Abstract
Ecological status assessment of watercourses is based on the calculation of quality indices using pollution sensitivity of targeted biological groups, including diatoms. The determination and quantification of diatom species is generally based on microscopic morphological identification, which requires expertise and is time-consuming and costly. In Europe, this morphological approach is legally imposed by standards and regulatory decrees by the Water Framework Directive (WFD). Over the past decade, a DNA-based molecular biology approach has newly been developed to identify species based on genetic criteria rather than morphological ones (i.e. DNA metabarcoding). In combination with high throughput sequencing technologies, metabarcoding makes it possible both to identify all species present in an environmental sample and to process several hundred samples in parallel. This article presents the results of two recent studies carried out on the WFD networks of rivers of Mayotte (2013–2018) and metropolitan France (2016–2018). These studies aimed at testing the potential application of metabarcoding for biomonitoring in the context of the WFD. We discuss the various methodological developments and optimisations that have been made to make the taxonomic inventories of diatoms produced by metabarcoding more reliable, particularly in terms of species quantification. We present the results of the application of this DNA approach on more than 500 river sites, comparing them with those obtained using the standardised morphological method. Finally, we discuss the potential of metabarcoding for routine application, its limits of application and propose some recommendations for future implementation in WFD.
Highlights
Since it came into force in 2000, the Water Framework Directive (WFD) has provided a common regulatory framework for the implementation of a water management policy in Europe (European Commission 2000)
Vasselon Valentin et al.: Diatoms DNA metabarcoding: French experience and developments by studying the biological characteristics of bioindicator communities living in aquatic environments
Some methodological biases were still limiting the production of reliable molecular taxonomic inventories through DNA metabarcoding, in terms of taxon quantification, thereby producing weak ecological status assessments
Summary
Since it came into force in 2000, the Water Framework Directive (WFD) has provided a common regulatory framework for the implementation of a water management policy in Europe (European Commission 2000) To facilitate their quality assessment, aquatic environments are classified by major water body categories (groundwaters, continental surface waters and coastal waters) and study sites are chosen to set up monitoring networks in each EU member state. Based on community composition and on relative abundance and ecological preferences of each diatom taxon in the phytobenthic community, it is possible to calculate values for WFD quality indices, such as the Biological Diatom Index (BDI) in France (Coste et al 2009) These make it possible to highlight pollution of physico-chemical origin, in particular nutrient and organic matter enrichment
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