Priyanka Chauhan, Pratibha Verma, Arpita Bhattacharya, Anushka Tripathi, Poonam C. Singh, S.K. Sharma, Aradhana Mishra
Abstract Plants produce a diverse range of secondary metabolites [SMs] such as alkaloids, terpenoids and phenolics, which play crucial roles in defense, signalling and human health applications like pharmaceuticals and nutraceuticals. Traditionally viewed as autonomous plant biosynthetic processes, several evidence reveals that profound influence of plant associated microbes (endophytes, rhizobacteria and phyllosphere communities) in engineering SM profiles. These microbes modulate SM biosynthesis through direct mechanism, including horizontal gene transfer of biosynthetic gene clusters, elicitation of stress responsive pathways via microbial elicitors (e.g. lipopolysaccharides), and metabolic cross feeding that supplies precursors or enzymes. Indirectly, they alter plant physiology by enhancing nutrient uptake, hormone signalling (e.g. auxins, jasmonate), and microbiome mediated priming against biotic/abiotic stresses. Recent metagenomic and metabolomic studies underscore microbiome -SM synergies in crop like rice and tomato, boosting yield of medicinally valuable compounds such as artemisinin in Artemisia annua . However, challenges persist in disentangling microbial causality from plant endogenous factors and scaling these interactions for agricultural biotechnology. This review synthesized multidisciplinary evidence on microbial engineering of plant SMs, highlighting molecular mechanisms, ecological contexts, and biotechnological prospects for sustainable crop improvement and novel drug discovery.