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Metabarcoding is a promising tool for identifying species of fish from their eggs and larvae

Before assuming adult form, most fish species go through egg and larval stages where they are collectively referred to as “Ichthyoplankton”. Understanding ichthyoplankton diversity and distribution patterns in aquatic environments provides invaluable information on the overall health of an ecosystem, its capacity to recover from disturbances and helps guide management and conservation efforts.

Until recently, past research has relied on difficult time-consuming visual identification techniques to determine the species within samples collected in the field. Today, DNA metabarcoding is a promising tool that is transforming this procedure by allowing for rapid and more accurate identification of species present in plankton samples, facilitating finer-scale community analyses to help address ecological questions.

In this study, metabarcoding was used to study the composition and distribution of ichthyoplankton species on the east coast of South Africa. The overall aim was to: (1) create a presence-absence matrix, (2) test for presence in a wide range of habitats and geographic distribution ranges, and (3) explore patterns in community composition in relation to prominent environmental features.

How OBIS was used in this study

Fish species detected by the metabarcoding analysis were cross referenced with occurrence records in OBIS, as well as the World Register of Marine Species (WoRMS) and Global Biodiversity Information Facility (GBIF) system. These online repositories were used to validate and confirm the distribution range, habitat and occurrence of the species found.

The findings confirmed previous research that the study area is an important spawning area for several fish species and for retention of their eggs and larvae. It was also determined that fish species community composition varies significantly with latitude, distance to coast, and distance to the shelf edge.

Fig1

Figure 1. This figure illustrates the proportional occurrence of ichthyoplankton species detected by metabarcoding and then categorised according to existing data on: (a) adult habitats, (b) ocean zones and (c) geographical distribution ranges (WoRMS; GBIF; OBIS).

Fig2

Figure 2. This figure illustrates the diversity of ichthyoplankton species found in the study area. Diversity was found to be highest in the north (closer to the tropics) and along the shelf edge.

DNA metabarcoding is a promising tool to simultaneously identify the species present in taxonomically complex samples. At the same time, due to current limitations, the authors suggest that it is best used as a complement to traditional methods rather than be used as a standalone technique. For example, DNA metabarcoding can result in an over or underestimate of species richness and diversity due to sampling limitations, e.g., sampling intensity, sampling depth, seasonality.

Further, as many species throughout the world do not yet have corresponding barcode records available in online reference libraries (e.g., BOLD and NCBI GenBank), this further reduces the possibility of species level identification using this technique. The authors encourage continued foundational biodiversity research to link DNA barcodes to taxonomically validated species to overcome this hurdle in future studies.

Full publication available at:

Govender, A., S.T. Fennessy, S.N. Porter and J.C. Groeneveld. 2023. Metabarcoding of ichthyoplankton communities associated with a highly dynamic shelf region of the southwest Indian Ocean. PLoS ONE 18(4): e0284961.