MYB6/bHLH13-AbSUS2 involved in sugar metabolism regulates root hair initiation of Abies beshanzuensis

Root hair is regarded as a pivotal complementary survival tactic for mycorrhizal plant like Abies beshanzuensis when symbiosis is disrupted. Relatively little is known about the mechanism underlying root hair morphogenesis in plant species that are strongly dependent on mycorrhizal symbiosis. Many of these species are endangered, and this knowledge is critical for ensuring their survival. Here, a MYB6/bHLH13-sucrose synthase 2 (AbSUS2) module was newly identified and characterized in A. beshanzuensis using bioinformatics, histochemistry, molecular biology, and transgenesis. Functional, expression pattern, and localization analysis showed that AbSUS2 participated in sucrose synthesis and was involved in root hair initiation in A. beshanzuensis. Additionally, the major enzymatic product of AbSUS2 was found to suppress root hair initiation in vitro. Our data further showed that a complex involving the transcription factors AbMYB6 and AbbHLH13 directly interacted with the promoter of AbSUS2 and strengthened its expression, thereby inhibiting root hair initiation in response to exogenous sucrose. Our findings offer novel insights into how root hair morphogenesis is regulated in mycorrhizal plants and also provide a new strategy for the preservation of endangered mycorrhizal plant species.

The effects of ERN1 on gene expression during early rhizobial infection in Lotus japonicus

Legumes develop root nodules in association with compatible rhizobia to overcome nitrogen deficiency. Rhizobia enter the host legume, mainly through infection threads, and induce nodule primordium formation in the root cortex. Multiple transcription factors have been identified to be involved in the regulation of the establishment of root nodule symbiosis, including ERF Required for Nodulation1 (ERN1). ERN1 is involved in a transcription network with CYCLOPS and NODULE INCEPTION (NIN). Mutation of ERN1 often results in misshapen root hair tips, deficient infection thread formation, and immature root nodules. ERN1 directly activates the expression of ENOD11 in Medicago truncatula to assist cell wall remodeling and Epr3 in Lotus japonicus to distinguish rhizobial exopolysaccharide signals. However, aside from these two genes, it remains unclear which genes are regulated by LjERN1 or what role LjERN1 plays during root nodule symbiosis. Thus, we conducted RNA sequencing to compare the gene expression profiles of wild-type L. japonicus and Ljern1-6 mutants. In total, 234 differentially expressed genes were identified as candidate LjERN1 target genes. These genes were found to be associated with cell wall remodeling, signal transduction, phytohormone metabolism, and transcription regulation, suggesting that LjERN1 is involved in multiple processes during the early stages of the establishment of root nodule symbiosis. Many of these candidate genes including RINRK1 showed decreased expression levels in Ljnin-2 mutants based on a search of a public database, suggesting that LjERN1 and LjNIN coordinately regulate gene expression. Our data extend the current understanding of the pleiotropic role of LjERN1 in root nodule symbiosis.

Pisum sativum has no competitive responses to neighbors: A case study in (non)reproducible plant biology

Plant-plant competition is ubiquitous in nature. However, studying below ground behavior of roots has always posed certain difficulties. Pea (Pisum sativum L.) has become a common study species for questions about how plant roots respond to neighboring plant roots and barriers in soil. However, published results point in several different directions. This has sometimes been interpreted as pea having sophisticated context dependent responses that can change in complex ways depending on its surroundings, but it could also just point to small statistical power resulting in type I or II statistical errors. To explore this further, here, we combine the result of five new experiments with published results to examine 18 unique experiments from 10 different studies and 6 cultivars of pea for a total of 254 replicate plants. We used a Bayesian hierarchical meta-analysis approach to estimating the likely effect size from the available data, as well as quantify heterogeneity among different experiments, studies and cultivars. The posterior distributions show that, at the coarsest possible scale of total root production, it is unlikely that P. sativum root growth is influenced by either neighbors or pot volume that varies primarily by depth. We find no evidence of publication bias and conclude that this is simply due to statistical sampling error and the scientific method combined with frequentist statistics operating as intended. We suggest that further work on pea should consider repeating experiments that reported finer scale root plasticity at the rhizosphere scale or consider exploring different pot geometries such as volume that varies by depth or width. We also suggest that more diversity in study species are needed to better understand the neighbor-volume response.

