研究業績

微生物生態工学研究チーム

論文（2020年以降）

2025

  1. Yuliar Y*, Tomita S, Hishinuma H, Yokota K. Involvement of iturin and surfactin in inhibition of a post-harvest fungal pathogen on green bell pepper. J. Plant. Protect. Res. (2025), Online ahead of print
  2. Isshiki R, Kuroda K, Tokizawa R, Shiiba C, Hino S, Yamano N, Tamaki H, Nakayama A, Narihiro T, Yamamoto K*.Draft genome sequences of six bacterial strains degrading the biodegradable plastic polyhydroxybutyrate (PHB). Microbiol Resour Announc (2025):e00105-25.DOI:10.1128/mra.00105-25
  3. Shayan MNM, Onodera T, Hirano R, Kuroda K, Narihiro T, Nakaya Y, Satoh H. Effects of snowmelt runoff on bacterial communities and antimicrobial resistance gene concentrations in an urban river in a cold climate region. Environ Sci Pollut Res Int. (2025)32(12):7641-7650. DOI: 10.1007/s11356-025-36168-y.
  4. Nakajima M, Nakai R, Hirakata Y, Kubota K, Satoh H, Nobu MK*, Narihiro T*, Kuroda K*. Minisyncoccus archaeiphilus gen. nov., sp. nov., a mesophilic, obligate parasitic bacterium and proposal of Minisyncoccaceae fam. nov., Minisyncoccales ord. nov., Minisyncoccia class. nov. and Minisyncoccota phyl. nov. formerly referred to as Candidatus Patescibacteria or candidate phyla radiation. Int J Syst Evol Microbiol. (2025) 75(2). DOI: 10.1099/ijsem.0.006668.
  5. Kuroda K*, Yamamoto K, Isshiki R, Tokizawa R, Shiiba C, Hino S, Yamano N, Usui E, Miyakawa T, Miura T, Kamino K, Tamaki H, Nakayama A*, Narihiro T*. Metagenomic and metatranscriptomic analyses reveal uncharted microbial constituents responsible for polyhydroxybutyrate biodegradation in coastal waters. J Hazard Mater. (2025) 13;487:137202. DOI: 10.1016/j.jhazmat.2025.137202.

2024

  1. Kurashita H, Hatamoto M, Tomita S, Yamaguchi T, Narihiro T*, Kuroda K*. Comprehensive Insights into Potential Metabolic Functions of Myxococcota in Activated Sludge Systems. Microbes Environ. (2024) 39(4). DOI: 10.1264/jsme2.ME24068.
  2. Fujii N, Kuroda K, Narihiro T, Aoi Y, Ozaki N, Ohashi A, Kindaichi T. Unique episymbiotic relationship between Candidatus Patescibacteria and Zoogloea in activated sludge flocs at a municipal wastewater treatment plant. Environ Microbiol Rep. (2024) 16(5):e70007. DOI: 10.1111/1758-2229.70007.
  3. Tomita S*, Nakai R, Kuroda K, Kurashita H, Hatamoto M, Yamaguchi T, Narihiro T*. Corallococcus caeni sp. nov., a novel myxobacterium isolated from activated sludge. Arch Microbiol. 21;206(7):317 (2024) DOI: 10.1007/s00203-024-04037-w.
  4. Takeuchi M, Fujiwara-Nagata E(equally contributed 1st author), Kuroda K, Sakata K, Narihiro T*, Kikuchi J*. Fecal metagenomic and metabolomic analyses reveal non-invasive biomarkers of Flavobacterium psychrophilum infection in ayu (Plecoglossus altivelis). mSphere 0:e00301-24. (2024) DOI:10.1128/msphere.00301-24
  5. Kuroda K*, Takai M, Sekiguchi T, IkarashiT, Kurashita H, Nakajima M, Nobu MK, Hatamoto M, Yamaguchi T, Nakaya Y, Satoh H, Yamauchi M, Yamada M, Narihiro T*. Development of an internal two-stage upflow anaerobic reactor integrating biostimulation strategies to enhance the degradation of aromatic compounds in wastewater from purified terephthalic acid and dimethyl terephthalate manufacturing processes. Water Res, 121762-121762 (2024). DOI: 10.1016/j.watres.2024.121762
  6. Fujiwara-Nagata E*, Nakase G, Kuroda K, Narihiro T, Eguchi M. Early prediction of environmental deterioration in a coastal fish farming area using lactic acid bacteria as an indicator. Fish Sci 90, 505–517.(2024). DOI:10.1007/s12562-024-01756-3
  7. Kuroda K*, Nakajima M (equally contributed 1st author), Nakai R, Hirakata Y, Kagemasa S, Kubota K, Noguchi T. Q. P, Yamamoto K, Satoh H, Nobu M. K, Narihiro T*. Microscopic and metatranscriptomic analyses revealed unique cross-domain parasitism between phylum Candidatus Patescibacteria/candidate phyla radiation and methanogenic archaea in anaerobic ecosystems. mBio, 15(3), e0310223. (2024). DOI:10.1128/mbio.03102-23
  8. Kuroda K*, Maeda R, Shinshima F, Urasaki K, Kubota K, Nobu MK, Noguchi TQP, Satoh H, Yamauchi M, Narihiro T*, Yamada M*. : Microbiological insights into anaerobic phenol degradation mechanisms and bulking phenomenon in a mesophilic upflow anaerobic sludge blanket reactor in long-term operation. Water Res. 1;253:121271. (2024). DOI:10.1016/j.watres.2024.121271
  9. Tomita S*, Nakai R, Kuroda K, Kurashita H, Hatamoto M, Yamaguchi T, Narihiro T*. Draft genome sequences of Corallococcus strains KH5-1 and NO1, isolated from activated sludge. Microbiol Resour Announc 13:e01104-23. (2024). DOI:10.1128/mra.01104-23
  10. Isshiki R, Fujitani H, Tsuneda S*. Variation in growth rates between cultures hinders the cultivation of ammonia-oxidizing bacteria. FEMS Microbiol Lett. 9;371:fnae013.(2024).　DOI:10.1093/femsle/fnae013

