Kazuo Isobe

I completed my Ph.D. in soil microbial ecology at The University of Tokyo in 2011. I have worked as an Assistant Professor at the University of Tokyo since 2011 and have conducted numerous international collaborations across Japan, China, and the U.S. In 2022, I joined the Institute of Ecology, College of Urban and Environmental Sciences at Peking University as a Tenure-track Associate Professor, where I launched a laboratory on soil microbial ecology.

Ph.D. The University of Tokyo, Japan, 2011

M.S.  The University of Tokyo, Japan, 2008

M.S. Waseda University, Japan, 2006

2022–  Tenure-track Associate Professor, Institute of Ecology, College of Urban and Environmental Sciences, Peking University

2016–2018  Researcher, Department of Ecology and Evolutionary Biology, University of California, Irvine. 

2011–2021  Assistant Professor, Graduate School of Agricultural and Life Sciences, The University of Tokyo

2010 JSPS  Research Associate, Graduate School of Agricultural and Life Sciences, The University of Tokyo

We are studying soil microbial communities' interaction with the environment and its consequences on ecosystem functions. In particular, we explore how soil microbial communities facilitate soil formation, nutrient cycling, and plant growth. 

Publication list

google scholar: https://scholar.google.com/citations?user=SNpIDY4AAAAJ&hl=en

 

(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)