Root photomorphogenesis in laboratory-maintained Arabidopsis seedlings

Investigation of Arabidopsis root skototropism with different distance settings

Plants can activate protective and defense mechanisms under biotic and abiotic stresses. Their roots naturally grow in the soil, but when they encounter sunlight in the top-soil layers, they may move away from the light source to seek darkness. Here we investigate the skototropic behavior of roots, which promotes their fitness and survival. Glutamate-like receptors (GLRs) of plants play roles in sensing and responding to signals, but their role in root skototropism is not yet understood. Light-induced tropisms are known to be affected by auxin distribution, mainly determined by auxin efflux proteins (PIN proteins) at the root tip. However, the role of PIN proteins in root skototropism has not been investigated yet. To better understand root skototropism and its connection to the distance between roots and light, we established five distance settings between seedlings and darkness to investigate the variations in root bending tendencies. We compared differences in root skototropic behavior across different expression lines of Arabidopsis thaliana seedlings (atglr3.7 ko, AtGLR3.7 OE, and pin2 knockout) to comprehend their functions. Our research shows that as the distance between roots and darkness increases, the root's positive skototropism noticeably weakens. Our findings highlight the involvement of GLR3.7 and PIN2 in root skototropism.

RAV1 mediates cytokinin signaling for regulating primary root growth in Arabidopsis

Root growth dynamics is an outcome of complex hormonal crosstalk. The primary root meristem size, for example, is determined by antagonizing actions of cytokinin and auxin. Here we show that RAV1, a member of the AP2/ERF family of transcription factors, mediates cytokinin signaling in roots to regulate meristem size. The rav1 mutants have prominently longer primary roots, with a meristem that is significantly enlarged and contains higher cell numbers, compared with wild-type. The mutant phenotype could be restored on exogenous cytokinin application or by inhibiting auxin transport. At the transcript level, primary cytokinin-responsive genes like ARR1, ARR12 were significantly downregulated in the mutant root, indicating impaired cytokinin signaling. In concurrence, cytokinin induced regulation of SHY2, an Aux/IAA gene, and auxin efflux carrier PIN1 was hindered in rav1, leading to altered auxin transport and distribution. This effectively altered root meristem size in the mutant. Notably, CRF1, another member of the AP2/ERF family implicated in cytokinin signaling, is transcriptionally repressed by RAV1 to promote cytokinin response in roots. Further associating RAV1 with cytokinin signaling, our results demonstrate that cytokinin upregulates RAV1 expression through ARR1, during post-embryonic root development. Regulation of RAV1 expression is a part of secondary cytokinin response that eventually represses CRF1 to augment cytokinin signaling. To conclude, RAV1 functions in a branch pathway downstream to ARR1 that regulates CRF1 expression to enhance cytokinin action during primary root development in Arabidopsis.

Algal Ocelloids and Plant Ocelli

Vision is essential for most organisms, and it is highly variable across kingdoms and domains of life. The most known and understood form is animal and human vision based on eyes. Besides the wide diversity of animal eyes, some animals such as cuttlefish and cephalopods enjoy so-called dermal or skin vision. The most simple and ancient organ of vision is the cell itself and this rudimentary vision evolved in cyanobacteria. More complex are so-called ocelloids of dinoflagellates which are composed of endocellular organelles, acting as lens- and cornea/retina-like components. Although plants have almost never been included into the recent discussions on organismal vision, their plant-specific ocelli had already been proposed by Gottlieb Haberlandt already in 1905. Here, we discuss plant ocelli and their roles in plant-specific vision, both in the shoots and roots of plants. In contrast to leaf epidermis ocelli, which are distributed throughout leaf surface, the root apex ocelli are located at the root apex transition zone and serve the light-guided root navigation. We propose that the plant ocelli evolved from the algal ocelloids, are part of complex plant sensory systems and guide cognition-based plant behavior.

Signaling events for photomorphogenic root development

A germinating seedling incorporates environmental signals such as light into developmental outputs. Light is not only a source of energy, but also a central coordinative signal in plants. Traditionally, most research focuses on aboveground organs' response to light; therefore, our understanding of photomorphogenesis in roots is relatively scarce. However, root development underground is highly responsive to light signals from the shoot and understanding these signaling mechanisms will give a better insight into early seedling development. Here, we review the central light signaling hubs and their role in root growth promotion of Arabidopsis thaliana seedlings.

Root growth direction in simulated microgravity is modulated by a light avoidance mechanism mediated by flavonols

In a microgravity environment, without any gravitropic signal, plants are not able to define and establish a longitudinal growth axis. Consequently, absorption of water and nutrients by the root and exposure of leaves to sunlight for efficient photosynthesis is hindered. In these conditions, other external cues can be explored to guide the direction of organ growth. Providing a unilateral light source can guide the shoot growth, but prolonged root exposure to light causes a stress response, affecting growth and development, and also affecting the response to other environmental factors. Here, we have investigated how the protection of the root from light exposure, while the shoot is illuminated, influences the direction of root growth in microgravity. We report that the light avoidance mechanism existing in roots guides their growth towards diminishing light and helps establish the proper longitudinal seedling axis in simulated microgravity conditions. This process is regulated by flavonols, as shown in the flavonoid-accumulating mutant transparent testa 3, which shows an increased correction of the root growth direction in microgravity, when the seedling is grown with the root protected from light. This finding may improve the efficiency of water and nutrient sourcing and photosynthesis under microgravity conditions, as they exist in space, contributing to better plant fitness and biomass production in space farming enterprises, necessary for space exploration by humans.

Interplay between glutathione and mitogen-activated protein kinase 3 via transcription factor WRKY40 under combined osmotic and cold stress in Arabidopsis

Glutathione (GSH) plays a fundamental role in plant defense. Recent reports showed that enhanced GSH content activates mitogen-activated protein kinases (MPKs). However, the molecular mechanism behind this GSH-mediated MPKs expression during environmental challenges is unexplored. Here, we found that under control and combined abiotic stress-treated conditions, GSH feeding activates MPK3 expression in Arabidopsis thaliana by inducing its promoter, as established through the promoter activation assay. Additionally, transgenic A. thaliana overexpressing the LeMPK3 gene (AtMPK3 line) showed increased γ-ECS expression, which was decreased in mpk3, the MPK3-depleted mutant. An in-gel kinase assay exhibited hyperphosphorylation of Myelin Basic Protein (MBP) in the GSH-fed AtMPK3 transgenic line. Under control and combined abiotic stress treated conditions, expression of transcription factor WRKY40 binding to MPK3 promoter was up-regulated under enhanced GSH condition. Interestingly, GSH feeding was rendered ineffective in altering MPK3 expression in the Atwrky40 mutant, emphasizing the involvement of WRKY40 in GSH-MPK3 interplay. This was further confirmed by a wrky40 co-transformation assay. The immunoprecipitation assay followed by ChIP-qPCR showed a significant increase in the binding of WRKY40 to MPK3 promoter, which further established MPK3-WRKY40 association upon GSH feeding. In conclusion, this study demonstrated that GSH modulates MPK3 expression via WRKY40 in response to stress.

