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Estuaries represent an important link between the land and the ocean. Heterotrophic microorganisms in the estuary are fuelled by a composite pool of both recalcitrant terrestrial organic carbon (OC) transported by rivers and labile OC produced by aquatic phototrophs. Bathyarchaeota that are widely distributed in estuarine sediments have unique metabolic functions in carbon metabolism. However, their ecology and physiological capacities are not fully understood. In this study, we coupled taxonomic composition with comprehensive geochemical data to investigate the distribution and the OC utilization potential of Bathyarchaeota in the sediment of Pearl River Estuary (PRE). The subgroups of Bathy-6, Bathy-8, Bathy-15 and Bathy-17 dominated in all sediment samples. Different bathyarchaeotal subgroups occupied different niches along the salinity gradient in the PRE sediment. Seasonal variations of …