Harnessing plant microbiomes for sustainable agriculture requires understanding not only whether they can boost crop performance, but also how ecological processes govern their assembly, stability, and functional contributions across environments. While we previously showed that seed tuber microbiomes can predict potato vigour using machine learning, it remained unclear how ecological processes shape tuber microbiome stability and functionality across host genotypes, tuber compartments, soil types, and years. Here, we analyzed the national-scale dataset of 240 field-collected potato seedlots, spanning six genotypes, two soil types, and two growing years, with a focus on the spatially distinct heel and eye compartments of the potato tuber. By profiling over 1200 bacterial and fungal communities and linking microbiome composition to plant performance, we show that plant genotype and tuber compartment are the strongest determinants of microbial diversity and composition. Compartment-specific enrichment of functional traits revealed spatial partitioning of microbial functions, with organic compound conversion and nitrogen cycling dominant in the heel, and energy metabolism enriched in the eye. Applying a macroecological abundance-occupancy framework, we identified a stable core microbiome of bacterial and fungal taxa that persisted across all environments and years. These core members were more strongly associated with plant growth-related traits than non-core taxa, and core taxa in different tuber compartments showed distinct correlations with taxa of potential pathogenic relevance. Together, our findings demonstrate that tuber compartments act as ecological filters that structure persistent, functionally specialised microbiomes linked to plant growth-related traits across environments. By providing an ecological and functional framework for compartment-resolved, stable core microbiomes, this study advances mechanistic understanding of plant-microbe interactions and identifies stable microbial partners as promising targets for improving potato resilience and productivity.
Potato growth and development are inhibited by drought stress, which in extreme situations jeopardises tuber yield and quality. Despite progress in understanding drought stress responses, the full regulatory network remains unclear. In this study, we found that the cell wall-localised expansin gene StEXLB1 was significantly induced by polyethylene glycol 6000 (PEG6000) and abscisic acid (ABA). StEXLB1-Overexpression (OE) reduced stomatal density and aperture, accompanied by enhancing drought tolerance. Conversely RNA interference (RNAi) lines exhibited the opposite effects. Further investigation revealed that the transcription factor StMYB55 directly promotes StEXLB1 transcription. Notably, StMYB55-OE resulted in stomatal phenotypes similar to those in StEXLB1-OE lines. Conversely, StMYB55-RNAi increased stomatal density and aperture, as well as reduced drought tolerance. StMYB55 interacts with the ABA receptor StPYL8 and the molecular chaperone StDnaJ3, respectively. This complex then acts to differentially suppress the transcript levels of key stomatal development factors (StSPCH and StFAMA). Genetic evidence showed that StPYL8-RNAi resulted in increased stomatal density and aperture, which was associated with decreased drought tolerance in potato. Collectively, this study suggests that the StMYB55/StPYL8-StEXLB1 module may participate in drought stress response, potentially via stomatal regulation, and provides candidate genes for breeding drought-tolerant potato varieties.
To enhance crop performance, intercropping strategies leverage volatile organic compound (VOC)-driven interactions with companion plants that constitutively emit VOCs. Despite the agricultural importance, the mechanisms and kinetics of VOC-mediated sensory transduction in receiver plants eavesdropping on neighbouring non-kin emitters remain largely unknown due to a lack of appropriate non-destructive analytical tools. In this work, we employ multiplexed salicylic acid (SA) and H2O2 nanosensors in Brassica rapa subsp. Chinensis (pak choy) plants to visualize, in real time, reactive oxygen species (ROS) and SA signal transduction following exposure to constitutively-released VOCs from neighbouring aromatic plants-namely sweet basil and spearmint. Unique emitter-specific temporal signatures of ROS and SA were observed in receiver pak choy: sweet basil VOCs induced concomitant generation of ROS and SA at 30 min, whereas spearmint VOCs triggered SA production at 30 min, followed by ROS accumulation. The temporal data enabled the formulation of a diffusion model that quantifies the VOC perception threshold that triggers the distinct early ROS and SA signalling. Transcriptomics analysis at 2 h revealed that both emitters evoke largely distinct changes in pak choy, likely stemming from variations in speed and sequence of the early signal transduction, leading to different phenotypic outcomes. Intercropping with sweet basil led to enhanced pak choy biomass, stress resilience and secondary metabolite accumulation, whereas spearmint as companions had a limited impact. Our study captures in real time, the VOC-induced rapid signalling in receiver plants and its ensuing effect on growth. These nanosensor-enabled findings represent an important advance in deciphering how emitter-specific volatile cues are integrated into plant responses, guiding rational selection of beneficial companion plants for improved yield and nutritional profiles in sustainable agriculture.
