研究業績

微生物生態工学研究グループ

論文（2020年以降）

2024

  1. Ishizuka Y, Yamashita R, Itoh H, Matsuura Y, Kikuchi Y, Shimoji H*. A potential risk and management of feces in the queenless ant. Insect. Soc. (2024). DOI:10.1007/s00040-024-00970-7
  2. 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.
  3. Nakai R*, Kusada H, Sassa F, Makino A, Morigasaki S, Hayashi H, Takaya N, Tamaki H*. Roseiterribacter gracilis gen. nov., sp. nov., a novel filterable alphaproteobacterium isolated from soil using a gel-filled microwell array device. PLoS One. 10;19(6):e0304366 (2024) DOI: 10.1371/journal.pone.0304366.
  4. Masuda Y, Mise K (equally contributed 1st author), Xu Z, Zhang Z, Shiratori Y, Senoo K, Itoh H* .Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome. Microbiome 12, 95 (2024) DOI: 10.1186/s40168-024-01812-1
  5. 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
  6. 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
  7. Morigasaki S, Matsui M (equally contributed 1st author), Ohtsu I, Doi Y, Kawano Y, Nakai R, Iwasaki W, Hayashi H, Takaya N*. Temporal and fertilizer-dependent dynamics of soil bacterial communities in buckwheat fields under long-term management. Sci Rep 14, 9896 (2024). DOI: 10.1038/s41598-024-60655-w
  8. Kuwata K*, Sato-Takabe Y*(equally contributed 1st author), Nakai R, Sugimura Y, Tazato N, Kunihiro T, Morohoshi S, Iwataki M, Hamasaki K, Shiozaki T. Novel aerobic anoxygenic phototrophic bacterium Jannaschia pagri sp. nov., isolated from seawater around a fish farm. Antonie van Leeuwenhoek 117, 70 (2024).DOI:10.1007/s10482-024-01971-z
  9. Kanbe H, Sano Y, Mise K, Kanie S, Ushijima N, Kawano K, Kihara M, Itoh H*. Lysinibacillus piscis sp. nov. isolated from the gut of mottled spinefoot Siganus fuscescens. Arch Microbiol. 21;206(5):228.(2024). DOI:10.1007/s00203-024-03937-1
  10. Kunito T*, Moro H, Mise K, Sawada K, Otsuka S, Nagaoka K, Fujita K. Ecoenzymatic stoichiometry as a temporally integrated indicator of nutrient availability in soils. Soil Science and Plant Nutrition, 1–24.(2024). DOI:10.1080/00380768.2024.2341669
  11. 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
  12. He Z, Naganuma T*, Nakai R, Uetake J, Hahn MW. Microbiomic Analysis of Bacteria Associated with Rock Tripe Lichens from Alpine Areas in Eastern Alps and Equatorial Africa. Curr Microbiol 81, 115 (2024). DOI:10.1007/s00284-024-03626-8
  13. 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
  14. 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
  15. Nakai R*, Munekawa S, Murai Y, Ohmura Y, Tani K. Diversity profiling of microbiomes associated with selected alpine plants and lichens from Mt. Suisho, Japan. Microbiol Resour Announc 13:e01270-23.(2024). Doi:10.1128/mra.01270-23
  16. Islam MS, Yamamoto K, Morita N, Yumoto I, Kato S, Nakai R*, Igarashi K*. Complete genome sequence of Opitutales bacterium strain ASA1, isolated from soil. Microbiol Resour Announc 13:e01032-23.(2024). DOI:10.1128/mra.01032-23
  17. Azuma S, Kawasuji H, Nakai R (equally contributed 1st author), Yamada H, Yoshida Y, Kawahara H, Suzuki M, Mori S, Hirata M, Sugie K, Niimi H, Morinaga Y*, Yamamoto Y*. The fatal case of “Pigmentibacter” bacteremia following aspiration pneumonia in elderly patient. J Infect Chemother. 2:S1341-321X(24)00028-X.(2024). DOI:10.1016/j.jiac.2024.01.019
  18. 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
  19. 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. Itoh​ H*, Sugisawa Y, Mise K, Xu Z, Kuniyasu M, Ushijima N, Kawano K, Kobayashi E, Shiratori Y, Masuda Y, Senoo K.: 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. Int. J. Syst. Evol. Microbiol., 73:9 (2023). 10.1099/ijsem.0.006073.
  6. Shimada S, Nakai R*, Aoki K, Miura S, Komori K, Kudoh S, Imura S, Ishii Y, Tateda K.: Complete genome sequence of Polynucleobacter sp. strain TUM22923 isolated from Antarctic lake sediment. Microbiology Resource Announcements, 12:7 (2023). DOI:10.1128/mra.00146-23.
  7. Shimada S*, Aoki K, Nakai R, Miura S, Komori K, Kudoh S, Imura S, Ishii Y, Tateda K.: Whole-Genome Sequences of Three Psychrotolerant Mycolicibacterium sp. Strains Isolated from Antarctic Soil. Microbiol. Resour. Announc., 12:6 (2023). DOI:10.1128/mra.00123-23.
  8. 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.
  9. Ishizawa S, Kaji Y, Shimizu Y, Kuroda M, Inoue D, Makino A, Nakai R, Tamaki H, Morikawa M, Ike M.: Spontaneous cell lysis by Pelomonas saccharophila MRB3 provides plant-available macronutrients in hydroponic growth media and accelerates biomass production of duckweed. J Water Environ Technol, 21:49 (2023). DOI:10.2965/jwet.22-054.
  10. Suzuki AC, Sugiura K, Tsujimoto M, Nakai R, McInnes SJ, Kagoshima H, Imura S.: A new species of bisexual Milnesium (Eutardigrada: Apochela) having aberrant claws from Innhovde, Dronning Maud Land, East Antarctica. Zoological Sci, 40 (2023). DOI:10.2108/zs220085.
  11. Nobu MK*, Nakai R*, Tamazawa S, Mori H, Toyoda A, Ijiri A, Suzuki S, Kurokawa K, Kamagata Y, Tamaki H.(*equal contribution): Unique H2-utilizing lithotrophy in serpentinite-hosted systems. ISME J, 17, 95-104 (2023) DOI:10.1038/s41396-022-01197-9.

