Assessing pelagic fish biomass through ddPCR Analysis of eDNA and eRNA

Aim:
This study investigates the use of environmental DNA (eDNA) and RNA (eRNA) as a tool for monitoring pelagic fish stocks across a large spatial scale. Specifically, we assess how well molecular concentrations correspond to fish biomass estimates from trawl surveys. We also compare eDNA and eRNA concentrations in surface waters and deeper layers to explore how these molecules are distributed through the water column.

Methods:
During the annual pelagic stock assessment cruise aboard R/V Jákup Sverri, quadruplicate water samples were collected at three depths: 5 m (surface), 60 m (midwater), and 500 m (bottom), using Niskin bottles mounted on a CTD (Conductivity, Temperature, Depth) rosette. In total, 332 samples were collected at 33 stations across the Faroe Islands’ Exclusive Economic Zone. DNA and RNA were extracted in the laboratory and quantified using digital droplet PCR (ddPCR) assays targeting mackerel (Scomber scombrus) and herring (Clupea harengus) from all locations. ddPCR data were then compared to biomass estimates from Catch Per Unit Effort (CPUE), to evaluate how well eDNA and eRNA reflect fish abundance across depths and locations.

Results and discussion:
All samples yielded high eDNA and eRNA concentrations; however, ddPCR results varied with sampling depth. Surface samples (5 m) produced ddPCR amplification results that closely mirrored CPUE-based biomass patterns. In contrast, ddPCR results from midwater (60 m) and bottom (500 m) samples did not reflect CPUE patterns, despite similar nucleic acid yields. Notably, ddPCR results for eDNA and eRNA were highly compatible, showing consistent spatial patterns across depths and stations.

Conclusions:
Our findings indicate that eDNA and eRNA from pelagic fish are most reliably detected—and biologically relevant—at the depth where the fish are actively present, with limited vertical dispersal of molecules. The strong correlation between eDNA and eRNA suggests both are reliable proxies for fish biomass, with eRNA potentially offering greater sensitivity due to its faster degradation rate. These findings lay the groundwork for ongoing work using vessel-based underway systems—drawing seawater from 5–8 m— as a practical, scalable tool for routine molecular monitoring of pelagic fish stocks.