東京大学大学院農学生命科学研究科土壌圏科学研究室

EN

研究業績

2021

  1. Zhengcheng Zhang, Zhenxing Xu, Yoko Masuda, Xueding Wang, Natsumi Ushijima, Yutaka Shiratori, Keishi Senoo, Hideomi Itoh (2021). Geomesophilobacter sediminis gen. nov., sp. nov., Geomonas propionica sp. nov. and Geomonas anaerohicana sp. nov., three novel membersin the family Geobacterecace isolated from river sediment and paddy soil. Systematic and Applied Microbiology, 44(5): 126233. doi: 10.1016/j.syapm.2021.126233
  2. Wei Wei, Kazuo Isobe, Yutaka Shiratori, Midori Yano, Sakae Toyoda, Keisuke Koba, Naohiro Yoshida, Haoyang Shen and Keishi Senoo (2021). Revisiting the involvement of ammonia oxidizers and denitrifiers in nitrous oxide emission from cropland soils. Environmental Pollution, 287:117494 (Available online 2 June 2021). doi: 10.1016/j.envpol.2021.117494
  3. Haoyang Shen, Yutaka Shiratori, Sayuri Ohta, Yoko Masuda, Kazuo Isobe and Keishi Senoo (2021). Mitigating N2O emissions from agricultural soils with fungivorous mites. The ISME Journal (Published online 04 March 2021). doi: 10.1038/s41396-021-00948-4
  4. Yoko Masuda, Yutaka Shiratori, Hirotomo Ohba, Takanori Ishida, Ryo Takano, Sakura Satoh, Weishou Shen, Nan Gao, Hideomi Itoh, Keishi Senoo (2021). Enhancement of the nitrogen-fixing activity of paddy soils owing to iron application. Soil Science and Plant Nutrition, 1888629 (Published online 17 Feb 2021). doi: 10.1080/00380768.2021.1888629

2020

  1. Hideomi Itoh, Zhenxing Xu, Yoko Masuda, Natsumi Ushijima, Chie Hayakawa, Yutaka Shiratori and Keishi Senoo (2020). Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov., isolated from terrestrial environments, and emended description of the genus Geomonas. International Journal of Systematic and Evolutionary Microbiology, 71(1): 004607. doi: 10.1099/ijsem.0.004607
  2. Chie Hayakawa, Taichi Kobayashi, Kazumichi Fujii and Keishi Senoo(2020). Fine root biomass stimulates microbial activity of glucose mineralization in buried humic horizon of volcanic ash soils. Soil Science and Plant Nutrition, 66(5): 724-733. doi: 10.1080/00380768.2020.1820757
  3. Yosuke Nojiri, Yuka Kaneko, Yoichi Azegami, Yutaka Shiratori, Nobuhito Ohte, Keishi Senoo, Shigeto Otsuka and Kazuo Isobe (2020). Dissimilatory Nitrate Reduction to Ammonium and Responsible Microbes in Japanese Rice Paddy Soil. Microbes Environ., 35(4): ME20069. doi: 10.1264/jsme2.ME20069
  4. Yoko Masuda, Haruka Yamanaka, Zhen-Xing Xu, Yutaka Shiratori, Toshihiro Aono, Seigo Amachi, Keishi Senoo and Hideomi Itoh (2020). Diazotrophic Anaeromyxobacter Isolates from Soils. Appl.Environ. Microbiol., 86: e00956-20. doi: 10.1128/AEM.00956-20
  5. Zhenxing Xu, Yoko Masuda, Chie Hayakawa, Natsumi Ushijima, Keisuke Kawano, Yutaka Shiratori, Keishi Senoo and Hideomi Itoh (2020). Description of Three Novel Members in the Family Geobacteraceae, Oryzomonas japonicum gen. nov., sp. nov., Oryzomonas sagensis sp. nov., and Oryzomonas ruber sp. nov.. Microorganisms, 8(5): 634. doi: 10.3390/microorganisms8050634
  6. Kazuo Isobe, Nicholas J. Bouskill, Eoin L. Brodie, Erika A. Sudderth, Jennifer B.H. Martiny (2020). Phylogenetic conservation of soil bacterial responses to simulated global changes. Philosophical Transactions of the Royal Society B: Biological Sciences.
  7. Mise, K., Koyama, Y., Matsumoto, A., Fujita, K., Kunito, T., Senoo, K., and Otsuka, S. (2020). Pectin drives microbial phosphorus solubilization in soil: Evidence from isolation-based and community-scale approaches. Eur J Soil Biol. 97: 103169.
  8. Reiko Fujimura, Yoichi Azegami, Wei Wei, Hiroko Kakuta, Yutaka Shiratori, Nobuhito Ohte, Keishi Senoo, Shigeto Otsuka and Kazuo Isobe (2020). Distinct Community Composition of Previously Uncharacterized Denitrifying Bacteria and Fungi across Different Land-Use Types. Microbes and Environments, 35(1). doi: 10.1264/jsme2.ME19064
  9. Nan Gao, Chaowei Zhou, Weishou Shen, Sayuri Ota, Yutaka Shiratori, Tomoyasu Nishizawa, Kazuo Isobe, Xinhua He, Hanjie Ying and Keishi Senoo (2019). Genome Sequence of Novoherbaspirillum sp. UKPF54, a Plant Growth-Promoting Rhizobacterial Strain with N2O-Mitigating Abilities, Isolated from Paddy Soil. Microbiology Resource Announcements, 9(3): e00999-19. doi: 10.1128/MRA.00999-19
  10. Kazumori Mise, Runa Maruyama, Yuichi Miyabara, Takashi Kunito, Keishi Senoo, Shigeto Otsuka (2020). Time-series analysis of phosphorus-depleted microbial communities in carbon/nitrogen-amended soils. Applied Soil Ecology,145: 103346. doi: 10.1016/j.apsoil.2019.08.008

