Metal containing engineered nanomaterials (ENMs) are now commonly used in various industrial and commercial applications. Many of these materials can be transformed during waste water treatment and ultimately enter terrestrial ecosystems via agriculturally applied biosolids. It is unclear how agriculturally important soil microbes will be affected by exposure to environmentally relevant, sublethal concentrations of ENMs and their transformation products (i.e., ions, aggregates, etc.). A method was developed, which puts O2 consumption responses in terms of viability, and tested by examining the toxic effects of Ag+, Zn2+, and Ni2+ ions on the plant growth promoting rhizobacterium (PGPR) Bacillus amyloliquefaciens GB03. The method was then used to examine the toxicity of Ag+, as-synthesized polyvinylpyrrolidone-coated silver ENM (PVP-AgENMs), and 100% sulfidized AgENM on B. amyloliquefaciens GB03, and two additional PGPRs Sinorhizobium meliloti 2011, and Pseudomonas putida UW4. S. meliloti was found to have the highest LC50 for Ag+ and PVP-AgENMs (6.6 and 207 μM, respectively), while B. amyloliquefaciens and P. putida exhibited LC50's for Ag+ and PVP-AgENMs roughly half those observed for S. meliloti. The authors observed species-specific O2 consumption responses to ENM and ion exposure. PVP-AgENMs were less toxic than ions on a molar basis, and abiotic dissolution likely explains a significant portion of the observed toxic responses. Our results suggest microbes may exhibit distinct metabolic responses to metal and ENM exposure, even when similar LC50's are observed. These findings together illustrate the importance of understanding species-specific toxic responses and the utility of examining O2 consumption for doing so.