1 Introduction
Large river systems are essential for providing critical foraging,
breeding ground, and nursery habitats for a variety of fauna and are
considered among the most productive ecosystems worldwide (Wang et al.,
2020a; Wang et al., 2021b). Fish, as consumers at high trophic levels in
river food webs, represent the sum of a wide range of complex trophic
interactions (Wang et al., 2018b). Linking the ecological indicators of
fish communities to human interference remains an important goal for
river managers (Zou et al., 2020). The distribution, composition and
diversity of fish communities are commonly used as proxies to assess an
ecosystem’s health and integrity. To appropriately manage and protect
aquatic ecosystems, it is essential to develop effective and
eco-friendly monitoring approaches to collect field data and obtain
biological parameters (Kumar et al., 2022; Shu et al., 2021).
Traditional monitoring of fish diversity has depended largely on census
methods such as electrofishing, gill/hoop/seine netting, and
dredging/trawling (Wang et al., 2020a; Wang et al., 2019a). However,
those methods have always been limited by their low sampling
efficiencies, destructiveness to organisms, and strict reliance on
taxonomic expertise (Sakata et al., 2020; Zhang et al., 2020). The
application of environmental DNA (eDNA) metabarcoding for fish diversity
analysis has emerged and offers a new avenue for characterizing fish
diversity in river ecosystems (Pont et al., 2018). It provides
cost-effective, dependable, rapid and continuous investigations for
monitoring and assessing fish diversity, which is crucial for the timely
and effective management and conservation of river and estuary
ecosystems (Garlapati et al., 2019).
The metabarcoding approach coupled with the use of eDNA is a potentially
powerful tool for surveying and assessing aquatic diversity. Numerous
studies have demonstrated the utility of eDNA metabarcoding for
assessing fish diversity (Rourke et al., 2022). Researchers have
successfully applied eDNA metabarcoding to monitor fish diversity in
freshwater and seawater samples from different habitats, especially in
streams, reservoirs, estuaries and oceans (Civade et al., 2016; Stoeckle
et al., 2017; Yao et al., 2022; Zou et al., 2020). The results from
these studies have shown that eDNA metabarcoding is a sound
biomonitoring tool for use in the conservation and management of aquatic
ecosystems (Nguyen et al., 2020). Currently, the application of eDNA
metabarcoding to monitor and assess biodiversity is at the forefront of
the available methods used by ecologists and conservation scientists
(Beng and Corlett, 2020; Bernos et al., 2023).
Many studies have compared eDNA results to those from traditional
methods and have shown a correlation between the results from the two
approaches (Lacoursière-Roussel et al., 2016; Port et al., 2016). In
some studies, eDNA analysis was superior for characterizing fish
biodiversity compared to traditional techniques such as electrofishing
and hoop netting (Nguyen et al.,
2020; Pont et al., 2018). In other studies, the results obtained from
eDNA have been comparable to those of traditional methods in which
fishes are caught through visual dive surveys and trawling (Port et al.,
2016; Zou et al., 2020). Previous studies have shown that eDNA
metabarcoding retains a higher diversity of taxa than the traditional
method; however, the practical application of eDNA in evaluating the
composition and structure of fish communities has been less explored,
and whether eDNA could replace traditional monitoring is still unknown.
The river systems of southern China, in a typical subtropical monsoon
climate zone, serve as reserves for biodiversity conservation. Due to
disproportionate use of coastal wetland resources and intense
anthropogenic activities (i.e., drainage, reclamation, and pollution),
subtropical river ecosystems (e.g., the Pearl River) have been badly
damaged, and their biodiversity and bioresources have seriously
declined. To investigate the distribution and composition of fish
communities in this area, eDNA metabarcoding studies combined with
electrofishing surveys were conducted. In addition, the diversity of
fluvial fishes observed by electrofishing with the characterization of
eDNA collected concurrently from rivers by metabarcoding was compared.
The objectives of our study include 1)
using a metabarcoding protocol to
assess the eDNA-based composition and diversity of fish communities; 2)
analysing the response between eDNA OTU richness and fish amounts (e.g.,
individual number and biomass); and 3) exploring the application of eDNA
in assessing environmental influences on fish diversity.