Elucidation of the complete degradation mechanism of N, N-dimethylformamide (DMF) and substrate preference within a synthetic bacterial consortium (DMF_syn) formed via a "top-down" strategy

The challenge posed by the chemical stability of N,N-dimethylformamide (DMF) renders its biological treatment a complex endeavor. Despite the isolation and characterization of numerous DMF-degrading bacterial strains, their limited adaptability to diverse environments has resulted in suboptimal efficacy in the treatment of actual DMF-containing wastewater. This research aims to address this predicament by employing a "top-down" approach to engineer a synthetic bacterial community termed DMFsyn. The mineralization of 0.5 % (v/v) DMF (similar to 4725 mg L-1) was efficiently carried out by DMFsyn within 4 days. Notably, robust DMF degradation capabilities across a broad spectrum of environmental conditions were observed. In scenarios where N,N-dimethylacetamide (DMAC) and N-methylpyrrolidone (NMP) coexisted with DMF, degradation followed a sequential pattern: NMP > DMAC > DMF. Through 16S rRNA gene sequencing, and metagenomic analysis, potential functional genes and species responsible for DMF degradation were unveiled. The active DMF degraders in DMFsyn, including Paracoccus aminovorans bin8, Hyphomicrobium sulfonivorans bin2, Hyphomicrobium zavarzinii bin0, Paracoccus zhejiangensis bin23, and Aquamicrobium lusatiense bin4, were substantiated by metaproteomic analysis. Furthermore, another DMF-mineralizing bacterium Aminobacter niigataensis DMFA1 was isolated from DMFsyn. Molecular dynamics simulations indicated that the preference for DMAC over DMF at the community level is dictated by the substrate specificity of DMFases from Sphingosinicella microcystinivorans bin6. By harnessing a multi-omics approach, conducting pure culture studies, and employing molecular simulations, an intricate mechanism governing DMF degradation and substrate preference within the DMFsyn was elucidated.