Tomonori Kindaichi

Last Updated :2024/05/07

Affiliations, Positions
Graduate School of Advanced Science and Engineering, Professor
Web Site
My research interests are discovery and enrichment of microorganisms that are useful for water treatment. In particular, I am focusing on (anaerobic ammonium oxidation) anammox bacteria that can efficiently remove ammonia in wastewater. Currently, our laboratory has three enrichment cultures of different species of anammox bacteria. Taking advantage of the different characteristics of each species, I am considering to apply it not only to the field of wastewater treatment but also to livestock wastewater and aquaculture wastewater.

Basic Information

Major Professional Backgrounds

  • 2023/10/01, Hiroshima University, Graduate School of Advanced Science and Engineering, Professor
  • 2020/04/01, 2023/09/30, Hiroshima University, Graduate School of Advanced Science and Engineering, Associate Professor
  • 2010/08/01, 2011/03/22, Aalborg University, Department of Biotechnology, Chemistry and Environmental Engineering, Visiting Researcher
  • 2007/04/01, 2020/03/31, Hiroshima University, Graduate School of Engineering, Assistant Professor
  • 2004/04/01, 2007/03/31, Hiroshima University, Graduate School of engineering, Research Associate

Educational Backgrounds

  • Hokkaido University, Graduate School, Division of Engineering, Urban and Environmental Engineering, Japan, 2001/04, 2004/03
  • Toyohashi University of Technology, Graduate School, Division of Engineering, Architecture and Civil Engineering, Japan, 1999/04, 2001/03
  • Toyohashi University of Technology, Faculty of Engineering, Japan, 1997/04, 1999/03
  • National Institute of Technology, Hakodate Colledge, Department of Civil Engineering, 1992/04, 1997/03

Academic Degrees

  • Doctor of Engineering, Hokkaido University
  • Master of Engineering, Toyohashi University of Technology

Educational Activity

  • [Bachelor Degree Program] School of Engineering : Cluster 4(Civil Engineering and Architecture) : Program of Civil and Environmental Engineering
  • [Master's Program] Graduate School of Advanced Science and Engineering : Division of Advanced Science and Engineering : Civil and Environmental Engineering Program
  • [Doctoral Program] Graduate School of Advanced Science and Engineering : Division of Advanced Science and Engineering : Civil and Environmental Engineering Program

Research Fields

  • Engineering;Civil engineering;Civil and environmental engineering
  • Environmental science;Environmental conservation;Environmental engineering and reduction of environmental burden
  • Biology;Basic biology;Biodiversity / Systematics

Research Keywords

  • wastewater treatment
  • environmental microbiology
  • anammox
  • nitrification

Affiliated Academic Societies

  • Japan Society of Civil Engineering, 1996
  • Japan Society on Water Environment, 2000
  • Japan Society of Microbial Ecology, 2002
  • Japan Society of Material Cycles and Waste Management, 2017
  • Japan Water Works Association, 2017
  • Japan Sewage Works Association, 2021
  • International Water Association, 2011
  • International Society for Microbial Ecology

Educational Activity

Course in Charge

  1. 2024, Undergraduate Education, 2Term, Experiments in Civil and Environmental Engineering
  2. 2024, Undergraduate Education, 2Term, Microbiology and Ecology for Engineering
  3. 2024, Undergraduate Education, 1Term, Sanitary and environmental engineering and exercise
  4. 2024, Undergraduate Education, 3Term, Design of Infrastructures
  5. 2024, Undergraduate Education, 1Term, Introduction of Civil and Environmental Engineering
  6. 2024, Undergraduate Education, Year, Graduation Thesis
  7. 2024, Graduate Education (Master's Program) , 1Term, Special Exercises on Civil and Environmental Engineering A
  8. 2024, Graduate Education (Master's Program) , 2Term, Special Exercises on Civil and Environmental Engineering A
  9. 2024, Graduate Education (Master's Program) , 3Term, Special Exercises on Civil and Environmental Engineering B
  10. 2024, Graduate Education (Master's Program) , 4Term, Special Exercises on Civil and Environmental Engineering B
  11. 2024, Graduate Education (Master's Program) , Academic Year, Special Study on Civil and Environmental Engineering
  12. 2024, Graduate Education (Master's Program) , 2Term, Advanced Environmental Protection Engineering
  13. 2024, Graduate Education (Doctoral Program) , Academic Year, Special Study on Civil and Environmental Engineering

