Characterization of the Major Capsid Genes (g23) of T4-Type Bacteriophages in the Wetlands of Northeast China

Microbial Ecology

Volumn 65, Issue 3, 2013, Pages 616-625

  Zheng, Chunyu ^a,b   Wang, Guanghua ^a   Liu, Junjie ^a,b   Song, Changchun ^a   Gao, Hongxing ^c   Liu, Xiaobing ^a  

^a NORTHEAST INSTITUTE OF GEOGRAPHY AND AGRICULTURAL ECOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c Jiansanjiang Administration of the Agricultural Reclamation of Heilongjiang Province   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CAREX LASIOCARPA; DEYEUXIA ANGUSTIFOLIA; MIRIDAE;

EID: 84876113735     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-012-0158-z     Document Type: Article

References (48)

1. Frost LS, Leplae R, Summers AO, Toussaint A (2005) Mobile genetic elements: the agents of open source evolution. Nature Rev Microbiol 3: 722-732.
2. Fuhrman JA (1999) Marine viruses and their biogeochemical and ecological effects. Nature 399: 541-548.
3. Mühling M, Fuller NJ, Millard A, Somerfield PJ, Marie D, Milson WH, Scanlan DJ, Post AF, Joint L, Mann NH (2005) Genetic diversity of marine Synechococcus and co-occurring cyanophage communities: evidence for viral control of phytoplankton. Environ Microbiol 7: 499-508.
4. Weinbauer MG, Winter C, Höfle MG (2002) Reconsidering transmission electron microscopy based estimates of viral infection of bacterioplankton using conversion factors derived from natural communities. Aquat Microb Ecol 27: 103-110.
5. Weinbauer MG (2004) Ecology of prokaryotic viruses. FEMS Microbiol Rev 28: 127-181.
6. Breitbart M, Rohwer F (2005) Here a virus, there a virus, everywhere the same virus? Trends Microbiol 13: 78-284.
7. Suttle CA (2005) Viruses in the sea. Nature 437: 356-361.
8. Filée J, Tétart F, Suttle CA, Krish HM (2005) Marine T4 type bacteriophages, a ubiquitous component of the dark matter of the biosphere. Proc Natl Acad Sci USA 102: 12471-12476.
9. Paul JH, Sullivan MB, Segall AM, Rohwer F (2002) Marine phage genomics. Comp Biochem Phys B 133: 463-476.
10. Weinbauer MG, Rassoulzadegan F (2004) Are viruses driving microbial diversification and diversity? Environ Microbiol 6: 1-11.
11. Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball KA (eds) (2005) Virus taxonomy: eighth report of the International Committee on Taxonomy of Viruses. Elsevier, London.
12. Wommack KE, Colwell RR (2000) Virioplankton: viruses in aquatic ecosystems. Microbiol Mol Biol Rev 64: 69-114.
13. Williamson KE, Radosevich M, Wommack KE (2005) Abundance and diversity of viruses in six Delaware soils. Appl Environ Microbiol 71: 3119-3125.
14. Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, Azam F, Rohwer F (2002) Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci USA 99: 14250-14255.
15. Williamson SJ, Rusch DB, Yooseph S, Halpern AL, Heidelberg KB, Glass JI, Andrews-Pfannkoch C, Fadrosh D, Miller CS, Sutton G, Frazier M, Venter JC (2008) The sorcerer II global ocean sampling expedition: metagenomic characterization of viruses within aquatic microbial samples. PLoS One 3: e1456.
16. Ackermann HW, Krisch HM (1997) A catalogue of T4-type bacteriophages. Arch Virol 142: 2329-2345.
17. Desplats C, Krisch HM (2003) The diversity and evolution of the T4-type bacteriophages. Res Microbiol 154: 259-267.
18. Tétart F, Desplats C, Kutateladze M, Monod C, Ackermann HW, Krisch HM (2001) Phylogeny of the major head and tail genes of the wide-ranging T4-type bacteriophages. J Bacteriol 183: 358-366.
19. Rohwer F, Edwards R (2002) The phage proteomic tree: a genome based taxonomy for phage. J Bacteriol 184: 4529-4535.
20. Fujii T, Nakayama N, Nishida M, Sekiya H, Kato N, Asakawa S, Kimura M (2008) Novel capsid genes (g23) of T4-type bacteriophages in a Japanese paddy field. Soil Biol Biochem 40: 1049-1059.
21. Keller JK (2011) Wetlands and the global carbon cycle: what might the simulated past tell us about the future? New Phytol 192: 789-792.
22. 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.
