The rhizosphere of a drought-tolerant plant species in Morocco: A refuge of high microbial diversity with no taxon preference

Arid and semi-arid areas are facing increasingly severe water deficits that are being intensified by global climate changes. Microbes associated with plants native to arid regions provide valuable benefits to plants, especially in water-stressed environments. In this study, we used 16S rDNA metabarcoding analysis to examine the bacterial communities in the bulk soil, rhizosphere and root endosphere of the plant Malva sylvestris L. in Morocco, along a gradient of precipitation. We found that the rhizosphere of M. sylvestris did not show significant differences in beta-diversity compared to bulk soil, although, it did display an increased degree of alpha-diversity. The endosphere was largely dominated by the genus Rhizobium and displayed remarkable variation between plants, which could not be attributed to any of the variables observed in this study. Overall, the effects of precipitation level were relatively weak, which may be related to the intense drought in Morocco at the time of sampling. The dominance of Rhizobium in a non-leguminous plant is particularly noteworthy and may permit the utilization of this bacterial taxon to augment drought tolerance; additionally, the absence of any notable selection of the rhizosphere of M. sylvestris suggests that it is not significatively affecting its soil environment.

Rhizobial-induced phosphatase GmPP2C61A positively regulates soybean nodulation

Symbiotic nitrogen fixation (SNF) is crucial for legumes, providing them with the nitrogen necessary for plant growth and development. Nodulation is the first step in the establishment of SNF. However, the determinant genes in soybean nodulation and the understanding of the underlying molecular mechanisms governing nodulation are still limited. Herein, we identified a phosphatase, GmPP2C61A, which was specifically induced by rhizobia inoculation. Using transgenic hairy roots harboring GmPP2C61A::GUS, we showed that GmPP2C61A was mainly induced in epidermal cells following rhizobia inoculation. Functional analysis revealed that knockdown or knock-out of GmPP2C61A significantly reduced the number of nodules, while overexpression of GmPP2C61A promoted nodule formation. Additionally, GmPP2C61A protein was mainly localized in the cytoplasm and exhibited conserved phosphatase activity in vitro. Our findings suggest that phosphatase GmPP2C61A serves as a critical regulator in soybean nodulation, highlighting its potential significance in enhancing symbiotic nitrogen fixation.

Molecular module GmPTF1a/b-GmNPLa regulates rhizobia infection and nodule formation in soybean

Nodulation begins with the initiation of infection threads (ITs) in root hairs. Though mutual recognition and early symbiotic signaling cascades in legumes are well understood, molecular mechanisms underlying bacterial infection processes and successive nodule organogenesis remain largely unexplored. We functionally investigated a novel pectate lyase enzyme, GmNPLa, and its transcriptional regulator GmPTF1a/b in soybean (Glycine max), where their regulatory roles in IT development and nodule formation were elucidated through investigation of gene expression patterns, bioinformatics analysis, biochemical verification of genetic interactions, and observation of phenotypic impacts in transgenic soybean plants. GmNPLa was specifically induced by rhizobium inoculation in root hairs. Manipulation of GmNPLa produced remarkable effects on IT and nodule formation. GmPTF1a/b displayed similar expression patterns as GmNPLa, and manipulation of GmPTF1a/b also severely influenced nodulation traits. LI soybeans with low nodulation phenotypes were nearly restored to HI nodulation level by complementation of GmNPLa and/or GmPTF1a. Further genetic and biochemical analysis demonstrated that GmPTF1a can bind to the E-box motif to activate transcription of GmNPLa, and thereby facilitate nodulation. Taken together, our findings potentially reveal novel mediation of cell wall gene expression involving the basic helix-loop-helix transcription factor GmPTF1a/b acts as a key early regulator of nodulation in soybean.

Both incompatible and compatible rhizobia inhabit the intercellular spaces of leguminous root nodules

In addition to rhizobia, many types of co-existent bacteria are found in leguminous root nodules, but their habitats are unclear. To investigate this phenomenon, we labeled Bradyrhizobium diazoefficiens USDA122 and Bradyrhizobium sp. SSBR45 with Discosoma sp. red fluorescent protein (DsRed) or enhanced green fluorescent protein (eGFP). USDA122 enhances soybean growth by forming effective root nodules, but SSBR45 does not form any nodules. Using low-magnification laser scanning confocal microscopy, we found that infected cells in the central zone of soybean nodules appeared to be occupied by USDA122. Notably, high-magnification microscopy after co-inoculation of non-fluorescent USDA122 and fluorescence-labeled SSBR45 also revealed that SSBR45 inhabits the intercellular spaces of healthy nodules. More unexpectedly, co-inoculation of eGFP-labeled USDA122 and DsRed-labeled SSBR45 (and vice versa) revealed the presence of USDA122 bacteria in both the symbiosomes of infected cells and in the apoplasts of healthy nodules. We then next inspected nodules formed after a mixed inoculation of differently-labeled USDA122, without SSBR45, and confirmed the inhabitation of the both populations of USDA122 in the intercellular spaces. In contrast, infected cells were occupied by single-labeled USDA122. We also observed Mesorhizobium loti in the intercellular spaces of active wild-type nodules of Lotus japonicus using transmission electron microscopy. Compatible intercellular rhizobia have been described during nodule formation of several legume species and in some mutants, but our evidence suggests that this type of colonization may occur much more commonly in leguminous root nodules.

Signaling in Legume-Rhizobia Symbiosis

Legumes represent an important source of food protein for human nutrition and animal feed. Therefore, sustainable production of legume crops is an issue of global importance. It is well-known that legume-rhizobia symbiosis allows an increase in the productivity and resilience of legume crops. The efficiency of this mutualistic association strongly depends on precise regulation of the complex interactions between plant and rhizobia. Their molecular dialogue represents a complex multi-staged process, each step of which is critically important for the overall success of the symbiosis. In particular, understanding the details of the molecular mechanisms behind the nodule formation and functioning might give access to new legume cultivars with improved crop productivity. Therefore, here we provide a comprehensive literature overview on the dynamics of the signaling network underlying the development of the legume-rhizobia symbiosis. Thereby, we pay special attention to the new findings in the field, as well as the principal directions of the current and prospective research. For this, here we comprehensively address the principal signaling events involved in the nodule inception, development, functioning, and senescence.

Effect of glyphosate on the growth and survival of rhizobia isolated from root nodules of grass pea (Lathyrus sativus L.)

Grass pea (L. sativus L.) is a widely cultivated crop worldwide, forming a symbiotic relationship with nitrogen-fixing rhizobia. Glyphosate is commonly used by farmers for weed control during agricultural processes. However, the application of this chemical herbicide negatively impacts soil fertility by affecting the nitrogen-fixing rhizobia. This study aimed to assess the effects of glyphosate on rhizobia isolated from healthy and robust Grass pea plants. Specifically, Grass pea plants exhibiting vigorous growth and a healthy appearance were intentionally selected to isolate rhizobia from their root nodules. The isolated rhizobia were then characterized based on their morphological features, biochemical properties, and resistance to abiotic traits. Rhizobial isolates from grass peas exhibited Gram-negative, rod-shaped morphology, milky colony color, and variable colony sizes. Additionally, the majority displayed smooth colony surfaces on yeast extract mannitol agar medium. Based on morphological and biochemical characteristics, the isolates could be grouped under the genus Rhizobium. Optimum growth conditions for these isolates were observed at temperatures between 28 and 38 °C, pH levels ranging from 5 to 8, and salt (NaCl) concentrations of 0.5% and 1%. At a concentration of 20 mL L-1, glyphosate inhibited 5.52-47% of the Rhizobium population. The inhibition percentage increased to 17.1-53.38% at a concentration of 40 mL L-1. However, when exposed to a higher concentration (60 mL/L) of glyphosate, 87% of the isolates were inhibited. The number of colonies after glyphosate exposure was significantly dependent on concentration, and there were notable differences between treatments with varying glyphosate concentrations (p < 0.05). Glyphosate negatively impacted the survival of grass pea rhizobia, leading to a reduction in the Rhizobium population (CFU). However, the effect varied between Rhizobium isolated from grass pea root nodules.

Cellular and molecular basis of symbiotic nodule development

Root nodule development plays a vital role in establishing the mutualistic relationship between legumes and nitrogen-fixing rhizobia. Two primary processes are involved in nodule development: formative cell divisions in the root cortex and the subsequent differentiation of nodule cells. The first process involves the mitotic reactivation of differentiated root cortex cells to form nodule primordium after perceiving symbiotic signals. The second process enables the nascent nodule primordium cells to develop into various cell types, leading to the creation of a functional nodule capable of supporting nitrogen fixation. Thus, both division and differentiation of nodule cells are crucial for root nodule development. This review provides an overview of the most recent advancements in comprehending the cellular and molecular mechanisms underlying symbiotic nodule development in legumes.

