Adaptation of Root Function by Nutrient-Induced Plasticity of Endodermal Differentiation

Root endodermal suberization induced by nitrate stress regulate apoplastic pathway rather than nitrate uptake in tobacco (Nicotiana tabacum L.)

Nitrogen levels and distribution in the rhizosphere strongly regulate the root architecture. Nitrate is an essential nutrient and an important signaling molecule for plant growth and development. Hydroponic experiments were conducted to investigate the differences in endodermal suberization in tobacco (Nicotiana tabacum L.) roots at three nitrate levels. Nitrogen accumulation was detected in the roots, shoots, and xylem sap. Nitrate influx on the root surface was also measured using the non-invasive self-referencing microsensor technique (SRMT). RNA-Seq analysis was performed to identify the genes related to endodermal suberization, nitrate transport, and endogenous abscisic acid (ABA) biosynthesis. The results showed that root length, root-shoot ratio, nitrate influx on the root surface, and NiA and NRT2.4 genes were regulated to maintain the nitrogen nutrient supply in tobacco under low nitrate conditions. Low nitrate levels enhanced root endodermal suberization and hence reduced the apoplastic transport pathway, and genes from the KCS, FAR, PAS2, and CYP86 families were upregulated. The results of exogenous fluridone, an ABA biosynthesis inhibitor, indicated that suberization of the tobacco root endodermis had no relevance to radial nitrate transport and accumulation. However, ABA enhances suberization, relating to ABA biosynthesis genes in the CCD family and degradation gene ABA8ox1.

The transcriptional integration of environmental cues with root cell type development

Plant roots navigate the soil ecosystem with each cell type uniquely responding to environmental stimuli. Below ground, the plant's response to its surroundings is orchestrated at the cellular level, including morphological and molecular adaptations that shape root system architecture as well as tissue and organ functionality. Our understanding of the transcriptional responses at cell type resolution has been profoundly enhanced by studies of the model plant Arabidopsis thaliana. However, both a comprehensive view of the transcriptional basis of these cellular responses to single and combinatorial environmental cues in diverse plant species remains elusive. In this review, we highlight the ability of root cell types to undergo specific anatomical or morphological changes in response to abiotic and biotic stresses or cues and how they collectively contribute to the plant's overall physiology. We further explore interconnections between stress and the temporal nature of developmental pathways and discuss examples of how this transcriptional reprogramming influences cell type identity and function. Finally, we highlight the power of single-cell and spatial transcriptomic approaches to refine our understanding of how environmental factors fine tune root spatiotemporal development. These complex root system responses underscore the importance of spatiotemporal transcriptional mapping, with significant implications for enhanced agricultural resilience.

An atlas of Brachypodium distachyon lateral root development

The root system of plants is a vital part for successful development and adaptation to different soil types and environments. A major determinant of the shape of a plant root system is the formation of lateral roots, allowing for expansion of the root system. Arabidopsis thaliana, with its simple root anatomy, has been extensively studied to reveal the genetic program underlying root branching. However, to get a more general understanding of lateral root development, comparative studies in species with a more complex root anatomy are required. Here, by combining optimized clearing methods and histology, we describe an atlas of lateral root development in Brachypodium distachyon, a wild, temperate grass species. We show that lateral roots initiate from enlarged phloem pole pericycle cells and that the overlying endodermis reactivates its cell cycle and eventually forms the root cap. In addition, auxin signaling reported by the DR5 reporter was not detected in the phloem pole pericycle cells or young primordia. In contrast, auxin signaling was activated in the overlying cortical cell layers, including the exodermis. Thus, Brachypodium is a valuable model to investigate how signaling pathways and cellular responses have been repurposed to facilitate lateral root organogenesis.

A Quantitative Computational Framework for Allopolyploid Single-Cell Data Integration and Core Gene Ranking in Development

Polyploidization drives regulatory and phenotypic innovation. How the merger of different genomes contributes to polyploid development is a fundamental issue in evolutionary developmental biology and breeding research. Clarifying this issue is challenging because of genome complexity and the difficulty in tracking stochastic subgenome divergence during development. Recent single-cell sequencing techniques enabled probing subgenome-divergent regulation in the context of cellular differentiation. However, analyzing single-cell data suffers from high error rates due to high dimensionality, noise, and sparsity, and the errors stack up in polyploid analysis due to the increased dimensionality of comparisons between subgenomes of each cell, hindering deeper mechanistic understandings. In this study, we develop a quantitative computational framework, called "pseudo-genome divergence quantification" (pgDQ), for quantifying and tracking subgenome divergence directly at the cellular level. Further comparing with cellular differentiation trajectories derived from single-cell RNA sequencing data allows for an examination of the relationship between subgenome divergence and the progression of development. pgDQ produces robust results and is insensitive to data dropout and noise, avoiding high error rates due to multiple comparisons of genes, cells, and subgenomes. A statistical diagnostic approach is proposed to identify genes that are central to subgenome divergence during development, which facilitates the integration of different data modalities, enabling the identification of factors and pathways that mediate subgenome-divergent activity during development. Case studies have demonstrated that applying pgDQ to single-cell and bulk tissue transcriptomic data promotes a systematic and deeper understanding of how dynamic subgenome divergence contributes to developmental trajectories in polyploid evolution.

Arabinosylation of cell wall extensin is required for the directional response to salinity in roots

Soil salinity is a major contributor to crop yield losses. To improve our understanding of root responses to salinity, we developed and exploited a real-time salt-induced tilting assay. This assay follows root growth upon both gravitropic and salt challenges, revealing that root bending upon tilting is modulated by Na+ ions, but not by osmotic stress. Next, we measured this salt-specific response in 345 natural Arabidopsis (Arabidopsis thaliana) accessions and discovered a genetic locus, encoding the cell wall-modifying enzyme EXTENSIN ARABINOSE DEFICIENT TRANSFERASE (ExAD) that is associated with root bending in the presence of NaCl (hereafter salt). Extensins are a class of structural cell wall glycoproteins known as hydroxyproline (Hyp)-rich glycoproteins, which are posttranslationally modified by O-glycosylation, mostly involving Hyp-arabinosylation. We show that salt-induced ExAD-dependent Hyp-arabinosylation influences root bending responses and cell wall thickness. Roots of exad1 mutant seedlings, which lack Hyp-arabinosylation of extensin, displayed increased thickness of root epidermal cell walls and greater cell wall porosity. They also showed altered gravitropic root bending in salt conditions and a reduced salt-avoidance response. Our results suggest that extensin modification via Hyp-arabinosylation is a unique salt-specific cellular process required for the directional response of roots exposed to salinity.

BIG enhances Arg/N-degron pathway-mediated protein degradation to regulate Arabidopsis hypoxia responses and suberin deposition

BIG/DARK OVEREXPRESSION OF CAB1/TRANSPORT INHIBITOR RESPONSE3 is a 0.5 MDa protein associated with multiple functions in Arabidopsis (Arabidopsis thaliana) signaling and development. However, the biochemical functions of BIG are unknown. We investigated a role for BIG in the Arg/N-degron pathways, in which substrate protein fate is influenced by the N-terminal residue. We crossed a big loss-of-function allele to 2 N-degron pathway E3 ligase mutants, proteolysis6 (prt6) and prt1, and examined the stability of protein substrates. Stability of model substrates was enhanced in prt6-1 big-2 and prt1-1 big-2 relative to the respective single mutants, and the abundance of the PRT6 physiological substrates, HYPOXIA-RESPONSIVE ERF2 (HRE2) and VERNALIZATION2 (VRN2), was similarly increased in prt6 big double mutants. Hypoxia marker expression was enhanced in prt6 big double mutants; this constitutive response required arginyl transferase activity and RAP-type Group VII ethylene response factor (ERFVII) transcription factors. Transcriptomic analysis of roots not only demonstrated increased expression of multiple hypoxia-responsive genes in the double mutant relative to prt6, but also revealed other roles for PRT6 and BIG, including regulation of suberin deposition through both ERFVII-dependent and independent mechanisms, respectively. Our results show that BIG acts together with PRT6 to regulate the hypoxia-response and broader processes in Arabidopsis.

