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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:4 Percentile:14.9(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

Characteristics of naturally grown biofilms in deep groundwaters and their heavy metal sorption property in a deep subsurface environment

Amano, Yuki; Iwatsuki, Teruki; Naganuma, Takeshi*

Geomicrobiology Journal, 34(9), p.769 - 783, 2017/03

 Times Cited Count:6 Percentile:22.94(Environmental Sciences)

Two biofilm samples were collected from anaerobic groundwater in a borehole drilled in the Tono area, Japan, to understand the effects of biofilms on the migration behavior of heavy metals in subsurface environments. Biofilms grown on in groundwater of sedimentary rocks and granite groundwater were characterized geochemically and microbiologically, and their heavy metal sorption capability was examined. Clone library analysis was constructed from the biofilms to evaluate microbial community composition. From the results of 16S rRNA gene analyses using clone libraries, it was found that these microbial community compositions in the biofilms were clearly different from the composition of unattached, planktonic microorganisms in the groundwater samples. Furthermore, the microbial community structures generated in each biofilm were different, depending on the groundwater type. It is shown that the community structure of biofilms lacked diversity in groundwater types obtained from sedimentary and granitic rocks. These results indicate that biofilms are formed in natural subsurface environments with site-specific community compositions. High amounts of heavy metals such as Fe, Ni, Cu, Zn, As, Cd, Pb, Th, and U accumulated in the biofilms, and their sorption properties varied in each elements. These results provide important insight on heavy metal sorption capability by biofilms.

Journal Articles

Cobalt(II) oxidation by biogenic Mn oxide produced by $$Pseudomonas$$ sp. strain NGY-1

Tanaka, Kazuya*; Yu, Q.; Sasaki, Keiko*; Onuki, Toshihiko

Geomicrobiology Journal, 30(10), p.874 - 885, 2013/08

 Times Cited Count:14 Percentile:39.5(Environmental Sciences)

no abstracts in English

Journal Articles

Zinc sorption during bio-oxidation and precipitation of manganese modifies the layer stacking of biogenic birnessite

Yu, Q.; Sasaki, Keiko*; Tanaka, Kazuya*; Onuki, Toshihiko; Hirajima, Tsuyoshi*

Geomicrobiology Journal, 30(9), p.829 - 839, 2013/07

 Times Cited Count:34 Percentile:72.58(Environmental Sciences)

no abstracts in English

Journal Articles

Manganese and arsenic oxidation performance of Bacterium-Yunotaki 86 (BY86) from Hokkaido, Japan, and the bacterium's Phylogeny

Ozaki, Takuo*; Wang, X.*; Onuki, Toshihiko

Geomicrobiology Journal, 30(7), p.559 - 565, 2013/05

 Times Cited Count:5 Percentile:15.55(Environmental Sciences)

The bacterium collected at Yunotaki, Hokkaido, Japan did not oxidized As(III) to As(V) in the absence of Mn. In the presence of Mn, however, As(III) was rapidly oxidized to As(V) on the cell surfaces. A phylogenetical study disclosed that BY86 was most losely related to Bacillus cereus with an identity of 99.90%.

Journal Articles

Redox buffer capacity in water-rock-microbe interaction systems in subsurface environments

Amano, Yuki; Sasao, Eiji; Niizato, Tadafumi; Iwatsuki, Teruki

Geomicrobiology Journal, 29(7), p.628 - 639, 2012/06

 Times Cited Count:4 Percentile:12.45(Environmental Sciences)

An incubation experiment was conducted to estimate redox buffer capacity of "water-rock-microbe" interaction systems in sedimentary rocks. The water chemistry, microbial growth and community structure were analyzed during the incubations. The dissolved oxygen (DO) concentrations and oxidation-reduction potential (ORP) values decreased notably in the presence of active microorganisms, whereas abiotic reactions did not lead to reducing conditions during incubation. The change in microbial community structure suggests that nitrate-reducing and sulfate-reducing bacteria played an important role in reduction of water by using lignite-derived organic matter. These results show that the microbial role is extremely important for the redox buffering capacity in sedimentary rock environments.

