Development and application of eDNA tools to assess the structure and function of coastal sea ecosystems (MARINe-DNA)

评估沿海海洋生态系统结构和功能的eDNA工具的开发和应用（MARINe-DNA）

• 批准号: NE/N006151/1
• 负责人: Michael Cunliffe
• 金额: $ 30.12万
• 依托单位: Marine Biological Association of the United Kingdom
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2015
• 资助国家: 英国
• 起止时间: 2015 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FN006151%2F1
• 关键词: Development; application; eDNA; tools; assess

This NERC highlight topic focuses on the use of eDNA as a new tool for 21st century ecology. Environmental DNA (eDNA) is defined in the call as 'free DNA present outside of any organism'. The aim of the call is to address the current knowledge gaps in the application of eDNA approaches to help understand community biodiversity and dynamics of ecosystem functioning. We will conduct a proof-of-concept investigation at Station L4, an exemplar coastal ocean ecosystem, and natural laboratory, in the English Channel off Plymouth, UK. Starting with a hydrodynamic model to spatially and temporally define the ecosystem (how large is the natural laboratory?) the project will then be split into three experimental phases: 1) eDNA methodological validation (developing the tools);2) 18-month temporal pelagic survey (testing the tools); and3) Comprehensive data analysis and model assimilation (did the tools work, what did they tell us, and are they useful?)Using a wide range of expertise from 4 different institutions (PML, MBA, NOC, and U.Exeter), we will investigate a spatially defined region, from estuarine to coastal, benthic to pelagic; and at a range of temporal resolutions building on NERC National Capability sampling regimes and biosensor deployment. E-metagenetic and e-metagenomic data (individual genes to whole genomes) will be used to answer cross-cutting science questions utilising current physicochemical and biological information collected in parallel at this important coastal site. Results from this project will provide a methodological template for the use of eDNA and remote eDNA biosensors in aquatic ecosystems. Downstream data will significantly advance our understanding of persistence of eDNA, and its potential impact on informing models of ecosystem functioning. Products of this research will have wider implications for the use of this tool on fisheries assessments, fish pathogen detection, conservation biology, environmental risk management (e.g. toxic algae blooms, human pathogens, ballast water regulations), with the wider aim of supporting biodiversity and nature's services through NERC's strategic pillar of "Managing environmental change".

这个 NERC 亮点主题重点关注 eDNA 作为 21 世纪生态学新工具的使用。环境 DNA (eDNA) 在呼吁中被定义为“存在于任何生物体外部的游离 DNA”。此次呼吁的目的是解决当前在应用 eDNA 方法方面的知识差距，以帮助了解社区生物多样性和生态系统功能的动态。我们将在英国普利茅斯附近英吉利海峡的 L4 站进行概念验证调查，L4 站是沿海海洋生态系统和自然实验室的典范。从水动力模型开始，在空间和时间上定义生态系统（自然实验室有多大？），然后该项目将分为三个实验阶段：1）eDNA 方法验证（开发工具）；2）18 个月的时间浮游调查（测试工具）； 3) 全面的数据分析和模型同化（这些工具是否有效，它们告诉了我们什么，它们有用吗？）利用来自 4 个不同机构（PML、MBA、NOC 和 U.Exeter）的广泛专业知识，我们将调查空间界定的区域，从河口到沿海，从海底到远洋；以及基于 NERC 国家能力采样制度和生物传感器部署的一系列时间分辨率。电子宏遗传学和电子宏基因组数据（单个基因到整个基因组）将用于利用在这个重要沿海地点并行收集的当前物理化学和生物信息来回答交叉科学问题。该项目的结果将为在水生生态系统中使用 eDNA 和远程 eDNA 生物传感器提供方法模板。下游数据将极大地促进我们对 eDNA 持久性及其对生态系统功能信息模型的潜在影响的理解。这项研究的成果将对该工具在渔业评估、鱼类病原体检测、保护生物学、环境风险管理（例如有毒藻华、人类病原体、压载水法规）方面的使用产生更广泛的影响，更广泛的目标是支持生物多样性和通过 NERC 的“管理环境变化”战略支柱来提供自然服务。

项目成果

Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current.

• DOI: 10.3389/fmicb.2018.01474
• 发表时间: 2018
• 期刊: Frontiers in microbiology
• 影响因子: 5.2
• 作者: Flaviani F;Schroeder DC;Lebret K;Balestreri C;Highfield AC;Schroeder JL;Thorpe SE;Moore K;Pasckiewicz K;Pfaff MC;Rybicki EP
• 通讯作者: Rybicki EP

A 17-year time-series of fungal environmental DNA from a coastal marine ecosystem reveals long-term seasonal-scale and inter-annual diversity patterns.

• DOI: 10.1098/rspb.2022.2129
• 发表时间: 2023-02-08
• 期刊: PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
• 影响因子: 4.7
• 作者: Chrismas, Nathan;Allen, Ro;Allen, Michael J.;Bird, Kimberley;Cunliffe, Michael
• 通讯作者: Cunliffe, Michael

Complex photobiont diversity in the marine lichen Lichina pygmaea

• DOI: 10.1017/s002531542100062x
• 发表时间: 2021-06-01
• 期刊: JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM
• 影响因子: 1.2
• 作者: Chrismas, Nathan A. M.;Allen, Ro;Cunliffe, Michael
• 通讯作者: Cunliffe, Michael

Limited congruence exhibited across microbial, meiofaunal and macrofaunal benthic assemblages in a heterogeneous coastal environment.

• DOI: 10.1038/s41598-018-33799-9
• 发表时间: 2018-10-19
• 期刊: Scientific reports
• 影响因子: 4.6
• 作者: Cronin-O'Reilly S;Taylor JD;Jermyn I;Allcock AL;Cunliffe M;Johnson MP
• 通讯作者: Johnson MP

Multi-year assessment of coastal planktonic fungi reveals environmental drivers of diversity and abundance

• DOI: 10.1038/ismej.2016.24
• 发表时间: 2016-09-01
• 期刊: ISME JOURNAL
• 影响因子: 11
• 作者: Taylor, Joe D.;Cunliffe, Michael
• 通讯作者: Cunliffe, Michael