2019

  1. Weishou Shen, Xinchun Yu, Nan Gao, Sayuri Ota, Yutaka Shiratori, Tomoyasu Nishizawa, Kazuo Isobe, Xinhua He and Keishi Senoo (2019). Genome Sequence of Arthrobacter sp. UKPF54-2, a Plant Growth-Promoting Rhizobacterial Strain Isolated from Paddy Soil. Microbiology Resource Announcements, 8(45): e01005-19. doi: 10.1128/MRA.01005-19
  2. Weishou Shen, Huaiwen Xue, Nan Gao, Yutaka Shiratori, Takehiro Kamiya, Toru Fujiwara, Kazuo Isobe, Keishi Senoo (2019). Effects of copper on nitrous oxide (N2O) reduction in denitrifiers and N2O emissions from agricultural soils. Biol. Fertil. Soils, 56: 39-51. doi: 10.1007/s00374-019-01399-y
  3. Midori Sakoda, Maika Mizusawa, Fumitaka Shiotsu, Nobuo Sakagami, Yong Guo, Yuji Masutomi, Daichi Fujii, Kazuo Isobe, Toru Fujiwara, Keishi Senoo, Tomoyasu Nishizawa (2019). Azoarcus sp. strain KH32C affects rice plant growth and the root-associated soil bacterial community in low nitrogen input paddy fields. Soil Sci. Plant Nutr., 65(5): 451-459. doi: 10.1080/00380768.2019.1666648
  4. Zhenxing Xu, Yoko Masuda, Hideomi Itoh, Natsumi Ushijima, Yutaka Shiratori, Keishi Senoo (2019). Geomonas oryzae gen. nov., sp. nov., Geomonas edaphica sp. nov., Geomonas ferrireducens sp. nov., Geomonas terrae sp. nov., Four Ferric-Reducing Bacteria Isolated From Paddy Soil, and Reclassification of Three Species of the Genus Geobacter as Members of the Genus Geomonas gen. nov.. Frontier in Microbiology,10: 2201. doi: 10.3389/fmicb.2019.02201
  5. Kazuo Isobe, Yuta Ise, Hiroyu Kato, Tomoki Oda, Christian E. Vincenot, Keisuke Koba, Ryunosuke Tateno, Keishi Senoo, Nobuhito Ohte (2019). Consequences of microbial diversity in forest nitrogen cycling: diverse ammonifiers and specialized ammonia oxidizers. The ISME Journal, 14: 12-25. doi: 10.1038/s41396-019-0500-2
  6. Nan Gao, Weishou Shen, Tomoyasu Nishizawa, Kazuo Isobe, Yong Guo, Hanjie Ying, Keishi Senoo (2019). Genome Sequences of Two Azospirillum sp. Strains, TSA2S and TSH100, Plant Growth-Promoting Rhizobacteria with N2O Mitigation Abilities. Microbiology Resource Announcements, 8(32): e00459-19. doi: 10.1128/MRA.00459-19
  7. 國頭 恭,諸 人誌,藤田一輝,美世一守,長岡一成,大塚重人 (2019). リン可給性をめぐる土壌微生物群集. 土と微生物. 73 (2): 41-54.
  8. 藤田一輝,諸 人誌,大塚重人,長岡一成,國頭 恭 (2019). 土壌中の養分利用性と微生物による酵素生産との関係: 資源配分モデルを中心に. 土と微生物. 73 (1): 10–23.
  9. Kazuo Isobe, Steven D. Allison, Banafshe Khalili, Adam C. Martiny, Jennifer B.H. Martiny (2019). Phylogenetic conservation of bacterial responses to soil nitrogen addition across continent. Nature Communications (2019) 10: 2499. doi: 10.1038/s41467-019-10390-y
  10. Yoko Masuda, Takashi Matsumoto, Kazuo Isobe and Keishi Senoo (2019). Denitrification in paddy soil as a cooperative process of different nitrogen oxide reducers, revealed by metatranscriptomic analysis of denitrification-induced soil microcosm. Soil Science and Plant Nutrition, 65: 342-345. doi: 10.1080/00380768.2019.1622401
  11. Mise, K., Moro, H., Kunito, T., Senoo, K., and Otsuka, S. (2019). Prokaryotic community structure of long-term fertilization field Andisols in central Japan. Microbiol. Resour. Announc., 8: e01551-18. doi: 10.1128/MRA.01551-18
  12. Tsunehiro Watanabe, Ryunosuke Tateno, Shogo Imada, Karibu Fukuzawa, Kazuo Isobe, Rieko Urakawa, Tomoki Oda, Nanae Hosokawa, Takahiro Sasai, Yoshiyuki Inagaki, Takuo Hishi, Hiroto Toda, Hideaki Shibata (2019). The effect of a freeze–thaw cycle on dissolved nitrogen dynamics and its relation to dissolved organic matter and soil microbial biomass in the soil of a northern hardwood forest. Biogeochemistry, 142(3): 319-338. doi: 10.1007/s10533-019-00537-w

