Herbicide-induced disruption of soil bacterial communities compromises microbial suppressiveness against Meloidogyne paranaensis in coffee agroforestry soil

Abstract

The application of herbicides in coffee agroforestry systems is increasing, yet the consequences for soil microbial suppressiveness against plant-parasitic nematodes remain poorly understood. We evaluated the impact of five herbicides – glyphosate, clethodim, flumioxazin, saflufenacil and pyroxasulfone – on the microbial-mediated suppressiveness of a herbicide-naïve coffee agroforestry soil against Meloidogyne paranaensis . In vivo bioassays quantified nematode infection in a model plant-tomato ( Solanum lycopersicum L. cv. 'Santa Clara') through gall and egg counts per gram of root across two independent experiments. In vitro chemotaxis assays measured the behavioural attraction of second-stage juveniles (J2) to herbicide-exposed microbiomes. Bacterial community structure, alpha diversity, and beta diversity were assessed by 16S rRNA gene amplicon sequencing, with LEfSe analysis to identify differentially abundant taxa. Saflufenacil and pyroxasulfone significantly increased gall and egg densities relative to the untreated control, whereas glyphosate and clethodim showed no significant effect. Microbiomes exposed to saflufenacil and pyroxasulfone attracted J2 (chemotaxis index > 0.6), whereas glyphosate-treated and control microbiomes were repellent. Sequencing revealed herbicide-specific shifts in bacterial community composition and diversity, with suppression-associated genera ( Chitinophaga , Bdellovibrio , Ramlibacter , Thermomonas ) depleted and xenobiotic-tolerant genera ( Sphingomonas , Cupriavidus ) enriched under saflufenacil and pyroxasulfone. These findings demonstrate that herbicide selection directly modulates the suppressiveness of soil microbiomes towards M. paranaensis , highlighting the need for microbiome-aware weed management strategies in perennial agroforestry systems.