Low nitrate under waterlogging triggers exodermal suberization to form a barrier to radial oxygen loss in rice roots

To acclimate to hypoxic waterlogged conditions, the roots of wetland plants form a radial oxygen loss (ROL) barrier that can promote oxygen diffusion to the root tips. We hypothesized that the low-nitrate concentrations that occur after molecular oxygen is consumed in waterlogged soils are an environmental trigger for ROL barrier formation in rice (Oryza sativa). We previously identified 128 tissue-specific up/downregulated genes during rice ROL barrier formation. The RiceXPro database showed that many of these genes were differentially regulated in response to nitrogen deficiency. Therefore, we assessed changes in the concentrations of ionic species of nitrogen under stagnant conditions, i.e. in a nutrient solution that mimics waterlogged soil conditions, and examined the effects of an increase or decrease of nitrate in the nutrient solution on ROL barrier formation and exodermal suberization. Preventing nitrate deficiency in the stagnant nutrient solution suppressed the formation of an ROL barrier. Conversely, a decrease in nitrate strongly induced ROL barrier formation, even under aerated conditions. In parallel with ROL barrier formation, suberin lamellae formed at the exodermis. Nitrate deficiency also promoted aerenchyma formation and the enlargement of root diameters. These findings suggest that the severe decline of nitrates under waterlogged conditions is an environmental cue for exodermal suberization to form an ROL barrier in rice roots.

Comparisons of two receptor-MAPK pathways in a single cell-type reveal mechanisms of signalling specificity

Cells harbour numerous receptor pathways to respond to diverse stimuli, yet often share common downstream signalling components. Mitogen-activated protein kinase (MPK) cascades are an example of such common hubs in eukaryotes. How such common hubs faithfully transduce distinct signals within the same cell-type is insufficiently understood, yet of fundamental importance for signal integration and processing in plants. We engineered a unique genetic background allowing direct comparisons of a developmental and an immunity pathway in one cell-type, the Arabidopsis root endodermis. We demonstrate that the two pathways maintain distinct functional and transcriptional outputs despite common MPK activity patterns. Nevertheless, activation of different MPK kinases and MPK classes led to distinct functional readouts, matching observed pathway-specific readouts. On the basis of our comprehensive analysis of core MPK signalling elements, we propose that combinatorial activation within the MPK cascade determines the differential regulation of an endodermal master transcription factor, MYB36, that drives pathway-specific gene activation.

Salt tolerance in mungbean is associated with controlling Na and Cl transport across roots, regulating Na and Cl accumulation in chloroplasts and maintaining high K in root and leaf mesophyll cells

Salinity tolerance requires coordinated responses encompassing salt exclusion in roots and tissue/cellular compartmentation of salt in leaves. We investigated the possible control points for salt ions transport in roots and tissue tolerance to Na+ and Cl- in leaves of two contrasting mungbean genotypes, salt-tolerant Jade AU and salt-sensitive BARI Mung-6, grown in nonsaline and saline (75 mM NaCl) soil. Cryo-SEM X-ray microanalysis was used to determine concentrations of Na, Cl, K, Ca, Mg, P, and S in various cell types in roots related to the development of apoplastic barriers, and in leaves related to photosynthetic performance. Jade AU exhibited superior salt exclusion by accumulating higher [Na] in the inner cortex, endodermis, and pericycle with reduced [Na] in xylem vessels and accumulating [Cl] in cortical cell vacuoles compared to BARI Mung-6. Jade AU maintained higher [K] in root cells than BARI Mung-6. In leaves, Jade AU maintained lower [Na] and [Cl] in chloroplasts and preferentially accumulated [K] in mesophyll cells than BARI Mung-6, resulting in higher photosynthetic efficiency. Salinity tolerance in Jade AU was associated with shoot Na and Cl exclusion, effective regulation of Na and Cl accumulation in chloroplasts, and maintenance of high K in root and leaf mesophyll cells.

Metabolic profiling of Citrus maxima L. seedlings in response to cadmium stress using UPLC-QTOF-MS

Cadmium (Cd) pollution significantly reduces agricultural crop yields. In our research, metabolomic changes in Citrus maxima L. subjected to Cd stress were investigated using ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) in tandem with multivariate analytical techniques. This integrative method, coupled with physiological evaluations, aimed to elucidate the core adaptive mechanisms to Cd stress. We found that under Cd stress, C. maxima seedlings exhibited elevated levels of reactive oxygen species, malondialdehyde, and electrolyte leakage. Furthermore, principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) demonstrated distinct a separation of the metabolome among the different treatment groups under Cd stress, indicating dynamic metabolic changes. Metabolic analysis suggested that genes involved are initially induced by Cd treatment, followed by the activation of the flavonoid biosynthesis pathway. This investigation provides new insights into the complex metabolic responses of C. maxima seedlings to Cd exposure.

Peroxidase in plant defense: Novel insights for cadmium accumulation in rice (Oryza sativa L.)

Phenylpropanoid biosynthesis plays crucial roles in the adaptation to cadmium (Cd) stress. Nevertheless, few reports have dabbled in physiological mechanisms of such super pathway regulating Cd accumulation in plants. Herein, by integrating transcriptomic, histological and molecular biology approaches, the present study dedicated to clarify molecular mechanism on how rice adapt to Cd stress via phenylpropanoid biosynthesis. Our analysis identified that the enhancement of phenylpropanoid biosynthesis was as a key response to Cd stress. Intriguingly, POD occupied a significant part in this process, with the number of POD related genes accounted for 26/29 of all upregulated genes in phenylpropanoid biosynthesis. We further used SHAM (salicylhydroxamic acid, the POD inhibitor) to validate that POD exhibited a negative correlation with the Cd accumulation in rice tissues, and proposed two intrinsic molecular mechanisms on POD in contributing to Cd detoxification. One strategy was that POD promoted the formation of lignin and CSs both in endodermis and exodermis for intercepting Cd influx. In detail, inhibited POD induced by external addition of SHAM decreased the content of lignin by 50.98-66.65 % and delayed percentage of the DTIP-CS to root length by 39.17-104.51 %. The other strategy was expression of transporter genes involved in Cd uptake, including OsIRT1, OsIRT2, OsZIP1 and OsZIP, negatively regulated by POD. In a word, our findings firstly draws a direct link between POD activity and the Cd accumulation, which is imperative for the breeding of rice with low-Cd-accumulating capacity in the future.

Imaging plant cell walls using fluorescent stains: The beauty is in the details

Plants continuously face various environmental stressors throughout their lifetime. To be able to grow and adapt in different environments, they developed specialized tissues that allowed them to maintain a protected yet interconnected body. These tissues undergo specific primary and secondary cell wall modifications that are essential to ensure normal plant growth, adaptation and successful land colonization. The composition of cell walls can vary among different plant species, organs and tissues. The ability to remodel their cell walls is fundamental for plants to be able to cope with multiple biotic and abiotic stressors. A better understanding of the changes taking place in plant cell walls may help identify and develop new strategies as well as tools to enhance plants' survival under environmental stresses or prevent pathogen attack. Since the invention of microscopy, numerous imaging techniques have been developed to determine the composition and dynamics of plant cell walls during normal growth and in response to environmental stimuli. In this review, we discuss the main advances in imaging plant cell walls, with a particular focus on fluorescent stains for different cell wall components and their compatibility with tissue clearing techniques. Lay Description: Plants are continuously subjected to various environmental stresses during their lifespan. They evolved specialized tissues that thrive in different environments, enabling them to maintain a protected yet interconnected body. Such tissues undergo distinct primary and secondary cell wall alterations essential to normal plant growth, their adaptability and successful land colonization. Cell wall composition may differ among various plant species, organs and even tissues. To deal with various biotic and abiotic stresses, plants must have the capacity to remodel their cell walls. Gaining insight into changes that take place in plant cell walls will help identify and create novel tools and strategies to improve plants' ability to withstand environmental challenges. Multiple imaging techniques have been developed since the introduction of microscopy to analyse the composition and dynamics of plant cell walls during growth and in response to environmental changes. Advancements in plant tissue cleaning procedures and their compatibility with cell wall stains have significantly enhanced our ability to perform high-resolution cell wall imaging. At the same time, several factors influence the effectiveness of cleaning and staining plant specimens, as well as the time necessary for the process, including the specimen's size, thickness, tissue complexity and the presence of autofluorescence. In this review, we will discuss the major advances in imaging plant cell walls, with a particular emphasis on fluorescent stains for diverse cell wall components and their compatibility with tissue clearing techniques. We hope that this review will assist readers in selecting the most appropriate stain or combination of stains to highlight specific cell wall components of interest.

