Unexpectedly low nitrogen acquisition and absence of root architecture adaptation to nitrate supply in a Medicago truncatula highly branched root mutant

CEP hormones at the nexus of nutrient acquisition and allocation, root development, and plant-microbe interactions

A growing understanding is emerging of the roles of peptide hormones in local and long-distance signalling that coordinates plant growth and development as well as responses to the environment. C-TERMINALLY ENCODED PEPTIDE (CEP) signalling triggered by its interaction with CEP RECEPTOR 1 (CEPR1) is known to play roles in systemic nitrogen (N) demand signalling, legume nodulation, and root system architecture. Recent research provides further insight into how CEP signalling operates, which involves diverse downstream targets and interactions with other hormone pathways. Additionally, there is emerging evidence of CEP signalling playing roles in N allocation, root responses to carbon levels, the uptake of other soil nutrients such as phosphorus and sulfur, root responses to arbuscular mycorrhizal fungi, plant immunity, and reproductive development. These findings suggest that CEP signalling more broadly coordinates growth across the whole plant in response to diverse environmental cues. Moreover, CEP signalling and function appear to be conserved in angiosperms. We review recent advances in CEP biology with a focus on soil nutrient uptake, root system architecture and organogenesis, and roles in plant-microbe interactions. Furthermore, we address knowledge gaps and future directions in this research field.

Control of the rhizobium-legume symbiosis by the plant nitrogen demand is tightly integrated at the whole plant level and requires inter-organ systemic signaling

Symbiotic nodules formed on legume roots with rhizobia fix atmospheric N₂. Bacteria reduce N₂ to NH₄ ⁺ that is assimilated into amino acids by the plant. In return, the plant provides photosynthates to fuel the symbiotic nitrogen fixation. Symbiosis is tightly adjusted to the whole plant nutritional demand and to the plant photosynthetic capacities, but regulatory circuits behind this control remain poorly understood. The use of split-root systems combined with biochemical, physiological, metabolomic, transcriptomic, and genetic approaches revealed that multiple pathways are acting in parallel. Systemic signaling mechanisms of the plant N demand are required for the control of nodule organogenesis, mature nodule functioning, and nodule senescence. N-satiety/N-deficit systemic signaling correlates with rapid variations of the nodules' sugar levels, tuning symbiosis by C resources allocation. These mechanisms are responsible for the adjustment of plant symbiotic capacities to the mineral N resources. On the one hand, if mineral N can satisfy the plant N demand, nodule formation is inhibited, and nodule senescence is activated. On the other hand, local conditions (abiotic stresses) may impair symbiotic activity resulting in plant N limitation. In these conditions, systemic signaling may compensate the N deficit by stimulating symbiotic root N foraging. In the past decade, several molecular components of the systemic signaling pathways controlling nodule formation have been identified, but a major challenge remains, that is, to understand their specificity as compared to the mechanisms of non-symbiotic plants that control root development and how they contribute to the whole plant phenotypes. Less is known about the control of mature nodule development and functioning by N and C nutritional status of the plant, but a hypothetical model involving the sucrose allocation to the nodule as a systemic signaling process, the oxidative pentose phosphate pathway, and the redox status as potential effectors of this signaling is emerging. This work highlights the importance of organism integration in plant biology.

The small peptide CEP1 and the NIN-like protein NLP1 regulate NRT2.1 to mediate root nodule formation across nitrate concentrations

