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.

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The movement of organisms facilitated by anthropogenic activities is a serious threat to marine diversity, especially for endemic species that may be outcompeted from non-indigenous species (NIS). In this study, we have analyzed communities inhabiting the north of the Gulf of Aqaba, Red Sea, employing environmental DNA (eDNA) metabarcoding. That gulf is especially rich in species and population endemism. We have detected NIS representing 36% of the total number of species found from eDNA. Primary producers were more abundant in the NIS than in the native fraction of species, suggesting that functional diversity could be altered if NIS thrive there. We discuss maritime traffic as a factor that may enhance the introduction of non-natives in this region and emphasize the importance of the control of these species that may threaten the rich endemic biota of the Red Sea.