The impact of the rhizobia-legume symbiosis on host root system architecture

Transcriptomic insights into the potential impacts of flavonoids and nodule-specific cysteine-rich peptides on nitrogen fixation in Vicia villosa and Vicia sativa

Vicia villosa (VV) and Vicia sativa (VS) are legume forages highly valued for their excellent nitrogen fixation. However, no research has addressed the mechanisms underlying their differences in nitrogen fixation. This study employed physiological, cytological, and comparative transcriptomic approaches to elucidate the disparities in nitrogen fixation between them. Our results showed that the total amount of nitrogen fixed was 60.45% greater in VV than in VS, and the comprehensive nitrogen response performance was 94.19% greater, while the nitrogen fixation efficiency was the same. The infection zone and differentiated bacteroid proportion in mature VV root nodules were 33.76% and 19.35% greater, respectively, than those in VS. The size of the VV genome was 15.16% larger than that of the VS genome, consistent with its greater biomass. A significant enrichment of the flavonoid biosynthetic pathway was found only for VV-specific genes, among which chalcone-flavonone isomerase, caffeoyl-CoA-O-methyltransferase and stilbene synthase were extremely highly expressed. The VV-specific genes also exhibited significant enrichment in symbiotic nodulation; genes related to nodule-specific cysteine-rich peptides (NCRs) comprised 61.11% of the highly expressed genes. qRT‒PCR demonstrated that greater enrichment and expression of the dominant NCR (Unigene0004451) were associated with greater nodule bacteroid differentiation and greater nitrogen fixation in VV. Our findings suggest that the greater total nitrogen fixation of VV was attributed to its larger biomass, leading to a greater nitrogen demand and enhanced fixation physiology. This process is likely achieved by the synergistic effects of high bacteroid differentiation along with high expression of flavonoid and NCR genes.

Legume-rhizobia symbiosis: Translatome analysis

Leguminous plants can establish endosymbiotic relationships with nitrogen-fixing soil rhizobacteria. Bacterial infection and nodule organogenesis are two independent but highly coordinated genetic programs that are active during this interaction. These genetic programs can be regulated along all the stages of gene expression. Most of the studies, for both eukaryotes and prokaryotes, focused on the transcriptional regulation level determining the abundance of mRNAs. However, it has been demonstrated that mRNA levels only sometimes correlate with the abundance or activity of the coded proteins. For this reason, in the past two decades, interest in the role of translational control of gene expression has increased, since the subset of mRNA being actively translated outperforms the information gained only by the transcriptome. In the case of legume-rhizobia interactions, the study of the translatome still needs to be explored further. Therefore, this review aims to discuss the methodologies for analyzing polysome-associated mRNAs at the genome-scale and their contribution to studying translational control to understand the complexity of this symbiotic interaction. Moreover, the Dual RNA-seq approach is discussed for its relevance in the context of a symbiotic nodule, where intricate multi-species gene expression networks occur.

Water deficit response in nodulated soybean roots: a comprehensive transcriptome and translatome network analysis

BACKGROUND

Soybean establishes a mutualistic interaction with nitrogen-fixing rhizobacteria, acquiring most of its nitrogen requirements through symbiotic nitrogen fixation. This crop is susceptible to water deficit; evidence suggests that its nodulation status-whether it is nodulated or not-can influence how it responds to water deficit. The translational control step of gene expression has proven relevant in plants subjected to water deficit.

RESULTS

Here, we analyzed soybean roots' differential responses to water deficit at transcriptional, translational, and mixed (transcriptional + translational) levels. Thus, the transcriptome and translatome of four combined-treated soybean roots were analyzed. We found hormone metabolism-related genes among the differentially expressed genes (DEGs) at the translatome level in nodulated and water-restricted plants. Also, weighted gene co-expression network analysis followed by differential expression analysis identified gene modules associated with nodulation and water deficit conditions. Protein-protein interaction network analysis was performed for subsets of mixed DEGs of the modules associated with the plant responses to nodulation, water deficit, or their combination.

CONCLUSIONS

Our research reveals that the stand-out processes and pathways in the before-mentioned plant responses partially differ; terms related to glutathione metabolism and hormone signal transduction (2 C protein phosphatases) were associated with the response to water deficit, terms related to transmembrane transport, response to abscisic acid, pigment metabolic process were associated with the response to nodulation plus water deficit. Still, two processes were common: galactose metabolism and branched-chain amino acid catabolism. A comprehensive analysis of these processes could lead to identifying new sources of tolerance to drought in soybean.

