Leverhulme funded PhD position on Earthworm Holobionts: The boom and bust of functional gains and decay in earthworm-associated microbial consortia

Earthworms are widely dispersed throughout sub-Arctic, temperate, and tropical soils, where they generally comprise the major fraction of soil macroorganismal biomass. The first person to fully recognize the key role of earthworms in contributing to the ecological functionality of soils was Charles Darwin – there is a pleasing symmetry in the fact that his first and last scientific publications were on the development of vegetable mould by worms (a topic that today would more likely be described in terms of carbon turnover). Indeed, worms have such an impact on soil development and processing of plant litter that they are frequently considered to be ecosystem engineers. Furthermore, earthworms are also considered sentinel organisms for soil health: they are sensitive to key pollutants including toxic metal ions, as well as many classes of agricultural biocides.

While there are, unsurprisingly, quite a number of published studies of earthworm microbiome research, many of these are essentially descriptive and lack compelling evidence for how a holobiont interacts with an external factor (for instance, analysing microbiomes in earthworms along a pollution gradient, but failing to show how or if microbiome changes may relate in any way to host biology). Metabolomics represents a form of biochemical profiling that is, arguably, the most downstream and direct measure of cellular phenotype, and integrates the effects of complex upstream regulatory mechanisms. There is almost nothing known about how earthworm microbiomes interact with earthworm metabolomes; nor is it known how microbial and host metabolism may interact to produce novel metabolites. A particularly interesting biofluid in this context is the coelomic fluid, which is also (for some earthworms, e.g. Eisenia spp.) very readily sampled using non-invasive techniques; There is also the potential for longitudinal sampling of individual worms and these are not home-office licenced techniques so are extremely tractable.

The project will focus on describing the earthworm holobiont – its microbiome and metabolome, and subsequently how this co-metabolome may affect other organisms – eg. soil and plant microbiomes. For instance, earthworm cocoons develop in soil, which is an environment full of predators and potential pathogens: there is unpublished evidence suggesting that cocoon microbes may contribute to the immunological defence of the cocoons and developing worms. Of relevance, several species of vertically-transmitted earthworm symbionts have been described that are passed to offspring via the cocoon – these may comprise some of these putative microbial probiotic defences. It is also possible to modulate earthworm microbiomes by antimicrobial treatment, which gives a simple route to starting to test the role of microbiome involvement in worm and soil health.

The student will address a number of key aims, designed to lead to PhD chapters:

• Characterize holometabolome and hologenome of a model earthworm species (E. andrei), including during cocoon development
• Characterize antimicrobial activity of novel earthworm/microbe metabolites to investigate their function in nature
• Adapt spatial metabolomics (via MS imaging) with microbial marker localization (e.g. by FISH)
• Characterize earthworm/microbiome exuded metabolome, and the effect on model soil/plant ecosystems (to be set up as controlled lab experiments in phytotron or similar) 

The student would join the Leverhulme Centre for the Holobiont (www.imperial.ac.uk/holobiont/), a multi-institutional research centre devoted to understanding interactions between multicellular hosts and their microbial symbionts.

Informal enquiries are welcomed and should be sent to Jake Bundy ([email protected])

• Supervised by Jake Bundy, Department of Metabolism, Digestion, and Reproduction, Imperial College, London
• Co- Supervised by Prof Marc-Emmanuel Dumas, Dr Peter Graystock, Prof Matthew Fisher

 The project will be based at Hammersmith, Sillwood and White city campus.

How to apply:

Please email Jake Bundy ([email protected]) and include in your application:

• Statement of Purpose
• Your CV
• At least two references to be sent directly to Jake Bundy from the referees.

Full applications made before 15^th April, will be considered at any time.

Funding and eligibility:

A fully funded 4 years Leverhulme Studentship, including tuition fees and a standard research council stipend. The fees and stipend cover UK home applicants and standard research council eligibility criteria apply:

https://www.ukri.org/what-we-offer/developing-people-and-skills/find-studentships-and-doctoral-training/get-a-studentship-to-fund-your-doctorate/

The successful applicant must hold, or be expected to complete, an MSc/MRes with merit/distinction in a relevant subject area. This is a multidisciplinary project and could suit someone with a biochemistry/chemistry background interested in applying their skills in the life sciences, or someone with a biology background interested in learning the analytical/bioinformatic skills.