Microbiology and

Molecular Ecology

Research Lead – Professor Michael Cunliffe

Microorganisms are the most abundant, diverse and important organisms in the marine environment. Marine microbial life maintains a healthy and functioning earth system, including being responsible for half of global primary production, underpinning food webs and cleaning up pollution.  

We are a marine microbial biology, ecology and evolution research group. We study microbes in their natural environment, including the open ocean and polar regions. We also study microbial cultures in the laboratory. Both approaches utilise a large research toolbox.  

Our skills and tools developed from studying marine microbial diversity are also being applied more broadly, such as with environmental DNA (eDNA) based approaches, to study all marine biodiversity from microbes to mammals.  

Our Research Impacts


Biomolecular observation of marine biodiversity

Biomolecules such as DNA and RNA are present in all life from viruses to vertebrates and through sequencing can be used to assess biodiversity. We have utilised environmental DNA and RNA sequencing to observe marine biodiversity across a range of ecosystems including the deep open ocean, polar regions, coastal waters and sediments. Our sequencing approach can capture all marine biodiversity, encompassing microbes, meiofauna and macrofauna. Recent examples of our work include showing latitudinal variation in the activity of Atlantic Ocean bacterioplankton (Allen et al 2023 Front. Mar. Sci.) and long-term patterns in coastal marine fungal diversity (Chrismas et al 2023 Proc. R. Soc. B.). As well as leading in this area, we are part of multiple international research networks developing and applying biomolecular marine observation. These science networks have set priorities for understanding and protecting the global ocean microbiome (Tara Ocean Foundation et al 2022 Nature Microbiology), developed multiomics approaches to be applied in the central Arctic Ocean to benchmark biodiversity change (Mock et al 2022 PloS Biology) and formed strategic biodiversity networks to implement omics-based approaches in ocean observation including applying FAIR data standards (Santi et al 2023 Front. Mar. Sci.). 

Living together – unravelling the mechanisms and impacts of microbial interactions

A substantial area of research activity has been on marine microbiomes and associated interactions, studying systems both in natura and in the laboratory, both between microbes and microbes with other organisms. We have characterized the interacting microbiomes of a range of marine organisms living in marine ecosystems including seaweeds (Bonthond et al 2022), lichens (Christmas et al 2021 JMBA) and polychaete worms (Dale et al 2019 FEMS Micro. Eco.). In the laboratory, we isolated a novel thraustochytrid parasite and associated host diatom and showed that the parasite targets ageing diatom cells in a similar way to selective animal predation on weaker prey individuals. Targeting of unhealthy cells improves the overall health of the diatom population, providing support for ‘healthy herd’ dynamics in a microbe-microbe interaction, a phenomenon typically associated with animal predators and their prey (Laundon et al 2021 ISME Journal).

Key Publications

17-year time-series of fungal environmental DNA from a coastal marine ecosystem reveals long-term seasonal-scale & inter-annual diversity patterns – Proceedings of the Royal Society B 

A cellular and molecular atlas reveals the basis of chytrid development – eLife  

E

Healthy herds in the phytoplankton: the benefit of selective parasitism – ISME Journal  

Latest Projects

Functional biology and ecology of planktonic marine fungi

Revealing the mechanistic basis of the roles of mycoplankton in the marine carbon cycle (MYCO-CARB). Funded by the European Research Council.

The Darwin Tree of Life Project

The Darwin Tree of Life project funded by the Wellcome Trust

Marine Coastal Biodiversity Long-term Observations (MARCO-BOLO)

MARCO-BOLO is co-funded by the European Union (Horizon GA#101082021) Horizon Europe/UKRI.

Marine biodiversity assessment and prediction across spatial, temporal and human scales (BIOcean5D)

BIOcean5D is co-funded by the European Union (Horizon GA#101059915), Horizon Europe/UKRI and SERI.


Our Team

Dr Michael Cunliffe

Professor Michael Cunliffe, Mem.MBA

Director of Science, Senior Research Fellow

Professor Michael Cunliffe, Mem.MBA

Director of Science, Senior Research Fellow

Dr Michael Cunliffe

micnli@mba.ac.uk

I received a degree in environmental biology from the University of Liverpool, and a MSc and PhD in Microbiology from the University of Manchester. After a postdoc at the University of Warwick, I joined the Marine Biological Association (MBA) in 2010 as a MBA Research Fellow (Group Leader). In 2014, I started a joint appointment between the MBA and the University of Plymouth, where I am currently a MBA Senior Research Fellow and Professor of Marine Microbiology in the School of Biological and Marine Sciences. I create knowledge through research and communicate knowledge through teaching, outreach and knowledge exchange activities. At the MBA I lead a diverse research group who study a range of topics in microbial biology, ecology, and evolution. Our research group works both in the lab and out in the marine environment, locally around Plymouth and in distant locations, including polar regions and the open ocean.

Research Group: Microbiology and Molecular Ecology

Dr Nathan Chrismas

Dr Nathan Chrismas

Postdoctoral Research Assistant

Dr Nathan Chrismas

Postdoctoral Research Assistant

Dr Nathan Chrismas

natchr@mba.ac.uk

My main research interests focus on the use of -omic approaches to understand the molecular mechanisms behind environmental adaptation in cyanobacteria, fungi, and lichens. My PhD work centred around understanding the evolution of polar and alpine cyanobacteria, including genome level adaptations of cyanobacteria to extreme cold environments. During my postdoctoral work at the MBA I’ve used bioinformatics to explore spatial and temporal dynamics of marine fungal communities as part of the ERC project MYCO-CARB and carried out transcriptomic analysis of the aquatic chytrid fungus Rhizoclosmatium globosum. I’m currently working on transcriptomic approaches to investigate the molecular response of the marine lichen Lichina pygmaea to tidal cycles and am developing my own research exploring molecular aspects of the lichen symbiosis. I have a strong interest in science outreach, with a particular passion for engaging with the rock climbing and hillwalking community about lichen diversity and conservation.

