Use of passive sampling in environmental DNA metabarcoding technology: Monitoring of fish diversity in the Jiangmen coastal waters

Abstract

Environmental DNA (eDNA) metabarcoding technology is proving to be the most up-to-date and promising method for monitoring marine fish diversity. Fish eDNA is usually collected on a filter membrane after the filtration of water. Not only does this require the use of specialized equipment, but the amount of filtered water needed is also difficult to meet. The recently proposed passive eDNA collection method can expand the sampling scale, providing new perspectives for monitoring marine biodiversity. The role of collection methods in eDNA surveys, however, remains unclear. In this study, a low-cost custom framework with two types of filter membrane materials was used to conduct passive submersion samplings at the north and south ends of Shangchuan Island, Jiangmen, China. After defined periods of submersion, the filter membranes were recovered and eDNA extracted. Metabarcoding techniques were applied to detect fish species information in the eDNA samples. A total of 106 marine fish species from 27 orders, 53 families, and 92 genera, including one cartilaginous fish, were identified in the samples. The majority of fish detected by active filtration were also found in the passively collected samples, within the same location. Both sampling methods, therefore, showed similar species richness. Passive sampling was effective in identifying fish species diversity and provided a higher spatial resolution owing to the sample replicates. Passive sampling was also more sensitive in detecting species that differ significantly in abundance (biomarkers) between different sampling depths. When active filtration is not possible, or when large-scale sampling is the purpose of the study, passive sampling methods certainly provide a promising alternative. The findings of our study provide guidance for fish surveys and continuous bio-stereoscopic monitoring in coastal waters.