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

海洋浮游生物对与气候变化有关的环境变化以及废物和污染物的排放迅速作出反应，这可能造成生物多样性的重大损失，并影响生态系统的复原力。了解具有重要生态意义的浮游生物物种动态的关键是对其进行采样、保存和识别的能力。然而，浮游动物和浮游植物组合的复杂性，众多的神秘和密切相关的物种和缺乏诊断特征的小型浮游生物构成了重要的障碍，我们了解浮游生物多样性和生态系统功能的模式。高通量测序（HTS）技术的最新进展已经证明了使用DNA元条形码捕获海洋浮游生物群落多样性的令人兴奋的潜力（Bucklin et al 2016; Le Bescot et al 2015）。与传统的方法相比，元条形码有可能揭示海洋浮游生物群落中隐藏的多样性，并有助于区分神秘物种。目前的元条形码编码方法是基于“短读”测序技术，其限制了条形码的长度，从而限制了可以识别物种的分类分辨率。第三代单分子测序平台（如Oxford Nanopore（ON）MinION）的最新发展提供了一个令人兴奋的机会，可以为更传统的HTS平台提供更便宜，更便携的替代品。重要的是，ON MinION是一种“长读”技术，因此能够对较长的条形码进行测序，从而可能导致物种识别达到较高的分类分辨率。该项目提供了一个令人兴奋和独特的机会，通过将第三代DNA元条形码应用于作为长期监测计划的一部分收集的样本，来解锁浮游生物群落的多样性苏格兰海岸观测站（Scottish Coastal Observatories，SCOBs）由苏格兰海洋科学公司（Marine Scotland Science）运营。自1997年以来，SCOBs每月收集的样本代表了一个独特的材料库，用于研究和了解气候变化导致的海洋浮游生物群落变化，这些变化可能对英国沿海生态系统的稳定性产生负面影响。将特别关注对水产养殖业、富营养化评估产生负面影响的生物群体，或被视为易受海洋酸化等不断变化的海洋环境影响的物种。该项目将为您提供最先进的测序方法，生物信息学和统计学方面的培训，以及使用浮游生物培养和先进的电子显微镜技术对浮游生物物种进行高水平的分类鉴定。您将被嵌入一个充满活力和活力的研究社区，并有机会与苏格兰海洋科学的政府研究科学家一起工作。您还将有机会展示并将您的结果整合到与浮游生物，海洋环境，气候变化和水产养殖业相关的许多国家和国际状况评估中，例如MSFD的英国远洋栖息地评估工作组，国际理事会探索海洋浮游植物和微生物生态学工作组，以及浮游动物生态学。

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.