1. Ikeda-Ohtsubo, W., M. Miyahara, T. Yamada, M., A. Watanabe, S. Fushinobu, T. Wakagi, H. Shoun, K. Miyauchi, G. Endo, Effectiveness of heat treatment to protect introduced denitrifying bacteria from eukaryotic predatory microorganisms in a pilot-scale bioreactor, J. Biosci. Bioeng., vol. 116 (6): p722-724 (2013)
2. Yamada, T., S. Araki, W. Ikeda-Ohtsubo, K. Okamura, A. Hiraishi, H. Ueda, Y. Ueda, K. Miyauchi and G. Endo, Community structure and population dynamics of ammonia oxidizers in composting processes of ammonia-rich livestock waste, Syst. Appl. Microbiol., vol. 36 (5): p359-367 (2013)
3. Ikeda-Ohtsubo, W., M. Miyahara, S.-W. Kim, T. Yamada, M. Matsuoka, A. Watanabe, S. Fushinobu, T. Wakagi, H. Shoun, K. Miyauchi, G. Endo, Bioaugmentation of a wastewater bioreactor system with the nitrous oxide-reducing denitrifier Pseudomonas stutzeri strain TR2, J. Biosci. Bioeng., vol. 115 (1): p37-42 (2013)
4. Yamada, T., H. Matsuoka, J. Son, S. Yoshikawa, H. Tsuji and A. Hiraishi, Nitrate removal properties of solid-phase denitrification processes using acid-blended poly(L-lactic acid) as the sole substrate, J. Phys.: Conf. Ser. 433 012036 (2013)
5. 山田剛史, 吉川成志, 片山傳喜, 平石明, 生分解性プラスチックを利用した生物学的脱窒処理技術 (第2編1章4節), 排水汚水処理技術集成 vol. 2, 株式会社エヌ・ティー・エス: p.113-120 (2013)
6. 山田剛史, 小さなハイパフォーマーとコーディネーター, needs (2013)

1. Kobayashi, K., T. Yamada, A. Hiraishi and S. Nakauchi, Real-time optical monitoring of microbial growth using optimal combination of light-emitting diodes, Opt. Eng., vol. 51 (12): p123201 (1-8) (2012)
2.Kaiya, S., O. Rubaba, N. Yoshida, T. Yamada, and A. Hiraishi, Characterization of Rhizobium naphthalenivorans sp. nov. with special emphasis on aromatic compound degradation and maltilocus sequence analysis of housekeeping genes, J. Gen. Appl. Microbiol. vol. 58: p.211-224 (2012)
3.Kaiya, S., S. Utsunomiya, S. Suzuki, N. Yoshida, H. Futamata, T. Yamada, A. Hiraishi, Isolation and function gene analyses of aromatic-hydrocarbon- degrading bacteria from a polychlorinated-dioxin-dechlorinating process, Microbes, Environ., vol. 27: p.127-135 (2012)
4.Miyahara, M., S.-W. Kim, S. Zhou, S. Fushinobu, T. Yamada, W. Ikeda-Ohtsubo, A. Watanabe, K. Miyauchi, G. Endo, T. Wakagi, H. Shoun, Survival of the aerobic denitrifier Pseudomonas stutzeri strain TR2 during co-cultures with activated sludge under the denitrifying conditions, Biosci. Biotech. Biochem. vol. 76: p.495-500 (2012)
5. Okamura, K., A. Takanashi, T. Yamada and A. Hiraishi, Ammonia-oxidizing activity and microbial community structure in hyper-acid Tea (Camellia sinensis) orchard soil, J. Phys.: Conf. Ser. 352 012052. (2012)

1. Okamura, K., Kawai, A., Yamada, T. and Hiraishi, A.: Acidipila rosea gen. nov., sp. nov., an acidophilic chemoorganotrophic bacterium belonging to the phylum Acidobacteria. FEMS Microbiol. Lett. 317(2): 138-142 (2011)
2. Yamada, T., Kikuchi, K., Yamauchi, T., Shiraishi, K., Ito, T., Okabe, S., Hiraishi, A., Ohashi, A., Harada, H., Kamagata, Y., Nakamura K., Sekiguchi, Y.:Ecophysiology of uncultured filamentous anaerobes belonging to the phylum KSB3 that cause bulking in methanogenic granular sludge. Appl. Environ. Microbiol. 77(6): 2081-2087 (2011)
3. Takahashi, M., Yamada, T., Tanno, N., Tsuji, H., Hiraishi, A.: Nitrate removal efficiency and bacterial community dynamics in a denitrification process using poly (L-lactic acid) as the solid substrate. Microbes Environ. vol. 26: 212-219 (2011)
4. 山田剛史, 平石明: 「ポリ乳酸」の新しい活用法 -生物学的脱窒プロセスにおける還元力供給材料-MATERIAL STAGE 3: p.23-26 (2011)
5. 山田剛史∗, 平石明, ポリ乳酸廃材を用いた環境浄化・エネルギー回収技術の開発と展望, 月刊ファインケミカル, vol. 40 (9): p12-19 (2011)

