Food for thought: how nutrients regulate root system architecture

Tryptophan regulates sorghum root growth and enhances low nitrogen tolerance

Over evolutionary time, plants have developed sophisticated regulatory mechanisms to adapt to fluctuating nitrogen (N) environments, ensuring that their growth is balanced with their responses to N stress. This study explored the potential of L-tryptophan (Trp) in regulating sorghum root growth under conditions of N limitation. Here, two distinct sorghum genotypes (low-N tolerance 398B and low-N sensitive CS3541) were utilized for investigating effect of low-N stress on root morphology and conducting a comparative transcriptomics analysis. Our foundings indicated that 398B exhibited longer roots, greater root dry weights, and a higher Trp content compared to CS3541 under low-N conditions. Furthermore, transcriptome analysis revealed substantial differences in gene expression profiles related to Trp pathway and carbon (C) and N metabolism pathways between the two genotypes. Additional experiments were conducted to assess the effects of exogenous Trp treatment on the interplay between sorghum root growth and low-N tolerance. Our observations showed that Trp-treated plants developed longer root and had elevated levels of Trp and IAA under low-N conditons. Concurrently, these plants demonstrated stronger physiological activities in C and N metabolism when subjected to low-N stress. These results underscored the pivotal role of Trp on root growth and low-N stress responses by balancing IAA levels and C and N metabolism. This study not only deepens our understanding of how plants maintain growth plasticity during environmental stress but also provides valuable insights into the availability of amino acid in crops, which could be instrumental in developing strategies for promoting crop resilience to N deficiency.

Combined application of zinc oxide and iron nanoparticles enhanced Red Sails lettuce growth and antioxidants enzymes activities while reducing the chromium uptake by plants grown in a Cr-contaminated soil

Soil contamination with chromium (Cr) is becoming a primary ecological and health concern, specifically in the Kasur and Sialkot regions of Pakistan. The main objective of the current study was to evaluate the impact of foliar application of zinc oxide nanoparticles (ZnO NPs) (0, 25, 50, 100 mg L-1) and Fe NPs (0, 5, 10, 20 mg L-1) in red sails lettuce plants grown in Cr-contaminated soil. Our results showed that both ZnO and Fe NPs improved plant growth, and photosynthetic attributes by minimizing oxidative stress in lettuce plants through the stimulation of antioxidant enzyme activities. At ZnO NPs (100 mgL-1), dry weights of shoots and roots and fresh weights of shoots and roots were improved by 53%, 58%, 34%, and 45%, respectively, as compared to the respective control plants. The Fe NPs treatment (20 mgL-1) increased the dry weight of shoots and the roots and fresh weights of shoots and roots by 53%, 76%, 42%, and 70%, respectively. Application of both NPs reduced the oxidative stress caused by Cr, as evident by the findings of the current study, i.e., at the ZnO NPs (100 mgL-1) and Fe NPs (20 mgL-1), the EL declined by 32% and 44%, respectively, in comparison with respective control plants. Moreover, Fe and ZnO NPs enhanced the Fe and Zn contents in red sails lettuce plants. Application of ZnO NPs at 100 mg L-1 and Fe NPs at 20 mg L-1, improved the Zn and Fe contents in plant leaves by 86%, and 68%, respectively, as compared to the control plants. This showed that the exogenous application of these NPs helped in Zn and Fe fortification in plants. At similar of concenteration ZnO NPs, CAT and APX activities were improved by 52% and 53%, respectively. Similarly, the POD contents were improved by 17% and 45% at 5 and 10 mg/L of Fe NPs. Furthermore, ZnO and Fe NPs limited the Cr uptake by plants, and the concentration of Cr in the leaves of lettuce was under the threshold limit. The exogenous application of ZnO NPs (100 mg L-1) and Fe NPs (20 mg L-1) reduced the Cr uptake in the leaves of red sails lettuce by 57% and 51%, respectively. In conclusion, ZnO and Fe NPs could be used for the improvement of plant growth and biomass as well as nutrient fortification in stressed environments. These findings not only underscore the efficacy of nanoparticle-assisted phytoremediation but also highlight its broader implications for sustainable agriculture and environmental health. However, future studies on other crops with molecular-level investigations are recommended for the validation of the results.

Soil health reduction following the conversion of primary vegetation covers in a semi-arid environment

A degraded forest is the outcome of a degradation process that has adverse effects on ecosystem functions and services. This phenomenon results in alterations of soil physicochemical and biological properties, which serve as valuable indicators for assessing soil health that has been recognized as a crucial component of soil quality. For several decades, the conversion of forested areas into rangeland has been documented in specific regions of the world. There is a widespread lack of global understanding regarding the lasting consequences of land degradation on soil health indicators. The present study aims to investigate the impact of forest degradation on soil health indicators in a mountainous semi-arid region located in northern Iran. The study area was predominantly forested, but due to human activities over the past 30 years, it has been transformed into three distinct land uses: forest, forest-rangeland ecotones and rangeland. In each of these land covers, a total of 20 litter (O-horizon) and 20 soil (from two depths of 0-15 and 15-30 cm) samples were collected in the summer (August 2022) season. According to our results, the highest litter thickness, P and Mg were in forest ecosystem, the lowest in rangeland ecosystem. The findings indicated that following the conversion of forest to rangeland, there was a decrease in soil aggregate stability, porosity, soil organic matter, POC, PON, NH4+, NO3- and nutrient levels, while soil bulk density increased. The forest ecosystem showed notably higher C and N stocks (45 and 5.21 Mg ha-1) in comparison to the rangeland (38 and 3.32 Mg ha-1) ecosystem. In addition, P, K, Ca, and Mg exhibited elevated levels within the total root of the forest ecosystem (2.12, 1.23, 0.71, and 0.38 %, respectively), whereas the lower values (1.29, 1.01, 0.43, and 0.23 %, respectively) were found in the rangeland ecosystem. Following the shift of land cover from forest to rangeland, soil fauna, microflora populations, soil enzymes and microbial activities decreased (about 1-2 times higher in the forestland). This research emphasizes the urgent need to advance sustainable management practices to prevent further degradation and promote the implementation of restoration or rehabilitation techniques in degraded forests. Despite being conducted in a semi-arid region situated in northern Iran, the findings of this study have considerable value for the sustainable management of soil and land conservation in various other semi-arid regions around the world.

Trichoderma guizhouense NJAU4742 augments morphophysiological responses, nutrient availability and photosynthetic efficacy of ornamental Ilex verticillata

Winterberry holly (Ilex verticillata [L.] A. Gray), a deciduous shrub producing glossy bright red berries, is a valuable ornamental and medicinal plant with good market prospects. However, the growth and development of I. verticillata are significantly affected by various stresses, and environmentally hazardous agrochemicals are often used to mitigate them. Trichoderma spp., ubiquitous soil-borne eco-friendly plant growth-promoting fungi, are potent biostimulants and biofertilizers and viable alternatives to agrochemicals for healthy and sustainable agriculture. In this study, the temporal efficacy of different dosages of the filamentous fungus Trichoderma guizhouense NJAU4742 in promoting morphophysiological responses of I. verticillata and the physicochemical properties and enzymatic activities of the substrate were investigated. Different concentrations of the strain T. guizhouense NJAU4742 spore suspension (C [0%], T1 [5%, v/m], T2 [10%, v/m] and T3 [15%, v/m]) were injected in the substrate contained in a pot in which 1-year-old I. verticillata was planted for temporal treatment (15, 45 and 75 days) under open-air conditions. The beneficial effects of T2 and/or T3 treatment for a long duration (75 days) were evident on the different root, aerial and photosynthetic traits; total contents of nitrogen (N), phosphorus (P) and potassium (K) in different tissues and the physicochemical properties of the substrate and its enzymatic activities (urease and invertase). Overall, the study revealed the potency of strain T. guizhouense NJAU4742 as a sustainable solution to improve the growth and development and ornamental value of I. verticillata.

