Long-term organic fertilization fosters modular microbial networks: A global analysis of soil bacteriome responses

Fertilization is a widely adopted agricultural practice with profound impacts on soil microbial communities. However, the global response of soil bacteriome to different fertilization strategies remains inadequately characterized. Here, we conducted an integrated analysis on over 2900 raw
bacterial amplicon sequencing samples from 82 studies worldwide to assess how microbial communities respond to inorganic (IF), organic (OF), and combined (IFOF) fertilization across environmental gradients. Results demonstrate that the effects of fertilization on community structure and diversity depend strongly on local soil properties, although OF maintained stable alpha-diversity across varying pH and experimental durations. Notably, meta-cooccurrence networks revealed that organic amendments (OF and IFOF) promoted microbial networks with higher complexity, modularity, and stability compared to IF and unfertilized controls, suggesting strengthened ecological resilience. The IFOF network contained several highly connected keystone taxa including Acidothermus, Devosia, and Bradyrhizobium, which exhibited sensitivity to gradients in soil nutrients, pH, and climate variables. Random forest models further confirmed the ecological importance of these taxa, achieving high accuracy (>90%) in classifying fertilization treatments. Moreover, threshold indicator taxon analysis quantified responses of these keystone taxa to environmental gradients, identifying optimal organic fertilization amendment rates to support keystone taxa (e.g., Bradyrhizobium abundance peaked at 15 tons per hectare per year). This study provides the first global-scale integration of sequencing data with meta-network analysis, revealing
how long-term fertilization influences soil microbial communities and associations.