2023

  1. Tomita S*, Kuroda K, Narihiro T*. : A small step to discover candidate biological control agents from preexisting bioresources by using novel nonribosomal peptide synthetases hidden in activated sludge metagenomes. PLoS One, 27;18(11):e0294843(2023). DOI:10.1371/journal.pone.0294843
  2. Maeda R, Ohike T, Ebe S, Noguchi TQP, Tomita S, Narihiro T*, Kuroda K*.: Green tuff supplementation improves plant growth and microbial interactions of soil aggregates and rhizosphere in cherry tomato (Solanum lycopersicum L. var. cerasiforme) cultivation. Rhizosphere, 28:100801 (2023). DOI:10.1016/j.rhisph.2023.100801.
  3. Kuroda K*, Tomita S, Kurashita H, Hatamoto M, Yamaguchi T, Hori T, Aoyagi T, Sato Y, Inaba T, Habe H, Tamaki H, Hagihara Y, Tamura T, Narihiro T*.: Metabolic implications for predatory and parasitic bacterial lineages in activated sludge wastewater treatment systems. Water Res. X, 20:100196 (2023). DOI:10.1016/j.wroa.2023.100196.
  4. Nakakubo K, Kariyazono K, Watari T, Yagi F, Kuroda K, Yamada M, Yamaguchi T, Yamauchi M*.: A novel cultivation method for growing oyster mushrooms with low potassium content using brewer’s grain, an agro-waste. Environ. Technol. Innov., 32:103240 (2023). DOI:10.1016/j.eti.2023.103240.
  5. Kuroda K*, Katahira T, Yamada M, Uezono I, Nakamura N, Yamaguchi T, Yamauchi M*.: Co-composting of sewage sludge with plant biomass, and analysis of microbiome relevant to plant growth promotion. Bioresour Technol Rep, 22:101401 (2023). DOI:10.1016/j.biteb.2023.101401.

