Effects of Biogas Slurry Substitution for Chemical Fertilizer on Soil Properties, Shallow Groundwater Quality and Soil Microbial Communities in Winter Wheat Cultivation

Substituting chemical fertilizer (CF) with biogas slurry (BS) is a promising strategy for sustainable agriculture, yet determining appropriate substitution ratios and their impacts remains challenging across different soil-crop systems. This study investigated five BS-to-CF ratios under an equal ammonium NH4+-N loading of approximately 60–63 kg/ha (R1: 100% BS; R2: 75% BS + 25% CF; R3: 50% BS + 50% CF; R4: 25% BS + 75% CF; R5: 0% BS + 100% CF) through field experiments to evaluate their impacts on soil properties, shallow groundwater quality, and soil microbial communities during winter wheat cultivation in the Huaihe–Yangtze River divide zone. Results demonstrated that the R4 treatment optimized the soil microenvironment under the conditions tested and achieved the highest winter wheat yield (5792.28 kg/ha), surpassing the pure CF treatment (R5) while increasing soil total nitrogen accumulation by 23.68%. Groundwater monitoring indicated that full chemical fertilization (R5) induced nitrate (NO3−-N) leaching risks, reaching NO3−-N concentrations up to 4.10 mg/L at a 1.5 m depth. Conversely, BS substitution treatments (R1–R4) were associated with lower nitrate concentrations in shallow groundwater than the CF treatment, without evidence of increased toxic heavy metal contamination or persistent dissolved organic matter pollution. High-throughput 16S rRNA sequencing revealed that partial BS substitution enriched essential functional microbial taxa, including Pseudomonadota, Actinomycetota, and Chloroflexota, that are potentially involved in organic matter degradation and nutrient cycling. Overall, partial substitution of CF with BS, particularly the R4 treatment, improved crop productivity, optimized soil microbial communities, and reduced groundwater pollution risk, providing scientific support for developing green, low-carbon farming systems.