研究業績 Publications

2010年

原著論文

  1. 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. (view abstract)

  2. 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. (view abstract)

  3. 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 (Erratum [2011] 47, 481-482). (view abstract)

  4. 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. (view abstract)

  5. 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. (view abstract)

  6. 6.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 (Corrigendum [2014] 60, 745). (view abstract)

  7. 7.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. (view abstract)

  8. 8.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 (Corrigendum [2014] 60, 746-748). (view abstract)


総説等

  1. 1.渡邉健史 2010:水田土壌に生息するメタン生成アーキア、生物工学会誌、88, 676. (view)


著書等

  1. 1.村瀬潤(分担執筆) 2010:集水域の中の水田、身近な水の環境科学-源流から干潟まで-、日本陸水学会東海支部 編、pp.92-102、朝倉書店、東京

  2. 2.浅川晋(分担執筆) 2010:湿地土壌の微生物,湿地環境と作物-環境と調和した作物生産をめざして-,坂上潤一・中園幹生・島村聡・奥田徹・伊藤治・石澤公明 編著, pp.82-89,養賢堂,東京

  3. 3.浅川晋・村瀬潤(分担執筆) 2010:水田の土壌環境と微生物相、身近な自然の保全生態学-生物の多様性を知る-、根本正之 編著, pp.149-173,培風館,東京

  4. 4.浅川晋・村瀬潤(分担執筆) 2010:生物群ごとの基本的な多様性調査法 微生物について、身近な自然の保全生態学-生物の多様性を知る-、根本正之 編著, pp.196-200,培風館,東京

  5. 5.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.



2009年

原著論文

  1. 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. (view abstract)

  2. 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. (view abstract)

  3. 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. (view abstract)

  4. 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. (view abstract)

  5. 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. (view abstract)

  6. 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. (view abstract)

  7. 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. (view abstract)

  8. 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. (view abstract)

  9. 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. (view abstract)

  10. 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. (view abstract)

  11. 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. (view abstract)

  12. 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. (view abstract)


総説等

  1. 1.橋本知義・浅川晋・村瀬潤・島野智之・高橋忠夫・岡田浩明・佐藤恵利華・豊田剛己 2009:原生生物や線虫から見た土壌生態系の解明と活用,日本土壌肥料学雑誌,80(2), 201-206

  2. 2.浅川晋 2009:微生物群集を鳥瞰する、化学と生物、47(7), 451-453


著書等

  1. 1.村瀬潤 2009:アメーバ、鞭毛虫、土壌の原生生物・線虫群集-その土壌生態系での役割-、日本土壌肥料学会 編、pp.23-30、博友社、東京

  2. 2.村瀬潤 2009:水田土壌生態系の機能における細菌-原生生物系の役割、土壌の原生生物・線虫群集-その土壌生態系での役割-、日本土壌肥料学会 編、 pp.94-114、博友社、東京

  3. 3.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.



2008年

原著論文

  1. 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. 2.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

  3. 3.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.

  4. 4.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

  5. 5.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

  6. 6.Jun Murase and Peter Frenzel 2008: Selective grazing of methanotrophs by protozoa in a rice field soil. FEMS Microbiol. Ecol., 65, 408-414

  7. 7.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

  8. 8.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

  9. 9.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


総説等

  1. 1.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

  2. 2.浅川晋・木村眞人・小野信一 2008:白鳥神社と水田農業(追補)ー愛知県旧作手村(現新城市作手地区)の白鳥神社と水田稲作の関わりについてー,農業と科学,598,11-14

  3. 3.浅川晋 2008:水田における微生物の機能と群集構造,バイオサイエンスとインダストリー,66(9),482-487

  4. 4.木村眞人 2008:水田土壌との40年近くを振り返って,肥料科学,30,1-62

  5. 5.浅川晋・鮫島玲子・齋藤明広・橋本知義 2008:部門別進歩総説,第3部門 土壌生物,土壌生物,日本土壌肥料学雑誌,79(6、部門別進歩総説特集号),557-560


著書等

  1. 6.浅川晋(分担執筆) 2008:農地から発生する温室効果ガス(メタン,亜酸化窒素)と微生物,微生物の事典,渡邉信・西村和子・内山裕夫・奥田徹・加来久敏・広木幹也 編, pp.317-318,朝倉書店,東京



2007年

原著論文

  1. 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. 2.Saman Bowatte, Susumu Asakawa, Masumi Okada, Kazuhiko Kobayashi and Makoto Kimura 2007: Effect of elevated atmospheric CO2concentration on ammonia oxidizing bacteria communities inhabiting in rice roots. Soil Sci. Plant Nutr., 53, 32-39.

  3. 1.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. 2.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. 3.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. 4.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. 5.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. 6.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. 7.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. 8.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. 9.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. 10.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. 11.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. 12.Jun Murase and Peter Frenzel 2007: A methane-driven microbial food web in a wetland rice soil. Environ. Microbiol. 9, 3025-3034.

  15. 13.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.


総説等

  1. 1.村瀬潤 2007:水田土壌の細菌群集の構造と機能に及ぼす原生動物の影響.土と微生物,61, 65-68.



2006年

原著論文

  1. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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


総説等

  1. 1.村瀬潤 2006:土壌中の遺伝子・遺伝情報 何ができるのか,何が分かるのか 9.土壌DNAの利用,新しい研究手法(その2)Stable Isotope Probing,日本土壌肥料学雑誌,77(2), 231-234

  2. 2.村瀬潤 2006:ドイツで学んだ水田土壌微生物,化学と生物,44(9), 640-644

  3. 3.村瀬潤 2006:ビールの国の水田土壌微生物,日本微生物生態学会誌,21(2),68-70

  4. 4.浅川晋 2006:水田土壌の機能と微生物群集構造,土と微生物,60(2),79-84


著書等

  1. 1.坂本充・村瀬潤・丸尾雅啓 2006:3-4 湖の富栄養化の現状,変動経過,原因,東アジアモンスーン域の湖沼と流域,坂本充・熊谷道夫編,pp.302-320,名古屋大学出版会,名古屋

  2. 2.村瀬潤・杉本敦子2006:5.4 水系のガス代謝,地球環境と生態系,武田博清・占部城太郎編,pp.225-242,共立出版,東京

  3. 3.村瀬潤 2006:陸水学事典 日本陸水学会編,講談社(項目執筆),東京