ABSTRACT
Prophages are abundant elements integrated into bacterial genomes and contribute to inter-strain genetic variability and, in some cases, modulate the environmental behavior of bacteria, such as pathogen virulence. Here, we described prophage occurrence and diversity in publicly available Erwinia genome assemblies, a genus containing plant pathogens. Prophage-like sequences were identified and taxonomically classified. Sequence diversity was analyzed through intergenomic similarities. Furthermore, we searched for anti-phage defense systems in Erwinia spp., such as DISARM, BREX, and CRISPR-Cas systems, and identified the putative targets of CRISPR spacers. We identified 939 prophage-like sequences in 221 Erwinia spp. genome assemblies. Only 243 prophage-like sequences were classified, all belonging to the Caudoviricetes class. The set of putative Erwinia prophages was mostly unique since only three sequences showed more than 70% intergenomic similarities to known Erwinia phages. Overall, the number and type of CRISPR-Cas systems were conserved within Erwinia species, with many spacers directed to the putative prophages identified. This study increased the knowledge of the diversity and distribution of Erwinia prophages, contributing to the characterization of genetic and ecological factors influencing Erwinia spp. environmental fitness.
ABSTRACT
Bacterial wilt caused by Ralstonia spp., soil-borne Gram-negative bacteria, is considered one of the most important plant diseases in tropical and subtropical regions of the world. A large number of bacteriophages capable of lysing or physiologically reprogramming cells of Ralstonia spp. have been reported in Asia. Despite the potential use of these organisms in the management of bacterial wilt, information on viruses that infect Ralstonia spp. is nonexistent in the Americas. We isolated a virus that infects Ralstonia spp. from a soil sample in the state of Minas Gerais, Brazil. Microscopy and genomic and phylogenetic analysis allowed us to classify the virus as a member of the family Podoviridae, genus Phikmvvirus. In spite of its relationship to Ralstonia virus RSB3, an Asian isolate, genomic and biological characteristics showed that the virus isolated in Brazil, tentatively named "Ralstonia virus phiAP1" (phiAP1), belongs to a new species. phiAP1 has EPS depolymerase activity and contains two putative virion-associated peptidoglycan hydrolases (VAPGHs), which reveals a robust mechanism of pathogenesis. Furthermore, phiAP1 specifically infects Ralstonia solanacearum, R. pseudosolanacearum and R. syzygii, causing cell lysis, but it was not able to infect thirteen other bacteria that were tested. Together, these characteristics highlight the biotechnological potential of this virus for the management of bacterial wilt.
