Details of the Researcher

PHOTO

Hiromi Kato
Section
Graduate School of Life Sciences
Job title
Specially Appointed Assistant Professor(Research)
Degree

  • 博士（農学） (Tokyo University of Agriculture and Technology)

Professional Memberships 5

  • 日本土壌微生物学会

  • 環境バイオテクノロジー学会

  • 日本ゲノム微生物学会

  • 日本農芸化学会

  • 日本微生物生態学会

Research Interests 4

  • Bacterial community

  • Bioremediation

  • soil

  • Environmental microbiology

Research Areas 1

  • Life sciences / Plant nutrition, soil science /

Papers 28

  1. Carbon Source Acts as a Deterministic Filter Shaping Microbial Succession and Rare-Abundant Decoupling in Soil Bacterial Communities

    Leonardo Stari, Hiromi Kato, Kouhei Kishida, Yoshiyuki Ohtsubo, Michio Kondoh, Yuji Nagata

    ISME Communications　2026/04/20

    Publisher: Oxford University Press (OUP)

    DOI： 10.1093/ismeco/ycag108 　

    eISSN： 2730-6151

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    Abstract The principles governing microbial community assembly and the interplay between deterministic selection and stochasticity remain central debates in ecology. We investigated how chemically diverse carbon sources act as ecological filters shaping soil bacterial communities. Using replicated microcosms amended with distinct substrates (glucose, succinate, naphthalene, phenanthrene, or γ-HCH) or under starvation, we tracked community trajectories via high-frequency 16S rRNA gene sequencing (29 timepoints, triplicate) and quantitative ecological modeling. Null model analysis confirmed the carbon source as the primary deterministic filter, enforcing high reproducibility (homogeneous selection governing ~74% of assembly among replicates) and overriding stochastic effects. Crucially, abundant (>1%) and rare (<0.1%) taxa exhibited decoupled assembly mechanisms. While abundant taxa were driven largely by dispersal limitation (~59%) and variable selection, the rare biosphere displayed a temporal regime shift. Unlike the immediate response of dominant taxa, rare taxa transitioned from stochastic isolation to strong deterministic selection (surging to ~50%) only during later successional stages. This reframes the rare biosphere as a "latent responder" reservoir recruited by metabolic byproducts rather than the primary substrate. Additionally, time-resolved interaction networks revealed that under severe stress from toxicity or starvation, interactions shifted from competitive exclusion to facilitation (e.g., necromass scavenging). These patterns provide strong empirical support for the Stress Gradient Hypothesis in a microbial context. Collectively, our findings demonstrate how deterministic filtering and stress-mediated cooperation jointly structure ecosystems, providing a high-resolution temporal dataset to further interrogate these fundamental ecological principles.

  2. Directional Colony Growth of Cupriavidus toward Sphingomonads.

    Hiromi Kato, Shoko Hirano, Chiaki Haga, Sayaka Sakogawa, Yoshiyuki Ohtsubo, Yuji Nagata

    Microbes and environments　41　(2)　2026

    DOI： 10.1264/jsme2.ME25087 　

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    Bacterial communities often originate from physical encounters between distinct species on solid surfaces; however, the mechanisms underlying these initial interactions remain unclear. The γ-hexachlorocyclohexane (γ-HCH; a toxic recalcitrant insecticide)-degrading consortium includes the surface-motile bacterium Cupriavidus sp. strain TKC and the γ-HCH-degrading Sphingobium sp. strain TKS. During a co-culture on R2A agar, TKC colonies exhibited directional colony growth (DCG), characterized by asymmetric expansion toward neighboring TKS colonies. When TKC colonies eventually overgrew TKS colonies, non-motile TKS cells were passively carried along the expanding TKC front, indicating that DCG facilitates the physical association and surface dispersal of Sphingobium cells. DCG activity was also observed against various strains of Sphingobium, Sphingomonas, and Novosphingobium, whereas extremely weak or no DCG activity was observed toward other bacterial groups, including representatives of α-, β-, and γ-proteobacteria as well as actinobacteria. These results indicate that TKC exhibits DCG selectively toward sphingomonads, recognizing taxon-specific cues rather than responding indiscriminately to neighboring colonies. Among the components tested, sphingosine reproducibly triggered DCG in a dose-dependent manner, and the inhibition of sphingolipid biosynthesis in Sphingobium with myriocin markedly suppressed the inducing effect. These results highlight the sphingosine-mediated induction of DCG as a molecular mechanism underlying the initial step in the spatial organization of bacterial communities on solid surfaces.

  3. Draft genome sequence of Cupriavidus sp. strain TKC, isolated from a γ-hexachlorocyclohexane-degrading community. International-journal

    Hiromi Kato, Yoshiyuki Ohtsubo, Shoko Hirano, Sachiko Masuda, Arisa Shibata, Ken Shirasu, Yuji Nagata

    Microbiology resource announcements　12　(12)　e0056723　2023/12/14

    DOI： 10.1128/MRA.00567-23 　

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    Cupriavidus sp. strain TKC was isolated from a microbial community enriched with γ-hexachlorocyclohexane (γ-HCH). This strain did not show γ-HCH-degrading activity but was one of the major members of the community. Here, we present the draft genome sequence of the strain TKC with a size of 7 Mb.

