1. Jun Murase, Manami Shibata, Chol Gyu Lee, Takeshi Watanabe, Susumu Asakawa, Makoto Kimura 2012: Incorporation of plant residue-derived carbon into the microeukaryotic community in a rice field soil revealed by DNA stable-isotope probing. FEMS Microbiol. Ecol., 79, 371-379.

1. Jun Murase, Kees Hordijk, Ichiro Tayasu, Paul L.E. Bodelier 2011: Strain-specific incorporation of methanotrophic biomass into eukaryotic grazers in a rice field soil revealed by PLFA-SIP. FEMS Microbiol. Ecol., 75, 284-290.
2. Chol Gyu Lee, Takeshi Watanabe, Yutaka Sato, Jun Murase, Susumu Asakawa, Makoto Kimura 2011: Bacterial populations assimilating carbon from 13C-labeled plant residue in soil: Analysis by a DNA-SIP approach. Soil Biol. Biochem., 43, 814-822.
3. Guanghua Wang, Zhenhua Yu, Junjie Liu, Jian Jin, Xiaobing Liu, Makoto Kimura 2011: Molecular analysis of the major capsid genes (g23) of T4-type bacteriophages in an upland black soil in Northeast China. Biol. Fertil. Soils, 47, 273-282.
4. Ryu Takahashi, Saman Bowatte, Katsutoshi Taki, Yoshinori Ohashi, Susumu Asakawa, Makoto Kimura 2011: High frequency of phage-infected bacterial cells in a rice field soil in Japan. Soil Sci. Plant Nutr., 57, 35-39.
5. Guanghua Wang, Susumu Asakawa, Makoto Kimura 2011: Spatial and temporal changes of cyanophage communities in paddy field soils as revealed by the capsid assembly protein gene g20, FEMS Microbiol. Ecol., 76, 352-359.
6. Takeshi Watanabe, Guanghua Wang, Jun Murase, Susumu Asakawa, Makoto Kimura 2011: Assimilation of glucose-derived carbon into methanogenic archaea in soil under unflooded condition. Appl. Soil Ecol., 48, 201-209.
7. Yong Li, Chol Gyu Lee, Takeshi Watanabe, Jun Murase, Susumu Asakawa, Makoto Kimura 2011: Identification of microbial communi-ties that assimilate substrate from root cap cells in an aerobic soil using a DNA-SIP approach. Soil Biol. Biochem., 43, 1928-1935.
8. Makoto Kimura, Susumu Asakawa 2011: Anaerobic microbially mediated processes. In "Handbook of Soil Sciences: Properties and Processes, Second Edition". P. M. Huang, Y. Li, M. E. Sumner (ed), pp. 26-32−26-41, CRC Press, Taylor & Francis Group, Boca Raton.
9. Takeshi Watanabe, Chol Gyu Lee, Jun Murase, Susumu Asakawa, Makoto Kimura 2011: Carbon flow into ammonia-oxidizing bacteria and archaea during decomposition of ¹³C-labeled plant residues in soil. Soil Sci. Plant Nutr., 57, 775-785.
9. D. O. Sigunga, M. Hoshino, J. C. Onyango, S. Asanuma, M. Kimura 2011: Pedological perspective of gully erosion sites within Kendu escarpment-Sondu Miriu Region, West Kenya. Afr. J. Environ. Sci. Technol., 5, 1050-1059.
   

1. Guanghua Wang, Jun Murase, Susumu Asakawa, Makoto Kimura 2010: Unique viral capsid assembly protein gene (g20) of cyanophages in the floodwater of a Japanese paddy field. Biol. Fertil. Soils, 46, 93-102
2. Saman Bowatte, Paul C.D. Newton, Ryu Takahashi, Makoto Kimura 2010: High frequency of virus-infected bacterial cells in a sheep grazed pasture soil in New Zealand. Soil Biol. Biochem., 42, 708-712
3. Takeshi Watanabe, Makoto Kimura, Susumu Asakawa 2010: Diversity of methanogenic archaeal communities in Japanese paddy field ecosystem, estimated by denaturing gradient gel electrophoresis. Biol. Fertil. Soils, 46, 343-353
4. Masatsugu Yamazaki, Taisuke Ohtsuka, Yasushi Kusuoka, Masayoshi Maehata, Hiroyuki Obayashi, Kiyoyuki Imai, Fujiyoshi Shibahara, Makoto Kimura 2010: The impact of nigorobuna crucian carp larvae/fry stocking and rice-straw application on the community structure of aquatic organisms in Japanese rice fields. Fish Sci., 76, 207-217
5. Jun Murase, Michio Kawasaki, Johan F. De Jonckneere 2010: Isolation of a new heterolobosean amoeba from a rice field soil: Vrihiamoeba italica gen. nov., sp. nov. Eur. J. Protistol., 46, 164-170
6. Makoto Kimura, Guangha Wang, Natsuko Nakayama, Susumu Asakawa 2010: Ubiquitous bacteriophage hosts in rice paddy  soil. In "Biocommunication in Soil Microorganisms", G. Witzany (ed), pp.189-213, Springer, Heidelberg, Dordrecht, London, New York.
7. Takeshi Watanabe, Guanghua Wang, Katsutoshi Taki, Yoshinori Ohashi, Makoto Kimura, Susumu Asakawa 2010: Vertical changes in bacterial and archaeal communities with soil depth in Japanese paddy fields. Soil Sci. Plant Nutr., 56, 705-715.
8. Shun Fujihara, Jun Murase, Cho Cho Tun, Tomoya Matsuyama, Makoto Ikenaga, Susumu Asakawa, Makoto Kimura 2010: Low diversity of T4-type bacteriophages in applied rice straw, plant residues and rice roots in Japanese rice soils: Estimation from major capsid gene (g23) composition. Soil Sci. Plant Nutr., 56, 800-812.
9. Guanghua Wang, Takeshi Watanabe, Jian Jin, Xiaobing Liu, Makoto Kimura, Susumu Asakawa 2010: Methanogenic archaeal communities in paddy field soils in north-east China as evaluated by PCR-DGGE, sequencing and real-time PCR analyses. Soil Sci. Plant Nutr., 56, 831-838.
   

1. Guanghua Wang, Motoki Hayashi, Masato Saito, Kazunari Tsuchiya , Susumu Asakawa, Makoto Kimura 2009: Survey of major capsid genes (g23) of T4-type bacteriophages in Japanese paddy field soils. Soil Biol. Biochem., 41, 13-20
   