Cytoskeleton as a roadmap navigating rhizobia to establish symbiotic root nodulation in legumes

Legumes enter into symbiotic associations with soil nitrogen-fixing rhizobia, culminating in the creation of new organs, root nodules. This complex process relies on chemical and physical interaction between legumes and rhizobia, including early signalling events informing the host legume plant of a potentially beneficial microbe and triggering the nodulation program. The great significance of this plant-microbe interaction rests upon conversion of atmospheric dinitrogen not accessible to plants into a biologically active form of ammonia available to plants. The plant cytoskeleton consists in a highly dynamic network and undergoes rapid remodelling upon sensing various developmental and environmental cues, including response to attachment, internalization, and accommodation of rhizobia in plant root and nodule cells. This dynamic nature is governed by cytoskeleton-associated proteins that modulate cytoskeletal behaviour depending on signal perception and transduction. Precisely localized cytoskeletal rearrangements are therefore essential for the uptake of rhizobia, their targeted delivery, and establishing beneficial root nodule symbiosis. This review summarizes current knowledge about rhizobia-dependent rearrangements and functions of the cytoskeleton in legume roots and nodules. General patterns and nodule type-, nodule stage-, and species-specific aspects of actin filaments and microtubules remodelling are discussed. Moreover, emerging evidence is provided about fine-tuning the root nodulation process through cytoskeleton-associated proteins. We also consider future perspectives on dynamic localization studies of the cytoskeleton during early symbiosis utilizing state of the art molecular and advanced microscopy approaches. Based on acquired detailed knowledge of the mutualistic interactions with microbes, these approaches could contribute to broader biotechnological crop improvement.

The Rpf107 gene, a homolog of LOR, is required for the symbiotic nodulation of Robinia pseudoacacia

MAIN CONCLUSION

Rpf107 is involved in the infection process of rhizobia and the maintenance of symbiotic nitrogen fixation in black locust root nodules. The LURP-one related (LOR) protein family plays a pivotal role in mediating plant defense responses against both biotic and abiotic stresses. However, our understanding of its function in the symbiotic interaction between legumes and rhizobia remains limited. Here, Rpf107, a homolog of LOR, was identified in Robinia pseudoacacia (black locust). The subcellular localization of Rpf107 was analyzed, and its function was investigated using RNA interference (RNAi) and overexpression techniques. The subcellular localization assay revealed that Rpf107 was mainly distributed in the plasma membrane and nucleus. Rpf107 silencing prevented rhizobial infection and hampered plant growth. The number of infected cells in the nitrogen fixation zone of the Rpf107-RNAi nodules was also noticeably lower than that in the control nodules. Notably, Rpf107 silencing resulted in bacteroid degradation and the premature aging of nodules. In contrast, the overexpression of Rpf107 delayed the senescence of nodules and prolonged the nitrogen-fixing ability of nodules. These results demonstrate that Rpf107 was involved in the infection of rhizobia and the maintenance of symbiotic nitrogen fixation in black locust root nodules. The findings reveal that a member of the LOR protein family plays a role in leguminous root nodule symbiosis, which is helpful to clarify the functions of plant LOR protein family and fully understand the molecular mechanisms underlying legume-rhizobium symbiosis.

A rare non-canonical splice site in Trema orientalis SYMRK does not affect its dual symbiotic functioning in endomycorrhiza and rhizobium nodulation

BACKGROUND

Nitrogen-fixing nodules occur in ten related taxonomic lineages interspersed with lineages of non-nodulating plant species. Nodules result from an endosymbiosis between plants and diazotrophic bacteria; rhizobia in the case of legumes and Parasponia and Frankia in the case of actinorhizal species. Nodulating plants share a conserved set of symbiosis genes, whereas related non-nodulating sister species show pseudogenization of several key nodulation-specific genes. Signalling and cellular mechanisms critical for nodulation have been co-opted from the more ancient plant-fungal arbuscular endomycorrhizal symbiosis. Studies in legumes and actinorhizal plants uncovered a key component in symbiotic signalling, the LRR-type SYMBIOSIS RECEPTOR KINASE (SYMRK). SYMRK is essential for nodulation and arbuscular endomycorrhizal symbiosis. To our surprise, however, despite its arbuscular endomycorrhizal symbiosis capacities, we observed a seemingly critical mutation in a donor splice site in the SYMRK gene of Trema orientalis, the non-nodulating sister species of Parasponia. This led us to investigate the symbiotic functioning of SYMRK in the Trema-Parasponia lineage and to address the question of to what extent a single nucleotide polymorphism in a donor splice site affects the symbiotic functioning of SYMRK.

RESULTS

We show that SYMRK is essential for nodulation and endomycorrhization in Parasponia andersonii. Subsequently, it is revealed that the 5'-intron donor splice site of SYMRK intron 12 is variable and, in most dicotyledon species, doesn't contain the canonical dinucleotide 'GT' signature but the much less common motif 'GC'. Strikingly, in T. orientalis, this motif is converted into a rare non-canonical 5'-intron donor splice site 'GA'. This SYMRK allele, however, is fully functional and spreads in the T. orientalis population of Malaysian Borneo. A further investigation into the occurrence of the non-canonical GA-AG splice sites confirmed that these are extremely rare.

CONCLUSION

SYMRK functioning is highly conserved in legumes, actinorhizal plants, and Parasponia. The gene possesses a non-common 5'-intron GC donor splice site in intron 12, which is converted into a GA in T. orientalis accessions of Malaysian Borneo. The discovery of this functional GA-AG splice site in SYMRK highlights a gap in our understanding of splice donor sites.

An emerging role of heterotrimeric G-proteins in nodulation and nitrogen sensing

MAIN CONCLUSION

A comprehensive understanding of nitrogen signaling cascades involving heterotrimeric G-proteins and their putative receptors can assist in the production of nitrogen-efficient plants. Plants are immobile in nature, so they must endure abiotic stresses including nutrient stress. Plant development and agricultural productivity are frequently constrained by the restricted availability of nitrogen in the soil. Non-legume plants acquire nitrogen from the soil through root membrane-bound transporters. In depleted soil nitrogen conditions, legumes are naturally conditioned to fix atmospheric nitrogen with the aid of nodulation elicited by nitrogen-fixing bacteria. Moreover, apart from the symbiotic nitrogen fixation process, nitrogen uptake from the soil can also be a significant secondary source to satisfy the nitrogen requirements of legumes. Heterotrimeric G-proteins function as molecular switches to help plant cells relay diverse stimuli emanating from external stress conditions. They are comprised of Gα, Gβ and Gγ subunits, which cooperate with several downstream effectors to regulate multiple plant signaling events. In the present review, we concentrate on signaling mechanisms that regulate plant nitrogen nutrition. Our review highlights the potential of heterotrimeric G-proteins, together with their putative receptors, to assist the legume root nodule symbiosis (RNS) cascade, particularly during calcium spiking and nodulation. Additionally, the functions of heterotrimeric G-proteins in nitrogen acquisition by plant roots as well as in improving nitrogen use efficiency (NUE) have also been discussed. Future research oriented towards heterotrimeric G-proteins through genome editing tools can be a game changer in the enhancement of the nitrogen fixation process. This will foster the precise manipulation and production of plants to ensure global food security in an era of climate change by enhancing crop productivity and minimizing reliance on external inputs.

Phylogeny and symbiotic effectiveness of indigenous rhizobial microsymbionts of common bean (Phaseolus vulgaris L.) in Malkerns, Eswatini

In most legumes, the rhizobial symbionts exhibit diversity across different environments. Although common bean (Phaseolus vulgaris L.) is one of the important legumes in southern Africa, there is no available information on the genetic diversity and N2-fixing effectiveness of its symbionts in Malkerns, Eswatini. In this study, we assessed the phylogenetic positions of rhizobial microsymbionts of common bean from Malkerns in Eswatini. The isolates obtained showed differences in morpho-physiology and N2-fixing efficiency. A dendrogram constructed from the ERIC-PCR banding patterns, grouped a total of 88 tested isolates into 80 ERIC-PCR types if considered at a 70% similarity cut-off point. Multilocus sequence analysis using 16S rRNA, rpoB, dnaK, gyrB, and glnII and symbiotic (nifH and nodC) gene sequences closely aligned the test isolates to the type strains of Rhizobium muluonense, R. paranaense, R. pusense, R. phaseoli and R. etli. Subjecting the isolates in this study to further description can potentially reveal novel species. Most of the isolates tested were efficient in fixing nitrogen and elicited greater stomatal conductance and photosynthetic rates in the common bean. Relative effectiveness (RE) varied from 18 to 433%, with 75 (85%) out of the 88 tested isolates being more effective than the nitrate fed control plants.