  4. 土壌微生物による化学合成農薬分解のフロンティア Invited Peer-reviewed

    永田裕二, 加藤広海, 大坪嘉行

    農薬学会誌　48　(2)　125-131　2023/08

    DOI： 10.1584/jpestics.W23-22 　

  5. Reconstruction of a Soil Microbial Network Induced by Stress Temperature Peer-reviewed

    Dailin Yang, Hiromi Kato, Kazutaka Kawatsu, Yutaka Osada, Toyohiro Azuma, Yuji Nagata, Michio Kondoh

    Microbiology Spectrum　10　(5)　2022/10/26

    Publisher: American Society for Microbiology

    DOI： 10.1128/spectrum.02748-22 　

    eISSN： 2165-0497

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    By combining amplicon-based diversity survey with recently developed nonlinear analytical tools, we successfully determined the interaction networks of more than 150 natural soil microbial genera under less or more temperature stress and explored the applicability of the stress gradient hypothesis to soil microbiota, shedding new light on the well-known hypothesis.

  6. CO2 -dependent High-yield Growth of a Heterotrophic Bacterium under Oligotrophic Conditions Invited Peer-reviewed

    Yuji Nagata, Hiromi Kato, Yoshiyuki Ohtsubo

    Journal of Environmental Biotechnology　22　(1)　9-13　2022/06

    DOI： 10.50963/jenvbio.22.1_9 　

  7. Genome evolution related to γ-hexachlorocyclohexane metabolic function in the soil microbial population. International-journal Peer-reviewed

    Hiromi Kato, Lijun Su, Ayami Tanaka, Honami Katsu, Yoshiyuki Ohtsubo, Shigeto Otsuka, Keishi Senoo, Yuji Nagata

    Bioscience, biotechnology, and biochemistry　2022/03/17

    DOI： 10.1093/bbb/zbac042 　

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    γ-Hexachlorocyclohexane (γ-HCH)-degrading strain, Sphingobium sp. TA15, was newly isolated from an experimental field soil from which the archetypal γ-HCH-degrading strain, S. japonicum UT26, was isolated previously. Comparison of the complete genome sequences of these two strains revealed that TA15 shares the same basic genome skeleton with UT26, but also has the variable regions that are presumed to have changed either from UT26 or from a putative common ancestor. Organization and localization of lin genes of TA15 were different with those of UT26. It was inferred that transposition of IS6100 plays a crucial role in these genome rearrangements. The accumulation of toxic dead-end products in TA15 was lower than in UT26, suggesting that TA15 utilizes γ-HCH more effectively than UT26. These results suggested that genome evolution related to the γ-HCH metabolic function in the soil microbial population is ongoing.

  8. Fungal Carbonyl Sulfide Hydrolase of Trichoderma harzianum Strain THIF08 and Its Relationship with Clade D β-Carbonic Anhydrases Peer-reviewed

    Yoshihito Masaki, Ryuka Iizuka, Hiromi Kato, Yuka Kojima, Takahiro Ogawa, Makoto Yoshida, Yasuhiko Matsushita, Yoko Katayama

    Microbes and Environments　36　(2)　ME20058-n/a　2021/05

    Publisher: Japanese Society of Microbial Ecology

    DOI： 10.1264/jsme2.me20058 　

    ISSN： 1342-6311

    eISSN： 1347-4405

  9. Microbial communities developing within bulk sediments under fish carcasses on a tidal flat Peer-reviewed

    Yasutake Kawamoto, Hiromi Kato, Yuji Nagata, Jotaro Urabe

    PLOS ONE　16　(2)　e0247220-e0247220　2021/02/25

    Publisher: Public Library of Science (PLoS)

    DOI： 10.1371/journal.pone.0247220 　

    eISSN： 1932-6203

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    Animal carcasses are often brought into tidal flats where they are at the boundary between terrestrial and marine ecosystems. Since these carcasses act as microhabitats with large amounts of energy and nutrients, they likely develop unique bacterial assemblages in the ambient sediment, which in turn may stimulate colonization of other organisms such as protozoans. However, little is known about the microbial assemblages colonized in sediment around animal carcasses in the tidal zone. Herein we examined the bacterial and ciliophoran assemblages developed in association with fish carcasses by incubating the carcasses in the Higashiyachi tidal flat (Sendai, Japan). We collected sediment samples at 2, 9, and 42 days of incubation and analyzed the bacterial and ciliophoran assemblages by 16S and 18S rRNA gene amplicon sequencing. We observed significant differences in the composition and relative abundance of bacterial and ciliophoran operational taxonomic units (OTUs) between the sediments with and without the carcasses. Our analyses suggest that these unique assemblages were created through the direct effects of the carcass and indirect effects through interactions between bacteria and ciliophorans. These results also suggest that animal carcasses developed a temporally unique microbial food web in the sediments close to the carcasses, although it disappeared for several weeks.