In situ Root Phenotypes of Cotton Seedlings Under Phosphorus Stress Revealed Through RhizoPot

Phosphorus (P) deficiency is a common challenge in crop production because of its poor mobility through the soil. The root system plays a significant role in P absorption from the soil and is the initial indicator of low P levels. However, the phenotypic dynamics and longevity of cotton roots under P stress remain unknown. In this study, RhizoPot, an improvised in situ root observation device, was used to monitor the dynamics of root phenotypes of cotton seedlings under P-deficient (PD) and P-replete (PR) conditions. Low P stress reduced P absorption and accumulation in the roots, leading to low dry weight accumulation. Cotton seedlings responded to low P stress by increasing the number of lateral roots, specific root length, branch density, root length density, and length of root hairs. Additionally, the life span of root hairs was prolonged. Low P stress also reduced the average diameter of roots, promoted root extension, expanded the root coverage area, and increased the range of P acquisition. Principal component analysis revealed that the net root growth rate, root length density, root dry weight, P absorption efficiency, average root hair length, and taproot daily growth significantly influenced the cotton root architecture. Collectively, these results show that low P stress reduces the net growth rate of cotton seedling roots and restricts plant growth. Plants respond to P deficiency by extending the life span of root hairs and increasing specific root length and lateral root branch density. This change in root system architecture improves the adaptability of plants to low P conditions. The findings of this study may guide the selection of cotton varieties with efficient P utilization.

The Arabidopsis HY2 Gene Acts as a Positive Regulator of NaCl Signaling during Seed Germination

Phytochromobilin (PΦB) participates in the regulation of plant growth and development as an important synthetase of photoreceptor phytochromes (phy). In addition, Arabidopsis long hypocotyl 2 (HY2) appropriately works as a key PΦB synthetase. However, whether HY2 takes part in the plant stress response signal network remains unknown. Here, we described the function of HY2 in NaCl signaling. The hy2 mutant was NaCl-insensitive, whereas HY2-overexpressing lines showed NaCl-hypersensitive phenotypes during seed germination. The exogenous NaCl induced the transcription and the protein level of HY2, which positively mediated the expression of downstream stress-related genes of RD29A, RD29B, and DREB2A. Further quantitative proteomics showed the patterns of 7391 proteins under salt stress. HY2 was then found to specifically mediate 215 differentially regulated proteins (DRPs), which, according to GO enrichment analysis, were mainly involved in ion homeostasis, flavonoid biosynthetic and metabolic pathways, hormone response (SA, JA, ABA, ethylene), the reactive oxygen species (ROS) metabolic pathway, photosynthesis, and detoxification pathways to respond to salt stress. More importantly, ANNAT1–ANNAT2–ANNAT3–ANNAT4 and GSTU19–GSTF10–RPL5A–RPL5B–AT2G32060, two protein interaction networks specifically regulated by HY2, jointly participated in the salt stress response. These results direct the pathway of HY2 participating in salt stress, and provide new insights for the plant to resist salt stress.

Nature and Nurture: Genotype-Dependent Differential Responses of Root Architecture to Agar and Soil Environments

Root development is crucial for plant growth and therefore a key factor in plant performance and food production. Arabidopsis thaliana is the most commonly used system to study root system architecture (RSA). Growing plants on agar-based media has always been routine practice, but this approach poorly reflects the natural situation, which fact in recent years has led to a dramatic shift toward studying RSA in soil. Here, we directly compare RSA responses to agar-based medium (plates) and potting soil (rhizotrons) for a set of redundant loss-of-function plethora (plt) CRISPR mutants with variable degrees of secondary root defects. We demonstrate that plt3plt7 and plt3plt5plt7 plants, which produce only a handful of emerged secondary roots, can be distinguished from other genotypes based on both RSA shape and individual traits on plates and rhizotrons. However, in rhizotrons the secondary root density and the total contribution of the side root system to the RSA is increased in these two mutants, effectively rendering their phenotypes less distinct compared to WT. On the other hand, plt3, plt3plt5, and plt5plt7 mutants showed an opposite effect by having reduced secondary root density in rhizotrons. This leads us to believe that plate versus rhizotron responses are genotype dependent, and these differential responses were also observed in unrelated mutants short-root and scarecrow. Our study demonstrates that the type of growth system affects the RSA differently across genotypes, hence the optimal choice of growth conditions to analyze RSA phenotype is not predetermined.

Root developmental responses to phosphorus nutrition

Phosphorus is an essential macronutrient for plant growth and development. Root system architecture (RSA) affects a plant's ability to obtain phosphate, the major form of phosphorus that plants uptake. In this review, I first consider the relationship between RSA and plant phosphorus-acquisition efficiency, describe how external phosphorus conditions both induce and impose changes in the RSA of major crops and of the model plant Arabidopsis, and discuss whether shoot phosphorus status affects RSA and whether there is a universal root developmental response across all plant species. I then summarize the current understanding of the molecular mechanisms governing root developmental responses to phosphorus deficiency. I also explore the possible reasons for the inconsistent results reported by different research groups and comment on the relevance of some studies performed under laboratory conditions to what occurs in natural environments.

Lighting Direction Affects Leaf Morphology, Stomatal Characteristics, and Physiology of Head Lettuce (Lactuca sativa L.)

