Understanding the genomics and specialised metabolites of the biopesticidal bacterium Burkholderia ambifaria

Harnessing beneficial interactions between microorganisms and plants can provide multiple solutions to food security by reducing chemical pesticide and fertilizer use, and improving crop yields. Burkholderia are Gram-negative, environmental bacteria that have been used as natural biotechnological agents for pollutant bioremediation and biological control of plant pathogens. They occur in high numbers at the roots of major crop species including maize and rice.

Burkholderia encode pathways that can fix atmospheric nitrogen and produce antimicrobial metabolites that kill a range of plant pathogens (bacteria, fungi and nematodes). However, the pathways that are most beneficial in plant interactions have not been systematically defined. The Burkholderia genome (8+ Mb) contains multiple large chromosomal replicons. The smallest, third chromosome (> 1Mb; c3) can be deleted, attenuating virulence but leaving rhizosphere fitness intact, opening up chromosome engineering as a means to harness Burkholderia's biotechnological potential.

Aim. The PhD will define the Burkholderia and plant genetic pathways involved in protective and growth promoting rhizosphere interactions, with an overall goal to engineer the most beneficial bacterial pathways onto a synthetic c3.

Objective 1 (Year 1). Screening Burkholderia strains for growth promotion and plant protection using Arabidopsis models. Multiple Burkholderia biocontrol strains are being genome sequenced as part of BBSRC antibiotic discovery genome mining (EM, 2014-17). The PhD will genetically characterise these strains (EM rotation) and establish Arabidopsis growth promotion assays (JM rotation), to identify the most bioactive Burkholderia. An Arabidopsis protection assay will be established (MG rotation) to determine how the bacterial pathogen, Xanthomonas is killed at the rhizosphere by Burkholderia, using a range of defence and hormone mutants to provide mechanistic insight.

Objective 2 (Year 2-3). Exploring the molecular basis for growth promotion and plant protection using post-genomic approaches. Global gene expression occurring in both Burkholderia and Arabidopsis during beneficial interactions will be determined using RNA-seq, defining the underlying transcriptional networks engaged in these processes (interdisciplinary rotations between EM and JM labs).

Objective 3 (Year 3-4). Synthetically engineer the Burkholderia c3 to encode specific growth promotion and pathogen control functions. Selected pathways identified from the global gene expression analysis will be engineered onto a synthetic third chromosome. They will be re-tested in a c3 mutant background, establishing which beneficial pathways remain effective in isolation, ultimately working towards the goal of producing a composite Burkholderia replicon for crop protection and plant growth promotion that can be utilized in environmentally adapted Burkholderia's.