Characterization of the microbiome and PAH-degrading organisms in contaminated estuarine sediments of the Elizabeth River, VA, USA

Sites along the Elizabeth River, VA are contaminated by industrial processes, including former creosoting facilities, resulting in increased concentrations of polycyclic aromatic hydrocarbons (PAHs) in estuarine sediments. To detect PAH-degrading organisms within sediment communities, DNA-SIP was performed with phenanthrene and fluoranthene using sediment from the former Republic Creosoting site. For these PAHs the most prominent degraders were identified as members of the Azoarcus and Hydrogenophaga genera, and Croceicoccus genera, respectively. Targeted cultivation of bacteria resulted in the isolation of 6 PAH-degrading strains, including one Hydrogenophaga strain highly similar to those detected in DNA-SIP experiments and well as strains within the Novosphingobium, Sphingobium, Stenotrophomonas, and Alcaligenes genera. 16S rRNA gene amplicon sequencing of four sites along the river with varying concentrations of PAHs, including Republic Creosoting, showed site-specific differences in bacterial communities, potentially related to the level of contamination. However, the relative abundance of genes associated with SIP-derived or PAH-degrading isolate sequences were low at all sites, suggesting that the identified organisms might be good target candidates for bioaugmentation to increase PAH removal in the affected sediments. Furthermore, this study confirms the value of both culture-based and culture-independent methods in identifying promising bacterial candidates for use in a precision bioremediation scheme.