Distinct Community Compositions of Prokaryotes, Eukaryotes, and Fishes Revealed Through Environmental <scp>DNA</scp> Analysis at Different Salinities Around Ishigaki Island, Okinawa, Japan

ABSTRACT Environmental DNA metabarcoding has proven effective for local biodiversity assessment with relatively low sampling effort and cost. However, it is still necessary to evaluate whether it can capture changing community composition along with environmental parameters such as salinity. Salinity is a fundamental abiotic feature that defines suitable habitats for many creatures, mainly due to osmotic considerations. We comprehensively investigated environmental DNA collected from two environments with different salinities, oligohaline (greater than salinity 0.5) and limnetic (less than salinity 0.5), using metabarcoding at different taxonomic levels: 16S prokaryotic universal metabarcoding, 18S eukaryotic universal metabarcoding, and MiFish fish‐specific metabarcoding. These results showed that shared and unique genera in each salinity displayed different patterns at all taxonomic levels. An nMDS plot revealed that community composition is clearly segregated between salinity groups based on 16S analysis, but overlaps slightly when based on MiFish results. This may reflect osmotic tolerance, as fish communities change gradually, whereas bacterial communities change dramatically with sharp thresholds. PERMANOVA showed that these two salinity groups have significantly different community compositions at 16S, 18S, and MiFish levels. We further estimated taxa that differed in abundance in each salinity. Our results revealed that saltwater indicator bacteria such as Planococcaceae and Woeseiaceae were significantly more abundant in oligohaline sites, demonstrating that metabarcoding is capable of detecting halophilic bacteria, even though differences in salinity are relatively small. Several potentially harmful taxa, that is, fish‐borne fluke, Haplorchis taichui , or toxic bloom‐forming dinoflagellates, Karlodinium , were detected in limnetic and oligohaline sites, respectively. Considering Ishigaki Island's great biodiversity and in view of public health, further monitoring utilizing eDNA metabarcoding is necessary.