Interactions, processes and biotechnological potential of microbiomes of freshwater macrophytes

Freshwater macrophytes harbour microbiomes in their rhizosphere, phyllosphere and endosphere, creating dynamic plant-microbe interactions modulating ecological processes. These interactions drive biogeochemical cycling (such as nitrogen and phosphorus), organic matter degradation and breakdown of emergent contaminants and thus promote water quality and ecosystem health. Recent research demonstrates that macrophyte microbiomes promote plant performance, stress resistance and phytoremediation in natural and constructed wetlands. But these interactions are highly dependent on environmental context. Disturbances like eutrophication, pollution and climate-related stresses can alter the microbial community structure, driving dysbiosis and induction of pathogenicity, methane release and the spread of antibiotic-resistant microbes. Here, we integrate newly gained insights into microbial diversity, community assembly and microbe-microbe and microbe-plant interactions with ecosystem impacts. We also highlight recent advances in microbiome engineering, synthetic ecology and genome-resolved techniques that help design microbial consortia in plant-microbe systems for wastewater remediation and reuse. Although progress has been made, significant research gaps exist in how microbial diversity translates into function, microbiome stability in response to environmental change and the experimental testing of microbial contributions. Overcoming these issues will help build predictive models and scalable, nature-based approaches to restore aquatic ecosystems and ensure sustainable water use in a circular bioeconomy.