Search

Legumes balance nitrogen acquisition from soil nitrate with symbiotic nitrogen fixation. Nitrogen fixation requires establishment of a new organ, which is a cytokinin dependent developmental process in the root. We found cytokinin biosynthesis is a central integrator, balancing nitrate signalling with symbiotic acquired nitrogen. Low nitrate conditions provide a permissive state for induction of cytokinin by symbiotic signalling and thus nodule development. In contrast, high nitrate is inhibitory to cytokinin accumulation and nodule establishment in the root zone susceptible to nodule formation. This reduction of symbiotic cytokinin accumulation was further exacerbated in cytokinin biosynthesis mutants, which display hypersensitivity to nitrate inhibition of nodule development, maturation and nitrogen fixation. Consistent with this, cytokinin application rescues nodulation and nitrogen fixation of biosynthesis mutants in a concentration dependent manner. These inhibitory impacts of nitrate on symbiosis occur in a Nlp1 and Nlp4 dependent manner and contrast with the positive influence of nitrate on cytokinin biosynthesis that occurs in species that do not form symbiotic root nodules. Altogether this shows that legumes, as exemplified by Lotus japonicus, have evolved a different cytokinin response to nitrate compared to non-legumes., Nodule development in legumes is a cytokinin dependent process. Here the authors show that high nitrate supply, which limits nodulation, suppresses cytokinin biosynthesis in Lotus japonicus which contrasts with the positive effect of nitrate on cytokinin biosynthesis in non-legumes

One of the longest standing theories and, therein-based, regulation-model of plant root development, posits the inhibitory action of auxin (IAA, indolylacetic acid) on elongation growth of root cells. This effect, as induced by exogenously supplied IAA, served as the foundation stone for root growth regulation. For decades, auxin ruled the day and only allowed hormonal side players to be somehow involved, or in some way affected. However, this copiously reiterated, apparent cardinal role of auxin only applies in roots immersed in solutions; it vanishes as soon as IAA-supplied roots are not surrounded by liquid. When roots grow in humid air, exogenous IAA has no inhibitory effect on elongation growth of maize roots, regardless of whether it is applied basipetally from the top of the root or to the entire residual seedling immersed in IAA solution. Nevertheless, such treatment leads to pronounced root-borne ethylene emission and lateral rooting, illustrating and confirming thereby induced auxin presence and its effect on the root — yet, not on root cell elongation. Based on these findings, a new root growth regulatory model is proposed. In this model, it is not IAA, but IAA-triggered ethylene which plays the cardinal regulatory role — taking effect, or not — depending on the external circumstances. In this model, in water- or solution-incubated roots, IAA-dependent ethylene acts due to its accumulation within the root proper by inhibited/restrained diffusion into the liquid phase. In roots exposed to moist air or gas, there is no effect on cell elongation, since IAA-triggered ethylene diffuses out of the root without an impact on growth.

Summary Serendipita vermifera ssp. bescii, hereafter referred to as S. bescii, is a root‐associated fungus that promotes plant growth in both its native switchgrass host and a variety of monocots and dicots. Winter wheat (Triticum aestivum L.), a dual‐purpose crop, used for both forage and grain production, significantly contributes to the agricultural economies of the Southern Great Plains, USA. In this study, we investigated the influence of S. bescii on growth and transcriptome regulation of nitrogen (N) and phosphorus (P) metabolism in winter wheat. Serendipita bescii significantly improved lateral root growth and forage biomass under a limited N or P regime. Further, S. bescii activated sets of host genes regulating N and P starvation responses. These genes include, root‐specific auxin transport, strigolactone and gibberellin biosynthesis, degradation of phospholipids and biosynthesis of glycerolipid, downregulation of ammonium transport and nitrate assimilation, restriction of protein degradation by autophagy and subsequent N remobilization. All these genes are hypothesized to regulate acquisition, assimilation and remobilization of N and P. Based on transcriptional level gene regulation and physiological responses to N or P limitation, we suggest S. bescii plays a critical role in modulating stress imposed by limitation of these two critical nutrients in winter wheat.

The volatile organic compounds (VOCs) produced by soil microbes modulated plant growth and development. Floccularia luteovirens, an edible mushroom, is beneficial to the growth of alpine meadow plants on the Qinghai-Tibet Plateau. We aimed to elucidate the physiological and molecular mechanisms underlying the mushroom fungal VOC-mediated plant growth and development. Here, we investigated the effects of VOCs produced by F. luteovirens on the root system development and seedling growth by integrating physiology, genetics, transcriptome and metabolome analysis using 1/2 MS medium-grown Arabidopsis thaliana seedlings. Treatment with F. luteovirens VOCs reduce primary root growth by aggravating auxin accumulation through the repression of the abundance of auxin efflux carrier PIN-FORMED 2 (PIN2) protein, whereas it increases the lateral root number of A. thaliana seedlings. In addition to modulating root system architecture, treatment with F. luteovirens VOCs markedly increased aboveground growth. The transcriptome and metabolome analyses further supported the notion that F. luteovirens VOCs modulate plant growth and development through the induction of carbon/nitrogen metabolism and antioxidant defense while repressing several secondary metabolism and amino acid catabolism pathways. These results suggested that application of F. luteovirens VOCs promote growth by inducing changes in root system architecture through auxin pathway and regulating metabolism in plants.

