Screening and characterization of prophages in Desulfovibrio genomes

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.

Figure 1

Identification and characterization strategies for Desulfovibrio prophages. The black rectangles represent the tools used for prophage identification and characterization. The white rectangles represent the input data and the gray rectangles represent the results obtained at each step represented by arrows.

Figure 2

Characteristics of prophage-like elements in Desulfovibrio. (A) Distribution of prophage-like elements in 46 Desulfovibrio genomes in each category: degenerate and complete. The bars represent the number of elements corresponding to the size range of the sequence found. (B) Frequency of integration of prophage-like elements in 17 closed bacterial genomes. (C) Correlation between the size of closed bacterial genomes and prophage-like elements.

Figure 3

Heatmap among 53 complete Desulfovibrio prophages. The map describes the similarity between two pairs of sequences.

Figure 4

Phylogenetic relationships between complete Desulfovibrio prophage sequences. In the phylogenetic tree we can distinguish 9 phylogenetic groups consisting of 21 subgroups. The putative viral families of the subgroups are indicated to the right of the tree.

Figure 5

Comparison of prophage sequences of subgroups A2, C1, E3 and I2. The collinearity between the sequences is represented by the conservation of the location of the blocks in all subgroups.