Metabolic signatures of Arabidopsis thaliana abiotic stress responses elucidate patterns in stress priming, acclimation, and recovery

The transcriptome landscape of Kumrogarh, a unique rice landrace showing the simultaneous presence of Sub1 and SK loci for submergence tolerance

To decipher the molecular mechanism behind submergence tolerance in a typical rice genotype (var. Kumrogarh), leaf transcriptome analysis was performed on submerged plant tissue with 7 and 14 days of induced submergence, followed by cataloguing the differentially expressed transcripts. Subsequent bioinformatics analysis identified 5,267 differentially expressed genes (DEGs), of which 2,657 were upregulated and 2,610 were downregulated in four comparative combinations: T7-C7, T14-T7, T14-T7, and C14-C7. A group of 41 co-expressed genes was found across all sets, while 1427, 558 and 83 transcripts were uniquely expressed in the T7-C7, T14-T7, and C14-C7 combinations, respectively. Constructed Ven diagram showed that 1428, 65, and 44 transcripts were commonly expressed in the paired combinations "T7-C7" and "T14-T7", "C14-C7" and "T7-C7", and "C14-C7" and "T14-T7". Gene ontology study functionally categorized the DEGs into molecular functions, biological processes, and cellular components. Additionally, nine transcription factor families were identified, including MYB, WRKY, bZIP, bHLH, SET domain, NAC domain, C2H2 zinc finger, E2F, and HSF, along with a set of differentially regulated signalling genes. Twelve genes related to submergence adaptation were selected for final validation through quantitative real-time PCR-based expression analysis, which demonstrated a strong association with a coefficient (R 2 = 0.716) after aligning with the RNA-Seq data. Derived results showed upregulation of gibberellin receptor GID1L2 (LOC_Os02g35940.1), ethylene-responsive element-binding protein (LOC_Os06g08360.1), glyceraldehyde-3-phosphate dehydrogenase (LOC_Os04g38600.1), decarboxylase (LOC_Os08g04540.1), sucrose synthase (LOC_Os03g22120.1), aldehyde dehydrogenase (LOC_Os12g07810.1), endonuclease/exonuclease/phosphatase family domain-containing protein (LOC_Os01g08780.1), polygalacturonase inhibitor 1 precursor (LOC_Os07g38130.1), transmembrane amino acid transporter protein (LOC_Os01g41420.1), and SAM-dependent carboxyl methyltransferase (LOC_Os02g48770.1). This study provides a comprehensive profile of leaf transcriptomics in a traditionally tall-type rice landrace containing both submergence-tolerant Sub1 and SK alleles, highlighting an area of research that remains largely unexplored. These remarkable findings have driven this investigation to decipher the interplay among these key genetic factors by hypothesizing a model leading to the development of a genetic network associated with improved survival under prolonged deep submergence of such a unique rice genotype.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-025-04277-7.

Static Magnetic Field Increases Polyhydroxyalkanoates Biosynthesis in Haloferax mediterranei: Parameter Optimization and Mechanistic Insights from Metabolomics

Polyhydroxyalkanoates (PHAs), as biosynthetic and biodegradable polymers, serve as alternatives to petroleum-based plastics, yet face critical cost barriers in large-scale production. While magnetic field (MF) stimulation enhances microbial activity, the optimal MF parameters and metabolic mechanisms for PHA biosynthesis remain unexplored. This study optimized magnetic field parameters to increase PHA biosynthesis in Haloferax mediterranei. A custom-engineered electromagnetic system identified 110 mT of static magnetic field (SMF) as the optimal level for biosynthesis, reaching 77.97 mg/(L·h) PHA volumetric productivity. A pulsed magnetic field caused oxidative stress and impaired substrate uptake despite increasing PHA synthesis. Prolonged SMF exposure (72 h) maximized PHA productivity, while 48 h of exposure attained 90% efficiency. Metabolomics revealed that SMF-driven carbon flux redirection via regulated butanoate metabolism led to a 2.10-fold increase in (R)-3-hydroxybutanoyl-CoA), while downregulating acetoacetate (0.51-fold) and suppressing PHA degradation (0.15-fold). This study pioneers the first application of metabolomics in archaea to decode SMF-induced metabolic rewiring in Haloferax mediterranei. Our findings establish SMF as a scalable bioenhancement tool, offering sustainable solutions for the circular bioeconomy.