Plants are exposed to numerous biotic and abiotic stresses, and light is one of the most important factors that influences the plant morphology. This study was carried out to examine how the lighting direction affected the plant morphology by investigating the growth parameters, epidermal cell elongation, stomatal properties, and physiological changes. Seedlings of two head lettuce (Lactuca sativa L.) cultivars, Caesar Green and Polla, were subjected to a 12 h photoperiod with a 300 μmol·m-2·s-1 photosynthetic photon flux density (PPFD) provided by light emitting diodes (LEDs) from three directions: the top, side, and bottom, relative to the plants. Compared with the top and side lighting, the bottom lighting increased the leaf angle and canopy by stimulating the epidermal cell elongation in leaf midrib, reduced the leaf number and root biomass, and induced large stomata with a low density, which is associated with reduced stomatal conductance and carbohydrate contents. However, the proline content and quantum yield exhibited no significant differences with the different lighting directions in both cultivars, which implies that the plants were under normal physiological conditions. In a conclusion, the lighting direction had a profound effect on the morphological characteristics of lettuce, where the plants adapted to the changing lighting environments.

Individuality, self and sociality of vascular plants

Vascular plants are integrated into coherent bodies via plant-specific synaptic adhesion domains, action potentials (APs) and other means of long-distance signalling running throughout the plant bodies. Plant-specific synapses and APs are proposed to allow plants to generate their self identities having unique ways of sensing and acting as agents with their own goals guiding their future activities. Plants move their organs with a purpose and with obvious awareness of their surroundings and require APs to perform and control these movements. Self-identities allow vascular plants to act as individuals enjoying sociality via their self/non-self-recognition and kin recognition. Flowering plants emerge as cognitive and intelligent organisms when the major strategy is to attract and control their animal pollinators as well as seed dispersers by providing them with food enriched with nutritive and manipulative/addictive compounds. Their goal in interactions with animals is manipulation for reproduction, dispersal and defence. This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.

Chloroplast avoidance movement: a novel paradigm of ROS signalling

The damaging effects of supra-optimal irradiance on plants, often turning to be lethal, may be circumvented by chloroplast avoidance movement which realigns chloroplasts to the anticlinal surfaces of cells (parallel to the incident light), essentially minimizing photon absorption. In angiosperms and many other groups of plants, chloroplast avoidance movement has been identified to be a strong blue light (BL)-dependent process being mediated by actin filaments wherein phototropins are identified as the photoreceptor involved. Studies through the last few decades have identified key molecular mechanisms involving Chloroplast Unusual Positioning 1 (CHUP1) protein and specific chloroplast-actin (cp-actin) filaments. However, the signal transduction pathway from strong BL absorption down to directional re-localization of chloroplasts by actin filaments is complex and ambiguous. Being the immediate cellular products of high irradiance absorption and having properties of remodelling actin as well as phototropin, reactive oxygen species (ROS) deemed to be more able and prompt than any other signalling agent in mediating chloroplast avoidance movement. Although ROS are presently being identified as fundamental component for regulating different plant processes ranging from growth, development and immunity, its role in avoidance movement have hardly been explored in depth. However, few recent reports have demonstrated the direct stimulatory involvement of ROS, especially H₂O₂, in chloroplast avoidance movement with Ca²⁺ playing a pivotal role. With this perspective, the present review discusses the mechanisms of ROS-mediated chloroplast avoidance movement involving ROS-Ca²⁺-actin communication system and NADPH oxidase (NOX)-plasma membrane (PM) H⁺-ATPase positive feed-forward loop. A possible working model is proposed.

PIN-mediated polar auxin transport facilitates root-obstacle avoidance

Plants sense mechanical stimuli to recognise nearby obstacles and change their growth patterns to adapt to the surrounding environment. When roots encounter an obstacle, they rapidly bend away from the impenetrable surface and find the edge of the barrier. However, the molecular mechanisms underlying root-obstacle avoidance are largely unknown. Here, we demonstrate that PIN-FORMED (PIN)-mediated polar auxin transport facilitates root bending during obstacle avoidance. We analysed two types of bending after roots touched barriers. In auxin receptor mutants, the rate of root movement during first bending was largely delayed. Gravity-oriented second bending was also disturbed in these mutants. The reporter assays showed that asymmetrical auxin responses occurred in the roots during obstacle avoidance. Pharmacological analysis suggested that polar auxin transport mediates local auxin accumulation. We found that PINs are required for auxin-assisted root bending during obstacle avoidance. We propose that rapid root movement during obstacle avoidance is not just a passive but an active bending completed through polar auxin transport. Our findings suggest that auxin plays a role in thigmotropism during plant-obstacle interactions.

Blue Light-Triggered Chemical Reactions Underlie Phosphate Deficiency-Induced Inhibition of Root Elongation of Arabidopsis Seedlings Grown in Petri Dishes

To tolerate phosphate (Pi) deficiency in the environment, plants alter their developmental and metabolic programs. In the past two decades, researchers have extensively used Petri dish-grown seedlings of the model plant Arabidopsis thaliana to study the molecular mechanisms underlying root developmental responses to Pi deficiency. A typical developmental response of the Petri dish-grown Arabidopsis seedlings to Pi deficiency is the inhibited growth of primary root (PR). This response is generally thought to enhance the production of lateral roots and root hairs, which increases the plant's ability to obtain Pi and is therefore regarded as an active cellular response. Here, we report that direct illumination of root surface with blue light is critical and sufficient for Pi deficiency-induced inhibition of PR growth in Arabidopsis seedlings. We further show that a blue light-triggered malate-mediated photo-Fenton reaction and a canonical Fenton reaction form an Fe redox cycle in the root apoplast. This Fe redox cycle results in the production of hydroxyl radicals that inhibit PR growth. In addition to revealing the molecular mechanism underlying Pi deficiency-induced inhibition of PR growth, our work demonstrated that this developmental change is not an active cellular response; instead, it is a phenotype resulting from root growth in transparent Petri dishes. This finding is significant because illuminated, transparent Petri dishes have been routinely used to study Arabidopsis root responses to environmental changes.

STO and GA negatively regulate UV-B-induced Arabidopsis root growth inhibition

Studies on UV-B-induced plant photomorphogenesis mainly focus on Arabidopsis shoots (hypocotyl, leaf, petiole, and stem) but less on roots. In the present research, the low-level UV-B (0.2 W·m-2) induced a decrease in the number of root cells in the meristem zone and an inhibition of the cell length in the maturation zone of roots in Arabidopsis thaliana L.Heynh (Col-0). UV-B-induced root growth inhibition was recovered by the addition of GA3 to culture media. GA3 played an important role in UV-B-induced inhibition of root growth. The cop1-4 mutant with more meristem cell and longer mature cells exhibited longer root length under low-level UV-B. COP1 acted as a positive regulator of root growth under UV-B, through regulation of cell division and elongation. The sto mutant exhibited a shorter root length under UV-B with similar cell length but fewer meristem cells compared with wild type (Col-0). STO only regulated cell division, but cell expansion was not affected. UV-B radiation also inhibited the root growth of uvr8 mutant, and the degree of inhibition was greater than for wild type (Ler). UV-B inhibited the growth of Arabidopsis root, possibly because it changes the GA signal and inhibited cell division and cell elongation, which be related to COP1 and STO genes.

