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 Science and Plant Nutrition

Volumn 56, Issue 6, 2010, Pages 800-812

  Fujihara, Shun ^a   Murase, Jun ^a   Tun, Cho Cho ^a   Matsuyama, Tomoya ^a   Ikenaga, Makoto ^a   Asakawa, Susumu ^a   Kimura, Makoto ^a  

^a NAGOYA UNIVERSITY   (Japan)

Author keywords

Diversity; G23 gene; Plant residue; Rice root; Rice straw; T4 type phage

Indexed keywords

BACTERIA (MICROORGANISMS); MIRIDAE; ORYZA SATIVA (JAPONICA CULTIVAR-GROUP);

EID: 78650061156     PISSN: 00380768     EISSN: 17470765     Source Type: Journal    
DOI: 10.1111/j.1747-0765.2010.00513.x     Document Type: Article

References (43)

1. Ackermann HW 2001: Frequency of morphological phage descriptions in the year 2000. Arch. Virol., 146, 843-857.
2. Asakawa S, Kimura M 2008: Comparison of bacterial community structures at main habitats in paddy field ecosystem based on DGGE analysis. Soil Biol. Biochem., 40, 1322-1329.
3. Breitbart M, Salamon P, Andresen B et al. 2002: Genomic analysis of uncultured marine viral communities. Proc. Natl Acad. Sci. USA, 99, 14250-14255.
4. 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.
5. Cahyani VR, Murase J, Asakawa S, Kimura M 2009b: Change in T4-type bacteriophage communities during the composting process of rice straw: estimation from major capsid gene (g23) sequences. Soil Sci. Plant Nutr., 55, 468-477.
6. Cahyani VR, Murase J, Ishibashi E, Asakawa S, Kimura M 2009a: 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.
7. Chibani-Chennoufi S, Bruttin A, Dillmann ML, Brussow H 2004: Phage-host interaction: an ecological perspective. J. Bacteriol., 186, 3677-3686.
8. Desplats C, Krisch HM 2003: The diversity and evolution of the T4-type bacteriophages. Res. Microbiol., 154, 259-267.
9. Edwards RA, Rohwer F 2005: Viral metagenomics. Nat. Rev. Microbiol., 3, 504-510.
10. Filée J, Tetart F, Suttle CA, Krisch HM 2005: Marine T4-type bacteriophages, a ubiquitous component of the dark matter of the biosphere. Proc. Natl Acad. Sci. USA, 102, 12471-12476.
11. Fujii T, Nakayama N, Nishida M et al. 2008: Novel capsid genes (g23) of T4-type bacteriophages in a Japanese paddy field. Soil Biol. Biochem., 40, 1049-1058.
12. Ikenaga M, Asakawa S, Muraoka Y, Kimura M 2003: Bacterial communities associated with nodal roots of rice plants along with the growth stages: estimation by PCR-DGGE and sequence analyses. Soil Sci. Plant Nutr., 49, 591-602.
13. Ikenaga M, Muraoka Y, Toyota K, Kimura M 2002: Community structure of the microbiota associated with nodal roots of rice plants along with the growth stages: estimation by PCR-RFLP analysis. Biol. Fertil. Soils, 36, 397-404.
14. Jia Z, Ishihara R, Nakajima Y, Asakawa S, Kimura M 2007: Molecular characterization of T4-type bacteriophages in a rice field. Environ. Microbiol., 9, 1091-1096.
15. Kimura M, Asakawa S 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, 20-29.
16. Kimura M, Jia Z, Nakayama N, Asakawa S 2008: Ecology of viruses in soils: past, present and future perspectives. Soil Sci. Plant Nutr., 54, 1-32.
17. 4). Soil Biol. Biochem., 36, 1399-1416.
18. 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.
19. Kumar S, Tamura K, Nei M 2004: MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform., 5, 150-163.
20. Lu Y, Watanabe A, Kimura M 2002: Contribution of plant-derived carbon to soil microbial biomass dynamics in a paddy rice microcosm. Biol. Fertil. Soils, 36, 136-142.
21. Mann NH 2003: Phages of the marine cyanobacterial picophytoplankton. FEMS Microbiol. Rev., 27, 17-34.
22. Matsuyama T, Nakajima Y, Matsuya K, Ikenaga M, Asakawa S, Kimura M 2007: Bacterial community in plant residues in a Japanese paddy field estimated by RFLP and DGGE analyses. Soil Biol. Biochem., 39, 463-472.
23. Minoda T, Kimura M 1994: Contribution of photosynthesized carbon to the methane emitted from paddy fields. Geophys. Res. Lett., 21, 2007-2010.
24. 4 emitted to the atmosphere from paddy fields. J. Geophys. Res., 101D, 21091-21097.
25. Moebus K 1992: Further investigations on the concentration of marine bacteriophages in the water around Helgoland, with reference to the phage-host systems encountered. Helgolander Meeresun., 46, 275-292.
26. Muraoka Y, Hamakawa E, Toyota K, Kimura M 2000: Observation of microbial colonization on the surface of rice roots along with their development and degradation. Soil Sci. Plant Nutr., 46, 491-502.
27. 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.
28. Nakayama N, Asakawa S, Kimura M 2009a: 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.
29. Nakayama N, Okumura M, Inoue K, Asakawa S, Kimura M 2007: Morphological analysis of viral communities in the floodwater of a Japanese paddy field. Soil Biol. Biochem., 39, 3187-3190.
30. Nakayama N, Tsuge T, Asakawa S, Kimura M 2009b: Morphology, host range and phylogenetic diversity of Sphingomonas phages in the floodwater of a Japanese paddy field. Soil Sci. Plant Nutr., 55, 53-64.
31. Okabe A, Oike H, Toyota K, Kimura M 2000: 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, 893-904.
32. Parker ML, Christensen AC, Boosman A, Stockard J, Young ET, Doermann AH 1984: Nucleotide sequence of bacteriophage T4 gene 23 and the amino acid sequence of its product. J. Mol. Biol., 180, 399-416.
33. Paul JH, Sullivan MS 2005: Marine phage genomics: what have we learned? Curr. Opin. Biotechnol., 16, 299-307.
34. 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.
35. 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.
36. 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.
37. 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.
38. Wang G, Hayashi M, Saito M, Tsuchiya K, Asakawa S, Kimura M 2009a: Survey of major capsid genes (g23) of T4-type bacteriophages in Japanese paddy field soils. Soil Biol. Biochem., 41, 13-20.
39. Wang G, Jin J, Asakawa S, Kimura M 2009b: Survey of major capsid genes (g23) of T4-type bacteriophages in rice fields in Northeast China. Soil Biol. Biochem., 41, 423-427.
40. Wang G, Murase J, Taki K et al. 2009c: Changes in major capsid genes (g23) of T4-type bacteriophages with soil depth in two Japanese rice fields. Biol. Fertil. Soils, 45, 521-529.
41. 4 carbon emitted from rice paddies. J. Geophys. Res., 104D, 23623-23629.
42. Weinbauer MG 2004: Ecology of prokaryotic viruses. FEMS Microbiol. Rev., 28, 127-181.
43. Weinbauer MG, Rassoulzadegan F 2004: Are viruses driving microbial diversification and diversity? Environ. Microbiol., 6, 1-11.