Genomics-informed insights into microbial degradation ofN,N-dimethylformamide

Abstract

Effective degradation of N,N-Dimethylformamide (DMF) is challenging as only few bacterial isolates are known to be capable of degrading DMF. Here, we analyzed 20,762 complete genomes and 28 constructed draft genomes for the genes associated with DMF degradation. We identified 952 genomes that harbor genes involved in DMF degradation, expanding the known diversity of prokaryotes with these metabolic capabilities. Our findings suggest horizontal acquisition of DMF-degrading gene via plasmids are important in the order Rhizobiales and genus Paracoccus, but not most other lineages. Degradation pathway analysis reveals that most putative DMF degraders using aerobic Pathway I will accumulate the methylamine (MA) intermediate, while members of the Paracoccus, Rhodococcus, Achromobacter, and Pseudomonas genera could potentially mineralize DMF completely under the aerobic condition. The aerobic DMF degradation via Pathway II is more common than thought and is primarily present in α-, β-Proteobacteria and Actinobacteria classes. Most putative DMF degraders could grow with supplied nitrate anaerobically (Pathway III), however, genes for the use of compound methyl-CoM to produce methane were not found in selected genomes. These analyses suggest that microbial consortia could be more advantageous in DMF degradation than pure culture, particularly for methane production under the anaerobic condition. The identified genomes form an important foundation for optimizing DMF degradation and have important applications for the bioremediation of DMF-containing wastewaters.