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

A novel mesophilic sulfate-reducing bacterium, designated strain HN2, 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 grew in a temperature range of 5-43 C (optimum, 35 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, 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 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 is JS1 (97.0% similarity). The average nucleotide identity (ANI) value between strain HN2 and D. JS1 was 79.8%. Based on the phenotypic and molecular genetic evidence, the isolate is assigned to the new species sp. nov. The type strain is HN2 (=DSM 101010 =NBRC 112213).

The Development of Fe-nodules surrounding biological material mediated by microorganisms

Yoshida, Hidekazu; Yamamoto, Koshi*; Amano, Yuki; Katsuta, Nagayoshi*; Hayashi, Toru*; Naganuma, Takeshi

Environmental Geology, 55(6), p.1363 - 1374, 2008/09

https://doi.org/10.1007/s00254-007-1087-x

Takashikozo is a phenomenon of Quaternary sediments in Japan. They are cylindrical Fe-oxyhydroxide nodules that form as plaques round plant roots. Structural features suggest that after the roots have decayed, the central space where the roots were situated acts as a flow path for oxidized water. Analysis of microbial 16S rDNA extracted from the nodules identified iron-oxidizing bacteria encrusted round the roots where they are the likely initiators of nodule formation. Geological history and nanofossil evidence suggest that these Fe-nodules may have been buried at a depth of up to several tens of meters for a least 100000 years in reducing Quaternary sediments. Thus Fe-oxyhydroxide nodules with water and rock by microbial mediation can persist under reducing conditions. The phenomenon is significant as an analogue of post-closure conditions in radioactive waste repositories, since it could influence nuclide migration.

Announced document collection of the 1st Information Exchange Meeting on Radioactive Waste Disposal Research Network (Joint research)

Nakayama, Shinichi; Nagasaki, Shinya*; Inagaki, Yaohiro*; Oe, Toshiaki*; Sasaki, Takayuki*; Sato, Seichi*; Sato, Tsutomu*; Tanaka, Satoru*; Tochiyama, Osamu*; Nagao, Seiya*; et al.

JAEA-Conf 2007-003, 120 Pages, 2007/03

JAEA-Conf-2007-003.pdf:53.18MB

The 1st information exchange meeting on Radioactive Waste Disposal Research Network was held in Nuclear Science Research Institute of Japan Atomic Energy Agency on August 4, 2006. Radioactive Waste Disposal Research Network was established by under Interorganization Atomic Energy Research Program of Japan Atomic Energy Agency, and the objective is to bring both research infrastructures and human expertise in Japan to an adequate performance level, thereby contributing to the development of the fundamental research area in the field of radioactive waste disposal. This lecture material is a collection of research presentations and discussions during the information exchange meeting.

Microbial activity in the subsurface environment of the Tono area and its relation to geochemical conditions -Study of the abundance and diversity of groundwater microorganisms-

Naganuma, Takeshi*; Iwatsuki, Teruki; Murakami, Yuki; Hama, Katsuhiro; Okamoto, Takuji*; Tanimoto, Daisuke*; Fujita, Yuka*; Watanabe, Fumiko*; Adachi, Nahomi*; Sato, Makoto*

JNC TY7400 2003-001, 116 Pages, 2003/05

JNC-TY7400-2003-001.pdf:4.97MB

The abundance and diversity of groundwater microorganisms was studied in the Tono area, central Japan. Total cell counts were estimated by epifluorescence microscopy. Cell viability, based on cell membrane integrity, respiration-based metabolism, and esterase activity was estimated to be from 0.001% to approximately 100% of the total counts. The distribution of microbial abundance wad related to a variety of environmental factors, including fracture numbers, hydrological, and geochemical conditions in the groundwater. In the groundwater, profiles of redox sensitive solutes such as sulphate and sulphide ions, abundance and viability of microbes, and sulphur isotope rations of sulphate ions suggest that microbial sulphate redution involving organic matter and subsequent pyrite precipiration are dominant redox reactions at the depths of the uranium ore body. Concentrations of both the sulphate and chloride increase with increasing depth. The dissoloved sulphate is surmised to have originated from dissolution of sulphate and sulphide minerals in a geologic marine formation precipitated in marine environments, in the upper part of the sedimentary rocks. Such a redox process in the water-mineral-microbe system is inferred to have continued from the time when the marine formation underwent uplift above sea-level, because sulphate-reducing bacteria can use sulphate ions dissolved in fresh water that infiltrates from the marine formation and organic matter located in the deeper sedimentary rocks. Calculations by using the sulphate-S contents of the rocks and the sulphate dissolution rate suggest that microbial sulphate redution alone could maintain sufficiently reducing conditions of preserve the uranium ore for several hundred thousand years, in the case where a hydrogeological system continues to exist without much change. On the other hand, iron-oxidizing/reducing bacteria seem to play an important role in iron redox cycling in the granite groundwater.

Deep subsurface microbial communities in the Tono area, central Japan

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

Genshiryoku Bakkuendo Kenkyu, 5(2), p.59 - 66, 1999/03

https://doi.org/10.3327/jnuce.5.59

None

Development of a radiation survey meter for space exploration

Yasuda, Hiroshi*; Yajima, Kazuaki*; Takada, Masashi*; Nakamura, Takashi*; Fukuda, Mitsuhiro*; Sato, Tatsuhiko; Naganuma, Takeshi*; Onishi, Takeo*

no journal, , 

A novel survey meter for application to future interplanetary exploration has been developed. It is expected that the survey meter will measure separately exact doses of various cosmic-ray particles at any places even on the ground of moon and Mars. This feature surpasses those of other onboard active monitors or present crew personal dosimeters.

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

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