Details of the Researcher

PHOTO

Kengo Kubota
Section
Graduate School of Environmental Studies
Job title
Associate Professor
Degree

  • 博士 (工学) (Nagaoka University of Technology)

Committee Memberships 9

  • 土木学会 東北支部　副幹事長

    2024/05 - Present

  • 日本水環境学会 原著論文編集部会　委員

    2023/07 - Present

  • 日本水環境学会 微生物生態と水環境工学研究委員会　幹事

    2020/04 - Present

  • 土木学会 環境工学委員会 副幹事長

    2023/04 - 2025/03

  • 土木学会 環境工学委員会　委員・幹事

    2021/04 - 2025/03

  • 土木学会 調査研究部門 土木学会論文集編集委員会 環境・資源編集小委員会(71小委員会)　委員

    2022/06 - 2024/06

  • 日本水環境学会 微生物生態と水環境工学研究委員会　幹事長

    2016/04 - 2020/03

  • 日本水環境学会 ポピュレーションダイナミクス研究委員会　幹事長

    2015/04 - 2016/03

  • 日本水環境学会 ポピュレーションダイナミクス研究委員会　幹事

    2011/01 - 2015/03

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Professional Memberships 4

  • International Water Association (IWA)

  • Japan Society of Civil Engineers

  • Japanese Society of Microbial Ecology

  • Japan Society on Water Environment

Research Interests 4

  • 温暖化対策技術

  • Development of wastewater treatment processes applicable for developing countries

  • Development of molecular tools

  • Environmental microbial community analysis

Research Areas 2

  • Social infrastructure (civil Engineering, architecture, disaster prevention) / Civil engineering (environmental systems) /

  • Environmental science/Agricultural science / Environmental load reduction/restoration technology /

Awards 17

  1. 社団法人 土木学会 東北支部 令和6年度 技術開発賞

    2025/05　社団法人 土木学会 東北支部　温度が無酸素環境下でのN2O除去プロセスに与える影響の評価

  2. 令和5年度下水道協会誌 奨励論文（学術部門）

    2023/06

  3. 第57回環境工学研究フォーラム 環境技術・プロジェクト賞

    2020/12　土木学会 環境工学委員会

  4. 第56回環境工学研究フォーラム 優秀ポスター発表賞

    2019/12　土木学会 環境工学委員会

  5. 平成27年度 科学技術分野の文部科学大臣表彰 若手科学者賞

    2015/04/15　文部科学省

  6. 第51回環境工学研究フォーラム 優秀ポスター発表賞

    2014/12/22　土木学会 環境工学委員会

  7. 5th International Conference on Microbial Ecology and Water Engineering (the International Water Association) Best Poster Award

    2013/07/10　the International Water Association

  8. 第48回 環境工学研究フォーラム 論文賞

    2012/11　土木学会 環境工学委員会

  9. 社団法人 土木学会 第65回年次学術講演会優秀講演者賞受賞

    2010/12　社団法人 土木学会

  10. 建設工学研究奨励賞

    2010/05　財団法人 建設工学研究振興会

  11. 第46回環境工学研究フォーラム 優秀ポスター発表賞

    2009/11　土木学会 環境工学委員会

  12. 土木学会東北支部技術開発賞

    2009/05/15　社団法人 土木学会 東北支部

  13. グリーンエネルギー革命による環境再生国際シンポジウム 優秀ポスター発表賞受賞

    2006/01　長岡技術科学大学 21世紀COEプログラム グリーンエネルギー革命による環境再生

  14. 社団法人 土木学会 第60回年次学術講演会優秀講演者賞受賞

    2005/12　社団法人 土木学会

  15. 社団法人 土木学会 第59回年次学術講演会優秀講演者賞受賞

    2004/12　社団法人 土木学会

  16. グリーンエネルギー革命による環境再生国際シンポジウム 優秀ポスター発表賞受賞

    2004/01　長岡技術科学大学 21世紀COEプログラム グリーンエネルギー革命による環境再生

  17. 社団法人 土木学会 第57回年次学術講演会優秀講演者賞受賞

    2002/11　社団法人 土木学会

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Papers 133

  1. Spatial, temporal, and biotic changes in the natural abundances of stable carbon and nitrogen isotopes in a biological treatment reactor Peer-reviewed

    Takashi Onodera, Kengo Kubota, Akinori Iguchi, Akihiro Nagamachi, Tadashi Tagawa, Gen Kanaya, Ayato Kohzu, Kazuaki Syutsubo

    Journal of Bioscience and Bioengineering　141　(2)　135-141　2026/02

    Publisher: Elsevier BV

    DOI： 10.1016/j.jbiosc.2025.11.002 　

    ISSN： 1389-1723

  2. Moderate oxidation–coagulation pretreatment for mitigating ultrafiltration membrane fouling by algae-laden water: Performance and mechanisms Peer-reviewed

    Jinlong Han, Qiuwen Wang, Li Sun, Mathias Ulbricht, Lukas Fischer, Houyun Yang, Xiao-Yang Liu, Zhijun Ren, Andrzej Kraslawski, Kengo Kubota, Yu-You Li

    Desalination　619　119522-119522　2026/02

    Publisher: Elsevier BV

    DOI： 10.1016/j.desal.2025.119522 　

    ISSN： 0011-9164

  3. Metabolic Potential of Candidatus Saccharimonadia Including Rare Lineages in Activated Sludge Peer-reviewed

    Shuka Kagemasa, Kyohei Kuroda, Ryosuke Nakai, Mikiko Sato, Yu‐You Li, Kengo Kubota

    Environmental Microbiology Reports　17　(6)　2025/11/06

    Publisher: Wiley

    DOI： 10.1111/1758-2229.70231 　

    ISSN： 1758-2229

    eISSN： 1758-2229

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    ABSTRACT Candidatus Saccharimonadia is a class‐level lineage of ultrasmall bacteria within the phylum Minisyncoccota (formerly Candidate Phyla Radiation or Ca . Patescibacteria), commonly found in activated sludge processes treating municipal wastewater. In this study, we aimed to elucidate the metabolic potential of Ca . Saccharimonadia by using shotgun metagenomic sequencing combined with a filtration‐based size‐fractionation approach for activated sludge from five wastewater treatment plants. A total of 65 high‐quality metagenomic bins were recovered, belonging to four orders and 19 families of Ca . Saccharimonadia, including previously unreported lineages in activated sludge. These bins had small genomes (approximately 0.46–1.73 Mbp) with limited metabolic capabilities, indicating dependency on other microorganisms. Notably, the order Ca . Saccharimonadales retained a type IV secretion system and effector gene cluster for parasitic interactions with the hosts, suggesting that Ca . Saccharimonadales bacteria may exhibit a parasitic lifestyle. Co‐occurrence network analysis showed that members of the order Ca . Saccharimonadales were significantly correlated with multiple lineages, including Actinobacteriota , for which a parasitic relationship has been previously demonstrated. Our results shed light on the potential ecophysiology of the diverse members of Ca . Saccharimonadia, providing a comprehensive understanding of Ca . Saccharimonadia in activated sludge.

  4. Enhanced biogas production through co-digestion of tapioca starch wastewater and duckweed in a continuous stirred tank reactor Peer-reviewed

    Sunisa Srisopa, Thanapat Thepubon, Pairaya Choeisai, Krit Choeisai, Kengo Kubota

    Engineering and Applied Science Research　52　(5)　499-505　2025/08

  5. Metabolic mechanism in biosynthesis of polyhydroxyalkanoate from terephthalic acid by mixed microbial consortium Peer-reviewed

    Lanjia Pan, Wardah Hayat Khan, Jie Li, Kengo Kubota, Qiang Wang, Yin Wang

    Chemical Engineering Journal　515　163695-163695　2025/07

    Publisher: Elsevier BV

    DOI： 10.1016/j.cej.2025.163695 　

    ISSN： 1385-8947

  6. Study of enhanced nitrogen removal performance and mechanism of iron-modified activated carbon in low-temperature environments Peer-reviewed

    Guangtao Li, Jinlong Han, Yunchang Wang, Shihong Wu, Liyan Ge, Xueqian An, Xiaoyang Liu, Wenfang Gao, Li Sun, Zhijun Ren, Kengo Kubota

    Journal of Environmental Chemical Engineering　13　(3)　116951-116951　2025/06

    Publisher: Elsevier BV

    DOI： 10.1016/j.jece.2025.116951 　

    ISSN： 2213-3437

  7. Mitigating nitrous oxide emission by a down-flow hanging sponge bioprocess enabling the removal of high concentration N2O Peer-reviewed

    Ryota Maeda, Mikiko Sato, Kiwamu Minamisawa, Kengo Kubota

    Chemical Engineering Journal　513　162885-162885　2025/06

    Publisher: Elsevier BV

    DOI： 10.1016/j.cej.2025.162885 　

    ISSN： 1385-8947

  8. Enhanced Molybdenum Recovery Achieved by a Complex of Porous Material-Immobilized Surface-Engineered Yeast in Development of a Sustainable Biosorption Technology Peer-reviewed

    Thiti Jittayasotorn, Kentaro Kojima, Audrey Stephanie, Kaho Nakamura, Hernando P. Bacosa, Kengo Kubota, Masanobu Kamitakahara, Chihiro Inoue, Mei-Fang Chien

    Microorganisms　13　(5)　1034-1034　2025/04/30

    Publisher: MDPI AG

    DOI： 10.3390/microorganisms13051034 　

    eISSN： 2076-2607

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    Molybdenum (Mo) is a critical industrial metal valued for its corrosion resistance and strength-enhancing properties. However, increasing demand necessitates more efficient and sustainable recovery methods. Bio-recovery of Mo by biosorption is a promising resolution, especially by the use of surface-engineered microbes that express metal binding proteins on its cell surface. This study investigates the potential of Saccharomyces cerevisiae strain ScBp6, which displays a molybdate-binding protein (ModE) on its cell surface, immobilized on porous materials. Our findings reveal that polyurethane sponges (PS) significantly outperform ceramic materials in yeast immobilization, entrapping 1.76 × 107 cells per sponge compared to 1.70 × 106 cells per ceramic cube. Furthermore, the yeast–PS complex demonstrated superior Mo adsorption, reaching 2.16 pg Mo per yeast cell under 10 ppm Mo conditions, comparable to free yeast cells (1.96 pg Mo per yeast cell). These results establish PS as an effective and scalable platform for Mo recovery, offering high biosorption efficiency, reusability, and potential for industrial wastewater treatment applications.

  9. 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. International-journal Peer-reviewed

    Meri Nakajima, Ryosuke Nakai, Yuga Hirakata, Kengo Kubota, Hisashi Satoh, Masaru K Nobu, Takashi Narihiro, Kyohei Kuroda

    International journal of systematic and evolutionary microbiology　75　(2)　006668　2025/02

    DOI： 10.1099/ijsem.0.006668 　

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    In the domain Bacteria, one of the largest, most diverse and environmentally ubiquitous phylogenetic groups, Candidatus Patescibacteria (also known as candidate phyla radiation/CPR), remains poorly characterized, leaving a major knowledge gap in microbial ecology. We recently discovered a novel cross-domain symbiosis between Ca. Patescibacteria and Archaea in highly purified enrichment cultures and proposed Candidatus taxa for the characterized species, including Ca. Minisyncoccus archaeophilus and the corresponding family Ca. Minisyncoccaceae. In this study, we report the isolation of this bacterium, designated strain PMX.108T, in a two-strain co-culture with a host archaeon, Methanospirillum hungatei strain DSM 864T (JF-1T), and hereby describe it as the first representative species of Ca. Patescibacteria. Strain PMX.108T was isolated from mesophilic methanogenic sludge in an anaerobic laboratory-scale bioreactor treating synthetic purified terephthalate- and dimethyl terephthalate-manufacturing wastewater. The strain could not grow axenically and is obligately anaerobic and parasitic, strictly depending on M. hungatei as a host. The genome was comparatively large (1.54 Mbp) compared to other members of the clade, lacked some genes involved in the biosynthesis pathway and encoded type IV pili-related genes associated with the parasitic lifestyle of ultrasmall microbes. The G+C content of the genomic DNA was 36.6 mol%. Here, we report the phenotypic and genomic properties of strain PMX.108T; we propose Minisyncoccus archaeiphilus gen. nov., sp. nov. to accommodate this strain. The type strain of the species is PMX.108T (=JCM 39522T). We also propose the associated family, order, class and phylum as Minisyncoccaceae fam. nov. Minisyncoccales nov., Minisyncoccia class. nov. and Minisyncoccota phyl. nov. within the bacterial kingdom Bacillati.

  10. Impact of Varying Temperatures on Performance and Stability of Hydroxyapatite (HAP)-Enhanced Granule-Type One-Stage Partial Nitritation/Anammox System Peer-reviewed

    Gaoxuefeng FENG, Yujie CHEN, Kengo KUBOTA, Yu-You LI

    Journal of JSCE　12　(2)　24-25027　2024/11

  11. 嫌気性膜分離法と一槽式HAP-PNA法の融合による濃縮浄化槽汚泥のリサイクル処理 Peer-reviewed

    郭広澤, 陳玉潔, 久保田健吾, 李玉友

    土木学会論文集　80　(25)　24-25013　2024/11

  12. Nondestructive and three-dimensional visualization by identifying elements using synchrotron radiation microscale X-ray CT reveals microbial and cavity distributions in anaerobic granular sludge Peer-reviewed

    Kampachiro Urasaki, Yuki Morono, Go-Ichiro Uramoto, Kentaro Uesugi, Masahiro Yasutake, Manato Akishiba, Guangze Guo, Yu-You Li, Kengo Kubota

    Applied and Environmental Microbiology　90　(8)　e00563-24　2024/08

    Publisher: American Society for Microbiology

    DOI： 10.1128/aem.00563-24 　

    ISSN： 0099-2240

    eISSN： 1098-5336

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    ABSTRACT We developed a nondestructive three-dimensional microbial visualization method utilizing synchrotron radiation X-ray microscale computed tomography to better understand the relationship between microorganisms and their surrounding habitats. The method was tested and optimized using a mixture of axenic Escherichia coli and Comamonas testosteroni . The osmium-thiocarbohydrazide-osmium method was used to stain all the microbial cells, and gold in situ hybridization was used to detect specific phylogenetic microbial groups. The stained samples were embedded in epoxy resin for microtomographic analysis. Differences in X-ray absorbances were calculated by subtracting the pre-L 3 -edge images from the post-L 3 -edge images to visualize the osmium and gold signals. Although we successfully detected cells stained with osmium, those labeled with gold were not detected, probably because of the insufficient density of gold atoms in the microbial cells. We then applied the developed technique to anaerobic granules and visualized the distribution of microbial cells and extracellular polymeric substances. Empty spaces were highlighted to determine the cavity distribution in granules. Numerous independent cavities of different sizes were identified in the granules. The developed method can be applied to various environmental samples for deeper insights into microbial life in their habitats. IMPORTANCE Microorganisms inhabit diverse environments and often form biofilms. One factor that affects their community structure is the surrounding physical environment. The arrangement of residential space within the formed biofilm plays a crucial role in the supply and transportation of substances, as well as the discharge of metabolites. Conventional approaches, such as scanning electron microscopy and confocal laser scanning microscopy combined with fluorescence in situ hybridization, have limitations as they provide information primarily from the biofilm surface and cross-sections. In this study, we developed a method for detecting microorganisms in biofilms using synchrotron radiation X-ray microscale computer tomography. The developed method allows nondestructive three-dimensional observation of biofilms at a single-cell resolution (voxel size of approximately 200 nm), facilitating an understanding of the relationship between microorganisms and their physical habitats.