Plants Grown in Parafilm-Wrapped Petri Dishes Are Stressed and Possess Altered Gene Expression Profile

Arabidopsis is used as a model species in numerous physiological and genetic studies. Most of them employ parafilm-wrapped sterile culture. Here we demonstrate that this method is prone to potential artifacts and can lead to erroneous conclusions. We compared the effect of different sealing methods including air-permeable paper tape and traditional parafilm on Arabidopsis seedling growth, root development and gene expression network. Although seedlings grown in Petri dishes after 1 week sealed with paper tape showed a similar growth phenotype to that of parafilm-sealed seedlings, more than 700 differentially expressed genes (DEG) were found, including stress and nutrition-responsive genes. In addition, more H₂O₂ was accumulated in the tissues of parafilm-sealed plants. After 14 days of growth, paper tape-sealed plants grew much better than parafilm-sealed ones and accumulated higher chlorophyll content, with 490 DEGs found. After 3 weeks of growth, paper tape-sealed plants had higher chlorophyll and better growth compared to parafilm-sealed ones; and only 10 DEGs were found at this stage. Thus, the obvious phenotype observed at the latter stage was a result of differential gene expression at earlier time points, mostly of defense, abiotic stress, nutrition, and phytohormone-responsive genes. More O₂ content was detected inside paper tape-sealed Petri dishes at early growth stage (7 days), and distinct difference in the CO₂ content was observed between parafilm-sealed and paper tape-sealed Petri dishes. Furthermore, the carbon source also influenced seedlings growth with different sealing methods. In conclusion, conventional sealing using parafilm was not the optimal choice, most likely because of the limited gas exchange and a consequent stress caused to plants.

Root Tropisms: Investigations on Earth and in Space to Unravel Plant Growth Direction

Root tropisms are important responses of plants, allowing them to adapt their growth direction. Research on plant tropisms is indispensable for future space programs that envisage plant-based life support systems for long-term missions and planet colonization. Root tropisms encompass responses toward or away from different environmental stimuli, with an underexplored level of mechanistic divergence. Research into signaling events that coordinate tropistic responses is complicated by the consistent coincidence of various environmental stimuli, often interacting via shared signaling mechanisms. On Earth the major determinant of root growth direction is the gravitational vector, acting through gravitropism and overruling most other tropistic responses to environmental stimuli. Critical advancements in the understanding of root tropisms have been achieved nullifying the gravitropic dominance with experiments performed in the microgravity environment. In this review, we summarize current knowledge on root tropisms to different environmental stimuli. We highlight that the term tropism must be used with care, because it can be easily confused with a change in root growth direction due to asymmetrical damage to the root, as can occur in apparent chemotropism, electrotropism, and magnetotropism. Clearly, the use of Arabidopsis thaliana as a model for tropism research contributed much to our understanding of the underlying regulatory processes and signaling events. However, pronounced differences in tropisms exist among species, and we argue that these should be further investigated to get a more comprehensive view of the signaling pathways and sensors. Finally, we point out that the Cholodny-Went theory of asymmetric auxin distribution remains to be the central and unifying tropistic mechanism after 100 years. Nevertheless, it becomes increasingly clear that the theory is not applicable to all root tropistic responses, and we propose further research to unravel commonalities and differences in the molecular and physiological processes orchestrating root tropisms.

HY5 Contributes to Light-Regulated Root System Architecture Under a Root-Covered Culture System

Light is essential for plant organogenesis and development. Light-regulated shoot morphogenesis has been extensively studied; however, the mechanisms by which plant roots perceive and respond to aboveground light are largely unknown, particularly because the roots of most terrestrial plants are usually located underground in darkness. To mimic natural root growth conditions, we developed a root-covered system (RCS) in which the shoots were illuminated and the plant roots could be either exposed to light or cultivated in darkness. Using the RCS, we observed that root growth of wild-type plants was significantly promoted when the roots were in darkness, whereas it was inhibited by direct light exposure. This growth change seems to be regulated by ELONGATED HYPOCOTYL 5 (HY5), a master regulator of photomorphogenesis. Light was found to regulate HY5 expression in the roots, while a HY5 deficiency partially abolished the inhibition of growth in roots directly exposed to light, suggesting that HY5 expression is induced by direct light exposure and inhibits root growth. However, no differences in HY5 expression were observed between illuminated and dark-grown cop1 roots, indicating that HY5 may be regulated by COP1-mediated proteasome degradation. We confirmed the crucial role of HY5 in regulating root development in response to light under soil-grown conditions. A transcriptomic analysis revealed that light controls the expression of numerous genes involved in phytohormone signaling, stress adaptation, and metabolic processes in a HY5-dependent manner. In combination with the results of the flavonol quantification and exogenous quercetin application, these findings suggested that HY5 regulates the root response to light through a complex network that integrates flavonol biosynthesis and reactive oxygen species signaling. Collectively, our results indicate that HY5 is a master regulator of root photomorphogenesis.

RhizoChamber-Monitor: a robotic platform and software enabling characterization of root growth

BACKGROUND

In order to efficiently determine genotypic differences in rooting patterns of crops, novel hardware and software are needed simultaneously to characterize dynamics of root development.

RESULTS

We describe a prototype robotic monitoring platform-the RhizoChamber-Monitor for analyzing growth patterns of plant roots automatically. The RhizoChamber-Monitor comprises an automatic imaging system for acquiring sequential images of roots which grow on a cloth substrate in custom rhizoboxes, an automatic irrigation system and a flexible shading arrangement. A customized image processing software was developed to analyze the spatio-temporal dynamics of root growth from time-course images of multiple plants. This software can quantify overall growth of roots and extract detailed growth traits (e.g. dynamics of length and diameter) of primary roots and of individual lateral roots automatically. It can also identify local growth traits of lateral roots (pseudo-mean-length and pseudo-maximum-length) semi-automatically. Two cotton genotypes were used to test both the physical platform and the analysis software.

