Fig. 1

Differentially expressed genes of the simplified soil microcosm in response to Trichoderma atroviride and/or Armillaria mellea introduction. a Venn diagram summarising the distribution of 28,405 differentially expressed genes (DEGs) of the simplified soil microcosm identified by the DESeq2 package [37] in four pairwise comparisons of the simplified soil microcosm incubated for 24 h either without exogenous fungi (SSM), with the biocontrol agent T. atroviride (SSM+T), with the plant pathogen A. mellea (SSM+A) or with both (SSM+T+A), in comparison with the simplified soil microcosm collected at the beginning of the experiment (SSM₀). Two additional pairwise comparisons (SSM+T+A vs. SSM+A and SSM+T+A vs. SSM+T) identified eight and 88 DEGs of A. mellea and T. atroviride, respectively. b Distribution of DEGs in the 17 selected Gene Ontology (GO) functional categories (GO identifiers are reported in brackets). Frequencies were calculated as a percentage of the total number of GO biological process terms obtained using the ARGOT2 function prediction tool [39]