2. Natsuko Nakayama, Susumu Asakawa, Makoto Kimura 2009: Comparison of g23 gene sequence diversity between Novosphingobium and Sphingomonas phages and phage communities in the floodwater of a Japanese paddy field. Soil Biol. Biochem., 41, 179-185
3. Natsuko Nakayama, Susumu Asakawa, Makoto Kimura 2009: Frequency of phage-infected bacterial cells in the floodwater of a Japanese paddy field. Soil Biol. Biochem., 41, 186-191
4. Takeshi Watanabe, Makoto Kimura, Susumu Asakawa 2009: Distinct members of a stable methanogenic archaeal community transcribe mcrA genes under flooded and drained conditions in Japanese paddy field soil. Soil Biol. Biochem., 41, 276-285
5. Guanghua Wang, Jian Jin, Susumu Asakawa, Makoto Kimura 2009: Survey of major capsid genes (g23) of T4-type bacteriophages in rice fields in Northeast China. Soil Biol. Biochem., 41, 423-427
6. Natsuko Nakayama, Takashi Tsuge, Susumu Asakawa, Makoto Kimura 2009: Morphology, host range and phylogenetic diversity of Sphingomonas phages in the floodwater of a Japanese paddy field. Soil Sci. Plant Nutr., 55, 53-64
7. Takeshi Watanabe, Vita Ratri Cahyani, Jun Murase, Eiji Ishibashi, Makoto Kimura, Susumu Asakawa 2009: Methanogenic archaeal communities developed in paddy fields in the Kojima Bay polder, estimated by denaturing gradient gel electrophoresis, real-time PCR and sequencing analyses. Soil Sci. Plant Nutr., 55, 73-79
8. Vita Ratri Cahyani, Jun Murase, Eiji Ishibashi, Susumu Asakawa, Makoto Kimura 2009: Phylogenetic positions of Mn²⁺-oxidizing bacteria and fungi isolated from Mn nodules in rice field subsoils. Biol. Fertil. Soils, 45, 337-346
9. Vita Ratri Cahyani, Jun Murase, Eiji Ishibashi, Susumu Asakawa, Makoto Kimura 2009: T4-type bacteriophage communities estimated from the major capsid genes (g23) in manganese nodules in Japanese paddy fields. Soil Sci. Plant Nutr., 55, 264-270
10. Guanghua Wang, Jun Murase, Katsutoshi Taki, Yoshinori Ohashi, Nanako Yoshikawa, Susumu Asakawa, Makoto Kimura 2009: Changes in major capsid genes (g23) of T4-type bacteriophages with soil depth in two Japanese rice fields. Biol. Fertil. Soils, 45, 521-529
11. Vita Ratri Cahyani, Jun Murase, Susumu Asakawa, Makoto Kimura 2009: Changes in T4-type bacteriophage communities during the composting process of rice straw: Estimation from the major capsid gene (g23) sequences. Soil Sci. Plant Nutr., 55, 468-477
12. Guanghua Wang, Jun Murase, Susumu Asakawa, Makoto Kimura 2009: Novel cyanophage photosynthetic gene psbA in the floodwater of a Japanese rice field. FEMS Microbiol. Ecol., 70, 79-86
13. Vita Ratri Cahyani, Makoto Kimura 2009: Succession and phylogenetic composition of microbial communities responsible for the composting process of rice straw. In "Composting: Processing, Materials and Approaches", J.C. Pereira and J.L. Bolin (eds), pp.69-112, Nova Science Publishers, New York.

1. Masashi Hatamoto, Takanori Tanahashi, Jun Murase, Kazuo Matsuya, Motoki Hayashi, Makoto Kimura and Susumu Asakawa 2008: Eukaryotic communities associated with the decomposition of rice straw compost in a Japanese rice paddy field estimated by DGGE analysis. Biol. Fertil. Soils, 44, 527-532
2. Makoto Kimura, Zhong-Jun Jia, Natsuko Nakayama and Susumu Asakawa 2008: Ecology of viruses in soils: Past, present and future perspectives. Soil Sci. Plant Nutr., 54, 1-32
3. Takeshi Fujii, Natsuko Nakayama, Mizuhiko Nishida, Hiroyuki Sekiya, Naoto Kato, Susumu Asakawa, Makoto Kimura 2008: Novel capsid genes (g23) of T4-type bacteriophages in a Japanese paddy field. Soil Biol. Biochem., 40, 1049-1058
4. Naoko Asari, Rie Ishihara, Yasunori Nakajima, Makoto Kimura, Susumu Asakawa 2008: Cyanobacterial communities of rice straw left on the surface of a paddy field. Biol. Fertil. Soils, 44, 605-612
5. Susumu Asakawa, Makoto Kimura 2008: Comparison of bacterial community structures at main habitats in
   paddy field ecosystem based on DGGE analysis. Soil Biol. Biochem., 40, 1322-1329
6. Akira Watanabe, Masahiro Kasuya, Ayumi Tsunekawa, Mieko Maeda, Atsuko Sugimoto, and Makoto Kimura 2008: Spatial and seasonal variations in CH4 in groundwater used for agriculture in central Japan. Agriculture, Ecosystems & Environment, 127, 207-214
7. Jun Murase and Peter Frenzel 2008: Selective grazing of methanotrophs by protozoa in a rice field soil. FEMS Microbiol. Ecol., 65, 408-414
   
8. Vita Ratri Cahyani, Jun Murase, Eiji Ishibashi, Susumu Asakawa, and Makoto Kimura 2008: Bacterial communities in Fe mottles in the plow pan layer of a Japanese rice field: estimation using PCR-DGGE and sequencing analyses. Soil Sci. Plant Nutr., 54, 711-717
9. Kokoro Yamabe, Hiroshi Maeda, Susumu Kokeguchi, Ichiro Tanimoto, Norihiro Sonoi, Susumu Asakawa, Shogo Takashiba 2008: Distribution of Archaea in Japanese patients with periodontitis and humoral immune response to the components. FEMS Microbiol. Lett., 287, 69-75
10. Naoki Osumi, Yoshihiro Kakehashi, Shiho Matsumoto, Kazunari Nagaoka, Junich Sakai, Kiyotaka Miyashita, Makoto Kimura, Susumu Asakawa 2008: Identification of the gene for disaggregatase from Methanosarcina mazei. Archaea, 2, 185-191

1. Tomoya Matsuyama, Yasunori Nakajima, Kazuo Matsuya, Makoto Ikenaga, Susumu Asakawa and  Makoto Kimura 2007: Bacterial community in plant residues in a Japanese paddy field estimated by RFLP and DGGE analyses. Soil Biol. Biochem., 39, 463-472
2. Saman Bowatte, Susumu Asakawa, Masumi Okada, Kazuhiko Kobayashi and Makoto Kimura 2007: Effect of elevated atmospheric CO₂ concentration on ammonia oxidizing bacteria communities inhabiting in rice roots. Soil Sci. Plant Nutr., 53, 32-39.
3. Naoko Asari, Rie Ishihara, Yasunori Nakajima, Makoto Kimura and Susumu Asakawa 2007: Succession and phylogenetic composition of eubacterial communities in rice straw during decomposition on the surface of paddy field soil. Soil Sci. Plant Nutr., 53, 56-65.
4. Zhongjun Jia, Rie Ishihara, Yasunori Nakajima, Susumu Asakawa and Makoto Kimura 2007: Molecular characterization of T4-type bacteriophages in a rice field. Environ. Microbiol., 9, 1091-1096.
5. Natsuko Nakayama, Mami Okumura, Katsuhiro Inoue, Susumu Asakawa and Makoto Kimura 2007: Seasonal variations in the abundance of virus-like particles and bacteria in the floodwater of a Japanese paddy field. Soil Sci. Plant Nutr., 53, 420-429.
6. Hiroyasu Kikuchi, Takeshi Watanabe, Zhongjun Jia, Makoto Kimura and Susumu Asakawa 2007:  Molecular analyses reveal stability of bacterial communities in bulk soil of a Japanese paddy field: Estimation by denaturing gradient gel electrophoresis of 16S rRNA genes amplified from DNA accompanied with RNA. Soil Sci. Plant Nutr., 53, 448-458.
7. Zhongjun Jia, Hiroyasu Kikuchi, Takeshi Watanabe, Susumu Asakawa and Makoto Kimura 2007: 

   Molecular identification of methane oxidizing bacteria in a Japanese rice field soil. Biol. Fertil. Soils, 44, 121-130.
8. Masahiro Kamiya, Susumu Asakawa and Makoto Kimura 2007: Molecular analysis of fungal communities of biodegradable plastics in two Japanese soils. Soil Sci. Plant Nutr., 53, 568–574.
9. Vita Ratri Cahyani, Jun Murase, Eiji Ishibashi, Susumu Asakawa and Makoto Kimura 2007:  Bacterial communities in manganese nodules in rice field subsoils: Estimation using PCR-DGGE and sequencing analyses. Soil Sci. Plant Nutr., 53, 575–584.
10. Atsuo Sugano, Hidetaka Tsuchimoto, Cho Cho Tun, Susumu Asakawa and Makoto Kimura 2007:  Succession and phylogenetic profile of eukaryotic communities in rice straw incorporated into a rice field: Estimation by PCR-DGGE and sequence analyses. Soil Sci. Plant Nutr., 53, 585–594.
11. Natsuko Nakayama, Mami Okumura, Katsuhiro Inoue, Susumu Asakawa and Makoto Kimura 2007: Abundance of bacteriophages of common heterotrophic bacteria in the floodwater of a Japanese paddy field. Soil Sci. Plant Nutr., 53, 595–605.
    
