Shinsei Iso, Yu Sato, Hiroyuki Kimura (2024) Impacts of groundwater pumping on subterranean microbial communities in a deep aquifer associated with an accretionary prism. Microorganisms 12: 679. (Abstract)

Toshio Mori, Satoaki Higashi, Hiroyuki Kimura, Hirokazu Kawagishi, Hirofumi Hirai (2023) Effects on microstructures of decayed wood particles in spent mushroom substrates on the enzymatic saccharification and fermentation properties. Bioresource Technology Reports 22: 101494. (Abstract)

Keita Miyake, Hiroyuki Kimura, Rei Narikawa (2022) Identification of significant residues for intermediate accumulation in phycocyanobilin synthesis. Photochemical & Photobiological Sciences 21: 437-446. (Abstract)

佐藤 悠、岡野憲司、木村浩之、本田孝祐（2021）原核生物における多様な温度適応機構．環境バイオテクノロジー学会誌　21巻，1号，p. 17-28．

森 智夫、岩田実子、木村浩之、河岸和洋、平井浩文（2020）木質バイオマスからのメタン発酵前処理に適した白色腐朽菌の選抜．日本きのこ学会誌　28巻，p. 56-61.

Yu Sato, Kenji Okano, Hiroyuki Kimura, Kohsuke Honda (2020) TEMPURA: Database of growth TEMPeratures of Usual and RAre prokaryotes. Microbes and Environments 35: ME20074. (Abstract)

Keita Miyake, Keiji Fushimi, Tomonori Kashimoto, Kaisei Maeda, Ni-Ni-Win, Hiroyuki Kimura, Masakazu Sugishima, Masahiko Ikeuchi, Rei Narikawa (2020) Functional diversification of two bilin reductases for light perception and harvesting in unique cyanobacterium Acaryochloris marina MBIC 11017. FEBS Journal 287: 4016-4031. (Abstract)

Makoto Matsushita, Shugo Ishikawa, Kenta Magara, Yu Sato, Hiroyuki Kimura (2020) The potential for CH₄ production by syntrophic microbial communities in diverse deep aquifers associated with an accretionary prism and its overlying sedimentary layers. Microbes and Environments 35: ME19103. (Abstract)

Hiroshi A. Takahashi, Hiroko Handa, Ayumi Sugiyama, Makoto Matsushita, Miyuki Kondo, Hiroyuki Kimura, Maki Tsujimura (2019) Filtration and exposure to benzalkonium chloride or sodium chloride to preserve water samples for dissolved inorganic carbon analysis. Geochemical Journal 53: 305-318. (Abstract)

Yu Sato, Hiroyuki Kimura (2019) Temperature-dependent expression of different guanine-plus-cytosine content 16S rRNA genes in Haloarcula strains of the class Halobacteria. Antonie van Leeuwenhoek 112: 187-201. (Abstract)

木村浩之、松下 慎、芦沼完太、津布久卓也（2019）付加体深部帯水層での微生物メタン生成とエネルギー生産システムの社会実装．日本微生物生態学会誌　34巻，2号，p. 43-48. (J-STAGE)

Makoto Matsushita, Kenta Magara, Yu Sato, Naoya Shinzato, Hiroyuki Kimura (2018) Geochemical and microbiological evidence for microbial methane production in deep aquifers of the Cretaceous accretionary prism. Microbes and Environments 33: 205-213. (Abstract)

Yu Sato, Taketomo Fujiwara, Hiroyuki Kimura (2017) Expression and function of different guanine-plus-cytosine content 16S rRNA genes in Haloarcula hispanica at different temperatures. Frontiers in Microbiology 8: 482. (Abstract)

Takunari Kono, Sandhya Mehrotra, Chikako Endo, Natsuko Kizu, Mami Matsuda, Hiroyuki Kimura, Eiichi Mizohata, Tsuyoshi Inoue, Tomohisa Hasunuma, Akiho Yokota, Hiroyoshi Matsumura, Hiroki Ashida (2017) A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea. Nature Communications 8: 14007. (Abstract)

Makoto Matsushita, Shugo Ishikawa, Kazushige Nagai, Yuichiro Hirata, Kunio Ozawa, Satoshi Mitsunobu, Hiroyuki Kimura (2016) Regional variation of CH₄ and N₂ production processes in the deep aquifers of an accretionary prism. Microbes and Environments 31: 329-338. (Abstract)

