Complex relationships: Exploring the role of the diatom microbiome in host-parasite interaction.


Complex relationships: Exploring the role of the diatom microbiome in host-parasite interaction.


Project Description


Professor Michael Cunliffe, Marine Biological Association – Contact me

Dr Miriam Reverter, School of Biological and Marine Sciences, University of Plymouth

Dr Katherine Helliwell, Marine Biological Association

Scientific background

Diatoms are a significant phytoplankton group. They fuel food webs and are major players in the global carbon cycle. Diatoms are particularly important in nutrient rich coastal waters and shelf seas. Despite our dependence on these critical components of the Earth system there is a limited understanding of marine diatom health and disease. A range of protists and some fungal parasites infect diatoms. Bacteria are also associated with diatoms as part of their microbiomes. At present we have a limited understanding of the role of bacterial microbiomes on parasite infection of marine diatoms. Given the importance of marine diatoms, it is critical that we now understand the relationship between marine diatoms, their bacterial microbiomes and parasite infection on their biomass and diversity, and establish the impacts on diatom ecosystem function, particularly their critical role in the marine carbon cycle.

Research methodology

The project will study the interaction of bacterial microbiomes and infecting parasites on marine diatom heath and function. Diatoms will be sampled from the coastal marine waters off Plymouth, targeting infected and uninfected diatoms using laser capture microscopy. Bacterial microbiomes of individual infected and uninfected diatoms will be compared using confocal microscopy and DNA/RNA metabarcode sequencing. Isolated cultures of diatoms, parasites and microbiome bacteria will also be studied in controlled laboratory-based experiments in different combinations to determine the interactions and impacts of the different components, including carbon processing and metabolite profiling.


Training will include fieldwork and sampling, including boat-based plankton sampling; Advanced microscopy, including laser capture and confocal; Metabolomics; Biomolecular techniques (e.g. DNA/RNA processing, PCR and sequencing); Bioinformatics analysis of metabarcode datasets including processing raw sequence data, data analysis, understanding and visualization, data stewardship; Science communication for academic and non-academic audiences, research publication writing.

Person specification

The applicant should have an interest in combining working with microbial communities from the natural environment and microbial cultures in the laboratory. The project will include bringing together a range of approaches and techniques outlined above, combining solo work and also being part of a team. Desired degree subjects include biology, marine biology, microbiology, environmental science and marine science.


  • 1 Laundon, Mock, Wheeler & Cunliffe (2021) Healthy herds in the phytoplankton: the benefit of selective parasitism. ISME J 15 2163–2166.
  • 2 Helliwell, Shibl & Amin (2021) The Diatom Microbiome: New Perspectives for Diatom-Bacteria Symbioses. The Molecular Life of Diatoms pp 679-712.Helliwell, Shibl & Amin (2021) The Diatom Microbiome: New Perspectives for Diatom-Bacteria Symbioses. The Molecular Life of Diatoms pp 679-712.
  • 3 Allen, Bird, Murrell & Cunliffe (2023) Latitudinal variation in the potential activity of Atlantic Ocean bacterioplankton revealed through 16S rRNA and 16S rRNA gene metabarcoding. Frontiers in Marine Science 10: 1241333.
  • 4 Roberts, Allen, Bird & Cunliffe (2020) Chytrid fungi shape bacterial communities on model particulate organic matter. Biology Letters 16 20200368.
  • 5 Klawonn, Van den Wyngaert, Parada, Arandia-Gorostidi, Whitehouse, Grossart & Dekas (2021) Characterizing the "fungal shunt": Parasitic fungi on diatoms affect carbon flow and bacterial communities in aquatic microbial food webs. PNAS 8 118(23) e2102225118.

Key Information

  • This project has been shortlisted for funding by the ARIES NERC DTP and will start on 1st October 2024. The closing date for applications is 23:59 on 10th January 2024.
  • Successful candidates who meet UKRI’s eligibility criteria will be awarded a NERC studentship, which covers fees, stipend (£18,622 p.a. for 2023/24) and research funding. International applicants are eligible for fully-funded ARIES studentships including fees. Please note however that ARIES funding does not cover additional costs associated with relocation to, and living in, the UK. We expect to award between 4 and 6 studentships to international candidates in 2024.
  • ARIES students benefit from bespoke graduate training and ARIES provides £2,500 to every student for access to external training, travel and conferences, on top of all Research Costs associated with the project. Excellent applicants from quantitative disciplines with limited experience in environmental sciences may be considered for an additional 3-month stipend to take advanced-level courses.
  • ARIES is committed to equality, diversity, widening participation and inclusion in all areas of its operation. We encourage enquiries and applications from all sections of the community regardless of gender, ethnicity, disability, age, sexual orientation and transgender status. Academic qualifications are considered alongside non-academic experience, and our recruitment process considers potential with the same weighting as past experience.
  • All ARIES studentships may be undertaken on a part-time or full-time basis, visa requirements notwithstanding.
  • For further information, please contact the supervisor. To apply for this Studentship follow the instructions at the bottom of the page or click the 'apply now' link.
  • ARIES is required by our funders to collect Equality and Diversity Information from all of our applicants. The information you provide will be used solely for monitoring and statistical purposes; it will remain confidential, and will be stored on the UEA sharepoint server. Data will not be shared with those involved in making decisions on the award of Studentships, and will have no influence on the success of your application. It will only be shared outside of this group in an anonymised and aggregated form. You will be ask to complete the form by the University to which you apply.
  • ARIES funding is subject to UKRI terms and conditions. Postgraduate Researchers are expected to live within reasonable distance of their host organisation for the duration of their studentship. See for more information

Applications open

Click this link to apply to University of Plymouth