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

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.

Role of Environmental Factors in Legume-Rhizobium Symbiosis: A Review

Legumes play a pivotal role in addressing global challenges of food and nutrition security by offering a sustainable source of protein and bioactive compounds. The capacity of legumes to establish symbiotic relationships with rhizobia bacteria enables biological nitrogen fixation (BNF), reducing the dependence on chemical fertilizers while enhancing soil health. However, the efficiency of this symbiosis is significantly influenced by environmental factors, such as soil acidity, salinity, temperature, moisture content, light intensity, and nutrient availability. These factors affect key processes, including rhizobia survival, nodule formation, and nitrogenase activity, ultimately determining the growth and productivity of legumes. This review summarizes current knowledge on legume-rhizobia interactions under varying abiotic conditions. It highlights the impact of salinity and acidity in limiting nodule development, soil temperature in regulating microbial community dynamics, and moisture availability in modulating metabolic and hormonal responses during drought and waterlogging. Moreover, the role of essential nutrients, including nitrogen, phosphorus, potassium, and trace elements such as iron, molybdenum, and boron, in optimizing symbiosis is critically analyzed.

The hidden language of plant-beneficial microbes: chemo-signaling dynamics in plant microenvironments

Plants and microorganisms coexist within complex ecosystems, significantly influencing agricultural productivity. Depending on the interaction between the plant and microbes, this interaction can either help or harm plant health. Microbes interact with plants by secreting proteins that influence plant cells, producing bioactive compounds like antibiotics or toxins, and releasing molecules such as N-acyl homoserine lactones to coordinate their behaviour. They also produce phytohormones which help regulate growth and stress responses in plants. Plants also interact with the associated microorganisms by exuding substances such as carbon and nitrogen sources, quorum-sensing molecules, peptide signals, secondary metabolites such as flavonoids and strigolactones. A successful exchange of chemical signals is essential for maintaining these associations, with significant implications for plant growth and development. This review explores the intricate array of signaling molecules and complex mechanisms governing plant-microbe interactions, elucidating the pivotal role of chemo-communication pathways. By examining these molecular dialogues, the review aims to deepen our understanding of chemo-signaling molecules, paving the way for future applications of these networks in promoting agricultural sustainability.

TML1 and TML2 synergistically regulate nodulation and affect arbuscular mycorrhiza in Medicago truncatula

Two symbiotic processes, nodulation and arbuscular mycorrhiza, are primarily controlled by the plant's need for nitrogen (N) and phosphorus (P), respectively. Autoregulation of nodulation (AON) and autoregulation of mycorrhizal symbiosis (AOM) both negatively regulate their respective processes and share multiple components-plants that make too many nodules usually have higher arbuscular mycorrhiza (AM) fungal root colonization. The protein TML (TOO MUCH LOVE) was shown to function in roots to maintain susceptibly to rhizobial infection under low N conditions and control nodule number through AON in Lotus japonicus. Medicago truncatula has two sequence homologs: MtTML1 and MtTML2. We report the generation of stable single and double mutants harboring multiple allelic variations in MtTML1 and MtTML2 using CRISPR-Cas9 targeted mutagenesis and screening of a transposon mutagenesis library. Plants containing single mutations in MtTML1 or MtTML2 produced two to three times the nodules of wild-type plants, whereas plants containing mutations in both genes displayed a synergistic effect, forming 20× more nodules compared to wild-type plants. Examination of expression and heterozygote effects suggests that genetic compensation may play a role in the observed synergy. Plants with mutations in both TMLs only showed mild increases in AM fungal root colonization at later timepoints in our experiments, suggesting that these genes may also play a minor role in AM symbiosis regulation. The mutants created will be useful tools to dissect the mechanism of synergistic action of MtTML1 and MtTML2 in M. truncatula symbiosis with beneficial microbes.

A mass spectrometry-based peptidomic dataset of the spermosphere in common bean (Phaseolus vulgaris L.) seeds

The spermosphere, a dynamic microenvironment surrounding germinating seeds, is shaped by the complex interactions between natural compounds exuded by seeds and seed-associated microbial communities. While peptides exuded by plants are known to influence microbiota diversity, little is known about those specifically exuded by seeds. In this study, we characterised the peptidome profile of the spermosphere for the first time using seeds from eight genotypes of common bean (Phaseolus vulgaris) grown in two contrasting production regions. An untargeted LC-MS/MS peptidomic analysis revealed 3,258 peptides derived from 414 precursor proteins of common bean in the spermosphere. This comprehensive peptidomic dataset provides valuable insights into the characteristics of peptides exuded by common bean seeds in the spermosphere. It can be used to identify peptides with potential antimicrobial or other biological activities, advancing our understanding of the functional roles of seed-exuded peptides in the spermosphere.