2022

  1. Mise K*, Iwasaki W*: Unexpected absence of ribosomal protein genes from metagenome-assembled genomes. ISME Commun, 2(1), 118 (2022). DOI:10.1038/s43705-022-00204-6.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. Shen W, Long Y, Qiu Z, Gao N, Masuda Y, Itoh H, Ohba H, Shiratori Y, Rajasecar A, Senoo, K*.. Investigation of rice yields and critical N losses from paddy soil under different N fertilization rates with iron application. Int J Environ Res Public Health, 19(14), 8707 (2022). DOI:10.3390/ijerph19148707.
  11. Itoh H*, Xu Z, Mise K, Masuda Y, Ushijima N, Hayakawa C, Shiratori Y, Senoo, K. Anaeromyxobacter oryzae sp. nov., Anaeromyxobacter diazotrophicus sp. nov. and Anaeromyxobacter paludicola sp. nov., isolated from paddy soils. Int J Syst Evol Microbiol, DOI:10.1099/ijsem.0.005546.
  12. Makino A, Nakai R*(equally contributed 1st author),, Yoneda Y, Toyama T, Tanaka Y, Meng X-Y, Mori K, Ike M, Morikawa M, Kamagata Y, Tamaki H. : Isolation of aquatic plant growth-promoting bacteria for the floating plant duckweed (Lemna minor). Microorganisms, 10:1564 (2022). DOI:10.3390/microorganisms10081564.
  13. He Z, Naganuma T, Nakai R, Imura S, Tsujimoto M, Convey P.: Microbiomic analysis of bacteria associated with rock tripe lichens in continental and maritime Antarctic regions. J Fungi, 8:817, (2022). DOI:10.3390/jof8080817.
  14. Liu Q, He Z(equally contributed 1st author), Naganuma T*, Nakai R, Rodriguez LM, Carreno R, Urbani F. (*equal contribution): Phylotypic diversity of bacteria associated with speleothems of a silicate cave in a Guiana Shield tepui. Microorganisms, 10:1395, (2022). DOI:10.3390/microorganisms10071395.
  15. Suda K, Aze T, Miyairi Y, Yokoyama Y, Matsui Y, Ueda H, Saito T, Sato T, Sawaki Y, Nakai R, Tamaki H, Takahashi H, Morikawa N, Ono S.: The origin of methane in serpentinite-hosted hyperalkaline hot spring at Hakuba Happo, Japan: Radiocarbon, methane isotopologue and noble gas isotope approaches. Earth Planet Sci Lett, 585:117510, (2022). DOI:10.1016/j.epsl.2022.117510.
  16. Ishigami K, Jang S, Itoh H, Kikuchi Y*. Obligate gut symbiotic association with Caballeronia in the mulberry seed bug Paradieuches dissimilis (Lygaeoidea: Rhyparochromidae). Microb Ecol, DOI:10.1007/s00248-022-02117-2.