VPT-like genes modulate Rhizobium-legume symbiosis and phosphorus adaptation

Although vacuolar phosphate transporters (VPTs) are essential for plant phosphorus adaptation, their role in Rhizobium-legume symbiosis is unclear. In this study, homologous genes of VPT1 (MtVPTs) were identified in Medicago truncatula to assess their roles in Rhizobium-legume symbiosis and phosphorus adaptation. MtVPT2 and MtVPT3 mainly positively responded to low and high phosphate, respectively. However, both mtvpt2 and mtvpt3 mutants displayed shoot phenotypes with high phosphate sensitivity and low phosphate tolerance. The root-to-shoot phosphate transfer efficiency was significantly enhanced in mtvpt3 but weakened in mtvpt2, accompanied by lower and higher root cytosolic inorganic phosphate (Pi) concentration, respectively. Low phosphate induced MtVPT2 and MtVPT3 expressions in nodules. MtVPT2 and MtVPT3 mutations markedly reduced the nodule number and nitrogenase activity under different phosphate conditions. Cytosolic Pi concentration in nodules was significantly lower in mtvpt2 and mtvpt3 than in the wildtype, especially in tissues near the base of nodules, probably due to inhibition of long-distance Pi transport and cytosolic Pi supply. Also, mtvpt2 and mtvpt3 could not maintain a stable cytosolic Pi level in the nodule fixation zone as the wildtype under low phosphate stress. These findings show that MtVPT2 and MtVPT3 modulate phosphorus adaptation and rhizobia-legume symbiosis, possibly by regulating long-distance Pi transport.

G-type receptor-like kinase AsNIP43 interacts with rhizobia effector nodulation outer protein P and is required for symbiosis

In the Rhizobium-Legume symbiosis, the nodulation outer protein P (NopP) effector is one of the key regulators for rhizobial infection and nodule organogenesis. However, the molecular mechanism through which host legume plants sense NopP remains largely unknown. Here, we constructed an nopP deletion mutant of Mesorhizobium huakuii and found that nopP negatively regulates nodulation on Chinese milk vetch (Astragalus sinicus). Screening for NopP interacting proteins in host plants using the yeast 2-hybrid system identified NopP interacting protein 43 (AsNIP43), which encodes a G-type receptor-like kinase (LecRLK). The B-lectin domain at the N terminus of AsNIP43 was essential in mediating its interaction with NopP, which was confirmed in vitro and in vivo. Subcellular localization, co-localization, and gene expression analyses showed that AsNIP43 and NopP function tightly associated with earlier infection events. RNA interference (RNAi) knockdown of AsNIP43 expression by hairy root transformation led to decreased nodule formation. AsNIP43 plays a positive role in symbiosis, which was further verified in the model legume Medicago truncatula. Transcriptome analysis indicated that MtRLK (a homolog of AsNIP43 in M. truncatula) may function to affect defense gene expression and thus to regulate early nodulation. Taken together, we show that LecRLK AsNIP43 is a legume host target that interacts with rhizobia effector NopP is essential for rhizobial infection and nodulation.

The Medicago SymCEP7 hormone increases nodule number via shoots without compromising lateral root number

Legumes acquire soil nutrients through nitrogen-fixing root nodules and lateral roots. To balance the costs and benefits of nodulation, legumes negatively control root nodule number by autoregulatory and hormonal pathways. How legumes simultaneously coordinate root nodule and lateral root development to procure nutrients remains poorly understood. In Medicago (Medicago truncatula), a subset of mature C-TERMINALLY ENCODED PEPTIDE (CEP) hormones can systemically promote nodule number, but all CEP hormones tested to date negatively regulate lateral root number. Here we showed that Medicago CEP7 produces a mature peptide, SymCEP7, that promotes nodulation from the shoot without compromising lateral root number. Rhizobial inoculation induced CEP7 in the susceptible root nodulation zone in a Nod factor-dependent manner, and, in contrast to other CEP genes, its transcription level was elevated in the ethylene signaling mutant sickle. Using mass spectrometry, fluorescence microscopy and expression analysis, we demonstrated that SymCEP7 activity requires the COMPACT ROOT ARCHITECTURE 2 receptor and activates the shoot-to-root systemic effector, miR2111. Shoot-applied SymCEP7 rapidly promoted nodule number in the pM to nM range at concentrations up to five orders of magnitude lower than effects mediated by root-applied SymCEP7. Shoot-applied SymCEP7 also promoted nodule number in White Clover (Trifolium repens) and Lotus (Lotus japonicus), which suggests that this biological function may be evolutionarily conserved. We propose that SymCEP7 acts in the Medicago shoot to counter balance the autoregulation pathways induced rapidly by rhizobia to enable nodulation without compromising lateral root growth, thus promoting the acquisition of nutrients other than nitrogen to support their growth.

Rhizobia induce SYMRK endocytosis in Phaseolus vulgaris root hair cells

PvSYMRK-EGFP undergoes constitutive and rhizobia-induced endocytosis, which rely on the phosphorylation status of T589, the endocytic YXXØ motif and the kinase activity of the receptor. Legume-rhizobia nodulation is a complex developmental process. It initiates when the rhizobia-produced Nod factors are perceived by specific LysM receptors present in the root hair apical membrane. Consequently, SYMRK (Symbiosis Receptor-like Kinase) becomes active in the root hair and triggers an extensive signaling network essential for the infection process and nodule organogenesis. Despite its relevant functions, the underlying cellular mechanisms involved in SYMRK signaling activity remain poorly characterized. In this study, we demonstrated that PvSYMRK-EGFP undergoes constitutive and rhizobia-induced endocytosis. We found that in uninoculated roots, PvSYMRK-EGFP is mainly associated with the plasma membrane, although intracellular puncta labelled with PvSymRK-EGFP were also observed in root hair and nonhair-epidermal cells. Inoculation with Rhizobium etli producing Nod factors induces in the root hair a redistribution of PvSYMRK-EGFP from the plasma membrane to intracellular puncta. In accordance, deletion of the endocytic motif YXXØ (YKTL) and treatment with the endocytosis inhibitors ikarugamycin (IKA) and tyrphostin A23 (TyrA23), as well as brefeldin A (BFA), drastically reduced the density of intracellular PvSYMRK-EGFP puncta. A similar effect was observed in the phosphorylation-deficient (T589A) and kinase-dead (K618E) mutants of PvSYMRK-EGFP, implying these structural features are positive regulators of PvSYMRK-EGFP endocytosis. Our findings lead us to postulate that rhizobia-induced endocytosis of SYMRK modulates the duration and amplitude of the SYMRK-dependent signaling pathway.

Role of Nod factor receptors and its allies involved in nitrogen fixation

Lysin motif (LysM)-receptor-like kinase (RLK) and leucine-rich repeat (LRR)-RLK mediated signaling play important roles in the development and regulation of root nodule symbiosis in legumes. The availability of water and nutrients in the soil is a major limiting factor affecting crop productivity. Plants of the Leguminosae family form a symbiotic association with nitrogen-fixing Gram-negative soil bacteria, rhizobia for nitrogen fixation. This symbiotic relationship between legumes and rhizobia depends on the signal exchange between them. Plant receptor-like kinases (RLKs) containing lysin motif (LysM) and/or leucine-rich repeat (LRR) play an important role in the perception of chemical signals from rhizobia for initiation and establishment of root nodule symbiosis (RNS) that results in nitrogen fixation. This review highlights the diverse aspects of LysM-RLK and LRR receptors including their specificity, functions, interacting partners, regulation, and associated signaling in RNS. The activation of LysM-RLKs and LRR-RLKs is important for ensuring the successful interaction between legume roots and rhizobia. The intracellular regions of the receptors enable additional layers of signaling that help in the transduction of signals intracellularly. Additionally, symbiosis receptor-like kinase (SYMRK) containing the LRR motif acts as a co-receptor with Nod factors receptors (LysM-RLK). Cleavage of the malectin-like domain from the SYMRK ectodomain is a mechanism for controlling SYMRK stability. Overall, this review has discussed different aspects of legume receptors that are critical to the perception of signals from rhizobia and their subsequent role in creating the mutualistic relationship necessary for nitrogen fixation. Additionally, it has been discussed how crucial it is to extrapolate the knowledge gained from model legumes to crop legumes such as chickpea and common bean to better understand the mechanism underlying nodule formation in crop legumes. Future directions have also been proposed in this regard.