TML1 AND TML2 SYNERGISTICALLY REGULATE NODULATION AND AFFECT ARBUSCULAR MYCORRHIZA IN MEDICAGO TRUNCATULA

Two symbiotic processes, nodulation and arbuscular mycorrhiza, are primarily controlled by the plant's need for nitrogen (N) and phosphorus (P), respectively. Autoregulation of Nodulation (AON) and Autoregulation of Mycorrhization (AOM) both negatively regulate their respective processes and share multiple components - plants that make too many nodules usually have higher AM fungal root colonization. The protein TML (TOO MUCH LOVE) was shown to function in roots to maintain susceptibly to rhizobial infection under low N conditions and control nodule number through AON in Lotus japonicus . M. truncatula has two sequence homologs: Mt TML1 and Mt TML2. We report the generation of stable single and double mutants harboring multiple allelic variations in MtTML1 and MtTML2 using CRISPR-Cas9 targeted mutagenesis and screening of a transposon mutagenesis library. Plants containing single mutations in Mt TML1 or Mt TML2 produced 2-3 times the nodules of wild-type plants whereas plants containing mutations in both genes displayed a synergistic effect, forming 20x more nodules compared to wild type plants. Examination of expression and heterozygote effects suggest genetic compensation may play a role in the observed synergy. Plants with mutations in both TMLs only showed mild increases in AM fungal root colonization at later timepoints in our experiments, suggesting these genes may also play a minor role in AM symbiosis regulation. The mutants created will be useful tools to dissect the mechanism of synergistic action of Mt TML1 and Mt TML2 in M. truncatula symbiosis with beneficial microbes.

The Compact Root Architecture 2 systemic pathway is required for the repression of cytokinins and miR399 accumulation in Medicago truncatula N-limited plants

Legume plants can acquire mineral nitrogen (N) either through their roots or via a symbiotic interaction with N-fixing rhizobia bacteria housed in root nodules. To identify shoot-to-root systemic signals acting in Medicago truncatula plants at N deficit or N satiety, plants were grown in a split-root experimental design in which either high or low N was provided to half of the root system, allowing the analysis of systemic pathways independently of any local N response. Among the plant hormone families analyzed, the cytokinin trans-zeatin accumulated in plants at N satiety. Cytokinin application by petiole feeding led to inhibition of both root growth and nodulation. In addition, an exhaustive analysis of miRNAs revealed that miR2111 accumulates systemically under N deficit in both shoots and non-treated distant roots, whereas a miRNA related to inorganic phosphate (Pi) acquisition, miR399, accumulates in plants grown under N satiety. These two accumulation patterns are dependent on Compact Root Architecture 2 (CRA2), a receptor required for C-terminally Encoded Peptide (CEP) signaling. Constitutive ectopic expression of miR399 reduced nodule numbers and root biomass depending on Pi availability, suggesting that the miR399-dependent Pi-acquisition regulatory module controlled by N availability affects the development of the whole legume plant root system.

Isolation and Characterization of High-Temperature-Tolerant Mutants of Bradyrhizobium diazoefficiens USDA110 by Carbon-Ion Beam Irradiation

Biofertilizers are promising technologies for achieving sustainable agriculture. However, high-temperature tolerance is a constraint that limits the function of microbial inoculants. To characterize the genetic changes responsible for the high-temperature tolerance of rhizobia, mutant screening was performed using Bradyrhizobium diazoefficiens USDA110. The wild-type cells were mutagenized with carbon-ion irradiation, and two mutant strains, designated M10 and M14, were obtained after a three-day heat-shock treatment at 43 °C. In particular, M14 showed superior growth at 36 °C, at which temperature growth of the wild type was extremely slow, whereas M14 grew more slowly than the wild type at 32 °C. Whole-genome sequencing revealed that M10 had seven point mutations, whereas M14 had eight point mutations together with a 1.27 Mb inversion. RNA sequencing showed that the number of differentially expressed genes greatly exceeded the actual number of induced mutations. In M14, a gene cluster associated with pyruvate metabolism was markedly downregulated, probably because of disjunction with the promoter region after inversion, and was considered to be the cause of the slow growth rate of M14 at 32 °C. Notably, transmembrane proteins, including porins, were enriched among the genes upregulated in both M10 and M14. M14 was confirmed to retain symbiotic functions with soybeans. These results indicate that high-temperature tolerance was conferred by random mutagenesis while the symbiotic functions of rhizobia was maintained.

