Fishing eDNA in One of the World’s Largest Rivers: A Case Study of Cross-Sectional and Depth Profile Sampling in the Yangtze

The world’s largest rivers are home to diverse,
endemic,
and threatened fish species. However, their sheer sizes make large-scale
biomonitoring challenging. While environmental DNA (eDNA) metabarcoding
has become an established monitoring approach in smaller freshwater
ecosystems, its suitability for large rivers may be challenged by
the sheer extent of their cross sections (>1 km wide and tens of
meters
deep). Here, we sampled fish eDNA from multiple vertical layers and
horizontal locations from two cross sections of the lower reach of
the Yangtze River in China. Over half of the ASVs (amplicon sequence
variants) were detected in only a single combination of the vertical
layers and horizontal locations, with ∼7% across all combinations.
We estimated the need to sample >100 L of water across the cross-sectional
profiles to achieve ASV richness saturation, which translates to ∼60
L of water at the species level. No consistent pattern emerged for
prioritizing certain depth and horizontal samples, yet we underline
the importance of sampling and integrating different layers and locations
simultaneously. Our study highlights the significance of spatially
stratified sampling and sampling volumes when using eDNA approaches.
Specifically, we developed and tested a scalable and broadly applicable
strategy that advances the monitoring and conservation of large rivers.