Plant growth promoting rhizobacteria (PGPR) application for coping with salinity and drought: a bibliometric network multi-analysis

Rhizobacteria play a crucial role in plant growth and yield, stimulating primary production and improving stress resistance. Climate change has several consequences worldwide that affect arable land and agriculture. Studies on plant-soil-microorganism interactions to enhance plant productivity and/or resistance to abiotic stress may open new perspectives. This strategy aims to make agricultural-relevant plant species able to complete their biological cycle in extreme soils with the help of inoculated or primed plant growth-promoting rhizobacteria (PGPR). We provide an overview of the evolution of interest in PGPR research in the last 30 years through: (i) a quantitative search on the Scopus database; (ii) keyword frequencies and clustering analysis, and (iii) a keyword network and time-gradient analysis. The review of scientific literature on PGPR highlighted an increase in publications in the last 15 years, and a specific time gradient on subtopics, such as abiotic stresses. The rise in PGPR as a keyword co-occurring with salinity and drought stresses aligns with the growing number of papers from countries directly or partly affected by climate change. The study of PGPR, its features, and related applications will be a key challenge in the next decades, considering climate change effects on agriculture. The increased interest in PGPR leads to deeper knowledge focused specifically on researching agriculturally sustainable solutions for soils affected by salinity and drought.

Physiological characterization of the tomato cutin mutant cd1 under salinity and nitrogen stress

MAIN CONCLUSION

We identified tomato leaf cuticle and root suberin monomers that play a role in the response to nitrogen deficiency and salinity stress and discuss their potential agronomic value for breeding. The plant cuticle plays a key role in plant-water relations, and cuticle's agronomic value in plant breeding programs is currently under investigation. In this study, the tomato cutin mutant cd1, with altered fruit cuticle, was physiologically characterized under two nitrogen treatments and three salinity levels. We evaluated leaf wax and cutin load and composition, root suberin, stomatal conductance, photosynthetic rate, partial factor productivity from applied N, flower and fruit number, fruit size and cuticular transpiration, and shoot and root biomass. Both nitrogen and salinity treatments altered leaf cuticle and root suberin composition, regardless of genotype (cd1 or M82). Compared with M82, the cd1 mutant showed lower shoot biomass and reduced partial factor productivity from applied N under all treatments. Under N depletion, cd1 showed altered leaf wax composition, but was comparable to the WT under sufficient N. Under salt treatment, cd1 showed an increase in leaf wax and cutin monomers. Root suberin content of cd1 was lower than M82 under control conditions but comparable under higher salinity levels. The tomato mutant cd1 had a higher fruit cuticular transpiration rate, and lower fruit surface area compared to M82. These results show that the cd1 mutation has complex effects on plant physiology, and growth and development beyond cutin deficiency, and offer new insights on the potential agronomic value of leaf cuticle and root suberin for tomato breeding.

Rewiring gene circuitry for plant improvement

Aspirations for high crop growth and yield, nutritional quality and bioproduction of materials are challenged by climate change and limited adoption of new technologies. Here, we review recent advances in approaches to profile and model gene regulatory activity over developmental and response time in specific cells, which have revealed the basis of variation in plant phenotypes: both redeployment of key regulators to new contexts and their repurposing to control different slates of genes. New synthetic biology tools allow tunable, spatiotemporal regulation of transgenes, while recent gene-editing technologies enable manipulation of the regulation of native genes. Ultimately, understanding how gene circuitry is wired to control form and function across varied plant species, combined with advanced technology to rewire that circuitry, will unlock solutions to our greatest challenges in agriculture, energy and the environment.

Nitrate transporter protein NPF5.12 and major latex-like protein MLP6 are important defense factors against Verticillium longisporum

Plant defense responses to the soil-borne fungus Verticillium longisporum causing stem stripe disease on oilseed rape (Brassica napus) are poorly understood. In this study, a population of recombinant inbred lines (RILs) using the Arabidopsis accessions Sei-0 and Can-0 was established. Composite interval mapping, transcriptome data, and T-DNA mutant screening identified the NITRATE/PEPTIDE TRANSPORTER FAMILY 5.12 (AtNPF5.12) gene as being associated with disease susceptibility in Can-0. Co-immunoprecipitation revealed interaction between AtNPF5.12 and the MAJOR LATEX PROTEIN family member AtMLP6, and fluorescence microscopy confirmed this interaction in the plasma membrane and endoplasmic reticulum. CRISPR/Cas9 technology was applied to mutate the NPF5.12 and MLP6 genes in B. napus. Elevated fungal growth in the npf5.12 mlp6 double mutant of both oilseed rape and Arabidopsis demonstrated the importance of these genes in defense against V. longisporum. Colonization of this fungus depends also on available nitrates in the host root. Accordingly, the negative effect of nitrate depletion on fungal growth was less pronounced in Atnpf5.12 plants with impaired nitrate transport. In addition, suberin staining revealed involvement of the NPF5.12 and MLP6 genes in suberin barrier formation. Together, these results demonstrate a dependency on multiple plant factors that leads to successful V. longisporum root infection.

Metal Homeostasis in Land Plants: A Perpetual Balancing Act Beyond the Fulfilment of Metalloproteome Cofactor Demands

One of life's decisive innovations was to harness the catalytic power of metals for cellular chemistry. With life's expansion, global atmospheric and biogeochemical cycles underwent dramatic changes. Although initially harmful, they permitted the evolution of multicellularity and the colonization of land. In land plants as primary producers, metal homeostasis faces heightened demands, in part because soil is a challenging environment for nutrient balancing. To avoid both nutrient metal limitation and metal toxicity, plants must maintain the homeostasis of metals within tighter limits than the homeostasis of other minerals. This review describes the present model of protein metalation and sketches its transfer from unicellular organisms to land plants as complex multicellular organisms. The inseparable connection between metal and redox homeostasis increasingly draws our attention to more general regulatory roles of metals. Mineral co-option, the use of nutrient or other metals for functions other than nutrition, is an emerging concept beyond that of nutritional immunity.

The OsDIR55 gene increases salt tolerance by altering the root diffusion barrier

The increased soil salinity is becoming a major challenge to produce more crops and feed the growing population of the world. In this study, we demonstrated that overexpression of OsDIR55 gene enhances rice salt tolerance by altering the root diffusion barrier. OsDIR55 is broadly expressed in all examined tissues and organs with the maximum expression levels at lignified regions in rice roots. Salt stress upregulates the expression of OsDIR55 gene in an abscisic acid (ABA)-dependent manner. Loss-function and overexpression of OsDIR55 compromised and improved the development of CS and root diffusion barrier, manifested with the decreased and increased width of CS, respectively, and ultimately affected the permeability of the apoplastic diffusion barrier in roots. OsDIR55 deficiency resulted in Na+ accumulation, ionic imbalance, and growth arrest, whereas overexpression of OsDIR55 enhances salinity tolerance and provides an overall benefit to plant growth and yield potential. Collectively, we propose that OsDIR55 is crucial for ions balance control and salt stress tolerance through regulating lignification-mediated root barrier modifications in rice.

