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/N006496/1
• 负责人: Julie Robidart
• 金额: $ 30.11万
• 依托单位: NATIONAL OCEANOGRAPHY CENTRE
• 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%2FN006496%2F1
• 关键词: Development; application; eDNA; tools; assess

SummarySeA-DNA: Development and application of eDNA tools to assess the structure and function of coastal sea ecosystems.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".

摘要SEA-DNA：EDNA工具的发展和应用，以评估沿海海洋生态系统的结构和功能。这个NERC的重点主题集中在EDNA作为21世纪生态学的新工具的使用上。环境DNA(EDNA)在电话会议中被定义为“存在于任何有机体外的自由DNA”。呼吁的目的是解决目前在应用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的英吉利海峡的L4站进行概念验证调查，L4站是沿海海洋生态系统的典范，也是自然实验室。从水动力学模型开始，在空间和时间上定义生态系统(自然实验室有多大？)然后该项目将被分成三个实验阶段：1)EDNA方法学验证(开发工具)；2)为期18个月的临时远洋调查(测试工具)；3)全面的数据分析和模型同化(工具起作用了吗，它们告诉我们什么，它们有用吗？)使用来自4个不同机构(PML，MBA，NOC和U·Exeter)的广泛专业知识，我们将调查一个空间定义的区域，从河口到海岸，海底到远洋；以及在一系列建立在NERC国家能力采样制度和生物传感器部署基础上的时间分辨率。将利用在这一重要沿海地点并行收集的当前物理化学和生物信息，利用电子元遗传学和电子元基因组数据(单个基因到整个基因组)来回答交叉科学问题。该项目的成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学模板。下游数据将大大促进我们对EDNA持续性的理解，以及它对生态系统功能模型的潜在影响。这项研究的成果将对渔业评估、鱼类病原体检测、养护生物学、环境风险管理(例如有毒藻类水华、人类病原体、压载水法规)的使用产生更广泛的影响，更广泛的目标是通过国家环境研究中心的战略支柱“管理环境变化”支持生物多样性和自然服务。

项目成果

Shining light on a deep-sea bacterial symbiont population structure with CRISPR.

• DOI: 10.1099/mgen.0.000625
• 发表时间: 2021-08
• 期刊: Microbial genomics
• 影响因子: 3.9
• 作者: Perez M;Angers B;Young CR;Juniper SK
• 通讯作者: Juniper SK

Bridging the Spatiotemporal Gap in Diazotroph Activity and Diversity With High-Resolution Measurements

• DOI: 10.3389/fmars.2020.568876
• 发表时间: 2020-09-29
• 期刊: FRONTIERS IN MARINE SCIENCE
• 影响因子: 3.7
• 作者: Benavides, Mar;Robidart, Julie
• 通讯作者: Robidart, Julie

Intra-host symbiont diversity in eastern Pacific cold seep tubeworms identified by the 16S-V6 region, but undetected by the 16S-V4 region

• DOI: 10.1371/journal.pone.0227053
• 发表时间: 2020-01-15
• 期刊: PLOS ONE
• 影响因子: 3.7
• 作者: Breusing, Corinna;Franke, Maximilian;Young, Curtis Robert
• 通讯作者: Young, Curtis Robert

Divergent paths in the evolutionary history of maternally transmitted clam symbionts

• DOI: 10.1098/rspb.2021.2137
• 发表时间: 2022-03-09
• 期刊: PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
• 影响因子: 4.7
• 作者: Perez，Maeva;Breusing，Corinna;Young，C. Robert
• 通讯作者: Young，C. Robert

FigS1.pdf from Divergent paths in the evolutionary history of maternally transmitted clam symbionts

FigS1.pdf 来自母系传播的蛤共生体进化史上的分歧路径

• DOI: 10.6084/m9.figshare.19323685
• 发表时间: 2022
• 作者: Perez M