Plants exude a wide variety of compounds into the rhizosphere, modulating soil functioning and diversity. The number of studies investigating exudation has exponentially increased over the past decades. Yet, the high inter-study variability of the results is slowing down our understanding of the root-soil interactions. Such variability is partly due to the absence of harmonized methodologies to collect and characterize exudation. Here, we discuss how various experimental aspects influence exudation profiles by performing a literature review, and we suggest best practices for different experimental setups. We discuss state-of-the art of spatially resolved exudate collection, collection in controlled vs field conditions, and plant growth setups ranging from hydroponics to soil. We highlight the importance of preparing experimental blanks, in situ vs ex situ exudate collection, various collection media and timing of collection, exudate storage and processing, and analytical considerations. We summarize best practices for experimental setup and reporting of parameters in an easily accessible table format to facilitate discussion of best practices in the field. An increased standardization in the field together with the systematic studies suggested will improve our knowledge on how plant exudation shapes interactions with organisms in soil.

Brassinosteroids (BR) are small endogenous phytohormones that are key regulators of plant growth, development, and stress resistance. They fulfil this role partially by modulating cell wall structure and composition through the control of genes involved in primary and secondary cell wall biosynthesis and metabolism. This affects the deposition of cellulose, lignin, and other components, and modifies the inner architecture of the wall, allowing it to adapt to the developmental status and environmental conditions. Here, we review the role of BR in cell wall modifications, highlighting recently described functions of BR in model plants in development and growth, such as cell layers interaction to regulate coordinated growth and tissue development for organ shape, skotomorphogenesis, and regulation of gravitropism for the orientation of plant growth direction against gravity. We also discuss the potential use of BR in crops to address current problems such as the need to maintain crop yield, quality, and wood production while increasing stress resistance. Among these approaches are the modification of BR biosynthesis and upregulated BR signalling, leading to increased crop development or wood deposition. We will also highlight how the use of exogenous BR applications can promote BR-related responses to improve plant fitness and productivity.

Trait-based approaches offer valuable perspectives for vegetation classification, but functional traits struggle to capture resource allocation among competing plants, showing limitations across scales. This study aimed to introduce plant architecture to enhance trait-based vegetation classification. From 2021 to 2023, 32 plots of Coastal Dwarf Forests (CDF) and Coastal Normal Forests (NCDF) along China’s eastern coast were surveyed. Their community characteristics were quantified, and classification and clustering models assessed the advantages of plant architecture in distinguishing these communities. The results indicated plant architecture traits are more critical for distinguishing different community types than leaf-based functional traits. Additionally, plant architecture traits are effective in clustering plant associations within the same community type. This is because plant architecture traits are closely linked to habitat, phylogeny, and community structure, providing a comprehensive description of vegetation, while functional traits reflect only partial habitat information related to soil nutrients. Our findings underscore the importance of plant architecture in optimizing trait-based vegetation classification and suggest that variations in the plasticity of plant architecture traits may support the classification of CDF as a distinct vegetation unit.

not-yet-known not-yet-known not-yet-known unknown In the context of climate change, associated with increasingly frequent water deficit and heat waves, there is an urgent need to maintain the performance of soybean the most extensively grown legume before it declines. The objective of this study was to explore which plant traits improve soybean resilience to heat and/or water stress, with a focus on traits involved in plant architecture and nutrient uptake. For this purpose, two soybean genotypes, already shown to have contrasted root architecture were grown under controlled conditions in the high-throughput phenotyping platform 4PMI where either optimal condition, heat waves, water stress or both heat waves and water stresses were applied during the vegetative stage. Under stress conditions the two genotypes displayed contrasted architectural features traits such as root width, root angle branching or number of roots. By correlating architectural to functional traits, related to water, carbon allocation and nutrient absorption, we were able to explain the stress susceptibility level of the two genotypes. This cross analysis of plant ecophysiology and architectural traits under different stresses provides new information on the adaptation of soybean and can inform future crop design, particularly under changing climatic conditions.

