IAP-24-096

Explorations of symbiosis along a parasite-mutualist continuum

What determines whether a microbe is a parasite, a mutualist or a saprophyte? Microbes exploit every conceivable niche on the planet and have a huge range of niches: they live intimately associated with organisms from other kingdoms as parasites or mutualists, but also live independently from other living organisms as saprophytes or autotrophs.

Even though microbes have a fundamental role shaping the planet’s ecosystems, for many species, we only have a limited idea of their true natural ecology. This is particularly true of many species of entomopathogenic fungi: parasites that are increasingly used as ecologically sustainable crop protection products to defend plants against herbivorous insects and other natural enemies. These fungi are distinctively unusual: they have the capability to live independently in the soil, but also to form symbiotic relationships with organisms in two different kingdoms: insects and plants. As saprophytes they live in the soil and metabolise soil carbon. In insects they are pathogens that cause major epidemics. In plants they grow endophytically inside the plant’s tissue and can help the plant in defending against pests and diseases.

This PhD will develop new understanding of the ecological niche inhabited by entomopathogenic fungi. The student will focus on one species of fungus, Beauveria bassiana, that is widely used as a crop protection product to defend plants against herbivorous insects. The project is motivated by both pure and applied research questions. The findings will provide novel fundamental knowledge about how this microbe has evolved to exploit such a diverse range of niches along the symbiotic continuum. However, there is also the potential to make major advances of strong relevance to sustainable agriculture: as farmers strive to replace ecologically damaging synthetic pesticides with biocontrol products formulated from natural microbes.

The specific objectives of this PhD are flexible and could be tailored to suit the interests of the successful candidate. In particular, whilst we have planned the project as an integrated study involving experimental, genomic and metagenomic analyses, there is scope to focus principally on some parts of this project more than others. At present we plan that the PhD student will tackle the following objectives:

1. Determine the extent to which the B. bassiana species-complex harbours ecologically specialised cryptic diversity with strains specialised to exploit parasitic, saprophytic and mutualistic niches.

2. Determine the extent that B. bassiana genotypes isolated from different ecological niches show genetic divergence and distinct genomic features.

3. Characterise the soil niche of B. bassiana by: (i) determining the soil properties that correlate with variation in relative abundance and (ii) investigating the diversity and composition of the soil fungal communities with which B. bassiana is associated.

The project could all be based entirely in the UK, exploiting research facilities and existing data-sets at Stirling and CEH. However, if the successful candidate is interested, we could explore options to include a fieldwork component with our existing collaborators in either Brazil or Chile.

Obj 1: To what extent do B. bassiana strains isolated from infected insects differ phenotypically from those isolated from soil? The student will test whether B. bassiana strains from these niches are ecologically specialised and whether phenotypic trade-offs occur in the quantitative ability of fungal strains to: (1) infect insects as parasites, (2) associate endophytically with plants, (3) grow as saprophytes. This will involve using a panel of fungal strains, testing their ability to: infect and kill insects, grow in plant tissue, and grow saprophytically on media in various conditions. This will enable the student to investigate the extent of specialisation and test whether trade-offs exist in the ability of insects to exploit different niches.

Obj 2: Genomic variation between insect-associated and soil-associated strains. Whilst some B. bassiana are implicated in parasitic infection, we have no knowledge of whether strains isolated from different niches show distinct patterns of gene gains/loss or divergent evolutionary processes. We will sequence and assemble high-quality full genomes for our panel of B. bassiana isolates and then study patterns of gene gain and loss across the phylogeny. We hypothesise Beauveria adaptation to an entomopathogenic lifestyle has been facilitated by phylogenetically distant, potentially inter-kingdom horizontal gene transfers, as has been observed in other insect-infecting fungi.

Obj 3: Beauveria niche utilisation in soils. The ability to persist and grow in the soil is vital to B. bassiana ecology, yet this niche is barely studied. We will undertake pioneering work by exploiting existing metagenomic data sets from UK soils that will enable us to test for the presence of B. bassiana in soil samples, quantify its abundance and investigate how it co-occurs with other soil microbes. This knowledge is exceptionally important to predict the impact of using B. bassiana as a biocontrol agent on microbial communities in agricultural soils.

Year 1

This 3.5 year studentship will begin with 6 months for project planning and then a literature review and training in key lab skills for working with insects, plants and fungal pathogens. The literature review could be developed into a published review article/meta-analysis. During this time the phenotypic characterisation of fungal strains as parasites, saprophytes and mutualists will begin.

Year 2

Year 2 will principally focus on genome reconstruction and annotation to investigate genomic correlates of niche utilisation.

Year 3

In year 3 the project will move to exploit our existing metagenomic data sets to investigate correlates of B. bassiana abundance in soil ecosystems.

Year 3.5

Thesis write up and submission. Publication of further research papers.

This PhD will principally be based in the vibrant multidisciplinary research environment at the University of Stirling. The PhD student will attend regular lab group meetings, along with weekly seminar series giving informal and formal opportunities for research presentation. The PhD student will also make regular trips to UKCEH for joint supervisory meetings and other research/training opportunities.

The candidate will receive training in subject specific and generic skills. These will include: insect husbandry, plant growth, pathogen handling and infection experimentation; advanced statistics (Stirling R course and other NERC training); pathogen molecular biology (eg DNA extraction, PCR, sequencing); bioinformatic skills for genome construction and annotation as well as metagenomic analysis.

The candidate will be expected to participate in training opportunities in a range of research and transferrable skills offered at Stirling University and through IAPETUS.

Training will be given in scientific communication skills, both writing and conference presentation, so that the candidate can successfully publish research papers and attend conferences during the PhD.