Legumes acquire fixed nitrogen (N) from the soil and through endosymbiotic association with diazotrophic bacteria. However, establishing and maintaining N2-fixing nodules are expensive for the host plant, relative to taking up N from the soil. Therefore, plants suppress symbiosis when N is plentiful and enhance symbiosis when N is sparse. Here, we show that the nitrate transporter MtNRT2.1 is required for optimal nodule establishment in Medicago truncatula under low-nitrate conditions and the repression of nodulation under high-nitrate conditions. The NIN-like protein (NLP) MtNLP1 is required for MtNRT2.1 expression and regulation of nitrate uptake/transport under low- and high-nitrate conditions. Under low nitrate, the gene encoding the C-terminally encoded peptide (CEP) MtCEP1 was more highly expressed, and the exogenous application of MtCEP1 systemically promoted MtNRT2.1 expression in a compact root architecture 2 (MtCRA2)-dependent manner. The enhancement of nodulation by MtCEP1 and nitrate uptake were both impaired in the Mtnrt2.1 mutant under low nitrate. Our study demonstrates that nitrate uptake by MtNRT2.1 differentially affects nodulation at low- and high-nitrate conditions through the actions of MtCEP1 and MtNLP1.

Effects of low nitrogen supply on nitrogen uptake, assimilation and remobilization in wild bermudagrass

The natural mechanism of underlying the low nitrogen (N) tolerance of wild bermudagrass (Cynodon dactylon (L.) Pers.) germplasm was important for reducing N fertilizer input to turf while also maintaining acceptable turf quality. The growth, N uptake, assimilation and remobilization of two wild bermudagrass accessions (C291, low N tolerant and C716, low N sensitive) were determined under low N (0.5 mM) and control N (5 mM) levels. C291 exhibited lower reduction in shoot and plant dry weight than C716. Furthermore, C291 presented a lower decrease in ¹⁵NO₃^- influx compared with C716, maintained its root dry weight and root surface and showed obviously enhanced CyNRT2.2 and CyNRT2.3 expression resulting in higher shoot NO₃^--N content than the control. Moreover, in C291, nitrate reductase (NR) activity had no significant difference with control, and cytosolic glutamine synthetase (GS1) protein content, glutamate synthetase (GOGAT) activity and glutamate dehydrogenase (GDH) activity higher than control, result in the soluble protein and free amino acid contents in the shoots did not differ compared with that in the control under low N conditions. Overall, the low N tolerant wild bermudagrass accessions adopted a low N supply based on improved root N uptake ability to achieve more nitrate to kept shoot N assimilation, and meanwhile increased N remobilization in the shoots, thereby maintaining a better N status in bermudagrass. The findings may help elucidate the low N tolerance mechanisms in bermudagrass and therefore facilitate genetic improvement of N use efficiency aiming to promote low-input turfgrass management.

Genotypic diversity and plasticity of root system architecture to nitrogen availability in oilseed rape

In the emerging new agricultural context, a drastic reduction in fertilizer usage is required. A promising way to maintain high crop yields while reducing fertilizer inputs is to breed new varieties with optimized root system architecture (RSA), designed to reach soil resources more efficiently. This relies on identifying key traits that underlie genotypic variability and plasticity of RSA in response to nutrient availability. The aim of our study was to characterize the RSA plasticity in response to nitrogen limitation of a set of contrasted oilseed rape genotypes, by using the ArchiSimple model parameters as screening traits. Eight accessions of Brassica napus were grown in long tubes in the greenhouse, under two contrasting levels of nitrogen availability. After plant excavation, roots were scanned at high resolution. Six RSA traits relative to root diameter, elongation rate and branching were measured, as well as nine growth and biomass allocation traits. The plasticity of each trait to nitrogen availability was estimated. Nitrogen-limited plants were characterized by a strong reduction in total biomass and leaf area. Even if the architecture traits were shown to be less plastic than allocation traits, significant nitrogen and genotype effects were highlighted on each RSA trait, except the root minimal diameter. Thus, the RSA of nitrogen-limited plants was primarily characterised by a reduced lateral root density, a smaller primary root diameter, associated with a stronger root dominance. Among the RSA traits measured, the inter-branch distance showed the highest plasticity with a level of 70%, in the same range as the most plastic allocation traits. This work suggests that lateral root density plays the key role in the adaptation of the root system to nitrogen availability and highlights inter-branch distance as a major target trait for breeding new varieties, better adapted to low input systems.

