Functional biology and ecology of aquatic fungi


Functional biology and ecology of aquatic fungi


Project Description


Dr Michael Cunliffe (Marine Biological Association of the UK)

Dr George Littlejohn (University of Plymouth)

Dr Katherine Helliwell (Marine Biological Association of the UK)

Scientific background

Fungi are well established as important components of aquatic ecosystems, however the functional roles that they fulfil remain poorly understood (Grossart & Rojas-Jimenez 2016). Recently, we have shown that fungi in marine waters regularly form blooms linked to specific environmental drivers, including particulate organic carbon (POC) availability (Taylor et al 2016). In a separate study using 13C-labelled diatom produced POC, we have identified specific aquatic fungi involved in POC cycling (Cunliffe et al 2017). These studies show that some aquatic fungi are saprotrophic, degrading POC via extracellular enzymes and feeding on dissolved organic degradation products osmotrophically.

Understanding the fundamental mechanisms that underpin biogeochemical processes in model microorganisms, including using ‘omics tools, is powerful and can reveal novel insights into microbial functioning in ecosystems. At present there are no model aquatic fungi available to understand fungal saprotrophy and POC cycling. This represents a knowledge gap that should be addressed in order to fully understand the functional roles that fungi fulfil in aquatic ecosystems.

Research methodology

The overarching aim of this PhD project is to utilise a new model fungus to understand the fundamental mechanisms that underpin aquatic fungal saprotrophy and particulate organic carbon (POC) cycling. The model has recently been developed in the Cunliffe Group at the Marine Biological Association (MBA) (paper in preparation). Preliminary analysis has shown that the fungus has a diverse range of novel POC-processing enzymes that will be assessed for their ecosystem functional roles and potential environmental biotechnological applications. Core resources developed include a genome sequence and established culturing techniques. These advances provide the platform for further experimentation to advance understanding of the ecology and biology of these important aquatic microorganisms. Experiments will determine how the fungus physically interacts with POC, including live cell imaging via confocal microscopy. The molecular machinery controlling POC degradation will also be assessed, including using ‘omics and CRISPR-Cas9 gene knock-out approaches.


The ARIES DTP provides comprehensive personal and professional development training alongside extensive opportunities for students to expand their multi-disciplinary outlook through interactions with a wide network of academic, research and industrial/policy partners.

The student will be registered at the University of Plymouth and based at the Marine Biological Association, also in Plymouth. Specific training will include: (i) Environmental microbiology, including fungi cultivation and physiological experimentation, ‘omics and associated bioinformatics; (ii) Microbial cell biology, including confocal microscopy and CRISPR-Cas9; (iii) Microbial biogeochemistry and ecophysiology.

Person specification

Students with a background in any of the following areas; biological sciences, molecular and/or cellular biology, microbiology, marine biology or aquatic biology should consider applying.

The successful candidate will be registered for a PhD in the University of Plymouth’s School of Biological and Marine Sciences, part of the Marine Institute.


  • Grossart, H.P., and Rojas-Jimenez, K. (2016) Aquatic fungi: targeting the forgotten in microbial ecology. Current Opinion in Microbiology 31: 140-145.
  • Taylor, J.D., and Cunliffe, M. (2016) Multi-year assessment of coastal planktonic fungi reveals environmental drivers of diversity and abundance. The ISME Journal 10: 2118-2128.
  • Cunliffe, M., Hollingsworth, A., Bain, C., and Taylor, J.D. (2017) Algal polysaccharide utilisation by saprotrophic planktonic marine fungi. Fungal Ecology 30: 135-138.
  • Helliwell K. E., Pandhal J., Cooper M, Longworth J., Kudahl U., Russo D., Tomsett E., Bunbury F., Salmon D., Smirnoff N., Wright P., and Smith A. G. (2018). Quantitative proteomics of a B12‐dependent alga grown in coculture with bacteria reveals metabolic tradeoffs required for mutualism. New Phytologist 217: 599-612.
  • Fones, H.N. & Littlejohn, G.R. (2018) From Sample to Data: Preparing, obtaining, and analyzing images of plant-pathogen interactions using confocal microscopy. Methods in Molecular Biology Methods 1734: 257-262

Open for applications

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