When does mutualism offer a competitive advantage? A game-theoretic analysis of host-host competition in mutualism

Due to their non-motile nature, plants rely heavily on mutualistic interactions to obtain resources and carry out services. One key mutualism is the plant-microbial mutualism in which a plant trades away carbon to a microbial partner for nutrients like nitrogen and phosphorous. Plants show much variation in the use of this partnership from the individual level to entire lineages depending upon ecological, evolutionary and environmental context. We sought to determine how this context dependency could result in the promotion, exclusion or coexistence of the microbial mutualism by asking if and when the partnership provided a competitive advantage to the plant. To that end, we created a 2 × 2 evolutionary game in which plants could either be a mutualist and pair with a microbe or be a non-mutualist and forgo the partnership. Our model includes both frequency dependence and density dependence, which gives us the eco-evolutionary dynamics of mutualism evolution. As in all models, mutualism only evolved if it could offer a competitive advantage and its net benefit was positive. However, surprisingly the model reveals the possibility of coexistence between mutualist and non-mutualist genotypes due to competition between mutualists over the microbially obtained nutrient. Specifically, frequency dependence of host strategies can make the microbial symbiont less beneficial if the microbially derived resources are shared, a phenomenon that increasingly reduces the frequency of mutualism as the density of competitors increases. In essence, ecological competition can act as a hindrance to mutualism evolution. We go on to discuss basic experiments that can be done to test and falsify our hypotheses.

Role of ethylene in effective establishment of the peanut-bradyrhizobia symbiotic interaction

Ethylene has been implicated in nitrogen fixing symbioses in legumes, where rhizobial invasion occurs via infection threads (IT). In the symbiosis between peanut (Arachis hypogaea L.) and bradyrhizobia, the bacteria penetrate the root cortex intercellularly and IT are not formed. Little attention has been paid to the function of ethylene in the establishment of this symbiosis. The aim of this article is to evaluate whether ethylene plays a role in the development of this symbiotic interaction and the participation of Nod Factors (NF) in the regulation of ethylene signalling. Manipulation of ethylene in peanut was accomplished by application of 1-aminocyclopropane-1-carboxylic acid (ACC), which mimics applied ethylene, or AgNO_3, which blocks ethylene responses. To elucidate the participation of NF in the regulation of ethylene signalling, we inoculated plants with a mutant isogenic rhizobial strain unable to produce NF and evaluated the effect of AgNO₃ on gene expression of NF and ethylene responsive signalling pathways. Data revealed that ethylene perception is required for the formation of nitrogen-fixing nodules, while addition of ACC does not affect peanut symbiotic performance. This phenotypic evidence is in agreement with transcriptomic data from genes involved in symbiotic and ethylene signalling pathways. NF seem to modulate the expression of ethylene signalling genes. Unlike legumes infected through IT formation, ACC addition to peanut does not adversely affect nodulation, but ethylene perception is required for establishment of this symbiosis. Evidence for the contribution of NF to the modulation of ethylene-inducible defence gene expression is provided.

Symbiotic Regulatory Genes Controlling Nodule Development in Pisum sativum L

Analyses of natural variation and the use of mutagenesis and molecular-biological approaches have revealed 50 symbiotic regulatory genes in pea (Pisum sativum L.). Studies of genomic synteny using model legumes, such as Medicago truncatula Gaertn. and Lotus japonicus (Regel) K. Larsen, have identified the sequences of 15 symbiotic regulatory genes in pea. These genes encode receptor kinases, an ion channel, a calcium/calmodulin-dependent protein kinase, transcription factors, a metal transporter, and an enzyme. This review summarizes and describes mutant alleles, their phenotypic manifestations, and the functions of all identified symbiotic regulatory genes in pea. Some examples of gene interactions are also given. In the review, all mutant alleles in genes with identified sequences are designated and still-unidentified symbiotic regulatory genes of great interest are considered. The identification of these genes will help elucidate additional components involved in infection thread growth, nodule primordium development, bacteroid differentiation and maintenance, and the autoregulation of nodulation. The significance of symbiotic mutants of pea as extremely fruitful genetic models for studying nodule development and for comparative cell biology studies of legume nodules is clearly demonstrated. Finally, it is noted that many more sequences of symbiotic regulatory genes remain to be identified. Transcriptomics approaches and genome-wide sequencing could help address this challenge.