  13. Evaluation of sewage treatment performance and duckweed biomass production efficiency in a primary sedimentation basin + duckweed pond + downflow hanging sponge (PSB + DWP + DHS) system Peer-reviewed

    Kengo Kubota, Takashi Otani, Teruki Hariu, Takumi Jin, Tadashi Tagawa, Masaaki Morikawa, Yu-You Li

    Journal of Water Process Engineering　65　105818　2024/08

    Publisher: Elsevier BV

    DOI： 10.1016/j.jwpe.2024.105818 　

    ISSN： 2214-7144

  14. Mass flow and microbial shifts in recirculated two-phase anaerobic digestion for biohythane production: Effect of hydraulic retention time Peer-reviewed

    Yu Qin, Aijun Zhu, Jing Wu, Lu Li, Toshimasa Hojo, Kengo Kubota, Yu-You Li

    Journal of Cleaner Production　468　143092　2024/08

    Publisher: Elsevier BV

    DOI： 10.1016/j.jclepro.2024.143092 　

    ISSN： 0959-6526

  15. Biomethane recovery and prokaryotic shifts in anaerobic co-digestion of food waste and paper waste in organic fraction of municipal solid waste: Effect of paper content Peer-reviewed

    Lu Li, Yi Bu, Wen Feng, Kengo Kubota, Yang Pan, Yong Huang, Yu-You Li, Yu Qin

    Bioresource Technology　406　130964　2024/08

    Publisher: Elsevier BV

    DOI： 10.1016/j.biortech.2024.130964 　

    ISSN： 0960-8524

  16. Microbiological insights into anaerobic phenol degradation mechanisms and bulking phenomenon in a mesophilic upflow anaerobic sludge blanket reactor in long-term operation Peer-reviewed

    Kyohei Kuroda, Ryota Maeda, Futaba Shinshima, Kampachiro Urasaki, Kengo Kubota, Masaru K. Nobu, Taro Q.P. Noguchi, Hisashi Satoh, Masahito Yamauchi, Takashi Narihiro, Masayoshi Yamada

    Water Research　253　121271　2024/04

    Publisher: Elsevier BV

    DOI： 10.1016/j.watres.2024.121271 　

    ISSN： 0043-1354

  17. Microscopic and metatranscriptomic analyses revealed unique cross-domain parasitism between phylum Candidatus Patescibacteria/candidate phyla radiation and methanogenic archaea in anaerobic ecosystems Peer-reviewed

    Kyohei Kuroda, Meri Nakajima, Ryosuke Nakai, Yuga Hirakata, Shuka Kagemasa, Kengo Kubota, Taro Q. P. Noguchi, Kyosuke Yamamoto, Hisashi Satoh, Masaru K. Nobu, Takashi Narihiro

    mBio　15　(3)　e03102-23　2024/03/13

    Publisher: American Society for Microbiology

    DOI： 10.1128/mbio.03102-23 　

    eISSN： 2150-7511

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    ABSTRACT To verify whether members of the phylum Candidatus Patescibacteria parasitize archaea, we applied cultivation, microscopy, metatranscriptomic, and protein structure prediction analyses on the Patescibacteria-enriched cultures derived from a methanogenic bioreactor. Amendment of cultures with exogenous methanogenic archaea, acetate, amino acids, and nucleoside monophosphates increased the relative abundance of Ca . Patescibacteria. The predominant Ca . Patescibacteria were families Ca . Yanofskyibacteriaceae and Ca . Minisyncoccaceae, and the former showed positive linear relationships ( r 2 ≥ 0.70) Methanothrix in their relative abundances, suggesting related growth patterns. Methanothrix and Methanospirillum cells with attached Ca . Yanofskyibacteriaceae and Ca . Minisyncoccaceae, respectively, had significantly lower cellular activity than those of the methanogens without Ca . Patescibacteria, as extrapolated from fluorescence in situ hybridization-based fluorescence. We also observed that parasitized methanogens often had cell surface deformations. Some Methanothrix -like filamentous cells were dented where the submicron cells were attached. Ca . Yanofskyibacteriaceae and Ca . Minisyncoccaceae highly expressed extracellular enzymes, and based on structural predictions, some contained peptidoglycan-binding domains with potential involvement in host cell attachment. Collectively, we propose that the interactions of Ca . Yanofskyibacteriaceae and Ca . Minisyncoccaceae with methanogenic archaea are parasitisms. IMPORTANCE Culture-independent DNA sequencing approaches have explored diverse yet-to-be-cultured microorganisms and have significantly expanded the tree of life in recent years. One major lineage of the domain Bacteria, Ca . Patescibacteria (also known as candidate phyla radiation), is widely distributed in natural and engineered ecosystems and has been thought to be dependent on host bacteria due to the lack of several biosynthetic pathways and small cell/genome size. Although bacteria-parasitizing or bacteria-preying Ca . Patescibacteria have been described, our recent studies revealed that some lineages can specifically interact with archaea. In this study, we provide strong evidence that the relationship is parasitic, shedding light on overlooked roles of Ca . Patescibacteria in anaerobic habitats.

  18. Dissolved organic matter composition and microbial community dynamics in two-phase multi-staged up-flow anaerobic sludge blanket treatment of tapioca starch processing wastewater Peer-reviewed

    Thanapat Thepubon, Phanwatt Phungsai, Pairaya Choeisai, Kengo Kubota

    Bioresource Technology Reports　24　101660　2023/12

    Publisher: Elsevier BV

    DOI： 10.1016/j.biteb.2023.101660 　

    ISSN： 2589-014X

  19. A novel method for the whole-cell detection of environmental microorganisms using hemin and tyramide signal amplification (Hemin-TSA) with a desired fluorescent dye Peer-reviewed

    Kampachiro Urasaki, Yu-You Li, Kengo Kubota

    Systematic and Applied Microbiology　46　(6)　126473-126473　2023/11

    Publisher: Elsevier BV

    DOI： 10.1016/j.syapm.2023.126473 　

    ISSN： 0723-2020

  20. Propidium monoazide - polymerase chain reaction reveals viable microbial community shifts in anaerobic membrane bioreactors treating domestic sewage at low temperature Peer-reviewed

    Jialing Ni, Jiayuan Ji, Yu-You Li, Kengo Kubota

    Bioresource Technology　387　129564　2023/11

    DOI： 10.1016/j.biortech.2023.129564 　

  21. Improved Properties and Enhancement Strategies of Hydroxyapatite-Based Functional Granular Sludge for a High-Rate Partial Nitritation/Anammox System Peer-reviewed

    Yujie Chen, Gaoxuefeng Feng, Guangze Guo, Kampachiro Urasaki, Kengo Kubota, Yu-You Li

    Environmental Science & Technology　57　(19)　7624-7633　2023/05/04

    Publisher: American Chemical Society (ACS)

    DOI： 10.1021/acs.est.3c00491 　

    ISSN： 0013-936X

    eISSN： 1520-5851

  22. Anammox upflow hybrid reactor: Nitrogen removal performance and potential for phosphorus recovery Peer-reviewed

    Ying Song, Jialing Ni, Yan Guo, Kengo Kubota, Wei-Kang Qi, Yu-You Li

    Chemosphere　313　137580-137580　2023/02

    Publisher: Elsevier BV

    DOI： 10.1016/j.chemosphere.2022.137580 　

    ISSN： 0045-6535

  23. Key factors improving the stability and the loading capacity of nitrogen removal in a hydroxyapatite (HAP)-enhanced one-stage partial nitritation/anammox process Peer-reviewed

    Yujie Chen, Yan Guo, Gaoxuefeng Feng, Kampachiro Urasaki, Guangze Guo, Yu Qin, Kengo Kubota, Yu-You Li

    Chemical Engineering Journal　452　139589-139589　2023/01

    Publisher: Elsevier BV

    DOI： 10.1016/j.cej.2022.139589 　

    ISSN： 1385-8947

  24. Novel Cross-domain Symbiosis between Candidatus Patescibacteria and Hydrogenotrophic Methanogenic Archaea Methanospirillum Discovered in a Methanogenic Ecosystem Peer-reviewed

    Kyohei Kuroda, Kengo Kubota, Shuka Kagemasa, Ryosuke Nakai, Yuga Hirakata, Kyosuke Yamamoto, Masaru K. Nobu, Takashi Narihiro

    Microbes and Environments　37　(4)　ME22063-n/a　2022/11

    Publisher: Japanese Society of Microbial Ecology

    DOI： 10.1264/jsme2.me22063 　

    ISSN： 1342-6311

    eISSN： 1347-4405

  25. Long term operation performance and membrane fouling mechanisms of anaerobic membrane bioreactor treating waste activated sludge at high solid concentration and high flux Peer-reviewed

    Guangze Guo, Yemei Li, Shitong Zhou, Yujie Chen, Kampachiro Urasaki, Yu Qin, Kengo Kubota, Yu-You Li

    Science of The Total Environment　846　157435-157435　2022/11

    Publisher: Elsevier BV

    DOI： 10.1016/j.scitotenv.2022.157435 　

    ISSN： 0048-9697

  26. Symbiosis between Candidatus Patescibacteria and Archaea Discovered in Wastewater-Treating Bioreactors Peer-reviewed

    Kyohei Kuroda, Kyosuke Yamamoto, Ryosuke Nakai, Yuga Hirakata, Kengo Kubota, Masaru K. Nobu, Takashi Narihiro

    mBio　13　(5)　e01711-22　2022/10/26

    Publisher: American Society for Microbiology

    DOI： 10.1128/mbio.01711-22 　

    eISSN： 2150-7511

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    One highly diverse phylogenetic group of Bacteria, Ca . Patescibacteria, remains poorly understood, but, from the few cultured representatives and metagenomic investigations, they are thought to live symbiotically or parasitically with other bacteria or even with eukarya.

  27. Fast formation of anammox granules using a nitrification-denitrification sludge and transformation of microbial community Peer-reviewed

    Lan Lin, Zibin Luo, Kyuto Ishida, Kampachiro Urasaki, Kengo Kubota, Yu-You Li

    Water Research　221　118751-118751　2022/08

    Publisher: Elsevier BV

    DOI： 10.1016/j.watres.2022.118751 　

    ISSN： 0043-1354

  28. 日本各地の下水処理活性汚泥の微生物群集構造とコア微生物群 Peer-reviewed

    久保田健吾, 佐藤幹子, 加藤裕之, 李玉友

    下水道協会誌　59　(717)　132-140　2022/07

  29. Diversity of Candidatus Patescibacteria in Activated Sludge Revealed by a Size-‍Fractionation Approach Peer-reviewed

    Shuka Kagemasa, Kyohei Kuroda, Ryosuke Nakai, Yu-You Li, Kengo Kubota

    Microbes and Environments　37　(2)　ME22027　2022/06

    Publisher: Japanese Society of Microbial Ecology

    DOI： 10.1264/jsme2.me22027 　

    ISSN： 1342-6311

    eISSN： 1347-4405

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    Uncultivated members of Candidatus Patescibacteria are commonly found in activated sludge treating sewage and are widely distributed in wastewater treatment plants in different regions and countries. However, the phylogenetic diversity of Ca. Patescibacteria is difficult to examine because of their low relative abundance in the environment. Since Ca. Patescibacteria members have small cell sizes, we herein collected small microorganisms from activated sludge using a filtration-based size-fractionation approach (i.e., 0.45-0.22‍ ‍μm and 0.22-0.1‍ ‍μm fractions). Fractionated samples were characterized using 16S rRNA gene amplicon and shotgun metagenomic sequence ana-lyses. The amplicon ana-lysis revealed that the relative abundance of Ca. Patescibacteria increased to 73.5% and 52.5% in the 0.45-0.22‍ ‍μm and 0.22-0.1‍ ‍μm fraction samples, respectively, from 5.8% in the unfractionated sample. The members recovered from the two size-fractionated samples included Ca. Saccharimonadia, Ca. Gracilibacteria, Ca. Paceibacteria, Ca. Microgenomatia, class-level uncultured lineage ABY1, Ca. Berkelbacteria, WS6 (Ca. Dojkabacteria), and WWE3, with Ca. Saccharimonadia being predominant in both fraction samples. The number of operational taxonomic units belonging to Ca. Patescibacteria was approximately 6-fold higher in the size-fractionated samples than in the unfractionated sample. The shotgun metagenomic ana-lysis of the 0.45-0.22‍ ‍μm fractioned sample enabled the reconstruction of 24 high-quality patescibacterial bins. The bins obtained were classified into diverse clades at the family and genus levels, some of which were rarely detected in previous activated sludge studies. Collectively, the present results suggest that the overall diversity of Ca. Patescibacteria inhabiting activated sludge is higher than previously expected.

  30. Sodium hypochlorite induced inhibition in anaerobic digestion and possible approach to maintain methane fermentation performance Peer-reviewed

    Jialing Ni, Jiayuan Ji, Kengo Kubota, Yu-You Li

    Bioresource Technology　352　127096-127096　2022/05

    Publisher: Elsevier BV

    DOI： 10.1016/j.biortech.2022.127096 　

    ISSN： 0960-8524

  31. Experimental adaptation of murine norovirus to calcium hydroxide International-journal Peer-reviewed

    Wakana Oishi, Mikiko Sato, Kengo Kubota, Ryoka Ishiyama, Reiko Takai-Todaka, Kei Haga, Kazuhiko Katayama, Daisuke Sano

    Frontiers in Microbiology, section Virology　13　848439　2022/03

    DOI： 10.3389/fmicb.2022.848439 　

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    Slaked lime (calcium hydroxide) is a commonly used disinfectant for fecal sludge. Although viruses are inactivated by lime treatment, whether RNA viruses adapt to lime treatment has not yet been determined. Here, we show that murine norovirus developed higher tolerance during serial passages with lime treatment. We compared synonymous and non-synonymous nucleotide diversities of the three open reading frames of viral genome and revealed that virus populations were subjected to enhanced purifying selection over the course of serial passages with lime treatment. Virus adaptation to lime treatment was coincident with amino acid substitution of lysine to arginine at position 345 (K345R) on the major capsid protein VP1, which accounted for more than 90% of the population. The infectious clones with the K345R produced using a plasmid-based reverse genetics system exhibited greater tolerance in a lime solution, which indicated that the specific amino acid substitution was solely involved in the viral tolerance in lime treatment.

  32. Niche differentiation of phenol-degrading microorganisms in UASB granular sludge as revealed by fluorescence in situ hybridization Peer-reviewed

    Kengo Kubota, Kei Igarashi, Masayoshi Yamada, Yasuyuki Takemura, Yu-You Li, Hideki Harada

    Engineering　9　61-66　2022/03

    Publisher: Elsevier BV

    DOI： 10.1016/j.eng.2021.05.012 　

    ISSN： 2095-8099

  33. Full-scale application of a down-flow hanging sponge reactor combined with a primary sedimentation basin for domestic sewage treatment Peer-reviewed

    Tsutomu Okubo, Tadashi Tagawa, Masanobu Takahashi, Akinori Iguchi, Mamoru Oshiki, Nobuo Araki, Kengo Kubota, Ahmed Tawfik, Shigeki Uemura, Hideki Harada

    Bioprocess and Biosystems Engineering　45　701-709　2022/01

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1007/s00449-022-02689-w 　

    ISSN： 1615-7591

    eISSN： 1615-7605

  34. Microbial characteristics in anaerobic membrane bioreactor treating domestic sewage: Effects of HRT and process performance Peer-reviewed

    Jialing Ni, Jiayuan Ji, Yu-You Li, Kengo Kubota

    Journal of Environmental Sciences　111　392-399　2022/01

    Publisher: Elsevier BV

    DOI： 10.1016/j.jes.2021.04.022 　

    ISSN： 1001-0742

  35. A successful start-up of an anaerobic membrane bioreactor (AnMBR) coupled mainstream partial nitritation-anammox (PN/A) system: A pilot-scale study on in-situ NOB elimination, AnAOB growth kinetics, and mainstream treatment performance Peer-reviewed

    Jiang Wu, Zhe Kong, Zibin Luo, Yu Qin, Chao Rong, Tianjie Wang, Taira Hanaoka, Shinichi Sakemi, Masami Ito, Shigeki Kobayashi, Masumi Kobayashi, Kai-Qin Xu, Takuro Kobayashi, Kengo Kubota, Yu-You Li

    Water Research　207　117783-117783　2021/12

    Publisher: Elsevier BV

    DOI： 10.1016/j.watres.2021.117783 　

    ISSN： 0043-1354

  36. Efficient phosphorus recovery by enhanced hydroxyapatite formation in a high loading anammox expanded bed reactor at 15 °C Peer-reviewed

    Haiyuan Ma, Yuanfan Zhang, Yi Xue, Kengo Kubota, Yu-You Li

    Chemical Engineering Journal　425　130636-130636　2021/12

    Publisher: Elsevier BV

    DOI： 10.1016/j.cej.2021.130636 　

    ISSN： 1385-8947

  37. 食品廃棄物を対象とした省エネルギー型小規模メタン発酵施設の物質・エネルギー収支の評価 Peer-reviewed

    丹野淳, 佐川剛史, 久保田健吾, 李玉友

    土木学会論文集G(環境)　77　(7)　III_367-III_373　2021/11

  38. PMA-PCR法を用いた高温嫌気性消化汚泥の微生物群集構造の解明 Peer-reviewed

    阿部天磨, 佐藤幹子, 矢口淳一, 李玉友, 久保田健吾

    土木学会論文集G(環境)　77　(7)　III_103-III_109　2021/11

  39. The impact of calcium supplementation on methane fermentation and ammonia inhibition of fish processing wastewater Peer-reviewed

    Eli Hendrik Sanjaya, Hui Cheng, Yu Qin, Kengo Kubota, Yu-You Li

    Bioresource Technology　337　125471-125471　2021/10

    Publisher: Elsevier BV

    DOI： 10.1016/j.biortech.2021.125471 　

    ISSN： 0960-8524

  40. Sequence-Specific Capture of Oligonucleotide Probes (SCOPE): a Simple and Rapid Microbial rRNA Quantification Method Using a Molecular Weight Cutoff Membrane International-journal Peer-reviewed

    Yasuyuki Takemura, Yuji Sekiguchi, Kazuaki Syutsubo, Hideki Harada, Tatsuo Omura, Yu-You Li, Kengo Kubota

    Applied and Environmental Microbiology　87　(20)　e01167-21　2021/09/28

    Publisher: American Society for Microbiology

    DOI： 10.1128/aem.01167-21 　

    ISSN： 0099-2240

    eISSN： 1098-5336

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    Microorganisms play integral roles in the earth’s ecosystem. Microbial populations and their activities significantly affect the global nutrient cycles.

