This study investigates the impact of hydroponic cultivation on plant-associated microbial communities in Epipremnum aureum (golden pothos) following the transition from soil-based to hydroponic growth systems. Three aqueous treatments were compared: tap water, distilled water, and mineral salts-added nutrient-enriched distilled water. Over a 3.5-month period, root, leaf, and nutrient solution samples were systematically collected and analyzed via 16S rRNA gene amplicon sequencing to track microbiome dynamics.

Hydroponic cultivation enables precise environmental control but its impact on plant-associated microbial communities remains underexplored. This study investigated microbiome shifts in Epipremnum aureum (golden pothos) following the transition from soil-based to hydroponic growth under three aqueous treatments including tap water, distilled water, and mineral salts-added nutrient-enriched distilled water. Over a three-and-a-half-month period, root tissues, leaf tissues, and nutrient solution samples were collected and analyzed through 16S rRNA gene amplicon sequencing. Key findings demonstrated marked declines in microbial diversity across hydroponic systems compared to soil-root microbiomes. Community restructuring was observed with aquatic-adapted Proteobacteria families becoming dominant in hydroponic environments, contrasting with soil-associated taxa. Temporal succession patterns indicated a gradual loss of terrestrial microbial groups and enrichment of hydroponic-specialized communities over the experimental period. Alpha diversity metrics and beta diversity analyses further revealed clear differentiation between soil-root and hydroponic microbiomes. Integrated measurements of physicochemical parameters such as pH, electrical conductivity, and nutrient ion concentrations provided contextual data for interpreting microbiome changes. This comprehensive dataset combines multi-compartment sampling of plant tissues and nutrient solutions with temporal tracking and environmental metadata, offering new insights into microbial community assembly during adaptation to hydroponic systems. The results support the development of microbiome-based strategies for optimizing plant-microbe interactions in controlled agricultural environments.