  10. Expression of an alcohol dehydrogenase gene in a heterotrophic bacterium induces carbon dioxide-dependent high-yield growth under oligotrophic conditions. International-journal Peer-reviewed

    Shinnosuke Inaba, Hironori Sakai, Hiromi Kato, Takayuki Horiuchi, Hirokazu Yano, Yoshiyuki Ohtsubo, Masataka Tsuda, Yuji Nagata

    Microbiology (Reading, England)　166　(6)　531-545　2020/04/20

    DOI： 10.1099/mic.0.000908 　

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    Sphingobium japonicum strain UT26, whose γ-hexachlorocyclohexane-degrading ability has been studied in detail, is a typical aerobic and heterotrophic bacterium that needs organic carbon sources for its growth, and cannot grow on a minimal salt agar medium prepared without adding any organic carbon sources. Here, we isolated a mutant of UT26 with the ability to grow to visible state on such an oligotrophic medium from a transposon-induced mutant library. This high-yield growth under oligotrophic conditions (HYGO) phenotype was CO2-dependent and accompanied with CO2 incorporation. In the HYGO mutant, a transposon was inserted just upstream of the putative Zn-dependent alcohol dehydrogenase (ADH) gene (adhX) so that the adhX gene was constitutively expressed, probably by the transposon-derived promoter. The adhX-deletion mutant (UT26DAX) harbouring a plasmid carrying the adhX gene under the control of a constitutive promoter exhibited the HYGO phenotype. Moreover, the HYGO mutants spontaneously emerged among the UT26-derived hypermutator strain cells, and adhX was highly expressed in these HYGO mutants, while no HYGO mutant appeared among UT26DAX-derived hypermutator strain cells, indicating the necessity of adhX for the HYGO phenotype. His-tagged AdhX that was expressed in Escherichia coli and purified to homogeneity showed ADH activity towards methanol and other alcohols. Mutagenesis analysis of the adhX gene indicated a correlation between the ADH activity and the HYGO phenotype. These results demonstrated that the constitutive expression of an adhX-encoding protein with ADH activity in UT26 leads to the CO2-dependent HYGO phenotype. Identical or nearly identical adhX orthologues were found in other sphingomonad strains, and most of them were located on plasmids, suggesting that the adhX-mediated HYGO phenotype may be an important adaptation strategy to oligotrophic environments among sphingomonads.

  11. Enumeration of Chemoorganotrophic Carbonyl Sulfide (COS)-degrading Microorganisms by the Most Probable Number Method Peer-reviewed

    Hiromi Kato, Takahiro Ogawa, Hiroyuki Ohta, Yoko Katayama

    Microbes and Environments　35　(2)　ME19139-n/a　2020/04

    Publisher: Japanese Society of Microbial Ecology

    DOI： 10.1264/jsme2.me19139 　

    ISSN： 1342-6311

    eISSN： 1347-4405

  12. Lessons from the genomes of lindane-degrading sphingomonads. International-journal Invited Peer-reviewed

    Nagata Y, Kato H, Ohtsubo Y, Tsuda M

    Environmental microbiology reports　11　(5)　630-644　2019/10

    DOI： 10.1111/1758-2229.12762 　

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    Bacterial strains capable of degrading man-made xenobiotic compounds are good materials to study bacterial evolution towards new metabolic functions. Lindane (γ-hexachlorocyclohexane, γ-HCH, or γ-BHC) is an especially good target compound for the purpose, because it is relatively recalcitrant but can be degraded by a limited range of bacterial strains. A comparison of the complete genome sequences of lindane-degrading sphingomonad strains clearly demonstrated that (i) lindane-degrading strains emerged from a number of different ancestral hosts that have recruited lin genes encoding enzymes that are able to channel lindane to central metabolites, (ii) in sphingomonads lin genes have been acquired by horizontal gene transfer mediated by different plasmids and in which IS6100 plays a role in recruitment and distribution of genes, and (iii) IS6100 plays a role in dynamic genome rearrangements providing genetic diversity to different strains and ability to evolve to other states. Lindane-degrading bacteria whose genomes change so easily and quickly are also fascinating starting materials for tracing the bacterial evolution process experimentally in a relatively short time period. As the origin of the specific lin genes remains a mystery, such genes will be useful probes for exploring the cryptic 'gene pool' available to bacteria.

