Interacting effect of diclofop-methyl on the rice rhizosphere microbiome and denitrification

A better knowledge of the intertwined effects of herbicides on plant physiology and microbiome as well as nutrient biogeochemical cycles are needed for environmental management. Here we studied the influence of herbicide diclofop-methyl (DM) on the rice root microbiome and its relationship with N cycle. To do so, we exposed rice seedlings to 100 μg/L DM and studied rhizosphere microbiota using MiSeq-pyrosequencing, root exudation by GC–MS, and denitrification activity by 15N isotope-tracing and qRT-PCR. The richness and diversity of rhizosphere microorganisms, significantly increased after DM exposure combined with an increase in root exudation of amino acids, sugars, and fatty acids. Transcription of denitrification-related gene and denitrification rate increased significantly in the rice rhizosphere. Our results suggest that DM strongly influenced the root exudation of bacteria nutrients, which affected root microbiome community and potentially influenced N cycle in rice rhizosphere. [Display omitted] •The rhizosphere microbiome acts as a highly evolved external functional milieu for plants.•The interactions between rhizosphere microbiota, exudates and plant stress remain poorly understood.•Herbicide (diclofop-methyl) affected rice root exudates.•The richness and diversity of rhizosphere microorganisms were significantly affected by root exudates.•The residual diclofop-methyl affected the rice root microbiome community and promoted the potential soil denitrification.