Discovering the genetic modules controlling root nodule symbiosis under abiotic stresses: salinity as a case study

Legumes form a symbiotic association with rhizobia and fix atmospheric nitrogen in specialized root organs known as nodules. It is well known that salt stress inhibits root nodule symbiosis by decreasing rhizobial growth, rhizobial infection, nodule number, and nitrogenase activity in diverse legumes. Despite this knowledge, the genetic and molecular mechanisms governing salt stress's inhibition of nodulation and nitrogen fixation are still elusive. In this Viewpoint, we summarize the most recent knowledge of the genetic mechanisms that shape this symbiosis according to the salt levels in the soil. We emphasize the relevance of modulating the activity of the transcription factor Nodule Inception to properly shape the symbiosis with rhizobia accordingly. We also highlight the knowledge gaps that are critical for gaining a deeper understanding of the molecular mechanisms underlying the adaptation of the root nodule symbiosis to salt-stress conditions. We consider that filling these gaps can help to improve legume nodulation and harness its ecological benefits even under salt-stress conditions.

Widely conserved AHL transcription factors are essential for NCR gene expression and nodule development in Medicago

Symbiotic nitrogen fixation by Rhizobium bacteria in the cells of legume root nodules alleviates the need for nitrogen fertilizers. Nitrogen fixation requires the endosymbionts to differentiate into bacteroids which can be reversible or terminal. The latter is controlled by the plant, it is more beneficial and has evolved in multiple clades of the Leguminosae family. The plant effectors of terminal differentiation in inverted repeat-lacking clade legumes (IRLC) are nodule-specific cysteine-rich (NCR) peptides, which are absent in legumes such as soybean where there is no terminal differentiation of rhizobia. It was assumed that NCRs co-evolved with specific transcription factors, but our work demonstrates that expression of NCR genes does not require NCR-specific transcription factors. Introduction of the Medicago truncatula NCR169 gene under its own promoter into soybean roots resulted in its nodule-specific expression, leading to bacteroid changes associated with terminal differentiation. We identified two AT-Hook Motif Nuclear Localized (AHL) transcription factors from both M. truncatula and soybean nodules that bound to AT-rich sequences in the NCR169 promoter inducing its expression. Whereas mutation of NCR169 arrested bacteroid development at a late stage, the absence of MtAHL1 or MtAHL2 completely blocked bacteroid differentiation indicating that they also regulate other NCR genes required for the development of nitrogen-fixing nodules. Regulation of NCRs by orthologous transcription factors in non-IRLC legumes opens up the possibility of increasing the efficiency of nitrogen fixation in legumes lacking NCRs.

A legume kinesin controls vacuole morphogenesis for rhizobia endosymbiosis

Symbioses between legumes and rhizobia require establishment of the plant-derived symbiosome membrane, which surrounds the rhizobia and accommodates the symbionts by providing an interface for nutrient and signal exchange. The host cytoskeleton and endomembrane trafficking systems play central roles in the formation of a functional symbiotic interface for rhizobia endosymbiosis; however, the underlying mechanisms remain largely unknown. Here we demonstrate that the nodulation-specific kinesin-like calmodulin-binding protein (nKCBP), a plant-specific microtubule-based kinesin motor, controls central vacuole morphogenesis in symbiotic cells in Medicago truncatula. Phylogenetic analysis further indicated that nKCBP duplication occurs solely in legumes of the clade that form symbiosomes. Knockout of nKCBP results in central vacuole deficiency, defective symbiosomes and abolished nitrogen fixation. nKCBP decorates linear particles along microtubules, and crosslinks microtubules with the actin cytoskeleton, to control central vacuole formation by modulating vacuolar vesicle fusion in symbiotic cells. Together, our findings reveal that rhizobia co-opted nKCBP to achieve symbiotic interface formation by regulating cytoskeletal assembly and central vacuole morphogenesis during nodule development.

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.

Interactions between hydrogen sulphide and rhizobia modulate the physiological and metabolism process during water deficiency-induced oxidative defense in soybean

Hydrogen sulphide (H₂ S), a new gas signal molecule, participates in the regulation of various abiotic stresses in plants. However, how the tandem working of H₂ S and rhizobia affects the adaptation of soybean to water deficiency is still unclear. In this study, we investigated the adaptation mechanism of H₂ S and rhizobia in soybean to water deficiency. Our results revealed that H₂ S and rhizobia jointly enhanced the leaf chlorophyll content and relative water content in plants, and caused an increase in the biomass of soybean seedlings under water deficiency. Besides, in the absence of water, H₂ S enhanced the biomass by affecting the number of nodules and nitrogenase activity during vegetative growth. The expression of nodulation marker genes including early nodulin 40 (GmENOD40), ERF required for nodulation (GmERN) and nodulation inception genes (GmNIN1a, GmNIN2a and GmNIN2b) were upregulated by H₂ S and rhizobia in the nodules. Moreover, the combined effect of H₂ S and rhizobia was proved to affect the enzyme activities and gene expression level of antioxidants, as well as osmotic protective substance content and related gene expression levels under water deficiency in soybean seedlings. In addition, the metabolomic results suggested that the combined effect of H₂ S and rhizobia remarkably promoted the contents of lipids and lipid-like molecules. Our results indicated that H₂ S and rhizobia synergistically reduced the oxidative damage caused by water deficiency through increasing the accumulation of metabolites and strengthening the plant antioxidant capacity.

Transcription Factors Controlling the Rhizobium-Legume Symbiosis: Integrating Infection, Organogenesis and the Abiotic Environment

Legume roots engage in a symbiotic relationship with rhizobia, leading to the development of nitrogen-fixing nodules. Nodule development is a sophisticated process and is under the tight regulation of the plant. The symbiosis initiates with a signal exchange between the two partners, followed by the development of a new organ colonized by rhizobia. Over two decades of study have shed light on the transcriptional regulation of rhizobium-legume symbiosis. A large number of transcription factors (TFs) have been implicated in one or more stages of this symbiosis. Legumes must monitor nodule development amidst a dynamic physical environment. Some environmental factors are conducive to nodulation, whereas others are stressful. The modulation of rhizobium-legume symbiosis by the abiotic environment adds another layer of complexity and is also transcriptionally regulated. Several symbiotic TFs act as integrators between symbiosis and the response to the abiotic environment. In this review, we trace the role of various TFs involved in rhizobium-legume symbiosis along its developmental route and highlight the ones that also act as communicators between this symbiosis and the response to the abiotic environment. Finally, we discuss contemporary approaches to study TF-target interactions in plants and probe their potential utility in the field of rhizobium-legume symbiosis.

GmNAC181 promotes symbiotic nodulation and salt tolerance of nodulation by directly regulating GmNINa expression in soybean

Soybean (Glycine max) is one of the most important crops world-wide. Under low nitrogen (N) condition, soybean can form a symbiotic relationship with rhizobia to acquire sufficient N for their growth and production. Nodulation signaling controls soybean symbiosis with rhizobia. The soybean Nodule Inception (GmNINa) gene is a central regulator of soybean nodulation. However, the transcriptional regulation of GmNINa remains largely unknown. Nodulation is sensitive to salt stress, but the underlying mechanisms are unclear. Here, we identified an NAC transcription factor designated GmNAC181 (also known as GmNAC11) as the interacting protein of GmNSP1a. GmNAC181 overexpression or knockdown in soybean resulted in increased or decreased numbers of nodules, respectively. Accordingly, the expression of GmNINa was greatly up- and downregulated, respectively. Furthermore, we showed that GmNAC181 can directly bind to the GmNINa promoter to activate its gene expression. Intriguingly, GmNAC181 was highly induced by salt stress during nodulation and promoted symbiotic nodulation under salt stress. We identified a new transcriptional activator of GmNINa in the nodulation pathway and revealed a mechanism by which GmNAC181 acts as a network node orchestrating the expression of GmNINa and symbiotic nodulation under salt stress conditions.

