Publications

• Scientific paper
• Book Chapters
• Magazine Articles
• Grants

Papers in peer-reviewed Scientific Journals

1. K. Matsui, and T. Miki. 2023. Microbial community composition and function in an urban waterway with combined sewer overflows before and after implementation of a stormwater storage pipe. PeerJ11:e14684 DOI 10.7717/peerj.14684. PDF
2. C. Terada, M. Nakamura, S.Y. Zhu, H. Iguchi, J. Takagi, K. Matsui, H. Shibata. 2022. Testing the measurement condition of the EcoPlate metabolic profiling for forest soil microbes in the Wakayama Experimental Forest of Hokkaido University. Jpn J For Environ.PDF
3. H. Lin, K. Matsui, R.J. Newton, and L. Guo. 2022. Disproportionate Changes in Composition and Molecular Size Spectra of Dissolved Organic Matter between Influent and Effluent from a Major Metropolitan Wastewater Treatment Plant. ACS ES&T Water 2:216-225. Abstract
4. M. Nakamura, C. Terada, K. Ito, K. Matsui, S. Niwa, M. Ishihara, T. Kenta, T. Yoshikawa, T. Kadoya, T. Hiura, H. Muraoka, K. Ishida, N. Agetsuma, R. Nakamura, H. Sakio, M. Takagi, A. S. Mori, M. K. Kimura, H. Kurokawa, T. Enoki, T. Seino, A. Takashima, H. Kobayashi, K. Matsumoto, K. Takahashi, R. Tateno, T. Yoshida, T. Nakaji, M. Maki, K. Kobayashi, K. Fukuzawa, K. Hoshizaki, K. Ohta, K. Kobayashi, M. Hasegawa, S. N. Suzuki, M. Sakimoto, Y. Kitagawa, A. Sakai, H. Kondo, T. Ichie, K. Kageyama, A. Hieno, S. Kato, T. Otani, Y. Utsumi, T. Kume, K. Homma, K. Kishimoto, K. Masaka, K. Watanabe, M. Toda, D. Nagamatsu, Y. Miyazaki, T. Yamashita, and N. Tokuchi. 2022. Evaluating the soil microbe community-level physiological profile using EcoPlate and soil properties at 33 forest sites across Japan. Ecological Research 37:432-445 PDF
5. K. Matsui, T. Fumoto, and H. Kawakami. 2019. Testing the repellent effects of construction materials on the attachment of the invasive golden mussel, Limnoperna fortunei, in a Japanese urban tidal river. Limnology 20: 131-136. Abstract
6. K. Matsui, and G. Endo. 2018. Mercury bioremediation by mercury resistance transposon-mediated in situ molecular breeding Applied Microbiology and Biotechnology 102: 3037-3048. Abstract
7. T. Miki, T. Yokokawa, P.J. Ke, I.F. Hsieh, C.H. Hsieh, T. Kume, K. Yoneya and K. Matsui. 2018. Statistical recipe for quantifying microbial functional diversity from EcoPlate metabolic profiling. Ecological Research 33: 249-260. Abstract
8. K. Matsui, Y. Yokoyama, K. Kamei, Y. Nakaguchi, M. Eguchi, A. Taniguchi, K. Takehara, and T. Fumoto. 2017. Bacterial community composition monitoring for the impact of combined sewer over-flow into Higashiyokobori-gawa waterway, and its remedial effects by building a stormwater storage pipe. Journal of Japan Society of Civil Engineers (Division G: Environmental Systems and Engineering) 73: 134-142. (Japanese) PDF
9. K. Takehara, and K. Matsui. 2017. Development of measurement technique of three dimensional flow fields around a microbe by using a differential interference contrast microscope. Journal of Japan Society of Civil Engineers (Division B1: Hydraulic Engineering) 73: I_673-I_678. (Japanese) PDF
10. K. Matsui, S. Yoshinami, M. Narita, M. F. Chien, L. Phung, S. Silver, and G. Endo. 2016. Mercury resistance transposons in Bacilli strains from different geographical regions. FEMS Microbiology Letters 363: fnw013. PDF
