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(Last updated on April 1, 2022)

·     *Isobe, K., Oka, H., Watanabe, T., Tateno, R., Senoo, K., Shibata, H., 2022. Soil microbial community response to winter climate change is phylogenetically conserved and highly resilient in a cool-temperate forest. Soil Biology and Biochemistry 165, 108499. doi:10.1016/j.soilbio.2021.108499

·     Enright, D.J., Frangioso, K.M., Isobe, K., Rizzo, D.M., *Glassman, S.I., 2022. Mega-fire in redwood tanoak forest reduces bacterial and fungal richness and selects for pyrophilous taxa that are phylogenetically conserved. Molecular Ecology 31, 2475–2493. doi:10.1111/mec.16399

·     Wei, W., *Isobe, K., Shiratori, Y., Yano, M., Toyoda, S., Koba, K., Yoshida, N., Shen, H., Senoo, K., 2021. Revisiting the involvement of ammonia oxidizers and denitrifiers in nitrous oxide emission from cropland soils. Environmental Pollution 287, 117494. doi:10.1016/j.envpol.2021.117494

·     *Shen, W., Xue, H., Gao, N., Shiratori, Y., Kamiya, T., Fujiwara, T., Isobe, K., Senoo, K., 2020. Effects of copper on nitrous oxide (N2O) reduction in denitrifiers and N2O emissions from agricultural soils. Biology and Fertility of Soils 56, 39–51. doi:10.1007/s00374-019-01399-y

·     *Isobe, K., Ise, Y., Kato, H., Oda, T., Vincenot, C.E., Koba, K., Tateno, R., Senoo, K., Ohte, N., 2020. 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

·     *Isobe, K., Bouskill, N.J., Brodie, E.L., Sudderth, E.A., *Martiny, J.B.H., 2020. Phylogenetic conservation of soil bacterial responses to simulated global changes. Philosophical Transactions of the Royal Society B: Biological Sciences 375, 20190242. doi:10.1098/rstb.2019.0242

·     Gao, N., Zhou, C., *Shen, W., Ota, S., Shiratori, Y., Nishizawa, T., Isobe, K., He, X., Ying, H., Senoo, K., 2020. Genome Sequence of Novoherbaspirillum sp. UKPF54, a Plant Growth-Promoting Rhizobacterial Strain with N2O-Mitigating Abilities, Isolated from Paddy Soil. Microbiology Resource Announcements 9, 6–8. doi:10.1128/MRA.00999-19

·     Fujimura, R., Azegami, Y., Wei, W., Kakuta, H., Shiratori, Y., Ohte, N., Senoo, K., Otsuka, S., *Isobe, K., 2020. Distinct Community Composition of Previously Uncharacterized Denitrifying Bacteria and Fungi across Different Land-Use Types. Microbes and Environments 35, n/a. doi:10.1264/jsme2.ME19064

·     Nojiri, Y., Kaneko, Y., Azegami, Y., Shiratori, Y., Ohte, N., Senoo, K., Otsuka, S., *Isobe, K., 2020. Dissimilatory Nitrate Reduction to Ammonium and Responsible Microbes in Japanese Rice Paddy Soil. Microbes and Environments 35, n/a. doi:10.1264/jsme2.ME20069

·     *Hosokawa, N., Isobe, K., Urakawa, R., Tateno, R., Fukuzawa, K., Watanabe, T., Shibata, H., 2020. Effect of root litter addition on nitrogen mineralization rate under laboratory low‐temperature conditions in soil from a Japanese northern hardwood forest. Ecological Research 35, 888–899. doi:10.1111/1440-1703.12154

·     *Isobe, K., Allison, S.D., Khalili, B., Martiny, A.C., *Martiny, J.B.H., 2019. Phylogenetic conservation of bacterial responses to soil nitrogen addition across continents. Nature Communications 10, 1–8. doi:10.1038/s41467-019-10390-y

·     *Watanabe, T., Tateno, R., Imada, S., Fukuzawa, K., Isobe, K., Urakawa, R., Oda, T., Hosokawa, N., Sasai, T., Inagaki, Y., Hishi, T., Toda, H., Shibata, H., 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, 319–338. doi:10.1007/s10533-019-00537-w

