2014年以降
*. Hisaya Kojima and Manabu Fukui. Sulfurisoma sediminicola gen. nov., sp. nov., a novel facultative autotroph isolated from a freshwater lake. International Journal of Systematic and Evolutionary Microbiology : in press.
2013年
*. Tomohiro Watanabe, Hisaya Kojima, Yoshinori Takano and Manabu Fukui. Diversity of sulfur-cycle prokaryotes in freshwater lake sediments investigated using aprA as functional marker gene. Systematic and Applied Microbiology 36: 436-443.2013.
*. Yoshinori Iizuka, Barbara Delmonte, Ikumi Oyabu, Torbjoern Karlin, Valter Maggi, Amuel Albani, Manabu Fukui, Takeo Hondoh and Margareta Hansson. Sulphate and chloride aerosols during Holocene and last glacial periods preserved in the Talos Dome Ice Core, a peripheral region of Antarctica. Tellus B 65: 20197.2013.
*. Miho Watanabe, Hisaya Kojima and Manabu Fukui. Desulfotomaculum intricatum sp. nov., a sulfate-reducer isolated from freshwater lake sediment. International Journal of Systematic and Evolutionary Microbiology 63: 3574-3578. 2013.
*.Takato Matsui, Hisaya Kojima, and Manabu Fukui. Effects of temperature on successive anaerobic decomposition of high-molecular organic matter under sulfate-reducing conditions. Estuarine, Coastal and Shelf Science 119: 139-144. 2013.
*. Akiko Kamono, Marianne Meyer, Thomas Cavalier-Smith, Manabu Fukui and Anne Maria Fiore-Donno. Exploring slime mould diversity in high altitude forests and grasslands by environmental RNA analysis. FEMS Microbiology Ecology 84: 98-108. 2013.
*. Yuriko Higashioka, Hisaya Kojima, Miho Watanabe and Manabu Fukui. Desulfatitalea tepidiphila gen. nov., sp. nov., a novel sulfate-reducing bacterium isolated from tidal flat sediment. International Journal of Systematic and Evolutionary Microbiology 63 : 761-765. 2013.
2012年
*. Yoshinori Takano, Jonathan James Tyler, Hisaya Kojima, Yusuke Yokoyama, Yukiko Tanabe, Takaharu Sato, Nanako O. Ogawa, Naohiko Ohkouchi, and Manabu Fukui. Holocene lake developments and glacial-isostatic uplift at Lake Skallen and Lake Oyako, Luetzow-Holm Bay, east Antarctica: based on biogeochemical facies and molecular signatures. Applied Geochemistry 27: 2546-2559. 2012.
*. Tomohiro Watanabe, Hisaya Kojima, and Manabu Fukui. Draft genome sequence of a psychrotolerant sulfur-oxidizing bacterium Sulfuricella denitrificans skB26 and proteomic insights into cold adaptation. Applied and Environmental Microbiology 78: 6545-6549. 2012.
*. Fumiko Nemoto, Hisaya Kojima, Akifumi Ohtaka and Manabu Fukui. Filamentous sulfur-oxidizing bacteria of the genus Thioploca from Lake Tonle Sap in Cambodia. Aquatic Microbial Ecology 66: 295-300. 2012.
*. Anne Maria Fiore-Donno, Akiko Kamono, Marianne Meyer, Martin Schnittler, Manabu Fukui and Thomas Cavalier-Smith. 18S rDNA phylogeny of Lanmproderma and allied genera (Stemonitales, Myxomycetes, Amoebozoa). PLoS ONE 7: e35359. 2012.
*. Hisaya Kojima, Masazumi Tsutsumi, Kanako Ishikawa, Tomoya Iwata, Marc Mussmann and Manabu Fukui. Distribution of putative denitrifying methane oxidizing bacteria of a freshwater lake. Systematic and Applied Microbiology. 35: 233-238. 2012.
*. Yuriko Higashioka, Hisaya Kojima, and Manabu Fukui. Isolation and characterization of novel sulfate-reducing bacterium capable anaerobic degradation of p-xylene. Microbes and Environments 27: 273-277. 2012.
*. Masanaori Fujii, Hisaya Kojima, Tomoya Iwata, Jotaro Urabe and Manabu Fukui. Dissolved organic carbon as major environmental factor affecting bacterioplankton communities in mountain lakes of eastern Japan. Microbial Ecology 63: 496-508. 2012.