  13. Suppression of substrate inhibition in phenanthrene-degrading Mycobacterium by co-cultivation with a non-degrading Burkholderia strain. Peer-reviewed

    Ogawa N, Kato H, Kishida K, Ichihashi E, Ishige T, Yoshikawa H, Nagata Y, Ohtsubo Y, Tsuda M

    165　(5)　625-637　2019/06

  14. Establishment of plasmid vector and allelic exchange mutagenesis systems in a mycobacterial strain that is able to degrade polycyclic aromatic hydrocarbon. International-journal Peer-reviewed

    Kouhei Kishida, Natsumi Ogawa, Eikichi Ichihashi, Hiromi Kato, Yuji Nagata, Yoshiyuki Ohtsubo, Masataka Tsuda

    Bioscience, biotechnology, and biochemistry　82　(7)　1169-1171　2018/07

    DOI： 10.1080/09168451.2018.1445522 　

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    Plasmid vector and allelic exchange mutagenesis systems were established for the genetic analysis of a phenanthrene-degrading mycobacterial strain, Mycobacterium sp. EPa45. Successful application of these systems revealed the necessity of the EPa45 phdI gene for the degradation of 1-hydroxy-2-naphthoate, which has been proposed to be an intermediate product in the degradation pathway of phenanthrene.

  15. Isotopic Fractionation of Sulfur in Carbonyl Sulfide by Carbonyl Sulfide Hydrolase of Thiobacillus thioparus THI115 Peer-reviewed

    Takahiro Ogawa, Shohei Hattori, Kazuki Kamezaki, Hiromi Kato, Naohiro Yoshida, Yoko Katayama

    MICROBES AND ENVIRONMENTS　32　(4)　367-375　2017/12

    DOI： 10.1264/jsme2.ME17130 　

    ISSN： 1342-6311

  16. Comparison of the complete genome sequences of four gamma-hexachlorocyclohexane-degrading bacterial strains: insights into the evolution of bacteria able to degrade a recalcitrant man-made pesticide Peer-reviewed

    Michiro Tabata, Satoshi Ohhata, Yuki Nikawadori, Kouhei Kishida, Takuya Sato, Toru Kawasumi, Hiromi Kato, Yoshiyuki Ohtsubo, Masataka Tsuda, Yuji Nagata

    DNA RESEARCH　23　(6)　581-599　2016/12

    DOI： 10.1093/dnares/dsw041 　

    ISSN： 1340-2838

    eISSN： 1756-1663

  17. Degradation of carbonyl sulfide by Actinomycetes and detection of clade D of beta-class carbonic anhydrase Peer-reviewed

    Takahiro Ogawa, Hiromi Kato, Mitsuru Higashide, Mami Nishimiya, Yoko Katayama

    FEMS MICROBIOLOGY LETTERS　363　(19)　fnw223　2016/10

    DOI： 10.1093/femsle/fnw223 　

    ISSN： 0378-1097

    eISSN： 1574-6968

  18. Complete genome sequence of Burkholderia caribensis Bcrs1W (NBRC110739), a strain co-residing with phenanthrene degrader Mycobacterium sp EPa45 Peer-reviewed

    Yoshiyuki Ohtsubo, Shouta Nonoyama, Natsumi Ogawa, Hiromi Kato, Yuji Nagata, Masataka Tsuda

    JOURNAL OF BIOTECHNOLOGY　228　67-68　2016/06

    DOI： 10.1016/j.jbiotec.2016.04.042 　

    ISSN： 0168-1656

    eISSN： 1873-4863

  19. Sulfur Isotopic Fractionation of Carbonyl Sulfide during Degradation by Soil Bacteria Peer-reviewed

    Kazuki Kamezaki, Shohei Hattori, Takahiro Ogawa, Sakae Toyoda, Hiromi Kato, Yoko Katayama, Naohiro Yoshida

    ENVIRONMENTAL SCIENCE & TECHNOLOGY　50　(7)　3537-3544　2016/04

    DOI： 10.1021/acs.est.5b05325 　

    ISSN： 0013-936X

    eISSN： 1520-5851

  20. Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance Peer-reviewed

    Hiromi Kato, Hiroshi Mori, Fumito Maruyama, Atsushi Toyoda, Kenshiro Oshima, Ryo Endo, Genki Fuchu, Masatoshi Miyakoshi, Ayumi Dozono, Yoshiyuki Ohtsubo, Yuji Nagata, Masahira Hattori, Asao Fujiyama, Ken Kurokawa, Masataka Tsuda

    DNA RESEARCH　22　(6)　413-424　2015/12

    DOI： 10.1093/dnares/dsv023 　

    ISSN： 1340-2838

    eISSN： 1756-1663

  21. Isolation of oxygenase genes for indigo-forming activity from an artificially polluted soil metagenome by functional screening using Pseudomonas putida strains as hosts Peer-reviewed

    Hirofumi Nagayama, Tomonori Sugawara, Ryo Endo, Akira Ono, Hiromi Kato, Yoshiyuki Ohtsubo, Yuji Nagata, Masataka Tsuda

    APPLIED MICROBIOLOGY AND BIOTECHNOLOGY　99　(10)　4453-4470　2015/05

    DOI： 10.1007/s00253-014-6322-2 　

    ISSN： 0175-7598

    eISSN： 1432-0614

  22. Complete genome sequence of a phenanthrene degrader, Mycobacterium sp. strain EPa45 (NBRC 110737), isolated from a phenanthrene-degrading consortium Peer-reviewed

