In the contaminated coastal sediments, variations of microbial community can reflect the impact of anthropogenic
activities. The identification, evaluation and monitoring of the potential bio-indicator species and biomarker
communities are vital for the ecological studies in sedimentary environments. Based on the highthroughput
sequencing, the microbial communitieswere characterized in the sediments along the Yangtze Estuary
and its coastal area. The results showed that the structure and composition of microbial communities varied
greatly among different sampling sites at the phyla level, especially for Euryarchaeota. Metabolic pathway and
quantitative PCR analyses suggested that the methane metabolism-related microbes were mainly included in
the phylum of Euryarchaeota. Elevated abundances of methane metabolism-related microbes were found at
Shidongkou (SDK) and Wusongkou (WSK), where microbes were seriously impacted by the wastewater treatment
plant (WWTP) effluent and urban runoff. By comparing with the Euryarchaeota inWWTP sludge, the relatively
high abundance of Euryarchaeota in sediment at SDK may be mainly related to the massive growth of
indigenous species, promoted by anthropogenic nutrients. Moreover, redundancy discriminant analysis and correlation
analysis revealed that methanogens and methanotrophs mainly respond to the nutrients and metals,
such as total organic carbon, total phosphorus, total nitrogen, SO4 2−, NO2
−, NH4+, Cr, and Zn, which were often related to human activities. Network analyses showed that the species related to the metabolism of methane may
play a vital role in the interassociation among different microbial communities. Therefore, methanogens,