Exploring Plant Resilience Through Secondary Metabolite Profiling: Advances in Stress Response and Crop Improvement

The metabolome, encompassing small molecules within organisms, provides critical insights into physiology, environmental influences, and stress responses. Metabolomics enables comprehensive analysis of plant metabolites, uncovering biomarkers and mechanisms underlying stress adaptation. Regulatory genes such as MYB and WRKY are central to secondary metabolite synthesis and environmental resilience. By integrating metabolomics with genomics, researchers can explore stress-related pathways and advance crop improvement efforts. This review examines metabolomic profiling under stress conditions, emphasizing drought tolerance mechanisms mediated by amino acids and organic acids. Additionally, it highlights the shikimate pathway's pivotal role in synthesizing amino acids and secondary metabolites essential for plant defense. These insights contribute to understanding metabolic networks that drive plant resilience, informing strategies for agricultural sustainability.

The effects of photosynthetic rate on respiration in light, starch/sucrose partitioning, and other metabolic fluxes within photosynthesis

In the future, plants may encounter increased light and elevated CO2 levels. How consequent alterations in photosynthetic rates will impact fluxes in photosynthetic carbon metabolism remains uncertain. Respiration in light (RL) is pivotal in plant carbon balance and a key parameter in photosynthesis models. Understanding the dynamics of photosynthetic metabolism and RL under varying environmental conditions is essential for optimizing plant growth and agricultural productivity. However, measuring RL under high light and high CO2 (HLHC) conditions poses challenges using traditional gas exchange methods. In this study, we employed isotopically nonstationary metabolic flux analysis (INST-MFA) to estimate RL and investigate photosynthetic carbon flux, unveiling nuanced adjustments in Camelina sativa under HLHC. Despite numerous flux alterations in HLHC, RL remained stable. HLHC affects several factors influencing RL, such as starch and sucrose partitioning, vo/vc ratio, triose phosphate partitioning, and hexose kinase activity. Analysis of A/Ci curve operational points reveals that HLHC's major changes primarily stem from CO2 suppressing photorespiration. Integration of these fluxes into a simplified model predicts changes in CBC labeling under HLHC. This study extends our prior discovery that incomplete CBC labeling is due to unlabeled carbon reimported during RL, offering insights into manipulating labeling through adjustments in photosynthetic rates.

Functional characterization reveals the importance of Arabidopsis ECA4 and EPSIN3 in clathrin mediated endocytosis and wall structure in apical growing cells

Localized clathrin mediated endocytosis is vital for secretion and wall deposition in apical growing plant cells. Adaptor and signalling proteins, along with phosphoinositides, are known to play a regulatory, yet poorly defined role in this process. Here we investigated the function of Arabidopsis ECA4 and EPSIN3, putative mediators of the process, in pollen tubes and root hairs. Homozygous eca4 and epsin3 plants exhibited altered pollen tube morphology (in vitro) and self-pollination led to fewer seeds and shorter siliques. These effects were augmented in eca4/epsin3 double mutant and quantitative polymerase chain reaction data revealed changes in phosphoinositide metabolism and flowering genes suggestive of a synergistic action. No visible changes were observed in root morphology, but atomic force microscopy in mutant root hairs showed altered structural stiffness. Imaging and FRET-FLIM analysis of ECA4 and EPSIN3 X-FP constructs revealed that both proteins interact at the plasma membrane but exhibit slightly different intracellular localization. FT-ICR-MS metabolomic analysis of mutant cells showed changes in lipids, amino acids and carbohydrate composition consistent with a role in secretion and growth. Characterization of double mutants of eca4 and epsin3 with phospholipase C genes (plc5, plc7) indicates that phosphoinositides (e.g. PtdIns(4,5)P2) are fundamental for a combined and complementary role of ECA4-EPSIN3 in cell secretion.

