Plants employ diverse strategies to cope with different types of heat stress. The response to short-term acute heat stress differs significantly from that to moderate heat stress followed by severe stress events. After experiencing moderate heat stress, plants exhibit a more robust response to subsequent severe stress, a phenomenon known as thermopriming or acquired thermotolerance. Thermopriming creates a memory by maintaining the heat stress (HS) memory-related genes in an alert state. In this work, we investigated the role of Arabidopsis Universal Stress Protein 1 (USP1) in plant heat stress responses. CRISPR-Cas9 generated knockout usp1 mutant lines showed no morphological changes during development and normal growth conditions. However, usp1 mutant plants showed enhanced levels of apoplast hydrogen peroxide and superoxide reactive oxygen species accumulation upon heat stress. Transcriptome analyses revealed that genes related to protein folding, electron transport, and oxidative phosphorylation are strongly upregulated in usp1 mutant plants. USP1 is essential for acquired thermotolerance, as usp1 mutants are compromised in heat stress memory but show normal responses to acute heat stress similar to hsfa2 mutants. Biochemical assays showed that USP1 functions as a molecular chaperone, protecting the transcription factor HSFA2 from heat-induced denaturation. Moreover, usp1 mutant plants show decreased transcript levels of heat stress response genes and reduced H3K4me3 enrichment at memory gene loci. These data show that USP1 plays an important role as a chaperone of HSFA2 in mediating plant heat stress memory.

Oxalotrophy refers to the ability of bacteria to utilize oxalate as a carbon and energy source. This is a critical process, with significant implications for the global carbon cycle. Oxalate-degrading bacteria play a key role in carbon sequestration through the oxalate-carbonate pathway, contributing to stable inorganic carbon pools. In this study, we identified and catalogued 19 enzymes and a transporter associated with various facets of oxalate metabolism to characterize the oxalotrophic potential of bacteria. Within this group, sets of enzymes were grouped into two functional categories in the context of carbon sequestration: a biomineralization toolkit for converting oxalate to inorganic carbon and an assimilation toolkit for incorporating oxalate into metabolic pathways such as amino acid biosynthesis and energy production. Using bioinformatic approaches, we analysed a collection of 536 bacterial genomes from desert and dryland strains spanning 81 genera to identify oxalotrophs. To validate our findings, we tested several bacterial strains for growth on media supplemented with exogenous oxalate. Notably, while multiple bacterial strains grew on oxalate media, two Pseudomonas species, namely JZ043 and JZ097, failed to grow despite genomic predictions suggesting otherwise. Further investigation of these strains revealed several non-conservative amino acid substitutions in the glyoxylate carboligase enzyme (EC 4.1.1.47), a key player in oxalate metabolism, suggesting a potential link between these mutations and their inability to metabolize oxalate. Our findings highlight the significance of our approach for identifying oxalotrophic bacteria and offer valuable insights into the molecular basis of oxalate metabolism.

Abstract N6-methyladenosine (m 6 A) is a key RNA modification that regulates transcript stability and translation. However, its function in plant viruses remains largely unclear. Here, we show that the positive-sense single-stranded +ssRNA Turnip mosaic virus (TuMV) relies on the host m 6 A machinery to support efficient infection. Our findings uncover a previously unrecognized nuclear phase in the TuMV life cycle, during which viral RNA undergoes extensive methylation by host enzymes. We identify a complex and non-canonical methylation landscape on the TuMV genome, where canonical DRACH motifs are embedded within clusters of additional virus-specific non-canonical m 6 A sites. Notably, we also detect the presence of another RNA modification, m 5 C (5-methylcytosine), in close proximity to m 6 A-marked regions. This coordinated methylation landscape appears to be critical for efficient viral polyprotein synthesis. In its absence, the virus displays aberrant methylation and reduced infectivity as observed in m 6 A writer and reader mutants. Based on this, we propose a “seeding” model in which initial m 6 A deposition at canonical sites nucleates the formation of a broader network of m 6 A and m 5 C marks, likely guided by RNA structure rather than sequence motifs alone.

