Metabarcoding vs Microscopy: Comparison of Methods To Monitor Phytoplankton Communities

Abstract

Phytoplankton are used worldwide to monitor the environmental status of aquatic systems. Long-time series of microscopy-analyzed phytoplankton are available from many monitoring stations. The microscopy method is, however, time-consuming and has shortcomings. DNA metabarcoding has been suggested as an alternative method, but the consistency between different methods needs further investigation. We performed a comparative study of microscopy and metabarcoding analyzing micro- and nanophytoplankton. For metabarcoding, 25-1000 mL of seawater was filtered, DNA extracted, and the 18S and 16S rRNA gene amplicons sequenced. For microscopy, based on the Utermöhl method, we evaluated the use of three metrics: abundance, biovolume, and carbon biomass. At the genus, species, and unidentified taxa levels, metabarcoding generally showed higher taxonomic diversity than microscopy, and diversity was already captured at the lowest filtration volume tested, 25 mL. Metabarcoding and microscopy displayed relatively similar distribution patterns at the group level. The results showed that the relative abundances of the 18S rRNA amplicon at the group level best fitted the microscopy carbon biomass metric. The results are promising for implementing DNA metabarcoding as a complement to microscopy in phytoplankton monitoring, especially if databases were improved and group-level indices could be applied to classify the environmental state of water bodies.