Medicago sativa and Medicago truncatula Show Contrasting Root Metabolic Responses to Drought

Drought is an environmental stressor that affects crop yield worldwide. Understanding plant physiological responses to stress conditions is needed to secure food in future climate conditions. In this study, we applied a combination of plant physiology and metabolomic techniques to understand plant responses to progressive water deficit focusing on the root system. We chose two legume plants with contrasting tolerance to drought, the widely cultivated alfalfa Medicago sativa (Ms) and the model legume Medicago truncatula (Mt) for comparative analysis. Ms taproot (tapR) and Mt fibrous root (fibR) biomass increased during drought, while a progressive decline in water content was observed in both species. Metabolomic analysis allowed the identification of key metabolites in the different tissues tested. Under drought, carbohydrates, abscisic acid, and proline predominantly accumulated in leaves and tapRs, whereas flavonoids increased in fibRs in both species. Raffinose-family related metabolites accumulated during drought. Along with an accumulation of root sucrose in plants subjected to drought, both species showed a decrease in sucrose synthase (SUS) activity related to a reduction in the transcript level of SUS1, the main SUS gene. This study highlights the relevance of root carbon metabolism during drought conditions and provides evidence on the specific accumulation of metabolites throughout the root system.

CEP receptor signalling controls root system architecture in Arabidopsis and Medicago

Root system architecture (RSA) influences the effectiveness of resources acquisition from soils but the genetic networks that control RSA remain largely unclear. We used rhizoboxes, X-ray computed tomography, grafting, auxin transport measurements and hormone quantification to demonstrate that Arabidopsis and Medicago CEP (C-TERMINALLY ENCODED PEPTIDE)-CEP RECEPTOR signalling controls RSA, the gravitropic set-point angle (GSA) of lateral roots (LRs), auxin levels and auxin transport. We showed that soil-grown Arabidopsis and Medicago CEP receptor mutants have a narrower RSA, which results from a steeper LR GSA. Grafting showed that CEPR1 in the shoot controls GSA. CEP receptor mutants exhibited an increase in rootward auxin transport and elevated shoot auxin levels. Consistently, the application of auxin to wild-type shoots induced a steeper GSA and auxin transport inhibitors counteracted the CEP receptor mutant's steep GSA phenotype. Concordantly, CEP peptides increased GSA and inhibited rootward auxin transport in wild-type but not in CEP receptor mutants. The results indicated that CEP-CEP receptor-dependent signalling outputs in Arabidopsis and Medicago control overall RSA, LR GSA, shoot auxin levels and rootward auxin transport. We propose that manipulating CEP signalling strength or CEP receptor downstream targets may provide means to alter RSA.

Evaluating maize phenotypic variance, heritability, and yield relationships at multiple biological scales across agronomically relevant environments

A challenge to improve an integrative phenotype, like yield, is the interaction between the broad range of possible molecular and physiological traits that contribute to yield and the multitude of potential environmental conditions in which they are expressed. This study collected data on 31 phenotypic traits, 83 annotated metabolites, and nearly 22,000 transcripts from a set of 57 diverse, commercially relevant maize hybrids across three years in central U.S. Corn Belt environments. Although variability in characteristics created a complex picture of how traits interact produce yield, phenotypic traits and gene expression were more consistent across environments, while metabolite levels showed low repeatability. Phenology traits, such as green leaf number and grain moisture and whole plant nitrogen content showed the most consistent correlation with yield. A machine learning predictive analysis of phenotypic traits revealed that ear traits, phenology, and root traits were most important to predicting yield. Analysis suggested little correlation between biomass traits and yield, suggesting there is more of a sink limitation to yield under the conditions studied here. This work suggests that continued improvement of maize yields requires a strong understanding of baseline variation of plant characteristics across commercially-relevant germplasm to drive strategies for consistently improving yield.

