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.

Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment

伊能 康平*; Hernsdorf, A. W.*; 今野 祐多*; 幸塚 麻里子*; 柳川 克則*; 加藤 信吾*; 砂村 道成*; 広田 秋成*; 東郷 洋子*; 伊藤 一誠*; et al.

ISME Journal, 12(1), p.31 - 47, 2018/01

https://doi.org/10.1038/ismej.2017.140

岐阜県瑞浪市の超深地層研究所において、深度300メートルの地下水を地下坑道から採取し、地下微生物の生態系を調査した。その結果、花崗岩深部でマグマ由来のメタンに依存した微生物生態系が存在す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。

On the design of experiments to study extreme field limits

Bulanov, S. S.*; Chen, M.*; Schroeder, C. B.*; Esarey, E.*; Leemans, W. P.*; Bulanov, S. V.; Esirkepov, T. Z.; 神門 正城; Koga, J. K.; Zhidkov, A. G.*; et al.

AIP Conference Proceedings 1507, p.825 - 830, 2012/12

https://doi.org/10.1063/1.4773805

We propose the experiments on the collision of intense laser pulses with energetic electron bunches and on the collision of two or more intense laser pulses for studying extreme field limits in the nonlinear interaction of electromagnetic waves. The regimes of dominant radiation reaction, which completely changes the electromagnetic wave matter interaction, will be revealed in such experiments. This will result in a new powerful source of ultra short high brightness -ray pulses. A possibility of the demonstration of the electron positron pair creation from vacuum in the collision of two or more intense laser pulses is discussed.

Identified charged hadron production in collisions at = 200 and 62.4 GeV

Adare, A.*; Afanasiev, S.*; Aidala, C.*; Ajitanand, N. N.*; 秋葉 康之*; Al-Bataineh, H.*; Alexander, J.*; 青木 和也*; Aphecetche, L.*; Armendariz, R.*; et al.

Physical Review C, 83(6), p.064903_1 - 064903_29, 2011/06

https://doi.org/10.1103/PhysRevC.83.064903

200GeVと62.4GeVでの陽子陽子の中心衝突からのの横運動量分布及び収量をRHICのPHENIX実験によって測定した。それぞれエネルギーでの逆スロープパラメーター、平均横運動量及び単位rapidityあたりの収量を求め、異なるエネルギーでの他の測定結果と比較する。またやスケーリングのようなスケーリングについて示して陽子陽子衝突における粒子生成メカニズムについて議論する。さらに測定したスペクトルを二次の摂動QCDの計算と比較する。

Measurement of neutral mesons in + collisions at = 200 GeV and scaling properties of hadron production

Adare, A.*; Afanasiev, S.*; Aidala, C.*; Ajitanand, N. N.*; Akiba, Y.*; Al-Bataineh, H.*; Alexander, J.*; Aoki, K.*; Aphecetche, L.*; Armendariz, R.*; et al.

Physical Review D, 83(5), p.052004_1 - 052004_26, 2011/03

https://doi.org/10.1103/PhysRevD.83.052004

RHIC-PHENIX実験で重心エネルギー200GeVの陽子陽子衝突からの, , と中間子生成の微分断面積を測定した。これらハドロンの横運動量分布のスペクトルの形はたった二つのパラメーター、、のTsallis分布関数でよく記述できる。これらのパラメーターはそれぞれ高い横運動量と低い横運動量の領域のスペクトルを決めている。これらの分布をフィットして得られた積分された不変断面積はこれまで測定されたデータ及び統計モデルの予言と一致している。

Defining the infrared systems for ITER

Reichle, R.*; Andrew, P.*; Counsell, G.*; Drevon, J.-M.*; Encheva, A.*; Janeschitz, G.*; Johnson, D. W.*; 草間 義紀; Levesy, B.*; Martin, A.*; et al.

Review of Scientific Instruments, 81(10), p.10E135_1 - 10E135_5, 2010/10

https://doi.org/10.1063/1.3491199

ITER will have wide angle viewing systems and a divertor thermography diagnostic which shall provide infrared coverage of the divertor and large parts of the first wall surfaces with spatial and temporal resolution adequate for operational purposes and higher resolved details of the divertor and other areas for physics investigations. We propose specifications for each system such that they jointly respond to the requirements. Risk analysis driven priorities for future work concern mirror degradation, interfaces with other diagnostics, radiation damage to refractive optics, reflections and the development of calibration and measurements methods for varying optical and thermal target properties.

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.

Spatial distribution of biofilm-forming Archaea in the deep sedimentary rock environment of the Horonobe area, Hokkaido, Japan

天野 由記; 別部 光里*; 佐藤 智文*; 望月 陽人; Thomas, B. C.*; Banfield, J. F.*

no journal, , 

The presence of microbes in deep subsurface environments may have important implications for the safety of underground repositories for high-level radioactive wastes. It has been suggested that biofilm may not exist in the deep subsurface due to low water flux, energy supply and physical space. We investigated spatial distribution of biofilm-forming Archaea, Candidatus Altiarchaeales, and the geochemical and microbiological properties of groundwater samples via study of boreholes drilled in the Horonobe Underground Research Laboratories (Horonobe URL), Horonobe area, Hokkaido, Japan. Samples were collected from four boreholes at 140, 250, 350 m below the surface in the Horonobe URL, and the time series changes of geochemistry, microbial abundance, and microbial diversity were monitored over several years. Analysis of metagenome and 16S rRNA genes by next generation sequencing indicates that the biofilms in methane- carbonate-rich groundwater were mainly dominated by Candidatus Altiarchaeales. Based on the section volume and the amount of discharged groundwater from the borehole, it is suggested that the biofilms occur within porous sedimentary rocks or fracture surfaces, rather than on the borehole walls. The biofilm accumulates heavy metals including 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. Thus, the presence of biofilms provides a mechanism for retardation of radionuclide migration in the subsurface. This is of practical interest from the perspective of geological disposal systems for high-level radioactive waste in the deep subsurface.