Biology and Fertility of Soils

, Volume 47, Issue 3, pp 273–282

Molecular analysis of the major capsid genes (g23) of T4-type bacteriophages in an upland black soil in Northeast China

  • Guanghua Wang
  • Zhenhua Yu
  • Junjie Liu
  • Jian Jin
  • Xiaobing Liu
  • Makoto Kimura
Original Paper

Abstract

Bacteriophages (phages) are the most abundant biological entities on the planet and are important as the greatest genomic reservoirs in both marine and terrestrial environments. In this study, we analysed T4-type phage communities in an upland black soil by monitoring g23 clones in DNA extracted from seasonal soil samples with no fertilizer, chemical fertilizers, chemical fertilizers plus manure, and natural restoration treatments. PCR products with degenerate primers MZIA1bis and MZIA6 were subjected to denaturing gradient gel electrophoresis. In total, 46 clones with different g23 sequences were obtained. Phylogenetic analyses indicated that T4-type phage communities in the upland black soil were distinctly different from those in marine environments and in an Antarctic lake, which strongly suggested that T4-type phage communities in soil differed from those in aquatic environments. Among 46 clones, 18 clones formed clusters with the clones from rice field soils, 14 clones formed three new clusters, and 13 clones were left as ungrouped, which indicated that T4-type phage communities in the upland black soil were relatively similar to those in rice field soils but that specific communities also inhabit in the upland black soil exclusively.

Keywords

g23 Major capsid gene Mollisol T4-type phage Upland soil Virus community 

References

  1. Ackermann HW (2003) Bacteriophage observations and evolution. Res Microbiol 154:245–251PubMedCrossRefGoogle Scholar
  2. Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, Azam F, Rohwer F (2002) Genomic analysis of uncultured marine viral communities. Pro Natl Acad Sci USA 99:14250–14255CrossRefGoogle Scholar
  3. Breitbart M, Miyake JH, Rohwer F (2004) Global distribution of nearly identical phage-encoded DNA sequences. FEMS Microbiol Lett 236:249–256PubMedCrossRefGoogle Scholar
  4. Edwards RA, Rohwer F (2005) Viral metagenomics. Nat Rev Microbiol 3:504–510PubMedCrossRefGoogle Scholar
  5. 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 Academic Press, London, pp 35–42Google Scholar
  6. Filée J, Tétart F, Suttle CA, Krisch HM (2005) Marine T4-type bacteriophages, a ubiquitous component of the dark matter of the biosphere. Pro Natl Acad Sci USA 102:12471–12476CrossRefGoogle Scholar
  7. Frost LS, Leplae R, Summers AO, Toussaint A (2005) Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 3:722–732PubMedCrossRefGoogle Scholar
  8. 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 40:1049–1059CrossRefGoogle Scholar
  9. Jia Z, Ishihara R, Nakajima Y, Asakawa S, Kimura M (2007) Molecular characterization of T4-type bacteriophages in a rice field. Environ Microbiol 9:1091–1096PubMedCrossRefGoogle Scholar
  10. Kimura M, Jia Z, Nakayama N, Asakawa S (2008) Viral ecology in soil: past, present, and future perspectives. Soil Sci Plant Nutr 54:1–32CrossRefGoogle Scholar
  11. Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163PubMedCrossRefGoogle Scholar
  12. 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 326:858–861PubMedCrossRefGoogle Scholar
  13. Nakayama N, Okumura M, Inoue K, Asakawa S, Kimura M (2007a) Seasonal variations in abundances of virus-like particles and bacteria in the floodwater of a Japanese paddy field. Soil Sci Plant Nutr 53:420–429CrossRefGoogle Scholar
  14. Nakayama N, Okumura M, Inoue K, Asakawa S, Kimura M (2007b) Morphological analysis of viral communities in the floodwater of a Japanese paddy field. Soil Biol Biochem 39:3187–3190CrossRefGoogle Scholar
  15. 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 41:179–185CrossRefGoogle Scholar
  16. 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 180:399–416PubMedCrossRefGoogle Scholar
  17. Paul JH, Sullivan MB (2005) Marine phage genomics: what have we learned? Curr Opin Biotechnol 16:299–307PubMedCrossRefGoogle Scholar
  18. Short CM, Suttle CA (2005) Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments. Appl Environ Microbiol 71:480–486PubMedCrossRefGoogle Scholar
  19. Srinivasiah S, Bhavsar J, Thapar K, Liles M, Schoenfeld T, Wommack KE (2008) Phages across the biosphere: contrasts of viruses in soil and aquatic environments. Res Microbiol 159:349–357PubMedCrossRefGoogle Scholar
  20. 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 24:4876–4882CrossRefGoogle Scholar
  21. Wang G, Hayashi M, Saito M, Tsuchiya K, Asakawa S, Kimura M (2009a) Diversity of major capsid genes (g23) of T4-type bacteriophages in Japanese paddy field soils. Soil Biol Biochem 41:13–20CrossRefGoogle Scholar
  22. 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 41:423–427CrossRefGoogle Scholar
  23. Wang G, Murase J, Taki K, Ohashi Y, Yoshikawa N, Asakawa S, Kimura M (2009c) Changes in major capsid genes (g23) of T4-type bacteriophages with soil depth in two Japanese rice fields. Biol Fertil Soils 45:521–529CrossRefGoogle Scholar
  24. Wang G, Murase J, Asakawa S, Kimura M (2010) Unique viral capsid assembly protein gene (g20) of cyanophages in the floodwater of a Japanese paddy field. Biol Fertil Soils 46:93–102CrossRefGoogle Scholar
  25. Weinbauer MG, Rassoulzadegan F (2004) Are viruses driving microbial diversification and diversity? Environ Microbiol 6:1–11PubMedCrossRefGoogle Scholar
  26. Wommack KE, Colwell RR (2000) Virioplankton: viruses in aquatic ecosystems. Microbiol Mol Biol Rev 64:69–114PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Guanghua Wang
    • 1
  • Zhenhua Yu
    • 1
    • 2
  • Junjie Liu
    • 1
    • 2
  • Jian Jin
    • 1
  • Xiaobing Liu
    • 1
  • Makoto Kimura
    • 3
  1. 1.Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and AgroecologyChinese Academy of SciencesHarbinChina
  2. 2.Graduate School of Chinese Academy of SciencesBeijingChina
  3. 3.Graduate School of Bioagricultural SciencesNagoya UniversityNagoyaJapan

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