Application of eDNA metabarcoding in the assessment of fish biodiversity in Philippine mangroves: Challenges and opportunities

Abstract

Biodiversity assessments are important in designing mangrove conservation and restoration programs. In the Philippines, conventional biodiversity assessment methods (e.g., trap nets, fish visual census) can be time-consuming, labor-intensive, and expensive. In recent years, environmental DNA (eDNA) metabarcoding has been an emerging tool for rapid biodiversity monitoring as it is fast, non-intrusive, and can provide broader detection of fauna. But, it is still subject to various field sampling and laboratory analysis constraints. Here, we applied the eDNA metabarcoding method to document and assess fish biodiversity in mangroves from two biogeographic regions in the Philippines: Oriental Mindoro in the West Philippine Sea and Sorsogon in the Northern Philippine Sea. Using 12S genetic markers from eDNA water samples, we detected 89 fish species from 44 families. Only twelve species were commonly detected in both sites. Several species were found in the Philippines’ list of economically important aquatic organisms while one species (Epinephelus fuscoguttatus) was classified as Vulnerable in IUCN’s Red List of Threatened Species. Seventy-six percent more species were detected in Sorsogon probably because the sampling sites were within a seascape of mangroves, seagrasses, and coral reefs. In contrast, the lesser species detected in Oriental Mindoro could probably be because of the more limited sampling points to coastal fringes. Our results serve as baseline data and the first obtained using this method in the country. However, we observed some limitations that should be addressed to improve the method: (1) lack or absence of a comprehensive reference database specific to Philippine aquatic organisms; (2) low eDNA reads which could be attributed to insufficient on-site filtration due to turbid seawaters common in Philippine mangroves; and (3) possible cross-contaminations that can affect comparative analyses. Despite these limitations, we were able to demonstrate the usefulness of this technique in doing rapid assessments which could address knowledge gaps in Philippine mangrove biodiversity studies and contribute to its conservation programs.