2022

  1. Kuroda K*, Kubota K, Kagemasa S, Nakai R, Hirakata Y, Yamamoto K, Nobu MK, Narihiro T*.: Novel cross-domain symbiosis between Candidatus Patescibacteria and hydrogenotrophic methanogenic archaea Methanospirillum discovered in a methanogenic ecosystem. Microbes Environ, 37(4):ME22063 (2022). DOI:10.1264/jsme2.ME22063.
  2. Kuroda K*, Yamamoto K, Nakai R, Hirakata Y, Kubota K, Nobu MK*, Narihiro T* (*Co-corresponding Author).: Symbiosis between Candidatus Patescibacteria and Archaea discovered in wastewater-treating bioreactors. mBio, 13(5):e0171122 (2022), DOI:10.1128/mbio.01711-22.
  3. Kuroda K*, Narihiro T*, Nakaya Y, Noguchi TQP, Maeda R, Nobu MK, Ohnishi Y, Kumaki Y, Aizawa T, Satoh H. Elucidation of the biodegradation pathways of bis(2-hydroxyethyl) terephthalate and dimethyl terephthalate under anaerobic conditions revealed by enrichment culture and microbiome analysis. Chem Eng J, 450(1): 137916 (2022). DOI:10.1016/j.cej.2022.137916.
  4. Maharjan N, Kuroda K, Silwal G, Toyama S, Ominato Y, Tsuchida Y, Araki N, Yamaguchi T, Ichitsubo M.: Implementation of design based learning for the development of SDGs educational games. J Technol and Sci Educ, 12(2): 496-509 (2022). DOI:10.3926/jotse.1578.
  5. Fujii N, Kuroda K, Narihiro T, Aoi Y, Ozaki N, Ohashi A, Kindaichi T.: Metabolic potential of the superphylum Patescibacteria reconstructed from activated sludge samples from a municipal wastewater treatment plant. Microbes Environ, 37(3): ME22012 (2022). DOI:10.1264/jsme2.ME22012.
  6. Oshiki M*, Netsu H*, Kuroda K*(equally contributed 1st author), Narihiro T, Fujii N, Kindaichi T, Suzuki Y, Watari T, Hatamoto M, Yamaguchi T, Araki N, Okabe S (*equal contribution).: Growth of nitrite-oxidizing Nitrospira and ammonia-oxidizing Nitrosomonas in marine recirculating trickling biofilter reactors. Environ Microbiol, 24(8): 3735-3750 (2022). DOI:10.1111/1462-2920.16085.
  7. Kagemasa S, Kuroda K, Nakai R, Li YY, Kubota K*: Diversity of Candidatus Patescibacteria in activated sludge revealed by a size-fractionation approach. Microbes Environ, 37(2): ME22027 (2022). DOI:10.1264/jsme2.ME22027.
  8. Kuroda K*, Narihiro T*, Shinshima F, Yoshida M, Yamaguchi H, Kurashita H, Nakahara N, Nobu MK, Noguchi TQP, Yamauchi M, Yamada M. (*Co-corresponding Author): High-rate cotreatment of purified terephthalate and dimethyl terephthalate manufacturing wastewater by a mesophilic upflow anaerobic sludge blanket reactor and the microbial ecology relevant to aromatic compound degradation. Water Res, 219: 118581 (2022). DOI:10.1016/j.watres.2022.118581.