2018

  1. Fujita, K., Kunito, T., Matsushita, J., Nakamura, K., Moro, H., Yoshida, S., Toda, H., Otsuka, S., and Nagaoka, K. (2018). Nitrogen supply rate regulates microbial resource allocation for synthesis of nitrogen- acquiring enzymes. PLoS ONE, 13: e0202086.
  2. Jeonghwan Jang, Naoaki Ashida, Ayaaki Kai, Kazuo Isobe, Tomoyasu Nishizawa, Shigeto Otsuka, Akira Yokota, Keishi Senoo and Satoshi Ishii (2018). Presence of Cu-type (NirK) and cd1-type (NirS) nitrite reductase genes in the denitrifying bacterium Bradyrhizobium nitroreducens sp. nov. Microbes Environ., 33: 326-331. doi: 10.1264/jsme2.ME18039
  3. Kazumori Mise, Kazuki Fujita, Takashi Kunito, Keishi Senoo and Shigeto Otsuka (2018). Phosphorus-mineralizing communities reflect nutrient-rich characteristics in Japanese arable Andisols. Microbes Environ., 33: 282-289. doi: 10.1264/jsme2.ME18043
  4. Kazuo Isobe, Hiroaki Oka, Tsunehiro Watanabe, Ryunosuke Tateno, Rieko Urakawa, Chao Liang, Keishi Senoo and Hideaki Shibata (2018). High soil microbial activity in the winter season enhances nitrogen cycling in a cool-temperate deciduous forest. Soil Biol Biochem, 124: 90-100. doi: 10.1016/j.soilbio.2018.05.028
  5. Pokchat Chutivisut, Kazuo Isobe, Sorawit Powtongsook, Wiboonluk Pungrasmi and Futoshi Kurisu (2018). Distinct Microbial Community Performing Dissimilatory Nitrate Reduction to Ammonium (DNRA) in a High C/NO3- Reactor. Microbes Environ, 33: 1342-6311. doi: 10.1264/jsme2.ME17193
  6. Kazuo Isobe, Junko Ikutani, Yunting Fang, Muneoki Yoh, Jiangming Mo, Yuichi Suwa, Makoto Yoshida, Keishi Senoo, Shigeto Otsuka and Keisuke Koba (2018). Highly abundant acidophilic ammonia-oxidizing archaea causes high rates of nitrification and nitrate leaching in nitrogen-saturated forest soils. Soil Biol. Biochem., 122: 220-227. doi: 10.1016/j.soilbio.2018.04.021
  7. 増田曜子 (2018). 水田土壌の鉄還元菌のもう一つの顔-窒素肥沃度を支えるキープレーヤー-. 土と微生物(Soil Microorganisms)72(1): 7-13
  8. Yoko Masuda, Hideomi Itoh, Yutaka Shiratori and Keishi Senoo (2018). Metatranscriptomic insights into microbial consortia driving methane metabolism in paddy soils. Soil Sci. Plant Nutr.,64(4): 455-464. doi: 10.1080/00380768.2018.1457409
  9. Zakaria M. Solaiman and Keishi Senoo (2018). Arbuscular mycorrhizal fungus causes increased condensed tannins concentrations in shoots but decreased in roots of Lotus japonicas. Rhizosphere, 5: 32-37. doi: 10.1016/j.rhisph.2017.11.006

2017

  • Nan Gao, Weishou Shen, Estefania Camargo, Yutaka Shiratori, Tomoyasu Nishizawa, Kazuo Isobe, Xinhua He, Keishi Senoo (2017). Nitrous oxide (N2O)-reducing denitrifier-inoculated organic fertilizer mitigates N2O emission from agricultural soils. Biol Fertil. Soils, 53: 885-898. doi: 10.1007/s00374-017-1231-z
  • Nanae Hosokawa, Kazuo Isobe, Rieko Urakawa, Ryunosuke Tateno, Karibu Fukuzawa, Tsunehiro Watanabe, Hideaki Shibata (2017). Soil freeze–thaw with root litter alters N transformations during the dormant season in soils under two temperate forests in northern Japan. Soil Biology and Biochemistry, 114: 270–278. doi: 10.1016/j.soilbio.2017.07.025
  • Akihiko Terada, Sho Sugawara, Keisuke Hojo, Yuki Takeuchi, Shohei Riya, Willie F Harper Jr, Tomoko Yamamoto, Megumi Kuroiwa, Kazuo Isobe, Chie Katsuyama, Yuichi Suwa, Keisuke Koba, Masaaki Hosomi (2017). Hybrid Nitrous Oxide Production from a Partial Nitrifying Bioreactor: Hydroxylamine Interactions with Nitrite. Environmental Science and Technology, 51: 2748–2756. doi: 10.1021/acs.est.6b05521
  • Fujita, K., Kunito, T., Moro, H., Toda, H., Otsuka, S., and Nagaoka, K. (2017). Microbial resource allocation for phosphatase synthesis reflects the availability of inorganic phosphorus across various soils. Biogeochemistry, 136: 325-339. doi: 10.1007/s10533-017-0398-6
  • Yabe, S., Sakai, Y., Abe, Y., Yokota, A., Také, A., Matsumoto, A., Sugiharto, A., Susilowati, D., Hamada, M., Nara, K., Sudiana, I M., and Otsuka, S. (2017). Dictyobacter aurantiacus gen. nov., sp. nov., a member of the family Ktedonobacteraceae, isolated from soil, and emended description of the genus Thermosporothrix. International Journal of Systematic and Evolutionary Microbiology, 67: 2615-2621. doi: 10.1099/ijsem.0.001985
  • Satoshi Ishii, Naoaki Ashida, Hiroki Ohno, Takahiro Segawa, Shuhei Yabe, Shigeto Otsuka, Akira Yokota, and Keishi Senoo (2017). Noviherbaspirillum denitrificans sp. nov., denitrifying bacterium isolated from rice paddy soil and Noviherbaspirillum autotrophicum sp. nov, denitrifying, facultatively autotrophic bacterium isolated from rice paddy soil, and proposal to reclassify Herbaspirillum massiliense as Noviherbaspirillum massiliense comb. nov. International Journal of Systematic and Evolutionary Microbiology, 67: 1841-1848. doi: 10.1099/ijsem.0.001875
  • Masuda Y, Itoh H, Shiratori Y, Isobe K, Otsuka S, Senoo K. (2017). Predominant but previously-unseen prokaryotic drivers of reductive nitrogen transformation in paddy soils, unveiled by metatranscriptomics. Microbes Environ., 32: 180-183