Chemotactic Host-Finding Strategies of Plant Endoparasites and Endophytes

Plants interact with microorganisms in the environment during all stages of their development and in most of their organs. These interactions can be either beneficial or detrimental for the plant and may be transient or long-term. In extreme cases, microorganisms become endoparastic or endophytic and permanently reside within a plant, while the host plant undergoes developmental reprogramming and produces new tissues or organs as a response to the invasion. Events at the cellular and molecular level following infection have been extensively described, however the mechanisms of how these microorganisms locate their plant hosts via chemotaxis remain largely unknown. In this review, we summarize recent findings concerning the signalling molecules that regulate chemotaxis of endoparasitic/endophytic bacteria, fungi, and nematodes. In particular, we will focus on the molecules secreted by plants that are most likely to act as guidance cues for microorganisms. These compounds are found in a wide range of plant species and show a variety of secondary effects. Interestingly, these compounds show different attraction potencies depending on the species of the invading organism, suggesting that cues perceived in the soil may be more complex than anticipated. However, what the cognate receptors are for these attractants, as well as the mechanism of how these attractants influence these organisms, remain important outstanding questions. Host-targeting marks the first step of plant-microorganism interactions, therefore understanding the signalling molecules involved in this step plays a key role in understanding these interactions as a whole.

Mechanisms in plant growth-promoting rhizobacteria that enhance legume-rhizobial symbioses

Nitrogen fixation is an important biological process in terrestrial ecosystems and for global crop production. Legume nodulation and N₂ fixation have been improved using nodule-enhancing rhizobacteria (NER) under both regular and stressed conditions. The positive effect of NER on legume-rhizobia symbiosis can be facilitated by plant growth-promoting (PGP) mechanisms, some of which remain to be identified. NER that produce aminocyclopropane-1-carboxylic acid deaminase and indole acetic acid enhance the legume-rhizobia symbiosis through (i) enhancing the nodule induction, (ii) improving the competitiveness of rhizobia for nodulation, (iii) prolonging functional nodules by suppressing nodule senescence and (iv) upregulating genes associated with legume-rhizobia symbiosis. The means by which these processes enhance the legume-rhizobia symbiosis is the focus of this review. A better understanding of the mechanisms by which PGP rhizobacteria operate, and how they can be altered, will provide opportunities to enhance legume-rhizobial interactions, to provide new advances in plant growth promotion and N₂ fixation.

Genome-Wide Identification of the CrRLK1L Subfamily and Comparative Analysis of Its Role in the Legume-Rhizobia Symbiosis

The plant receptor-like-kinase subfamily CrRLK1L has been widely studied, and CrRLK1Ls have been described as crucial regulators in many processes in Arabidopsis thaliana (L.), Heynh. Little is known, however, about the functions of these proteins in other plant species, including potential roles in symbiotic nodulation. We performed a phylogenetic analysis of CrRLK1L subfamily receptors of 57 different plant species and identified 1050 CrRLK1L proteins, clustered into 11 clades. This analysis revealed that the CrRLK1L subfamily probably arose in plants during the transition from chlorophytes to embryophytes and has undergone several duplication events during its evolution. Among the CrRLK1Ls of legumes and A. thaliana, protein structure, gene structure, and expression patterns were highly conserved. Some legume CrRLK1L genes were active in nodules. A detailed analysis of eight nodule-expressed genes in Phaseolus vulgaris L. showed that these genes were differentially expressed in roots at different stages of the symbiotic process. These data suggest that CrRLK1Ls are both conserved and underwent diversification in a wide group of plants, and shed light on the roles of these genes in legume–rhizobia symbiosis.