12. Takeshi Watanabe, Makoto Kimura, and Susumu Asakawa 2007: Dynamics of methanogenic archaeal communities based on rRNA analysis and their relation to methanogenic activity in Japanese paddy field soils. Soil Biol. Biochem., 39, 2877-2887.
13. Natsuko Nakayama, Mami Okumura, Katsuhiro Inoue, Susumu Asakawa and Makoto Kimura 2007: Morphological analysis of viral communities in the floodwater of a Japanese paddy field. Soil Biol. Biochem., 39, 3187-3190.
14. Jun Murase and Peter Frenzel 2007: A methane-driven microbial food web in a wetland rice soil. Environ. Microbiol. 9, 3025-3034.
15. Zhong-Jun Jia, Atsuo Sugano, Naoko Asari, Cho Cho Tun, Rie Ishihara, Susumu Asakawa and Makoto Kimura 2007:  Molecular characterization of methane-oxidizing bacteria associated with rice straw decomposition in a rice field. Soil Sci. Plant Nutr., 53, 729-739

2006

1. Nagamitsu Maie, Heike Knicker, Akira Watanabe, and Makoto Kimura 2006: Heterocyclic N in the highly humified humic acids extracted from the subsoil of paddy fields and surface ando soils. Org. Geochem., 37(1), 12-19.
2. Taketoshi Shibagaki-Shimizu, Natsuko Nakayama, Yasunori Nakajima, Kazuo Matsuya, Makoto Kimura, and Susumu Asakawa 2006: Phylogenetic study on a bacterial community in the floodwater of a Japanese paddy field estimated by sequencing 16S rDNA fragments after denaturing gradient gel electrophoresis. Biol. Fertil. Soils, 42(4), 362-365.
3. Guanghua Wang, Xiaozeng Han, Natsuko Nakayama, Takeshi Watanabe, Akira Watanabe, and Makoto Kimura 2006: Soil organic matter dynamics in lands continuously cultivated with maize and soybean in Heilongjiang Province, Northeast China: Estimation from natural 13C abundance. Soil Sci. Plant Nutr., 52(2), 139-144.
4. Takeshi Watanabe, Makoto Kimura, and Susumu Asakawa 2006: Community structure of methanogenic archaea in paddy field soil under double cropping (rice-wheat). Soil Biol. Biochem., 38, 1264-1274.
5. Natsuko Nakayama, Akiko Okabe, Koki Toyota, Makoto Kimura, and Susumu Asakawa 2006: Phylogenetic distribution of bacteria isolated from the floodwater of a Japanese paddy field. Soil Sci.Plant Nutr., 52(3), 305-312.
6. Saman Bowatte, Zhongjun Jia, Rie Ishihara, Yasunori Nakajima, Susumu Asakawa and Makoto Kimura 2006: Molecular analysis of the ammonia oxidizing bacterial community in the surface soil layer of a Japanese paddy field. Soil Sci. Plant Nutr., 52(4), 427-431.
7. Makoto Kimura and Susumu Asakawa 2006: Comparison of community structures of microbiota at main habitats in the rice field ecosystems based on phospholipid fatty acid analysis. Biol. Fertil. Soils, 43(1), 20-29.
8. Saman Bowatte, Rie Ishihara, Susumu Asakawa and Makato Kimura 2006: Characterization of ammonia oxidizing bacteria associated with weeds in a Japanese paddy field using amoA gene fragments. Soil Sci. Plant Nutr., 52(5), 593-600.
9. Jun Murase, Matthias Noll, and Peter Frenzel 2006: The impact of protists on activity and structure of the bacterial community in a rice field soil. Appl. Environ. Microbiol., 72, 5436-5444
10. Jun Murase, Yuri Matsui, Masahiko Katoh, Atsuko Sugimoto, and Makoto Kimura 2006: Incorporation of 13C-labeled rice straw carbon into microbial communities in submerged rice field soil and the percolating water. Soil Biol. Biochem., 38, 3483-3491
    

Back to Lab. of Soil Biology and Chemistry

2005

1. Atsuo Sugano, Hidetaka Tsuchimoto, Cho Cho Tun, Susumu Asakawa and Makoto Kimura 2005: Succession and phylogenetic profile of eubacterial communities in rice straw incorporated into a rice field: estimation by PCR-DGGE analysis. Soil Sci. Plant Nutr., 51, 51-60
2. Jun Murase, Miho Shimizu, Motoki Hayashi, Kazuo Matsuya, and Makoto Kimura 2005: Vertical changes in bacterial communities in percolating water of a Japanese paddy field as revealed by PCR-DGGE. Soil Sci. Plant Nutr., 50, 83-90
3. Tomoko Hashimoto-Yasuda, Makoto Ikenaga, Susumu Asakawa, Han-Yong Kim, Masumi Okada, Kazuhiko Kobayashi, and Makoto Kimura 2005: Effect of free-air CO2 enrichment (FACE) on methanogenic archaeal communities inhabiting rice roots in a Japanese rice field. Soil Sci. Plant Nutr., 51(1), 91-100
4. Akira Watanabe, Hiromi Yamada, and Makoto Kimura 2005: Analysis of temperature effects on seasonal and interannual variation in CH4 emission from rice-planted pots. Agr. Ecosyst. Environ., 105(1-2), 439-443
5. Makoto Kimura 2005: Populations, community composition and biomass of aquatic organisms in the floodwater of rice fields and effects of field management. Soil Sci. Plant Nutr., 51, 159-181
6. Masatsugu Yamazaki, Masumi Okada, Kazuhiko Kobayashi, and Makoto Kimura 2005: Effect of free-air CO2 enrichment (FACE) on the community structure of aquatic organisms in the floodwater of a Japanese paddy field during the flooding period of rice cultivation. Soil Sci. Plant Nutr., 51(2), 271-279
7. Masahiko Katoh, Jun Murase, and Makoto Kimura 2005: Effect of rice straw amendment on dissolved organic and inorganic carbon and cationic nutrients in percolating water from a flooded paddy soil: A microcosm experiment using 13C-enriched rice straw. Org. Geochem., 36(5), 803-811
8. Ainin Niswati, Jun Murase, and Makoto Kimura 2005: Comparison of bacterial communities associated with microcrustaceans from the floodwater of a paddy field microcosm: estimation based on DGGE pattern and sequence analyses. Soil Sci. Plant Nutr., 51, 281-290
9. Takanori Tanahashi, Jun Murase, Kazuo Matsuya, Susumu Asakawa, and Makoto Kimura 2005: Bacterial community responsible for the decomposition of rice straw compost in a Japanese rice paddy field as determined with denaturing gradient gel electrophoresis of amplified 16S rDNA and 16S rRNA fragments. Soil Sci. Plant Nutr., 51(3), 351-360
10. Ainin Niswati, Jun Murase, and Makoto Kimura 2005: Effect of application of rice straw and compost on the bacterial communities associated with Moina sp. in the floodwater of a paddy soil microcosm: estimation based on DGGE pattern and sequence analyses. Soil Sci. Plant Nutr., 51(4), 565-571
11. Atsuo Sugano, Hidetaka Tsuchimoto, Cho Cho Tun, Makoto Kimura, and Susumu Asakawa 2005: Succession of methanogenic archaea in rice straw incorporated into a Japanese rice field: estimation by PCR-DGGE and sequence analyses. Archaea, 1(6), 391-397
12. Jun Murase and Atsuko Sugimoto 2005: Inhibitory effect of light on methane oxidation in the pelagic water column of a mesotrophic lake (Lake Biwa, Japan). Limnol. Oceanogr., 50, 1339-1343
13. Jun Murase, Yuji Sakai, Aya Kametani, and Astuko Sugimoto 2005: Dynamics of methane in a mesotrophic Lake Biwa, Japan. Ecol. Res., 20, 377-385
    

