Using Environmental DNA (eDNA) to Illuminate the Ocean’s Twilight Zone

The fauna of the ocean’s vast mesopelagic zone is relatively poorly studied due to the technological and logistical challenges of accessing the region. The analysis of environmental DNA (eDNA) shows great promise for efficiently characterizing aquatic biodiversity and may provide new insight into the presence of mesopelagic animals, including rare and undiscovered species that could be missed by traditional sampling approaches. Here, we assess the utility of eDNA for characterizing mesopelagic animal biodiversity. We describe the results from an August 2018 cruise in Slope Water off the northeast United States. Water samples for eDNA analysis were collected using Niskin bottles during 6 CTD casts. Sampling depths were selected based on the real-time presence of biomass as indicated by the shipboard Simrad EK60 echosounder. Metabarcoding of the 18S V9 gene region was used to assess super-specific taxonomic diversity. Environmental DNA metabarcoding results were compared with those from a net-collected (MOCNESS) plankton sample, and the efficiencies of each sampling method for detecting biodiversity were evaluated. We found that the MOCNESS sampling recovered more taxa, which is perhaps expected given the greater volume sampled by the net. However, we also found that the eDNA approach was especially useful for detecting gelatinous animals, many of which we not detected by metabarcoding the net sample. Future eDNA studies that seek to identify rare or undescribed species will benefit from large-volume in situ sampling methods.