Research Activities

Academic Papers

  1. Analysis of size distribution and areal cell density of ammonia-oxidizing bacterial microcolonies in relation to substrate microprofile in biofilms, Biotechnology and Bioengineering, 85(1), 86-95, 20040101
  2. Eco-physiological interaction between nitrifying bacteria and heterotrophic bacteria in autotrophic nitrifying biofilms as determined by MAR-FISH, Applied and Environmental Microbiology, 70(3), 1641-1650, 20040301
  3. MAR-FISH-An Ecophysiological approach to link phylogenetic affiliation and in situ metabolic activity of microorganisms at a single-cell resolution, Microbes and Environments, 19(2), 83-98, 20040601
  4. Effects of hydroxylamine on microbial community structure and function of autotrophic nitrifying biofilms determined by in situ hybridization and the use of microelectrodes., Water Science and Technology, 49(11-12), 61-68, 20040801
  5. Fate of C-14-labeled microbial products derived from nitrifying bacteria in autotrophic nitrifying biofilms, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 71(7), 3987-3994, 20050701
  6. Eco-physiology of autotrophic nitrifying biofilms, WATER SCIENCE AND TECHNOLOGY, 52(7), 225-232, 20051001
  7. Community structure, abundance, and in situ activity of nitrifying bacteria in river sediments as determined by the combined use of molecular techniques and microelectrodes, ENVIRONMENTAL SCIENCE & TECHNOLOGY, 40(5), 1532-1539, 20060301
  8. Community structures and activities of nitrifying and denitrifying bacteria in industrial wastewater-treating biofilms, BIOTECHNOLOGY AND BIOENGINEERING, 94(4), 762-772, 20060705
  9. Population dynamics and in situ kinetics of nitrifying bacteria in autotrophic nitrifying biofilms as determined by real-time quantitative PCR, BIOTECHNOLOGY AND BIOENGINEERING, 94(6), 1111-1121, 20060820
  10. Quantification of anaerobic ammonium-oxidizing bacteria in enrichment cultures by real-time PCR, WATER RESEARCH, 41(4), 785-794, 20070201
  11. Development of high-rate anaerobic ammonium-oxidizing (anammox) biofilm reactors, WATER RESEARCH, 41(8), 1623-1634, 20070401
  12. Development of a super high-rate Anammox reactor and in situ analysis of biofilm structure and function, WATER SCIENCE AND TECHNOLOGY, 55(8-9), 9-17, 20070401
  13. Estimation of the emission factors of PAHs by traffic with the model of atmospheric dispersion and deposition from heavy traffic road, WATER SCIENCE AND TECHNOLOGY, 56(1), 233-242, 20070401
  14. ★, In situ activity and spatial organization of anaerobic ammonium-oxidizing (anammox) bacteria in biofilms, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 73(15), 4931-4939, 20070801
  15. Estimation of river discharge loadings of PAHs in a suburban river in 
Hiroshima Prefecture, Japan., Journal of Water and Environment Technology, 7(2), 109-120, 20090601
  16. Nitro-PAHs and PAHs in Atmospheric Particulate Matters and Sea Sediments in Hiroshima Bay Area, Japan, WATER AIR AND SOIL POLLUTION, 207(1-4), 263-271, 20100301
  17. Biological oxidation of dissolved methane in effluents from anaerobic reactors using a down-flow hanging sponge reactor, WATER RESEARCH, 44(5), 1409-1418, 20100301
  18. Modelling of wet deposition of atmospheric polycyclic aromatic hydrocarbons by the consecutive measurements in an urban area, Japan, WATER SCIENCE AND TECHNOLOGY, 62(8), 1922-1930, 20100801
  20. ★, Enrichment of marine anammox bacteria in Hiroshima Bay sediments, WATER SCIENCE AND TECHNOLOGY, 63(5), 964-969, 20110301
  21. ★, Enrichment Using an Up-flow Column Reactor and Community Structure of Marine Anammox Bacteria from Coastal Sediment, MICROBES AND ENVIRONMENTS, 26(1), 67-73, 20110305
  22. Enrichment and identification of methane-oxidizing bacteria by using down-flow hanging sponge bioreactors under low methane concentration, ANNALS OF MICROBIOLOGY, 61(3), 683-687, 20110901
  23. Dissolved methane oxidation and competition for oxygen in down-flow hanging sponge reactor for post-treatment of anaerobic wastewater treatment, BIORESOURCE TECHNOLOGY, 102(22), 10299-10304, 20111101
  24. ★, Development of anammox reactor equipped with a degassing membrane to improve biomass retention, WATER SCIENCE AND TECHNOLOGY, 66(2), 451-456, 20120701
  25. Influence of temperature and salinity on microbial structure of marine anammox bacteria, WATER SCIENCE AND TECHNOLOGY, 66(5), 958-964, 20120901
  26. PAHs concentration and toxicity in organic solvent extracts of atmospheric particulate matter and sea sediments, WATER SCIENCE AND TECHNOLOGY, 66(5), 983-992, 20120901
  27. Anaerobic treatment of municipal wastewater at ambient temperature: Analysis of archaeal community structure and recovery of dissolved methane, WATER RESEARCH, 46(17), 5756-5764, 20121101
  28. ★, Ecophysiological role and function of uncultured Chloroflexi in an anammox reactor, WATER SCIENCE AND TECHNOLOGY, 66(12), 2556-2561, 20121201
  29. Photocatalytic decomposition of atmospheric toxic substances on the TiO2-loaded glasses set on the roadside of a highway, Journal of Water and Environment Technology, 10(4), 399-408, 20121201
