Soil microbiome and ecological traits depending on fertilization and climate in organic input agricultural ecosystem

Soil microbiome is crucial for ecosystem functions, and its response to fertilization varies with climate. There are no comprehensive generalizations about the ecological mechanisms underlying climate-dependent responses of soil microbiome to fertilization. To clarify these responses and mechanisms, 321 observations from 62 studies were meta-analyzed. Soil organic matter content and pH increased more with organic fertilization in hot and wet climates than in cold and dry climates. Microbial α-diversity decreased with mineral fertilization (NPK), particularly in hot and wet climates, owing to rapid losses of soil organic carbon driven by high microbial activity. The abundance of r-strategists (i.e., Proteobacteria and Bacteroidota) increased by 82.34% on average with organic fertilizers in hot and wet climates, driven by favorable hydrothermal conditions and sufficient nutrients. In contrast, the abundance of K-strategists (i.e., Acidobacteriota and Actinobacteriota) decreased by an average of 32.18%. Compared to NPK, organic fertilizers optimized soil nutrient and organic matter status, thereby increasing the proportion of generalists and microbial niche breadth and reducing niche overlap among microbial groups, especially in hot and wet climates. Organic inputs increased microbial network complexity and reduced network vulnerability (47.50% and 35.87% decreases, respectively, compared with those under NPK). All these ecological traits, optimized by organic fertilization in hot and wet climates, support the maintenance and stability of microbial diversity. This meta-analysis offers insights into the ecological patterns of fertilization effects on soil microbial diversity across climates, highlighting the potential drivers of microbiome stability in agricultural ecosystems under shifting climatic regimes.