CONCLUSIONS

The combination of hardware and software is expected to facilitate quantification of root geometry and its spatio-temporal growth patterns, and therefore to provide opportunities for high-throughput root phenotyping in support of crop breeding to optimize root architecture.

Sense of space: Tactile sense for exploratory behavior of roots

In soil, plant roots grow in heterogeneous environments. Plant roots are always facing the difficulty of searching effectively the patchy natural resources, such as water, oxygen, ions and mineral nutrition. Numerous studies reported that root apex navigation enables roots to explore complex environments. In this short communication, we characterize how growing maize roots explore narrow space available with two experimental settings: tactile exploration of narrow glass tube and circumnutation in free space. We also discuss root growth in the soil in terms of foraging behavior guided by the sensory root apex.

Combined Effects of Elevated O3 Concentrations and Enhanced UV-B Radiation of the Biometric and Biochemical Properties of Soybean Roots

Enhanced ultraviolet-B (UV-B) radiation and elevated tropospheric ozone alone may inhibit the growth of agricultural crops. However, research regarding their combined effects on growth and biochemical properties of roots is still scarce. Using open top chambers, we monitored the response of growth, secondary metabolites, endogenous hormones and enzyme activities of soybean roots to elevated O3 and enhanced UV-B individually and in combination at stages of branching, flowering and podding. Our results indicated that the root biomass decreased by 23.6, 25.2, and 27.7%, and root oxidative capacity declined by11.2, 39.9, and 55.7% exposed to elevated O3, enhanced UV-B, and O3 + UV-B, respectively, compared to the control treatment. Concentrations of quercetin and ABA were significantly increased, while concentrations of total polyphenol and P-coumaric acid responded insignificantly to elevated O3, enhanced UV-B, and O3 + UV-B during the whole period of soybean growth. Elevated O3, enhanced UV-B and O3 + UV-B showed significant negative effects on superoxide dismutase (EC 1.15.1.1) activity at flowering stage, on activities of peroxidase (EC 1.11.1.7) and catalase (EC 1.11.1.6) at podding stage, on ascorbate peroxidase activity during the whole period of soybean growth. Moreover, compared to hormones and enzyme activity, secondary metabolisms showed stronger correlation with root growth exposed to elevated O3 and enhanced UV-B individually and in combination. Our study concluded that combined effects of O3 and UV-B radiation significantly exacerbated the decline of soybean root growth, and for annual legumes, the inhibited root growth exposed to O3 and/or UV-B radiation was mostly associated with secondary metabolisms (especially flavonoids).

Multiple Routes of Light Signaling during Root Photomorphogenesis

Plants dynamically adjust their architecture to optimize growth and performance under fluctuating light environments, a process termed photomorphogenesis. A variety of photomorphogenic responses have been studied extensively in the shoots, where diverse photoreceptors and signaling molecules have been functionally characterized. Notably, accumulating evidence demonstrates that the underground roots also undergo photomorphogenesis, raising the question of how roots perceive and respond to aboveground light. Recent findings indicate that root photomorphogenesis is mediated by multiple signaling routes, including shoot-to-root transmission of mobile signaling molecules, direct sensing of light by the roots, and light channeling through the plant body. In this review we discuss recent advances in how light signals are transmitted to the roots to trigger photomorphogenic responses.

Dissection of HY5/HYH expression in Arabidopsis reveals a root-autonomous HY5-mediated photomorphogenic pathway

ELONGATED HYPOCOTYL 5 (HY5), a member of the bZIP gene family, is a positive regulator of the light signaling pathway in Arabidopsis thaliana. Whereas the hy5 mutant exhibits an elongated hypocotyl when grown in the light, the hy5 homolog (hyh) mutant does not. Although the functions of HY5 and HYH in light-mediated seedling development have been revealed, the tissue-specific expression patterns of HY5 and HYH and their interconnected regulation are largely unknown. Here, we report that HY5 regulates HYH expression in roots and contributes to root growth under different light conditions. We generated HY5 and HYH transcriptional and translational fusion reporter lines to investigate their expression patterns. HY5 was constitutively expressed in all root tissues, while HYH was predominantly expressed in root xylem cells. Root growth after a dark-to-light transition was perturbed in the hy5 and hy5hyh mutant lines, but not in the hyh mutant line, indicating that HY5 plays a major role in light-regulated root growth. Light-induced HY5/HYH expression occurred autonomously in roots. HYH expression in roots was decreased in the hy5 mutant, suggesting that HY5 regulates HYH expression. Collectively, these results indicate that an organ-specific HY5-mediated pathway controls root photomorphogenic development independently of light signaling in the shoot.

Expression of Root Genes in Arabidopsis Seedlings Grown by Standard and Improved Growing Methods

Roots of Arabidopsis thaliana seedlings grown in the laboratory using the traditional plant-growing culture system (TPG) were covered to maintain them in darkness. This new method is based on a dark chamber and is named the improved plant-growing method (IPG). We measured the light conditions in dark chambers, and found that the highest light intensity was dramatically reduced deeper in the dark chamber. In the bottom and side parts of dark chambers, roots were almost completely shaded. Using the high-throughput RNA sequencing method on the whole RNA extraction from roots, we compared the global gene expression levels in roots of seedlings from these two conditions and identified 141 differently expressed genes (DEGs) between them. According to the KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment, the flavone and flavonol biosynthesis and flavonoid biosynthesis pathways were most affected among all annotated pathways. Surprisingly, no genes of known plant photoreceptors were identified as DEGs by this method. Considering that the light intensity was decreased in the IPG system, we collected four sections (1.5 cm for each) of Arabidopsis roots grown in TPG and IPG conditions, and the spatial-related differential gene expression levels of plant photoreceptors and polar auxin transporters, including CRY1, CRY2, PHYA, PHYB, PHOT1, PHOT2, and UVR8 were analyzed by qRT-PCR. Using these results, we generated a map of the spatial-related expression patterns of these genes under IPG and TPG conditions. The expression levels of light-related genes in roots is highly sensitive to illumination and it provides a background reference for selecting an improved culture method for laboratory-maintained Arabidopsis seedlings.

