微生物生態工学研究グループ

成果発表

論文（2015年以降）

2023

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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*(*Co-corresponding authors): 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. (*Co-corresponding Author): 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*, 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*, Yoneda Y, Toyama T, Tanaka Y, Meng X-Y, Mori K, Ike M, Morikawa M, Kamagata Y, Tamaki H. (*equal contribution): 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*, 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. Yamamoto K, Yamamoto N, Ayukawa S, Yasutake Y, Ishiya K, N Nakashima.: Scaffold size-dependent effect on the enhanced uptake of antibiotics and other compounds by Escherichia coli and Pseudomonas aeruginosa. Sci Rep, 12:5609 (2022). DOI:10.1038/s41598-022-09635-6.
  17. 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.
  18. Yamamoto K, Yoneda Y, Makino A, Tanaka Y, Meng XY, Hashimoto J, Shin-Ya K, Satoh N, Fujie M, Toyama T, Mori K, Ike M, Morikawa M, Kamagata Y, Tamaki H.: Complete Genome Sequence of Luteitalea sp. Strain TBR-22. Microbiol Resour Announc. 11(2): e00455-21 (2022). DOI:10.1128/mra.00455-21.
  19. Yamamoto K, Yoneda Y, Makino A, Tanaka Y, Meng XY, Hashimoto J, Shin-Ya K, Satoh N, Fujie M, Toyama T, Mori K, Ike M, Morikawa M, Kamagata Y, Tamaki H.: Draft Genome Sequence of Bryobacteraceae Strain F-183. Microbiol Resour Announc. 11(2): e00453-21 (2022). DOI:10.1128/mra.00453-21.
  20. Ishiya K, Kosaka H, Inaoka T, Kimura K, Nakashima N.,: Comparative genome analysis of three Komagataeibacter strains used for practical production of nata-de-coco. Frontiers in Microbiology, 12:798010 (2022). DOI:10.3389/fmicb.2021.798010.
  21. Ishiya K, Nakashima N.,: Comparative Genome Analysis Reveals Accumulation of Single-Nucleotide Repeats in Pathogenic Escherichia Lineages. Current Issues in Molecular Biology, 44(2) 498-504 (2022). DOI:10.3390/cimb44020034.

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. Ishiya K, Aburatani S.,: Multivariate statistical monitoring system for microbial population dynamics. Physical Biology, 19(1) (2021). DOI:10.1088/1478-3975/ac3ad6.
  5. Kurashita H, Kuroda K, 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.
  6. Shimada S*, Nakai R*, Aoki K, Kudoh S, Imura S, Shimoeda N, Ohno G, Watanabe K, Miyazaki Y, Ishii Y, Tateda K. (*equal contribution): 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.
  7. 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).
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. Kurth JM, Nobu MK, Tamaki H, de Jonge N, Berger S, Jetten MSM, Yamamoto K, Mayumi D, Sakata S, Bai L, Cheng L, Nielsen JL, Kamagata Y, Wagner T, Welte CU.: Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds. ISME J., 15: 3549–3565(2021). DOI:10.1038/s41396-021-01025-6.
  17. Yoneda Y*, Yamamoto K*, Makino A, Tanaka Y, Meng XY, Hashimoto J, Shin-Ya K, Satoh N, Fujie M, Toyama T, Mori K, Ike M, Morikawa M, Kamagata Y, Tamaki H. (*equal contribution): Novel Plant-Associated Acidobacteria Promotes Growth of Common Floating Aquatic Plants, Duckweeds. Microorganisms 9:1133 (2021) DOI:10.3390/microorganisms9061133.
  18. 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.
  19. Yamamoto K, Kusada H, Kamagata Y, Tamaki H.: Parallel evolution of enhanced biofilm formation and phage-resistance in Pseudomonas aeruginosa during adaptation process in spatially heterogeneous environments. Microorganisms 9:569 (2021). DOI:10.3390/microorganisms9030569.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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. Kosakamoto H, Yamauchi T, Akuzawa-Tokita Y, Nishimura K, Soga T, Murakami T, Mori H, Yamamoto K, Miyazaki R, Koto A, Miura M, Obata F: Local necrotic cells trigger systemic immune activation via gut microbiome dysbiosis in Drosophila, Cell Rep. 32(3) 107938 (2020). DOI:10.1016/j.celrep.2020.107938.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.