2016

  • Satoshi Ishii, Kazuki Jokai, Shigeto Otsuka, Keishi Senoo and Satoshi Okabe (2016). Denitrification and Nitrate-Dependent Fe(II)-Oxidation in Various Pseudogulbenkiania Strains. Microbes Environ. 31: 293-298. doi:10.1264/jsme2.ME16001
  • Shiozaki, T., Ijichi, M., Isobe, K., Hashihama, F., Nakamura, K., Ehama, M., Hayashizaki, K., Takahashi, K., Hamasaki, K., Furuya, K. (2016). Nitrification and it influence on biogeochemical cycles from the equatorial Pacific to the Arctic Ocean. The ISME Journal, 10: 2184–2197. doi:10.1038/ismej.2016.18
  • Gao N, Shen W, Kakuta H, Tanaka N, Fujiwara T, Nishizawa T, Takaya N, Nagamine T, Isobe K, Otsuka S, Senoo K (2016). Inoculation with nitrous oxide (N2O)-reducing denitrifier strains simultaneously mitigates N2O emission from pasture soil and promotes growth of pasture plants. Soil Biol. Biochem. 97: 83-91. doi:10.1016/j.soilbio.2016.03.004
  • Kunito, T., Isomura, I., Sumi, H., Park, H.-D., Toda, H., Otsuka, S., Nagaoka, K., Saeki, K., and Senoo (2016). Aluminum and acidity suppress microbial activity and biomass in acidic forest soils. Soil Biol. Biochem. 97: 23-30. doi:10.1016/j.soilbio.2016.02.019
  • Graham EB, Knelman JE, Schindlbacher A, Siciliano S, Breulmann M, Yannarell A, Beman J, Abell G, Philippot L, Prosser J, Foulquier A, Yuste J, Glanville H, Jones D, Angel R, Salminen J, Newton RJ, Bürgmann H, Ingram LJ, Hamer U, Siljanen HM, Peltoniemi K, Potthast K, Bañeras L, Hartmann M, Banerjee S, Yu R, Nogaro G, Richter A, Koranda M, Castle S, Goberna M, Song B, Chatterjee A, Nunes OC, Lopes AR, Cao Y, Kaisermann A, Hallin S, Strickland MS, Garcia-Pausas J, Barba J, Kang H, Isobe K, Papaspyrou S, Pastorelli R, Lagomarsino A, Lindström E, Basiliko N, Nemergut DR (2016). Microbes as engines of ecosystem function: when does community structure enhance predictions of ecosystem processes? Front. Microbiol. 7: 214. doi:10.3389/fmicb.2016.00214
  • Urakawa, R., Ohte, N., Shibata, H., Isobe, K., Tateno, R., Oda, T., Hishi, T., Fukushima, K., Inagaki, Y., Hirai, K., Oyanagi, N., Nakata, N., Toda, H., Kenta, T., Kuroiwa, M., Watanabe, T., Fukuzawa, K., Tokuchi, N., Ugawa, S., Enoki, T., Nakanishi, A., Saigusa, N., Yamao, and Kotani, A. (2016). Factors contributing to nitrogen mineralization and nitrification rates of forest soils in the Japanese archipelago. Forest Ecol Manage. 361: 382-396. doi:10.1016/j.foreco.2015.11.033

