Environmental DNA Metabarcoding Reveals Distinct Spatial and Seasonal Patterns in Estuarine Fish Communities in Taiwan

To understand the spatial and seasonal variations of fish communities in Taiwanese estuaries, this study collected environmental DNA (eDNA) water samples and assessed environmental parameters from four estuaries in northeastern, southeastern, northwestern, and southwestern Taiwan between February and December 2023. The 12S rRNA genetic marker was used as a mini-barcode to detect fish compositions in 16 samples. Assessment of environmental parameters revealed that (1) there were significant differences between estuaries but no differences between seasons; (2) the northwestern estuary exhibited the greatest seasonal variation; and (3) the greatest spatial variation was exhibited in summer. Fish community analysis revealed that (1) fish diversity was highest in the northeastern estuary and lowest in the southeastern estuary; (2) fish compositions significantly differed among the estuaries; (3) fish compositions in the southeastern estuary exhibited the greatest seasonal variation, and those in the northeastern estuary exhibited the smallest seasonal variation; (4) fish compositions in winter slightly differed from those in the other seasons; and (5) invasive fish species were present in all estuaries. In summary, the fish compositions in Taiwanese estuaries were influenced by local environmental variables and ocean currents.