Identical physical principles dictate the formulation of transpiration and sap flow. Yet, a hiatus separates the ways the conduction of water in the vapor and liquid phases are dimensioned, leading to the elaboration of conflicting response mechanisms to water stress. An analysis prompted by the discrepancy between the dimensionality assigned to water vapor conductance for transpiration and that assigned to hydraulic conductance for sap flow reveals that capacitance combines with conductance to determine the respective transport rates. For transpiration, the capability of air to accept or release water vapor qualified as pneumatic capacitance, derived from theory, is equal to the reciprocal of the barometric pressure. The conductance is set by the network of diffusive and convective air paths where stomatal aperture is the ruling biological component. For sap flow the current view is that the proportionality between flux density and motive water potential difference is the hydraulic conductance, disregarding that its physical dimensions lump conductance and capacitance. Plant hydraulic capacitance derives from measured water retention curves. It varies according to water potential which is determined by the metabolic regulation of living cell osmolarity. Hydraulic conductance is set by abiotic factors: friction and water column cohesion in dead xylem conduits. Lumping the two properties into a single parameter erroneously defined as plant hydraulic conductance confounds the factors affecting sap flow, precluding a scientifically sound investigation of plant hydraulics.

The rhizosphere is a key interface between plants, microbes and the soil which influences plant health and nutrition and modulates terrestrial biogeochemical cycling processes. Recently it has been shown that the rhizosphere environment is far more dynamic than previously recognized, with evidence emerging for diurnal rhythmicity in rhizosphere chemistry and in the composition of rhizosphere microbial communities. Rhythmicity of the rhizosphere microbiome is in part linked to the host plant's circadian rhythm, although evidence also points to some heterotrophic rhizosphere bacteria and fungi possessing rhythmicity. We review the evidence for diurnal rhythmicity in the composition and abundance of rhizosphere microbial communities, and its link to the plant circadian clock. Factors which may drive microbial rhythmicity in the rhizosphere are discussed, including diurnal change in the flux and composition of root exudates, rhizosphere physico-chemical properties and plant immunity mechanisms. The potential contributions of microbial processes to community rhythmicity are considered, including self-sustained microbial rhythms, bacterial movement into and out of the rhizosphere, and microbe-microbe interactions. We also consider evidence that changes in microbial composition mediated by the plant circadian clock may affect microbial function and its significance for plant health and broader soil biogeochemical cycling processes. We identify key knowledge gaps and approaches which could help to resolve the spatial and temporal variation and functional significance of rhizosphere microbial rhythmicity. This includes unravelling the factors which determine the oscillation of microbial activity, growth and death, and cross-talk with the host over diurnal time frames. We conclude that diurnal rhythmicity is an inherent characteristic of the rhizosphere environment and that temporal factors should be considered and reported in experimental studies conducted on the rhizosphere.

The present study investigated the linkage between days to flowering (DTF) and Growth Habit (GH) in pigeonpea using QTL mapping, QTL-seq, and GWAS approaches. The linkage map developed here is the largest to date, spanning 1825.56 cM with 7987 SNP markers. In total, eight and four QTLs were mapped for DTF and GH, respectively, harboring 78 pigeonpea orthologs of Arabidopsis flowering time genes. Corroboratively, QTL-seq analysis identified a single linked QTL for both traits on chromosome 3, possessing 15 genes with genic variants. Together, these 91 genes were clustered primarily into autonomous, photoperiod, and epigenetic pathways. Further, we identified 39 associations for DTF and 111 associations for GH through GWAS in the QTL regions. Of these, nine associations were consistent and constituted nine haplotypes (five late, two early, one each for super-early and medium duration). The involvement of multiple genes explained the range of allelic effects and the presence of multiple LD blocks. Further, the linked QTL on chromosome 3 was fine-mapped to the 0.24 Mb region with a LOD score of 8.56, explaining 36.47% of the phenotypic variance. We identified a 10 bp deletion in the first exon of TFL1 gene of the ICPL20338 variety, which may affect its interaction with the Apetala1 and Leafy genes, resulting in determinate GH and early flowering. Further, the genic marker developed for the deletion in the TFL1 gene could be utilized as a foreground marker in marker-assisted breeding programs to develop early-flowering pigeonpea varieties.

