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Journal Articles

The Succession of bacterial community structure in groundwater from a 250-m gallery in the Horonobe Underground Research Laboratory

Ise, Kotaro; Sasaki, Yoshito; Amano, Yuki; Iwatsuki, Teruki; Nanjo, Isao*; Asano, Takahiro*; Yoshikawa, Hideki

Geomicrobiology Journal, 34(6), p.489 - 499, 2017/07

 Times Cited Count:2 Percentile:72.72(Environmental Sciences)

We investigated the change in bacterial community structure after drilling boreholes, 09-V250-M02 and 09-V250-M03 in the 250 m depth research gallery of Horonobe Underground Research Laboratory (URL). In 09-V250-M02, $$varepsilon$$-Proteobacteria was predominantly detected in the clone library analyses of the groundwater samples conducted immediately after drilling the borehole. All these $$varepsilon$$-Proteobacteria clones are closely related to ${{it Arcobacter spp}}$. which is known as sulfide oxidizing chemoautotrophic bacteria. After four years, the microbial structure was drastically changed and most detected OTUs were uncultured species such as candidate division OP9 and Chloroflexi relatives which are frequently detected in deep-sea sediments.

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

AA2016-0002.pdf:2.21MB

 Times Cited Count:26 Percentile:2.76(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:473 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

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.

Oral presentation

Planktonic and attached microbes in deep subsurface

Sasaki, Yoshito; Asano, Takahiro*; Ise, Kotaro; Sato, Tomofumi; Murakami, Hiroaki; Amamiya, Hiroki; Amano, Yuki; Iwatsuki, Teruki; Yoshikawa, Hideki

no journal, , 

no abstracts in English

Oral presentation

Microbial structure change in the groundwater samples from two boreholes at depths of -250m in Horonobe Underground Research Laboratory

Ise, Kotaro; Nanjo, Isao; Amamiya, Hiroki; Amano, Yuki; Iwatsuki, Teruki; Asano, Takahiro*; Kageyama, Koji*; Sasaki, Yoshito; Yoshikawa, Hideki

no journal, , 

no abstracts in English

Oral presentation

Development of evaluation code for microbial effect on HLW disposal, 1; Prediction for redox environment by microbial reaction in site experiment

Yoshikawa, Hideki; Amano, Yuki; Sasaki, Yoshito; Ito, Tsuyoshi*; Ise, Kotaro; Iwatsuki, Teruki

no journal, , 

An insite experiment was conducted to understand for microbial effect on backfill of 140m underground tunnel, the contribution of the microbial reaction in backfill material on redox change of the tunnel environment was suggested.

Oral presentation

Development of evaluation code for microbial effect on HLW disposal, 2; Sensitivity analysis of microbial colloid effects on radionuclide transport by COLFRAC

Ise, Kotaro; Ito, Tsuyoshi; Amano, Yuki; Yoshikawa, Hideki

no journal, , 

To evaluate microbial colloid-facilitated radionuclide transport in fractured porous media, we conducted sensitivity analyses using a two dimentional numerical code, COLFRAC-mrl. The targeted domain is 100 $$times$$ 0.2 m granitic rock which contain strait fracture in the center. The fracture aperture was set to 1.18$$times$$10$$^{-3}$$ m and groundwater velocity in the fracture was set to 50 m/y. The results of sensitivity analyses showed that if there are microbe in the order of 10$$^{10}$$ cells/L in the groundwater, these microbe have possibilities to facilitate radionuclide transport.

Oral presentation

Changes in microbial community composition and geochemistry during excavation shaft and galleries of the Horonobe Underground Research Laboratory

Amano, Yuki; Sasaki, Yoshito; Nanjo, Isao*; Amamiya, Hiroki; Mizuno, Takashi; Ise, Kotaro; Yoshikawa, Hideki

no journal, , 

Continuous monitoring of groundwater chemistry of the boreholes during the facility construction indicated that the salinity around 140 m have not changed from the beggining to date. Water pressures within the area several tens to hundreds meter from the shafts also went down in process of time. Regarding the chemical disturbance in the area, the redox potencial of the groundwaters in the monitoring boreholes showed reducing condition nevertheless the gallery is in oxidized condition. However, microbial community structure changed considerably from the beggining to date. These results indicate that microbial redox reaction could contribute to maintain of reducing conditions in the groundwater system, despite of hydrochemical disturbance caused by facility construction.

Oral presentation

Reduction of red iron oxide by iron reducing bacteria cultured from Yoshida Nakamichi site in Tottori City, Tottori Prefecture

Lee, S.*; Taniguchi, Tomoko*; Ise, Kotaro; Yoshikawa, Hideki

no journal, , 

In this study, we investigated the reduction ability of red iron oxide by iron reducing bacteria cultured from Yoshida Nakamichi site in Tottori City, Tottori Prefecture. We report that the results of comparison of morphological characteristic for red iron oxide between commercial product and buried cultural properties.