Drought can activate many stress responses in plant growth and development, including the synthesis of epidermal wax and the induction of abscisic acid (ABA), and increased wax accumulation will improve plant drought resistance. Therefore, an examination of wax biosynthesis genes could help to better understand the molecular mechanism of environmental factors regulating wax biosynthesis and the wax associated stress response. Here, we identified the MdCER2 gene from the 'Gala' (Malus× domestica Borkh.) variety of domestic apple, which is a homolog of Arabidopsis AtCER2. It possesses a transferase domain and the protein localizes on the cell membrane. The MdCER2 gene was constitutively expressed in apple tissues and was induced by drought treatment. Finally, we transformed the MdCER2 gene into Arabidopsis to identify its function, and found ectopic expression of MdCER2 promoted accumulation of cuticular wax in both leaves and stems, decreased water loss and permeability in leaves, increased lateral root number, changed plant ABA sensitivity, and increased drought resistance.

The rice root system consists of three types of roots; main root, L-type and S-type lateral root (LR). These component roots are morphologically and histologically different, which is termed as heterorhizy. Root system hydraulic architecture is related to the unique features of component roots. We hypothesized that each component root contributes in different degrees to water uptake of the whole root system. Rice varieties IRAT 109 and Taichung 65 were grown in pots filled with soil under continuous waterlogged (CWL) and drought (CD) conditions until two weeks after heading. Morphology and histological structures of roots, which may regulate radial water movement, were compared among the three component roots. Moreover, hydraulic conductivity (Lpr) of the root system, which represents the water uptake ability, were measured with a pressure chamber. Based on a model that Lpr of the whole root system is a product of Lpr of each of the component roots and their surface areas, we found that the differences in Lpr between the two varieties and the plants grown under different soil water conditions for any of the component roots did not support the corresponding differences in the measured Lpr of the whole root system. In contrast, a significant and positive correlation was found between Lpr of the whole root system and the percentage of surface area of S-type LR but not for the other component roots. These results indicate S-type LR might have a higher contribution to Lpr of the whole root system than the other component roots.

Soil is a primary source of water and inorganic nutrients vital for plant growth. In particular, the rhizosphere, a microecological region around the plant roots, is enriched with root exudates that enable beneficial microbial communities to form. Plant growth-promoting rhizobacteria (PGPR) are rhizosphere bacteria that contribute to the improvement of plant growth through diverse physiological mechanisms. Identifying PGPR is beneficial for agriculture because their use can effectively increase the productivity of plants without the harmful side effects of chemical fertilizers. To further enrich the pool of PGPR that contribute to abiotic stress resistance in plants, we screened roughly 491 bacteria that had previously been isolated in soil from Gotjawal in Jeju island, South Korea. Among several candidates, the application of Bacillus subtilis strain GOT9, led to the enhancement of drought and salt stress tolerance in Arabidopsis. In agreement with the increased stress tolerance phenotypes, its application resulted in increases in the transcripts of various drought stress- and salt stress-inducible genes in the absence or presence of the stresses. Furthermore, the treatment resulted in improved lateral root growth and development in Arabidopsis. GOT9 also led to enhanced tolerance against drought and salt stresses and to upregulation of drought-inducible genes in Brassica, a closely related crop to Arabidopsis. Taken together, these results show that GOT9 could be utilized as a biotic resource that effectively minimizes damage to plants from environmental stresses.

Plant growth-promoting rhizobacteria (PGPR) stimulate plant growth, but the underlying mechanism is poorly understood. In this study, we asked whether PROTEIN PHOSPHATASE 2A (PP2A), a regulatory molecular component of stress, growth, and developmental signaling networks in plants, contributes to the plant growth responses induced by the PGPR Azospirillum brasilense (wild type strain Sp245 and auxin deficient strain FAJ0009) and Pseudomonas simiae (WCS417r). The PGPR were co-cultivated with Arabidopsis wild type (WT) and PP2A (related) mutants. These plants had mutations in the PP2A catalytic subunits (C), and the PP2A activity-modulating genes LEUCINE CARBOXYL METHYL TRANSFERASE 1 (LCMT1) and PHOSPHOTYROSYL PHOSPHATASE ACTIVATOR (PTPA). When exposed to the three PGPR, WT and all mutant Arabidopsis revealed the typical phenotype of PGPR-treated plants with shortened primary root and increased lateral root density. Fresh weight of plants generally increased when the seedlings were exposed to the bacteria strains, with the exception of catalytic subunit double mutant c2c5. The positive effect on root and shoot fresh weight was especially pronounced in Arabidopsis mutants with low PP2A activity. Comparison of different mutants indicated a significant role of the PP2A catalytic subunits C2 and C5 for a positive response to PGPR., The present study was supported by the Bionær program of the Research Council of Norway (‘Biofresh’ project no. 255613/E50).

When dealing with plant roots, a multiscale description of the functional root structure is needed. Since the beginning of 21st century, new devices such as laser confocal microscopes have been accessible for coarse root structure measurements, including three-dimensional (3D) reconstruction. Most researchers are familiar with using simple 2D geometry visualization that does not allow quantitative determination of key morphological features from an organ-like perspective. We provide here a detailed description of the quantitative methods available for 3D analysis of root features at single-cell resolution, including root asymmetry, lateral root analysis, cell size and nuclear organization, cell-cycle kinetics, and chromatin structure analysis. Quantitative maps of the root apical meristem (RAM) are shown for different species, including Arabidopsis thaliana (L.), Heynh, Nicotiana tabacum L., Medicago sativa L., and Setaria italica (L.) P. Beauv. The 3D analysis of the RAM in these species showed divergence in chromatin organization and cell volume distribution that might be used to study root zonation for each root tissue. Detailed protocols and possible pitfalls in the usage of the marker lines are discussed. Therefore, researchers who need to improve their quantitative root biology portfolio can use them as a reference.

