Taxonomy and identification of bacteria associated with acute oak decline

Abstract

Acute oak decline (AOD) is a relatively newly described disorder affecting native oak species in Britain. Symptomatic trees are characterised by stem bleeds from vertical fissures, necrotic lesions in the live tissue beneath and larval galleries of the two spotted oak buprestid (Agrilus biguttatus). Several abiotic and biotic factors can be responsible for tree death, however the tissue necrosis and stem weeping is thought to be caused by a combination of bacterial species. Following investigations of the current episode of AOD which began in 2008, numerous strains belonging to several different bacteria in the family Enterobacteriaceae have been consistently isolated from symptomatic tissue. The majority of these enterobacteria were found to be novel species, subspecies and even genera, which have now been formally classified. The most frequently isolated species from symptomatic oak are Gibbsiella quercinecans, Brenneria goodwinii and Rahnella victoriana. Identification of these bacteria is difficult due to similarities in colony morphology, phenotypic profile and 16S rRNA gene sequences. Current identification relies heavily on gyrB gene amplification and sequencing, which is time consuming and laborious. However, newer techniques based on detection of single nucleotide polymorphisms show greater promise for rapid and reliable identification of the bacteria associated with AOD.

Keywords: Acute oak decline; Brenneria goodwinii; Gibbsiella quercinecans; Taxonomy.

Fig. 1

Symptoms of acute oak decline a external symptoms of weeping stem bleeds b cracked bark plates caused by necrotic underlying tissue c lesions in the inner bark d Agrilus biguttatus larval galleries in close proximity to necrotic lesions

Fig. 2

Current distribution of acute oak decline in Britain (all sites verified as of 2014)

Fig. 3

Maximum likelihood tree based on concatenated partial gene sequences of gyrB, rpoB, atpD and infB of members of the genera Brenneria, Lonsdalea phylogenetically related species. The phylogenetic analysis was inferred using the general time reversible model with estimated gamma distribution with invariant sites (G + I) in MEGA 7 (Kumar et al. 2016). Bootstrap values after 500 replicates are expressed as percentages. Cronobacter sakazakii is included as an outgroup; gene sequences were obtained from the genome sequencing database (http://www.ncbi.nlm.nih.gov). Bar 0.05 substitutions per site

Fig. 4

Maximum likelihood tree based on concatenated partial gene sequences of gyrB, rpoB, atpD and infB of members of the genera Rahnella, Gibbsiella and phylogenetically related species. The phylogenetic analysis was inferred using the General Time Reversible model with estimated gamma distribution with invariant sites (G + I) in MEGA 7 (Kumar et al. 2016). Bootstrap values after 500 replicates are expressed as percentages. Xenorhabdus nematophila is included as an outgroup; gene sequences were obtained from the genome sequencing database (http://www.ncbi.nlm.nih.gov). Bar 0.05 substitutions per site