How the flow and sediment pulse influencing the distribution and functional gene composition of bacterial communities? Case study of the lower Yellow River, China

•Bacterial communities and functional groups before/during/after WSR was analyzed.•Hydrodynamic change of WSR was the main cause to communities difference.•Anammox group became the main groups during WSR since the worse water quality.•The communities and functional groups of bacteria could gradually recover after WSR. Discharge containing large amount of sediment will cause a series of ecological effects on downstream river systems. To solve the siltation problem of Yellow River and Xiaolangdi reservoirs, water and sediment regulation has been carried out since 2000. To clarify the impact of the regulation on bacterial communities in the lower Yellow River, the composition of bacterial communities and functional groups in the riverbed and suspended sediment was analyzed by high-throughput sequencing and functional annotation of prokaryotic taxa method. The results showed that the overall diversity index of the Yellow River bacterial community was 3.014–7.045, and at a medium level compared to other large rivers in China. During the water and sediment regulation, the bacterial diversity index slightly decreased compared to the previous stage, while significantly increased at the post-stage of regulation, consideringrelatively small changes in chemical factors among three stages, it was thought that the The variation of bacterial community diversity was more influenced by the fluctuations of discharge, turbulent kinetic energy and sediment concentration. The relationship between suspended and riverbed samples to environmental factors also showed differences at three stages of regulation. During the regulation, increasing discharge and high velocity caused the ammoxidation related groups, such as nitrate and nitrite ammoxidation groups, to displace nitrification, nitrate reduction, and nitrate respiration groups, hence inhibit the water purification capabilities, while at the post-stage, the functional group of most sites recovered to similar level to the pre-stage. In summary, we reveal a characteristic pattern on how the microorganism in the high sediment river respond to the severe disturbance.