Glutamine (Gln), the first organic nitrogen (N) produced during primary N assimilation, is increasingly recognised as a signalling molecule in plants. Here, we show that Gln, supplied as the sole N source, promotes root hair elongation in Arabidopsis seedlings compared with NH4NO3. This response is dose-dependent and persists even under high NH4NO3 concentrations. Transcriptomic and gene expression analyses showed that Gln represses the negative regulator GLABRA2 while inducing the positive regulators ROOT HAIR DEFECTIVE6 (RHD6), RHD6-LIKE2, and RHD6-LIKE4, which control root hair development. Consistently, the rhd6-1 mutant failed to develop root hairs in response to Gln, demonstrating that Gln-induced root hair elongation depends on the RHD6 pathway. Gln also induces defence gene expression. Our pharmacological studies revealed that proper pectin methyl-esterification is required for both Gln-induced root hair elongation and defence gene expression, highlighting the importance of cell wall integrity in perceiving exogenous Gln. Furthermore, we show that Gln perception at the root apex triggers root hair elongation-a response that relies on defence hormone signalling, particularly ethylene, as demonstrated by pharmacological and genetic analyses. Together, these findings suggest that Gln integrates nutrient sensing, cell wall integrity, and defence hormone signalling to regulate root hair elongation in Arabidopsis.
Cucumber (Cucumis sativus L.) requires frequent irrigation due to its shallow root system and high transpiration rate of the aboveground parts. However, it is also prone to waterlogging damage. Therefore, understanding its response to waterlogging is crucial for breeding waterlogging-tolerant varieties. Although Rho of Plants GTPases play well-established roles in regulating development and stress signalling, their functions in plant adaptation to waterlogging stress has yet to be fully elucidated. Here, we identified nine CsROP genes in the cucumber genome, which exhibit evolutionary diversification but retain conserved functional domains. Functional analysis revealed that CsROP2 acts as a negative regulator of adventitious root formation. It modulates auxin accumulation in hypocotyl vascular bundles, thereby suppressing adventitious root development and enhancing waterlogging sensitivity. The HD-Zip I transcription factor CsTBH directly binds the CsROP2 promoter and activates its expression. Our study uncovers a CsTBH-CsROP2 module that governs adventitious rooting and waterlogging tolerance by modulating auxin homeostasis. These findings provide new insights into the crosstalk between developmental programmes and stress signalling pathways and offer potential genetic targets for improving stress resilience in cucumber and other crops.
Maintaining cellular photosensitivity while preventing damage from excessive light energy is a crucial challenge for plants, and negative feedback inhibition of photoreceptors plays a vital role in achieving this balance. Here, we uncover a regulatory mechanism involved in the UVR8-mediated UV-B signalling pathway. Through a combination of genetic, biochemical and cross-species analyses, we identified Arabidopsis BIC1 and BIC2, along with their orthologs in eggplant (Solanum melongena L.), as functionally conserved negative regulators in UV-B signalling. Through physical association with UVR8, BIC proteins likely stabilise its inactive dimeric state, which in turn attenuates UV‑B‑triggered monomerization and downstream transcriptional activation of the photoreceptor. Overexpression of BIC proteins in both eggplant and Arabidopsis promote hypocotyl elongation under UV-B, while the bic1bic2 double mutant exhibits enhanced photomorphogenesis. Notably, the uvr8-6bic1bic2 triple mutant displays an intermediate phenotype between the uvr8-6 and bic1bic2 parents, revealing a mutual regulatory relationship: BIC proteins inhibit UVR8 activity at the protein level, while UVR8 promotes BIC transcription via HY5. Heterologous overexpression of eggplant SmBIC proteins in Arabidopsis phenocopies the elongated hypocotyl phenotype of Arabidopsis BIC-overexpressors, further supporting functional conservation. Mechanistically, BICs attenuate UVR8-dependent transcriptional activation of HY5 without directly binding to the HY5 promoter. We establish a self-regulatory negative feedback loop in which HY5 activates BIC expression upon UV-B exposure, and BICs reciprocally suppress UVR8-mediated HY5 transactivation by stabilising the UVR8 dimer. This non-proteolytic regulatory circuit enables precise fine-tuning of photomorphogenic responses to fluctuating UV-B environments. Our study expands the functional repertoire of BIC proteins beyond blue light signalling and defines a conserved mechanism for attenuating UV-B responses essential for environmental adaptation in terrestrial plants.
