Restoration of submerged vegetation modulates microbial communities to decrease nitrogen and phosphorus loads in sediment-water systems.

• Restoration of submerged vegetation mitigated nutrient loads in sediment-water systems. • Submerged vegetation reduced the abundance of most nitrogen cycling genes and increased that of phosphorus cycling genes. • Diversity differently affects sediment nutrients and microbiomes, mainly due to plant life cycles. The release of nitrogen and phosphorus from sediments, known as internal nutrient loading, plays a crucial role in determining the eutrophic state of lakes and the timeframe for their ecological recovery. The restoration of submerged macrophytes is considered an effective measure to improve lake eutrophication. However, the impact of submerged macrophytes restoration on the storage and transformation mechanisms of nitrogen and phosphorus in lake sediment-water systems has not yet been systematically studied. This study constructed two submerged macrophyte communities with species richness of either two or five and monitored the physicochemical characteristics, nitrogen and phosphorus dynamics, and the structural and functional changes of sediment microbiomes in the plant-water-sediment system during three growth stages of the plants (May, July, and October). Our results demonstrated that the presence of submerged vegetation effectively reduced the nitrogen and phosphorus loads in the sediment-water system, encompassing their chemical forms, active concentrations, and release fluxes. Simultaneously, the restoration of submerged vegetation altered the composition of sediment microbial communities and the nitrogen and phosphorus cycling functions. Following the restoration, the abundance of functional genes associated with nitrogen fixation, organic nitrogen metabolism, nitrate reduction, and nitrification exhibited an average decrease of 2.95 %. In contrast, the abundance of genes involved in denitrification and nitrogen limitation response regulation increased by 20.24 %, while those related to phosphorus cycling processes showed a 7.29 % increase. Additionally, submerged macrophyte communities with varying richness differentially affected lake nitrogen and phosphorus loads, as well as the structure and function of sediment microbiomes, primarily related to the life cycle stages of the submerged macrophytes. These findings highlight the crucial role of submerged plants in maintaining lake nutrient balance and sediment microbiomes, providing valuable insights into how the restoration of submerged vegetation affects nutrient cycling in aquatic ecosystems. [Display omitted] [ABSTRACT FROM AUTHOR]