Additional file 1: Concentration of the soil microorganism in the
simplified soil microcosm.
Additional file 2: Primer sequences of the microcosm genes analysed
by real-time RT-PCR.
Additional file 3: RNA-Seq sequencing and mapping results for each
replicate.
Additional file 4: Distribution of read pair alignments to the genomes
of the soil microorganisms. (A, B) Distribution of read pair alignments to
the 13 soil microorganisms calculated with the Samtools software [30]
and expressed as a percentage (%) of total alignments to the microcosm
genome. (C, D) Distribution of unique read pairs mapping to genes of
the 13 soil microorganisms, counted using HTSeq [32] and expressed as a
percentage (%) of total unique read pairs mapping to genes in the
microcosm genome. (E, F) Percentage (%) of expressed genes (more
than one read pair) calculated as compared to the total predicted genes
for each soil microorganism. Mean and standard error values of three
replicates are reported for each condition: the simplified soil microcosm
collected at the beginning of the experiment (SSM0) and 24 h after
incubation either without exogenous fungi (SSM), with the biocontrol
agent Trichoderma atroviride (SSM+T), with the plant pathogen Armillaria
mellea (SSM+A) or with both (SSM+T+A).
Additional file 5: Expression levels of genes of the simplified soil
microcosm.
Additional file 6: Pearson’s correlation coefficients among replicates
and conditions for RNA-Seq analysis.
Additional file 7: Clustering and functional annotation results of
differentially expressed genes.
Additional file 8: Proportion of expressed and differentially expressed
genes for each soil microorganism.
Additional file 9: Distribution of differentially expressed genes of each soil
microorganism in 18 clusters, based on the expression profiles.
Additional file 10: Metabolic pathways of the simplified soil microcosm,
modulated by incubation in the soil matrix. Metabolic pathways
deactivated (left panels) and activated (right panels) by 24 h incubation
in the soil matrix (A) without reinforced modulation (cluster 1) and (B)
with reinforced modulation (cluster 15) in the presence of Armillaria
mellea and Trichoderma atroviride combined. Metabolic pathways
modulated by the introduction of (C) T. atroviride (cluster 3), (D) A. mellea
(cluster 5), or (E) both (cluster 7). KEGG pathways were visualised using
the iPath2 tool [48], the pathways of upregulated (green) and
downregulated (red) genes were highlighted, and a section of the most
relevant pathways is reported for each panel.
Additional file 11: Biological networks of Gene Ontology (GO) terms.
GO biological process terms of the simplified soil microcosm,
upregulated by incubation in the soil matrix with similar expression
profiles in the presence or absence of Armillaria mellea and Trichoderma
atroviride (cluster 1). Significantly enriched GO terms (P < 0.001) were
identified using the BiNGO tool [42] and visualised with Cytoscape
software [43]. The colour scale legend indicates the level of significance
for enriched GO terms. White nodes indicate not significantly
overrepresented categories.
Additional file 12: Key differentially expressed genes discussed in the
manuscript, based on their functional categories and expression profiles.
Each sheet contains the genes in each cluster discussed.