Flooding stress is a primary environmental barrier that severely limits the widespread adoption of direct-seeded rice systems. Under submerged conditions, rapid coleoptile elongation serves as a vital morphological strategy that facilitates anaerobic germination and successful seedling establishment, yet its underlying molecular mechanisms remain poorly understood. Through a genome-wide association study, we identified a critical locus governing anaerobic coleoptile elongation, in which OsCsLF6, encoding a mixed-linkage glucan (MLG) synthase, was characterized as the causal gene. Genetic and biochemical analyses demonstrated that OsCsLF6 positively regulated coleoptile elongation by directly mediating MLG deposition into the primary cell wall. Mechanistically, we identified OsERF74, an AP2/ERF transcription factor, as an upstream master repressor that directly binds to a conserved core cis-element within the OsCsLF6 promoter. Under submergence, OsERF74 deficiency (oserf74 mutants) completely releases this transcriptional suppression, triggering a substantial upregulation of OsCsLF6 expression and subsequent hyper-accumulation of cell wall MLG. In contrast, constitutive overexpression of OsERF74 persistently blocks MLG biosynthesis. Crucially, a natural single-nucleotide polymorphism located within the OsERF74 binding element in the promoter defines two distinct haplotypes. The elite haplotype (Hap1) effectively disrupts OsERF74 binding affinity, which in turn attenuates transcriptional repression and sustains high OsCsLF6 expression, ultimately driving accelerated MLG synthesis and coleoptile elongation. Our findings establish a condition-specific OsERF74-OsCsLF6 regulatory module that serves as a central biochemical hub orchestrating cell wall remodelling during anaerobic germination. This module thus represents a promising molecular target and elite genetic resource for molecular breeding of flood-tolerant and direct-seeded rice varieties.
Reactive oxygen species (ROS) are pivotal signalling molecules that coordinate various aspects of plant development. Although ROS has been implicated in controlling stem cell fate within the shoot apical meristem (SAM), its specific role in rice panicle development and grain yield formation remains largely unexplored. Here, OsSRO1a, a plant-specific redox-regulated protein, is identified as a key mediator linking ROS signalling to panicle morphogenesis. Disruption of OsSRO1a leads to severe defects in branching and spikelet formation, alongside abolished responsiveness to ROS perturbation. ROS were found to accumulate in the inflorescence meristem and branch meristem, where they oxidise OsSRO1a at cysteine 387, promoting polymerisation and driving condensation through its intrinsically disordered region IDR3. OsSRO1a condensates recruit the GATA transcription factor NL1 into nuclear foci, enhancing NL1's transcriptional activity and upregulating downstream targets involved in meristem development and redox responses. Together, these results uncover a mechanism whereby ROS-induced condensation of a redox-sensitive protein orchestrates transcriptional reprogramming to shape inflorescence architecture, providing new insights into the integration of redox signalling and developmental regulation in crops.
Sucrose non-fermenting-1-related protein kinase (SnRK) is a plant serine/threonine kinase that mediates stress signaling, yet its function in the mangrove Avicennia marina remains unexplored. In this study, we identified 46 SnRK genes in A. marina, classifying them into three subfamilies with high phylogenetic conservation. Family expansion occurred mainly through 20 segmental duplication events under purifying selection (Ka/Ks < 1). Promoter regions were enriched in stress- and hormone-responsive elements, and expression profiling showed distinct tissue-specific and stress-responsive patterns. Our study specifically focused on the functional characterization of AmSnRK2.7. AmSnRK2.7-overexpressed Arabidopsis thaliana increases salt tolerance by altering the expression of ion transport genes and mediating Na+ efflux from the roots. Further investigation revealed that AmSnRK2.7 interacts with and phosphorylates AmENO2 (enolase, a key enzyme in the glycolysis pathway). Meanwhile, measurements of ATP content in wild type, AmSnRK2.7-overexpressed Arabidopsis lines and the atsnrk2.6 (homologous gene of AmSnRK2.7 in A. thaliana) mutant confirm that the AmSnRK2.7-AmENO2 module can affect the energy-driven Na+ efflux. Our findings provide key insights into the role of SnRK gene family in mangrove adaptation to saline intertidal habitat, and suggest AmSnRK2.7-AmENO2 module plays a role in salt tolerance.
