Facing chemical contamination of aquatic ecosystems, it is crucial to understand how fluctuation in structural and functional microbial biodiversity due to environmental changes modulates the sensitivity of microbiomes to chemical stress, as these communities play a significant role in ecosystem function and services. To address this challenge, the combination of metabolomics and metagenomics is particularly relevant as it allows for the assessment of microbial activity and taxonomic and genic diversity, respectively. The aim of this study is to characterize the relationship between the fluctuation of microbial activity (i.e. meta-metabolome) and the structural biodiversity (diversity of species and genes) due to changing environmental conditions over the course of a year. Periphytic biofilms were colonized monthly on glass slides in a hypereutrophic pilot pond. After quenching and freeze-drying, samples were split for both omics. The meta-metabolome was extracted using biphasic extraction and further analysed through LC-HRMS-based untargeted metabolites. Data processing and metabolite annotation were performed using a combination of Mzmine3, GNPS tools and Sirius5. Shotgun whole genome sequencing was carried out on an Illumina NextSeq 2000 platform. Taxonomic assignation was performed with Kraken2 by using the NCBI RefSeq V208 nt, while relative abundance was further determined at the genus level using Brachen. The annotated datasets were further analysed by using phyloseq and vegan R packages to determine alpha and beta-diversity following rarefaction normalisation. The results showed significant shift in the richness and evenness of both the meta-metabolome and the microbiome. Further ordination and PERMANOVA based on (un)weighted UniFrac distances highlighted significant phylogenetic discrepancies in periphyton between month. Microbiome and meta-metabolome relationship over the year according to environmental conditions will be further explored through neural network analyses (mmvec). Altogether, these results will support better understanding of potential functional impairment of microbiomes by the chemical stress in the global changes context.Read less <