23. Liu J, Wang G, Zheng C, Yuan X, Jin J, Liu X (2011) Specific assemblages of major capsid genes (g23) of T4-type bacteriophages isolated from upland black soils in Northeast China. Soil Biol Biochem 43: 1980-1984.
24. Wang G, Hayashi M, Saito M, Tsuchiya K, Asakawa S, Kimura M (2009) Survey of major capsid genes (g23) of T4-type bacteriophages in Japanese paddy field soils. Soil Biol Biochem 41: 13-20.
25. Wang G, Jin J, Asakawa S, Kimura M (2009) Survey of major capsid genes (g23) of T4-type bacteriophages in rice fields in Northeast China. Soil Biol Biochem 41: 423-427.
26. Wang G, Yu Z, Liu J, Jin J, Liu X, Kimura M (2011) Molecular analysis of the major capsid genes (g23) of T4-type bacteriophages in an upland black soil in Northeast China. Biol Fert Soils 47: 273-282.
27. McJannet D, Wallace J, Keen R, Hawdon A, Kemei J (2012) The filtering capacity of a tropical riverine wetland: I. Water balance. Hydrol Process 26: 40-52.
28. Burton TM, Uzarski DG (2009) Biodiversity in protected coastal wetlands along the west coast of Lake Huron. Aquat Ecosyst Health 12: 63-76.
29. Jackson EF, Jackson CR (2008) Viruses in wetland ecosystems. Freshwater Biol 53: 1214-1227.
30. Mausbach MJ, Parker WB (2001) Background and history of the concept of hydric soils. In: Richardson JL, Vepraskas MJ (eds) Wetland soils. Lewis, New York, pp 19-34.
31. Gutknecht JLM, Goodman RM, Balser TC (2006) Linking soil process and microbial ecology in freshwater wetland ecosystems. Plant Soil 289: 17-33.
32. Zhao KY (1999) Wetland in China. Science Press, Beijing.
33. Liu XT, Ma XH (2000) Influence of large scale reclamation on natural environment and regional environmental protection in the Sanjiang Plain. Sci Geogr Sin 20: 14-19 (in Chinese with English abstract).
34. Wang W, Jia N, Zhou X, Wang Y (2011) Long-term change in land management from subtropical wetland to paddy field shifts soil microbial community structure as determined by PLFA and T-RFLP. Pol J Ecol 59: 37-44.
35. He Y, Zhang MX (2001) Study on wetland loss and its reasons in China. Chin Geogr Sci 11: 241-245.
36. Casas V, Rohwer F (2007) Phage metagenomics. Methods Enzymol 421: 259-268.
37. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24: 4876-4882.
38. Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5: 150-163.
39. Letunic I, Bork P (2006) Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinform 23: 127-128.
40. Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-8235.
41. Butina TV, Belykh OI, Maksimenko SY, Belikov SI (2010) Phylogenetic diversity of T4-like bacteriophages in Lake Baikal, East Siberia. FEMS Microbiol Lett 309: 122-129.
42. Huang HZ, Cheng K, Xu M, Zhao YJ (2011) Genetic diversity of T4 virioplankton, inferred from g23 gene, in Wuhan Donghu Lake. China Environ Sci 31: 44-447 (in Chinese with English abstract).
43. López-Bueno A, Tamames J, Velázquez D, Moya A, Quesada A, Alcamí A (2009) High diversity of the viral community from an Antarctic lake. Science 326: 858-861.
44. Nakayama N, Asakawa S, Kimura M (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.
45. Liu J, Wang G, Wang Q, Liu J, Jin J, Liu X (2012) Phylogenetic diversity and assemblage of major capsid genes (g23) of T4-type bacteriophages in paddy field soils during rice growth season in Northeast China. Soil Sci Plant Nutr. doi: 10. 1080/00380768. 2012. 703610.
46. Wang G, Murase J, Taki K, Ohashi Y, Yoshikawa N, Asakawa S, Kimura M (2009) Changes in major capsid genes (g23) of T4-type bacteriophages with soil depth in two Japanese rice fields. Biol Fert Soils 5: 521-529.
47. Fujihara S, Murase J, Tun CC, Matsuyama T, Ikenaga M, Asakawa S, Kimura M (2010) Low diversity of T4-type bacteriophages in applied rice straw, plant residues and rice roots in Japanese rice soils: estimation from major capsid (g23) composition. Soil Sci Plant Nutr 56: 800-812.
48. Wang G, Asakawa S, Kimura M (2011) Spatial and temporal changes of cyanophage communities in paddy field soils as revealed by capsid assembly protein gene g20. FEMS Microbiol Ecol 76: 352-359.