Paenibacillus lentimorbus alleviates nutrient deficiency-induced stress in Zea mays by modulating root system architecture, auxin signaling, and metabolic pathways

KEY MESSAGE

Paenibacillus lentimorbus reprograms auxin signaling and metabolic pathways for modulating root system architecture to mitigate nutrient deficiency in maize crops. The arable land across the world is having deficiency and disproportionate nutrients, limiting crop productivity. In this study, the potential of plant growth-promoting rhizobacteria (PGPR) viz., Pseudomonas putida, Paenibacillus lentimorbus, and their consortium was explored for growth promotion in maize (Zea mays) under nutrient-deficient conditions. PGPR inoculation improved the overall health of plants under nutrient-deficient conditions. The PGPR inoculation significantly improved the root system architecture and also induced changes in root cortical aerenchyma. Based on plant growth and physiological parameters inoculation with P. lentimorbus performed better as compared to P. putida, consortium, and uninoculated control. Furthermore, expression of auxin signaling (rum1, rul1, lrp1, rtcs, rtcl) and root hair development (rth)-related genes modulated the root development process to improve nutrient acquisition and tolerance to nutrient-deficient conditions in P. lentimorbus inoculated maize plants. Further, GC-MS analysis indicated the involvement of metabolites including carbohydrates and organic acids due to the interaction between maize roots and P. lentimorbus under nutrient-deficient conditions. These findings affirm that P. lentimorbus enhance overall plant growth by modulating the root system of maize to provide better tolerance to nutrient-deficient condition.

Root system architecture associated zinc variability in wheat (Triticum aestivum L.)

Root system architecture (RSA) plays a fundamental role in nutrient uptake, including zinc (Zn). Wheat grains are inheritably low in Zn. As Zn is an essential nutrient for plants, improving its uptake will not only improve their growth and yield but also the nutritional quality of staple grains. A rhizobox study followed by a pot study was conducted to evaluate Zn variability with respect to RSA and its impact on grain Zn concentration. The grain Zn content of one hundred wheat varieties was determined and grown in rhizoboxes with differential Zn (no Zn and 0.05 mg L-1 ZnSO4). Seedlings were harvested 12 days after sowing, and root images were taken and analyzed by SmartRoot software. Using principal component analysis, twelve varieties were screened out based on vigorous and weaker RSA with high and low grain Zn content. The screened varieties were grown in pots with (11 mg ZnSO4 kg-1 soil) and without Zn application to the soil. Zinc translocation, localization, and agronomic parameters were recorded after harvesting at maturity. In the rhizobox experiment, 4% and 8% varieties showed higher grain Zn content with vigorous and weaker RSA, respectively, while 45% and 43% varieties had lower grain Zn content with vigorous and weaker RSA. However, the pot experiment revealed that varieties with vigorous root system led to higher grain yield, though the grain Zn concentration were variable, while all varieties with weaker root system had lower yield as well as grain Zn concentration. Zincol-16 revealed the highest Zn concentration (28.07 mg kg-1) and grain weight (47.9 g). Comparatively higher level of Zn was localized in the aleurone layer than in the embryonic region and endosperm. It is concluded that genetic variability exists among wheat varieties for RSA and grain Zn content, with a significant correlation. Therefore, RSA attributes are promising targets for the Zn biofortification breeding program. However, Zn localization in endosperm needs to be further investigated to achieve the goal of reducing Zn malnutrition.

Potassium transporter KUP9 regulates plant response to K+ deficiency and affects carbohydrate allocation in A.thaliana

Due to the essential roles of K+ in plants, its up to 10% share in plant dry matter, and its mostly low availability in soil, effective potassium management poses a significant challenge for the plant. To enable efficient uptake and allocation of K+, numerous transporters and channels have evolved. During the last two decades, efforts have been made to characterise these transport proteins in Arabidopsis thaliana using knock-out mutants. Several KT/HAK/KUP transporters have been assigned specific functions. In this work, we contribute to an understanding of the role of AtKUP9 in plant adaptation to low K+ availability. We found that in vitro, atkup9 has reduced lateral root growth under low-K conditions, and root apical meristem proliferation is reduced in lateral roots compared with the primary root. We also documented AtKUP9 expression in both roots and shoots and showed that AtKUP9 expression is modulated during plant ontogeny and as a result of K+ deprivation. Altered carbohydrate allocation was also documented in atkup9. Mutants exported more soluble saccharides from leaves under K+ rich conditions and, under K+ deficiency, atkup9 accumulated more soluble saccharides in the shoots. A possible role of AtKUP9 in these processes is discussed.

Strategies of Molecular Signal Integration for Optimized Plant Acclimation to Stress Combinations

Plant growth and survival in their natural environment require versatile mitigation of diverse threats. The task is especially challenging due to the largely unpredictable interaction of countless abiotic and biotic factors. To resist an unfavorable environment, plants have evolved diverse sensing, signaling, and adaptive molecular mechanisms. Recent stress studies have identified molecular elements like secondary messengers (ROS, Ca2+, etc.), hormones (ABA, JA, etc.), and signaling proteins (SnRK, MAPK, etc.). However, major gaps remain in understanding the interaction between these pathways, and in particular under conditions of stress combinations. Here, we highlight the challenge of defining "stress" in such complex natural scenarios. Therefore, defining stress hallmarks for different combinations is crucial. We discuss three examples of robust and dynamic plant acclimation systems, outlining specific plant responses to complex stress overlaps. (a) The high plasticity of root system architecture is a decisive feature in sustainable crop development in times of global climate change. (b) Similarly, broad sensory abilities and apparent control of cellular metabolism under adverse conditions through retrograde signaling make chloroplasts an ideal hub. Functional specificity of the chloroplast-associated molecular patterns (ChAMPs) under combined stresses needs further focus. (c) The molecular integration of several hormonal signaling pathways, which bring together all cellular information to initiate the adaptive changes, needs resolving.

Monitoring nutrients in plants with genetically encoded sensors: achievements and perspectives

Understanding mechanisms of nutrient allocation in organisms requires precise knowledge of the spatiotemporal dynamics of small molecules in vivo. Genetically encoded sensors are powerful tools for studying nutrient distribution and dynamics, as they enable minimally invasive monitoring of nutrient steady-state levels in situ. Numerous types of genetically encoded sensors for nutrients have been designed and applied in mammalian cells and fungi. However, to date, their application for visualizing changing nutrient levels in planta remains limited. Systematic sensor-based approaches could provide the quantitative, kinetic information on tissue-specific, cellular, and subcellular distributions and dynamics of nutrients in situ that is needed for the development of theoretical nutrient flux models that form the basis for future crop engineering. Here, we review various approaches that can be used to measure nutrients in planta with an overview over conventional techniques, as well as genetically encoded sensors currently available for nutrient monitoring, and discuss their strengths and limitations. We provide a list of currently available sensors and summarize approaches for their application at the level of cellular compartments and organelles. When used in combination with bioassays on intact organisms and precise, yet destructive analytical methods, the spatiotemporal resolution of sensors offers the prospect of a holistic understanding of nutrient flux in plants.

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.

