Plant-microbial partnerships and their underlying molecular mechanisms are indispensable, natural drivers of improved nutrient acquisition and stress tolerance in the face of climate-driven environmental challenges. Modern multi-omics tools, when coupled with artificial intelligence and synthetic biology, enable the precise design of targeted bioinoculants and synthetic microbial consortia. Translating these advanced microbiome-based strategies into scalable, field-level agricultural applications provides a sustainable path toward securing global food production while maintaining soil health. Global climate change imposes multifaceted abiotic and biotic stresses on crops, disrupting physiological and molecular processes and threatening agricultural productivity. Plant-associated microbes represent an underexplored yet powerful ally in enhancing crop resilience. This review presents current knowledge of plant–microbe interactions and the molecular mechanisms governing plant stress physiology, with an emphasis on climate-resilient and sustainable farming. Hence, ever-changing environmental cues pose a significant burden on agricultural productivity, and plant-associated microbial communities modulate a cascade of physiological and molecular responses, including production of phytohormones, signaling, regulation of reactive oxygen species homeostasis, and activation of plant immune responses to help plants withstand stress and enhance productivity. Moreover, root exudates, phytohormones, and quorum sensing mediate the central communication networks, facilitating plant–microbe cross talk. Additionally, the advances in OMICs approaches aid in disentangling the molecular underpinnings of these interactions by providing mechanistic insights and potential candidate gene targets for crop improvement and stress resilience. In the post-genomic era, integrating artificial intelligence and big data analysis to optimize microbiome-based strategies for sustainable agriculture is a new frontier for disentangling plant–microbe symbiosis to improve soil health, enhance crop yields, and improve stress tolerance. Thus, by integrating the ecological, physiological, and molecular perspectives, this review highlights the transformative potential of harnessing plant–microbe symbiosis for climate-resilient and sustainable agriculture. This review provides an up-to-date synthesis of plant–microbe interactions and their molecular roles in enhancing plant tolerance to multiple abiotic and biotic stresses under climate change scenarios. It integrates physiological, molecular, and omics-based perspectives across diverse microbial groups, including bacteria, fungi, archaea, and viruses. The review also highlights the potential of microbial symbiosis, together with emerging OMICS, AI, and Big Data approaches, to improve climate resilience and support sustainable agriculture.
Time-resolved metabolome–transcriptome integration reveals circadian regulation of floral scent biosynthesis in Nyctanthes arbor-tristis, linking volatile emission to transcriptional control and ecological timing. Nyctanthes arbor-tristis is a nocturnal plant known for its intense floral scent. However, the reported molecular regulation of its volatile organic compound (VOC) biosynthesis remains enigmatic. In this study, we investigated the temporal floral VOCs analysis using GC–FID and GC–MS at five time points between 6 PM and 6 AM. Fifteen major VOCs were identified, including green leaf volatiles (GLVs), terpenoids, and phenylpropanoids/benzenoids (PBs). Among them, 4-ketoisophorone was the most abundant constituent at all time points, showing a peak concentration at midnight (18.8 ± 3.4
Rootstock genotype shaped grapevine physiology and associated microbial communities, with the strongest compositional shifts consistently observed in the phyllosphere across contrasting growing seasons. Rootstocks contribute to grapevine adaptation to biotic and abiotic stresses, including drought, and influence associated microbial communities relevant to nutrient dynamics and stress resilience. However, integrated analyses of rhizosphere and phyllosphere microbiomes remain limited, particularly for newly developed drought-tolerant rootstocks (M2 and M4). This study tested the hypothesis that rootstock genotype influences vine physiology and vegetative growth while shaping microbial community composition and functional potential in the rhizosphere and phyllosphere. The study was conducted from 2023 to 2024 on Vitis vinifera cv. Barbera grafted onto six rootstocks (1103 Paulsen, 140 Ruggeri, SO4, Kober 5BB, M2, and M4). Phyllosphere and rhizosphere samples were collected at grapevine flowering and veraison, together with measurements of leaf gas exchange and stem water potential (Ψstem). Vegetative growth was assessed at the end of each season through leaf area, node number, and pruning weight. Microbial communities were profiled through 16S rRNA gene and ITS amplicon sequencing. Across both years, despite contrasting weather conditions, rootstock genotype affected vine performance, while the strongest differences in microbial communities were observed in the phyllosphere. Notably, M2 and M4 maintained higher Ψstem than the other rootstocks, indicating greater drought tolerance. Phyllosphere microbiome composition appeared to be shaped by rootstock-related differences in vine physiology and vegetative growth, likely through local microenvironmental changes affecting microbial assembly. Expanding integrative research linking plant physiology and microbiome ecology could clarify how rootstock-mediated traits influence grapevine-associated microbiomes and their potential contribution to microbial terroir, ultimately supporting more resilient and sustainable viticulture under climate change.
