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Journal Articles

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.*; Amano, Yuki; Thomas, B. C.*; et al.

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

 Times Cited Count:8 Percentile:18.27(Multidisciplinary Sciences)

Journal Articles

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

Ino, Kohei*; Hernsdorf, A. W.*; Konno, Yuta*; Kozuka, Mariko*; Yanagawa, Katsunori*; Kato, Shingo*; Sunamura, Michinari*; Hirota, Akinari*; Togo, Yoko*; Ito, Kazumasa*; et al.

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

In this study, we found the dominance ofanaerobic methane-oxidizing archaea in groundwater enriched in sulfate and methane from a 300-m deep underground borehole in granitic rock.

Journal Articles

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

Horiike, Takumi*; Dotsuta, Yuma*; Nakano, Yuriko*; Ochiai, Asumi*; Utsunomiya, Satoshi*; Onuki, Toshihiko; Yamashita, Mitsuo*

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

 Times Cited Count:7 Percentile:42.79(Biotechnology & Applied Microbiology)

Radioactive strontium ($$^{90}$$Sr) leaked into the ocean from the Fukushima Daiichi Nuclear Power Plant after the nuclear accident. Since the removal of Sr using general adsorbents is not efficient at high salinity, this study investigated removal of soluble Sr from a saline solution by biogenic carbonate minerals. An isolate, Bacillus sp. strain TK2d, from marine sediment removed more than 99 % of Sr in a saline solution. Sr adsorbed at the cell surface and then carbonate minerals containing Sr developed outside the cells.

Journal Articles

Effect of flavin compounds on uranium(VI) reduction- kinetic study using electrochemical methods with UV-vis spectroscopy

Yamasaki, Shinya*; Tanaka, Kazuya; Kozai, Naofumi; Onuki, Toshihiko

Applied Geochemistry, 78, p.279 - 286, 2017/03

 Times Cited Count:1 Percentile:89.08(Geochemistry & Geophysics)

This study examined the rate constant for the U(VI) reduction process by three flavin analogues, which are redox-active biomolecules secreted from anaerobic bacteria, to elucidate their substituent group effect on the U(VI) reduction rate by electrochemical methods. The formation of the U(IV) was monitored by UV-vis spectrometry in the presence of the flavins. The rate constant for the U(VI) reduction by the flavins was determined. The apparent reduction potential of U(VI) increased about 0.2 V in the presence of the mediators, which strongly suggests that the biological electron mediator makes the U(VI) reduction possible even under more oxidative conditions.

Journal Articles

Potential for microbial H$$_{2}$$ and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments

Hernsdorf, A. W.*; Amano, Yuki; Miyakawa, Kazuya; Ise, Kotaro; Suzuki, Yohei*; Anantharaman, K.*; Probst, A. J.*; Burstein, David*; Thomas, B. C.*; Banfield, J. F.*

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


 Times Cited Count:42 Percentile:2.88(Ecology)

To evaluate the potential for interactions between microbial communities and disposal systems, we explored the structure and metabolic function of a sediment-hosted subsurface ecosystem associated with Horonobe Underground Research Center, Hokkaido, Japan. Overall, the ecosystem is enriched in organisms from diverse lineages and many are from phyla that lack isolated representatives. The majority of organisms can metabolize H$$_{2}$$, often via oxidative [NiFe] hydrogenases or electron-bifurcating [FeFe] hydrogenases that enable ferredoxin-based pathways, including the ion motive Rnf complex. Many organisms implicated in H$$_{2}$$ metabolism are also predicted to catalyze carbon, nitrogen, iron, and sulfur transformations. Notably, iron-based metabolism was predicted in a bacterial lineage where this function has not been predicted previously and in an ANME-2d archaeaon that is implicated in methane oxidation. We infer an ecological model that links microorganisms to sediment-derived resources and predict potential impacts of microbial activity on H$$_{2}$$ accumulation and radionuclide migration.

Journal Articles

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.*; Amano, Yuki; Ise, Kotaro; et al.

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

 Times Cited Count:632 Percentile:0.02(Microbiology)

The tree of life is one of the most important organizing principles in biology. Gene surveys suggest the existence of an enormous number of branches, but even an approximation of the full scale of The Tree has remained elusive. Here, we use newly available information from genomes of uncultivated organisms, along with other published sequences, to present a new version of the Tree of life, with Bacteria, Archaea and Eukaryotes included. The depiction is both a global overview and a snapshot of the diversity within each major lineage. The results imply the predominance of bacterial diversification and underline the importance of organisms lacking isolated representatives, with substantial evolution concentrated in a major radiation of such organisms.

Journal Articles

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

Ino, Kohei*; Konno, Yuta*; Kozuka, Mariko*; Hirota, Akinari*; Togo, Yoko*; Fukuda, Akari*; Komatsu, Daisuke*; Tsunogai, Urumu*; Tanabe, Akifumi*; Yamamoto, Satoshi*; et al.

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

 Times Cited Count:14 Percentile:32.4(Environmental Sciences)

To understand the subsurface biosphere, borehole investigation was conducted for 300-m deep granitic rocks at the Mizunami underground research laboratory, Japan. The initial biomass was the highest with the flourish of aerobic H$$_{2}$$-oxidizing Hydrogenophaga spp., whereas an uncultivated lineage of the phylum Nitrospirae became predominant after three years with decreasing biomass. The common occurrence of many species of Nitrospirae and Chlorobi phyla at the geographically distinct sites and the exclusive detection of their phylogenetically related environmental sequences from deep groundwaters and terrestrial hot springs, suggest that these bacteria are indigenous and potentially adapted to the deep terrestrial subsurface.

