Investigation of coastal benthic diatom communities using the <scp><i>rbc</i>L</scp> marker with nanopore sequencing in Urban Marine environments

Marine benthic diatoms are one of the most important groups in coastal primary production and photosynthesis, and the number of molecular studies revealing diatom biodiversity is increasing. In this study, we investigated diatom composition using environmental DNA metabarcoding based on the rbcL gene using MinION (Oxford Nanopore) at 11 sampling sites along the Istanbul coasts of the Sea of Marmara in 2023. We identified 261 species belonging to 121 genera, and among them, Nitzschia (19.6%; 24 species) and Navicula (17.1%; 21 species) were the most abundant genera, followed by Licmophora (6.9%) and Nanofrustulum (6.1%). At the species level, the highest number of reads was assigned to Nitzschia inconspicua, Navicula perminuta, and Nanofrustulum shiloi. Redundancy analysis (RDA) showed that pH was the major driving factor related to taxon abundance at the genera and species levels. Metabarcoding results revealed the presence of new taxa for the Sea of Marmara such as Minutocellus, Pierrecomperia, Perideraion, Rhoikoneis, Sternimirus, and Synedropsis, which had not been formerly detected by traditional monitoring methods. Since there are few studies on marine diatom monitoring using rbcL gene markers, our results could support the use of this marker to reveal the diversity of marine benthic diatoms from urban coasts.