University of Exeter funding: NERC FRESH Biosciences PhD

Quantifying the role of microbial community dynamics in triggering the production of nuisance chemicals in freshwater ecosystems. PhD in Biosciences (NERC FRESH) Ref: 3782

About the award


Lead Supervisor Name

Dr Chris Lowe, Department of Biosciences, College of Life and Environmental Sciences, University of Exeter

Additional supervisors

Dr Rupert Perkins, School of Earth and Ocean Sciences, Cardiff University

Prof Angus Buckling, Centre for Ecology and Conservation, University of Exeter

Chris Rockey, South West Water

Nicolas Tromas, University of Montreal

The NERC Centre for Doctoral Training in Freshwater Biosciences and Sustainability (GW4 FRESH CDT) provides a world-class doctoral research and training environment, for the next generation of interdisciplinary freshwater scientists equipped to tackle future global water challenges. GW4 FRESH harnesses freshwater scientists from four of the UK’s most research-intensive universities (Bath, Bristol, Cardiff and Exeter) plus world-class research organisations the Centre for Ecology and Hydrology (CEH) and British Geological Survey (BGS). 

For an overview of the GW4 FRESH CDT please see website

Note, the research projects listed are in competition with other studentship projects available across the GW4 FRESH CDT Partnership. Up to 14 studentships will be awarded to the best applicants.

Full Project Description

Blooms of cyanobacteria are a serious global threat to freshwater habitats and to water security. Bloom incidence is on the rise globally as a result of environmental warming and in response to nutrient loading from agricultural, urban, and industrial sources. Cyanobacteria can impair freshwater habitats and drinking water quality, as a direct result of forming high biomass blooms, and by producing secondary metabolites, such as toxins and persistent taste and odour compounds. Critically, while studies often show correlations between cyanobacteria abundance and environmental factors (e.g. nutrient concentrations and ratios, temperature, rainfall, and sunlight), the association between cellular abundance and concentrations of nuisance metabolites is often weak. Consequently, conservation and management practices are currently constrained by a limited understanding of mechanisms that drive or constrain the presence of nuisance cyanobacteria and metabolites.

Recent studies show that interactions within freshwater microbial communities can strongly influence the abundance of nuisance species and nuisance metabolite production. For example, microbial community composition and dynamics can provide better predictions of bloom outbreaks than environmental data and interactions between strains of the same cyanobacterial species can modify toxin production and species persistence. Consequently, there is growing evidence that understanding inter- and intra-specific interactions within microbial communities is likely to be key to management of nuisance cyanobacteria in freshwater habitats. Here we aim to extend these approaches by combining field monitoring, and in-vitro experiments using simplified microbial communities, to understand the relative importance of inter- and intra-specific interactions within microbial communities for determining cyanobacterial abundance and nuisance metabolite production.

The proposed project will focus on water supply reservoirs within Cornwall with a history of cyanobacterial blooms and will build on an existing study conducted by the supervisory team demonstrating a link between Microcystis sp. diversity and microcystin toxin production. In conjunction with staff at South West Water the student will monitor target reservoirs over one year and characterise standard environmental parameters (e.g. nutrient concentrations, temperature, turbidity), microbial community composition, and common nuisance compounds (i.e. Microcystin – one of the most problematic cyanotoxins, Geosmin and 2-MIB – the major causative chemicals for taste and odour problems in drinking water). The student will receive expert training in each component of the field study - SWW water will provide training in water chemistry analysis, training in metabolite profiling will be provided by Tromas (Montreal) and Perkins (Cardiff), training in microbial community profiling using 16S amplicon sequencing (conduced at the Exeter sequencing service) will be provided by Lowe (Exeter) and Tromas, and training in multivariate data analysis will be provided by Lowe, Buckling (Exeter), and Tromas. The fieldwork will be complemented by experimental studies aimed at isolating the effects of e.g. intraspecific diversity in targeted nuisance species on growth dynamics and secondary metabolite production and on the interactions between concentrations of key nutrients and intraspecific diversity. The experimental studies will be conducted at the University of Exeter, Penryn campus where we have extensive facilities for the isolation, growth, and characterisation of environmental microbial isolates. This component of the project will be guided by Lowe and Buckling who have extensive experience in experimental microbial ecology. The student will also benefit from expertise in the broader research community at Penryn which includes other world leading experts in aquatic microbial ecology (e.g. Yvon-Durocher, Gaze, Vos).

