Supplementary Information
Supplementary Dataset S1. GC-MS profiles of fungal spent media and peak attribution. Worksheet 1 reports for each sample the retention time (min), the peak area (%), the name of the possible compound and probability of attribution. Tg, Th, Tv, Tt, indicates T.gamsii , T. harzianum , T. velutinumand T. tomentosum , respectively. Worksheet 2 matrices with the 76 compounds identified with >80% probability and grouped on the basis of chemical class. The matrices report percentage and dimensionless values for the peak area. File type .xlsx
Supplementary Dataset S2. List of total upregulated Differentially Expressed Genes (DEGs). Each datasheet contains the list of DEGs, with fold change of >2; padj <0.01 for each strain and fungal spent media treatment. For each gene information on functional annotation and pangenome is present. Fungal codes are as indicated above. File type .xlsx
Supplementary Dataset S3. List of total downregulated Differentially Expressed Genes (DEGs). Each datasheet contains the list of DEGs, with fold change of < -2 and padj<0.01, retrieved for each strain and fungal spent media treatment. For each gene information on functional annotation and pangenome is present. Fungal codes are as indicated above. File type .xlsx
Supplementary Dataset S4. Statistically significant DEGs present in the core genome of the strains. The list of DEGs with fold change of >|2|; P value <0.01, from genes present in the core genome of the strains is reported. File type .xlsx
Supplementary Dataset S5. List of unique DEGs. For each strain, each datasheet contains the list of unique upregulated and downregulated DEGs retrieved from the intersection of the 4 sets (corresponding to Trichoderma species). For each gene, information on fold change, padj, functional annotation and pangenome details is present. File types .xlsx
Supplementary Dataset S6. List of core DEGs resulted from the nested model of the likelihood ratio test (nLRT). For each gene fold change and padj are reported. The effect column indicates the term of the model (strain, fungus, or strain:fungus) being tested. In column sign, significance after BH correction for false discovery rate is reported with “*” for padj<0.05 ; “**” for padj<0.01
Supplementary Figure S1. Effects of Trichoderma spent media on S. meliloti growth and plant-growth promotion phenotypes . a) growth inhibition b) Auxin (IAA) inhibition of production; c) biosurfactants production; d) total EPS production; e) reducing EPS production, f) root biofilm formation
Supplementary Figure S2 - Effect of S. meliloti-Trichoderma on symbiotic phenotypes . a) root length; b) stem length; c) shoot length; d) dry weight; e) number of leaves; f) number of nodules. Different letters indicate significant differences at P <0.05
Supplementary Table S1. S. meliloti response to spent fungal growth media . Results from one-way ANOVA evaluating the effect on rhizobial growth of different fungi on each S. melilotistrains for 1W, 2W and 3W spent media are reported.
Supplementary Table S2 . Effect of coinoculation ofS. meliloti strains with Trichoderma (condition) on symbiosis quality . Results from ANOVA are shown for the different phenotypes recorded. Asterisks indicate statistically significant differences (*, p<0.05; **, p<0.01; ***, p<0.001).