The GPAT4/6/8 clade functions in Arabidopsis root suberization nonredundantly with the GPAT5/7 clade required for suberin lamellae

Lipid polymers such as cutin and suberin strengthen the diffusion barrier properties of the cell wall in specific cell types and are essential for water relations, mineral nutrition, and stress protection in plants. Land plant-specific glycerol-3-phosphate acyltransferases (GPATs) of different clades are central players in cutin and suberin monomer biosynthesis. Here, we show that the GPAT4/6/8 clade in Arabidopsis thaliana, which is known to mediate cutin formation, is also required for developmentally regulated root suberization, in addition to the established roles of GPAT5/7 in suberization. The GPAT5/7 clade is mainly required for abscisic acid-regulated suberization. In addition, the GPAT5/7 clade is crucial for the formation of the typical lamellated suberin ultrastructure observed by transmission electron microscopy, as distinct amorphous globular polyester structures were deposited in the apoplast of the gpat5 gpat7 double mutant, in contrast to the thinner but still lamellated suberin deposition in the gpat4 gpat6 gpat8 triple mutant. Site-directed mutagenesis revealed that the intrinsic phosphatase activity of GPAT4, GPAT6, and GPAT8, which leads to monoacylglycerol biosynthesis, contributes to suberin formation. GPAT5/7 lack an active phosphatase domain and the amorphous globular polyester structure observed in the gpat5 gpat7 double mutant was partially reverted by treatment with a phosphatase inhibitor or the expression of phosphatase-dead variants of GPAT4/6/8. Thus, GPATs that lack an active phosphatase domain synthetize lysophosphatidic acids that might play a role in the formation of the lamellated structure of suberin. GPATs with active and nonactive phosphatase domains appear to have nonredundant functions and must cooperate to achieve the efficient biosynthesis of correctly structured suberin.

Exogenous abscisic acid induces the formation of a suberized barrier to radial oxygen loss in adventitious roots of barley (Hordeum vulgare)

BACKGROUND AND AIMS

Internal root aeration is essential for root growth in waterlogged conditions. Aerenchyma provides a path for oxygen to diffuse to the roots. In most wetland species, including rice, a barrier to radial oxygen loss (ROL) allows more of the oxygen to diffuse to the root tip, enabling root growth into anoxic soil. Most dryland crops, including barley, do not form a root ROL barrier. We previously found that abscisic acid (ABA) signalling is involved in the induction of ROL barrier formation in rice during waterlogging. Although rice typically does not form a tight ROL barrier in roots in aerated conditions, an ROL barrier with suberized exodermis was induced by application of exogenous ABA. Therefore, we hypothesized that ABA application could also trigger root ROL barrier formation with hypodermal suberization in barley.

METHODS

Formation of an ROL barrier was examined in roots in different exogenous ABA concentrations and at different time points using cylindrical electrodes and Methylene Blue staining. Additionally, we evaluated root porosity and observed suberin and lignin modification. Suberin, lignin and Casparian strips in the cell walls were observed by histochemical staining. We also evaluated the permeability of the apoplast to a tracer.

KEY RESULTS

Application of ABA induced suberization and ROL barrier formation in the adventitious roots of barley. The hypodermis also formed lignin-containing Casparian strips and a barrier to the infiltration of an apoplastic tracer (periodic acid). However, ABA application did not affect root porosity.

CONCLUSIONS

Our results show that in artificial conditions, barley can induce the formation of ROL and apoplastic barriers in the outer part of roots if ABA is applied exogenously. The difference in ROL barrier inducibility between barley (an upland species) and rice (a wetland species) might be attributable to differences in ABA signalling in roots in response to waterlogging conditions.

Function and induction of the root barrier to radial O2 loss. A commentary on 'Exogenous abscisic acid induces the formation of a suberized barrier to radial oxygen loss in adventitious roots of barley (Hordeum vulgare)'

This article comments on:

Katsuhiro Shiono and Haruka Matsuura, Exogenous abscisic acid induces the formation of a suberized barrier to radial oxygen loss in adventitious roots of barley (Hordeum vulgare), Annals of Botany, Volume 133, Issue 7, 6 June 2024, Pages 931–940 https://doi.org/10.1093/aob/mcae010

Elucidating the intricacies of the H2S signaling pathway in gasotransmitters: Highlighting the regulation of plant thiocyanate detoxification pathways

In recent decades, there has been increasing interest in elucidating the role of sulfur-containing compounds in plant metabolism, particularly emphasizing their function as signaling molecules. Among these, thiocyanate (SCN-), a compound imbued with sulfur and nitrogen, has emerged as a significant environmental contaminant frequently detected in irrigation water. This compound is known for its potential to adversely impact plant growth and agricultural yield. Although adopting exogenous SCN- as a nitrogen source in plant cells has been the subject of thorough investigation, the fate of sulfur resulting from the assimilation of exogenous SCN- has not been fully explored. There is burgeoning curiosity in probing the fate of SCN- within plant systems, especially considering the possible generation of the gaseous signaling molecule, hydrogen sulfide (H2S) during the metabolism of SCN-. Notably, the endogenous synthesis of H2S occurs predominantly within chloroplasts, the cytosol, and mitochondria. In contrast, the production of H2S following the assimilation of exogenous SCN- is explicitly confined to chloroplasts and mitochondria. This phenomenon indicates complex interplay and communication among various subcellular organelles, influencing signal transduction and other vital physiological processes. This review, augmented by a small-scale experimental study, endeavors to provide insights into the functional characteristics of H2S signaling in plants subjected to SCN--stress. Furthermore, a comparative analysis of the occurrence and trajectory of endogenous H2S and H2S derived from SCN--assimilation within plant organisms was performed, providing a focused lens for a comprehensive examination of the multifaceted roles of H2S in rice plants. By delving into these dimensions, our objective is to enhance the understanding of the regulatory mechanisms employed by the gasotransmitter H2S in plant adaptations and responses to SCN--stress, yielding invaluable insights into strategies for plant resilience and adaptive capabilities.

Hydrolysis of riboflavins in root exudates under iron deficiency and alkaline stress

Riboflavins are secreted under iron deficiency as a part of the iron acquisition Strategy I, mainly when the external pH is acidic. In plants growing under Fe-deficiency and alkaline conditions, riboflavins have been reported to accumulate inside the roots, with very low or negligible secretion. However, the fact that riboflavins may undergo hydrolysis under alkaline conditions has been so far disregarded. In this paper, we report the presence of riboflavin derivatives and products of their alkaline hydrolysis (lumichrome, lumiflavin and carboxymethylflavin) in nutrient solutions of Cucumis sativus plants grown under different iron regimes (soluble Fe-EDDHA in the nutrient solution, total absence of iron in the nutrient solution, or two different doses of FeSO4 supplied as a foliar spray), either cultivated in slightly acidic (pH 6) or alkaline (pH 8.8, 10 mM bicarbonate) nutrient solutions. The results show that root synthesis and exudation of riboflavins is controlled by shoot iron status, and that exuded riboflavins undergo hydrolysis, especially at alkaline pH, with lumichrome being the main product of hydrolysis.

Endodermal suberin restricts root leakage of cesium: a suitable tracer for potassium

An urgent challenge within crop production is to maintain productivity in a world plagued by climate change and its associated plant stresses, such as heat, drought and salinity. A key factor in this endeavor is to understand the dynamics of root suberization, and its role in plant-water relations and nutrient transport. This study focuses on the hypothesis that endodermal suberin, acts as a physical barrier preventing radial potassium (K) movement out of the vascular tissues during translocation. Previous attempts to experimentally support this idea have produced inconsistent results. We developed a Laser Ablation-Inductively Coupled Plasma-Mass Spectrometry (LA-ICP-MS) method, allowing us to visualize the distribution of mineral elements and track K movement. Cesium (Cs), dosed in optimized concentrations, was found to be an ideal tracer for K, due to its low background and similar chemical/biological properties. In suberin mutants of Arabidopsis thaliana, we observed a positive correlation between suberin levels and K translocation efficiency, indicating that suberin enhances the plant's ability to retain K within the vascular tissues during translocation from root to shoot. In barley (Hordeum vulgare), fully suberized seminal roots maintained higher K concentrations in the stele compared to younger, less suberized root zones. This suggests that suberization increases with root maturity, enhancing the barrier against K leakage. In nodal roots, suberin was scattered towards the phloem in mature root zones. Despite this incomplete suberization, nodal roots still restrict outward K movement, demonstrating that even partial suberin barriers can significantly reduce K loss. Our findings provide evidence that suberin is a barrier to K leakage during root-to-shoot translocation. This understanding is crucial to maintain crop productivity in the face of climate change.

