Both plant and bacterial nitrate reductases contribute to nitric oxide production in Medicago truncatula nitrogen-fixing nodules

Differential regulation of the "phytoglobin-nitric oxide respiration" in Medicago truncatula roots and nodules submitted to flooding

Flooding induces hypoxia in plant tissues, impacting various physiological and biochemical processes. This study investigates the adaptive response of the roots and nitrogen-fixing nodules of Medicago truncatula in symbiosis with Sinorhizobium meliloti under short-term hypoxia caused by flooding. Four-week-old plants were subjected to flooding for 1-4 days. Physiological parameters as well as the expression of the senescence marker gene MtCP6 remained unchanged after 4 days of flooding, indicating no senescence onset. Hypoxia was evident from the first day, as indicated by the upregulation of hypoxia marker genes (MtADH, MtPDC, MtAlaAT, MtERF73). Nitrogen-fixing capacity was unaffected after 1 day but markedly decreased after 4 days, while energy state (ATP/ADP ratio) significantly decreased from 1 day and was more affected in nodules than in roots. Nitric oxide (NO) production increased in roots but decreased in nodules after prolonged flooding. Nitrate reductase (NR) activity and expression of genes associated with Phytoglobin-NO (Pgb-NO) respiration (MtNR1, MtNR2, MtPgb1.1) were upregulated, suggesting a role in maintaining energy metabolism under hypoxia, but the use of M. truncatula nr1 and nr2 mutants, impaired in nitrite production, indicated the involvement of these two genes in ATP regeneration during initial flooding response. The addition of sodium nitroprusside or tungstate revealed that Pgb-NO respiration contributes significantly to ATP regeneration in both roots and nodules under flooding. Altogether, these results highlight the importance of NR1 and Pgb1.1 in the hypoxic response of legume root systems and show that nodules are more sensitive than roots to hypoxia.

Soil application of graphitic carbon nitride nanosheets alleviate cadmium toxicity by altering subcellular distribution, chemical forms of cadmium and improving nitrogen availability in soybean (Glycine max L.)

Cadmium (Cd)-contamination impairs biological nitrogen fixation in legumes (BNF), threatening global food security. Innovative strategies to enhance BNF and improve plant resistance to Cd are therefore crucial. This study investigates the effects of graphitic carbon nitride nanosheets (g-C3N4 NSs) on soybean (Glycine max L.) in Cd contaminated soil, focusing on Cd distribution, chemical forms and nitrogen (N) fixation. Soybean plants were treated with 100 mg kg-1 g-C3N4 NSs, with or without 10 mg kg-1 Cd for 4 weeks. Soil addition of g-C3N4 NSs alleviated Cd toxicity and promote soybean growth via scavenging Cd-mediated oxidative stress and improving photosynthesis. Compared to Cd treatment, g-C3N4 NSs increased shoot and root dry weights under Cd toxicity by 49.5% and 63.4%, respectively. g-C3N4 NSs lowered Cd content by 35.7%-54.1%, redistributed Cd subcellularly by increasing its proportion in the cell wall and decreasing it in soluble fractions and organelles, and converted Cd from high-toxicity to low-toxicity forms. Additionally, g-C3N4 NSs improved the soil N cycle, stimulated nodulation, and increased the N-fixing capacity of nodules, thus increasing N content in shoots and roots by 12.4% and 43.2%, respectively. Mechanistic analysis revealed that g-C3N4 NSs mitigated Cd-induced loss of endogenous nitric oxide in nodules, restoring nodule development. This study highlights the potential of g-C3N4 NSs for remediating Cd-contaminated soil, reducing Cd accumulation, and enhancing plant growth and N fixation, offering new insights into the use of carbon nanomaterials for soil improvement and legume productivity under metal(loid)s stress.

Dynamics of hemoglobins during nodule development, nitrate response, and dark stress in Lotus japonicus

Legume nodules express multiple leghemoglobins (Lbs) and non-symbiotic hemoglobins (Glbs), but how they are regulated is unclear. Here, we study the regulation of all Lbs and Glbs of Lotus japonicus in different physiologically relevant conditions and mutant backgrounds. We quantified hemoglobin expression, localized reactive oxygen species (ROS) and nitric oxide (NO) in nodules, and deployed mutants deficient in Lbs and in the transcription factors NLP4 (associated with nitrate sensitivity) and NAC094 (associated with senescence). Expression of Lbs and class 2 Glbs was suppressed by nitrate, whereas expression of class 1 and 3 Glbs was positively correlated with external nitrate concentrations. Nitrate-responsive elements were found in the promoters of several hemoglobin genes. Mutant nodules without Lbs showed accumulation of ROS and NO and alterations of antioxidants and senescence markers. NO accumulation occurred by a nitrate-independent pathway, probably due to the virtual disappearance of Glb1-1 and the deficiency of Lbs. We conclude that hemoglobins are regulated in a gene-specific manner during nodule development and in response to nitrate and dark stress. Mutant analyses reveal that nodules lacking Lbs experience nitro-oxidative stress and that there is compensation of expression between Lb1 and Lb2. They also show modulation of hemoglobin expression by NLP4 and NAC094.

Nitric Oxide in Fungi: Production and Function

Nitric oxide (NO) is synthesized in all kingdoms of life, where it plays a role in the regulation of various physiological and developmental processes. In terms of endogenous NO biology, fungi have been less well researched than mammals, plants, and bacteria. In this review, we summarize and discuss the studies to date on intracellular NO biosynthesis and function in fungi. Two mechanisms for NO biosynthesis, NO synthase (NOS)-mediated arginine oxidation and nitrate- and nitrite-reductase-mediated nitrite reduction, are the most frequently reported. Furthermore, we summarize the multifaceted functions of NO in fungi as well as its role as a signaling molecule in fungal growth regulation, development, abiotic stress, virulence regulation, and metabolism. Finally, we present potential directions for future research on fungal NO biology.

The underestimated role of plant root nitric oxide emission under low-oxygen stress

The biotic release of nitric oxide (NO), a greenhouse gas, into the atmosphere contributes to climate change. In plants, NO plays a significant role in metabolic and signaling processes. However, little attention has been paid to the plant-borne portion of global NO emissions. Owing to the growing significance of global flooding events caused by climate change, the extent of plant NO emissions has been assessed under low-oxygen conditions for the roots of intact plants. Each examined plant species (tomato, tobacco, and barley) exhibited NO emissions in a highly oxygen-dependent manner. The transfer of data obtained under laboratory conditions to the global area of farmland was used to estimate possible plant NO contribution to greenhouse gas budgets. Plant-derived and stress-induced NO emissions were estimated to account for the equivalent of 1 to 9% of global annual NO emissions from agricultural land. Because several stressors induce NO formation in plants, the actual impact may be even higher.

NPF and NRT2 from Pisum sativum Potentially Involved in Nodule Functioning: Lessons from Medicago truncatula and Lotus japonicus

In addition to absorbing nitrogen from the soil, legumes have the ability to use atmospheric N2 through symbiotic nitrogen fixation. Therefore, legumes have developed mechanisms regulating nodulation in response to the amount of nitrate in the soil; in the presence of high nitrate concentrations, nodulation is inhibited, while low nitrate concentrations stimulate nodulation and nitrogen fixation. This allows the legumes to switch from soil nitrogen acquisition to symbiotic nitrogen fixation. Recently, particular interest has been given to the nitrate transporters, such as Nitrate Transporter1/Peptide transporter Family (NPF) and Nitrate Transporter 2 (NRT2), having a role in the functioning of nodules. Nitrate transporters of the two model plants, Lotus japonicus and Medicago truncatula, shown to have a positive and/or a negative role in nodule functioning depending on nitrate concentration, are presented in this article. In particular, the following transporters were thoroughly studied: (i) members of NPF transporters family, such as LjNPF8.6 and LjNPF3.1 in L. japonicus and MtNPF1.7 and MtNPF7.6 in M. truncatula, and (ii) members of NRT2 transporters family, such as LjNRT2.4 and LjNRT2.1 in L. japonicus and MtNRT2.1 in M. truncatula. Also, by exploiting available genomic and transcriptomic data in the literature, we have identified the complete PsNPF family in Pisum sativum (69 sequences previously described and 21 new that we have annotated) and putative nitrate transporters candidate for playing a role in nodule functioning in P. sativum.