Fusarium oxysporum, a global soil-borne pathogen, causes severe disease in various cultivated plants. The mechanism underlying infection and resistance remains largely elusive. Vernicia fordii, known as the tung tree, suffers from disease caused by F. oxysporum f. sp. fordiis (Fof-1), while its sister species V. montana displays high resistance to Fof-1. To investigate the process of infection and resistance ability, we demonstrated that Fof-1 can penetrate the epidermis of root hairs and then centripetally invade the cortex and phloem in both species. Furthermore, Fof-1 spread upwards through the root xylem in susceptible V. fordii trees, whereas it failed to infect the root xylem in resistant V. montana trees. We found that D6 PROTEIN KINASE LIKE 2 (VmD6PKL2) was specifically expressed in the lateral root xylem and was induced after Fof-1 infection in resistant trees. Transgenic analysis in Arabidopsis and tomato revealed that VmD6PKL2 significantly enhanced resistance in both species, whereas the d6pkl2 mutant displayed reduced resistance against Fof-1. Additionally, VmD6PKL2 was identified to interact directly with synaptotagmin (VmSYT3), which is specifically expressed in the root xylem and mediates the negative regulation responding to Fof-1. Our data suggested that VmD6PKL2 could act as a resistance gene against Fof-1 through suppression of VmSYT3-mediated negative regulation in the lateral root xylem of the resistant species. These findings provide novel insight into Fusarium wilt resistance in plants.

Shade-intolerant plants rapidly elongate their stems, branches, and leaf stalks to compete with neighboring vegetation, maximizing sunlight capture for photosynthesis. This rapid growth adaptation, known as the shade-avoidance response (SAR), comes at a cost: reduced biomass, crop yield, and root growth. Significant progress has been made on the mechanistic understanding of hypocotyl elongation during SAR; however, the molecular interpretation of root growth repression is not well understood. Here, we explore the mechanisms by which SAR induced by low red:far-red light restricts primary and lateral root (LR) growth. By analyzing the whole-genome transcriptome, we identified a core set of shade-induced genes in roots of Arabidopsis (Arabidopsis thaliana) and tomato (Solanum lycopersicum) seedlings grown in the shade. Abiotic and biotic stressors also induce many of these shade-induced genes and are predominantly regulated by WRKY transcription factors. Correspondingly, a majority of WRKY genes were among the shade-induced genes. Functional analysis using transgenics of these shade-induced WRKYs revealed that their role is essentially to restrict primary root and LR growth in the shade; captivatingly, they did not affect hypocotyl elongation. Similarly, we also found that ethylene hormone signaling is necessary for limiting root growth in the shade. We propose that during SAR, shade-induced WRKY26, 45, and 75, and ethylene reprogram gene expression in the root to restrict its growth and development.

SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors play critical roles in regulating diverse aspects of plant growth and development, including vegetative phase change, plant architecture, anthocyanin accumulation, lateral root growth, etc. In the present study, 15 SPL genes were identified based on the genome data of Codonopsis pilosula, a well-known medicinal plant. Phylogenetic analysis clustered CpSPLs into eight groups (G1-G8) along with SPLs from Arabidopsis thaliana, Solanum lycopersicum, Oryza sativa and Physcomitrella patens. CpSPLs in the same group share similar gene structure and conserved motif composition. Cis-acting elements responding to light, stress and phytohormone widely exist in their promoter regions. Our qRT-PCR results indicated that 15 CpSPLs were differentially expressed in different tissues (root, stem, leaf, flower and calyx), different developmental periods (1, 2 and 3 months after germination) and various conditions (NaCl, MeJA and ABA treatment). Compared with the control, overexpression of CpSPL2 or CpSPL10 significantly promoted not only the growth of hairy roots, but also the accumulation of total saponins and lobetyolin. Our results established a foundation for further investigation of CpSPLs and provided novel insights into their biological functions. As far as we know, this is the first experimental research on gene function in C. pilosula.

miR390 is a highly conserved miRNA in plant lineages known to function in growth and development processes, such as lateral root development, and in responses to salt and metal stress. In the ecological model species, Nicotiana attenuata, miR390's biological function remains unknown, which we explore here with a gain‐of‐function analysis with plants over‐expressing (OE‐) N. attenuata miR390 (Na‐miR390) in glasshouse and natural environments. OEmiR390 plants showed normal developmental processes, including lateral root formation or reproductive output, in plants grown under standard conditions in the glasshouse. OEmiR390 plants did not have dramatically altered interactions with arbuscular mycorrhizal fungi (AMF), Fusarium pathogens, or herbivores. However, Na‐miR390 regulated the plant's tolerance of herbivory. Caterpillar feeding elicits the accumulation of a suite of phytohormones, including auxin and jasmonates, which further regulate host‐tolerance. The increase in Na‐miR390 abundance reduces the accumulation of auxin but does not influence levels of other phytohormones including jasmonates (JA, JA‐Ile), salicylic acid (SA), and abscisic acid (ABA). Na‐miR390 overexpression reduces reproductive output, quantified as capsule production, when plants are attacked by herbivores. Exogenous auxin treatments of herbivore‐attacked plants restored capsule production to wild‐type levels. During herbivory, Na‐miR390 transcript abundances are increased; its overexpression reduces the abundances of auxin biosynthesizing YUCCA and ARF (mainly ARF4) transcripts during herbivory. Furthermore, the accumulation of auxin‐regulated phenolamide secondary metabolites (caffeoylputrescine, dicaffeoylspermidine) is also reduced. In N. attenuata, miR390 functions in modulating tolerance responses of herbivore‐attacked plants.

