Researcher basic information

• Doctor of Philosophy, The University of Tokyo, Oct. 2020
• Master of Agricultural and Life Sciences, The University of Tokyo, Mar. 2017

• https://researchmap.jp/ms33?lang=en

• https://orcid.org/0000-0003-3565-3119
• https://jglobal.jst.go.jp/detail?JGLOBAL_ID=201901001402360072

• https://orcid.org/0000-0003-3565-3119

• 201901001402360072

• Metagenomics
• Genomics
• Bioinformatics
• Soil microorganisms
• Community ecology
• Plant-microbe symbiosis
• Isolation and cultivation
• Microbial community structure
• Biogeochemistry
• Nitrogen fixation
• Phosphorus cycling

• Life Science, Applied microbiology
• Life Science, Plant nutrition and soil science
• Life Science, Genome biology
• Life Science, System genome science
• Life Science, Ecology and environment
• Environmental Science/Agriculture Science, Environmental dynamic analysis
• Informatics, Life, health and medical informatics

• Master's degree program, Graduate School of Environmental Science
• Doctoral (PhD) degree program, Graduate School of Environmental Science

Research activity information

• Isolation and global occurrence of nitrogen-fixing Acidobacteriota in soil environments
  Hideomi Itoh; Kazumori Mise; Miyu Kuniyasu; Sawa Wasai-Hara; Natsumi Ushijima
  Oxford University Press (OUP), 18 Jun. 2026, [Lead author, Corresponding author], [International Magazine]
  Scientific journal, Abstract
  
  Acidobacteriota, one of the most abundant and ubiquitous bacterial phyla in soils, are well recognized for their role in carbon cycling. In contrast, their roles in soil nitrogen cycling remain largely unexplored, although recent metagenome-assembled genome (MAG) analyses suggest that Acidobacteriota may harbor genes involved in nitrogen cycling. Here, we provide culture-based evidence of diazotrophy within this phylum and demonstrate the widespread occurrence of nitrogen-fixing Acidobacteriota across diverse soil types. From grassland and agricultural soils, we isolated five Acidobacteriota strains representing novel taxonomic lineages, four of which harbor functional nitrogenase (nif) gene clusters. These strains were capable of fixing atmospheric nitrogen in vitro and/or in soil microcosms, as evidenced by acetylene reduction, N2-dependent growth, transcription of nif genes, incorporation of 15N into biomass and soil, and inhibition of nitrogenase activity by ammonium. Furthermore, global-scale meta-analysis of soil metagenomes revealed that nif-harboring Acidobacteriota are widely distributed and locally dominant across soil types. These results demonstrate the nitrogen-fixing capability of Acidobacteriota at the organismal level, complementing MAG-based inferences, and underscore their adaptive capacity in nitrogen-limited environments and their potential contribution to terrestrial nitrogen fixation. We also propose novel taxa within the class Terriglobia of the phylum Acidobacteriota, including diazotrophic strains, comprising one novel family, three novel genera, and four novel species: Koromonadaceae fam. nov., Koromonas soli gen. nov., sp. nov., Koromonas humicola sp. nov., Oryzophilus luti gen. nov., sp. nov., and Humiphilus diazotrophicus gen. nov., sp. nov.
• Global terrestrial distribution of N₂O-reducing Acidobacteriota members
  Kazumori Mise; Sawa Wasai-Hara; Hideomi Itoh
  Oxford University Press (OUP), 27 Mar. 2026, [Lead author, Corresponding author], [International Magazine]
  Scientific journal, Nitrous oxide (N2O) is a potent greenhouse gas, and soil is its largest terrestrial source. Microbial N2O reductase (NosZ) is the only known enzyme capable of reducing N2O to N2, making nosZ-harboring prokaryotes important sinks in terrestrial ecosystems. Despite being among the most abundant and ubiquitous bacterial phyla in soil, the potential role of Acidobacteriota in N2O reduction remains largely unexplored. In this study, we addressed this gap using genomic, metagenomic, and physiological analyses. We first analyzed 199,602 prokaryotic genomes, including genomes from both isolated strains and metagenome-assembled genomes. We found that 491 Acidobacteriota genomes harbored nosZ, predominantly the Sec-dependent NosZ gene (nosZII). Global metagenomic analysis of 321 soil samples revealed that Acidobacteriota nosZII is one of the most abundant groups of nosZ and distributed across different continents. Among Acidobacteriota, nosZII from the class Vicinamibacteria was the most prevalent in the soils. Finally, we provide the physiological evidence of N2O-reducing activity in Acidobacteriota by demonstrating that the Vicinamibacteria type strain, Luteitalea pratensis KCTC52215T, can reduce N2O. Taken together, these findings highlight the previously overlooked potential role of Acidobacteriota as a global N2O sink and underscore the need to include them in future studies on soil N2O dynamics.
• Betaproteobacterial clade II nosZ activated under high N₂O concentrations in paddy soil microcosms
  Kazumori Mise; Yoko Masuda; Keishi Senoo; Hideomi Itoh
  Mar. 2025, [Lead author, Corresponding author], [International Magazine]

