Marine Fish Detection by Environmental DNA (eDNA) Metabarcoding Approach in the Pelabuhan Ratu Bay, Indonesia

Diversity studies in marine ecosystems have experienced many developments with molecular applications through the environmental DNA (eDNA) metabarcoding approach. This method has widely used in identifying rare species, invasive species, and biodiversity information in both freshwater and marine water environments. In this study, the eDNA metabarcoding approach was the first applied to estimate fish diversity surrounding the Pelabuhan Ratu Bay waters. Five liters of seawater samples have been collected from five spots of the surrounding port area. The metabarcoding technique was applied out by using combination DNA barcoding and the next-generation sequencing (NGS) method by MiSeq platform. The MiFish Pipeline for data analyzing to get species estimation and reads numbers for quantifying the fish abundance in this location. DNA successfully identified 20 species, which commercially in the traditional fish market in Pelabuhan Ratu. Then, the eDNA metabarcoding revealed that 44 marine fish species representing 36 genera, 24 families, and ten orders exist in Pelabuhan Ratu Bay's surrounding water. Several marine fish not included in economically but have ecological value in marine fish diversity. Furthermore, fish fall into the category of vulnerable fish (Thunnus obesus), poisonous fish (Acanthurus lineatus, Acanthurus xanthopterus, Siganus vermiculatus, and Siganus fuscescens), and migratory fish. Regular surveys to determine the fluctuations and effects of human activities are necessary to monitor marine diversity, both the effect of over-exploitation and potential pollution from the coastal areas around the Pelabuhan Ratu Bay.