Independent Regulation of Symbiotic Nodulation by the SUNN Negative and CRA2 Positive Systemic Pathways

Plant systemic signaling pathways allow the integration and coordination of shoot and root organ metabolism and development at the whole-plant level depending on nutrient availability. In legumes, two systemic pathways have been reported in the Medicago truncatula model to regulate root nitrogen-fixing symbiotic nodulation. Both pathways involve leucine-rich repeat receptor-like kinases acting in shoots and proposed to perceive signaling peptides produced in roots depending on soil nutrient availability. In this study, we characterized in the M. truncatula Jemalong A17 genotype a mutant allelic series affecting the Compact Root Architecture2 (CRA2) receptor. These analyses revealed that this pathway acts systemically from shoots to positively regulate nodulation and is required for the activity of carboxyl-terminally encoded peptides (CEPs). In addition, we generated a double mutant to test genetic interactions of the CRA2 systemic pathway with the CLAVATA3/EMBRYO SURROUNDING REGION peptide (CLE)/Super Numeric Nodule (SUNN) receptor systemic pathway negatively regulating nodule number from shoots, which revealed an intermediate nodule number phenotype close to the wild type. Finally, we showed that the nitrate inhibition of nodule numbers was observed in cra2 mutants but not in sunn and cra2 sunn mutants. Overall, these results suggest that CEP/CRA2 and CLE/SUNN systemic pathways act independently from shoots to regulate nodule numbers.

Connecting the dots between computational tools to analyse soil-root water relations

In recent years, many computational tools, such as image analysis, data management, process-based simulation, and upscaling tools, have been developed to help quantify and understand water flow in the soil-root system, at multiple scales (tissue, organ, plant, and population). Several of these tools work together or at least are compatible. However, for the uninformed researcher, they might seem disconnected, forming an unclear and disorganized succession of tools. In this article, we show how different studies can be further developed by connecting them to analyse soil-root water relations in a comprehensive and structured network. This 'explicit network of soil-root computational tools' informs readers about existing tools and helps them understand how their data (past and future) might fit within the network. We also demonstrate the novel possibilities of scale-consistent parameterizations made possible by the network with a set of case studies from the literature. Finally, we discuss existing gaps in the network and how we can move forward to fill them.

CRootBox: a structural-functional modelling framework for root systems

Background and Aims

Root architecture development determines the sites in soil where roots provide input of carbon and take up water and solutes. However, root architecture is difficult to determine experimentally when grown in opaque soil. Thus, root architecture models have been widely used and been further developed into functional-structural models that simulate the fate of water and solutes in the soil-root system. The root architecture model CRootBox presented here is a flexible framework to model root architecture and its interactions with static and dynamic soil environments.

Methods

CRootBox is a C++-based root architecture model with Python binding, so that CRootBox can be included via a shared library into any Python code. Output formats include VTP, DGF, RSML and a plain text file containing coordinates of root nodes. Furthermore, a database of published root architecture parameters was created. The capabilities of CRootBox for the unconfined growth of single root systems, as well as the different parameter sets, are highlighted in a freely available web application.

Key results

The capabilities of CRootBox are demonstrated through five different cases: (1) free growth of individual root systems; (2) growth of root systems in containers as a way to mimic experimental setups; (3) field-scale simulation; (4) root growth as affected by heterogeneous, static soil conditions; and (5) coupling CRootBox with code from the book Soil physics with Python to dynamically compute water flow in soil, root water uptake and water flow inside roots.

Conclusions

CRootBox is a fast and flexible functional-structural root model that is based on state-of-the-art computational science methods. Its aim is to facilitate modelling of root responses to environmental conditions as well as the impact of roots on soil. In the future, this approach will be extended to the above-ground part of the plant.

Root Development in Medicago truncatula: Lessons from Genetics to Functional Genomics

This decade introduced "omics" approaches, such as genomics, transcriptomics, proteomics, and metabolomics in association with reverse and forward genetic approaches, developed earlier, to try to identify molecular pathways involved in the development or in the response to environmental conditions as well as in animals and plants. This review summarizes studies that utilized "omics" strategies to unravel the root development in the model legume Medicago truncatula and how external factors such as soil mineral status or the presence of bacteria and fungi affect root system architecture in this species. We also compare these "omics" data to the knowledges concerning the Arabidopsis thaliana root development, nowadays considered as the model of allorhiz root systems. However, unlike legumes, this species is unable to interact with soil nitrogen-fixing rhizobia and arbuscular-mycorrhizal (AM) fungi to develop novel root-derived symbiotic structures. Differences in root organization, development, and regulatory pathways between these two model species have been highlighted.