Studying the effect of tissue-specific expression of the K1 gene encoding LysM-receptor-like kinase on the development of symbiosis in peas

To study the role of pea LysM receptor-like kinase K1 in the coordination of the infection process, starting in epidermis and nodule organogenesis in the root cortex of plants, during the development of rhizobium-legume symbiosis, the genetic constructs in which K1 gene was cloned under the control of tissue-specific promoter pLeEXT1 of tomato Lycopersicon esculentum extensin gene and the constitutive promoter of cauliflower mosaic virus (CaMV35S, cauliflower mosaic virus 35S) were obtained. During the transformation of the Nod- mutant line, the k1-1, with two types of constructs, the restoration of nodule formation was observed, which indicated the possible participation of K1 in the control not only early, but also later stages of symbiosis development in pea.

ERN1 and CYCLOPS coordinately activate NIN signaling to promote infection thread formation in Lotus japonicus

Legumes engage in symbiosis with nitrogen-fixing soil bacteria, collectively called rhizobia, under nitrogen-limited conditions. In many legumes, the root invasion of rhizobia is mediated by infection threads (ITs), tubular invaginations of the host cell wall and plasma membrane, developed from infection foci of deformed root hairs. IT formation is regulated by a series of signal transduction in host root. Nodulation signals activate the host transcription factor (TF), CYCLOPS, which directly induces expression of two TF genes, ERF REQUIRED FOR NODULATION1 (ERN1) and NODULE INCEPTION (NIN), essential for IT development. Here, we explored the relationship among these three symbiotic TF genes in the model legume Lotus japonicus and examined how their interplay contributes to IT formation. qRT-PCR analysis showed that NIN expression induced by rhizobial infection was attenuated in ern1-1, and further declined in cyclops-3 ern1-1. ERN1 overexpression led to induction of NIN expression in cyclops-3 ern1-1 in the presence of rhizobia. Thus, in addition to CYCLOPS, ERN1 is able to increase the NIN expression level depending on infection. Furthermore, consistent with this transcriptional hierarchy, ectopic expression of ERN1 as well as NIN suppressed the IT-deficient cyclops-3 phenotype, but ERN1 failed to confer ITs in the nin-2 root. However, the ern1-1 symbiotic epidermal phenotype was not suppressed by the NIN ectopic expression. The cyclops-3 ern1-1 double mutant was less sensitive to rhizobial infection than the single mutants and defective in the symbiotic root hair response at earlier stages. This more severe phenotype of the double mutant suggests a role for ERN1 that independent of the CYCLOPS-mediated transcriptional regulation. We conclude that ERN1 is involved in regulating NIN expression in addition to CYCLOPS, and these TFs coordinately promote the symbiotic root hair response and IT development. Our data help to reveal the extensive role of ERN1 in root nodule symbiosis signaling.

Transcriptomic Analysis With the Progress of Symbiosis in 'Crack-Entry' Legume Arachis hypogaea Highlights Its Contrast With 'Infection Thread' Adapted Legumes

In root-nodule symbiosis, rhizobial invasion and nodule organogenesis is host controlled. In most legumes, rhizobia enter through infection threads and nodule primordium in the cortex is induced from a distance. But in dalbergoid legumes like Arachis hypogaea, rhizobia directly invade cortical cells through epidermal cracks to generate the primordia. Herein, we report the transcriptional dynamics with the progress of symbiosis in A. hypogaea at 1 day postinfection (dpi) (invasion), 4 dpi (nodule primordia), 8 dpi (spread of infection in nodule-like structure), 12 dpi (immature nodules containing rod-shaped rhizobia), and 21 dpi (mature nodules with spherical symbiosomes). Expression of putative ortholog of symbiotic genes in 'crack entry' legume A. hypogaea was compared with infection thread-adapted model legumes. The contrasting features were i) higher expression of receptors like LYR3 and EPR3 as compared with canonical Nod factor receptors, ii) late induction of transcription factors like NIN and NSP2 and constitutive high expression of ERF1, EIN2, bHLH476, and iii) induction of divergent pathogenesis-responsive PR-1 genes. Additionally, symbiotic orthologs of SymCRK, ROP6, RR9, SEN1, and DNF2 were not detectable and microsynteny analysis indicated the absence of a RPG homolog in diploid parental genomes of A. hypogaea. The implications are discussed and a molecular framework that guides crack-entry symbiosis in A. hypogaea is proposed.