2015

  • Wei, W., Isobe, K., Nishizawa, T., Zhu, L., Shiratori, Y., Ohte, N., Koba, K., Otsuka, S., Senoo, K. (2015). Higher diversity and abundance of denitrifying microorganisms in environments than considered previously. ISME J. 9: 1954-1965. doi:10.1038/ismej.2015.9 (press release)
  • Ali, M., Oshiki, M., Awata, T., Isobe, K., Kimura, Z., Yoshikawa, H., Hira, D., Kindaichi, T., Satoh, H., Fujii, T., and Okabe, S. (2015) Physiological Characterization of Anaerobic Ammonium Oxidizing Bacterium “Candidatus Jettenia caeni”. Environ Microbiol. online publication. 17: 2172-2189. doi:10.1111/1462-2920.12674
  • Shi, J., Ohte N., Tokuchi, N., Isobe, K., Urakawa, R., Imamura, N., Oda, T., Suzuki, M. (2015). Soil nitrogen transformation dynamics in a suburban forest near Tokyo Metropolitan Area under high nitrogen deposition: A case study using stable isotope tracer techniques. Bull. Tokyo Univ. For.132, 17-34
  • Umezawa, K., Takeda, K., Ishida, T., Sunagawa, N., Makabe, A., Isobe, K., Koba, K., Ohno,H., Samejima, M., Nakamura, N., Igarashi, K., Yoshida M. (2015). A novel pyrroloquinoline quinone-dependent 2-Keto-D-Glucose dehydrogenase from Pseudomonas aureofaciens. J. Bacteriol online publication 197: 1322-1329. doi:10.1128/JB.02376-14
  • Isobe, K., Ohte, N., Oda, T., Murabayashi, S., Wei, W., Senoo, K., Tokuchi, N., and Tateno, R. (2015). Microbial regulation of nitrogen dynamics along the hillslope of a natural forest. Front. Environ. Sci. 2: 63. doi:10.3389/fenvs.2014.00063
  • Wei, W., Isobe, K., Shiratori, Y., Nishizawa, T., Ohte, N., Ise, Y., Otsuka, S., Senoo, K. (2015). Development of PCR primers targeting fungal nirK to study fungal denitrification in the environment. Soil Biol Biochem. 81: 282-286. doi:10.1016/j.soilbio.2014.11.026
  • Urakawa, R., Ohte, N., Shibata, H., Tateno, R., Hishi, T., Fukushima, K., Inagaki, Y., Hirai, K., Oda, T., Oyanagi, N., Nakata, N., Toda, H., Kenta, T., Fukuzawa, K., Watanabe, T., Tokuchi, N., Nakaji, T., Saigusa, N., Yamao, Y., Nakanishi, A., Enoki, T., Ugawa, S., Hayakawa, A., Kotani, A., Kuroiwa, M., and Isobe, K. (2015). Biogeochemical nitrogen properties of forest soils in the Japanese archipelago. Ecol Res. 30: 1-2. doi:10.1007/s11284-014-1212-8

2014

2013

2012

  • Isobe, K., Koba, K., Suwa, Y., Ikutani, J., Fang, Y., Yoh, M., Mo, J., Otsuka, S., and Senoo, K. (2012). High abundance of ammonia-oxidizing archaea in acidified subtropical forest soils in southern China after long-term N deposition. FEMS Microbiol. Ecol. 80, 193–203. doi:10.1111/j.1574-6941.2011.01294.x
  • Yoshida, M., Ishii, S., Fujii, D., Otsuka, S., and Senoo, K. (2012). Identification of Active Denitrifiers in Rice Paddy Soil by DNA- and RNA-Based Analyses. Microbes Environ. 27, 456–461. doi:10.1264/jsme2.ME12076
  • Isobe, K., Koba, K., Suwa, Y., Ikutani, J., Kuroiwa, M., Fang, Y., Yoh, M., Mo, J., Otsuka, S., and Senoo, K. (2012). Nitrite transformations in an N-saturated forest soil. Soil Biol. Biochem. 52, 61–63. doi:10.1016/j.soilbio.2012.04.006.
  • Nishiyama, M., Sugita, R., Otsuka, S., and Senoo, K. (2012). Community structure of bacteria on different types of mineral particles in a sandy soil. Soil Sci. Plant Nutr. 58, 562–567. doi:10.1080/00380768.2012.729226.
  • Nishizawa, T., Tago, K., Oshima, K., Hattori, M., Ishii, S., Otsuka, S., and Senoo, K. (2012). Complete genome sequence of the denitrifying and N2O-reducing bacterium Azoarcus sp. strain KH32C. J. Bacteriol. 194, 1255. doi:10.1128/JB.06618-11
  • Koba, K., Fang, Y., Mo, J., Zhang, W., Lu, X., Liu, L., Zhang, T., Takebayashi, Y., Toyoda, S., Yoshida, N., et al. (2012). The 15 N natural abundance of the N lost from an N-saturated subtropical forest in southern China. J. Geophys. Res. Biogeosciences 117. doi:10.1029/2010JG001615
  • Nishizawa, T., Tago, K., Uei, Y., Ishii, S., Isobe, K., Otsuka, S., and Senoo, K. (2012). Advantages of functional single-cell isolation method over standard agar plate dilution method as a tool for studying denitrifying bacteria in rice paddy soil. AMB Express 2, 50. doi:10.1186/2191-0855-2-50