Effects of Soil Rhizobia Abundance on Interactions between a Vector, Pathogen, and Legume Plant Host

Soil rhizobia promote nitrogen fixation in legume hosts, maximizing their tolerance to different biotic stressors, plant biomass, crop growth, and yield. While the presence of soil rhizobia is considered beneficial for plants, few studies have assessed whether variation in rhizobia abundance affects the tolerance of legumes to stressors. To address this, we assessed the effects of variable soil rhizobia inoculum concentrations on interactions between a legume host (Pisum sativum), a vector insect (Acyrthosiphon pisum), and a virus (Pea enation mosaic virus, PEMV). We showed that increased rhizobia abundance reduces the inhibitory effects of PEMV on the nodule formation and root growth in 2-week-old plants. However, these trends were reversed in 4-week-old plants. Rhizobia abundance did not affect shoot growth or virus prevalence in 2- or 4-week-old plants. Our results show that rhizobia abundance may indirectly affect legume tolerance to a virus, but effects varied based on plant age. To assess the mechanisms that mediated interactions between rhizobia, plants, aphids, and PEMV, we measured the relative expression of gene transcripts related to plant defense signaling. Rhizobia concentrations did not strongly affect the expression of defense genes associated with phytohormone signaling. Our study shows that an abundance of soil rhizobia may impact a plant's ability to tolerate stressors such as vector-borne pathogens, as well as aid in developing sustainable pest and pathogen management systems for legume crops. More broadly, understanding how variable rhizobia concentrations can optimize legume-rhizobia symbiosis may enhance the productivity of legume crops.

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.

H2 S works synergistically with rhizobia to modify photosynthetic carbon assimilation and metabolism in nitrogen-deficient soybeans

Hydrogen sulfide (H₂ S) performs a crucial role in plant development and abiotic stress responses by interacting with other signalling molecules. However, the synergistic involvement of H₂ S and rhizobia in photosynthetic carbon (C) metabolism in soybean (Glycine max) under nitrogen (N) deficiency has been largely overlooked. Therefore, we scrutinised how H₂ S drives photosynthetic C fixation, utilisation, and accumulation in soybean-rhizobia symbiotic systems. When soybeans encountered N deficiency, organ growth, grain output, and nodule N-fixation performance were considerably improved owing to H₂ S and rhizobia. Furthermore, H₂ S collaborated with rhizobia to actively govern assimilation product generation and transport, modulating C allocation, utilisation, and accumulation. Additionally, H₂ S and rhizobia profoundly affected critical enzyme activities and coding gene expressions implicated in C fixation, transport, and metabolism. Furthermore, we observed substantial effects of H₂ S and rhizobia on primary metabolism and C-N coupled metabolic networks in essential organs via C metabolic regulation. Consequently, H₂ S synergy with rhizobia inspired complex primary metabolism and C-N coupled metabolic pathways by directing the expression of key enzymes and related coding genes involved in C metabolism, stimulating effective C fixation, transport, and distribution, and ultimately improving N fixation, growth, and grain yield in soybeans.

Balancing nitrate acquisition strategies in symbiotic legumes

MAIN CONCLUSION

Legumes manage both symbiotic (indirect) and non-symbiotic (direct) nitrogen acquisition pathways. Understanding and optimising the direct pathway for nitrate uptake will support greater legume growth and seed yields. Legumes have multiple pathways to acquire reduced nitrogen to grow and set seed. Apart from the symbiotic N2-fixation pathway involving soil-borne rhizobia bacteria, the acquisition of nitrate and ammonia from the soil can also be an important secondary nitrogen source to meet plant N demand. The balance in N delivery between symbiotic N (indirect) and inorganic N uptake (direct) remains less clear over the growing cycle and with the type of legume under cultivation. In fertile, pH balanced agricultural soils, NO3- is often the predominant form of reduced N available to crop plants and will be a major contributor to whole plant N supply if provided at sufficient levels. The transport processes for NO3- uptake into legume root cells and its transport between root and shoot tissues involves both high and low-affinity transport systems called HATS and LATS, respectively. These proteins are regulated by external NO3- availability and by the N status of the cell. Other proteins also play a role in NO3- transport, including the voltage dependent chloride/nitrate channel family (CLC) and the S-type anion channels of the SLAC/SLAH family. CLC's are linked to NO3- transport across the tonoplast of vacuoles and the SLAC/SLAH's with NO3- efflux across the plasma membrane and out of the cell. An important step in managing the N requirements of a plant are the mechanisms involved in root N uptake and the subsequent cellular distribution within the plant. In this review, we will present the current knowledge of these proteins and what is understood on how they function in key model legumes (Lotus japonicus, Medicago truncatula and Glycine sp.). The review will examine their regulation and role in N signalling, discuss how post-translational modification affects NO3- transport in roots and aerial tissues and its translocation to vegetative tissues and storage/remobilization in reproductive tissues. Lastly, we will present how NO3-influences the autoregulation of nodulation and nitrogen fixation and its role in mitigating salt and other abiotic stresses.

