Transcriptomic responses of plant-associated bacterial isolates to 4-hydroxycinnamic acid
Plant-derived specialised metabolites are increasingly recognised as major determinants of microbiome assembly, enabling plants to selectively recruit microorganisms adapted to their chemical environment. Among these metabolites, 4-hydroxycinnamic acid (4-HCA) has recently emerged as a key ecological signal that shapes plant-associated bacterial communities. However, whether bacterial responsiveness to 4-HCA can be exploited as a rational criterion for identifying plant-beneficial microorganisms and the molecular mechanisms underlying this adaptation remain largely unknown. We hypothesised that bacteria exhibiting positive growth responses to 4-HCA represent metabolically specialised, microbiome-adapted organisms with enhanced potential as plant growth-promoting bacteria (PGPB) and biological control agents (BCAs). To test this hypothesis, we isolated 39 culturable bacterial strains from the rhizosphere, phyllosphere, and endosphere of cotton (Gossypium spp.) genotypes differing in their tolerance to Cotton Leaf Curl Disease (CLCuD). The isolates were screened for growth responses to 4-HCA, plant growth-promoting characteristics, and their capability of inducing stress-tolerance in plant monoassociation assays. The collection was dominated by members of the genera Bacillus, Serratia, Agromyces, and Microbacterium, with Bacillus safensis AB30 (Bs), Serratia nematodiphila AB14 (Sn), and Microbacterium schleiferi AB1 (Ms) exhibiting significantly enhanced growth in the presence of 4-HCA. Candidate strains tolerating 4-HCA also exhibited remarkable plant growth-promoting (PGP) characteristics such as nitrogen fixation, phosphorus and zinc solubilisation, siderophore production, phytohormone production, and salt tolerance. To evaluate the practical relevance of metabolite-guided bacterial selection, representative 4-HCA-responsive strains were assembled into a synthetic microbial community (SynCom). The SynCom efficiently co-utilized 4-HCA and glucose, significantly enhanced cotton growth following seed biopriming, and consistently reduced the severity of Cotton Leaf Curl Disease under greenhouse conditions. Comparative transcriptomic analyses revealed that adaptation to 4-HCA involved extensive but strain-specific transcriptional reprogramming rather than a universal bacterial response. Differentially expressed genes were associated with oxidative stress mitigation, respiratory metabolism, aromatic compound utilisation, membrane-associated functions, and resource allocation, highlighting multiple physiological strategies for adaptation to this plant-derived metabolite. Several previously uncharacterized genes also displayed conserved regulation across responsive strains, suggesting novel components of bacterial adaptation to phenolic-rich environments. Collectively, our findings demonstrate that 4-HCA functions as a host-controlled ecological filter that can be exploited to identify microbiome-adapted, plant-beneficial bacteria that are not only capable of thriving in plant compartments but have also acquired beneficial PGP and biocontrol traits. By integrating metabolite-guided bacterial selection, we propose a targeted SynCom development rather than random bioformulations, for sustainable agriculture.
Plant-derived specialised metabolites are increasingly recognised as major determinants of microbiome assembly, enabling plants to selectively recruit microorganisms adapted to their chemical environment. Among these metabolites, 4-hydroxycinnamic acid (4-HCA) has recently emerged as a key ecological signal that shapes plant-associated bacterial communities. However, whether bacterial responsiveness to 4-HCA can be exploited as a rational criterion for identifying plant-beneficial microorganisms and the molecular mechanisms underlying this adaptation remain largely unknown. We hypothesised that bacteria exhibiting positive growth responses to 4-HCA represent metabolically specialised, microbiome-adapted organisms with enhanced potential as plant growth-promoting bacteria (PGPB) and biological control agents (BCAs). To test this hypothesis, we isolated 39 culturable bacterial strains from the rhizosphere, phyllosphere, and endosphere of cotton (Gossypium spp.) genotypes differing in their tolerance to Cotton Leaf Curl Disease (CLCuD). The isolates were screened for growth responses to 4-HCA, plant growth-promoting characteristics, and their capability of inducing stress-tolerance in plant monoassociation assays. The collection was dominated by members of the genera Bacillus, Serratia, Agromyces, and Microbacterium, with Bacillus safensis AB30 (Bs), Serratia nematodiphila AB14 (Sn), and Microbacterium schleiferi AB1 (Ms) exhibiting significantly enhanced growth in the presence of 4-HCA. Candidate strains tolerating 4-HCA also exhibited remarkable plant growth-promoting (PGP) characteristics such as nitrogen fixation, phosphorus and zinc solubilisation, siderophore production, phytohormone production, and salt tolerance. To evaluate the practical relevance of metabolite-guided bacterial selection, representative 4-HCA-responsive strains were assembled into a synthetic microbial community (SynCom). The SynCom efficiently co-utilized 4-HCA and glucose, significantly enhanced cotton growth following seed biopriming, and consistently reduced the severity of Cotton Leaf Curl Disease under greenhouse conditions. Comparative transcriptomic analyses revealed that adaptation to 4-HCA involved extensive but strain-specific transcriptional reprogramming rather than a universal bacterial response. Differentially expressed genes were associated with oxidative stress mitigation, respiratory metabolism, aromatic compound utilisation, membrane-associated functions, and resource allocation, highlighting multiple physiological strategies for adaptation to this plant-derived metabolite. Several previously uncharacterized genes also displayed conserved regulation across responsive strains, suggesting novel components of bacterial adaptation to phenolic-rich environments. Collectively, our findings demonstrate that 4-HCA functions as a host-controlled ecological filter that can be exploited to identify microbiome-adapted, plant-beneficial bacteria that are not only capable of thriving in plant compartments but have also acquired beneficial PGP and biocontrol traits. By integrating metabolite-guided bacterial selection, we propose a targeted SynCom development rather than random bioformulations, for sustainable agriculture.