Integrating Direct Experimental Fishing and Environmental DNA Metabarcoding to Assess Fish Biodiversity in the Cibareno River, Indonesia, to Support Fishway Design

A fishway is an engineered structure designed to help fish navigate past artificial barriers in rivers such as dams, weirs and regulators. An effective fishway design requires an understanding of fish biodiversity and migration requirements of the local community. To support the conceptual design of a fishway at Caringin Weir in the Cibareno River in Indonesia, we conducted a fish biodiversity assessment using experimental fishing and an eDNA metabarcoding survey. In early 2022, experimental fishing was conducted at six sampling sites upstream and downstream of the planned weir, and the sites were surveyed seven times during the wet and dry seasons. Environmental DNA sampling was conducted once during the wet season at each of the six sites. A total of 72 aquatic species were detected, comprising 40 fish species and seven crustacean species captured during experimental fishing and 36 fish species identified through eDNA metabarcoding. Twelve fish species (18.46%) were detected using both methods. The total number of all species caught and species richness in experimental fishing varied significantly between upstream and downstream areas (p < 0.05), but there were no significant differences between seasons (p > 0.05). There was also a significant difference in the species richness upstream and downstream using eDNA metabarcoding (p < 0.05). There were also numerous diadromous species, further highlighting the need for an effective fishway design to enable these species to complete their migrations. Based on the species present, migratory behaviour and economic importance, we prioritised six fish and crustacean species to be considered during fishway design: Anguilla marmorata, Tor tambra, Barbodes binotatus, Sicyopterus sp., Rhyacichthys aspro and Macrobrachium sp.