Phytoplankton Metabarcoding vs Microscopy

Phytoplankton is used worldwide to monitor the environmental state of aquatic systems. Long-time series of microscopy-analyzed phytoplankton are available from many monitoring stations. The traditional microscopy method is however time-consuming and has shortcomings, such as the low resolution of certain taxa. Metabarcoding has been suggested as an alternative method, but the consistency between different methods needs illumination. We performed a comparative study of microscopy and DNA metabarcoding, by analyzing micro- and nanophytoplankton at 5 coastal sites in the northern Baltic Sea during an autumn sampling. The results are promising for implementing DNA metabarcoding as a complement to microscopy in phytoplankton monitoring, especially if group-level indexes can be applied to classify the environmental state of water bodies.