Journal Articles

Screening of cesium-accumulating mutant of radioresistant bacterium ${it Deinococcus radiodurans}$ by ion beam breeding technology

Sato, Katsuya; Ueda, Ryoshiro*; Hase, Yoshihiro; Narumi, Issey*; Ono, Yutaka

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

Journal Articles

Improvement of symbiotic performance of ${it Sinorhizobium}$ with ${it Vigna marina}$ under high salt conditions using the ion beam mutation breeding

Maruyama, Yudai*; Takeda, Kiyoko*; Tomooka, Norihiko*; Sato, Katsuya; Ono, Yutaka; Yokoyama, Tadashi*

JAEA-Review 2015-022, JAEA Takasaki Annual Report 2014, P. 99, 2016/02

Journal Articles

Breeding of high ethanol producing yeast by screening from mutant library

Ogino, Chiaki*; Kahar, P.*; Lee, J. M.*; Sato, Katsuya; Ono, Yutaka; Kondo, Akihiko*

JAEA-Review 2015-022, JAEA Takasaki Annual Report 2014, P. 105, 2016/02

Journal Articles

Accumulation of cesium and its association with intracellular polyphosphate in ${it Deinococcus radiodurans}$

Ueda, Ryoshiro*; Sato, Katsuya; Hayashi, Hidenori*; Narumi, Issey*; Ono, Yutaka

JAEA-Review 2015-022, JAEA Takasaki Annual Report 2014, P. 101, 2016/02

Journal Articles

Genome sequence analysis of high ethyl caproate producing sake yeasts generated by ion beam breeding, 2

Masubuchi, Takashi*; Toguchi, Kazuki*; Hayashi, Hidenori*; Ikenaga, Hiroshi*; Sato, Katsuya; Ono, Yutaka

JAEA-Review 2015-022, JAEA Takasaki Annual Report 2014, P. 106, 2016/02

Journal Articles

Carbon steel corrosion induced by microbial community in soil environment and its analysis

Hirano, Shinichi*; Nagaoka, Toru*; Ise, Kotaro; Amano, Yuki; Matsumoto, Norio*

Zairyo To Kankyo, 64(12), p.535 - 539, 2015/12

To obtain the knowledge about the corrosion ability and its mechanism as a target the soil environment microorganisms, lake mud was cultured with metallic iron. As a result, corrosion of carbon steel was observed with sulfate reduction and methane producing activity in brackish medium with lactate as substrate. Inhibition test of SRB and MPA suggested that SRB plays a major role for this corrosion, and MPA enhanced corrosion activity by the coexistence of SRB.

Journal Articles

Sorption of trivalent cerium by a mixture of microbial cells and manganese oxides; Effect of microbial cells on the oxidation of trivalent cerium

Onuki, Toshihiko; Jiang, M.*; Sakamoto, Fuminori; Kozai, Naofumi; Yamasaki, Shinya*; Yu, Q.; Tanaka, Kazuya; Utsunomiya, Satoshi*; Xia, X.*; Yange, K.*; et al.

Geochimica et Cosmochimica Acta, 163, p.1 - 13, 2015/08

 Times Cited Count:10 Percentile:49.12(Geochemistry & Geophysics)

The association of Ce(III) with the microbial cell surface and the formation of Ce phosphate nano-particles are responsible for suppressing the oxidation of Ce(III) to Ce(IV) in the mixtures.

Journal Articles

Development of cesium-accumulating bacteria by ion beam breeding technology

Sato, Katsuya; Ueda, Ryoshiro; Hase, Yoshihiro; Narumi, Issey*; Ono, Yutaka

JAEA-Review 2014-050, JAEA Takasaki Annual Report 2013, P. 117, 2015/03

Journal Articles

Molecular analysis of polyphosphate biosynthesis-related genes in ${it Deinococcus radiodurans}$

Ueda, Ryoshiro; Sato, Katsuya; Hayashi, Hidenori*; Narumi, Issey*; Ono, Yutaka

JAEA-Review 2014-050, JAEA Takasaki Annual Report 2013, P. 118, 2015/03

Journal Articles

Genome analysis of the high temperature tolerant mutant of ${it Bradyrhizobium japonicum}$ USDA110 generated by ion-beam irradiation

Takeda, Kiyoko*; Sato, Katsuya; Narumi, Issey*; Ono, Yutaka; Otsu, Naoko*; Yokoyama, Tadashi*

JAEA-Review 2014-050, JAEA Takasaki Annual Report 2013, P. 120, 2015/03

Journal Articles

Thermotolerant mutants of entomopathogenic fungi obtained by ion beam- and $$gamma$$ ray-induced mutagenesis

Saito, Tsutomu*; Fitriana, Y.*; Sato, Katsuya; Ono, Yutaka; Narumi, Issey*

JAEA-Review 2014-050, JAEA Takasaki Annual Report 2013, P. 121, 2015/03

Journal Articles

Screening of yeast strain for ethanol fermentation after carbon ion beam irradiation

Ogino, Chiaki*; Yamada, Ryosuke*; Sato, Katsuya; Ono, Yutaka

JAEA-Review 2014-050, JAEA Takasaki Annual Report 2013, P. 122, 2015/03

Journal Articles

Genome analysis of high ethyl caproate producing sake yeasts generated by ion beam breeding

Masubuchi, Takashi*; Hyuga, Hirokazu*; Ueda, Ryoshiro; Hayashi, Hidenori*; Ikenaga, Hiroshi*; Sato, Katsuya; Ono, Yutaka

JAEA-Review 2014-050, JAEA Takasaki Annual Report 2013, P. 123, 2015/03

118 (Records 1-20 displayed on this page)