Articles
Phytoplankton analysis using environmental DNA: new tools to evaluate water bodies ecological status
Received : 19 February 2026;
Published : 10 March 2026
References
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Abstract
Phytoplankton is a key biological element for biomonitoring water bodies due to its role in their functioning and its rapid response to human-induced environmental pressures. In France, a biotic index (IPLAC) has been developed to assess the ecological quality of water bodies. It is based on the identification and counting of phytoplankton species using optical microscopy. While optical microscopy has certain shortcomings, such as the difficulty of identifying certain small or cryptic species, the metabarcoding approach avoids these pitfalls and is therefore of interest for biomonitoring. In this context, the PhytoDOM project has enabled the development of biotic indices based on metabarcoding sequencing of phytoplankton DNA. The first steps were dedicated to developing protocols for phytoplankton sampling, preparations for sequencing (DNA extraction, PCR amplification of DNA), and analysing the data obtained from sequencing (bioinformatic pipeline). The data produced made it possible to assess the relevance of using species identified by metabarcoding to calculate the IPLAC's MCS metric and showed that this approach is not conclusive. Subsequently, a taxonomy-free metric (MCA) and an ecological network topology index (MCT) were developed and tested on 599 samples collected from 186 metropolitan lakes and showed a significant ability to predict phosphorus levels.
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