Background and aims Kandelia obovata, a dominant mangrove species in China, produces complex buttress roots and prop roots in intertidal wetlands where high quantities of nitric oxide (NO) are produced by reducing sediments. NO, a key signaling molecule, participates in an array of plant physiological and developmental processes. However, it is unclear whether NO functions in K. obovata root system establishment. Methods Here, we used a transcriptomic approach to investigate the potential role of NO in the regulation of K. obovata lateral root development and growth. Transcript profiles and bioinformatics analyses were used to characterize potential regulatory mechanisms. Results NO enhanced K. obovata lateral root development and growth in a dose-dependent manner. RNA-seq analysis identified 1,593 differentially expressed genes (DEGs), of which 646 and 947 were up- and down-regulated in roots treated with NO donor. Functional annotation analysis demonstrated that the starch and sucrose pathway was significantly induced in response to NO. A suite of DEGs involved in hormone signal transduction and cell wall metabolism was also differentially regulated by NO. Taken together, our results suggest that a complex interaction between energy metabolism, multiple hormone signaling pathways, and cell wall biosynthesis is required for the NO regulation on lateral root development and growth in mangrove plant K. obovata. Conclusion NO appears to contribute to the formation of the unique root system of mangrove plants.

Hydrogen sulfide (H2S) is considered the third gas signal molecule in recent years. A large number of studies have shown that H2S not only played an important role in animals but also participated in the regulation of plant growth and development and responses to various environmental stresses. Waterlogging, as a kind of abiotic stress, poses a serious threat to land-based waterlogging-sensitive plants, and which H2S plays an indispensable role in response to. In this review, we summarized that H2S improves resistance to waterlogging stress by affecting lateral root development, photosynthetic efficiency, and cell fates. Here, we reviewed the roles of H2S in plant resistance to waterlogging stress, focusing on the mechanism of its promotion to gained hypoxia tolerance. Finally, we raised relevant issues that needed to be addressed.

The interaction between legume plants and soil bacteria rhizobia results in the formation of new organs on the plant roots, symbiotic nodules, where rhizobia fix atmospheric nitrogen. Symbiotic nodules represent a perfect model to trace how the pre-existing regulatory pathways have been recruited and modified to control the development of evolutionary “new” organs. In particular, genes involved in the early stages of lateral root development have been co-opted to regulate nodule development. Other regulatory pathways, including the players of the KNOX-cytokinin module, the homologues of the miR172-AP2 module, and the players of the systemic response to nutrient availability, have also been recruited to a unique regulatory program effectively governing symbiotic nodule development. The role of the NIN transcription factor in the recruitment of such regulatory modules to nodulation is discussed in more details.

To date, synthetic herbicides are the main tools used for weed control, with consequent damage to both the environment and human health. In this respect, searching for new natural molecules and understanding their mode of action could represent an alternative strategy or support to traditional management methods for sustainable agriculture. Protodioscin is a natural molecule belonging to the class of steroid saponins, mainly produced by monocotyledons. In the present paper, protodioscin’s phytotoxic potential was assessed to identify its target and the potential mode of action in the model plant Arabidopsis thaliana. The results highlighted that the root system was the main target of protodioscin, which caused a high inhibitory effect on the primary root length (ED50 50 μM) with morphological alteration, accompanied by a significant increase in the lateral root number and root hair density. Through a pharmacological and microscopic approach, it was underlined that this saponin modified both auxin distribution and transport, causing an auxin accumulation in the region of root maturation and an alteration of proteins responsible for the auxin efflux (PIN2). In conclusion, the saponin protodioscin can modulate the root system of A. thaliana by interfering with the auxin transport (PAT).

Background The root distribution in the soil is one of the elements that comprise the root system architecture (RSA). In monocots, RSA comprises radicle and crown roots, each of which can be basically represented by a single curve with lateral root branches or approximated using a polyline. Moreover, RSA vectorization (polyline conversion) is useful for RSA phenotyping. However, a robust software that can enable RSA vectorization while using noisy three-dimensional (3D) volumes is unavailable. Results We developed RSAtrace3D, which is a robust 3D RSA vectorization software for monocot RSA phenotyping. It manages the single root (radicle or crown root) as a polyline (a vector), and the set of the polylines represents the entire RSA. RSAtrace3D vectorizes root segments between the two ends of a single root. By utilizing several base points on the root, RSAtrace3D suits noisy images if it is difficult to vectorize it using only two end nodes of the root. Additionally, by employing a simple tracking algorithm that uses the center of gravity (COG) of the root voxels to determine the tracking direction, RSAtrace3D efficiently vectorizes the roots. Thus, RSAtrace3D represents the single root shape more precisely than straight lines or spline curves. As a case study, rice (Oryza sativa) RSA was vectorized from X-ray computed tomography (CT) images, and RSA traits were calculated. In addition, varietal differences in RSA traits were observed. The vector data were 32,000 times more compact than raw X-ray CT images. Therefore, this makes it easier to share data and perform re-analyses. For example, using data from previously conducted studies. For monocot plants, the vectorization and phenotyping algorithm are extendable and suitable for numerous applications. Conclusions RSAtrace3D is an RSA vectorization software for 3D RSA phenotyping for monocots. Owing to the high expandability of the RSA vectorization and phenotyping algorithm, RSAtrace3D can be applied not only to rice in X-ray CT images but also to other monocots in various 3D images. Since this software is written in Python language, it can be easily modified and will be extensively applied by researchers in this field.