2019

  1. Takeshita K, Yamada T, Kawahara Y, Narihiro T, Ito M, Kamagata Y, Shinzato N: Tripartite symbiosis of an anaerobic scuticociliate with two hydrogenosome-associated endosymbionts, a Holospora-related alphaproteobacterium and a nethanogenic archaeon. Appl Environ Microbiol. 85(24). pii: e00854-19. (2019). DOI:10.1128/AEM.00854-19.
  2. Wang HZ, Lv XM, Yi Y, Zheng D, Gou M, Nie Y, Hu B, Nobu MK, Narihiro T, Tang YQ. Using DNA-based stable isotope probing to reveal novel propionate- and acetate-oxidizing bacteria in propionate-fed mesophilic anaerobic chemostats. Sci Rep. 9(1):17396 (2019). DOI:10.1038/s41598-019-53849-0. 
  3. Zheng D, Wang HZ, Gou M, Nobu MK, Narihiro T, Hu B, Nie Y, Tang YQ. Identification of novel potential acetate-oxidizing bacteria in thermophilic methanogenic chemostats by DNA stable isotope probing. Appl Microbiol Biotechnol. 103(20):8631-8645 (2019). DOI:10.1007/s00253-019-10078-9. 
  4. Chen SC, Weng CY, Lai MC, Tamaki H, Narihiro T: Comparative genomic analyses reveal trehalose synthase genes as the signature in genus Methanoculleus. Marine Genomics. 47, 100673 (2019). DOI:10.1016/j.margen.2019.03.008.
  5. Wang HZ, Yan YC, Gou M, Yi Y, Xia ZY, Nobu MK, Narihiro T, Tang YQ: Response of propionate-degrading methanogenic microbial communities to inhibitory conditions. Applied Biochemistry and Biotechnology, 189 (1), 233-248 (2019). DOI:10.1007/s12010-019-03005-1.
  6. Yamada T, Harada J, Kurobe M, Giri S, Nobu MK, Narihiro T, Tsuji H, Daimon H. Draft genome sequence of Thermodesulfovibrio sp. strain Kuro-1, a thermophilic, lactate-degrading anaerobe isolated from a thermophilic anaerobic digestion reactor. Microbiol Resour Announc. 8(29). pii: e00709-19 (2019) . DOI:10.1128/MRA.00709-19.
  7. Sun H, Narihiro T, Ma X, Zhang XX, Ren H, Ye L: Diverse aromatic-degrading bacteria present in a highly enriched autotrophic nitrifying sludge. Sci Total Environ. 666:245-251 (2019). DOI:10.1016/j.scitotenv.2019.02.172.
  8. Leng L, Nobu MK, Narihiro T, Yang P, Amy Tan GY, Lee PH: Shaping microbial consortia in coupling glycerol fermentation and carboxylate chain elongation for Co-production of 1,3-propanediol and caproate: pathways and mechanisms. Water Res. 148:281-291 (2019). DOI:10.1016/j.watres.2018.10.063.
  9. Narihiro T, Nobu MK, Hori T, Aoyagi T, Sato Y, Inaba T, et al.: Effects of the wastewater flow rate on interactions between the genus Nitrosomonas and diverse populations in an activated sludge microbiome. Microbes Environ. 34(1):89-94 (2019). DOI:10.1264/jsme2.ME18108.
  10. Hirakata Y, Hatamoto M, Oshiki M, Watari T, Kuroda K, Araki N, Yamaguchi T. Temporal variation of eukaryotic community structures in UASB reactor treating domestic sewage as revealed by 18S rRNA gene sequencing, Sci Rep. 4;9(1):12783 (2019). DOI:10.1038/s41598-019-49290-y.
  11. Yagi F, Minami Y, Yamada M, Kuroda K, Yamauchi M. Development of animal feeding additives from mushroom waste media of shochu lees, International Journal of Recycling of Organic Waste in Agriculture, 8(2) :215–220 (2019). DOI:10.1007/s40093-018-0234-6.
  12. Maharjan N, Kuroda K, Okada M, Nakamura S, Aburatani H, Yamaguchi T, Ichitsubo M. Generic skills assessment through implementation of group based learning to understand SDGs, Journal of Education and practice, 10(6): 14–23 (2019). DOI:10.7176/JEP
  13. Itoh H, Jang S, Takeshita K, Ohbayashi T, Ohnishi N, Meng XY, Mitani Y, Kikuchi Y. Host-symbiont specificity determined by microbe-microbe competition in an insect gut. Proc Natl Acad Sci U S A. 116(45):22673-22682 (2019). DOI:10.1073/pnas.1912397116.
  14. Xu Z, Masuda Y, Itoh H, Ushijima N, Shiratori Y, Senoo K. Geomonas oryzae gen. nov., sp. nov., Geomonas edaphica sp. nov., Geomonas ferrireducens sp. nov., Geomonas terrae sp. nov., Four Ferric-Reducing Bacteria Isolated From Paddy Soil, and Reclassification of Three Species of the Genus Geobacter as Members of the Genus Geomonas gen. nov. Front. Microbiol. 25(10):2201 (2019). DOI:10.3389/fmicb.2019.02201.
  15. Itoh, H., Kawano, K., Kihara, M.: Draft Genome Sequence of Agarivorans sp. Strain Toyoura001, Isolated from an Abalone Gut. Microbiol Resour Announc. 8(19):e00169-19 (2019). DOI:10.1128/MRA.00169-19.
  16. Ohbayashi, T., Itoh, H., Lachat, J., Kikuchi, Y., and Mergaert, P.: Burkholderia gut symbionts associated with European and Japanese populations of the dock bug Coreus marginatus (Coreoidea : Coreidae). Microbes Environ. 34(2):219-222 (2019). DOI:10.1264/jsme2.ME19011.
  17. Faluaburu MS, Nakai R, Imura S, Naganuma T: Phylotypic characterization of mycobionts and photobionts of rock tripe lichen in East Antarctica. Microorganisms 7(7):203 (2019). DOI:10.3390/microorganisms7070203.
  18. Yamamoto K, Hackley K, Kelly W, Panno S, Sekiguchi Y, Sanford R, Liu WT, Kamagata Y, Tamaki H. Diversity and geochemical community assembly processes of the living rare biosphere in a sand-and-gravel aquifer ecosystem in the Midwestern United States. Sci. Rep. 9(1):13484 (2019). DOI:10.1038/s41598-019-49996-z.
  19. Nishioka T, Marian M, Kobayashi I, Kobayashi Y, Yamamoto K, Tamaki H, Suga H, Shimizu K. Microbial basis of Fusarium wilt suppression by Allium cultivation. Sci. Rep. 9(1):1715 (2019). DOI:10.1038/s41598-018-37559-7.

