Defining pH-associated ecological clusters and their responses to agricultural intensification

Soil pH is a major factor influencing the participation of soil microorganisms in biogeochemical processes. However, different microbial taxa exhibit varied responses to pH levels, and their ecological functions remain unclear. This gap limits our understanding of the precise pathways through which pH affects the structure and function of soil microbial communities. In this study, we identified seven ecological clusters based on their responses to pH: Acidophile, Conditioned Acidophile, Alkaliphile, Conditioned Alkaliphile, Opportunist, Conservative, and Liberalist. Acidophiles and Conditioned Acidophiles exhibited a positive correlation with nutrient cycling functions, whereas Alkaliphiles and Conditioned Alkaliphiles showed a negative correlation. Additionally, agricultural intensification (farmland vs. greenhouse) with frequent perturbation of soil pH directly or indirectly influences the abundance of pH-associated ecological clusters. Acidophiles and Opportunists were enriched in intensive agriculture soils, while Liberals were predominantly found in traditional agriculture soils. Changes in microbial community composition significantly influence soil ecosystem functions, with Acidophiles, Liberalists, and Opportunists potentially serving as the primary contributors to nutrient cycling functions, animal & zoonotic pathogens, and plant beneficial microbes, respectively. Our results highlight the complex interactions between soil pH, microbial ecological clusters, and soil functionality, emphasizing the need for targeted agricultural management practices to maintain soil health.