Journal Articles

Yeast genes involved in uranium tolerance and uranium accumulation; A Functional screening using the nonessential gene deletion collection

Sakamoto, Fuminori; Nankawa, Takuya; Onuki, Toshihiko; Fujii, Tsutomu*; Iefuji, Haruyuki*

Geomicrobiology Journal, 29(5), p.470 - 476, 2012/05

 Times Cited Count:6 Percentile:17.72(Environmental Sciences)

We screened 4908 non-essential gene deletion mutant yeast strains for uranium sensitivity and low accumulation by growth in agar medium containing uranium. All mutant strains grew successfully on agar media containing 0 or 0.5 mM uranium for one week at 30 centigrade. Thirteen strains with single gene deletions showed reduced growth in the agar medium containing 0.5 mM uranium and were identified as uranium-sensitive mutant strains. The phosphate transporter genes of PHO86, PHO84, PHO2, and PHO87 were among the deleted genes in the uranium-sensitive mutant strains, suggesting that genes concerned with phosphate transport contribute to uranium tolerance. Seventeen single-deletion strains showed lower uranium accumulation than the wild-type after exposure to agar medium containing 0.5 mM uranium, and were identified as mutant strains with low uranium accumulation.

Journal Articles

Response of ${it Saccharomyces cerevisiae}$ to heavy element stress; Lead vs. uranium

Sakamoto, Fuminori; Onuki, Toshihiko; Fujii, Tsutomu*; Iefuji, Haruyuki*

Geomicrobiology Journal, 27(3), p.240 - 244, 2010/05

 Times Cited Count:8 Percentile:24.43(Environmental Sciences)

We have examined the responses of ${it Saccharomyces cerevisiae}$ in media containing Pb$$^{2+}$$ ions and compared it to those in media containing UO$$_{2}$$$$^{2+}$$ ions to elucidate the stress effects of heavy elements. Cultivation of ${it S. cerevisiae}$ in a medium containing 1.0$$times$$10$$^{-4}$$ M Pb showed nearly the same growth as that in the control medium while growth was inhibited in the medium containing 1.0$$times$$10$$^{-3}$$ M Pb. Backscattering electron image analyses of thin sections of cells showed that Pb had accumulated inside the cells. Two-dimensional (2D) gel electrophoresis analysis of the proteins extracted from the ${it S. cerevisiae}$ exposed to Pb$$^{2+}$$ ions showed that several specific protein spots were expressed after cultivation with Pb, that did not appear in the control medium. Our results suggest that Pb$$^{2+}$$ more weakly inhibits the growth of ${it S. cerevisiae}$ than UO$$_{2}$$$$^{2+}$$, and produces different stresses in ${it S. cerevisiae}$ than UO$$_{2}$$$$^{2+}$$.

Journal Articles

Association of actinides with microorganisms and clay; Implications for radionuclide migration from waste-repository sites

Onuki, Toshihiko; Kozai, Naofumi; Sakamoto, Fuminori; Ozaki, Takuo; Nankawa, Takuya; Suzuki, Yoshinori; Francis, A. J.*

Geomicrobiology Journal, 27(3), p.225 - 230, 2010/04

 Times Cited Count:16 Percentile:20.75(Environmental Sciences)

The recent research results on the interation of heavy-elements and microorganisms are shown. (1) Adsorption of Pu(IV), Th(IV) and Eu(III)-DFO complexes on bacteria, (2) Biodegradation of Eu(III) in the presence of malic acids.

Journal Articles

Effects of citrate, NTA, and EDTA on the reduction of U(VI) by ${it Shewanella putrefaciens}$

Suzuki, Yoshinori; Tanaka, Kazuya; Kozai, Naofumi; Onuki, Toshihiko

Geomicrobiology Journal, 27(3), p.245 - 250, 2010/04

 Times Cited Count:27 Percentile:58.32(Environmental Sciences)

${it Shewanella putrefaciens}$ was cultured in the anarobic medium containing U(VI)-organic complexes. The weak complexes were reduced to U(IV) and uraninite was formed. The strong complexes were reduced to U(IV)-complexes remaining in the solution. These results suggest that organic acids affect the bioreduction behavior of U(VI).

Journal Articles

Metal sorption to $$Pseudomonas fluorescens$$; Influence of pH, ionic strength and metal concentrations

Takenaka, Yoko*; Saito, Takumi*; Nagasaki, Shinya*; Tanaka, Satoru*; Kozai, Naofumi; Onuki, Toshihiko

Geomicrobiology Journal, 24(3-4), p.205 - 210, 2007/09

 Times Cited Count:8 Percentile:25.82(Environmental Sciences)

no abstracts in English

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