2018

  1. Mei R, Nobu MK, Narihiro T, Yu J, Sathyagal A, Willman E, et al.: Novel Geobacter species and diverse methanogens contribute to enhanced methane production in media-added methanogenic reactors. Water Res. 147:403-12 (2018). DOI:10.1016/j.watres.2018.10.026.
  2. Narihiro T, Nobu MK, Bocher BTW, Mei R, Liu WT: Co-occurrence network analysis reveals thermodynamics-driven microbial interactions in methanogenic bioreactors. Environ Microbiol Rep. 10(6):673-85 (2018). DOI:10.1111/1758-2229.12689.
  3. Hidalgo-Ahumada CAP, Nobu MK, Narihiro T, Tamaki H, Liu WT, Kamagata Y, et al.: Novel energy conservation strategies and behaviour of Pelotomaculum schinkii driving syntrophic propionate catabolism. Environ Microbiol. 20(12):4503-11 (2018). DOI:10.1111/1462-2920.14388.
  4. Harada J, Yamada T, Giri S, Hamada M, Nobu MK, Narihiro T, et al.: Draft genome sequence of Moorella sp. strain Hama-1, a novel acetogenic bacterium isolated from a thermophilic digestion reactor. Genome Announcements. 6(24) (2018). DOI:10.1128/genomeA.00517-18.
  5. Masuda, Y., Itoh, H., Shiratori, Y., Senoo, K.: Metatranscriptomic insights into microbial consortia driving methane metabolism in paddy soils. Soil Sci. Plant Nutr. 64(4):455-464 (2018). DOI:10.1080/00380768.2018.1457409.
  6. Itoh, H., Hori, T., Sato, Y., Nagayama, A., Tago, K., Hayatsu, M., Kikuchi, Y.: Infection dynamics of insecticide-degrading symbionts from soil to insects in response to insecticide spraying. ISME J. 12:909-920 (2018). DOI:10.1038/s41396-017-0021-9.
  7. Naganuma T, Iinuma Y, Nishiwaki H, Murase R, Masaki K, Nakai R: Enhanced bacterial growth and gene expression of D-amino acid dehydrogenase with D-glutamate as the sole carbon source. Front Microbiol. 9:2097 (2018). DOI:10.3389/fmicb.2018.02097.