Kyohei Baito, Satomi Imai, Makoto Matsushita, Miku Otani, Yu Sato, Hiroyuki Kimura (2015) Biogas production using anaerobic groundwater containing a subterranean microbial community associated with the accretionary prism. Microbial Biotechnology 8: 837-845. (Abstract)

木村浩之（2015）付加体のメタンと地下圏微生物を利用した分散型発電システム. Electronics Communications No. 31, 2-8．

Koji Mori, Atsushi Yamazoe, Akira Hosoyama, Shoko Ohji, Nobuyuki Fujita, Jun-ichiro Ishibashi, Hiroyuki Kimura, Ken-ichiro Suzuki (2014) Thermotoga profunda sp. nov., and Thermotoga caldifontis sp. nov., anaerobic thermophilic bacteria isolated from terrestrial hot springs. International Journal of Systematic and Evolutionary Microbiology 64: 2128-2136. (Abstract)

Masanori Kaneko, Yoshinori Takano, Yoshito Chikaraishi, Susumu Asakawa, Takeshi Watanabe, Seigo Shima, Nanako O. Ogawa, Martin Krüger, Makoto Matsushita, Hiroyuki Kimura, Naohiko Ohkouchi (2014) Quantitative analysis of coenzyme F430 in environmental samples: a new diagnostic tool for methanogenesis and anaerobic methane oxidation. Analytical Chemistry 86: 3633-3638. (Abstract)

木村浩之、松下 慎、梅藤恭平、今井里弥、津島一平、大谷実来、佐藤 悠（2014）陸上掘削による地域資源革命 〜付加体の地下圏微生物を利用したメタン・水素ガス生産〜．月刊地球　Vol. 36，No. 2，p. 101-108.（海洋出版）

Chie Katsuyama, Hiroaki Nashimoto, Kazuyo Nagaosa, Tomotaka Ishibashi, Rakeshi Kinoshita, Hideki Yoshikawa, Kazuhiro Aoki, Takahiro Asano, Toshito Sasaki, Rumi Sohrin, Daisuke Komatsu, Urumu Tsunogai, Hiroyuki Kimura, Yuichi Suwa, Kenji Kato (2013) Occurrence and potential activity of denitrifiers and methanogens in groundwater at 140 m depth in Pliocene diatomaceous mudstone of northern Japan. FEMS Microbiology Ecology 86: 532-543. (Abstract)

Yoshihiro Fujiwara, Takashi Okutani, Hiroyuki Kimura (2013) First occurrence of Alviniconcha from Japanese waters (Gastropoda: Provannidae). Venus 71: 217-219.

Hiroyuki Kimura, Kousuke Mori, Toshiro Yamanaka, Jun-Ichiro Ishibashi (2013) Growth temperatures of archaeal communities can be estimated from the guanine-plus-cytosine contents of 16S rRNA gene fragments. Environmental Microbiology Reports 5: 468-474. (Abstract)

木村浩之（2013）付加体の深部地下圏に生息する微生物群集を利用した自立分散型エネルギー生産システム．ケミカルエンジニヤリング　Vol. 58，No. 5，p. 8-13.（化学工業社）

木村浩之（2013）南西日本の地下圏微生物を利用した付加体エネルギー生産システム．クリーンエネルギー　Vol. 22， No. 5，p. 27-32.（日本工業出版）

木村浩之（2013）付加帯エネルギー生産システム 〜地下圏微生物を利用した新たな創エネ技術〜．配管技術　Vol. 55, No. 1，p. 31-36.（日本工業出版）

木村浩之（2013）付加帯の地下圏微生物を使ったエネルギー生産システム．太陽エネルギー　Vol. 39，No. 1，p. 15-20.（JSES）

Shohei Hattori, Hiroaki Nashimoto, Hiroyuki Kimura, Keisuke Koba, Keita Yamada, Mikio Shimizu, Hiroshi Watanabe, Muneoki Yoh, Naohiro Yoshida (2012) Hydrogen and carbon isotope fractionation by thermophilic hydrogenotrophic methanogens from a deep aquifer under coculture with fermenters. Geochemical Journal 46: 193-200. (Abstract)

Koji Mori, Takao Iino, Jun-Ichiro Ishibashi, Hiroyuki Kimura, Ken-Ichiro Suzuki (2012) Meiothermus hypogaeus sp. nov., a novel moderately thermophilic bacterium isolated from a Japanese hot spring. International Journal of Systematic and Evolutionary Microbiology 62: 112-117. (Abstract)