Preliminary symbiotic performance of indigenous soybean (Glycine max)-nodulating rhizobia from agricultural soils of Tanzania

Globally, the increase in human population continues to threaten the sustainability of agricultural systems. Despite the fast-growing population in Sub-Saharan Africa (SSA) and the efforts in improving the productivity of crops, the increase in the yield of crops per unit area is still not promising. The productivity of crops is primarily constrained by inadequate levels of soil nutrients to support optimum crop growth and development. However, smallholder farmers occasionally use fertilizers, and the amount applied is usually small and does not meet plant requirements. This is due to the unaffordability of the cost of fertilizers, which is enough to suffice the crop requirement. Therefore, there is a need for alternative affordable and effective fertilization methods for sustainable intensification and improvement of the smallholder farming system's productivity. This study was designed to evaluate the symbiotic performance of indigenous soybean nodulating rhizobia in selected agricultural soils of Tanzania. In total, 217 rhizobia isolates were obtained from three agroecological zones, i.e., eastern, northern, and southern highlands. The isolates collected were screened for N2 fixing abilities under in vitro (nitrogen-free medium) and screen house conditions. The results showed varying capabilities of isolates in nitrogen-fixing both under in vitro and screen house conditions. Under in vitro experiment, 22% of soybean rhizobia isolates were identified to have a nitrogen-fixing capability on an N-free medium, with the highest N2-fixing diameter of 1.87 cm. In the screen house pot experiment, results showed that soybean rhizobia isolate significantly (P < 0.001) influenced different plant growth and yield components, where the average shoot dry weight ranged from 2.49 to 10.98 g, shoot length from 41 to 125.27 cm whilst the number of leaves per plant ranged from 20 to 66. Furthermore, rhizobia isolates significantly (P = 0.038) increased root dry weight from 0.574 to 2.17 g. In the case of symbiotic parameters per plant, the number of nodules was in the range of 0.33–22, nodules dry weight (0.001–0.137 g), shoot nitrogen (2.37–4.97%), total nitrogen (53.59–6.72 g), and fixed nitrogen (46.878–0.15 g) per plant. In addition, the results indicated that 51.39% of the tested bacterial isolates in this study were ranked as highly effective in symbiosis, suggesting that they are promising as potential alternative biofertilizers for soybean production in agricultural soils of Tanzania to increase productivity per unit area while reducing production cost.

Innovative Rhizosphere-Based Enrichment under P-Limitation Selects for Bacterial Isolates with High-Performance P-Solubilizing Traits

The use of phosphate solubilizing bacteria (PSB) as inoculants for the rhizosphere is a well-known strategy to mitigate P-deficiency in plants. However, despite the multiple modes of action to render P available for plants, PSB often fail to deliver in the field as their selection is often based on a single P-solubilizing trait assessed in vitro. Anticipating these shortcomings, we screened 250 isolates originating from rhizosphere-based enriched consortia for the main in vitro P-solubilizing traits, and subsequently grouped the isolates through trait-based HCPC (hierarchical clustering on principal components). Representative isolates of each cluster were tested in an in planta experiment to compare their in vitro P-solubilizing traits with their in planta performance under conditions of P-deprivation. Our data convincingly show that bacterial consortia capable to mitigate P-deficiency in planta were enriched in bacterial isolates that had multiple P-solubilizing traits in vitro and that had the capacity to mitigate plant P-stress in planta under P-deprived conditions. Furthermore, although it was assumed that bacteria that looked promising in vitro would also have a positive effect in planta, our data show that this was not always the case. Opposite, lack of performance in vitro did not automatically result in a lack of performance in planta. These results corroborate the strength of the previously described in planta-based enrichment and selection technique for the isolation of highly efficient rhizosphere competent PSB. IMPORTANCE With the growing awareness on the ecological impact of chemical phosphate fertilizers, research concerning the use of phosphate solubilizing bacteria (PSB) as a sustainable alternative for, or addition to these fertilizers is of paramount importance. In previous research, we successfully implemented a plant-based enrichment technique for PSB, which simultaneously selected for the rhizosphere competence and phosphate solubilizing characteristics of bacterial suspensions. Current research follows up on our previous findings, whereas we screened 250 rhizobacteria for their P-solubilizing traits and were able to substantiate the results obtained from the enriched suspensions at a single-isolate level. With this research, we aim for a paradigm shift toward the plant-based selection of PSB, which is a more holistic approach compared to the plate-based methods. We emphasize the strength of the previously described plant-based enrichment and selection technique for the isolation of highly efficient and diverse PSB.