2017

  1. Nobu MK, Narihiro T, Liu M, Kuroda K, Mei R, Liu WT: Thermodynamically diverse syntrophic aromatic compound catabolism. Environ. Microbiol. 18: 2495-2506 (2017). DOI:10.1111/1462-2920.13922.
  2. Mei R, Nobu MK, Narihiro T, Kuroda K, Muñoz Sierra J, Wu Z, Ye L, Lee PKH, Lee PH, van Lier JB, McInerney MJ, Kamagata Y, Liu WT: Operation-driven heterogeneity and overlooked feed-associated populations in global anaerobic digester microbiome. Water Res. 124:77-84 (2017). DOI:10.1016/j.watres.2017.07.050.
  3. Okamoto T, Aino K, Narihiro T, Matsuyama H, Yumoto I: Analysis of microbiota involved in the aged natural fermentation of indigo. World J. Microbiol. Biotechnol. 33:70 (2017). DOI:10.1007/s11274-017-2238-1.
  4. Jia, H., Hanate, M., Aw, W., Itoh, H., Saito, K., Kobayashi, S., Hachimura, S., Fukuda, S., Tomita, M., Hasebe, Y., Kato, H.: Eggshell membrane powder ameliorates intestinal inflammation by facilitating the restitution of epithelial injury and alleviating microbial dysbiosis. Sci. Rep. 7: 43993 (2017). DOI:10.1038/srep43993.
  5. Masuda, Y., Itoh, H., Shiratori, Y., Isobe, K., Otsuka, S., Senoo, K.: Predominant but previously-overlooked prokaryotic drivers of reductive nitrogen transformation in paddy soils, revealed by metatranscriptomics. Microbes Environ. 32:180-183 (2017). DOI:10.1264/jsme2.ME16179.
  6. Itoh, H., Matsuura, Y., Hosokawa, T., Fukatsu T., Kikuchi, Y.: Obligate gut symbiotic association in the sloe bug Dolycoris baccarum (Hemiptera: Pentatomidae). Appl. Entomol. Zool. 52:51-59 (2017). DOI:10.1007/s13355-016-0453-0.
  7. Hahn MW, Schmidt J, Koll U, Rohde M, Verbarg S, Pitt A, Nakai R, Naganuma T, Lang E: Silvanigrella aquatica gen. nov., sp. nov., isolated from a freshwater lake, description of Silvanigrellaceae fam. nov. and Silvanigrellales ord. nov., reclassification of the order Bdellovibrionales in the class Oligoflexia, reclassification of the families Bacteriovoracaceae and Halobacteriovoraceae in the new order Bacteriovoracales ord. nov., and reclassification of the family Pseudobacteriovoracaceae in the order Oligoflexales. Int J Syst Evol Microbiol. 67(8):2555-2568 (2017). DOI:10.1099/ijsem.0.001965.

