Microbes or microorganisms are the primary producers of ecosystem services for biogeochemical cycles of the earth and biological systems. Xenobiotics mark a new anthropogenic era, "the Anthropocene," and they represent a source of artificial selection of the structure and composition of microbial biodiversity. As a result, anthropogenic disturbances are detrimental to microbial systems and induce adaptive changes or damage in their metagenomic repertories. During resistance and recovery, the ecological processes governing the assembly of microbial communities cannot be dissociated from those of microbial evolution. This work stems from the transdisciplinary intersection of ecotoxicology, microbial ecology, metagenomics and bioinformatics. The main goal is to understand the adaptive signatures of microbial resistance and resilience in two models. The first is environmental (E) composed of a lake-bound watershed contaminated by heavy metals. The second model is hostassociated (HA), consisting of an experimental system of perch (Perca flavescens) intoxicated with cadmium using two steady and gradual regimes. Three novelties summarize the work of this doctoral thesis. Firstly, the phenomenon of taxon-function decoupling has been demonstrated for the first time, in the E system under selective pollution gradient, and second, within the cutaneous microbiota in the HA system during its recovery stage. Third, the microbiota assembly modelling in the HA system suggested mixed effects of ontogenesis, and selective pressure during the period of resistance and recovery. The increase in cadmium bioaccumulation in liver tissues of perch can argue the persistence of the long-term effects of selection during the recovery stage. In conclusion, our work showed that the adaptation of microbial metagenomic repertories could be revealed through functional and taxonomic redundancy patterns observed at the scale of taxon-function decoupling. The gap between functional and taxonomic diversity reflects an adaptive strategy by horizontal gene transfer among environmental communities microbial under gradual disruption In the HA system, the microbiota assembly shows a gradient of neutral and non-neutral processes. Finally, the taxonomic drift is a significant ecological force, more effective in the environmental system than in the intestinal system during and after the disruption.