Spatial Patterns and Composition Traits of Soil Microbial Nitrogen-Metabolism Genes in the Robinia pseudoacacia Forests at a Regional Scale

Microbial-driven processes related to the nitrogen-metabolism (N-metabolism) in soil are critical for ecosystem functioning and stability. There are spatial patterns of microbial-mediated nitrogen processes, but we still lack an overview of the soil N-metabolism genes of single nitrogen-fixing tree species pure forests at a regional scale. Here, we investigated the spatial variation and drivers of microbial N-metabolism genes in the rhizosphere soil of Robinia pseudoacacia on the Loess Plateau by metagenomic technology. We found that the distance-decay of soil N functional gene similarities in Robinia pseudoacacia forests on the Loess Plateau spanning a geographic distance of 230 km was significant (p < 0.001). The gene composition and co-occurrence patterns in the process of soil microbial N-metabolism were very different, and they were mainly driven by soil pH and MAP (mean annual precipitation). The proportion of positive links and edges co-occurrence networks between N functional genes increased with increasing pH, suggesting that increasing pH promoted connections between functional genes. The relative frequencies of N-metabolism pathways were consistent on the Loess Plateau, the abundance of ammonia assimilation pathway was highest, and the abundance of the nitrogen fixation pathway was the lowest; only the abundance of the nitrogen fixation pathway was not significantly different. The bacterial and archaeal communities involved in soil nitrogen metabolism were significantly different. Structural equation modeling showed that decreases in soil pH and MAP mainly affected the increase in nitrogen functional gene abundance through an increase in the diversity of N-metabolism microorganisms. In conclusion, this study provides a baseline for biogeographic studies of soil microbe functional genes.

Harnessing rhizobacteria to fulfil inter-linked nutrient dependency on soil and alleviate stresses in plants

Plant rhizo-microbiome comprises of complex microbial communities that colonizes at the interphase of plant roots and soil. Plant-growth-promoting rhizobacteria (PGPR) in the rhizosphere provides important ecosystem services ranging from release of essential nutrients for enhancing soil quality and improving plant health to imparting protection to plants against rising biotic and abiotic stresses. Hence, PGPR serve as restoring agents to rejuvenate soil health and mediate plant fitness in the facet of changing climate. Though, it is evident that nutrients availability in soil are managed through inter-linked mechanisms, how PGPR expediate these processes remain less recognized. Promising results of PGPR inoculation on plant growth are continually reported in controlled environmental conditions, however, their field application often fails due to competition with native microbiota and low colonization efficiency in roots. The development of highly efficient and smart bacterial synthetic communities by integrating bacterial ecological and genetic features provides better opportunities for successful inoculant formulations. This review provides an overview of the inter-play between nutrient availability and disease suppression governed by rhizobacteria in soil followed by the role of synthetic bacterial communities in developing efficient microbial inoculants. Moreover, an outlook on the beneficial activities of rhizobacteria in modifying soil characteristics to sustainably boost agroecosystem functioning is also provided.