2016

  1. Mei R, Narihiro T, Nobu MK, Liu WT: Effects of heat shocks on microbial community structure and microbial activity of a methanogenic enrichment degrading benzoate. Lett. Appl. Microbiol. 63: 356-362. (2016). DOI:10.1111/lam.12629.
  2. Shinzato N, Aoyama H, Saitoh S, Nikoh N, Nakano K, Shimoji M, Shinzato M, Satou K, Teruya K, Hirano T, Yamada T, Nobu MK, Tamaki H, Shirai Y, Park S, Narihiro T, Liu WT, Kamagata Y: Complete genome sequence of the intracellular bacterial symbiont TC1 in the anaerobic ciliate Trimyema compressum. Genome Announc. 4: pii: e01032-16 (2016). DOI:10.1128/genomeA.01032-16.
  3. Nobu MK, Narihiro T, Kuroda K, Mei R, Liu WT: Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methyl-reducing methanogen. ISME J. 10:2478-87 (2016). DOI:10.1038/ismej.2016.33.
  4. Mei R, Narihiro T, Nobu MK, Kuroda K, Liu WT: Evaluating digestion efficiency in full-scale anaerobic digesters by identifying active microbial populations through the lens of microbial activity. Sci Rep. 6:34090 (2016). DOI:10.1038/srep34090.
  5. Narihiro T, Kusada H, Yoneda Y, Tamaki H: Draft genome sequences of Methanoculleus horonobensis strain JCM 15517, Methanoculleus thermophilus strain DSM 2373, and Methanofollis ethanolicus strain JCM 15103, hydrogenotrophic methanogens belonging to the family Methanomicrobiaceae. Genome Announc. 4: pii: e00199-16 (2016). DOI:10.1128/genomeA.00199-16.
  6. Narihiro T, Nobu MK, Tamaki H, Kamagata Y, Liu WT: Draft Genome sequence of Syntrophomonas wolfei subsp. methylbutyratica strain 4J5T (JCM 14075), a mesophilic butyrate- and 2-methylbutyrate-degrading syntroph. Genome Announc. 4: pii: e00047-16 (2016). DOI:10.1128/genomeA.00047-16.
  7. Kuroda K, Nobu MK, Mei R, Narihiro T, Bocher BT, Yamaguchi T, Liu WT: A single-granule-level approach reveals ecological heterogeneity in an upflow anaerobic sludge blanket reactor. PLoS One 11: e0167788 (2016). DOI:journal.pone.0167788.
  8. Narihiro T, Nobu MK, Tamaki H, Kamagata Y, Sekiguchi Y, Liu WT: Comparative genomics of syntrophic branched-chain fatty acid degrading bacteria. Microbes Environ. 31:288-292 (2016). DOI:10.1264/jsme2.ME16057.
  9. Narihiro T, Kanosue Y, Hiraishi A: Cultural, transcriptomic, and proteomic analyses of water-stressed cells of actinobacterial strains isolated from compost: Ecological implications in the fed-batch composting process. Microbes Environ. 31:127-136 (2016). DOI:10.1264/jsme2.ME15199.
  10. Dao HT, Kuroda K, Nakahara N, Danshita T, Hatamoto M, Yamaguchi T. 16S rRNA gene-based comprehensive analysis of microbial community compositions in a full-scale leachate treatment system, J Biosci Bioeng. 122(6):708-715 (2016). DOI:10.1016/j.jbiosc.2016.06.003.
  11. Hirakata Y, Oshiki M, Kuroda K, Hatamoto M, Kubota K, Yamaguchi T, Harada H, Araki N. Effects of Predation by Protists on Prokaryotic Community Function, Structure, and Diversity in Anaerobic Granular Sludge. Microbes Environ. 31(3):279-87 (2016). DOI:10.1264/jsme2.ME16067.
  12. Maharjan N, Kuroda K, Dehama K, Hatamoto M, Yamaguchi T. Development of slow sponge sand filter (SpSF) as a post-treatment of UASB-DHS reactor effluent treating municipal wastewater. Water Sci Technol. 74(1):65-72 (2016). DOI:10.2166/wst.2016.164.
  13. Nakai R, Fujisawa T, Nakamura Y, Baba T, Nishijima M, Karray F, Sayadi S, Isoda H, Naganuma T, Niki H: Genome sequence and overview of Oligoflexus tunisiensis Shr3T in the eighth class Oligoflexia of the phylum Proteobacteria. Stand Genomic Sci. 11:90 (2016). DOI:10.1186/s40793-016-0210-6.
  14. Nakai R, Fujisawa T, Nakamura Y, Nishide H, Uchiyama I, Baba T, Toyoda A, Fujiyama A, Naganuma T, Niki H: Complete genome sequence of Aurantimicrobium minutum type strain KNCT, a planktonic ultramicrobacterium isolated from river water. Genome Announc. 4(3): e00616-16 (2016). DOI:10.1128/genomeA.00616-16.
  15. Mayumi D, Mochimaru H, Tamaki T, Yamamoto K, Yoshioka H, Suzuki Y, Kamagata Y, Sakata S. Methane production from coal by a single methanogen. Science 354(6309): 222-225 (2016). DOI:10.1126/science.aaf8821.
  16. Tamazawa S*, Yamamoto K*, Takasaki K, Mitani Y, Hanada S, Kamagata Y, Tamaki H. In situ gene expression responsible for sulfide oxidation and CO2 fixation of an uncultured large sausage-shaped Aquificae bacterium in a sulfidic hot spring. Microbes Environ. 31(2):194-198 (2016). DOI:10.1264/jsme2.ME16013.

