Abstract
Temperate phages play important roles in bacterial communities but have been largely overlooked, particularly in non-pathogenic bacteria. In rhizobia the presence of temperate phages has the potential to have significant ecological impacts but few examples have been described. Here we characterize a novel group of 5 Rhizobium leguminosarum prophages, capable of sustaining infections across a broad host range within their host genus. Genome comparisons identified further putative prophages infecting multiple Rhizobium species isolated globally, revealing a wider family of 10 temperate phages including one previously described lytic phage, RHEph01, which appears to have lost the ability to form lysogens. Phylogenetic discordance between prophage and host phylogenies suggests a history of active mobilization between Rhizobium lineages. Genome comparisons revealed conservation of gene content and order, with the notable exception of an approximately 5 kb region of hypervariability, containing almost exclusively hypothetical genes. Additionally, several horizontally acquired genes are present across the group, including a putative antirepressor present only in the RHEph01 genome, which may explain its apparent inability to form lysogens. In summary, both phenotypic and genomic comparisons between members of this group of phages reveals a clade of viruses with a long history of mobilization within and between Rhizobium species.
Highlights
Bacteriophages are ubiquitous in bacterial populations and contribute significantly to the ecology and evolution of microbial communities
Genes encoded on temperate phages can have significant ecological effects, such as the shiga toxin genes encoded on STX phages that make Shigella bacteria highly virulent (Allison, 2007) or photosynthesis genes encoded on Prochlorococcus phages (Lindell et al, 2004)
The vTRX32-1 phage family represents a novel group of temperate phages isolated within Rhizobium leguminosarum bv. trifolii (Rlt) strains
Summary
Bacteriophages (phages) are ubiquitous in bacterial populations and contribute significantly to the ecology and evolution of microbial communities. Temperate phages—phages capable of integrating into the bacterial genome—in particular, occupy a multitude of roles in bacterial communities (Harrison and Brockhurst, 2017); like purely lytic phages they can infect and kill susceptible bacteria, contributing to population turnover and driving selection for resistance (Paterson et al, 2010). As integrated phages—“prophages”—they can provide competitive advantages to their hosts—which are known as “lysogens” (Brown et al, 2009); Lytic phage particles produced from the lysogen population at low rates infect and kill non-lysogens—likely to be unrelated competitors—and act as anti-competitor “weapons” during competition. Temperate phages can be significant players in microbial ecosystems. In terrestrial environments, very little is known about the lives of these genetic symbionts
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