Comparative proteomics analysis of root and nodule mitochondria of soybean

Legumes perform symbiotic nitrogen fixation through rhizobial bacteroids housed in specialised root nodules. The biochemical process is energy-intensive and consumes a huge carbon source to generate sufficient reducing power. To maintain the symbiosis, malate is supplied by legume nodules to bacteroids as their major carbon and energy source in return for ammonium ions and nitrogenous compounds. To sustain the carbon supply to bacteroids, nodule cells undergo drastic reorganisation of carbon metabolism. Here, a comprehensive quantitative comparison of the mitochondrial proteomes between root nodules and uninoculated roots was performed using data-independent acquisition proteomics, revealing the modulations in nodule mitochondrial proteins and pathways in response to carbon reallocation. Corroborated our findings with that from the literature, we believe nodules preferably allocate cytosolic phosphoenolpyruvates towards malate synthesis in lieu of pyruvate synthesis, and nodule mitochondria prefer malate over pyruvate as the primary source of NADH for ATP production. Moreover, the differential regulation of respiratory chain-associated proteins suggests that nodule mitochondria could enhance the efficiencies of complexes I and IV for ATP synthesis. This study highlighted a quantitative proteomic view of the mitochondrial adaptation in soybean nodules.

In Vitro: The Extraordinary Enhancement in Rutin Accumulation and Antioxidant Activity in Philodendron "Imperial Red" Plantlets Using Ti-Mo-Ni-O Nanotubes as a Novel Elicitor

Rutin, a flavonoid phytochemical compound, plays a vital role in human health. It is used in treating capillary fragility and has anti-Alzheimer, anti-inflammatory, and antioxidant effects. In this study, Ti-Mo-Ni-O nanotubes (NTs) were used, for the first time, in an unprecedented plant biotechnology application, wherein in vitro Philodendron shoots (Philodendron erubescens) known as "Imperial Red" were targeted for rutin accumulation. The antioxidant responses and the accumulation of rutin were evaluated in treated Philodendron erubescens (P. erubescens) shoots using 5.0 mg/L of Ti-Mo-Ni-O NTs. The total phenolic content and total flavonoid content were estimated, and an ABTS+ assay, FRAP assay, and iron metal chelation assay were performed. The application of Ti-Mo-Ni-O NTs enhanced the rutin content considerably from 0.02 mg/g to 2.96 mg/g for dry-weight shootlet extracts. Therefore, the use of Ti-Mo-Ni-O NTs is proposed to be a superior alternative to elevate the rutin content. The aim of the current study is to target P. erubescens shoots grown in vitro for the accumulation of rutin compounds using Ti-Mo-Ni-O NT powder, to determine the quantitative and qualitative accumulation of rutin via HPLC-DAD analysis, and to estimate the antioxidant activity of P. erubescens shoot extract. This study presents a novel methodology for utilizing nano-biotechnology in the synthesis of plant secondary metabolites.

Microbe-dependent and independent nitrogen and phosphate acquisition and regulation in plants

Nitrogen (N) and phosphorus (P) are the most important macronutrients required for plant growth and development. To cope with the limited and uneven distribution of N and P in complicated soil environments, plants have evolved intricate molecular strategies to improve nutrient acquisition that involve adaptive root development, production of root exudates, and the assistance of microbes. Recently, great advances have been made in understanding the regulation of N and P uptake and utilization and how plants balance the direct uptake of nutrients from the soil with the nutrient acquisition from beneficial microbes such as arbuscular mycorrhiza. Here, we summarize the major advances in these areas and highlight plant responses to changes in nutrient availability in the external environment through local and systemic signals.

Different responses of Sinorhizobium sp. upon Pb and Zn exposure: Mineralization versus complexation

Lead (Pb) and zinc (Zn) have been discharged into environment and may negatively impact ecological security. Rhizobia has gained attention due to their involvement in the restoration of metal polluted soils. However, little is known about the responses of rhizobia under Pb and Zn stress, especially the roles played by extracellular polymeric substances (EPS) in the resistance of these two metals. Here, Sinorhizobium sp. C10 was isolated from soil around a mining area and was exposed to a series of Pb/Zn treatments. The cell morphology and surface mineral crystals, EPS content and fluorescent substances were determined. In addition, the extracellular polysaccharides and proteins were characterized by attenuated total reflection infrared spectroscopy (ATR-IR) and X-ray photoelectron spectroscopy (XPS). The results showed that Zn stress induced the synthesis of EPS by C10 cells. Functional groups of polysaccharides (CO) and proteins (C-O/C-N) were involved in complexation with Zn. In contrast, C10 resisted Pb stress by forming lead phosphate (Pb3(PO4)2) on the cell surface. Galactose (Gal) and tyrosine played key roles in resistance to the Zn toxicity, whereas glucosamine (N-Glc) was converted to glucose in large amounts during extracellular Pb precipitation. Together, this study demonstrated that C10 possessed different strategies to detoxify the two metals, and could provide basis for bioremediation of Pb and Zn polluted sites.

