Anthropogenic pressures on riparian communities: insights from genomic tools

Riparian ecosystems, situated at the interface of aquatic and terrestrial environments, support exceptionally high biodiversity and provide critical ecosystem functions, including nutrient cycling, habitat provision, and cross-boundary energy transfer. Despite their ecological importance, these systems face increasing anthropogenic pressures such as pollution, hydrological alteration, and habitat degradation, which threaten their biodiversity and functioning. Understanding how riparian communities respond to such stressors requires an integrative perspective that considers three key dimensions: organismal composition, ecological interactions, and evolutionary processes. This thesis combines genomic approaches with stress-ecology experiments to investigate how riparian invertebrate communities respond to human-induced stressors across these dimensions. In Chapter I, community metabarcoding was applied to assess how exposure to the mosquito control biocide Bacillus thuringiensis israelensis (Bti) alters chironomid emergence dynamics. A novel direct PCR metabarcoding workflow was developed, providing a cost-effective and reliable tool to capture community composition. Results indicated that altered emergence patterns were less driven by strong taxon-specific sensitivities than initially hypothesized. In Chapter II, gut content metabarcoding of riparian spiders was used to evaluate how hydrological drought reshapes trophic interactions across aquatic-terrestrial boundaries. A bleach-wash protocol was validated to remove external DNA contamination, enabling reliable dietary analyses. Results uncovered cryptic diversity within Tetragnatha spiders and showed species-specific responses to drought, suggesting that shifts in ecological niches and competition, rather than changes in prey availability, structured riparian predator populations. In Chapter III, an experimental evolution framework was applied to Chironomus riparius populations chronically exposed to Bti and copper. Population genomic analyses revealed pollutant-specific signatures of selection, linked to midgut cell repair in Bti-exposed populations and to detoxification pathways under copper exposure. These findings provide mechanistic insights into how genomic adaptation can occur within only a few generations, even before consistent phenotypic changes are detectable. Taken together, the findings demonstrate that genomic tools can substantially refine our understanding of riparian communities by resolving hidden diversity, clarifying mechanisms underlying ecological interactions, and uncovering genetic pathways of adaptation. Beyond methodological advances, this thesis highlights the interconnectedness of ecological and evolutionary processes in shaping community resilience under anthropogenic stress. By integrating composition, interaction, and evolution, the work provides a framework for anticipating how riparian ecosystems, and other connected habitats, may persist, reorganize, or decline under ongoing global change.