2011

  • Isobe, K., Koba, K., Otsuka, S., and Senoo, K. (2011). Nitrification and nitrifying microbial communities in forest soils. J. For. Res. 16, 351–362. doi:10.1007/s10310-011-0266-5
  • Kuroiwa, M., Koba, K., Isobe, K., Tateno, R., Nakanishi, A., Inagaki, Y., Toda, H., Otsuka, S., Senoo, K., Suwa, Y., et al. (2011). Gross nitrification rates in four Japanese forest soils: heterotrophic versus autotrophic and the regulation factors for the nitrification. J. For. Res. 16, 363–373. doi:10.1007/s10310-011-0287-0
  • Isobe, K., Koba, K., Ueda, S., Senoo, K., Harayama, S., and Suwa, Y. (2011). A simple and rapid GC/MS method for the simultaneous determination of gaseous metabolites. J. Microbiol. Methods 84, 46–51. doi:10.1016/j.mimet.2010.10.009.
  • Isobe, K., Suwa, Y., Ikutani, J., Kuroiwa, M., Makita, T., Takebayashi, Y., Yoh, M., Otsuka, S., Senoo, K., Ohmori, M., et al. (2011). Analytical Techniques for Quantifying 15N/14N of Nitrate, Nitrite, Total Dissolved Nitrogen and Ammonium in Environmental Samples Using a Gas Chromatograph Equipped with a Quadrupole Mass Spectrometer. Microbes Environ. 26, 46–53. doi:10.1264/jsme2.ME10159
  • Ishii, S., Ikeda, S., Minamisawa, K., and Senoo, K. (2011). Nitrogen Cycling in Rice Paddy Environments: Past Achievements and Future Challenges. Microbes Environ. 26, 282–292. doi:10.1264/jsme2.ME11293
  • Tago, K., Ishii, S., Nishizawa, T., Otsuka, S., and Senoo, K. (2011). Phylogenetic and Functional Diversity of Denitrifying Bacteria Isolated from Various Rice Paddy and Rice-Soybean Rotation Fields. Microbes Environ. 26, 30–35. doi:10.1264/jsme2.ME10167
  • Ishii, S., Ohno, H., Tsuboi, M., Otsuka, S., and Senoo, K. (2011). Identification and isolation of active N2O reducers in rice paddy soil. ISME J. 5, 1936–45. doi:10.1038/ismej.2011.69
  • Ishii, S., Ashida, N., Otsuka, S., and Senoo, K. (2011). Isolation of oligotrophic denitrifiers carrying previously uncharacterized functional gene sequences. Appl. Environ. Microbiol. 77, 338–42. doi:10.1128/AEM.02189-10
  • Ishii, S., Tago, K., Nishizawa, T., Oshima, K., Hattori, M., and Senoo, K. (2011). Complete genome sequence of the denitrifying and N(2)O-reducing bacterium Pseudogulbenkiania sp. strain NH8B. J. Bacteriol. 193, 6395–6. doi:10.1128/JB.06127-11

2010

2009

  • Ishii, S., Yamamoto, M., Kikuchi, M., Oshima, K., Hattori, M., Otsuka, S., and Senoo, K. (2009). Microbial populations responsive to denitrification-inducing conditions in rice paddy soil, as revealed by comparative 16S rRNA gene analysis. Appl. Environ. Microbiol. 75, 7070–8. doi:10.1128/AEM.01481-09.
  • Ishii, S., Kadota, K., and Senoo, K. (2009). Application of a clustering-based peak alignment algorithm to analyze various DNA fingerprinting data. J. Microbiol. Methods 78, 344–50. doi:10.1016/j.mimet.2009.07.005.
  • Yamamoto, S., Otsuka, S., Murakami, Y., Nishiyama, M., and Senoo, K. (2009). Genetic diversity of gamma-hexachlorocyclohexane-degrading sphingomonads isolated from a single experimental field. Lett. Appl. Microbiol. 49, 472–7. doi:10.1111/j.1472-765X.2009.02691.x.
  • Ueda, H., Otsuka, S., and Senoo, K. (2009). Community composition of bacteria co-cultivated with microalgae in non-axenic algal cultures. Microbiol. Cult. Collect., 21–25.
  • Yoshida, M., Ishii, S., Otsuka, S., and Senoo, K. (2009). Temporal shifts in diversity and quantity of nirS and nirK in a rice paddy field soil. Soil Biol. Biochem. 41, 2044–2051. doi:10.1016/j.soilbio.2009.07.012.
  • Isobe, K., Otsuka, S., Sudiana, I., Nurkanto, A., and Senoo, K. (2009). Community composition of soil bacteria nearly a decade after a fire in a tropical rainforest in East Kalimantan , Indonesia. J. Gen. Appl. Microbiol. 337, 329–337.

2008

  • Saito, T., Ishii, S., Otsuka, S., Nishiyama, M., and Senoo, K. (2008). Identification of Novel Betaproteobacteria in a Succinate-Assimilating Population in Denitrifying Rice Paddy Soil by Using Stable Isotope Probing. Microbes Environ. 23, 192–200. doi:10.1264/jsme2.23.192.
  • Otsuka, S., Sudiana, Im., Komori, A., Isobe, K., Deguchi, S., Nishiyama, M., Shimizu, H., and Senoo, K. (2008). Community Structure of Soil Bacteria in a Tropical Rainforest Several Years After Fire. Microbes Environ. 23, 49–56. doi:10.1264/jsme2.23.49.