Transcription factors WOX11 and LBD16 function with histone demethylase JMJ706 to control crown root development in rice

Crown roots are the main components of root systems in cereals. Elucidating the mechanisms of crown root formation is instrumental for improving nutrient absorption, stress tolerance, and yield in cereal crops. Several members of the WUSCHEL-related homeobox (WOX) and lateral organ boundaries domain (LBD) transcription factor families play essential roles in controlling crown root development in rice (Oryza sativa). However, the functional relationships among these transcription factors in regulating genes involved in crown root development remain unclear. Here, we identified LBD16 as an additional regulator of rice crown root development. We showed that LBD16 is a direct downstream target of WOX11, a key crown root development regulator in rice. Our results indicated that WOX11 enhances LBD16 transcription by binding to its promoter and recruiting its interaction partner JMJ706, a demethylase that removes histone H3 lysine 9 dimethylation (H3K9me2) from the LBD16 locus. In addition, we established that LBD16 interacts with WOX11, thereby impairing JMJ706-WOX11 complex formation and repressing its own transcriptional activity. Together, our results reveal a feedback system regulating genes that orchestrate crown root development in rice, in which LBD16 acts as a molecular rheostat.

Response of the root anatomical structure of Carex moorcroftii to habitat drought in the Western Sichuan Plateau of China

MAIN CONCLUSION

The anatomical structures of Carex moorcroftii roots showing stronger plasticity during drought had a lower coefficient of variation in cell size in the same habitats, while those showing weaker plasticity had a higher coefficient of variation. The complementary relationship between these factors comprises the adaptation mechanism of the C. moorcroftii root to drought. To explore the effects of habitat drought on root anatomy of hygrophytic plants, this study focused on roots of C. moorcroftii. Five sample plots were set up along a soil moisture gradient in the Western Sichuan Plateau to collect experimental materials. Paraffin sectioning was used to obtain root anatomy, and one-way ANOVA, correlation analysis, linear regression analysis, and RDA ranking were applied to analyze the relationship between root anatomy and soil water content. The results showed that the root transverse section area, thickness of epidermal cells, exodermis and Casparian strips, and area of aerenchyma were significantly and positively correlated with soil moisture content (P < 0.01). The diameter of the vascular cylinder and the number and total area of vessels were significantly and negatively correlated with the soil moisture content (P < 0.01). The plasticity of the anatomical structures was strong for the diameter and area of the vascular cylinder and thickness of the Casparian strip and epidermis, while it was weak for vessel diameter and area. In addition, there was an asymmetrical relationship between the functional adaptation of root anatomical structure in different soil moisture and the variation degree of root anatomical structure in the same soil moisture. Therefore, the roots of C. moorcroftii can shorten the water transport distance from the epidermis to the vascular cylinder, increase the area of the vascular cylinder and the number of vessels, and establish a complementary relationship between the functional adaptation of root anatomical structure in different habitats and the variation degree of root anatomical structure in the same habitat to adapt to habitat drought. This study provides a scientific basis for understanding the response of plateau wetland plants to habitat changes and their ecological adaptation strategies. More scientific experimental methods should be adopted to further study the mutual coordination mechanisms of different anatomical structures during root adaptation to habitat drought for hygrophytic plants.

Symplasmic and transmembrane zinc transport is modulated by cadmium in the Cd/Zn hyperaccumulator Sedum alfredii

This study investigated the influence of Cd (25 µM) on Zn accumulation in a hyperaccumulating (HE) and a non-hyperaccumulating (NHE) ecotype of Sedum alfredii Hance at short-term supply of replete (Zn5, 5 µM) and excess (Zn400, 400 µM) Zn. Cd inhibited Zn accumulation in both ecotypes, especially under Zn400, in organs with active metal sequestration, i.e. roots of NHE and shoots of HE. Direct biochemical Cd/Zn competition at the metal-protein interaction and changes in transporter gene expression contributed to the observed accumulation patterns in the roots. Specifically, in HE, Cd stimulated SaZIP4 and SaPCR2 under Zn5, but downregulated SaIRT1 and SaZIP4 under Zn400. However, Cd downregulated related transporter genes, except for SaNRAMP1, in NHE, irrespective of Zn. Cadmium stimulated casparian strip (CSs) development in NHE, as part of the defense response, while it had a subtle effect on the (CS) in HE. Moreover, Cd delayed the initiation of the suberin lamellae (SL) in HE, but stimulated SL deposition in NHE under both Zn5 or Zn400. Changes in suberization were mainly ascribed to suberin-biosynthesis-related genes and hormonal signaling. Altogether, Cd regulated Zn accumulation mainly via symplasmic and transmembrane transport in HE, while Cd inhibited both symplasmic and apoplasmic Zn transport in NHE.

Arabidopsis class II TPS controls root development and confers salt stress tolerance through enhanced hydrophobic barrier deposition

KEY MESSAGE

The mechanism of conferring salt tolerance by AtTPS9 involves enhanced deposition of suberin lamellae in the Arabidopsis root endodermis, resulting in reduction of Na+ transported to the leaves. Members of the class I trehalose-6-phosphate synthase (TPS) enzymes are known to play an important role in plant growth and development in Arabidopsis. However, class II TPSs and their functions in salinity stress tolerance are not well studied. We characterized the function of a class II TPS gene, AtTPS9, to understand its role in salt stress response and root development in Arabidopsis. The attps9 mutant exhibited significant reduction of soluble sugar levels in the leaves and formation of suberin lamellae (SL) in the endodermis of roots compared to the wild type (WT). The reduction in SL deposition (hydrophobic barriers) leads to increased apoplastic xylem loading, resulting in enhanced Na+ content in the plants, which explains salt sensitivity of the mutant plants. Conversely, AtTPS9 overexpression lines exhibited increased SL deposition in the root endodermis along with increased salt tolerance, showing that regulation of SL deposition is one of the mechanisms of action of AtTPS9 in conferring salt tolerance to Arabidopsis plants. Our data showed that besides salt tolerance, AtTPS9 also regulates seed germination and root development. qRT-PCR analyses showed significant downregulation of selected SNF1-RELATED PROTEIN KINASE2 genes (SnRK2s) and ABA-responsive genes in the mutant, suggesting that AtTPS9 may regulate the ABA-signaling intermediates as part of the mechanism conferring salinity tolerance.

Suberin deficiency and its effect on the transport physiology of young poplar roots

The precise functions of suberized apoplastic barriers in root water and nutrient transport physiology have not fully been elucidated. While lots of research has been performed with mutants of Arabidopsis, little to no data are available for mutants of agricultural crop or tree species. By employing a combined set of physiological, histochemical, analytical, and transport physiological methods as well as RNA-sequencing, this study investigated the implications of remarkable CRISPR/Cas9-induced suberization defects in young roots of the economically important gray poplar. While barely affecting overall plant development, contrary to literature-based expectations significant root suberin reductions of up to 80-95% in four independent mutants were shown to not evidently affect the root hydraulic conductivity during non-stress conditions. In addition, subliminal iron deficiency symptoms and increased translocation of a photosynthesis inhibitor as well as NaCl highlight the involvement of suberin in nutrient transport physiology. The multifaceted nature of the root hydraulic conductivity does not allow drawing simplified conclusions such as that the suberin amount must always be correlated with the water transport properties of roots. However, the decreased masking of plasma membrane surface area could facilitate the uptake but also leakage of beneficial and harmful solutes.

How exogenous ligand enhances the efficiency of cadmium phytoextraction from soils?

Many experiments showed that exogenous ligands could enhance cadmium (Cd) phytoextraction efficiency in soils. Previous studies suggested that the dissociation and the apoplastic uptake of Cd complex could not fully explain the increase of root Cd uptake. Two hypotheses are evaluated to explain enhanced Cd uptake in the presence of ligand: i) enhanced apoplastic uptake of complex due to reduced apoplastic resistance and ii) complex internalization by membrane transporters. RESULTS: show that the ligand affinity for Cd is a key characteristic determining the potential mechanism for enhanced Cd uptake. When low molecular weight organic acids are applied, the complex dissociation could generally be fast (> 10-3.3 s-1) and result in the increased Cd uptake. When hydrophilic aminopolycarboxylic acids (APCAs) are applied in experiments without water or temperature stresses to the plant, the root water uptake flux could very likely be high (> 10-7.8 dm s-1), and the strong apoplastic complex uptake could enhance the root Cd uptake. When lipophilic APCAs are applied, the strong internalization of the complex by membrane transporters could result in the increased Cd uptake if the maximum internalization rate is high (> 10-12 mol dm-2 s-1). However, the complex internalization by membrane transporters must be experimentally confirmed.

