Microbial modulation of soil pH: A self-benefiting mechanism exemplified by Bacillus

Most studies focus on how microorganisms respond to environmental changes, yet much less is known about how microorganisms alter their surroundings. In this study, we employed Bacillus, a model genus known for their resilience and broad application, to investigate the hypothesis that microorganisms can alter environmental conditions to better suit their needs. Using a combination of global soil dataset analysis and controlled laboratory experiments, we explored the adaptive strategies and mechanisms by which microorganisms respond to varying soil pH conditions. Our results from global soil dataset analysis revealed that soil pH significantly influenced the abundance, diversity, and functional capacity of Bacillus, with the highest abundance observed at around pH 6.5. When inoculated in acidic or alkaline soil for 35 days, Bacillus shifted the pH towards neutrality. Compared with control (CK), only Bacillus inoculation significantly decreased alkaline soil pH from 8.13 to 7.36, and raised acidic soil pH by 5.86–5.91. Metabolic profiling indicated pH-dependent modulation: alkaline metabolites (e.g., laurylamine) were enriched in acidic medium of pH 5 (1529-fold), while acidic metabolites (e.g., organic acids) increased in alkaline medium of pH 8 (1.5-fold), reflecting an adaptive pH stress response. Microbial community analysis revealed that the inoculation of Bacillus not only altered the native microbial compositions but also showed close associations with specific microbial taxa, which were speculated to have a potential cooperative role in regulating soil pH. Our findings highlight that microorganisms can modify their environment in predictable ways, offering valuable insights into microbe-environment interactions.