**4. Conclusions**

Genome analysis of *Pseudomonas veronii* strain VI4T1 and *Pseudomonas* sp. VI4.1 not only revealed the presence of key genes involved in the catabolism of aromatic and aliphatic hydrocarbons but also a diverse set of genes involved in plant growth promotion, stress regulation, and adaptation. Experimental evidence for both hydrocarbon degradation and plant growth promotion confirmed the

degradative and versatile metabolic properties. These features make both sequenced strains promising candidates for testing and designing di fferent plant–bacteria systems to perform phytoremediation experiments, and contribute in this way to the development of a cost-e ffective and eco-friendly method to remediate polluted environments.

**Supplementary Materials:** The following are available online at http://www.mdpi.com/2073-4425/10/6/443/s1, Figure S1: Side and top view of the custom-made sandwich di ffusion system to isolate hydrocarbon-degrading bacteria, Figure S2: Multiple sequence alignment of the Rieske unit of the *nahAc* gene of bacterial isolates from the oil-polluted soil in Bóbrka. Reference strain is *Pseudomonas putida* plasmid with *nahAc* encoded on plasmid pAK5, Figure S3: Circular genome views of strains VI4T1 and VI4.1 in addition to the major EGGNOG categories distribution (in %), Figure S4: Visualizations of the SPAdes genome assembly and plasmidSPAdes assemblies of strains VI4T1 and VI4.1. Closed circular plasmids with coverage (in red), are indicated and results of the BLAST searches are shown in the tables, Figure S5: Rudimentary conjugative 40 kb plasmid of pVI4T1-1, showing some T4SS genes (*mpfABCDEH*), and other genes involved in conjugation (*parA*, *parB*, *fmdA*, *hbpA*), Figure S6: Toluene degradation operon to o-cresol for strain VI4.1, Figure S7: ( **A**) Comparative analyses of upper toluene/m-xylene degradation operon to generate *m*-toluate. (**B**) *meta*-cleavage pathway of catechol to acetyl Co-A degradation and C. *ortho*-cleavage pathway, Figure S8: Comparative analyses of the toluene V degradation operon (*todABC1C2DFGHI*), and proposed biochemical pathways for toluene degradation to acetyl-CoA, Figure S9: Comparative analyses of the benzene degradation operon (*bedABC1C2D*), and proposed biochemical pathways, Figure S10: Example of positive result to the motility assay, Table S1: The list of carbon sources catabolized by VI4T1 and VI4.1 tested with the GEN-III array (Biolog).

**Author Contributions:** V.I. and S.T. executed the main part of the experimental work and wrote the manuscript. Y.D. assisted with the isolation of the hydrocarbon degrading strains and genome annotation. B.M.M. genome sequenced the bacteria strains under supervision of J.V.H., S.W.G. and J.V., experts in phyllo- and phyto-remediation, critically reviewed the manuscripts. M.P-E. performed the PTR-TOF analyses at UAntwerp and revised the manuscript.

**Funding:** V.I. was supported by a BOF PhD gran<sup>t</sup> from Hasselt University and by Grant G0D0916N. S.T. was supported by a PhD gran<sup>t</sup> from FWO-Flanders and the Methusalem project 08M03VGRJ. M.P.-E. was supported by the Methusalem funding of the Flemish Community through the Research Council of the University of Antwerp and by the Flemish Science Foundation (FWO, Brussels).

**Acknowledgments:** We thank the director of the The Ignacy Łuksiewicz's Museum of Oil and Gas Industry in Bóbrka for granting access to the Bóbrka forest sampling site. We thank Łukasz Kowalkowski for assisting with the sampling.

**Conflicts of Interest:** No conflict of interest.
