Little is known about the potential impacts of accidental or incidental releases of manufactured nanomaterials to microbial ecosystem services (e.g., nutrient cycling). Here, quantum dots (QDs) coated with cationic polyethylenimine (PEI) were more toxic to pure cultures of nitrogen-cycling bacteria than QDs coated with anionic polymaleic anhydride-alt-1-octadecene (PMAO). Nitrifying bacteria (i.e., Nitrosomonas europaea) were much more susceptible than nitrogen fixing (i.e., Azotobacter vinelandii, Rhizobium etli, and Azospirillum lipoferum) and denitrifying bacteria (i.e., Pseudomonas stutzeri). Antibacterial activity was mainly exerted by the QDs rather than by their organic coating or their released QD components (e.g., Cd and Zn), which under the near-neutral pH tested (to minimize QD weathering) were released into the bacterial growth media at lower levels than their minimum inhibitory concentrations. Sublethal exposure to QDs stimulated the expression of genes associated with nitrogen cycling. QD-PEI (10 nM) induced three types of nitrogenase genes (nif, anf, and vnf) in A. vinelandii, and one ammonia monooxygenase gene (amoA) in N. europaea was up-regulated upon exposure to 1 nM QD-PEI. We previously reported up-regulation of denitrification genes in P. stutzeri exposed to low concentrations of QD-PEI. (1) Whether this surprising stimulation of nitrogen cycling activities reflects the need to generate more energy to overcome toxicity (in the case of nitrification or denitrification) or to synthesize organic nitrogen to repair or replace damaged proteins (in the case of nitrogen fixation) remains to be determined.