• Peer reviewed papers since 2007
• Non-peer reviewed papers since 2007
• Books

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

• Nishizawa, T., Quan, A., Kai, A., Tago, K., Ishii, S., Shen, W., Isobe, K., Otsuka, S., and Senoo, K. (2014). Inoculation with N2-generating denitrifier strains mitigates N2O emission from agricultural soil fertilized with poultry manure. Biol. Fertil. Soils 50: 1001–1007. doi:10.1007/s00374-014-0918-7
• Isobe, K., and Ohte, N. (2014). Ecological Perspectives on Microbes Involved in N-Cycling. Microbes Environ. 29: 4–16. doi:10.1264/jsme2.ME13159
• Wei, W., Isobe, K., Shiratori, Y., Nishizawa, T., Ohte, N., Otsuka, S., and Senoo, K. (2014). N2O emission from cropland field soil through fungal denitrification after surface applications of organic fertilizer. Soil Biol. Biochem. 69: 157–167. doi:10.1016/j.soilbio.2013.10.044
• 磯部一夫, 大手信人 (2014). 森林の窒素循環研究に対する微生物生態学的アプローチ 森林立地 56: 89-95
• 大手信人, 磯部一夫, 徳地直子 (2014). 森林集水域における窒素循環研究の今日的な課題とそれに対するストラテジー 日本水文科学会誌 44: 135-145

2013

• Itoh, H., Ishii, S., Shiratori, Y., Oshima, K., Otsuka, S., Hattori, M., and Senoo, K. (2013). Seasonal Transition of Active Bacterial and Archaeal Communities in Relation to Water Management in Paddy Soils. Microbes Environ. 28, 370–380. doi:10.1264/jsme2.ME13030
• Otsuka, S., Suenaga, T., Vu, H. T., Ueda, H., Yokota, A., and Senoo, K. (2013). Brevifollis gellanilyticus gen. nov., sp. nov., a gellan-gum-degrading bacterium of the phylum Verrucomicrobia. Int. J. Syst. Evol. Microbiol. 63, 3075–8. doi:10.1099/ijs.0.048793-0
• Otsuka, S., Ueda, H., Suenaga, T., Uchino, Y., Hamada, M., Yokota, A., and Senoo, K. (2013). Roseimicrobium gellanilyticum gen. nov., sp. nov., a new member of the class Verrucomicrobiae. Int. J. Syst. Evol. Microbiol. 63, 1982–6. doi:10.1099/ijs.0.041848-0
• Nishizawa, T., Uei, Y., Tago, K., Isobe, K., Otsuka, S., and Senoo, K. (2013). Taxonomic composition of denitrifying bacterial isolates is different among three rice paddy field soils in Japan. Soil Sci. Plant Nutr. 59, 305–310. doi:10.1080/00380768.2013.773256.
• Thi Vu, H., Itoh, H., Ishii, S., Senoo, K., and Otsuka, S. (2013). Identification and Phylogenetic Characterization of Cobalamin Biosynthetic Genes of Ensifer adhaerens. Microbes Environ. 28, 153–155. doi:10.1264/jsme2.ME12069

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

• Yoshida, M., Ishii, S., Otsuka, S., and Senoo, K. (2010). nirK-Harboring Denitrifiers Are More Responsive to Denitrification- Inducing Conditions in Rice Paddy Soil Than nirS-Harboring Bacteria. Microbes Environ. 25, 45–48. doi:10.1264/jsme2.ME09160
• Murakami, Y., Otsuka, S., and Senoo, K. (2010). Abundance and Community Structure of Sphingomonads in Leaf Residues and Nearby Bulk Soil. Microbes Environ. 25, 183–189. doi:10.1264/jsme2.ME10114
• Koba, K., Isobe, K., Takebayashi, Y., Fang, Y. T., Sasaki, Y., Saito, W., Yoh, M., Mo, J., Liu, L., Lu, X., et al. (2010). Delta15N of soil N and plants in a N-saturated, subtropical forest of southern China. Rapid Commun. Mass Spectrom. 24, 2499–506. doi:10.1002/rcm.4648
• Ishii, S., Yamamoto, M., Tago, K., Otsuka, S., and Senoo, K. (2010). Microbial populations in various paddy soils respond differently to denitrification-inducing conditions, albeit background bacterial populations are similar. Soil Sci. Plant Nutr. 56, 220–224. doi:10.1111/j.1747-0765.2010.00453.x
• Vu, H. T., Otsuka, S., Ueda, H., and Senoo, K. (2010). Cocultivated bacteria can increase or decrease the culture lifetime of Chlorella vulgaris. J. Gen. Appl. Microbiol. 418, 413–418.
• Ishii, S., Tago, K., and Senoo, K. (2010). Single-cell analysis and isolation for microbiology and biotechnology: methods and applications. Appl. Microbiol. Biotechnol. 86, 1281–92. doi:10.1007/s00253-010-2524-4
• Ueda, H., Otsuka, S., and Senoo, K. (2010). Bacterial Communities Constructed in Artificial Consortia of Bacteria and Chlorella vulgaris. Microbes Environ. 25, 36–40. doi:10.1264/jsme2.ME09177
• Ashida, N., Ishii, S., Hayano, S., Tago, K., Tsuji, T., Yoshimura, Y., Otsuka, S., and Senoo, K. (2010). Isolation of functional single cells from environments using a micromanipulator: application to study denitrifying bacteria. Appl. Microbiol. Biotechnol. 85, 1211–7. doi:10.1007/s00253-009-2330-z

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.