Comparative study of benthic diatom community using 18S rDNA metabarcoding and light microscopy in the Bosphorus, Turkey

Abstract

Diatoms are one of the major algal groups having an important role in the aquatic systems in which they constitute the main primary production with dinoflagellates in the coastal regions, and can contribute to photosynthesis at great rates. There had been intense effort to reveal diatom community with light microscopy (LM) and scanning electron microscopy (SEM), on the other hand, DNA barcoding techniques had been an interest to understand the microbiome in the last decades. Barcoding provided rapid response on the targeted organisms and introduced many new species. Recently, monocultural molecular studies showed that species could be described with accurate and reliable results. DNA metabarcoding approaches yielded to determine the whole organisms with available DNA data in the sample and major advances on next-generation sequencing platforms enable to widen the application of metabarcoding approach to various environmental samples. The aim of this study was to perform a comparative assessment of the diatom community structures in Bosphorus of Istanbul, Turkey by LM and 18S rDNA metabarcoding. Diatom samples were collected by brushing from the submerged stones of 10 cm of area taken from the coast of Beykoz on the Asian part of the Bosphorus, Istanbul and processed for LM and metabarcoding in June 2020. To concentrate the sample, the scrapes of the biofilm filtered from a 0.22-micron filter, and eDNA was extracted from that filter paper using MN ‡ ‡ ‡