Check out Patrick's first paper from his dissertation, "Prevalence of an Insect-Associated Genomic Region in Environmentally Acquired Burkholderiaceae Symbionts" published in Applied and Environmental Microbiology!
Patrick joined the lab just a couple months after the COVID crisis began. Since he couldn’t perform lab work during the shutdowns, he quickly and impressively pivoted to learn to assemble and annotate the genomes of Caballeronia symbionts. Patrick became our lab’s expert in bacterial genome analyses and performed a comparative analysis of eight new symbiont genomes we collected plus over 200 genomes he downloaded from GenBank. He explored the prevalence, origin, and function of a genomic region which had previously been identified as a symbiosis-associated genomic island. In the process, he also generated the most comprehensive whole-genome phylogeny of the Burkholderiaceae to date.
Symbiosis islands are horizontally transferred regions of microbial genomes that encode the machinery for symbiosis. The best documented example is the rhizobial symbiosis island, which has been transferred many times between diverse bacteria, resulting in transmission of the rhizobial lifestyle to previously nonsymbiotic bacteria. A putative symbiosis island for the bug-Caballeronia symbiosis was detected by a 2020 study that compared five symbiotic Caballeronia and related Paraburkholderia genomes. If true, this would be exciting because it would suggest that machinery for the bug-Caballeronia symbiosis might be easily transferred between bacteria.
In a comprehensive 229-genome comparison encompassing the entire Burkholderiaceae family, Patrick found that this contiguous genomic region likely evolved in the ancestor of the Caballeronia and Paraburkholderia (after the split from Burkholderia sensu stricto), which might help explain why these two genera are much better at forming symbiotic partnerships with bugs compared to Burkholderia s.s. Interestingly, however, the genes within the region all appear to be ancestral to the Burkholderiaceae family, perhaps indicating that the machinery for this symbiosis was co-opted from other functions.
But is this region is a symbiosis island? In the end, Patrick detected only two instances of likely horizontal transfer of the region. He found that it is usually located on the chromosome (not plasmids, which are more mobile), and that is does not posses any of the mobility elements (e.g. phage elements) that would facilitate horizontal transfer. He concluded that although this region is associated with the symbiosis and merits further investigation, we probably can't call it a symbiosis island. The machinery for bug-Caballeronia symbiosis does not appear to be as easily transferred between disparate lineages as the legume-rhizobium symbiosis.
Congratulations to Patrick on this impressive achievement - even moreso in the face of a pandemic!
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