Mechanisms of Aluminum Toxicity Impacting Root Growth in Shatian Pomelo

Aluminum (Al) toxicity in acidic soils poses significant challenges to crop growth and development. However, the response mechanism of Shatian pomelo (Citrus maxima 'Shatian Yu') roots to Al toxicity remains poorly understood. This study employed root phenotype analysis, physiological response index measurement, root transcriptome analysis, and quantitative PCR (qPCR) validation to investigate the effects of Al toxicity on Shatian pomelo roots. The findings revealed that Al toxicity inhibited root growth and development, resulting in reduced root biomass, total root length, total root surface area, root volume, average root diameter, and root tip count. Antioxidant enzyme activities (peroxidase, superoxide dismutase, ascorbate peroxidase, and catalase activity) and soluble protein content increased with rising Al toxicity, whereas malondialdehyde content initially increased and then declined. Additionally, Al toxicity stress increased Al (1439.25%) content and decreased boron (B, 50.64%), magnesium (Mg, 42.04%), calcium (Ca, 46.02%), manganese (Mn, 86.75%), and iron (Fe, 69.92%) levels in the roots. RNA sequencing (RNA-seq) analysis identified 3855 differentially expressed genes (DEGs) between 0 mmol/L Al (control) and 4 mmol/L Al (Al toxicity) concentrations, with 1457 genes up-regulated and 2398 down-regulated, indicating a complex molecular regulatory response. The qPCR results further validated these findings. This study elucidates the response mechanisms of Shatian pomelo roots to Al toxicity stress, providing insights into the regulatory pathways involved. The findings offer valuable reference points for breeding Al-resistant Shatian pomelo varieties. The results of this study provide important genetic tools and technical support for the screening and breeding of highly resistant varieties of Shatian pomelo. On the one hand, by detecting the key indexes (such as antioxidant enzyme activity and nutrient absorption capacity) of Shatian pomelo, varieties with excellent anti-Al toxicity characteristics can be selected. On the other hand, the Al-resistant genes identified in this study, such as TFM1 and ALERTFA0, can be used to develop molecular markers, assisted marker breeding, or transgenic breeding to accelerate the breeding process of Al-resistant strains.

Acetic acid: a cheap but chief metabolic regulator for abiotic stress tolerance in plants

As sessile organisms, plants constantly face a variety of abiotic stresses, such as drought, salinity, and metal/metalloid toxicity, all of which possess significant threats to plant growth and yield potential. Improving plant resilience to such abiotic stresses bears paramount importance in practicing sustainable agriculture worldwide. Acetic acid/acetate has been recognized as an important metabolite with multifaceted roles in regulating plant adaptation to diverse abiotic stresses. Recent studies have elucidated that acetic acid can potentiate plants' inherent mechanisms to withstand the adverse effects of abiotic stresses through the regulation of lipid metabolism, hormone signaling, epigenetic changes, and physiological defense mechanisms. Numerous studies also underpin the potential use of acetic acid in boosting crop production under unfavorable environmental conditions. This review provides a comprehensive update on the understanding of how acetic acid regulates plant photosynthesis, acts as an antitranspirant, detoxifies reactive oxygen species to alleviate oxidative stress, interacts with phytohormones to regulate physiological processes, and improves soil fertility and microbial diversity, with a specific focus on drought, salinity, and metal toxicity. We also highlight the eco-friendly and economic potential of acetic acid that may attract farmers from developing countries to harness the benefits of acetic acid application for boosting abiotic stress resistance in crops. Given that acetic acid is a widely accessible, inexpensive, and eco-friendly compound, the revelation of acetic acid-mediated regulatory pathways and its crosstalk with other signaling molecules will have significant importance in developing a sustainable strategy for mitigating abiotic stresses in crops.

Elevated Temperature Effects on Protein Turnover Dynamics in Arabidopsis thaliana Seedlings Revealed by 15N-Stable Isotope Labeling and ProteinTurnover Algorithm

