Fungicide-induced modifications in soil microbial profiles and enzyme activities: a controlled, plant-free soil microcosm study under contrasting agro-management systems

Abstract

Soil microbial communities are key indicators of bio-geochemical processes; however, their response to fungicides across various agro-management systems requires further investigation. Under controlled microcosm conditions, we evaluated the effects of the fungicides Carbendazim and Iprodione at recommended and higher rates of application on bacterial community composition, enzymatic activities, and predictive functional profiles in Typic Haplustoll soils from conventional monoculture and conservation crop rotation systems in Argentina. High-throughput 16S rRNA gene sequencing, enzymatic assays (β-glucuronidase, β-glucosidase, xylanase), and functional inference using Tax4Fun2 were used to assess microbial responses. Iprodione induced greater shifts in bacterial diversity and community structure, resulting in significant reductions in the phyla Proteobacteria and Acidobacteria, along with increases in the phylum Firmicutes. Enzymatic activity was more severely inhibited by Carbendazim, particularly within monoculture settings. Functional predictions indicated that Iprodione suppressed pathways related to amino acid and carbohydrate metabolism, energy production, and nitrogen cycling genes (nirK, nosZ), while Carbendazim exhibited milder effects. Although crop rotation alleviated some of these negative effects, both fungicides altered predicted microbial functional profiles. Iprodione had a stronger effect on the bacterial community structure and the predicted functional profiles, while Carbendazim showed stronger inhibition on enzymatic activity, especially in monoculture soils. These results provide mechanistic insight, under controlled microcosm conditions, into the potential susceptibility of soil microbial communities and enzyme activities of soil to fungicide exposure, highlighting the need of refined management strategies for preserving soil microbiological integrity.