Genomic analysis of bacteria in the Acute Oak Decline pathobiome

The United Kingdom’s native oak are under serious threat from Acute Oak Decline (AOD). Stem tissue necrosis is a primary symptom of AOD and several novel bacteria are associated with necrotic lesions. Two members of the lesion pathobiome, Brenneria goodwinii and Gibbsiella quercinecans, have been identified as causative agents of necrosis. However, additional bacteria including Lonsdalea britannica and Rahnella spp. have been detected in the lesion microbiome, but their role in the decline is unclear. Consequently, information on the genome-encoded virulence factors that mediate lesion formation is critical to understand the role of these bacteria as pathogens amongst AOD lesion microbiota. Here, the whole genomes of lesion isolates were sequenced, annotated and compared against canonical bacterial phytopathogens and non-pathogenic symbionts. Genome-wide virulence factor clustering demonstrated that all studied members of the AOD lesion microbiota possessed genes associated with phytopathogens. However, the genome of B. goodwinii was characteristic of a necrogenic phytopathogen, corroborating ecological and metatranscriptomic studies that implicate it as the key causal agent of AOD lesions. Furthermore, we investigated the genome sequence of other AOD lesion microbiota to understand the lifestyle of organisms isolated from a complex pathobiome. We demonstrate that in combination with empirical ecological and metatranscriptomic data, whole genome sequencing provides key insights into the lifestyle of bacterial species as phytopathogens or non-pathogenic symbionts in complex pathosystems.

Keywords: Acute Oak Decline (AOD), Brenneria goodwinii, Gibbsiella quercinecans, necrosis, pathobiome, phytopathogens.