Culture-Independent Analysis of Linuron-Mineralizing Microbiota and Functions in on-Farm Biopurification Systems via DNA-Stable Isotope Probing: Comparison with Enrichment Culture.

Our understanding of the microorganisms involved in biodegradation of xenobiotics, like pesticides, in natural and engineered environments is poor. On-farm biopurification systems (BPSs) treat farm-produced pesticide-contaminated wastewater to reduce surface water pollution. BPSs are a labor and cost-efficient technology but are still mainly operated as black box systems. We used DNA-stable isotope probing (DNA-SIP) and classical enrichment to be informed about the organisms responsible for degradation of the phenylurea herbicide linuron in a BPS matrix. DNA-SIP identified , , and an unknown genus as the dominant linuron assimilators. While linuron-degrading strains have been isolated repeatedly, has never been associated before with linuron degradation. Genes and mobile genetic elements (MGEs) previously linked to linuron catabolism were enriched in the heavy DNA-SIP fractions, suggesting their involvement in linuron assimilation. BPS material free cultivation of linuron degraders from the same BPS matrix resulted in a community dominated by , while was not observed. Our study provides evidence for the role of in linuron biodegradation in a BPS, alongside other organisms like , and further shows that cultivation results in a biased representation of the linuron-assimilating bacterial populations.