Integrating metabolomics and transcriptomics for SynCom-driven rhizomicrobiome engineering in salinity-stressed rice

Ensuring food security is increasingly difficult as salinity stress, intensified by climate change, reduces crop yields and causes frequent harvest failures, especially in coastal regions. Synthetic community (SynCom)-driven rhizomicrobiome engineering offers a promising approach to enhance rice resilience by improving stress responses, nutrient uptake, and osmoprotection. Supported by metabolomic and transcriptomic analyses, SynCom interventions reveal mechanisms underlying plant adaptation to saline environments. This review evaluates the potential of SynCom in mitigating salinity stress in rice through multi-omics integration and identifies key research clusters, emerging themes, and regional knowledge gaps. Using a PRISMA-guided systematic review and bibliometric analysis of Scopus and ScienceDirect databases, 989 articles were screened, with 15 selected for detailed analysis. Results indicate distinct thematic clusters and influential studies shaping current understanding. Metabolomic and transcriptomic insights highlight essential tolerance mechanisms such as ion homeostasis, osmoprotectant synthesis, and antioxidant defense. Significant gaps remain, particularly in region-specific studies relevant to Indonesia’s saline agroecosystems. By mapping the research landscape, this review outlines a roadmap for incorporating SynCom-based bioengineering into climate-smart rice production, aiming to enhance productivity, sustain soil health, and strengthen long-term food security.