Does environmental DNA reflect the actual phytoplankton diversity in the aquatic environment? Case study of marine mucilage in the Sea of Marmara

The present study was designed to assess the effectiveness of the eDNA metabarcoding approach to determine the phytoplankton composition in the marine environment with a special focus on mucilage episodes in the Sea of Marmara. For this purpose, the samples were collected from 5 different sites located in the Sea of Marmara and the northern Aegean Sea during the mucilage episode in June 2021. The phytoplankton diversity was analyzed morphologically and by 18S rRNA gene amplicon sequencing, and the dataset of both methods was compared, accordingly. The results showed significant differences between methods in terms of composition and the abundance of the phytoplankton groups. While Miozoa was the most abundant group by metabarcoding, light microscopy (LM) indicated a dominance of Bacillariophyta. Katablepharidophyta was found at lower abundances by the metabarcoding (representing < 1% of the community); the members of this phylum were not observed by a microscope. At the lower taxonomic levels, Chaetoceros was the only genus detected in all samples by both methods. Additionally, while mucilage-forming Gonyaulax fragilis, Cylindrotheca closterium, and Thalassiosira rotula were detected to species-level by LM, metabarcoding was able to determine these organisms at the genus level. On the other hand, the genus Arcocellulus was found in all metabarcoding datasets and not detected by microscopy. The results indicated that metabarcoding can detect a greater number of genera and reveal taxa that were overlooked by light microscopy but to develop a complete picture of phytoplankton diversity in the sample, microscopical observations still are in need.