Dependence on Nitrogen Availability and Rhizobial Symbiosis of Different Accessions of Trifolium fragiferum, a Crop Wild Relative Legume Species, as Related to Physiological Traits

Biological nitrogen fixation by legume-rhizobacterial symbiosis in temperate grasslands is an important source of soil nitrogen. The aim of the present study was to characterize the dependence of different accessions of T. fragiferum, a rare crop wild relative legume species, from their native rhizobia as well as additional nitrogen fertilization in controlled conditions. Asymbiotically cultivated, mineral-fertilized T. fragiferum plants gradually showed signs of nitrogen deficiency, appearing as a decrease in leaf chlorophyll concentration, leaf senescence, and a decrease in growth rate. The addition of nitrogen, and the inoculation with native rhizobia, or both treatments significantly prevented the onset of these symptoms, leading to both increase in plant shoot biomass as well as an increase in tissue concentration of N. The actual degree of each type of response was genotype-specific. Accessions showed a relatively similar degree of dependence on nitrogen (70–95% increase in shoot dry mass) but the increase in shoot dry mass by inoculation with native rhizobia ranged from 27 to 85%. In general, there was no correlation between growth stimulation and an increase in tissue N concentration by the treatments. The addition of N or rhizobial inoculant affected mineral nutrition at the level of both macronutrient and micronutrient concentration in different plant parts. In conclusion, native rhizobial strains associated with geographically isolated accessions of T. fragiferum at the northern range of distribution of the species represent a valuable resource for further studies aimed at the identification of salinity-tolerant N₂-fixing bacteria for the needs of sustainable agriculture, as well as in a view of understanding ecosystem functioning at the level of plant-microorganism interactions.

Delineation of mechanistic approaches of rhizosphere microorganisms facilitated plant health and resilience under challenging conditions

Sustainable agriculture demands the balanced use of inorganic, organic, and microbial biofertilizers for enhanced plant productivity and soil fertility. Plant growth-enhancing rhizospheric bacteria can be an excellent biotechnological tool to augment plant productivity in different agricultural setups. We present an overview of microbial mechanisms which directly or indirectly contribute to plant growth, health, and development under highly variable environmental conditions. The rhizosphere microbiomes promote plant growth, suppress pathogens and nematodes, prime plants immunity, and alleviate abiotic stress. The prospective of beneficial rhizobacteria to facilitate plant growth is of primary importance, particularly under abiotic and biotic stresses. Such microbe can promote plant health, tolerate stress, even remediate soil pollutants, and suppress phytopathogens. Providing extra facts and a superior understanding of microbial traits underlying plant growth promotion can stir the development of microbial-based innovative solutions for the betterment of agriculture. Furthermore, the application of novel scientific approaches for facilitating the design of crop-specific microbial biofertilizers is discussed. In this context, we have highlighted the exercise of "multi-omics" methods for assessing the microbiome's impact on plant growth, health, and overall fitness via analyzing biochemical, physiological, and molecular facets. Furthermore, the role of clustered regularly interspaced short palindromic repeats (CRISPR) based genome alteration and nanotechnology for improving the agronomic performance and rhizosphere microbiome is also briefed. In a nutshell, the paper summarizes the recent vital molecular processes that underlie the different beneficial plant-microbe interactions imperative for enhancing plant fitness and resilience under-challenged agriculture.

Salicylic Acid in Root Growth and Development

In plants, salicylic acid (SA) is a hormone that mediates a plant’s defense against pathogens. SA also takes an active role in a plant’s response to various abiotic stresses, including chilling, drought, salinity, and heavy metals. In addition, in recent years, numerous studies have confirmed the important role of SA in plant morphogenesis. In this review, we summarize data on changes in root morphology following SA treatments under both normal and stress conditions. Finally, we provide evidence for the role of SA in maintaining the balance between stress responses and morphogenesis in plant development, and also for the presence of SA crosstalk with other plant hormones during this process.

Phenotyping seedlings for selection of root system architecture in alfalfa (Medicago sativa L.)

BACKGROUND

The root system architecture (RSA) of alfalfa (Medicago sativa L.) affects biomass production by influencing water and nutrient uptake, including nitrogen fixation. Further, roots are important for storing carbohydrates that are needed for regrowth in spring and after each harvest. Previous selection for a greater number of branched and fibrous roots significantly increased alfalfa biomass yield. However, phenotyping root systems of mature alfalfa plant is labor-intensive, time-consuming, and subject to environmental variability and human error. High-throughput and detailed phenotyping methods are needed to accelerate the development of alfalfa germplasm with distinct RSAs adapted to specific environmental conditions and for enhancing productivity in elite germplasm. In this study methods were developed for phenotyping 14-day-old alfalfa seedlings to identify measurable root traits that are highly heritable and can differentiate plants with either a branched or a tap rooted phenotype. Plants were grown in a soil-free mixture under controlled conditions, then the root systems were imaged with a flatbed scanner and measured using WinRhizo software.

