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

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.

Comparison of species-specific qPCR and metabarcoding methods to detect small pelagic fish distribution from open ocean environmental DNA

“…Surveys using eDNA have been performed in rivers, lakes, and coastal areas [5][6][7][8][9]. However, the eDNA method faces more challenges in the open ocean [10,11]. The validity of 'eDNA survey in the open ocean' (hereafter OceanDNA) is unclear, given the lower density of creatures like fish and zooplankton in the open ocean [10,11].…”

“…However, the eDNA method faces more challenges in the open ocean [10,11]. The validity of 'eDNA survey in the open ocean' (hereafter OceanDNA) is unclear, given the lower density of creatures like fish and zooplankton in the open ocean [10,11]. For example, zooplankton were detected in the coastal region, but not in the open waters, in 1.5 L water samples using COI metabarcoding [11].…”

Message in a Bottle: Archived DNA Reveals Marine Heatwave-Associated Shifts in Fish Assemblages

“…In addition, metabarcoding of the stomachs of larval fishes can then identify actual prey items that were consumed by larvae. Evaluating the larval prey field and gut contents through metabarcoding will help us to finally understand the drivers of recruitment volatility in coastal pelagic and other fishes, allowing for improved prediction of forage fish population dynamics (Barbato et al, 2019; Erdozain et al, 2019; Garcia-Vazquez et al, 2021; Mariac et al, 2018; Nielsen et al, 2021; Pitz et al, 2020; Sydeman et al, 2020).…”

Framing Cutting-Edge Integrative Deep-Sea Biodiversity Monitoring via Environmental DNA and Optoacoustic Augmented Infrastructures

“…Unfortunately, imaging does not always allow sufficiently high taxonomical precision, and generally requires the physical collection of samples to validate species identification. Furthermore, organisms' attraction to or avoidance of submerged infrastructures is likely to cause some degree of bias toward the local communities (Widder et al, 2005;Aguzzi et al, 2019;Rountree et al, 2020;Garcia-Vazquez et al, 2021).…”

“…Significant advances in molecular methodology and bioinformatics, accompanied by a steady increase in computational power, have made "omics" technologies and data increasingly accessible, with great potential to fill gaps in biodiversity monitoring capabilities of deep-sea cabled observatories (Heidelberg et al, 2010;Garcia-Vazquez et al, 2021). One of the more recent contributions of "omics" to biodiversity monitoring is linked to the collection and analysis of genetic material extracted directly from environmental samples (sediment, water, ice, and air, etc.…”