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。它帮助我们了解物种之间如何相互关联，环境变化如何导致物种分化，以及个体种群如何通过进化过程适应当地环境。它对于量化微生物群落中的物种多样性也特别有用，而使用标准显微镜无法轻易观察和评估这些微生物群落的物种多样性。重要的是，自然环境中的 DNA 也可以用于“法医”方式。皮肤、血液、粪便或粘液中的 DNA 痕迹可用于识别最近出现在当地环境中的物种。鉴于 DNA 测序技术的最新发展，这种“环境 DNA”(eDNA) 有望彻底改变我们探测环境中生物多样性的方式，特别是在很难可靠采样的海洋环境中。传统上，我们使用专门的抓斗和网来调查海洋群落中比微生物更大的物种。然而，与此类设备相比，对周围水中的游离 eDNA 进行采样可能更快、更便宜且破坏性更小。使用微量 eDNA 还可以识别环境中无法可靠采样的物种，这些物种要么是稀有、体型较小，要么是善于躲避网捕和抓捕。 eDNA 作为水生环境采样工具的实用性主要在淡水系统中进行了测试，只有少数研究在海洋环境中测试了该方法。因此，需要结合实验室实验和现场调查来进一步评估潜力。作为重要的第一阶段，我们需要确定鱼类和无脊椎动物的 eDNA 在分解到无法检测的程度之前在海洋环境中持续存在多长时间。这将告诉我们 eDNA 衍生的物种列表如何反映采样点的物种群落。我们将进行一系列实验室实验，使我们能够量化 eDNA 分解率，并确定影响这种分解率的主要环境变量。然后，我们将致力于开发可靠检测这些物种组 DNA 所需的实验室和现场方法，然后在我们将在实验室水族箱中组装的实验群落中测试这些方法。测试 eDNA 作为调查和监测海洋物种的工具的能力的一个重要阶段是使用传统方法（例如网）和 eDNA 方法调查自然环境。我们将在对渔业、保护和环境监测非常重要的两个英国海洋栖息地（即河口和近岸陆架海）进行这项工作。我们还将在南大洋这一开阔的海洋栖息地进行这项工作，南大洋是渔业和鲸鱼等海洋巨型动物的重要栖息地。我们将直接将 eDNA 方法的数据与传统方法的数据进行比较，以询问 eDNA 是否准确捕获鱼类和无脊椎动物群落，以及该方法是否具有额外的能力来告知我们通常稀有或难以采样的物种的存在，其中一些对于科学来说可能是新的。最后，我们将使用 eDNA 衍生物种列表来重建采样地点的食物网。我们将利用这些数据来测试海洋群落在空间和时间上的稳定性，以及温度等环境变量如何影响其组成和稳定性。这些分析的结果将深入了解 eDNA 的作用，帮助我们了解未来气候变化可能如何影响捕捞物种。