Betaproteobacteria dominance and diversity shifts in the bacterial community of a PAH-contaminated soil exposed to phenanthrene

In this study, the PAH-degrading bacteria of a constructed wetland collecting road runoff has been studied through DNA stable isotope probing. Microcosms were spiked with 13C-phenanthrene at 34 or 337 ppm, and bacterial diversity was monitored over a 14-day period. At 337 ppm, PAH degraders became dominated after 5 days by Betaproteobacteria, including novel Acidovorax, Rhodoferax and Hydrogenophaga members, and unknown bacteria related to Rhodocyclaceae. The prevalence of Betaproteobacteria was further demonstrated by phylum-specific quantitative PCR, and was correlated with a burst of phenanthrene mineralization. Striking shifts in the population of degraders were observed after most of the phenanthrene had been removed. Soil exposed to 34 ppm phenanthrene showed a similar population of degraders, albeit only after 14 days. Results demonstrate that specific Betaproteobacteria are involved in the main response to soil PAH contamination, and illustrate the potential of SIP approaches to investigate PAH biodegradation in soil. ► We explored PAH-degrading bacteria on a chronically polluted site by stable isotope probing. ► Betaproteobacteria appeared as the main phenanthrene degraders in soil. ► Most soil PAH degraders were poorly related to bacteria isolated so far. ► Diversity shifts occurred in the community of degraders when the PAH became less available. On a site collecting road runoff, implementation of stable isotope probing to identify soil bacteria responsible for phenanthrene degradation, led to the discovery of new Betaproteobacteria distantly related to known PAH degraders.