Protein-Based Liquid Fertilizers Improve Soil Fertility and Stabilize the Soil Microbiome in Water-Saving and Drought-Resistance Rice Paddies

Replacing synthetic nitrogen fertilizer with protein-based liquid fertilizers (PLFs) is a promising strategy for sustainable crop production, yet its impacts on soil fertility and soil microbiomes remain poorly understood. In a field experiment, we compared Control (unfertilized, CK; urea, CKU) with PLFs applied at 50% (C1) and 100% (C2) substitution rates across three formulations (P1–P3) at the tillering-stage topdressing fertilization, and assessed soil properties, microbial communities and functional genes. Partial substitution significantly increased soil pH by 8.2–10.0% and enhanced phosphorus and potassium availability (e.g., total P by 21.1%, available P by 59.6%), whereas full substitution maintained soil nitrogen at levels comparable to urea. The integrated fertility index (IFI) ranged from 1.60 to 1.78 and was significantly higher under C1 than under C2 and the Control. Metagenomic analysis revealed that microbial α- and β-diversity, community composition, and all 25 C/N/P functional gene groups showed no significant responses to fertilization, and field block effects often exceeded treatment effects. However, co-occurrence network analysis revealed that C1 and C2 increased network edges by 10.3% and 96.6% relative to the Control, and raised mean degree from 2.90 (CK) to 3.20 (C1) to 5.70 (C2). Structural equation modeling indicated that treatment directly shaped functional gene profiles (β = +0.41), while fertility–community–function pathways were weak, and fertilization explained 76.4% of IFI variation but only 17.3% of functional variation. Overall, these findings demonstrate that partial substitution of PLFs, particularly the silicon-enriched formulation, represents a possible strategy for improving soil fertility while preserving the soil microbiome.