteria appear to play critical ecosystem roles as primary producers and they are likely central to sulfur cycling in the deep subsurface.


Vast metabolic and phylogenetic diversity shared across deep subsurface environments

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.


Existence and the role of subsurface biofilm in the deep sedimentary rock environment of the Horonobe area, Hokkaido, Japan

天野 由記; 別部 光里*; 遠藤 貴志*; 根本 一昭*; 佐藤 智文*; Thomas, B. C.*; Banfield, J. F.*

no journal, , 

We investigated the geochemical and microbial properties of groundwater samples and the habitat of biofilm collected from a borehole drilled in the Horonobe Underground Research Laboratories (Horonobe URL) at Horonobe area, Hokkaido, Japan. Samples were collected from a borehole at 140 m below the surface in the Horonobe URL, and the time series changes of geochemistry, microbial abundance, and microbial diversity were monitored for four days. To understand the ecological role of the biofilm in the deep subsurface, we analyzed metagenomically derived genome data from the groundwater samples. From the results of microscopic observation, it is indicated that abundant biofilm were collected in the groundwater samples. Analysis of 16S rRNA gene by next generation sequencing indicates that the biofilms were dominated by Candidatus Altiarchaeales (SM1 Euryarchaeon) in the methane- carbonate-rich groundwater. The genomes encode autotrophic metabolism that fix CO$$_{2}$$ via the Wood-Ljungdahl pathway and reductive tricarboxylic acid (TCA) cycles. The genes for polysaccharide biosynthesis were detected in the SM1 genomes. Biofilm phase were also characterized with accumulation/sorption of heavy metals such as Cr, Fe, Ni, Cu, Pb, Ce, Nd, U and Th. From the calculation of the bioaccumulation factor for the concentration of heavy metals, it is possible that the biofilms selectively accumulate heavy metals according to their metabolic activity. Hence, it is necessary to evaluate mechanisms of interaction between heavy metals, microbial community structure and metabolic activities of biofilms. The biofilm-mineral interaction provides an implication for the possible retardation of radionuclide migration in subsurface hydrology, which is of practical interest in geological disposal systems for high-level radioactive waste.

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