Location: University of Exeter, Streatham Campus, Exeter EX4 4QJ
This project is one of a number that are in competition for funding from the NERC Great Western Four+ Doctoral Training Partnership (GW4+ DTP). The GW4+ DTP consists of the Great Western Four alliance of the University of Bath, University of Bristol, Cardiff University and the University of Exeter plus five Research Organisation partners: British Antarctic Survey, British Geological Survey, Centre for Ecology and Hydrology, the Natural History Museum and Plymouth Marine Laboratory. The partnership aims to provide a broad training in earth and environmental sciences, designed to train tomorrow’s leaders in earth and environmental science. For further details about the programme please see http://nercgw4plus.ac.uk/
Marine copepods are the most numerous animals on the planet and are part of zooplankton living at the surface throughout the world’s oceans. They are thought to contribute more to marine secondary productivity than all other groups of organisms combined. They exert top-down control of microbial populations (bacteria and eukaryotes), are an essential food source for larval and some adult fish, and are a dominant factor in the role of oceanic surface waters as the world’s largest carbon sink. It is increasingly recognized that parasitism, particularly in the plankton, is a major structuring force in marine ecology, a realization that has highlighted how understudied are the prevalence and impact of parasitic organisms in marine planktonic systems. Despite the enormous biomass of copepods and their ecological importance in marine ecosystems, very little is known about their own pathogens, which are likely to have a very significant, but unknown impact of their role as key ecological players. This project will use plankton samples collected at regular intervals from marine observatories to investigate copepod parasites and, using genetic methods, what effects they have on diversity and abundance of copepods populations, and how these effects vary over seasonal cycles. These new data will be related to long term copepod historic records from the Continuous Plankton Recorder (CPR) to better understand links between copepod-parasite dynamics in response to increasing sea surface temperatures brought about by climate change.
Project Aims and Methods
The project will include some or all of the following elements:
1. Collecting zooplankton samples from a fixed marine observatory and from research ship cruises, and process them for a range of analyses: genetic identification of host and parasites using metagenomics; microscopic copepod identification and abundance and histopathology/transmission electron microscopy to characterise the cellular and physiological effects of parasites on their copepod hosts.
2. Determining the relationship between the changes in copepod diversity and abundance across an annual cycle, and that of their parasites (as determined by molecular biology and microscopy).
3. Use of culturing experiments to measure the effects of raised temperature, pH and dissolved CO2 on ellobiopsid parasites (also recorded on CPR samples) of Calanus copepods prevalence and virulence in a model copepod system.
4. Performing hindcast analysis to link physiological and diversity data to physical and long-term CPR copepod records to model the effect of different climate change scenarios on copepod populations around the UK coast, incorporating data generated during the PhD.
This is an interdisciplinary project, developing and integrating skills in cutting edge molecular biology, bioinformatics, modelling, ecology, and morphological assays, including histology. There is significant scope for the student to be involved in choosing the specific research direction within these areas, with flexibility regarding the balance between the four objectives, although the integrative aspect of the project will be retained. Additionally, the work will result in other outcomes, such as insight into the ‘dark matter’ of diversity – microbes, particularly those associated with larger organisms – and in gaining much insight into host-symbiont relationships, including microbiomes, and the development of the pathobiome model of microbe-mediated disease.
Training will be provided in all necessary aspects of the project: copepod biology, ecology, and evolution (NHM), sampling techniques and sample fixing/processing (Cefas, MBA, NHM), identification and imaging of copepods, molecular biology (nucleic acid extraction, PCR, sequencing; Exeter, NHM), microscopy (identification and counts from fixed material, histology, and transmission electron microscopy; Cefas), and analytical techniques (sequence-based bioinformatics, phylogenetics, and environmental modelling; NHM, Exeter, MBA). The student will also have the opportunity to join Cefas and MBA sampling cruises to collect their own samples and marine observatories managed by MBA.
References / Background reading list
Cleary AC, Durbin EG (2016) Unexpected prevalence of parasite 18S rDNA sequences in winter among Antarctic marine protists, Journal of Plankton Research 38: 401–417.
De Vargas, C., Audic, S., Henry, N., Decelle, J., Mahé, F., Logares, R., Lara, E., Berney, C. et al. (2015) Eukaryotic plankton diversity in the sunlit ocean. Science, 348, 1261605.
Skovgaard A (2014) Dirty tricks in the plankton: diversity and role of marine parasitic protists. Acta Protozoologica 53: 51-62.
Ward GM, Neuhauser S, Groben R, Ciaghi S, Berney C, Romac S, Bass D (2018) Environmental sequencing fills the gap between parasitic haplosporidians and free-living giant amoebae. J Euk Microbiol, Jan 16. doi: 10.1111/jeu.12501.