Fig. 2
Clustering of differentially expressed genes (DEGs) of the simplified soil microcosm based on expression profiles. Heat map diagram of fold change values for the simplified soil microcosm incubated for 24 h either without exogenous fungi (SSM), with the biocontrol agent Trichoderma atroviride (SSM+T), with the plant pathogen Armilalria mellea (SSM+A) or with both (SSM+T+A), calculated as compared to the simplified soil microcosm collected at the beginning of the experiment (SSM0). Genes modulated by 24 h incubation in the soil matrix (SSM/SSM0 ≥ 2) were classified as: genes with similar expression profiles in the presence or absence of A. mellea and T. atroviride alone and combined (cluster 1), genes with similar expression profiles in the presence or absence of A. mellea and T. atroviride with reinforced modulation (cluster 15) or no modulation (cluster 16) in the presence of A. mellea and T. atroviride combined, and genes with specific profiles in the presence of T. atroviride and/or A. mellea (clusters 9–14). Genes not affected by incubation in the soil matrix (SSM/SSM0 < 2) were classified as: genes modulated by T. atroviride alone (cluster 2) or combined with A. mellea (cluster 3), and genes modulated by A. mellea alone (cluster 4) or combined with T. atroviride (cluster 5). Three clusters grouped genes modulated by the presence of A. mellea and T. atroviride combined (cluster 6), by the presence of A. mellea and T. atroviride alone and combined (cluster 7), and by the presence of A. mellea or T. atroviride alone (cluster 8). The heat map diagram was visualised using MultiExperiment Viewer [38] according to the colour scale legend shown