Background Moso bamboo, the fastest growing plant on earth, is an important source for income in large areas of Asia, mainly cultivated in China. Lateral organ boundaries domain (LBD) proteins, a family of transcription factors unique to plants, are involved in multiple transcriptional regulatory pathways and play important roles in lateral organ development, pathogen response, secondary growth, and hormone response. The LBD gene family has not previously been characterized in moso bamboo (Phyllostachys edulis). Results In this study, we identified 55 members of the LBD gene family from moso bamboo and found that they were distributed non-uniformly across its 18 chromosomes. Phylogenetic analysis showed that the moso bamboo LBD genes could be divided into two classes. LBDs from the same class share relatively conserved gene structures and sequences encoding similar amino acids. A large number of hormone response–associated cis-regulatory elements were identified in the LBD upstream promoter sequences. Synteny analysis indicated that LBDs in the moso bamboo genome showed greater collinearity with those of O. sativa (rice) and Zea mays (maize) than with those of Arabidopsis and Capsicum annuum (pepper). Numerous segmental duplicates were found in the moso bamboo LBD gene family. Gene expression profiles in four tissues showed that the LBD genes had different spatial expression patterns. qRT–PCR assays with the Short Time-series Expression Miner (STEM) temporal expression analysis demonstrated that six genes (PeLBD20, PeLBD29, PeLBD46, PeLBD10, PeLBD38, and PeLBD06) were consistently up-regulated during the rapid growth and development of bamboo shoots. In addition, 248 candidate target genes that function in a variety of pathways were identified based on consensus LBD binding motifs. Conclusions In the current study, we identified 55 members of the moso bamboo transcription factor LBD and characterized for the first time. Based on the short-time sequence expression software and RNA-seq data, the PeLBD gene expression was analyzed. We also investigated the functional annotation of all PeLBDs, including PPI network, GO, and KEGG enrichment based on String database. These results provide a theoretical basis and candidate genes for studying the molecular breeding mechanism of rapid growth of moso bamboo.

Shade-intolerant plants rapidly elongate their stems, branches, and leaf stalks to compete with their neighboring vegetation to maximize sunlight capture for photosynthesis. This rapid growth adaptation, known as the shade avoidance response (SAR), comes at a cost; reduced biomass, crop yield, and root growth. Significant progress has been made on the mechanistic understanding of hypocotyl elongation during SAR; however, the molecular account of how root growth is repressed is not well understood. Here, we explore the mechanisms by which low red:far-red induced SAR restrict the primary and lateral root (LR) growth. By analyzing whole-genome transcriptome, we identified a core set of shade-induced genes in the roots of Arabidopsis and tomato seedlings grown in the shade. Abiotic and biotic stressors also induce many of these shade-induced genes and are predominantly regulated by the WRKY transcription factors. Correspondingly, a majority of the WRKYs were also among the shade-induced genes. Functional analysis using transgenics of these shade-induced WRKYs revealed their role is essentially to restrict primary root and LR growth in the shade, and captivatingly, they did not affect hypocotyl elongation. Similarly, we also show that ethylene hormone signaling is necessary to limit root growth in the shade. Our study proposes that during SAR, shade-induced WRKY26, 45, and 75, and ethylene reprogram gene expression in the root to restrict its growth and development. The reduced growth of root organs helps the plant divert its critical resources to the elongating organs in the shoot to ensure competitiveness under limiting photosynthetic radiation.One sentence summaryShade represses root growth by inducing WRKY transcription factors.

Mycorrhizal helper bacteria (MHB) play an important role in mediating mycorrhizal symbiosis, which improves the growth and nutrient uptake of plants. This study examined the growth-promoting effects and mechanisms of pine growth after inoculation with the MHB Bacillus pumilus HR10 and/or Hymenochaete sp. Rl. The effect of B. pumilus HR10 on Hymenochaete sp. Rl growth, enzyme activity and gene expression related to mycorrhiza formation were determined. The growth, root activity, nitrogen, phosphorus, and potassium content and chlorophyll fluorescence activity of Pinus thunbergii and the mycorrhizal colonization intensity of Hymenochaete sp. Rl-inoculated pine seedlings after inoculation with B. pumilus HR10 were also evaluated. The results showed that B. pumilus HR10 promoted growth, regulated the expression of mycorrhizal-related genes and affected the β-1,3-glucanase activity of Hymenochaete sp. Rl. The mycorrhizal colonization intensity of pine seedlings co-inoculated with B. pumilus HR10 and Hymenochaete sp. Rl was 1.58-fold higher than seedlings inoculated with only Hymenochaete sp. Rl. Inoculation with B. pumilus HR10 and/or Hymenochaete sp. Rl increased lateral root number and root activity of pine seedlings and chlorophyll fluorescence activity of pine needles compared with the control. Bacillus pumilus HR10 facilitated nutrient uptake by enhancing the mycorrhizal proliferation of pine and induced greater photosynthesis and root activity of pine seedlings, which confirms its role as an outstanding plant-growth-promoting rhizobacterium. These findings improve our understanding of the mechanism of B. pumilus HR10 promotion of mycorrhizal symbiosis.