L-System model for the growth of arbuscular mycorrhizal fungi, both within and outside of their host roots

Development of arbuscular mycorrhizal fungal colonization of roots and the surrounding soil is the central process of mycorrhizal symbiosis, important for ecosystem functioning and commercial inoculum applications. To improve mechanistic understanding of this highly spatially and temporarily dynamic process, we developed a three-dimensional model taking into account growth of the roots and hyphae. It is for the first time that infection within the root system is simulated dynamically and in a spatially resolved way. Comparison between data measured in a calibration experiment and simulated results showed a good fit. Our simulations showed that the position of the fungal inoculum affects the sensitivity of hyphal growth parameters. Variation in speed of secondary infection and hyphal lifetime had a different effect on root infection and hyphal length, respectively, depending on whether the inoculum was concentrated or dispersed. For other parameters (branching rate, distance between entry points), the relative effect was the same independent of inoculum placement. The model also indicated that maximum root colonization levels well below 100%, often observed experimentally, may be a result of differential spread of roots and hyphae, besides intrinsic plant control, particularly upon localized placement of inoculum and slow secondary infection.

Small-peptide signals that control root nodule number, development, and symbiosis

Many legumes have the capacity to enter into a symbiotic association with soil bacteria generically called 'rhizobia' that results in the formation of new lateral organs on roots called nodules within which the rhizobia fix atmospheric nitrogen (N). Up to 200 million tonnes of N per annum is fixed by this association. Therefore, this symbiosis plays an integral role in the N cycle and is exploited in agriculture to support the sustainable fixation of N for cropping and animal production in developing and developed nations. Root nodulation is an expendable developmental process and competency for nodulation is coupled to low-N conditions. Both nodule initiation and development is suppressed under high-N conditions. Although root nodule formation enables sufficient N to be fixed for legumes to grow under N-deficient conditions, the carbon cost is high and nodule number is tightly regulated by local and systemic mechanisms. How legumes co-ordinate nodule formation with the other main organs of nutrient acquisition, lateral roots, is not fully understood. Independent mechanisms appear to regulate lateral roots and nodules under low- and high-N regimes. Recently, several signalling peptides have been implicated in the local and systemic regulation of nodule and lateral root formation. Other peptide classes control the symbiotic interaction of rhizobia with the host. This review focuses on the roles played by signalling peptides during the early stages of root nodule formation, in the control of nodule number, and in the establishment of symbiosis. Here, we highlight the latest findings and the gaps in our understanding of these processes.

Reduced frequency of lateral root branching improves N capture from low-N soils in maize

Suboptimal nitrogen (N) availability is a primary constraint for crop production in developing countries, while in developed countries, intensive N fertilization is a primary economic, energy, and environmental cost for crop production. We tested the hypothesis that under low-N conditions, maize (Zea mays) lines with few but long (FL) lateral roots would have greater axial root elongation, deeper rooting, and greater N acquisition than lines with many but short (MS) lateral roots. Maize recombinant inbred lines contrasting in lateral root number and length were grown with adequate and suboptimal N in greenhouse mesocosms and in the field in the USA and South Africa (SA). In low-N mesocosms, the FL phenotype had substantially reduced root respiration and greater rooting depth than the MS phenotype. In low-N fields in the USA and SA, the FL phenotype had greater rooting depth, shoot N content, leaf photosynthesis, and shoot biomass than the MS phenotype. The FL phenotype yielded 31.5% more than the MS phenotype under low N in the USA. Our results are consistent with the hypothesis that sparse but long lateral roots improve N capture from low-N soils. These results with maize probably pertain to other species. The FL lateral root phenotype merits consideration as a selection target for greater crop N efficiency.