2007

  • Kuramochi, N., S. Otsuka, M. Nishiyama, and K. Senoo. (2007). Presence of linA-homologous DNA sequences in different types of soil and their sequence diversity. Microbes Environ. 22:399-404.
  • Kotani-Tanoi, T., M. Nishiyama, S. Otsuka, K. Senoo. (2007). Single particle analysis reveals that bacterial community structures are semi-specific to the type of their inhabiting soil particle. Soil Sci. Plant Nutr. 53:740-743.
  • Harada, N., M. Nishiyama, S. Otsuka, and S. Matsumoto. (2007). Enhanced methanogenesis in the vicinity of rice straw residues in surface layers of a paddy soil. Soil Microorganisms 61:17-21.
  • Senoo, K., Z. Solaiman, S. Tanaka, M. Kawaguchi, H. Imaizumi-Anraku, S. Akao, A. Tanaka, and H. Obata. (2007). Isolation and characterization of arbuscules from roots of an increased arbuscule forming mutant of Lotus japonicus. Ann. Bot. 100:1599-1603.

Non-peer reviewed papers since 2007

  • 増田曜子, 伊藤英臣, 白鳥豊, 妹尾啓史 (2020). 水田土壌における鉄還元菌窒素固定の発見と応用-マイクロバイオーム解析から低窒素農業へ-. 土と微生物 74(1): 2-7.
  • 増田曜子, 伊藤英臣, 白鳥豊, 妹尾啓史 (2020). 水田土壌における鉄還元菌窒素固定の発見と応用. 化学と生物 58(3): 143-150.
  • 妹尾啓史, 野尻秀昭, 西山真 (2018). 機構紹介 東京大学微生物科学イノベーション連携研究機構. バイオサイエンスとインダストリー 76(5): 432-434
  • 語り手:服部勉, 聞き手:藤村玲子 (2018). 国際土壌10年企画「服部勉先生(東北大名誉教授)へのインタビュー」から. 土と微生物(Soil Microorganisms)72(1): 2-6
  • 和穎朗太, 藤井一至, 磯部一夫, 平舘俊太郎, 伊田奈緒美, 西村拓, 常田岳志, 光延聖, 妹尾啓史 (2016). 土壌の物質循環機能を多角的にみる―最先端手法が切り拓く新たな姿. 日本土壌肥料学雑誌 87(4): 283-288
  • 妹尾啓史 (2016). 農耕地からの一酸化二窒素ガス発生を削減し作物生産性を向上する微生物資材の開発に向けて. JATAFFジャーナル vol.4, No.5: 67
  • 妹尾啓史 (2015). 温室効果ガスと土壌微生物. 土と微生物(Soil Microorganisms)69(1): 10-15
  • 磯部一夫, 妹尾啓史 (2015). 環境中の脱窒微生物に関する研究の進展. バイオサイエンスとインダストリー Vol.73: 373-377
  • 西山雅也, 杉田亮平, 田野井孝子, 大塚重人, 妹尾啓史 (2015). 土壌粒子の微生物. 土と微生物(Soil Microorganisms)69(2): 84-86
  • 妹尾啓史 (2014). 土壌メタゲノム・菌株ゲノム情報を活用した農耕地からの亜酸化窒素ガス発生原因微生物の特定・分離と性状解析. IFO Res. Commun. 28: 31-49
  • 妹尾啓史 (2014). 水田土壌の脱窒微生物研究の新たな展開-現象の発見から一世紀を経て見えてきたその姿-. 肥料科学 第35号: 19-33
  • 石井聡, 吉田愛美, 伊藤英臣, 妹尾啓史 (2013). N2Oを消去する水田の微生物. 生物の科学 遺伝 67巻5号(2013年9月号): 562-567
  • 石井聡, 多胡加奈子, 妹尾啓史 (2011). 水田土壌で機能する脱窒微生物群の特定とN2O低減化への利用の可能性 セミナー室 土壌圏における窒素循環と微生物ーN2Oの動態を中心として(3). 化学と生物 Vol.49(7): 479-484
  • 浅川晋, 長岡一成, 関口博之, 浦嶋泰文, 須賀有子, 西澤智康, 太田寛行, 山崎真嗣, 妹尾啓史 (2011). 分子生態学的な微生物解析手法の土壌肥料研究への活用. 日本土壌肥料学雑誌 82巻2号: 170-175
  • 大塚重人, 西山雅也 (2011). 土壌微生物の多様性. 生物の科学 遺伝 Vol.65(3): 198-19924-29
  • 大塚重人 (2011). 微細藻類と共存して培養される難培養細菌の継代培養法および系統分類に関する研究. IFO Res. Commun. 25: 69-91
  • 伊藤英臣, 石井聡, 妹尾啓史. シンポジウム記録 微生物ゲノムが拓く水産の新しい潮流 農業環境分野へのメタゲノム解析の展開. 日本水産学会誌 77巻2号: 254
  • 妹尾啓史, 石井聡 (2010). Stable isotope probing(SIP)法を用いた土壌で機能する微生物の特定. Radioisotopes 59: 703-705
  • 石井聡, 大塚重人 (2010). Single cell isolation技術で何ができるか. 化学と生物 48: 666-668
  • 石井聡, 妹尾啓史 (2010). Functional single cell分離が明かす水田土壌脱窒菌の機能と生態. 土と微生物 64: 72-76
  • 西山雅也, 妹尾啓史 (2009). 土壌の物理的構造と細菌のすみか. 生物工学会誌 87:419-421
  • 妹尾啓史, 石井聡, 芦田直明, 大塚重人 (2009). 土壌環境で機能している微生物 を探る. 生物工学会誌 87: 422-424
  • 妹尾啓史, 對馬誠也 (2009). 土壌の生物性の遺伝子診断ー現状と将来展望ー. 圃場と土壌. 4月号: 6-10
  • 妹尾啓史 (2008). 農薬分解菌. 科学 78: 198-199