1. Yahai Lu, Akira Watanabe, and Makoto Kimura 2004: Contribution of plant photosynthates to dissolved organic carbon in a flooded rice soil. Biogeochemistry, 71, 1-15
2. Masatsugu Yamazaki, Yukihiro Hamada, Nobuchika Kamimoto, Takashi Momii and Makoto Kimura 2004: Habitats of aquatic organisms in a paddy field during flooding period. Edaphologia, 74, 1-10
3. Akira Watanabe, Nobuhisa Machida, Kazushi Takahashi, Shigeru Kitamura, and Makoto Kimura 2004: Flow of photosynthesized carbon from rice plants into the paddy soil ecosystem at different stages of rice growth. Plant Soil, 258, 151-160
4. Yahai Lu, Jun Murase, Akira Watanabe, Atsuko Sugimoto, and Makoto Kimura 2004: Linking microbial community dynamics to rhizosphere carbon flow in a wetland rice soil. FEMS Microbiol. Ecol., 48, 179-186
5. Takeshi Watanbe, Susumu Asakawa, Asumi Nakamura, Kazunari Nagaoka and Makoto Kimura 2004: DGGE method for analyzing 16S rDNA of methanogenic archaeal community in paddy field soil. FEMS Microbiol. Lett., 232, 153-163
6. Nagamitsu Maie, Akira Watanabe, and Makoto Kimura 2004: Chemical characteristics and potential source of fulvic acids leached from the plow layer of paddy soil. Geoderma, 120, 309-323
7. Masatsugu Yamazaki, Nobuhiro Yasuda, Toshimasa Yamada, Koich Ota, and Makoto Kimura 2004: Comparison of aquatic organisms communities between paddy fields under rice-duck (Aigamo) farming and paddy fields under conventional farming. Soil Sci. Plant Nutr., 50(3), 375-383
8. Ainin Niswati, Jun Murase, Susumu Asakawa, and Makoto Kimura 2004: Analysis of communities of ammonia oxidizers, methanotrophs, and methanogens associated with microcrustaceans in the floodwater of a rice field microcosm. Soil Sci. Plant Nutr., 50, 447-455
9. Vita Ratri Cahyani, Kazuo Matsuya, Susumu Asakawa and Makoto Kimura 2004: Succession and phylogenetic profile of methanogenic archaeal communities during the composting process of rice straw estimated by PCR-DGGE analysis. Soil Sci. Plant Nutr., 50, 555-563
10. Makoto Ikenaga, Susumu Asakawa, Yoshitetsu Muraoka and Makoto Kimura 2004: Community structure of Eukaryotes in rice roots estimated by PCR-DGGE pattern and sequence analyses. Soil Sci. Plant Nutr., 50, 583-589
11. Vita Ratri Cahyani, Kazuo Matsuya, Susumu Asakawa and Makoto Kimura 2004: Succession and phylogenetic profile of eukaryotic communities in the composting process of rice straw estimated by PCR-DGGE analysis. Biol. Fertil. Soils, 40, 334-344
12. Makoto Ikenaga, Susumu Asakawa, Yoshitetsu Muraoka and Makoto Kimura 2004: Methanogenic archaeal communities in rice roots grown in flooded soil pots: estimation by PCR-DGGE and sequence analyses. Soil Sci. Plant Nutr., 50, 701-711
13. Masatsugu Yamazaki, Yukihiro Hamada, Nobuchika Kamimoto, Takashi Momii, and Makoto Kimura 2004: Composition and structure of aquatic organisms communities in various water conditions of a paddy. Ecol. Res., 19, 645-653
14. Masahiko Kato, Jun Murase, Motoki Hayashi, Kazuo Matsuya, and Makoto Kimura 2004: Nutrient leaching from the plow layer by water percolation and accumulation in the subsoil in an irrigated paddy field. Soil Sci. Plant Nutr., 50, 721-729
15. Masahiko Kato, Jun Murase, and Makoto Kimura 2004: Sites and processes of nutrient accumulation in the subsoil through water percolation from the plow layer in a submerged paddy soil microcosm. Soil Sci. Plant Nutr., 50, 731-738
16. Takanori Tanahashi, Jun Murase, Kazuo Matsuya, Susumu Asakawa, and Makoto Kimura 2004: Microbial communities responsible for the decomposition of rice straw compost in a Japanese rice paddy field determined by phospholipid fatty acid (PLFA) analysis. Soil Sci. Plant Nutr., 50, 1229-1236
17. Makoto Kimura, Jun Murase, and Yahai Lu 2004: Carbon cycling in rice field ecosystems in the context of input, decomposition and translocation of organic materials and the fates of their end products (CO₂ and CH₄). Soil Biol. Biochem., 36, 1399-1416