ARR1/12-mediated cytokinin signaling negatively regulates the accumulation of glycosylated flavonoids, thereby increasing plant susceptibility to As(III) stress. Cytokinins negatively regulate arsenic stress tolerance in plants through cytokinin-signaling type-B Arabidopsis response regulators (B-ARRs), specifically ARR1 and ARR12. However, the mechanism by which cytokinin signaling regulates plant metabolite dynamics, particularly antioxidant flavonoids, in response to arsenic toxicity remains largely unknown. Here, we hypothesized that ARR1/12-mediated cytokinin signaling modulates flavonoid metabolism to regulate arsenite [As(III)] tolerance. By comparing the global metabolic changes in roots of the arr1 12 double mutant (rD) and wild-type (WT) plants, we found that As(III) stress globally reduced metabolite abundance in WT roots. Importantly, the rD mutant accumulated significantly more flavonoids, most in glycosylated forms, than WT under As(III) exposure, which was supported by the specific upregulation of UDP-glycosyltransferase genes involved in flavonoid glycosylation. Accordingly, exogenous application of the glycosylated quercitrin-enhanced As(III) tolerance in WT roots, strengthening that the increase of glycosylated flavonoids in rD roots was beneficial for plant survival under As(III) exposure. Our data collectively strongly support that the increased glycosylation of flavonoids in the rD mutant improves their antioxidant functionality, thereby enhancing the As(III) stress tolerance. This study provides a new insight into the negative role of cytokinin signaling in repressing glycosylated flavonoid accumulation, causing increased susceptibility of plants to As(III) stress. Manipulation of cytokinin signaling or flavonoid glycosylation is, therefore, a promising approach for heavy metal stress mitigation in crops.
Plant immunity depends on coordinated control of signaling gain, molecular persistence, RNA fate, interorganismal exchange and timely attenuation, defining testable routes to durable disease control. Plant immunity is often reviewed as a sequence of receptor activation, transcriptional reprogramming, and antimicrobial output. That organization is useful, but it obscures a central mechanistic problem: immune performance depends on coupled control of protein abundance, RNA fate, interorganismal exchange and response termination. Here, we develop an evidence-weighted protein–RNA control-loop framework that is explicitly differentiated from receptor-, proteostasis-, RNA-silencing- and extracellular-vesicle-centered reviews. The framework organizes plant–pathogen interactions around five experimentally tractable control variables: signaling gain, molecular persistence, RNA routing, interorganismal exchange and memory versus cost. We evaluate how pattern-recognition receptors and nucleotide-binding leucine-rich-repeat receptors set signaling gain; ubiquitination, SUMOylation, proteasomal turnover and autophagy determine persistence; RNA-binding proteins, alternative splicing, N6-methyladenosine (m6A), translation and decay route immune messages; and vesicular or non-vesicular ribonucleoprotein carriers mediate cross-kingdom RNA exchange. For each layer, we distinguish association from physical mechanism, causal perturbation, and crop-level validation. Receptor synergy, resistosome signaling, selected proteolytic circuits and several cross-kingdom RNA interference mechanisms are strongly supported, whereas generalized roles for immune m6A, stress-granule routing, vesicle-exclusive RNA transport and durable epigenetic memory remain incompletely demonstrated. The framework yields testable predictions and a stage-gated roadmap for engineered receptors, host- and spray-induced gene silencing, proteostasis or RNA-binding-protein engineering, and multi-omics breeding. Durable resistance should therefore be judged not by maximal defense activation, but by sufficient gain, correct routing, appropriate persistence and timely attenuation with acceptable yield and environmental costs.