RESULTS

The branched root plants had a significantly greater number of tertiary roots and significantly longer tertiary roots relative to the tap rooted plants. Additionally, the branch rooted population had significantly more secondary roots > 2.5 cm relative to the tap rooted population. These two parameters distinguishing phenotypes were confirmed using two machine learning algorithms, Random Forest and Gradient Boosting Machines. Plants selected as seedlings for the branch rooted or tap rooted phenotypes were used in crossing blocks that resulted in a genetic gain of 10%, consistent with the previous selection strategy that utilized manual root scoring to phenotype 22-week-old-plants. Heritability analysis of various root architecture parameters from selected seedlings showed tertiary root length and number are highly heritable with values of 0.74 and 0.79, respectively.

CONCLUSIONS

The results show that seedling root phenotyping is a reliable tool that can be used for alfalfa germplasm selection and breeding. Phenotypic selection of RSA in seedlings reduced time for selection by 20 weeks, significantly accelerating the breeding cycle.

Root hairs vs. trichomes: Not everyone is straight!

Trichomes show 47 morphological phenotypes, while literature reports only two root hair phenotypes in all plants. However, could hair-like structures exist below-ground in a similar wide range of morphologies like trichomes? Genetic mutants and root hair stress phenotypes point to the possibility of uncharacterized morphological variation existing belowground. For example, such root hairs in Arabidopsis (Arabidopsis thaliana) can be wavy, curled, or branched. We found hints in the literature about hair-like structures that emerge before root hairs belowground. As such, these early emerging hair structures can be potential exceptions to the contrasting morphological variation between trichomes and root hairs. Here, we show a previously unreported 'hooked' hair structure growing below-ground in common bean. The unique 'hooking' shape distinguishes the 'hooked hair' morphologically from root hairs. Currently, we cannot fully characterize the phenotype of our observation due to the lack of automated methods for phenotyping root hairs. This phenotyping bottleneck also handicaps the discovery of more morphology types that might exist below-ground as manual screening across species is slower than computer-assisted high-throughput screening.

Arbuscular Mycorrhizal Fungus Alters Root System Architecture in Camellia sinensis L. as Revealed by RNA-Seq Analysis

Arbuscular mycorrhizal fungus (AMF), forming symbiosis with most terrestrial plants, strongly modulates root system architecture (RSA), which is the main characteristic of root in soil, to improve plant growth and development. So far, the studies of AMF on tea plant seedlings are few and the relevant molecular mechanism is not deciphered. In this study, the 6-month-old cutting seedlings of tea plant cultivar "Wancha No.4" were inoculated with an AMF isolate, Rhizophagus intraradices BGC JX04B and harvested after 6 months of growth. The indexes of RSA and sugar contents in root were determined. The transcriptome data in root tips of mycorrhizal and non-mycorrhizal cutting seedlings were obtained by RNA-sequence (Seq) analysis. The results showed that AMF significantly decreased plant growth, but increased the sucrose content in root and the higher classes of lateral root (LR) formation (third and fourth LR). We identified 2047 differentially expressed genes (DEGs) based on the transcriptome data, and DEGs involved in metabolisms of phosphorus (42 DEGs), sugar (39), lipid (67), and plant hormones (39) were excavated out. Variation partitioning analysis showed all these four categories modulated the RSA. In phosphorus (P) metabolism, the phosphate transport and release (DEGs related to purple acid phosphatase) were promoted by AMF inoculation, while DEGs of sugar transport protein in sugar metabolism were downregulated. Lipid metabolism might not be responsible for root branching but for AMF propagation. With respect to phytohormones, DEGs of auxin (13), ethylene (14), and abscisic acid (5) were extensively affected by AMF inoculation, especially for auxin and ethylene. The further partial least squares structural equation modeling analysis indicated that pathways of P metabolism and auxin, as well as the direct way of AMF inoculation, were of the most important in AMF promoting root branching, while ethylene performed a negative role. Overall, our data revealed the alterations of genome-wide gene expression in tea plant roots after inoculation with AMF and provided a molecular basis for the regulatory mechanism of RSA (mainly root branching) changes induced by AMF.