C4 photosynthesis increases the efficiency of carbon fixation by spatially separating high concentrations of molecular oxygen from rubisco. The specialized leaf anatomy required for this separation evolved independently many times. C4 root systems are highly branched, an adaptation thought to support high rates of photosynthesis; however, little is known about the molecular mechanisms that have driven the evolution of C4 root system architecture (RSA). Using a mutant screen in the C4 model plant Setaria italica, we identify siaux1-1 and siaux1-2 as RSA mutants, and use CRISPR/cas9-mediated genome editing and overexpression to confirm the importance of the locus. As AUX1 is not necessary for lateral root emergence in S. viridis, the species from which S. italica was domesticated, we conducted an analysis of auxin responsive elements in the promoters of auxin-responsive gene families in S. italica, and explore the molecular basis of SiAUX1’s role in seedling development using an RNAseq analysis of wild type and siaux1-1 plants. Finally, we use a root coordinate system to compare cell-by-cell meristem structures in siaux1-1 and wild type Setaria plants, observing changes in the distribution of cell volumes in all cell layers and a dependence in the frequency of protophloem and protoxylem strands on siAUX1.

Summary Vesicular-arbuscular (VA) mycorrhizal fungi and ectomycorrhizal fungi were observed together in the same root system, and even within the same root apices, of seedlings of Eucalyptus dumosa A. Cunn. ex Schau. On a population basis, there was a succession of two overlapping mycorrhizal epidemics-VA mycorrhizas followed by ectomycorrhizas. This succession was interpreted as follows. Early build-up of VA mycorrhizas was related to initial higher inoculum potential of that fungus and to rapidity of colonization of individual roots. The ectomycorrhizal fungus was more successful later in achieving secondary infections by hyphal spread and in colonization of lateral root branches. The ectomycorrhizal fungus had no difficulty infecting pre-existing VA mycorrhizas, but the ectomycorrhizal sheath provided a barrier to subsequent VA mycorrhizal infections. While the proportion of VA mycorrhizas to ectomycorrhizas changed between two and five months, the overall proportion of mycorrhizal roots remained constant, suggesting that there could be competition between the different fungi for limiting substrate.

SUMMARY Low activities of the monomeric aluminium (Al) species, Al3+, Al(OH)2+ and Al(OH)2+ in solution reduce root growth and root hair development in soybean [Glycine max (L.) Merr.]. Calcium (Ca) ameliorates to a certain extent the toxic effects of Al on root growth, but the interactive effects of Ca and Al on root hair development are not known. In the absence of added Al in solution culture, Ca concentration over the range 500–2000 μM had little effect on root growth or root hair development of soybean cv. Fitzroy. Where the sum of the activities of the monomeric Al species was 2 μM, taproot elongation and lateral root development of soybean was suppressed in solution with 500 μM Ca. The length of the root hair zone was only 10% of that in plants not exposed to Al, and scanning electron microscopy revealed a low density of root hairs. Increasing the Ca concentration to 2000 μM largely overcame these deleterious effects. The results are discussed in relation to the role of root hairs as infection sites for Bradyrhizobium, and the known effects of Al in suppressing nodulation in soybean.

Homogeneously developed oak (Quercus robur L.) microcuttings were challenged in a Petri-dish system with the mycobionts Piloderma croceum J. Erikss. & Hjortst. and Paxillus involutus (Batsch) Fr. Non-destructive observations over 10 wk followed by d. wt measurements at the end of the assays served to precisely characterize root and shoot development, dynamics of mycorrhizal colonization and morphological ratio. In the system, plant development, and especially root morphogenesis, had more similarities to those of stump cuttings or of older seedlings than to those of 3-month-old seedlings. Whereas Paxillus involutus displayed early mycorrhizal colonization and had no significant morphological effects on the host Piloderma croceum modified markedly the entire plant development before a delayed mycorrhiza formation. The latter mycobiont stimulated elongation and production of the lateral root system and also increased the leaf surface. However, no corresponding weight increases were noted, which was reflected by significant increase of both specific root length and specific leaf area. These differential effects are discussed in relation to data concerning carbon requirement and auxin production of the mycobionts. The developed system was shown to be highly suitable for comparative studies with diverse mycobionts on recognition and physiological balance between partners before, and in the early stage of, formation of mycorrhizas.