1. Masatsugu Yamazaki, Yukihiro Hamada, Nobutika Kamimoto, Takashi Momii, Yoshimi Aiba, Nobuhiro Yasuda, Shinya Mizuno, Shigekata Yoshida and Makoto Kimura 2003: Changes in the community structure of aquatic organisms after midseason drainage in the floodwater of Japanese paddy fields. Soil Sci. Plant Nutr, 49(1), 125-135
2. Ainin Niswati, Jun Murase and Makoto Kimura 2003: Effect of application of rice straw and compost on the community structure of bacteria associated with microcrustaceans in the floodwater of a paddy field microcosm. Soil Sci. Plant Nutr., 49(2), 191-200
3. Asumi Nakamura, Cho Cho Tun, Susumu Asakawa and Makoto Kimura 2003: Microbial community responsible for the decomposition of rice straw in a paddy field: estimation by phospholipid fatty acid analysis. Biol. Fertil. Soils, 38, 288-295
4. Makoto Ikenaga, Susumu Asakawa, Yoshitetsu Muraoka and Makoto Kimura 2003: Bacterial community associated with nodal roots of rice plants along with the growth stages: Estimation by PCR-DGGE  and sequence analyses. Soil Sci. Plant Nutr., 49(4), 591-602
5. Vita Ratri Cahyani, Kazuo Matsuya, Susumu Asakawa and Makoto Kimura 2003: Succession and phylogenetic composition of bacterial communities responsible for the composting process of rice straw estimated by PCR-DGGE analysis. Soil Sci. Plant Nutr., 49(4), 619-630
6. Makoto Ikenaga, Susumu Asakawa, Yoshitetsu Muraoka and Makoto Kimura 2003: Phylogenetic study on CTO primer-amplified ammonia-oxidizing bacteria and ｧ-Proteobacteria associated with rice roots grown in a flooded paddy soil. Soil Sci. Plant Nutr., 49(5), 719-727
7. Yahai Lu, Akira Watanabe and Makoto Kimura 2003: Carbon dynamics of rhizodeposits, root- and shoot-residues during the off-crop season of rice. Soil Biol. Biochem., 35, 1223-1230
8. Masahiko Kato, Akiko Iwata, Ichiro Shaku, Yasunori Nakajima, Kazuo Matsuya and Makoto Kimura 2003: Impact of water percolation on nutrient leaching from an irrigated paddy field in Japan. Soil Use & Management, 19, 298-304
9. Susumu Asakawa and Kazunari Nagaoka 2003: Methanoculleus bourgensis, Methanoculleus olentangyi and Methanoculleus oldenburgensis are subjective synonyms. Int. J. Syst. Evol. Microbiol. 53, 1551-1552
10. Akira Hoshino, Hideo Sawada and Makoto Kimura 2003: Influence of Surface Coating Materials on the Degradability of Biodegradable Plastic Film in Soil. Soil Sci. Plant Nutr., 49(6), 903-907
11. Jun Murase, Kumiko Itoh, Mayuko Kano and Makoto Kimura 2003: Molecular analysis of ｧ-Proteobacterial ammonia oxidizer populations in surface layers of a submerged paddy soil micrososm. Soil Sci. Plant Nutr., 49(6), 909-913

1. Nagamitsu Maie, Akira Watanabe, Kikuko Hayamizu and Makoto Kimura 2002: Comparison of chemical characteristics of Type A humic acids extracted from subsoils of paddy fields and surface ando soils. Geoderma, 106, 1-19 　
2. Masatsugu Yamazaki, Yukihiro Hamada, Nobutika Kamimoto, Takashi Momii and Makoto Kimura 2002:Effect of spring plowing on the spatial distribution of aquatic organisms in a paddy field during the off-crop season under drained conditions. Edaphologia, , 25-33
3. Ainin Niswati, Makoto Ikenaga and Makoto Kimura 2002: Microbiota associated with microcrustacean in the floodwater of a Japanese paddy field estimated by RFLP analysis. Soil Sci. Plant Nutr., 48(2), 185-193
4. Wayan Sabe Ardjasa, Ho Ando and Makoto Kimura 2002: Fate of basal N and growth of crops cultivated under cassava-based intercropping system with reference to K application rate. Soil Sci. Plant Nutr.,48(3), 365-370
5. Akira Hoshino, Masao Tsuji, Kazuhiko Fukuda, Miki Nonagase, Hideo Sawada and Makoto Kimura 2002: Changes in molecular structure of biodegradable plastics during degradation in soils estimated by FT-IR and NMR.Soil Sci. Plant Nutr., 48(4), 469-473
6. Miho Shimizu, Yasunori Nakajima, Kazuo Matsuya and Makoto Kimura 2002: Comparison of phospholipid fatty acid composition in percolating water, floodwater, and the plow layer soil during the rice cultivation period in a Japanese paddy field. Soil Sci. Plant Nutr., 48(4), 595-600
7. Makoto Kimura 2002: Community structure of fauna and microbiota in paddy field ecosystems. 17th World Congr. Soil Sci., No.1871: 1-11, August 14-21, Thailand
8. Yahai Lu, Akira Watanabe and Makoto Kimura 2002: Contribution of plant-derived carbon to soil microbial biomass dynamics in a paddy rice microcosm. Biol. Fertil. Soils, 36,136-142
9. Vita Ratri Cahyani, Akira Watanabe, Kazuo Matsuya, Susumu Asakawa and Makoto Kimura 2002: Succession of microbiota estimated by phospholipid fatty acid analysis and changes in organic constituents during the composting process of rice straw. Soil Sci. Plant Nutr., 48(5), 735-743
10. Makoto Kimura, Taketoshi Shibagaki, Yasunori Nakajima, Kazuo Matsuya, and Makoto Ikenaga 2002: Community structure of the microbiota in the floodwater of a Japanese paddy field estimated by restriction fragment length polymorphism and denaturing gradient gel electrophoresis pattern analyses. Biol. Fertil. Soils 36, 306-312
11. Makoto Ikenaga, Yoshitetsu Muraoka, Koki Toyota and Makoto Kimura 2002: Community structure of the microorganisms associated with nodal roots of rice plants along with the growth stages: Estimation by PCR-RFLP analysis. Biol. Fertil.Soils, 36, 397-404
12. Yahai Lu, Akira Watanabe and Makoto Kimura 2002: Input and distribution of photosynthesized carbon in a flooded rice soil. Global Biogeochem. Cycles 16,1085, doi:10.1029/2002GB001864
13. Cho Cho Tun, Makoto Ikenaga, Susumu Asakawa and Makoto Kimura 2002: Community structure of bacteria and fungi responsible for rice straw decomposition in a paddy field estimated by PCR-RFLPanalysis. Soil Sci. Plant Nutr., 48(6), 805-813
14. Yuji Sakai, Jun Murase, Atsuko Sugimoto, Kenji Okubo, and Eiichiro Nakayama 2002: Resuspension of bottom sediment by an internal wave in Lake Biwa. Lakes and Reservoirs 7, 339-344
15. Shigekazu Yamamuro, Hideto Ueno, Hiroshi Yamada,Yumiko Takahashi, Yoko Shiga, Syuko Miyahara, Tsutomu Shimonihara, Jun Murase, Junta Yanai, Mizuhiko Nishida 2002: Uptake of carbon and nitrogen through roots of rice and corn plants, grown in soils treated with 13C and 15N dual-labeled cattle manure compost. Soil Sci. Plant Nutr. 48(6), 787-795
16. Miho Shimizu, Motoki Hayashi, Kazuo Matsuya, Jun Murase and Makoto Kimura 2002: Comparison of microbial communities in percolating water from plow layer and subsoil layer estimated by phospholipid fatty acids (PLFA) analysis. Soil Sci. Plant Nutr., 48(6), 877-881

