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Tanimoto, Kazuya*; Kato, Shingo*; Tokunaga, Kohei; Hamamura, Natsuko*; Okuma, Moriya*; Mitsunobu, Satoshi*
Environmental Microbiology, 27(12), p.e70212_1 - e70212_18, 2025/12
Times Cited Count：0 Percentile：0.00(Microbiology)
isolated from the radioactive element-containing water in Fukushima Daiichi Nuclear Power Station Unit 2Dotsuta, Yuma; Taniguchi, Itsuki*; Goto, Yasuhiro*; Hayashi, Tetsuya*; Kurokawa, Ken*; Warashina, Tomoro*; Kanai, Akio*; Kitagaki, Toru
Microbiology Resource Announcements (Internet), 14(10), p.e00769-25_1 - e00769-25_3, 2025/10
Four bacteria strains with yellow-colored colonies which were Isolated from the radioactively element-containing water in Fukushima Daiichi Nuclear Power Station Unit 2 were identified as . Here, we present the complete genome sequences of these species assembled via a combination of short-read and long-read sequencing techniques.
sp. nov., a novel hydrogen-producing bacterium isolated from a deep diatomaceous shale formationUeno, Akio*; Sato, Kiyoshi*; Tamamura, Shuji*; Murakami, Takuma*; Inomata, Hidenori*; Tamazawa, Satoshi*; Amano, Yuki; Miyakawa, Kazuya; Naganuma, Takeshi*; Igarashi, Toshifumi*
International Journal of Systematic and Evolutionary Microbiology, 75(6), p.006802_1 - 006802_11, 2025/06
Times Cited Count：0 Percentile：0.00(Microbiology)no abstracts in English
Uchijima, Tomoki*; Kato, Shingo*; Tanimoto, Kazuya*; Shiraishi, Fumito*; Hamamura, Natsuko*; Tokunaga, Kohei; Makita, Hiroko*; Kondo, Momoko*; Okuma, Moriya*; Mitsunobu, Satoshi*
FEMS Microbiology Ecology, 101(6), p.fiaf051_1 - fiaf051_15, 2025/05
Times Cited Count：3 Percentile：81.72(Microbiology)Chemolithotrophic neutrophilic iron (Fe)-oxidizing bacteria, which mainly belong to the family Gallionellaceae, universally prevail in terrestrial environments changing Fe cycling. However, they are typically recognized as difficult-to-culture microbes. Despite efforts, there are few Fe(II)-oxidizing lithotroph isolates; hence, their physiological and ecological knowledge remains limited. This limitation is largely owing to difficulties in their cultivation, and we hypothesize that the difficulty exists because substrate and mineral concentrations in the cultivation medium are not tuned to a specific environmental condition under which these organisms live. To address this hypothesis, this study proposes a novel custom-made medium approach for chemolithotrophic Fe(II)-oxidizing bacteria; a method that manipulates medium components through diligent analysis of field environment. A new custom-made medium simulating energy substrates and nutrients under the field condition was prepared by modifying both chemical composition and physical setup in the glass-tube medium. In particular, the modification of the physical setup in the tube had a significant effect on adjusting dissolved Fe(II) and O
concentrations to the field environment. Using the medium, Gallionellaceae members were successfully enriched and a new Gallionellaceae species was isolated from a natural hot spring site. Compared with conventional medium, the custom-made medium has significantly higher ability in enriching Gallionellaceae members.
sp. strain V2501 isolated from 250 m below the ground level in Horonobe, Hokkaido, JapanUeno, 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
archaea host diverse and interacting extrachromosomal elementsShi, L.-D.*; West-Roberts, J.*; Schoelmerich, M. C.*; Penev, P. I.*; Chen, L.-X.*; Amano, Yuki; Lei, S.*; Sachdeva, R.*; Banfield, J. F.*
Nature Microbiology (Internet), 9(9), p.2422 - 2433, 2024/09
Times Cited Count：5 Percentile：61.57(Microbiology)Warashina, Tomoro*; Sato, Asako*; Hinai, Hiroshi; Shaikhutdinov, N.*; Shagimardanova, E.*; Mori, Hiroshi*; Tamaki, Satoshi*; Saito, Motofumi*; Sanada, Yukihisa; Sasaki, Yoshito; et al.
Applied and Environmental Microbiology, 90(4), p.e02113-23_1 - e02113-23_23, 2024/04
Times Cited Count：2 Percentile：13.04(Biotechnology & Applied Microbiology)Esser, S. P.*; Rahlff, J.*; Zhao, W.*; Predl, M.*; Plewka, J.*; Sures, K.*; Wimmer, F.*; Lee, J.*; Adam, P. S.*; McGonigle, J.*; et al.
