PLEASE NOTE: Application deadline date 08 Jan 2024. Applications are no longer being accepted for this project
Project Overview
The project will develop, optimize, and validate a rapid eDNA-based approach for marine and coastal biodiversity assessment, covering the full range of biodiversity from microbes to mammals. The project will be based around the Plymouth Sound National Marine Park and the Western English Channel, encompassing a range of habitats.
Project Description
Biodiversity assessment is now possible with environmental DNA (eDNA) metabarcoding, however further innovation in eDNA-based monitoring is needed to support the broader application of the approach. The coastal marine environment contains vast biodiversity that underpin ecosystem functions and services, representing invaluable natural capital. The application of rapid eDNA-based approaches in coastal marine biodiversity assessment could support informed decision making, prediction and environmental management. The project will develop, optimize, and validate a new rapid eDNA-based approach for marine and coastal biodiversity assessment. The full range of marine biodiversity will be covered, from viruses to vertebrates, as well as targeting of key species of interest. This innovative project will include using autonomous eDNA sampling and rapid metabarcoding. As well as new sampling, the project will also have available existing long-term eDNA datasets for method validation. The project will be based around the Plymouth Sound National Marine Park, the UK’s first national marine park, and the Western Channel Observatory (WCO) biodiversity reference site in the Western English Channel, encompassing a range of habitats, including seagrass meadows, open water, kelp forests and artificial (e.g. marinas). The PhD student will work in the recently established Marine Microbiome Centre of Excellence (MMCE) with facilities including dedicated eDNA laboratory space. There will also be opportunity to contribute to the international Ocean Biomolecular Observing Network (OBON), an endorsed programme of the UN Decade of Ocean Science for Sustainable Development that will understand ocean life by analysing biomolecules, and the associated WCO Biomolecular Observing Network (WCO BON).
The INSPIRE DTP programme provides comprehensive personal and professional development training alongside extensive opportunities for students to expand their multidisciplinary outlook through interactions with a wide network of academic, research and industrial/policy partners. The student will be registered at the University of Southampton and hosted at Marine Biological Association (MBA) in Plymouth.
Specific training will include: marine fieldwork and sampling including working on a research vessel and the use of autonomous eDNA sampling via the Robotic Cartridge Sampling Instrument (RoCSI); biomolecular laboratory techniques including eDNA processing, PCR and sequencing; bioinformatics analysis of metabarcode datasets including processing raw sequence data using the DADA2 pipeline, data analysis using the vegan package in R, understanding and visualization; eDNA data stewardship including depositing following FAIR principles at the MBA-based marine biodiversity data archive (DASSH); Science communication for academic (e.g. science conference presentations) and non-academic audiences (e.g. ‘popular science’ articles), research publication writing.
Santi et al (2023) European marine omics biodiversity observation network: a strategic outline for the implementation of omics approaches in ocean observation. Frontiers in Marine Science 10: 1118120.
Tara Ocean Foundation, Tara Oceans, European Molecular Biology Laboratory (EMBL) et al (2022) Priorities for ocean microbiome research. Nature Microbiology 7, 937–947.
Chrismas et al (2023) A 17-year time-series of fungal environmental DNA from a coastal marine ecosystem reveals long-term seasonal-scale and inter-annual diversity patterns. Proceedings of the Royal Society B 290: 20222129.