Biofortification of common bean (Phaseolus vulgaris L.) with iron and zinc: Achievements and challenges

Micronutrient deficiencies (hidden hunger), particularly in iron (Fe) and zinc (Zn), remain one of the most serious public health challenges, affecting more than three billion people globally. A number of strategies are used to ameliorate the problem of micronutrient deficiencies and to improve the nutritional profile of food products. These include (i) dietary diversification, (ii) industrial food fortification and supplements, (iii) agronomic approaches including soil mineral fertilisation, bioinoculants and crop rotations, and (iv) biofortification through the implementation of biotechnology including gene editing and plant breeding. These efforts must consider the dietary patterns and culinary preferences of the consumer and stakeholder acceptance of new biofortified varieties. Deficiencies in Zn and Fe are often linked to the poor nutritional status of agricultural soils, resulting in low amounts and/or poor availability of these nutrients in staple food crops such as common bean. This review describes the genes and processes associated with Fe and Zn accumulation in common bean, a significant food source in Africa that plays an important role in nutritional security. We discuss the conventional plant breeding, transgenic and gene editing approaches that are being deployed to improve Fe and Zn accumulation in beans. We also consider the requirements of successful bean biofortification programmes, highlighting gaps in current knowledge, possible solutions and future perspectives.

Decrypting the multi-functional biological activators and inducers of defense responses against biotic stresses in plants

Plant diseases are still the main problem for the reduction in crop yield and a threat to global food security. Additionally, excessive usage of chemical inputs such as pesticides and fungicides to control plant diseases have created another serious problem for human and environmental health. In view of this, the application of plant growth-promoting rhizobacteria (PGPR) for controlling plant disease incidences has been identified as an eco-friendly approach for coping with the food security issue. In this review, we have identified different ways by which PGPRs are capable of reducing phytopathogenic infestations and enhancing crop yield. PGPR suppresses plant diseases, both directly and indirectly, mediated by microbial metabolites and signaling components. Microbial synthesized anti-pathogenic metabolites such as siderophores, antibiotics, lytic enzymes, hydrogen cyanide, and several others act directly on phytopathogens. The indirect mechanisms of reducing plant disease infestation are caused by the stimulation of plant immune responses known as initiation of systemic resistance (ISR) which is mediated by triggering plant immune responses elicited through pathogen-associated molecular patterns (PAMPs). The ISR triggered in the infected region of the plant leads to the development of systemic acquired resistance (SAR) throughout the plant making the plant resistant to a wide range of pathogens. A number of PGPRs including Pseudomonas and Bacillus genera have proven their ability to stimulate ISR. However, there are still some challenges in the large-scale application and acceptance of PGPR for pest and disease management. Further, we discuss the newly formulated PGPR inoculants possessing both plant growth-promoting activities and plant disease suppression ability for a holistic approach to sustaining plant health and enhancing crop productivity.

The ROP2 GTPase Participates in Nitric Oxide (NO)-Induced Root Shortening in Arabidopsis

Nitric oxide (NO) is a versatile signal molecule that mediates environmental and hormonal signals orchestrating plant development. NO may act via reversible S-nitrosation of proteins during which an NO moiety is added to a cysteine thiol to form an S-nitrosothiol. In plants, several proteins implicated in hormonal signaling have been reported to undergo S-nitrosation. Here, we report that the Arabidopsis ROP2 GTPase is a further potential target of NO-mediated regulation. The ROP2 GTPase was found to be required for the root shortening effect of NO. NO inhibits primary root growth by altering the abundance and distribution of the PIN1 auxin efflux carrier protein and lowering the accumulation of auxin in the root meristem. In rop2-1 insertion mutants, however, wild-type-like root size of the NO-treated roots were maintained in agreement with wild-type-like PIN1 abundance in the meristem. The ROP2 GTPase was shown to be S-nitrosated in vitro, suggesting that NO might directly regulate the GTPase. The potential mechanisms of NO-mediated ROP2 GTPase regulation and ROP2-mediated NO signaling in the primary root meristem are discussed.

Auxin efflux carrier ZmPIN1a modulates auxin reallocation involved in nitrate-mediated root formation

BACKGROUND

Auxin plays a crucial role in nitrate (NO₃^-)-mediated root architecture, and it is still unclear that if NO₃^- supply modulates auxin reallocation for regulating root formation in maize (Zea mays L.). This study was conducted to investigate the role of auxin efflux carrier ZmPIN1a in the root formation in response to NO₃^- supply.

RESULTS

Low NO₃^- (LN) promoted primary root (PR) elongation, while repressed the development of lateral root primordia (LRP) and total root length. LN modulated auxin levels and polar transport and regulated the expression of auxin-responsive and -signaling genes in roots. Moreover, LN up-regulated the expression level of ZmPIN1a, and overexpression of ZmPIN1a enhanced IAA efflux and accumulation in PR tip, while repressed IAA accumulation in LRP initiation zone, which consequently induced LN-mediated PR elongation and LR inhibition. The inhibition rate of PR length, LRP density and number of ZmPIN1a-OE plants was higher than that of wild-type plants after auxin transport inhibitor NPA treatment under NN and LN conditions, and the degree of inhibition of root growth in ZmPIN1a-OE plants was more obvious under LN condition.

CONCLUSION

These findings suggest that ZmPIN1a was involved in modulating auxin levels and transport to alter NO₃^--mediated root formation in maize.

Integration of reactive oxygen species and nutrient signalling to shape root system architecture

Yield losses due to nutrient deficiency are estimated as the primary cause of the yield gap worldwide. Understanding how plant roots perceive external nutrient status and elaborate morphological adaptations in response to it is necessary to develop reliable strategies to increase crop yield. In the last decade, reactive oxygen species (ROS) were shown to be key players of the mechanisms underlying root responses to nutrient limitation. ROS contribute in multiple ways to shape the root system in response to nutritional cues, both as direct effectors acting on cell wall architecture and as second messengers in signalling pathways. Here, we review the mutual interconnections existing between perception and signalling of the most common forms of the major macronutrients (nitrogen, phosphorus and potassium), and ROS in shaping plant root system architecture. We discuss recent advances in dissecting the integration of these elements and their impact on morphological traits of the root system, highlighting the functional ductility of ROS and enzymes implied in ROS metabolism, such as class III peroxidases.

Molinia caerulea alters forest Quercus petraea seedling growth through reduced mycorrhization

Oak regeneration is jeopardized by purple moor grass, a well-known competitive perennial grass in the temperate forests of Western Europe. Below-ground interactions regarding resource acquisition and interference have been demonstrated and have led to new questions about the negative impact of purple moor grass on ectomycorrhizal colonization. The objective was to examine the effects of moor grass on root system size and ectomycorrhization rate of oak seedlings as well as consequences on nitrogen (N) content in oak and soil. Oak seedlings and moor grass tufts were planted together or separately in pots under semi-controlled conditions (irrigated and natural light) and harvested 1 year after planting. Biomass, N content in shoot and root in oak and moor grass as well as number of lateral roots and ectomycorrhizal rate in oak were measured. Biomass in both oak shoot and root was reduced when planting with moor grass. Concurrently, oak lateral roots number and ectomycorrhization rate decreased, along with a reduction in N content in mixed-grown oak. An interference mechanism of moor grass is affecting oak seedlings performance through reduction in oak lateral roots number and its ectomycorrhization, observed in conjunction with a lower growth and N content in oak. By altering both oak roots and mycorrhizas, moor grass appears to be a species with a high allelopathic potential. More broadly, these results show the complexity of interspecific interactions that involve various ecological processes involving the soil microbial community and need to be explored in situ.

SUE4, a novel PIN1-interacting membrane protein, regulates acropetal auxin transport in response to sulfur deficiency

Sulfur (S) is an essential macronutrient for plants and a signaling molecule in abiotic stress responses. It is known that S availability modulates root system architecture; however, the underlying molecular mechanisms are largely unknown. We previously reported an Arabidopsis gain-of-function mutant sulfate utilization efficiency4 (sue4) that could tolerate S deficiency during germination and early seedling growth with faster primary root elongation. Here, we report that SUE4, a novel plasma membrane-localized protein, interacts with the polar auxin transporter PIN1, resulting in reduced PIN1 protein levels and thus decreasing auxin transport to the root tips, which promotes primary root elongation. Moreover, SUE4 is induced by sulfate deficiency, consistent with its role in root elongation. Further analyses showed that the SUE4-PIN1 interaction decreased PIN1 levels, possibly through 26 S proteasome-mediated degradation. Taken together, our finding of SUE4-mediated root elongation is consistent with root adaptation to highly mobile sulfate in soil, thus revealing a novel component in the adaptive response of roots to S deficiency.