·     Gao, N., *Shen, W., Nishizawa, T., Isobe, K., Guo, Y., Ying, H., Senoo, K., 2019. Genome Sequences of Two Azospirillum sp. Strains, TSA2S and TSH100, Plant Growth-Promoting Rhizobacteria with N2O Mitigation Abilities. Microbiology Resource Announcements 8, e00459-19. doi:10.1128/MRA.00459-19

·     *Shen, W., Yu, X., Gao, N., Ota, S., Shiratori, Y., Nishizawa, T., Isobe, K., He, X., Senoo, K., 2019. Genome Sequence of Arthrobacter sp. UKPF54-2, a Plant Growth-Promoting Rhizobacterial Strain Isolated from Paddy Soil. Microbiology Resource Announcements 8, 7–9. doi:10.1128/MRA.01005-19

·     *Masuda, Y., Matsumoto, T., Isobe, K., Senoo, K., 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

·     Sakoda, M., Mizusawa, M., Shiotsu, F., Sakagami, N., Guo, Y., Masutomi, Y., Fujii, D., Isobe, K., Fujiwara, T., Senoo, K., *Nishizawa, T., 2019. Azoarcus sp. strain KH32C affects rice plant growth and the root-associated soil bacterial community in low nitrogen input paddy fields. Soil Science and Plant Nutrition 65, 451–459. doi:10.1080/00380768.2019.1666648

·     *Isobe, K., Ikutani, J., Fang, Y., Yoh, M., Mo, J., Suwa, Y., Yoshida, M., Senoo, K., Otsuka, S., Koba, K., 2018. Highly abundant acidophilic ammonia-oxidizing archaea causes high rates of nitrification and nitrate leaching in nitrogen-saturated forest soils. Soil Biology and Biochemistry 122, 220–227. doi:10.1016/j.soilbio.2018.04.021

·     Chutivisut, P., Isobe, K., Powtongsook, S., *Pungrasmi, W., Kurisu, F., 2018. Distinct Microbial Community Performing Dissimilatory Nitrate Reduction to Ammonium (DNRA) in a High C/NO3− Reactor. Microbes and Environments 33, 264–271. doi:10.1264/jsme2.ME17193

·     *Isobe, K., Oka, H., Watanabe, T., Tateno, R., Urakawa, R., Liang, C., Senoo, K., Shibata, H., 2018. High soil microbial activity in the winter season enhances nitrogen cycling in a cool-temperate deciduous forest. Soil Biology and Biochemistry 124, 90–100. doi:10.1016/j.soilbio.2018.05.028

·     Jang, J., Ashida, N., Kai, A., Isobe, K., Nishizawa, T., Otsuka, S., Yokota, A., Senoo, K., *Ishii, S., 2018. Presence of Cu-Type (NirK) and cd1-Type (NirS) Nitrite Reductase Genes in the Denitrifying Bacterium Bradyrhizobium nitroreducens sp. nov. Microbes and Environments 33, 326–331. doi:10.1264/jsme2.ME18039

·     *Terada, A., Sugawara, S., Hojo, K., Takeuchi, Y., Riya, S., Harper, W.F., Yamamoto, T., Kuroiwa, M., Isobe, K., Katsuyama, C., Suwa, Y., Koba, K., Hosomi, M., 2017. Hybrid Nitrous Oxide Production from a Partial Nitrifying Bioreactor: Hydroxylamine Interactions with Nitrite. Environmental Science & Technology 51, 2748–2756. doi:10.1021/acs.est.6b05521

·     *Masuda, Y., Itoh, H., Shiratori, Y., Isobe, K., Otsuka, S., Senoo, K., 2017. Predominant but Previously-overlooked Prokaryotic Drivers of Reductive Nitrogen Transformation in Paddy Soils, Revealed by Metatranscriptomics. Microbes and Environments 32, 180–183. doi:10.1264/jsme2.ME16179

·     *Hosokawa, N., Isobe, K., Urakawa, R., Tateno, R., Fukuzawa, K., Watanabe, T., Shibata, H., 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