2001

1. Aiko Nakano, Kazushi Takahashi, Roger T. Koide and Makoto Kimura 2001: Determination of the nitrogen source for arbuscular mycorrhizal fungi by 15N application to soil and plants. Mycorrhiza, 10(6), 267-273
2. Aiko Nakano, Kazushi Takahashi and Makoto Kimura 2001: Effect of host shoot clipping on carbon and nitrogen sources for arbuscular mycorrhizal fungi. Mycorrhiza, 10(6), 287-293
3. Nagamitsu Maie, Akira Watanabe and Makoto Kimura 2001: Origin and properties of humus in the subsoil of irrigated rice paddies. IV. Effect of water percolation on the binding type of humus in a submerged plow layer soil. Soil Sci. Plant Nutr., 47(1), 1-8
4. Akira Hoshino, Hideo Sawada, Masahisa Yokota, Masao Tsuji, Kazuhiko Fukuda and Makoto Kimura 2001: Influence of weather conditions and soil properties on degradation of biodegradable plastics in soil. Soil Sci. Plant Nutr., 47(1), 35-43
5. Wayan Sabe Ardjasa, Ho Ando and Makoto Kimura 2001: Comparison of soil erosion among red-yellow podzolic fields under various cassava-based cropping patterns. Soil Sci. Plant Nutr., 47(1), 101-112
6. Guang-Hua Wang, Yasunori Nakajima, Ichiro Shaku and Makoto Kimura 2001: Effect of fungicide Thiram on microbial communities of rice seed surface estimated by culture-dependent and culture-independent (PCR-RFLP) methods. Soil Sci. Plant Nutr., 47(2), 303-314
7. Masatsugu Yamazaki, Yukihiro Hamada, Nobuchika Kamimoto, Takashi Momii and Makoto Kimura2001:Spatial distribution of aquatic organisms in a paddy field during off-crop season under drained conditions. Edaphologia, 68, 23-31
8. Makoto Kimura, Hiroyoshi Kishi, Akiko Okabe and Nagamitsu Maie 2001: Phospholipid fatty acid composition of microbiota in the percolating water from a rice paddy microcosm. Soil Sci. Plant Nutr.,47(3), 533-545
9. Makoto Kimura, Mariko Miyaki, Ko-Ichiro Fujinaka and Nagamitsu Maie 2001: Microbiota responsible for the decomposition of rice straw in a submerged paddy soil estimated from phospholipid fatty acid composition.Soil Sci. Plant Nutr., 47(3), 569-578
10. Masatsugu Yamazaki, Yukihiro Hamada, Takeo Ibuka, Takashi Momii and Makoto Kimura2001:Aquatic organisms in the floodwater of a Japanese paddy field under a long-term fertilizer trial. Soil Sci. Plant Nutr., 47(3), 587-599
11. Akira Watanaba, Hiromi Yamada and Makoto Kimura 2001: Effects of shifting growth stage and regulating temperature on seasonal variation of CH4 emission from rice. Global Biogeochem. Cycles, 15(3), 729-739
12. Abdul Kadir Salam, Afandi, Nanik Sriyani and Makoto Kimura 2001: Soil enzymatic activities in a hilly coffee Plantation in Lampung Province, South Sumatra Indonesia, managed by plant cover. Soil Sci. Plant Nutr., 47(4), 695-702
13. Dayeri Dianou, Taro Miyaki, Susumu Asakawa, Hiroyuki Morii, Kazunari Nagaoka, Hiroshi Oyaizu, and Satoshi Matsumoto 2001: Methanoculleus chikugoensis sp. nov., a novel methanogenic archaeon isolated from paddy field soil in Japan, and DNA-DNA hybridization among Methanoculleus species. Int. J. Syst. Evol. Microbiol., 51, 1663-1669

2000

1. Nagamitsu Maie, Akira Watanabe, Katsutoshi Taki, Hideji Yano and Makoto Kimura 2000: Comparison of humus composition in the subsoil of Japanese paddy and upland fields.Soil Sci. Plant Nutr., 46(1), 163-175
2. Akiko Okabe, Koki Toyota and Makoto Kimura2000:Seasonal variations of phospholipid fatty acid composition in the floodwater of a Japanese paddy field under a long-term fertilizer trial. Soil Sci. Plant Nutr.,46(1),177-188
3. Itoh, K., Toyota, K. and Kimura, M. 2000: Effects of soil solarization and fumigation on root rot of melon caused by Phomopsis sclerotioides and on soil microbial community. Jpn. J. Sci. Soil Plant Nutr. 71(2),154-164
4. Koki Toyota, Makoto Kimura, Seiichi Takechi and Shiro Kuninaga 2000: Comparison of microbial community structure between soils suppressive and conducive to Fusarium-wilt of radish. Soil Microorganisms, 54(1), 69-79
5. Koki Toyota and Makoto Kimura 2000: Suppression of Ralstonia solanacearum in soil following colonization by other strains of R. solanacearum. Soil Sci. Plant Nutr., 46(2), 449-459
6. Yoshiteru Muraoka, Eitaro Hamakawa, Koki Toyota and Makoto Kimura 2000: Observation of microbial colonization on the surface of rice roots along with their development and degradation. Soil Sci. Plant Nutr., 46(2), 491-502
7. Akira Watanabe, Masako Kajiwara, Shigekata Yoshida and Makoto Kimura 2000: Effect of planting density on methane emission from a rice paddy.Environ. Sci., 13(2), 223-227
8. Koki Toyota and Makoto Kimura 2000: Microbial community indigenous to the earthworm Eisenia foetida. Biol. Fertil. Soils, 31(3-4), 187-190
9. Koki Toyota, Makoto Kimura and Tadataka Kinoshita 2000: Microbiological factors affecting the colonization of tomato roots by Ralstonia solanacearum YU1Rif43lux. Soil Sci. Plant Nutr., 46(3), 643-653
10. Wayan Sabe Ardjasa, Ho Ando and Makoto Kimura : Establishment of sustainable cropping patterns in the transmigration area in South Sumatra, Indonesia. J. ISSAAS., 6(2), 13-27
11. Akiko Okabe,Hiroe Oike, Koki Toyota and Makoto Kimura2000:Comparison of phospholipid fatty acid composition in floodwater and plow layer soil during the rice cultivation period in a Japanese paddy field.Soil Sci. Plant Nutr.,46(4), 893-904

1999

1. Abdul Kadir Salam, Yessi Desvia, Edi Sutanto, Tamaluddin Syam, Sutopo Ghani Nugroho and Makoto Kimura 1999: Activities of soil enzymes in different land-use systems in middle terrace areas of Lampung Province, South Sumatra, Indonesia. Soil Sci. Plant Nutr., 45(1), 89-99
2. Koki Toyota, Karl Ritz, Shiro Kuninaga and Makoto Kimura 1999: Impact of fumigation with metam sodium upon soil microbial community structure in two Japanese soils. Soil Sci. Plant Nutr.,45(1), 207-223
3. Aiko Nakano, Takahashi and Makoto Kimura 1999: Carbon origin of arbuscular mycorrhizal fungi: Estimation fromδ13C values of spores. Mycorrhiza, 9, 41-47
4. Makoto Kimura and Cho Cho Tun 1999: Microscopic observation of the decomposition process of leaf sheath of rice straw and colonizing microorganisms during the cultivation period of paddy rice. Soil Sci. plant Nutr., 45(2), 427-4377
5. Misako Taniguchi, Wilbur Ventura, Koki Toyota and Makoto Kimura 1999: Epibiotic microorganisms associated with microcrustaceans in overlying water of Philippine paddy fields. Soil Sci. Plant Nutr., 45(3), 757-766
6. Akira Watanabe and Makoto Kimura 1999: Influence of chemical properties of soils on methane emission from rice paddies. Commun. Soil Sci. Plant Anal., 30(17&18), 2449-2463
7. Akira Watanabe, Takuya Takeda and Makoto Kimura 1999: Evaluation of carbon origins of CH4 emitted from rice paddies. J. Geophys. Res., 104(D19), 13623-23630
8. Abdul Kadir Salam, Edi Sutanto, Yessi Desvia, Ainin Niswati, Dermiyati and Makoto Kimura 1999: Activities of soil enzymes in fields continuously cultivated with cassava, sugarcane, and pineapple in middle terrace areas of Lampung Province, South Sumatra, Indonesia. Soil Sci. Plant Nutr.,45(4), 803-809
9. Hiroyo Nishide, Koki Toyota and Makoto Kimura 1999: Effects of soil temperature and anaerobiosis on degradation of biodegradable plastics in soil and their degrading microorganisms. Soil Sci. Plant Nutr., 45(4), 963-972
10. Koki Toyota, Chikayo Hiraiwa (Nojiri) and Makoto Kimura 1999: Phenotypic characterization of a mutant of Burkholderia cepacia MRT11 defective in rhizosphere competence. Microbes and Environments, 14(4), 201-208
11. Charlchai Tanavud, Chao Yongchalermchai, Makoto Kimura, Masaharu Komamura and Abdollah bennui 1999: Land use changes and its environmental consequence in Songkla Lake basin. Thai J. Agric. Sci., 32(2), 211-228

