Glyphosate-Induced Shifts in Edaphic Microbiota: A Comparative Study of Bacterial and Fungal Responses in Historical Milpa Soils

Glyphosate is the most widely used herbicide worldwide and in Mexico; however, its effects on soil microbiota in traditional agroecosystems remain unclear. We evaluated bacterial, archaeal, and fungal responses to commercial glyphosate in three representative karst soils of the Yucatán Peninsula (black Leptosol, red Leptosol, and red Cambisol) historically associated with the Mayan milpa system. The high-throughput sequencing of the 16S rRNA V4 and ITS1 regions was used to assess diversity patterns and differential abundance. Glyphosate application did not significantly alter alpha or beta diversity; however, fifteen taxa classified at the genus level exhibited shifts in relative abundance. Most bacterial taxa were depauperated in treated soils, whereas others, such as Arthrobacter, were enriched after application, indicating the presence of tolerant or resistant bacteria that may play a role in glyphosate degradation. Cordyceps, an entomopathogenic fungus, was depleted, indicating potential for natural pest control. The similarity of the core microbiota between samples with and without glyphosate application indicates that these communities are resilient. Overall, under short-term exposure, glyphosate induced compositional shifts in specific taxa without major effects on community structure but with potential implications for soil functionality and resilience in the Mayan milpa.