Propagation Methods Decide Root Architecture of Chinese Fir: Evidence from Tissue Culturing, Rooted Cutting and Seed Germination

The root is the main organ of a plant for absorbing resources and whose spatial distribution characteristics play an important role in the survival of seedlings after afforestation. Chinese fir (Cunninghamia lanceolata) is one of China’s most important plantation species. To clarify the effects of propagation methods on root growth and spatial distribution characteristics of Chinese fir trees, sampled trees cultivated by seed germination, tissue culture, and asexual cutting of Chinese fir were taken as the research objects. The root morphology, geometric configuration, and spatial distribution characteristics of different trees were analyzed. The influence of geometric root morphology on its spatial distribution pattern was explored by correlation analysis, and the resource acquisition characteristics reflected by the roots of Chinese fir trees with different propagation methods are discussed. The main results showed that the root mean diameter (1.56 mm, 0.95 mm, and 0.97 mm), root volume (2.98 m3, 10.25 m3, and 4.07 m3), root tip count (397, 522, and 440), main root branch angle (61°, 50° and 32°) and other geometric configurations of Chinese fir under seed germination, tissue culture and rooted cutting respectively, were significantly different, which resulted in different distribution characteristics of roots in space. Chinese fir seed germination had noticeable axial roots, and the growth advantage was obvious in the vertical direction. A fishtail branch structure (TI = 0.87) was constructed. The shallow root distribution of tissue culture and rooted cutting was obvious, and belonged to the fork branch structure (TI = 0.71 and 0.74, respectively). There was a tradeoff in the spatial growth of the root system of Chinese fir trees with different propagation methods to absorb nutrients from heterogeneous soil patches. A negative correlation was present between the root system and root amplitude. There was an opposite spatial growth trend of Chinese fir trees with different propagation methods in the vertical or horizontal direction. In conclusion, selecting suitable propagation methods to cultivate Chinese fir trees is beneficial to root development and the “ideal” configuration formation of resource acquisition to improve the survival rate of Chinese fir afforestation.

Multiple forms of vitamin B6 regulate salt tolerance by balancing ROS and abscisic acid levels in maize root

Salt stress causes osmotic stress, ion toxicity and oxidative stress, inducing the accumulation of abscisic acid (ABA) and excessive reactive oxygen species (ROS) production, which further damage cell structure and inhibit the development of roots in plants. Previous study showed that vitamin B6 (VB6) plays a role in plant responses to salt stress, however, the regulatory relationship between ROS, VB6 and ABA under salt stress remains unclear yet in plants. In our study, we found that salt stress-induced ABA accumulation requires ROS production, in addition, salt stress also promoted VB6 (including pyridoxamine (PM), pyridoxal (PL), pyridoxine (PN), and pyridoxal 5'-phosphate (PLP)) accumulation, which involved in ROS scavenging and ABA biosynthesis. Furthermore, VB6-deficient maize mutant small kernel2 (smk2) heterozygous is more susceptible to salt stress, and which failed to scavenge excessive ROS effectively or induce ABA accumulation in maize root under salt stress, interestingly, which can be restored by exogenous PN and PLP, respectively. According to these results, we proposed that PN and PLP play an essential role in balancing ROS and ABA levels under salt stress, respectively, it laid a foundation for VB6 to be better applied in crop salt resistance than ABA.

The Role of Sulfur in Agronomic Biofortification with Essential Micronutrients

Sulfur (S) is an essential macronutrient for plants, being necessary for their growth and metabolism and exhibiting diverse roles throughout their life cycles. Inside the plant body, S is present either in one of its inorganic forms or incorporated in an organic compound. Moreover, organic S compounds may contain S in its reduced or oxidized form. Among others, S plays roles in maintaining the homeostasis of essential micronutrients, e.g., iron (Fe), copper (Cu), zinc (Zn), and manganese (Mn). One of the most well-known connections is homeostasis between S and Fe, mainly in terms of the role of S in uptake, transportation, and distribution of Fe, as well as the functional interactions of S with Fe in the Fe-S clusters. This review reports the available information describing the connections between the homeostasis of S and Fe, Cu, Zn, and Mn in plants. The roles of S- or sulfur-derived organic ligands in metal uptake and translocation within the plant are highlighted. Moreover, the roles of these micronutrients in S homeostasis are also discussed.

Root penetration ability and plant growth in agroecosystems

Root penetration ability is critical for plant growth and development. When roots encounter soil impedance, hormones are activated that affect cells and tissues, leading to changes in root morphology and configuration that often increase root penetration ability. Factors, such as root system architecture, root anatomic traits, rhizosphere exudation and root-induced phytohormones, influencing root penetration ability and how they affect plant performance under soil impedance were summarized. Root penetration ability affects plant capturing water and nutrients, and thus determines plant performance and productivity in adverse environments. Great efforts have been made in searching for the underlying mechanisms of root penetration ability, and tools have been developed for phenotyping variability in root penetration ability. Therefore, with the continued development of agroecosystems based on the advocated low input costs and controlled tillage, crops or genotypes of a crop species with stronger root penetration ability may have the potential for developing new varieties with enhanced adaptation and grain yield under mechanical impedance in soil.

Lotus japonicus HAR1 regulates root morphology locally and systemically under a moderate nitrate condition in the absence of rhizobia

The local and long-distance signaling pathways mediated by the leucine-rich repeat receptor kinase HAR1 suppress root branching and promote primary root length in response to nitrate supply. The root morphology of higher plants changes plastically to effectively absorb nutrients and water from the soil. In particular, legumes develop root organ nodules, in which symbiotic rhizobia fix atmospheric nitrogen in nitrogen-poor environments. The number of nodules formed in roots is negatively regulated by a long-distance signaling pathway that travels through shoots called autoregulation of nodulation (AON). In the model plant Lotus japonicus, defects in AON genes, such as a leucine-rich repeat receptor kinase HYPERNODULATION ABERRANT ROOT FORMATION 1 (HAR1), an orthologue of CLAVATA1, and the F-box protein TOO MUCH LOVE (TML), induce the formation of an excess number of nodules. The loss-of-function mutant of HAR1 exhibits a short and bushy root phenotype in the absence of rhizobia. We show that the har1 mutant exhibits high nitrate sensitivity during root development. The uninfected har1 mutant significantly increased lateral root number and reduced primary root length in the presence of 3 mM nitrate, compared with the wild-type and tml mutant. Grafting experiments indicated that local and long-distance signaling pathways via root- and shoot-acting HAR1 additively regulated root morphology under the moderate nitrate concentrations. These findings allow us to propose that HAR1-mediated signaling pathways control the root system architecture by suppressing lateral root branching and promoting primary root elongation in response to nitrate availability.