  41. Important effects of temperature on treating real municipal wastewater by a submerged anaerobic membrane bioreactor: Removal efficiency, biogas, and microbial community Peer-reviewed

    Jiayuan Ji, Jialing Ni, Akito Ohtsu, Naoko Isozumi, Yisong Hu, Runda Du, Yujie Chen, Yu Qin, Kengo Kubota, Yu-You Li

    Bioresource Technology　336　125306-125306　2021/09

    Publisher: Elsevier BV

    DOI： 10.1016/j.biortech.2021.125306 　

    ISSN： 0960-8524

  42. Evaluation of microbial community succession and trophic transfer using microscopic, molecular and stable isotope ratio analysis in a sponge-based sewage treatment system Peer-reviewed

    Takashi Onodera, Yasuyuki Takemura, Kengo Kubota, Rina Kato, Tsutomu Okubo, Gen Kanaya, Kazuaki Syutsubo, Shigeki Uemura

    Biochemical Engineering Journal　171　108002-108002　2021/07

    Publisher: Elsevier BV

    DOI： 10.1016/j.bej.2021.108002 　

    ISSN： 1369-703X

  43. Achieving superior nitrogen removal performance in low-strength ammonium wastewater treatment by cultivating concentrated, highly dispersive, and easily settleable granule sludge in a one-stage partial nitritation/anammox-HAP reactor Peer-reviewed

    Yan Guo, Chenglei Xie, Yujie Chen, Kampachiro Urasaki, Yu Qin, Kengo Kubota, Yu-You Li

    Water Research　200　117217-117217　2021/07

    Publisher: Elsevier BV

    DOI： 10.1016/j.watres.2021.117217 　

    ISSN： 0043-1354

  44. Application of two anaerobic membrane bioreactors with different pore size membranes for municipal wastewater treatment International-journal Peer-reviewed

    Jiayuan Ji, Satoshi Sakura, Jialing Ni, Yujie Chen, Yisong Hu, Akito Ohtsu, Rong Chen, Hui Cheng, Yu Qin, Toshimasa Hojo, Kengo Kubota, Yu-You Li

    Science of the Total Environment　745　140903　2020/11

  45. 環境DNA解析に基づく宮城県名取川水系中流域における水生昆虫群集構造の時系列変化 Peer-reviewed

    内田典子, 久保田健吾, 会田俊介, 風間聡

    応用生態工学　23　(1)　21-36　2020/09

  46. Temperature-phased anaerobic co-digestion of food waste and paper waste with and without recirculation: biogas production and microbial structure Peer-reviewed

    Lu Li, Zhe Kong, Yu Qin, Jing Wu, Arjun Zhu, Benyi Xiao, Jialing Ni, Kengo Kubota, Yu-You Li

    Science of the Total Environment　724　138168　2020/07

  47. Effect of treated sewage characteristics on duckweed biomass production and microbial communities International-journal Peer-reviewed

    Hiroshi Iwano, Syo Hatohara, Tadashi Tagawa, Hideyuki Tamaki, Yu-You Li, Kengo Kubota

    Water Science and Technology　82　(2)　292-302　2020/07

    DOI： 10.2166/wst.2020.168 　

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    Duckweed biomass production in a duckweed pond fed with three differently treated sewage (i.e. sewage treated by primary sedimentation (PS); conventional activated sludge process (CAS); and downflow hanging sponge process (DHS)) was evaluated in order to assess the effects of water quality on biomass yield. Higher and stable biomass production was observed when the duckweed pond was fed with PS or DHS-effluent than with CAS-effluent, evidently due to the difference in nutrient loads. Availability of nutrients, especially phosphorus, affected the biomass production rate: higher the nutrient, faster the production. Microbial community analysis revealed that the members of Rhizobiales were likely to contribute to stable and high biomass growth. From the results of the study, a sewage treatment system consisting of a primary sedimentation followed by a duckweed pond and a tertiary treatment unit can be proposed to maximize biomass production without compromising treatment objectives. Size and operational parameters of the duckweed pond should be determined primarily based on the nutrient availability in the influent water to maximize duckweed growth.

  48. Aquatic insect community structure revealed by eDNA metabarcoding derives indices for environmental assessment Peer-reviewed

    Noriko Uchida, Kengo Kubota, Shunsuke Aita, So Kazama

    PeerJ　8　e9176　2020/06

    DOI： 10.7717/peerj.9176 　

    ISSN： 2167-8359

  49. EDTA-FISH: A simple and effective approach to reduce non-specific adsorption of probes in fluorescence in situ hybridization (FISH) for environmental samples Peer-reviewed

    Yuki Morono, Kengo Kubota, Daisuke Tsukagoshi, Takeshi Terada

    Microbes and Environments　35　(3)　ME20062　2020/06

    DOI： 10.1264/jsme2.ME20062 　

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    Fluorescence in situ hybridization (FISH) is a widely used molecular technique in microbial ecology. However, the non-specific adsorption of fluorescent probes and resulting high intensity of background signals from mineral particles hampers the specific detection of microbial cells in grain-rich environmental samples, such as subseafloor sediments. We herein demonstrated that a new buffer composition containing EDTA efficiently reduced the adsorption of probes without compromising the properties of the FISH-based probing of microbes. The inclusion of a high concentration of EDTA in the buffer in our protocol provides a simple and effective approach for reducing the background in FISH for environmental samples.

  50. Uncovering viable microbiome in anaerobic sludge digesters by propidium monoazide (PMA)-PCR Peer-reviewed

    Jialing Ni, Shingo Hatori, Yin Wang, Yu-You Li, Kengo Kubota

    Microbial Ecology　2020/05

  51. Simultaneous nitrogen removal and phosphorus recovery using an anammox expanded reactor operated at 25˚C Peer-reviewed

    Haitian Ma, Yi Xue, Yuanfan Zhang, Takuro Kobayashi, Kengo Kubota, Yu-You Li

    Water Research　172　115510　2020/04

    DOI： 10.1016/j.watres.2020.115510 　

    ISSN： 0043-1354

    eISSN： 1879-2448

  52. メタバーコーディングと定量PCRから得た水生昆虫環境DNA量と水生昆虫現存量の関係 Peer-reviewed

    内田典子, 久保田健吾, 会田俊介, 風間聡

    土木学会論文集G(環境)　75　(7)　III_281-III_288　2019/12

    Publisher: Japan Society of Civil Engineers

    DOI： 10.2208/jscejer.75.7_III_281 　

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    <p> Invertebrate species DNA of the cytochrome oxidase subunit 1 region were quantified using environmental DNA (eDNA) extracted from river water using quantitative PCR (qPCR). Subsequently, metabarcoding was conducted to obtain the proportion of stream insects of six taxonomic orders (Ephemeroptera, Plecoptera, Trichoptera, Diptera, Odonata, Coleoptera) in the community. Finally, eDNA concentrations of the six taxonomic groups were calculated by multiplying the proportion of each taxonomy and the quantified invertebrate DNA concentration. As a result, aquatic insect eDNA concentrations displayed significant positive correlations with aquatic insect individuals collected by the conventional surber net sampling (Spearman's rank correlation = 0.74, p < 0.01). Furthermore, positive correlations were observed between the population densities and eDNA concentrations for orders Ephemeroptera, Plecoptera, and Dipetra. These results indicate that the combination of eDNA metabarcoding and qPCR can be an effective way to estimate the abundance of stream insect.</p>

  53. ウキクサ亜科植物を用いた都市下水処理水からのバイオエネルギー生産 Peer-reviewed

    岩野寛, 鳩原翔, 多川正, 玉木秀幸, 李玉友, 久保田健吾

    下水道協会誌　56　(685)　127-134　2019/11

  54. Successful operation performance and syntrophic micro-granule in partial nitritation and anammox reactor treating low-strength ammonia wastewater Peer-reviewed

    Rong Chen, Jiayuan Ji, Yujie Chen, Yasuyuki Takemura, Yuan Liu, Kengo Kubota, Haiyuan Ma, Yu-You Li

    Water Research　155　288-299　2019/05

    Publisher: Elsevier BV

    DOI： 10.1016/j.watres.2019.02.041 　

    ISSN： 0043-1354

  55. Co-production of biohydrogen and biomethane from food waste and paper waste via recirculated two-phase anaerobic digestion process: Bioenergy yields and metabolic distribution Peer-reviewed

    Yu Qin, Lu Li, Jing Wu, Benyi Xiao, Toshimasa Hojo, Kengo Kubota, Jun Cheng, Yu-You Li

    Bioresource Technology　276　325-334　2019/03

  56. Health impact of agricultural drainage water for farmers in the West Nile Delta Peer-reviewed

    Tsutomu Okubo, Akinori Iguchi, Shuya Tanaka, Shota Uchida, Tadashi Tagawa, Mamoru Oshiki, Nobuo Araki, Ahmed Tawfik, Masanobu Takahashi, Kengo Kubota, Hideki Harada, Shigeki Uemura

    International Journal of Environmental Research　13　319-325　2019/03

  57. Characterization of microbial community and main functional groups of prokaryotes in thermophilic anaerobic co-digestion of food waste and paper waste Peer-reviewed

    Lu Li, Yu Qin, Zhe Kong, Jing Wu, Kengo Kubota, Yu-You Li

    Science of The Total Environment　652　709-717　2019/02

  58. Using partial nitrification and anammox to remove nitrogen from low-strength wastewater by co-immobilizing biofilm inside a moving bed bioreactor Peer-reviewed

    Rong Chen, Yasuyuki Takemura, Yuan Liu, Jiayuan Ji, Satoshi Sakuma, Kengo Kubota, Haiyuan Ma, Yu-You Li

    ACS Sustainable Chemistry & Engineering　7　(1)　1353-1361　2019/01

    Publisher: American Chemical Society (ACS)

    DOI： 10.1021/acssuschemeng.8b05055 　

    ISSN： 2168-0485

    eISSN： 2168-0485

  59. 最初沈殿池+DHSシステムに付加する下水処理水の灌漑利用のための消毒システムの開発 Peer-reviewed

    景政柊蘭, 長町晃宏, 井口晃徳, 久保田健吾, 高橋優信, 原田秀樹, 押木守, 荒木信夫, 大久保努, 上村繁樹, 多川正

    土木学会論文集G(環境)　74　(7)　III_333-III_340　2018/12

  60. Anaerobic treatment of N, N-dimethylformamide-containing wastewater by co-culturing two sources of inoculum Peer-reviewed

    Zhe Kong, Lu Li, Rei Kurihara, Kengo Kubota, Yu-You Li

    Water Research　139　228-239　2018/08/01

    Publisher: Elsevier Ltd

    DOI： 10.1016/j.watres.2018.03.078 　

    ISSN： 1879-2448 0043-1354

  61. Response of morphology and microbial community structure of granules to influent COD/SO42 – ratios in an upflow anaerobic sludge blanket (UASB) reactor treating starch wastewater Peer-reviewed

    Xueqin Lu, Jialing Ni, Guangyin Zhen, Kengo Kubota, Yu-You Li

    Bioresource Technology　256　456-465　2018/05/01

    Publisher: Elsevier Ltd

    DOI： 10.1016/j.biortech.2018.02.055 　

    ISSN： 1873-2976 0960-8524

  62. Defining microbial community composition and seasonal variation in a sewage treatment plant in India using a down-flow hanging sponge reactor Peer-reviewed

    Naoki Nomoto, Masashi Hatamoto, Yuga Hirakata, Muntjeer Ali, Komal Jayaswal, Akinori Iguchi, Tsutomu Okubo, Masanobu Takahashi, Kengo Kubota, Tadashi Tagawa, Shigeki Uemura, Takashi Yamaguchi, Hideki Harada

    APPLIED MICROBIOLOGY AND BIOTECHNOLOGY　102　(10)　4381-4392　2018/05

    DOI： 10.1007/s00253-018-8864-1 　

    ISSN： 0175-7598

    eISSN： 1432-0614

  63. Microfluidic PCR amplification and MiSeq amplicon sequencing techniques for high-throughput detection and genotyping of human pathogenic RNA viruses in human feces, sewage, and oysters Peer-reviewed

    Mamoru Oshiki, Takayuki Miura, Shinobu Kazama, Takahiro Segawa, Satoshi Ishii, Masashi Hatamoto, Takashi Yamaguchi, Kengo Kubota, Akinori Iguchi, Tadashi Tagawa, Tsutomu Okubo, Shigeki Uemura, Hideki Harada, Naohiro Kobayashi, Nobuo Araki, Daisuke Sano

    Frontiers in Microbiology　9　830　2018/04/27

    Publisher: Frontiers Media S.A.

    DOI： 10.3389/fmicb.2018.00830 　

    ISSN： 1664-302X

  64. Corrigendum to: Characteristics of DO, organic matter, and ammonium profile for practical-scale DHS reactor under various organic load and temperature conditions (Environmental Technology, (2018), 39, 7, (907-916), 10.1080/09593330.2017.1316319) Peer-reviewed

    Naoki Nomoto, Muntjeer Ali, Komal Jayaswal, Akinori Iguchi, Masashi Hatamoto, Tsutomu Okubo, Masanobu Takahashi, Kengo Kubota, Tadashi Tagawa, Shigeki Uemura, Takashi Yamaguchi, Hideki Harada

    Environmental Technology (United Kingdom)　39　(7)　907-916　2018/04/03

    Publisher: Taylor and Francis Ltd.

    DOI： 10.1080/09593330.2017.1316319 　

    ISSN： 0959-3330 1479-487X

  65. エジプトの高校生を対象とした「水」に関する環境教育プログラムの開発と実践 Peer-reviewed

    大久保勉, 上村繁樹, 井口晃徳, 多川正, 押木守, 久保田健吾, 荒木信夫, 原田秀樹, Ahmed Tawfik, 市村禎二郎

    下水道協会誌　55　(665)　76-82　2018/03

  66. Characterization of sludge properties for sewage treatment in a practical-scale down-flow hanging sponge reactor: Oxygen consumption and removal of organic matter, ammonium, and sulfur Peer-reviewed

    Naoki Nomoto, Masashi Hatamoto, Muntjeer Ali, Komal Jayaswal, Akinori Iguchi, Tsutomu Okubo, Masanobu Takahashi, Kengo Kubota, Tadashi Tagawa, Shigeki Uemura, Takashi Yamaguchi, Hideki Harada

    Water Science and Technology　77　(3)　608-616　2018/02/01

    Publisher: IWA Publishing

    DOI： 10.2166/wst.2017.557 　

    ISSN： 0273-1223

  67. Phase separation and microbial distribution in the hyperthermophilic-mesophilic-type temperature-phased anaerobic digestion (TPAD) of waste activated sludge (WAS) Peer-reviewed

    Yu Qin, Atsushi Higashimori, Li-Jie Wu, Toshimasa Hojo, Kengo Kubota, Yu-You Li

    BIORESOURCE TECHNOLOGY　245　401-410　2017/12

    DOI： 10.1016/j.biortech.2017.08.124 　

    ISSN： 0960-8524

    eISSN： 1873-2976

  68. Treatment performance of practical-scale down-flow hanging sponge reactor using sixth-generation hard sponge media Peer-reviewed

    Tsutomu Okubo, Akinori Iguchi, Masanobu Takahashi, Kengo Kubota, Shigeki Uemura, Hideki Harada

    DESALINATION AND WATER TREATMENT　91　48-54　2017/10

    DOI： 10.5004/dwt.2017.20815 　

    ISSN： 1944-3994

    eISSN： 1944-3986

  69. Phylogenetic diversity and in situ detection of eukaryotes in anaerobic sludge digesters Peer-reviewed

    Miri Matsubayashi, Yusuke Shimada, Yu-You Li, Hideki Harada, Kengo Kubota

    PLOS ONE　12　(3)　e0172888　2017/03

    DOI： 10.1371/journal.pone.0172888 　

    ISSN： 1932-6203

  70. Removal of human pathogenic viruses in a down-flow hanging sponge (DHS) reactor treating municipal wastewater and health risks associated with utilization of the effluent for agricultural irrigation Peer-reviewed

    Naohiro Kobayashi, Mamoru Oshiki, Toshihiro Ito, Takahiro Segawa, Masashi Hatamoto, Tsuyoshi Kato, Takashi Yamaguchi, Kengo Kubota, Masanobu Takahashi, Akinori Iguchi, Tadashi Tagawa, Tsutomu Okubo, Shigeki Uemura, Hideki Harada, Toshiki Motoyama, Nobuo Araki, Daisuke Sano

    WATER RESEARCH　110　389-398　2017/03

    DOI： 10.1016/j.watres.2016.10.054 　

    ISSN： 0043-1354

  71. Sulfidogenesis process to strengthen re-granulation for biodegradation of methanolic wastewater and microorganisms evolution in an UASB reactor Peer-reviewed

    Xueqin Lu, Guangyin Zhen, Jialing Ni, Kengo Kubota, Yu-You Li

    WATER RESEARCH　108　137-150　2017/01

    DOI： 10.1016/j.watres.2016.10.073 　

    ISSN： 0043-1354

  72. Application of DHS Reactor to Sewage Treatment in a Developing Country: Performance during Start-Up Period and under High Organic Load Condition Peer-reviewed

    NOMOTO Naoki, KUBOTA Kengo, TAGAWA Tadashi, UEMURA Shigeki, YAMAGUCHI Takashi, HARADA Hideki, TYAGI Vinay Kumar, ALI Muntjeer, JAYASWAL Komal, MAHARJAN Namita, IGUCHI Akinori, HATAMOTO Masashi, OKUBO Tsutomu, TAKAHASHI Masanobu

    Journal of Japan Society on Water Environment　40　(1)　11-19　2017

    Publisher: Japan Society on Water Environment

    DOI： 10.2965/jswe.40.11 　

    ISSN： 0916-8958

    More details Close

    A full-scale UASB (Up-flow Anaerobic Sludge Blanket) -DHS (Down-flow Hanging Sponge) system, which is a sewage treatment technology for developing countries, was applied in India, and its performance was evaluated. In the initial phase of start-up (up to the 3rd month) , the DHS system showed a 60% CODCr removal efficiency. Up to the 9th month, the operation of the DHS reactor was affected by various unforeseeable situations, e.g. inappropriate volume of DHS influent. However, from the 9th month onwards, a stable flow was received by the DHS reactor. From the 9th to the 12th month, the average CODCr in the DHS effluent was 92 (&plusmn;20) mg L-1. During this period, organic load fluctuated from 2.59 to 12.59 kg-CODCr m-3 day-1, and was high. However, the organic load and removal of the DHS reactor were directly proportional to each other. As a result, it was clarified that this system can maintain its organic matter treatment performance even under high organic load. Also start-up of the DHS reactor was achieved without maintenance, despite some common problem that can be seen in developing countries. It was shown that the DHS reactor is an appropriate sewage treatment technology for developing countries.

