Fig. 3

Resistome dynamic changes along time, as revealed through the evolution of alpha and beta diversity indices and ARG composition. A Antibiotic resistance genes (ARGs) counts per million reads (CPM); B richness and Simpson’s indices calculated with the ARG–CPM matrix; and C Principal Coordinates Analysis, using Bray–Curtis distance, at ARG level for the 210 industry samples (n = 55 for T1, n = 70 for T2, n = 85 for T3). The centroid of each ellipse represents the group mean, and the shape is defined by the covariance within each group. Adonis test values are indicated at Table S1. Distance to the centroid values were employed to evaluate the homogeneity of variances within each group. Only significant p values (p < 0.05) obtained from the Wilcoxon signed-rank test analysis are indicated. D Barplot of the 14 ARG classes detected and E the 7 ARG classes associated with resistance to antibiotics of critical importance calculated by adding ARG abundances according to the antibiotic classes they confer resistance to (Suppl. File 4). Each bar represents the average value for samples belonging to the same Surface and Time groups, indicated at the top and bottom of the plot, respectively. MLSP refers to macrolides, lincosamides, streptogramins, pleuromutilins