The emerging roles of nitric oxide and its associated scavengers-phytoglobins-in plant symbiotic interactions

A key feature in the establishment of symbiosis between plants and microbes is the maintenance of the balance between the production of the small redox-related molecule, nitric oxide (NO), and its cognate scavenging pathways. During the establishment of symbiosis, a transition from a normoxic to a microoxic environment often takes place, triggering the production of NO from nitrite via a reductive production pathway. Plant hemoglobins [phytoglobins (Phytogbs)] are a central tenant of NO scavenging, with NO homeostasis maintained via the Phytogb-NO cycle. While the first plant hemoglobin (leghemoglobin), associated with the symbiotic relationship between leguminous plants and bacterial Rhizobium species, was discovered in 1939, most other plant hemoglobins, identified only in the 1990s, were considered as non-symbiotic. From recent studies, it is becoming evident that the role of Phytogbs1 in the establishment and maintenance of plant-bacterial and plant-fungal symbiosis is also essential in roots. Consequently, the division of plant hemoglobins into symbiotic and non-symbiotic groups becomes less justified. While the main function of Phytogbs1 is related to the regulation of NO levels, participation of these proteins in the establishment of symbiotic relationships between plants and microorganisms represents another important dimension among the other processes in which these key redox-regulatory proteins play a central role.

Plasma-generated nitric oxide water: A promising strategy to combat bacterial dormancy (VBNC state) in environmental contaminant Micrococcus luteus

The viable but non-culturable (VBNC) is an inactive state, and certain bacteria can enter under adverse conditions. The VBNC state challenges the environment, food safety, and public health since VBNCs may resuscitate and pose a risk to human health. The aim of this study was to investigate the effect of plasma-generated nitric oxide water (PG-NOW) on airborne contaminant Micrococcus luteus (M. luteus) and examine its potential to induce the VBNC state. The essential conditions for bacteria to enter VBNC state are low metabolic activity and rare or no culturable counts. The results indicated that PG-NOW effectively eliminates M. luteus, and the remaining bacteria are in culturable condition. Moreover, the conventional cultured-based method combined with a propidium iodide monoazide quantitative PCR (PMAxxTM-qPCR) showed no significant VBNC induction and moderate culturable counts. Results from the qPCR revealed that gene levels in PG-NOW treated bacteria related to resuscitation-promoting factors, amino acid biosynthesis, and fatty acid metabolism were notably upregulated. PG-NOW inactivated M. luteus showed negligible VBNC formation and alleviated infection ability in lung cells. This study provides new insights into the potential use of PG-NOW reactive species for the prevention and control of the VBNC state of M. luteus.

Exogenous Putrescine Modulates Nitrate Reductase-Dependent NO Production in Cucumber Seedlings Subjected to Salt Stress

Polyamines (PAs) are small aliphatic compounds that participate in the plant response to abiotic stresses. They also participate in nitric oxide (NO) production in plants; however, their role in this process remains unknown. Therefore, the study aimed to investigate the role of putrescine (Put) in NO production in the roots of cucumber seedlings subjected to salt stress (120 mM NaCl) for 1 and 24 h. In salinity, exogenous Put can regulate NO levels by managing NO biosynthesis pathways in a time-dependent manner. In cucumber roots exposed to 1 h of salinity, exogenous Put reduced NO level by decreasing nitrate reductase (NR)-dependent NO production and reduced nitric oxide synthase-like (NOS-like) activity. In contrast, during a 24 h salinity exposure, Put treatment boosted NO levels, counteracting the inhibitory effect of salinity on the NR and plasma membrane nitrate reductase (PM-NR) activity in cucumber roots. The role of endogenous Put in salt-induced NO generation was confirmed using Put biosynthesis inhibitors. Furthermore, the application of Put can modulate the NR activity at the genetic and post-translational levels. After 1 h of salt stress, exogenous Put upregulated CsNR1 and CsNR2 expression and downregulated CsNR3 expression. Put also decreased the NR activation state, indicating a reduction in the level of active dephosphorylated NR (dpNR) in the total enzyme pool. Conversely, in the roots of plants subjected to 24 h of salinity, exogenous Put enhanced the NR activation state, indicating an enhancement of the dpNR form in the total NR pool. These changes were accompanied by a modification of endogenous PA content. Application of exogenous Put led to an increase in the amount of Put in the roots and reduced endogenous spermine (Spm) content in cucumber roots under 24 h salinity. The regulatory role of exogenous Put on NO biosynthesis pathways may link with plant mechanisms of response to salt stress.

Polyethylene and polyvinyl chloride microplastics promote soil nitrification and alter the composition of key nitrogen functional bacterial groups

Microplastics (MPs) contamination in soils seriously threatens agroecosystems globally. However, very few studies have been done on the effects of MPs on the soil nitrogen cycle and related functional microorganisms. To assess MP's impact on the soil nitrogen cycle and related functional bacteria, we carried out a one-month soil incubation experiment using typical acidic soil. The soil was amended with alfalfa meal and was spiked with 1% and 5% (mass percentage) of low-density polyethylene (LDPE) and polyvinyl chloride (PVC) MPs. Our results showed that both LDPE and PVC addition significantly increased soil nitrification rate and nitrate reductase activity, which could further promote soil denitrification. The relative abundance of diazotrophs, ammonium oxidizing, and denitrifying bacterial groups were significantly altered with MPs addition. Moreover, the MPs treatments greatly enhanced denitrifying bacteria richness. Redundancy analysis showed that nitrate reductase activity was the most significant factor affecting the soil functional bacterial community. Correlation analysis shows that Nitrosospira genus might be for the improvement of soil nitrification rate. Our results implied that MPs exposure could significantly affect the soil nitrogen cycling in farmland ecosystems by influencing essential nitrogen functional microorganisms and related enzymatic activities.

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.

Group VII ethylene response factors, MtERF74 and MtERF75, sustain nitrogen fixation in Medicago truncatula microoxic nodules

Group VII ethylene response factors (ERF-VII) are plant-specific transcription factors (TFs) known for their role in the activation of hypoxia-responsive genes under low oxygen stress but also in plant endogenous hypoxic niches. However, their function in the microaerophilic nitrogen-fixing nodules of legumes has not yet been investigated. We investigated regulation and the function of the two Medicago truncatula ERF-VII TFs (MtERF74 and MtERF75) in roots and nodules, MtERF74 and MtERF75 in response to hypoxia stress and during the nodulation process using an RNA interference strategy and targeted proteolysis of MtERF75. Knockdown of MtERF74 and MtERF75 partially blocked the induction of hypoxia-responsive genes in roots exposed to hypoxia stress. In addition, a significant reduction in nodulation capacity and nitrogen fixation activity was observed in mature nodules of double knockdown transgenic roots. Overall, the results indicate that MtERF74 and MtERF75 are involved in the induction of MtNR1 and Pgb1.1 expression for efficient Phytogb-nitric oxide respiration in the nodule.

