Harmful cyanobacteria in UK freshwater ecosystems


A cynobacterial bloom in freshwater

The PhD project will investigate the molecular diversity, toxins and interactions with associated microbial assemblages to build a better understanding of cyanobacteria blooms in freshwater ecosystems.

The studentship is part of the Southampton Partnership for Innovative Training of Future Investigators Researching the Environment (SPITFIRE) funded by NERC and starts 1 October 2018.

Apply for this course

Read the eligibility criteria and application guidance below, then apply via the Spitfire Online Application Service.

Application deadline: 5 January 2018.

Research focus

Cyanobacteria blooms occur in freshwater sources across the world. They are a hazard for drinking water supplies and recreation because they produce diverse toxins ranging from skin irritants to liver- and neurotoxins (1).

Nutrient pollution, elevated temperatures and low flow conditions encourage the proliferation of such harmful blooms. This means that blooms are likely to increase in the future due to climate change and rising demands for water.

We therefore need a better understanding of the toxins produced by cyanobacteria blooms, the molecular diversity of blooms and their impact on the microbial ecology of lakes.

The aims of the project are:

  • to assess cyanobacterial species composition and community structure, and toxin production in freshwater ecosystems in the UK.
  • to perform a comprehensive description of microbial assemblages co-occurring with cyanobacteria and their interactions.
  • evaluate the effect of seasonal environmental variables related to future climatic-driven environmental change on these freshwater cyanobacterial and associated microbial assemblages. 

Supervision and training

The student will receive training in:

  • molecular techniques and bioinformatics for microbial diversity and ecological analyses.
  • identification and quantification of cyanobacteria toxins by liquid chromatography-mass spectrometry.
  • water chemistry analyses.
  • freshwater field work.
  • laboratory microbial culture incubation experiments.

The student will also have opportunities to gain experience in public outreach.

The student will be registered at the University of Southampton and hosted at both the Natural History Museum and the Centre for Ecology and Hydrology, Edinburgh.

The student will also work with existing collaborators in the UK such as Prof. Geoffrey A. Codd and Dr Peter Hunter in relation to toxins (University of Stirling), have opportunities to travel to New Zealand and Australia to work with existing collaborators on this project. 


PhD student will carry out field work as part of the routine lake monitoring programmes at CEH, and cyanobacterial bloom samples will be analysed using environmental DNA, high throughput sequencing, bioinformatics and community structure analysis techniques. Toxins will be identified and quantified, and toxin genes investigated using molecular tools (2). Laboratory-based manipulation culture experiments in combination with DNA and sequence analysis will be performed to evaluate the effect of abiotic variables such as nutrients, temperature and light on the interactions between cyanobacteria and associated freshwater bacterial and microbial assemblages.


Long-term monitoring of cyanobacteria in UK freshwaters has provided some understanding of environmental variables that play a role in the formation of cyanobacteria blooms (2). However many of the assessments are based on poor taxonomic resolution of the community. There is little information on individual species autoecology as their small size and limited morphological features make identification of cyanobacteria difficult.

Comprehensive molecular assessments are needed to sufficiently resolve cyanobacterial taxa composition to improve our understanding of species responses to environmental drivers. It has also become apparent that diverse bacterioplankton (3) and microbial eukaryotes, including fungi and ciliates, are associated with cyanobacteria blooms, but interactions between cyanobacteria and microbial assemblages have not been sufficiently investigated.

These interactions may be important for understanding cyanobacteria population development and toxin production. 


This project is open to applicants who meet the SPITFIRE eligibility and other exceptional applicants.

SPITFIRE seeks excellent prospective research students regardless of their particular scientific background. We aim to recruit the best students rather than to fill particular projects. We put a huge amount of effort into the recruitment process to meet this objective. 

Minimum Academic Eligibility Criteria: 

  • BSc/MSci 2:1
  • and/or Masters (MSc or MRes) at Merit/Distinction level (>60%).
  • and/or evidence of significant relevant professional experience equivalent to Masters level.

How to apply

Apply using the Spitfire Online Application Service, please include:

  • A short statement of your research interests and rationale for your choice of project(s) - in the Personal Statement section of the application form
  • Curriculum vitae - giving details of your academic record and stating your research interests.
  • Names of two current academic referees - with an institutional email addresses in the Reference section of the application form. On submission of your online application your referees will be automatically emailed requesting they send a reference to us directly by email.
  • Academic transcripts and IELTS/TOEFL certificate if applicable.

As far as possible please upload all documents in pdf format.

Interview dates

For successful candidates are:

  • Thursday 22 February 2018
  •  Friday 23 February 2018
  • Thursday 1 March 2018
  • Friday 2 March 2018

Please note they are all day events and will be allocated based on interview panel availability.

General enquiries should be directed to the SPITFIRE Team on spitfire@southampton.ac.uk

The deadline for applications is 5 January 2018.

Any questions?

You are encouraged to contact potential supervisors by email to discuss project-specific aspects of the proposed research at an early stage.

If you have any questions about the project please contact

Main supervisor: Dr Anne D. Jungblut


1) Carvalho et al (2013) Sustaining recreational quality of European lakes: minimising the health risks from algal blooms through phosphorus control. Journal of Applied Ecology 50: 315-323 doi: 10.1111/1365-2664.12059

2) Jungblut AD, Neilan BA (2006) Molecular identification and evolution of the cyclic peptide hepatotoxins, microcystin and nodularin, synthetase genes in three orders of cyanobacteria. Archives of Microbiology 185: 107-114. doi: 10.1007/s00203-005-0073-5

3 ) Woodhouse JN, Kinsela AS, Nicholas C, Bowling LC, Honeyman GL, Holliday JK, Neilan BA (2016) Microbial communities reflect temporal changes in cyanobacterial composition in a shallow ephemeral freshwater lake. The ISME Journal 10: 1337-1351. doi: 10.1038/ismej.2015.218

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Southampton Partnership for Innovative Training of Future Investigators Researching the Environment

This a joint PhD training partnership between the Natural History Museum and SPITFIRE a NERC Doctoral Training Partnership (DTP) creating an innovative multi-disciplinary experience for the effective training of future leaders in environmental science, engineering, technology development, business, and policy.

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