In this study, we functionally characterized the GRAS transcription factor gene GhSCL5 in upland cotton. Transcriptome analysis, RT-qPCR validation, and public transcriptome data from the CottonOmics database demonstrated that the expression of GhSCL5 was significantly induced by exogenous γ-polyglutamic acid (γ-PGA), polyethylene glycol (PEG)-simulated drought, and natural drought conditions. These results indicate that GhSCL5 participates in the drought stress response of cotton. Drought is a major abiotic stress limiting cotton production. The GRAS protein family participates in plant development and abiotic stress responses, but the roles of many cotton GRAS members remain unclear. Here, we characterized GhSCL5, a GRAS family gene in upland cotton (Gossypium hirsutum) whose expression was induced by natural drought, polyethylene glycol (PEG), and exogenous γ-polyglutamic acid (γ-PGA). Silencing GhSCL5 by virus-induced gene silencing (VIGS) reduced cotton drought tolerance, as indicated by decreased catalase (CAT) and peroxidase (POD) activities, lower proline (Pro) accumulation and leaf relative water content (RWC), and increased malondialdehyde (MDA) content under drought stress. Conversely, heterologous overexpression of GhSCL5 in Arabidopsis thaliana enhanced drought tolerance and maintained longer primary roots under mannitol-induced osmotic stress. Transcriptome profiling identified 7061 differentially expressed genes (DEGs) in GhSCL5-silenced cotton leaves under drought stress, comprising 3140 upregulated and 3921 downregulated genes. Notably, upregulated DEGs were enriched in pathways, including plant-pathogen interaction, plant hormone signal transduction, the plant MAPK signaling pathway, amino sugar and nucleotide sugar metabolism, phenylpropanoid biosynthesis, and arginine and proline metabolism, while downregulated DEGs were enriched in photosynthesis, plant hormone signal transduction, starch and sucrose metabolism, carbon fixation in photosynthetic organisms, glyoxylate and dicarboxylate metabolism, and photosynthesis–antenna protein. Importantly, the plant hormone signal transduction pathway was enriched with both upregulated and downregulated DEGs, suggesting that this pathway may represent a significant component of the transcriptional response. Within the plant hormone signal transduction pathway, genes associated with abscisic acid (ABA) and auxin were the most abundant, which indicates that these two hormonal systems might be key factors in the response associated with GhSCL5. Collectively, these findings suggest that GhSCL5 may contribute to drought tolerance through processes related to antioxidant defense, osmotic adjustment, and carbon metabolism, with transcriptomic evidence suggesting a potential involvement of ABA and Auxin signaling.
PAE8 and PAE9 double mutants reduce auxin concentration and enhance Arabidopsis thaliana resistance in a pathogen-dependent manner. Pectin O-acetylation is a key plant cell wall modification that influences developmental processes and stress responses. pectin acetylesterases (PAEs) are cell wall-modifying enzymes that are responsible for removing the acetyl group from pectin. In this study, we investigated the roles of PAE8 and PAE9 in regulating pectin O-acetylation, auxin concentration, and plant defense in Arabidopsis thaliana rosette leaves. Quantitative real-time PCR (qPCR) was conducted to evaluate the transcriptional profiles of PAE8 and PAE9 in 3- to 8-week-old rosette leaves that represent successive vegetative developmental stages, showing maximum expression at week 8 for both genes. The double mutant plants (pae8/pae9) showed significantly higher cell wall acetylation levels compared to the wild-type plants (Col-0) across all examined developmental stages. Indole-3-acetic acid (IAA) concentration was reduced in pae8/pae9 compared to Col-0 at week 8. Fourier-transform infrared spectroscopy (FTIR) analysis confirmed a significant difference in cell wall acetylation between Col-0 and pae8/pae9. Detached leaf assay for 8-week-old rosette leaves demonstrated that pae8/pae9 plants exhibit enhanced resistance to Fusarium oxysporum, Macrophomina phaseolina, Aspergillus flavus, Pseudomonas viridiflava, and Pectobacterium carotovorum, whereas the bacterial growth of Pseudomonas syringae pv. tomato and Pectobacterium atrosepticum was not significantly different from Col-0 under the tested conditions. Together, altered pectin structure and reduced auxin concentration in pae8/pae9 may contribute to pathogen-dependent resistance although auxin’s direct role remains to be determined. These findings highlight PAE8 and PAE9 as key regulators of pectin O-acetylation and suggest a potential link between cell wall acetylation, reduced IAA concentration, and pathogen-dependent defense responses.