Signaling by reactive molecules and antioxidants in legume nodules

Legume nodules are symbiotic structures formed as a result of the interaction with rhizobia. Nodules fix atmospheric nitrogen into ammonia that is assimilated by the plant and this process requires strict metabolic regulation and signaling. Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are involved as signal molecules at all stages of symbiosis, from rhizobial infection to nodule senescence. Also, reactive sulfur species (RSS) are emerging as important signals for an efficient symbiosis. Homeostasis of reactive molecules is mainly accomplished by antioxidant enzymes and metabolites and is essential to allow redox signaling while preventing oxidative damage. Here, we examine the metabolic pathways of reactive molecules and antioxidants with an emphasis on their functions in signaling and protection of symbiosis. In addition to providing an update of recent findings while paying tribute to original studies, we identify several key questions. These include the need of new methodologies to detect and quantify ROS, RNS, and RSS, avoiding potential artifacts due to their short lifetimes and tissue manipulation; the regulation of redox-active proteins by post-translational modification; the production and exchange of reactive molecules in plastids, peroxisomes, nuclei, and bacteroids; and the unknown but expected crosstalk between ROS, RNS, and RSS in nodules.

Nitric Oxide Metabolic Pathway in Drought-Stressed Nodules of Faba Bean (Vicia faba L.)

Drought is an environmental stress that strongly impacts plants. It affects all stages of growth and induces profound disturbances that influence all cellular functions. Legumes can establish a symbiosis with Rhizobium-type bacteria, whose function is to fix atmospheric nitrogen in organs called nodules and to meet plant nitrogen needs. Symbiotic nitrogen fixation (SNF) is particularly sensitive to drought. We raised the hypothesis that, in drought-stressed nodules, SNF inhibition is partly correlated to hypoxia resulting from nodule structure compaction and an increased O2 diffusion barrier, and that the nodule energy regeneration involves phytoglobin-nitric oxide (Pgb-NO) respiration. To test this hypothesis, we subjected faba bean (Vicia faba L.) plants nodulated with a Rhizobium laguerreae strain to either drought or osmotic stress. We monitored the N2-fixation activity, the energy state (ATP/ADP ratio), the expression of hypoxia marker genes (alcohol dehydrogenase and alanine aminotransferase), and the functioning of the Pgb-NO respiration in the nodules. The collected data confirmed our hypothesis and showed that (1) drought-stressed nodules were subject to more intense hypoxia than control nodules and (2) NO production increased and contributed via Pgb-NO respiration to the maintenance of the energy state of drought-stressed nodules.

Role of Nitric Oxide of Bacterial Origin in the Medicago truncatula-Sinorhizobium meliloti Symbiosis

Nitric oxide (NO) is a small ubiquitous gaseous molecule that has been found in many host-pathogen interactions. NO has been shown to be part of the defense arsenal of animal cells and more recently of plant cells. To fight this molecular weapon, pathogens have evolved responses consisting of adaptation to NO or degradation of this toxic molecule. More recently, it was shown that NO could also be produced by the pathogen and contributes likewise to the success of the host cell infection. NO is also present during symbiotic interactions. Despite growing knowledge about the role of NO during friendly interactions, data on the specificity of action of NO produced by each partner are scarce, partly due to the multiplicity of NO production systems. In the nitrogen-fixing symbiosis between the soil bacterium Sinorhizobium meliloti and the model legume Medicago truncatula, NO has been detected at all steps of the interaction, where it displays various roles. Both partners contribute to NO production inside the legume root nodules where nitrogen fixation occurs. The study focuses on the role of bacterial NO in this interaction. We used a genetic approach to identify bacterial NO sources in the symbiotic context and to test the phenotype in planta of bacterial mutants affected in NO production. Our results show that only denitrification is a source of bacterial NO in Medicago nodules, giving insight into the role of bacteria-derived NO at different steps of the symbiotic interaction. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Nitrate–Nitrite–Nitric Oxide Pathway: A Mechanism of Hypoxia and Anoxia Tolerance in Plants

Oxygen (O₂) is the most crucial substrate for numerous biochemical processes in plants. Its deprivation is a critical factor that affects plant growth and may lead to death if it lasts for a long time. However, various biotic and abiotic factors cause O₂ deprivation, leading to hypoxia and anoxia in plant tissues. To survive under hypoxia and/or anoxia, plants deploy various mechanisms such as fermentation paths, reactive oxygen species (ROS), reactive nitrogen species (RNS), antioxidant enzymes, aerenchyma, and adventitious root formation, while nitrate (NO₃⁻), nitrite (NO₂⁻), and nitric oxide (NO) have shown numerous beneficial roles through modulating these mechanisms. Therefore, in this review, we highlight the role of reductive pathways of NO formation which lessen the deleterious effects of oxidative damages and increase the adaptation capacity of plants during hypoxia and anoxia. Meanwhile, the overproduction of NO through reductive pathways during hypoxia and anoxia leads to cellular dysfunction and cell death. Thus, its scavenging or inhibition is equally important for plant survival. As plants are also reported to produce a potent greenhouse gas nitrous oxide (N₂O) when supplied with NO₃⁻ and NO₂⁻, resembling bacterial denitrification, its role during hypoxia and anoxia tolerance is discussed here. We point out that NO reduction to N₂O along with the phytoglobin-NO cycle could be the most important NO-scavenging mechanism that would reduce nitro-oxidative stress, thus enhancing plants’ survival during O₂-limited conditions. Hence, understanding the molecular mechanisms involved in reducing NO toxicity would not only provide insight into its role in plant physiology, but also address the uncertainties seen in the global N₂O budget.

Intracellular production of reactive oxygen species and a DAF-FM-related compound in Aspergillus fumigatus in response to antifungal agent exposure

Fungi are ubiquitously present in our living environment and are responsible for crop and infectious diseases. Developing new antifungal agents is constantly needed for their effective control. Here, we investigated fungal cellular responses to an array of antifungal compounds, including plant- and bacteria-derived antifungal compounds. The pathogenic fungus Aspergillus fumigatus generated reactive oxygen species in its hyphae after exposure to the antifungal compounds thymol, farnesol, citral, nerol, salicylic acid, phenazine-1-carbonic acid, and pyocyanin, as well as under oxidative and high-temperature stress conditions. The production of nitric oxide (NO) was determined using diaminofluorescein-FM diacetate (DAF-FM DA) and occurred in response to antifungal compounds and stress conditions. The application of reactive oxygen species or NO scavengers partly suppressed the inhibitory effects of farnesol on germination. However, NO production was not detected in the hyphae using the Greiss method. An LC/MS analysis also failed to detect DAF-FM-T, a theoretical product derived from DAF-FM DA and NO, in the hyphae after antifungal treatments. Thus, the cellular state after exposure to antifungal agents may be more complex than previously believed, and the role of NO in fungal cells needs to be investigated further.

Nitric Oxide Metabolism Affects Germination in Botrytis cinerea and Is Connected to Nitrate Assimilation

Nitric oxide regulates numerous physiological processes in species from all taxonomic groups. Here, its role in the early developmental stages of the fungal necrotroph Botrytis cinerea was investigated. Pharmacological analysis demonstrated that NO modulated germination, germ tube elongation and nuclear division rate. Experimental evidence indicates that exogenous NO exerts an immediate but transitory negative effect, slowing down germination-associated processes, and that this effect is largely dependent on the flavohemoglobin BCFHG1. The fungus exhibited a “biphasic response” to NO, being more sensitive to low and high concentrations than to intermediate levels of the NO donor. Global gene expression analysis in the wild-type and ΔBcfhg1 strains indicated a situation of strong nitrosative and oxidative stress determined by exogenous NO, which was much more intense in the mutant strain, that the cells tried to alleviate by upregulating several defense mechanisms, including the simultaneous upregulation of the genes encoding the flavohemoglobin BCFHG1, a nitronate monooxygenase (NMO) and a cyanide hydratase. Genetic evidence suggests the coordinated expression of Bcfhg1 and the NMO coding gene, both adjacent and divergently arranged, in response to NO. Nitrate assimilation genes were upregulated upon exposure to NO, and BCFHG1 appeared to be the main enzymatic system involved in the generation of the signal triggering their induction. Comparative expression analysis also showed the influence of NO on other cellular processes, such as mitochondrial respiration or primary and secondary metabolism, whose response could have been mediated by NmrA-like domain proteins.