    Hiromi Kato, Natsumi Ogawa, Yoshiyuki Ohtsubo, Kenshiro Oshima, Atsushi Toyoda, Hiroshi Mori, Yuji Nagata, Ken Kurokawa, Masahira Hattori, Asao Fujiyama, Masataka Tsuda

    Genome Announcements　3　(4)　e00782-15　2015

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.00782-15 　

    ISSN： 2169-8287

  23. Complete genome sequence of a phenanthrene degrader, Burkholderia sp. HB-1 (NBRC 110738) Peer-reviewed

    Yoshiyuki Ohtsubo, Azusa Moriya, Hiromi Kato, Natsumi Ogawa, Yuji Nagata, Masataka Tsuda

    Genome Announcements　3　(6)　e01283-15　2015

    Publisher: American Society for Microbiology

    DOI： 10.1128/genomeA.01283-15 　

    ISSN： 2169-8287

  24. Design and Experimental Application of a Novel Non-Degenerate Universal Primer Set that Amplifies Prokaryotic 16S rRNA Genes with a Low Possibility to Amplify Eukaryotic rRNA Genes Peer-reviewed

    Hiroshi Mori, Fumito Maruyama, Hiromi Kato, Atsushi Toyoda, Ayumi Dozono, Yoshiyuki Ohtsubo, Yuji Nagata, Asao Fujiyama, Masataka Tsuda, Ken Kurokawa

    DNA RESEARCH　21　(2)　217-227　2014/04

    DOI： 10.1093/dnares/dst052 　

    ISSN： 1340-2838

    eISSN： 1756-1663

  25. Carbonyl Sulfide Hydrolase from Thiobacillus thioparus Strain THI115 Is One of the beta-Carbonic Anhydrase Family Enzymes Peer-reviewed

    Takahiro Ogawa, Keiichi Noguchi, Masahiko Saito, Yoshiko Nagahata, Hiromi Kato, Akashi Ohtaki, Hiroshi Nakayama, Naoshi Dohmae, Yasuhiko Matsushita, Masafumi Odaka, Masafumi Yohda, Hiroshi Nyunoya, Yoko Katayama

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY　135　(10)　3818-3825　2013/03

    DOI： 10.1021/ja307735e 　

    ISSN： 0002-7863

  26. Genomic features of Lactococcus lactis IO-1, a lactic acid bacterium that utilizes xylose and produces high levels of L-lactic acid. Peer-reviewed

    Shimizu-Kadota M, Kato H, Shiwa Y, Oshima K, Machii M, Araya-Kojima T, Zendo T, Hattori M, Sonomoto K, Yoshikawa H

    Bioscience, biotechnology, and biochemistry　77　(9)　1804-1808　2013

    Publisher: Japan Society for Bioscience, Biotechnology, and Agrochemistry

    DOI： 10.1271/bbb.130080 　

    ISSN： 0916-8451

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    Lactococcus lactis IO-1 (JCM7638) produces <small>L</small>-lactic acid predominantly when grown at high xylose concentrations, and its utilization is highly desired in the green plastics industry. Therefore it is worthwhile studying its genomic traits. In this study, we focused on (i) genes of possible horizontal transfer derivation (prophages, the nisin-sucrose transposon, and several restriction-modification systems), and (ii) genes for the synthetic pathways of amino acids and vitamins in the IO-1 genome. In view of the results of this analysis, we consider their meanings in strain IO-1.

  27. Vertical Distribution of Carbonyl Sulfide at Mt. Fuji, Japan Peer-reviewed

    Hiromi Kato, Yasuhito Igarashi, Yukiko Dokiya, Yoko Katayama

    WATER AIR AND SOIL POLLUTION　223　(1)　159-167　2012/01

    DOI： 10.1007/s11270-011-0847-0 　

    ISSN： 0049-6979

    eISSN： 1573-2932

  28. Degradation of ambient carbonyl sulfide by Mycobacterium spp. in soil Peer-reviewed

    Hiromi Kato, Masahiko Saito, Yoshiko Nagahata, Yoko Katayama

    MICROBIOLOGY-SGM　154　249-255　2008/01

    DOI： 10.1099/mic.0.2007/011213-0 　

    ISSN： 1350-0872

Show all ︎Show first 5

Misc. 35

  1. Dynamic spectral decomposition of soil microbial community

    長田穣, STARI Leonardo, 加藤広海, 永田裕二, 大坪嘉行, 近藤倫生

    日本生態学会大会講演要旨(Web)　71st　2024

  2. Hitchhiking phenomenon in which Paenibacillus sp.NK-L2 transports an organochlorine pesticide-degrading bacterial strain

