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Research article - Peer-reviewed, 2017

The best of both worlds: a combined approach for analyzing microalgal diversity via metabarcoding and morphology-based methods

Groendahl, Sophie; Kahlert, Maria; Fink, Patrick


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) pyro-sequencing 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.

Published in

2017, volume: 12, number: 2

Authors' information

Groendahl, Sophie
University of Cologne
Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment
Fink, Patrick
University of Cologne
Fink, Patrick
Heinrich Heine University Düsseldorf

UKÄ Subject classification

Environmental Sciences

Publication Identifiers


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