Perspectives from an eDNA metabarcoding pilot project in the Banggai MPA, Central Sulawesi, Indonesia

Abstract

The Banggai MPA is one of many Indonesian MPAs established or reestablished as a result of the shift from regency to provincial level governance over waters 0–4 NM from shore under Act 23/2014. The MPA covers a substantial proportion of Banggai Archipelago coastal ecosystems and around 90% of endangered Banggai cardinalfish (Pterapogon kauderni) endemic habitat. An expedition in 1998 reported high fish biodiversity; however, logistics and taxonomic expertise requirements mean that similar methods are not realistic for collecting baseline or monitoring biodiversity data to support MPA management. A pilot project in 2018 collected water samples (four shallow-water coastal sites, three replicates per site) around Banggai Island for environmental DNA (eDNA) metabarcoding using two molecular markers: COI mtDNA and 12S rRNA. COI data were overwhelmingly dominated by a few phytoplankton species, reflecting challenges using this marker in areas with dense phytoplankton, and could not be analyzed further. The 12S rRNA sequences were processed and aggregated into amplicon sequence variants (ASVs) using the Anacapa Toolkit. These data provide a snapshot of fish diversity by site, although accumulation curves indicate three samples per site is insufficient to provide a comprehensive record. Identified taxa overlapped and exceeded in number those detected in 1998. The percentage of ASVs unassigned at species and genus level (e.g., gobies and cardinalfishes) and taxonomic ambiguities indicate a need for combined classical taxonomic and barcoding studies to enhance nucleotide databases (GenBank/BOLD), ideally with regional voucher specimen repositories. Furthermore, the study revealed the need for further capacity building in metabarcoding data analysis.