Environmental DNA analysis at multiple taxonomic levels highlights geographic variation in subtropical coastal marine communities

Abstract

In this study, environmental DNA was used to assess marine diversity across the southern part of Okinawa Island, Japan, located in the subtropics. Diversity analysis was performed for prokaryotes and eukaryotes. Differences in diversity were detected between the west side of Okinawa (an area exposed to groundwater influenced by land-derived loads) and the east side (an area where coral reefs, beaches, and seagrass beds coexist). In particular, the community composition of prokaryotes, for which 16S rRNA metabarcoding analysis was performed, differed markedly between the east and west sides of the island. Differences in the composition of eukaryotic communities between the east and west coasts are relatively unclear, likely due to the fact that 18S rRNA metabarcoding targets a wide range of species (including almost all eukaryotic taxonomic groups), making it difficult to identify differences. On the other hand, MiFish analysis indicated that distributions of various fish species differed markedly between the east and west coasts of the island, suggesting a close relationship between differences in the coastal environment and the habitat selection by fish. We show that prokaryotic communities can be evaluated using eDNA analysis in order to monitor extensive geographic environments via water cycles. This can then be used to promote understanding of geographic variations of marine community structures of eukaryotes, including fish.

Fig. 1

A bar plot for prokaryotes at the phylum level. The top 20 taxa that appear most frequently and others are shown.

Fig. 2

A bar plot for eukaryotes at the phylum level. The top 20 taxa that appear most frequently and others are shown.

Fig. 3

A bar plot for fishes at the species level. The top 20 taxa that appear most frequently and others are shown.

Fig. 4

Left: nMDS plot of community similarities of prokaryotes. Groups are based on results of a cluster analysis set to 2 clusters. Right: diversity index of prokaryotes.

Fig. 5

Left: nMDS plot of community similarities of eukaryotes. Groups are based on the results of cluster analysis set to 2 clusters. Right: diversity index of eukaryotes.

Fig. 6

Left: nMDS plot of community similarities of fishes. Groups are based on results of a cluster analysis set to 2 clusters. Right: diversity index of fishes.

Fig. 7

Map showing survey sites around southern Okinawa Island.