Real Life challenges this project will address

Nuisance chemicals produced by cyanobacteria represent a global challenge to freshwater ecosystems, compromising ecological function and subsequently impacting ecosystem services such as drinking water production. Consequently, strategies to limit or mitigate the abundance of nuisance cyanobacteria or prevent the production of harmful compounds are key for the conservation of freshwater habitats and for water security.

What you should know about this project

Globally, freshwater cyanobacteria threaten freshwater ecosystems, water security, and human health via the production of toxins and other nuisance compounds. This project will assess microbial interactions as triggers for nuisance compound production with the ultimate aim of predicting and mitigating the impact of cyanobacterial blooms on freshwater systems. The project will be supervised by experts in cyanobacteria and algal physiology, microbial community dynamics, and water quality management.

What expertise you will develop

The student will develop a range of skills in aquatic microbial ecology including field sampling and survey design, microbial community profiling using high throughput sequencing, chemical analysis via mass spectrometry, and lab experimental approaches to characterising microbial physiology and species interactions. The student will also gain insight into drinking water treatment processes and the engineering challenges posed by nuisance cyanobacteria.

Why this project is novel

Whilst research shows a strong association between environmental factors and the abundance of nuisance species, the associations between the environment, cellular abundance, and nuisance metabolite production are poorly understood. While there are clearly direct links between e.g. environmental factors and nuisance species abundance, there is also a potentially critical role for interactions within microbial communities in driving or constraining the production of nuisance chemicals. Here we will examine the role of inter- and intra-specific microbial interactions as determinants of nuisance metabolite production in freshwater habitats.

Project specific enquiries should be directed to the lead supervisor, Dr Chris Lowe

Entry requirements

Applicants must demonstrate an outstanding academic record: at least a 2:1 undergraduate degree or equivalent, or relevant masters degree.

In addition to your academic record, selection will be based on the following criteria:

  • Why you are keen to pursue a freshwater bioscience PhD
  • What experience you have of freshwater research and interdisciplinary work
  • Whether you have the necessary personal and academic skills to complete a PhD project
  • Whether this scheme is suited to you and likely to best contribute to your career.

English requirements

If English is not your first language you will need to have achieved at least 6.5 in IELTS (and no less than 6.5 in any section) by the start of the programme.

How to apply

You will need to complete an application to the GW4 FRESH CDT for an “offer of funding”.

Please complete the application form at also sending a copy of your CV and a covering letter to the CDT by 9:00 on 16th December 2019.

After the closing deadline all applications and CVs will be forwarded to the lead Supervisor of the project(s) you have selected. They will interview you at a mutually convenient date in January 2020 (tbc) and submit their preferred candidate to FRESH CDT.

Shortlisted candidates will be invited to a panel interview in Cardiff in the week commencing 17th February 2020.  Further details will be included in the shortlisting letter.

For further details regarding the application process please see the following web page

You do NOT need to apply to the University of Exeter at this stage - only those applicants who are successful in obtaining an offer of funding from the DTP will be required to submit an application to study at Exeter.

Data Protection

During the application process, the University may need to make certain disclosures of your personal data to third parties to be able to administer your application, carry out interviews and select candidates.  These are not limited to, but may include disclosures to:

  • the selection panel and/or management board or equivalent of the relevant programme, which is likely to include staff from one or more other HEIs;
  • administrative staff at one or more other HEIs participating in the relevant programme.

Such disclosures will always be kept to the minimum amount of personal data required for the specific purpose. Your sensitive personal data (relating to disability and race/ethnicity) will not be disclosed without your explicit consent.


Application deadline:16th December 2019
Value:3.5 year studentship consisting of full UK/EU tuition fees, as well as a Doctoral Stipend matching UK Research Council National Minimum (£15,009 for 2019/20)
Duration of award:per year
Contact: PGR Enquiries