Crosstalk between H2 S and NO: an emerging signalling pathway during waterlogging stress in legume crops

In legumes, waterlogging is a major detrimental factor leading to huge yield losses. Generally, legumes lack tolerance to submergence, and conventional breeding to develop tolerant varieties are limited due to the lack of tolerant germplasm and potential target genes. Moreover, our understanding of the various signalling cascades, their interactions and key pathways induced during waterlogging is limited. Here, we focus on the role of two important plant signalling molecules, viz. hydrogen sulphide (H₂ S) and nitric oxide (NO), during waterlogging stress in legumes. Plants and soil microbes produce these signalling molecules both endogenously and exogenously under various stresses, including waterlogging. NO and H₂ S are known to regulate key physiological pathways, such as stomatal closure, leaf senescence and regulation of numerous stress signalling pathways, while NO plays a pivotal role in adventitious root formation during waterlogging. The crosstalk between H₂ S and NO is synergistic because of the resemblance of their physiological effects and proteomic functions, which mainly operate through cysteine-dependent post-translational modifications via S-nitrosation and persulfidation. Such knowledge has provided novel platforms for researchers to unravel the complexity associated with H₂ S-NO signalling and interactions with plant stress hormones. This review provides an overall summary on H₂ S and NO, including biosynthesis, biological importance, crosstalk, transporter regulation as well as understanding their role during waterlogging using 'multi-omics' approach. Understanding H₂ S and NO signalling will help in deciphering the metabolic interactions and identifying key regulatory genes that could be used for developing waterlogging tolerance in legumes.

Common gene expression patterns are observed in rice roots during associations with plant growth-promoting bacteria, Herbaspirillum seropedicae and Azospirillum brasilense

Non-legume plants such as rice and maize can form beneficial associations with plant growth-promoting bacteria (PGPB) such as Herbaspirillum seropedicae and Azospirillum brasilense. Several studies have shown that these PGPB promote plant growth via multiple mechanisms. Our current understanding of the molecular aspects and signaling between plants like rice and PGPB like Herbaspirillum seropedicae is limited. In this study, we used an experimental system where H. seropedicae could colonize the plant roots and promote growth in wild-type rice. Using this experimental setup, we identified 1688 differentially expressed genes (DEGs) in rice roots, 1 day post-inoculation (dpi) with H. seropedicae. Several of these DEGs encode proteins involved in the flavonoid biosynthetic pathway, defense, hormone signaling pathways, and nitrate and sugar transport. We validated the expression pattern of some genes via RT-PCR. Next, we compared the DEGs identified in this study to those we previously identified in rice roots during associations with another PGPB, Azospirillum brasilense. We identified 628 genes that were differentially expressed during both associations. The expression pattern of these genes suggests that some of these are likely to play a significant role(s) during associations with both H. seropedicae and A. brasilense and are excellent targets for future studies.

Physiological mechanism of the response to Cr(VI) in the aerobic denitrifying ectomycorrhizal fungus Pisolithus sp.1

Pisolithus sp. 1 (P sp. 1) is an ectomycorrhizal fungus (EMF) with a strong Cr(VI) tolerance and reduction ability. The noninvasive microttest technique (NMT), real-time quantitative PCR (qRT-PCR), and the three-dimensional excitation-emission matrix (3D-EEM) were used to deeply explore the physiological mechanism of the P sp. 1 response to Cr(VI) and investigate the relationship between Cr(VI) reduction and denitrification in P sp. Cr(VI) induced the strongest elevations in nitrate reductase (NR) activity and NO production in the mycelia after treatment with Cr(VI) for 48 h under aerobic conditions. The NR inhibitor tungstate significantly inhibited Cr(VI) reduction, proton efflux and the expression of the NR gene (niaD) and NiR gene (niiA). In addition, NO was generated via NR-regulated denitrification. Combined treatments with Cr(VI) and the NO scavenger carboxy-PTIO (cPTIO) significantly increased O₂^-, H₂O₂ and MDA contents and reduced SDH, CAT, GSH, GR and GSNOR activity. Therefore, the NR-driven aerobic denitrifying process requires protons, and the generated NO reduces the oxidative stress effect of Cr(VI) on mycelia by reducing ROS accumulation and lipid peroxidation, enhancing mycelial and CAT activity, and promoting GSH recycling and regeneration. Psp.1 can also secrete humic acid-like and protein-like substances to combine with Cr(III) in a culture system.

Integrated Proteomics and Metabolomics Analysis of Nitrogen System Regulation on Soybean Plant Nodulation and Nitrogen Fixation

The specific mechanisms by which nitrogen affects nodulation and nitrogen fixation in leguminous crops are still unclear. To study the relationship between nitrogen, nodulation and nitrogen fixation in soybeans, dual-root soybean plants with unilateral nodulation were prepared by grafting. At the third trifoliate leaf (V3) to fourth trifoliate leaf (V4) growth stages (for 5 days), nitrogen nutrient solution was added to the non-nodulated side, while nitrogen-free nutrient solution was added to the nodulated side. The experiment was designed to study the effects of exogenous nitrogen on proteins and metabolites in root nodules and provide a theoretical reference for analyzing the physiological mechanisms of the interaction between nitrogen application and nitrogen fixation in soybean root nodules. Compared with no nitrogen treatment, exogenous nitrogen regulated the metabolic pathways of starch and sucrose metabolism, organic acid metabolism, nitrogen metabolism, and amino acid metabolism, among others. Additionally, exogenous nitrogen promoted the synthesis of signaling molecules, including putrescine, nitric oxide, and asparagine in root nodules, and inhibited the transformation of sucrose to malic acid; consequently, the rhizobia lacked energy for nitrogen fixation. In addition, exogenous nitrogen reduced cell wall synthesis in the root nodules, thus inhibiting root nodule growth and nitrogen fixation.

What do we know from the transcriptomic studies investigating the interactions between plants and plant growth-promoting bacteria?

Major crops such as corn, wheat, and rice can benefit from interactions with various plant growth-promoting bacteria (PGPB). Naturally, several studies have investigated the primary mechanisms by which these PGPB promote plant growth. These mechanisms involve biological nitrogen fixation, phytohormone synthesis, protection against biotic and abiotic stresses, etc. Decades of genetic and biochemical studies in the legume-rhizobia symbiosis and arbuscular mycorrhizal symbiosis have identified a few key plant and microbial signals regulating these symbioses. Furthermore, genetic studies in legumes have identified the host genetic pathways controlling these symbioses. But, the same depth of information does not exist for the interactions between host plants and PGPB. For instance, our knowledge of the host genes and the pathways involved in these interactions is very poor. However, some transcriptomic studies have investigated the regulation of gene expression in host plants during these interactions in recent years. In this review, we discuss some of the major findings from these studies and discuss what lies ahead. Identifying the genetic pathway(s) regulating these plant-PGPB interactions will be important as we explore ways to improve crop production sustainably.

Specialization in a Nitrogen-Fixing Symbiosis: Proteome Differences Between Sinorhizobium medicae Bacteria and Bacteroids

Using tandem mass spectrometry (MS/MS), we analyzed the proteome of Sinorhizobium medicae WSM419 growing as free-living cells and in symbiosis with Medicago truncatula. In all, 3,215 proteins were identified, over half of the open reading frames predicted from the genomic sequence. The abundance of 1,361 proteins displayed strong lifestyle bias. In total, 1,131 proteins had similar levels in bacteroids and free-living cells, and the low levels of 723 proteins prevented statistically significant assignments. Nitrogenase subunits comprised approximately 12% of quantified bacteroid proteins. Other major bacteroid proteins included symbiosis-specific cytochromes and FixABCX, which transfer electrons to nitrogenase. Bacteroids had normal levels of proteins involved in amino acid biosynthesis, glycolysis or gluconeogenesis, and the pentose phosphate pathway; however, several amino acid degradation pathways were repressed. This suggests that bacteroids maintain a relatively independent anabolic metabolism. Tricarboxylic acid cycle proteins were highly expressed in bacteroids and no other catabolic pathway emerged as an obvious candidate to supply energy and reductant to nitrogen fixation. Bacterial stress response proteins were induced in bacteroids. Many WSM419 proteins that are not encoded in S. meliloti Rm1021 were detected, and understanding the functions of these proteins might clarify why S. medicae WSM419 forms a more effective symbiosis with M. truncatula than S. meliloti Rm1021.[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.