木村浩之 (2012) 微生物分子温度計による地下圏の温度プロファイリング. 総特集：モホ点描-超深部掘削で何が分かるのか？　月刊地球　Vol. 34，No. 4，p. 201-206.（海洋出版）

木村浩之（2012）地下圏微生物利用の新エネルギー生産システム −発電システムへの応用−．特集：新エネルギー最前線．化学装置　Vol. 54，No. 10，p. 38-41.（工業通信）

木村浩之、小澤邦雄、増田俊明（2012）地下圏微生物を利用した付加帯エネルギー生産システム. 特集：エネルギー利用のライセンス新技術．ケミカルエンジニヤリング　Vol. 57，No. 7，p. 38-41.（化学工業社）

Hiroyuki Kimura, Robert Young, Asuncion Martinez, Edward F. DeLong (2011) Light-induced transcriptional responses associated with proteorhodopsin-enhanced growth in a marine flavobacterium. ISME Journal 5: 1641-1651. (Abstract)

Ryouichi Higashi, Akira Tsukagoshi, Hiroyuki Kimura, Kenji Kato (2011) Male dimorphism in a new interstitial species of the genus Microloxoconcha (Podocopida: Ostracoda). Journal of Crustacean Biology 31: 142-152. (Abstract)

Do Manh Hao, Tomokazu Tashiro, Miharu Kato, Rumi Sohrin, Chie Katsuyama, Kazuyo Nagaosa, Hiroyuki Kimura, and Kenji Kato (2010) Population dynamics of Crenarchaeota and Euryarchaeota in the mixing front of river and marine waters. Microbes and Environments 25: 126-132. (Abstract)

Hiroyuki Kimura, Kousuke Mori, Hiroaki Nashimoto, Satoshi Hanada, Kenji Kato (2010) In situ biomass production of hot spring sulfur-turf microbial mat. Microbes and Environments 25: 140-143. (Abstract)

Hiroyuki Kimura, Hiroaki Nashimoto, Mikio Shimizu, Shohei Hattori, Keita Yamada, Keisuke Koba, Naohiro Yoshida, Kenji Kato (2010) Microbial methane production in deep aquifer associated with the accretionary prism in Southwest Japan. ISME Journal 4: 531-541. (Abstract)

Hiroyuki Kimura, Kousuke Mori, Hiroaki Nashimoto, Shohei Hattori, Keita Yamada, Keisuke Koba, Naohiro Yoshida, Kenji Kato (2010) Biomass production and energy source of thermophiles in a Japanese alkaline geothermal pool. Environmental Microbiology 12: 480-489. (Abstract)

Hiroyuki Kimura, Kousuke Mori, Tomokazu Tashiro, Kenji Kato, Toshiro Yamanaka, Jun-Ichiro Ishibashi, Satoshi Hanada (2010) Culture-independent estimation of optimal and maximum growth temperatures of archaea in subsurface habitats based on the G+C content in 16S rRNA gene sequences. Geomicrobiology Journal 27: 114-122. (Abstract)

Kenji Kato, Kazuyo Nagaosa, Hiroyuki Kimura, Chie Katsuyama, Katsunori Hama, Takanori Kunimaru, Urumu Tsunogai, Kazuhiro Aoki (2009) Unique distribution of deep groundwater bacteria constrained by geological setting. Environmental Microbiology Reports 1: 569-574. (Abstract)

Shingo Kato, Katsunori Yamanagawa, Michinari Sunamura, Yoshinori Takano, Jun-Ichiro Ishibashi, Takeshi Kakegawa, Motoo Utsumi, Toshiro Yamanaka, Tomohiro Toki, Takuroh Noguchi, Kensei Kobayashi, Arimichi Moroi, Hiroyuki Kimura, Yutaka Kawarabayasi, Katsumi Marumo, Tetsuro Urabe, Akihiko Yamagishi (2009) Abundance of Zetaproteobacteria within crustal fluids in back-arc hydrothermal fields of the Southern Mariana Trough. Environmental Microbiology 11: 3210-3222. (Abstract)

Shingo Kato, Kurt Hara, Hiroko Kasai, Takashi Teramura, Michinari Sunamura, Jun-ichiro Ishibashi, Takeshi Kakegawa, Toshiro Yamanaka, Hiroyuki Kimura, Katsumi Marumo, Tetsuro Urabe, Akihiko Yamagishi (2009) Spatial distribution, diversity and composition of bacterial communities in sub-seafloor fluids at a deep-sea hydrothermal field of the Suiyo seamount. Deep-Sea Research Part I 56: 1844-1855. (Abstract)

