Abstract
Summary Lake and adjoining river ecosystems are ecologically and economically valuable and are heavily threatened by anthropogenic activities. Determining the inherent capacity of ecosystems for polycyclic aromatic hydrocarbon (PAH) biodegradation can help quantify environmental impacts on the functioning of ecosystems, especially on that of the microbial community. Here, PAH biodegradation potential was compared between sediments collected from a lake bay (LS) and an adjoining river (RS) ecosystem. Microbial community composition, function, and their co‐occurrence patterns were also explored. In the RS, the biodegradation rates ( K D ) of pyrene or PAH were almost two orders of magnitude higher than those in the LS. Sediment functional community structure and network interactions were dramatically different between the LS and RS. Although PAH degradation genes ( p450aro , quinoline , and qorl ) were detected in the LS, the community activity of these genes needed to be biostimulated for accelerated bioremediation. In contrast, functional communities in the RS were capable of spontaneous natural attenuation of PAH. The degradation of PAH in the RS also required coordinated response of the complex functional community. Taken together, elucidating functions and network interactions in sediment microbial communities and their responses to environmental changes are very important for the bioremediation of anthropogenic toxic contaminants.