·     Gao, N., *Shen, W., Camargo, E., Shiratori, Y., Nishizawa, T., Isobe, K., He, X., Senoo, K., 2017. Nitrous oxide (N2O)-reducing denitrifier-inoculated organic fertilizer mitigates N2O emissions from agricultural soils. Biology and Fertility of Soils 53, 885–898. doi:10.1007/s00374-017-1231-z

·     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 Biology and Biochemistry 97, 83–91. doi:10.1016/j.soilbio.2016.03.004

·     *Shiozaki, T., Ijichi, M., Isobe, K., Hashihama, F., Nakamura, K., Ehama, M., Hayashizaki, K., Takahashi, K., Hamasaki, K., Furuya, K., 2016. Nitrification and its influence on biogeochemical cycles from the equatorial Pacific to the Arctic Ocean. The ISME Journal 10, 2184–2197. doi:10.1038/ismej.2016.18

·     *Graham, E.B., Knelman, J.E., Schindlbacher, A., Siciliano, S., Breulmann, M., Yannarell, A., Beman, J.M., Abell, G., Philippot, L., Prosser, J., Foulquier, A., Yuste, J.C., Glanville, H.C., Jones, D.L., Angel, R., Salminen, J., Newton, R.J., Bürgmann, H., Ingram, L.J., Hamer, U., Siljanen, H.M.P., Peltoniemi, K., Potthast, K., Bañeras, L., Hartmann, M., Banerjee, S., Yu, R.-Q., Nogaro, G., Richter, A., Koranda, M., Castle, S.C., Goberna, M., Song, B., Chatterjee, A., Nunes, O.C., Lopes, A.R., Cao, Y., Kaisermann, A., Hallin, S., Strickland, M.S., Garcia-Pausas, J., Barba, J., Kang, H., Isobe, K., Papaspyrou, S., Pastorelli, R., Lagomarsino, A., Lindström, E.S., Basiliko, N., Nemergut, D.R., 2016. Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes? Frontiers in Microbiology 7, 1–10. 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, M., Toda, H., Kenta, T., Kuroiwa, M., Watanabe, T., Fukuzawa, K., Tokuchi, N., Ugawa, S., Enoki, T., Nakanishi, A., Saigusa, N., Yamao, Y., Kotani, A., 2016. Factors contributing to soil nitrogen mineralization and nitrification rates of forest soils in the Japanese archipelago. Forest Ecology and Management 361, 382–396. doi:10.1016/j.foreco.2015.11.033

·     *Isobe, K., Ohte, N., Oda, T., Murabayashi, S., Wei, W., Senoo, K., Tokuchi, N., Tateno, R., 2015. Microbial regulation of nitrogen dynamics along the hillslope of a natural forest. Frontiers in Environmental Science 2, 1–8. 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 Biology and Biochemistry 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, M., 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., Isobe, K., 2015. Biogeochemical nitrogen properties of forest soils in the Japanese archipelago. Ecological Research 30, 1–2. doi:10.1007/s11284-014-1212-8

·     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. Journal of Bacteriology 197, 1322–1329. doi:10.1128/JB.02376-14

·     Ali, M., Oshiki, M., Awata, T., Isobe, K., Kimura, Z., Yoshikawa, H., Hira, D., Kindaichi, T., Satoh, H., Fujii, T., *Okabe, S., 2015. Physiological characterization of anaerobic ammonium oxidizing bacterium ‘C andidatus J ettenia caeni.’ Environmental Microbiology 17, 2172–2189. doi:10.1111/1462-2920.12674

·     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. The ISME Journal 9, 1954–1965. doi:10.1038/ismej.2015.9

·     *Isobe, K., Ohte, N., 2014. Ecological Perspectives on Microbes Involved in N-Cycling. Microbes and Environments 29, 4–16. doi:10.1264/jsme2.ME13159

·     Wei, W., *Isobe, K., Shiratori, Y., Nishizawa, T., Ohte, N., Otsuka, S., Senoo, K., 2014. N2O emission from cropland field soil through fungal denitrification after surface applications of organic fertilizer. Soil Biology and Biochemistry 69, 157–167. doi:10.1016/j.soilbio.2013.10.044