Plants associate with diverse microbial communities that influence growth and health. Although plant immune regulatory networks are known to balance defense activation and microbial accommodation during pathogen attack, how they coordinate beneficial plant-microbe interactions across complex microbial contexts remains unclear. Here, we systematically screened 39 immune-pathway mutants using individual plant growth-promoting bacteria (PGPBs), binary combinations, and synthetic and natural communities. We identified the bik1-1 mutant as exhibiting a broad defect in growth promotion across multiple beneficial microbial systems. Extensive genetic analyses using independent BIK1 CRISPR and T-DNA insertion alleles, as well as overexpression lines, demonstrated that the growth promotion defect observed in the bik1-1 line is not caused by loss of BIK1 function but is instead associated with a chromosomal fragment duplication. Although induced systemic resistance (ISR) and beneficial bacteria-mediated pathogen protection remain intact in bik1-1, immune activation is elevated during beneficial interactions. Microbiome profiling revealed reduced diversity and altered community structure, and microbiome transfer experiments indicated that host immune status influences selection of microbial taxa associated with growth promotion. These findings indicate that balanced immune signaling is a key determinant of plant-microbiome compatibility across diverse microbial contexts.

Microbial communities associated with desert plants play a pivotal role in enhancing host survival under extreme environmental stressors, including drought, salinity, and nutrient limitation. The Desert Plant Endophyte Microbial Collection is one of the largest curated repositories of 2500 cultivable endophytic bacteria isolated from 23 native desert plant species across Saudi Arabia, Jordan, and Pakistan. Representing a broad spectrum of arid microhabitats from inland deserts and mountain wadis to coastal mangroves and date palm oases, the collection supports integrative studies on microbial ecology and plant-microbe interactions in water-limited ecosystems. A central component of this initiative is the Desert Plant Endophyte Genome Database, which currently hosts whole-genome sequences of 534 endophytic bacterial isolates annotated with extensive ecological metadata, assembly statistics, functional traits, and host associations. The database interface provides tools for genome exploration, metadata filtering, and functional gene mining, enabling users to identify taxa and traits of agronomic interest, particularly for applications in sustainable agriculture and sustainable desert revegetation. By combining genomic, ecological, and functional data, the Desert Plant Endophyte Genome Database serves as a foundational platform for the development of targeted microbial inoculants and fosters data-driven research into desert microbiomes and plant resilience mechanisms.

Abstract Drought is a major consequence of climate change and significantly limits crop productivity. Plant growth-promoting bacteria offer a promising solution to mitigate drought stress. The root endophyte Pseudomonas argentinensis SA190 has been shown to enhance plant performance under drought stress conditions, but the mechanistic basis of SA190’s beneficial effects remained unclear. Given the pivotal role of sulfur-containing compounds in abiotic stress responses, we investigated multiple sulfur-related Arabidopsis mutants under drought stress. We found that SA190 enhances sulfate uptake and promotes glutathione (GSH) accumulation in shoots under stress conditions. SA190 treatment improved the GSH/GSSG ratio, indicating an enhanced redox balance under drought. Selective inhibition of Arabidopsis GSH biosynthesis using buthionine sulfoximine (BSO) confirmed the essential contribution of bacterial GSH to drought stress. In addition, by generation and use of bacterial mutants deficient in the GSH synthesis pathway, we show that the bacteria directly provide Arabidopsis with either GSH or it’s precursor γ-EC. In summary, SA190 promotes drought tolerance by supplying the host plant with additional GSH thereby maintaining cellular redox homeostasis and enhancing drought stress resilience.

The activation of immune Mitogen Activated Protein Kinases (MAPKs) is one of the earliest cellular responses following pathogen attack leading to the phosphorylation of appropriate cytosolic or nuclear targets to regulate cellular processes. In this work, we show that the Arabidopsis nuclear protein DEK2 is a target of MPK6 and regulator of plant defense against bacterial and fungal plant pathogens. Transcriptomic analysis unveils that AtDEK2 modulates transcription of defense-related genes, as well as genes associated with hormone synthesis and signaling. Chromatin immunoprecipitation sequencing (ChIP-Seq) analysis reveals that DEK2 potentially binds to TGGGC(C/T) motifs of ZNF, bZIP, WRKY and TCP transcription factors. DEK2 orchestrates diverse chromatin-related processes. Our findings suggest that DEK2 is recruited to specific chromatin regions by transcription factors and functions as a reader of the bivalent histone mark H3K4me3K27me3.

Global warming affects plant growth and yield, posing a major threat to global food security. Male sexual reproduction is the most sensitive stage for plant yield under elevated temperature (eT). We show here that under eT conditions, plant growth and male reproduction depend on the ethylene-mediated activity of the histone demethylase REF6. Although eT-compromised plant performance of wild-type plants can be fortified by treatment with the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC), ref6 mutant plants are insensitive to ACC, showing that ethylene-dependent eT-induced genes depend on REF6 histone demethylase activity. Sexual reproduction and yield, including pollen viability and germination, are strongly compromised in ethylene and ref6 mutants under eT conditions. Intriguingly, we demonstrate that the bacterial endophyte Enterobacter sp. SA187 deploys ethylene-mediated REF6 to protect plant growth and reproduction to eT. These results show that microbiome-assisted approaches can help to ensure food safety under changing climate conditions.