    松添華子, 岸田なつみ, 加藤広海, 岸田康平, 大坪嘉行, 永田裕二

    日本農芸化学会大会講演要旨集(Web)　2024　2024

    ISSN： 2186-7976

  3. A mutant of Cupriavidus strain exhibiting thin-colony-expansion phenotype

    平野翔子, XIONG Zhiyu, 加藤広海, 岸田康平, 大坪嘉行, 永田裕二

    日本農芸化学会大会講演要旨集(Web)　2024　2024

    ISSN： 2186-7976

  4. Formation of an organochlorine insecticide-degrading bacterial community by Sphingobium-Cupriavidus strains

    XIONG Zhiyu, 平野翔子, 岸田なつみ, 加藤広海, 岸田康平, 大坪嘉行, 永田裕二

    日本農芸化学会大会講演要旨集(Web)　2024　2024

    ISSN： 2186-7976

  5. Reconstruction of an organochlorine insecticide-degrading bacterial community

    手塚隆博, 岸田なつみ, 加藤広海, 岸田康平, 大坪嘉行, 永田裕二

    日本農芸化学会大会講演要旨集(Web)　2024　2024

    ISSN： 2186-7976

  6. Cupriavidus sp.TKC株におけるThin Colony Expansion表現型の機構解明

    平野翔子, XIONG Zhiyu, 加藤広海, 岸田康平, 大坪嘉行, 永田裕二

    日本微生物生態学会大会(Web)　37th　2024

  7. 非移動性の環境汚染物質分解細菌株が移動性細菌株により運ばれるヒッチハイク現象

    松添華子, 岸田なつみ, 加藤広海, 岸田康平, 大坪嘉行, 永田裕二

    環境バイオテクノロジー学会大会プログラム講演要旨集　2024　2024

  8. γ-HCH分解性Sphingobium属株と非分解性Cupriavidus属株のコミュニティ形成

    ZHIYU Xiong, 平野翔子, 岸田なつみ, 加藤広海, 岸田康平, 大坪嘉行, 永田裕二

    環境バイオテクノロジー学会大会プログラム講演要旨集　2024　2024

  9. 単離細菌株を用いた有機塩素系殺虫剤分解細菌コミュニティの構成原理の解明

    手塚隆博, 加藤広海, 岸田康平, 大坪嘉行, 岸田なつみ, 永田裕二

    環境バイオテクノロジー学会大会プログラム講演要旨集　2024　2024

  10. Cupriavidus sp.TKC株のThin Colony Expansion表現型に関与する推定Histidine Kinase遺伝子の同定

    平野翔子, ZHIYU Xiong, 加藤広海, 岸田康平, 大坪嘉行, 永田裕二

    環境バイオテクノロジー学会大会プログラム講演要旨集　2024　2024

  11. Temperature-Induced Reconstruction of Soil Microbial Networks

    YANG Dailin, AZUMA Toyohiro, KATO Hiromi, NAGATA Yuji, KONDOH Michio

    日本生態学会大会講演要旨(Web)　69th　2022

  12. Rewired Community Networks of Soil Microbiota Induced by Increased Temperature

    YANG Dailin, AZUMA Toyohiro, KATO Hiromi, NAGATA Yuji, KONDOH Michio

    日本生態学会大会講演要旨(Web)　68th　2021

  13. Time series analysis for Microbial Interaction

    東豊浩, 加藤広海, 長田穣, 近藤倫生

    日本生態学会大会講演要旨(Web)　67th　2020

  14. 土壌細菌叢の液体培養系における遷移の動態解析

    東豊浩, 加藤広海, 長田穣, 永田裕二, 近藤倫生

    日本微生物生態学会大会(Web)　33rd　2019

  15. 生態学は生物群集デザインに活用できるか?