  30. Phosphate recovery as concentrated solution from treated wastewater by a PAO-enriched biofilm reactor, WATER RESEARCH, 47(6), 2025-2032, 20130415
  31. ★, High and stable substrate specificities of microorganisms in enhanced biological phosphorus removal plants, ENVIRONMENTAL MICROBIOLOGY, 15(6), 1821-1831, 20130601
  32. ★, Physiological Characterization of an Anaerobic Ammonium-Oxidizing Bacterium Belonging to the Candidatus Scalindua" Group", APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 79(13), 4145-4148, 20130701
  33. Cultivation of Planktonic Anaerobic Ammonium Oxidation (Anammox) Bacteria Using Membrane Bioreactor, MICROBES AND ENVIRONMENTS, 28(4), 436-443, 20131220
  34. Hydrogen sulfide generation suppression by nitrate addition – application to solid waste landfill site, American Journal of Environmental Protection, 3(5), 267-274, 20141101
  35. Biological oxidation of Mn(II) coupled with nitrification for removal and recovery of minor metals by downflow hanging sponge reactor, WATER RESEARCH, 68, 545-553, 20150101
  36. Suppressing hydrogen sulfide generation by nitrate or oxygen addition in column percolation experiment, American Journal of Environmental Protection, 4(1), 55-61, 20150201
  37. ★, Biomass Yield Efficiency of the Marine Anammox Bacterium, Candidatus Scalindua sp.," is Affected by Salinity", MICROBES AND ENVIRONMENTS, 30(1), 86-91, 20150213
  38. Physiological characterization of anaerobic ammonium oxidizing bacterium CandidatusJettenia caeni'", ENVIRONMENTAL MICROBIOLOGY, 17(6), 2172-2189, 20150601
  39. Loading and removal of PAHs in a wastewater treatment plant in a separated sewer system, WATER RESEARCH, 80, 337-345, 20150901
  40. Characterisation of the in situ ecophysiology of novel phylotypes in nutrient removal activated sludge treatment plants, PLOS ONE, 1-13, 20150904
  41. PAH contents in road dust on principal roads collected nationwide in Japan and their influential factors, WATER SCIENCE AND TECHNOLOGY, 72(7), 1062-1071, 20151018
  42. ★, Nitrogen removal using an anammox membrane bioreactor at low temperature., Water Science & Technology, 72(12), 2148-2153, 20151218
  43. ★, Phylogenetic diversity and ecophysiology of candidate phylum Saccharibacteria in activated sludge., FEMS Microbiology Ecology, 92(6), 1-11, 20160601
  44. ★, Effects of organic matter in livestock manure digester liquid on microbial community structure and in situ activity of anammox granules., Chemosphere, 159, 300-307, 20160613
  45. Source identification of nitrous oxide emission pathways from a single-stage nitritation-anammox granular reactor, Water Research, 102, 147-157, 20161001
  46. Dominant Candidatus Accumulibacter phosphatis enriched in response to phosphate concentrations in EBPR process., Microbes and Environments, 32(3), 260-267, 20170927
  47. Genetic diversity of marine anaerobic ammonium-oxidizing bacteria as revealed by genomic and proteomic analyses of Candidatus Scalindua japonica'", ENVIRONMENTAL MICROBIOLOGY REPORTS, 9(5), 550-561, 20171001
  48. Concentrated landfill leachate treatment with a combined system including electro-ozonation and composite adsorbent augmented sequencing batch reactor process, PROCESS SAFETY AND ENVIRONMENTAL PROTECTION, 111, 253-262, 20171001
  49. Loading and removal of PAHs, fragrance compounds, triclosan and toxicity by composting process from sewage sludge, SCIENCE OF THE TOTAL ENVIRONMENT, 605, 860-866, 20171215
  50. Production of biogenic manganese oxides coupled with methane oxidation in a bioreactor for removing metals from wastewater, WATER RESEARCH, 130, 224-233, 20180301
  51. Draft genome sequence of Mn(II)-oxidizing Pseudomonas resinovorans strain MO-1., Genome Announcements, 6(11), e00088-18-e00088-18, 20180301
  52. ★, Specificities and Efficiencies of Primers Targeting Candidatus Phylum Saccharibacteria in Activated Sludge, MATERIALS, 11(7), 20180701
  53. Pollutant Removal from Synthetic Aqueous Solutions with a Combined Electrochemical Oxidation and Adsorption Method, INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH, 15(7), 20180701
  54. ★, Effects of Salts on the Activity and Growth of "Candidatus Scalindua sp.", a Marine Anammox Bacterium, MICROBES AND ENVIRONMENTS, 33(3), 336-339, 20180930
  55. Pollutants removal from synthetic wastewater by the combined electrochemical, adsorption and sequencing batch reactor (SBR), ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY, 161, 137-144, 20181015
  56. Biogas purification performance of new water scrubber packed with sponge carriers, JOURNAL OF CLEANER PRODUCTION, 214, 103-111, 20190320
  57. Investigation of prospective factors that control Kouleothrix (Type 1851) filamentous bacterial abundance and their correlation with sludge settleability in full-scale wastewater treatment plants, PROCESS SAFETY AND ENVIRONMENTAL PROTECTION, 124, 137-142, 201904
  58. Stormwater inflow loading of polycyclic aromatic hydrocarbons into urban domestic wastewater treatment plant for separate sewer system, WATER SCIENCE AND TECHNOLOGY, 79(7), 1426-1436, 20190401
  59. Integrated biological-physical process for biogas purification effluent treatment, JOURNAL OF ENVIRONMENTAL SCIENCES-CHINA, 83, 110-122, 20190901
