Abstract:
Novel traits introduced by recombination and horizontal gene transfer can alter microbial interactions
and increase the risk and severity of disease outbreaks. In this work I use the Ralstonia solanacearum
species complex (RSSC) to investigate links between mobile genetic elements (MGEs) and the
emergence of two disease outbreaks in South America and Indonesia. The first outbreak is caused
by the parallel expansion of two distantly related lineages, one of which displays the broadest host
range ever documented for Ralstonia. I defined a family of previously unrecognized integrative and
conjugative elements (ICEs) exchanged between the two lineages during the outbreak. These ICEs
encode two specialized accessory genes integration sites that carry either metabolism or defence
related genes. The ICE associated with the outbreak carries genes involved in the degradation of
reactive xenobiotics and plant-derived metabolites, thereby potentially enhancing metabolic capacity
of the two lineages. The second investigated outbreak of banana-infecting R. syzygii subsp.
celebesensis (Rsc) was first detected in Indonesia, a centre of wild host diversity. My work sampling,
sequencing, and analysing isolates from Sulawesi and Java provides new insight into the origins of
the novel lineage that threatens global banana production. Comparative analyses revealed that Rsc
exhibits significant prophage enrichment in the context of an otherwise reduced genome. Genome
assemblies of isolate pairs sampled from the same host individuals revealed extensive structural
variation and MGEs exchange, underscoring the role MGEs can play during active infection. In the
final part of my work, I show how prophage movement shapes microbial interactions by altering strain
carriage of loci mediating contact dependent inhibition (CDI) across the whole RSSC. I found RSSC
have the largest repertoires of CDI loci ever discribed for bacteria. This amplification is linked with
prophage-mediated introduction of entire loci into hotspots on the chromosome. CDI loci cluster into
four types, all of which are predicted to carry toxin and immunity genes, which are in turn subject to
rapid diversification via homologous recombination. Collectively, these findings provide insight into
how a globally significant plant pathogen has expanded its repertoire of antagonistic loci through
MGEs, thereby enhancing its competitive ability and capacity to establish successful infections. This
knowledge can in turn be used to develop novel strategies for infection prevention.
Recombination