SeaDNA - Assessing marine biodiversity and structure using environmental DNA: from groundtruthing to food web structure and stability

SeaDNA - 使用环境 DNA 评估海洋生物多样性和结构：从地面实况到食物网结构和稳定性

基本信息

批准号：
NE/N005996/1
负责人：
Eoin O'Gorman
金额：
$ 11.69万
依托单位：
Imperial College London
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%2FN005996%2F1
关键词：
SeaDNA Assessing marine biodiversity structure

项目摘要

DNA evidence has revolutionised our understanding of the natural world. It has helped us to appreciate how species are related to one other, how environmental change can lead to species divergence and how individual populations become adapted through evolutionary processes to their local environments. It has also been particularly useful in quantifying the diversity of species in communities of microorganisms that cannot readily be seen and assessed using standard microscopy. Importantly, DNA in the natural environment can also be used in a "forensic" manner. Traces of DNA from skin, blood, faeces or mucous can be used to identify which species have recently been present in the local environment. Given recent developments in DNA sequencing technology, this "environmental DNA" (eDNA) promises to revolutionise the way we probe biodiversity in our environment, particularly in marine environments that can be very difficult to sample reliably. Traditionally we have used specialist grabs and nets to survey species larger than microbes in marine communities. However, sampling free eDNA in surrounding water is potentially faster, less expensive and less destructive than such gears. Use of trace eDNA also holds potential to identify species that are not reliably sampled in the environment, either because they are rare, small, or adept at avoiding nets and grabs. The utility of eDNA as a tool for sampling aquatic environments has been mostly tested in freshwater systems, and there are only a handful of studies that have tested the approach in the marine environment. Thus, there is a need to further evaluate the potential using a combination of laboratory experiments and field surveys. As an important first stage, we need to establish how long eDNA from fish and invertebrates persists in the marine environment before it is broken down beyond the point of detectability. This will tell us how well an eDNA-derived species list reflects the species community at the sampling site. We will conduct a set of laboratory experiments that will enable us to quantify the rate of eDNA break-down, and identify main environmental variables that influence this rate of decay. We will then aim to develop the laboratory and field methods needed to reliably detect DNA from these species groups, before testing these methods in experimental communities that we will assemble in laboratory aquaria. An important stage in testing the ability of eDNA to be used as a tool in surveying and monitoring marine species is to survey the natural environment using both traditional methods (e.g. nets), and eDNA methods. We will do this in two UK marine habitats that are important for fisheries, conservation and environmental monitoring, namely estuaries and inshore shelf seas. We will also do this in an open ocean habitat, the Southern Ocean, which is an important habitat for fisheries and oceanic megafauna such as whales. We will directly compare data from eDNA methods to those from traditional methods to ask if eDNA accurately captures the fish and invertebrate communities, and if the method has the added ability to inform us on the presence of species that are typically rare or difficult to sample, some of which may be new to science. Finally, we will use the eDNA derived species lists to reconstruct the food webs present in our sampling locations. We will use these data to test how stable marine communities are over space and time, and how environmental variables such as temperature affect their composition and stability. The results of these analyses will provide insight into the role of eDNA in helping us to understand how future climate change may affect fished species.

DNA证据彻底改变了我们对自然世界的理解。它帮助我们欣赏了物种与一个彼此之间的关系，环境变化如何导致物种差异以及如何通过进化过程到其当地环境来适应各个种群。它在量化微生物群落的多样性方面也特别有用，这些物种的多样性无法轻易使用标准显微镜进行评估。重要的是，自然环境中的DNA也可以以“法医”方式使用。皮肤，血液，粪便或粘液中的DNA痕迹可用于识别最近在当地环境中存在哪些物种。鉴于DNA测序技术的最新发展，这种“环境DNA”（EDNA）有望改变我们在环境中探测生物多样性的方式，尤其是在海洋环境中，很难可靠地采样。传统上，我们利用专家抢夺和网络调查海洋社区中比微生物大的物种。但是，与此类齿轮相比，在周围水中抽样无EDNA的可能性更快，更便宜，破坏性更低。痕量EDNA的使用还具有识别在环境中不可靠采样的物种，因为它们稀有，小或熟练地避免了网和抢夺。 EDNA作为抽样水生环境的工具的实用性主要在淡水系统中进行了测试，并且只有少数研究在海洋环境中测试了该方法。因此，有必要使用实验室实验和现场调查的组合进一步评估潜力。作为重要的第一阶段，我们需要确定在海洋环境中，在海洋环境中持续多长时间，直到埃德纳被遗忘了，然后才能将其分解为可检测性点。这将告诉我们EDNA衍生的物种清单在抽样场所的物种社区的表现如何。我们将进行一组实验室实验，使我们能够量化EDNA分解的速率，并确定影响这种衰减速率的主要环境变量。然后，我们将旨在开发可靠地检测到这些物种群体的DNA所需的实验室和现场方法，然后在实验社区中测试这些方法，这些方法我们将在实验室水族箱中聚集。测试EDNA用作测量和监测海洋物种工具的能力的一个重要阶段是使用传统方法（例如NETS）和EDNA方法调查自然环境。我们将在两个对渔业，保护和环境监测至关重要的英国海洋栖息地，即河口和近海货架海。我们还将在南大洋的开阔海洋栖息地中这样做，这是渔业和海洋巨型群岛（例如鲸鱼）的重要栖息地。我们将直接将数据从EDNA方法与传统方法的数据进行比较，以询问Edna是否准确地捕获了鱼类和无脊椎动物群落，以及该方法是否具有附加能力，可以告知我们存在通常很少或难以采样的物种的存在，其中一些可能是科学的新物种。最后，我们将使用Edna衍生的物种清单来重建我们采样位置中存在的食物网。我们将使用这些数据来测试稳定的海洋社区在空间和时间上的稳定方式，以及温度等环境变量如何影响其组成和稳定性。这些分析的结果将为我们了解埃德娜在帮助我们了解未来气候变化如何影响捕食物种方面的作用。