  60. Dual nitrogen and oxygen isotope fractionation during anaerobic ammonium oxidation by anammox bacteria, ISME JOURNAL, 13(10), 2426-2436, 20191001
  61. Degradation and volatilization process of fragrance materials and triclosan in wastewater treatment plant - Comparison between field survey and laboratory experiment -, ENVIRONMENTAL TECHNOLOGY & INNOVATION, 16, 20191101
  62. Cross-linked chitosan/zeolite as a fixed-bed column for organic micropollutants removal from aqueous solution, optimization with RSM and artificial neural network, JOURNAL OF ENVIRONMENTAL MANAGEMENT, 250, 20191115
  63. Comprehensive review of polycyclic aromatic hydrocarbons in water sources, their effects and treatments, SCIENCE OF THE TOTAL ENVIRONMENT, 696, 20191215
  64. Mn(II) oxidation and manganese-oxide reduction on the decolorization of an azo dye, INTERNATIONAL BIODETERIORATION & BIODEGRADATION, 146, 20200101
  65. Integrated anammox-biochar in synthetic wastewater treatment: Performance and optimization by artificial neural network, JOURNAL OF CLEANER PRODUCTION, 243, 20200101
  66. Anti-bacterial Effects of MnO2 on the Enrichment of Manganese-oxidizing Bacteria in Downflow Hanging Sponge Reactors, MICROBES AND ENVIRONMENTS, 35(4), 20200101
  67. Multiple organic substrates support Mn(II) removal with enrichment of Mn(II)-oxidizing bacteria, JOURNAL OF ENVIRONMENTAL MANAGEMENT, 259, 20200401
  68. PAHs emission source analysis for air and water environments by isomer ratios - Comparison by modified Cohen's d, SCIENCE OF THE TOTAL ENVIRONMENT, 715, 20200501
  69. Pesticides in aquatic environments and their removal by adsorption methods, CHEMOSPHERE, 253, 20200801
  70. Bioelectrical methane production with an ammonium oxidative reaction under the no organic substance condition, Microbes and Environments, 36(2), 20210601
  71. ★, Cometabolism of the Superphylum Patescibacteria with Anammox Bacteria in a Long-Term Freshwater Anammox Column Reactor, WATER, 13(2), 20210102
  72. Treatment of landfill leachate with different techniques: an overview, WATER REUSE, 11(1), 66-96, 20210301
  73. Triggering Growth via Growth Initiation Factors in Nature: A Putative Mechanism for in situ Cultivation of Previously Uncultivated Microorganisms, FRONTIERS IN MICROBIOLOGY, 12, 20210504
  74. Performance optimization of a chitosan/anammox reactor in nitrogen removal from synthetic wastewater, JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING, 9(3), 20210601
  75. ★, Reactor performance and microbial community structure of single-stage partial nitritation anammox membrane bioreactors inoculated with Brocadia and Scalindua enrichment cultures, Biochemical Engineering Journal, 170, 20210601
  76. Effects of recirculating aquaculture system wastewater on anammox performance and community structure, Processes, 9, 20210721
  77. Photodegradation of fragrance materials and triclosan in water: Direct photolysis and photosensitized degradation, Environmental Technology & Innovation, 23, 20210801
  78. Mutualistic relationship between Nitrospira and concomitant heterotrophs, Environmental Microbiology Reports, 14, 130-137, 20220201
  79. Environmental factors affecting the community of methane-oxidizing bacteria, Microbes and Environments, 37, ME21074-ME21074, 20220301
  80. Biological methane production coupled with sulfur oxidation in a microbial electrosynthesis system without organic substrates, Journal of Environmental Sciences, 116, 68-78, 20220601
  81. ★, Metabolic potential of the superphylum Patescibacteria reconstructed from activated sludge samples from a municipal wastewater treatment plant., Microbes and Environments, 37(3), ME22012-ME22012, 20230601
  82. Growth of nitrite-oxidizing Nitrospira and ammonia-oxidizing Nitrosomonas in marine recirculating trickling biofilter reactors, Environmental Microbiology, 24(8), 3735-3750, 20220801
  83. Cultivation of previously uncultured sponge-associated bacteria using advanced cultivation techniques: A perspective on possible key mechanisms, FRONTIERS IN MARINE SCIENCE, 9, 20220830
  84. Indoor thermal environment and energy performance in a central air heating system using a heat pump for a house with underfloor space for heat distribution, Building Services Engineering Research and Technology, 43(6), 755-766, 20221101
  85. Contaminant Removal from Wastewater by Microalgal Photobioreactors and Modeling by Artificial Neural Network, WATER, 14(24), 20221201
  86. Influence of pH and concentration on the growth of bacteria-fungus and benzo[a]pyrene degradation, ENVIRONMENTAL TECHNOLOGY & INNOVATION, 29, 20230201
  87. New microbial electrosynthesis system for methane production from carbon dioxide coupled with oxidation of sulfide to sulfate, Journal of Environmental Sciences (China), 125, 786-797, 20230301
  88. ★, Candidatus Scalindua, a Biological Solution to Treat Saline Recirculating Aquaculture System Wastewater, Processes, 11(3), 20230301
  89. Detection of domestic-use chemicals in urban storm drains during dry days in a separated sewer area, Environmental Science: Water Research and Technology, 20230301

