The difference of activity of the nanoparticles mentioned in your question can be determined both by the properties of the materials and nature of the microorganisms. The properties may depend on kind of the material of the nanoparticle, its size, shape, etc. But the microorganism may be more or less resistant to the surrounding conditions, including the interaction of different nanoparticles. The resistance (or susceptibility) can be determined by the adapting to these and other environmental conditions, and what is the connection with the construction of various defense mechanisms which enable it to survive under the circumstances.

In the case of bacteria can have for example gram-positive or gram negative nature and ability to produce less or more egzobacterial mucus which often help to isolate the bacteria from environmental conditions. Usually the substances contained in these mucus can determined difference on microbial activities .