  Polycyclic aromatic hydrocarbons (PAHs) are highly toxic, carcinogenic
substances. On soils contaminated with PAHs, crop cultivation, animal husbandry
and even the survival of microflora in the soil are greatly perturbed,
depending on the degree of contamination. Most microorganisms cannot tolerate
PAH-contaminated soils, however, some microbial strains can adapt to these
harsh conditions and survive on contaminated soils. Analysis of the metagenomes
of contaminated environmental samples may lead to discovery of PAH-degrading
enzymes suitable for green biotechnology methodologies ranging from
biocatalysis to pollution control. In the present study, our goal was to apply
a metagenomic data search to identify efficient novel enzymes in remediation of
PAH-contaminated soils. The metagenomic hits were further analyzed using a set
of bioinformatics tools to select protein sequences predicted to encode
well-folded soluble enzymes. Three novel enzymes (two dioxygenases and one
peroxidase) were cloned and used in soil remediation microcosms experiments.
The novel enzymes were found to be efficient for degradation of naphthalene and
phenanthrene. Adding the inorganic oxidant CaO2 further increased the degrading
potential of the novel enzymes for anthracene and pyrene. We conclude that
metagenome mining paired with bioinformatic predictions, structural modelling
and functional assays constitutes a powerful approach towards novel enzymes for
soil remediation.