Nature Microbiology (Internet), 8(9), p.1619 - 1633, 2023/09
Times Cited Count：14 Percentile：81.39(Microbiology)
MethanoperedenaceaeNishimura, Hiroki*; Kozuka, Mariko*; Fukuda, Akari*; Ishimura, Toyoho*; Amano, Yuki; Beppu, Hikari*; Miyakawa, Kazuya; Suzuki, Yohei*
Environmental Microbiology Reports (Internet), 15(3), p.197 - 205, 2023/06
Times Cited Count：4 Percentile：31.50(Environmental Sciences)The family Methanoperedenaceae archaea mediate anaerobic oxidation of methane (AOM). We newly developed a high-pressure laboratory incubation system and investigated groundwater from 214- and 249-m deep boreholes at Horonobe Underground Research Laboratory, Japan, where the high and low abundances of Methanoperedenaceae archaea have been revealed, respectively. We incubated the samples amended with or without amorphous Fe(III) and 
C-labelled methane at an in-situ pressure of 1.6 MPa. After three to seven-day incubation, AOM activities were not detected from the 249-m sample but from the 214-m sample. The AOM rates were 93.7
40.6 and 27.737.5 nM/day with and without Fe(III) amendment. Suspended particulates were not visible in the 249-m sample on the filter, while they were abundant and contained amorphous Fe(III) and Fe(III)-bearing phyllosilicates in the 214-m sample. This supports the in-situ activity of Fe(III)-dependent AOM in the deep subsurface borehole.
sp. DN11 and its potential use for removal of radioiodine from contaminated aquifersSasamura, Seiya*; Onuki, Toshihiko*; Kozai, Naofumi; Amachi, Seigo*
Frontiers in Microbiology (Internet), 14, p.1162788_1 - 1162788_7, 2023/04
Times Cited Count：9 Percentile：65.06(Microbiology) sp. DN11 previously isolated from gasoline-contaminated groundwater contained a gene cluster involved in bacterial iodate (IO
) respiration. This study determined if strain DN11 performed iodate respiration and assessed its potential use to remove and sequester radioactive iodine (
I) from subsurface contaminated aquifers. Strain DN11 grew anaerobically with iodate as the sole electron acceptor. After the growth of strain DN11 on iodate, silver-impregnated zeolite was added to the spent medium to remove iodide from the aqueous phase. In the presence of 200 
M iodate as the electron acceptor, more than 98% of iodine was successfully removed from the aqueous phase. These results suggest that strain DN11 is potentially helpful for bioaugmentation of I-contaminated subsurface aquifers.
sp. nov., a mesophilic sulfate-reducing deltaproteobacterium isolated from a deep siliceous mudstone formationUeno, 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
Times Cited Count：13 Percentile：53.93(Microbiology)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).
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：20 Percentile：58.80(Biotechnology & Applied Microbiology)Radioactive strontium (
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.
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：8 Percentile：22.66(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, 
-Proteobacteria was predominantly detected in the clone library analyses of the groundwater samples conducted immediately after drilling the borehole. All these -Proteobacteria clones are closely related to 
. 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.
Amano, Yuki; Iwatsuki, Teruki; Naganuma, Takeshi*
Geomicrobiology Journal, 34(9), p.769 - 783, 2017/03
Times Cited Count：9 Percentile：25.57(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.
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：1468 Percentile：99.96(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.
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：34 Percentile：70.74(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-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.
Katsuyama, Chie*; Nashimoto, Hiroaki*; Nagaosa, Kazuyo*; Ishibashi, Tomotaka*; Furuta, Kazuki*; Kinoshita, Takeshi*; Yoshikawa, Hideki; Aoki, Kazuhiro; Asano, Takahiro*; Sasaki, Yoshito; et al.
FEMS Microbiology Ecology, 86(3), p.532 - 543, 2013/12
Times Cited Count：16 Percentile：37.24(Microbiology)Anaerobic microbial activity has a major influence on the subsurface environment, and should be considered in subsurface activities including the construction of radioactive waste repositories. We investigated denitrification and methanogenesis in anoxic groundwater from 140 m depth in two boreholes, where the redox potential fluctuated. The average maximum potential denitrification rates, measured under anaerobic conditions in the two boreholes using an 
N tracer. Methanogenesis candidates were detected by 16S rRNA gene analysis. Although the stable isotope signatures suggested that some of the dissolved methane was of biogenic origin, no potential for methane production was evident during the incubations. The groundwater at 140 m depth did not contain oxygen, had an Eh ranging from -144 to 6.8 mV, and was found to be a potential field for denitrification.
following ionizing radiation-induced mutagenesisShinohara, Shinobu*; Fitriana, Y.*; Sato, Katsuya; Narumi, Issey*; Saito, Tsutomu*
FEMS Microbiology Letters, 349(1), p.54 - 60, 2013/12
Times Cited Count：14 Percentile：33.07(Microbiology)
sp. strain NGY-1Tanaka, Kazuya*; Yu, Q.; Sasaki, Keiko*; Onuki, Toshihiko
Geomicrobiology Journal, 30(10), p.874 - 885, 2013/08
Times Cited Count：23 Percentile：50.47(Environmental Sciences)no abstracts in English
Yu, Q.; Sasaki, Keiko*; Tanaka, Kazuya*; Onuki, Toshihiko; Hirajima, Tsuyoshi*
Geomicrobiology Journal, 30(9), p.829 - 839, 2013/07
Times Cited Count：38 Percentile：68.99(Environmental Sciences)no abstracts in English