2021

  1. Shimoji H, Itoh H*, Matsuura Y, Yamashita R, Hori T, Hojo MK, Kikuchi Y.. Worker-dependent gut symbiosis in an ant. (*co-1st and co-corresponding author), ISME Communications, 1(1), 1-10 (2021). DOI:10.1038/s43705-021-00061-9.
  2. Sato Y, Jang S, Takeshita K, Itoh H, Koike H, Tago K, Hayatsu M, Tomoyuki H, Kikuchi Y.. Insecticide resistance by a host-symbiont reciprocal detoxification. Nature communications, 12(1), 1-8 (2021). DOI:10.1038/s41467-021-26649-2.
  3. Mise K, Masuda Y, Senoo K, Itoh H. Undervalued pseudo-nifH sequences in public databases distort metagenomic insights into biological nitrogen fixers. mSphere, 6(6), e00785-21 (2021). DOI:10.1128/msphere.00785-21.
  4. 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.
  5. Shimada S, Nakai R(equally contributed 1st author),, Aoki K, Kudoh S, Imura S, Shimoeda N, Ohno G, Watanabe K, Miyazaki Y, Ishii Y, Tateda K. : Characterization of the First Cultured Psychrotolerant Representative of Legionella from Antarctica Reveals Its Unique Genome Structure. Microbiol Spectr., 9:e00424-21 (2021). DOI=10.1128/Spectrum.00424-21.
  6. 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).
  7. 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.
  8. 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.
  9. 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.
  10. Zhang Z, Xu Z, Masuda Y, Wang X, Ushijima N, Shiratori Y, Senoo K, Itoh H.: Geomesophilobacter sediminis gen. nov., sp. nov., Geomonas propionica sp. nov. and Geomonas anaerohicana sp. nov., three novel members in the family Geobacterecace isolated from river sediment and paddy soil. Syst Appl Microbiol, 44(5), 126233 (2021). DOI=10.1016/j.syapm.2021.126233.
  11. Xu Z, Masuda Y, Wang X, Ushijima N, Shiratori Y, Senoo K, Itoh H.: Genome-based taxonomic rearrangement of the order Geobacterales including the description of Geomonas azotofigens sp. nov. and Geomonas diazotrophica sp. nov.. Front Microbiol, 12:737531 (2021). DOI=10.3389/fmicb.2021.737531.
  12. 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.
  13. Nakai R*, Kusada H*, Sassa F, Morigasaki S, Hayashi H, Takaya N. Tamaki H.(*equal contribution): Draft genome sequence of novel filterable Rhodospirillales bacterium strain TMPK1, isolated from soil. Microbiol Resour Announc, 10:e00393-21 (2021). DOI=10.1128/MRA.00393-21.
  14. Nakai R, Wakana I, Niki H.: Internal microbial zonation during the massive growth of marimo, a lake ball of Aegagropila linnaei in Lake Akan. iScience 24:102720 (2021). DOI:10.1016/j.isci.2021.102720.
  15. 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.
  16. Iwashita T, Tanaka H, Tamaki H, Nakai R, Yoneda Y, Makino A, Toyama T, Kamagata Y, Morikawa M, Mori K.: Isolation and characterization of novel plant growth-promoting bacteria from frond of duckweeds. Jpn. J. Water Treat. Biol. 57:1-9 (2021). DOI:10.2521/jswtb.57.1.
  17. Shimada S, Nakai R, Aoki K, Shimoeda N, Ohno G, Kudoh S, Imura S, Watanabe K, Miyazaki Y, Ishii Y, Tateda K.: Chasing waterborne pathogens in Antarctic human-made and natural environments with special reference to Legionella spp. Appl. Environ. Microbiol. 87:e02247-20 (2021). DOI:10.1128/AEM.02247-20.
  18. Itoh H, Xu Z, Masuda Y, Ushijima N, Hayakawa C, Shiratori Y, Senoo, K.: Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov., isolated from terrestrial environments, and emended description of the genus Geomonas. Int. J. Syst. Evol. Microbiol. 71: 004607 (2021). DOI:10.1099/ijsem.0.004607.
  19. Masuda Y, Shiratori Y, Ohba H, Ishida T, Takano R, Satoh S, Shen W, Nan G, Itoh H, Senoo K.: Enhancement of the nitrogen-fixing activity of paddy soils owing to iron application. Soil Sci. Plant Nutr. (2021). DOI:10.1080/00380768.2021.1888629.