Non-host resistance refers to the immunity of plant species to virtually all isolates of a potential pathogen and represents an underexplored avenue for breeding and engineering disease resistance. In domesticated and wild barley, cell surface-localized lectin receptor kinases (LecRKs) contribute to determining the host status to leaf rust fungi, which pose a major threat to global cereal production. Here, we identify a conserved family of leaf rust glycoside hydrolases as ligands for these barley LecRKs and show that direct ligand-receptor binding triggers immune responses. This mechanism of pathogen perception is conserved across multiple cereal species and can be functionally transferred between them. We also uncover previously uncharacterized recognition specificities among distinct LecRK variants, expanding the repertoire of LecRK-mediated rust pathogen detection. Our findings define a molecular mechanism underlying non-host resistance in cereals and provide a basis for harnessing non-host rust resistance across diverse crop-pathogen systems.

Frequent drought and variable rainfall limit tree establishment in drylands. Over a 4-month field trial, we examined how early acacia seedling transplantation and irrigation pulses shape desert soil microbiomes, and whether irrigation primarily stabilizes transplant-associated trajectories rather than driving them. Moisture formed the dominant environmental gradient across treatments, while early transplantation shifted bulk-soil stoichiometric ratios, with water and vegetation lowering C/N and altering nutrient context. Using 16S rRNA gene and ITS2 region amplicon sequencing together with time-series generalized Lotka-Volterra modeling, we assessed changes in community composition and inferred interaction signs at phylum and genus resolution. Seedling transplantation exerted a stronger influence on microbial diversity and genus-level composition, whereas irrigation mainly modified the magnitude and stability of inferred interaction patterns. Phylum-level responses were comparatively stable, but genus-level trajectories diverged across vegetation × irrigation combinations. Model-based growth tendencies and inferred interaction signs were consistent with resilience in non-watered bare soil, opportunistic responses under irrigation in bare soil, and a shift toward more negative inferred associations in vegetated non-watered soil, whereas irrigated vegetated soil showed higher connectivity and a higher proportion of positive inferred links. Together, these results frame early transplantation as a discrete window of microbiome assembly in desert soils and support a testable hypothesis for nursery-to-field workflows. Irrigation may primarily function as a stabilizing input to a seedling-associated microbiome state, while establishment outcomes and functional mechanisms require direct validation.

Haloxylon salicornicum is a desert plant well-adapted to extreme arid environments. This study explores how this species adjusts its metabolism in response to diurnal and seasonal environmental changes. Herein, we examined its metabolic responses across two soil types (clay and sandy), two seasons (winter and summer), and two timings (dawn and midday), focusing on water status and primary metabolites’ profiling via untargeted metabolomics.The variation in soil properties at 1 m depth did not significantly affect the metabolic responses of H. salicornicum plants, while notable changes occurred across seasons and timings. During winter, the plants’ water status was relatively higher (water potential − 1 MPa), facilitating the activation of anabolic pathways, specifically carbon fixation and the biosynthesis of carbohydrates and amino acids, thereby allowing growth and accumulation of reserves. In summer, however, water potential decreased sharply ( − 5 MPa), leading to the stimulation of catabolic processes, particularly starch breakdown, to sustain carbon metabolism and maintain energy production. Additionally, the plants accumulated antioxidants like ascorbate, glutathione, and caffeic acid to combat oxidative stress caused by heat and drought. Overall, H. salicornicum exhibited remarkable metabolic flexibility, especially through nocturnal activity, to survive harsh desert conditions. These findings contribute to understanding the mechanisms by which desert plants endure extreme stress and lay the groundwork for future genetic studies.

A central regulator of condensate formation in mammals is the Ras GTPase-activating protein SH3 domain-binding protein (G3BP) family of RNA-binding proteins. In Arabidopsis, G3BP homologs can also form condensates and exhibit diverse expression patterns and subcellular localization. Previously, we identified G3BP1 as a negative regulator of plant immunity that is phosphorylated at Ser257 in vivo. Here, we generated phospho-mimic (G3BP1D) and phospho-dead (G3BP1A) variants and expressed them in Arabidopsis, revealing that the phosphorylation state of G3BP1 affects susceptibility to bacterial infection by influencing ROS production and salicylic acid (SA) accumulation. G3BP1 phosphorylation also influences stomatal immunity by maintaining stomatal opening, thereby modulating pre-invasive defense mechanisms. Furthermore, we show that phosphorylation at Ser257 contributes to the stabilization of G3BP1 by limiting its degradation. Collectively, these findings identify G3BP1 phosphorylation as an important regulatory mechanism in plant immunity and provide new insights into the role of RNA-binding proteins in plant defense responses.