2015

  1. Nobu MK, Narihiro T, Tamaki H, Qiu YL, Sekiguchi Y, Woyke T, Goodwin L, Davenport KW, Kamagata Y, Liu WT: The genome of Syntrophorhabdus aromaticivorans strain UI provides new insights for syntrophic aromatic compound metabolism and electron flow. Environ Microbiol, 17(12):4861-4872 (2015)
  2. Nobu MK, Narihiro T, Rinke C, Kamagata Y, Tringe SG, Woyke T, Liu WT: Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor. ISME J. 9: 1710-1722 (2015).
  3. Hori T, Aoyagi T, Itoh H, Narihiro T, Oikawa A, Suzuki K, Ogata A, Friedrich MW, Conrad R, Kamagata Y: Isolation of microorganisms involved in reduction of crystalline iron (III) oxides in natural environments. Frontiers in Microbiol, 6: e368 (2015).
  4. Narihiro T, Nobu MK, Kim NK, Kamagata Y, Liu WT: The nexus of syntrophy-associated microbiota in anaerobic digestion revealed by long-term enrichment and community survey. Environ Microbiol. 17(5):1707-20 (2015)
  5. Narihiro T, Kim NK, Mei R, Nobu MK, Liu WT: Microbial community analysis of anaerobic reactors treating soft drink wastewater. PLOS One, 10(3):e0119131 (2015)
  6. Kuroda K, Chosei T, Nakahara N, Hatamoto M, Wakabayashi T, Kawai T, Araki N, Syutsubo K, Yamaguchi T. High organic loading treatment for industrial molasses wastewater and microbial community shifts corresponding to system development. Bioresour Technol. 196:225-34 (2015).
  7. Kuroda K, Hatamoto M, Nakahara N, Abe K, Takahashi M, Araki N, Yamaguchi T. Community composition of known and uncultured archaeal lineages in anaerobic or anoxic wastewater treatment sludge, Microb Ecol, 69(3): 586–596 (2015).
  8. Aida AA, Kuroda K, Yamamoto M, Nakamura A, Hatamoto M, Yamaguchi T. Diversity Profile of Microbes Associated with Anaerobic Sulfur Oxidation in an Upflow Anaerobic Sludge Blanket Reactor Treating Municipal Sewage. Microbes Environ. 30(2):157-63 (2015).
  9. Watari T, Thanh NT, Tsuruoka N, Tanikawa D, Kuroda K, Huong NL, Tan NM, Hai HT, Hatamoto M, Syutsubo K, Fukuda M, Yamaguchi T. Development of a BR-UASB-DHS system for natural rubber processing wastewater treatment. Environ Technol. 37(4):459-465 (2015).
  10. Hirakata Y, Oshiki M, Kuroda K, Hatamoto M, Kubota K, Yamaguchi T, Harada H, Araki N. Identification and Detection of Prokaryotic Symbionts in the Ciliate Metopus from Anaerobic Granular Sludge. Microbes Environ. 30(4):335-8 (2015).
  11. Tourlousse DM, Matsuura N, Sun L, Toyonaga M, Kuroda K, Ohashi A, Cruz R, Yamaguchi T, Sekiguchi Y. Draft Genome Sequence of Bacteroidales Strain TBC1, a Novel Isolate from a Methanogenic Wastewater Treatment System. Genome Announc. 3(5). pii: e01168-15 (2015).
  12. Matsuura N, Tourlousse DM, Sun L, Toyonaga M, Kuroda K, Ohashi A, Cruz R, Yamaguchi T, Sekiguchi Y. Draft Genome Sequence of Anaerolineae Strain TC1, a Novel Isolate from a Methanogenic Wastewater Treatment System. Genome Announc. 3(5). pii: e01104-15 (2015).
  13. Hatamoto M, Saito Y, Dehama K, Nakahara N, Kuroda K, Takahashi M, Yamaguchi T. Microbial community structure of a simultaneous nitrogen and phosphorus removal reactor following treatment in a UASB-DHS system. Water Sci Technol. 71(3):454-61 (2015).
  14. Watari T, Tanikawa D, Kuroda K, Nakamura A, Fujii N, Yoneyama F, Wakisaka O, Hatamoto M, Yamaguchi T. Development of UASB-DHS system for treating industrial wastewater containing ethylene glycol. Journal of Water and Environment Technology, 13(2), 131–140 (2015).
  15. Takeshita, K., Matsuura, Y., Itoh, H., Navarro, R., Hori, T., Sone, T., Kamagata, Y., Mergaert, P., Kikuchi, Y.: Burkholderia of plant-beneficial group are symbiotically associated with bordered plant bugs (Heteroptera: Pyrrhocoroidea: Largidae). Microbes Environ. 30:321-329 (2015).
  16. Navarro, R. R., Aoyagi, T., Kimura, M., Itoh, H., Sato, Y., Kikuchi, Y., Ogata, A., Hori, T.: High resolution dynamics of microbial communities during dissimilatory selenate reduction in an anoxic soil. Environ. Sci. Technol. 49: 7684–7691 (2015).
  17. Aoyagi, T., Hanada, S., Itoh, H., Sato, Y., Ogata, A., Friedrich, M. W., Kikuchi, Y., Hori, T.: Ultra-high-sensitivity stable-isotope probing of rRNA by high-throughput sequencing of isopycnic centrifugation gradients. Environ. Microbiol. Rep. 7: 282-287 (2015). 
  18. Tago, K., Okubo, T., Itoh, H., Kikuchi, Y., Hori, T., Sato, Y., Nagayama, A., Hayashi, K., Ikeda, S., Hayatsu, M.: Insecticide-degrading Burkholderia symbionts of the stinkbug naturally occupy various environments of sugarcane fields in a southeast island of Japan. Microbs Environ. 30: 29-36 (2015).
  19. Aoyagi T., Kimura M., Yamada N., Navarro R.R., Itoh H., Ogata A., Sakoda A., Katayama Y., Takasaki M., Hori T.: Dynamic transition of chemolithotrophic sulfur-oxidizing bacteria in response to amendment with nitrate in deposited marine sediments. Front. Microbiol. 6:426 (2015).
  20. Nakai R, Baba T, Niki H, Nishijima M, Naganuma T: Aurantimicrobium minutum gen. nov., sp. nov., a novel ultramicrobacterium of the family Microbacteriaceae, isolated from river water. Int J Syst Evol Microbiol 65(11): 4072-4079 (2015).