LACK OF SYMBIONT ACCOMMODATION controls intracellular symbiont accommodation in root nodule and arbuscular mycorrhizal symbiosis in Lotus japonicus

Nitrogen-fixing rhizobia and arbuscular mycorrhizal fungi (AMF) form symbioses with plant roots and these are established by precise regulation of symbiont accommodation within host plant cells. In model legumes such as Lotus japonicus and Medicago truncatula, rhizobia enter into roots through an intracellular invasion system that depends on the formation of a root-hair infection thread (IT). While IT-mediated intracellular rhizobia invasion is thought to be the most evolutionarily derived invasion system, some studies have indicated that a basal intercellular invasion system can replace it when some nodulation-related factors are genetically modified. In addition, intracellular rhizobia accommodation is suggested to have a similar mechanism as AMF accommodation. Nevertheless, our understanding of the underlying genetic mechanisms is incomplete. Here we identify a L. japonicus nodulation-deficient mutant, with a mutation in the LACK OF SYMBIONT ACCOMMODATION (LAN) gene, in which root-hair IT formation is strongly reduced, but intercellular rhizobial invasion eventually results in functional nodule formation. LjLAN encodes a protein that is homologous to Arabidopsis MEDIATOR 2/29/32 possibly acting as a subunit of a Mediator complex, a multiprotein complex required for gene transcription. We also show that LjLAN acts in parallel with a signaling pathway including LjCYCLOPS. In addition, the lan mutation drastically reduces the colonization levels of AMF. Taken together, our data provide a new factor that has a common role in symbiont accommodation process during root nodule and AM symbiosis.

Symbiosis between plants and beneficial microbes such as nitrogen-fixing bacteria and arbuscular mycorrhizal fungi has enabled plant colonization of new environments. Root nodule symbiosis with nitrogen-fixing rhizobia enables sessile plants to survive in a nitrogen-deficient environment. To establish the symbiosis, host plant cells need to accommodate rhizobia during nodule development, a process mediated by a plant-derived intracellular structure called the infection thread (IT). In this study, we show that LACK OF SYMBIONT ACCOMMODATION (LAN) is involved in intracellular rhizobia accommodation in the model leguminous plant Lotus japonicus. LjLAN encodes a putative subunit of Mediator complex, a multiprotein complex that has a fundamental role as an activator of gene transcription. Mutation analysis suggests that LjLAN is required for root hair IT formation, which enables swift and efficient rhizobial accommodation. Moreover, we show that LjLAN is required for symbiosis with arbuscular mycorrhizal fungi. These data add a new component to the molecular mechanism relevant to the establishment of root nodule and arbuscular mycorrhizal symbiosis.

Regulation and functional diversification of root hairs

Root hairs result from the polar outgrowth of root epidermis cells in vascular plants. Root hair development processes are regulated by intrinsic genetic programs, which are flexibly modulated by environmental conditions, such as nutrient availability. Basic programs for root hair development were present in early land plants. Subsequently, some plants developed the ability to utilize root hairs for specific functions, in particular, for interactions with other organisms, such as legume-rhizobia and host plants-parasites interactions. In this review, we summarize the molecular regulation of root hair development and the modulation of root hairs under limited nutrient supply and during interactions with other organisms.

Improved Phytophthora resistance in commercial chickpea (Cicer arietinum) varieties negatively impacts symbiotic gene signalling and symbiotic potential in some varieties

Breeding disease-resistant varieties is one of the most effective and economical means to combat soilborne diseases in pulse crops. Commonalities between pathogenic and mutualistic microbe colonization strategies, however, raises the concern that reduced susceptibility to pathogens may simultaneously reduce colonization by beneficial microbes. We investigate here the degree of overlap in the transcriptional response of the Phytophthora medicaginis susceptible chickpea variety 'Sonali' to the early colonization stages of either Phytophthora, rhizobial bacteria or arbuscular mycorrhizal fungi. From a total of 6476 genes differentially expressed in Sonali roots during colonization by any of the microbes tested, 10.2% were regulated in a similar manner regardless of whether it was the pathogenic oomycete or a mutualistic microbe colonizing the roots. Of these genes, 49.7% were oppositely regulated under the same conditions in the moderately Phytophthora resistant chickpea variety 'PBA HatTrick'. Chickpea varieties with improved resistance to Phytophthora also displayed lower colonization by rhizobial bacteria and mycorrhizal fungi leading to an increased reliance on N and P from soil. Together, our results suggest that marker-based breeding in crops such as chickpea should be further investigated such that plant disease resistance can be tailored to a specific pathogen without affecting mutualistic plant:microbe interactions.