We identified IAA13 negatively associated with lateral root number by comparing the differential expressed genes between Bupleurum chinense and B. scorzonerifolium. Dried roots of the genus Bupleurum L. are used as a herbal medicine for diseases in Asia. Bupleurum chinense has a greater number of lateral roots than B. scorzonerifolium, but the genetic mechanisms for such differences are largely unknown. We (a) compared the transcriptome profiles of the two species and (b) identified a subset of candidate genes involved in auxin signal transduction and explored their functions in lateral root development. By isoform sequencing (Iso-Seq) analyses of the whole plant, more unigenes were found in B. scorzonerifolium (118,868) than in B. chinense (93,485). Given the overarching role of indole-3-acetic acid (IAA) as one of the major regulators of lateral root development, we identified 539 unigenes associated with auxin signal transduction. Fourteen and 44 unigenes in the pathway were differentially expressed in B. chinense and B. scorzonerifolium, respectively, and 3 unigenes (LAX2, LAX4, and IAA13) were expressed in both species. The number of lateral root primordia increased after exogenous auxin application at 8 h and 12 h in B. scorzonerifolium and B. chinense, respectively. Since overexpression of IAA13 in Arabidopsis reduced the number of lateral roots, we hypothesized that IAA13 is involved in the reduction of the number of lateral roots in B. scorzonerifolium.

Background: Cucumber is an economically important crop cultivated worldwide. However, it is susceptible to various stresses due to weak and shallow root systems, limiting its productivity. Lateral roots (LRs) are critical for plant stress tolerance and productivity. Increasing evidence showed that gibberellins (GAs) play important roles, positively or negatively, in LR development in many plants. Therefore, it is of great importance for cucumber production to study the role of GAs in LR development. Results: The application of various concentrations of GA3 and uniconazole, a GA biosynthesis inhibitor, on germinated cucumber seeds for 5 days showed that GAs regulated cucumber LR development in a concentration-dependent manner. 1 µM, 10 µM, 50 µM and 100 µM GA3 significantly increased secondary root length, tertiary root number and length. It is worthy note that 50 µM GA3 treatment showed strong effects in increasing root dry weight and the root/shoot dry weight ratio. Pairwise comparisons between GA3-treated roots and Control at 2, 3 and 5 days after germination (DAG) identified 417 down-regulated genes enriched for GA metabolism-related processes and 447 up-regulated genes enriched for cell wall metabolism-related processes in GA3-treated roots. Linear factorial modeling was also performed to systematically identify DEGs and a total of 3523 non-redundant DEGs were identified in our RNA-seq data. Of these, most of the genes involved in auxin and cell wall metabolisms were up-regulated in GA3-treated roots. Conclusions: GAs positively regulate LR development in cucumber putatively associated with enhanced IAA and cell wall metabolisms. Our findings not only shed light on LR regulation mediated by GA but also offer an important resource for functional studies of candidate genes putatively involved in the regulation of LR development in cucumber and other crops.

Lateral root (LR) formation is an example of plant post-embryonic organogenesis event. LRs are issued from non-dividing cells entering consecutive steps of formative divisions, proliferation and elongation. The chromatin remodeling protein PICKLE negatively regulates auxin-mediated LR formation through a mechanism that is not yet known. Here we show that PICKLE interacts with RETINOBLASTOMA-RELATED 1 (RBR1) to repress theLATERAL ORGAN BOUNDARIES-DOMAIN 16(LBD16) promoter activity. Since LBD16 function is required for the formative division of LR founder cells, repression mediated by the PKL-RBR1 complex negatively regulates formative division and LR formation. Inhibition of LR formation by PKL-RBR1 is counteracted by auxin indicating that in addition to auxin-mediated transcriptional responses, the fine-tuned process of LR formation is also controlled at the chromatin level in an auxin-signaling dependent manner.

Matrix metalloproteinases (MMPs) are zinc‐dependent endo‐peptidases that in mammals are known to be involved in remodeling the extracellular matrix (ECM) in developmental and pathological processes. In this study, we report At5‐MMP of Arabidopsis thaliana to be important for root development and root bacterial communities. At5‐MMP is mainly localized in the root vasculature and lateral root, an At5‐MMP T‐DNA insertion mutant (mmp5 KO) showed reduced root growth and a lower number of root apexes, causing reduced water uptake from the soil. Subsequently, mmp5 KO is sensitive to drought stress. Inhibited auxin transport was accompanied with resistance to indole‐3‐acetic acid (IAA), 2, 4‐dichlorophenoxyacetic acid (2, 4‐D), and 1‐naphthaleneacetic acid (NAA). The content of endogenous abscisic acid (ABA) was lower in roots of mmp5 KO than in wild type. Genes responsive to ABA as well as genes encoding enzymes of the proline biosynthesis were expressed to a lower extent in mmp5 KO than in wild type. Moreover, drought stress modulated root‐associated bacterial communities of mmp5 KO: the number of Actinobacteria increased. Therefore, At5‐MMP modulates auxin/ABA signaling rendering the plant sensitive to drought stress and recruiting differential root bacterial communities.

Abiotic stresses increasingly threaten existing ecological and agricultural systems across the globe. Plant roots perceive these stresses in the soil and adapt their architecture accordingly. This review provides insights into recent discoveries showing the importance of root system architecture (RSA) and plasticity for the survival and development of plants under heat, cold, drought, salt, and flooding stress. In addition, we review the molecular regulation and hormonal pathways involved in controlling RSA plasticity, main root growth, branching and lateral root growth, root hair development, and formation of adventitious roots. Several stresses affect root anatomy by causing aerenchyma formation, lignin and suberin deposition, and Casparian strip modulation. Roots can also actively grow toward favorable soil conditions and avoid environments detrimental to their development. Recent advances in understanding the cellular mechanisms behind these different root tropisms are discussed. Understanding root plasticity will be instrumental for the development of crops that are resilient in the face of abiotic stress., Recent discoveries show the importance of root system architecture plasticity for the survival and growth of plants under several abiotic stresses.