Pandemics originating from zoonotic viruses have posed significant threats to human health and agriculture. Recent discoveries have revealed that wild-rice plants also harbor viral pathogens capable of severely impacting rice production, a cornerstone food crop. In this study, we conducted virome analysis on ~1000 wild-rice individual colonies and discovered a novel single-strand positive-sense RNA virus prevalent in these plants. Through comprehensive genomic characterization and comparative sequence analysis, this virus was classified as a new species in the genus Polerovirus, designated Rice less tiller virus (RLTV). Our investigations elucidated that RLTV could be transmitted from wild-rice to cultivated rice via a specific insect vector, the aphid Rhopalosiphum padi, causing less tiller disease symptoms in rice plants. We generated an infectious cDNA clone for RLTV and demonstrated systemic infection of rice cultivars and induction of severe disease symptoms following mechanical inoculation or stable genetic transformation. We further illustrated transmission of RLTV from stable transgenic lines to healthy rice plants by the aphid vector, leading to the development of disease symptoms. Notably, our database searches showed that RLTV and another polerovirus isolated from a wild plant species are widely circulating not only in wild rice but also cultivated rice around the world. Our findings provide strong evidence for a wild plant origin for rice viruses and underscore the imminent threat posed by aphid-transmitted rice Polerovirus to rice cultivar.

Plants maintain iron (Fe) homeostasis under varying environmental conditions by balancing processes such as Fe uptake, transport, and storage. In Arabidopsis, POPEYE (PYE), a basic helix-loop-helix (bHLH) transcription factor (TF), has been shown to play a crucial role in regulating this balance. In recent years, the mechanisms regulating Fe uptake have been well established but the upstream transcriptional regulators of Fe transport and storage are still poorly understood. In this study, we report that ELONGATED HYPOCOTYL5 (HY5), a basic leucine zipper (bZIP) TF which has recently been shown to play a crucial role in Fe homeostasis, interacts with PYE. Molecular, genetic and biochemical approaches revealed that PYE and HY5 have overlapping as well as some distinct roles in regulation of Fe deficiency response. We found that HY5 and PYE both act as a repressor of Fe transport genes such as YSL3, FRD3 NPF5.9, YSL2, NAS4, and OPT3. HY5 was found to directly bind on the promoter of these genes and regulate intercellular Fe transport. Further analysis revealed that HY5 and PYE directly interact at the same region on PYE and NAS4 promoter. Overall, this study revealed that HY5 regulates Fe homeostasis by physically interacting with PYE as well as independently.

Pollen, a pivotal stage in the plant reproductive cycle, is highly sensitive to temperature fluctuations, impacting seed quality and quantity. While the importance of understanding pollen temperature limtits (Tmin, Topt, Tmax – collectively PTLs) is recognized, a comprehensive synthesis of underlying drivers is lacking. Here, we examined PTLs, correlating them with vegetative tissue thermotolerance and assessing variability at the intra- and interspecific levels across 198 species with contrasting phylogeny, cultivation history, biology and ecology. At the species level, the PTLs range from 6.1 to 39.5 0C, with considerable differences among growth forms and cultivation histories. Positive correlations were found between PTLs and leaf/stem temperature tolerances. Notably, pollen cold tolerances varied significantly across species populations, while Topt and Tmax values remained stable. Phylogenetic analysis revealed family-level conservation in pollen cold tolerance, contrasting with heat tolerance’s independence from evolutionary history. Climate emerged as a significant PTL driver, with species at higher elevations and latitudes exhibiting enhanced cold and heat tolerance. Cultivated species displayed narrower temperature tolerances (10.3-39.9 °C) than their wild counterparts (5.2-42.3 °C), highlighting potential crop vulnerabilities to global warming. Herbaceous plants exhibited superior tolerance to both low and high temperatures compared to shrubs and trees, reflecting divergent thermal conditions during anthesis. This study illuminates complex relationships between pollen temperature limits, plant characteristics, and environmental factors, providing crucial insights into climate change impacts on plant reproduction.

Drought is one of the most devastating causes of yield losses in crops like maize and the anticipated increases in severity and duration of drought spells due to climate change pose an imminent threat to agricultural productivity. To understand the drought response, phenotypic and molecular studies are typically performed at a given time point after drought onset, representing a steady-state adaptation response. Because growth is a dynamic process, we monitored the drought response with high temporal resolution and examined cellular and transcriptomic changes after rehydration at 4 and 6 days after leaf four appearance. These data showed that the division zone activity is a determinant for full organ growth recovery upon rehydration. Moreover, a prolonged maintenance of cell division by the ectopic expression of PLASTOCHRON1 extends the ability to resume growth after rehydration. The transcriptome analysis also indicated that GROWTH-REGULATING FACTORS (GRFs) affected leaf growth by impacting cell division duration, which was confirmed by a prolonged recovery potential of the GRF1-overexpression line after rehydration. Finally, we used a multiplex genome editing approach to evaluate the most promising differentially expressed genes from the transcriptome study and as such narrowed down the gene space from forty to seven genes for future functional characterization.