Ethylene, a Hormone at the Center-Stage of Nodulation

Nodulation is the result of a beneficial interaction between legumes and rhizobia. It is a sophisticated process leading to nutrient exchange between the two types of symbionts. In this association, within a nodule, the rhizobia, using energy provided as photosynthates, fix atmospheric nitrogen and convert it to ammonium which is available to the plant. Nodulation is recognized as an essential process in nitrogen cycling and legume crops are known to enrich agricultural soils in nitrogenous compounds. Furthermore, as they are rich in nitrogen, legumes are considered important as staple foods for humans and fodder for animals. To tightly control this association and keep it mutualistic, the plant uses several means, including hormones. The hormone ethylene has been known as a negative regulator of nodulation for almost four decades. Since then, much progress has been made in the understanding of both the ethylene signaling pathway and the nodulation process. Here I have taken a large view, using recently obtained knowledge, to describe in some detail the major stages of the process. I have not only reviewed the steps most commonly covered (the common signaling transduction pathway, and the epidermal and cortical programs), but I have also looked into steps less understood (the pre-infection step with the plant defense response, the bacterial release and the formation of the symbiosome, and nodule functioning and senescence). After a succinct review of the ethylene signaling pathway, I have used the knowledge obtained from nodulation- and ethylene-related mutants to paint a more complete picture of the role played by the hormone in nodule organogenesis, functioning, and senescence. It transpires that ethylene is at the center of this effective symbiosis. It has not only been involved in most of the steps leading to a mature nodule, but it has also been implicated in host immunity and nodule senescence. It is likely responsible for the activation of other hormonal signaling pathways. I have completed the review by citing three studies which makes one wonder whether knowledge gained on nodulation in the last decades is ready to be transferred to agricultural fields.

Possible Role of 1-Aminocyclopropane-1-Carboxylate (ACC) Deaminase Activity of Sinorhizobium sp. BL3 on Symbiosis with Mung Bean and Determinate Nodule Senescence

Sinorhizobium sp. BL3 forms symbiotic interactions with mung bean (Vigna radiata) and contains lrpL-acdS genes, which encode the 1-aminocyclopropane-1-carboxylate (ACC) deaminase enzyme that cleaves ACC, a precursor of plant ethylene synthesis. Since ethylene interferes with nodule formation in some legumes and plays a role in senescence in plant cells, BL3-enhancing ACC deaminase activity (BL3(+)) and defective mutant (BL3(-)) strains were constructed in order to investigate the effects of this enzyme on symbiosis and nodule senescence. Nodulation competitiveness was weaker in BL3(-) than in the wild-type, but was stronger in BL3(+). The inoculation of BL3(-) into mung bean resulted in less plant growth, a lower nodule dry weight, and smaller nodule number than those in the wild-type, whereas the inoculation of BL3(+) had no marked effects. However, similar nitrogenase activity was observed with all treatments; it was strongly detected 3 weeks after the inoculation and gradually declined with time, indicating senescence. The rate of plant nodulation by BL3(+) increased in a time-dependent manner. Nodules occupied by BL3(-) formed smaller symbiosomes, and bacteroid degradation was more prominent than that in the wild-type 7 weeks after the inoculation. Changes in biochemical molecules during nodulation were tracked by Fourier Transform Infrared (FT-IR) microspectroscopy, and the results obtained confirmed that aging processes differed in nodules occupied by BL3 and BL3(-). This is the first study to show the possible role of ACC deaminase activity in senescence in determinate nodules. Our results suggest that an increase in ACC deaminase activity in this strain does not extend the lifespan of nodules, whereas the lack of this activity may accelerate nodule senescence.

