EDNA metabarcoding of small plankton samples to detect fish larvae and their preys from Atlantic and Pacific waters

Eva Garcia-Vazquez,Alba Ardura,Sara Fernandez,Oriane Georges

doi:10.1038/s41598-021-86731-z

Abstract

Zooplankton community inventories are the basis of fisheries management for containing fish larvae and their preys; however, the visual identification of early-stage larvae (the “missing biomass”) is difficult and laborious. Here, eDNA metabarcoding was employed to detect zooplankton species of interest for fisheries from open and coastal waters. High-Throughput sequencing (HTS) from environmental samples using small water volumes has been proposed to detect species of interest whose DNA is the most abundant. We analyzed 6-L water samples taken from subtropical and tropical waters using Cytochrome oxidase I (COI) gene as metabarcode. In the open ocean, several commercial fish larvae and invertebrate species important in fish diet were found from metabarcodes and confirmed from individual barcoding. Comparing Atlantic, Mediterranean, Red Sea, and Pacific samples we found a lower taxonomic depth of OTU assignments in samples from tropical waters than in those from temperate ones, suggesting large gaps in reference databases for those areas; thus a higher effort of zooplankton barcoding in tropical oceans is highly recommended. This and similar simplified sampling protocols could be applied in early detection of species important for fisheries.

Highlights

Zooplankton community inventories are the basis of fisheries management for containing fish larvae and their preys; the visual identification of early-stage larvae is difficult and laborious
Ardura et al.[11] have shown that DNA Barcoding is a promising methodology for ichthyoplankton inventory, and Fuentes et al.[12] have applied quantitative Polymerase Chain Reaction for quantifying toxic algae, but individualization is still necessary, and new developments are still needed for application in large-scale routine surveys
The list of Operational Taxonomic Units (OTUs) found in all the samples and their taxonomic assignments is in Supplementary Table 3

Summary

Introduction

Zooplankton community inventories are the basis of fisheries management for containing fish larvae and their preys; the visual identification of early-stage larvae (the “missing biomass”) is difficult and laborious. Comparing Atlantic, Mediterranean, Red Sea, and Pacific samples we found a lower taxonomic depth of OTU assignments in samples from tropical waters than in those from temperate ones, suggesting large gaps in reference databases for those areas; a higher effort of zooplankton barcoding in tropical oceans is highly recommended This and similar simplified sampling protocols could be applied in early detection of species important for fisheries. The new methods of HTS on environmental samples, generically called metabarcoding, can help in species detection and inventory, as has been proven for Polarstern ballast water[13,14,15], open waters16, estuaries[17], marine b enthos[18] and biofouling c ommunities[19], among others They are employed for prokaryotes and some specific taxonomic groups like ciliates, in large oceanic expeditions like Tara. Being the standardization of the process very important[23,24], if appropriate controls are included along the data generation process, DNA metabarcoding will provide a valuable tool in ecosystem assessments[25]

Methods

Results

Conclusion