Contemporary evolution rivals the effects of rhizobium presence on community and ecosystem properties in experimental mesocosms

Because genotypes within a species commonly differ in traits that influence other species, whole communities, or even ecosystem functions, evolutionary change within one key species may affect the community and ecosystem processes. Here we use experimental mesocosms to test how the evolution of reduced cooperation in rhizobium mutualists in response to 20 years of nitrogen fertilization compares to the effects of rhizobium presence on soil nitrogen availability and plant community composition and diversity. The evolution of reduced rhizobium cooperation caused reductions in soil nitrogen, biological nitrogen fixation, and leaf nitrogen concentrations that were as strong as, or even stronger than, experimental rhizobium inoculation (presence/absence) treatments. Effects of both rhizobium evolution and rhizobium inoculation on legume dominance, plant community composition, and plant species diversity were often smaller in magnitude, but suggest that rhizobium evolution can alter the relative abundance of plant functional groups. Our findings indicate that the consequences of rapid microbial evolution for ecosystems and communities can rival the effects resulting from the presence or abundance of keystone mutualists.

Are legumes different? Origins and consequences of evolving nitrogen fixing symbioses

Nitrogen fixing symbioses between plants and bacteria are ancient and, while not numerous, are formed in diverse lineages of plants ranging from microalgae to angiosperms. One symbiosis stands out as the most widespread one is that between legumes and rhizobia, leading to the formation of nitrogen-fixing nodules. The legume family is one of the largest and most diverse group of plants and legumes have been used by humans since the beginning of agriculture, both as high nitrogen food, as well as pastures and rotation crops. One open question is whether their ability to form a nitrogen-fixing symbiosis has contributed to legumes' success, and whether legumes have any unique characteristics that have made them more diverse and widespread than other groups of plants. This review examines the evolutionary journey that has led to the diversification of legumes, in particular its nitrogen-fixing symbiosis, and asks four questions to investigate which legume traits might have contributed to their success: 1. In what ways do legumes differ from other plant groups that have evolved nitrogen-fixing symbioses? In order to answer this question, the characteristics of the symbioses, and efficiencies of nitrogen fixation are compared between different groups of nitrogen fixing plants. 2. Could certain unique features of legumes be a reason for their success? This section examines the manifestations and possible benefits of a nitrogen-rich 'lifestyle' in legumes. 3. If nitrogen fixation was a reason for such a success, why have some species lost the symbiosis? Formation of symbioses has trade-offs, and while these are less well known for non-legumes, there are known energetic and ecological reasons for loss of symbiotic potential in legumes. 4. What can we learn from the unique traits of legumes for future crop improvements? While exploiting some of the physiological properties of legumes could be used to improve legume breeding, our increasing molecular understanding of the essential regulators of root nodule symbioses raise hope of creating new nitrogen fixing symbioses in other crop species.

The CYCLOPS Response Element in the NIN Promoter Is Important but Not Essential for Infection Thread Formation During Lotus japonicus-Rhizobia Symbiosis

The establishment of the legume-rhizobia symbiosis, termed the root-nodule symbiosis (RNS), requires elaborate interactions at the molecular level. The host plant-derived transcription factor NODULE INCEPTION (NIN) is known to be crucial for RNS, regulating associated processes such as alteration of root hair morphology, infection thread formation, and cell division during nodulation. This emphasizes the importance of the precise spatiotemporal regulation of NIN expression for the establishment of RNS; however, the detailed role of NIN promoter sequences in this process remains unclear. The daphne mutant, a nin mutant allele containing a chromosomal translocation approximately 7 kb upstream of the start codon, does not form nodules but does form infection threads, indicating that the region within 7 kb of the NIN start codon contributes to NIN expression during infection thread formation. CYCLOPS binds to a CYCLOPS response element (CYC-RE) in the NIN promoter, and cyclops mutants are defective in infection thread formation. Here, we performed complementation analysis in nin mutants, using various truncated forms of the NIN promoter, and found that the CYC-RE is important for infection thread formation. Additionally, the CYC-RE deletion mutant, generated through CRISPR/Cas9 technology, displayed a significant reduction in infection thread formation, indicating that the CYC-RE is important for the fine-tuning of NIN expression during this process. However, the fact that infection thread formation is not completely abolished in the CYC-RE deletion mutant suggests that cis and trans factors other than CYCLOPS and the CYC-RE may cooperatively regulate NIN expression for the induction of infection thread formation. [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.

Effector-triggered inhibition of nodulation: A rhizobial effector protease targets soybean kinase GmPBS1-1

Type III protein secretion systems of nitrogen-fixing rhizobia deliver effector proteins into leguminous host cells to promote or inhibit the nodule symbiosis. However, mechanisms underlying effector-triggered inhibition of nodulation remain largely unknown. Nodulation outer protein T (NopT) of Sinorhizobium sp. NGR234 is an effector protease related to the Pseudomonas effector Avirulence protein Pseudomonas phaseolicola B (AvrPphB). Here, we constructed NGR234 mutants producing different NopT variants and found that protease activity of NopT negatively affects nodulation of smooth crotalaria (Crotalaria pallida). NopT variants lacking residues required for autocleavage and subsequent lipidation showed reduced symbiotic effects and were not targeted to the plasma membrane. We further noticed that Sinorhizobium fredii strains possess a mutated nopT gene. Sinorhizobium fredii USDA257 expressing nopT of NGR234 induced considerably fewer nodules in soybean (Glycine max) cv. Nenfeng 15 but not in other cultivars. Effector perception was further examined in NopT-expressing leaves of Arabidopsis (Arabidopsis thaliana) and found to be dependent on the protein kinase Arabidopsis AvrPphB Susceptible 1 (AtPBS1) and the associated resistance protein Arabidopsis Resistance to Pseudomonas syringae 5 (AtRPS5). Experiments with Nicotiana benthamiana plants indicated that the soybean homolog GmPBS1-1 associated with AtRPS5 can perceive NopT. Further analysis showed that NopT cleaves AtPBS1 and GmPBS1-1 and thus can activate these target proteins. Insertion of a DKM motif at the cleavage site of GmPBS1-1 resulted in increased proteolysis. Nodulation tests with soybeans expressing an autoactive GmPBS1-1 variant indicated that activation of a GmPBS1-1-mediated resistance pathway impairs nodule formation in cv. Nenfeng 15. Our findings suggest that legumes face an evolutionary dilemma of either developing effector-triggered immunity against pathogenic bacteria or establishing symbiosis with suboptimally adapted rhizobia producing pathogen-like effectors.

At the Crossroads of Salinity and Rhizobium-Legume Symbiosis

Legume roots interact with soil bacteria rhizobia to develop nodules, de novo symbiotic root organs that host these rhizobia and are mini factories of atmospheric nitrogen fixation. Nodulation is a sophisticated developmental process and is sensitive to several abiotic factors, salinity being one of them. While salinity influences both the free-living partners, symbiosis is more vulnerable than other aspects of plant and microbe physiology, and the symbiotic interaction is strongly impaired even under moderate salinity. In this review, we tease apart the various known components of rhizobium-legume symbiosis and how they interact with salt stress. We focus primarily on the initial stages of symbiosis since we have a greater mechanistic understanding of the interaction at these stages.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Pseudogenization of the rhizobium-responsive EXOPOLYSACCHARIDE RECEPTOR in Parasponia is a rare event in nodulating plants

BACKGROUND

Nodule symbiosis with diazotrophic Frankia or rhizobium occurs in plant species belonging to ten taxonomic lineages within the related orders Fabales, Fagales, Cucurbitales, and Rosales. Phylogenomic studies indicate that this nitrogen-fixing nodulation trait has a single evolutionary origin. In legume model plants, the molecular interaction between plant and rhizobium microsymbiont is mapped to a significant degree. A specific LysM-type receptor kinase, LjEPR3 in Lotus japonicus and MtLYK10 in Medicago truncatula, was found to act in a secondary identity-based mechanism, controlling intracellular rhizobium infection. Furthermore, LjEPR3 showed to bind surface exopolysaccharides of Mesorhizobium loti, the diazotrophic microsymbiont of L. japonicus. EPR3 orthologous genes are not unique to legumes. Surprisingly, however, its ortholog EXOPOLYSACCHARIDE RECEPTOR (EPR) is pseudogenized in Parasponia, the only lineage of non-legume plants that nodulate also with rhizobium.

RESULTS

Analysis of genome sequences showed that EPR3 orthologous genes are highly conserved in nodulating plants. We identified a conserved retrotransposon insertion in the EPR promoter region in three Parasponia species, which associates with defected transcriptional regulation of this gene. Subsequently, we studied the EPR gene of two Trema species as they represent the sister genus of Parasponia for which it is assumed it lost the nitrogen-fixing nodulation trait. Both Trema species possess apparently functional EPR genes that have a nodulation-specific expression profile when introduced into a Parasponia background. This indicates the EPR gene functioned in nodulation in the Parasponia-Trema ancestor.