Effects of nitrogen levels on gene expression and amino acid metabolism in Welsh onion

Background

Welsh onion constitutes an important crop due to its benefits in traditional medicine. Nitrogen is an important nutrient for plant growth and yield; however, little is known about its influence on the mechanisms of Welsh onion regulation genes. In this study, we introduced a gene expression and amino acid analysis of Welsh onion treated with different concentrations of nitrogen (N0, N1, and N2 at 0 kg/ha, 130 kg/ha, and 260 kg/ha, respectively).

Results

Approximately 1,665 genes were differentially regulated with different concentrations of nitrogen. Gene ontology enrichment analysis revealed that the genes involved in metabolic processes, protein biosynthesis, and transportation of amino acids were highly represented. KEGG analysis indicated that the pathways were related to amino acid metabolism, cysteine, beta-alanine, arginine, proline, and glutathione. Differential gene expression in response to varying nitrogen concentrations resulted in different amino acid content. A close relationship between gene expression and the content of amino acids was observed.

Conclusions

This work examined the effects of nitrogen on gene expression and amino acid synthesis and provides important evidence on the efficient use of nitrogen in Welsh onion.

Molecular responses of legumes to abiotic stress: post-translational modifications of proteins and redox signaling

Legumes include several major crops that can fix atmospheric nitrogen in symbiotic root nodules, thus reducing the demand for nitrogen fertilizers and contributing to sustainable agriculture. Global change models predict increases in temperature and extreme weather conditions. This scenario might increase plant exposure to abiotic stresses and negatively affect crop production. Regulation of whole plant physiology and nitrogen fixation in legumes during abiotic stress is complex, and only a few mechanisms have been elucidated. Reactive oxygen species (ROS), reactive nitrogen species (RNS), and reactive sulfur species (RSS) are key players in the acclimation and stress tolerance mechanisms of plants. However, the specific redox-dependent signaling pathways are far from understood. One mechanism by which ROS, RNS, and RSS fulfil their signaling role is the post-translational modification (PTM) of proteins. Redox-based PTMs occur in the cysteine thiol group (oxidation, S-nitrosylation, S-glutathionylation, persulfidation), and also in methionine (oxidation), tyrosine (nitration), and lysine and arginine (carbonylation/glycation) residues. Unraveling PTM patterns under different types of stress and establishing the functional implications may give insight into the underlying mechanisms by which the plant and nodule respond to adverse conditions. Here, we review current knowledge on redox-based PTMs and their possible consequences in legume and nodule biology.

Structural Modeling and in planta Complementation Studies Link Mutated Residues of the Medicago truncatula Nitrate Transporter NPF1.7 to Functionality in Root Nodules

Symbiotic nitrogen fixation is a complex and regulated process that takes place in root nodules of legumes and allows legumes to grow in soils that lack nitrogen. Nitrogen is mostly acquired from the soil as nitrate and its level in the soil affects nodulation and nitrogen fixation. The mechanism(s) by which legumes modulate nitrate uptake to regulate nodule symbiosis remain unclear. In Medicago truncatula, the MtNPF1.7 transporter has been shown to control nodulation, symbiosis, and root architecture. MtNPF1.7 belongs to the nitrate/peptide transporter family and is a symporter with nitrate transport driven by proton(s). In this study we combined in silico structural predictions with in planta complementation of the severely defective mtnip-1 mutant plants to understand the role of a series of distinct amino acids in the transporter's function. Our results support hypotheses about the functional importance of the ExxE(R/K) motif including an essential role for the first glutamic acid of the motif in proton(s) and possibly substrate transport. Results reveal that Motif A, a motif conserved among major facilitator transport (MFS) proteins, is essential for function. We hypothesize that it participates in intradomain packing of transmembrane helices and stabilizing one conformation during transport. Our results also question the existence of a putative TMH4-TMH10 salt bridge. These results are discussed in the context of potential nutrient transport functions for MtNPF1.7. Our findings add to the knowledge of the mechanism of alternative conformational changes as well as symport transport in NPFs and enhance our knowledge of the mechanisms for nitrate signaling.

The Lotus japonicus NPF3.1 Is a Nodule-Induced Gene That Plays a Positive Role in Nodule Functioning

Nitrogen-fixing nodules are new organs formed on legume roots as a result of the beneficial interaction with the soil bacteria, rhizobia. Proteins of the nitrate transporter 1/peptide transporter family (NPF) are largely represented in the subcategory of nodule-induced transporters identified in mature nodules. The role of nitrate as a signal/nutrient regulating nodule functioning has been recently highlighted in the literature, and NPFs may play a central role in both the permissive and inhibitory pathways controlling N₂-fixation efficiency. In this study, we present the characterization of the Lotus japonicus LjNPF3.1 gene. LjNPF3.1 is upregulated in mature nodules. Promoter studies show transcriptional activation confined to the cortical region of both roots and nodules. Under symbiotic conditions, Ljnpf3.1-knockout mutant's display reduced shoot development and anthocyanin accumulation as a result of nutrient deprivation. Altogether, LjNPF3.1 plays a role in maximizing the beneficial outcome of the root nodule symbiosis.

Bacterial nitric oxide metabolism: Recent insights in rhizobia

Nitric oxide (NO) is a reactive gaseous molecule that has several functions in biological systems depending on its concentration. At low concentrations, NO acts as a signaling molecule, while at high concentrations, it becomes very toxic due to its ability to react with multiple cellular targets. Soil bacteria, commonly known as rhizobia, have the capacity to establish a N₂-fixing symbiosis with legumes inducing the formation of nodules in their roots. Several reports have shown NO production in the nodules where this gas acts either as a signaling molecule which regulates gene expression, or as a potent inhibitor of nitrogenase and other plant and bacteria enzymes. A better understanding of the sinks and sources of NO in rhizobia is essential to protect symbiotic nitrogen fixation from nitrosative stress. In nodules, both the plant and the microsymbiont contribute to the production of NO. From the bacterial perspective, the main source of NO reported in rhizobia is the denitrification pathway that varies significantly depending on the species. In addition to denitrification, nitrate assimilation is emerging as a new source of NO in rhizobia. To control NO accumulation in the nodules, in addition to plant haemoglobins, bacteroids also contribute to NO detoxification through the expression of a NorBC-type nitric oxide reductase as well as rhizobial haemoglobins. In the present review, updated knowledge about the NO metabolism in legume-associated endosymbiotic bacteria is summarized.

NO Network for Plant-Microbe Communication Underground: A Review

Mechanisms governing plant-microbe interaction in the rhizosphere attracted a lot of investigative attention in the last decade. The rhizosphere is not simply a source of nutrients and support for the plants; it is rather an ecosystem teeming with diverse flora and fauna including different groups of microbes that are useful as well as harmful for the plants. Plant-microbe interaction occurs via a highly complex communication network that involves sophisticated machinery for the recognition of friend and foe at both sides. On the other hand, nitric oxide (NO) is a key, signaling molecule involved in plant development and defense. Studies on legume-rhizobia symbiosis suggest the involvement of NO during recognition, root hair curling, development of infection threads, nodule development, and nodule senescence. A similar role of NO is also suggested in the case of plant interaction with the mycorrhizal fungi. Another, insight into the plant-microbe interaction in the rhizosphere comes from the recognition of pathogen-associated molecular patterns (PAMPs)/microbe-associated molecular patterns (MAMPs) by the host plant and thereby NO-mediated activation of the defense signaling cascade. Thus, NO plays a major role in mediating the communication between plants and microbes in the rhizosphere. Interestingly, reports suggesting the role of silicon in increasing the number of nodules, enhancing nitrogen fixation, and also the combined effect of silicon and NO may indicate a possibility of their interaction in mediating microbial communication underground. However, the exact role of NO in mediating plant-microbe interaction remains elusive. Therefore, understanding the role of NO in underground plant physiology is very important, especially in relation to the plant's interaction with the rhizospheric microbiome. This will help devise new strategies for protection against phytopathogens and enhancing plant productivity by promoting symbiotic interaction. This review focuses on the role of NO in plant-microbe communication underground.

