Metagenomics research on PAH biodegradation in the lower reaches of the Shiwuli River in Chaohu, China

Metagenomics is a powerful tool for investigating functional microorganisms, molecular mechanisms and genes involved in the degradation of polycyclic aromatic hydrocarbons (PAHs) <i>in situ</i> complex environments. In this study, we selected three land use types in the lower reaches of the Shiwuli River in Chaohu and applied metagenomics technology. The results revealed that <i>Rhodoplanes</i> and <i>Bradyrhizobium</i> were the abundant PAH-degrading microorganisms across the three land use types. Based on the functional annotation and PAH degradation pathway, it was found that the <i>in situ</i> microbial communities of the three land use types shared common metabolic pathways for phenanthrene degradation. In addition, a unique metabolic pathway for PAH degradation was identified in the agricultural land. Only <i>Patulibacter</i> contributed to <i>flnE</i> (KO14604) in the agricultural land, which was involved in the metabolic pathway of fluorene degradation. Results of this study suggested that the <i>in situ</i> degradation of PAHs was not completed by a single genus, and it involved the synergy effects of different PAH-degrading microorganisms. There was no significant difference between the compositions and relative abundances of PAH-degrading microorganisms in the three land use types and those presented in the Kyoto Encyclopedia of Genes and Genomes Orthology (KO). However, the same microorganism contributed to different functional genes in different samples. Genes encoding protocatechuic acid 4,5-dioxygenase were widely distributed and relatively abundant. Therefore, this gene may serve as an indicator of PAH degradation potential. Among all the factors, the total organic carbon and nitrate nitrogen contents exhibited significant influences on the functional genes (KO) related to PAH degradation (<i>p</i> < 0.05).