As the single link between leaves and the rest of the plant, petioles must develop conductive tissues according to the water influx and sugar outflow of the leaf lamina. A scaling relationship between leaf area and anatomical traits of xylem and phloem is expected to improve the efficiency of these tissues. However, the different constraints compromising the functionality of both tissues (e.g., risk of cavitation) must not be disregarded. Additionally, plants present two main leaf habits (deciduous and evergreen) that may have different strategies to produce and package their petiole conduits to cope with environmental restrictions. In this study, we explore, in a diverse group of 33 oak species, the relationships between petiole anatomical traits, leaf area, stomatal conductance and photosynthesis rate. Results showed allometric scaling between anatomical structure of xylem and phloem with leaf area. We also found how photosynthesis and stomatal conductance at leaf-level are correlated with anatomical traits in the petiole. Nonetheless, the main novelty is how oaks present a different strategy depending on the leaf habit. Deciduous species tend to increase their diameters to achieve a greater leaf-specific conductivity. By contrast, evergreen oaks develop larger xylem conductive areas for a given leaf area than deciduous ones. This trade-off between safety-efficiency in petioles has never been attributed to the leaf habit of the species.

Plants are an intrinsic part of the soil community, which is comprised of a diverse range of organisms that interact in the rhizosphere through continuous molecular communications. The plant-microbe continuum forms a network of underground nutrient and information highways that benefit both plant and microbial communities, as well as ultimately serve as a significant sink for atmospheric CO 2. The molecular dialogue at the rhizosphere interface is crucial not only for plants to discriminate between harmful, benign, and beneficial microorganisms but also to actively participate in crop productivity and resilience to environmental stresses. Although many facets of the chemistry of inter-organism communication remain to be discovered, and the molecular mechanisms that underly hormone-regulated symbiosis are largely unexplored, biological fertilization is an attractive tool for the sustainable production of high-value crops. Here, we discuss our increasing knowledge of the chemical repertoire that underpins plant-microbe communication and host-range specificity, highlighting how the regulated production of reactive oxygen species (ROS) is used in inter-organism communication between plants and microbes and within the communities that shape the soil microbiome.

Plants differ widely in how soil drying affects stomatal conductance ( g s) and leaf water potential ( ψ leaf), and in the underlying physiological controls. Efforts to breed crops for drought resilience would benefit from a better understanding of these mechanisms and their diversity. We grew 12 diverse genotypes of common bean ( Phaseolus vulgaris L.) and four of tepary bean ( P. acutifolius; a highly drought resilient species) in the field under irrigation and terminal drought, and quantified responses of g s and ψ leaf, and their controls (soil water potential [ ψ soil], evaporative demand [Δ w] and plant hydraulic conductance [ K]). We hypothesized that (i) common beans would be more ”isohydric” (i.e., exhibit strong stomatal closure in drought, minimizing ψ leaf decline) than tepary beans, and that genotypes with larger ψ leaf decline (more ”anisohydric”) would exhibit (ii) smaller increases in Δ w, due to less suppression of evaporative cooling by stomatal closure and hence less canopy warming, but (iii) larger K declines due to ψ leaf decline. Contrary to our hypotheses, we found that half of the common bean genotypes were similarly anisohydric to most tepary beans; that isohydric genotypes experienced less canopy warming and hence smaller increases in Δ w in drought, and similar declines in K; and that stomatal closure was similar in isohydric and anisohydric genotypes. g s and ψ leaf were virtually insensitive to drought in one tepary genotype (G40068). Our results highlight the potential importance of non-stomatal mechanisms for leaf cooling, and the variability in drought resilience traits among closely related crop legumes.

