Over the past decade, our research group has found that plant responses to combined abiotic stresses are unique and cannot be inferred from studying plants exposed to individual stresses. Adaptive mechanisms involve changes in gene expression, ion regulation, hormonal balance, and metabolite biosynthesis or degradation. Understanding how these mechanisms integrate from stress perception to biochemical and physiological adjustments is a major challenge in abiotic stress signaling studies. Today, vast amounts of -omics data (genomics, transcriptomics, proteomics, metabolomics, phenomics) are readily available. Additonally, each –omic level is regulated and influenced by the others, highlighting the complexity of plant metabolism’s response to stress. Considering abscisic acid (ABA) as a key regulator in plant abiotic stress responses, in our study, ABA-deficient plants (flc) underwent single or combined salinity and heat stresses were evaluated and different -omics analyses were conducted. Significant changes in biomass, photosynthesis, ions, transcripts, and metabolites occurred in mutant plants under single or combined stresses. Exogenous ABA application in flc mutants did not fully recover plant phenotypes or metabolic levels but induced cellular reprogramming with changes in specific markers. Multi-omic analysis aimed to identify ABA-dependent, ABA-independent, or stress-dependent markers in plant responses to single or combined stresses. We demonstrated that studying different -omics together identifies specific markers for each stress condition not detectable individually. Our findings provide insight into specific metabolic markers in plant responses to single and combined stresses, highlighting specific regulation of metabolic pathways, ion absorption, and physiological responses crucial for plant tolerance to climate change.

Root exudates play an essential role in plant-soil-abiotic stress interactions. However, we still know little about the influence of stress combinations on the root exudation profile. Using targeted and untargeted metabolomics, here we test the effect of drought, heat stress, and their combination on the maize root exudates, also considering the differences that might exist between root types (seminal and primary) and root zones (apical and sub-apical). In addition, we built an analytical framework that relate the root exudation profile with the characterization of the rhizosphere bacterial community, enabling us to dissect the interactions between specific root exudates and microbial taxa. Our results suggest that the composition of root exudates has a different outcome according to the single or combined stress and to the root zone but not between root types. Further, we found that stress-specific exudates influence the relative abundance of specific microbial taxa, some of which are known to be beneficial microorganisms. Therefore, the stress-specific root exudate composition selecting specific microbial taxa, here observed, represent a contribute on the effects of climate changes on crops increasing thus the potential impact on the current trend of crafting agricultural practices within a wider point of view of plants-microbe-environment interactions.

Microbial-based biostimulants can improve crop productivity by modulating cell metabolic pathways including hormonal balance. However, little is known about the microbial-mediated molecular changes causing yield increase. The present study elucidates the metabolomic modulation occurring in pepper (Capsicum annuum L.) leaves at the vegetative and reproductive phenological stages in response to microbial-based biostimulants containing the arbuscular mycorrhizal fungi Rhizoglomus irregularis and Funneliformis mosseae as well as Trichoderma koningii. Application of endophytic fungi significantly increased total fruit yield by 23.7% compared to that of untreated plants. Multivariate statistics indicated that the biostimulant treatment substantially altered the shape of the metabolic profile of pepper. Compared to the untreated control, the plants treated with microbial biostimulants presented with modified gibberellin, auxin, and cytokinin production and distribution. The biostimulant treatment also induced secondary metabolism and caused carotenoids, saponins, and phenolic compounds to accumulate in the plants. Differential metabolomic signatures indicated diverse and concerted biochemical responses in the plants following the colonisation of their roots by beneficial microorganisms. The above findings demonstrated a clear link between microbial-mediated yield increase and a strong up-regulation of hormonal and secondary metabolic pathways associated with growth stimulation and crop defence to environmental stresses.