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Journal Articles

Complete genome sequence of ${it Thiomicrospira}$ sp. strain V2501 isolated from 250 m below the ground level in Horonobe, Hokkaido, Japan

Ueno, Akio*; Sato, Kiyoshi*; Tamamura, Shuji*; Murakami, Takuma*; Inomata, Hidenori*; Tamazawa, Satoshi*; Amano, Yuki; Miyakawa, Kazuya; Naganuma, Takeshi*; Igarashi, Toshifumi*

Microbiology Resource Announcements (Internet), 13(11), p.e00108-24_1 - e00108-24_4, 2024/11

https://doi.org/10.1128/mra.00108-24

Journal Articles

${it Desulfovibrio subterraneus}$ sp. nov., a mesophilic sulfate-reducing deltaproteobacterium isolated from a deep siliceous mudstone formation

Ueno, Akio*; Tamazawa, Satoshi*; Tamamura, Shuji*; Murakami, Takuma*; Kiyama, Tamotsu*; Inomata, Hidenori*; Amano, Yuki; Miyakawa, Kazuya; Tamaki, Hideyuki*; Naganuma, Takeshi*; et al.

International Journal of Systematic and Evolutionary Microbiology, 71(2), p.004683_1 - 004683_10, 2021/02

https://doi.org/10.1099/ijsem.0.004683
 Times Cited Count：11 Percentile：59.45(Microbiology)

A novel mesophilic sulfate-reducing bacterium, designated strain HN2$$^{rm T}$$, was isolated from groundwater sampled from the subsurface Miocene Wakkanai Formation located in Horonobe, Hokkaido, Japan. The cells were Gram-negative rods, with motility conferred by a single polar flagellum. The isolate expressed desulfoviridin, but no catalase or oxidase activities was detected. Strain HN2$$^{rm T}$$ grew in a temperature range of 5-43 $$^{circ}$$C (optimum, 35 $$^{circ}$$C) and in a pH range of 6.5-7.5 (optimum, pH 7.0-7.3). It used sulfate, thiosulfate, dimethyl sulfoxide, anthraquinone-2,6-disulfonate, Fe$$^{3+}$$, and manganese oxide as electron acceptors, but not elemental sulfur, nitrite, or nitrate. The bacterium showed very weak growth with sulfite as the electron acceptor. The strain fermented pyruvate and cysteine in the absence of sulfate, but not malate or succinate. The bacterium did not require NaCl, but tolerated up to 4% NaCl (w/v). Strain HN2$$^{rm T}$$ did not require vitamins. The G+C content of the genomic DNA was 56.66 mol%. A 16S rRNA gene sequence analysis showed that the closest recognized relative of strain HN2$$^{rm T}$$ is ${it Desulfovibrio psychrotolerans}$ JS1$$^{rm T}$$ (97.0% similarity). The average nucleotide identity (ANI) value between strain HN2$$^{rm T}$$ and D. ${it psychrotolerans}$ JS1$$^{rm T}$$ was 79.8%. Based on the phenotypic and molecular genetic evidence, the isolate is assigned to the new species ${it Desulfovibrio subterraneus}$ sp. nov. The type strain is HN2$$^{rm T}$$ (=DSM 101010$$^{rm T}$$ =NBRC 112213$$^{rm T}$$).

Journal Articles

A Proposed method to estimate in situ dissolved gas concentrations in gas-saturated groundwater

Tamamura, Shuji*; Miyakawa, Kazuya; Aramaki, Noritaka*; Igarashi, Toshifumi*; Kaneko, Katsuhiko*

Groundwater, 56(1), p.118 - 130, 2018/01

http://doi.org/10.1111/gwat.12573

Groundwater saturated with gas forms bubble under atmospheric pressure, bothering most authorized methods to determine in-situ dissolved gas concentrations. To circumvent this problem, a simple theory to quantify effect of $rm bubble formation on in-situ dissolved gas concentration was developed: Pressure ({it P$_{i},rm original $}$ [bar]) of a gas component "${it i}$" (e.g., CH$$_{4}$$, CO$$_{2}$$ and H$$_{2}$$) in equilibrium with in-situ dissolved concentration (${it C $_{i},rm original $}$ [mol L $$^{-1}$$]) was related to partial pressure of the $rm bubble ({it P $_{i},rm bubble $}$ [bar]) emerged from groundwater in the form: ${it P$_{i},rm original $}$ = ${it P $_{i},rm bubble $}$ + $$Delta$$ ${it P}$ (k${it i}$' ${it P $_{i},rm bubble $}$/($$Sigma$$ ${it j}$k${it j}$' ${it P $_{ j },rm bubble $}$)), where $$Delta$$ ${it P}$ [bar] is groundwater pressure difference before and after the $rm bubble formation, and j refers to all gas components in the system including "{it i.}$" The k${it $_{i}$}$' and k${it $_{j}$}$' corresponds to the Henry's constant [bar L mol$$^{-1}$$] of ${it i}$ (k${it $_{i}$}$) and ${it j}$ (k${it $_{j}$}$), respectively, except for k$$_{CO2}$$', which is pH-dependent function. Dissolved CH$$_{4}$$ concentrations were successfully estimated by the model within the error of $$pm$$ 4.0% from the direct measurements by the sealed sampler method. Similar TIC concentration in the groundwater before and after the rm bubble formation was consistent with the model prediction. The wide application of the model is suggested without selecting sampling locations.