    近藤倫生, 東豊浩, 加藤広海, 川津一隆, 長田穣, 永田裕二

    日本生物工学会大会講演要旨集　71st　2019

  16. Mycobacterium sp.EPa45株におけるフェナントレン分解遺伝子群の転写解析

    市橋永吉, 小川なつみ, 加藤広海, 岸田康平, 野々山翔太, 永田裕二, 大坪嘉行, 津田雅孝

    日本ゲノム微生物学会年会要旨集　13th　2019

  17. フェナントレン分解Mycobacterium株の遺伝子破壊系構築とビフェニル分解への転写応答

    市橋永吉, 小川なつみ, 岸田康平, 加藤広海, 永田裕二, 大坪嘉行, 津田雅孝

    日本ゲノム微生物学会年会要旨集　12th　2018

  18. 難分解性芳香族化合物分解コンソーシアム由来の分解細菌Mycobacteirum sp.EPa45株における生育阻害機構

    小川なつみ, 加藤広海, 岸田康平, 市橋永吉, 永田裕二, 大坪嘉行, 津田雅孝

    日本農芸化学会大会講演要旨集(Web)　2018　2018

    ISSN： 2186-7976

  19. 土壌細菌叢のノトバイオロジー

    加藤広海

    アグリバイオ　2　107-109　2018

  20. 汚染物質分解コンソーシアムにおけるキープレイヤーとオーディエンス

    加藤広海, 小川なつみ, 津田雅孝, 永田裕二

    環境バイオテクノロジー学会誌　1　15-20　2018

  21. 土壌細菌叢メタゲノムの時間的変動

    加藤広海, 津田雅孝

    生体の科学　68　(2)　160-164　2017

    Publisher: 金原一郎記念医学医療振興財団 ; 1949-

    DOI： 10.11477/mf.2425200600 　

    ISSN： 0370-9531

  22. 土壌細菌叢の化学的撹乱に対するロバスト性

    加藤広海, 津田雅孝

    化学と生物 今日の話題　55　446-447　2017

    DOI： 10.1271/kagakutoseibutsu.55.446 　

  23. 土壌細菌叢のメタ16S・ショットガンメタゲノム解析

    加藤広海, 津田雅孝

    メタゲノム解析・実験プロトコール-ヒト常在細菌叢から環境メタゲノムまでサンプル調製と解析のコツ-　107-114　2016/12

    Publisher: 羊土社

  24. 土壌微生物のノトバイオロジー

    加藤広海, 森宙史, 永山浩史, 大坪嘉行, 永田裕二, 黒川顕, 津田雅孝

    日本農芸化学会大会講演要旨集(Web)　2016　2016

    ISSN： 2186-7976

  25. 再構築された土壌微生物群集の超長期培養

    加藤広海, 渡来直生, 森宙史, 大坪嘉行, 永田裕二, 黒川顕, 黒川顕, 津田雅孝

    日本微生物生態学会大会(Web)　31st　2016

  26. 移植された土壌微生物の定着過程と,その安定性について

    加藤広海, 森宙史, 丸山史人, 永山浩史, 大坪嘉行, 永田裕二, 黒川顕, 津田雅孝

    日本ゲノム微生物学会年会要旨集　9th　2015

  27. メタゲノム情報を基盤とした土壌細菌コミュニティの解析

    加藤広海, 小川なつみ, 津田雅孝

    日本微生物生態学会和文誌　30　(2)　57-64　2015

    Publisher: Japanese Society of Microbial Ecology

    DOI： 10.20709/jsmeja.30.2_57 　

  28. 土壌微生物の移植メタゲノム

    加藤広海, 森宙史, 丸山史人, 豊田敦, 永山浩史, 大坪嘉行, 永田裕二, 藤山秋佐夫, 黒川顕, 津田雅孝

    日本ゲノム微生物学会年会要旨集　8th　2014

  29. 撹乱に対する土壌微生物のレジリエンス

    加藤広海, 森宙史, 丸山史人, 豊田敦, 堂園亜由美, 大坪嘉行, 永田裕二, 藤山秋佐夫, 黒川顕, 津田雅孝

    日本ゲノム微生物学会年会要旨集　7th　2013

  30. 芳香族化合物汚染土壌における経時的メタゲノムによって明らかになった土壌微生物の適応反応

    加藤広海, 森宙史, 豊田敦, 大坪嘉行, 丸山史人, 堂園亜由美, 永田裕二, 藤山秋佐夫, 黒川顕, 津田雅孝

    日本農芸化学会大会講演要旨集(Web)　2012　2012

    ISSN： 2186-7976

  31. Solexaを用いた土壌メタゲノム解析における情報解析~汚染化に伴う菌叢と代謝遺伝子の変動を追う~

    加藤広海, 豊田敦, 大坪嘉行, 丸山史人, 府中玄樹, 遠藤諒, 森宙史, 堂園亜由美, 宮腰昌利, 永田裕二, 藤山秋佐夫, 黒川顕, 津田雅孝

    日本ゲノム微生物学会年会要旨集　4th　2010

  32. Solexaを用いた土壌メタゲノム解析における情報解析

    森宙史, 加藤広海, 堂園亜由美, 大坪嘉行, 宮腰昌利, 丸山史人, 豊田敦, 藤山秋佐夫, 藤山秋佐夫, 永田裕二, 津田雅孝, 黒川顕

    日本ゲノム微生物学会年会要旨集　4th　2010

  33. 第二世代シークエンサーを用いた土壌汚染に対する微生物遺伝子プールの変動解析,および汚染物質分解酵素遺伝子の取得

    加藤広海, 豊田敦, 大坪嘉行, 丸山史人, 遠藤諒, 府中玄樹, 森宙史, 堂園亜由美, 宮腰昌利, 永田裕二, 藤山秋佐夫, 黒川顕, 津田雅孝

    日本農芸化学会大会講演要旨集　2010　2010

  34. 第二世代シークエンサを用いた,土壌汚染に伴う微生物の適応反応の解析

    加藤広海, 森宙史, 豊田敦, 大坪嘉行, 丸山史人, 府中玄樹, 遠藤諒, 堂園亜由美, 宮腰昌利, 永田裕二, 藤山秋佐夫, 黒川顕, 津田雅孝

    環境バイオテクノロジー学会大会プログラム講演要旨集　40th　2010

  35. 芳香族化合物による土壌撹乱における微生物遺伝子プールの変動

    加藤広海, 大坪嘉行, 永田裕二, 津田雅孝

    環境バイオテクノロジー学会誌　10　(2)　63-70　2010

    Publisher: 環境バイオテクノロジー学会

    ISSN： 1347-1856

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Books and Other Publications 2