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).

2019

  1. Ichitsubo M (Ed.), Yamaguchi T, Fujii K, Maharjan N, Drier B, Kuroda K, Maruyama N, Takimoto Y, Putra AA, Thao TP, Ohmine N, Arata T, Kurashita H, Kotsusa M. SDGs Fun Learning Book – A bright future for all of us -, Maruzen-Yushodo Co., Ltd., Tokyo, Japan (2019).
  2. Nakai R, Imura S, Naganuma T: Chapter 2: Patterns of microorganisms inhabiting Antarctic freshwater lakes with special reference to aquatic moss pillars, pp.25-43, In: Castro-Sowinski S (ed) The Ecological Role of Micro-organisms in the Antarctic Environment, Springer Polar Sciences, (2019).

2018

  1. Itoh, H., Tago, K., Hayatsu, M., Kikuchi, Y.: Detoxifying symbiosis: microbe-mediated detoxification of phytotoxins and pesticides in insects. Nat. Prod. Rep. 35(5):434-454 (2018).
  2. Haruta S, Yamamoto K. Model microbial consortia as tools for understanding complex microbial communities. Curr. Genomics 19(8):723-733 (2018).

2017

  1. Narihiro T, Kamagata Y: Genomics and metagenomics in microbial ecology: recent advances and challenges. Microbes Environ. 32:1-4 (2017).

2016

  1. Narihiro T, Kamagata Y: Anaerobic Cultivation, pp. 2.1.2-1-2.1.2-12. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC (2016).
  2. Kamagata Y, Narihiro T: Symbiosis studies in microbial ecology. Microbes Environ. 31: 201-203 (2016).
  3. Narihiro T: Microbes in the water infrastructure: underpinning our society. Microbes Environ. 31:89-92 (2016).
  4. Kudoh S, Takahashi KT, Ishihara T, Tsujimoto M, Nakai R, Suzuki AC, Tanabe Y, Uchida M, Imura S: Limnological parameters in Sôya Coats lakes between the 55th and 56th Japanese Antarctic Research Expeditions in 2014–2015 —Long-term monitoring study —. JARE Data Reports, 344 (Terrestrial Biology 14): 1-7 (2016).

2015

  1. Narihiro T, Nobu MK, Mei R, Liu WT: Microbial Community Involved in Anaerobic Purified Terephthalic Acid Treatment Process, pp. 31-48. In Fang HHP, Zhang T. (ed.), Anaerobic Biotechnology: Environmental Protection and Resource Recovery. World Scientific Publishing, Singapore (2015).
  2. Narihiro T, Sekiguchi Y: Primers: Functional Genes and 16S rRNA Genes for Methanogens, pp. 79-139. In McGenity TJ, Timmis KN, Nogales B. (ed.), Hydrocarbon and Lipid Microbiology Protocols. Springer Berlin Heidelberg, New York (2015).
  3. Kudoh S, Takahashi KT, Ishihara T, Tsujimoto M, Nakai R, Suzuki AC, Tanabe Y, Uchida M, Imura S: Meteorological data from ice-free areas in Yukidori Zawa, Langhovde, Kizahashi Hama, Skarvsnes and Skallen in Sôya Coast, East Antarctica during 2014– 2015. JARE Data Reports, 339 (Terrestrial Biology 11): 1-6 (2015).

邦文総説・解説・論文・書籍・教科書等

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).

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).
  8. 石谷孔司, 油谷幸代: バイオインフォマティクスによる微生物群集解析の新展開, 化学と生物 60(2) 52-54(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).

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)

