Soil microbial community structure is an effective indicator to reflect changes in soil quality. Little is known about the effect of alpine meadow degradation on the soil bacterial and fungal community. In this study, we used the Illumina MiSeq sequencing method to analyze the microbial community structure of alpine meadow soil in five different degradation levels (i.e., non-degraded (ND), slightly degraded (LD), moderately degraded (MD), severely degraded (SD), and very severely degraded (VD))

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... in the Qinghai-Tibet Plateau. Proteobacteria, Actinobacteria, and Acidobacteria were the mainly bacterial phyla in meadow soil across all five degradation levels investigated. Basidiomycota was the mainly fungal phylum in ND; however, we found a shift from Basidiomycota to Ascomycota with an increase (severity) in degradation level. The overall proportion of Cortinariaceae exhibited high fungal variability, and reads were highest in ND (62.80%). Heatmaps of bacterial genera and fungal families showed a two-cluster sample division on a genus/family level: (1) an ND and LD group and (2) an SD, VD, and MD group. Redundancy analysis (RDA) showed that 79.7%and 71.3% of the variance in bacterial and fungal composition, respectively, could be explained by soil nutrient conditions (soil organic carbon, total nitrogen, and moisture) and plant properties (below-ground biomass). Our results indicate that meadow degradation affects both plant and soil properties and consequently drives changes in soil microbial community structure.