Application of environmental DNA metabarcoding to identify fish
community characteristics in subtropical river systems
Fish play vital roles in river ecosystems; however, traditional
investigations of fish usually cause certain ecological damage.
Extracting DNA from aquatic environments and identifying DNA sequences
offers an alternative, non-invasive approach for detecting fish species.
In this study, environmental DNA (eDNA), coupled with PCR and
next-generation sequencing, and electrofishing were used to compare
their effects in identifying fish community characteristics. In three
subtropical rivers of southern China, fish specimens and eDNA in water
were collected from headwaters to estuaries. Both eDNA OTU richness and
individual abundance (including number and biomass) could group 38
sampling sites into eight spatial zones with significant differences in
local fish community composition. Compared with the order-/family-level
grouping, the genus-/species-level grouping could more accurately
recognize the differences between upstream zones I − III, midstream
zones IV − V, and downstream zones VI – VIII. From headwaters to
estuary, two environmental gradients significantly influenced the
longitudinal distribution of fish species, including the first gradient
composed of habitat and physical water parameters and the second
gradient composed of chemical water parameters. The high regression
coefficient of alpha diversity between eDNA and electrofishing methods
as well as the accurate recognition of dominant, alien, and biomarker
species at each spatial zone indicated that eDNA could characterize fish
community attributes at a similar level of traditional approach.
Generally, our results demonstrated that eDNA metabarcoding can be used
as an effective tool in revealing fish composition and diversity, which
is important for using the eDNA technique in aquatic field monitoring.