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The influence of long-term fertilization on arbuscular mycorrhizal fungi community composition was investigated. Soil samples were taken from a long-term field experiment which was conducted for 5 years to explore the effect of three treatments: control (non-fertilization), conventional (mineral fertilizers-NPK), and alternative (organic fertilizers-farmyard manure). The highest values of AMF community composition were found in the alternative fertilization system after the thirty year of its utilization. After the thirty year the conventional fertilization system showed lower AMF diversity compared to alternative fertilization system. In conclusion the alternative fertilization system enhanced mycorrhizal effectiveness that contributes to increase wheat growth after a long-term experiment. Our findings also suggest that inputs of organic matter source can change positively the AMF community composition, and these results highlight the importance of considering the long-term effect of mineral and organic fertilizers on the AMF community diversity. Thus, the long-term utilization of an alternative fertilization system with continuous input of organic matter may exploit positive situations of jointly beneficial biotic and abiotic conditions. [ABSTRACT FROM AUTHOR]