The potential of exact sequence variants (ESVs) to interpret and assess the impact of agricultural pressure on stream diatom assemblages revealed by DNA metabarcoding

Land-use imposes an important potential threat on the aquatic ecosystems of riverine habitats. In this study, DNA metabarcoding was used to assess the effect of land-use on diatom assemblages, with a special focus on cropland area as an integrative proxy for several direct-acting pressures. The so-called taxonomy-free approach was tested using exact sequence variants (ESVs) without pre-clustering and without assigning them to traditional taxonomy. Our hypothesis is that the taxonomy-free approach gives better interpretation of the effect of agricultural land use and it provides a more efficient index to indicate agricultural stress than the classical method with taxonomical clustering. Classical ordination techniques (PCA, NMDS) were performed to study the effects of cropland area proportion on diatom assemblages and a modified version of the Zelinka-Marvan equation for the index development. Results showed that (i) although ESVs provided better results when studying land-use effects on diatoms, taxonomic assignment after analysis was necessary to give ecological interpretations and that (ii) a better performing index could be developed by using the taxonomy-free approach. By using ESVs without taxonomic assignment, information on the ecology of sequences belonging to the same species and of unassigned sequences could be kept. New types of clustering methods are welcome in the future of biomonitoring where the delimitation of taxonomic units should be refined based on a higher emphasis on their ecology rather than on morphological or genetical criteria.

Automated summary

This study assessed the impact of land-use on diatom assemblages using DNA metabarcoding and tested a taxonomy-free approach for a better interpretation of agricultural stress. Results showed that the taxonomy-free approach provided better insights into the effects of agricultural land use and could lead to the development of more efficient indices. Furthermore, it demonstrated the importance of retaining ecological information by using exact sequence variants without taxonomic assignment.