Climate-resilient crops: Lessons from xerophytes

Developing climate-resilient crops is critical for future food security and sustainable agriculture under current climate scenarios. Of specific importance are drought and soil salinity. Tolerance traits to these stresses are highly complex, and the progress in improving crop tolerance is too slow to cope with the growing demand in food production unless a major paradigm shift in crop breeding occurs. In this work, we combined bioinformatics and physiological approaches to compare some of the key traits that may differentiate between xerophytes (naturally drought-tolerant plants) and mesophytes (to which the majority of the crops belong). We show that both xerophytes and salt-tolerant mesophytes have a much larger number of copies in key gene families conferring some of the key traits related to plant osmotic adjustment, abscisic acid (ABA) sensing and signalling, and stomata development. We show that drought and salt-tolerant species have (i) higher reliance on Na for osmotic adjustment via more diversified and efficient operation of Na+ /H+ tonoplast exchangers (NHXs) and vacuolar H+ - pyrophosphatase (VPPases); (ii) fewer and faster stomata; (iii) intrinsically lower ABA content; (iv) altered structure of pyrabactin resistance/pyrabactin resistance-like (PYR/PYL) ABA receptors; and (v) higher number of gene copies for protein phosphatase 2C (PP2C) and sucrose non-fermenting 1 (SNF1)-related protein kinase 2/open stomata 1 (SnRK2/OST1) ABA signalling components. We also show that the past trends in crop breeding for Na+ exclusion to improve salinity stress tolerance are counterproductive and compromise their drought tolerance. Incorporating these genetic insights into breeding practices could pave the way for more drought-tolerant and salt-resistant crops, securing agricultural yields in an era of climate unpredictability.

How plants sense and respond to osmotic stress

Drought is one of the most serious abiotic stresses to land plants. Plants sense and respond to drought stress to survive under water deficiency. Scientists have studied how plants sense drought stress, or osmotic stress caused by drought, ever since Charles Darwin, and gradually obtained clues about osmotic stress sensing and signaling in plants. Osmotic stress is a physical stimulus that triggers many physiological changes at the cellular level, including changes in turgor, cell wall stiffness and integrity, membrane tension, and cell fluid volume, and plants may sense some of these stimuli and trigger downstream responses. In this review, we emphasized water potential and movements in organisms, compared putative signal inputs in cell wall-containing and cell wall-free organisms, prospected how plants sense changes in turgor, membrane tension, and cell fluid volume under osmotic stress according to advances in plants, animals, yeasts, and bacteria, summarized multilevel biochemical and physiological signal outputs, such as plasma membrane nanodomain formation, membrane water permeability, root hydrotropism, root halotropism, Casparian strip and suberin lamellae, and finally proposed a hypothesis that osmotic stress responses are likely to be a cocktail of signaling mediated by multiple osmosensors. We also discussed the core scientific questions, provided perspective about the future directions in this field, and highlighted the importance of robust and smart root systems and efficient source-sink allocations for generating future high-yield stress-resistant crops and plants.

Choreographing root architecture and rhizosphere interactions through synthetic biology

Climate change is driving extreme changes to the environment, posing substantial threats to global food security and bioenergy. Given the direct role of plant roots in mediating plant-environment interactions, engineering the form and function of root systems and their associated microbiota may mitigate these effects. Synthetic genetic circuits have enabled sophisticated control of gene expression in microbial systems for years and a surge of advances has heralded the extension of this approach to multicellular plant species. Targeting these tools to affect root structure, exudation, and microbe activity on root surfaces provide multiple strategies for the advancement of climate-ready crops.

Outer apoplastic barriers in roots: prospects for abiotic stress tolerance

Floods and droughts are becoming more frequent as a result of climate change and it is imperative to find ways to enhance the resilience of staple crops to abiotic stresses. This is crucial to sustain food production during unfavourable conditions. Here, we analyse the current knowledge about suberised and lignified outer apoplastic barriers, focusing on the functional roles of the barrier to radial O2 loss formed as a response to soil flooding and we discuss whether this trait also provides resilience to multiple abiotic stresses. The barrier is composed of suberin and lignin depositions in the exodermal and/or sclerenchyma cell walls. In addition to the important role during soil flooding, the barrier can also restrict radial water loss, prevent phytotoxin intrusion, salt intrusion and the main components of the barrier can impede invasion of pathogens in the root. However, more research is needed to fully unravel the induction pathway of the outer apoplastic barriers and to address potential trade-offs such as reduced nutrient or water uptake. Nevertheless, we suggest that the outer apoplastic barriers might act as a jack of all trades providing tolerance to multiple abiotic and/or biotic stressors.

A suberized exodermis is required for tomato drought tolerance

Plant roots integrate environmental signals with development using exquisite spatiotemporal control. This is apparent in the deposition of suberin, an apoplastic diffusion barrier, which regulates flow of water, solutes and gases, and is environmentally plastic. Suberin is considered a hallmark of endodermal differentiation but is absent in the tomato endodermis. Instead, suberin is present in the exodermis, a cell type that is absent in the model organism Arabidopsis thaliana. Here we demonstrate that the suberin regulatory network has the same parts driving suberin production in the tomato exodermis and the Arabidopsis endodermis. Despite this co-option of network components, the network has undergone rewiring to drive distinct spatial expression and with distinct contributions of specific genes. Functional genetic analyses of the tomato MYB92 transcription factor and ASFT enzyme demonstrate the importance of exodermal suberin for a plant water-deficit response and that the exodermal barrier serves an equivalent function to that of the endodermis and can act in its place.

IlNRAMP5 is required for cadmium accumulation and the growth in Iris lactea under cadmium exposures

Iris lactea is potentially applied for remediating Cd-contaminated soils due to the strong ability of Cd uptake and accumulation. However, its molecular mechanism underlying Cd uptake pathway remains unknown. Here, we report a member of NRAMP (Natural Resistance-Associated Macrophage Protein) family, IlNRAMP5, is involved in Cd/Mn uptake and the growth in I. lactea response to Cd. IlNRAMP5 was localized onto the plasma membrane, and was induced by Cd. It was expressed in the root cortex rather than the central vasculature, and in leaf vascular bundle and mesophyll cells. Heterologous expression in yeast showed that IlNRAMP5 could transport Cd and Mn, but not Fe. Knockdown of IlNRAMP5 triggered a significant reduction in Cd uptake, further diminishing the accumulation of Cd. In addition, silencing IlNRAMP5 disrupted Mn homeostasis by lowering Mn uptake and Mn allocation, accompanied by remarkably inhibiting photosynthesis under Cd conditions. Overall, the findings suggest that IlNRAMP5 plays versatile roles in Cd accumulation by mediating Cd uptake, and contributes to maintain the growth via modulating Mn homeostasis in I. lactea under Cd exposures. This would provide a mechanistic understanding Cd phytoremediation efficiency in planta.

The evolutionary innovation of root suberin lamellae contributed to the rise of seed plants

Seed plants overtook ferns to become the dominant plant group during the late Carboniferous, a period in which the climate became colder and dryer1,2. However, the specific innovations driving the success of seed plants are not clear. Here we report that the appearance of suberin lamellae (SL) contributed to the rise of seed plants. We show that the Casparian strip and SL vascular barriers evolved at different times, with the former originating in the most recent common ancestor (MRCA) of vascular plants and the latter in the MRCA of seed plants. Our results further suggest that most of the genes required for suberin formation arose through gene duplication in the MRCA of seed plants. We show that the appearance of the SL in the MRCA of seed plants enhanced drought tolerance through preventing water loss from the stele. We hypothesize that SL provide a decisive selective advantage over ferns in arid environments, resulting in the decline of ferns and the rise of gymnosperms. This study provides insights into the evolutionary success of seed plants and has implications for engineering drought-tolerant crops or fern varieties.

