Impacts of chlorimuron-ethyl on rhizosphere nitrogen cycling functional genes and microbial remediation by Chenggangzhangella methanolivorans CHL1 in soybean systems

The herbicide chlorimuron-ethyl (CE) is widely applied in soybean fields, but the long-term accumulation of its residues in soil poses risks to soil health and nitrogen cycling. Although many CE-degrading microbial strains are known, its impact on rhizosphere nitrogen cycling functional genes and microbial communities, as well as the effectiveness of remediation by CE-degraders remain unclear. Chenggangzhangella methanolivorans CHL1 is a novel CE-degrading bacterium with promising potential for herbicide bioremediation. Here, we tested CE at recommended (low-dose) and fivefold doses (high-dose) in field and pot experiments. Subsequently, we integrated soil physicochemical properties and metagenomic sequencing data to evaluate CE’s effects and CHL1-driven remediation of soybean rhizosphere nitrogen cycling functional genes and microbial communities. Results showed that CHL1 significantly decreased soil CE residues, shortened the half-life of CE by more than 50%, and alleviated CE-induced inhibition of soybean growth and nodulation. Notably, CE exposure reduced taxa associated with nitrogen fixation ( Bradyrhizobium ) and denitrification (Nocardioides) but enriched taxa associated with nitrification (Nitrososphaerota and Nitrospirota) in the soybean rhizosphere. Moreover, CE had consistent effects on the gene abundances of these nitrogen cycling-related modules, especially those related to nitrogen fixation. The inhibition rates of nifD , nifH , and nifK reached approximately 85.0%–93.3% across different stages. Furthermore, functional contribution analysis showed a transient increase in the contributions of Nitrososphaerota and Nitrospirota to nitrification-related functions. In contrast, the contribution of Bradyrhizobium to nitrogen fixation and denitrification-related functions was persistently reduced. These changes were accompanied by reductions in NH4 ± -N levels, increases in NO3 – -N levels, and decreases in soil pH. Importantly, by degrading CE, CHL1 alleviated the inhibition of the abundances of taxa and genes associated with nitrogen fixation and denitrification. For nitrogen fixation-associated genes, CHL1 reduced the inhibition rates to 2.7%–64.5% under CE exposure. CHL1 also reduced the CE induced enrichment of taxa and functional genes associated with nitrification, which was accompanied by partial recovery of soil nitrogen forms and pH. These findings enhance our understanding of how CHL1 mitigates CE-induced shifts in rhizosphere nitrogen cycling-related microbial and functional profiles. They also provide scientific support for the field application of degrading bacteria in soil remediation.