Evaluation of freshwater faunal biodiversity has been an essential method for the assessment of ecosystem health. The Environment Agency (EA), UK and other regulators have been applying mainly classical taxonomic and morphology-based analysis of benthic macroinvertebrates for biomonitoring of river and lake ecosystems, by either measuring biodiversity or identifying indicator species that can provide information on environment quality. The downside of morphology-based approaches is that they are very demanding. They require taxonomic expertise, the analysis of samples is time consuming and specimens in many cases, cannot be identified to a taxonomic level lower than genus. By employing molecular techniques we have the ability to overcome these difficulties. Using cytochrome oxidase subunit I (COI) barcodes we can accurately identify specimens and resolve taxonomic issues, while with Next Generation Sequencing (NGS) we can achieve high taxonomic resolution for DNA extracted directly from bulk samples (environmental DNA).
In the context of this work we will populate a reference library for about 200 freshwater macroinvertebrate indicator species in the UK, using barcode analysis of the COI mtDNA gene along with classical taxonomic identification. Using this library and the sequences already available in databases (BOLD) we will be able to test the application of large community analysis of benthic macroinvertebrates from bulk environmental samples, through 454 Roche pyrosequencing. Furthermore, we will apply a barcoding analysis system for the identification of Chironomid Pupal Exuviae (CPE Technique), a method which is also extensively used by the EA for the monitoring of lake ecosystems. This work will set a framework for the direct application of molecular methods for the assessment and monitoring of river and lake ecosystem health.
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