Comparative Analysis of Cd Uptake and Tolerance in Two Mangrove Species (Avicennia marina and Rhizophora stylosa) with Distinct Apoplast Barriers

Mangrove plants demonstrate an impressive ability to tolerate environmental pollutants, but excessive levels of cadmium (Cd) can impede their growth. Few studies have focused on the effects of apoplast barriers on heavy metal tolerance in mangrove plants. To investigate the uptake and tolerance of Cd in mangrove plants, two distinct mangrove species, Avicennia marina and Rhizophora stylosa, are characterized by unique apoplast barriers. The results showed that both mangrove plants exhibited the highest concentration of Cd2+ in roots, followed by stems and leaves. The Cd2+ concentrations in all organs of R. stylosa consistently exhibited lower levels than those of A. marina. In addition, R. stylosa displayed a reduced concentration of apparent PTS and a smaller percentage of bypass flow when compared to A. marina. The root anatomical characteristics indicated that Cd treatment significantly enhanced endodermal suberization in both A. marina and R. stylosa roots, and R. stylosa exhibited a higher degree of suberization. The transcriptomic analysis of R. stylosa and A. marina roots under Cd stress revealed 23 candidate genes involved in suberin biosynthesis and 8 candidate genes associated with suberin regulation. This study has confirmed that suberized apoplastic barriers play a crucial role in preventing Cd from entering mangrove roots.

Making watercress (Nasturtium officinale) cropping sustainable: genomic insights into enhanced phosphorus use efficiency in an aquatic crop

Watercress (Nasturtium officinale) is a nutrient-dense salad crop with high antioxidant capacity and glucosinolate concentration and with the potential to contribute to nutrient security as a locally grown outdoor aquatic crop in northern temperate climates. However, phosphate-based fertilizers used to support plant growth contribute to the eutrophication of aquatic habitats, often pristine chalk streams, downstream of farms, increasing pressure to minimize fertilizer use and develop a more phosphorus-use efficient (PUE) crop. Here, we grew genetically distinct watercress lines selected from a bi-parental mapping population on a commercial watercress farm either without additional phosphorus (P-) or under a commercial phosphate-based fertilizer regime (P+), to decipher effects on morphology, nutritional profile, and the transcriptome. Watercress plants sustained shoot yield in P- conditions, through enhanced root biomass, but with shorter stems and smaller leaves. Glucosinolate concentration was not affected by P- conditions, but both antioxidant capacity and the concentration of sugars and starch in shoot tissue were enhanced. We identified two watercress breeding lines, with contrasting strategies for enhanced PUE: line 60, with highly plastic root systems and increased root growth in P-, and line 102, maintaining high yield irrespective of P supply, but less plastic. RNA-seq analysis revealed a suite of genes involved in cell membrane remodeling, root development, suberization, and phosphate transport as potential future breeding targets for enhanced PUE. We identified watercress gene targets for enhanced PUE for future biotechnological and breeding approaches enabling less fertilizer inputs and reduced environmental damage from watercress cultivation.

Quantitative Time-Course Analysis of Osmotic and Salt Stress in Arabidopsis thaliana Using Short Gradient Multi-CV FAIMSpro BoxCar DIA

A major limitation when undertaking quantitative proteomic time-course experimentation is the tradeoff between depth-of-analysis and speed-of-analysis. In high complexity and high dynamic range sample types, such as plant extracts, balance between resolution and time is especially apparent. To address this, we evaluate multiple compensation voltage (CV) high field asymmetric waveform ion mobility spectrometry (FAIMSpro) settings using the latest label-free single-shot Orbitrap-based DIA acquisition workflows for their ability to deeply quantify the Arabidopsis thaliana seedling proteome. Using a BoxCarDIA acquisition workflow with a -30 -50 -70 CV FAIMSpro setting, we were able to consistently quantify >5000 Arabidopsis seedling proteins over a 21-min gradient, facilitating the analysis of ∼42 samples per day. Utilizing this acquisition approach, we then quantified proteome-level changes occurring in Arabidopsis seedling shoots and roots over 24 h of salt and osmotic stress, to identify early and late stress response proteins and reveal stress response overlaps. Here, we successfully quantify >6400 shoot and >8500 root protein groups, respectively, quantifying nearly ∼9700 unique protein groups in total across the study. Collectively, we pioneer a short gradient, multi-CV FAIMSpro BoxCarDIA acquisition workflow that represents an exciting new analysis approach for undertaking quantitative proteomic time-course experimentation in plants.

Root radial apoplastic transport contributes to shoot cadmium accumulation in a high cadmium-accumulating rice line

Radial transport of cadmium (Cd) in roots governs the amount of Cd loaded into xylem vessels, where Cd ions are translocated upward into shoots, while the mechanism of differential Cd radial transport between the high Cd-accumulating rice line Lu527-8 and the normal rice line Lu527-4 remains ambiguous. A higher Cd distribution in cross sections and root apoplast and higher bypass flow of Cd were found in Lu527-8, explaining a greater Cd translocation through the apoplastic pathway. The lower relative area of the epidermis and the constant relative area of the cortex in Lu527-8 opened-up root radial transport for Cd. Deposition of apoplastic barriers (Casparian strips and suberin lamellae) was stimulated by Cd, which effectively prevented Cd from entering the stele through the apoplastic pathway. In Lu527-8, apoplastic barriers were further from the root apex with lower expression of genes responsible for biosynthesis of Casparian strips and suberin lamellae, enhancing radial transport of Cd. Our data revealed that the higher radial apoplastic transport of Cd played an integral role in Cd translocation, contributed to a better understanding of the mechanism involved in high Cd accumulation in Lu527-8 and helped achieve the practical application of phytoextraction.

Time course of changes in the transcriptome during russet induction in apple fruit

BACKGROUND

Russeting is a major problem in many fruit crops. Russeting is caused by environmental factors such as wounding or moisture exposure of the fruit surface. Despite extensive research, the molecular sequence that triggers russet initiation remains unclear. Here, we present high-resolution transcriptomic data by controlled russet induction at very early stages of fruit development. During Phase I, a patch of the fruit surface is exposed to surface moisture. For Phase II, moisture exposure is terminated, and the formerly exposed surface remains dry. We targeted differentially expressed transcripts as soon as 24 h after russet induction.

RESULTS

During moisture exposure (Phase I) of 'Pinova' apple, transcripts associated with the cell cycle, cell wall, and cuticle synthesis (SHN3) decrease, while those related to abiotic stress increase. NAC35 and MYB17 were the earliest induced genes during Phase I. They are therefore linked to the initial processes of cuticle microcracking. After moisture removal (Phase II), the expression of genes related to meristematic activity increased (WOX4 within 24 h, MYB84 within 48 h). Genes related to lignin synthesis (MYB52) and suberin synthesis (MYB93, WRKY56) were upregulated within 3 d after moisture removal. WOX4 and AP2B3 are the earliest differentially expressed genes induced in Phase II. They are therefore linked to early events in periderm formation. The expression profiles were consistent between two different seasons and mirrored differences in russet susceptibility in a comparison of cultivars. Furthermore, expression profiles during Phase II of moisture induction were largely identical to those following wounding.

CONCLUSIONS

The combination of a unique controlled russet induction technique with high-resolution transcriptomic data allowed for the very first time to analyse the formation of cuticular microcracks and periderm in apple fruit immediately after the onset of triggering factors. This data provides valuable insights into the spatial-temporal dynamics of russeting, including the synthesis of cuticles, dedifferentiation of cells, and impregnation of cell walls with suberin and lignin.

ABA-dependent suberization and aquaporin activity in rice (Oryza sativa L.) root under different water potentials

Drought is one of the most stressful environments limiting crop growth and yield throughout the world. Therefore, most efforts have been made to document drought-derived genetic and physiological responses and to find better ways to improve drought tolerance. The interaction among them is unclear and/or less investigated. Therefore, the current study is to find a clue of metabolic connectivity among them in rice root experiencing different levels of drought condition. We selected 19 genes directly involved in abscisic acid (ABA) metabolism (6), suberization (6), and aquaporins (AQPs) activity (7) and analyzed the relatively quantitative gene expression using qRT-PCR from rice roots. In addition, we also analyzed proline, chlorophyll, and fatty acids and observed cross-sectional root structure (aerenchyma) and suberin lamella deposition in the endodermis. All drought conditions resulted in an obvious development of aerenchyma and two- to fourfold greater accumulation of proline. The limited water supply (-1.0 and -1.5 MPa) significantly increased gene expression (ABA metabolism, suberization, and AQPs) and developed greater layer of suberin lamella in root endodermis. In addition, the ratio of the unsaturated to the saturated fatty acids was increased, which could be considered as an adjusted cell permeability. Interestingly, these metabolic adaptations were an exception with a severe drought condition (hygroscopic coefficient, -3.1 MPa). Accordingly, we concluded that the drought-tolerant mechanism in rice roots is sophisticatedly regulated until permanent wilting point (-1.5 MPa), and ABA metabolism, suberization, and AQPs activity might be independent and/or concurrent process as a survival strategy against drought.