"Feature Detection" vs. "Predictive Coding" Models of Plant Behavior

In this article we consider the possibility that plants exhibit anticipatory behavior, a mark of intelligence. If plants are able to anticipate and respond accordingly to varying states of their surroundings, as opposed to merely responding online to environmental contingencies, then such capacity may be in principle testable, and subject to empirical scrutiny. Our main thesis is that adaptive behavior can only take place by way of a mechanism that predicts the environmental sources of sensory stimulation. We propose to test for anticipation in plants experimentally by contrasting two empirical hypotheses: “feature detection” and “predictive coding.” We spell out what these contrasting hypotheses consist of by way of illustration from the animal literature, and consider how to transfer the rationale involved to the plant literature.

Root cap-dependent gravitropic U-turn of maize root requires light-induced auxin biosynthesis via the YUC pathway in the root apex

Gravitropism refers to the growth or movement of plants that is influenced by gravity. Roots exhibit positive gravitropism, and the root cap is thought to be the gravity-sensing site. In some plants, the root cap requires light irradiation for positive gravitropic responses. However, the mechanisms regulating this phenomenon are unknown. We herein report that maize roots exposed to white light continuously for ≥1-2h show increased indole-3-acetic acid (IAA) levels in the root tips, especially in the transition zone (1-3mm from the tip). Treatment with IAA biosynthesis inhibitors yucasin and l-kynurenine prevented any increases in IAA content and root curvature under light conditions. Analyses of the incorporation of a stable isotope label from tryptophan into IAA revealed that some of the IAA in roots was synthesized in the root apex. Furthermore, Zmvt2 and Zmyuc gene transcripts were detected in the root apex. One of the Zmyuc genes (ZM2G141383) was up-regulated by light irradiation in the 0-1mm tip region. Our findings suggest that IAA accumulation in the transition zone is due to light-induced activation of Zmyuc gene expression in the 0-1mm root apex region. Light-induced changes in IAA levels and distributions mediate the maize root gravitropic U-turn.

Genetic Homogeneity Revealed Using SCoT, ISSR and RAPD Markers in Micropropagated Pittosporum eriocarpum Royle- An Endemic and Endangered Medicinal Plant

Pittosporum eriocarpum Royle, a medicinally important taxon, is endemic to Uttarakhand region of Himalaya. It has become endangered due to over-collection and the loss of habitats. As raising plants through seeds in this plant is problematic, a reliable protocol for micropropagation using nodal explants has been developed. High shoot regeneration (95%) occurred in MS medium augmented with BA 0.4mg/l in combination IBA 0.6mg/l. In vitro regenerated shoots were rooted in MS medium supplemented with three auxins, of which 0.6 mg/l indole butyric acid proved to be the best for rooting (90%) with maximum number of roots per shoot. Thereafter, rooted plants were hardened and nearly 73% of rooted shoots were successfully acclimatized and established in the field. Start codon targeted (SCoT), inter simple sequence repeats (ISSR) and random amplified polymorphic DNA (RAPD) markers were used to validate the genetic homogeneity amongst nine in vitro raised plantlets with mother plant. DNA fingerprints of in vitro regenerated plantlets displayed monomorphic bands similar to mother plant, indicating homogeneity among the micropropagated plants with donor mother plant. The similarity values were calculated based on SCoT, ISSR and RAPD profiles which ranged from 0.89 to 1.00, 0.91 to 1.00 and 0.95 to 1.00 respectively. The dendrograms generated through Unweighted Pair Group Method with arithmetic mean (UPGMA) analysis revealed 97% similarity amongst micropropagated plants with donor mother plant, thus confirming genetic homogeneity of micropropagated clones. This is the first report on micropropagation and genetic homogeneity assessment of P. eriocarpum. The protocol would be useful for the conservation and large scale production of P. eriocarpum to meet the demand for medicinal formulations and also for the re-introduction of in vitro grown plants in the suitable natural habitats to restore the populations.

MES Buffer Affects Arabidopsis Root Apex Zonation and Root Growth by Suppressing Superoxide Generation in Root Apex

In plants, growth of roots and root hairs is regulated by the fine cellular control of pH and reactive oxygen species (ROS). MES, 2-(N-morpholino)ethanesulfonic acid as one of the Good's buffers has broadly been used for buffering medium, and it is thought to suit for plant growth with the concentration at 0.1% (w/v) because the buffer capacity of MES ranging pH 5.5-7.0 (for Arabidopsis, pH 5.8). However, many reports have shown that, in nature, roots require different pH values on the surface of specific root apex zones, namely meristem, transition zone, and elongation zone. Despite the fact that roots always grow on a media containing buffer molecule, little is known about impact of MES on root growth. Here, we have checked the effects of different concentrations of MES buffer using growing roots of Arabidopsis thaliana. Our results show that 1% of MES significantly inhibited root growth, the number of root hairs and length of meristem, whereas 0.1% promoted root growth and root apex area (region spanning from the root tip up to the transition zone). Furthermore, superoxide generation in root apex disappeared at 1% of MES. These results suggest that MES disturbs normal root morphogenesis by changing the ROS homeostasis in root apex.

The TOR Complex: An Emergency Switch for Root Behavior

Target of rapamycin (TOR) kinase is known to be a controller of cell growth and aging, which determines the fine balance between growth rates and energy availabilities. It has been reported that many eukaryotes express TOR genes. In plants, TOR signaling modifies growth and development in response to a plant's energy status. An example of TOR action can be found in the root apices, which are active organs that explore the soil environment via vigorous growth and numerous tropisms. The exploratory nature of root apices requires a large energy supply for signaling, as well as for cell division and elongation. In the case of negative tropisms, roots must respond quickly to avoid patches of unfavorable soil conditions, again by consuming precious energy reserves. Here we review the current findings on TOR signaling in plants and animals, and propose possible roles for this important complex in driving plant root negative tropisms, particularly during light escape and salt avoidance behavior.

GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems

Root systems develop different root types that individually sense cues from their local environment and integrate this information with systemic signals. This complex multi-dimensional amalgam of inputs enables continuous adjustment of root growth rates, direction, and metabolic activity that define a dynamic physical network. Current methods for analyzing root biology balance physiological relevance with imaging capability. To bridge this divide, we developed an integrated-imaging system called Growth and Luminescence Observatory for Roots (GLO-Roots) that uses luminescence-based reporters to enable studies of root architecture and gene expression patterns in soil-grown, light-shielded roots. We have developed image analysis algorithms that allow the spatial integration of soil properties, gene expression, and root system architecture traits. We propose GLO-Roots as a system that has great utility in presenting environmental stimuli to roots in ways that evoke natural adaptive responses and in providing tools for studying the multi-dimensional nature of such processes.

