Plants function as integral components of soil ecosystems, embedded within diverse microbial consortia that engage in continuous chemical and informational exchange. This molecular dialog governs how plants distinguish harmful, neutral, and beneficial microbes, transforming the rhizosphere into a dynamic signaling interface. Microbial interactions operate along a chemical continuum in which metabolites, volatiles, peptides, and other small molecules act across aqueous, lipidic, and chemically heterogeneous microenvironments to shape recognition and response. The physicochemical organization of rhizosphere metabolites may influence their diffusion, stability, and accessibility, although direct evidence for these effects remains limited. Within this framework, plant recognition is reinterpreted as a fluid, context-dependent communication process rather than a binary separation of immunity and symbiosis. This review synthesizes recent advances in the molecular architecture of this continuum, from receptor-mediated signaling to metabolite-driven ecological filtering, and examines how these overlapping systems determine host specificity, community stability, and adaptive resilience. Special attention is given to the regulatory roles of reactive oxygen species (ROS), phytohormones, and redox metabolites as both stress indicators and inter-organismal communicators. By integrating biochemical, ecological, and systems perspectives, this review highlights implications for developing microbiome-based, climate-smart, and sustainable agricultural practices.
Germination of urediniospores marks the onset of infection by Neophysopella tropicalis, the causal agent of Asian grapevine leaf rust, yet the molecular mechanisms enabling this obligate biotrophic fungus to establish infection remain largely unknown. We combined transcriptomics, histological analyses, and functional assays to identify and characterize candidate effector proteins deployed during the earliest stages of pathogenesis. RNA sequencing of in vitro-germinated urediniospores identified 303 genes encoding predicted secreted proteins bearing hallmarks of fungal effectors, grouped into 142 sequence families and revealing a remarkably diverse repertoire of effector candidates. Fifteen highly expressed N. tropicalis effector candidate (NtEC) genes, representing thirteen distinct sequence families, were selected for expression profiling by reverse transcription quantitative PCR across infection stages. Chitin-targeted fluorescence microscopy provided a developmental framework for interpreting expression across germination, penetration, and early colonization. Although identified during germination, seven NtECs accumulated transcripts predominantly during host penetration and early biotrophic colonization, suggesting specialized roles in infection establishment. Using the Type III Secretion System of Pseudomonas fluorescens EtHAn, we demonstrated that three NtECs (NtEC-05, NtEC-09, and NtEC-10) strongly suppressed AvrB-triggered hypersensitive cell death in Nicotiana benthamiana, while three others (NtEC-11, NtEC-12, and NtEC-13) exhibited moderate immune-suppressing activity. Together, these findings provide the first comprehensive characterization of the N. tropicalis effector repertoire, demonstrating that early infection involves coordinated, sequential deployment of evolutionarily diverse effectors associated with plant immune suppression. This work establishes an integrated framework for discovery and functional prioritization of rust fungus effectors and provides a valuable molecular resource for future studies on grapevine–rust interactions.
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.
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.
RNA N6-methyladenosine (m6A) modifications dynamically modulate RNA stability, splicing, and translation in plants, influencing developmental and stress response processes. In this review, we provide an overview of the key protein complexes involved in RNA m6A modification, including methyltransferases, demethylases, and m6A-binding proteins. We then demonstrate that m6A modulates vegetative growth, reproductive processes, responses to stresses, and hormone signaling. In agronomically important crops, RNA m6A modifications affect stress resilience, developmental timing, and quality traits, such as drought tolerance, salt resistance, male fertility, pollen viability, and fruit maturation. Furthermore, we elucidate the molecular mechanisms of RNA m6A. Finally, we explore advancements in m6A detection technologies, highlighting emerging trends and future directions. These strategies provide a conceptual framework for moving plant m6A research from descriptive epitranscriptomics toward trait-oriented crop and forest tree improvement.
