## 3 Results
### Overexpression in Secondary Metabolism  
Within the 90% cut-off, 11 out of the 20 predicted secondary metabolite gene clusters with antiSMASH were identified among the overexpressed genes, observing variations in expression depending on the analyzed condition (Figure 8). In region 1, where the closet predicted metabolite was pyrrolnitrin, the overexpression of the described gene cluster prnABCD was observed [22]. Pyrrolnitrin is a phenylpyrrole derivative, with antifungal activity, originally isolated from _Pseudomonas pyrrocinia_, but found in other proteobacteria [50; 51]. The presence of glycerol, glucose, and mannose in liquid culture was determinant for an increased gene expression in stationary phase (GLY, GLU, MAN), showing less determination for FRU and SGS. Under conditions of liquid culture with glycerol in death phase of growth (GYS) and solid culture with glycerol in exponential phase (SGE), the gene expression was low or irrelevant. In region 2, the core cluster pchR-pchDHIEFKCBA for enantio/iso-pyochelin, as well as the protein-dependent ABC transporter encoded by the fetABCDEF operon, were significantly overexpressed in liquid cultures, and particularly in GYS and MAN. During these conditions, the overexpression of the determinant genes for enantio/iso-pyochelin synthesis, fetA and pchEF [21; 52], stood out among the related genes. Figure 8: Heat map for secondary metabolism cluster predicted for _Pseudomonas_ sp., strain L5B5 and overexpression of genes through RNA-seq analyses. GLY: RNA extracted from liquid culture (NB) supplemented with glycerol in stationary phase; GLU: RNA extracted from liquid culture (NB) supplemented with glucose in stationary phase; MAN: RNA extracted from liquid culture (NB) supplemented with mannose in stationary phase; FRU: RNA extracted from liquid culture (NB) supplemented with fructose in stationary phase; SGS: RNA extracted from solid culture (NA) supplemented with glycerol in stationary phase; SGE: RNA extracted from solid culture (NA) supplemented with glycerol in exponential phase. Genes of the predicted cluster in region 3, which likely encodes some phenazine-type compound, were differentially expressed under SGS condition, with minor or irrelevant expression in the rest ones. The relation of expressed genes determined the operon structures present in strain L5B5, with the core cluster phzABCDEFG [53], the transcriptional regulators via quorum sensing phzRI [54] and the transamidase phzH, which enable the bacteria containing this mechanism to produce both phenazine-1-carboxylic acid (PCA) and phenazine-1-carboxamide (PCN) [55]. Region 4, with antifungal pyoluteorin as the closest metabolite identified, was observed to be overexpressed for every analyzed condition, but more particularly in the two solid culture conditions. In this dataset, the two pair of operons involved in synthesis and transportation of pyoluteorin, pltLABCDEFG, and pltRM, as well as pltPIJKNO and pltZ operons, respectively, were differentially expressed [56; 57]. Orfamide-type cyclic lipopeptides (CLPs), identified as the closest metabolite likely produced by gene cluster in region 5, are biosurfactants synthesized by _Pseudomonas_ with insectical activity and involved in the biocontrol of plant pathogens. Up to eight different ordamides has been described so far, Orfamide A-H, in _Pseudomonas protegens_ strains Pf-5 and CHA0, as well as in _Pseudomonas_ sp. strains CMR5c and CMR12a [19; 58; 59]. Cluster prediction derived in the identification of auxiliary genes described in _P. protegens_ Pf-5, such as RND efflux system upstream of the core biosynthetic genes ofaABC, and a putative glyoxalase family protein (phnB-like) and a heme transporter CcmD, radical SAM domain-containing protein (rSAM), downstream of two transporter genes (macA and macB) and luxR type transcriptional regulator gene. Core biosynthetic genes were overexpressed in all conditions analyzed, especially in GLU, FRU, and SGS, where auxiliary genes upstream and downstream were highly expressed as well.