Functional Differentiation and Metabolic Interactions of Microbial Communities Associated with Submerged and Emergent Aquatic Macrophytes

Microbial communities associated with aquatic macrophytes participate in lake biogeochemical cycling, but how macrophyte habitat and nutrient level impact their functional differentiation and metabolic interactions remains unclear. Metagenomics and genome-scale metabolic modeling were used to characterize these communities on submerged (Vallisneria natans and Hydrilla verticillata) and emergent (Phragmites australis and Zizania latifolia) macrophytes across nutrient levels in Xuanwu Lake. Communities associated with macrophytes harbored more abundant carbon (C) and nitrogen (N) metabolic genes than planktonic communities, particularly in the rhizosphere. Metabolic interaction modules (MIMs) centered on hub taxa differed in structure and predicted function between the rhizosphere and phyllosphere of submerged macrophytes. In the rhizosphere, a Halobacteriota hub was predicted to receive carbohydrates and nitrogen compounds mainly from Burkholderiales, and its MIM showed predicted carbon degradation and denitrification potential, which was greater under higher nutrient levels. In the phyllosphere, a Thermoproteota hub was predicted to receive ammonium and urea from, and supply urea to, its partners, and its MIM showed predicted nitrification and nitrogen reduction potential; under higher nutrient levels, a Pseudomonadota hub showed lower predicted nitrogen transfer potential. Overall, macrophyte habitat and nutrient level were both associated with microbial metabolic interactions and predicted C and N cycling potential, providing new insights into biogeochemical cycling in freshwater lakes.