The Oxidative Paradox in Low Oxygen Stress in Plants

Reactive oxygen species (ROS) are part of aerobic environments, and variations in the availability of oxygen (O2) in the environment can lead to altered ROS levels. In plants, the O2 sensing machinery guides the molecular response to low O2, regulating a subset of genes involved in metabolic adaptations to hypoxia, including proteins involved in ROS homeostasis and acclimation. In addition, nitric oxide (NO) participates in signaling events that modulate the low O2 stress response. In this review, we summarize recent findings that highlight the roles of ROS and NO under environmentally or developmentally defined low O2 conditions. We conclude that ROS and NO are emerging regulators during low O2 signalling and key molecules in plant adaptation to flooding conditions.

Nitric oxide production and signalling in algae

Nitric oxide (NO) was the first identified gaseous messenger and is now well established as a major ubiquitous signalling molecule. The rapid development of our understanding of NO biology in embryophytes came with the partial characterization of the pathways underlying its production and with the decrypting of signalling networks mediating its effects. Notably, the identification of proteins regulated by NO through nitrosation greatly enhanced our perception of NO functions. In comparison, the role of NO in algae has been less investigated. Yet, studies in Chlamydomonas reinhardtii have produced key insights into NO production through the identification of NO-forming nitrite reductase and of S-nitrosated proteins. More intriguingly, in contrast to embryophytes, a few algal species possess a conserved nitric oxide synthase, the main enzyme catalysing NO synthesis in metazoans. This latter finding paves the way for a deeper characterization of novel members of the NO synthase family. Nevertheless, the typical NO-cyclic GMP signalling module transducing NO effects in metazoans is not conserved in algae, nor in embryophytes, highlighting a divergent acquisition of NO signalling between the green and the animal lineages.

Rhizobia: highways to NO

The interaction between rhizobia and their legume host plants conduces to the formation of specialized root organs called nodules where rhizobia differentiate into bacteroids which fix atmospheric nitrogen to the benefit of the plant. This beneficial symbiosis is of importance in the context of sustainable agriculture as legumes do not require the addition of nitrogen fertilizer to grow. Interestingly, nitric oxide (NO) has been detected at various steps of the rhizobium-legume symbiosis where it has been shown to play multifaceted roles. Both bacterial and plant partners are involved in NO synthesis in nodules. To better understand the role of NO, and in particular the role of bacterial NO, at all steps of rhizobia-legumes interaction, the enzymatic sources of NO have to be elucidated. In this review, we discuss different enzymatic reactions by which rhizobia may potentially produce NO. We argue that there is most probably no NO synthase activity in rhizobia, and that instead the NO2- reductase nirK, which is part of the denitrification pathway, is the main bacterial source of NO. The nitrate assimilation pathway might contribute to NO production but only when denitrification is active. The different approaches to measure NO in rhizobia are also addressed.

PGPR Mediated Alterations in Root Traits: Way Toward Sustainable Crop Production

The above ground growth of the plant is highly dependent on the belowground root system. Rhizosphere is the zone of continuous interplay between plant roots and soil microbial communities. Plants, through root exudates, attract rhizosphere microorganisms to colonize the root surface and internal tissues. Many of these microorganisms known as plant growth promoting rhizobacteria (PGPR) improve plant growth through several direct and indirect mechanisms including biological nitrogen fixation, nutrient solubilization, and disease-control. Many PGPR, by producing phytohormones, volatile organic compounds, and secondary metabolites play important role in influencing the root architecture and growth, resulting in increased surface area for nutrient exchange and other rhizosphere effects. PGPR also improve resource use efficiency of the root system by improving the root system functioning at physiological levels. PGPR mediated root trait alterations can contribute to agroecosystem through improving crop stand, resource use efficiency, stress tolerance, soil structure etc. Thus, PGPR capable of modulating root traits can play important role in agricultural sustainability and root traits can be used as a primary criterion for the selection of potential PGPR strains. Available PGPR studies emphasize root morphological and physiological traits to assess the effect of PGPR. However, these traits can be influenced by various external factors and may give varying results. Therefore, it is important to understand the pathways and genes involved in plant root traits and the microbial signals/metabolites that can intercept and/or intersect these pathways for modulating root traits. The use of advanced tools and technologies can help to decipher the mechanisms involved in PGPR mediated determinants affecting the root traits. Further identification of PGPR based determinants/signaling molecules capable of regulating root trait genes and pathways can open up new avenues in PGPR research. The present review updates recent knowledge on the PGPR influence on root architecture and root functional traits and its benefits to the agro-ecosystem. Efforts have been made to understand the bacterial signals/determinants that can play regulatory role in the expression of root traits and their prospects in sustainable agriculture. The review will be helpful in providing future directions to the researchers working on PGPR and root system functioning.

Importance of the Rhizosphere Microbiota in Iron Biofortification of Plants

Increasing the iron content of plant products and iron assimilability represents a major issue for human nutrition and health. This is also a major challenge because iron is not readily available for plants in most cultivated soils despite its abundance in the Earth's crust. Iron biofortification is defined as the enhancement of the iron content in edible parts of plants. This biofortification aims to reach the objectives defined by world organizations for human nutrition and health while being environment friendly. A series of options has been proposed to enhance plant iron uptake and fight against hidden hunger, but they all show limitations. The present review addresses the potential of soil microorganisms to promote plant iron nutrition. Increasing knowledge on the plant microbiota and plant-microbe interactions related to the iron dynamics has highlighted a considerable contribution of microorganisms to plant iron uptake and homeostasis. The present overview of the state of the art sheds light on plant iron uptake and homeostasis, and on the contribution of plant-microorganism (plant-microbe and plant-plant-microbe) interactions to plant nutritition. It highlights the effects of microorganisms on the plant iron status and on the co-occurring mechanisms, and shows how this knowledge may be valued through genetic and agronomic approaches. We propose a change of paradigm based on a more holistic approach gathering plant and microbial traits mediating iron uptake. Then, we present the possible applications in plant breeding, based on plant traits mediating plant-microbe interactions involved in plant iron uptake and physiology.

Nitrogen and Phosphorus Signaling and Transport During Legume-Rhizobium Symbiosis

Nitrogen (N) and phosphorus (P) are the two predominant mineral elements, which are not only essential for plant growth and development in general but also play a key role in symbiotic N fixation in legumes. Legume plants have evolved complex signaling networks to respond to both external and internal levels of these macronutrients to optimize symbiotic N fixation in nodules. Inorganic phosphate (Pi) and nitrate (NO₃ ^-) are the two major forms of P and N elements utilized by plants, respectively. Pi starvation and NO₃ ^- application both reduce symbiotic N fixation via similar changes in the nodule gene expression and invoke local and long-distance, systemic responses, of which N-compound feedback regulation of rhizobial nitrogenase activity appears to operate under both conditions. Most of the N and P signaling and transport processes have been investigated in model organisms, such as Medicago truncatula, Lotus japonicus, Glycine max, Phaseolus vulgaris, Arabidopsis thaliana, Oryza sativa, etc. We attempted to discuss some of these processes wherever appropriate, to serve as references for a better understanding of the N and P signaling and transport during symbiosis.

