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Identification and Analysis of Prophages and Phage Remnants in Soil Bacteria

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Book cover Biocommunication in Soil Microorganisms

Part of the book series: Soil Biology ((SOILBIOL,volume 23))

Abstract

Soils serve as a shelter for wide range of bacteria and virus monotypes, which include tailed, spherical, and filamentous particle. The existence of temperate phages, i.e., prophages, and their significance in soil hosts is not well understood. Whole genome sequence data and outcome of prophage detection methods in bacterial genomes indicate that prophage sequences pervade prokaryotic genomes. Lysogenic state is considered as mutual coexistence of host bacteria and prophage which improves host fitness leading to phage-mediated horizontal gene transfer and also favors the prophage genome to be a permanent associate of the host. Using the database of cryptic prophage elements and phage remnants available at http://bicmku.in:8082, we focus on the methods for systematic and definitive identification of prophages in a collection of soil bacteria and the importance of phage-mediated gene transfer in the evolution of prokaryotes. A total of 200 bacterial genomes with no prophage reports were taken up for the study. Employing a proteome comparison method using protein similarity approach (PSA) yielded 30 prophage-like elements. By the genome comparison method using dinucleotides relative abundance difference (DRAD), 52 prophage elements were identified. Comparative analysis of other available methods against the above approaches developed here will be discussed. Detailed analysis of locus will help in understanding the contribution of prophages to the microbial communities in soil.

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Acknowledgments

Bioinformatics facilities provided by Department of Biotechnology, Government of India under Centre of Excellence. CSIR and UGC RFSMS for fellowship to KVS.

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Authors and Affiliations

  1. Centre of Excellence in Bioinformatics School of Biotechnology, Madurai Kamaraj University, Madurai, 625021, Tamil Nadu, India

    K. V. Srividhya & S. Krishnaswamy

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  1. K. V. Srividhya
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  2. S. Krishnaswamy
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Correspondence to S. Krishnaswamy .

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  1. Telos - Philosophische Praxis, Vogelsangstr. 18c18c, Bürmoos, 5111, Austria

    Günther Witzany

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Srividhya, K.V., Krishnaswamy, S. (2011). Identification and Analysis of Prophages and Phage Remnants in Soil Bacteria. In: Witzany, G. (eds) Biocommunication in Soil Microorganisms. Soil Biology, vol 23. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-14512-4_5

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