Bioremediation 3.0: Engineering Pollutant-Removing Bacteria in the Times of Systemic Biology
Dvorak, P., Nikel, P.I., Damborsky, J., de Lorenzo, V.
BIOTECHNOLOGY ADVANCES 7: 845-866 (2017)
Elimination or at least mitigation of the toxic effects of chemical waste released to the environment by industrial and urban activities relies on the catalytic activities of microorganisms in the environment. Because of their capacity to evolve rapidly, bacteria possess the biochemical power to tackle a large number of molecules either mobilized from their geological repositories through human action (e.g., hydrocarbons, heavy metals) or generated through chemical synthesis (e.g., xenobiotic compounds). While naturally occurring microbes have already a considerable ability to get rid of many environmental pollutants without any external intervention, the onset of genetic engineering in the 1980s opened the possibility to rationally design bacteria for the catabolism of specific compounds that could eventually be released into the environment as the bioremediation agents. Alas, the complexity of this endeavour and the lack of fundamental knowledge made such a recombinant DNA-based bioremediation to be virtually abandoned one decade later. Yet, in a twist of events, the last few years have witnessed the emergence of new systemic fields (including systems and synthetic biology, and metabolic engineering) that allow revisiting the same environmental pollution challenges through more powerful approaches. Furthermore, the focus on contaminated sites and chemicals has been broadened with the phenomenal problems of anthropogenic CO2 emissions or the accumulation of plastic waste at a global scale. In this article, we analyze how contemporary systemic biology is helping to bring the design of bioremediation agents back to the core of Environmental Biotechnology. To this end, we inspect a number of recent strategies for catabolic pathway construction and optimization and we bring them together by proposing an engineering workflow. Moreover, we examine upstream (e.g., protein engineering) and downstream (e.g., dispersal strategies) approaches that boost the impact of the catalytic activities at stake.