The investigation of microbial communities and their interactions with their environments is a field of research that engaged the scientific community for several decades. We study in the laboratory microorganisms isolated from freshwater and atmospheric ecosystems in different conditions. The aim of this internship was to optimize the metabolomic workflows of four microorganisms (Pseudomonas syringae, Rhodococcus rhodococcus, Microcystis aeruginosa, Chlorella spp.) from extraction to annotation of compounds. Objectives: i) Optimize metabolome extraction protocol for each microorganism, ii) Implementation of a PeakForest database with MetaCyc and NPATLAS databases, iii) Annotation of microorganism's metabolomes.