Beneficial interactions between plant roots and rhizosphere microorganisms are pivotal for plant fitness. Nevertheless, the molecular mechanisms controlling the feedback between root architecture and microbial community structure remain elusive in maize. Here, we demonstrate that transcriptomic gradients along the longitudinal root axis associate with specific shifts in rhizosphere microbial diversity. Moreover, we have established that root-derived flavones predominantly promote the enrichment of bacteria of the taxa Oxalobacteraceae in the rhizosphere, which in turn promote maize growth and nitrogen acquisition. Genetic experiments demonstrate that LRT1-mediated lateral root development coordinates the interactions of the root system with flavone-dependent Oxalobacteraceae under nitrogen deprivation. In summary, these experiments reveal the genetic basis of the reciprocal interactions between root architecture and the composition and diversity of specific microbial taxa in the rhizosphere resulting in improved plant performance. These findings may open new avenues towards the breeding of high-yielding and nutrient-efficient crops by exploiting their interaction with beneficial soil microorganisms.

Strains of Bacillus thuringiensis (Bt) are commonly commercialized as bioinoculants for insect pest control, but their benefits go beyond their insecticidal property: they can act as plant growth-promoters. Auxins play a major role in the plant growth promotion. However, the mechanism of auxin production by the Bacilli group, and more specifically by Bt strains, is unclear. In previous work, the plant growth-promoting rhizobacterium (PGPR) B. thuringiensis strain RZ2MS9 increased the corn roots. This drew our attention to the strain's auxin production trait, earlier detected in vitro. Here, we demonstrate that in its genome, RZ2MS9 harbours the complete set of genes required in two pathways that are used for Indole acetic acid (IAA) production. We also detected that the strain produces almost five times more IAA during the stationary phase. The bacterial application increased the shoot dry weight of the Micro-Tom (MT) tomato by 24%. The application also modified MT root architecture, with an increase of 26% in the average lateral root length and inhibition of the axial root. At the cellular level, RZ2MS9-treated MT plants presented elongated root cortical cells with intensified mitotic activity. Altogether, these are the best characterized auxin-associated phenotypes. Besides that, no growth alteration was detected in the auxin-insensitive diageotropic (dgt) plants either with or without the RZ2MS9 inoculation. Our results suggest that auxins play an important role in the ability of B. thuringiensis RZ2MS9 to promote MT growth and provide a better understanding of the auxin production mechanism by a Bt strain.

In the world due to climate change, plants face numerous biotic and abiotic stresses. These biotic and abiotic stresses strictly reduce plant growth which ultimately affects the production or yield of the crop. To overcome the negative effect of these stresses plants endogenously produce some compounds or they are exogenously applied which mitigates the stress. Hydrogen sulfide (H2S) is one of those compounds that help the plant to tolerate these stresses. H2S signaling related to plant growth is very complex and it is interactions between auxin, H2S, and actin-binding proteins that are responsible for controlling the root growth by making changes in the transportation and distribution of auxins, which are responsible for root formation. In this chapter we focus on H2S signaling under stress conditions and its importance in the growth and development of roots.

Plants have developed multiple strategies to respond to salt stress. In order to identify new traits related to salt tolerance, with potential breeding application, the research focus has recently been shifted to include root system architecture (RSA) and root plasticity. Using a simple but effective root phenotyping system containing soil (rhizotrons), RSA of several tomato cultivars and their response to salinity was investigated. We observed a high level of root plasticity of tomato seedlings under salt stress. The general root architecture was substantially modified in response to salt, especially with respect to position of the lateral roots in the soil. At the soil surface, where salt accumulates, lateral root emergence was most strongly inhibited. Within the set of tomato cultivars, H1015 was the most tolerant to salinity in both developmental stages studied. A significant correlation between several root traits and aboveground growth parameters was observed, highlighting a possible role for regulation of both ion content and root architecture in salt stress resilience.

Fire blight caused by Erwinia amylovora affects pome fruit worldwide, generating serious economic losses. Despite the abundant literature on E. amylovora infection mechanisms of aerial plant organs, root infection routes remain virtually unexplored. Assessing these infection pathways is necessary for a full understanding of the pathogen's ecology. Using the pathosystem Pyrus communis–E. amylovora and different experimental approaches including a green fluorescent protein transformant (GFP1) and epifluorescence microscopy (EFM) and laser confocal scanning microscopy (LCSM), we demonstrated the pathogen's ability to infect, colonize and invade pear roots and cause characteristic fire blight symptoms both in the aerial part and in the root system. Plant infections after soil irrigation with E. amylovora-contaminated water were favored by root damage, which agreed with EFM and LCSM observations. E. amylovora GFP1 cells formed aggregates/biofilms on root surfaces and invaded the cortex through wounds and sites of lateral root emergence. Sugars, sugar-alcohols and amino acids typically secreted by roots, favored the in vitro biofilm development by E. amylovora. Migration of E. amylovora cells to aerial tissues mainly occurred after xylem penetration. Overall, our findings revealed, for the first time, common root infection patterns between E. amylovora and well-known soil borne plant pathogens and endophytes.