Dissecting the assays to assess microbial tolerance to toxic chemicals in bioprocessing

•Tolerance to toxic chemicals is a limiting issue in industrial bioprocesses.•Industrial practice should guide tolerance assay design.•Many parameters affect tolerance assays.•High-throughput assays play a key role in tolerance engineering.

Microbial strains are increasingly used for the industrial production of chemicals and biofuels, but the toxicity of components in the feedstock and product streams limits process outputs. Selected or engineered microbes that thrive in the presence of toxic chemicals can be assessed using tolerance assays. Such assays must reasonably represent the conditions the cells will experience during the intended process and measure the appropriate physiological trait for the desired application. We review currently used tolerance assays, and examine the many parameters that affect assay outcomes. We identify and suggest the use of the best-suited assays for each industrial bioreactor operating condition, discuss next-generation assays, and propose a standardized approach for using assays to examine tolerance to toxic chemicals.