Genomic analysis of Burkholderia ambifaria identifies key specialised metabolites for biopesticidal applications

Burkholderia bacteria are renowned for the biosynthesis of an extensive repertoire of specialised metabolites encoded by biosynthetic gene clusters (BGCs). Burkholderia ambifaria is a historical biopesticide and produces multiple antimicrobials with activity against nematodes, fungi and bacteria. We evaluated the distribution of antimicrobial activity and BGCs across the species which, despite their biopesticidal potency, is poorly understood.

Genomic analysis of 64-B. ambifaria whole-genomes revealed considerable diversity. Pathway prediction identified 1272 BGCs across 64 strains that were de-replicated to 38 distinct BGCs. Known BGCs accounted for 13 of the BGCs; 7 of which corresponded to known antimicrobials, and included enacyloxins and bactobolins. The antimicrobial activity of the strains was assessed in a classical overlay assay against animal and plant pathogens. The combined genome mining and in vitro activity screens identified a potent anti-Gram-positive and anti-Oomycete compound, cepacin. A damping-off disease model with the pathogen Pythium ultimum and legume Pisum sativum (garden peas) highlighted cepacin as a key specialised metabolite in crop protection. B. ambifaria strain persistence in a mouse inhalation infection model was reduced by removal of the third replicon, whilst retaining the biopesticidal properties of the B. ambifaria strain.

This work highlights the diversity and prevalence of specialised metabolites in B. ambifaria, and the importance of the potent antimicrobial cepacin in protection against damping-off disease in agriculture. Construction of a B. ambifaria strain that retained biopesticidal properties yet was attenuated for persistence within a murine infection model provides a potential route towards developing safe biopesticidal agent.