GR24 enhances wheat performance by optimizing plant-arbuscular mycorrhizal fungi (AMF) interactions. Signaling molecules such as strigolactones (SLs) play essential regulatory roles in the rhizosphere by facilitating plant–soil communication and strengthening plant–microbe interactions. These molecules are crucial for promoting AMF colonization and the stable establishment of a symbiotic association, thereby supporting plant adaptation under stress conditions. This study aimed to evaluate the potential of seed priming with the synthetic strigolactone analogue GR24 to enhance AMF colonization, nutrient uptake, and the morpho-physiological performance of wheat. A factorial experiment was conducted in a completely randomized design under greenhouse conditions, with four GR24 concentrations (0, 2.5, 5, and 10 μM) and two AMF inoculation treatments (with and without AMF). Results showed that the addition of 5 μM GR24 combined with AMF significantly enhanced plant growth and physiological performance. Specifically, total dry weight (TDW), total chlorophyll content, stomatal conductance, photosynthetic rate, and the uptake of N, K, Fe, and Zn increased by 41
Integrating conventional breeding, omics, and CRISPR-based genome editing can overcome genetic and antinutrient constraints, enabling efficient iron biofortification of millets for sustainable and nutrition-secure food systems. Iron (Fe) deficiency remains one of the most widespread forms of micronutrient malnutrition. Biofortification of staple crops has emerged as a particularly sustainable and scalable strategy to combat this issue. Millets are nutrient-dense staple cereals with exceptional nutritional quality and climate resilience. However, genetic variations and the presence of antinutrients limit Fe content in millets, which highlights the necessity of advancing biofortification strategies. This review examines the present state of multi-dimensional strategies and discusses the future prospects for efficient iron biofortification in millets. We analyzed the efforts made for Fe biofortification in millets, ranging from conventional breeding practices to next-generation molecular approaches. Recent advances in omics have enhanced understanding of Fe uptake, transport, and storage in millets. Furthermore, CRISPR/Cas-based genome editing is discussed for the regulated expression of key Fe-transporter genes and targeted knockout of genes responsible for antinutrients. A multidisciplinary approach is essential to develop high-yielding and Fe-rich millet varieties that can contribute to sustainable nutrition security.
We established a protocol for reliable nuclear visualization in Charophyceae, revealed diverse nuclear organization across cell types and species, and identified suitable cells for genome size estimation via flow cytometry. Charophyceae are multicellular green algae closely related to land plants and are established model systems for understanding plant evolution. Yet key cellular parameters like genome size remain poorly characterized. We combined fluorescence microscopy, transmission electron microscopy (TEM), and flow cytometry to characterize nuclear diversity across cell types and species of Characeae and to identify a cell type suitable for genome size estimation. Among three DNA-intercalating fluorochromes, propidium iodide labeled nuclei most reliably. Nuclear morphology varied widely across cell types: mononucleated cells were found in vegetative apical cells, the coronula of oogonia, and spermatogenous filaments of antheridia, whereas multinucleation predominated in other tissues, e.g., cortical cells, spine cells, stipulodes and rhizoids. Nuclei in Chara hispida showed a significant gradient in cross-sectional area along the thallus axis. In the apical internodes, nuclei were larger and more heterogeneous, whereas in the basal internodes they were smaller and more uniform, which is consistent with possible endopolyploidy. TEM confirmed the nuclear identity of crescent-shaped structures. Relatively large nuclei were found in rhizoids and spine cells. Only Sphaerochara canadensis showed an organized nuclei pattern. Whole-thallus preparations did not yield a defined nuclear peak by flow cytometry, but antheridia of Chara tomentosa produced a sharp peak, from which a genome size of 5.32 pg (1C) was estimated. The protocol established here provides a simple, reproducible framework for visualizing nuclei and estimating genome size in Charophyceae, and helps address longstanding questions in this group, such as the mechanisms and functions of multinucleation, the site of meiosis, and genome evolution.