Deserts cover one-third of Earth's land and support life forms uniquely adapted to extreme climatic and environmental conditions. Restoring these ecosystems remains difficult and costly, yet knowledge of native plants, soils, and their associated microbiomes offers promising solutions. This review outlines the drivers and consequences of desertification feedback loops and explains how microbial adaptations sustain soil functions under stress. We highlight the role of plant-microbe-soil interactions in shaping functional networks that support restoration and the development of synergistic plant communities. We also highlight how the integration of ecological frameworks such as niche differentiation, network theory, and stoichiometric balance reveals new directions for restoration efforts. In this framework, emerging microbiome-based strategies can offer a path to transform barren or degraded landscapes into diverse, resilient vegetative islands.

Transposon mutagenesis is a powerful tool for investigating gene function in bacteria, particularly in newly discovered species. In this study, we applied the hyperactive EZ-Tn5 transposase system to Pseudomonas argentinensis SA190, an endophytic bacterium known for enhancing plant resilience under drought stress. By leveraging the random amplification of transposon ends (RATE)-PCR method, we successfully mapped the insertion sites of the transposon within the SA190 genome. This approach enabled the precise identification of disrupted genes, offering insights into their roles in bacterial function and interaction with host plants. Our comprehensive protocol, including competent cell preparation, transformation, and insertion site mapping, provides a reliable framework for future studies aiming to explore gene function through mutagenesis. Key features • The use of the hyperactive EZ-Tn5 transposase system ensures efficient and detectable random mutagenesis across the Pseudomonas argentinensis SA190 genome, facilitating comprehensive gene disruption studies. • The technique is employed to identify and map the transposon insertion sites, allowing for precise determination of gene function and its impact on bacterial phenotypes. • This method enables the exploration of a broad range of gene functions within SA190, particularly those involved in plant growth promotion and stress tolerance. • This method can be readily adapted to generate mutant libraries in other bacterial species, emphasizing its transferability.

Mitogen-activated protein kinase (MAPK) cascades play critical roles in plant immunity by phosphorylating downstream effectors that regulate stress responses. While MAPK-mediated transcriptional regulation has been well examined, the involvement of MAPKs in post-transcriptional and post-translational regulation is still poorly understood. In this study, we identify the RNA binding-protein AtG3BP1 as a phosphorylation target of MPK3, MPK4, and MPK6 and demonstrate that phosphorylation of AtG3BP1 at Ser257 modulates key aspects of Arabidopsis immunity. Using phospho-mimic (G3BP1D) and phospho-dead (G3BP1A) mutants, we investigated the functional consequences of AtG3BP1 phosphorylation. Our data indicate that phosphorylation of AtG3BP1 promotes susceptibility to bacterial infection, suppresses accumulation of reactive oxygen species (ROS), and downregulates salicylic acid (SA) biosynthesis. Furthermore, we demonstrate that AtG3BP1 phosphorylation influences stomatal immunity by maintaining stomatal opening, thereby regulating pre-invasive defense mechanisms. Additionally, we provide evidence that phosphorylation stabilizes AtG3BP1 and prevents its degradation via the proteasome, thus leading to sustained immune signaling. These findings validate AtG3BP1 as a central integrator of MAPK signaling during plant immunity and reveal a new level of post-translational control. This study enhances our understanding of plant defense mechanisms and provides potential targets for engineering disease-resistant crops. ### Competing Interest Statement The authors have declared no competing interest.

Global climate change increasingly challenges agriculture with flooding and salinity. Among strategies to enhance crop resilience to these stresses, we tested several endophytic bacterial strains from mangroves, which are permanently exposed to flooding and high salinity. We show several strains that can enhance flooding and salinity tolerance in Arabidopsis and rice plants. Two strains and their combination massively enhanced the growth and yield of Oryza sativa cv. Nipponbare under both soil and hydroponic growth conditions with and without salt treatment. The bacteria-induced transcriptome changes in O. sativa roots, particularly related to ABA-signaling and lignin and suberin deposition in root tissues, explain the altered responses of colonized rice plants to hypoxic and saline stress conditions. Importantly, bacterially colonized rice plants exhibited enhanced yield and improved grain quality. These results show that microbes can be a powerful tool for enhancing the yield and resilience of rice to hypoxic and saline stress conditions.

