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

DNA证据彻底改变了我们对自然界的理解。它帮助我们理解了物种是如何相互联系的，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。它在量化微生物群落中的物种多样性方面也特别有用，这些微生物群落不容易用标准显微镜观察和评估。重要的是，自然环境中的DNA也可以用于“法医”的方式。皮肤、血液、粪便或粘液中的DNA痕迹可以用来识别哪些物种最近出现在当地环境中。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索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，我们使用专家抓取和渔网来调查海洋生物群落中比微生物大的物种。然而，在周围水域中对自由埃德纳进行采样可能比这样的装置更快、更便宜、破坏性更小。使用微量EDNA也有可能识别在环境中没有可靠采样的物种，要么是因为它们很稀有，要么是因为它们体型较小，要么是因为它们擅长躲避渔网和捕食。EDNA作为水生环境采样工具的效用大多在淡水系统中进行了测试，只有少数几项研究在海洋环境中测试了这种方法。因此，有必要结合实验室实验和实地调查进一步评估这一潜力。作为一个重要的第一阶段，我们需要确定来自鱼类和无脊椎动物的EDNA在海洋环境中持续多久，然后才被分解到超出可检测的点。这将告诉我们，EDNA衍生的物种名单在多大程度上反映了采样点的物种群落。我们将进行一系列实验室实验，使我们能够量化EDNA分解的速度，并确定影响这种腐烂速度的主要环境变量。然后，我们将致力于开发所需的实验室和现场方法，以可靠地检测这些物种群体的DNA，然后在我们将在实验室水族馆组装的实验社区中测试这些方法。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(如网)和EDNA方法调查自然环境。我们将在两个对渔业、养护和环境监测非常重要的英国海洋栖息地进行这项工作，即河口和近岸陆架海。我们还将在一个开阔的海洋栖息地--南大洋--进行这项工作，这是渔业和鲸鱼等海洋大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是否准确地捕获了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是否存在典型的稀有或难以采样的物种，其中一些可能是科学上的新物种。最后，我们将使用Edna衍生的物种列表来重建我们采样地点存在的食物网。我们将使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它们的组成和稳定性。这些分析的结果将提供对EDNA在帮助我们了解未来气候变化可能如何影响鱼类物种方面所起的作用的洞察。

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.