Heterologous expression of NcNPF6.3-1 promotes nitrogen and phosphorus accumulation in plants and improves nutrient removal efficiency in eutrophic water, indicating that this gene plays an important role in nutrient acquisition and has potential for phytoremediation applications. Nitrogen (N) and phosphorus (P) are essential mineral nutrients for plant growth. However, their excessive application can lead to water eutrophication. Aquatic plants provide an environmentally friendly and sustainable strategy for the ecological restoration of eutrophic aquatic ecosystems. Water lily (Nymphaea L.) is known to purify eutrophic water, yet the molecular mechanisms underlying its nutrient uptake remain unclear. In this study, we identified and characterized NcNRT1/PTR6.3-1 (NcNPF6.3-1), a nitrate transporter family member from Nymphaea colorata Peter, which is exclusively localized to the plasma membrane. Heterologous expression of NcNPF6.3-1 (NcNPF6.3-1-Ex) in rice (Oryza sativa L.) significantly promoted flowering and increased grain yield under moderate-N (N1: 0.27 g N/kg soil) and low-N (N2: 0.09 g N/kg soil) levels. Furthermore, NcNPF6.3-1-Ex lines exhibited enhanced total N and total P accumulation under N2 conditions. Notably, in simulated eutrophic water, NcNPF6.3-1-Ex lines showed substantially higher removal efficiencies of nitrate nitrogen (NO3−-N), ammonium nitrogen (NH4+-N), and total P compared with the wild type. These results demonstrate that NcNPF6.3-1 enhances plant nutrient absorption and accumulation while effectively reducing nutrient concentrations in eutrophic water, highlighting its potential application in phytoremediation and ecological restoration of nutrient-polluted aquatic ecosystems.
Mg-based nanoparticles have the potential to improve plant growth, photosynthetic pigments, metabolites, nutrients’ acquisition, and antioxidant defense system. They can increase plant tolerance by mitigating abiotic and biotic stresses and may provide sustainable solutions to agricultural output. Magnesium (Mg) is one of the important macronutrients and a significant cofactor for numerous biological activities of living organisms. It is crucial for plant development and important for metabolic functions, such as photosynthesis, since it is the central atom of the chlorophyll molecule and thus has a direct impact on trapping and converting light energy. Magnesium containing nanoparticles (Mg NPs) have been explored as a potential approach to improve crop yield and enhance stress tolerance in plants. Because of their physicochemical characteristics, such as small size, high surface area, and high reactivity, Mg NPs have demonstrated great promise in agriculture. Mg NPs are favored compared to other NPs, because Mg is non-toxic and biologically essential. Mg NPs play a major role in enhancing agronomic characteristics, nutrient acquisition, photosynthetic productivity, secondary metabolites, and antioxidant defense system. Mg NPs are capable of neutralizing abiotic and biotic stresses through interaction with plant growth hormones, signal transduction, nutrient uptake regulation, and stress-responsive pathways. They possess antibacterial, antifungal, and nematocidal action by inhibiting plant pathogens and suppressing disease occurrence. Mg NPs also induce the growth and activity of plant growth-promoting soil microorganisms, thus promoting plant growth. However, high concentrations of Mg NPs may reduce crop yield, likely due to NP-induced oxidative stress. This review highlights the role of Mg NPs in plants, including their impact on metal translocation, nutrient and metabolite acquisition, agronomic characteristics, antioxidant defense, stress alleviation, and growth and activity of beneficial microorganisms in soil. It also discusses future prospects, challenges, and risks involved in the application of Mg-based nanomaterials to sustainable agriculture.
