Cultivable Rhizosphere Microbial Community Structure in the Yaqui Valley’s Agroecosystems

Agricultural practices affect the physical, chemical, and biological properties of soil in agroecosystems. This study evaluated the impact of food production strategies on the rhizosphere microbial communities in the Yaqui Valley, Mexico, on key crops (Medicago sativa, Brassica oleracea, Asparagus officinalis, Phaseolus vulgaris, Citrus sinensis, Zea mays, Solanum tuberosum, Triticum durum, and an undisturbed native ecosystem). Soil samples were collected from 30 cm depths across one-hectare fields and analyzed for bulk density, pH, organic matter content, and electrical conductivity. Standardized methods were used for these analyses, along with microbial isolation through culturing, PCR amplification, and DNA sequencing for microbial identification. The use of synthetic fertilizers in the region was linked to increased salinity and soil compaction. Organic matter content was notably low at ≤1.4%, which negatively impacted microbial diversity. A total of 317 microbial strains were isolated, with bacteria comprising 73% and fungi 27%. Bacillus was the most dominant bacterial genus (41% of isolates), while Aspergillus was the most abundant fungal genus (31% of isolates). Crop-specific microbial strains were identified. This study provides the first detailed insight into how agricultural practices shape microbial communities in the Yaqui Valley’s major crops, highlighting the link between soil properties and microbial diversity.