Monitoring marine plankton biodiversity and community dynamics using third-generation DNA metabarcoding

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Marine plankton respond rapidly to environmental change associated with climate change and also emissions of waste and pollutants, which may cause significant losses in biodiversity and impact ecosystem resilience. Key to understanding the dynamics of ecologically important plankton species is the ability to sample, preserve and identify them. However, the complexity of zooplankton and phytoplankton assemblages, with numerous cryptic and closely related species and the lack of diagnostic characteristics for small plankton constitute important impediments to our understanding of patterns of plankton biodiversity and ecosystem function. Recent advances in high throughput sequencing (HTS) technologies have demonstrated exciting potential to capture the diversity of marine plankton communities (Bucklin et al 2016; Le Bescot et al 2015) using DNA metabarcoding. In contrast to more conventional approaches, metabarcoding has the potential to uncover the hidden diversity in marine planktonic communities and help distinguish between cryptic species. Current approaches to metabarcoding are based on 'short-read' sequencing technology which restricts the length of the barcode and consequently limits the taxonomic resolution to which species can be identified. The recent development of third-generation single molecule sequencing platforms such as the Oxford Nanopore (ON) MinION offers an exciting opportunity to provide a cheaper and more portable alternative to more conventional HTS platforms. Importantly, the ON MinION is a 'long-read' technology and is therefore able to sequence longer barcodes potentially resulting in species identification to a high taxonomic resolution.This project provides an exciting and unique opportunity to unlock the diversity of the plankton community by applying third-generation DNA metabarcoding to samples collected as part of a long-term monitoring programme (Scottish Coastal Observatories - SCObs) run by Marine Scotland Science. Monthly samples collected by SCObs since 1997 represent a unique bank of material to study and understand climate change driven changes in marine plankton communities which can have a negative impact on the stability of coastal ecosystems in the UK. Particular focus will be on groups of organisms that have a negative impact on the aquaculture industry, eutrophication assessments, or species seen as vulnerable to impacts of the changing marine environment such as ocean acidification. This project will provide you with training in state-of-the-art sequencing methods, bioinformatics and statistics, as well as high level taxonomic identification of plankton species using plankton culture and advanced electron microscopy techniques. You will be embedded within a vibrant and dynamic research community and have the opportunity to work alongside governmental research scientists at Marine Scotland Science. You will also have the opportunity to present and integrate your results into a number of national and international status assessments related to plankton, the marine environment, climate change and the aquaculture industry such as the UK Pelagic Habitat Assessment WG for the MSFD, the International Council for the Exploration of the Sea WGs on Phytoplankton and Microbial Ecology, and Zooplankton Ecology.