Fig. 2: Microbial community of alfalfa silage initiated by endophytes.

a The box-and-whiskers plot shows the Shannon index of silage microbial community in PB (silage fermentation by phyllosphere bacteria) and EN (endophytes) at three time points of 9, 30, and 60 days of fermentation. The box depicts the interquartile range (IQR) between the 25th and 75th percentiles respectively, the top of the box is the first quartile, the bottom is the third quartile, and the line within the box represents the median. The whiskers extend 1.5 times the IQR from the top and bottom of the box, respectively. Significant differences using two-tailed Welch’s t-test (n = 3, biologically independent samples). b PCA based on silage microbial community (n = 9, biologically independent samples). c Genus dynamics of silage microbial communities. The colors highlighted the phylum information. The circle size indicates the relative abundance, and the red font indicates lactic acid bacteria (LAB). Significant differences using two-tailed Welch’s t-test (n = 3, biologically independent samples). *P < 0.05; **P < 0.01; ***P < 0.001. d Co-occurrence network of microbial communities for the groups of PB and EN. LAB were highlighted in orange. Co-occurrence networks of microbial community were also shown for PB (e) and EN (f) respectively. LAB were highlighted in pink, and the key LAB was highlighted in red. The orange line represents negative correlation, and the blue line represents positive correlation (Spearman correlation > |0.6| and P < 0.05).