  20. Ishigami K, Jang S, Itoh H, Kikuchi Y.: Insecticide resistance governed by gut symbiosis in a rice pest, Cletus punctiger, under laboratory conditions. Biol. Lett. 17:20200780 (2021). DOI:10.1098/rsbl.2020.0780.
  21. Jang S, Mergaert P, Ohbayashi T, Ishigami K, Shigenobu S, Itoh H, Kikuchi Y.: Dual oxidase enables insect gut symbiosis by mediating respiratory network formation. Proc. Natl. Acad. Sci. U S A 118: e2020922118 (2021). DOI:10.1073/pnas.2020922118.
  22. 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.
  23. 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.
  24. 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. Waite DW, Chuvochina M, Pelikan C, Parks DH, Yilmaz P, Wagner M, Loy A, Naganuma T, Nakai R, Whitman WB, Hahn MW, Kuever J, Hugenholtz P.: Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities. Int. J. Syst. Evol. Microbiol. 70:5972-6016 (2020). DOI:10.1099/ijsem.0.004213.
  4. Nakajima Y, Kojima K, Kashiyama Y, Doi S, Nakai R, Sudo Y, Kogure K, Yoshizawa S: Bacterium lacking a known gene for retinal biosynthesis constructs functional rhodopsins. Microbes Environ. 35: ME20085 (2020). DOI:10.1264/jsme2.ME20085.
  5. 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.
  6. 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.
  7. Nakai R, Naganuma T, Tazato N, Morohoshi S, Koide T.: Cell plasticity and genomic structure of a novel filterable Rhizobiales bacterium that belongs to a widely distributed lineage. Microorganisms, 8(9): 1373 (2020), DOI:10.3390/microorganisms8091373.
  8. 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.
  9. Masuda Y, Yamanaka H, Xu Z, Shiratori Y, Aono T, Amachi S, Senoo K, Itoh H. Diazotrophic Anaeromyxobacter isolated from soils. Appl. Environ. Microbiol. 86:e00956-20(2020). DOI:10.1128/AEM.00956-20.
  10. Kawano K, Ushijima N, Kihara M, Itoh H. Patiriisocius marinistellae gen. nov., sp. nov., isolated from the starfish Patiria pectinifera, and reclassification of Ulvibacter marinus as a member of the genus Patiriisocius comb. nov. Int. J. Syst. Evol. Microbiol. (2020). DOI:10.1099/ijsem.0.004254.
  11. Xu, Z.; Masuda, Y.; Hayakawa, C.; Ushijima, N.; Kawano, K.; Shiratori, Y.; Senoo, K.; Itoh, H. Description of Three Novel Members in the Family Geobacteraceae, Oryzomonas japonicum gen. nov., sp. nov., Oryzomonas sagensis sp. nov., and Oryzomonas ruber sp. nov.. Microorganisms 8:634 (2020). DOI:10.3390/microorganisms8050634.
  12. Shimada S*, Nakai R*, Aoki K, Shimoeda N, Ohno G, Miyazaki Y, Kudoh S, Imura S, Watanabe K, Ishii Y, Tateda K (*equal contribution): Complete genome sequence of novel psychrotolerant Legionella strain TUM19329, isolated from Antarctic lake sediment. Microbiol Resour Announc. 9(16):e00253-20 (2020).  DOI:10.1128/MRA.00253-20.
  13. 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.
  14. 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. Nakai R: Size matters: ultra-small and filterable microorganisms in the environment. Microbes Environ 35(2) (2020) . DOI=10.1264/jsme2.ME20025.
  2. 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: 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).
  2. 中井亮佑, 仁木宏典: マイクロバイオーム解析で明らかとなった巨大マリモの内部の微生物たち, 化学と生物, 60(10): 492-495, (2022).
  3. 河野圭丞, 伊藤英臣: 土壌から獲得した微生物がメダカ腸内の日和見菌の定着を抑制する. 日本土壌微生物学会誌 土と微生物, 76(1):28-29(2022).
  4. 伊藤英臣: 土壌微生物学会への思い. 日本土壌微生物学会誌 土と微生物, 76(1):32-33(2022).
  5. 伊藤英臣: 農耕地の窒素循環と農業害虫に関わる土壌微生物の研究. 日本土壌肥料学会誌 日本土壌学肥料雑誌ー土壌、肥料、植物栄養ー, 93(5)(2022) in press.
  6. 中井亮佑, 草田裕之, 玉木秀幸: 培養技術の革新で迫る未知微生物の実態. 環境バイオテクノロジー学会誌, 22(1): 75-80(2022).
  7. 中井亮佑: 環境ゲノミクス / Environmental genomics、遺伝学の百科事典 -継承と多様性の源-, 分担執筆 (8. 微生物と遺伝学 の一項目を担当), 丸善出版(2022).

