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

• Published in: Biofouling (Chur, Switzerland) Vol. 31; no. 3; pp. 241 - 251
• Main Authors: Pochon, Xavier, Zaiko, Anastasija, Hopkins, Grant A., Banks, Jonathan C., Wood, Susanna A.
• Format: Journal Article
• Language: English
• Published: England Taylor & Francis 01-01-2015
• Subjects: 18S rRNA gene; Animals; Bacillariophyceae; Biodiversity; Biofilms; Ciona savignyi; Communities; Computational Biology; Devices; Diatoms; DNA - isolation & purification; DNA Barcoding, Taxonomic; High-Throughput Nucleotide Sequencing; High-throughput sequencing (HTS); Marine; Metazoa; non-indigenous species (NIS); operational taxonomic unit (OTU); Phylogeny; RNA, Ribosomal, 18S - genetics; Sampling; Seawater; Sequence Analysis, DNA; Sequencing; Sponges; Underwater; underwater sampling devices; Urochordata; High-throughput sequencing (HTS); operational taxonomic unit (OTU); Ciona savignyi; underwater sampling devices; 18S rRNA gene; non-indigenous species (NIS)
• ISSN: 0892-7014; 1029-2454
• DOI: 10.1080/08927014.2015.1028923

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. Perspex
TM
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.