Functional biology and ecology of aquatic fungi

Primary supervisor: Dr Michael Cunliffe (University of Plymouth, Marine Biological Association)

Secondary supervisor: Dr George Littlejohn (University of Plymouth)

Additional supervisor: Dr Katherine Helliwell (Marine Biological Association)

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 programme 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.

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.

Research background

Model microorganisms that are used in laboratory-based experiments have proven invaluable in progressing our understanding of the roles that microbes have in biogeochemical cycles. 

For example, the Cunliffe Group at the MBA has used model bacteria to determine the underpinning mechanisms used for carbon processing, including the application of ‘omics tools (Cunliffe, 2011, Cunliffe, 2013, Cunliffe, 2016). We have recently shown that an analogous approach is achievable with aquatic fungi (Cunliffe et al., 2017).

Aims and objectives

Using a new model aquatic fungus, the PhD student will conduct a series of revolutionary experiments that will define the biology that underpins the functional roles of fungal saprotrophs in the aquatic carbon cycle.

Aim 1. Establish the molecular basis of saprotrophy in model fungi. The new model fungus will be used in a series of experiments to identify and characterise the molecular machinery (genes and enzymes) controlling POC degradation. 

Initial experiments will determine basic physiological properties, including growth substrate range, POC degradation/DOC production rates and growth kinetics (rate, yields, etc.), which will be used to establish optimal experimental conditions. 

Based on these parameters, cultures will be grown and used to identify key functional enzymes and genes. The biochemical properties of extracellular enzymes, including CAZymes, will be characterised. Intracellular and extracellular proteins will be isolated and sequenced using an LC MS/MS proteomics platform. 

Complementary analysis will also be performed to isolate mRNA from the cultures, which will be sequenced using the transcriptomics platform HiSeq. Bioinformatics analysis of the protein and mRNA sequences will identify the key enzymes (intra-and extracellular), genes and metabolic pathways that drive fungal POC degradation.

Aim 2. Establish saprotroph-POC interaction in model fungi. Using the new model fungus, a series of experiments will be conducted to characterise how saprotrophic fungi physically interact with POC. 

Interaction will be characterised primarily using confocal laser scanning microscopy and combinations of specific diagnostic fluorescent dyes to stain fungal cell walls and fluorescently-labelled lectins (carbohydrate-binding proteins). 

Fungi/POC interactions that will be characterised and quantified include attachment and growth on/within POC, hyphal development, POC penetration and degradation.  


Using an ecologically and biogeochemically validated model system, the PhD student will have characterised the biological properties of saprotrophic aquatic fungi that underpin their roles in the carbon cycle, including identifying the key genes, enzymes and metabolic pathways involved in POC processing, and establishing how fungi physically interact with POC.  

Development and training opportunities

The PhD student will join a large research team funded through the recently awarded European Research Council (ERC) Consolidator Grant - MYCO-CARB Revealing the mechanistic basis of the roles of mycoplankton in the carbon cycle. 

This will provide substantial supplementary resources and collaboration opportunities, including dedicated bioinformatics support.

Contingency and risk mitigation

The model fungus is already established within the Cunliffe group at the MBA. The annotated genome sequence is available and pilot experiments have been conducted to demonstrate that the organism is viable for the proposed research (e.g. protein extraction protocols are successful).


This project has been shortlisted for funding by the ARIES NERC Doctoral Training Partnership. Undertaking a PhD with ARIES will involve attendance at training events.

ARIES is committed to equality & diversity, and inclusion of students of any and all backgrounds. All ARIES Universities have Athena Swan Bronze status as a minimum.  

Applicants from quantitative disciplines who may have limited environmental science experience may be considered for an additional 3-month stipend to take appropriate advanced-level courses.

Usually, only UK and EU nationals who have been resident in the UK for three years are eligible for a stipend. Shortlisted applicants will be interviewed on 26/27 February 2019.

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