*. Masazumi Tsutsumi, Hisaya Kojima, and Manabu Fukui. Vertical profiles of abundance and potential activity of methane-oxidizing bacteria in sediment of Lake Biwa, Japan. Microbes and Environments 27: 67-71. 2012.
2011年
*. Fumiko Nemoto, Hisaya Kojima, and Manabu Fukui. Diversity of freshwater Thioploca species and their specific association with filamentous bacteria of the phylum Chloroflexi. Microbial Ecology 62：753-764.2011.
*. Hisaya Kojima, and Manabu Fukui. Sulfuritalea hydrogenivorans gen. nov., sp. nov., a novel facultative autotroph isolated from a freshwater lake. International Journal of Systematic and Evolutionary Microbiology 61: 1651-1655. 2011.
*. Masazumi Tsutsumi, Tomoya Iwata, Hisaya Kojima, and Manabu Fukui. Spatiotemporal variations in an assemblage of closely related planktonic aerobic methanotrophs. Freshwater Biology 56: 342-351. 2011.
*. Yuriko Higashioka, Hisaya Kojima and Manabu Fukui. Temperature-dependent differences in community structure of bacteria involved in degradation of petroleum hydrocarbons under sulfate-reducing conditions. Journal of Applied and Microbiology 110: 314-322. 2011.
*. Kyoko Kubo, Katrin Knittel, Rudolf Amann, Manabu Fukui and Katsumi Matsuura. Sulfur-metabolizing bacteria populations in microbial mats of the Nakabusa hot spring, Japan. Systematic and Applied Microbiology 34: 293-302, 2011.
2010年
*. Hisaya Kojima, and Manabu Fukui. Sulfuricella denitrificans gen. nov., sp. nov., a novel sulfur-oxidizing autotroph isolated from a freshwater lake. International Journal of Systematic and Evolutionary Microbiology 60:2862-2866. 2010.
*. Keiichi Tabuchi, Hisaya Kojima, and Manabu Fukui. Seasonal changes in organic matter mineralization in a sublittoral sediment and temperature-driven decoupling of key processes. Microbial Ecology 60: 551-560. 2010.
*. Masanaori Fujii, Yoshinori Takano, Hisaya Kojima, Tamotsu Hoshino, Ryoichi Tanaka and Manabu Fukui. Microbial community structure, pigment composition, and nitrogen source of red snow in Antarctica. Microbial Ecology 59: 466-4775.2010.
*. Anne Fiore-Donno, Akiko Kamono, Ema Chao, Manabu Fukui and Thomas Cavalier-Smith. Invalidation of hyperamoeba by transferring its species to other genera of Myxogastria. Journal of Eukaryotic Biology 52: 189-196. 2010.
2009年
*. Akiko Kamono, Hisaya Kojima, Jun Matsumoto, Kimitaka Kawamura and Manabu Fukui. Airborne Myxomycete spore: Detection using molecular techniques, Naturwissenschaften 96: 147-151.2009.
*. Masazumi Tsutsumi, Hisaya Kojima, Shigeru Uemura, Kiyomi Ono, Akihiro Sumida, Toshihiko Hara and Manabu Fukui. Structure and activity of soil-inhabiting methanotrophic communities in northern forest of Japan. Soil Biology and Biochemistry 41: 403-408.2009.
*. Yuriko Higashioka, Hisaya Kojima, Tatsunori Nakagawa, Shinya Sato and Manabu Fukui. A novel n-alkane-degrading bacterium as a minor member of p-xylene-degrading sulfate-reducing consortium. Biodegradation 20: 383-390.2009.
*. Yuriko Higashioka, Hisaya Kojima, Shinya Sato, Manabu Fukui. Microbial community analysis at crude oil-contaminated soils targeting the 16S ribosomal RNA, xylM, C23O, and bcr genes. Journal of Applied Microbiology, 107: 126-135. 2009.
*. Hisaya Kojima, Tomoya Iwata, and Manabu Fukui. DNA-based analysis of planktonic methanotrophs in a stratified lake. Freshwater Biology 54: 1501-1509.2009.
*. Akiko Kamono, Jun Matsumoto, Hisaya Kojima, and Manabu Fukui. Characterization of myxomycete communities in soil by reverse transcription polymerase chain reaction (RT-PCR)-based method. Soil Biology and Biochemistry 41: 1324-1330. 2009.
*. Hisaya Kojima, Haruo Fukuhara and Manabu Fukui. Community structure of microorganisms asssociated with reddish-brown iron-rich snow. Systematic and Applied Microbiology 32: 429-437, 2009.