1. Matsuzawa, Y., Kimura, Z., Nishimura, Y., Shibayama, M., Hiraishi, A.: Removal of hydrophobic organic contaminants from aqueous solutions by sorption onto biodegradable polyesters. J. Water Resour. Prot. 2: 214-221 (2010).
2. Narihiro, T., Kaiya, S., Futamata, H., Hiraishi, A.: Removal of polychlorinated dioxins by semi-aerobic fed-batch composting with biostimulation of “Dehalococcoides”. J. Biosci. Bioeng. 109(3): 249-256 (2010).
3. Hiraishi, A.: Environmental applications. In Poly(lactic acid): Synthesis, Structures, Properties, Processing, and Applications, ed. by Auras, R., Lim, L.-T., Selke, S. E. M., and Tsuji, H., Wiley, pp. 477-485 (2010).
4. Miyahara, M., Kim, S.-W., Fushinobu, S., Takaki, K., Yamada, T., Watanabe, A., Miyauchi, K., Endo, G., Wakagi, T., and Shoun, H.: Potential of aerobic denitrification by Pseudomonas stutzeri TR2 to reduce nitrous oxide emissions from wastewater treatment plants. Appl. Environ. Microbiol. 76 (14): 4619-4629 (2010)
5. 山田剛史: ポリ乳酸の廃水処理技術利用への展望 ―プロセス内で機能する微生物群に迫る―.微生物生態学会誌 25:14-15 (2010)

1. Futamata, H., Kaiya, S., Sugawara, M., Hiraishi, A.: Phylogenetic and Transcriptional analyses of a tetrachloroethene-dechlorinating "Dehalococcoides" enrichment culture TUT2264 and its reductive-dehalogenase genes. Microbes Environ. 24(4): 330-337 (2009).
2. Okamura, K., Takata, K., Hiraishi, A.: Intrageneric relationships of members of the genus Rhodopseudomonas. J. Gen. Appl. Microbiol. 55(6): 468-479 (2009).
3. Okamura, K., Kanbe, T., Hiraishi, A.: Rhodoplanes serenus sp. nov., a purple non-sulfur bacterium isolated from pond water. Int. J. Syst. Evol. Microbiol. 59(3): 531-535 (2009).
4. Fujii, Y., Hiraishi, A.: Combined use of cyanoditolyl tetrazolium staining and flow cytometry for detection of metabolically active bacteria in a fed-batch composting process. Microbes Environ. 24(1): 57-63 (2009).
5. Okamura, K., Hisada, T., Kanbe, T., Hiraishi, A.: Rhodovastum atsumiense gen. nov., sp. nov., a phototrophic alphaproteobacterium isolated from paddy soil. J. Gen. Appl. Microbiol. 55(1): 43-50 (2009).
6. Yamada, T., Sekiguchi, Y.: Cultivation of uncultured Chloroflexi subphyla: significance and ecophysiology formerly uncultured Chloroflexi ‘subphylum I’ with natural and biotechnological relevance. Microbes Environ. 24(2): 205-216 (2009)

1. Miyazawa, K., Kobayashi, K., Nakauchi, S., and Hiraishi, A.: In situ detection and identification of microorganisms at single-colony resolution by spectral imaging. Opt. Rev. 15(6): 285-291 (2008).
2. Hiraishi, A. (2008) Biodiversity of dehalorespiring bacteria with special emphasis on polychlorinated biphenyl/dioxin dechlorinators. Microbes Environ. 23(1): 1-12.
3. Yamada, T., Suzuki, A., Ueda, H., Ueda, Y., Miyauchi, K., Endo, G.: Successions of bacterial community in composting cow dung wastes with or without hyperthermophilic pre-treatment. Appl. Microbiol. Biotechnol. 81: 771-781 (2008)
4. 平石明: 微生物の分類.遺伝子から見た応用微生物学,熊谷英彦,加藤暢夫,村田幸作,阪井康能(編著),朝倉書店,東京,pp. 96-112 (2008).
5. 平石明: 複合微生物群集によるダイオキシンの分解除去技術.土壌・地下水汚染の浄化および修復技術,エヌ・ティー・エス,東京,pp. 128-136 (2008).
6. 平石明: 水処理におけるバイオプラスチックの利用.バイオプラスチックの高機能化・再資源化技術,エヌ・ティー・エス,東京,pp. 296-308 (2008).

