The toxicity of single walled carbon nanotubes (SWCNTs) to a model bacterium, Escherichia coli ATCC 8739 was investigated. Estimates of E. coli viability following treatment with SWCNTs were similar using four viability methods: plate count, galactosidase enzyme assay, LIVE/DEAD® Baclight™ assay, and RNA quantificatio. Pristine SWCNTs, carboxylic functionalized SWCNTs (SWCNT-COOHs) and hydroxyl functionalized SWCNTs (SWCNTOHs) were used to assess toxicity. Regardless of the length of SWCNTs, the toxicity was in the following order: SWCNT-OHs < SWCNTs < SWCNT-COOHs. While there was no difference in the impact of short and long SWCNT-OHs, the long pristine SWCNTs and SWCNT-COOHs were more toxic than the corresponding short SWCNTs. The viability of cells exposed to all three types of SWCNTs was greater with increasing cell density. Alterations of cell morphology ware observed after the cells were exposed to SWCNTs. Entrapment of cells in alginate and polyvinyl alcohol (PVA) as a means to limit the antibacterial effect of SWCNTs was examined. The results showed that cell entrapment could reduce the bactericidal effects of SWCNTs. Calcium alginate and PVA provided equivalent cell protection against SWCNTs. The toxicity of SWCNTs for entrapped cells depended on the length and concentrations of SWCNTs, the presence of functional groups, and the initial cell density. Transcriptomic and proteomic analyses were used to study the molecular mechanisms by which SWCNTs induce bactericidal activity. Expression levels of genes and proteins, particularly phage shock proteins (Psp) that are known to react under membrane stress such as iv pspA, pspB, and pspC, changed following cell exposure to SWCNTs. Expression of the Psp operon was affected by the length, concentration, and functionalization of SWCNTs. Overall, this study provided multiple methods that can be used to quantify the toxicity of SWCNTs for bacterial cells. A way to mitigate the bactericidal effects of SWCNTs was identified and verified. Gene and protein expression, particularly expression of the Psp operon, were reported in cells stressed by exposure to SWCNTs.