Environmental genomics and more generally omics, have influenced the paradigm of microbes response to toxics and pollutants and the understanding of who is affected and how this happens. Nanomaterials are promising nano-scaled objects that have revolutionized the technology and enabled the marketing of a dizzying number of products, routinely used by consumers. The nano-size feature endows these materials with properties that are different from their non-nano counterparts, allowing major innovation in technology. Besides, the nano-size aspect promotes interactions at the cellular and macromolecular level, with potential consequences. A tiny alteration in nanomaterial design (size, shape, surface charge, coating or functionalization, aggregation trend…) can upset their toxicological profile and the interaction with biological systems. The nanomaterials that are released by the use of nano-enabled products and technologies, end their life-cycle in all environmental compartments, air, water, soil, sediments, including humans. This worrying spreading together with their potential biological impacts, rate them as emerging contaminants. Recognizing that innovation in technology is needed and even inevitable, we used DNA metabarcoding and metabolomics not to expose the toxicity and the environmental impact of nanomaterials on bacteria, but to contribute to a safer and eco-design approach of these objects. Safety considerations, since the design first steps and during the entire life-cycle of new-generation nanomaterials, is one of the challenges of the Labex SERENADE. We aim to contribute to design nanomaterials with a reduced environmental impact over their life-cycle, on a plant-bacteria-soil model. For that purpose, we took advantage of the versatile profile of nanomaterials to modulate their interactions with biological systems, by using microbial enzymatic activities, and omics (metabarcoding and metabolomics) to examine the impact of particle size, coating, and inherent activity behaviour towards terrestrial ecosystems. How nanomaterials shaped the bacterial community in the unplanted soil, the rhizosphere and plant roots was considered by focusing on the core consortia of these compartments. The communication will emphasis on cerium oxide nanomaterials, as an example of safer-by-design approach. This work is a contribution to the Labex Serenade (ANR-11-LABX-0064) funded by the “Investissements d’Avenir” French Government program of the French National Research Agency (ANR) through the A*MIDEX project (ANR-11-IDEX-0001-02).