Soil and Genotype Shape the Sugarcane Phytobiome for Enhanced Environmental Adaptation

Soil properties critically shape sugarcane growth and its microbiome, yet their influence on gene expression remains unclear. We investigated the combined effects of soil type (clayey and sandy loam) and sugarcane genotype (IACSP-5503 and IACSP-6007) on microbiome composition and plant transcriptional profiles. Bacterial communities from soils and stalk tissues, as well as transcriptomes of 48-h sprouted buds grown for 10 months, were analysed. Results showed that IACSP-5503 (adapted to low-fertility soils) and IACSP-6007 (less adapted) recruited endophytic microbiota in a soil–genotype-dependent manner. In sandy loam, IACSP-5503 promoted diverse plant growth-promoting bacteria (PGPB) (including Burkholderia, Leifsonia and Mycobacterium), associated with nitrogen fixation, hormone production and stress tolerance, while IACSP-6007 displayed reduced PGPB diversity and transcriptomic signatures of nutrient deficiencies. Conversely, in clayey soil, IACSP-6007 recruited more PGPBs (such as Pseudomonas, Bacillus and Klebsiella) linked to nutrient acquisition and defence responses. Both genotypes exhibited enhanced expression of defence- and antioxidant-related genes in clayey soil, suggesting priming effects. Overall, our findings reveal soil-dependent, genotype-specific microbial recruitment strategies, particularly in IACSP-5503, reflecting adaptive responses to nutrient-poor conditions. The combined 16S metataxonomic and transcriptome data offered insights into how soil and genotype shape microbial recruitment and transcriptional plasticity in sugarcane.