1. Futamata, H., Hiraishi, A.: Biodiversity and ecophysiology of anaerobic dehalogenating microorganisms: implications for bioremediation. Curr. Trends Microbiol. 3: 63-92 (2007).
2. Hisada, T., Okamura, K., Hiraishi, A.: Isolation and characterization of phototrophic purple nonsulfur bacteria from Chloroflexus and cyanobacterial mats in hot springs. Microbes Environ. 22(4): 405-411 (2007).
3. Okamura, K., Hisada, T., Hiraishi, A.: Characterization of thermotolerant purple nonsulfur bacteria isolated from hot-spring Chloroflexus mats and the reclassification of "Rhodopseudomonas cryptolactis" Stadtwald-Demchick et al. 1990 as Rhodoplanes cryptolactis nom. rev., comb. nov. J. Gen. Appl. Microbiol. 53(6): 357-361 (2007).
4. Futamata, H., Yoshida, N., Kurogi, T., Kaiya, S., Hiraishi, A.: Reductive dechlorination of chloroethenes by Dehalococcoides-containing cultures enriched from a polychlorinated-dioxin-contaminated microcosm. ISME J. 1: 471-479 (2007).
5. Takebayashi, S., Narihiro, T., Fujii, Y., Hiraishi, A.: Water availability is a critical determinant of a population shift From Proteobacteria to Actinobacteria during start-up operation of mesophilic fed-batch composting. Microbes Environ. 22(3): 279-289 (2007).
6. Okubo, Y., Hiraishi, A.: Population dynamics and acetate utilization kinetics of two different species of phototrophic purple nonsulfur bacteria in a continuous co-culture system. Microbes Environ. 22(1): 82-88 (2007).
7. Suzuki, S., Hiraishi, A.: Novosphingobium naphthalenivorans sp. nov., a naphthalene-degrading bacterium isolated from polychlorinated-dioxin-contaminated environments. J. Gen. Appl. Microbiol. 53(4): 221-228 (2007).
8. Khan, S. T., Horiba, Y., Takahashi, N., Hiraishi, A.: Activity and community composition of denitrifying bacteria in poly(3-hydroxybutyrate-co-3-hydroxyvalerate)-using solid-phase denitrification processes. Microbes Environ. 22(1): 20-31 (2007).
9. Yamada, T., Yamauchi, T., Shiraishi, K., Hugenholtz, P., Ohashi, A., Harada, H., Kamagata, Y., Nakamura, K., Sekiguchi, Y.: Characterization of filamentous bacteria, belonging to candidate phylum KSB3, that are associated with bulking in methanogenic granular sludges. ISME J. 1: 246-255 (2007).
10. Yamada, T., Imachi, H., Hanada, S., Ohashi, A., Harada, H., Kamagata, Y., Sekiguchi Y.: Bellilinea caldifistulae gen. nov., sp. nov. and Longilinea arvoryzae gen. nov., sp. nov., strictly anaerobic, filamentous bacteria of the phylum Chloroflexi isolated from methanogenic propionate-degrading consortia. Int. J. Syst. Evol. Microbiol. 57:2299-2306 (2007)
11. Yamada, T., Miyauchi, K., Ueda, H., Ueda, Y., Sugawara, H., Nakai, Y., Endo G.: Composting cattle dung wastes by using a hyperthermophilic pre-treatment process: characterization by physicochemical and molecular biological analysis. 104:408-415 (2007)
12. 平石明: 微生物によるダイオキシンの分解と生物学的環境技術の開発.資源環境対策 43(2): 78-82 (2007).
13. 平石明: 生分解性プラスチックを利用した残留性汚染化学物質の吸着除去.工業材料 55(5): 72-75 (2007).
14. 平石明: 生分解プラスチックを用いた水中の窒素除去技術.プラスチックス 58(5): 44-47 (2007).
15. 山田剛史, 宮内啓介, 上田英代, 上田裕一, 遠藤銀朗: 有機資源の循環利用に必要な環境保全型コンポスト製造技術の開発. 環境バイオテクノロジー学会誌 7(2):111-117 (2007)