  73. PMA-qPCR法へのLED光源の適用とろ過濃縮の影響 Peer-reviewed

    類家渉, 山本歩, 矢口淳一, 久保田健吾, 李玉友

    土木学会論文集G(環境)　72　(7)　III_315-III_323　2016/12

    DOI： 10.2208/jscejer.72.III_315 　

  74. 一次沈澱+DHSシステムによる衛生指標微生物の処理性能評価 Peer-reviewed

    長町晃宏, 井口晃徳, 瀬戸雄太, 久保田健吾, 押木守, 荒木信夫, 大久保努, 上村繁樹, 高橋優信, 原田秀樹, 多川正

    土木学会論文集G(環境)　72　(7)　III_187-III_195　2016/12

    DOI： 10.2208/jscejer.72.III_187 　

  75. Development of a new non-aeration-based sewage treatment technology: Performance evaluation of a full-scale down-flow hanging sponge reactor employing third-generation sponge carriers Peer-reviewed

    Tsutomu Okubo, Kengo Kubota, Takashi Yamaguchi, Shigeki Uemura, Hideki Harada

    WATER RESEARCH　102　(October)　138-146　2016/10

    DOI： 10.1016/j.watres.2016.06.035 　

    ISSN： 0043-1354

  76. Effects of Predation by Protists on Prokaryotic Community Function, Structure, and Diversity in Anaerobic Granular Sludge Peer-reviewed

    Yuga Hirakata, Mamoru Oshiki, Kyohei Kuroda, Masashi Hatamoto, Kengo Kubota, Takashi Yamaguchi, Hideki Harada, Nobuo Araki

    MICROBES AND ENVIRONMENTS　31　(3)　279-287　2016/09

    DOI： 10.1264/jsme2.ME16067 　

    ISSN： 1342-6311

  77. Effect of influent COD/SO42- ratios on biodegradation behaviors of starch wastewater in an upflow anaerobic sludge blanket (UASB) reactor Peer-reviewed

    Xueqin Lu, Guangyin Zhen, Jialing Ni, Toshimasa Hojo, Kengo Kubota, Yu-You Li

    BIORESOURCE TECHNOLOGY　214　(August)　175-183　2016/08

    DOI： 10.1016/j.biortech.2016.04.100 　

    ISSN： 0960-8524

    eISSN： 1873-2976

  78. Long-term operation performance and variation of substrate tolerance ability in an anammox attached film expanded bed (AAFEB) reactor Peer-reviewed

    Yanlong Zhang, Qigui Niu, Haiyuan Ma, Shilong He, Kengo Kubota, Yu-You Li

    BIORESOURCE TECHNOLOGY　211　31-40　2016/07

    DOI： 10.1016/j.biortech.2016.03.055 　

    ISSN： 0960-8524

    eISSN： 1873-2976

  79. Upgrading of mesophilic anaerobic digestion of waste activated sludge by thermophilic pre-fermentation and recycle: Process performance and microbial community analysis Peer-reviewed

    Li-Jie Wu, Atsushi Higashimori, Yu Qin, Toshimasa Hojo, Kengo Kubota, Yu-You Li

    FUEL　169　(April)　7-14　2016/04

    DOI： 10.1016/j.fuel.2015.11.091 　

    ISSN： 0016-2361

    eISSN： 1873-7153

  80. Comparison of hyper-thermophilic-mesophilic two-stage with single-stage mesophilic anaerobic digestion of waste activated sludge: Process performance and microbial community analysis Peer-reviewed

    Li-Jie Wu, Atsushi Higashimori, Yu Qin, Toshimasa Hojo, Kengo Kubota, Yu-You Li

    CHEMICAL ENGINEERING JOURNAL　290　(April)　290-301　2016/04

    DOI： 10.1016/j.cej.2016.01.067 　

    ISSN： 1385-8947

    eISSN： 1873-3212

  81. Evaluation of water distribution and oxygen mass transfer in sponge support media for a down-flow hanging sponge reactor Peer-reviewed

    Uemura, S, Okubo, T, Maeno, K, Takahashi, M, Kubota, K, Harada, H

    International Journal of Environmental Research　10　(2)　265-272　2016/04

  82. Effect of ammonia inhibition on microbial community dynamic and process functional resilience in mesophilic methane fermentation of chicken manure Peer-reviewed

    Qigui Niu, Kengo Kubota, Wei Qiao, Zhaoqian Jing, Yanlong Zhang, Li Yu-You

    JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY　90　(12)　2161-2169　2015/12

    DOI： 10.1002/jctb.4527 　

    ISSN： 0268-2575

    eISSN： 1097-4660

  83. Biocatalysis conversion of methanol to methane in an upflow anaerobic sludge blanket (UASB) reactor: Long-term performance and inherent deficiencies Peer-reviewed

    Xueqin Lu, Guangyin Zhen, Mo Chen, Kengo Kubota, Yu-You Li

    BIORESOURCE TECHNOLOGY　198　691-700　2015/12

    DOI： 10.1016/j.biortech.2015.09.073 　

    ISSN： 0960-8524

    eISSN： 1873-2976

  84. Identification and Detection of Prokaryotic Symbionts in the Ciliate Metopus from Anaerobic Granular Sludge Peer-reviewed

    Yuga Hirakata, Mamoru Oshiki, Kyohei Kuroda, Masashi Hatamoto, Kengo Kubota, Takashi Yamaguchi, Hideki Harada, Nobuo Araki

    MICROBES AND ENVIRONMENTS　30　(4)　335-338　2015/12

    DOI： 10.1264/jsme2.ME15154 　

    ISSN： 1342-6311

  85. Hythane (H-2 + CH4) production from petrochemical wastewater containing mono-ethylene glycol via stepped anaerobic baffled reactor Peer-reviewed

    Ahmed Elreedy, Ahmed Tawfik, Kengo Kubota, Yusuke Shimada, Hideki Harada

    INTERNATIONAL BIODETERIORATION & BIODEGRADATION　105　252-261　2015/11

    DOI： 10.1016/j.ibiod.2015.09.015 　

    ISSN： 0964-8305

    eISSN： 1879-0208

  86. UASB型ANAMMOXプロセスの処理性能に及ぼす基質濃度変化の影響 Peer-reviewed

    馬海元, 張彦隆, 何士龍, 牛啓桂, 久保田健吾, 李玉友

    土木学会論文集G(環境)　71　(7)　III_397-III_404　2015/11

    DOI： 10.2208/jscejer.71.III_397 　

  87. Evaluation of functional microbial community's difference in full-scale and lab-scale anaerobic digesters feeding with different organic solid waste: Effects of substrate and operation factors Peer-reviewed

    Qigui Niu, Takuro Kobayashi, Yasuyuki Takemura, Kengo Kubota, Yu-You Li

    BIORESOURCE TECHNOLOGY　193　110-118　2015/10

    DOI： 10.1016/j.biortech.2015.05.107 　

    ISSN： 0960-8524

    eISSN： 1873-2976

  88. Comparing mesophilic and thermophilic anaerobic digestion of chicken manure: Microbial community dynamics and process resilience Peer-reviewed

    Qigui Niu, Yasuyuki Takemura, Kengo Kubota, Yu-You Li

    Waste Management　43　114-122　2015/09

    Publisher: Elsevier BV

    DOI： 10.1016/j.wasman.2015.05.012 　

    ISSN： 0956-053X

  89. Rapid and sensitive identification of marine bacteria by an improved in situ DNA hybridization chain reaction (quickHCR-FISH) Peer-reviewed

    Tsuyoshi Yamaguchi, Bernhard Maximilian Fuchs, Rudolf Amann, Shuji Kawakami, Kengo Kubota, Masashi Hatamoto, Takashi Yamaguchi

    SYSTEMATIC AND APPLIED MICROBIOLOGY　38　(6)　400-405　2015/09

    DOI： 10.1016/j.syapm.2015.06.007 　

    ISSN： 0723-2020

  90. In situ DNA-hybridization chain reaction (HCR): a facilitated in situ HCR system for the detection of environmental microorganisms Peer-reviewed

    Tsuyoshi Yamaguchi, Shuji Kawakami, Masashi Hatamoto, Hiroyuki Imachi, Masanobu Takahashi, Nobuo Araki, Takashi Yamaguchi, Kengo Kubota

    ENVIRONMENTAL MICROBIOLOGY　17　(7)　2532-2541　2015/07

    DOI： 10.1111/1462-2920.12745 　

    ISSN： 1462-2912

    eISSN： 1462-2920

  91. Operation performance and granule characterization of upflow anaerobic sludge blanket (UASB) reactor treating wastewater with starch as the sole carbon source Peer-reviewed

    Xueqin Lu, Guangyin Zhen, Adriana Ledezma Estrada, Mo Chen, Jialing Ni, Toshimasa Hojo, Kengo Kubota, Yu-You Li

    BIORESOURCE TECHNOLOGY　180　264-273　2015/03

    DOI： 10.1016/j.biortech.2015.01.010 　

    ISSN： 0960-8524

    eISSN： 1873-2976

  92. 途上国のための新規下水処理装置”DHS”におけるスポンジ担体の水の流れと酸素の取込特性の評価 Peer-reviewed

    大久保努, 高橋優信, 久保田健吾, 原田秀樹, 時田政輝, 上村繁樹, 前野一夫

    実験力学　15　(1)　30-37　2015/03

    DOI： 10.11395/jjsem.15.30 　

  93. Molecular Diversity of Eukaryotes in Municipal Wastewater Treatment Processes as Revealed by 18S rRNA Gene Analysis Peer-reviewed

    Kengo Matsunaga, Kengo Kubota, Hideki Harada

    MICROBES AND ENVIRONMENTS　29　(4)　401-407　2014/12

    DOI： 10.1264/jsme2.ME14112 　

    ISSN： 1342-6311

  94. Metagenomic characterization of 'Candidatus Defluviicoccus tetraformis strain TFO71', a tetrad-forming organism, predominant in an anaerobic-aerobic membrane bioreactor with deteriorated biological phosphorus removal Peer-reviewed

    Masaru K. Nobu, Hideyuki Tamaki, Kengo Kubota, Wen-Tso Liu

    ENVIRONMENTAL MICROBIOLOGY　16　(9)　2739-2751　2014/09

    DOI： 10.1111/1462-2920.12383 　

    ISSN： 1462-2912

    eISSN： 1462-2920

  95. 実証規模DHSリアクターの処理性能と硝化細菌群に及ぼすスポンジ担体の影響 Peer-reviewed

    大久保努, 井口晃德, 久保田健吾, 山口隆司, 上村繁樹, 原田秀樹

    下水道協会誌　51　(623)　121-128　2014/09

  96. Metaproteomic Identification of Diazotrophic Methanotrophs and Their Localization in Root Tissues of Field-Grown Rice Plants

    Zhihua Bao, Takashi Okubo, Kengo Kubota, Yasuhiro Kasahara, Hirohito Tsurumaru, Mizue Anda, Seishi Ikeda, Kiwamu Minamisawa

    Applied and Environmental Microbiology　80　(16)　5043-5052　2014/08

  97. Gold-ISH: a nano-size gold particle-based phylogenetic identification compatible with NanoSIMS. International-journal Peer-reviewed

    Kengo Kubota, Yuki Morono, Motoo Ito, Takeshi Terada, Shogo Itezono, Hideki Harada, Fumio Inagaki

    Systematic and applied microbiology　37　(4)　261-6　2014/06

    DOI： 10.1016/j.syapm.2014.02.003 　

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    The linkage of microbial phylogenetic and metabolic analyses by combining ion imaging analysis with nano-scale secondary ion mass spectrometry (NanoSIMS) has become a powerful means of exploring the metabolic functions of environmental microorganisms. Phylogenetic identification using NanoSIMS typically involves probing by horseradish peroxidase-mediated deposition of halogenated fluorescent tyramides, which permits highly sensitive detection of specific microbial cells. However, the methods require permeabilization of target microbial cells and inactivation of endogenous peroxidase activity, and the use of halogens as the target atom is limited because of heavy background signals due to the presence of halogenated minerals in soil and sediment samples. Here, we present "Gold-ISH," a non-halogen phylogenetic probing method in which oligonucleotide probes are directly labeled with Undecagold, an ultra-small gold nanoparticle. Undecagold-labeled probes were generated using a thiol-maleimide chemical coupling reaction and they were purified by polyacrylamide gel electrophoresis. The method was optimized with a mixture of axenic (13)C-labeled Escherichia coli and Methanococcus maripaludis cells and applied to investigate sulfate-reducing bacteria in an anaerobic sludge sample. Clear gold-derived target signals were detected in microbial cells using NanoSIMS ion imaging. It was concluded that Gold-ISH can be a useful approach for metabolic studies of naturally occurring microbial ecosystems using NanoSIMS.

  98. Microbial community composition of a down-flow hanging sponge (DHS) reactor combined with an up-flow anaerobic sludge blanket (UASB) reactor for the treatment of municipal sewage Peer-reviewed

    Kengo Kubota, Mikio Hayashi, Kengo Matsunaga, Akinori Iguchi, Akiyoshi Ohashi, Yu-You Li, Takashi Yamaguchi, Hideki Harada

    BIORESOURCE TECHNOLOGY　151　(January)　144-150　2014/01

    DOI： 10.1016/j.biortech.2013.10.058 　

    ISSN： 0960-8524

    eISSN： 1873-2976

  99. Kinetic analysis on gaseous and aqueous product formation by mixed anaerobic hydrogen-producing cultures Peer-reviewed

    Fang Fang, Yang Mu, Guo-Ping Sheng, Han-Qing Yu, Yu-You Li, Kengo Kubota, Hideki Harada

    INTERNATIONAL JOURNAL OF HYDROGEN ENERGY　38　(35)　15590-15597　2013/11

    DOI： 10.1016/j.ijhydene.2013.03.157 　

    ISSN： 0360-3199

    eISSN： 1879-3487

  100. 実証規模下水処理UASB-DHSシステムにおける後段DHSリアクターの微生物群集構造解析と脱窒細菌群の定量 Peer-reviewed

    井口晃德, 大久保努, 立花真, 永井寛之, 上村繁樹, 山口隆司, 久保田健吾, 原田秀樹

    土木学会論文集G (環境)　69　(7)　III_539-III_546　2013/11

    Publisher: Japan Society of Civil Engineers

    DOI： 10.2208/jscejer.69.III_539 　

    ISSN： 2185-6648

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    Bacterial community structure in municipal wastewater treatment practical-scale 3rd generation (G3) and 6th generation (G6) type Down-flow Hanging sponge (DHS) reactor was investigated by rRNA clone analysis and real-time PCR analysis. 16S rRNA gene clone-based analysis revealed different microbial composition between high-water-temperature period and low-water-temperature period was observed. Clone-based bacterial diversity was increased in high-temperature period. By contrast in low-temperature period, those composition was dramatically changed to lower diversity. Denitrifying bacteria was quantified by real-time PCR, which indicated that denitrifying bacteria were present in a ratio almost the same amount regardless of the height of the reactor. PCR-based quantifying analysis also revealed that DHS sponge can be retained denitrifying bacteria as well as activated sludge process.

