Abstract

Background The widespread use and environmental persistence of the herbicide glyphosate raise significant concerns for human and ecological health. Developing efficient and sustainable remediation strategies is therefore crucial. Microbial degradation and biocontrol are two promising approaches. This study aimed to isolate and characterize a bacterial strain capable of both degrading glyphosate and antagonizing soil-borne fungal pathogens, and to evaluate its impact on soil microbial communities. Results This study isolated and characterized a novel bacterial strain, NPDY10, identified as Paenibacillus ottowii, which exhibits dual beneficial functions: efficient glyphosate degradation and broad-spectrum antagonism against soil-borne fungal pathogens. Under optimal conditions (pH 7–7.5, 30–35 °C), strain NPDY10 completely degraded 400 mg L⁻¹ of glyphosate within four days, utilizing the herbicide as a carbon source. Metabolic profiling via UPLC-MS/MS confirmed glyphosate degradation via the aminomethylphosphonic acid (AMPA) pathway In a rice paddy field trial, the application of NPDY10 reduced glyphosate levels in paddy water, and a visible foam layer formed, serving as a visual indicator of active metabolism. Furthermore, strain NPDY10 demonstrated broad-spectrum antifungal activity in vitro, inhibiting 17 plant-pathogenic fungi with inhibition rates ranging from 60.00% to 92.00%. Analysis of soil microbial communities in a subsequent maize cultivation season revealed that NPDY10 treatment increased bacterial diversity and suppressed the relative abundance of pathogenic fungal genera such as Fusarium and Gibberella. Conclusion Paenibacillus ottowii NPDY10 represents a promising multi-functional agent for sustainable agriculture, potentially combining glyphosate bioremediation with direct and indirect biocontrol effects through modulation of soil microbial communities, thereby contributing to improved soil health.