The functional characterization of LjNRT2.4 indicates a novel, positive role of nitrate for an efficient nodule N2 -fixation activity

Atmospheric nitrogen (N₂₎ -fixing nodules are formed on the roots of legume plants as result of the symbiotic interaction with rhizobia. Nodule functioning requires high amounts of carbon and energy, and therefore legumes have developed finely tuned mechanisms to cope with changing external environmental conditions, including nutrient availability and flooding. The investigation of the role of nitrate as regulator of the symbiotic N₂ fixation has been limited to the inhibitory effects exerted by high external concentrations on nodule formation, development and functioning. We describe a nitrate-dependent route acting at low external concentrations that become crucial in hydroponic conditions to ensure an efficient nodule functionality. Combined genetic, biochemical and molecular studies are used to unravel the novel function of the LjNRT2.4 gene. Two independent null mutants are affected by the nitrate content of nodules, consistent with LjNRT2.4 temporal and spatial profiles of expression. The reduced nodular nitrate content is associated to a strong reduction of nitrogenase activity and a severe N-starvation phenotype observed under hydroponic conditions. We also report the effects of the mutations on the nodular nitric oxide (NO) production and content. We discuss the involvement of LjNRT2.4 in a nitrate-NO respiratory chain taking place in the N₂ -fixing nodules.

Physiological significance of pedospheric nitric oxide for root growth, development and organismic interactions

Nitric oxide (NO) is essential for plant growth and development, as well as interactions with abiotic and biotic environments. Its importance for multiple functions in plants means that tight regulation of NO concentrations is required. This is of particular significance in roots, where NO signalling is involved in processes, such as root growth, lateral root formation, nutrient acquisition, heavy metal homeostasis, symbiotic nitrogen fixation and root-mycorrhizal fungi interactions. The NO signal can also be produced in high levels by microbial processes in the rhizosphere, further impacting root processes. To explore these interesting interactions, in the present review, we firstly summarize current knowledge of physiological processes of NO production and consumption in roots and, thereafter, of processes involved in NO homeostasis in root cells with particular emphasis on root growth, development, nutrient acquisition, environmental stresses and organismic interactions.

The outcomes of the functional interplay of nitric oxide and hydrogen sulfide in metal stress tolerance in plants

Phytotoxicity of metals constraints plants health, metabolism and productivity. The sustainable approaches for minimizing major metals-accrued phytotoxicity have been least explored. The gasotransmitters signaling molecules such as nitric oxide (NO) and hydrogen sulfide (H₂S) play a significant role in the mitigation of major consequences of metals stress. Versatile gaseous signaling molecules, NO and H₂S are involved in the regulation of various physiological processes in plants and their tolerance to abiotic stresses. However, literature available on NO or H₂S stand alone, and the major insights into the roles of NO and/or H₂S in plant tolerance, particularly to metals, remained unclear. Given above, this paper aimed to (a) briefly overview metals and highlight their major phytotoxicity; (b) appraises literature reporting potential mechanisms underlying the roles of NO and H₂S in plant-metal tolerance; (c) crosstalk on NO and H₂S in relation to plant metal tolerance. Additionally, major aspects so far unexplored in the current context have also been mentioned.

Effectiveness of nitrogen fixation in rhizobia

Biological nitrogen fixation in rhizobia occurs primarily in root or stem nodules and is induced by the bacteria present in legume plants. This symbiotic process has fascinated researchers for over a century, and the positive effects of legumes on soils and their food and feed value have been recognized for thousands of years. Symbiotic nitrogen fixation uses solar energy to reduce the inert N2 gas to ammonia at normal temperature and pressure, and is thus today, especially, important for sustainable food production. Increased productivity through improved effectiveness of the process is seen as a major research and development goal. The interaction between rhizobia and their legume hosts has thus been dissected at agronomic, plant physiological, microbiological and molecular levels to produce ample information about processes involved, but identification of major bottlenecks regarding efficiency of nitrogen fixation has proven to be complex. We review processes and results that contributed to the current understanding of this fascinating system, with focus on effectiveness of nitrogen fixation in rhizobia.

Nitric oxide production is involved in maintaining energy state in Alfalfa (Medicago sativa L.) nodulated roots under both salinity and flooding

In Medicago sativa nodulated roots, NR-dependent NO production is involved in maintaining energy state, presumably through phytoglobin NO respiration, under both salinity and hypoxia stress. The response to low and average salinity stress and to a 5 day-long flooding period was analyzed in M. sativa nodulated roots. The two treatments result in a decrease in the biological nitrogen fixation capacity and the energy state (evaluated by the ATP/ADP ratio), and conversely in an increase nitric oxide (NO) production. Under salinity and hypoxia treatments, the use of either sodium tungstate, an inhibitor of nitrate reductase (NR), or carboxy-PTIO, a NO scavenger, results in a decrease in NO production and ATP/ADP ratio, meaning that NR-dependent NO production participates to the maintenance of the nodulated roots energy state.

Identification of client iron-sulfur proteins of the chloroplastic NFU2 transfer protein in Arabidopsis thaliana

Iron-sulfur (Fe-S) proteins have critical functions in plastids, notably participating in photosynthetic electron transfer, sulfur and nitrogen assimilation, chlorophyll metabolism, and vitamin or amino acid biosynthesis. Their maturation relies on the so-called SUF (sulfur mobilization) assembly machinery. Fe-S clusters are synthesized de novo on a scaffold protein complex and then delivered to client proteins via several transfer proteins. However, the maturation pathways of most client proteins and their specificities for transfer proteins are mostly unknown. In order to decipher the proteins interacting with the Fe-S cluster transfer protein NFU2, one of the three plastidial representatives found in Arabidopsis thaliana, we performed a quantitative proteomic analysis of shoots, roots, and seedlings of nfu2 plants, combined with NFU2 co-immunoprecipitation and binary yeast two-hybrid experiments. We identified 14 new targets, among which nine were validated in planta using a binary bimolecular fluorescence complementation assay. These analyses also revealed a possible role for NFU2 in the plant response to desiccation. Altogether, this study better delineates the maturation pathways of many chloroplast Fe-S proteins, considerably extending the number of NFU2 clients. It also helps to clarify the respective roles of the three NFU paralogs NFU1, NFU2, and NFU3.

Medicago truncatula Phytoglobin 1.1 controls symbiotic nodulation and nitrogen fixation via the regulation of nitric oxide concentration

In legumes, phytoglobins (Phytogbs) are known to regulate nitric oxide (NO) during early phase of the nitrogen-fixing symbiosis and to buffer oxygen in functioning nodules. However, their expression profile and respective role in NO control at each stage of the symbiosis remain little-known. We first surveyed the Phytogb genes occurring in Medicago truncatula genome. We analyzed their expression pattern and NO production from inoculation with Sinorhizobium meliloti up to 8 wk post-inoculation. Finally, using overexpression and silencing strategy, we addressed the role of the Phytogb1.1-NO couple in the symbiosis. Three peaks of Phytogb expression and NO production were detected during the symbiotic process. NO upregulates Phytogbs1 expression and downregulates Lbs and Phytogbs3 ones. Phytogb1.1 silencing and overexpression experiments reveal that Phytogb1.1-NO couple controls the progression of the symbiosis: high NO concentration promotes defense responses and nodular organogenesis, whereas low NO promotes the infection process and nodular development. Both NO excess and deficiency provoke a 30% inhibition of nodule establishment. In mature nodules, Phytogb1.1 regulates NO to limit its toxic effects while allowing the functioning of Phytogb-NO respiration to maintain the energetic state. This work highlights the regulatory role played by Phytogb1.1-NO couple in the successive stages of symbiosis.

