Metabarcoding analysis of marine zooplankton confirms the ecological role of a sheltered bight along an exposed continental shelf

Abstract

Zooplankton plays an essential role in marine ecosystems as the link between primary producers (phytoplankton) and higher trophic levels in food webs, and as a dynamic pool of recruits for invertebrates and fish. Zooplankton communities are diverse with a patchy distribution at different spatial scales, influenced by oceanographic processes. The continental shelf of eastern South Africa is narrow and exposed to the western‐boundary Agulhas Current, with some shelter against strong directional flow provided by the broader KwaZulu‐Natal Bight, a coastal offset adjacent to an estuary. We compared zooplankton species richness, diversity and relative abundance of key taxa among sheltered and exposed shelf areas using metabarcoding and community analysis, to explore the ecological role of the bight in a highly dynamic ocean region. Metabarcoding recovered higher richness and diversity at a finer resolution than could previously be achieved with traditional microscopy. Of 271 operational taxonomic units (OTUs) recovered through metabarcoding, 63% could be matched with >95% sequence similarity to reference barcodes. OTUs were dominated by malacostracan crustaceans (161 spp.), ray‐finned fishes (45 spp.) and copepods (28 spp.). Species richness, diversity and the relative abundance of key taxa differed between sheltered and exposed shelf areas. Lower species richness in the bight was partly attributed to structurally homogeneous benthic habitats, and an associated reduction of meroplanktonic species originating from local benthic–pelagic exchange. High relative abundance of a ray‐finned fish in the bight, as observed based on fish eggs and read counts, confirmed that the bight is an important fish spawning area. Overall, zooplankton metabarcoding outputs were congruent with findings of previous ecological research using more traditional methods of observation.

Metabarcoding of ichthyoplankton communities associated with a highly dynamic shelf region of the southwest Indian Ocean

“…Individual tow net samples ( S1 Table ) were homogenized for 45 s using a consumer blender (Defy PB7354X, 350 W and 22,000 rpm) [ 43 ]. Three subsamples per homogenate were taken to increase sequencing depth and improve diversity estimates.…”

“…The pooled products were consolidated into a single sample for each tow-net haul, to create 88 libraries with equimolar concentrations (5 ng/μl). Illumina Miseq sequencing was performed at the KZN Research and Innovation Platform (KRISP, South Africa) following the protocols outlined in [ 43 ].…”

Towards exhaustive community ecology via DNA metabarcoding

“…By combining primers optimized for different phyla, they were able to characterize at high resolution the diversity of the major taxonomic groups, including fish, crustaceans, echinoderms, molluscs, cnidarians and more. Govender et al (2022) included up to four different reverse primers within the same PCR reaction, all targeting the same DNA fragment. In principle an even larger number of primers could be combined, to maximize the number of taxa that are amplified at high resolution, and the multiplex might include primers targeting different genomic regions, if they have comparable performance (see below).…”

Insights into Ecological & Evolutionary Processes via Community Metabarcoding

“…Species sorting is a dominant driver in community assembly in the studied kettle hole zooplankton metacommunity. Likewise Govender et al (2022) used a metabarcoding approach to highlight the point that, while sheltered bight areas have lower pelagic zooplankton diversity due to structurally homogeneity, they actually represent important fish spawning grounds (with important ramifications for fisheries and higher-level consumers). In this case, diversity measures could thus not be used as a proxy for ecological importance.…”