Introducing a Novel, Broad Host Range Temperate Phage Family Infecting Rhizobium leguminosarum and Beyond

• Published in: Frontiers in microbiology Vol. 12; p. 765271
• Main Authors: Ford, Sam, Moeskjær, Sara, Young, Peter, Santamaría, Rosa I., Harrison, Ellie
• Format: Journal Article
• Language: English
• Published: Frontiers Media S.A 09-11-2021
• Subjects: Microbiology; phage ecology; phage evolution; prophage; rhizobia; temperate phage
• ISSN: 1664-302X; 1664-302X
• DOI: 10.3389/fmicb.2021.765271

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.