Genomic analysis of bacteria in the Acute Oak Decline pathobiome

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The UK’s native oak is under serious threat from Acute Oak Decline (AOD). Stem tissue necrosis is a primary symptom
of AOD and several bacteria are associated with necrotic lesions. Two members of the lesion pathobiome, Brenneria
goodwinii and Gibbsiella quercinecans, have been identified as causative agents of tissue necrosis. However, additional
bacteria including Lonsdalea britannica and Rahnella species have been detected in the lesion microbiome, but their role
in tissue degradation is unclear. Consequently, information on potential genome-encoded mechanisms for tissue
necrosis is critical to understand the role and mechanisms used by bacterial members of the lesion pathobiome in the
aetiology of AOD. Here, the whole genomes of bacteria isolated from AOD-affected trees were sequenced, annotated
and compared against canonical bacterial phytopathogens and non-pathogenic symbionts. Using orthologous gene
inference methods, shared virulence genes that retain the same function were identified. Furthermore, functional
annotation of phytopathogenic virulence genes demonstrated that all studied members of the AOD lesion microbiota
possessed genes associated with phytopathogens. However, the genome of B. goodwinii was the most characteristic of
a necrogenic phytopathogen, corroborating previous pathological and metatranscriptomic studies that implicate it as the
key causal agent of AOD lesions. Furthermore, we investigated the genome sequences of other AOD lesion microbiota
to understand the potential ability of microbes to cause disease or contribute to pathogenic potential of organisms
isolated from this complex pathobiome. The role of these members remains uncertain but some such as G.
quercinecans may contribute to tissue necrosis through the release of necrotizing enzymes and may help more
dangerous pathogens activate and realize their pathogenic potential or they may contribute as secondary/opportunistic
pathogens with the potential to act as accessory species for B. goodwinii. We demonstrate that in combination with
ecological data, whole genome sequencing provides key insights into the pathogenic potential of bacterial species
whether they be phytopathogens, part-contributors or stimulators of the pathobiome.
Original languageEnglish
Number of pages15
JournalMicrobial Genomics
Issue number1
Publication statusPublished - 8 Jan 2019

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