  101. パームオイル工場廃液を処理するラグーンシステムからのメタンガス放出量の測定 Peer-reviewed

    谷川大輔, 久保田健吾, 佐瀬信哉, 珠坪一晃, Chen Sau Soon, Yunus Mohammed, Faisal Mohammed, 山口隆司, 原田秀樹

    土木学会論文集G (環境)　69　(4)　157-165　2013/11

    DOI： 10.2208/jscejer.69.157 　

  102. Characterization of the retained sludge in a down-flow hanging sponge (DHS) reactor with emphasis on its low excess sludge production Peer-reviewed

    Takashi Onodera, Kengo Matsunaga, Kengo Kubota, Ryoko Taniguchi, Hideki Harada, Kazuaki Syutsubo, Tsutomu Okubo, Shigeki Uemura, Nobuo Araki, Masayoshi Yamada, Masahito Yamauchi, Takashi Yamaguchi

    Bioresource Technology　136　169-175　2013

    Publisher: Elsevier Ltd

    DOI： 10.1016/j.biortech.2013.02.096 　

    ISSN： 1873-2976 0960-8524

  103. Nutrient Removal and Phosphorus Recovery from Municipal Sewage Using Anaerobic/Anoxic Sequencing Batch Reactor. Peer-reviewed

    SAKAMOTO Kenichi, YAMAGUCHI Takashi, HATAMOTO Masashi, TAKAHASHI Masanobu, KUBOTA Kengo, ARAKI Nobuo, YAMAZAKI Shinichi, OKUBO Tsutomu, UEMURA Shigeki, HARADA Hideki

    Journal of Japan Society of Civil Engineers, Ser. G (Environmental Research)　69　(7)　III_121-III_127　2013

    Publisher: Japan Society of Civil Engineers

    DOI： 10.2208/jscejer.69.III_121 　

    ISSN： 2185-6648

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    &nbsp;In this study, nitrogen and phosphorus were removed by using denitrifying phosphate-accumulating organisms (DPAOs). An anaerobic / anoxic sequencing batch reactor (A2SBR) was operated to culture the DPAOs. A2SBR system achieved 77% of nitrogen and 83% of phosphorus removal efficiency in a system feeding actual sewage. The result showed that this system is suitable for the nutrient removal of sewage treatment. The A2SBR sample was then subjected to microbial community analysis using FISH method and the result showed that a stable treatment process was performed at 15% or more of PAOs ratio. Additionally, a hydroxyapatite precipitation (HAP) reactor was applied as the downstream system. As a result 29% of phosphorus was recovered from the sewage by the calcium-added physicochemical technology. This HAP reactor became applicable with concentration of the phosphorus around ten-fold, although influent phosphorus was as low as about 4 mg-P/L.

  104. Effects of nickel ion on microbial community structures under high salt concentration environment and isolation of novel nickel resistant microorganisms Peer-reviewed

    SHIBUYA Sachiko, ISHIKAWA Ayumi, TAMAKI Hideyuki, HARADA Hideki, KUBOTA Kengo

    Journal of Japan Society of Civil Engineers, Ser. G (Environmental Research)　69　(7)　III_241-III_248　2013

    Publisher: Japan Society of Civil Engineers

    DOI： 10.2208/jscejer.69.III_241 　

    ISSN： 2185-6648

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    &nbsp;Effects of nickel ion on microbial community structures under high salt concentration environment were investigated. Nickel resistant microbial cultures were enriched in a chemostat reactor by feeding landfill leachate in which nickel (II) chloride was added. Stable enrichment was established up to 2 mM of nickel (II) chloride addition. Microbial community structures of enrichment cultures were analyzed by pyrosequencing. Drastic community change, even at class level, was observed when nickel (II) chloride concentration was increased. In the culture enriched with 2 mM of nickel ion, Nitratireductor were the dominant genus, indicating that they are likely to have nickel resistance under the high salt concentration environment. Novel nickel resistant microorganisms, including the member of Nitratireductor, were isolated from the reactor.

  105. 18S rRNA遺伝子情報を用いた排水処理汚泥の真核生物群集構造解析 Peer-reviewed

    松永健吾, 久保田健吾, Erica Vonasek, 竹村泰幸, 原田秀樹

    土木学会論文集G (環境)　68　(7)　III_13-III_20　2012/11

    Publisher: Japan Society of Civil Engineers

    DOI： 10.2208/jscejer.68.III_13 　

    ISSN： 2185-6648

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    Eukaryotic communities in two different wastewater processes, a full-scale anaerobic/aerobic activated sludge process and a pilot-scale Down-flow hanging sponge (DHS) process, was evaluated by constrcting 18S rRNA gene clone library. The clones close to the member of Opercularia was found to be a dominant eukaryote in anaerobic and aerobic activated sludges, whereas the clones affiliated to phylum Arthropoda were the most predominant in the DHS sludges. Eukaryotic communities of the activated sludges as revealed by 18S rRNA gene clone library were in agreement with published data determined by microscopic observation. On the other hand, eukaryotic communities as revealed by 18S rRNA gene clone library and microscopic observation were significantly different in the case of the DHS sluges; therefore, it was suggested that both molecular and microscopic approaches need to be conducted. The molecular approach can also reveal unidentified eukaryotic gene sequences, which might be important for understanding wastewater treatment processes.

  106. Detection of single-copy functional genes in prokaryotic cells by two-pass TSA-FISH with polynucleotide probes Peer-reviewed

    Shuji Kawakami, Takuya Hasegawa, Hiroyuki Imachi, Takashi Yamaguchi, Hideki Harada, Akiyoshi Ohashi, Kengo Kubota

    JOURNAL OF MICROBIOLOGICAL METHODS　88　(2)　218-223　2012/02

    DOI： 10.1016/j.mimet.2011.11.014 　

    ISSN： 0167-7012

  107. Characterization of sulfide-oxidizing microbial mats developed inside a full-scale anaerobic digester employing biological desulfurization Peer-reviewed

    Takuro Kobayashi, Yu-You Li, Kengo Kubota, Hideki Harada, Takeki Maeda, Han-Qing Yu

    APPLIED MICROBIOLOGY AND BIOTECHNOLOGY　93　(2)　847-857　2012/01

    DOI： 10.1007/s00253-011-3445-6 　

    ISSN： 0175-7598

  108. Microbial Community Structure Analysis of Landfill Leachate-Treating Reactor by Using Molecular and Cultivation Techniques Peer-reviewed

    ISHIKAWA Ayumi, SHIBUYA Sachiko, TAMAKI Hideyuki, HARADA Hideki, KUBOTA Kengo

    Journal of Japan Society of Civil Engineers, Ser. G (Environmental Research)　68　(7)　III_21-III_30　2012

    Publisher: Japan Society of Civil Engineers

    DOI： 10.2208/jscejer.68.III_21 　

    ISSN： 2185-6648

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    &nbsp;Microbial community structure of a landfill leachate-treating nitrifying reactor was investigated by using molecular cloning and cultivation techniques. The most dominant phylum in the community was the Proteobacteria, which covers 65% of the clone library. In addition, candidate division TM7, OD1, and TM6 were also found as major groups. Clones close to the microorganisms capable of degrading persistent organic matters and of oxidizing ammonia and nitrite in marine environments were retrieved. Total 312 strains were isolated from agar- and gellan gum-based media, in which the isolates close to PAH degraders were obtained. Furthermore, phylogenetically novel microorganisms were also isolated.

  109. Hybridization Chain Reaction (HCR) 法を用いた新規高感度FISH法の開発 Peer-reviewed

    山口剛士, 川上周司, 幡本将史, 高橋優信, 久保田健吾, 井町寛之, 荒木信夫, 山口隆司

    土木学会論文集G (環境)　67　(7)　III_93-III_98　2011/11

  110. 分子量分画膜を用いた迅速・簡便な配列特異的rRNA定量法の開発 Peer-reviewed

    竹村泰幸, 関口勇地, 原田秀樹, 久保田健吾

    土木学会論文集G (環境)　67　(7)　III_85-III_92　2011/11

  111. UASB-DHSシステムによる高濃度フェノール廃水の連続処理特性とUASB内微生物叢解析 Peer-reviewed

    山田真義, 久保田健吾, 高橋優信, 田中秀治, 山口隆司, 長野晃弘, 原田秀樹, 山内正仁

    土木学会論文集G (環境)　67　(7)　III_75-III_84　2011/11

  112. パームオイル圧搾廃液 (POME) を処理する密閉型嫌気性消化槽の処理特性と微生物群集構造 Peer-reviewed

    渋谷幸子, 久保田健吾, 谷川大輔, 射手園章吾, 珠坪一晃, 山口隆司, 関口勇地, S. S. Chen, M. F, M. Yunus, 原田秀樹

    土木学会論文集G (環境)　67　(7)　III_59-III_68　2011/11

  113. 微生物コミュニティレベルでみる高級脂肪酸阻害メカニズム Peer-reviewed

    射手園章吾, 久保田健吾, 谷川大輔, 珠坪一晃, 関口勇地, 山口隆司, 原田秀樹

    土木学会論文集G (環境)　67　(7)　III_51-III_58　2011/11

  114. Novel Online Monitoring and Alert System for Anaerobic Digestion Reactors Peer-reviewed

    Fang Dong, Quan-Bao Zhao, Wen-Wei Li, Guo-Ping Sheng, Jin-Bao Zhao, Yong Tang, Han-Qing Yu, Kengo Kubota, Yu-You Li, Hideki Harada

    ENVIRONMENTAL SCIENCE & TECHNOLOGY　45　(20)　9093-9100　2011/10

    DOI： 10.1021/es202245f 　

    ISSN： 0013-936X

  115. Anaerobic degradation of palm oil mill effluent (POME) Peer-reviewed

    W. Yoochatchaval, S. Kumakura, D. Tanikawa, T. Yamaguchi, M. F. M. Yunus, S. S. Chen, K. Kubota, H. Harada, K. Syutsubo

    WATER SCIENCE AND TECHNOLOGY　64　(10)　2001-2008　2011

    DOI： 10.2166/wst.2011.782 　

    ISSN： 0273-1223

  116. 無曝気方式の新規下水処理技術の開発 −第三世代型担体を適用した実規模DHSリアクターの処理性能評価− Peer-reviewed

    大久保努, 山口隆司, 久保田健吾, 原田秀樹

    土木学会論文集G　66　149-158　2010/09

    DOI： 10.2208/jscejg.66.149 　

  117. 都市下水処理UASB-DHSシステムにおけるG3型DHSリアクターの微生物群集構造解析 Peer-reviewed

    久保田健吾, 林幹大, 松永健吾, 大橋晶良, 李玉友, 山口隆司, 原田秀樹

    土木学会論文集G　66　56-64　2010/03

    DOI： 10.2208/jscejg.66.56 　

  118. DHS-USB方式による埋立地浸出水の省エネルギー型窒素除去システムの開発 Peer-reviewed

    大久保努, 渡辺悠介, 大浦一恵, 久保田健吾, 李玉友, 原田秀樹

    土木学会論文集G　66　9-16　2010/02

    DOI： 10.2208/jscejg.66.9 　

  119. Detection of single copy genes by two-pass tyramide signal amplification fluorescence in situ hybridization (two-pass TSA-FISH) with single oligonucleotide probes Peer-reviewed

    Shuji Kawakami, Kengo Kubota, Hiroyuki Imachi, Takashi Yamaguchi, Hideki Harada, Akiyoshi Ohashi

    Microbes and Environments　25　(1)　15-21　2010

    DOI： 10.1264/jsme2.ME09180 　

    ISSN： 1342-6311

  120. Characterization of start-up performance and archaeal community shifts during anaerobic self-degradation of waste-activated sludge Peer-reviewed

    Takuro Kobayashi, Daisuke Yasuda, Yu-You Li, Kengo Kubota, Hideki Harada, Han-Qing Yu

    BIORESOURCE TECHNOLOGY　100　(21)　4981-4988　2009/11

    DOI： 10.1016/j.biortech.2009.05.043 　

    ISSN： 0960-8524

  121. 下水処理UASB後段のDHSにおける余剰汚泥量の抑制要因の評価 Peer-reviewed

    松永健吾, 小野寺崇, 上村繁樹, 山田真義, 山内正仁, 高橋優信, 久保田健吾, 原田秀樹, 山口隆司

    環境工学研究論文集　46　623-628　2009/11

  122. 機能遺伝子を標的としたtwo-pass TSA-FISH法による環境中未培養微生物の機能推定 Peer-reviewed

    長谷川拓也, 川上周司, 久保田健吾, 井町寛之, 大橋晶良, 原田秀樹

    環境工学研究論文集　46　537-544　2009/11

  123. バイオガスの生物脱硫に寄与する硫黄マットの反応環境と微生物生態 Peer-reviewed

    小林拓朗, 李玉友, 久保田健吾, 原田秀樹

    環境技術　38　(9)　642-651　2009/09

    Publisher: Society of Environmental Conservation Engineering

    DOI： 10.5956/jriet.38.642 　

    ISSN： 0388-9459

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    Hydrogen sulfide in a biogas can be removed economically by adding a small amount of air into the headspace of a digester. A microbial mat developed in the headspace of the digester as a result of the sulfide oxidation. Microbial mats containing sulfur filaments developed in the headspace of the digester. Little is known about microbial ecology and the environment in the digester with a biological desulfurization system. This study is an attempt to clarify the internal environment and the microbial ecology in the mats. The result of microelectrode experiments revealed that the O2/S2- supply ratio as a reaction-controlling factor was 0.45 which is a suitable range for sulfur formation. The results of CARD-FISH analysis suggested that Sulfurimonas sp. related bacteria were active sulfur-oxidizing bacteria producing sulfur from H2S and responsible for the formation of filamentous sulfur.

  124. 硫黄酸化細菌を利用したメタン発酵槽の微好気環境下におけるバイオガス脱硫 Peer-reviewed

    小林拓朗, 李玉友, 久保田健吾, 原田秀樹, 前田武己, 河合和保, 吉田尊彦

    土木学会論文集G　65　(2)　104-113　2009/06

    Publisher: Japan Society of Civil Engineers

    DOI： 10.2208/jscejg.65.104 　

    ISSN： 1880-6082

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    Biological removal of hydrogen sulfide in biogas, which was produced from an anaerobic digester treating cattle manure with a HRT of 25 days, was carried out by adding a low amount of air to the headspace of the digester (approximately 1% of oxygen concentration in the digester). The concentration of hydrogen sulfide was successfully reduced from 3,500 ppm to a low level of 1,100 ppm after air adding. A microbial mat with an elemental sulfur content of 90% per g-TS was developed in the headspace of the digester as a result of the sulfide oxidation. Cloning analysis revealed that close-relatives of Halothiobacillus neapolitanus and Sulfurimonas sp., both known as sulfide oxidizer, were predominant in the mat and might be responsible for the sulfide oxidation and for the elemental sulfur accumulation under microaerophilic environment. A microbial sulfide oxidation activity test demonstrated that the wetness of the mat is important to the microbial sulfide oxidation activity. These results suggest that an appropriate design for microbial habitat in a digester is one of the important factors for the biological hydrogen sulfide removal.

  125. Effects of seed sludge on fermentative characteristics and microbial community structures in thermophilic hydrogen fermentation of starch Peer-reviewed

    Yohei Akutsu, Yu-You Li, Madan Tandukar, Kengo Kubota, Hideki Harada

    INTERNATIONAL JOURNAL OF HYDROGEN ENERGY　33　(22)　6541-6548　2008/11

    DOI： 10.1016/j.ijhydene.2008.08.038 　

    ISSN： 0360-3199

  126. DHSリアクターによる無曝気方式硝化プロセスの処理特性 Peer-reviewed

    服部賢, 小地沢俊宏, 渡辺悠介, タンドカール・マダン, 久保田健吾, 李玉友, 原田秀樹

    環境工学研究論文集　45　317-324　2008/11

    Publisher: Japan Society of Civil Engineers

    DOI： 10.11532/proes1992.45.317 　

    ISSN： 1341-5115

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    The objective of this study is to evaluate applicability of DHS reactor to nitrification process receiving a high strength ammonium influent. The most prominent advantage of DHS reactor is no need for external aeration because sponge carriers are exposed to air. DHS reactor in this study was operated with an artificial wastewater composed of ammonium-nitrogen solely (completely organic free) at ambient temperature. The total experimental period of 350·days was divided into 4 phases according to ammonium-nitrogen loading rate. The maximum nitrification rate of 1.78 kg-N·m-3·d-1 was observed at a HRT of 6 h and at an ammonium-nitrogen loading rate of 2.00 kg-N·m-3·d-1. The maximum oxygen uptake rate was estimated from nitrogen elimination rate to be 66 g-O2·g-VSS-1·d-1. Nitrification potential of DHS reactor was verified to be comparable to other types of nitrification processes equipped with external aeration. There is a need of further investigation to enhance the nitrification performance by overcoming the restriction of partial oxygen permeation into carrier-sponge inward depth.

