Résumé
Tropical estuaries are hyper-diverse ecosystems, hosting essential
habitats for freshwater, euryhaline and marine life. Understanding how
biological communities are distributed in these systems has long been a
challenge because of their inherent dynamic nature, and the diversity of
interacting natural pressures and anthropogenic stressors they are
subjected to. In this study, we used environmental DNA (eDNA)
metabarcoding to examine the structure of multi-taxonomic communities in
estuarine ecosystems (diatoms, crustacean, fish and eukaryote as a whole)
and their relationships with environmental drivers in three differentially
impacted locations facing the Great Barrier Reef in Central Queensland
(Australia). We first demonstrated that eDNA signals from sediment and
water matrices provide complementary information, and that both should be
monitored for a more holistic understanding of community trajectories in
anthropogenically-impacted aquatic environments. We also observed that,
independently of the taxonomic group considered, communities were
primarily structured by the ecological conditions of the estuary. A
within-estuary differentiation along an upstream-downstream gradient was
detected but only for small-bodied organisms, which further adds credence
of eDNA approaches as an ecologically relevant tool for monitoring
fine-scale biodiversity patterns even in profoundly dynamic environments.
Finally, the different communities exhibited contrasting response
patterns, in terms of diversity, composition and uniqueness, to the
anthropogenic gradient. Hence, our findings emphasize the need for
multi-taxonomic assessments, for which eDNA is well-suited, to better
understand the impacts of multiple stressors on biodiversity, and thereby
assist decision makers in the protection and management of tropical
estuaries.