  
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• Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome
  Yoko Masuda; Kazumori Mise; Zhenxing Xu; Zhengcheng Zhang; Yutaka Shiratori; Keishi Senoo; Hideomi Itoh
  Springer Science and Business Media LLC, 24 May 2024, [Lead author, Corresponding author]
  Scientific journal, Abstract
  
  Background
  
  Biological nitrogen fixation is a fundamental process sustaining all life on earth. While distribution and diversity of N₂-fixing soil microbes have been investigated by numerous PCR amplicon sequencing of nitrogenase genes, their comprehensive understanding has been hindered by lack of de facto standard protocols for amplicon surveys and possible PCR biases. Here, by fully leveraging the planetary collections of soil shotgun metagenomes along with recently expanded culture collections, we evaluated the global distribution and diversity of terrestrial diazotrophic microbiome.
  
  Results
  
  After the extensive analysis of 1,451 soil metagenomic samples, we revealed that the Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous groups of diazotrophic microbiome in the soils with different geographic origins and land usage types, with particular predominance in anaerobic soils (paddy soils and sediments).
  
  Conclusion
  
  Our results indicate that Deltaproteobacteria is a core bacterial taxon in the potential soil nitrogen fixation population, especially in anaerobic environments, which encourages a careful consideration on deltaproteobacterial diazotrophs in understanding terrestrial nitrogen cycling.

  
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• Lysinibacillus piscis sp. nov. isolated from the gut of mottled spinefoot Siganus fuscescens
  Hiyu Kanbe; Yuki Sano; Kazumori Mise; Shusei Kanie; Natsumi Ushijima; Keisuke Kawano; Minoru Kihara; Hideomi Itoh
  Springer Science and Business Media LLC, 21 Apr. 2024
  Scientific journal

  
  Experimental
• Ecoenzymatic stoichiometry as a temporally integrated indicator of nutrient availability in soils
  Takashi Kunito; Hitoshi Moro; Kazumori Mise; Kozue Sawada; Shigeto Otsuka; Kazunari Nagaoka; Kazuki Fujita
  Informa UK Limited, 16 Apr. 2024
  Scientific journal
• Mesoterricola silvestris gen. nov., sp. nov., Mesoterricola sediminis sp. nov., Geothrix oryzae sp. nov., Geothrix edaphica sp. nov., Geothrix rubra sp. nov., and Geothrix limicola sp. nov., six novel members of Acidobacteriota isolated from soils
  Hideomi Itoh; Yumi Sugisawa; Kazumori Mise; Zhenxing Xu; Miyu Kuniyasu; Natsumi Ushijima; Keisuke Kawano; Emiko Kobayashi; Yutaka Shiratori; Yoko Masuda; Keishi Senoo
  Microbiology Society, 06 Sep. 2023
  Scientific journal, Forty-eight Acidobacteriota strains were isolated from soils and sediments in Japan. Among them, six representative strains, designated W79^T, W786^T, Red222^T, Red802^T, Red803^T, and Red804^T, were subjected to the taxonomic classification. These six strains are Gram-stain-negative, non-spore-forming, rod-shaped, and facultative anaerobic bacterium that can reduce ferric iron. Phylogenetic and phylogenomic trees based on 16S rRNA genes and multiple single-copy gene sequences showed that strains Red222^T, Red802^T, Red803^T, and Red804^T formed a cluster with the type strains of Geothrix species, but strains W79^T and W786^T created an independent cluster from any other type strains. The former four strains shared 97.95–99.08% similarities of 16S rRNA gene sequence with the type strains of the genus Geothrix, whereas the latter two strains 94.86–95.49% similarities. The average amino acid identity of strains W79^T and W786^T were <63 % to any other type strains, which were below the genus delineation thresholds. Moreover, colonies of these two strains were white, while those of the other four isolated strains were reddish-yellow as well as the type strain Geothrix fermentans H-5^T. Although the known type strains of Geothrix species have been reported to be non-motile, five strains (W79^T, W786^T, Red222^T, Red803^T, and Red804^T) except for strain Red802^T displayed motility. Furthermore, multiple genomic, phylogenetic, and phenotypic features supported the discrimination between these isolated strains. Based on the study evidence, we propose these six isolates as novel members within the Acidobacteriota/Holophagae/Holophagales/Holophagaceae, comprising two novel species of a novel genus, Mesoterricola silvestris gen. nov., sp. nov., and Mesoterricola sediminis sp. nov., and four novel species of the genus Geothrix: Geothrix oryzae sp. nov., Geothrix edaphica sp. nov., Geothrix rubra sp. nov., and Geothrix limicola sp. nov.

