Melatonin acts as a multifunctional regulator of plant stress adaptation by reprogramming primary and secondary metabolism and coordinating ROS, nitric oxide, and phytohormone signalling. Integrating metabolomics with transcriptomics and proteomics provides new insights into these mechanisms and highlights melatonin as a promising strategy for enhancing crop resilience and productivity under diverse environmental stresses. Plants, being sessile, are continuously exposed to diverse environmental challenges, which disrupt cellular homeostasis and reduce crop productivity. To survive under such conditions, plants have evolved complex defence mechanisms involving metabolic reprogramming and coordinated molecular signalling networks. Among the regulatory molecules involved in stress adaptation, melatonin (N-acetyl-5-methoxytryptamine) has emerged as a multifunctional signalling compound that plays a pivotal role in plant growth, development, and stress tolerance. Acting as a potent antioxidant and signalling regulator, melatonin modulates multiple metabolic pathways associated with energy metabolism, amino acid biosynthesis, carbohydrate metabolism, and secondary metabolite production. These metabolic adjustments enhance the accumulation of osmoprotectants, antioxidants, and defence-related metabolites, thereby improving plant resilience under stress. Recent advances in metabolomics, together with transcriptomics and proteomics, have provided deeper insights into melatonin-mediated metabolic regulation in plants. High-throughput analytical platforms such as liquid chromatography-mass spectrometry (LC-MS), gas chromatography-mass spectrometry (GC-MS), and nuclear magnetic resonance (NMR) enable comprehensive profiling of stress-responsive metabolites and reveal how melatonin orchestrates metabolic network reprogramming. Emerging evidence indicates that melatonin interacts with reactive oxygen species, nitric oxide, and multiple phytohormones to regulate gene expression, protein abundance, and metabolite accumulation, thereby integrating stress perception with physiological adaptation. This review summarises current knowledge on melatonin biosynthesis, signalling pathways, cross-talk and its role in regulating primary and secondary metabolism under diverse stresses. Emphasis has been laid on metabolomics-driven insights and multi-omics integration to elucidate the molecular mechanisms underlying melatonin-mediated stress tolerance and to support strategies to improve crop resilience and productivity.

Microbial compatibility is an important consideration for synthetic communities (SynCom) function, but its ecological and physiological consequences for plant-microbe interactions remain insufficiently understood. We investigated compatible and incompatible Bacillus-based SynComs and their effects on tomato growth, rhizosphere microbiome assembly, and microbial network organization. Compatible co-cultures exhibited enhanced co-culture phenotypes, including merged colony morphology, enhanced biofilm formation, and altered growth dynamics, whereas incompatible combinations formed demarcation zones, indicative of antagonism. The compatible pair NMCN6+LNXM12 showed higher attached biomass and relative indole-3-acetic acid production compared with most incompatible or single-strain inoculations. Greenhouse experiments revealed that compatible SynComs significantly promoted tomato growth, increased plant height, root length, photosynthesis, and stomatal conductance, while incompatible combinations showed distinct soluble sugar responses rather than consistent evidence of plant stress. Amplicon sequencing revealed treatment-associated variation in rhizosphere bacterial community composition. Compatible SynComs were associated with enrichment of specific bacterial taxa and produced more interconnected and stable co-occurrence networks, whereas incompatible combinations showed distinct taxonomic profiles and comparatively fragmented microbial associations. Community composition differed significantly among individual treatments but not among broader compatibility categories with unequal within-group dispersion. Collectively, the observed co-culture, plant, and microbiome responses highlight differences among the selected Bacillus combinations that cannot be attributed to compatibility alone. These findings may provide the selection of Bacillus strain combinations for further evaluation as plant inoculants.

Alternative splicing (AS) is a pivotal post-transcriptional mechanism for plant thermal adaptation, yet its dynamics in heat-tolerant woody species remain poorly understood. Here, we map the temperature-resolved AS landscape of the highly thermotolerant woody plant Rhododendron hainanense by combining Iso-Seq with RNA-seq. Transcriptomic profiling revealed a graded regulatory architecture: moderate heat (37 °C) elicited a targeted proteostatic response, whereas severe heat (42 °C) provoked a massive transcriptome expansion. Notably, this global AS surge coincided with a widespread downregulation of core splicing factors, a correlation suggesting that a more permissive splicing environment may contribute to the rapid generation of diverse stress-responsive isoforms. The heat shock protein (HSP) family emerged as the principal hub of this AS-associated diversification; the core chaperone genes ClpB1, HSP83, and HSP70 generated the greatest transcript complexity, with HSP83 alone producing 29 distinct AS transcripts that resolved into three temperature-dependent expression groups. Within the heat shock factor network, HSFA2 showed the strongest and most sustained induction, and DAP-seq identified in vitro HSFA2 binding at the promoters of ClpB1, HSP83, and HSP70, supporting these core chaperones as putative direct DNA-binding targets. Functional complementation in Arabidopsis further showed that three structurally distinct HSFA2 splice variants each restored thermotolerance to the hsfa2 mutant and consistently induced expression of the core ATP-dependent chaperone arm, suggesting that this central chaperone-induction capacity is retained across the tested splice variants in this heterologous system. Together, these findings provide a comprehensive atlas of temperature-modulated AS in a thermotolerant woody plant and support a model in which splicing-mediated diversification of the HSP chaperone network contributes to heat adaptation, offering post-transcriptional insights for breeding climate-resilient crops.