Institution: University of Bristol
Lead Supervisor: Dr Marian Yallop
This project, building on previous NERC and water company funded research, aims to identify the organisms responsible for producing secondary metabolites (Geosmin and 2-Methylisoborneol) which impart tastes and odours to drinking water. Our previous research indicates that actinobacteria, benthic cyanobacteria and planktonic organisms may be producers of these metabolites but proof of production can only be achieved by linking the presence of the secondary metabolite genes to individual species. Identifying the main producing organisms is essential if we are to devise suitable control methods and reduce the impact of these undesirable metabolites. The problem is complex as the source of organisms could be from water bodies or associated catchments.
The student will: 1) gain skills in fieldwork, sampling sites in the local area, and learn how to culture potential isolates in the laboratory (supervised by Dr Marian Yallop); 2) carry out DNA extraction, undertake gene-specific amplification, using taxon-specific PCR primers, and carry out bioinformatics on those samples (with Dr Gary Barker); 3) locate, download, align, and assemble published gene and metagenome sequences and conduct phylogenetic analyses on the resulting alignments (supervised by Dr Tom Williams). The student will benefit from joining well-resourced laboratories and a large team of researchers working in aquatic microbiology. Fieldwork costs for travel and sterile sampling and culturing consumables will be covered by the £500 RTSG. Costs for the laboratory work will be supplemented through existing funds and will utilise the School’s Genomics Facility laboratory space and equipment. We envisage that information gathered through this research will contribute towards a scientific publication, co-authored by the student. The project will be of interest to students with a mathematical background (especially the bioinformatics/phylogenetics components, which will make use of Bayesian statistical methods but will also involve learning a great deal about lake ecology, molecular biology and microbial metabolism.
Indicative timescale for project (subject to change)
Weeks 1-3 Sample collection in local water bodies (within a 50 mile radius of Bristol), microscopy and establishment of cultures for organisms of interest.
Weeks 4-6 DNA extraction from a wide range of terrestrial and aquatic samples (potentially including new culture isolates), followed by PCR using primers specific for geosmin and MIB synthase genes for a range taxa including cyanobacteria and actinobacteria.
Weeks 7-9 Database searching for terpene synthase gene family members from annotated genes in NCBI and by similarity searching from published metagenomes, followed by phylogenetic analysis to reveal the full taxonomic distribution and evolutionary history of these genes.
Week 10 Completion of database records and involvement in any outputs, including planned scientific publication.