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.

Localized osmotic stress activates systemic responses to N limitation in Medicago truncatula-Sinorhizobium symbiotic plants

In mature symbiotic root nodules, differentiated rhizobia fix atmospheric dinitrogen and provide ammonium to fulfill the plant nitrogen (N) demand. The plant enables this process by providing photosynthates to the nodules. The symbiosis is adjusted to the whole plant N demand thanks to systemic N signaling controlling nodule development. Symbiotic plants under N deficit stimulate nodule expansion and activate nodule senescence under N satiety. Besides, nodules are highly sensitive to drought. Here, we used split-root systems to characterize the systemic responses of symbiotic plants to a localized osmotic stress. We showed that polyéthylène glycol (PEG) application rapidly inhibited the symbiotic dinitrogen fixation activity of nodules locally exposed to the treatment, resulting to the N limitation of the plant supplied exclusively by symbiotic dinitrogen fixation. The localized PEG treatment triggered systemic signaling stimulating nodule development in the distant untreated roots. This response was associated with an enhancement of the sucrose allocation. Our analyses showed that transcriptomic reprogramming associated with PEG and N deficit systemic signaling(s) shared many targets transcripts. Altogether, our study suggests that systemic N signaling is a component of the adaptation of the symbiotic plant to the local variations of its edaphic environment.

The role of microbial interactions on rhizobial fitness

Rhizobia are soil bacteria that can establish a nitrogen-fixing symbiosis with legume plants. As horizontally transmitted symbionts, the life cycle of rhizobia includes a free-living phase in the soil and a plant-associated symbiotic phase. Throughout this life cycle, rhizobia are exposed to a myriad of other microorganisms that interact with them, modulating their fitness and symbiotic performance. In this review, we describe the diversity of interactions between rhizobia and other microorganisms that can occur in the rhizosphere, during the initiation of nodulation, and within nodules. Some of these rhizobia-microbe interactions are indirect, and occur when the presence of some microbes modifies plant physiology in a way that feeds back on rhizobial fitness. We further describe how these interactions can impose significant selective pressures on rhizobia and modify their evolutionary trajectories. More extensive investigations on the eco-evolutionary dynamics of rhizobia in complex biotic environments will likely reveal fascinating new aspects of this well-studied symbiotic interaction and provide critical knowledge for future agronomical applications.

Enhance of tomato production and induction of changes on the organic profile mediated by Rhizobium biofortification

Introduction

The extensive use of chemical fertilizers has served as a response to the increasing need for crop production in recent decades. While it addresses the demand for food, it has resulted in a decline in crop productivity and a heightened negative environmental impact. In contrast, plant probiotic bacteria (PPB) offer a promising alternative to mitigate the negative consequences of chemical fertilizers. PPB can enhance nutrient availability, promote plant growth, and improve nutrient uptake efficiency, thereby reducing the reliance on chemical fertilizers.

Methods

This study aimed to evaluate the impact of native Rhizobium strains, specifically Rhizobium calliandrae LBP2-1, Rhizobium mayense NSJP1-1, and Rhizobium jaguaris SJP1- 2, on the growth, quality, and rhizobacterial community of tomato crops. Various mechanisms promoting plant growth were investigated, including phosphate solubilization, siderophore production, indole acetic acid synthesis, and cellulose and cellulase production. Additionally, the study involved the assessment of biofilm formation and root colonization by GFP-tagged strains, conducted a microcosm experiment, and analyzed the microbial community using metagenomics of rhizospheric soil.

Results

The results showed that the rhizobial strains LBP2-1, NSJP1-1 and SJP1-2 had the ability to solubilize dicalcium phosphate, produce siderophores, synthesize indole acetic acid, cellulose production, biofilm production, and root colonization. Inoculation of tomato plants with native Rhizobium strains influenced growth, fruit quality, and plant microbiome composition. Metagenomic analysis showed increased Proteobacteria abundance and altered alpha diversity indices, indicating changes in rhizospheric bacterial community.

Discussion

Our findings demonstrate the potential that native Rhizobium strains have to be used as a plant probiotic in agricultural crops for the generation of safe food and high nutritional value.