11. K. Matsui, T. Yokokawa, M. Ueta, Y. Michikoshi, A. Mizuguti, H. Matsuda, and T. Miki. 2016. How can we identify and evaluate the possible adverse effects on biological diversity with a scientifically sound manner under the Cartagena Protocol on Biosafety: Perspective. Japanese Journal of Ecology 66: 325-335. (Japanese) PDF
12. K. Matsui. 2015. Horizontal gene transfer in microbial ecosystem. Japanese Journal of Protozoology 48: 31-43. (Japanese) PDF
13. T. Miki, T. Yokokawa, K. Matsui. 2014. Biodiversity and multifunctionality in a microbial community: a novel theoretical approach to quantify functional redundancy.Proceedings of the Royal Society B 281: 20132498. PDF
14. Z. Kawabata, T. Minamoto, M. N. Honjo, K. Uchii, H. Yamanaka, A. A. Suzuki, Y. Kohmatsu, K. Asano, T. Itayama, T. Ichijo, K. Omori, N. Okuda, M. Kakehashi, M. Nasu, K. Matsui, M. Matsuoka, H. Kong, T. Takahara, D. Wu, and R. Yonekura. 2011. Environment-KHV-carp-human linkage as a model for environmental diseases. Ecological Research 26: 1011-1016. Abstract
15. K. Uchii, A. Telschow, T. Minamoto, H. Yamanaka, M. N. Honjo, K. Matsui, and Z. Kawabata. 2011. Transmission dynamics of an emerging infectious disease in wildlife through host reproductive cycles. The ISME Journal 5: 244-251. PDF
16. M. F. Chien, M. Narita, K. H. Lin, K. Matsui, C. C. Huang, and G. Endo. 2010. Organomercurials removal by heterogeneous merB genes harboring bacterial strains. Journal of Bioscience and Bioengineering 110: 94-98. Abstract
17. M. N. Honjo, T. Minamoto, K. Matsui, K. Uchii, H. Yamanaka, A. A. Suzuki, Y. Kohmatsu, T. Iida, and Z. Kawabata. 2010. Quantification of cyprinid herpesvirus 3 in environmental water by using an external standard virus. Applied and Environmental Microbiology 76: 161-168. PDF
18. K. Uchii, K. Matsui, T. Iida, and Z. Kawabata. 2009. Distribution of the introduced cyprinid herpesvirus 3 in a wild population of common carp (Cyprinus carpio). Journal of Fish Diseases 32: 857-864. PDF
19. R. Yonekura, H. Yamanaka, A. Ushimaru, K. Matsui, K. Uchii, and A. Maruyama. 2008. Allochthonous prey subsidies provide an asymmetric growth benefit to invasive bluegills over native cyprinids under the competitive conditions in a pond. Biological Invasions 11:1347-1355. PDF
20. K. Matsui, M. Honjo, Y. Kohmatsu, K. Uchii, R. Yonekura, and Z. Kawabata. 2008. Detection and significance of koi herpesvirus (KHV) in freshwater environments. Freshwater Biology 53: 1262-1272. PDF
21. T. Miki, K. Matsui, T. Yokokawa, T. Nishida, Y. Kobayashi, and K. Uchii. 2007. Microbial pool and biodiversity. Japanese Journal of Ecology 57: 424-431. (Japanese)
22. K. Matsui, M. Narita, and G. Endo. 2007. Transoceanic and transcontinental dispersal of bacteria and genes: Global dissemination of mercury resistance bacteria and mercury resistance genes. Japanese Journal of Ecology 57: 390-397. (Japanese)
23. K. Uchii, N. Okuda, R. Yonekura, Z. Karube, K. Matsui, and Z. Kawabata. 2007. Trophic polymorphism in bluegill sunfish (Lepomis macrochirus) introduced into Lake Biwa: Evidence from stable isotope analysis. Limnology 8: 59-63. Abstract
    