Publications such as books

  1. 2022/02/01, Wastewater Treatment: Current and Future Techniques, Cometabolism of the superphylum Patescibacteria with anammox bacteria in a long-term freshwater anammox column reactor, 2022, 202202, Scholarly Book, Joint work, English, Suguru Hosokawa, Kyohei Kuroda, Takashi Narihiro, Yoshiteru Aoi, Noriatsu Ozaki, Akiyoshi Ohashi, Tomonori Kindaichi, 978-3-0365-3274-5, 252, 13


  1. 2022/11/03, Research Paper Award 2021 Of the Microbes and Environments, 日本微生物生態学会 2021年M&E論文賞選考委員会 Editor in Chies, Bioelectrical Methane Production with an Ammonium Oxidative Reaction under the No Organic Substance Condition
  2. 2007/09, The Best Poster Award, Japanese Society of Microbial Ecology, In situ physiology of candidate division TM7 in a wastewater treatment plant
  3. 2006/08, Best Poster Award, International Society for Microbial Ecology, Microbial community structure in a super high-rate ANAMMOX biofilm


  1. Patent, JP6719092, 2020/06/18
  2. Patent, JP6651118, 2020/01/24
  3. Patent, JP6016062, 2016/10/07
  4. Patent, JP5582388, 2014/07/25
  5. Patent, JP5004105, 2012/06/01