An increasing number of studies use next generation sequencing (NGS) to analyze complex communities, but is the method sensitive enough when it comes to identification and quantification of species? We compared NGS with morphology-based identification methods in an analysis of microalgal (periphyton) communities. We conducted a mesocosm experiment in which we allowed two benthic grazer species to feed upon benthic biofilms, which resulted in altered periphyton communities. Morphology-based identification and 454 (Roche) pyrosequencing of the V4 region in the small ribosomal unit (18S) rDNA gene were used to investigate the community change caused by grazing. Both the NGS-based data and the morphology-based method detected a marked shift in the biofilm composition, though the two methods varied strongly in their abilities to detect and quantify specific taxa, and neither method was able to detect all species in the biofilms. For quantitative analysis, we therefore recommend using both metabarcoding and microscopic identification when assessing the community composition of eukaryotic microorganisms.

Algal dry massThis csv file contains the algal dry mass (mg/ml).Algal cell numberThis csv file contains the algal cell number (cells/cm3) obtained with morphology-based approach.Algal biovolumeThis csv file contains the algal biovolume (µm/cm3) obtained with morphology-based approach.Sequence abundanceThis csv file contains the sequence abundances obtained with the DNA metabarcoding approach.Sequence dataThis csv file contains the sequences used to construct the phylogenetic tree, pairwise identity and taxonomic identity.