Preparation of plants for developmental and cellular imaging by light-sheet microscopy

Long-term fluorescence live-cell imaging experiments have long been limited by the effects of excitation-induced phototoxicity. The advent of light-sheet microscopy now allows users to overcome this limitation by restricting excitation to a narrow illumination plane. In addition, light-sheet imaging allows for high-speed image acquisition with uniform illumination of samples composed of multiple cell layers. The majority of studies conducted thus far have used custom-built platforms with specialized hardware and software, along with specific sample handling approaches. The first versatile commercially available light-sheet microscope, Lightsheet Z.1, offers a number of innovative solutions, but it requires specific strategies for sample handling during long-term imaging experiments. There are currently no standard procedures describing the preparation of plant specimens for imaging with the Lightsheet Z.1. Here we describe a detailed protocol to prepare plant specimens for light-sheet microscopy, in which Arabidopsis seeds or seedlings are placed in solid medium within glass capillaries or fluorinated ethylene propylene tubes. Preparation of plant material for imaging may be completed within one working day.

Roles of proteome dynamics and cytokinin signaling in root to hypocotyl ratio changes induced by shading roots of Arabidopsis seedlings

In nature, root systems of most terrestrial plants are protected from light exposure by growing in a dark soil environment. Hence, in vitro cultivation in transparent Petri dishes leads to physiological perturbations, but the mechanisms underlying root-mediated light perception and responses have not been fully elucidated. Thus, we compared Arabidopsis thaliana seedling development in transparent and darkened Petri dishes at low light intensity (20 µmol m(-2) s(-1)), allowing us to follow (inter alia) hypocotyl elongation, which is an excellent process for studying interactions of signals involved in the regulation of growth and developmental responses. To obtain insights into molecular events underlying differences in seedling growth under these two conditions, we employed liquid chromatography-mass spectrometry (LC-MS) shotgun proteomics (available via the PRIDE deposit PXD001612). In total, we quantified the relative abundances of peptides representing 1,209 proteins detected in all sample replicates of LC-MS analyses. Comparison of MS spectra after manual validation revealed 48 differentially expressed proteins. Functional classification, analysis of available gene expression data and literature searches revealed alterations associated with root illumination (inter alia) in autotrophic CO2 fixation, C compound and carbohydrate metabolism, and nitrogen metabolism. The results also indicate a previously unreported role for cytokinin plant hormones in the escape-tropism response to root illumination. We complemented these results with reverse transcription followed by quantitative PCR (RT-qPCR), chlorophyll fluorescence and detailed cytokinin signaling analyses, detecting in the latter a significant increase in the activity of the cytokinin two-component signaling cascade in roots and implicating the cytokinin receptor AHK3 as the major mediator of root to hypocotyl signaling in responses to root illumination.

Pectins, ROS homeostasis and UV-B responses in plant roots

Light from the sun contains far-red, visible and ultra violet (UV) wavelength regions. Almost all plant species have been evolved under the light environment. Interestingly, several photoreceptors, expressing both in shoots and roots, process the light information during the plant life cycle. Surprisingly, Arabidopsis root apices express besides the UVR8 UV-B receptor, also root-specific UV-B sensing proteins RUS1 and RUS2 linked to the polar cell-cell transport of auxin. In this mini-review, we focus on reactive oxygen species (ROS) signaling and possible roles of pectins internalized via endocytic vesicle recycling system in the root-specific UV-B perception and ROS homeostasis.

"Rhizoponics": a novel hydroponic rhizotron for root system analyses on mature Arabidopsis thaliana plants

BACKGROUND

Well-developed and functional roots are critical to support plant life and reach high crop yields. Their study however, is hampered by their underground growth and characterizing complex root system architecture (RSA) therefore remains a challenge. In the last few years, several phenotyping methods, including rhizotrons and x-ray computed tomography, have been developed for relatively thick roots. But in the model plant Arabidopsis thaliana, in vitro culture remains the easiest and preferred method to study root development, which technically limits the analyses to young seedlings.

RESULTS

We present here an innovative design of hydroponic rhizotrons (rhizoponics) adapted to Arabidopsis thaliana. The setup allows to simultaneously characterize the RSA and shoot development from seedling to adult stages, i.e. from seed to seed. This system offers the advantages of hydroponics such as control of root environment and easy access to the roots for measurements or sampling. Being completely movable and low cost, it can be used in controlled cabinets. We chose the case of cadmium treatment to illustrate potential applications, from cell to organ levels.

CONCLUSIONS

Rhizoponics makes possible, on the same plants of Arabidopsis, RSA measurements, root sampling and characterization of aerial development up to adult size. It therefore provides a valuable tool for addressing fundamental questions in whole plant physiology.

How and why do root apices sense light under the soil surface?

Light can penetrate several centimeters below the soil surface. Growth, development and behavior of plant roots are markedly affected by light despite their underground lifestyle. Early studies provided contrasting information on the spatial and temporal distribution of light-sensing cells in the apical region of root apex and discussed the physiological roles of plant hormones in root responses to light. Recent biological and microscopic advances have improved our understanding of the processes involved in the sensing and transduction of light signals, resulting in subsequent physiological and behavioral responses in growing root apices. Here, we review current knowledge of cellular distributions of photoreceptors and their signal transduction pathways in diverse root tissues and root apex zones. We are discussing also the roles of auxin transporters in roots exposed to light, as well as interactions of light signal perceptions with sensing of other environmental factors relevant to plant roots.

UV-B Induced Generation of Reactive Oxygen Species Promotes Formation of BFA-Induced Compartments in Cells of Arabidopsis Root Apices

UV-B radiation is an important part of the electromagnetic spectrum emitted by the sun. For much of the period of biological evolution organisms have been exposed to UV radiation, and have developed diverse mechanisms to cope with this potential stress factor. Roots are usually shielded from exposure to UV by the surrounding soil, but may nevertheless be exposed to high energy radiation on the soil surface. Due to their high sensitivity to UV-B radiation, plant roots need to respond rapidly in order to minimize exposure on the surface. In addition to root gravitropism, effective light perception by roots has recently been discovered to be essential for triggering negative root phototropism in Arabidopsis. However, it is not fully understood how UV-B affects root growth and phototropism. Here, we report that UV-B induces rapid generation of reactive oxygen species which in turn promotes the formation of BFA-induced compartments in the Arabidopsis root apex. During unilateral UV-B irradiation of roots changes in auxin concentration on the illuminated side have been recorded. In conclusion, UV-B-induced and ROS-mediated stimulation of vesicle recycling promotes root growth and induces negative phototropism.