  
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• Unexpected absence of ribosomal protein genes from metagenome-assembled genomes
  Kazumori Mise; Wataru Iwasaki
  Oxford University Press (OUP), 28 Nov. 2022, [Lead author, Corresponding author]
  Scientific journal, Abstract
  
  Metagenome-assembled genomes (MAGs) have revealed the hidden diversity and functions of uncultivated microbes, but their reconstruction from metagenomes remains a computationally difficult task. Repetitive or exogenous sequences, such as ribosomal RNA and horizontally transferred genes, are frequently absent from MAGs because of misassembly and binning errors. Here, we report that ribosomal protein genes are also often absent from MAGs, although they are neither repetitive nor exogenous. Comprehensive analyses of more than 190,000 MAGs revealed that these genes could be missing in more than 20–40% of near-complete (i.e., with completeness of 90% or higher) MAGs. While some uncultivated environmental microbes intrinsically lack some ribosomal protein genes, we found that this unexpected absence is largely due to special evolutionary patterns of codon usage bias in ribosomal protein genes and algorithmic characteristics of metagenomic binning, which is dependent on tetranucleotide frequencies of contigs. This problem reflects the microbial life-history strategy. Fast-growing microbes tend to have this difficulty, likely because of strong evolutionary pressures on ribosomal protein genes toward the efficient assembly of ribosomes. Our observations caution those who study genomics and phylogeny of uncultivated microbes, the diversity and evolution of microbial genes in the central dogma, and bioinformatics in metagenomics.

  
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• Anaeromyxobacter oryzae sp. nov., Anaeromyxobacter diazotrophicus sp. nov. and Anaeromyxobacter paludicola sp. nov., isolated from paddy soils
  Hideomi Itoh; Zhenxing Xu; Kazumori Mise; Yoko Masuda; Natsumi Ushijima; Chie Hayakawa; Yutaka Shiratori; Keishi Senoo
  Microbiology Society, 03 Oct. 2022
  Scientific journal, Three bacterial strains (Red232^T, Red267^T and Red630^T) were isolated from paddy soils sampled in Japan. Cells of these strains were Gram-stain-negative, facultative anaerobic, long rod-shaped with monotrichous flagella or pilus-like structures for motility, and formed red colonies on agar plates. Phylogenetic trees based on 16S rRNA gene and multiple single-copy gene sequences showed that the three strains formed a cluster with the type strains of Anaeromyxobacter species, independent from any other strain genera. Similarity values of the 16S rRNA gene sequences and genomes among the three isolated strains and the type strain of Anaeromyxobacter, Anaeromyxobacter dehalogenans 2CP-1^T, were 95.4–97.4% for 16S rRNA gene sequence, 75.3–79.5% for average nucleotide identity, 19.6–21.7% for digital DNA–DNA hybridization and 64.1–72.6% for average amino acid identity, all of which are below the species delineation thresholds. Nitrogenase genes were observed in the genomes of the three novel strains, but not in A. dehalogenans 2CP-1^T. Moreover, multiple genomic, physiological and chemotaxonomic features supported the discrimination between these three strains. Based on the evidence in this study, the three isolates represent three novel independent species for which the following names are proposed: Anaeromyxobacter oryzae sp. nov., Anaeromyxobacter diazotrophicus sp. nov. and Anaeromyxobacter paludicola sp. nov. The type strains are Red232^T (=NBRC 114074^T=MCCC 1K03954^T), Red267^T (=NBRC 114075^T=MCCC 1K04211^T), and Red630^T (=NBRC 114076^T=MCCC 1K03957^T), respectively.
• Undervalued Pseudo-nifH Sequences in Public Databases Distort Metagenomic Insights into Biological Nitrogen Fixers
  Kazumori Mise; Yoko Masuda; Keishi Senoo; Hideomi Itoh
  American Society for Microbiology, 22 Dec. 2021, [Lead author, Corresponding author]
  Scientific journal, Nitrogen-fixing microbes affect biogeochemical cycling, agricultural productivity, and microbial ecosystems, and their distributions have been investigated intensively using genomic and metagenomic sequencing. Currently, insights into nitrogen fixers in the environment have been acquired by homology searches against nitrogenase genes, particularly the nifH gene, in public databases.