Chie Katsuyama, Naho Kondo, Yuichi Suwa, Takao Yamagishi, Masayuki Ito, Nobuhito Ohte, Hiroyuki Kimura, Kazuyo Nagaosa, Kenji Kato (2008) Denitrification activity and relevant bacteria revealed by nitrite reductase gene fragments in soil of temperate mixed forest. Microbes and Environments 23: 337-345. (Abstract) (日本微生物生態学会2009年度論文賞)

Takayuki Takenaka, Tomokazu Tashiro, Ayumi Ozaki, Hitomi Takakubo, Yutaka Yamamoto, Tomoko Maruyama, Kazuyo Nagaosa, Hiroyuki Kimura, Kenji Kato (2007) Planktonic bacterial population dynamics with environmental changes in coastal areas of Suruga Bay. Microbes and Environments 22: 257-267. (Abstract)

Takeshi Naganuma, Tatsuo Miyoshi, Hiroyuki Kimura (2007) Phylotype diversity of deep-sea hydrothermal vent prokaryotes trapped by 0.2- and 0.1-um-pore-size filters. Extremophiles 11: 637-646. (Abstract)

Hiroyuki Kimura, Jun-Ichiro Ishibashi, Harue Masuda, Kenji Kato, Satoshi Hanada (2007) Selective phylogenetic analysis targeting 16S rRNA genes of hyperthermophilic archaea in the deep-subsurface hot biosphere. Applied and Environmental Microbiology 73: 2110-2117. (Abstract)

Hosam Elsaied, Hiroyuki Kimura, Takeshi Naganuma (2007) Composition of archaeal, bacterial, and eukaryal RuBisCO genotypes in three Western Pacific arc hydrothermal vent systems. Extremophiles 11: 191-202. (Abstract)

Takeshi Naganuma, Hiroyuki Kimura, Risa Karimoto, Nikolay V. Pimenov (2006) Abundance of planktonic thraustochytrids and bacteria and the concentration of particulate ATP in the Greenland and Norwegian Seas. Polar Bioscience 20: 37-45. (Contents)

Hiroyuki Kimura, Maki Sugihara, Kenji Kato, Satoshi Hanada (2006) Selective phylogenetic analysis targeted at 16S rRNA genes of thermophiles and hyperthermophiles in deep-subsurface geothermal environments. Applied and Environmental Microbiology 72: 21-27. (Abstract)

Takeshi Naganuma, Hosam E. Elsaied, Daiki Hoshii, Hiroyuki Kimura (2005) Bacterial emdosymbioses of gutless tube-dwelling worms in nonhydrothermal vent habitats. Marine Biotechnology 7: 416-428. (Abstract)

Hiroyuki Kimura, Maki Sugihara, Hiroyuki Yamamoto, Bharat K.C. Patel, Kenji Kato, Satoshi Hanada (2005) Microbial community in a geothermal aquifer associated with the subsurface of the Great Artesian Basin, Australia. Extremophiles 9: 407-414. (Abstract)

Tatsunori Nakagawa, Jun-ichiro Ishibashi, Akihiro Maruyama, Toshiro Yamanaka, Yusuke Morimoto, Hiroyuki Kimura, Tesuro Urabe, Manabu Fukui (2004) Analysis of dissimilatory sulfite reductase and 16S rRNA gene fragments from deep-sea hydrothermal sites of the Suiyo seamount, Izu-Bonin Arc, Western Pacific. Applied and Environmental Microbiology 70: 393-403. (Abstract)

Hiroyuki Kimura, Ryuji Asada, Andrew Masta, Takeshi Naganuma (2003) Distribution of microorganisms in the subsurface of the Manus Basin hydrothermal vent field, Papua New Guinea. Applied and Environmental Microbiology 69: 644-648. (Abstract)

Hiroyuki Kimura, Yukimasa Higashide, Takeshi Naganuma (2003) Endosymbiotic microflora of the vestimentiferan tubeworm (Lamellibrachia sp.) from a bathyal cold-seep. Marine Biotechnology 5: 593-603. (Abstract)

Hiroyuki Kimura, Makoto Sato, Yuichi Sasayama, Takeshi Naganuma (2003) Molecular characterization and in situ localization of endosymbiotic 16S rRNA and RuBisCO genes in the pogonophoran tissue. Marine Biotechnology 5: 261-269. (Abstract)

木村浩之、長沼 毅（2003）西太平洋マヌス海盆における海底熱水噴出域深部の地下微生物圏. 地学雑誌 112：250-261.

