Long-term study on three different cultivation system

Soil is an important factor for agricultural production and it is not just the medium for plant growth, therefore the use of organic farming agriculture is receiving so much attention, as it reduces the environmental impact and improves the quality of the soil. In this paper, we assessed the long-term effect of agricultural management of two organic cropping systems (Org_C and Org_M) and a conventional system (Inorg) with the same crops history, on bacterial and fungal soil community structure through high-throughput sequencing analysis and their interaction with soil physicochemical properties and crop yield.Results showed that crop yield during the last cycle were similar among the three cropping systems. There were no significant differences in bacterial diversity among cropping systems while for fungal diversity was higher in Inorg. Org_C showed significantly higher soil organic carbon and nutrients (TN, NH4+, Mg and B), the key soil properties that influenced the change of bacterial community structure. Although, there were no soil properties significantly related to changes in the fungal community structure. SIMPER analysis accounted for 75% of the overall dissimilarities between Inorg and the two organic cropping systems (Org_M or Org_C) for Proteobacteria, Gemmatimonadetes, Bacteriodetes and Actinobacteria. While for fungi, Olpidiomycota, Basidiomycota and Ascomycota accounted for 74% of dissimilarities between Inorg and Org_C. Effect size (LEfSe) showed 33 bacterial and 22 fungal biomarkers to screen under different taxonomic levels across the three cropping systems. These results suggest that long-term application of compost (Org_C) not only increased organic material and nutrient but change bacterial and fungal community structure and we have identified specific microorganisms. Moreover, a-diversity indices may not be suitable indicators to assess the microbial response to management practices in agriculture.