  
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• Environmental Atlas of Prokaryotes Enables Powerful and Intuitive Habitat-Based Analysis of Community Structures
  Kazumori Mise; Wataru Iwasaki
  Elsevier BV, Oct. 2020, [Lead author]
  Scientific journal
• Invention of Artificial Rice Field Soil: A Tool to Study the Effect of Soil Components on the Activity and Community of Microorganisms Involved in Anaerobic Organic Matter Decomposition
  Yu Maeda; Kazumori Mise; Wataru Iwasaki; Akira Watanabe; Susumu Asakawa; Rasit Asiloglu; Jun Murase
  Japanese Society of Microbial Ecology, Sep. 2020
  Scientific journal
• Eukaryotic Microbial Communities in Japanese Arable Andisols Investigated by Amplicon Sequencing of 18S rRNA Genes
  Kazumori Mise; Shigeto Otsuka
  American Society for Microbiology, 04 Jun. 2020, [Lead author, Corresponding author]
  Scientific journal, Compared with the well-studied soil prokaryotic communities, little is known about soil eukaryotic communities. Here, we investigated the eukaryotic community structures in 43 arable soils using amplicon sequencing of 18S rRNA genes. Major taxonomic groups, such as Fungi, Holozoa, and Stramenopiles, were detected in all samples.
• Pectin drives microbial phosphorus solubilization in soil: Evidence from isolation-based and community-scale approaches
  Kazumori Mise; Yuki Koyama; Arisa Matsumoto; Kazuki Fujita; Takashi Kunito; Keishi Senoo; Shigeto Otsuka
  Elsevier BV, Mar. 2020, [Lead author, Corresponding author]
  Scientific journal
• Time-series analysis of phosphorus-depleted microbial communities in carbon/nitrogen-amended soils
  Kazumori Mise; Runa Maruyama; Yuichi Miyabara; Takashi Kunito; Keishi Senoo; Shigeto Otsuka
  Jan. 2020, [Lead author, Corresponding author]
  Scientific journal
• Microorganisms enhancing phosphorus availability in arable soils
  Takashi Kunito; Hitoshi Moro; Kazuki Fujita; Kazumori Mise; Kazunari Nagaoka; Shigeto Otsuka
  Oct. 2019
  Japanese, Scientific journal
• Prokaryotic Community Structure of Long-Term Fertilization Field Andisols in Central Japan
  Kazumori Mise; Hitoshi Moro; Takashi Kunito; Keishi Senoo; Shigeto Otsuka
  17 Jan. 2019, [Lead author, Corresponding author]
  Scientific journal
• Phosphorus-mineralizing Communities Reflect Nutrient-Rich Characteristics in Japanese Arable Andisols
  Kazumori Mise; Kazuki Fujita; Takashi Kunito; Keishi Senoo; Shigeto Otsuka
  2018, [Lead author]
  Scientific journal

• Society of Genome Microbiology, Japan
• Japanese Society for Bioinformatics
• Japanese Society of Microbial Ecology
• Ecological Society of Japan
• Japanese Society of Soil Microbiology
• Japanese Society of Soil Science and Plant Nutrition