木村浩之、朝田隆二、 長沼 毅（2003）Leg193：海底熱水域直下の地下微生物圏−マヌス海盆における海底熱水掘削と微生物分布調査−. 特集：深海掘削と新しい地球生命学．月刊地球　号外40号，p. 126-132.（海洋出版株式会社）

Hosam Elsaied, Hiroyuki Kimura, Takeshi Naganuma (2002) Molecular characterization and endosymbiotic localization of the gene encoding D-ribulose 1,5-bisphoshate carboxylase-oxygenase (RuBisCO) form II in the deep-sea vestimentiferan trophosome. Microbiology-SGM 148: 1947-1957. (Abstract)

Koji Nagao, Hiroyuki Kimura, Takeshi Naganuma (2002) Overlooked microbial agents in aquaculture: thraustochytrids. In: Cheng-Sheng Lee, Pat O'bryen (Eds). Microbial approaches to aquatic nutrition within environmentally sound aquaculture production systems. pp. 109-117.

Hiroyuki Kimura, Makoto Sato, Chino Sugiyama, Takeshi Naganuma (2001) Coupling of thraustochytrids and POM, and of bacterio- and phytoplankton in a semi-enclosed coastal area: implication for different substrate preference by the planktonic decomposers. Aquatic Microbial Ecology 25: 293-300. (Abstract)

Hiroyuki Kimura, Takeshi Naganuma (2001) Thraustochytrids: a forgotten agent of the marine microbial food chain. Aquatic Ecosystem Health & Management 4: 13-18. (Abstract)

木村浩之、長沼 毅（2001）沿岸域における浮遊性ヤブレツボカビ類の生態学的役割．海洋と生物　132（Vol. 23，No. 1），p. 19-25. （生物研究社）

Jean-Marie Auzende, Junichiro Ishibashi, Yannick Beaudoin, Jean-Luc Charlou, Jean Delteil, Jean-Pierre Donval, Yves Fouquet, Jean-Pierre Gouillou, Benoit Ildefonse, Hiroyuki Kimura, Yoshio Nishio, Joel Radford-Knoery, Etienne Ruellan (2000) The eastern and western tips of Manus Basin (Papua, New Guinea) explored by submersible; MANAUTE cruise. Comptes Rendus de l'Academie des Sciences -Serie IIA- Earth and Planetary Sciences 331: 119-126. (Abstract)

Jean-Marie Auzende, JunIchiro Ishibashi, Yannick Beaudoin, Yves Bouquet, Hiroyuki Kimura, Yoshiro Nishio, Joel Radford-Knoery, Etienne Ruellan (2000) Extensive magmatic and hydrothermal activity documented in Manus Basin. EOS 81: 452-453.

Jean-Mari Auzende, Junichiro Ishibashi, Yannick Beaudoin, Jean-Luc Charlou, Jean Detail, Jean-Pierre Donald, Yves Fouquet, Benoit Ildefonse, Hiroyuki Kimura, Yoshio Nishio, Joel Radford-Knoery, Etienne Ruellan (2000) Rift propagation and extensive off-axis volcanic and hydrothermal activity in Manus Basin (Papua New Guinea): MANUTE Cruise. InterRidge News 9: 21-25.

Hiroyuki Kimura, Tatsuhiro Fukuba, Takeshi Naganuma (1999) Biomass of thraustochytrid protoctists in coastal water. Marine Ecology Progress Series 189: 27-33. (Abstract)

木村浩之、東出幸真、長沼 毅（1999) 深海生物ハオリムシの体内と体外の微生物相〜類似と相違〜．JAMSTEC深海研究　第15号，I. 生物学編，p. 25-33.

長沼 毅、木村浩之、高杉秀美、植田浩義、小山田 潔（1999）ベントナイト微生物学地球深部研究および地層処分研究への応用の一例．月刊海洋　号外19，p. 133-138. （海洋出版株式会社）

Takeshi Naganuma, Hidemi Takasugi, Hiroyuki Kimura (1998) Abundance of thraustochytrids in coastal plankton. Marine Ecology Progress Series 162: 105-110. (Abstract)