Among nanomaterials, nano-sized zero-valent iron particles represent a new generation of products used for environmental remediation strategies and are considered to be a valid option for treating contaminated soil and groundwater systems. In the USA, nZVI treatment is a well-accepted practice, whereas until recently, few applications have been carried out in Europe, a region that lacks regulations for nZVI environmental remediation practices. A paucity of research that assesses the health and environmental risks of nZVI treatment is currently impeding its commercialisation. A variety of possible nZVI toxicity mechanisms toward bacteria have been investigated, including the disruption of cell membrane integrity, the interference with respiration, DNA or protein damage, and oxidative stress by the generation of reactive oxygen species. High intracellular ROS concentrations can activate redox-sensitive pathways, which in turn can lead to the activation of a variety of scavenging enzymes. Regardless of the exact mechanism, nZVI toxicity on the microbial community is not well understood, although previous studies have indicated that toxicity seems to be dose- and species-dependent. The identification and validation of new markers to assess nanomaterial toxicity are Ginsenoside-Ro needed and “omic” tools would provide complementary information to the classical ecotoxicological tests that are currently available. Hence, the transcriptional changes of bacterial genes such as those encoding enzymes involved in the nitrogen biogeochemical cycle and nitrite reductase, DNA replication, glycolysis, and the cellular oxidative stress response can provide information about the impact of nanoparticles on environmental microorganisms. Proteomics is also recognised as a valuable tool in ecotoxicology research; the term ‘ecotoxicoproteomics’ is used to define protein profiling techniques developed for the purpose of identifying new treatment-related markers that are capable of providing information about early responses to a toxicant. Therefore, damage to the microbial cell envelope could serve as a basis for new ecotoxicity assays involving nanomaterials. In this study, the abundance of several membrane proteins was significantly reduced following nZVI exposure. Among them, 8 protein spots that were dramatically affected by nZVI treatment were identified as porins and transporters. ABC transporters play important roles in nutrient uptake and the export of toxic substances. Interestingly, we found that the iron ABC transporter Atractylenolide-III periplasmic protein, PST 4066 and TonB-dependent siderophore receptor, both which are involved in iron uptake, were downregulated. An abundance of iron promotes the formation of ROS, in turn leading to the damage of key cellular components, and thus, the decreased abundance of both proteins should diminish the availability of iron within the cell. We hypothesise that a similar scenario, such as the upregulation of the expression of this stress responsive protein, may occur in P. stutzeri following nZVI exposure. Fe-superoxide dismutase, which acts as superoxide scavenger was also found to be upregulated. Similar results have been reported in P. stutzeri following quantum dots exposure.