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Arbuscular mycorrhizal fungi (AMF) play vital roles in sustaining soil productivity and plant communities. However, adaption and differentiation of AMF in response to commonly used fertilization remain poorly understood. In this study, we showed that the AMF community composition was primarily driven by soil physiochemical changes associated with chronic inorganic and organic fertilization of 37 years in Mollisols. High-throughput sequencing indicated that inorganic fertilizer negatively affected AMF diversity and richness, implying a reduction of mutualism in plant–AMF symbiosis; however, a reverse trend was observed for the application of inorganic fertilizer combined with manure. With regards to AMF community composition, order  Glomerales  was dominant, but varied significantly among different fertilization treatments. All fertilization treatments decreased family  Glomeraceae  and genus  Funneliformis , while  Rhizophagus  abundance increased. Plant-growth-promoting-microorganisms of family  Claroideoglomeraceae  and genus  Claroideoglomus  were stimulated by manure application, and likely benefited pathogen suppression and phosphorus (P) acquisition. Family  Gigasporaceae  and genus  Gigaspora  were negatively correlated with available P in soil. Additionally, redundancy analysis further suggested that soil available P, organic matter and pH were the most important factors in shaping AMF community composition. These results provide strong evidence for niche differentiation of phylogenetically distinct AMF populations under different fertilization regimes. Manure likely contributes to restoration and maintenance of plant–AMF symbiosis, and the balanced fertilization would favor the growth of beneficial AMF communities as one optimized management in support of sustainable agriculture in Mollisols.

Chronic fertilization of 37 years alters the phylogenetic structure of soil arbuscular mycorrhizal fungi in Chinese Mollisols