  127. 余剰活性汚泥の嫌気性自己分解によるメタン発酵スタートアップ方法およびその過程における微生物群構造の変化 Peer-reviewed

    小林拓朗, 安田大介, 李玉友, 久保田健吾, 原田秀樹, 岡庭良安

    水環境学会誌　31　(9)　525-532　2008/09

    Publisher: Japan Society on Water Environment

    DOI： 10.2965/jswe.31.525 　

    ISSN： 0916-8958

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    The start-up of mesophilic anaerobic digestion from waste activated sludge with internal inoculum was carried out in a laboratory-scale completely mixed reactor. The microbial community shift during the start-up period was monitored by molecular techniques. The self-degradation period, when the digester was operated in batch mode, consists of two characteristic phases, acidogenic (A) phase and methanogenic (M) phase. During the A phase, Volatile Fatty Acid (VFA) accumulation and a low level of methane production were observed. On the other hand, during the M phase, rapid VFA degradation and an increase in methane production were observed. Clone analysis results suggest that after self-degradation, Methanosarcina and Methanoregula were predominant at day 30, while the former was detected at low level (4%) and the latter was not detected at day 0. The population dynamics of the archaeal community were investigated by Real-time PCR. During the transition from A phase to M phase, the digester showed a significant increase by one order in the Methanosarcina rRNA gene. A significant positive correlation between the population of Methanosarcina and methane production rate was observed.

  128. デンプンの高温水素発酵細菌群の構造解析 Peer-reviewed

    堆洋平, 李玉友, 久保田健吾, 原田秀樹

    生物工学会誌　86　(4)　157-163　2008/04

    Publisher:

    ISSN： 0919-3758

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    Microbial community structures in thermophilic hydrogen fermentation (55℃) were analyzed by molecular methods, including polymerase chain reaction-denatured gel gradient electrophoresis (PCR-DGGE), real-time PCR, and cloning methods. Samples used for analyses were obtained from five identical completely stirred tank reactors (CSTRs) of thermophilic hydrogen fermentation from starch, which were seeded with five different types of inoculum. The closest relatives of the genus Thermoanaerobacterium, which is known to be a typical hydrogen producer, predominated in all reactors. However, microbial community structures abundant in each reactor were different, indicating that the type of inoculum is one of the important factors for thermophilic hydrogen fermentation.

  129. Evaluation of enzymatic cell treatments for application of CARD-FISH to methanogens Peer-reviewed

    Kengo Kubota, Hiroyuki Imachi, Shuji Kawakami, Kohei Nakamura, Hideki Harada, Akiyoshi Ohashi

    JOURNAL OF MICROBIOLOGICAL METHODS　72　(1)　54-59　2008/01

    DOI： 10.1016/j.mimet.2007.10.006 　

    ISSN： 0167-7012

  130. Two-pass TSA-FISH法によるメタン生成古細菌のmcr遺伝子の検出 Peer-reviewed

    川上周司, 久保田健吾, 井町寛之, 原田秀樹, 大橋晶良

    環境工学研究論文集　43　143-148　2006/11

    Publisher: Japan Society of Civil Engineers

    DOI： 10.11532/proes1992.43.143 　

    ISSN： 1341-5115

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    Applicability and reliability of two-pass tyramide signal amplification-fluorescence in situ hybridization (two-pass TSA-FISH) with PCR generated polydeoxyribonucleotide probes, specific for chromosomal encoded gene, methyl coenzyme M reductase (mcr) in Methanococcus vannielli, was tested and evaluated. The probes were labeled with dinitrophenol (DNP) and the efficiency of probe-labeling was improved by optimizing the concentrations of DNP-labeled nucleotide and Mg2+ in PCR mixture. The target mcr gene was successfully detected, which was again verified by the disappearance of the signals after treating the target with DNase prior to hybridization or washing with high stringency buffer. However, a few nonspecific signals were observed when the method was applied to pure cultures of Methanoculleus bourgensis and Escherichia coli.

  131. Visualization of mcr mRNA in a methanogen by fluorescence in situ hybridization with an oligonucleotide probe and two-pass tyramide signal amplification (two-pass TSA-FISH) Peer-reviewed

    Kengo Kubota, Akiyoshi Ohashi, Hiroyuki Imachi, Hideki Harada

    JOURNAL OF MICROBIOLOGICAL METHODS　66　(3)　521-528　2006/09

    DOI： 10.1016/j.mimet.2006.02.002 　

    ISSN： 0167-7012

  132. Improved in situ hybridization efficiency with locked-nucleic-acid-incorporated DNA probes Peer-reviewed

    Kengo Kubota, Akiyoshi Ohashi, Hiroyuki Imachi, Hideki Harada

    APPLIED AND ENVIRONMENTAL MICROBIOLOGY　72　(8)　5311-5317　2006/08

    DOI： 10.1128/AEM.03039-05 　

    ISSN： 0099-2240

  133. メタン生成古細菌にCARD-FISH法を適用するための細胞壁処理 Peer-reviewed

    久保田健吾, 大橋晶良, 井町寛之, 原田秀樹

    環境工学研究論文集　40　363-371　2003/11

    Publisher: Japan Society of Civil Engineers

    DOI： 10.11532/proes1992.40.363 　

    ISSN： 1341-5115

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    Cell wall treatment methods were investigated to apply CARD (catalyzed reporter deposition)-FISH (fluorescence in situ hybridization) technique for the detection of methanogenic archaea. To determine the effective treatment for enhancing the cell wall permeability, we employed purely cultured methanogens, which have any one of four different types of cell wall: s-layer, pseudomurein, sheath and methanochondroitin, and tested pretreatments such as lysozyme-EDTA, detergents, proteinase K, pseudomurein endopeptidase extracted from Methanothermobacter wolfei, and freeze and thaw cycle. Of eight tested methanogens, six species were successfully detected by CARD-FISH, but some of them stained heterogeneously. Applicability of CARD-FISH with the treatments, proteinase K and pseudomurein endopeptidase, was evaluated using anaerobic digested sludge. As results, CARD-FISH was successfully applied for the detection of methanogens in anaerobic digested sludge with proteinase K treatment.

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Misc. 12

  1. Recent advances and challenges in low-cost biosynthesis of polyhydroxyalkanoates: A review

    Lanjia Pan, Yang Zhang, Jie Li, Qingsheng Qi, Shuhua Wang, Kengo Kubota, Yin Wang

    International Journal of Biological Macromolecules　331　148379-148379　2025/11

    Publisher: Elsevier BV

    DOI： 10.1016/j.ijbiomac.2025.148379 　

    ISSN： 0141-8130

  2. Mitigating nitrous oxide emission by an ultra-fast bioprocess enabling the removal of high concentration N2O

    Ryota Maeda, Mikiko Sato, Kiwamu Minamisawa, Kengo Kubota

    bioRxiv　2024/10/08

    Publisher: Cold Spring Harbor Laboratory

    DOI： 10.1101/2024.10.08.615939 　

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    Abstract Nitrous oxide (N₂O) is known as a greenhouse gas as well as an ozone-depleting substance. Wastewater treatment process is one of the sources of N2O emission, and the high concentrations of N₂O in off-gas were reported from an anaerobic ammonium oxidation process. This study developed a novel N₂O removal process using a down-flow hanging sponge reactor to remove high concentrations of N₂O. More than 96% removal efficiencies were achieved for up to 300 ppm N₂O with 3 min gas retention time (GRT), and more than 99% removal efficiency was obtained for 2,000 ppm N2O with 18 min GRT. A maximum removal rate of 161 ± 26 mg-N/L-reactor/day was achieved, that was over 10 times faster than the pioneering process. Kinetic analysis indicated that the N₂O dissolution rate is a crucial factor in determining the N₂O removal rate in the reactor. Various N₂O reducers belonging to both clade I and II were detected in reactors, andAzonexuswas thought to play a key role.

  3. Towards an understanding of Candidate phyla radiation (CPR)/Candidatus Patescibacteria from perspectives of wastewater treatment systems

    Kuroda Kyohei, Narihiro Takashi, Fujii Naoki, Nakajima Meri, Kagemasa Shuka, Nakai Ryosuke, Satoh Hisashi, Kubota Kengo, Kindaichi Tomonori

    Japanese Society of Microbial Ecology　38　(1)　2-13　2023/03/01

    Publisher: Japanese Society of Microbial Ecology

    DOI： 10.20709/jsmeja.38.1_2 　

    eISSN： 2424-1989

  4. Recent Progress in Cutting-edge Monitoring Tools for Microbiomes in Engineered Systems Peer-reviewed

    Akihiko TERADA, Tomoyuki HORI, Kengo KUBOTA, Futoshi KURISU, Ikuro KASUGA, Tomonori KINDAICHI, Tsukasa ITO

    Journal of Japan Society on Water Environment　45　(3)　91-105　2022/05

    Publisher: Japan Society on Water Environment

    DOI： 10.2965/jswe.45.91 　

    ISSN： 0916-8958

    eISSN： 1881-3690

  5. Microbial community dynamics in anaerobic digesters treating organic fraction of municipal solid waste Peer-reviewed

    Vinay Kumar Tyagi, Akansha Bhatia, Kengo Kubota, Ankur Rajpal, Banafsha Ahmed, Abid Ali Khan, A.A. Kazmi, Manish Kumar

    Environmental Technology & Innovation　21　101303-101303　2021/02

    Publisher: Elsevier BV

    DOI： 10.1016/j.eti.2020.101303 　

    ISSN： 2352-1864

  6. Characterization of downflow hanging sponge reactors with regard to structure, process function, and microbial community compositions Invited Peer-reviewed

    Masashi Hatamoto, Tsutomu Okubo, Kengo Kubota, Takashi Yamaguchi

    Applied Microbiology and Biotechnology　102　(24)　10345-10352　2018/12/01

    DOI： 10.1007/s00253-018-9406-6 　

    ISSN： 0175-7598

    eISSN： 1432-0614

  7. 嫌気性処理における微生物群集構造解析 Invited

    久保田健吾

    環境システム計測制御学会　22　(4)　36-40　2018/03

  8. Construction of a Cell Surface Engineered Yeast Aims to Selectively Recover Molybdenum, a Rare Metal Peer-reviewed

    Mei-Fang Chien, Naoya Ikeda, Kengo Kubota, Chihiro Inoue

    Solid State Phenomena　262　421-424　2017/09

  9. 微生物生態と水環境工学に関する最新研究動向

    栗栖太, 伊藤司, 青井議輝, 久保田健吾, 佐藤弘泰, 金田一智規, 井上謙吾, 寺田昭彦

    水環境学会誌　39　(12)　444-451　2016/12

  10. 総論 水処理分野における顕微鏡観察 Invited

    久保田健吾

    水環境学会誌　38　(10)　360-364　2015/10

    Publisher: 日本水環境学会 ; 1992-

    ISSN： 0916-8958

  11. CARD-FISH for environmental microorganisms: Technical advancement and future applications Invited Peer-reviewed

    Kengo Kubota

    Microbes and Environments　28　(1)　3-12　2013

    DOI： 10.1264/jsme2.ME12107 　

    ISSN： 1342-6311 1347-4405

  12. Two-pass TSA-FISH法を用いた微生物機能遺伝子の視覚的検出技術 Peer-reviewed

    長谷川拓也, 川上周司, 井町寛之, 大橋晶良, 原田秀樹, 久保田健吾

    環境バイオテクノロジー学会誌　10　(2)　97-103　2010/12

    Publisher: 環境バイオテクノロジー学会

    ISSN： 1347-1856

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Books and Other Publications 6