24. M. Honjo, K. Matsui, N. Ishii, M. Nakanishi, and Z. Kawabata. 2007. Viral abundance and its related factors in a stratified lake. Archiv fur Hydrobiology 168: 105-112. Abstract
    
25. K. Matsui, K. Yusa, H. Sugawara, M. Narita, and G. Endo. 2007. Development of bacterial biosensor for detecting organomercurials using organomercurial lyase gene and bioluminescence reporter system. Journal of Japan Society on Water Environment 30: 77-81. (Japanese)
26. K. Uchii, K. Matsui, R. Yonekura, K. Tani, T. Kenzaka, M. Nasu, and Z. Kawabata. 2006. Genetic and physiological characterization of the intestinal bacterial microbiota of bluegill (Lepomis macrochirus) with three different feeding habits. Microbial Ecology 51: 277-283. Abstract
    
27. G. Endo, K. Matsui, and M. Narita. 2006. Horizontal gene transfer in environmental purification microorganisms: consideration of the use of living modified organisms in the uncontained environments from the evidence of mercury resistance genes as microbial common properties. Journal of Environmental Biotechnology 6: 27-32. (Japanese)
28. M. Honjo, K. Matsui, M. Ueki, R. Nakamura, J. A. Fuhrman, and Z. Kawabata. 2006. Diversity of virus-like agents killing Microcystis aeruginosa in a hyper-eutrophic pond. Journal of Plankton Research 28: 407-412. PDF
    
29. K. Matsui, M. Narita, H. Ishii, and G. Endo. 2005. Participation of the recA determinant in the transposition of class II transposon mini-TnMERI1. FEMS Microbiology Letters 253: 309-314. PDF
    
30. M. Ueki, K. Matsui, K. Choi, and Z. Kawabata. 2004. The enhancement of conjugal plasmid pBHR1 transfer between bacteria in the presence of extracellular metabolic products produced by Microcystis aeruginosa. FEMS Microbiology Ecology 51: 1-8. PDF
    
31. N. Ishii, K. Matsui, S. Fuma, H. Takeda, and Z. Kawabata. 2004. Release of transforming plasmid DNA from actively growing genetically engineered Escherichia coli. FEMS Microbiology Letters 240: 151-154. PDF
    
32. K. Matsui, N. Ishii, M. Honjo, and Z. Kawabata. 2004. Use of the SYBR Green I fluorescent dye and a centrifugal filter device for rapid determination of dissolved DNA concentration in fresh water. Aquatic Microbial Ecology 36: 99-105. PDF
    
33. M. Narita, K. Matsui, C. C. Huang, Z. Kawabata, and G. Endo. 2004. Dissemination of TnMERI1-like mercury resistance transposons among Bacillus isolated from worldwide environmental samples. FEMS Microbiology Ecology 48: 47-55. PDF
    
34. K. Matsui, N. Ishii, and Z. Kawabata. 2003. Microbial interactions affecting the natural transformation of Bacillus subtilis in a model aquatic ecosystem. FEMS Microbiology Ecology 45: 211-218. PDF
    
35. K. Matsui, N. Ishii, and Z. Kawabata. 2003. Release of extracellular transformable plasmid DNA from Escherichia coli cocultivated with algae. Applied and Environmental Microbiology 69: 2399-2404. PDF
    
36. K. Matsui, M-S. Jun, M. Ueki, and Z. Kawabata. 2001. Functional succession of bacterioplankton on the basis of carbon source utilization ability by BIOLOG plates. Ecological Research 16: 905-912. Abstract
    
37. K. Matsui, M. Honjo, and Z. Kawabata. 2001. Estimation of the fate of dissolved DNA in thermally stratified lake water from the stability of exogenous plasmid DNA. Aquatic Microbial Ecology 26: 95-102. PDF
    
38. K. Matsui, N. Ishii, and Z. Kawabata. 2001. Survival of genetically modified Escherichia coli carrying extraneous antibiotic resistance gene through microbial interactions. Bulletin of Environmental Contamination and Toxicology 66: 139-145. Abstract
    
39. K. Matsui, S. Kono, A. Saeki, N. Ishii, M-G. Min, and Z. Kawabata. 2000. Direct and indirect interactions for coexistence in a species defined microcosm. Hydrobiologia 435: 109-116. Abstract
    
40. A. Gupta, K. Matsui, J.F. Lo, and S. Silver. 1999. Molecular basis for resistance to silver in Salmonella. Nature Medicine 5: 183-188. PDF
    
41. S. Silver, A. Gupta, K. Matsui, and J. F. Lo. 1999. Resistance to Ag(I) cations in bacteria: environments, genes and proteins. Metal-Based Drugs 6: 315-320. PDF
    
