Graduate Thesis Or Dissertation
 

Phylogeny and Evolution of Gall-Associated Plant Pathogenic Bacteria

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  • Gall-associated phytopathogens have unique evolutionary histories that haveshaped both their modes of infection and genomic structures. Pathogenicity of the gall-associated plant pathogens of the Rhodococcus, Agrobacterium, and Rathayibactergenera is mediated by horizontally acquired virulence loci. The relative ease of gainand loss of the virulence loci has confounded accurate characterization of thesebacteria, especially those characterizations made prior to the use of molecular markersfor genotyping. Work presented in this thesis uses whole genome guided approaches todiscern the intra- and inter- species genetic diversity in the three genera described.Rhodococcus fascians is the causal agent of leafy gall disease. We tested thehypothesis that R. fascians is comprised of a single species level group and show thattwo distinct clades with up to six species level groups are able to cause symptomsconsistent with leafy gall disease. These data reveal previously unknown chromosomaldiversity within this group of phytopathogenic bacteria. Four lines of evidence thatmake use of whole genome sequences indicate that the species are acted on by distinctselective pressures and have unique evolutionary histories. Further, a set of horizontallyacquired virulence loci is correlated with the pathogenic phenotype, regardless ofchromosomal lineage. These data suggest that delimitation of phytopathogenicRhodococcus isolates requires careful consideration with respect to both thechromosomal genotype as well as the presence of virulence loci.Rathayibacter spp. are vector mediated plant pathogens that infect nematodegalls in the seed heads of several grass species. Rathayibacter toxicus, a Select Agentin the U.S., has been shown to produce corynetoxins, nucleoside antibiotics that alsocause neurotoxic effects in mammals, when infected by a bacteriophage. As R. toxicusencodes a clustered regularly interspersed short palindromic repeats (CRISPR) systemthat acts as an adaptive immune system against foreign DNA in bacteria, we studiedthe CRISPR array evolution for insights into the ecology of bacteria-phage interactions.We predicted that over half of the spacers encoded in R. toxicus are functional intargeting the phage, while the bacteria still show susceptibility to the phage. These datasuggest a complex homeostatic interaction whereby neither bacteria nor phagepopulations are eliminated. Further, our results challenge past conclusions on theefficacy of CRISPR-mediated immunity.Lastly, we generated a set of tools to facilitate comparative genomics researchand accurate species and strain identification. Data are integrated into a website(http: gall-id.cgrb.oregonstate.edu ) to facilitate their use by all researchers, regardlessof computational proclivity.
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