Figure 1.
Pseudomonas phylogenetic tree.
A phylogenetic tree of different Pseudomonas species based on the comparison of four different housekeeping genes sequences (16s rDNA, gyrB, rpoB, rpoD). The P. putida cluster is highlighted and the strain W15Oct28 is indicated in red. W15Oct28 closest relative is the P. putida type strain NBRC14164T.
Table 1.
Whole genome comparison (Average Nucleotide Identitybased on BLAST [ANIb]) between different P. putida group strains, including W15Oct28.
Figure 2.
Phylogeny of TonB-dependent receptors.
Neighbor joining tree based on the alignment of amino acid sequences of the 56 TonB dependent receptors (TBDR) detected in the genome of W15oct28 (green font) and a selection of known ferric-pyoverdine receptors from different sequenced Pseudomonas genomes (black font). W15oct28 TBDRs that are regulated through sigma-anti-sigma factors are indicated with a red node. Grey surface indicates part of the tree that contains all ferric-pyoverdine receptors that form a separate cluster.
Table 2.
Pattern of pyoverdines utilization by the pvdL-pyoverdine-negative mutant.
Figure 3.
Genes involved in the production of secondary metabolites.
A. Genes involved in the production of putisolvins in strain W15Oct28 (top) and strain P. putida PCL1145 (bottom): psoA, psoB, and psoC are the genes encoding NRPS enzymes with their condensation (C), adenylation (A) domains showing the predicted activated amino acid, and the T domain for the thioester attachment of the activated amino acid. The two thioesterase domains responsible for the detachment of the completed peptide at the end of psoC are also indicated (TE). The macA and macB genes correspond to a transporter, the oprM gene coding for an efflux system porin, and the two orphan luxR genes are shown in red. The amino acids predicted to be activated by the different A domains by the antiSMASH analysis are indicated without mentioning whether they are in the D- or L- form. B. The ten genes cluster possibly involved in the biosynthesis of a secondary metabolite. The cluster is preceded by a gene encoding an AraC regulator. See the text for details. C. The incomplete safracin gene cluster of W15Oct28 compared to the complete safracin gene cluster of P. fluorescens A2-2.
Figure 4.
Antagonistic activity and role of pyoverdine in the antagonism.
A. Antagonistic activity of the P. putida W15Oct28 strain against Pseudomonas aeruginosa, Curtobacterium flaccumfaciens, and Pseudomonas syringae. The pyoverdine-negative pvdO 2C5 transposon mutant has lost its antagonism against P. aeruginosa while the ΔpsoB putisolvin-negative mutant keeps a reduced, but still visible level of antagonism. B. The pyoverdine genes clusters: the arrows indicate the places of transposon insertions causing the loss of pyoverdine production and of the antagonism.
Table 3.
Antagonistic activity of P. putida W15Oct28 against different microorganisms.
Figure 5.
Fractionation of the antagonistic activity by HPLC.
HPCL fractionation of a crude extract from a culture supernatant of P. putida W15Oct28 grown in M9-glucose medium: A, chromatography of crude extraction of W15Oct28 cultured in M9 minimal medium for 48 hours; B, chromatography of crude extraction of W15Oct28 cultured in M9 minimal medium for 48 hours plus 5 days stay at 6°C. The yield of fraction 1 and 4 were increased with longer time of cultivation. Fractions 1 to 4 were spotted on an agar plate inoculated with P. aeruginosa PAO1 (upper left, fraction 1, upper right, fraction 2, lower left, fraction 3, lower right, fraction 4). The green line represents the acetonitrile gradient.
Figure 6.
Gene clusters coding for components of different secretion systems: amyloid, curli, type I, type II, type IV, type V (autotransporters) and type VI secretion systems. The genes in yellow for type VI secretion represent the different VgrG effector proteins.