Global warming poses a threat to plant survival, impacting growth and agricultural yield. Protein turnover, a critical regulatory mechanism balancing protein synthesis and degradation, is crucial for the cellular response to environmental changes. We investigated the effects of elevated temperature on proteome dynamics in Arabidopsis thaliana seedlings using 15N-stable isotope labeling and ultra-performance liquid chromatography-high resolution mass spectrometry, coupled with the ProteinTurnover algorithm. Analyzing different cellular fractions from plants grown under 22 °C and 30 °C growth conditions, we found significant changes in the turnover rates of 571 proteins, with a median 1.4-fold increase, indicating accelerated protein dynamics under thermal stress. Notably, soluble root fraction proteins exhibited smaller turnover changes, suggesting tissue-specific adaptations. Significant turnover alterations occurred with redox signaling, stress response, protein folding, secondary metabolism, and photorespiration, indicating complex responses enhancing plant thermal resilience. Conversely, proteins involved in carbohydrate metabolism and mitochondrial ATP synthesis showed minimal changes, highlighting their stability. This analysis highlights the intricate balance between proteome stability and adaptability, advancing our understanding of plant responses to heat stress and supporting the development of improved thermotolerant crops.

Research Progress on Plant Responses to Stress Combinations in the Context of Climate Change

In the context of climate change, the frequency and intensity of extreme weather events are increasing, environmental pollution and global warming are exacerbated by anthropogenic activities, and plants will experience a more complex and variable environment of stress combinations. Research on plant responses to stress combinations is crucial for the development and utilization of climate-adaptive plants. Recently, the concept of stress combinations has been expanded from simple to multifactorial stress combinations (MFSCs). Researchers have realized the complexity and necessity of stress combination research and have extensively employed composite gradient methods, multi-omics techniques, and interdisciplinary approaches to integrate laboratory and field experiments. Researchers have studied the response mechanisms of plant reactive oxygen species (ROS), phytohormones, transcription factors (TFs), and other response mechanisms under stress combinations and reached some generalized conclusions. In this article, we focus on the research progress and methodological dynamics of plant responses to stress combinations and propose key scientific questions that are crucial to address, in the context of plant responses to stress assemblages, conserving biodiversity, and ensuring food security. We can enhance the search for universal pathways, identify targets for stress combinations, explore adaptive genetic responses, and leverage high-technology research. This is in pursuit of cultivating plants with greater tolerance to stress combinations and enabling their adaptation to and mitigation of the impacts of climate change.

Role of Epigenetic Factors in Response to Stress and Establishment of Somatic Memory of Stress Exposure in Plants

All species are well adapted to their environment. Stress causes a magnitude of biochemical and molecular responses in plants, leading to physiological or pathological changes. The response to various stresses is genetically predetermined, but is also controlled on the epigenetic level. Most plants are adapted to their environments through generations of exposure to all elements. Many plant species have the capacity to acclimate or adapt to certain stresses using the mechanism of priming. In most cases, priming is a somatic response allowing plants to deal with the same or similar stress more efficiently, with fewer resources diverted from growth and development. Priming likely relies on multiple mechanisms, but the differential expression of non-coding RNAs, changes in DNA methylation, histone modifications, and nucleosome repositioning play a crucial role. Specifically, we emphasize the role of BRM/CHR17, BRU1, FGT1, HFSA2, and H2A.Z proteins as positive regulators, and CAF-1, MOM1, DDM1, and SGS3 as potential negative regulators of somatic stress memory. In this review, we will discuss the role of epigenetic factors in response to stress, priming, and the somatic memory of stress exposures.

Multi-stress resilience in plants recovering from submergence

Submergence limits plants' access to oxygen and light, causing massive changes in metabolism; after submergence, plants experience additional stresses, including reoxygenation, dehydration, photoinhibition and accelerated senescence. Plant responses to waterlogging and partial or complete submergence have been well studied, but our understanding of plant responses during post-submergence recovery remains limited. During post-submergence recovery, whether a plant can repair the damage caused by submergence and reoxygenation and re-activate key processes to continue to grow, determines whether the plant survives. Here, we summarize the challenges plants face when recovering from submergence, primarily focusing on studies of Arabidopsis thaliana and rice (Oryza sativa). We also highlight recent progress in elucidating the interplay among various regulatory pathways, compare post-hypoxia reoxygenation between plants and animals and provide new perspectives for future studies.