NIN-Like Proteins: Interesting Players in Rhizobia-Induced Nitrate Signaling Response During Interaction with Non-Legume Host Arabidopsis thaliana

Nitrogen is an essential macronutrient and a key cellular messenger. Plants have evolved refined molecular systems to sense the cellular nitrogen status. This is exemplified by the root nodule symbiosis between legumes and symbiotic rhizobia, where nitrate availability inhibits this mutualistic interaction. Additionally, nitrate also functions as a metabolic messenger, resulting in nitrate signaling cascades which intensively crosstalk with other physiological pathways. Nodule inception-like proteins (NLPs) are key players in nitrate signaling and regulate nitrate-dependent transcription during legume-rhizobia interactions. Nevertheless, the coordinated interplay between nitrate signaling pathways and rhizobacteria-induced responses remains to be elucidated. In our study, we investigated rhizobia-induced changes in the root system architecture of the non-legume host arabidopsis under different nitrate conditions. We demonstrate that rhizobium-induced lateral root growth and increased root hair length and density are regulated by a nitrate-related signaling pathway. Key players in this process are AtNLP4 and AtNLP5, because the corresponding mutants failed to respond to rhizobia. At the cellular level, AtNLP4 and AtNLP5 control a rhizobia-induced decrease in cell elongation rates, while additional cell divisions occurred independently of AtNLP4. In summary, our data suggest that root morphological responses to rhizobia are coordinated by a newly considered nitrate-related NLP pathway that is evolutionarily linked to regulatory circuits described in legumes.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Integration of nutrient and water availabilities via auxin into the root developmental program

In most soils, the spatial distribution of nutrients and water in the rooting zone of plants is heterogeneous and changes over time. To access localized resources more efficiently, plants induce foraging responses by modulating individual morphological root traits, such as the length of the primary root or the number and length of lateral roots. These adaptive responses require the integration of exogenous and endogenous nutrient- or water-related signals into the root developmental program. Recent studies corroborated a central role of auxin in shaping root architectural traits in response to fluctuating nutrient and water availabilities. In this review, we highlight current knowledge on nutrient- and water-related developmental processes that impact root foraging and involve auxin as a central player. A deeper understanding and exploitation of these auxin-related processes and mechanisms promises advances in crop breeding for higher resource efficiency.

Nodulating white lupins take advantage of the reciprocal interplay between N and P nutritional responses

The low bioavailability of nutrients, especially nitrogen (N) and phosphorus (P), is one of the most limiting factors for crop production. In this study, under N- and P-free nutrient solution (-N-P), nodulating white lupin plants developed some nodules and analogous cluster root structures characterized by different morphological, physiological, and molecular responses than those observed upon single nutrient deficiency (strong acidification of external media, a better nutritional status than -N+P and +N-P plants). The multi-elemental analysis highlighted that the concentrations of nutrients in white lupin plants were mainly affected by P availability. Gene-expression analyses provided evidence of interconnections between N and P nutritional pathways that are active to promote N and P balance in plants. The root exudome was mainly characterized by N availability in nutrient solution, and, in particular, the absence of N and P in the nutrient solution triggered a high release of phenolic compounds, nucleosides monophosphate and saponines by roots. These morphological, physiological, and molecular responses result from a close interplay between N and P nutritional pathways. They contribute to the good development of nodulating white lupin plants when grown on N- and P-free media. This study provides evidence that limited N and P availability in the nutrient solution can promote white lupin-Bradyrhizobium symbiosis, which is favourable for the sustainability of legume production.

Diverse phosphate and auxin transport loci distinguish phosphate tolerant from sensitive Arabidopsis accessions

Phosphorus (P) is an essential element for plant growth often limiting agroecosystems. To identify genetic determinants of performance under variable phosphate (Pi) supply, we conducted genome-wide association studies on five highly predictive Pi starvation response traits in 200 Arabidopsis (Arabidopsis thaliana) accessions. Pi concentration in Pi-limited organs had the strongest, and primary root length had the weakest genetic component. Of 70 trait-associated candidate genes, 17 responded to Pi withdrawal. The PHOSPHATE TRANSPORTER1 gene cluster on chromosome 5 comprises PHT1;1, PHT1;2, and PHT1;3 with known impact on P status. A second locus featured uncharacterized endomembrane-associated auxin efflux carrier encoding PIN-LIKES7 (PILS7) which was more strongly suppressed in Pi-limited roots of Pi-starvation sensitive accessions. In the Col-0 background, Pi uptake and organ growth were impaired in both Pi-limited pht1;1 and two pils7 T-DNA insertion mutants, while Pi -limited pht1;2 had higher biomass and pht1;3 was indistinguishable from wild-type. Copy number variation at the PHT1 locus with loss of the PHT1;3 gene and smaller scale deletions in PHT1;1 and PHT1;2 predicted to alter both protein structure and function suggest diversification of PHT1 is a key driver for adaptation to P limitation. Haplogroup analysis revealed a phosphorylation site in the protein encoded by the PILS7 allele from stress-sensitive accessions as well as additional auxin-responsive elements in the promoter of the "stress tolerant" allele. The former allele's inability to complement the pils7-1 mutant in the Col-0 background implies the presence of a kinase signaling loop controlling PILS7 activity in accessions from P-rich environments, while survival in P-poor environments requires fine-tuning of stress-responsive root auxin signaling.

The potential use of Chlamydomonas reinhardtii and Chlorella sorokiniana as biostimulants on maize plants

Nitrogen deficiency and drought stress are among the major stresses faced by plants with negative consequence on crop production. The use of plant biostimulants is a very promising application in agriculture to improve crop yield, but especially to prevent the effect of abiotic stresses. Algae-derived biostimulants represent an efficient tool to stimulate the root development: while macroalgae have already been widely adopted as a source of biostimulants to improve plants growth and resilience, far less information is available for microalgae. The objective of this work is to investigate the stimulant ability on maize roots of two green algae species, Chlamydomonas reinhardtii and Chlorella sorokiniana, being respectively the model organism for Chlorophyta and one of the most promising species for microalgae cultivation at industrial scale. The results obtained demonstrate that both C. reinhardtii and C. sorokiniana cells promoted the development of maize root system compared to the untreated negative control. C. sorokiniana specifically increased the number of secondary roots, while improved micro-nutrients accumulation on roots and shoots was measured in the case of C. reinhardtii treated plants. When these microalgae-derived biostimulants were applied on plants grown in stress conditions as nitrogen deficiency, improved development of the root system was measured in the case of plants treated with C. sorokiniana biomass. Microalgae cultivation for biostimulant production can thus be considered as a bio-based process providing solutions for improving plant resilience toward stress conditions.

Evaluation of the relationship between root nutrients and root biomass in lands under different management practices

Mastering ecological dynamics necessitates identifying the substance cycles in biomass. In terms of sustainable soil productivity, the nutrient content of below-ground biomass is just as significant as the above-ground biomass, which fluctuates depending on land use. Yet, there were limited studies on determining the quantity of plant nutrient stocks, particularly in the below-ground biomass, in rangeland, forest, and plantation areas coexisting in the same ecological zone. In this regard, it is expected that the findings of this study will contribute to the literature. For this purpose in mind, distinct samples were taken from three depth levels (0-10 cm, 10-20 cm, 20-30 cm) to determine root biomass and nutrient stocks of roots in neighboring rangeland, forest, and plantation areas, and roots were divided into diameter classes, and below-ground biomass amounts and nutritional contents of below-ground biomass were determined. According to the results obtained, the total root biomass in the rangelands is 8.02 Mg ha^-1, total root biomass was 5.95 Mg ha^-1 in forest areas, and in plantation areas, the total root biomass is 6.94 Mg ha^-1. Root biomass in the 0-10 cm soil layer constituted 78% of the total biomass. Also, for all land uses, the highest below-ground biomass concentrations were observed for Al, Fe, K, Mg, and Ca. The amounts of Al, Fe, K and Mg in the below-ground biomass followed the sequence of rangeland, plantation, and forest from high to low. Nutrient stocks in below-ground biomass and the effects of increases in root biomass on plant growth should be evaluated by future studies.