CONCLUSION

We conclude that nodule-specific expression of EPR3 orthologous genes is shared between the legume and Parasponia-Trema lineage, suggesting an ancestral function in the nitrogen-fixing nodulation trait. Pseudogenization of EPR in Parasponia is an exceptional case in nodulating plants. We speculate that this may have been instrumental to the microsymbiont switch -from Frankia to rhizobium- that has occurred in the Parasponia lineage and the evolution of a novel crack entry infection mechanism.

Innovation and appropriation in mycorrhizal and rhizobial Symbioses

Most land plants benefit from endosymbiotic interactions with mycorrhizal fungi, including legumes and some nonlegumes that also interact with endosymbiotic nitrogen (N)-fixing bacteria to form nodules. In addition to these helpful interactions, plants are continuously exposed to would-be pathogenic microbes: discriminating between friends and foes is a major determinant of plant survival. Recent breakthroughs have revealed how some key signals from pathogens and symbionts are distinguished. Once this checkpoint has been passed and a compatible symbiont is recognized, the plant coordinates the sequential development of two types of specialized structures in the host. The first serves to mediate infection, and the second, which appears later, serves as sophisticated intracellular nutrient exchange interfaces. The overlap in both the signaling pathways and downstream infection components of these symbioses reflects their evolutionary relatedness and the common requirements of these two interactions. However, the different outputs of the symbioses, phosphate uptake versus N fixation, require fundamentally different components and physical environments and necessitated the recruitment of different master regulators, NODULE INCEPTION-LIKE PROTEINS, and PHOSPHATE STARVATION RESPONSES, for nodulation and mycorrhization, respectively.

Lotus japonicus HAR1 regulates root morphology locally and systemically under a moderate nitrate condition in the absence of rhizobia

The local and long-distance signaling pathways mediated by the leucine-rich repeat receptor kinase HAR1 suppress root branching and promote primary root length in response to nitrate supply. The root morphology of higher plants changes plastically to effectively absorb nutrients and water from the soil. In particular, legumes develop root organ nodules, in which symbiotic rhizobia fix atmospheric nitrogen in nitrogen-poor environments. The number of nodules formed in roots is negatively regulated by a long-distance signaling pathway that travels through shoots called autoregulation of nodulation (AON). In the model plant Lotus japonicus, defects in AON genes, such as a leucine-rich repeat receptor kinase HYPERNODULATION ABERRANT ROOT FORMATION 1 (HAR1), an orthologue of CLAVATA1, and the F-box protein TOO MUCH LOVE (TML), induce the formation of an excess number of nodules. The loss-of-function mutant of HAR1 exhibits a short and bushy root phenotype in the absence of rhizobia. We show that the har1 mutant exhibits high nitrate sensitivity during root development. The uninfected har1 mutant significantly increased lateral root number and reduced primary root length in the presence of 3 mM nitrate, compared with the wild-type and tml mutant. Grafting experiments indicated that local and long-distance signaling pathways via root- and shoot-acting HAR1 additively regulated root morphology under the moderate nitrate concentrations. These findings allow us to propose that HAR1-mediated signaling pathways control the root system architecture by suppressing lateral root branching and promoting primary root elongation in response to nitrate availability.

NIN-Like Proteins: Interesting Players in Rhizobia-Induced Nitrate Signaling Response During Interaction with Non-Legume Host Arabidopsis thaliana

Nitrogen is an essential macronutrient and a key cellular messenger. Plants have evolved refined molecular systems to sense the cellular nitrogen status. This is exemplified by the root nodule symbiosis between legumes and symbiotic rhizobia, where nitrate availability inhibits this mutualistic interaction. Additionally, nitrate also functions as a metabolic messenger, resulting in nitrate signaling cascades which intensively crosstalk with other physiological pathways. Nodule inception-like proteins (NLPs) are key players in nitrate signaling and regulate nitrate-dependent transcription during legume-rhizobia interactions. Nevertheless, the coordinated interplay between nitrate signaling pathways and rhizobacteria-induced responses remains to be elucidated. In our study, we investigated rhizobia-induced changes in the root system architecture of the non-legume host arabidopsis under different nitrate conditions. We demonstrate that rhizobium-induced lateral root growth and increased root hair length and density are regulated by a nitrate-related signaling pathway. Key players in this process are AtNLP4 and AtNLP5, because the corresponding mutants failed to respond to rhizobia. At the cellular level, AtNLP4 and AtNLP5 control a rhizobia-induced decrease in cell elongation rates, while additional cell divisions occurred independently of AtNLP4. In summary, our data suggest that root morphological responses to rhizobia are coordinated by a newly considered nitrate-related NLP pathway that is evolutionarily linked to regulatory circuits described in legumes.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Posttranslational regulation of transporters important for symbiotic interactions

Coordinated sharing of nutritional resources is a central feature of symbiotic interactions, and, despite the importance of this topic, many questions remain concerning the identification, activity, and regulation of transporter proteins involved. Recent progress in obtaining genome and transcriptome sequences for symbiotic organisms provides a wealth of information on plant, fungal, and bacterial transporters that can be applied to these questions. In this update, we focus on legume-rhizobia and mycorrhizal symbioses and how transporters at the symbiotic interfaces can be regulated at the protein level. We point out areas where more research is needed and ways that an understanding of transporter mechanism and energetics can focus hypotheses. Protein phosphorylation is a predominant mechanism of posttranslational regulation of transporters in general and at the symbiotic interface specifically. Other mechanisms of transporter regulation, such as protein-protein interaction, including transporter multimerization, polar localization, and regulation by pH and membrane potential are also important at the symbiotic interface. Most of the transporters that function in the symbiotic interface are members of transporter families; we bring in relevant information on posttranslational regulation within transporter families to help generate hypotheses for transporter regulation at the symbiotic interface.

The miR156b-GmSPL9d module modulates nodulation by targeting multiple core nodulation genes in soybean

Symbiotic nodulation is initiated in the roots of legumes in response to low nitrogen and rhizobial signal molecules and is dynamically regulated by a complex regulatory network that coordinates rhizobial infection and nodule organogenesis. It has been shown that the miR156-SPL module mediates nodulation in legumes; however, conclusive evidence of how this module exerts its function during nodulation remains elusive. Here, we report that the miR156b-GmSPL9d module regulates symbiotic nodulation by targeting multiple key regulatory genes in the nodulation signalling pathway of soybean. miR156 family members are differentially expressed during nodulation, and miR156b negatively regulates nodulation by mainly targeting soybean SQUAMOSA promoter-binding protein-like 9d (GmSPL9d), a positive regulator of soybean nodulation. GmSPL9d directly binds to the miR172c promoter and activates its expression, suggesting a conserved role of GmSPL9d. Furthermore, GmSPL9d was coexpressed with the soybean nodulation marker genes nodule inception a (GmNINa) and GmENOD40-1 during nodule formation and development. Intriguingly, GmSPL9d can bind to the promoters of GmNINa and GmENOD40-1 and regulate their expression. Our data demonstrate that the miR156b-GmSPL9d module acts as an upstream master regulator of soybean nodulation, which coordinates multiple marker genes involved in soybean nodulation.

Mechanisms underlying legume-rhizobium symbioses

Legumes, unlike most land plants, can form symbiotic root nodules with nitrogen-fixing bacteria to secure nitrogen for growth. The formation of nitrogen-fixing nodules on legume roots requires the coordination of rhizobial infection at the root epidermis with cell division in the cortex. The nodules house the nitrogen-fixing rhizobia in organelle-like structures known as symbiosomes, which enable nitrogen fixation and facilitate the exchange of metabolites between the host and symbionts. In addition to this beneficial interaction, legumes are continuously exposed to would-be pathogenic microbes; therefore the ability to discriminate pathogens from symbionts is a major determinant of plant survival under natural conditions. Here, we summarize recent advances in the understanding of root nodule symbiosis signaling, transcriptional regulation, and regulation of plant immunity during legume-rhizobium symbiosis. In addition, we propose several important questions to be addressed and provide insights into the potential for engineering the capacity to fix nitrogen in legume and non-legume plants.