42. Z. Kawabata, M-G. Min, K. Matsui, and N. Ishii. 1998. Factors affecting the survival of genetically engineered Escherichia coli bearing a plasmid in a paddy field microcosm. International Journal of Environmental Studies 55: 77-85. Abstract
    
43. M-G. Min, Z. Kawabata, K. Matsui, and N. Ishii. 1997. Fate of a genetically engineered Escherichia coli bearing a plasmid in a paddy field microcosm. International Journal of Environmental Studies 52: 75-88. Abstract
    
44. Z. Kawabata, M-G. Min, K. Matsui, and N. Ishii. 1996. A simple method for counting Escherichia coli sensitive and resistant to antibiotics in a bacterial community. Japanese Journal of Water Treatment Biology 32: 61-66. PDF
    
45. Z. Kawabata, K. Matsui, K. Okazaki, M. Nasu, N. Nakano, and T. Sugai. 1995. Synthesis of a species-defined microcosm with protozoa. Journal of Protozoology Research 5: 23-26. PDF
    

Book Chapters

1. K. Matsui. 2012. Dynamics of genetic information: Horizontal gene transfer in microbial world. In: Frontiers in freshwater ecology, T. Yoshida, M. Kagami, and G-M. Kato, eds., pp. 132-141., Kyoritsu Syuppan, Tokyo, Japan (In Japanese).
2. Educational outreach working group in Japanese Society of Microbial Ecology (20 people including K. Matsui) eds. 2004. Introduction of Microbial Ecology, 237pp., Nikkagiren Syuppan, Tokyo, Japan (In Japanese).
3. Z. Kawabata, and K. Matsui. 2003. Genes in aquatic environment. Contribution of bacterial horizontal gene transfer for the diversity of genetic information. In: Recommendation of biodiversity science, T. Ohgushi, eds., pp. 136-157., Maruzen Syuppan, Tokyo, Japan (In Japanese).

Magazine Articles

1. T. Miki, M. Nakamura, H. Kurokawa, K. Matsui. 2022. “Idea Paper” for sharing diverse research ideas. Ecological Research 37: 450-454. Abstract
2. T. Miki, M. Nakamura, K. Matsui, H. Mizoguchi, E. Tamaki. 2020. Promoting the sharing of ideas via “Idea Papers”. Ecological Research 35: 575-578. Abstract
3. K. Matsui, and T. Yokokawa. 2016. How can we identify and evaluate the possible adverse effects on biological diversity with a scientifically sound manner under the Cartagena Protocol on Biosafety: Introduction. Japanese Journal of Ecology 66: 287-289. (Japanese)
4. M. Sato, C. C. Huang, M. Narita, K. Matsui, and G. Endo. 2005. Characterization of arsenic resistance transposon and ars-operon in Bacillus isolated from the sediment of Minamata Bay, Japan. Bulletin of Institute for Environmental Protection, Tohoku Gakuin University 16: 3-8. (Japanese)

