Giving the Eastern Canadian Diatom Index (IDEC) a makeover using metabarcoding: first considerations and challenges

The Eastern Canada Diatom Index (Indice Diatomées de l'Est du Canada; IDEC) was developed to assess stream biological integrity from diatom assemblages. Since the first version of the IDEC in the early 2000s, the number of sites monitored with this bioassessment tool has increased steadily in the province of Quebec. This resulted in a significant increase in samples, which in turn resulted in an increased need for highly qualified personnel to carry out microscopic diatom identification. Time constraints and costs also represent limitations of microscopic analysis. There is thus a necessity to develop a more rapid tool for diatom assemblage analysis to maintain high-quality diatom-based stream monitoring in the province of Quebec. DNA metabarcoding targeting diatoms represents an interesting avenue in overcoming the limitations associated with traditional taxonomic analyses by microscopy. This preliminary study was conducted to investigate the potential use of diatom DNA metabarcoding for assessing stream biological integrity in Quebec. A total of 56 sampling sites were visited for biofilm collection in August of 2019 and again in August of 2020 (except for 15 sites that were visited only one of the two years). Genomic DNA was extracted from freeze-dried biofilms and sequenced using HTS targeting the rbcL barcode. Overall, diatom assemblage structure using DNA metabarcoding was similar to that based on microscopy. IDEC scores calculated from microscopy- and DNA-derived diatom assemblages were also comparable. The results are promising and justify conducting a similar study at a larger scale with more diverse stream types, regions, and impairment status, with the final objective of developing a new version of the IDEC based on diatom DNA.