Effects of net type, tow duration, and day or night sampling on the metagenetic composition of marine zooplankton

AbstractDNA metabarcoding to determine the species composition and diversity of marine zooplankton communities is a rapidly advancing field, where the standardization of methods has yet to be fully achieved. The calibration of metagenetic composition with species records from traditional morphology-based sampling is particularly challenging because molecular identification does not rely on the presence of intact specimens. We used an experimental approach to compare the effects of sampling gear (ring-, Manta- and WP2 net), day and night (DN) sampling, and tow duration (5-, 10- and 15-minute tows) on the metagenetic composition of marine zooplankton samples collected in coastal waters of eastern South Africa. High-throughput sequencing of the cytochrome c oxidase subunit I (COI) gene region, followed by taxonomic assignment of amplicon sequence variants at 97% similarity to barcode records, was used to identify species in samples. Metabarcoding detected a total of 224 species, of which 92% matched prior occurrence records. Malacostraca was the best-represented taxonomic class (49%) followed by Copepoda (21%), Actinopterygii (21%), and Gastropoda (9%). Metagenetic species counts ranged from 9–61 species per tow, with high proportions of private species in replicate tows. Mean species counts did not differ significantly between net types, DN samples, or tow durations, respectively. Proportionate representation among classes remained within a narrow range, except when sampling deeper habitats with a smaller mesh size. DN samples showed no evidence of daily vertical migration of zooplankton. The consistency of metagenetic composition across net types, tow duration and DN sampling treatments reflects high detection sensitivity of individual-based sampling, allowing for greater flexibility in planning of zooplankton sampling regimes.