Submerged macrophyte restoration drives microbial community reassembly and functional adaptation for synergistic water quality improvement

• Submerged macrophytes reshaped microbial communities • Taxa linked to nutrient cycling and organic matter degradation were enriched • Heterogeneous selection predominated in microbial assembly mechanisms • Sediment nutrients drive microbial assembly • The synergistic interaction of submerged macrophytes and microorganisms was elucidated Urban lakes are important in sustaining urban ecological equilibrium through microclimate regulation, biodiversity support, and provision of ecosystem services. Submerged macrophyte restoration has emerged as a promising strategy to rehabilitate disturbed lake ecosystems, as these plants not only improve water clarity and nutrient cycling but also shape microhabitats that support microbial communities pivotal for biogeochemical processes. However, current studies predominantly focus on microbial α-diversity, lacking systematic comparisons of microbial succession and cascade purification mechanisms between restored ((H zone) and non-restored (P zone) zones during long-term macrophyte recovery. This study aimed to elucidate the mechanisms underlying submerged macrophyte-microorganism synergies in anthropogenically disturbed urban lakes by analyzing microbial structure, diversity, ecological functions, and environmental drivers across restored and non-restored areas. Results demonstrated that submerged macrophyte restoration reshaped sediment microbial communities, enhancing community stability and enriching taxa linked to nutrient cycling, heavy metal detoxification, and organic matter degradation. Sediment nutrient concentrations were identified as primary environmental drivers of microbial assembly. The submerged macrophyte integrated with microorganisms improved the lake ecological quality through habitat-driven niche creation and functional specialization, exudate-driven co-metabolism, and allelopathic suppression of competitors. These findings highlight the critical role of submerged macrophyte-microbe co-regulation in restoring polluted urban lakes, offering novel insights for sustainable management of anthropogenically disturbed aquatic ecosystems.