Transcripts showing opposite (positive values in solid and negative in liquid or vice versa) and significant (coefficient of variation between solid and liquid cultures higher than 0.7) abundances (Fig. 4C, F, I, L, O, R, U; Fig. 5C, F, I, L).

Average log2 abundance values from three biological replicates of the MII with respect to MI in solid (S) and liquid (L) cultures. Only transcripts with significant abundances are shown (log2 abundance greater than ±1 in liquid and/or solid cultures). Functions (according to Gene bank, Gene Ontology, Conserved Domain, and KEGG and StrepDB databases): Primary metabolism (DNA/RNA replication, aerobic and anaerobic energy production, glycolysis and glyconeogenesis, pentose phosphate pathway, amino acid metabolism, nucleotide metabolism, translation, protein folding, RNA/protein processing, nucleases/RM methylases); secondary metabolism (secondary metabolites synthesis); differentiation (TTA bldA targets, Bld and Whi proteins); regulatory genes (transcriptional regulators, kinases, other regulatory genes); transposons - insertion sequences; conjugation – recombination - mutagenesis; stress and defense proteins; catabolism - degradation; lipid metabolism; transporters and secreted (ABC transporters, transporters and secreted proteins). Genes with “unknown” functions (Table S1) were not included.