Metabolic fingerprints of rhizosphere microbial communities differ due to increased nitrogen availability and cultivation methods of rice (Oryza sativa)

Microbial metabolic activities in the rhizosphere are essential for plant nutrition and yield. The study was carried out during 2023–2024 at ICAR-Indian Agricultural Research Institute, New Delhi to profile the rhizosphere metabolic community fingerprints using Biolog EcoPlateTM assays in rice (Oryza sativa L.) grown on neutral soil under conventional flooded (CF) and aerobic [simulating direct-seeded rice (DSR)] methods, with high (HN, 150 kg N/ha) or low (LN, 25 kg N/ha) nitrogen (N). The experiment was laid out in a randomised block design (RBD). Average well colour development (AWCD) of total and class-specific substrates, diversity indices, and principal component analysis (PCA) were used to assess community-level metabolic activity, diversity, and carbon source utilisation patterns (CSUP). Low-N treatments (CFLN, DSRLN) showed higher AWCD (1.45 and 1.31, respectively) and broader substrate utilisation, indicating enhanced microbial activity and metabolic flexibility. The low-N treatment under DSR (DSRLN) had the most metabolically diverse and even communities, whereas the CF system (CFLN) favoured heterotrophic, oligotrophic communities adapted to anoxia. CSUP revealed differential catabolism of amino and carboxylic acids, with marginal variation in amine and polymer utilisation. PCA separated the CSUP along nitrogen and cultivation methods, high-N CF method (CFHN) favoured copiotrophic degradation of aromatics and polymers, while low-N DSR (DSRLN) promoted oxidative metabolism of keto acids, benzoates, and disaccharides. Functional indices reflected niche-specific adaptation, with DSRLN exhibiting the highest Shannon diversity and CFLN dominated by specialists for distinct carbon classes. Nitrogen availability and cultivation methods act as filters shaping rhizosphere metabolic activity, flexibility, and community stability, influencing sustainable rice cultivation. Therefore, understanding the management of rhizosphere microbiome under DSR is critical to unlock its potential as a sustainable, water-saving alternative to conventional flooded rice.