Projects that commenced in 2015


Supervisors: Prof Richard Wall (University of Bristol), Dr Eric Morgan (University of Bristol), Dr Ailsa Milnes (Zoetis Animal Health).

In environments where poor land quality precludes crop production, livestock represent the primary contribution to agricultural production and food security. Domestic sheep in particular are hardy and well-adapted to marginal land and harsh climates. However, sheep suffer from a wide range of parasites and disease problems, one of the most persistent and damaging of which in the UK is psoroptic mange, known as scab. Scab is caused by infestation by a parasitic mite, Psoroptes ovis. The mites cause a debilitating and destructive clinical disease; there are believed to be over 7,000 outbreaks of scab in UK flocks each year costing the UK sheep industry over £8 million per year from mortality, reduced weight gain and the costs of treatment. Despite a number of recent scab education campaigns, there is no evidence that scab prevalence has been reduced.

Recent research at the University of Bristol has highlighted the risk factors associated with scab outbreaks, quantified the prevalence of the disease and suggested that regional or local scab management programmes may be a more effective use of time and resource than any attempted national eradication programme. However, at present there is considerable confusion about the best approaches to scab management, both in terms of the compounds to apply, when to apply them in relation to seasonal husbandry practices and in terms of farm/region scale effects.

The aim of this project therefore, is to develop a systems model which incorporates different farm types and husbandry approaches, incorporating farmer behaviour, to identify optimum management approaches to scab control under specific husbandry regimes.

Supervisors: Dr James Hodge (University of Bristol), Dr Seirian Sumner, (University of Bristol), Dr Sean Rands (University of Bristol)

Over a third of global crops (84% European crops) are dependent on pollinators (predominantly bees) with a value of ~£120 billion. Food production has kept up with postwar increase in population through the extensive use of pesticides, with development of resistance becoming an increasing problem. The neonicotinoids represent 15% of the worldwide insecticide market valued at ~$1 billion/year, but their pervasive use is widely thought to be a major contributory factor towards the 50% decrease of bees since the 1970s. This has resulted in a two-year ban on the neonicotinoids allowing scientists to determine their safety, mechanism of action and compatibility with global food security.

We aim to exploit the genetic tractability of Drosophila to determine the mechanism of action of neonicotinoids and generation of resistance. Our pilot data reveals that field relevant doses of neonicotinoids have a similar detrimental effect on fly and bee viability, longevity, locomotion and memory.


Supervisors: Dr Wynand van der Goes van Naters (Cardiff University), Dr Mike Birkett (Cardiff University).

This project investigates how the olfactory system of the emerging agricultural pest Drosophila suzukii encodes host odours, and aims to identify attractive ligands and their mixtures that can be used as baits in traps. Endemic to eastern Asia, D. suzukii was first recorded in Spain in 2008 and has since invaded northwards in Europe, reaching the UK in September 2012. D. suzukii is an extreme generalist feeder: the fly lays its eggs in fruit from diverse plant families including strawberry, grape and blueberry. How a generalist insect selects its hosts is a central question in insect-plant relationships.

By electrophysiology at the resolution of single sensory neurons, we will test hypotheses of how the olfactory system encodes odours from fruit hosts. Are there shared key ligands in the bouquets emitted by the different hosts, which thereby activate common subpopulations of sensory neurons in the olfactory system that mediate behavioural attraction, or do different host bouquets activate mutually exclusive groups of sensory neurons? Our knowledge of the olfactory system of the model organism Drosophila melanogaster will inform our research on D. suzukii. Assays measuring behavioural attraction to pure single odorants and to multicomponent blends will provide quantitative readouts of processing of olfactory information, and a mathematical model which relates output to input will give insight into the importance of blend recognition. Blends that are attractive in the laboratory are valuable candidate baits for traps to monitor and control D. suzukii populations in orchards.

Supervisors: Prof Eshwar Mahenthiralingam (Cardiff University), Prof Jim Murray (Cardiff University), Prof Murray Grant (University of Exeter)

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.