Genome-Wide Identification and Characterization of the Soybean DEAD-Box Gene Family and Expression Response to Rhizobia

DEAD-box proteins are a large family of RNA helicases that play important roles in almost all cellular RNA processes in model plants. However, little is known about this family of proteins in crops such as soybean. Here, we identified 80 DEAD-box family genes in the Glycine max (soybean) genome. These DEAD-box genes were distributed on 19 chromosomes, and some genes were clustered together. The majority of DEAD-box family proteins were highly conserved in Arabidopsis and soybean, but Glyma.08G231300 and Glyma.14G115100 were specific to soybean. The promoters of these DEAD-box genes share cis-acting elements involved in plant responses to MeJA, salicylic acid (SA), low temperature and biotic as well as abiotic stresses; interestingly, half of the genes contain nodulation-related cis elements in their promoters. Microarray data analysis revealed that the DEAD-box genes were differentially expressed in the root and nodule. Notably, 31 genes were induced by rhizobia and/or were highly expressed in the nodule. Real-time quantitative PCR analysis validated the expression patterns of some DEAD-box genes, and among them, Glyma.08G231300 and Glyma.14G115100 were induced by rhizobia in root hair. Thus, we provide a comprehensive view of the DEAD-box family genes in soybean and highlight the crucial role of these genes in symbiotic nodulation.

A roadmap of plant membrane transporters in arbuscular mycorrhizal and legume-rhizobium symbioses

Most land plants live in close contact with beneficial soil microbes: the majority of land plant species establish symbiosis with arbuscular mycorrhizal fungi, while most legumes, the third largest plant family, can form a symbiosis with nitrogen-fixing rhizobia. These microbes contribute to plant nutrition via endosymbiotic processes that require modulating the expression and function of plant transporter systems. The efficient contribution of these symbionts involves precisely controlled integration of transport, which is enabled by the adaptability and plasticity of their transporters. Advances in our understanding of these systems, driven by functional genomics research, are rapidly filling the gap in knowledge about plant membrane transport involved in these plant-microbe interactions. In this review, we synthesize recent findings associated with different stages of these symbioses, from the pre-symbiotic stage to nutrient exchange, and describe the role of host transport systems in both mycorrhizal and legume-rhizobia symbioses.

Computationally Reconstructed Interactome of Bradyrhizobium diazoefficiens USDA110 Reveals Novel Functional Modules and Protein Hubs for Symbiotic Nitrogen Fixation

Symbiotic nitrogen fixation is an important part of the nitrogen biogeochemical cycles and the main nitrogen source of the biosphere. As a classical model system for symbiotic nitrogen fixation, rhizobium-legume systems have been studied elaborately for decades. Details about the molecular mechanisms of the communication and coordination between rhizobia and host plants is becoming clearer. For more systematic insights, there is an increasing demand for new studies integrating multiomics information. Here, we present a comprehensive computational framework integrating the reconstructed protein interactome of B. diazoefficiens USDA110 with its transcriptome and proteome data to study the complex protein-protein interaction (PPI) network involved in the symbiosis system. We reconstructed the interactome of B. diazoefficiens USDA110 by computational approaches. Based on the comparison of interactomes between B. diazoefficiens USDA110 and other rhizobia, we inferred that the slow growth of B. diazoefficiens USDA110 may be due to the requirement of more protein modifications, and we further identified 36 conserved functional PPI modules. Integrated with transcriptome and proteome data, interactomes representing free-living cell and symbiotic nitrogen-fixing (SNF) bacteroid were obtained. Based on the SNF interactome, a core-sub-PPI-network for symbiotic nitrogen fixation was determined and nine novel functional modules and eleven key protein hubs playing key roles in symbiosis were identified. The reconstructed interactome of B. diazoefficiens USDA110 may serve as a valuable reference for studying the mechanism underlying the SNF system of rhizobia and legumes.

Suppression of LjBAK1-mediated immunity by SymRK promotes rhizobial infection in Lotus japonicus

An important question in biology is how organisms can associate with different microbes that pose no threat (commensals), pose a severe threat (pathogens), and those that are beneficial (symbionts). The root nodule symbiosis serves as an important model system for addressing such questions in the context of plant-microbe interactions. It is now generally accepted that rhizobia can actively suppress host immune responses during the infection process, analogous to the way in which plant pathogens can evade immune recognition. However, much remains to be learned about the mechanisms by which the host recognizes the rhizobia as pathogens and how, subsequently, these pathways are suppressed to allow establishment of the nitrogen-fixing symbiosis. In this study, we found that SymRK (Symbiosis Receptor-like Kinase) is required for rhizobial suppression of plant innate immunity in Lotus japonicus. SymRK associates with LjBAK1 (BRASSINOSTEROID INSENSITIVE 1-Associated receptor Kinase 1), a well-characterized positive regulator of plant innate immunity, and directly inhibits LjBAK1 kinase activity. Rhizobial inoculation enhances the association between SymRK and LjBAK1 in planta. LjBAK1 is required for the regulation of plant innate immunity and plays a negative role in rhizobial infection in L. japonicus. The data indicate that the SymRK-LjBAK1 protein complex serves as an intersection point between rhizobial symbiotic signaling pathways and innate immunity pathways, and support that rhizobia may actively suppress the host's ability to mount a defense response during the legume-rhizobium symbiosis.

Light-induced mobile factors from shoots regulate rhizobium-triggered soybean root nodulation

Symbiotic nitrogen fixation is an energy-expensive process, and the light available to plants has been proposed to be a primary influencer. We demonstrate that the light-induced soybean TGACG-motif binding factor 3/4 (GmSTF3/4) and FLOWERING LOCUS T (GmFTs), which move from shoots to roots, interdependently induce nodule organogenesis. Rhizobium-activated calcium- and calmodulin-dependent protein kinase (CCaMK) phosphorylates GmSTF3, triggering GmSTF3–GmFT2a complex formation, which directly activates expression of nodule inception (NIN) and nuclear factor Y (NF-YA1 and NF-YB1). Accordingly, the CCaMK–STF–FT module integrates aboveground light signals with underground symbiotic signaling, ensuring that the host plant informs its roots that the aboveground environment is prepared to sustainably supply the carbohydrate necessary for symbiosis. These results suggest approaches that could enhance the balance of carbon and nitrogen in the biosphere.

Nod factor receptor complex phosphorylates GmGEF2 to stimulate ROP signaling during nodulation

The establishment of the symbiotic interaction between rhizobia and legumes involves the Nod factor signaling pathway. Nod factor recognition occurs through two plant receptors, NFR1 and NFR5. However, the signal transduction mechanisms downstream of NFR1-NFR5-mediated Nod factor perception remain largely unknown. Here, we report that a small guanosine triphosphatase (GTPase), GmROP9, and a guanine nucleotide exchange factor, GmGEF2, are involved in the soybean-rhizobium symbiosis. We show that GmNFR1α phosphorylates GmGEF2a at its N-terminal S86, which stimulates guanosine diphosphate (GDP)-to-GTP exchange to activate GmROP9 and that the active form of GmROP9 can associate with both GmNFR1α and GmNFR5α. We further show that a scaffold protein, GmRACK1, interacts with active GmROP9 and contributes to root nodule symbiosis. Collectively, our results highlight the symbiotic role of GmROP9-GmRACK1 and support the hypothesis that rhizobial signals promote the formation of a protein complex comprising GmNFR1, GmNFR5, GmROP9, and GmRACK1 for symbiotic signal transduction in soybean.

Rhizobium symbiosis modulates the accumulation of arsenic in Medicago truncatula via nitrogen and NRT3.1-like genes regulated by ABA and linalool

Arsenic (As) contamination is a worldwide problem and threatens human health. Here, we found that Rhizobium symbiosis can improve the tolerance to arsenate [As(V)], and a wild type R. meliloti Rm5038 symbiosis can significantly decrease the accumulation of As in Medicago truncatula shoots. The As content in plants could be decreased by nitrogen and the mutation of nitrate transporter NRT3.1. The expression of M. truncatula NRT3.1-like gene NRT3.1L1 could reverse the As(V)-tolerance phenotype of the Arabidopsis nrt3.1 mutant. Rm5038 symbiosis significantly increased the level of nitrogen in the shoot and reduced the expression of NRT3.1Ls in plants afflicted by As(V). The genetic analyses of aba2-1, pyr1/pyl1/2/4/5/8, and abi1-2/abi2-2/hab1-1/pp2ca-1 mutants revealed that abscisic acid (ABA) signaling regulates the tolerance of plants to As(V). ABA and linalool could promote the expression of NRT3.1Ls, however, their root biosynthesis was inhibited by ammonium, the first form of nitrogen fixed by Rhizobium symbiosis. Moreover, ABA and linalool may also control As and nitrate accumulation in Rhizobium symbionts via signaling pathways other than ammonia and NRT3.1Ls. Thus, Rhizobium symbiosis modulates the accumulation of As in plants via nitrogen and NRT3.1Ls regulated by ABA and linalool, which provides novel approaches to reduce As accumulation in legume crops.

