Global diversity and distribution of prophages are lineage-specific within the Ralstonia solanacearum plant pathogenic bacterium species complex

Abstract

Ralstonia solanacearum is a destructive plant pathogenic bacterium and the causative agent of bacterial wilt disease, infecting over 200 plant species worldwide. In addition to chromosomal genes, its virulence is mediated by mobile genetic elements including integrated DNA of bacteriophages, i.e. prophages, which may carry fitness-associated auxiliary genes or modulate host gene expression. Although experimental studies have characterised several prophages that shape R. solanacearum virulence, the global diversity, distribution, and wider functional gene content of R. solanacearum prophages is unknown. In this study, prophages were identified in a diverse collection of 192 R. solanacearum draft genome assemblies originating from six continents. Prophages were identified bioinformatically and their diversity investigated using genetic distance measures, gene content, GC, and total length. Prophage distribution was characterised using metadata on R. solanacearum geographic origin and lineage classification (phylotypes), and their functional gene content was assessed by identifying putative prophage-encoded auxiliary genes. In total, 343 intact prophages were identified, forming ten genetically distinct clusters. These included five prophage clusters belonging to the Inoviridae, Myoviridae, and Siphoviridae phage families, and five uncharacterised clusters, possibly representing novel, previously undescribed phages. The prophages had broad geographical distribution being present across multiple continents. However, they were generally host phylogenetic lineage-specific, and overall, prophage diversity was proportional to the genetic diversity of their hosts. The prophages contained a myriad of auxiliary genes involved in metabolism and virulence of both phage and bacteria. Our results show that while R. solanacearum prophages are highly diverse globally, they make lineage-specific contributions to the R. solanacearum accessory genome, which could result from shared coevolutionary history.

Influence of insertion sequences on population structure of phytopathogenic bacteria in the Ralstonia solanacearum species complex

“…We found that there was significant congruence between the trees overall and independently within lineages, suggesting that genetically similar hosts contain similar IS. These findings mirror those of a recent study conducted on RSSC prophages (41) which found similar lineage-specific distributions and detected significant congruence between prophage content and the host phylogenetic tree. Therefore, multiple mobile genetic elements in RSSC appear to track the evolution of their hosts and act as sources of genetic diversity between lineages.…”

“…IS movement between bacterial lineages has previously been attributed to plasmids (72,73), integrative and conjugative elements (74), and, rarely, prophages (73). Both integrative and conjugative elements and prophages have both been found to be lineage-specific (40,41) and therefore may have limited movement between lineages. However, RSSC strains are naturally competent and is capable of being transformed with DNA from different lineages (75)(76)(77).…”

“…Considerable variation exists between and within R. solanacearum lineages regarding their metabolic versatility (35), tolerance to environmental stresses including starvation and low temperatures (36,37), and disease severity (38). This has been linked to a diverse accessory genome (39,40) which includes mobile genetic elements such as prophages (29,41). A recent analysis of RSSC prophages found that, while prophages were highly diverse, they were generally bacterial host phylotype-specific (41).…”

“…This has been linked to a diverse accessory genome (39,40) which includes mobile genetic elements such as prophages (29,41). A recent analysis of RSSC prophages found that, while prophages were highly diverse, they were generally bacterial host phylotype-specific (41). In addition, prophage content tightly followed the host phylogeny with genetically similar hosts containing similar prophages.…”

Genomic and functional analysis of phage‐mediated horizontal gene transfer in Pseudomonas syringae on the plant surface

“…They found that many of the prophages were inducible, released from O157 cells and transferred to other E. coli strains. Numerous prophages carrying virulence factors including genes for T3SEs have recently been identified in the plant pathogenic bacterium Ralstonia solanacearum (Greenrod et al ., 2021), but phage‐mediated HGT has not been functionally demonstrated for a phytopathogen.…”