Books

  • 妹尾啓史 (2021). 第1章 土壌微生物と人類および作物生産 (p1-7), 第6章 土壌微生物による有機物の無機化と物質循環 (p79-94), 第7章 水田土壌の微生物の動態 (p95-107). In エッセンシャル土壌微生物学 作物生産のための基礎. 南澤究, 妹尾啓史(著・編), 青山正和, 齋藤明広, 齋藤雅典(著). 講談社
  • Otsuka, S (2019). Roseimicrobium. In Bergey's Manual of Systematics of Archaea and Bacteria. Whitman W.B. (Ed.), John Wiley & Sons, Inc., in association with Bergey’s Manual Trust, (Published online) DOI: 10.1002/9781118960608.gbm01550.  
  • Otsuka, S (2019). Brevifollis. In Bergey's Manual of Systematics of Archaea and Bacteria. Whitman W.B. (Ed.), John Wiley & Sons, Inc., in association with Bergey’s Manual Trust, (Published online) DOI: 10.1002/9781118960608.gbm01545.  
  • 妹尾啓史 (2019). 分子生物学と土壌生化学 In 土壌生化学. p.128-143. 朝倉書店
  • 磯部一夫 (2018). 森林土壌微生物の構成と養分動態へのかかわり. 森林科学シリーズ7 森林と土壌. p101-151. 共立出版
  • 妹尾啓史 (2018). 第7章 土壌中の生物とその働き In 土壌サイエンス入門 第2版. 木村眞人, 南條正巳(編). p139-149. 文永堂出版
  • 大塚重人 (2018). 第3章 土壌微生物の種類と特徴 In 土壌微生物学. 豊田剛己(編). p17-29. 朝倉書店
  • 大塚重人 (2018). コラム:もしも土壌微生物がいなかったら In 土壌サイエンス入門 第2版. 木村眞人, 南條正巳(編). p168. 文永堂出版
  • 大塚重人 (2015). 6-12 土壌に有機物と窒素を供給する万能生物シアノバクテリア In 土のひみつ. 日本土壌肥料学会「土のひみつ」編集グループ(編). p182-183. 朝倉書店
  • 妹尾啓史 (2014). 水田の微生物. 環境と微生物の事典 日本微生物生態学会編. p184-185. 朝倉書店
  • 大塚重人 (2013). 第5章 微生物の分類と同定 In 土壌微生物実験法 (第3版). 日本土壌微生物学会(編). p32-38. 養賢堂
  • 大塚重人, 磯部一夫, 青野俊裕 (2013). 第3章 土壌実験法 (p42-56) および 大塚重人, 磯部一夫. 第7章 土壌微生物の計数 (p207-208). In 実験農芸化学. 東京大学大学院農学生命科学研究科応用生命化学専攻・応用生命工学専攻(編). 朝倉書店
  • Satoshi Ishii, Koji Kadota and Keishi Senoo (2011). Clustering-Based Peak Alignment Algorithm for Objective and Quantitative Analysis of DNA Fingerprinting Data. In Handbook of Molecular Microbial Ecology I, Metagenomics and Complementary Approaches. Ed. Frans J. de Bruijn. p67-73. Wiley-Blackwell
  • 妹尾啓史, 石井聡 (2010). 水田土壌で機能する脱窒細菌群集の土壌DNAに基づく特定とSingle-Cell Isolation In 難培養微生物研究の最新技術Ⅱ~ゲノム解析を中心とした最前線と将来展望~. p184-196. シーエムシー出版
  • 伊藤秀臣, 石井聡, 妹尾啓史 (2010). 水田土壌のメタゲノム解析 In メタゲノム解析技術の最前線. p215-221. シーエムシー出版
  • 大塚重人 (2010). 第9章 細菌−9.4 シアノバクテリア In IFO 微生物学概論. 大嶋,荒井,駒形,杉山,中瀬,本田,宮道(編). p270-275. 培風館
  • 妹尾啓史 (2008). 農業環境と微生物 7.1 農地から派生する窒素 リン酸による環境汚染と微生物 In 微生物の事典. 渡邉, 西村, 内山, 奥田, 加来, 広木(編). p316-317. 朝倉書店
  • 大塚重人 (2008). I 概説−地球・人間・微生物 1 微生物学の歴史 In 微生物の事典. 渡邉, 西村, 内山, 奥田, 加来, 広木(編). p3-10. 朝倉書店
  • 渡邉信&大塚重人 (2008). I 概説−地球・人間・微生物 2 地球と微生物 In 微生物の事典.渡邉, 西村, 内山, 奥田, 加来, 広木(編). p11-22. 朝倉書店
  • 大塚重人 (2008). I 概説−地球・人間・微生物 3 生物界における微生物のグループと系統進化上の位置 3-(5) シアノバクテリア In 微生物の事典. 渡邉, 西村, 内山, 奥田, 加来, 広木(編). p32. 朝倉書店
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