Nutrient carriers at the heart of plant nutrition and sensing

Plants require water and several essential nutrients for their development. The radial transport of nutrients from the soil to the root vasculature is achieved through a combination of three different pathways: apoplastic, symplastic, and transcellular. A common feature for these pathways is the requirement of carriers to transport nutrients across the plasma membrane. An efficient transport of nutrients across the root cell layers relies on a large number of carriers, each of them having their own substrate specificity, tissular and subcellular localization. Polarity is also emerging as a major feature allowing their function. Recent advances on radial transport of nutrients, especially carrier mediated nutrient transport will be discussed in this review, as well as the role of transporters as nutrient sensors.

Cell-type-specific transcriptomics reveals that root hairs and endodermal barriers play important roles in beneficial plant-rhizobacterium interactions

Growth- and health-promoting bacteria can boost crop productivity in a sustainable way. Pseudomonas simiae WCS417 is such a bacterium that efficiently colonizes roots, modifies the architecture of the root system to increase its size, and induces systemic resistance to make plants more resistant to pests and pathogens. Our previous work suggested that WCS417-induced phenotypes are controlled by root cell-type-specific mechanisms. However, it remains unclear how WCS417 affects these mechanisms. In this study, we transcriptionally profiled five Arabidopsis thaliana root cell types following WCS417 colonization. We found that the cortex and endodermis have the most differentially expressed genes, even though they are not in direct contact with this epiphytic bacterium. Many of these genes are associated with reduced cell wall biogenesis, and mutant analysis suggests that this downregulation facilitates WCS417-driven root architectural changes. Furthermore, we observed elevated expression of suberin biosynthesis genes and increased deposition of suberin in the endodermis of WCS417-colonized roots. Using an endodermal barrier mutant, we showed the importance of endodermal barrier integrity for optimal plant-beneficial bacterium association. Comparison of the transcriptome profiles in the two epidermal cell types that are in direct contact with WCS417-trichoblasts that form root hairs and atrichoblasts that do not-implies a difference in potential for defense gene activation. While both cell types respond to WCS417, trichoblasts displayed both higher basal and WCS417-dependent activation of defense-related genes compared with atrichoblasts. This suggests that root hairs may activate root immunity, a hypothesis that is supported by differential immune responses in root hair mutants. Taken together, these results highlight the strength of cell-type-specific transcriptional profiling to uncover "masked" biological mechanisms underlying beneficial plant-microbe associations.

Bacterial community and root endodermis: a complementary relationship

There are feedforward and feedback loops along the microbiota-root-shoot axis to maintain plant growth or defense under environmental stresses. Here, we highlight a reciprocal interaction between the endodermis and the plant-bacterial community, which stabilizes the diffusion barriers to maintain nutrient homeostasis under nutritional stress.

Next-generation ABACUS biosensors reveal cellular ABA dynamics driving root growth at low aerial humidity

The plant hormone abscisic acid (ABA) accumulates under abiotic stress to recast water relations and development. To overcome a lack of high-resolution sensitive reporters, we developed ABACUS2s-next-generation Förster resonance energy transfer (FRET) biosensors for ABA with high affinity, signal-to-noise ratio and orthogonality-that reveal endogenous ABA patterns in Arabidopsis thaliana. We mapped stress-induced ABA dynamics in high resolution to reveal the cellular basis for local and systemic ABA functions. At reduced foliar humidity, root cells accumulated ABA in the elongation zone, the site of phloem-transported ABA unloading. Phloem ABA and root ABA signalling were both essential to maintain root growth at low humidity. ABA coordinates a root response to foliar stresses, enabling plants to maintain foraging of deeper soil for water uptake.

Nitrate_dependent suberization regulates cadmium uptake and accumulation in maize

In this study, effect of nitrate-dependent suberization in maize root on cadmium (Cd) uptake and accumulation was investigated. Suberization in maize roots was significantly lower in plants grown with a high nitrate supply compared with low nitrate. This decrease was seen in the total amount of suberin, in which the aliphatic suberin amount was significantly decreased, whereas no difference in aromatic suberin content between different N-treatments. RNA-sequencing showed that suberin biosynthesis genes were upregulated in low nitrate treatment, which correlated well with the increased suberin content. Bioimaging and xylem sap analysis showed that reduced exodermal and endodermal suberization in roots of plants grown under high nitrate promoted radial Cd transport along the crown root. The enhanced suberization in crown roots of plants grown in low nitrate restricted the radial transport of Cd from epidermis to cortex via decreased accessibility to Cd related transporters at the plasmalemma. Also, under low nitrate supply, the Cd transport gene ZmNramp5 was upregulated in the crown root, which may enhance Cd uptake by root tip where exodermis and endodermis were not fully suberized. These results suggest that high nitrate supply enhances Cd uptake and radial transport in maize roots by reducing exodermal and endodermal suberization.

Transcriptome analysis reveals different mechanisms of selenite and selenate regulation of cadmium translocation in Brassica rapa

Selenium (Se) inhibits cadmium (Cd) root-to-shoot translocation and accumulation in the shoots of pak choi; however, the mechanism by which Se regulates Cd retention in roots is still poorly understood. A time-dependent hydroponic experiment was conducted to compare the effects of selenite and selenate on Cd translocation and retention in the roots. The underlying mechanisms were investigated regarding Se biotransformation and metal transportation in roots using HPLC and transcriptome analyses. Selenite showed reducing effects on Cd translocation and accumulation in shoots earlier than selenate. Selenite is mainly biotransformed into selenomethionine (80% of total Se in roots) at 72 h, while SeO42- was the dominant species in the selenate treatments (68% in shoots). Selenite up-regulated genes involved in the biosynthesis of lignin, suberin, and phytochelatins and those involved in stress signaling, thereby helping to retain Cd in the roots, whereas essentially, selenate had opposite effects and impaired the symplastic and apoplastic retention of Cd. These results suggest that cell-wall reinforcement and Cd retention in roots may be the key processes by which Se regulates Cd accumulation, and faster biotransformation into organic seleno-compounds could lead to earlier effects.

Integrated physio-biochemical and transcriptomic analysis revealed mechanism underlying of Si-mediated alleviation to cadmium toxicity in wheat

Cadmium (Cd) contamination has resulted in serious reduction of crop yields. Silicon (Si), as a beneficial element, regulates plant growth to heavy metal toxicity mainly through reducing metal uptake and protecting plants from oxidative injury. However, the molecular mechanism underlying Si-mediated Cd toxicity in wheat has not been well understood. This study aimed to reveal the beneficial role of Si (1 mM) in alleviating Cd-induced toxicity in wheat (Triticum aestivum) seedlings. The results showed that exogenous supply of Si decreased Cd concentration by 67.45% (root) and 70.34% (shoot), and maintained ionic homeostasis through the function of important transporters, such as Lsi, ZIP, Nramp5 and HIPP. Si ameliorated Cd-induced photosynthetic performance inhibition through up-regulating photosynthesis-related genes and light harvesting-related genes. Si minimized Cd-induced oxidative stress by decreasing MDA contents by 46.62% (leaf) and 75.09% (root), and helped re-establish redox homeostasis by regulating antioxidant enzymes activities, AsA-GSH cycle and expression of relevant genes through signal transduction pathway. The results revealed molecular mechanism of Si-mediated wheat tolerance to Cd toxicity. Si fertilizer is suggested to be applied in Cd contaminated soil for food safety production as a beneficial and eco-friendly element.