2019

  1. 黒田恭平, 蔵下はづき, 幡本将史, 青井透. 自活性線虫とBacillales目細菌を優占化させた廃棄物利用型の土壌改良資材, アグリバイオ 2019年12月臨時増刊号, 株式会社 北隆館, 3(14): 41–42 (1329–1330) (2019).
  2. 幡本将史，平片悠河，黒田恭平，山口隆司. 次世代シーケンサーを適用した嫌気性処理の微生物生態解析，用水と廃水，61(4): 42–49 (2019).
  3. 黒田恭平, 高津佐愛実, 徳田裕二郎, 池田匠児, 平片悠河, 幡本将史, 山田真義, 山口隆司, 八木史郎, 山内正仁. 下水汚泥堆肥を用いたマッシュルーム栽培培地中の微生物叢解析と培地内優占微生物の分離培養, 土と微生物, 73(2),62–70 (2019).
  4. 山内正仁, 島田温史, 山田真義, 徳田裕二郎, 八木史郎, 黒田恭平, 香西直子, 山本雅史. 下水汚泥を用いた食用きのこ量産化技術の開発ときのこ栽培過程で発生するCO2の農業利用への検討, 土木学会論文集G (環境) (環境工学研究論文集第56巻), 75(7): 443–450 (2019).
  5. 市坪 誠, 中村成芳, 黒田恭平, 山田宏，油谷英明, 山口隆司. 教材及び教授法と協調したコンピテンス評価の基礎的研究, 工学教育, 67(1): 42–47 (2019).
  6. 中井亮佑: とっても小さいやつらを追って－謎だらけの「辺境微生物」の世界、講談社ブルーバックス，2019.03.02 (2019).
  7. 中井亮佑: 精密ろ過膜を通り抜ける「ろ過性細菌」，バイオサイエンスとインダストリー(B&I)，77(1): 56-57 (2019).

2018

  1. 成廣 隆：微生物機能で水素社会を実現する？ 生物工学会誌 96(11): 657 (2018)
  2. 蔵下はづき，平片悠河，高木素紀，幡本将史，牧慎也，山口隆司，青井透，黒田恭平. 連作障害の生じたレンコン栽培土壌の分子生物学的解析および有用微生物優占化土壌改良資材の施肥効果の評価，土木学会論文集G (環境) (環境工学研究論文集第55巻)，74(7), 255–264 (2018)．
  3. 山田真義，山内正仁，徳田裕二郎，池田匠児，八木史郎，樗木直也，黒田恭平，原田陽，山口隆司. 下水汚泥堆肥の利用によるマッシュルームの生産性向上と廃培地の農業利用への検討，土木学会論文集G (環境) (環境工学研究論文集第55巻)，74(7): 101–109 (2018)．
  4. 中村成芳，黒田恭平，森本真理，油谷英明，山口隆司，市坪誠. 自然科学基礎教育における技術者育成のための協同学習を取り入れた授業モジュール，工学教育，66(4): 31–37 (2018)．
  5. 黒田恭平，中村成芳，岡田美鈴，山口隆司，市坪誠，油谷英明. 世界課題との関連性を持たせた専門教育 –英語によるアクティブ・ラーニング–，日本高専学会誌，23(2): 11–16 (2018)．
  6. 中井 亮佑: 追跡！辺境微生物 砂漠・温泉から北極・南極まで，築地書館，pp204, (2018).

2017

  1. 山内正仁，池田匠児，新原悠太郎，山田真義，八木史郎，黒田恭平，原田陽，山口隆司. 下水汚泥堆肥を用いたマッシュルーム栽培技術の開発，土木学会論文集G (環境) (環境工学研究論文集第54巻)，73(7): 397–405 (2017).
  2. 黒田恭平, 幡本将史, 山口隆司, 渡部紀一, 南條忠彦, 山内正仁, 山田真義. 低温 (20ºC) UASB反応器及び常温DHS反応器を組み合わせたシステムによる模擬醤油製造廃水の高負荷連続処理, 水環境学会誌, 40(2) :67–75 (2017).
  3. 中井亮佑: 超微小バクテリアは何者か？，生物工学会誌，95(7): 405 (2017).

2016

  1. 黒田恭平，段下剛志，牧慎也，山口隆司，市坪誠. 多様性を持たせたグループワークによる汎用的能力の向上とその評価手法の確立，工学教育，65(1): 58–65 (2016)．
  2. 山内正仁，池田匠児，山崎寛登，山田真義，八木史郎，黒田恭平，原田陽，山口隆司. 下水汚泥と地域バイオマスを用いた食用きのこ栽培技術の開発，土木学会論文集G (環境) (環境工学研究論文集第53巻)，72(7): 515–522.
  3. 中井亮佑: 小さいサイズの極限－生物はどこまで小さくなれるのか？，生物の科学 遺伝，70: 199-203. (2016).
  4. 伊藤英臣: 土壌微生物が斑点米カメムシを育む. 日本土壌壌微生物学会誌 土と微生物. 70: pp 87 (2016).
  5. 山本京祐：マイノリティとして生きる微生物, 生物工学会誌, 94(10):639 (2016).

2015

  1. 伊藤英臣, 菊池義智: 昆虫に新機能を賦与する微生物. 難培養微生物研究の最新技術Ⅲ (シーエムシー出版) pp 95-100 (2015).
  2. 伊藤英臣: 昆虫と土壌微生物の共生：農業害虫カメムシ-土壌間の殺虫剤分解菌の動態解明. 日本土壌壌微生物学会誌 土と微生物. 69(1): pp 34-38 (2015).

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

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