Our review illustrates how the dexamethasone-inducible LhGR/pOp system has been used across numerous tissues/organs and plant species, and summarizes the resources and inducer application procedures established to date. The establishment of groundbreaking molecular biology tools has enabled the rapid advancement of research based on the model plant Arabidopsis, which currently strongly benefits non-model but economically important species. Spatiotemporal control of transgene expression via the chemically inducible system GR-LhG4/pOp has proven to be a particularly powerful, universal and non-invasive experimental approach. This review characterizes the mechanism of action of GR-LhG4/pOp and synthesizes information on available GR-LhG4 transgenic lines and inductor (dexamethasone) application procedures across various plant tissues. Moreover, feasible experimental approaches are depicted that range from classical ones aiming at selected genes overexpression or silencing to highly innovative ones, like those integrating the GR-LhG4/pOp system with CRISPR-Cas for targeted ablation of specific cell types. Information about the existing GR-LhG4/pOp lines from non-Arabidopsis plants is also provided, in hope that this sophisticated but universal research tool will become more exploited in crop research.
The review highlights that anthocyanin accumulation in Brassica napus is driven by strong up-regulation of key upstream biosynthetic genes and demonstrates that RNA-seq is an effective strategy for identifying candidate regulators underlying purple-leaf pigmentation in rapeseed. Rapeseed is planted worldwide as an oilseed crop and has been developed as a multifunctional plant. Anthocyanins are important secondary metabolites that play diverse roles in plant development, stress tolerance, and human health. They contribute to the color variation and nutritional value of plants. Many color variants with high-anthocyanin content have been reported in rapeseed species. To provide a comprehensive overview of the biosynthesis, accumulation, and molecular regulation mechanisms of anthocyanins in Brassica napus, this review summarizes research advances on the leaf, stem, seed, and flower color variants, focusing on identification of key genes regulating anthocyanins biosynthesis, accumulation, and regulation by MYB–bHLH–WD40 complexes in the plant. The review also explores how environmental cues such as light and temperature modulate anthocyanin accumulation in rapeseed and highlights the progress and challenges in understanding anthocyanin metabolism in rapeseed. Furthermore, we discuss a simplified procedure to isolate the candidate gene controlling the anthocyanins biosynthesis in Brassica napus, offering insights for basic research.
One of the primary salt-tolerance mechanisms in the three Disakisperma species involves salt excretion via bicellular salt glands. Salt excretion out of the leaves is one of the ways to avoid the toxicity of sodium and chloride ions under salinity. Among grasses (Poaceae), about 30 species are capable of salt excretion. The genus Disakisperma is in a sister clade to the salt excretors and has C4 metabolism, which is advantageous for salinity tolerance. For three Disakisperma species, D. eleusine, D. dubium, and D. obtusiflorum, we confirmed NAD-ME biochemical C4 subtype by the Western blotting for the main decarboxylases and NAD-ME anatomical type by the transmission electron microscopy. Under 200 mM and 400 mM NaCl treatments, photosynthetic and transpiration rates, as well as leaf sizes, decreased progressively. Nevertheless, all plants successfully completed their life cycle and produced viable seeds, demonstrating that all three species are halophytes characterized by moderate salt tolerance. All species possess bicellular salt glands on both adaxial and abaxial leaf surfaces. Crystals observed on their cap cells contain mainly sodium, potassium and chloride. Salt-excreting function is related to special subcellular structures as partitioning membranes and numerous mitochondria in the basal cell. Therefore, we presume that one of the salt-tolerance mechanisms of three Disakisperma species is ion excretion via specialized salt glands.
