Root exudates affect phenanthrene biodegradation, bacterial community and functional gene expression in sand microcosms

Polycyclic aromatic hydrocarbon (PAH) degradation may be increased in plant rhizosphere, but the role of plants in PAH degradation is not clearly understood. We investigated the effect of ryegrass root exudates on phenanthrene (PHE) degradation, PHE degrading bacterial population and functional gene expression in sand microcosms inoculated with bacteria from an industrial PAH polluted soil. Dominant bacteria were identified using 16S rDNA based temporal thermal gradient electrophoresis (TTGE). Functional PAH-ring hydroxylating dioxygenase (PAH-RHDα) genes (DNA) and transcripts (RNA) were quantified through real-time PCR and RT-PCR. Without root exudates PHE degradation was rapid and complete within 5 days. Herbaspirillum sp. and Pseudomonas putida were the dominant strains. Percentage of PAH-RHDα relative to 16S rRNA, both for genes and transcripts, was the highest after only two days and then decreased. With phenanthrene and root exudates as carbon sources, only 50% of the PHE was degraded in 10 days. P. putida-related bacteria were also detected with other strains related to Pseudomonas sp. and Paenibacillus. PHE degradation was reduced, and the percentage of PAH-RHDα transcripts was lower with root exudates than with only PHE, but increased over the incubation, while PAH-RHDα gene copy number was higher.

► Microcosms with PHE spiked sand inoculated with soil bacteria were used.
► The effect of root exudates addition on PHE degradation and genes was investigated.
► Without root exudates PHE degradation was rapid and complete within 5 days.
► Root exudates decreased PHE degradation and the percentage of PAH-RHDα transcripts.
► Partially different dominant bacteria were detected with and without root exudates.