PhD Research Projects: NERC GW4+ DTP - TrematodeDNA - Using environmental DNA to quantify the abund

Trematodes (e.g. schistosomes and liver flukes) are among the most ecologically, economically and medically-important parasites of humans, livestock and wild animals in the world today. Many species of trematodes have an aquatic phase during their life history when they infect a freshwater snail intermediate host, before going on to infect mammalian definitive hosts. Knowledge of the abundance of these species within aquatic environments is important to help understand and control infection rates. However, assessing trematode abundance in freshwaters is currently laborious and requires specialist identification skills, precluding assessment of disease risk across broad spatial scales. There is huge potential to improve understanding of parasite abundance in freshwaters through environmental DNA (eDNA), traces of DNA released in the environment during excretion, decomposition and reproduction (Bass et al. 2015; Thomsen & Willerslev 2015). Remarkably, the potential of these methods for determining the abundance of globally-important parasite species of humans, livestock and wildlife has not yet been fully assessed, let alone widely exploited.

This project aims to develop and deploy an eDNA toolkit to rapidly assess abundance of trematode species in freshwaters. Metabarcoding methods will be used to reconstruct eukaryotic assemblages in these systems, and develop ecological models of infection risk.

Objective A: Developing the toolkit: i) How reliable is eDNA data as an indicator of trematode species presence? ii) Does eDNA reflect abundance in the natural environment? The project will experimentally address these questions to calibrate the field investigation.

Objective B: Field investigations. In the Lake Chilwa catchment in Malawi traditional and eDNA approaches will be compared when assessing trematode species abundance within gastropod hosts. Infection risk will be modelled from local environmental variables, including pool dimensions, livestock and human density, vegetation and water chemistry/physical parameters.

Objective C: Metabarcoding. Full eukaryotic assemblages will be characterised from discovery-orientated eDNA metabarcode profiles. These data will be compared to data collected in-situ during field sampling. The project will aim to develop both data-driven and systems-based models describing how the abiotic and biotic environment influence trematode occurrence and abundance.

The project will combine state-of-the-art eDNA capture and metagenomic methods with experimental laboratory work in Bristol, and fieldwork on freshwaters in Africa. The PhD will provide the opportunity to develop advanced molecular and bioinformatics skills, alongside skills in the modelling of ecological networks and infection risk scenarios.

Alternative second supervisors:

Dr Joanne Lello (Cardiff University)

Prof Mark Eisler (University of Bristol)

Funding Notes

Part of the GW4+ competition. For further details on how to apply see View Website

Supervisors: Dr Genner, Dr Morgan and Dr Bridle