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Assessing water quality using eDNA from diatoms

Researchers from the University and Canton of Geneva (Switzerland), the University Pierre and Marie Curie (Paris, France) and the Laboratory “Adaptation et Diversité en milieu marin” (Roscoff, France) published a study to assess the potential of the eDNA approach for identification and quantification of diatoms from environmental samples.

In June 2015, Amorim Visco et al. published a paper entitled “Environmental monitoring: inferring diatom index from next-generation sequencing data”. This study corresponds to the first use of environmental DNA to infer a diatom biotic index.

Summary: Diatoms are widely used as bio-indicators for the assessment of water quality in rivers and streams. Classically, the diatom biotic indices are based on the relative abundance of morphologically identified species weighted by their autoecological value. Obtaining such indices is time-consuming, costly and requires excellent taxonomic expertise, which is not always available. In this study, the Authors tested the possibility to overcome these limitations by using a Next Generation Sequencing approach to identify and quantify diatoms found in environmental DNA and RNA samples. They analysed 27 river sites in the Geneva area (Switzerland), in order to compare the values of the Swiss Diatom Index (DI-CH) computed either by microscopic quantification or directly from sequencing data. Despite gaps in the reference database and variations in relative abundance of analysed species, a significant correlation was demonstrated between morphological and molecular data indicating similar biological quality status for the majority of sites. This proof-of-concept study demonstrates the potential of the eDNA approach for identification and quantification of diatoms in environmental samples, opening new avenues towards the routine application of genetic tools for bioassessment and biomonitoring of aquatic ecosystems.

Reference: Amorim Visco, J., Apothéloz-Perret-Gentil, L., Cordonier, A., Esling, P., Pillet, L., Pawlowski, J. 2015. Environmental monitoring: inferring diatom index from next-generation sequencing data. Environmental Science and Technology. DOI: 10.1021/es506158m.