Understanding molecular mechanisms of interactions between nanoparticles and bacteria is important and essential to develop nanotechnology for medical and environmental applications. Quantum dots (QDs) are specific nanoparticles with unique optical properties and high photochemical stability. In the present study, direct interactions were observed between cationic QDs and bacteria. Distinct fluorescence quenching patterns were developed when cationic QDs interacted with Gram negative and Gram positive bacteria. The aggregation of QDs on bacterial surface as well as fluorescence quenching depends upon the chemical composition and structure of the bacterial cell envelopes. The presence of lipopolysaccharide is unique to Gram-negative bacterial surface and provides negatively charge areas for absorbing cationic QDs. The effects of lipopolysaccharide were proved on fluorescence quenching of cationic QDs. In contrast to Gram-negative bacteria, the presence of teichoic acids is unique to Gram-positive bacterial cell wall and provides negatively charged sites for cationic QDs along the chain of teichoic-acid molecules, which may protect QDs from aggregation and fluorescence quenching. This study may not only provide insight into behaviors of QDs on bacterial cell surfaces but also open a new avenue for designing and applying QDs as biosensors in microbiology, medicine, and environmental science. (C) 2015 Elsevier Inc. All rights reserved.