Abstract
Bacteria of the genus Desulfovibrio belong to the group of Sulphate Reducing Bacteria (SRB). SRB generate significant liabilities in the petroleum industry, mainly due to their ability to microbiologically induce corrosion, biofilm formation and H2S production. Bacteriophages are an alternative control method for SRB, whose information for this group of bacteria however, is scarce. The present study developed a workflow for the identification of complete prophages in Desulfovibrio. Poly-lysogenesis was shown to be common in Desulfovibrio. In the 47 genomes analyzed 53 complete prophages were identified. These were classified within the order Caudovirales, with 69.82% belonging to the Myoviridade family. More than half the prophages identified have genes coding for lysozyme or holin. Four of the analyzed bacterial genomes present prophages with identity above 50% in the same strain, whose comparative analysis demonstrated the existence of colinearity between the sequences. Of the 17 closed bacterial genomes analyzed, 6 have the CRISPR-Cas system classified as inactive. The identification of bacterial poly-lysogeny, the proximity between the complete prophages and the possible inactivity of the CRISPR-Cas in closed bacterial genomes analyzed allowed the choice of poly-lysogenic strains with prophages belonging to the Myoviridae family for the isolation of prophages and testing of related strains for subsequent studies.
Highlights
Viruses have a diversity of hosts and are considered obligate intracellular parasites
The identified prophage-like sequences have an average size of 25.5 kb, the smallest (3.6 kb) found in D. vulgaris DP4 and the largest (57.1 kb) in D. fairfieldensis CCUG45958 (Supplementary Table S1). 41.40% (53) of the prophage-like elements were classified as complete prophages and 58.60% (75) as degenerate prophages (Fig. 2A)
All the complete prophages presented structural components related to the order Caudovirales, which allowed the classification of 69.82% (37) of them into the Myoviridae family, 22.64% (12) into Siphoviridae and 7.54% (4) into the Podoviridae family (Supplementary Table S2)
Summary
Viruses have a diversity of hosts and are considered obligate intracellular parasites. Prophages remain in the lysogenic state until the lytic cycle is activated through chemical and physical stresses or by spontaneous induction[5,6] While they are present in the bacterial genome, these prophages are directly related to the genome diversity of the host cell, contributing positively or not, to bacterial fitness[7,8]. The replication and integration of the bacteriophage genetic material into the host strain can be avoided through the CRISPR-Cas system[15] This system is characterized by a genomic region composed by spacers alternated with small palindromic sequences and associated with Cas proteins. This is the first analysis of prophages present in this important SRB genus
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