Diversity of the active phenanthrene degraders in PAH-polluted soil is shaped by ryegrass rhizosphere and root exudates

Root exudates can stimulate microbial degradation within the rhizosphere, but their exact roles are embedded within the complicated rhizospheric effects. In the present study, we applied both C-12- and C-13-phenanthrene to distinguish the effects of root exudates within ryegrass rhizosphere on phenanthrene degradation via DNA stable isotope probing (DNA-SIP). A significant increase of phenanthrene biodegradation efficiency (10.7%) was found in ryegrass rhizosphere compared to bulk soils, but not in soils supplemented with ryegrass root exudates. Results from high-throughput sequencing and computational analyses suggested that treatments with both ryegrass rhizosphere and root exudates markedly increased total bacterial populations and shaped the composition of the active phenanthrene-degrader community. Of all the phenanthrene-degraders belonging to eight bacterial classes revealed by DNA-SIP, only Aiphaproteobacteria and Nitrososphaeria were shared between bulk soils, ryegrass rhizosphere and soils supplemented with ryegrass root exudates. Sphingobacteriia and Actinobacteria were active phenanthrene-degraders within both ryegrass rhizosphere and soils supplemented with ryegrass root exudates, whereas others were observed only in bulk soils or soils supplemented with ryegrass root exudates. Most of the degraders were linked to phenanthrene degradation for the first time based on their incorporation of C-13-phenanthrene. In C-13-phenanthrene microcosms, the relative abundance of PAH-RHD alpha genes and active phenanthrene-degraders was strongly correlated with phenanthrene degradation efficiency. Compared to the rhizosphere, root exudates provided a minor contribution to the abundance of PAH-RHD alpha gene. This study helps in better understanding the roles of root exudates supplement in the phenanthrene biodegradation process within the rhizosphere and provides theoretical insights into the mechanisms of enhanced phenanthrene degradation via phytoremediation at PAH-contaminated sites.