2021

  1. Kurashita H, Kuroda K*(equally contributed 1st author), Maki S, Sato T, Takagi M, Goto M, Kariya T, Hatamoto M, Tomita S, Narihiro T.Chemical and microbial characteristics of blackening disease in lotus (Nelumbo nucifera Gaertn.) caused by Hirschmanniella diversa Sher. Agronomy, 11(12): 2517 (2021). DOI:10.3390/agronomy11122517.
  2. Kuroda K, Kurashita H, Takagi M, Narihiro T, Hatamoto M, Yamaguchi T.: Phylogenetic analyses of the lotus root-parasitic nematodes Hirschmanniella diversa Sher and H. imamuri Sher based on the 18S ribosomal RNA (rRNA) gene and 5.8S rRNA gene/internal transcribed spacer region. Nematol Res., 51: 5-9 (2021).
  3. Kuroda K, Narihiro T, Nobu MK, Tobo A, Yamauchi M, Yamada M.: Ecogenomics reveals microbial metabolic networks in a psychrophilic methanogenic bioreactor treating soy sauce production wastewater. Microbes Environ 36(4) (2021). DOI=10.1264/jsme2.ME21045.
  4. Yamada T, Hamada M, Kurobe M, Narihiro T, Tsuji H, Daimon H.: Complete Genome Sequence of Gelria sp. Strain Kuro-4, a Thermophilic Anaerobe Isolated from a Thermophilic Anaerobic Digestion Reactor Treating Poly (L-Lactic Acid). Microbiol Resour Announc 10 (33), e00544-21. DOI=10.1128/MRA.00544-21.
  5. Kuroda K, Shinshima F, Tokunaga S, Noguchi TQP, Yamauchi M, Nobu MK, Narihiro T, Yamada M.: Assessing the effect of green tuff as novel natural inorganic carrier on methane producing activity of anaerobic sludge microbiome. Environ Technol Innov 24: 101835 (2021). DOI=10.1016/j.eti.2021.101835.
  6. Nakai R, Naganuma T, Tazato N, Kunihiro T, Morohoshi S, Koide T, Kusada H, Tamaki H, Narihiro T. Characterization of Terrihabitans soli gen. nov., sp. nov., a novel 0.2 μm-filterable soil bacterium belonging to a widely distributed lineage of Hyphomicrobiales (Rhizobiales). Diversity 13(9):422 (2021). DOI=10.3390/d13090422.
  7. Tu Z, Lopes, HFS, Narihiro T, Yumoto I.: The mechanism underlying of long-term stable indigo reduction state in indigo fermentation using sukumo (composted Polygonum tinctorium leaves). Front Microbiol. DOI:10.3389/fmicb.2021.698674.
  8. Hosokawa S, Kuroda K, Narihiro T, Aoi Y, Ozaki N, Ohashi A, Kindaichi T.: Cometabolism of the superphylum Patescibacteriawith anammox bacteria in a long-term freshwater anammox column reactor. Water 13(2):208 (2021). DOI:10.3390/w13020208.
  9. Kurashita H, Kuroda K., Narihiro T, Takagi M, Goto M, Ikeda S, Hirakata Y, Hatamoto M, Maki S, Yamaguchi T, Aoi T.: Accurate evaluation of blackening disease in lotus (Nelumbo nucifera Gaertn.) using a quantitative PCR-based assay for Hirschmanniella diversa Sher and H. imamuri Sher. Crop Protection 139 105380 (2021). DOI:10.1016/j.cropro.2020.105380.
  10. Omine T, Kuroda K (equally contributed 1st author), Hatamoto M, Yamaguchi T, Yamauchi M, Yamada M. Reduction of alkalinity supplementation for acid-based wastewater treatment using a thermophilic multi-feed upflow anaerobic sludge blanket reactor. Environ Technol. 27:1-11 (2021). DOI:10.1080/09593330.2019.1620864.

2020

  1. Mei R, Nobu MK, Narihiro T, Liu WT.: Metagenomic and Metatranscriptomic Analyses Revealed Uncultured Bacteroidales Populations as the Dominant Proteolytic Amino Acid Degraders in Anaerobic Digesters. Frontiers in Microbiology 11:593006 (2020). DOI:10.3389/fmicb.2020.593006 .
  2. Quaiyum S, Igarashi K, Narihiro T, Kato S.: Microbial Community Analysis of Anaerobic Enrichment Cultures Supplemented with Bacterial Peptidoglycan as the Sole Substrate. Microbes and Environments. 35:ME20002 (2020). DOI:10.1264/jsme2.ME20002 .
  3. Chen YT, Zeng Y, Li J, Zhao XY, Yi Y, Gou M, Kamagata Y, Narihiro T, Nobu MK, Tang YQ.: Novel syntrophic isovalerate-degrading bacteria and their energetic cooperation with methanogens in methanogenic chemostats. Environmental Science & Technology 54(15):9618-9628 (2020). DOI:10.1021/acs.est.0c01840.
  4. Nobu MK, Narihiro T, Mei R, Kamagata Y, Lee PKH, Lee PH, McInerney MJ, Liu WT: Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses. Microbiome. 8(1):111. (2020). DOI:10.1186/s40168-020-00885-y.
  5. Kuroda K, Kurashita H, Arata T, Miyata A, Kawazoe M, Nobu MK, Narihiro T, Ohike T, Hatamoto M, Maki S, Yamaguchi T: Influence of Green Tuff Fertilizer Application on Soil Microorganisms, Plant Growth, and Soil Chemical Parameters in Green Onion (Allium fistulosum L.) Cultivation. Agronomy, 10: 929 (2020). DOI:10.3390/agronomy10070929.
  6. Wang HZ, Li J, Yi Y, Nobu MK, Narihiro T, Tang YQ: Response to inhibitory conditions of acetate-degrading methanogenic microbial community. Journal of Bioscience and Bioengineering 129 (4), 476-485 (2020). DOI:10.1016/j.jbiosc.2019.10.006.
  7. Chen YT, Zeng Y, Wang HZ, Zheng D, Kamagata Y, Narihiro T, Nobu MK, Tang YQ: Different interspecies electron transfer patterns during mesophilic and thermophilic syntrophic propionate degradation in chemostats. Microb Ecol. (2020).  DOI:10.1007/s00248-020-01485-x.