Isolation and Characterization of High-Efficiency Rhizobia From Western Kenya Nodulating With Common Bean

Common bean is one of the primary protein sources in third-world countries. They form nodules with nitrogen-fixing rhizobia, which have to be adapted to the local soils. Commercial rhizobial strains such as Rhizobium tropici CIAT899 are often used in agriculture. However, this strain failed to significantly increase the common bean yield in many places, including Kenya, due to the local soils' low pH. We isolated two indigenous rhizobial strains from the nodules of common bean from two fields in Western Kenya that have never been exposed to commercial inocula. We then determined their ability to fix nitrogen in common beans, solubilize phosphorus, and produce indole acetic acid. In greenhouse experiments, common bean plants inoculated with two isolates, B3 and S2 in sterile vermiculite, performed better than those inoculated with CIAT899 or plants grown with nitrogen fertilizer alone. In contrast to CIAT899, both isolates grew in the media with pH 4.8. Furthermore, isolate B3 had higher phosphate solubilization ability and produced more indole acetic acid than the other two rhizobia. Genome analyses revealed that B3 and S2 are different strains of Rhizobium phaseoli. We recommend fieldwork studies in Kenyan soils to test the efficacy of the two isolates in the natural environment in an effort to produce inoculants specific for these soils.

Sweet Modifications Modulate Plant Development

Plant development represents a continuous process in which the plant undergoes morphological, (epi)genetic and metabolic changes. Starting from pollination, seed maturation and germination, the plant continues to grow and develops specialized organs to survive, thrive and generate offspring. The development of plants and the interplay with its environment are highly linked to glycosylation of proteins and lipids as well as metabolism and signaling of sugars. Although the involvement of these protein modifications and sugars is well-studied, there is still a long road ahead to profoundly comprehend their nature, significance, importance for plant development and the interplay with stress responses. This review, approached from the plants' perspective, aims to focus on some key findings highlighting the importance of glycosylation and sugar signaling for plant development.

Interaction of Symbiotic Rhizobia and Parasitic Root-Knot Nematodes in Legume Roots: From Molecular Regulation to Field Application

Legumes form two types of root organs in response to signals from microbes, namely, nodules and root galls. In the field, these interactions occur concurrently and often interact with each other. The outcomes of these interactions vary and can depend on natural variation in rhizobia and nematode populations in the soil as well as abiotic conditions. While rhizobia are symbionts that contribute fixed nitrogen to their hosts, parasitic root-knot nematodes (RKN) cause galls as feeding structures that consume plant resources without a contribution to the plant. Yet, the two interactions share similarities, including rhizosphere signaling, repression of host defense responses, activation of host cell division, and differentiation, nutrient exchange, and alteration of root architecture. Rhizobia activate changes in defense and development through Nod factor signaling, with additional functions of effector proteins and exopolysaccharides. RKN inject large numbers of protein effectors into plant cells that directly suppress immune signaling and manipulate developmental pathways. This review examines the molecular control of legume interactions with rhizobia and RKN to elucidate shared and distinct mechanisms of these root-microbe interactions. Many of the molecular pathways targeted by both organisms overlap, yet recent discoveries have singled out differences in the spatial control of expression of developmental regulators that may have enabled activation of cortical cell division during nodulation in legumes. The interaction of legumes with symbionts and parasites highlights the importance of a comprehensive view of root-microbe interactions for future crop management and breeding strategies.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Overexpression of alfalfa SIMK promotes root hair growth, nodule clustering and shoot biomass production

Nitrogen-fixing rhizobia and legumes have developed complex mutualistic mechanism that allows to convert atmospheric nitrogen into ammonia. Signalling by mitogen-activated protein kinases (MAPKs) seems to be involved in this symbiotic interaction. Previously, we reported that stress-induced MAPK (SIMK) shows predominantly nuclear localization in alfalfa root epidermal cells. Nevertheless, SIMK is activated and relocalized to the tips of growing root hairs during their development. SIMK kinase (SIMKK) is a well-known upstream activator of SIMK. Here, we characterized production parameters of transgenic alfalfa plants with genetically manipulated SIMK after infection with Sinorhizobium meliloti. SIMKK RNAi lines, causing strong downregulation of both SIMKK and SIMK, showed reduced root hair growth and lower capacity to form infection threads and nodules. In contrast, constitutive overexpression of GFP-tagged SIMK promoted root hair growth as well as infection thread and nodule clustering. Moreover, SIMKK and SIMK downregulation led to decrease, while overexpression of GFP-tagged SIMK led to increase of biomass in above-ground part of plants. These data suggest that genetic manipulations causing downregulation or overexpression of SIMK affect root hair, nodule and shoot formation patterns in alfalfa, and point to the new biotechnological potential of this MAPK.