Enhancing neotropical fish monitoring using dietary DNA of detrivorous natural samplers

Neotropical freshwater fish face alarming biodiversity loss, yet current
capture-based monitoring methods are costly, invasive, and heavily reliant
on taxonomic expertise. There is an urgent need for more efficient and
accurate biomonitoring tools to assess the impacts of increasing
anthropogenic pressures. Natural samplers are emerging as a promising
biomonitoring tool - living organisms that, through feeding, aggregate the
DNA of species in their immediate environment. Here, we investigated
whether abundant and widely distributed freshwater shrimp could provide
reliable snapshots of local fish assemblages in large neotropical rivers
using multi-marker metabarcoding analysis of their dietary DNA (dDNA).
Shrimp dDNA analysis revealed almost as many species (68 species) as an
intensive 10-day inventory of the study area (70 species), and nearly
three times more species than gillnet-based methods commonly used in
surveillance programs. The generalist and opportunistic feeding behaviour
of these detritivorous organisms enabled detection of a broad spectrum of
species, including small fish typically overlooked by traditional surveys.
The vast majority of fish taxa were identified at the species level thanks
to nearly exhaustive barcoding reference databases, demonstrating the high
taxonomic resolution of this approach. Synthesis and applications: The
relative ease of sampling and processing makes shrimp dDNA analysis
particularly suitable for rapid biodiversity assessments, complementing
observational approaches that provide data on fish abundance, biomass, or
condition. As the cost of molecular analyses continues to decrease, this
method offers an efficient tool for implementing large-scale monitoring
programs in neotropical rivers and detecting localized ecosystem impacts
of anthropogenic disturbances.