E151 (sym15), a pleiotropic mutant of pea (Pisum sativum L.), displays low nodule number, enhanced mycorrhizae, delayed lateral root emergence, and high root cytokinin levels

In legumes, the formation of rhizobial and mycorrhizal root symbioses is a highly regulated process which requires close communication between plant and microorganism. Plant mutants that have difficulties establishing symbioses are valuable tools for unravelling the mechanisms by which these symbioses are formed and regulated. Here E151, a mutant of Pisum sativum cv. Sparkle, was examined to characterize its root growth and symbiotic defects. The symbioses in terms of colonization intensity, functionality of micro-symbionts, and organ dominance were compared between the mutant and wild type. The endogenous cytokinin (CK) and abscisic acid (ABA) levels and the effect of the exogenous application of these two hormones were determined. E151 was found to be a low and delayed nodulator, exhibiting defects in both the epidermal and cortical programmes though a few mature and functional nodules develop. Mycorrhizal colonization of E151 was intensified, although the fungal functionality was impaired. Furthermore, E151 displayed an altered lateral root (LR) phenotype compared with that of the wild type whereby LR emergence is initially delayed but eventually overcome. No differences in ABA levels were found between the mutant and the wild type, but non-inoculated E151 exhibited significantly high CK levels. It is hypothesized that CK plays an essential role in differentially mediating the entry of the two micro-symbionts into the cortex; whereas it would inhibit the entry of the rhizobia in that tissue, it would promote that of the fungus. E151 is a developmental mutant which may prove to be a useful tool in further understanding the role of hormones in the regulation of beneficial root symbioses.

Functional analysis of duplicated Symbiosis Receptor Kinase (SymRK) genes during nodulation and mycorrhizal infection in soybean (Glycine max)

Association between legumes and rhizobia results in the formation of root nodules, where symbiotic nitrogen fixation occurs. The early stages of this association involve a complex of signalling events between the host and microsymbiont. Several genes dealing with early signal transduction have been cloned, and one of them encodes the leucine-rich repeat (LRR) receptor kinase (SymRK; also termed NORK). The Symbiosis Receptor Kinase gene is required by legumes to establish a root endosymbiosis with Rhizobium bacteria as well as mycorrhizal fungi. Using degenerate primer and BAC sequencing, we cloned duplicated SymRK homeologues in soybean called GmSymRKα and GmSymRKβ. These duplicated genes have high similarity of nucleotide (96%) and amino acid sequence (95%). Sequence analysis predicted a malectin-like domain within the extracellular domain of both genes. Several putative cis-acting elements were found in promoter regions of GmSymRKα and GmSymRKβ, suggesting a participation in lateral root development, cell division and peribacteroid membrane formation. The mutant of SymRK genes is not available in soybean; therefore, to know the functions of these genes, RNA interference (RNAi) of these duplicated genes was performed. For this purpose, RNAi construct of each gene was generated and introduced into the soybean genome by Agrobacterium rhizogenes-mediated hairy root transformation. RNAi of GmSymRKβ gene resulted in an increased reduction of nodulation and mycorrhizal infection than RNAi of GmSymRKα, suggesting it has the major activity of the duplicated gene pair. The results from the important crop legume soybean confirm the joint phenotypic action of GmSymRK genes in both mycorrhizal and rhizobial infection seen in model legumes.

The soybean (Glycine max) nodulation-suppressive CLE peptide, GmRIC1, functions interspecifically in common white bean (Phaseolus vulgaris), but not in a supernodulating line mutated in the receptor PvNARK

Legume plants regulate the number of nitrogen-fixing root nodules they form via a process called the Autoregulation of Nodulation (AON). Despite being one of the most economically important and abundantly consumed legumes, little is known about the AON pathway of common bean (Phaseolus vulgaris). We used comparative- and functional-genomic approaches to identify central components in the AON pathway of common bean. This includes identifying PvNARK, which encodes a LRR receptor kinase that acts to regulate root nodule numbers. A novel, truncated version of the gene was identified directly upstream of PvNARK, similar to Medicago truncatula, but not seen in Lotus japonicus or soybean. Two mutant alleles of PvNARK were identified that cause a classic shoot-controlled and nitrate-tolerant supernodulation phenotype. Homeologous over-expression of the nodulation-suppressive CLE peptide-encoding soybean gene, GmRIC1, abolished nodulation in wild-type bean, but had no discernible effect on PvNARK-mutant plants. This demonstrates that soybean GmRIC1 can function interspecifically in bean, acting in a PvNARK-dependent manner. Identification of bean PvRIC1, PvRIC2 and PvNIC1, orthologues of the soybean nodulation-suppressive CLE peptides, revealed a high degree of conservation, particularly in the CLE domain. Overall, our work identified four new components of bean nodulation control and a truncated copy of PvNARK, discovered the mutation responsible for two supernodulating bean mutants and demonstrated that soybean GmRIC1 can function in the AON pathway of bean.

