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世界的理解。它帮助我们了解物种之间是如何相互联系的，环境变化是如何导致物种分化的，以及个体种群是如何通过进化过程适应当地环境的。它在量化微生物群落的物种多样性方面也特别有用，这些微生物群落的物种多样性很难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”方式。来自皮肤、血液、粪便或粘液的DNA痕迹可以用来识别最近在当地环境中出现的物种。鉴于DNA测序技术的最新发展，这种“环境DNA”（eDNA）有望彻底改变我们在环境中探测生物多样性的方式，特别是在很难可靠取样的海洋环境中。传统上，我们使用专业的抓斗和网来调查海洋群落中比微生物大的物种。然而，在周围的水中取样游离eDNA可能比这种装置更快、更便宜、破坏性更小。痕量eDNA的使用还具有识别在环境中无法可靠取样的物种的潜力，这些物种要么是稀有的，要么是小的，要么是善于躲避渔网和捕获。eDNA作为水生环境采样工具的效用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，有必要利用实验室实验和实地调查相结合的方法进一步评价其潜力。作为重要的第一步，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才会被分解到无法检测的程度。这将告诉我们edna衍生的物种列表在多大程度上反映了采样地点的物种群落。我们将进行一系列实验室实验，这将使我们能够量化eDNA分解的速度，并确定影响这一衰变速度的主要环境变量。然后，我们将致力于开发可靠地检测这些物种群体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作为海洋物种调查和监测工具的能力的一个重要阶段是同时使用传统方法（如网）和eDNA方法调查自然环境。我们将在两个对渔业、保护和环境监测都很重要的英国海洋栖息地，即河口和近海大陆架海域进行这项研究。我们还将在开放的海洋栖息地南大洋进行这项工作，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，可以告诉我们通常罕见或难以采样的物种的存在，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。这些分析的结果将帮助我们深入了解eDNA在帮助我们了解未来气候变化如何影响鱼类方面的作用。

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.