The Role of Nitric Oxide in Nitrogen Fixation by Legumes

The legume-rhizobia symbiosis is an important process in agriculture because it allows the biological nitrogen fixation (BNF) which contributes to increasing the levels of nitrogen in the soil. Nitric oxide (⋅NO) is a small free radical molecule having diverse signaling roles in plants. Here we present and discuss evidence showing the role of ⋅NO during different stages of the legume-rhizobia interaction such as recognition, infection, nodule development, and nodule senescence. Although the mechanisms by which ⋅NO modulates this interaction are not fully understood, we discuss potential mechanisms including its interaction with cytokinin, auxin, and abscisic acid signaling pathways. In matures nodules, a more active metabolism of ⋅NO has been reported and both the plant and rhizobia participate in ⋅NO production and scavenging. Although ⋅NO has been shown to induce the expression of genes coding for NITROGENASE, controlling the levels of ⋅NO in mature nodules seems to be crucial as ⋅NO was shown to be a potent inhibitor of NITROGENASE activity, to induce nodule senescence, and reduce nitrogen assimilation. In this sense, LEGHEMOGLOBINS (Lbs) were shown to play an important role in the scavenging of ⋅NO and reactive nitrogen species (RNS), potentially more relevant in senescent nodules. Even though ⋅NO can reduce NITROGENASE activity, most reports have linked ⋅NO to positive effects on BNF. This can relate mainly to the regulation of the spatiotemporal distribution of ⋅NO which favors some effects over others. Another plausible explanation for this observation is that the negative effect of ⋅NO requires its direct interaction with NITROGENASE, whereas the positive effect of ⋅NO is related to its signaling function, which results in an amplifier effect. In the near future, it would be interesting to explore the role of environmental stress-induced ⋅NO in BNF.

The role of nitrite and nitric oxide under low oxygen conditions in plants

Plant tissues, particularly roots, can be subjected to periods of hypoxia due to environmental circumstances. Plants have developed various adaptations in response to hypoxic stress and these have been described extensively. Less well-appreciated is the body of evidence demonstrating that scavenging of nitric oxide (NO) and the reduction of nitrate/nitrite regulate important mechanisms that contribute to tolerance to hypoxia. Although ethylene controls hyponasty and aerenchyma formation, NO production apparently regulates hypoxic ethylene biosynthesis. In the hypoxic mitochondrion, cytochrome c oxidase, which is a major source of NO, also is inhibited by NO, thereby reducing the respiratory rate and enhancing local oxygen concentrations. Nitrite can maintain ATP generation under hypoxia by coupling its reduction to the translocation of protons from the inner side of mitochondria and generating an electrochemical gradient. This reaction can be further coupled to a reaction whereby nonsymbiotic haemoglobin oxidizes NO to nitrate. In addition to these functions, nitrite has been reported to influence mitochondrial structure and supercomplex formation, as well as playing a role in oxygen sensing via the N-end rule pathway. These studies establish that nitrite and NO perform multiple functions during plant hypoxia and suggest that further research into the underlying mechanisms is warranted.

The Hemoglobin Bjgb From Bradyrhizobium diazoefficiens Controls NO Homeostasis in Soybean Nodules to Protect Symbiotic Nitrogen Fixation

Legume-rhizobia symbiotic associations have beneficial effects on food security and nutrition, health and climate change. Hypoxia induced by flooding produces nitric oxide (NO) in nodules from soybean plants cultivated in nitrate-containing soils. As NO is a strong inhibitor of nitrogenase expression and activity, this negatively impacts symbiotic nitrogen fixation in soybean and limits crop production. In Bradyrhizobium diazoefficiens, denitrification is the main process involved in NO formation by soybean flooded nodules. In addition to denitrification, nitrate assimilation is another source of NO in free-living B. diazoefficiens cells and a single domain hemoglobin (Bjgb) has been shown to have a role in NO detoxification during nitrate-dependent growth. However, the involvement of Bjgb in protecting nitrogenase against NO in soybean nodules remains unclear. In this work, we have investigated the effect of inoculation of soybean plants with a bjgb mutant on biological nitrogen fixation. By analyzing the proportion of N in shoots derived from N₂-fixation using the ¹⁵N isotope dilution technique, we found that plants inoculated with the bjgb mutant strain had higher tolerance to flooding than those inoculated with the parental strain. Similarly, reduction of nitrogenase activity and nifH expression by flooding was less pronounced in bjgb than in WT nodules. These beneficial effects are probably due to the reduction of NO accumulation in bjgb flooded nodules compared to the wild-type nodules. This decrease is caused by an induction of expression and activity of the denitrifying NO reductase enzyme in bjgb bacteroids. As bjgb deficiency promotes NO-tolerance, the negative effect of NO on nitrogenase is partially prevented and thus demonstrates that inoculation of soybean plants with the B. diazoefficiens bjgb mutant confers protection of symbiotic nitrogen fixation during flooding.

Potential Pathway of Nitrous Oxide Formation in Plants

Plants can produce and emit nitrous oxide (N₂O), a potent greenhouse gas, into the atmosphere, and several field-based studies have concluded that this gas is emitted at substantial amounts. However, the exact mechanisms of N₂O production in plant cells are unknown. Several studies have hypothesised that plants might act as a medium to transport N₂O produced by soil-inhabiting microorganisms. Contrarily, aseptically grown plants and axenic algal cells supplied with nitrate (NO₃) are reported to emit N₂O, indicating that it is produced inside plant cells by some unknown physiological phenomena. In this study, the possible sites, mechanisms, and enzymes involved in N₂O production in plant cells are discussed. Based on the experimental evidence from various studies, we determined that N₂O can be produced from nitric oxide (NO) in the mitochondria of plants. NO, a signaling molecule, is produced through oxidative and reductive pathways in eukaryotic cells. During hypoxia and anoxia, NO₃ in the cytosol is metabolised to produce nitrite (NO₂), which is reduced to form NO via the reductive pathway in the mitochondria. Under low oxygen condition, NO formed in the mitochondria is further reduced to N₂O by the reduced form of cytochrome c oxidase (CcO). This pathway is active only when cells experience hypoxia or anoxia, and it may be involved in N₂O formation in plants and soil-dwelling animals, as reported previously by several studies. NO can be toxic at a high concentration. Therefore, the reduction of NO to N₂O in the mitochondria might protect the integrity of the mitochondria, and thus, protect the cell from the toxicity of NO accumulation under hypoxia and anoxia. As NO₃ is a major source of nitrogen for plants and all plants may experience hypoxic and anoxic conditions owing to soil environmental factors, a significant global biogenic source of N₂O may be its formation in plants via the proposed pathway.

Plant Nitrate Reductases Regulate Nitric Oxide Production and Nitrogen-Fixing Metabolism During the Medicago truncatula-Sinorhizobium meliloti Symbiosis

Nitrate reductase (NR) is the first enzyme of the nitrogen reduction pathway in plants, leading to the production of ammonia. However, in the nitrogen-fixing symbiosis between legumes and rhizobia, atmospheric nitrogen (N₂) is directly reduced to ammonia by the bacterial nitrogenase, which questions the role of NR in symbiosis. Next to that, NR is the best-characterized source of nitric oxide (NO) in plants, and NO is known to be produced during the symbiosis. In the present study, we first surveyed the three NR genes (MtNR1, MtNR2, and MtNR3) present in the Medicago truncatula genome and addressed their expression, activity, and potential involvement in NO production during the symbiosis between M. truncatula and Sinorhizobium meliloti. Our results show that MtNR1 and MtNR2 gene expression and activity are correlated with NO production throughout the symbiotic process and that MtNR1 is particularly involved in NO production in mature nodules. Moreover, NRs are involved together with the mitochondrial electron transfer chain in NO production throughout the symbiotic process and energy regeneration in N₂-fixing nodules. Using an in vivo NMR spectrometric approach, we show that, in mature nodules, NRs participate also in the regulation of energy state, cytosolic pH, carbon and nitrogen metabolism under both normoxia and hypoxia. These data point to the importance of NR activity for the N₂-fixing symbiosis and provide a first explanation of its role in this process.