  1. Visualization of Microorganisms in Bioprocesses

    Tsuyoshi Yamaguchi, Kengo Kubota

    2018/01

  2. Nanoscale Secondary-Ion Mass Spectrometry Imaging of Biological Structures

    Kengo Kubota, Yuki Morono, Motoo Ito

    2017/03/25

  3. Protocol for in situ detection of functional genes of microorganisms by two-pass TSA-FISH

    Kengo Kubota, Shuji Kawakami

    2016

  4. 顕微鏡の基礎, 進化する顕微鏡, 嫌気性廃水処理の微生物

    久保田健吾

    2014/07

  5. 微生物検出向け新規高感度FISH法の開発

    山口隆司, 山口剛士, 幡本将史, 中村明靖, 川上周司, 久保田健吾

    2013/10

  6. 水浄化技術の最新動向

    山口隆司, 高橋優信, 幡本将史, 川上周司, 久保田健吾, 原田秀樹, 山田真義, 山内正仁, 荒木信夫, 山崎慎一

    2011/06

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Presentations 85

  1. PMA-PCR 法を用いた高温嫌気性消化汚泥の微生物群集構造解析

    阿部天磨, 李玉友, 久保田健吾

    第55回日本水環境学会　2021/03/10

  2. 水道管路網の時空間ピンポイント劣化予測に用いる水質情報の同定に関する研究

    三浦耀平, 久保田健吾, 丸尾知佳子, 水谷大二郎, 佐野大輔

    第55回日本水環境学会　2021/03/10

  3. サイズ分画した活性汚泥の微生物学的特性把握

    景政柊蘭, 久保田健吾, 李玉友, 黒田恭平, 中井亮佑

    第55回日本水環境学会　2021/03/10

  4. 最初沈殿池+ウキクサ亜科植物培養池+DHSリアクターを用いた実下水処理およびバイオマス生産のオンサイト実験

    大谷尭, 神拓海, 李玉友, 久保田健吾

    第55回日本水環境学会　2021/03/10

  5. Heminを用いた微生物の新規視覚的検出法の開発

    浦崎幹八郎, 李玉友, 久保田健吾

    第55回日本水環境学会　2021/03/10

  6. 下水処理プロセス中のテトラサイクリン系耐性菌の探索

    丸山涼介, 久保田健吾, 李玉友

    第55回日本水環境学会　2021/03/10

  7. PMA-PCR法を⽤いた嫌気性消化汚泥の微⽣物叢解析：中温と⾼温の⽐較

    阿部天磨, 矢口淳一, 李玉友, 久保田健吾

    令和2年度 土木学会東北支部 技術研究発表会　2021/03/06

  8. 異なる産業廃⽔を処理するグラニュール汚泥の微⽣物群集の⽐較

    三浦花梨, 針生紗雪, 浦崎幹八郎, 庄子俊男, 久保田健吾

    令和2年度 土木学会東北支部 技術研究発表会　2021/03/06

  9. Diversity and Metabolic Characteristics of Patescibacteria in Activated Sludge

    景政柊蘭, LI Yu-You, 久保田健吾, 黒田恭平, 中井亮佑

    日本水環境学会シンポジウム講演集　2021

  10. 長期連続メタン発酵処理による初沈汚泥とウキクサのエネルギー資源化

    神拓海, 岩野寛, 大谷尭, 李玉友, 久保田健吾

    第57回環境工学研究フォーラム　2020/12/10

  11. 最初沈殿池+ウキクサ亜科植物培養槽+DHSリアクターを用いた下水処理およびバイオマス生産のオンサイト実証実験

    大谷尭, 神拓海, 李玉友, 久保田健吾

    第57回環境工学研究フォーラム　2020/12/10

  12. 初沈汚泥とウキクサの連続メタン発酵によるエネルギー資源化

    神拓海, 大谷尭, 岩野寛, 李玉友, 久保田健吾

    第54回日本水環境学会　2020/03/16

  13. 日本各地の下水処理場における微生物群集構造の比較解析

    久保田健吾, 佐藤幹子, 李玉友, 加藤裕之

    54回日本水環境学会　2020/03/17

  14. 最初沈殿池+ウキクサ亜科植物+DHS を用いた下水処理システムの屋外実証実験

    大谷尭, 神拓海, 李玉友, 久保田健吾

    第54回日本水環境学会　2020/03/18

  15. Gene-FISH法を用いた薬剤耐性関連遺伝子の視覚的検出の試み

    丸山涼介, 久保田健吾, 李玉友

    第54回日本水環境学会　2020/03/16

  16. メタン発酵に及ぼすヘキサンの影響

    丹野淳, 久保田健吾, 覃宇, 李玉友

    第54回日本水環境学会　2020/03/16

  17. 0.2 µm分画した活性汚泥の微生物学的特性の把握

    景政柊蘭, 久保田健吾, 李玉友

    第54回日本水環境学会　2020/03/16

  18. 精密質量分析を用いた下水処理における溶存有機物の動態解明

    高橋真, 久保田健吾, 佐藤幹子, 李玉友, 石井淑大, 栗栖太

    第54回日本水環境学会　2020/03/16

  19. 季節別運転管理に伴う活性汚泥の微生物群集構造の変遷

    大野裕之, 佐藤幹子, 李玉友, 久保田健吾

    第54回日本水環境学会　2020/03/16

  20. 微生物群集の空間分布可視化のための元素標識技術の開発

    浦崎幹八郎, 李玉友, 浦本豪一郎, 諸野祐樹, 久保田健吾

    第54回日本水環境学会　2020/03/16

  21. 環境DNAによる河川生物群集の時空間特性解析

    内田典子, 風間聡, 会田俊介, 久保田健吾

    令和元年度 土木学会東北支部 技術研究発表会　2020/03/07

  22. ウキクサと初沈汚泥の連続メタン発酵処理によるエネルギー資源化

    神拓海, 大谷尭, 岩野寛, 李玉友, 久保田健吾

    令和元年度 土木学会東北支部 技術研究発表会　2020/03/07

  23. 日本各地の下水処理場を対象とした溶存有機物と微生物群集の関係性の評価

    高橋真, 石井淑大, 栗栖太, 佐藤幹子, 李玉友, 久保田健吾

    第56回環境工学研究フォーラム　2019/12/03

  24. Characteristics of dissolved DNA in activated sludge

    S. Kagemasa, Y.-Y. Li, K. Kubota

    8th IWA Microbial Ecology and Water Engineering Specialist Conference　2019/11/18

  25. Detection and quantification of viable microbiome in anaerobic sludge digester using propidium monoazide (PMA)-PCR

    J. Ni, S. Hatori, Y. Wang, Y.Y. Li, K. Kubota

    8th IWA Microbial Ecology and Water Engineering Specialist Conference　2019/11/18

  26. 最初沈殿池越流水を供するウキクサ亜科植物培養槽における溶存有機物の消長

    大谷尭, 岩野寛, 石井淑大, 栗栖太, 久保田健吾, 李玉友

    第56回下水道研究発表会　2019/08/07

  27. 下水処理プロセスにおける微生物群集構造と溶存有機物組成の関係性の解明

    高橋真, 久保田健吾, 佐藤幹子, 李玉友, 石井淑大, 栗栖太

    平成30年度 土木学会東北支部 技術研究発表会　2019/03

  28. 下水一次処理水中のウキクサ亜科植物の生長に影響を与える物質の探索

    大谷尭, 岩野寛, 久保田健吾, 李玉友, 栗栖太, 石井淑大

    平成30年度 土木学会東北支部 技術研究発表会　2019/03

  29. DHS担体付着汚泥の微生物群集構造の遷移

    加藤莉奈, 大久保努, 上村繁樹, 久保田健吾, 小野寺崇, 竹村泰幸

    第53回日本水環境学会　2019/03

  30. 連続流式一槽式アナモックスプロセスによる常温低濃度アンモニア排水の処理

    陳玉潔, 陳栄, 竹村泰幸, 紀佳淵, 佐久間智士, 久保田健吾, 李玉友

    第53回日本水環境学会　2019/03

  31. 下水一次処理水に含まれるウキクサ亜科植物の生長に影響を与える物質の探索

    大谷尭, 岩野寛, 石井淑大, 李玉友, 栗栖太, 久保田健吾

    第53回日本水環境学会　2019/03

  32. 活性汚泥中の溶存態DNA解析による微生物群集の動態解明

    景政柊蘭, 久保田健吾, 李玉友

    第53回日本水環境学会　2019/03

  33. 下水処理における微生物群集構造と溶存有機物組成の関係性の解明

    高橋真, 久保田健吾, 佐藤幹子, 李玉友, 石井淑大, 栗栖太

    第53回日本水環境学会　2019/03

  34. ウキクサ亜科植物を用いたエネルギー自立型下水処理システムの適用性の評価

    岩野寛, 大谷尭, 多川正, 玉木秀幸, 李玉友, 久保田健吾

    第53回日本水環境学会　2019/03

  35. 最初沈殿池+DHSシステムに付加する下水処理水の灌漑利用のための消毒システムの開発

    景政柊蘭, 長町晃宏, 井口晃徳, 久保田健吾, 高橋優信, 原田秀樹, 押木守, 荒木信夫, 大久保努, 上村繁樹, 多川正

    第55回環境工学研究フォーラム　2018/12

  36. Duckweed for advanced sewage treatment and bioenergy production International-presentation

    Hiroshi Iwano, Syo Hatohara, Tadashi Tagawa, Hideyuki Tamaki, Yu-You Li, Kengo Kubota

    15th Specialized Conference on Small Water & Wastewater Systems and 7th Specialized Conference on Resources Oriented Sanitation　2018/10

  37. A Novel Sewage Treatment System Using Duckweed International-presentation

    Hiroshi Iwano, Syo Hatohara, Tadashi Tagawa, Hideyuki Tamaki, Yu-You Li, Kengo Kubota

    Water and Environment Technology Conference 2018　2018/07

  38. ウキクサ亜科植物による下水処理水からの健康関連微生物除去の評価

    鳩原翔, 岩野寛, 久保田健吾, 李玉友, 多川正, 玉木秀幸

    平成29年度 土木学会東北支部 技術研究発表会　2018/03

  39. ウキクサ亜科植物を用いた下水処理における健康関連微生物除去性能の評価

    鳩原翔, 岩野寛, 久保田健吾, 多川正, 玉木秀幸, 李玉友

    第52回日本水環境学会　2018/03

  40. 分子量分画膜を用いた迅速・簡便な新規rRNA直接定量法による環境微生物群のマルチプレックス定量

    竹村泰幸, 李玉友, 原田秀樹, 関口勇地, 久保田健吾

    第52回日本水環境学会　2018/03

  41. 嫌気性消化槽におけるPMA-PCR法を用いた生菌由来DNAに基づく微生物群集構造の解析

    倪 嘉苓, 久保田健吾, 羽鳥伸吾, 李玉友

    第52回日本水環境学会　2018/03

  42. 初沈+DHS下水処理システムにおける安全な処理水の再利用を実現する消毒システムの開発

    景政柊蘭, 長町晃宏, 多川正, 井口晃徳, 久保田健吾, 原田秀樹, 押木守, 荒木信夫, 大久保努, 上村繁樹

    第52回日本水環境学会　2018/03

  43. ウキクサ亜科植物を用いたエネルギー自立型下水処理システムの開発

    岩野寛, 鳩原翔, 久保田健吾, 多川正, 玉木秀幸, 李玉友

    第52回日本水環境学会　2018/03

  44. ウキクサ亜科植物を用いた下水処理水からのバイオエネルギー生産

    岩野寛, 久保田健吾, 玉木秀幸, 李玉友

    第72回土木学会年次学術講演会　2017/09

  45. 一槽式アナッモクスプロセスに及ぼす有機酸の影響

    郭延, 牛啓桂, 北條俊昌, 久保田健吾, 李玉友

    第20回日本水環境学会シンポジウム　2017/09

  46. PMA-PCR法を用いた生菌由来DNAに基づく嫌気性消化槽内微生物群集構造解析

    倪嘉苓, 久保田健吾, 羽鳥伸吾, 李玉友

    第20回日本水環境学会シンポジウム　2017/09

  47. 微生物可視化技術の新展開 Invited

    久保田健吾

    【東日本支部】2017年度 生物工学フォーラム「微生物のシングルセル解析」　2017/08/21

  48. ウキクサを介した下水処理水からのバイオエネルギー生産

    岩野寛, 久保田健吾, 玉木秀幸, 李玉友

    第54回下水道研究発表会　2017/08

  49. Diversity of phages in an anaerobic sludge digester International-presentation

    Jialing Ni, Kengo Kubota, Shinobu Kazama, Yu-You Li

    IUMS2017　2017/07

  50. Comparison of three primer sets for eukaryotic diversity study in wastewater treatment plant International-presentation

    Lu Li, Kengo Kubota, Jialing Ni, Yu-You Li

    IUMS2017　2017/07

  51. Long-term Monitoring of Anaerobic Sludge Digester: Microbial Dynamics during Restart-up Period and Steady State International-presentation

    Kengo KUBOTA, Yusuke SHIMADA, Kyohei KURODA, Hideki HARADA, Yu-You LI

    WET (Water and Environment Technology Conference) 2017　2017/07

  52. P-46 廃水汚泥内apsA mRNA発現微生物群の高感度FISH法による検出(ポスター発表)

    大塚 勇輝, 久保田 健吾, 山口 隆司, 荒木 信夫, 原田 秀樹, 川上 周司

    日本微生物生態学会講演要旨集　2009

  53. P-123 機能遺伝子を標的としたtwo-pass TSA-FISH法による環境中未培養微生物の検出(ポスター発表)

    長谷川 拓也, 川上 周司, 久保田 健吾, 井町 寛之, 大橋 晶良, 原田 秀樹

    日本微生物生態学会講演要旨集　2009

  54. P-79 生物脱硫を行うメタン発酵槽に存在するフィラメント硫黄生成細菌(ポスター発表)

    小林 拓朗, 李 玉友, 久保田 健吾, 原田 秀樹

    日本微生物生態学会講演要旨集　2009

  55. 都市下水処理UASB+DHSシステムにおけるDHSリアクターの微生物叢解析

    久保田健吾, 林幹大, タンドカール マダン, 山口隆司, 原田秀樹

    土木学会第63回年次学術講演会　2008/09

  56. Microbial community structure in a down-flow hanging sponge reactor International-presentation

    M. Hayashi, M. Tandular, T. Yamaguchi, H. Harada

    12th international symposium on microbial ecology　2008/08

  57. 機能遺伝子に基づく微生物のシングルセルレベルでの視覚的検出技術の開発

    農芸化学会2008年度大会　2008/03

  58. 10-188 Analysis of the microbial mats oxidizing hydrogen sulfide into sulfur filaments under microaerophilic environment(Microbial community analysis)

    Kobayashi Takuro, Li Yuyou, Kubota Kengo, Harada Hideki

    2008

  59. LNA/DNAプローブのFISH法への適用 -交雑効率の改善と特異性評価-

    大橋晶良, 大河原正博, 井町寛之, 原田秀樹

    第62回 土木学会全国大会　2007/09

  60. PB-29 In situ visualization of single copy genes at the cellular level by ultra sensitive two-pass TSA-FISH with oligonucleotide probes(Monitoring,Poster presentation B) :

    Kawakami Shuji, Kubota Kengo, Imachi Hiroyuki, Harada Hideki, Yamguchi Takashi, Ohashi Akiyoshi

    2007

  61. PB-16 Microbial community shift during cultivating a inoculum for mesophilic anaerobic digestion from waste activated sludge and cattle manure(Waste water treatment ecosystem,Poster presentation B) :

    Kobayashi Takuro, Yasuda Daisuke, Kubota Kengo, Li Yu-You, Harada Hideki

    2007

  62. Improvement of in situ hybridization efficiency of rRNA-targeted probes using locked nucleic acid International-presentation

    A. Ohashi, H. Imachi, H. Harada

    11th International Symposium on Microbial Ecology　2006/08

  63. FISH法における低交雑サイトへのLNA/DNAプローブの適用

    大橋晶良, 井町寛之, 原田秀樹

    第40回日本水環境学会　2006/03

  64. Enhanced in situ hybridization efficiency with LNA-incorporated probes International-presentation

    A. Ohashi, H. Imachi, H. Harada

    The 6th international symposium on Green Energy Revolution　2006/01

  65. 人工核酸プローブを用いたFISH法

    大橋晶良, 井町寛之, 原田秀樹

    第21回日本微生物生態学会　2005/11

  66. Two-pass TSA-FISH法によるmRNAの検出

    大橋晶良, 井町寛之, 原田秀樹

    日本農芸化学会関東支部2005年度大会　2005/10

  67. Two-pass TSA-FISH法による微生物genome上のシングルコピー遺伝子の検出

    大橋晶良, 井町寛之, 原田秀樹

    第60回土木学会全国大会　2005/09

  68. CARD-FISH for Detection of Functional Gene of Methanogens International-presentation

    A. Ohashi, H. Imachi, H. Harada

    The ASM 105th General Meeting　2005/06

  69. Dual TSA-FISH法による機能遺伝子の検出

    大橋晶良, 井町寛之, 原田秀樹

    第39回日本水環境学会　2005/03

  70. A-21 FISH with nucleic acid analog probe(MONITORING,(2) Oral presentation)

    Kubota Kengo, Ohashi Akiyoshi, Imachi Hiroyuki, Harada Hideki

    2005

  71. Detection of mRNA by CARD-FISH for physiological identification of prokaryotes International-presentation

    A. Ohashi, H. Imachi, H. Harada

    The 4th international symposium on Green Energy Revolution　2005/01

  72. CARD-FISH法によるシングルセルレベルでのmRNAの視覚化

    大橋晶良, 井町寛之, 原田秀樹

    第20回日本微生物生態学会　2004/11

  73. Detection and Visualization of Methanogen by Fluorescence in situ Hybridization and Catalyzed Reporter Deposition with 16S rRNA- or mcr mRNA-targeted Oligonucleotide Probe International-presentation

    The 3rd international symposium on Green Energy Revolution　2004/09

  74. 機能遺伝子を標的としたCARD-FISH法による微生物の特異的検出

    大橋晶良, 井町寛之, 原田秀樹

    第59回土木学会全国大会　2004/09

  75. Detection and identification of methanogens by CARD-FISH targeting mcrA mRNA International-presentation

    A. Ohashi, H. Imachi, H. Harada

    10th International Symposium on Microbial Ecology　2004/08

  76. Applicability of catalyzed reporter deposition and fluorescence in situ hybridization (CARD-FISH) for visualization of methanogens International-presentation

    A. Ohashi, H. Imachi, H. Harada

    10th World Congress of Anaerobic Digestion　2004/08

  77. CARD-FISH法による機能遺伝子mcrA検出の試み

    大橋晶良, 井町寛之, 原田秀樹

    第38回日本水環境学会　2004/03

  78. A-23 CARD-FISH法によるシングルセルレベルでのmRNAの視覚化(モニタリング,口頭発表)

    久保田 健吾, 大橋 晶良, 井町 寛之, 原田 秀樹

    日本微生物生態学会講演要旨集　2004

  79. Specific identification of methanogens by CARD-FISH International-presentation

    A. Ohashi, H. Imachi, H. Harada

    The 1st international symposium on Green Energy Revolution　2004/01

  80. メタン生成古細菌にCARD-FISH法を適用するための細胞壁処理

    大橋晶良, 井町寛之, 原田秀樹

    第40回環境フォーラム　2003/11

  81. Fluorescence in situ hybridization combined with catalyzed reporter deposition for in situ analysis of metanogens in anaerobic digested sludge International-presentation

    A. Ohashi, H. Imachi, H. Harada

    IWA ASIAN WATERQUAL2003　2003/10

  82. 高感度CARD-FISH法による16S rRNA含量の少ない環境微生物の検出

    大橋晶良, 原田秀樹

    第37回日本水環境学会　2003/03

  83. Tyramide Signal Amplificationによるメタン生成古細菌の検出

    大橋晶良, 原田秀樹

    第57回土木学会全国大会　2002/09

  84. 高感度FISH法による低16S rRNA含量微生物の検出

    大橋晶良, 原田秀樹

    第36回日本水環境学会　2002/03

  85. Digoxigeninを標識したDNAプローブを用いた微生物の検出

    大橋晶良, 原田秀樹

    第19回土木学会関東支部新潟会　2001/10

Show all Show first 5

Research Projects 25

  1. 嫌気性廃水処理システムの成否を左右する極小寄生微生物の全容解明と制御技術の創成

    黒田 恭平, 成廣 隆, 佐藤 久, 久保田 健吾, 山田 真義, 野口 太郎, 中島 芽梨

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 基盤研究(B)

    Institution: 国立研究開発法人産業技術総合研究所

    2025/04 - 2028/03

  2. 低温メタン発酵技術革新による新規創・省エネルギー型廃水処理システムの構築

    山田 真義, 久保田 健吾

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 基盤研究(C)

    Institution: 鹿児島工業高等専門学校

    2024/04/01 - 2027/03/31

  3. 極小未知細菌群の実態を解明する -活性汚泥から切り拓く微生物新世界-

    中井 亮佑, 久保田 健吾, 黒田 恭平, 景政 柊蘭

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 基盤研究(B)

    Institution: 国立研究開発法人産業技術総合研究所

    2023/04/01 - 2027/03/31

  4. 廃水処理における除去メカニズム解明のためのウイルスの視覚的・特異的検出技術の開発

    久保田 健吾, 佐野 大輔

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 挑戦的研究(萌芽)