1. Nagamitsu Maie, Akira Watanabe and Makoto Kimura 1998: Origin and properties of humus in the subsoil of irrigated rice paddies. II. Effects of subsoil constituents and drainage on the accumulation of organic matter leached from the plow layer soil. Soil Sci. Plant Nutr., 44(1), 77-91
2. Akira Watanabe, Mariko Yoshida and Makoto Kimura 1998: Contribution of rice straw carbon to CH4 emission from rice paddies using 13C-enriched rice straw. J. Geophys.. Res., 103(D7), 8237-8242
3. Akira Watanabe and Makoto Kimura 1998: Factors affecting variation in CH4 emission from paddy fields grown with different rice cultivars. J. Geophys.. Res., 103(D15), 18947-18952
4. Nagamitsu Maie, Akira Watanabe and Makoto Kimura 1998: Origin and properties of humus in the subsoil of irrigated rice paddies. III. Changes in binding type of humus in submerged plow layer soil. Soil Sci. Plant Nutr., 44(3), 331-345
5. Jamalam Lumbanraja, Sutopo Ghani Nugroho, Ainin Niswati, Wayan Sabe Ardjasa, Netera Subadiyasa, Nyoman Arya, Hiroki Haraguchi and Makoto Kimura 1998: Methane emission from Indonesian rice fields with special references to the effects of yearly and seasonal variations, rice variety, soil type and water management. Hydrological Processes, 12(13-14), 2057-2072
6. Akira Watanabe and Makoto Kimura 1998: Effect of rice straw application on CH4 emission from paddy fields. IV. Influence of rice straw incorporated during the previous cropping period. Soil Sci. Plant Nutr., 44(4), 507-512
7. Tadashiro Koyama and Makoto Kimura 1998: Inhibitors for the methane fermentation in paddy soils. Soil Sci. Plant Nutr., 44(4), 667-674

1. Katayama, A. Ukai, T. and Itoh, T. (1997) Ubiquitous capability to substitute chlorine of chlorothalonil in bacteria. J. Pesticide Sci. 22: 12-16
2. Ikeda, K., Toyota, K. and Kimura, M. (1997) Effects of soil compaction on the microbial populations of melon and maize rhizoplane. Plant and Soil, 189: 91-96.
3. Koyama, T. and Kimura, M. (1997) Methane emission fluxes from rice paddies and the methane productive potential in the soils. Nutrient Cycling in Agroecosystems, 49: 129-138
4. Kimura, M. (1997) Sources of methane emitted from paddy fields. Nutrient Cycling in Agroecosystems, 49: 153-161
5. Murase, J. and Kimura, M. (1997) Anaerobic re-oxidation of Mn2+, Fe2+, S0 and S2- in submerged paddy soils. Biol. Fertil. Soils., 25: 302-306
6. Fujimura, Y. and Katayama, A. (1997) Estimation of DDT availability to DDT-degrading baterium in soil by direct extraction method of bacterial cells. Chemosphere, 35: 335-341
7. Subadiyasa, N., Arya, N. and Kimura, M. (1997) Methane emission form paddy fields in Bali Island, Indonesia. Soil Sci. Plant Nutr., 43: 387-394
8. Lumbanraja, J., Nugroho, S.G., Suprapto, H., Sunyoto, Ardjasa, W.S. and Kimura, M. (1997) Methane emissions from paddy fields in Bali Island, Indonesia. Soil Sci. Plant Nutr., 43: 479-482
9. Kimura, M., Yamashita, T. and Ikka, T. (1997) Bacterial numbers and biomass in leachate from submerged paddy soils. Soil Sci. Plant Nutr., 43: 575-585
10. Syam, T., Nishide, H., Salam, A.K., Utomo, U., Mahi, A.K., Lumbanraja, J., Nugroho, S.G. and Kimura, M. (1997) Land Use and Cover Changes in a Upper Terrace area of South Sumatra, Indonesia (from 1970 to 1990). Soil Sci. Plant Nutr., 43: 587-599
11. Taniguchi, M., Toyota, K. and Kimura, M. (1997) Epibiotic bacteria associated with microcrustaceans in the overlying water of paddy fields. Soil Sci. PlantNutr., 43: 633-641
12. Taniguchi, M., Toyota, K. and Kimura, M. (1997) Seasonal variation of microcrustaceans and microbial flora on their surface in the overlying water of a Japanese paddy field. Soil Sci. Plant Nutr., 43: 651-664
13. Sutopo Ghani Nugroho, Jamalam Lumbanraja, Hermanus Suprapto, Sunyoto, Wayan Saba Ardjasa and Makoto Kimura (1997) Effect of rice variety on methane emission from an Indonesian paddy field. Soil Sci. Plant Nutr., 43: 799-809
14. Maie, N., Watanabe, A., and Kimura, M. (1997) Origin and properties of humus in subsoil in irrigated rice paddies. I. Organic matter leached from plow layer and their accumulation in subsoil. Soil Sci. Plant Nutr., 43: 901-910
15. Toyota, K. and Ikeda, K. (1997) Relative importance of motility and antibiosis in the rhizoplane competence of a biocontrol agent Pseudomonas fluorescens MelRC2Rif. Biol. Fert. Soils, 25: 416-420

1. Jun Murase and Makoto Kimura (1996) Methane production and its fate in paddy fields. IX. Methane flux distribution and decomposition of methane in the subsoil during the growth period of rice plants.Soil Sci. Plant Nutr., 42(1), 187-190
2. Sutopo Ghani Nugroho, Jamalam Lumbanraja, Hermanus Suprapto, Sunyoto, Wayan Saba Ardjasa, Hiroki Haraguchi and Makoto Kimura (1996) Three-year measurement of methane emission froman Indonesian paddy field. Plant Soil,181(April II), 287-293
3. Tomomi Minoda, Makoto Kimura and E. Wada (1996) Photosynthates as dominant source of CH4 and CO2 in soil water and CH4 emitted to the atmosphere from paddy fields.J. Geopys. Res., 101(D15), 21091-21097
4. Toyota, K., Young、I. M. and Ritz, K. (1996) Effects of soil matric potential and bulk density on the growth of Fusarium oxysporum f. sp. raphani Soil Biology & Biochemistry, 28:1139-1145.
5. Toyota, K. and Kimura, M. (1996) Growth of the bacterial wilt pathogen Pseudomonas solanacearum introduced into soil colonized by individual soil bacteria.Soil Biology & Biochemistry, 28:1489-1494.
6. Toyota, K., Ritz, K. and Young, I. M. (1996) Microbiological factors affecting the colonisation of soil aggregates by Fusarium oxysporum f. sp. raphani Soil Biology & Biochemistry, 28: 1513-1521
7. Toyota, K., Ritz, K. and Young, I. M. (1996) Survival of bacterial and fungal populations following chloroform-fumigation: The effect of soil matric potential and bulk density.Soil Biology & Biochemistry, 28:1545-1547
8. Mori, T. Fujie, K. Kuwatsuka, S. and Katayama, A. (1996) Accelerated microbial degradation of chlorothalonil in soil amended with farmyard manure, Soil Sci. Plant Nutr. 42: 315-322
9. Fujimura, Y., Kuwatsuka, S. and Katayama, A. (1996) Bioavailability and biodegradation rate of DDT by Bacillus sp. B75 in the presence of dissolved humic substances, Soil. Sci. Plant. Nutr., 42: 375-381
10. Watanabe, A., Fujimori, H., Nagai, Y., Miyajima, T. and Kuwatsuka, S. (1996) Analysis of the green fraction of humic acids, European Journal of Soil Science, 47: 197-204

