Application of antibiotics for the selective isolation of previously uncultured bacteria from activated sludge

Wastewater treatment plants (WWTPs) are essential in urban areas, ensuring the protection of both human health and the environment. Among the various technologies used for wastewater treatment, activated sludge (AS) is by far the most widespread. AS contains a complex microbial community responsible for degrading organic materials, facilitating resource recovery, and returning treated water to the environment. Understanding the composition of these microbial communities is crucial for optimizing WWTP processes. While DNA-based studies have identified which bacterial taxa are commonly found in the activated sludge and provided clues into their specific roles, culture-based methods are necessary to validate these observations. However, isolating environmental bacteria remains challenging due to the difficulty in replicating their specific growth conditions in the laboratory and competition from fast-growing bacteria. In this project, dispersed bacteria from AS were cultured in media containing ultrafiltered, sterilized AS fluid, supplemented with one of eleven antibiotics to modify microbial structure.The results showed that this method reduced microbial diversity and altered microbial composition in an antibiotic-specific manner. Although this method did not facilitate the isolation of previously uncultured genera, we successfully isolated 26 species of which 8 were novel. Five of these represent taxa previously found in AS, demonstrating that the isolation strategy can be used to obtain ecosystem-relevant species. Further attempts could be focused on tailoring growth conditions for targeting bacteria of interest after modifying the microbial profile.