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Enhancing neotropical fish monitoring using dietary DNA of detrivorous natural samplers

Bonnet, Baptiste1; Condachou, Céline2; Lassalle, Gilles1; Besnard, Anne-Laure1; Roussel, Jean-marc1; Covain, Raphael3; Le Bail, Pierre-Yves1; Vigouroux, Régis4; Murienne, Jerome2; Brosse, Sébastien2; Lalague, Hadrien4; Quemere, Erwan1

Published Mar 18, 2026 on Dryad. https://doi.org/10.5061/dryad.tht76hfdg

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Abstract

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.