Diplodia sapinea causes Diplodia tip blight (DTB) and is recognised as an opportunistic necrotrophic pathogen affecting conifers. While DTB is associated with abiotic stress, the impact of biotic stress in the host on D. sapinea’s lifestyle shift is unknown. Observed co-occurrences of D. sapinea and Melampsora pinitorqua, causing pine twisting rust on Scots pine ( Pinus sylvestris), instigated an investigation into their interaction with and influence on the defence mechanisms of the host. We hypothesised that M. pinitorqua infections predispose the trees to D. sapinea by stressing the host and altering the shoot metabolites. Trees in a pine plantation in central Sweden were sampled over time to study pathogen biomass and host metabolites. The symptoms of both pathogens were consistent over years, and the preceding season’s symptoms affected the metabolic starting points pre-infection and M. pinitorqua’s proliferation. Symptoms of M. pinitorqua altered shoot metabolites more than fungal biomass, with co-symptomatic trees exhibiting elevated M. pinitorqua biomass. D. sapinea’s biomass pre-symptoms was independent of previous disease symptoms and infection by M. pinitorqua. Some trees showed tolerance to M. pinitorqua, with delayed rust infections and minimal DTB symptoms. This trait may improve the resilience of pine plantations, but more work is needed.

Peach Leaf Curl Disease, caused by the fungus Taphrina deformans, is characterized by reddish hypertrophic and hyperplasic leaf areas. To comprehend the biochemical imbalances caused by the disease an integrated approach including metabolomics, lipidomics, proteomics and complementary biochemical techniques was undertaken. Symptomatic and asymptomatic areas were dissected from leaves with increasing extension of the disease. A differential metabolic behaviour was identified in symptomatic areas with respect to either asymptomatic areas or healthy leaves. Symptomatic areas showed an altered chloroplastic functioning and composition which differs from the typical senescence process and includes decrease in the photosynthetic machinery, alteration in plastidic lipids, and decreased starch, carotenoid and chlorophyll biosynthesis. In symptomatic areas, alteration in redox-homeostasis proteins and in triacylglycerols content, peroxidation and double bond index were observed. Proteomic data revealed induction of host enzymes involved in auxin and jasmonate biosynthesis together with up-regulation of phenylpropanoid and mevalonate pathways and down-regulation of the plastidic methylerythritol phosphate route. Amino acid pools were affected, with up-regulation of proteins involved in asparagine synthesis. Overall, we conclude that curled areas exhibited a metabolic shift towards functioning as a sink tissue importing sugars and producing energy through fermentation and respiration and reductive power via the pentose phosphate route.

Soybean ( Glycine max [L.] Merr) is among the most important agricultural seed crops and source of vegetable protein. Further yield improvements per unit land area are needed to meet future demand and avoid destruction of more natural lands. Mesophyll conductance ( gm) in C 3 crops quantifies the ease with which CO 2 can transfer from the sub-stomatal cavity to Rubisco within the mesophyll. Increasing gm is in theory most attractive as it would increase photosynthesis, yield potential and water-use efficiency. Most measurements of gm have been made during steady-state light saturated photosynthesis. However, in field crop canopies, light fluctuations are frequent and the speed with which gm can increase following shade to sun transitions is likely important to crop carbon gain. Is there variability in gm that could be used in breeding? If so, indirect selection could be expected to have already increased gm and be apparent when comparing wild ancestors of soybean ( Glycine soja) to a domesticated high-yielding cultivar. The elite LD11 was compared with four ancestor accessions collected from the assumed area of domestication by concurrent measurements of gas exchange and carbon isotope discrimination (∆ 13C). This allowed estimation of gm both through induction following transfer to high light and at steady-state. The results have shown 1) gm was a significant limitation to soybean photosynthesis both at steady-state and through light induction, especially when the major biochemical limitation was in vivo Rubisco activity and, 2) compared to the ancestral accessions, the elite LD11 showed a large and significant increase in gm at both steady-state and through light induction, which also corresponded to a substantial increase in leaf level CO2 assimilation and water use efficiency.

The comprehension of the reciprocal interaction between root development and its co-adapted beneficial microbes in response to elevated CO 2 (eCO 2) will facilitate the identification of nutrient-efficient cultivars for a sustainable agriculture. Here systemically morphological, anatomical, chemical and gene expression assays performed under eCO 2 highlight the divergent root differentiation driven endodermal barrier development with respect to the L-/S-shaped lateral roots under low nitrogen conditions in rice. Next, by metabolome and endodermal-cell specific RNA sequencing we showed that rice adapted to eCO 2 by spatially recruiting diazotrophs through flavonoid secretion in L-shaped lateral roots. To the end, using a rice Casparian strip mutant Oscasp1-1 we validated such root differentiation driven specific recruitment of a diazotrophic family Oxalobacteraceae implicated in plant tolerance to low nitrogen availability. Our work indicates that rice could coordinate nutrient uptake and root differentiation by the recruitment of diazotrophs in L-shaped lateral roots under climate change.