Abstract
Summary Despite its long‐term use in bioremediation, bioaugmentation of contaminated sites with microbial cells continues to be a source of controversy within environmental microbiology. This largely results from its notoriously unreliable performance record. In this article, we argue that the unpredictable nature of the approach comes from the initial strain selection step. Up until now, this has been dictated by the search for catabolically competent microorganisms, with little or no consideration given to other essential features that are required to be functionally active and persistent in target habitats. We describe how technical advances in molecular biology and analytical chemistry, now enable assessments of the functional diversity and spatial distribution of microbial communities to be made in situ . These advances now enable microbial populations, targeted for exploitation, to be differentiated to the cell level, an advance that is bound to improve microbial selection and exploitation. We argue that this information‐based approach is already proving to be more effective than the traditional ‘black‐box’ approach of strain selection. The future perspectives and opportunities for improving selection of effective microbial strains for bioaugmentation are also discussed.