Emily Cooper

Emily Cooper, BSc, MRes, AMRSC

PhD Student

Emily Cooper, BSc, MRes, AMRSC

PhD Student

Emily Cooper

emicoo@mba.ac.uk

Poppy Diver

Poppy Diver, MEarthSci

PhD Student

Poppy Diver, MEarthSci

PhD Student

Poppy Diver

popdiv@mba.ac.uk

I am a PhD researcher on a NERC-funded INSPIRE Doctoral Training Partnership between the MBA and the University of Southampton. I am interested in the ecology of marine fungi and their role in biogeochemical processes. My primary research aims are to characterise the key functional traits of marine fungi and to develop a mechanistic basis for their incorporation into plankton community models.

Much of my work utilises a selection of model marine yeast strains from the MBA Fungal Culture Collection. By monitoring yeast cell morphology and physiology across a range of nutrient conditions in the lab, I aim to better understand their ecological function in the dynamic marine environment. Using observations of cell size and growth rate, I draw functional comparisons with other plankton groups.

Before my PhD, I researched the influence of trace metal availability on marine ammonia oxidation as part of the OceanBug group at the University of Oxford. I joined the team as a 4th year MEarthSci student and continued as a research assistant on the APPELS (A Probe of the Periodic Elements for Life in the Sea) project.

Cell and Molecular Support Technician Rob Moore

Rob Moore BSc MRes

Cell and Molecular Support Technician

Rob Moore BSc MRes

Cell and Molecular Support Technician

As the cell and molecular support technician for the MBA, I am responsible for maintaining the MBA’s algal culture and providing general laboratory maintenance for the research teams so they can conduct their investigations. I’m also helping the MBA to move into their recently renovated and purpose-built laboratory by setting up equipment and laboratory spaces for the future. I have a Bachelor of Science and a Master of Research from the University of Plymouth in marine biology and in my undergraduate degree, my project examined anthropogenic noise pollution on jellyfish polyp settlement rates. During my placement year, I gained practical skills in a marine science research facility assisting in a range of projects. In my post-graduate degree, I investigated tempo-spatial patterns of growth rate in juvenile plaice around the South-west of England using a range of molecular metrics. I am interested in using molecular techniques to answer questions in marine biology such as examining how marine life is responding to climate change.

PhD student Beth Tindal-Jones smiling sat next to a microscope

Beth Tindall-Jones BSc, MRes

PhD Student

Beth Tindall-Jones BSc, MRes

PhD Student

PhD student Beth Tindal-Jones smiling sat next to a microscope

betjon@mba.ac.uk

I am PhD student working in the Cunliffe group at the MBA and Exeter University. My project is looking into the fundamental biology behind the interactions of marine fungi and macroalgae, establishing and understanding the life cycle of various marine fungi when associated with different types of macroalgae. From this I will also be assessing the biotechnological potential of these interactions. I have always had a passion for marine life from a very young age. This passion has lead me to study Marine Biology at both undergraduate and master’s level at Newcastle and Plymouth University respectively. I am delighted to be continuing with the joy of studying marine life in this next step of my education.

Rebekkah Uhl standing in lab coat with research equipment

Rebekka Uhl BSc MRes

Research Assistant

Rebekka Uhl BSc MRes

Research Assistant

Rebekkah Uhl standing in lab coat with research equipment

rebuhl@mba.ac.uk

I am a research technician for the Darwin Tree of Life project and am responsible for collecting, identifying and sometimes culturing marine specimen, as well as carrying out DNA barcoding for molecular identification. I completed my BSc in Biology at the University of St Andrews, where I worked on my dissertation with Prof David Paterson, studying benthic diatom locomotion and how their speed and extracellular polymeric substance composition is influenced by external stressors. Subsequently I completed an MRes where I was working on identifying the function of a carbohydrate processing enzyme, HexD. I moved to Plymouth to satiate my interests in marine biology, working for the husbandry team at the National Marine Aquarium before the MBA. I have a big interest in marine life, in particular the smaller easily missed things that are often spectacular. In my free time, I am also a keen climber and sea swimmer!

  

Dr Joanna Warwick-Dugdale

Post Doctoral Research Assistant

Dr Joanna Warwick-Dugdale

Post Doctoral Research Assistant

joadug@mba.ac.uk

I am fascinated by how communities of the smallest marine organisms (i.e. prokaryotes; algae; viruses) function to drive systems at the largest scales (e.g. global nutrient cycling). Previously I have focused on the characterization of Open Ocean and Coastal viral communities, key players of global biogeochemistry who remain largely underexplored. To accomplish this, I developed a hybrid, long- and short-read viral metagenomic method during my PhD, a NERC DTP with Dr Ben Temperton at the University of Exeter (UoE) and Plymouth Marine Laboratory (PML). During my first post-doctoral position at the UoE I further developed this method to include viral communities that are ‘active’ in host cells and applied it to the investigation of a hypoxic marine environment, work that is highly relevant to the reduction in oxygen levels of ever-growing areas of the Global Ocean. Currently I am conducting Horizon Europe funded research with Professor Michael Cunliffe, investigating temporal and spatial patterns in marine biodiversity of the Western Channel Observatory and other European time series. I will also establish long-read (MinION) sequencing at the MBA and investigate how it could be leveraged for monitoring marine ecosystem change.