Early detection of eukaryotic communities from marine biofilm using high-throughput sequencing: an assessment of different sampling devices

Marine biofilms are precursors for colonization by larger fouling organisms, including non-indigenous species (NIS). In this study, high-throughput sequencing (HTS) of 18S rRNA metabarcodes was used to investigate four sampling methods (modified syringe, sterilized sponge, underwater tape and sterilized swab) for characterizing eukaryotic communities in marine biofilms. PerspexTM plates were sampled in and out of water. DNA collected with tape did not amplify. Otherwise, there were no statistical differences in communities among the remaining three sampling devices or between the two environments. Sterilized sponges are recommended for ease of use underwater. In-depth HTS analysis identified diverse eukaryotic communities, dominated by Metazoa and Chromoalveolata. Among the latter, diatoms (Bacillariophyceae) were particularly abundant (33% of reads assigned to Chromalveolata). The NIS Ciona savignyi was detected in all samples. The application of HTS in marine biofilm surveillance could facilitate early detection of NIS, improving the probability of successful eradication.