·     *Nishizawa, T., Quan, A., Kai, A., Tago, K., Ishii, S., Shen, W., Isobe, K., Otsuka, S., Senoo, K., 2014. Inoculation with N2-generating denitrifier strains mitigates N2O emission from agricultural soil fertilized with poultry manure. Biology and Fertility of Soils 50, 1001–1007. doi:10.1007/s00374-014-0918-7

·     *Nishizawa, T., Uei, Y., Tago, K., Isobe, K., Otsuka, S., Senoo, K., 2013. Taxonomic composition of denitrifying bacterial isolates is different among three rice paddy field soils in Japan. Soil Science and Plant Nutrition 59, 305–310. doi:10.1080/00380768.2013.773256

·     *Nishizawa, T., Tago, K., Uei, Y., Ishii, S., Isobe, K., Otsuka, S., 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

·     *Isobe, K., Koba, K., Suwa, Y., Ikutani, J., Fang, Y., Yoh, M., Mo, J., Otsuka, S., Senoo, K., 2012. High abundance of ammonia-oxidizing archaea in acidified subtropical forest soils in southern China after long-term N deposition. FEMS Microbiology Ecology 80, 193–203. doi:10.1111/j.1574-6941.2011.01294.x

·     *Isobe, K., Koba, K., Suwa, Y., Ikutani, J., Kuroiwa, M., Fang, Y., Yoh, M., Mo, J., Otsuka, S., Senoo, K., 2012. Nitrite transformations in an N-saturated forest soil. Soil Biology and Biochemistry 52, 61–63. doi:10.1016/j.soilbio.2012.04.006

·     Kuroiwa, M., *Koba, K., Isobe, K., Tateno, R., Nakanishi, A., Inagaki, Y., Toda, H., Otsuka, S., Senoo, K., Suwa, Y., Yoh, M., Urakawa, R., Shibata, H., 2011. Gross nitrification rates in four Japanese forest soils: heterotrophic versus autotrophic and the regulation factors for the nitrification. Journal of Forest Research 16, 363–373. doi:10.1007/s10310-011-0287-0

·     *Isobe, K., Koba, K., Otsuka, S., Senoo, K., 2011. Nitrification and nitrifying microbial communities in forest soils. Journal of Forest Research 16, 351–362. doi:10.1007/s10310-011-0266-5

·     Isobe, K., Suwa, Y., Ikutani, J., Kuroiwa, M., Makita, T., Takebayashi, Y., Yoh, M., Otsuka, S., Senoo, K., Ohmori, M., *Koba, K., 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 and Environments 26, 46–53. doi:10.1264/jsme2.ME10159

·     Isobe, K., Koba, K., Ueda, S., Senoo, K., Harayama, S., *Suwa, Y., 2011. A simple and rapid GC/MS method for the simultaneous determination of gaseous metabolites. Journal of Microbiological Methods 84, 46–51. doi:10.1016/j.mimet.2010.10.009

·     *Koba, K., Isobe, K., Takebayashi, Y., Fang, Y.T., Sasaki, Y., Saito, W., Yoh, M., Mo, J., Liu, L., Lu, X., Zhang, T., Zhang, W., Senoo, K., 2010. δ 15 N of soil N and plants in a N-saturated, subtropical forest of southern China. Rapid Communications in Mass Spectrometry 24, 2499–2506. doi:10.1002/rcm.4648

·     *Isobe, K., Otsuka, S., Sudiana, Im., Nurkanto, A., Senoo, K., 2009. Community composition of soil bacteria nearly a decade after a fire in a tropical rainforest in East Kalimantan, Indonesia. The Journal of General and Applied Microbiology 55, 329–37. doi:10.2323/jgam.55.329

·     *Otsuka, S., Sudiana, Im., Komori, A., Isobe, K., Deguchi, S., Nishiyama, M., Shimizu, H., Senoo, K., 2008. Community Structure of Soil Bacteria in a Tropical Rainforest Several Years After Fire. Microbes and Environments 23, 49–56. doi:10.1264/jsme2.23.49

Isobe's research group is seeking highly motivated Ph.D. students and post-doctoral fellows interested in soil microbial ecology and plant-microbe interactions. Please feel free to contact Kazuo Isobe (contact: kazuo.isobe@pku.edu.cn)