Rare Earth Elements (REEs) are naturally present in the environment and in biological systems, but little is still known about the effect of their agricultural application on the growth of soil microorganisms. We investigated by flow cytometry the growth of some bacteria strains, very important in agricultural science, in presence of increasing levels of either a mix of REEs nitrates or lanthanum nitrate alone by an in vitro assay miniaturized procedure. We used it to fix the dangerous range of REEs nitrates and Lanthanum nitrate concentrations and their DL100 on bacterial viability, evaluated by flow cytometry, and then we compared the results with those obtained by in vitro standard culture (agar medium in Petri plate). We also tried to study, by Biolog technology, the changes in metabolism which occurred when bacteria are treated with a critical concentration of REEs nitrates and lanthanum nitrate alone.