    Institution: 東北大学

    2022/06/30 - 2025/03/31

    More details Close

    廃水処理汚泥における視覚的な微生物検出において、その空間分布の可視化は数十μm程度の汚泥切片を作成することで行われる。一方で、３次元的な廃水処理汚泥の形状から得られる情報は多い。そのため、廃水処理汚泥中の微生物の可視化に際しては、非破壊で形状を維持したままの可視化が望ましい。そこで廃水処理汚泥を3次元的に、非破壊で可視化する手法の開発を行った。具体的には微生物細胞への特定元素標識と吸収端X線による元素識別を組み合わせた新たな廃水処理汚泥の3次元可視化手法の確立である。 廃水処理汚泥のCT測定のための準備として、汚泥の物理的固定法と標識元素の吸収端エネルギーを用いた検出方法について検討した。サンプルのドリフトを防ぐための処理として、エポキシ樹脂による包埋を行った。微生物細胞に標識した特定元素の検出特性については、オスミウムと金について検討した。2種類の純菌の混合物を対象として、微生物細胞に標識した特定元素の検出を行ったところ、オスミウムの特異的検出に成功した一方で、金は、gold-ISH法により特異的に標識した条件において、差分が明確には得られなかった。XRFおよびSEM-EDX分析では金のシグナルが確認されたため、金は微生物細胞に標識されていたが、減算法による特異的検出に必要な密度まで達しなかったと考えられる。続いてオスミウムにより染色したグラニュール汚泥を放射光X線μCT撮影に供し、特異的可視化を実施した。その結果、グラニュール汚泥中の3次元的な空隙の分布などを視覚的に明らかにすることができた。

  5. 脱炭素化に向けた創エネ・リン資源回収型下水高度処理システムの開発

    李 玉友, 北條 俊昌, 安井 英斉, 増田 周平, 久保田 健吾, 佐野 大輔, 覃 宇

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 基盤研究(A)

    Institution: 東北大学

    2022/04/01 - 2025/03/31

  6. 都市下水から薬を創り出す：棄てられたヒト免疫細胞由来遺伝子を活用した抗体医薬開発

    佐野 大輔, 野地 智法, 斉藤 繭子, 久保田 健吾

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 挑戦的研究(開拓)

    Institution: 東北大学

    2021/07/09 - 2025/03/31

    More details Close

    本研究は、都市下水から回収した抗体遺伝子を用いて抗体医薬の合成を行う手法の開発に取り組むものである。研究初年度である令和3年度においては、文献情報をもとに免疫細胞由来遺伝子を増幅するためのプライマーを設計し、都市下水から抽出した総DNAを鋳型として用いたPCRを行い、都市下水から免疫細胞由来遺伝子の増幅産物を取得することを試みた。都市下水は3000xgで30分遠心分離し、得られた沈殿物を下水濃縮サンプルとした。プライマーは複数の組み合わせを合成し、試行錯誤的に下水濃縮サンプルから抽出した総DNAに適用した。その結果、目的遺伝子と思われる増幅産物を得ることに成功した。得られた増幅産物に対して配列解析を行ったところ、ヒト免疫グロブリン由来の遺伝子配列が得られていることが確認された。この結果により、都市下水中に免疫細胞由来遺伝子が存在していることが証明され、本研究のコンセプトが成立可能であることが示された。続いて、得られた増幅産物に対して次世代シーケンシングを行うための前処理を行なった。最終的に、十分な量と純度を持つサンプルが得られたため、次世代シーケンス解析を開始した。

  7. 未培養微小真核生物群の生態・機能解明による活性汚泥食物環モデルの再構築

    久保田 健吾, 山田 剛史

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 基盤研究(B)

    Institution: 東北大学

    2021/04/01 - 2024/03/31

  8. Realization of a novel metallic resource recovery technology by introducing the advanced molecule biotechnology method

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Fund for the Promotion of Joint International Research (Fostering Joint International Research (B))

    Institution: Tohoku University

    2019/10/07 - 2023/03/31

  9. 未知廃水処理微生物群のメタゲノム解析による統合代謝ネットワークの解明

    久保田 健吾

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 国際共同研究加速基金(国際共同研究強化(A))

    Institution: 東北大学

    2021 - 2023

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    本研究では、廃水処理に関与する微生物群およびそれらの代謝を明らかにすることを目的の１つとしている。基課題研究で、廃水処理汚泥中には普遍的だが存在率が少ない微生物群が存在することを明らかにした。これらの微生物群の代謝機能をメタゲノム解析により解析しようとした場合、解析に十分なクオリティのゲノムビンの構築が通常のメタゲノム解析では困難である。しかしながら廃水処理微生物群を包括的に理解するためには、それらの微生物群を無視することはできない。そこでそれらの微生物群のゲノムビンを獲得し、ゲノム情報に基づいた代謝機能を解明するために、標的とする微生物群のシーケンスデータ回収量を増やす方法について検討を行った。存在量が少ないとはいえ、サンプル間によってその割合が大きく変わるため、まずは標的とする微生物群が多く存在しているサンプルを選定した。下水および産業廃水を処理するバイオリアクターからサンプリングした汚泥を、アンプリコンシーケンシングにより解析し、汚泥内に存在する微生物群の相対存在率を求めた。その結果、一部において他よりも高い相対存在率を示すサンプルが見られたため、これらのバイオリアクター内の汚泥を標的として実験を進めることとした。次に、シーケンス解析においてより多くのリード数を得るための前処理方法について検討を行った。前処理方法の詳細については、現在も検討中であるため詳細は割愛する。この前処理方法により、これまでゲノムビンを構築できなかった様々な微生物群についても代謝機能を推定することが可能となり、廃水処理汚泥内での役割を解明できるようになると考えられる。

  10. Modeling of biological wastewater treatment processes as aggregation of microbial metabolisms of organic matters

    KURISU FUTOSHI

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Challenging Research (Exploratory)

    Institution: The University of Tokyo

    2019/06/28 - 2022/03/31

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    Influent wastewater, treated water and activated sludge were collected from domestic wastewater treatment plants, to analyze dissolved organic matter at the compound species level using high-resolution mass spectrometry and the microbial community responsible for the organic matter degradation. The results showed that the microbial community structure was not found to be related to the influent composition, whereas it was related to the treated water, indicating a relationship between the treated water and microbial composition as a product of microbial metabolism. In addition, we were able to establish a method for estimating the organic matter in treated wastewater that is utilized by the microorganisms.

  11. Development of fundamental technologies for rare metal recovery by exploring metal responsible bioresource

    Chien Mei-Fang

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

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

    Institution: Tohoku University

    2019/04/01 - 2022/03/31

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    This study aimed to discover the metal-responsible bioresources, to construct novel metal-recovery microorganisms, and to develop a biosystem by applying metal-recovery microorganisms. Regarding the search for bioresources, we succeeded in obtaining binding protein genes of two rare metals, molybdenum and nickel, in finding microorganisms that have detoxification genes for the toxic metals arsenic and mercury in a special structure, and in analyzing the expression of genes that contribute to the uptake of arsenic, cadmium, and zinc from hyperaccumulator plants. Regarding the construction of metal-recovery microorganisms, we succeeded in producing molybdenum-adsorbing yeast and nickel- and cobalt-adsorbing Escherichia coli cells, and were also able to study the fixation carriers for these microorganisms. These results have published six papers in academic journals and given seven presentations in academic conferences.

  12. Development of municipal wastewater system by using anaerobic microoragnism

    Li Yu-You

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

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

    Institution: Tohoku University

    2019/04/01 - 2022/03/31

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    In this study, a new system combining an anaerobic membrane bioreactor (AnMBR) and a one-stage partial nitritation/anammox (PNA) reactor was developed to realize energy-saving/energy-creation in the treatment of municipal wastewater. Both small scale and pilot scale experiments were conducted in a wastewater treatment plant. The methanogenic performance and membrane operation for AnMBR were studied by changing the HRT from 24 to 6 hours and temperature from 25 to 15 ℃. The effluent COD was stable < 50 mg/L, always met the discharge standards. The one-stage PNA reactor could reduce the effluent BOD to 10 mg/L or less and T-N (total nitrogen) to 10 mg/L or less with an HRT of 2 h, thereby achieving the target values. This research proved that applying mainstream AnMBR in temperate climates can significantly reduce electricity demand and achieve energy positive.

  13. Elucidating microbial functions involved in sewage treatment

    Kubota Kengo

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

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

    Institution: Tohoku University

    2018/04/01 - 2021/03/31

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    The purpose of this study was to elucidate microorganisms involved in sewage treatment by amplicon and metagenome analyses and single cell detection techniques. The microbial community structure and core microorganisms of activated sludge in Japanese sewage treatment plants were uncovered. Metagenomic analysis of uncultured microorganisms Patescibacteria revealed their functions. PMA-PCR allowed the analysis of microbial community based on cell viability. We also developed a hemin-based microbial detection technique.

  14. Application of SERS for understanding microbial metabolism at single-cell resolution

    Kubota Kengo, HATORI Shingo

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Challenging Exploratory Research

    Institution: Tohoku University

    2016/04/01 - 2019/03/31

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    In this study, we focus on a method using Raman scattering for elucidation of microbial metabolism. After cultivation with deuterium containing media, microbial metabolism was measured based on the appearance of C-D bond peak. In addition, surface enhanced Raman scattering (SERS) was applied to enhance the sensitivity. After washing the excess gold nanoparticles, an enhancer was added to perform gold enhancement reaction. The Raman spectrum derived from the C-D bond was enhanced. On the other hand, since the disappearance of the Raman spectrum from E. coli cells due to the light emission from gold nanoparticles was also observed, further optimization of the experimental protocol is necessary.

  15. Analysis of salt-resistant Escherichia coli strains using transcriptome analysis

    Masago Yoshifumi, INABA Manami

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Challenging Exploratory Research

    2015/04/01 - 2018/03/31

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    This study tested a hypothesis that a part of Escherichia coli in coastal area acquires resistance against salt (sodium chloride), and they cannot be detected using ordinary selection media”. A field survey at a coastal area in Japan found higher concentration of E. coli using selective agar supplemented with salt compared to the ordinary agar in summer season. But the salt-resistant E. coli strains isolated from the water samples showed low growth rates in salt-supplemented media, indicating that salt inhibits growth of salt-resistant E. coli strains. These finding implies that E. coli in coastal water shows lower overall decay rates due to the strains possessing salt-resistance.

  16. Selective metagenomic analysis of novel viruses in water environment

    Masago Yoshifumi, SAITO Mayuko, KAZAMA Shinobu

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

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

    2015/04/01 - 2018/03/31

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    This study aimed at developing effective detection methods for novel human RNA viruses from domestic wastewater using selective metagenomic analysis. Capture probe-based selection followed by next-generation sequencing using illumina MiSeq platform enabled to detect virus genome with relatively low concentration in wastewater. Viral metagenomic analysis revealed that most viral genome sequences are not homologous to any sequences in the database. Based on the metagenome, we constructed contigs that are expected to be from novel viruses. We also confirmed that virus genome with the contig sequence are present in wastewater samples throughout the study period.

  17. A study on innovation of sewage treatment technology by using anaerobic membrane bioreactor

    LI Yu-You

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

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

    Institution: Tohoku University

    2014/04/01 - 2017/03/31

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    An experimental study on the innovation sewage treatment by using anaerobic membrane reactor (AnMBR) was conducted. The effects of HRT, temperature and sewage composition on treatment performance of AnMBR were investigated. The treatment performance was evaluated by suing two type of membranes, flat sheet membrane and hollow fiber membrane, and a total of four different sewages including three artificial sewages containing surfactants (AE, LAS) and SS (toilet paper) respectively, and real sewage. The COD removal was high as 95-97% for artificial sewages. In the all experiments, AE removal was over 90%, but the LAS removal was only about 50%.

  18. Physiological and genetic characterization of uncultured methanogenic archaea via an ultra-high sensitive fluorescence in situ hybridization technique

    IMACHI Hiroyuki, KUBOTA Kengo, SAITO Yayoi

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Challenging Exploratory Research

    Institution: Japan Agency for Marine-Earth Science and Technology

    2013/04/01 - 2016/03/31

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    The investigation of uncultured methanogens is a significant challenge in comprehensive understanding global carbon cycle. In this study, we aimed to gain physiological and genetic information of taxonomically new methanogens by obtaining genomic sequences and isolate. For this purpose, we first performed mcrA and 16S rRNA gene-based clone analyses on methanogenic sludges to explore taxonomically novel methanogens. Through the analyses, we found a novel methanogen group, which may represent the eighth order of methanogen. To obtain genetic information of the methanogen, we tried to do specific sorting of the methanogen cells using a combination of an ultra-high sensitive fluorescence in situ hybridization (FISH) technique (i.e., two-pass tyramide signal amplification FISH with polynucleotide probes) and fluorescence-activated cell sorting. However, unfortunately, the targeted methanogen cells could not be detected by the FISH technique even after several cell wall treatments.

  19. Development of a novel in situ hybridization method using gold nano particle for nanoSIMS analysis

    Kubota Kengo, MORONO YUKI

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Challenging Exploratory Research

    Institution: Tohoku University

    2013/04/01 - 2016/03/31

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    We developed a novel in situ hybridization method using ultra-small gold nano-particle-labeled oligonucleotide probe for phylogenetic identification of environmental microorganisms during nanoSIMS analysis, and proposed as Gold-ISH. Lactate-assimilating sulfate reducing bacteria in an anaerobic wastewater treatment reactor were identified by using the proposed method.

  20. Innovation of Non-Aerated Aerobic DHS Bioprocess for Extremely Energy-saving Wastewater Treatment Technology

    Harada Hideki, UEMURA SHIGEKI, KUBOTA KENGO, OKUBO TSUTOMU

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

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

    Institution: Tohoku University

    2011/04/01 - 2016/03/31

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    To expand the applicability of DHS bioprocess, various wastewaters were tested by using DHS bioreactor in combination with other pre-treatment technologies. Mainly, the applicability of landfill leachate and nitrification of phenol-containing wastewater was investigated. The effects of salt concentration on nitrification were quantitatively evaluated. Physico-chemical and microbial approaches were used clarify DHS treatment mechanisms.

  21. Development of a method for eva l uat i ng the host range of bacteriophages

    IMACHI Hiroyuki, KUBOTA Kengo

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Challenging Exploratory Research

    Institution: Japan Agency for Marine-Earth Science and Technology

    2011 - 2012

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    We developed a novel phage-host range evaluation method using EdU (5-ethynyl-2’-deoxyuridine) labeled phages, which consists of the following four steps. (i) Fluorescently labeled phages are added to a microbial consortium, and host cells are infected and fluorescently labeled. (ii) Fluorescent cells are sorted by FACS. (iii) 16S rRNA gene sequences retrieved from sorted cells are analyzed, and specific oligonucleotide probes for FISH are designed. (iv) Cells labeled with both fluorescently labeled phage and FISH probe are identified as host cells.

  22. Development of functional gene-based cell enrichment method for understating microbial community in wastewater treatment systems

    KUBOTA Kengo

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

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

    Institution: Tohoku University

    2010 - 2011

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    We developed a method to enrich microbial cells after CARD-FISH. Effects of solvents to microbial community were also investigated. Microbial community of a phenol-degrading anaerobic reactor was analyzed. Specific FISH probes were designed and applied to decipher spatial distribution of major microorganisms involved in phenol degradation.

  23. Construction of future forecast map and environmental policy scenario of water and the hygiene in Asian developing countries

    HARADA Hideki, SHIKURA Shigeo, UEMURA Shigeki, KUBOTA Kengo, YAMADA Masayoshi

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

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

    Institution: Tohoku University

    2008 - 2010

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    The present conditions of water and hygiene were investigated in India, Uzbekistan, Malaysia, Vietnam, etc. We put emphasis on urban sewage treatment and river water pollution in India, salt damage of agricultural land by irrigation water in Uzbekistan, and pollution in the water bodies by palm oil and gum production wastewater in Malaysia and Vietnam, respectively. By analyzing those findings, appropriate environmental policy scenarios were proposed for each country.

  24. Development of energy-saving novel wastewater treatment systems

    HARADA Hideki, LI Yu-you, KUBOTA Kengo, OHASHI Akiyoshi

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

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

    Institution: Tohoku University

    2007 - 2010

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    Sewage treatment mechanisms in terms of excess sludge production and microbial community structures of a UASB-DHS system was investigated. In addition, applicability of DHS reactor to a wastewater containing high strength of ammonium-nitrogen and a landfill leachate was also investigated. New media for DHS reactor was introduced in a reactor in India, and investigated its start-up characteristics under on-site practical conditions.

  25. Development of gene FISH for environmental microbiology

    KUBOTA Kengo

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Young Scientists (Start-up)

    Institution: Tohoku University

    2008 - 2009

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    In this study, gene FISH is developed for environmental microbiology. Two-pass TSA-FISH with oligonucleotide or polynucleotide probes successfully developed for detection of single copy genes in prokaryotic cells. Application of the technique to environmental samples was also successful ; further application of this technique for environmental microbial autecology is possible.

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