You shall not pass! (unless you’re stress resistant): Selection-driven restructuring and transient invasion in freshwater mussel microbiomes under antimicrobial exposure

Global declines of freshwater mussel populations and of the ecosystem services they provide have been linked to anthropogenic stressors including pollution, but the impacts of antibiotic spillover, e.g. through aquaculture or pharmaceutical wastewater effluents, on mussel health are unclear. Mussel-associated microbiomes contribute to key benthic processes such as nutrient cycling and organic matter transformation. While adverse effects on fish gut microbiomes are increasingly recognized, ecological impacts of antibiotic discharge on microbiomes of non-target organisms like mussels are poorly understood, with unknown consequences for the functioning of aquatic habitats. Using 16S rRNA gene sequencing, we investigated how exposure to florfenicol and peracetic acid via rearing water effluents affected the microbiome of Anodonta cygnea. Under baseline conditions, the microbiome was distinct from water and dominated by taxa like Ferruginibacter aligning with its suspension-feeding lifestyle. Both compounds significantly altered microbial community structure, with temporal convergence of the host microbiome with external water microbiota. Observed shifts were characterized by the enrichment of detoxifying Dechloromonas and Sphingomonas as well as modulatory taxa like Aureispira and Nannocystis, with core commensals persisting across treatments. Co-application of peracetic acid and florfenicol increased florfenicol concentrations in water, highlighting potential compound interactions that may alter florfenicol degradation dynamics and could increase antibiotic pressure in aquatic habitats. Although the stability of core taxa indicates partial resilience rather than complete dysbiosis after single exposure, this study highlights potential ecological implications of antibiotic spillover in freshwater environments, as exemplified here by aquaculture but relevant for risk assessments of other pollution sources.