DNA methylation dynamics in a coastal foundation seagrass species under abiotic stressors

DNA methylation (DNAm) has been intensively studied in terrestrial plants in response to environmental changes, but its dynamic changes in a temporal scale remain unexplored in marine plants. The seagrass Posidonia oceanica ranks among the slowest-growing and longest-living plants on Earth, and is particularly vulnerable to sea warming and local anthropogenic pressures. Here, we analysed the dynamics of DNAm changes in plants collected from coastal areas differentially impacted by eutrophication (i.e. oligotrophic, Ol; eutrophic, Eu) and exposed to abiotic stressors (nutrients, temperature increase and their combination). Levels of global DNAm (% 5-mC) and the expression of key genes involved in DNAm were assessed after one, two and five weeks of exposure. Results revealed a clear differentiation between plants, depending on environmental stimuli, time of exposure and plants' origin. % 5-mC levels were higher during the initial stress exposure especially in Ol plants, which upregulated almost all genes involved in DNAm. Contrarily, Eu plants showed lower expression levels, which increased under chronic exposure to stressors, particularly to temperature. These findings show that DNAm is dynamic in P. oceanica during stress exposure and underlined that environmental epigenetic variations could be implicated in the regulation of acclimation and phenotypic differences depending on local conditions.

Applications of Metabolomics for the Elucidation of Abiotic Stress Tolerance in Plants: A Special Focus on Osmotic Stress and Heavy Metal Toxicity

Plants undergo metabolic perturbations under various abiotic stress conditions; due to their sessile nature, the metabolic network of plants requires continuous reconfigurations in response to environmental stimuli to maintain homeostasis and combat stress. The comprehensive analysis of these metabolic features will thus give an overview of plant metabolic responses and strategies applied to mitigate the deleterious effects of stress conditions at a biochemical level. In recent years, the adoption of metabolomics studies has gained significant attention due to the growing technological advances in analytical biochemistry (plant metabolomics). The complexity of the plant biochemical landscape requires sophisticated, advanced analytical methods. As such, technological advancements in the field of metabolomics have been realized, aided much by the development and refinement of separatory techniques, including liquid and gas chromatography (LC and GC), often hyphenated to state-of-the-art detection instruments such as mass spectrometry (MS) or nuclear resonance magnetic (NMR) spectroscopy. Significant advances and developments in these techniques are briefly highlighted in this review. The enormous progress made thus far also comes with the dawn of the Internet of Things (IoT) and technology housed in machine learning (ML)-based computational tools for data acquisition, mining, and analysis in the 4IR era allowing for broader metabolic coverage and biological interpretation of the cellular status of plants under varying environmental conditions. Thus, scientists can paint a holistic and comprehensive roadmap and predictive models for metabolite-guided crop improvement. The current review outlines the application of metabolomics and related technological advances in elucidating plant responses to abiotic stress, mainly focusing on heavy metal toxicity and subsequent osmotic stress tolerance.

The Plant Metabolic Changes and the Physiological and Signaling Functions in the Responses to Abiotic Stress

Global climate change has altered, and will further alter, rainfall patterns and temperatures likely causing more frequent drought and heat waves, which will consequently exacerbate abiotic stresses of plants and significantly decrease the yield and quality of crops. On the one hand, the global demand for food is ever-increasing owing to the rapid increase of the human population. On the other hand, metabolic responses are one of the most important mechanisms by which plants adapt to and survive to abiotic stresses. Here we therefore summarize recent progresses including the plant primary and secondary metabolic responses to abiotic stresses and their function in plant resistance acting as antioxidants, osmoregulatory, and signaling factors, which enrich our knowledge concerning commonalities of plant metabolic responses to abiotic stresses, including their involvement in signaling processes. Finally, we discuss potential methods of metabolic fortification of crops in order to improve their abiotic stress tolerance.

Reprogramming of Plant Central Metabolism in Response to Abiotic Stresses: A Metabolomics View

Abiotic stresses rewire plant central metabolism to maintain metabolic and energy homeostasis. Metabolites involved in the plant central metabolic network serve as a hub for regulating carbon and energy metabolism under various stress conditions. In this review, we introduce recent metabolomics techniques used to investigate the dynamics of metabolic responses to abiotic stresses and analyze the trend of publications in this field. We provide an updated overview of the changing patterns in central metabolic pathways related to the metabolic responses to common stresses, including flooding, drought, cold, heat, and salinity. We extensively review the common and unique metabolic changes in central metabolism in response to major abiotic stresses. Finally, we discuss the challenges and some emerging insights in the future application of metabolomics to study plant responses to abiotic stresses.