JAEA Reports

Gas composition related to the Horonobe Underground Research Laboratory Project

Miyakawa, Kazuya; Tamamura, Shuji*; Nakata, Kotaro*; Hasegawa, Takuma*

JAEA-Data/Code 2016-021, 60 Pages, 2017/03

JAEA-Data-Code-2016-021.pdf:3.87MB
JAEA-Data-Code-2016-021-appendix(CD-ROM).zip:0.45MB

The Japan Atomic Energy Agency has been involved in ongoing research in the Horonobe area for the purposes of geoscientific research, and research and development (R&D) on technologies to be used for the geological disposal of high-level radioactive waste. The chemistry of groundwater and dissolved gas from deep boreholes has been obtained since H13 fiscal year for R&D on technologies related to geological characterization. Horonobe Research Institute for the Subsurface Environment (H-RISE) has investigated a resources development on promoting effective use of coal bed buried in Hokkaido including the Horonobe area using microbial communities. The data of dissolved gas from the Horonobe groundwater have also been obtained along with the microbiological research by H-RISE. Central Research Institute of Electric Power Industry (CRIEPI) has conducted R&D on technology of groundwater geochronology which is one of technologies to be used for the geological disposal, and noble gas data from the Horonobe groundwater have been obtained by CRIEPI. This report shows a data set which comprises gas data obtained from the Horonobe underground research project during the period from H13 fiscal year to H27 fiscal year.

Journal Articles

Possibility of formic and acetic acids as active substrates for methanogenesis in the groundwater in Horonobe, Hokkaido

Tamamura, Shuji*; Endo, Ryo*; Shimizu, Satoru*; Iwatsuki, Teruki; Amano, Yuki; Omi, Yasushi*; Igarashi, Toshifumi*

Journal of MMIJ, 128(10,11), p.570 - 575, 2012/10

http://doi.org/10.2473/journalofmmij.128.570

no abstracts in English

Oral presentation

Analysis of microbial community structure in deep underground diatomaceous/siliceous mudstone formations and factors determining microbial community structure

Tamazawa, Satoshi*; Ueno, Akio*; Murakami, Takuma*; Miyakawa, Kazuya; Tamamura, Shuji*; Kiyama, Tamotsu*; Inomata, Hidenori*; Naganuma, Takeshi*; Kaneko, Katsuhiko*; Igarashi, Toshifumi*

no journal, , 

no abstracts in English

Oral presentation

Isolation and characterization of a novel fermentative bacterium in the phylum Bacteroidetes from a deep subsurface diatomaceous mudstone formation

Tamazawa, Satoshi*; Ueno, Akio*; Tamaki, Hideyuki*; Tamamura, Shuji*; Murakami, Takuma*; Kiyama, Tamotsu*; Inomata, Hidenori*; Miyakawa, Kazuya; Naganuma, Takeshi*; Kaneko, Katsuhiko*

no journal, , 

no abstracts in English

Oral presentation

A Novel bacterium, ${it Mangrovibacterium}$ sp. strain Z1-71, isolated from the terrestrial subsurface environment and its co-cultivation within a methanogenic archaeon

Ueno, Akio*; Tamazawa, Satoshi*; Tamamura, Shuji*; Murakami, Takuma*; Inomata, Hidenori*; Amano, Yuki; Miyakawa, Kazuya; Naganuma, Takeshi*; Igarashi, Toshifumi*

no journal, , 

no abstracts in English

Oral presentation

A Novel bacterium isolated from the terrestrial subsurface environment and its co-cultivation with a methanogenic archaeon

Ueno, Akio*; Sato, Kiyoshi*; Tamamura, Shuji*; Murakami, Takuma*; Inomata, Hidenori*; Tamazawa, Satoshi*; Amano, Yuki; Miyakawa, Kazuya; Naganuma, Takeshi*; Igarashi, Toshifumi*

no journal, , 

no abstracts in English

Oral presentation

Characterization of a novel fermentative iron-reducing Bacteroidetes bacterium isolated from deep subsurface diatomaceous mudstone formation

Tamazawa, Satoshi*; Ueno, Akio*; Tamaki, Hideyuki*; Tamamura, Shuji*; Murakami, Takuma*; Kiyama, Tamotsu*; Inomata, Hidenori*; Miyakawa, Kazuya; Naganuma, Takeshi*; Kaneko, Katsuhiko*

no journal, , 

no abstracts in English

10 (Records 1-10 displayed on this page)
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