Oral presentation

Microbiological considerations relevant to a deep geological repository; Research review and perspective

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

no journal, , 

no abstracts in English

Oral presentation

Spatial distribution of microbial populations and carbon cycle in the subsurface environment of the Horonobe area, Hokkaido, Japan

Amano, Yuki; Ise, Kotaro; Terashima, Motoki; Sasaki, Yoshito; Amamiya, Hiroki; Yoshikawa, Hideki

no journal, , 

Microorganisms are widely distributed in the subsurface environments. However, the distribution, role and rate of metabolisms, and the origin of the activity are not well known. In this study, we investigated deep groundwater samples of sedimentary rocks, which is contained supersuturated methane and carbon dioxide, using boreholes in the Horonobe Underground Research Laboratory (URL), in the northern part of Hokkaido, Japan. Abundant methanogens were detected in the groundwater, and 80% of them were related to Methanoregula boonei and Methanobacterium flexile that can utilize hydrogen and carbon dioxide as methanogenesis. Phylotypes clustered within the phylum Firmicutes, beta-Proteobacteria, delta-Proteobacteria and Candidatte division TM7 were dominant in the groundwater samples. Laboratory experiment using culture a technique showed that humic substances purified from Horonobe area could be degraded by microorganisms. Our results suggest that microbial spatial distribution in the subsurface environment was correlate closely with geochemical conditions, such as redox condition and carbon sources.

Oral presentation

Drilling effect on subsurface microbial community structure in groundwater from the -250 m gallery at the Horonobe Underground Research Laboratory, Japan

Ise, Kotaro; Amano, Yuki; Sasaki, Yoshito; Yoshikawa, Hideki

no journal, , 

We investigated the changes in geochemical and microbial characteristics by using molecular techniques to characterize subsurface microbial community structure response toward oxygen intrusion. Therefore we collected groundwater samples from a borehole at -250 m gallery of Horonobe Underground Research Laboratory. The first sampling was conducted right after the borehole was drilled. In this sample, $$varepsilon$$-Proteobacteria dominated and accounted for 65% of total clone library. All these $$varepsilon$$-Proteobacteria clones are closely related to ${it Arcobacter}$ spp. which is known as sulfide oxidizer and which can growth chemoautrophically. And after two years, the microbial structure was drastically changed and most detected clones were uncultured species such as candidate division WS6, JS1 relatives which are frequently detected in deep-sea sediments.

Oral presentation

An Analogue study for heavy metal adsorption onto biofilm in the deep subsurface environment of the Horonobe area, Hokkaido, Japan

Amano, Yuki; Ise, Kotaro; Ito, Tsuyoshi; Nemoto, Kazuaki; Tachi, Yukio

no journal, , 

We characterized the geochemical and microbial structures of biofilm samples formed with groundwater from boreholes in the subsurface environment at Horonobe area, Japan. The biofilm samples were grown naturally into the sampling tubes made by nylon under in-situ geochemical conditions. The heavy metal sorption capacities of these biofilms were also determined to evaluate the effects of microorganims on radionuclides transport in HLW systems. From the results of heavy metal analyses, it is revealed that high content of elements was accumulated in the biofilms, and each elements was not accumulated in quantity in the same proportion and had different sorption properties. We could find no discernible correlation between those elements accumulated in the biofilms and the composition of groundwaters. It is assumed that these differences depend on the microbial community structure that composed of biofilms. That is to say, it is possible that microorganims that compose the biofilms selectively accumulate heavy metals according to their metabolic activity. Analyses of 16S rDNA utilizing next generation sequencing indicates that the biofilms were dominated by the phylum Nitrospirae, Proteobacteria, and JS1 and SM1 as Candidate phylum. Over 40% of the detected sequences belong to groups of uncultured microorganisms. These results possibly show the similar characteristics of natural biofilms formed on fracture-surfaces in the subsurface environments. Hence, it is necessary to evaluate mechanisms of interaction between heavy metals, microbial community structure and metabolic activities of biofilms.

Oral presentation

Study of microbial ecology in sedimentary rocks and granite using the underground research laboratories

Amano, Yuki; Sasaki, Yoshito; Ise, Kotaro; Iwatsuki, Teruki

no journal, , 

The Japan Atomic Energy Agency has been constructing an Underground Research Laboratory (URL) in the Horonobe and Mizunami area, Japan to establish general techniques for the assessment of deep geological environments. To evaluate the microbial effects on geological disposal, groundwater chemistry and microbial community composition in and around the URLs were investigated. Microbial numbers were determined by direct count using fluorescent microscopy. Culture-independent techniques were used to determine the diversity and metabolic activity of the microbial community in groundwater samples collected from the boreholes. The results shows microbial community structure, abundance, and their size distribution depend on the geology, pore size, and geochemistry. In this presentation, we will discuss about the research of microbial ecology in Horonobe and Mizunami area.

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