欧文総説・解説・BOOK CHAPTERS

2020

  1. Ichitsubo M (Ed.), Aburatani H (Ed.), Fujii K, Murayama K, Okada M, Sugihara Y, Kuroda K, Maharjan N, Ichitsubo H, Sumits K, L3 Inc. (Molly JD). Transforming for Sustainability –The guide for your action on the SDG 7 & 9–, Maruzen-Yushodo Co., Ltd., Tokyo, Japan (2020).

邦文総説・解説・論文・書籍・教科書等

2024

  1. 黒田恭平, 成廣隆 (2024). フェノール含有廃水処理の成否を左右する運転条件と微生物群を特定, 環境と測定技術, 一般社団法人日本環境測定分析協会, Vol. 51, No. 12, pp. 3–8.
  2. 黒田恭平, 成廣隆: PET関連物質および原料製造廃水の嫌気的分解微生物の発見, バイオサイエンスとインダストリー(B&I), 一般財団法人バイオインダストリー協会, 82(2), 164–166 (2024).

2023

  1. 黒田恭平, 成廣隆: ショットガンメタゲノム解析の理論と未知微生物へのアプローチ（第6章第2節）, ゲノム編集の最新技術と医薬品・遺伝子治療・農業・水畜産物・有用物質生産への活用, 技術情報協会, 375–386 (2023).
  2. 黒田恭平, 成廣隆, 藤井直樹, 中島芽梨, 景政柊蘭, 中井亮佑, 佐藤久, 久保田健吾, 金田一智規, Candidate phyla radiation (CPR)／Candidatus Patescibacteriaの実態を廃水処理システムの視点から理解する, 日本微生物生態学会誌, 38(1): 2–13, (2023).
  3. 富田駿, 篠原弘亮, 横田健治, Pseudomonas tolaasiiによるきのこの細菌病害に対する生物的防除戦略 -微生物の様々な機能を駆使してきのこを病気から守る- , 化学と生物, 61(3):116-124, (2023).

2022

  1. 片平智仁, 原田隆大, 潟龍平, 上薗一郎, 中村憲知, 山田真義, 黒田恭平, 碇智, 山口隆司, 山内正仁, 新規下水汚泥肥料の量産化技術の開発と茶栽培への適用, 土木学会論文集G (環境) (環境工学研究論文集第59巻), 78(7): 223–231, (2022).

2021

  1. 山内正仁, 原田隆大, 山田真義, 潟龍平, 黒田恭平, 片平智仁, 碇智, 山口隆司: 下水汚泥肥料およびマッシュルーム廃菌床の茶栽培への適用, 土木学会論文集G (環境) (環境工学研究論文集第58巻), 77(7): 161-168(2021).
  2. 横田健治, 富田駿, 篠原弘亮, きのこを褐変化させる毒素tolaasinを解毒する細菌, バイオサイエンスとインダストリー, 79(3):214-215, (2021).

2020

  1. 成廣 隆, NOBU Masaru K., LENG Ling, 玉木 秀幸: ［NiFe］ヒドロゲナーゼ類縁エネルギー保存システムの分子進化, 地学雑誌, 129(6):825-835(2020).
  2. 前田稜太, 川添未裕, 大池達矢, 野口太郎, 幡本将史, 牧慎也, 山口隆司, 黒田恭平: 緑色凝灰岩の加工廃材がミニトマトとニンジンの収量、土壌化学性および土壌微生物性に与える影響評価, 土木学会論文集G (環境) (環境工学研究論文集第56巻) , 76(7), 337–348(2020).
  3. 穐田南海, 蔵下はづき, 島武男, 村田岳, 幡本将史, 山口隆司, 青井透, 黒田恭平. し尿汚泥を利活用した土壌改良資材施用によるカンショ栽培実圃場の細菌・線虫群集構造変化, 土木学会論文集G (環境) (環境工学研究論文集第56巻) , 76(7), 141–148(2020).
  4. 山田真義, 山内正仁, 黒田恭平, 宮原将志, 原田隆大, 園田寛人, 片平智仁, 丁字哲治, 山口隆司. 霧島連山硫黄山噴火に伴う汚濁水が河川環境及び水稲栽培に与える影響調査, 土木学会論文集G (環境) (環境工学研究論文集第56巻) , 76(7), 383–392(2020).

特許

2024

  1. 山内正仁，黒田恭平，佐々木俊郎，碇智. 低カリウムきのこの生産方法，特許第7589937号.

2023

2022