Light-dependent control of redox balance and auxin biosynthesis in plants

Auxin, indole-3-acetic acid (IAA), plays a crucial role for morphogenesis, development, growth, and tropisms in many plant species. Auxin biosynthesis is accomplished via specific pathways depending on several enzymes starting from amino acid, tryptophan. Auxin biosynthesis in maize is particularly active at the tip of coleoptile expressing abundant YUCCA (YUC) protein, which is essential for auxin biosynthesis. In vitro experiment demonstrated that precursor of auxin molecule; indole-3-acetaldehyde (IAAld) was generated by illumination of the mixture of tryptophan and flavin in non-enzymatic manner. In addition, we have detected immediate production of reactive oxygen species (ROS) in illuminated Arabidopsis root cells. In this perspective, we are proposing the non-enzymatic regulation of redox homeostasis and auxin biosynthesis throughout the plant body under variable environmental light conditions.

Light as stress factor to plant roots - case of root halotropism

Despite growing underground, largely in darkness, roots emerge to be very sensitive to light. Recently, several important papers have been published which reveal that plant roots not only express all known light receptors but also that their growth, physiology and adaptive stress responses are light-sensitive. In Arabidopsis, illumination of roots speeds-up root growth via reactive oxygen species-mediated and F-actin dependent process. On the other hand, keeping Arabidopsis roots in darkness alters F-actin distribution, polar localization of PIN proteins as well as polar transport of auxin. Several signaling components activated by phytohormones are overlapping with light-related signaling cascade. We demonstrated that the sensitivity of roots to salinity is altered in the light-grown Arabidopsis roots. Particularly, light-exposed roots are less effective in their salt-avoidance behavior known as root halotropism. Here we discuss these new aspects of light-mediated root behavior from cellular, physiological and evolutionary perspectives.

The actin cytoskeleton is a suppressor of the endogenous skewing behaviour of Arabidopsis primary roots in microgravity

Before plants can be effectively utilised as a component of enclosed life-support systems for space exploration, it is important to understand the molecular mechanisms by which they develop in microgravity. Using the Biological Research in Canisters (BRIC) hardware on board the second to the last flight of the Space Shuttle Discovery (STS-131 mission), we studied how microgravity impacts root growth in Arabidopsis thaliana. Ground-based studies showed that the actin cytoskeleton negatively regulates root gravity responses on Earth, leading us to hypothesise that actin might also be an important modulator of root growth behaviour in space. We investigated how microgravity impacted root growth of wild type (ecotype Columbia) and a mutant (act2-3) disrupted in a root-expressed vegetative actin isoform (ACTIN2). Roots of etiolated wild-type and act2-3 seedlings grown in space skewed vigorously toward the left, which was unexpected given the reduced directional cue provided by gravity. The left-handed directional root growth in space was more pronounced in act2-3 mutants than wild type. To quantify differences in root orientation of these two genotypes in space, we developed an algorithm where single root images were converted into binary images using computational edge detection methods. Binary images were processed with Fast Fourier Transformation (FFT), and histogram and entropy were used to determine spectral distribution, such that high entropy values corresponded to roots that deviated more strongly from linear orientation whereas low entropy values represented straight roots. We found that act2-3 roots had a statistically stronger skewing/coiling response than wild-type roots, but such differences were not apparent on Earth. Ultrastructural studies revealed that newly developed cell walls of space-grown act2-3 roots were more severely disrupted compared to space-grown wild type, and ground control wild-type and act2-3 roots. Collectively, our results provide evidence that, like root gravity responses on Earth, endogenous directional growth patterns of roots in microgravity are suppressed by the actin cytoskeleton. Modulation of root growth in space by actin could be facilitated in part through its impact on cell wall architecture.

Root apex transition zone as oscillatory zone

Root apex of higher plants shows very high sensitivity to environmental stimuli. The root cap acts as the most prominent plant sensory organ; sensing diverse physical parameters such as gravity, light, humidity, oxygen, and critical inorganic nutrients. However, the motoric responses to these stimuli are accomplished in the elongation region. This spatial discrepancy was solved when we have discovered and characterized the transition zone which is interpolated between the apical meristem and the subapical elongation zone. Cells of this zone are very active in the cytoskeletal rearrangements, endocytosis and endocytic vesicle recycling, as well as in electric activities. Here we discuss the oscillatory nature of the transition zone which, together with several other features of this zone, suggest that it acts as some kind of command center. In accordance with the early proposal of Charles and Francis Darwin, cells of this root zone receive sensory information from the root cap and instruct the motoric responses of cells in the elongation zone.

GSA-1/ARG1 protects root gravitropism in Arabidopsis under ammonium stress

Gravitropism plays a critical role in plant growth and development, plant stability and acclimation to changes in water and nutrient availability. Ammonium (NH4(+)) is well known to have profound effects on root growth, but its impacts on gravitropism are poorly understood. To determine which genes are essential for the maintenance of root gravitropism under NH4(+) stress, we isolated and identified an NH4 (+)-sensitive mutant, gsa-1 (gravitropism sensitive to ammonium-1), in Arabidopsis thaliana, using an agar plate root reorientation assay. We found that, under NH4(+) stress, gsa-1 displayed increased loss of root gravitropism. Gene cloning and sequencing revealed that gsa-1 contains a G to C transversion mutation at the highly conserved 5'-GT splice position of intron 10 of ARG1 (ALTERED RESPONSE TO GRAVITY1), known to participate in the transduction of the root gravity signal. Genetic complement tests established the locus of GSA-1/ARG1 and its role in resistance to NH4 (+) inhibition on root gravitropism. GSA-1/ARG1 is required for normal AUX1 expression and basipetal auxin transport in root apices. In addition, PIN-FORMED2 (PIN2) is proposed as a target in the reduction of root gravitropism under NH4(+) stress, a response which can be antagonized by the GSA-1/ARG1-dependent pathway. These results suggest that GSA-1/ARG1 protects root gravitropism in Arabidopsis thaliana under ammonium stress.