Different New Fertilizers Differentially Modulate Wheat Yield, Rhizosphere Microbiota and Soil Fertility

The use of alternative fertilizers offers a promising approach to improving soil health and crop productivity, yet their relative effects on rhizosphere microbial communities remain insufficiently understood. This two-year field study on the Huang-Huai Plain, China, assessed the impacts of controlled-release fertilizer (CRF), organic fertilizer (OF), and microbial fertilizer (MF), relative to a conventional synthetic fertilizer (CF), on soil properties, wheat yield, and microbial community composition. Soil chemical parameters, microbial diversity (via 16S rRNA and ITS sequencing), and wheat yield were analyzed. OF significantly enhanced soil organic matter (14.97%), available nitrogen (28.70%), phosphorus (20.59%), potassium (33.06%), and grain yield (17.58%) compared to CF, likely due to sustained nutrient release and stimulation of microbial activity. In contrast, CRF decreased soil organic matter (−19.2%) and phosphorus availability, with only modest yield improvement (3.50%). MF enriched plant-beneficial taxa, including Bacillus and Arthrobacter, and improved yield by 9.39%. Fungal communities showed greater responsiveness to fertilizer type than bacterial communities, with OF and CRF promoting notable increases in fungal diversity. LEfSe analysis revealed treatment-specific microbial biomarkers such as Saccharothrix (OF), Azotobacter (CRF), and Nitrospira (MF), while correlation analysis linked Cyphellophora (OF) and Epicoccum (CRF) to yield enhancement. These findings underscore the potential of organic amendments to simultaneously boost soil fertility, microbial diversity, and crop productivity, outperforming controlled-release and microbial fertilizers. MF demonstrated promise for microbiome-targeted interventions, whereas CRF may pose risks to long-term soil health. This study supports microbiome-informed, organic-inclusive fertilization strategies for sustainable agriculture.