1. Katayama, A., Mori, T., and Kuwatsuka, S.(1995) Abiotic dissipation of chlorothalonil in soil accelerated by amendment with high applications of farmyard manure, Soil Biol. Biochem., 27, 147-151　
2. Watanabe, A. and Kimura, M. (1995) Methane production and its fate in paddy fields. VIII. Seasonal variations in the amount of methane retained in soil, Soil Sci. Plant Nutr., 41, 225-233
3. Watanabe, A., Satoh, Y., and Kimura, M. (1995) Estimation of the increase in CH₄ emission from paddy soils by rice straw application, Plant Soil, 173, 225-231
4. Watanabe, A., Kajiwara, M., Tashiro, T., and Kimura, M. (1995) Influence of rice cultivar on methane emission from paddy fields, Plant Soil, 176, 51-56
5. Toyota K., Kamesaka T. and Kimura M.(1995) Autecology of Fusarium oxysporum f. sp. raphani in soils suppressive and conducive to Fusarium-wilt of radish. FEMS Microbiol. Ecol., 16, 261-268
6. Toyota K., Kitamura M. and Kimura M. (1995) Suppression of Fusarium oxysporum f. sp. raphani in soil following colonization by other Fusariumspp. Soil Biol. Biochem., 27, 41-46
7. Lee, S-J., Katayama, A. and Kimura, M. (1995) Microbial degradation of paraquat sorbed to plant residues. J. Agric. Food Chem., 43, 1343-1347
8. Yang, Z. Q. and Kimura, M. (1995) Solubility fractionation of Zn, Cu and Cd in soils applied with sewage sludges and their potential availability to plant. Envron. Sci., 8, 369-378
9. Yang, Z. Q. and Kimura, M. (1995) Time course of Zn Cu and Cd redistribution in soil amended with sewage sludges. Environ. Sci., 8, 379-386
10. Yuan, H-L., Toyota, K. and Kimura, M. (1995) Observation with scanning electron microscope of microbial succession on lignite along with weathering. Bull. Jpn. Soc. Microb. Ecol., 10, 53-58
11. Yuan, H-L., Toyota, K. and Kimura, M. (1995) Mechanisms of biodegradation of lignite piled in the open air. Bull. Jpn. Soc. Microb. Ecol., 10, 59-65

1. Fujimura, Y., Katayama, A., and Kuwatsuka, S.(1994) Inhibitory action of dissolved humic substances on growth of soil bacteria degrading DDT, Soil Sci. Plant Nutr., 40, 525-530
2. Jermsawatdipong, P., Murase, J., Prabuddham, P., Hasathon, T., Khomthong, N., Naklang, K., Watanabe, A., Haraguchi, H., and Kimura, M.(1994) Methane emission from plots with differences in fertilizer application in Thai paddy fields. Soil Sci. Plant Nutr., 40, 63-71
3. Minoda, T., and Kimura, M.(1994) Contribution of photosymthesized carbon to the methane emitted from paddy fields. Geophys. Res. Letters, 21(18), 2007-2010
4. Murase, J., and Kimura, M. (1994) Methane production and its fate in paddy fields IV. Sources of microorganisms and substrates responsible for anaerobic methane oxidation in subsoil. Soil Sci. Plant Nutr., 40, 57-61
5. Murase, J., Topark-Ngarm, B., Adachi, T., Losirikul, M., and Kimura, M.(1994) Studies on saline soils in Khon Kaen Region, Northeast Thailand. V. Nitrification and nitrifying bacteria. Soil Sci. Plant Nutr., 40, 173-177
6. Murase, J., and Kimura, M.(1994) Methane production and its fate in paddy fields. VI. Anaerobic oxidation of methane in plow layer soil. Soil Sci. Plant Nutr., 40, 505-514
7. Murase, J., and Kimura, M.(1994) Methane production and its fate in paddy fields. VII. Electron acceptors responsible for anaerobic methane oxidation. Soil Sci. Plant Nutr., 40, 647-654
8. Nugroho, S.G., Lumbanraja, J., Suprapto, H., Sunyoto, Ardjasa, W.S., Haraguchi, H., and Kimura, M. (1994) Methane Emission from an Indonesian Paddy Field Subjected to Several Fertilizer Treatments. Soil Sci. Plant Nutr., 40, 275-281.
9. Nugroho, S.G., Lumbanraja, J., Suprapto, H., Sunyoto, Ardjasa, W.S., Haraguchi, H., and Kimura, M.(1994) Effect of Intermittent Irrigation on Methane Emission from an Indonesian Paddy Field. Soil Sci. Plant Nutr., 40, 609-615
10. Toyota, K., Miyashita, K., and Kimura, M.(1994) Introduction of a chitinase gene into Pseudomonas stutzeri A18 isolated from the surface of chlamydospores of Fusarium oxysporum f. sp. raphani. Soil Biol. Biochem., 26, 413-416
11. Toyota, K., and Kimura, M. (1994) Earthworms disseminate a soil-borne plant pathogen, Fusarium oxysporum f. sp. raphani. Biol. Fertil. Soils, 18, 32-36　　
12. Toyota, K., Yamamoto, K., and Kimura, M.(1994) Mechanisms of suppression of Fusarium oxysporumf. sp. raphani in soils so-called suppressive to Fusarium-wilt of radish. Soil Sci. Plant Nutr., 40, 373-380
13. Toyota, K., Yamamoto, K., and Kimura, M.(1994) Isolation and characterization of bacteria responsible for the suppression of Fusarium oxysporum f. sp. raphani on the host rhizoplane. Soil Sci. Plant Nutr., 40, 381-390
14. Watanabe, A., Kimura, M., Kasuya, M., Kotake, M., and Katoh, T.(1994) Methane in groundwater used for Japanese agriculture: Its relationship to other physico-chemical properties and possible tropospheric source strength. Geophys. Res. Letters, 21, 41-44
15. Watanabe, A., Murase, J., Katoh, K., and Kimura, M.(1994) Methane production and its fate in paddy fields. V. Fate of methane remained in paddy soil at harvesting stage. Soil Sci. Plant Nutr., 40, 221-230
16. Watanabe, A., Katoh, K., and Kimura, M.(1994) Effect of rice straw application on CH4 emission from paddy fields. III. Effect of incorporation site of rice straw on CH4 emission rates and their variation among shoots of a rice plant. Soil Sci. Plant Nutr., 40, 497-504
17. Watanabe, A., Itoh, K., Arai, S., and Kuwatsuka, S.(1994) Comparison of composition of humic and fulvic acids prepared by the IHSS method and NAGOYA method. Soil Sci. Plant Nutr., 40, 601-608
18. Yuan, H.-L., Toyota, K., Watanabe, A., and Kimura, M. (1994) Changes of chemical properties and microbial succession of lignites with weathering. Bull. Jpn. Soc. Microb. Ecol., 9, 45-53
19. Kimura, M., Toyota, K., Iwatsuki, M., and Sawada, H.(1994) Effects of soil conditions on biodegradation of plastics and responsible microorganisms. In "Biodegradable Plastics and Polymers" Doi, Y. and Fukuda, K. (eds.) p.92-106, Elsevier, Amsterdam .