Grants

1. 2024-2026. JSPS Kakenhi (B) (Grant-in-Aid for Scientific Research). Clarifying the ecological changes from upstream to downstream in sewer systems and the establishment of antibiotic-resistant bacteria. Principal Investigator (PI)
2. 2023. River Fund of The River Foundation, Japan. Dynamics of antibiotic resistance coliforms in urban river and sewage. Principal Investigator (PI).
3. 2020-2022. JSPS Kakenhi (B) (Grant-in-Aid for Scientific Research 20H04348). Characterization of antibiotic resistant bacteria in sewer ecosystem for the embodiment of the one health approach. Principal Investigator (PI)
4. 2019-2021. JSPS Kakenhi (B) (Grant-in-Aid for Scientific Research 19H03309). Elucidation how the individual epidemiology parameter gives to infectious disease expansion and the whole ecosystem. Project member (PI: T. Miki)
5. 2019-2021. JSPS Kakenhi (C) (Grant-in-Aid for Scientific Research 19K12357). Evaluation of the dissemination and the infection mechanism of drug-resistant bacteria in aquatic ecosystem. Project member (PI: Y. Kobayashi)
6. 2018. Research Foundation on marine environment re-generation and creation in Osaka Bay area. Distribution of antibiotics resistant bacteria in Osaka Bay and the influence from the inflowing rivers. Principal Investigator (PI).
7. 2017. Research Fellowships from Graduate School of Science and Engineering, Kindai University. Dynamics of antibiotic resistant bacteria in urban river and the impact of combined sewer over-flow (CSO). Principal Investigator (PI).
8. 2017. River Fund of The River Foundation, Japan. Impact of combined sewer over-flow (CSO) for the dynamics of antibiotics resistant bacteria and their genes in urban river. Principal Investigator (PI).
9. 2016-2018. JSPS Kakenhi (C) (Grant-in-Aid for Scientific Research 16K07529). Evaluation of microbial dispersal and environmental selection; using mercury resistant bacteria as probe. Principal Investigator (PI)
10. 2016. Research Fellowships from Graduate School of Science and Engineering, Kindai University. Construction of closed experimental ecosystem for evaluation of Genetically Modified Microbes on biodiversity. Principal Investigator (PI).
11. 2014-2015 Research Project at Research Institute for Humanity and Nature (RHIN). Co-creating Heuristic and Autonomous Risk-recognition system and Value-Action Networking for Futurability (CHAR’s VAN for the Future). Project member (PI: I. C. Handoh)
12. 2013-2015. Japan Sewage Works Association Foundation. Bacterial community composition monitoring for the impact of combined sewer over-flow (CSO) into Higashiyokobori-gawa and Dotonbori-gawa waterway. Principal Investigator (PI).
13. 2013. Research Fellowships from Graduate School of Science and Engineering, Kindai University. Analysis of aero-microbial diversity of Asian dust and their participation for ecosystems. Principal Investigator (PI).
14. 2012. Nippon Life Insurance Foundation. Microbial. Microbial diversity in urban river and their contribution for in situ water treatment. Principal Investigator (PI).
15. 2010. Research Fellowships from Graduate School of Science and Engineering, Kindai University. Application of bio-polyurethane for microbiological water treatment. Principal Investigator (PI).
16. 2009-2013. MEXT-Supported Program for the Strategic Research Foundation at Private Universities. Advanced biotechnological researches for environmental conservation and healthy life. Contributed Researcher (PI: G. Endo in Tohoku Gakuin University)
17. 2008. Research Fellowships of Kindai University SR-03. Application of mercury resistance transposon for evaluation of the bacterial gene transfer frequency. Principal Investigator (PI).
18. 2008-2010. JSPS Kakenhi (C) (Grant-in-Aid for Scientific Research 20570027). Estimation of the bacterial horizontal gene transfer frequency in environment from the transposition of mercury resistance transposon. Principal Investigator (PI)
19. 2006-2007. Grant-in-Aid for Young Scientists 18810040 (Start-up). Environmental parameters affecting the survival of cyprinid herpesvirus 3 in freshwater. Principal Investigator (PI).
20. 2006-2008. JSPS Kakenhi (Grant-in-Aid for Exploratory Research 18651039). Bioremediation of contaminated environment by heavy metal resistance transposon-mediated in situ molecular breeding. Contributed Researcher (PI: G. Endo)
21. 2006-2011. Research Project at Research Institute for Humanity and Nature (RHIN). Effects of Environmental Change on the Interactions between Pathogens and Humans (C-06). Project member (PI: Z. Kawabata)
22. 2004-2006. JSPS Kakenhi (A) (Grant-in-Aid for Scientific Research 16207001). Analysis of different processes of gene transfer in aquatic ecosystems using the Aquatron. Contributed Researcher (PI: Z. Kawabata)
23. 2003-2005. Grant-in-Aid for JSPS Fellows 03J09436 (PD). Application of horizontal gene transfer among bacteria to clean-up contaminated ecosystem: A new bioremediation strategy. Principal Investigator (PI).
24. 2001-2003. JSPS Kakenhi (A) (Grant-in-Aid for Scientific Research 13309009). Analysis of gene transfer and expression mechanisms in aquatic ecosystems using the Aquatron. Contributed Researcher (PI: Z. Kawabata)
25. 2002. Kurita Water and Environment Foundation. Fundamental research using microbial ecosystem for bioremediation of contaminated environments. Principal Investigator (PI).
26. 2000-2002. Grant-in-Aid for JSPS Fellows 00J03345 (DC2). Characterization of biological factors in the horizontal gene transfer among bacteria using experimental ecosystems. Principal Investigator (PI).