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.


Supervisors: Prof Angus Buckling (University of Exeter), Prof Richard ffrench-Constant (University of Exeter), Dr Edze Westra (University of Exeter)

The bacterium Bacillus thuringiensis is the main bio-pesticide used to control insect crop pests and is widely used in agriculture in the UK. The bacterium is produced in large-scale fermentations, but this method often suffers from contaminations with viruses that feed on the bacteria (bacteriophages; phages), resulting in large economical losses. An estimated 30% of the bacterial fermentation batches suffer from phage infections and there is therefore a pressing need to develop phage-resistant B. thuringiensis strains to replace the current phage-sensitive variants. Here we will manipulate B. thuringiensis phage-resistance through its CRISPR-Cas systems. CRISPR-Cas systems are bacterial adaptive immune systems and unlike alternative phage-resistance strategies of bacteria, CRISPR-Cas can potentially provide cost-free resistance to unlimited numbers of phage species. In addition to increasing production of bacteria, the resultant B. thuringiensis genotypes are likely to have greater biocontrol properties, because their in vivo growth will not be compromised by phages. However, a main hurdle for using CRISPR-Cas to generate phage-resistant bacteria is that bacteria frequently evolve phage resistance through other mechanisms, and such resistant mutants are expected to have reduced virulence in hosts as well as being outcompeted by phage sensitive bacteria.

We have recently shown how we can predict and manipulate the environmental conditions that promote the evolution of different resistance mechanisms, and we have identified conditions where the bacterium Pseudomonas aeruginosa exclusively utilizes CRISPR-Cas-mediated resistance. Here, we aim to investigate (i) the conditions where B. thuringiensis CRISPR-Cas-mediated phage resistance evolves; (ii) the level of protection offered by CRISPR-Cas-mediated phage immunity; and (iii) any in vitro costs associated with this resistance. Once we have pre-evolved phage resistant B. thuringiensis, we will (iv) investigate their biocontrol efficacy in insect hosts.


Supervisors: Dr Michael Birkett (Rothamtsed), Prof Murray Grant (University of Exeter).

Trichoderma species are ubiquitous soil saprotrophs utilized in agriculture for their biocontrol activities. Some strains additionally possess the ability to activate induced systemic resistance (ISR) to a broad range of pathogens. Other strains have been shown to stimulate plant growth through the production of plant-growth-promoting (PGP) compounds, although both traits are rarely found together. This project focuses upon a novel, free-living, strain of T. hamatum, which exhibits biocontrol and plant growth promotion (PGP) capabilities in both monocots and dicots, controls plant diseases caused by pre- and post-emergence pathogens, can induce systemic resistance and modify root architecture, even in species where no increase in canopy development is evident (e.g. maize & wheat). As with other biocontrol/PGP solutions, field application presents many challenges. Complex cross-talk occurs during beneficial rhizosphere interactions and is influenced by the climate, soil type, time of year and host genotype, e.g. in tomato-T. atroviride and T. harzianum interactions. Therefore, there is significant added value in studies that seek to understand and exploit the chemical ecology that underpins beneficial traits conferred by Trichoderma in the rhizosphere.

This project will use an interdisciplinary approach to elucidate the novel bioactive chemistry produced by T. hamatumthat contributes to these agronomically important traits. Bioassay-guided fractionation (using advanced chromatographic/spectroscopic analysis i.e. MS and NMR) will be used to identify bioactive natural products from microcosm extracts of Trichoderma hamatum that provide protection of lettuce (Lactuca sativa) or brassicas against the soil pathogen Sclerotinia sclerotorium (Ss). In-soil capture of the identified chemical signals, from Trichoderma isolates and the host plants will be carried out by the insertion of reverse-phase coated fibres into Trichoderma-amended soil environment of plants, in the presence or absence of Ss, and then elution/analysis of the captured compounds. This technique will shed light on the identity of the causal metabolites involved in potential enhancement of root defence against herbivores eg. clover root weevils, Sitona lepidus.