Specific foraminiferal marker of the V9 18S rRNA gene

Environmental biomonitoring is a prerequisite for adapted and efficient evaluation of ecosystem degradation due to anthropogenic pressure or climate change. Among the different habitat, estuaries are efficient model as this ecotone is a crossroad of multiple anthropogenic and natural stressors. However, due to the multiple origins of stressors, the detection of anthropogenic pressure is challenging. The fact that in estuaries, abundant natural stressors often lead to negative quality assessments has been coined the “Estuarine quality paradox”. To solve this issue, the application of molecular approaches to successful bioindicators like Foraminifera is promising. However, the development and the validation of different sampling protocols, molecular procedures and data analyses remains to be completed before such a tool can be routinely applied. We conducted an environmental DNA survey of six estuaries along the French Atlantic coast, using a metabarcoding approach targeting foraminiferal clades. RDA analysis based on the distribution of 99 taxa showed that 40% of the variance was explained by the physical and chemical composition of the sediment and the climatic conditions. Our results demonstrate that estuarine environments possess a large stock of dormant or propagules stage with only a few taxa dominating the community composition. These findings underline the importance of the so called “rare biosphere” in estuarine ecosystems. Indeed, this diversity component in multiple stressor environments may constitute an important reservoir of species actively contributing to the community dynamics. Environmental DNA biomonitoring opens new perspectives to resolve the “estuarine quality paradox” by providing complementary information to the classical morphological approaches.