Enterobacter sp. SA187, is a plant growth-promoting bacterium (PGPB) with potential to enhance abiotic stress tolerance in various crops. This study evaluated the impact of inoculation of SA187 to salinity and heat stress tolerance of Solanum lycopersicum L, tomato. Different alterations in the physiological, biochemical and molecular responses against the salt and heat stress due to the beneficial association of tomato plants with SA187 were investigated. Colonization by SA187 significantly enhanced tomato plants growth under both saline and heat stress condition. It induced an enhancement of > 90 % in the morphological and physiological processes resulting in an increased root hair growth and higher plant biomass. The inoculation also caused a 65 % decline in Na+/K+ ratio, increased chlorophyll content and improved the antioxidant enzyme activity of Superoxidase dismutase (SOD), Peroxidase (POD), and Catalase (CAT), particularly under salt and heat stress conditions. The RNA-seq analysis produced clean reads that ranged from 33,812,161 to 44,114,539 across the different groups of treatment, which were successfully assembled into 35,825 annotated genes. Transcriptomic analysis of the genes involved in the enhancement of the physiological and biochemical processes revealed at least a 2-fold increase in the expression of NHX3 and ERF4 in leaves, SOS2, SOS4, and SULTR3;5 in leaves and roots. For heat stress, SA187-colonized tomato plants displayed higher expression of heat shock protein genes in leaves such as HSP17.4B, HSP17.6, HSP22.0, and HSP26.5. These findings show the possibility of using the Enterobacter sp. SA187 as a sustainable solution for enhancing crop tolerance and productivity in challenging environmental conditions.

Certain microbes have considerable potential as biocontrol agents against various pathogens, but they coexist with other microbial species in complex networks of interactions that influence their function in a host-dependent manner. These interactions and underlying mechanisms are still largely unknown. In this review we focus on Pseudomonas, a versatile genus of bacteria with adaptable physiological and metabolic traits, functioning as both symbionts and pathogens. We review the direct antagonism pathways Pseudomonas uses to inhibit different pathotypes and its role in indirectly inducing systemic defense responses in plants. We provide insights into bacterial coexistence and interactions in host plant-microbe and microbe-microbe relationships, considering pairwise and community dynamics. Understanding these interactions will help optimize synthetic communities and improve practices for sustainable agriculture.

The complex and mutual interactions between plants and their associated microbiota are key for plant survival and fitness. From the myriad of microbes that exist in the soil, plants dynamically engineer their surrounding microbiome in response to varying environmental and nutrient conditions. The notion that the rhizosphere bacterial and fungal community acts in harmony with plants is widely acknowledged, yet little is known about how these microorganisms interact with each other and their host plants. Here, we explored the interaction of two well-studied plant beneficial endophytes, Enterobacter sp. SA187 and the fungus Serendipita indica. We show that these microbes show inhibitory growth in vitro but act in a mutually positive manner in the presence of Arabidopsis as a plant host. Although both microbes can promote plant salinity tolerance, plant resilience is enhanced in the ternary interaction, revealing that the host plant has the ability to positively orchestrate the interactions between microbes to everyone's benefit. In conclusion, this study advances our understanding of plant-microbiome interaction beyond individual plant-microbe relationships, unveiling a new layer of complexity in how plants manage microbial communities for optimal growth and stress resistance.

Desert ecosystems have limited resources and harsh climatic conditions and cannot support cropping in most farming models. Recently, microbial applications have emerged as promising strategies to enhance plant survival and adaptation in such extreme environments. However, the beneficial microbes and our understanding of their functional roles and adaptation mechanisms in desert ecosystems remain underexplored. This study reports the isolation and characterization of the Pseudomonas sp. R4-79 strain from the arid environment of Wadi Rum, Jordan, associated with the desert plant Ifloga spicata. The genome of Pseudomonas sp. R4-79, sequenced at 275 × PacBio coverage, consists of a 6.18 Mbp chromosome encoding 5,445 proteins, including gene clusters for siderophores, phenazines, hydrogen cyanide, and phytohormones, as well as secretion systems (T2SS, T4SS, T6SS, and TAT). Genomic and phenotypic analyses revealed that Pseudomonas sp. R4-79 belongs to the genus P. granadensis and exhibits plant growth-promoting attributes and substantial biocontrol potential. Pseudomonas sp. R4-79 effectively suppressed key phytopathogens, including the necrotrophic fungus Botrytis cinerea in vitro, as well as Pseudomonas syringae pv. tomato DC3000 and root-knot nematodes (Meloidogyne incognita) in vivo in Arabidopsis and tomato. This work suggests that P. granadensis R4-79 could represent an effective biocontrol agent to improve crop yield in sustainable agriculture.