1. Iizuka, T., Tokura, M., Jojima, Y., Hiraishi, A., Yamanaka, S., Fudou, R.: Enrichment and phylogenetic analysis of moderately thermophilic myxobacteria from hot springs in Japan. Microbes Environ. 21(3): 189-199 (2006).
2. Yoshida, N., Fujii, H., Hiraishi, A.: A modified cyanoditolyl tetrazolium reduction method for differential detection of metabolically active gram-positive and gram-negative bacteria. Microbes Environ. 21(4): 272-277 (2006).
3. Ando, T., Suzuki, H., Nishimura, S., Tanaka, T., Hiraishi, A., Kikuchi, Y.: Characterization of extracellular RNAs produced by the marine photosynthetic bacterium Rhodovulum sulfidophilum. J. Biochem. 139(4): 805-811 (2006).
4. Okubo, Y., Futamata, H., Hiraishi, A.: Characterization of phototrophic purple nonsulfur bacteria forming colored microbial mats in a swine wastewater ditch. Appl. Environ. Microbiol. 72(9): 6225-6233 (2006).
5. Maruyama, T., Park, H.-D., Ozawa, K., Tanaka, Y., Tatsuo, S., Hamana, K., Hiraishi, A., Kato, K. (2006) Sphingosinicella microcystinivorans gen. nov., sp. nov., a microcystin-degrading bacterium. Int. J. Syst. Evol. Microbiol. 56(1): 85-89 (2006).
6. Yamada, T., Sekiguchi, Y., Imachi, H., Kamagata, Y., Ohashi, A., Harada, H.: Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi. Int. J. Syst. Evol. Microbiol. 56: 1331-1340 (2006).
7. 平石明: 脱ハロ呼吸細菌"Dehalococcoides"と環境修復--PCBやダイオキシンなどの脱塩素化能をもつ菌への期待.化学と生物 44(5): 292-294 (2006).
8. 平石明,二又裕之: 生分解性ポリマーを利用した新しい水処理・環境浄化技術.水処理技術 47(7): 301-311 (2006).

1. Hiraishi, A., Sakamaki, N., Miyakoda, H., Maruyama, T., Kato, K., Futamata, H.: Estimation of "Dehalococcoides" populations in lake sediment contaminated with low levels of polychlorinated dioxins. Microbes Environ. 20(4): 216-226 (2005).
2. Hiraishi, A., Kaiya, S., Miyakoda, H., Futamata, H.: Biotransformation of polychlorinated dioxins and microbial community dynamics in sediment microcosms at different contamination levels. Microbes Environ. 20(4): 227-242 (2005).
3. Okubo, Y., Futamata, H., Hiraishi, A.: Distribution of phototrophic purple nonsulfur bacteria in wastewater environments and their capacity for utilization of lower fatty acids. Microbes Environ. 20(3): 135-143 (2005).
4. Shimomura, K., Kaji, S., Hiraishi, A.: Chryseobacterium shigense sp. nov., a yellow-pigmented, aerobic bacterium isolated from a lactic acid beverage. Int. J. Syst. Evol. Microbiol. 55(5):1903-1906 (2005).
5. Yoshida, N., Takahashi, N., and Hiraishi, A.: Phylogenetic characterization of a polychlorinated-dioxin-dechlorinating microbial community by use of microcosm studies. Appl. Environ. Microbiol. 71(8): 4325-4334 (2005).
6. Shinoda, Y., Akagi, J., Uchihashi, Y., Hiraishi, A., Yukawa, H., Yurimoto, H., Sakai, Y., Kato N.: Anaerobic degradation of aromatic compounds by Magnetospirillum strains: isolation and degradation genes. Biosci. Biotechnol. Biochem. 69(8): 1483-1491 (2005).
7. Kubota, M., Kazuyoshi Kawahara, K., Sekiya, K., Uchida, T., Hattori, Y., Futamata, H., Hiraishi, A.: Nocardioides aromaticivorans sp. nov., a dibenzofuran-degrading bacterium isolated from dioxinpolluted environments. Syst. Appl. Microbiol. 28(2): 165-174 (2005).
8. Horiba, Y., Khan, S. T., Hiraishi, A.: Characterization of the microbial community and culturable denitrifying bacteria in a solid-phase denitrification process using poly(-caprolactone) as the carbon and energy source. Microbes Environ. 20(1): 25-33 (2005).
9. Futamata H, Nagano Y, Watanabe K., Hiraishi A.: Unique kinetic properties of phenol-degrading variovorax strains responsible for efficient trichloroethylene degradation in a chemostat enrichment culture. Appl. Environ. Microbiol.. 71(2): 904-911 (2005).
10. Miyazawa, K., Kobayashi, K., Nakauchi, S., Hiraishi, A.: In situ detection and identification of microorganisms at single colony resolution using spectral imaging technique. Lect. Notes Comput. Sci. 3540: 419-428 (2005).
11. Narihiro, T., Hiraishi, A.: Microbiology of fed-batch composting. Microbes Environ. 20(1): 1-13 (2005).
12. Imhoff, J, F., Hiraishi, A., Suling: Anoxygenic phototrophic purple bacteria. In Bergey's Manual of Systematic Bacteriology, Second Edition, Vol. 2, The Proteobacteria, Part A Introductory Essays, ed. by D. J. Brenner, N. R. Krieg, and J. T. Staley, Editor-in-Chief G. M. Garrity, Springer, pp. 119-132 (2005).
13. Imhoff, J, F., Hiraishi, A.: Aerobic bacteria containing bacteriochlorophyll and belonging to the Alphaproteobacteria. In Bergey's Manual of Systematic Bacteriology, Second Edition, Vol. 2, The Proteobacteria, Part A Introductory Essays, ed. by D. J. Brenner, N. R. Krieg, and J. T. Staley, Editor-in-Chief G. M. Garrity, Springer, pp. 119-132 (2005).
14. Yamada, T., Sekiguchi, Y., Imachi, H., Kamagata, Y., Ohashi, A., Harada, H.: Diversity, localization, and physiological properties of filamentous microbes belonging to Chloroflexi subphylum I in mesophilic and thermophilic methanogenic sludge granules. Appl. Environ. Microbiol. 71: 7493-7503 (2005).
15. 山田剛史, 関口勇地,鎌形洋一,白石皓二,Philip Hugenholtz,井町寛之,大橋晶良, 原田秀樹: 嫌気性廃水処理グラニュール汚泥のバルキングに関する門レベルで未培養な糸状性細菌群. 水環境学会誌 28 (1): 37-42 (2005)