Synergistic anti-oxidative effects of Pongamia pinnata against nickel mediated by Rhizobium pisi and Ochrobacterium pseudogrignonense

Nickel is widely spread by different anthropogenic activities and shows toxicity for plant growth and development. Whether rhizobia symbiotically fix nitrogen can eliminate or reduce nickel toxic effect on plant or not is still unknown. This study was aimed to investigate the effect of different rhizobia genus inoculation on growth, nitrogen fixing ability, metal accumulation and enzymatic antioxidative balance of Pongamia pinnnaa. Inoculation with Rhizobium pisi and Ochrobacterium pseudogrignonense increased the all the growth parameters both in 0 and 40 mg/kg nickel as comparison with control. Only shoot length increased in presence of nitrogen as compared with no supply of nitrogen. Nitrogen content also increased both in rhizobia inoculation as compared to no nitrogen supply and non-inoculation control, respectively. Nickel uptake was higher in shoots and leaves but lower in roots in case of inoculation as compared to non-inoculation control. Rhizobia inoculation improved the plant antioxidant capacity by increasing the activity of enzymatic scavengers catalase (CAT), superoxide dismutase (SOD), peroxidase (POD) and ascorbate (GR). However, 40 mg/kg of nickel adding showed mostly effect on the activity CAT, SOD, POD in leaves. All the enzymatic activity showed a significant increase in absence of nitrogen supply as compared nitrogen supply. Our results suggested that rhizobia inoculation effectively mediated nickel stress for legume plants by increasing nitrogen supplement and inducing antioxidant capacity.

An NADPH oxidase regulates carbon metabolism and the cell cycle during root nodule symbiosis in common bean (Phaseolus vulgaris)

BACKGROUND

Rhizobium-legume symbiosis is a specific, coordinated interaction that results in the formation of a root nodule, where biological nitrogen fixation occurs. NADPH oxidases, or Respiratory Burst Oxidase Homologs (RBOHs) in plants, are enzymes that generate superoxide (O2 •-). Superoxide produces other reactive oxygen species (ROS); these ROS regulate different stages of mutualistic interactions. For example, changes in ROS levels are thought to induce ROS scavenging, cell wall remodeling, and changes in phytohormone homeostasis during symbiotic interactions. In common bean (Phaseolus vulgaris), PvRbohB plays a key role in the early stages of nodulation.

RESULTS

In this study, to explore the role of PvRbohB in root nodule symbiosis, we analyzed transcriptomic data from the roots of common bean under control conditions (transgenic roots without construction) and roots with downregulated expression of PvRbohB (by RNA interference) non-inoculated and inoculated with R. tropici. Our results suggest that ROS produced by PvRBOHB play a central role in infection thread formation and nodule organogenesis through crosstalk with flavonoids, carbon metabolism, cell cycle regulation, and the plant hormones auxin and cytokinin during the early stages of this process.

CONCLUSIONS

Our findings provide important insight into the multiple roles of ROS in regulating rhizobia-legume symbiosis.

Perception of lipo-chitooligosaccharides by the bioenergy crop Populus

Populus sp. is a developing feedstock for second-generation biofuel production. To ensure its success as a sustainable biofuel source, it is essential to capitalize on the ability of Populus sp. to associate with beneficial plant-associated microbes (e.g., mycorrhizal fungi) and engineer Populus sp. to associate with non-native symbionts (e.g., rhizobia). Here, we review recent research into the molecular mechanisms that control ectomycorrhizal associations in Populus sp. with particular emphasis on the discovery that ectomycorrhizal fungi produce lipochitooligosaccharides capable of activating the common symbiosis pathway. We also present new evidence that lipo-chitooligosaccharides produced by both ectomycorrhizal fungi and various species of rhizobia that do not associate with Populus sp. can induce nuclear calcium spiking in the roots of Populus sp. Thus, we argue Populus sp. already possesses the molecular machinery necessary for perceiving rhizobia, and the next step in engineering symbiosis with rhizobia should be focused on inducing bacterial accommodation and nodule organogenesis. The gene Nodule INception is central to these processes, and several putative orthologs are present in Populus sp. Manipulating the promoters of these genes to match that of plants in the nitrogen-fixing clade may be sufficient to introduce nodulation in Populus sp.

Soybean Yellow Stripe-like 7 is a symbiosome membrane peptide transporter important for nitrogen fixation

Legumes form a symbiosis with rhizobia that convert atmospheric nitrogen (N2) to ammonia and provide it to the plant in return for a carbon and nutrient supply. Nodules, developed as part of the symbiosis, harbor rhizobia that are enclosed in a plant-derived symbiosome membrane (SM) to form an organelle-like structure called the symbiosome. In mature nodules exchanges between the symbionts occur across the SM. Here we characterize Yellow Stripe-like 7 (GmYSL7), a Yellow stripe-like family member localized on the SM in soybean (Glycine max) nodules. It is expressed specifically in infected cells with expression peaking soon after nitrogenase becomes active. Unlike most YSL family members, GmYSL7 does not transport metals complexed with phytosiderophores. Rather, it transports oligopeptides of between four and 12 amino acids. Silencing GmYSL7 reduces nitrogenase activity and blocks infected cell development so that symbiosomes contain only a single bacteroid. This indicates the substrate of YSL7 is required for proper nodule development, either by promoting symbiosome development directly or by preventing inhibition of development by the plant. RNAseq of nodules where GmYSL7 was silenced suggests that the plant initiates a defense response against rhizobia with genes encoding proteins involved in amino acid export downregulated and some transcripts associated with metal homeostasis altered. These changes may result from the decrease in nitrogen fixation upon GmYSL7 silencing and suggest that the peptide(s) transported by GmYSL7 monitor the functional state of the bacteroids and regulate nodule metabolism and transport processes accordingly. Further work to identify the physiological substrate for GmYSL7 will allow clarification of this role.

Conditional sanctioning in a legume-Rhizobium mutualism

Legumes are high in protein and form a valuable part of human diets due to their interaction with symbiotic nitrogen-fixing bacteria known as rhizobia. Plants house rhizobia in specialized root nodules and provide the rhizobia with carbon in return for nitrogen. However, plants usually house multiple rhizobial strains that vary in their fixation ability, so the plant faces an investment dilemma. Plants are known to sanction strains that do not fix nitrogen, but nonfixers are rare in field settings, while intermediate fixers are common. Here, we modeled how plants should respond to an intermediate fixer that was otherwise isogenic and tested model predictions using pea plants. Intermediate fixers were only tolerated when a better strain was not available. In agreement with model predictions, nodules containing the intermediate-fixing strain were large and healthy when the only alternative was a nonfixer, but nodules of the intermediate-fixing strain were small and white when the plant was coinoculated with a more effective strain. The reduction in nodule size was preceded by a lower carbon supply to the nodule even before differences in nodule size could be observed. Sanctioned nodules had reduced rates of nitrogen fixation, and in later developmental stages, sanctioned nodules contained fewer viable bacteria than nonsanctioned nodules. This indicates that legumes can make conditional decisions, most likely by comparing a local nodule-dependent cue of nitrogen output with a global cue, giving them remarkable control over their symbiotic partners.

Shoot-derived miR2111 controls legume root and nodule development

Legumes control their nodule numbers through the autoregulation of nodulation (AON). Rhizobia infection stimulates the production of root-derived CLE peptide hormones that are translocated to the shoot where they regulate a new signal. We used soybean to demonstrate that this shoot-derived signal is miR2111, which is transported via phloem to the root where it targets transcripts of Too Much Love (TML), a negative regulator of nodulation. Shoot perception of rhizobia-induced CLE peptides suppresses miR2111 expression, resulting in TML accumulation in roots and subsequent inhibition of nodule organogenesis. Feeding synthetic mature miR2111 via the petiole increased nodule numbers per plant. Likewise, elevating miR2111 availability by over-expression promoted nodulation, while target mimicry of TML induced the opposite effect on nodule development in wild-type plants and alleviated the supernodulating and stunted root growth phenotypes of AON-defective mutants. Additionally, in non-nodulating wild-type plants, ectopic expression of miR2111 significantly enhanced lateral root emergence with a decrease in lateral root length and average root diameter. In contrast, hairy roots constitutively expressing the target mimic construct exhibited reduced lateral root density. Overall, these findings demonstrate that miR2111 is both the critical shoot-to-root factor that positively regulates root nodule development and also acts to shape root system architecture.