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

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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.