1. 特許出願2012-022257、山田剛史 他4 名、電子供与体供給剤および、それを用いた環境浄化方法, 出願人:山田剛史 他4 名、出願日:2012 年2 月3 日.
2. 特許出願2009-264383、平石明 他2 名、電子供与体供給剤、電子供与体供給剤の製造方法および、それを用いた環境浄化方法、出願人:豊橋技術科学大学、出願 日:2009 年11 月31 日.
3. 特許出願2008-83062、上田裕一 他4 名、有機廃棄物の堆肥化方法、出願人:有限会社日本ライフセンター、出願日:2008 年3 月27 日.
4. 特許出願2005-103710、平石明 他4 名、微生物の汚染物質分解能力測定方法、出願人:豊橋技術科学大学 外1名、出願日:2005 年3 月31 日.
5. 特許出願2004-356749、平石明 他1 名、余剰汚泥の発生抑制方法、出願人:豊橋技術科学大学 外1名、出願日:2004 年12 月9 日.
6. 特許出願2004-84001、平石明 他3 名、汚染物質の浄化方法、出願人:豊橋技術科学長 他1 名、出願日:2004 年3 月23 日.
7. 特許出願2004-83996、平石明 他3 名、微生物剤、これを用いる汚染物質の浄化方法、出願人:豊橋技術科学長 他1 名、出願日:2004 年3 月23 日.
8. 特許出願2004-82651、平石明 他3 名、複合微生物製剤、その製造方法、および有機塩素系化合物で汚染された物質の浄化方法、出願人:平石明 他1 名、出願日:2004 年3 月22 日.
9. 特許出願2004-65989、平石明 他1 名、廃水処理方法、出願人:平石明 他1 名、出願日:2004 年3 月9 日.
10. 特許出願2003-361430、平石明 他1 名、余剰汚泥の発生抑制方法、出願人:オルガノ株式会社 外1名、出願日:2003 年10 月22 日.
11. 特許出願2003-168941、平石明、微生物の分子生物学的同定技術、出願人:平石明他1 名、出願日:2003 年6 月13 日.
12. 特許出願2002-380888、平石明 他1 名、環境浄化方法、窒素除去方法および集積培養方法、出願人:平石明 他1 名、出願日:2002 年12 月27 日.
13. 特許出願2002-167428、平石明 他2 名、難分解性有機物吸着剤と難分解性有機物含有水の浄化方法ならびに難分解性有機物含有水浄化システム、出願人:科学技術振興事業団、出願日:2002 年6 月7 日.