Nano-selenium (nano-Se) fertilizers are emerging as a promising strategy to alleviate selenium (Se) deficiency in rice-producing regions, where Se deficiency affects nearly one billion people globally. However, their impacts on Se bioavailability, rhizosphere microbial ecology, and nutrient cycling in flooded paddy soils remain poorly understood. In this study, a field experiment was conducted to evaluate biologically synthesized nano-Se (BSeNP) and chemically synthesized nano-Se (CSeNP) in terms of Se uptake, soil–plant Se dynamics, and microbial community responses in a rice system. Both nano-Se treatments significantly enhanced Se accumulation in stems, leaves, and grains. BSeNP induced stronger Se enrichment in vegetative tissues, whereas both treatments achieved comparable increases in grain Se content relative to the control. Soil Se decreased gradually during plant growth while plant Se increased, reflecting efficient nano-Se dissolution, sustained rhizosphere availability, and effective root-to-shoot translocation.
High-throughput 16S rRNA gene sequencing revealed substantial microbial restructuring, characterized by increased abundance of Proteobacteria and enrichment of Se-transforming genera, including Burkholderia, Rhodobacter, and Sphingomonas. Co-occurrence network and functionalprediction analyses indicated enhanced nitrogen and sulfur cycling pathways, increased ABC transporter activity, and elevated microbial metabolic and redox functions, particularly under BSeNP. Correlation analyses demonstrated strong coupling between plant Se accumulation, soil nutrients, and microbial functional traits, highlighting coordinated plant–soil–microbe interactions.
Collectively, biosynthesized nano-Se exhibited superior biofortification potential and ecological compatibility compared with chemically synthesized forms, providing a bio-based and sustainable approach for improving Se nutrition and soil microbial function in paddy agroecosystems.