Succession and phylogenetic composition of eubacterial communities in rice straw during decomposition on the surface of paddy field soil

Soil Science and Plant Nutrition

Volumn 53, Issue 1, 2007, Pages 56-65

  Asari, Naoko ^a   Ishihara, Rie ^a   Nakajima, Yasunori ^b   Kimura, Makoto ^a   Asakawa, Susumu ^a  

^a NAGOYA UNIVERSITY   (Japan)

^b AICHI PREFECTURAL UNIVERSITY   (Japan)

Author keywords

Bacterial communities; Paddy field; PCR DGGE; Rice straw; Soil surface

Indexed keywords

ACTINOBACTERIA; ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); BACTEROIDETES; DELTAPROTEOBACTERIA; GAMMAPROTEOBACTERIA; GEMMATIMONADETES; NEGIBACTERIA; SPIROCHAETALES; SPIROCHAETES;

EID: 33845869561     PISSN: 00380768     EISSN: 17470765     Source Type: Journal    
DOI: 10.1111/j.1747-0765.2007.00110.x     Document Type: Article

References (22)

1. Akasaka H, Izawa T, Ueki K, Ueki A 2003: Phylogeny of numerically abundant culturable anaerobic bacteria associated with degradation of rice plant residue in Japanese paddy field soil. FEMS Microbiol. Ecol., 43, 149-161.
2. Aoki S 1996: http://aoki2.si.gunma-u.ac.jp/bb0/BlackBox0.html
3. Cahyani VR, Matsuya K, Asakawa S, Kimura M 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, 619-630.
4. Canale-Parola E 1992: Free-living saccarolytic spirochetes: The genus Spirochaeta. In The Prokaryotes: A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications, 2nd Edn, Vol. 4. Eds A Balows, HG Trüper, M Dworkin, W Harder and KH Schleifer, pp. 3524-3536. Springer-Verlag, New York.
5. Dawid W 2000: Biology and global distribution of myxo-bacteria in soils. FEMS Microbiol. Rev., 24, 403-427.
6. Hashimoto H, Matsuzaki T 1976: Use of straws (Wararui no Riyo). In Utilization of Organic Matter (Yukibutsu no Riyo), pp. 96-110. Rural Culture Association (Nosangyoson Bunka Kyokai), Tokyo (in Japanese).
7. Kimura M, Miyaki M, Fujinaka K, Maie N 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, 569-578.
8. 4). Soil Biol. Biochem., 36, 1399-1416.
9. Kimura M, Tun CC 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, 427-437.
10. Lüdemann H, Arth I, Liesack W 2000: Spatial changes in the bacterial community structure along a vertical oxygen gradient in flooded paddy soil cores. Appl. Environ. Microbiol., 66, 754-762.
11. Muyzer G, De Waal EC, Uitterlinden AG 1993: Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol., 59, 695-700.
12. Nakamura A, Tun CC, Asakawa S, Kimura M 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.
13. Ponnamperuma FN 1984: Straw as a source of nutrients for wetland rice. In Organic Matter and Rice, Ed. International Rice Research Institute, pp. 117-136. International Rice Research Institute, Los Banõs.
14. Shibagaki-Shimizu T, Nakayama N, Nakajima Y, Matsuya K, Kimura M, Asakawa S 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, 362-365.
15. Shiga H, Ohyama N, Maeda K, Suzuki M 1985: An evaluation of different organic materials based on their decomposition patterns in paddy soils. Bull. Natl. Agric. Res. Cent., 5, 1-9 (in Japanese with English summary).
16. Sugano A, Tsuchimoto H, Tun CC, Asakawa S, Kimura M 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.
17. Tanahashi T, Murase J, Matsuya K, Hayashi M, Kimura M, Asakawa S 2005: Bacterial communities responsible for the decomposition of rice straw compost in a Japanese rice paddy field estimated by DGGE analysis of amplified 16S rDNA and 16S rRNA fragments. Soil Sci. Plant Nutr., 51, 351-360.
18. Tun CC, Ikenaga M, Asakawa S, Kimura M 2002: Community structure of bacteria and fungi responsible for rice straw decomposition in a paddy field estimated by PCR-RFLP analysis. Soil Sci. Plant Nutr., 48, 805-813.
19. Tun CC, Kimura M 2000: Microscopic observation of the decomposition process of leaf blade of rice straw and colonizing microorganisms in a Japanese paddy field soil during the cultivation period of paddy rice. Soil Sci. Plant Nutr., 46, 127-137.
20. Uemori A, Shinmura Y, Iida S, Kutsuna K 1970: Studies on the treating method of the rice straw caused by the adoption of the combine. (I) Plowing method of rice straw. Bull. Toyama Agric. Exp. Stn, 4, 7-15 (in Japanese with English summary).
21. 4 emission from paddy fields. I. Effect of weathering of rice straw in the field during off-crop season. Soil Sci. Plant Nutr., 39, 701-706.
22. Weber S, Stubner S, Conrad R 2001: Bacterial populations colonizing and degrading rice straw in anoxic paddy soil. Appl. Environ. Microbiol., 67, 1318-1327.