Phosphate Suppression of Arbuscular Mycorrhizal Symbiosis Involves Gibberellic Acid Signaling

Most land plants entertain a mutualistic symbiosis known as arbuscular mycorrhiza with fungi (Glomeromycota) that provide them with essential mineral nutrients, in particular phosphate (Pi), and protect them from biotic and abiotic stress. Arbuscular mycorrhizal (AM) symbiosis increases plant productivity and biodiversity and is therefore relevant for both natural plant communities and crop production. However, AM fungal populations suffer from intense farming practices in agricultural soils, in particular Pi fertilization. The dilemma between natural fertilization from AM symbiosis and chemical fertilization has raised major concern and emphasizes the need to better understand the mechanisms by which Pi suppresses AM symbiosis. Here, we test the hypothesis that Pi may interfere with AM symbiosis via the phytohormone gibberellic acid (GA) in the Solanaceous model systems Petunia hybrida and Nicotiana tabacum. Indeed, we find that GA is inhibitory to AM symbiosis and that Pi may cause GA levels to increase in mycorrhizal roots. Consistent with a role of endogenous GA as an inhibitor of AM development, GA-defective N. tabacum lines expressing a GA-metabolizing enzyme (GA methyltransferase-GAMT) are colonized more quickly by the AM fungus Rhizoglomus irregulare, and exogenous Pi is less effective in inhibiting AM colonization in these lines. Systematic gene expression analysis of GA-related genes reveals a complex picture, in which GA degradation by GA2 oxidase plays a prominent role. These findings reveal potential targets for crop breeding that could reduce Pi suppression of AM symbiosis, thereby reconciling the advantages of Pi fertilization with the diverse benefits of AM symbiosis.

Can Inoculation With the Bacterial Biostimulant Enterobacter sp. Strain 15S Be an Approach for the Smarter P Fertilization of Maize and Cucumber Plants?

Phosphorus (P) is an essential nutrient for plants. The use of plant growth-promoting bacteria (PGPB) may also improve plant development and enhance nutrient availability, thus providing a promising alternative or supplement to chemical fertilizers. This study aimed to evaluate the effectiveness of Enterobacter sp. strain 15S in improving the growth and P acquisition of maize (monocot) and cucumber (dicot) plants under P-deficient hydroponic conditions, either by itself or by solubilizing an external source of inorganic phosphate (Pi) [Ca₃(PO₄)₂]. The inoculation with Enterobacter 15S elicited different effects on the root architecture and biomass of cucumber and maize depending on the P supply. Under sufficient P, the bacterium induced a positive effect on the whole root system architecture of both plants. However, under P deficiency, the bacterium in combination with Ca₃(PO₄)₂ induced a more remarkable effect on cucumber, while the bacterium alone was better in improving the root system of maize compared to non-inoculated plants. In P-deficient plants, bacterial inoculation also led to a chlorophyll content [soil-plant analysis development (SPAD) index] like that in P-sufficient plants (p < 0.05). Regarding P nutrition, the ionomic analysis indicated that inoculation with Enterobacter 15S increased the allocation of P in roots (+31%) and shoots (+53%) of cucumber plants grown in a P-free nutrient solution (NS) supplemented with the external insoluble phosphate, whereas maize plants inoculated with the bacterium alone showed a higher content of P only in roots (36%) but not in shoots. Furthermore, in P-deficient cucumber plants, all Pi transporter genes (CsPT1.3, CsPT1.4, CsPT1.9, and Cucsa383630.1) were upregulated by the bacterium inoculation, whereas, in P-deficient maize plants, the expression of ZmPT1 and ZmPT5 was downregulated by the bacterial inoculation. Taken together, these results suggest that, in its interaction with P-deficient cucumber plants, Enterobacter strain 15S might have solubilized the Ca₃(PO₄)₂ to help the plants overcome P deficiency, while the association of maize plants with the bacterium might have triggered a different mechanism affecting plant metabolism. Thus, the mechanisms by which Enterobacter 15S improves plant growth and P nutrition are dependent on crop and nutrient status.

Environmental and Cultivation Factors Affect the Morphology, Architecture and Performance of Root Systems in Soilless Grown Plants

Soilless culture systems are currently one of the fastest-growing sectors in horticulture. The plant roots are confined into a specific rootzone and are exposed to environmental changes and cultivation factors. The recent scientific evidence regarding the effects of several environmental and cultivation factors on the morphology, architecture, and performance of the root system of plants grown in SCS are the objectives of this study. The effect of root restriction, nutrient solution, irrigation frequency, rootzone temperature, oxygenation, vapour pressure deficit, lighting, rootzone pH, root exudates, CO2, and beneficiary microorganisms on the functionality and performance of the root system are discussed. Overall, the main results of this review demonstrate that researchers have carried out great efforts in innovation to optimize SCS water and nutrients supply, proper temperature, and oxygen levels at the rootzone and effective plant–beneficiary microorganisms, while contributing to plant yields. Finally, this review analyses the new trends based on emerging technologies and various tools that might be exploited in a smart agriculture approach to improve root management in soilless cropping while procuring a deeper understanding of plant root–shoot communication.

Genome-wide analysis of the soybean root transcriptome reveals the impact of nitrate on alternative splicing

In plants, nitrate acts not only as a signaling molecule that affects plant development but also as a nutrient. The development of plant roots, which directly absorb nutrients, is greatly affected by nitrate supply. Alternative gene splicing plays a crucial role in the plant stress response by increasing transcriptome diversity. The effects of nitrate supply on alternative splicing (AS), however, have not been investigated in soybean roots. We used high-quality high-throughput RNA-sequencing data to investigate genome-wide AS events in soybean roots in response to various levels of nitrate supply. In total, we identified 355 nitrate-responsive AS events between optimal and high nitrate levels (NH), 335 nitrate-responsive AS events between optimal and low nitrate levels (NL), and 588 nitrate-responsive AS events between low and high nitrate levels (NLH). RI and A3SS were the most common AS types; in particular, they accounted for 67% of all AS events under all conditions. This increased complex and diversity of AS events regulation might be associated with the soybean response to nitrate. Functional ontology enrichment analysis suggested that the differentially splicing genes were associated with several pathways, including spliceosome, base excision repair, mRNA surveillance pathway and so on. Finally, we validated several AS events using reverse transcription-polymerase chain reaction to confirm our RNA-seq results. In summary, we characterized the features and patterns of genome-wide AS in the soybean root exposed to different nitrate levels, and our results revealed that AS is an important mechanism of nitrate-response regulation in the soybean root.

Nitrate Modulates Lateral Root Formation by Regulating the Auxin Response and Transport in Rice

Nitrate (NO3-) plays a pivotal role in stimulating lateral root (LR) formation and growth in plants. However, the role of NO3- in modulating rice LR formation and the signalling pathways involved in this process remain unclear. Phenotypic and genetic analyses of rice were used to explore the role of strigolactones (SLs) and auxin in NO3--modulated LR formation in rice. Compared with ammonium (NH4+), NO3- stimulated LR initiation due to higher short-term root IAA levels. However, this stimulation vanished after 7 d, and the LR density was reduced, in parallel with the auxin levels. Application of the exogenous auxin α-naphthylacetic acid to NH4+-treated rice plants promoted LR initiation to levels similar to those under NO3- at 7 d; conversely, the application of the SL analogue GR24 to NH4+-treated rice inhibited LR initiation to levels similar to those under NO3- supply by reducing the root auxin levels at 10 d. D10 and D14 mutations caused loss of sensitivity of the LR formation response to NO3-. The application of NO3- and GR24 downregulated the transcription of PIN-FORMED 2(PIN2), an auxin efflux carrier in roots. LR number and density in pin2 mutant lines were insensitive to NO3- treatment. These results indicate that NO3- modulates LR formation by affecting the auxin response and transport in rice, with the involvement of SLs.

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.

