Metabarcoding of ichthyoplankton communities from the entrance of the Gulf of California (March, 2016)

This study aimed to identify species of marine ichthyoplankton communities from the entrance of the Gulf of California, using morphological and DNA metabarcoding methods. Twenty-eight zooplankton samples were collected by vertical trawls in the study area, from 2 to 8 March 2016. A total of 742 marine fish larvae and 333 fish eggs were separated and morphologically identified to the most precise taxonomic level or typified, respectively. Subsequently, larvae and eggs were pooled by sampling station for DNA extraction. A 12S amplicon library (167-185 bp) was constructed and sent for high-throughput sequencing on an Illumina HiSeq (2X150 bp) platform. The Obitools bioinformatic pipeline was implemented for assembly and quality control of amplicon sequences. Ecotag and BLAST searches were performed for taxonomic assignment of amplicons (similarity ≥97%) when compared with 12S fish sequences from GenBank. Metabarcoding results showed a similar number of orders, families and genera to the morphological method. However, at the species level, the DNA metabarcoding method revealed 17 species that were not recognized by the morphological method, indicating that the DNA method was more precise and contributed to the knowledge of the species richness of fishes that spawn in the study area. Furthermore, our presence/absence results aligned largely with the more common ichthyoplankton species found in most oceanographic surveys in the region. A comparison with a previous study performed in the same oceanographic survey indicates concordance with the spatial distribution of Benthosema panamense, which was delimited by temperature. However, differences with the spatial distribution of Diaphus pacificus were observed, likely because this species was concealed within unidentified eggs. In conclusion, DNA metabarcoding is a valuable complement to traditional morphological identification in ichthyoplankton research and can contribute to finding some undetected members of ichthyoplankton communities as well as geographical differences in their species richness.