The cytoskeleton regulates cell division, intracellular transport and cell-wall patterning, but its roles in secondary growth and long-term stress responses in woody plants remain poorly understood. We classify individual claims as direct functional evidence from woody species (Level I), correlative or functionally non-specific evidence from woody systems (Level II), mechanisms demonstrated only in non-woody models (Level III), or relationships untested in woody plants (Hypothesis). Direct functional evidence remains concentrated in Populus. In hybrid poplar, PagPCaP1a promotes salt-induced microtubule depolymerisation, while its genetic inhibition improves salt tolerance. Separate studies report that tubulin perturbation alters developing xylem pectin and xylan extractability and leaf stomatal kinetics. Woody studies associate microtubule-related factors with cambial cytokinesis, reaction wood, microfibril angle and xylem anatomy, but do not establish causality. Microtubule-cellulose synthase coupling and actin-dependent trafficking are supported mainly by non-woody models, whereas proposed cytoskeletal roles in secondary-wall delivery, xylem programmed cell death, wood mechanics, hydraulic safety, stress memory and immunity remain untested. Resolving these gaps requires cell-type-specific perturbation and live imaging in cambium and developing xylem, combined with wall, anatomical, mechanical and hydraulic measurements across woody lineages and validation in whole trees.
Pre-harvest sprouting (PHS) represents a major threat to global food security under increasingly variable climatic conditions. Current understanding is largely derived from controlled laboratory studies, whereas field PHS is a multi-scale phenomenon resulting from interactions among genetic regulation, spike and grain traits, heterogeneous environmental conditions, and agronomic management. Our knowledge of PHS mechanisms under field conditions remains limited, and a systematic, integrated control framework is still lacking. In this review, we synthesise advances in the genetic architecture, physiological regulation, phenotypic determinants, and environmental factors of PHS in cereals, with emphasis on integrating multi-scale regulatory networks with environmental drivers. We particularly focus on laboratory-field discrepancies and how environmental heterogeneity influences grain quality deterioration and PHS outcomes under field conditions., and further evaluate current control strategies for PHS, including breeding, agronomic management, and chemical regulation, especially their limitations, environmental dependence, and associated trade-offs in practical application. Finally, we propose that future PHS control will require integrating field-relevant phenotypes, genotype × environment × management interactions, multi-scale predictive modelling, and decision-support systems to improve field-level resilience to PHS under increasingly variable climatic conditions.
Droughts increasingly threaten crop productivity in nutrient-depleted tropical soils. We investigated how water limitation influences rhizomicrobial traits (microbial biomass and functional community composition, enzyme activities) and nitrogen (N) uptake in three sorghum genotypes Makueni local (Mkl), Gadam (Gd), and IESH 22012 (IESH) under well-watered and drought conditions. Depth-specific (0-30 and 30-60 cm) 15N labelling traced N uptake at flowering and grain-filling. Drought reduced grain N content across all genotypes but shoot N only in IESH. Gd enhanced 15N recovery in grains via post-anthesis uptake from both depths under drought, whereas Mkl and IESH rather reallocated N within the plants towards the grain. Compared to well-watered conditions, rhizosphere chitinase activity declined in Mkl under drought, while leucine aminopeptidase (LAP) activity remained unchanged. Under drought, microbial biomass decreased at flowering but recovered at grain-filling, coinciding with enhanced arbuscular mycorrhiza fungi (AMF) colonisation. At grain-filling, AMF associations with specific bacterial taxa aligned with grain N recovery, N-utilisation efficiency, and LAP activity, displaying complementary roles within the plant-AMF-bacterial functional consortia in sustaining N acquisition. Overall, N acquisition in sorghum shifted in a genotype-specific manner from reliance on microbial activity under well-watered conditions to selective AMF-bacterial partnership at grain-filling under drought. These responses highlight the significant role of rhizosphere functional dynamics in sorghum N nutrition during reproductive stages under concomitant drought and nutrient limitation.