SPL14/17 act downstream of strigolactone signalling to modulate rice root elongation in response to nitrate supply

Nitrogen (N) is an essential major nutrient for food crops. Although ammonium (NH₄⁺ ) is the primary N source of rice (Oryza sativa), nitrate (NO₃^- ) can also be absorbed and utilized. Rice responds to NO₃^- application by altering its root morphology, such as root elongation. Strigolactones (SLs) are important modulators of root length. However, the roles of SLs and their downstream genes in NO₃^- -induced root elongation remain unclear. Here, the levels of total N and SL (4-deoxyorobanchol) and the responses of seminal root (SR) lengths to NH₄⁺ and NO₃^- were investigated in rice plants. NO₃^- promoted SR elongation, possibly due to short-term signal perception and long-term nutrient function. Compared with NH₄⁺ conditions, higher SL signalling/levels and less D53 protein were recorded in roots of NO₃^- -treated rice plants. In contrast to wild-type plants, SR lengths of d mutants were less responsive to NO₃^- conditions, and application of rac-GR24 (SL analogue) restored SR length in d10 (SL biosynthesis mutant) but not in d3, d14, and d53 (SL-responsive mutants), suggesting that higher SL signalling/levels participate in NO₃^- -induced root elongation. D53 interacted with SPL17 and inhibited SPL17-mediated transactivation from the PIN1b promoter. Mutation of SPL14/17 and PIN1b caused insensitivity of the root elongation response to NO₃^- and rac-GR24 applications. Therefore, we conclude that perception of SLs by D14 leads to degradation of D53 via the proteasome system, which releases the suppression of SPL14/17-modulated transcription of PIN1b, resulting in root elongation under NO₃^- supply.

Friends, neighbours and enemies: an overview of the communal and social biology of plants

Plants were traditionally seen as rather passive actors in their environment, interacting with each other only in so far as they competed for the same resources. In the last 30 years, this view has been spectacularly overturned, with a wealth of evidence showing that plants actively detect and respond to their neighbours. Moreover, there is evidence that these responses depend on the identity of the neighbour, and that plants may cooperate with their kin, displaying social behaviour as complex as that observed in animals. These plant-plant interactions play a vital role in shaping natural ecosystems, and are also very important in determining agricultural productivity. However, in terms of mechanistic understanding, we have only just begun to scratch the surface, and many aspects of plant-plant interactions remain poorly understood. In this review, we aim to provide an overview of the field of plant-plant interactions, covering the communal interactions of plants with their neighbours as well as the social behaviour of plants towards their kin, and the consequences of these interactions. We particularly focus on the mechanisms that underpin neighbour detection and response, highlighting both progress and gaps in our understanding of these fascinating but previously overlooked interactions.

Looking for Root Hairs to Overcome Poor Soils

Breeding new cultivars allowing reduced fertilization and irrigation is a major challenge. International efforts towards this goal focus on noninvasive methodologies, platforms for high-throughput phenotyping of large plant populations, and quantitative description of root traits as predictors of crop performance in environments with limited water and nutrient availability. However, these high-throughput analyses ignore one crucial component of the root system: root hairs (RHs). Here, we review current knowledge on RH functions, mainly in the context of plant hydromineral nutrition, and take stock of quantitative genetics data pointing at correlations between RH traits and plant biomass production and yield components.

Biochemical and Genetic Approaches Improving Nitrogen Use Efficiency in Cereal Crops: A Review

Nitrogen is an essential nutrient required in large quantities for the proper growth and development of plants. Nitrogen is the most limiting macronutrient for crop production in most of the world's agricultural areas. The dynamic nature of nitrogen and its tendency to lose soil and environment systems create a unique and challenging environment for its proper management. Exploiting genetic diversity, developing nutrient efficient novel varieties with better agronomy and crop management practices combined with improved crop genetics have been significant factors behind increased crop production. In this review, we highlight the various biochemical, genetic factors and the regulatory mechanisms controlling the plant nitrogen economy necessary for reducing fertilizer cost and improving nitrogen use efficiency while maintaining an acceptable grain yield.

Compatibility of X-ray computed tomography with plant gene expression, rhizosphere bacterial communities and enzyme activities

Non-invasive X-ray computed tomography (XRCT) is increasingly used in rhizosphere research to visualize development of soil-root interfaces in situ. However, exposing living systems to X-rays can potentially impact their processes and metabolites. In order to evaluate these effects, we assessed the responses of rhizosphere processes 1 and 24 h after a low X-ray exposure (0.81 Gy). Changes in root gene expression patterns occurred 1 h after exposure with down-regulation of cell wall-, lipid metabolism-, and cell stress-related genes, but no differences remained after 24 h. At either time point, XRCT did not affect either root antioxidative enzyme activities or the composition of the rhizosphere bacterial microbiome and microbial growth parameters. The potential activities of leucine aminopeptidase and phosphomonoesterase were lower at 1 h, but did not differ from the control 24 h after exposure. A time delay of 24 h after a low X-ray exposure (0.81 Gy) was sufficient to reverse any effects on the observed rhizosphere systems. Our data suggest that before implementing novel experimental designs involving XRCT, a study on its impact on the investigated processes should be conducted.

Root-Apex Proton Fluxes at the Centre of Soil-Stress Acclimation

Proton (H⁺) fluxes in plant roots play critical roles in maintaining root growth and facilitating plant responses to multiple soil stresses, including fluctuations in nutrient supply, salt infiltration, and water stress. Soil mining for nutrients and water, rates of nutrient uptake, and the modulation of cell expansion all depend on the regulation of root H⁺ fluxes, particularly at the root apex, mediated primarily by the activity of plasma membrane (PM) H⁺-ATPases. Here, we summarize recent findings on the regulatory mechanisms of H⁺ fluxes at the root apex under three abiotic stress conditions - phosphate deficiency, salinity stress, and water deficiency - and present an integrated physiomolecular view of the functions of H⁺ fluxes in maintaining root growth in the acclimation to soil stress.

Root architecture and hydraulics converge for acclimation to changing water availability

Because of intense transpiration and growth, the needs of plants for water can be immense. Yet water in the soil is most often heterogeneous if not scarce due to more and more frequent and intense drought episodes. The converse context, flooding, is often associated with marked oxygen deficiency and can also challenge the plant water status. Under our feet, roots achieve an incredible challenge to meet the water demand of the plant's aerial parts under such dramatically different environmental conditions. For this, they continuously explore the soil, building a highly complex, branched architecture. On shorter time scales, roots keep adjusting their water transport capacity (their so-called hydraulics) locally or globally. While the mechanisms that directly underlie root growth and development as well as tissue hydraulics are being uncovered, the signalling mechanisms that govern their local and systemic adjustments as a function of water availability remain largely unknown. A comprehensive understanding of root architecture and hydraulics as a whole (in other terms, root hydraulic architecture) is needed to apprehend the strategies used by plants to optimize water uptake and possibly improve crops regarding this crucial trait.

Hormonal regulation of root hair growth and responses to the environment in Arabidopsis

The main functions of plant roots are water and nutrient uptake, soil anchorage, and interaction with soil-living biota. Root hairs, single cell tubular extensions of root epidermal cells, facilitate or enhance these functions by drastically enlarging the absorptive surface. Root hair development is constantly adapted to changes in the root's surroundings, allowing for optimization of root functionality in heterogeneous soil environments. The underlying molecular pathway is the result of a complex interplay between position-dependent signalling and feedback loops. Phytohormone signalling interconnects this root hair signalling cascade with biotic and abiotic changes in the rhizosphere, enabling dynamic hormone-driven changes in root hair growth, density, length, and morphology. This review critically discusses the influence of the major plant hormones on root hair development, and how changes in rhizosphere properties impact on the latter.

