Copy of Sequencing the meiofaunal metagenome of the marine/freshwater interface in key estuarine ecosystems

河口是重要的过渡性栖息地，受到当地和全球人类活动的重大影响（即它们是居住、工业化、污染和娱乐的主要中心）。河口通常被认为是生物多样性低的系统；可能是由于大型动物的α -多样性较低。相比之下，小动物多样性（小于45um的动物，以线虫为主）是可观的，大多数河口估计有大约200种线虫栖息，数量从惊人的106-108只/m2不等，贡献了50-90%的后生动物动物物种丰富度（存在的物种总数）。微区系生物多样性在沉积物生态系统过程中发挥着重要作用，对碳、氮、硫循环、水柱过程、污染物分布、二次生产、食物链过程和沉积物稳定性等具有调节作用。减数动物显然是生态系统功能的关键组成部分，但使用标准形态学方法研究减数动物群落需要高技能的分类学家，而且非常耗时。这不仅限制了生态学研究中有意义的样本量的分析，而且不同种类的小动物生物的小尺寸和形态相似性导致了对形态分类方法可靠性的严重怀疑。由于这些限制，正在开发形态学方法和新的分子遗传学方法相结合的方法来评估线虫的生物多样性。也许该领域最令人兴奋的发展是应用大规模平行测序（MPS）的潜力，以阐明微生物或微量动物样品的分子群落组成。这项全新的技术能够同时对成千上万的DNA短链进行测序（在4小时内），这些DNA短链可以用作物种识别标签。到目前为止，使用标准的克隆和测序方法是不可能做到这一点的，而MPS也代表着令人难以置信的物有所值，在这种类型的应用中，每个序列的成本不到5便士。MPS技术的可用性，加上最近在线虫分类群的系统发育和生态关系方面的重大进展，现在提供了一个分子和生物信息学框架，可以用来实时准确地表征小动物的生物多样性。这些进展使假设得以发展和检验，以阐明微生态生物多样性与生物/非生物过程之间的关系。此外，这些方法将促进水动力模型的发展，该模型可用于根据流量和沉积物组成之间的关系预测小型动物群落的时空组成。目前的提案旨在为河口生态系统中一系列底物类型的生态重要河口物种创建新的生物多样性基因组序列资源，这些底物类型以持续的（默西）和恢复的（泰晤士河）工业和城市污染物制度为特征。这些数据将用于解决以生物和非生物为中心的生态假设，并将产生预测的32万个新序列读数，有效地表征英国河口小型动物的重要组成部分，从而为理解海洋沉积物中的生态系统功能提供一个平台。然后，这些数据可以与来自砂质沉积物的补充数据集相结合，用于开发成本效益高、节省时间、基于DNA芯片的小型动物群落识别工具（例如用于生物监测和生态毒理学研究），从而推动海洋沉积物中生物多样性-生态系统功能的研究（学术和商业）。

Estuaries are key transitional habitats that are significantly affected by local and global human activities (ie they are main centres of habitation, industrialization, pollution and recreation). Estuaries are typically considered to be low biodiversity systems; probably due to the presence of low alpha diversity of macrofauna. In contrast, meiofaunal diversity (animals smaller than 45um, dominated by nematodes) is substantial, with most estuaries estimated to be inhabited by approximately 200 species of nematodes, with numbers ranging from a staggering 106-108 animals/m2, contributing to between 50-90% of the metazoan faunal species richness (the total numbers of species present). Meiofaunal biodiversity plays a very important role in sediment ecosystem processes, contributing to the regulation of carbon, nitrogen, and sulphur cycling, water column processes, pollutant distribution, secondary production, food chain processes, and stability of sediments. Meiofauna are clearly key components of ecosystem functioning, but studying meiofaunal communities using standard morphological approaches requires highly-skilled taxonomists and is incredibly time consuming. Not only does this restrict the analysis of meaningful sample sizes in ecological studies, but the small size and morphological similarities of different species of meiofaunal organisms have led to severe doubts regarding the reliability of morphological taxonomic approaches. As a result of these constraints, combinations of morphological approaches and new molecular genetic methods are being developed for nematode biodiversity assessments. Perhaps the most exciting development in this field is the potential to apply massively parallel sequencing (MPS), to elucidate the molecular community composition of microbial, or meiofaunal samples. This brand new technology has the ability to simultaneously sequence hundreds of thousands of short strands of DNA (in four hours), that can be used as species identification tags. To date, this has never been possible using standard cloning and sequencing methods and MPS also represents incredible value for money, with each sequence in this type of application costing less than 5p. The availability of MPS technology, in addition to recent significant advances in the knowledge of the phylogenetic and ecological relationships of nematode taxa, now offers a molecular and bioinformatic framework that can be used to accurately characterise meiofaunal biodiversity in real time. Such advances allow hypotheses to be developed and tested to elucidate relationships between meiofaunal biodiversity and biotic/abiotic processes. Moreover, these methods will facilitate the development of hydrodynamic models that can be used to predict the spatial and temporal composition of meiofaunal communities according to the relationships between flow rates and sediment composition. The current proposal seeks to create novel biodiversity genome sequence resources for ecologically important estuarine species throughout a range of substrate types in estuarine ecosystems characterized by ongoing (Mersey) and recovering (Thames) industrial and municipal pollutant regimes. The data will be used to address biotic- and abiotic-focused ecological hypotheses, and will generate a predicted c. 320,000 novel sequence reads, effectively characterizing a significant component of the UK's estuarine meiofauna, thus providing a platform for understanding ecosystem functioning in marine sediments. These data can then be combined with complimentary datasets derived from sandy sediments and be used to develop cost-effective, time-saving, DNA chip-based meiofaunal community identification tools (e.g. for biomonitoring and ecotoxicology studies), thus, driving forward research (academic and commercial) into biodiversity-ecosystem functioning in marine sediments.