  1. NGSアプリケーション メタゲノム解析実験プロトコール

    加藤広海, 津田雅孝

    羊土社　2016

  2. 生態適応科学

    加藤広海, 東北大学生態適応グローバルCOE編

    日経BP社　2013/02

Presentations 8

  1. 土壌細菌叢メタゲノムの時間的変動と細菌間相互作用 Invited

    Kato Hiromi

    第 61 回日本放線菌学会学術講演会　2017/11/16

  2. 利用する：汚染物質分解コンソーシアムにおける非分解菌の役割 Invited

    加藤広海, 小川なつみ, 大坪嘉行, 永田裕二, 津田雅孝

    環境微生物系学会合同大会　2017/08/31

  3. 難分解性有機塩素系殺虫剤の分解細菌コミュニティにおける非分解菌の役割

    2017/03/17

  4. 有機塩素系殺虫剤γ-hexachlorocyclohexane分解コミュニティのメタゲノム解析

    大坪嘉行, 津田雅孝, 永田裕二

    第11回日本ゲノム微生物学会年会　2017/03/02

  5. 再構築された土壌微生物群集の超長期培養 Invited

    加藤広海, 渡来直生, 森宙史, 大坪嘉行, 永田裕二, 黒川顕, 津田雅孝

    日本微生物生態学会 第31回大会　2016/10/22

  6. Robustness of soil microbiome against chemical disturbance International-presentation Invited

    Hiromi Kato, Masataka Tsuda

    The 8th Asian Symposium on Microbial Ecology　2016/09/30

  7. 土壌微生物のノトバイオロジー Invited

    加藤広海

    日本農芸化学会2016年度大会　2016/03/27

  8. 土壌の撹乱によるマイクロバイオームの変動. Invited

    2015/10/05

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Research Projects 5

  1. 土壌微生物機能発揮の鍵となる群集・メタゲノム構造の特定

    近藤 倫生, 川津 一隆, 永田 裕二, 大坪 嘉行, 加藤 広海

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 学術変革領域研究(A)

    Institution: 東北大学

    2021/09/10 - 2026/03/31

  2. Development of practical use of useful bacteria by understanding their behavior in the environment

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (B)

    Institution: Tohoku University

    2019/04/01 - 2022/03/31

  3. Soil-derived bacterial consortium capable of degrading chemical pollutant: interaction between pollutant-degrader and co-residing non-degraders

    Tsuda Masataka

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (B)

    Institution: Tohoku University

    2017/04/01 - 2020/03/31

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    Our previous study has indicated that (i) growth of some environmental bacterial strains capable of degrading phenanthrene (a representative chemical pollutant) is drastically inhibited by this compound, and (ii) such inhibition is significantly suppressed by the co-residence of various phenanthrene-non-degrading bacterial strains. Our present comprehensive analysis of such growth inhibition and its suppression phenomena revealed their details and the mechanisms that govern each phenomenon, consequently providing a novel type of interaction between different bacterial species.

  4. Soil gnotobiology: Microbial transplantation beween soils

    Kato Hiromi

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Young Scientists (B)

    Institution: Tohoku University

    2016/04/01 - 2019/03/31

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    We performed microbial transplantation between the two different types of soil (brown forest soil and andisol) to evaluate effect of physicochemical and microbial factors on microbial community formation in the soils. We showed that higher mixing ratio of andisol resulted in high levels of viable cells and actinomycetes regardless of the parental communities, implying the dominating effect of physicochemical factors on microbial colonization in the soils. Furthermore, we found that dominant bacteria in the initial step of the colonization exhibited the promoting ability of other bacterial growth, implying sequential growth networks among bacteria during the microbial colonization in the soils.

  5. Behavior of environmental bacteria in microbial community and oligotrophic growth state

    Nagata Yuji, KATO HIROMI

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Challenging Exploratory Research

    Institution: Tohoku University

    2016/04/01 - 2018/03/31

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    We studied on behavior of environmental bacteria in microbial community and oligotrophic growth state by using a bacteria degrading recalcitrant organochlorine insecticide and a microbial community from which the bacterial strain was isolated as models. We showed (i) the importance of non-degrading bacterial strains in the community and (ii) the generality of the phenomenon that environmental bacteria can grow on the solid minimal salt medium without addition of any carbon source accompanying CO2 fixation by expression of the alcohol dehydrogenase gene, and obtained a lot of knowledge leading to the elucidation of the mechanisms of these phenomena. A theoretical foundation for the practical application of bacteria in real environments has been established.