2021

  1. 妹尾啓史, 増田曜子, 伊藤英臣, 白鳥豊, 大峽広智, Zhenxing Xu, 山中遥加, 石田敬典, 髙野諒, 佐藤咲良, Shen Weishou. 水田土壌における鉄還元菌窒素固定の学術的基盤解明と低窒素農業への応用 -低炭素社会の実現を目指して. 日本土壌微生物学会誌 土と微生物, 75(2):60-65(2021).
  2. 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).
  3. 中井亮佑: 極地に生きる未知微生物は何者か？, 極限環境生物学会誌, 19, 25-31(2021).
  4. 増田曜子, 伊藤英臣: 土壌圏の新たな微生物生態をあぶり出すメタトランスクリプトーム解析, 北隆館, アグリバイオ, 5(1):13-17(2021).
  5. 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. 戎崎俊一, 西原秀典, 黒川顕, 森宙史, 鎌形洋一, 玉木秀幸, 中井亮佑, 大島拓, 原正彦, 鈴木鉄兵, 丸山茂徳: 原子炉間欠泉に駆動された冥王代原初代謝経路, 地学雑誌, 129(6):779-804(2020).
  2. 中井亮佑, 長沼毅: 微生物の世界に新しい「門」が誕生！ 砂漠で見つけた超すごいやつ、講談社ブルーバックス, 2020.11.17(2020).
  3. 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).
  4. 小西怜生, 重盛俊弥, 田村瑠菜, 伊藤英臣, 菊池義智, 樋口博也: 共生細菌を保持したホソハリカメムシ（カメムシ目：ヘリカメムシ科）の発育零点と有効積算温度から推定した年間世代数、日本応用動物昆虫学会, 日本応用動物昆虫学会誌, 64(3):125-131(2020).
  5. 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).
  6. 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).
  7. 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).
  8. 増田曜子, 伊藤英臣, 白鳥豊, 妹尾啓史. 水田土壌における鉄還元菌窒素固定の発見と応用－マイクロバイオーム解析から低窒素農業へ－, 日本土壌微生物学会誌　土と微生物, 74(1):1-7(2020).
  9. 河野圭丞, 伊藤英臣. 土壌圏最大微生物ダークマター「アシドバクテリア」の単離培養と生態解析. 日本土壌微生物学会誌　土と微生物, 74(1):42(2020).
  10. 増田曜子, 伊藤英臣, 白鳥豊, 妹尾啓史. 水田土壌における鉄還元窒素固定の発見と応用　オミクス解析から低窒素農業へ, 日本農芸化学会誌 化学と生物 58(3):143-150(2020)
  11. 妹尾啓史, 増田曜子, 伊藤英臣, 野田口理孝, 田畑亮, 岡安浩次, 澤井優, 鈴木孝征, 黒谷賢一, 藤雅子, Yuniar Devi Utami, 清水幸子, 西條雄介, 大森良弘, 藤原徹, 白鳥豊, 太田沙由理. 理想の農業を追求する－サステイナブルで革新的な食糧生産を支える基礎研究と現場技術. 日本土壌肥料学会誌 日本土壌学肥料雑誌ー土壌、肥料、植物栄養ー, 91(2):94-98(2020)

特許

2023

  • 木原稔、伊藤英臣、渡辺康之： 魚介類養殖方法、プロバイオティクス細菌液、およびプロバイオティクス細菌含有飼料. 特許第7377478号

2022

  • 伊藤英臣、木原稔： アガリボランス（Agarivorans）属細菌、その変異株である細菌、海藻分解用細菌並びにアガー、アルギン酸、フコイダン、カラギーナン、ペクチン及びキシラン分解用細菌. 特許第7141637号