Establishing the correlation of metabolites and rhizobacterial composition on the roots of Senna alexandrina

Abstract

Senna alexandrina is widely recognised for its production of anthraquinone derivatives, central to its pharmacological properties. Like many plants, its growth and secondary metabolism are influenced by interactions with rhizosphere microorganisms. Rhizobacteria are essential in facilitating nutrient cycling, enhancing stress resilience, and influencing plant metabolic processes. Plant-derived metabolites shape microbial community composition by providing selective substrates or signalling molecules. The aim of this study was to examine the correlation between the metabolite profiles of roots and the associated rhizobacterial communities in S. alexandrina at the early growth and flowering stages. S. alexandrina was cultivated under controlled conditions and sampled at two developmental stages, early vegetative and flowering. Rhizosphere soil was collected for microbial genomic analysis using full-length 16S rRNA sequencing, with reads processed and classified against the SILVA database. Root tissues were extracted using methanol and analysed by UHPLC qTOF-MS, followed by multivariate statistical analysis and GNPS-based molecular networking to profile stage-specific metabolites. The study demonstrates that plant developmental stage profoundly shapes rhizosphere microbial diversity, community structure, and metabolomic composition. Early growth stages are marked by higher α-diversity, broader phylum-level representation, and denser, more cooperative co-occurrence networks, reflecting a microbiome that supports mutualistic interactions and nutrient cycling. In contrast, the flowering stage exhibits reduced diversity, narrower ecological niches, and increased dominance of Proteobacteria, accompanied by looser and more competitive network structures. Metabolomic profiling identified rhein as a key early-stage metabolite linked to stress signalling, whereas flavonoids and phosphatidic acids predominated the flowering stage in VIP plot analysis, reflecting reproductive development and hormone regulation. Molecular networking further highlighted anthraquinones, flavonoids, and lipids as core metabolite families, each exhibiting distinct enrichment patterns across the stages. These findings highlight that Senna alexandrina undergoes coordinated shifts in both rhizobacterial composition and metabolite production across developmental stages, underscoring the importance of plant–microbe interactions in shaping growth, reproduction, and the medicinal value.