Environmental DNA metabarcoding for the detection of the silverlip pearl oyster (Pinctada maxima) offshore of Eighty Mile Beach in northwest Australia

Abstract

Effective fishery management relies on accurate knowledge of the spatial distribution of stocks of target species to efficiently focus fishing efforts. However, the distribution and abundance of species such as the silverlip pearl oyster (Pinctada maxima) can be difficult to determine with traditional survey methods since populations are patchy, often occur in low densities, and individuals can be quite cryptic, living partially buried in sediment. Environmental DNA is increasingly used to survey marine species and has proven to be particularly useful in detecting rare or elusive organisms. Here, we compared the presence of silverlip pearl oysters detected via eDNA metabarcoding to traditional towed video surveys offshore of Eighty Mile Beach, northwest Australia. Seawater samples were collected at the end of towed video transects and sites were categorised into shallow (<40 m depth) or deep (40 m +) groups. We applied an oyster-specific 16S metabarcoding assay as well as a universal 18S assay to identify potential indicator taxa associated with the presence of pearl oysters. Using the 16S assay, we detected silverlip pearl oysters at three of the 12 sites sampled, and found that eDNA records generally matched towed video transect data, with both survey methods detecting the target species predominantly in inshore waters at depths <40 m. Our results indicate that metabarcoding of seawater eDNA can be applied to detect cryptic species of commercial importance but highlight limitations around detecting organisms at very low abundances.