fluorescens Pf-5 in natural habitats.

Temperate bacteriophages similar to those encoded by prophages 03 and 06 are capable of development through both lysogenic and lytic pathways, and the presence of prophages can protect the host from superinfection by closely related bacteriophages [60]. On the other hand, the lytic pathway ultimately results in phage-induced host cell lysis, and it has been reported that the presence of virulent bacteriophages can adversely affect rhizosphere-inhabiting strains of P. fluorescens [62–64]. Similarly bacteriophage tail-like bacteriocins such as the one encoded by prophage 01 are capable of killing both closely and more distantly related strains of bacteria, presumably through destabilization of the cell membrane [65–69]. Temperate bacteriophages YM155 and bacteriophage-like Saracatinib concentration elements also are an important part of the bacterial flexible gene pool and actively

participate in horizontal gene transfer [60, 70]. Among the putative lysogenic conversion genes in P. fluorescens Pf-5 are two copies of llpA, located adjacent to prophages 01 and 04. These genes encode low-molecular weight bacteriocins resembling plant BIBF 1120 supplier mannose-binding lectins that kill sensitive strains of Pseudomonas spp. via a yet-unidentified mechanism [71]. The fact that both llpA copies reside near prophage repressor genes, as well as the involvement of a recA-dependent SOS response in LlpA production by a different strain of Pseudomonas [72], suggests that the association of llpA genes with prophages is not accidental and that the prophages may be involved in the regulation of bacteriocin production in P. fluorescens Pf-5. The analysis of MGEs revealed at least 66 CDSs not present in the original Pf-5 genome annotation (data are summarized in supplemental Tables). The bulk of these newly predicted CDSs fall in the category of conserved

below hypothetical genes of bacterial or phage origin. Predicted products of the remaining novel CDSs exhibit similarity to proteins of diverse enzymatic, regulatory, and structural functions and include a phage integrase, an ATP-dependent DNA ligase, an endonuclease, plasmid partitioning and stabilization proteins, a NADH-dependent FMN reductase, an acytransferase, a PrtN-like transcriptional regulator, a Com-like regulatory protein, a P-pilus assembly and an integral membrane protein. Taken together, the analyses of six prophage regions and two GIs in the Pf-5 genome indicate that these structures have evolved via exchange of genetic material with other Pseudomonas spp. and extensive recombination. Transposition is unlikely to have played a major role in this evolution, as the genome of Pf-5 is nearly devoid of transposons and IS elements that are common in certain other Pseudomonas genomes.