**4. Conclusions**

Complex pollutants such as diesel require multiple microorganisms for their degradation. We have shown here that an effective autochthonous bacterial consortium can be constructed by successive enrichment cultivation of soils from contaminated sites. By metagenomic analysis of the consortium, growing on diesel and on specific aliphatic and polyaromatic hydrocarbons, we have been able to determine the bacterial genera composition of the consortium, the genes and enzymes implicated in diesel degradation and the specific degradative roles of the major populations within the consortium. The functional redundancy observed in the metagenome might be related to the plasticity that allows the populations to adapt to changes in the environment, and therefore conferring robustness to the degrading hydrocarbon system.

**Supplementary Materials:** The following are available online at http://www.mdpi.com/2073-4425/10/6/456/s1. Table S1: Relative abundance of the diesel-degrading consortium based on 16S rRNA gene and CDSs from the metagenome annotations. Table S2: Statistics of the 16S rRNA and whole-metagenome shotgun sequencing and processing of reads. Table S3: CDSs for alkanes and PAHs initial hydroxylation and others involved in central aromatic metabolism. Figure S1: Growth curves of the diesel-degrading consortium in each of the substrates used in this study. Figure S2: Detailed GC-FID results of aliphatic and aromatic hydrocarbons fractions remaining after microcosms treatments.

**Author Contributions:** Conceptualization, D.G.-S., M.R.-N., M.M., R.M., and R.R.; methodology, D.G.-S., M.G., O.P.J., and M.R.-N.; software, D.G.-S. and M.R.-N.; validation, R.R., M.M., R.M., and M.R.-N.; formal analysis, D.G.-S., M.G., O.P.J., M.R.-N., M.M., R.M., and R.R.; investigation, D.G.-S., M.G., and O.P.J.; resources, D.G.-S., M.G., O.P.J., M.R.-N., R.M., M.M., and R.R.; data curation, D.G.-S. and M.R.-N.; writing—original draft preparation, D.G.-S. and R.R.; writing—review and editing, D.G.-S., M.R.-N., M.M., and R.R.; visualization, D.G.-S., and M.G.; supervision, D.G.-S., M.R.-N., R.M., M.M., and R.R.; project administration, M.M., R.M., and R.R.; funding acquisition, M.M., R.M., and R.R.

**Funding:** This research was funded by GREENER-H2020 (EU), gran<sup>t</sup> number 826312, Ministerio de Ciencia, Innovación y Universidades/FEDER EU, gran<sup>t</sup> number RTI2018-0933991-B-I00 and the BIOXISOIL project, gran<sup>t</sup> number LIFE11/ENV/ES/000505. D.G.-S. was granted by the MECD FPU fellowship program, gran<sup>t</sup> number FPU14/03965.

**Acknowledgments:** We thank Mª José Sierra Herráiz for her advice on the selection of alfalfa seeds and their optimal growth conditions in the culture chamber.

**Conflicts of Interest:** The authors declare no conflict of interest.