Signalling Overlaps between Nitrate and Auxin in Regulation of The Root System Architecture: Insights from the Arabidopsis thaliana

Nitrate (NO3-) and auxin are key regulators of root growth and development, modulating the signalling cascades in auxin-induced lateral root formation. Auxin biosynthesis, transport, and transduction are significantly altered by nitrate. A decrease in nitrate (NO3-) supply tends to promote auxin translocation from shoots to roots and vice-versa. This nitrate mediated auxin biosynthesis regulating lateral roots growth is induced by the nitrate transporters and its downstream transcription factors. Most nitrate responsive genes (short-term and long-term) are involved in signalling overlap between nitrate and auxin, thereby inducing lateral roots initiation, emergence, and development. Moreover, in the auxin signalling pathway, the varying nitrate supply regulates lateral roots development by modulating the auxin accumulation in the roots. Here, we focus on the roles of nitrate responsive genes in mediating auxin biosynthesis in Arabidopsis root, and the mechanism involved in the transport of auxin at different nitrate levels. In addition, this review also provides an insight into the significance of nitrate responsive regulatory module and their downstream transcription factors in root system architecture in the model plant Arabidopsis thaliana.

Cryptic variation in RNA-directed DNA-methylation controls lateral root development when auxin signalling is perturbed

Maintaining the right balance between plasticity and robustness in biological systems is important to allow adaptation while maintaining essential functions. Developmental plasticity of plant root systems has been the subject of intensive research, but the mechanisms underpinning robustness remain unclear. Here, we show that potassium deficiency inhibits lateral root organogenesis by delaying early stages in the formation of lateral root primordia. However, the severity of the symptoms arising from this perturbation varies within a natural population of Arabidopsis and is associated with the genetic variation in CLSY1, a key component of the RNA-directed DNA-methylation machinery. Mechanistically, CLSY1 mediates the transcriptional repression of a negative regulator of root branching, IAA27, and promotes lateral root development when the auxin-dependent proteolysis pathway fails. Our study identifies DNA-methylation-mediated transcriptional repression as a backup system for post-translational protein degradation which ensures robust development and performance of plants in a challenging environment.

Developmental plasticity of plant root systems has been intensively studied, but the mechanisms underpinning robustness remain unclear. Here, the authors show that DNA-methylation-mediated transcriptional repression serves as a backup system to control lateral root development when auxin signalling is perturbed.

Epigenetic regulation: another layer in plant nutrition

Uptake, assimilation, and recycling of nutrients are essential for optimal plant growth and development. A large number of studies have contributed significantly to highlight the major features that shape an efficient utilization of nutrients in plants, especially at the transcriptional level. However, only a few examples have explored the epigenetic mechanisms that are intrinsically associated to the transcriptional reprogramming events in response to nutritional fluctuations. In this review, we gather the chromatin-based mechanisms that have been described in response to variations of nutrients availability. At this time of genome and epigenome editing, such mechanisms could potentially represent new targets for crop improvement.

High-throughput three-dimensional visualization of root system architecture of rice using X-ray computed tomography

BACKGROUND

X-ray computed tomography (CT) allows us to visualize root system architecture (RSA) beneath the soil, non-destructively and in a three-dimensional (3-D) form. However, CT scanning, reconstruction processes, and root isolation from X-ray CT volumes, take considerable time. For genetic analyses, such as quantitative trait locus mapping, which require a large population size, a high-throughput RSA visualization method is required.

RESULTS

We have developed a high-throughput process flow for the 3-D visualization of rice (Oryza sativa) RSA (consisting of radicle and crown roots), using X-ray CT. The process flow includes use of a uniform particle size, calcined clay to reduce the possibility of visualizing non-root segments, use of a higher tube voltage and current in the X-ray CT scanning to increase root-to-soil contrast, and use of a 3-D median filter and edge detection algorithm to isolate root segments. Using high-performance computing technology, this analysis flow requires only 10 min (33 s, if a rough image is acceptable) for CT scanning and reconstruction, and 2 min for image processing, to visualize rice RSA. This reduced time allowed us to conduct the genetic analysis associated with 3-D RSA phenotyping. In 2-week-old seedlings, 85% and 100% of radicle and crown roots were detected, when 16 cm and 20 cm diameter pots were used, respectively. The X-ray dose per scan was estimated at < 0.09 Gy, which did not impede rice growth. Using the developed process flow, we were able to follow daily RSA development, i.e., 4-D RSA development, of an upland rice variety, over 3 weeks.

CONCLUSIONS

We developed a high-throughput process flow for 3-D rice RSA visualization by X-ray CT. The X-ray dose assay on plant growth has shown that this methodology could be applicable for 4-D RSA phenotyping. We named the RSA visualization method 'RSAvis3D' and are confident that it represents a potentially efficient application for 3-D RSA phenotyping of various plant species.

Transcriptome Changes Induced by Different Potassium Levels in Banana Roots

Potassium plays an important role in enhancing plant resistance to biological and abiotic stresses and improving fruit quality. To study the effect of potassium nutrient levels on banana root growth and its regulation mechanism, four potassium concentrations were designed to treat banana roots from no potassium to high potassium. The results indicated that K2 (3 mmol/L K2SO4) treatment was a relatively normal potassium concentration for the growth of banana root, and too high or too low potassium concentration was not conducive to the growth of banana root. By comparing the transcriptome data in each treatment in pairs, 4454 differentially expressed genes were obtained. There were obvious differences in gene function enrichment in root systems treated with different concentrations of potassium. Six significant expression profiles (profile 0, 1, 2, 7, 9 and 13) were identified by STEM analysis. The hub genes were FKF1, HsP70-1, NRT1/PTR5, CRY1, and ZIP11 in the profile 0; CYP51 in profile 1; SOS1 in profile 7; THA, LKR/SDH, MCC, C4H, CHI, F3'H, 2 PR1s, BSP, TLP, ICS, RO, chitinase and peroxidase in profile 9. Our results provide a comprehensive and systematic analysis of the gene regulation network in banana roots under different potassium stress.

Machine Learning Approaches to Improve Three Basic Plant Phenotyping Tasks Using Three-Dimensional Point Clouds

Developing automated methods to efficiently process large volumes of point cloud data remains a challenge for three-dimensional (3D) plant phenotyping applications. Here, we describe the development of machine learning methods to tackle three primary challenges in plant phenotyping: lamina/stem classification, lamina counting, and stem skeletonization. For classification, we assessed and validated the accuracy of our methods on a dataset of 54 3D shoot architectures, representing multiple growth conditions and developmental time points for two Solanaceous species, tomato (Solanum lycopersicum cv 75 m82D) and Nicotiana benthamiana Using deep learning, we classified lamina versus stems with 97.8% accuracy. Critically, we also demonstrated the robustness of our method to growth conditions and species that have not been trained on, which is important in practical applications but is often untested. For lamina counting, we developed an enhanced region-growing algorithm to reduce oversegmentation; this method achieved 86.6% accuracy, outperforming prior methods developed for this problem. Finally, for stem skeletonization, we developed an enhanced tip detection technique, which ran an order of magnitude faster and generated more precise skeleton architectures than prior methods. Overall, our improvements enable higher throughput and accurate extraction of phenotypic properties from 3D point cloud data.

Inoculation with the mycorrhizal fungus Rhizophagus irregularis modulates the relationship between root growth and nutrient content in maize (Zea mays ssp. mays L.)

Plant root systems play a fundamental role in nutrient and water acquisition. In resource-limited soils, modification of root system architecture is an important strategy to optimize plant performance. Most terrestrial plants also form symbiotic associations with arbuscular mycorrhizal fungi to maximize nutrient uptake. In addition to direct delivery of nutrients, arbuscular mycorrhizal fungi benefit the plant host by promoting root growth. Here, we aimed to quantify the impact of arbuscular mycorrhizal symbiosis on root growth and nutrient uptake in maize. Inoculated plants showed an increase in both biomass and the total content of twenty quantified elements. In addition, image analysis showed mycorrhizal plants to have denser, more branched root systems. For most of the quantified elements, the increase in content in mycorrhizal plants was proportional to root and overall plant growth. However, the increase in boron, calcium, magnesium, phosphorus, sulfur, and strontium was greater than predicted by root system size alone, indicating fungal delivery to be supplementing root uptake.