Phenanthrene biodegradation by sphingomonads and its application in the contaminated soils and sediments: A review

• Autecological properties of sphingomonads in phenanthrene degradation.
• Catabolic aspect of sphingomonads: genes, enzymes and biochemical pathways involved.
• Phylogeny of the genes taking part in soil phenanthrene bioremediation.
• Relevance of genomic studies in soil PAH degrading sphingomonads research.

Polycyclic aromatic hydrocarbons (PAHs), a class of hazardous chemicals ubiquitous in many ecosystems, are of great concern due to their potential toxicity, carcinogenicity, teratogenicity, and mutagenicity. Phenanthrene, a low-molecular-weight hydrophobic PAH, binds to particulates in the soil and sediments, thus inhibiting biological uptake. In such PAH-contaminated environments, some well-adapted microorganisms, such as the sphingomonads (belonging to the Family Sphingomonadaceae in α-Proteobacteria) can degrade phenanthrene, whether in isolation or cometabolized with other PAHs. Some of the members of sphingomonads, consisting of the Sphingomonas, Sphingobium, Novosphingobium, and Sphingopyxis genera, have adjusted well to contaminated soil environments compared to most bacterial genera that degrade PAHs. This is manifested in phenanthrene, which has been found to induce strong up-regulation of extradiol cleavage pathway enzymes in sphingomonads with similar gene and enzyme homology to Sphingobium yanoikuyae B1, where enzymes like ring-hydroxylating dioxygenase, putative biphenyl-2,3-diol 1,2-dioxygenase, and catechol 2,3-dioxygenase are encoded by bphA2cA1c, bphA1[a-e]A2[a-e] (which both require bphA3bphA4) and bphC genes, respectively. With meta- and ortho-cleavage pathway routes, this has made sphingomonads a well-adapted group of microorganisms. This review will focus on taxonomic, autecological and genetic features of sphingomonads which impact on their ability to metabolize phenanthrene at different rates and under different conditions.