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。它帮助我们理解物种之间的关系，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。它还特别适用于量化微生物群落中的物种多样性，这些微生物群落无法使用标准显微镜轻易观察和评估。重要的是，自然环境中的DNA也可以用于"法医"方式。皮肤、血液、粪便或粘液中的DNA痕迹可用于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测环境中生物多样性的方式，特别是在海洋环境中，很难可靠地取样。传统上，我们使用专业的抓斗和渔网来调查海洋群落中比微生物大的物种。然而，在周围的水中采样游离的eDNA可能比这种齿轮更快，更便宜，破坏性更小。使用微量eDNA也有可能识别出环境中无法可靠采样的物种，因为它们要么是稀有的，要么是小的，要么是善于避免渔网和抓斗。eDNA作为水生环境取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，进一步评估其潜力。作为重要的第一步，我们需要确定鱼类和无脊椎动物的eDNA在海洋环境中存在多久，然后才被分解到无法检测的程度。这将告诉我们一个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分解的速率，并确定影响这种衰变速率的主要环境变量。然后，我们将致力于开发可靠地检测这些物种群体的DNA所需的实验室和现场方法，然后在实验室水族馆中组装的实验社区中测试这些方法。在测试DNA作为调查和监测海洋物种的工具的能力方面，一个重要阶段是使用传统方法（例如网）和DNA方法调查自然环境。我们将在两个对渔业、保护和环境监测很重要的英国海洋栖息地，即河口和近海陆架海，开展这项工作。我们还将在一个开放的海洋栖息地，即南大洋，这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来告知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它们的组成和稳定性。这些分析的结果将有助于深入了解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.