Full-Length 16S rRNA Sequencing Reveals That Silicon Fertilization Enhances Sugarcane Yield and Heavy Metal Tolerance by Reshaping the Rhizosphere Microbiome

Silicon (Si) depletion in intensively managed tropical soils may limit the performance of silicophilic crops such as sugarcane. This field study investigated granular and powdered Si-enriched compound fertilizers applied at a product rate of low (1000 kg·hm−2) and high (1250 kg·hm−2) doses, evaluating impacts on: (1) sugarcane agronomic traits and edaphic properties; (2) heavy metal accumulation in plant tissues and rhizosphere soil; and (3) rhizosphere bacterial communities via PacBio sequencing of full-length 16S rRNA genes. Our findings indicated that high-dose Si application (HP) significantly boosted sugarcane growth in the second cropping season (2022) compared with the control (CK), with stalk height increasing by 12.43%, stalk diameter by 8.93%, sucrose content by 21.41%, available stalk number by 21.33%, single stalk weight by 35.21%, and theoretical yield by 64.16%. High-dose powdered Si increased available nitrogen (33.89%), phosphorus (29.05%), potassium (43.42%), and soil Si (42.18%). Si amendments reduced toxic metals (Cd, Pb, Cr) by 56–75% in tissues and enriched putatively beneficial bacterial taxa (e.g., Aquabacterium, Candidatus Koribacter). Microbial community analysis revealed dose-dependent shifts in bacterial diversity, with the enrichment of putatively beneficial taxa, such as Candidatus Solibacter and Kitasatospora, in the high-dose treatment groups. A ternary plot analysis further revealed treatment-enriched genera distinct from the control. Moreover, redundancy analysis identified available potassium, soil pH, and Si as the key edaphic factors shaping rhizosphere bacterial community composition. This study offers a theoretical foundation for its application to sustainable farming towards food security. Further studies are required to explore the individual roles of these bacterial strains in the silicon-mediated plant growth.