Selective autophagy has emerged as a critical component of plant immunity, yet its role as a dedicated antimicrobial mechanism, xenophagy, remains conceptually underdeveloped. In plants, xenophagy extends beyond bulk degradation to function as a highly regulated, cargo-specific pathway that targets invading pathogens and their effector molecules for autophagic clearance. Recent evidence demonstrates that selective autophagy receptors, particularly NBR1, integrate ubiquitin-mediated recognition with ATG8-dependent sequestration, enabling the elimination of bacterial, fungal, and viral components. However, this process is not merely degradative but operates at the intersection of immune signaling, proteostasis, and cellular decision-making. Here, we synthesize current advances in plant xenophagy and propose a unifying framework in which xenophagy appears to function as a cell-autonomous immune hub comprising three interconnected modules: cargo recognition, selective sequestration, and autophagic execution, dynamically modulated by pathogen-derived countermeasures. We further examine how pathogens subvert or exploit host autophagic machinery, revealing xenophagy as a contested interface in plant-pathogen interactions. By integrating molecular, cellular, and cross-kingdom perspectives, we highlight key conceptual gaps, including the specificity of cargo selection, the regulatory logic of receptor engagement, and the coordination between autophagy and canonical immune pathways. Resolving these gaps will be essential for repositioning xenophagy as a central determinant of plant immune competence, with significant implications for engineering disease-resistant crops.
Understanding the molecular mechanisms underlying plant responses to various stresses is crucial for improving crop productivity under stressful conditions. However, how plants prioritize the activation of pathways to balance disease resistance with drought and salt tolerance remains unclear. Here, we identify two regulatory modules centered on the rice protein OsSRLD, which negatively regulates disease resistance and positively regulates drought/salt tolerance. Upregulation of OsSRLD increases ABA content and reduces ROS levels under both normal and stressed conditions, suggesting its involvement in ABA signaling and ROS homeostasis. As an E3 ligase, OsSRLD interacts with OsIMα1a (a positive regulator of disease resistance) and promotes its ubiquitination and degradation via the 26S proteasome. Additionally, OsIMα1a interacts with OsWRKY53 (a positive regulator of disease resistance but a negative regulator of salt tolerance), thereby promoting the nuclear accumulation of OsWRKY53. Consistently, both overexpression of OsSRLD and knockout of OsIMα1a resulted in downregulation of OsWRKY53-activated genes and upregulation of OsWRKY53-inactivated genes. Furthermore, OsSRLD interacts with and stabilizes OsDIP1 (a positive regulator of drought and salt tolerance) via an E3 ligase-independent pathway. Together, our findings reveal that OsSRLD-OsIMα1a-OsWRKY53 and OsSRLD-OsDIP1 modules balance disease resistance and drought/salt tolerance through both E3 ligase-dependent and E3 ligase-independent pathways.
Proper anther dehiscence is essential for successful pollination and male fertility in flowering plants. However, many gaps remain in the regulatory mechanisms underlying anther dehiscence in plants, including a possible role for abscisic acid (ABA) in anther dehiscence. Here, we reported a member of 9-cis-epoxycarotenoid dioxygenase family (NCED), OsNCED5, which regulates proper anther dehiscence for male fertility in rice. OsNCED5 encodes a chloroplast-localized ABA biosynthetic enzyme highly expressed in anther during the late phase. Disruption of OsNCED5 by CRISPR/Cas9-mediated mutagenesis led to the reduction of ABA accumulation in anthers, thus the failure of secondary cell wall (SCW) thickening in anther endothecium due to loss of lignin biosynthesis, which eventually resulting in indehiscent anthers and significantly reduced fertility. Further analysis indicated that OsNCED5 probably confer a conserved fertility regulation mechanism between japonica and indica subspecies. Taken together, we have identified a key OsNCED regulator involved anther dehiscence -based male fertility, and provide a valuable genetic resource for fertility improvement in rice.
