Understanding the genomics and specialised metabolites of the biopesticidal bacterium Burkholderia ambifaria
Lead Research Organisation:
CARDIFF UNIVERSITY
Department Name: School of Biosciences
Abstract
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.
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.
Organisations
Publications
Webster G
(2020)
Culturable diversity of bacterial endophytes associated with medicinal plants of the Western Ghats, India.
in FEMS microbiology ecology
Beaton A
(2018)
Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies.
in FEMS microbiology letters
Mullins AJ
(2020)
Genomic Assemblies of Members of Burkholderia and Related Genera as a Resource for Natural Product Discovery.
in Microbiology resource announcements
Webster G
(2019)
Genome Sequences of Two Choline-Utilizing Methanogenic Archaea, Methanococcoides spp., Isolated from Marine Sediments.
in Microbiology resource announcements
Webster G
(2019)
The Genome Sequences of Three Paraburkholderia sp. Strains Isolated from Wood-Decay Fungi Reveal Them as Novel Species with Antimicrobial Biosynthetic Potential.
in Microbiology resource announcements
Mullins AJ
(2019)
Genome mining identifies cepacin as a plant-protective metabolite of the biopesticidal bacterium Burkholderia ambifaria.
in Nature microbiology
Mullins AJ.
(2019)
Burkholderia bacteria: natural alternatives to synthetic pesticides
Studentship Projects
Project Reference | Relationship | Related To | Start | End | Student Name |
---|---|---|---|---|---|
BB/M009122/1 | 30/09/2015 | 31/03/2024 | |||
1646512 | Studentship | BB/M009122/1 | 30/09/2015 | 29/09/2019 | Alex Mullins |
Description | We investigated the antimicrobial capacity of a bacterium called Burkholderia ambifaria by analysing multiple strains using a combination of genome-based informatics and lab-based assays. We systematically defined the antimicrobial profiles of different strains against a collection of diverse plant pathogens. Following these analyses, we identified the genes responsible for the production of an antimicrobial compound called cepacin. The role of this compound in the biological control of pathogens was investigated by creating a cepacin-deficient mutant and comparing it to the cepacin-producing strain in a plant-pathogen model by inoculating pea seeds with either version of the bacterium and challenging the seeds with a plant pathogen called Pythium. We observed significant protection of seedlings by the cepacin-producing strain and significantly reduced protection by the cepacin-deficient mutant. This confirmed that cepacin was a key metabolite produced by Burkholderia ambifaria in the biological control of a specific plant pathogen. |
Exploitation Route | The outcomes of this funding are currently being advanced in a BBSRC grant (BB/S007652/1) in collaboration with the University of Warwick to explore several aspects of Burkholderia bacteria as biological control (biopesticide) agents: safety, efficacy, and persistence. The human safety aspect will focus on attenuation of promising biopesticidal strains, or hererologously expressing key antimicrobial pathways in closely-related environmental species such as Paraburkholderia species. Further research will explore the efficacy of different Burkholderia species in a biological control capacity to identify optimal strains. Finally, the persistence of these bacteria in the soil following inoculation of seeds and their influence on the rhizosphere community will be investigated over a growth season of the model crop Pisum sativum (pea plant). I am employed as a postdoctoral researcher on this grant. |
Sectors | Agriculture Food and Drink Environment |
Description | Annual Conference Travel Grant |
Amount | £238 (GBP) |
Funding ID | GA001269 |
Organisation | Microbiology Society |
Sector | Learned Society |
Country | United Kingdom |
Start | 03/2019 |
End | 04/2019 |
Description | Cardiff School of Biosciences - Nature Masterclass |
Amount | £600 (GBP) |
Organisation | Cardiff University |
Sector | Academic/University |
Country | United Kingdom |
Start | 01/2018 |
End | 01/2018 |
Description | Exploiting the untapped biosynthetic potential of the bacterium Burkholderia ambifaria |
Amount | £2,400 (GBP) |
Organisation | Cardiff University |
Sector | Academic/University |
Country | United Kingdom |
Start | 01/2020 |
End | 07/2020 |
Description | President's Fund |
Amount | £1,200 (GBP) |
Organisation | Society for Applied Microbiology |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 07/2017 |
End | 08/2017 |