Ethylene and jasmonic acid act as negative modulators during mutualistic symbiosis between Laccaria bicolor and Populus roots

The plant hormones ethylene, jasmonic acid and salicylic acid have interconnecting roles during the response of plant tissues to mutualistic and pathogenic symbionts. We used morphological studies of transgenic- or hormone-treated Populus roots as well as whole-genome oligoarrays to examine how these hormones affect root colonization by the mutualistic ectomycorrhizal fungus Laccaria bicolor S238N. We found that genes regulated by ethylene, jasmonic acid and salicylic acid were regulated in the late stages of the interaction between L. bicolor and poplar. Both ethylene and jasmonic acid treatments were found to impede fungal colonization of roots, and this effect was correlated to an increase in the expression of certain transcription factors (e.g. ETHYLENE RESPONSE FACTOR1) and a decrease in the expression of genes associated with microbial perception and cell wall modification. Further, we found that ethylene and jasmonic acid showed extensive transcriptional cross-talk, cross-talk that was opposed by salicylic acid signaling. We conclude that ethylene and jasmonic acid pathways are induced late in the colonization of root tissues in order to limit fungal growth within roots. This induction is probably an adaptive response by the plant such that its growth and vigor are not compromised by the fungus.

Ethylene in mutualistic symbioses

Ethylene (ET) is a gaseous phytohormone that participates in various plant physiological processes and essentially contributes to plant immunity. ET conducts its functions by regulating the expression of ET-responsive genes or in crosstalk with other hormones. Several recent studies have shown the significance of ET in the establishment and development of plant-microbe interactions. Therefore, it is not surprising that pathogens and mutualistic symbionts target ET synthesis or signaling to colonize plants. This review introduces the significance of ET metabolism in plant-microbe interactions, with an emphasis on its role in mutualistic symbioses.

Multiple impacts of the plant growth-promoting rhizobacterium Variovorax paradoxus 5C-2 on nutrient and ABA relations of Pisum sativum

Resolving the physiological mechanisms by which rhizobacteria enhance plant growth is difficult, since many such bacteria contain multiple plant growth-promoting properties. To understand further how the 1-aminocyclopropane-1-carboxylate (ACC) deaminase (ACCd)-containing rhizobacterium Variovorax paradoxus 5C-2 affects plant growth, the flows and partitioning of mineral nutrients and abscisic acid (ABA) and ABA metabolism were studied in pea (Pisum sativum) plants following rhizosphere bacterial inoculation. Although root architecture was not affected, inoculation increased root and shoot biomass, and stomatal conductance, by 20, 15, and 24%, respectively, and increased N, P, K, Ca, and Mg uptake by 16, 81, 50, 46, and 58%, respectively. P deposition in inoculated plant roots was 4.9 times higher than that in uninoculated controls. Rhizobacterial inoculation increased root to shoot xylem flows and shoot to root phloem flows of K by 1.8- and 2.1-fold, respectively. In control plants, major sinks for K deposition were the roots and upper shoot (43% and 49% of total uptake, respectively), while rhizobacterial inoculation increased K distribution to the lower shoot at the expense of other compartments (xylem, phloem, and upper shoot). Despite being unable to metabolize ABA in vitro, V. paradoxus 5C-2 decreased root ABA concentrations and accumulation by 40-60%. Although inoculation decreased xylem ABA flows, phloem ABA flows increased. Whether bacterial ACCd attenuates root to shoot ABA signalling requires further investigation, since ABA is critical to maintain growth of droughted plants, and ACCd-containing organisms have been advocated as a means of minimizing growth inhibition of plants in drying soil.

Ethylene supports colonization of plant roots by the mutualistic fungus Piriformospora indica

The mutualistic basidiomycete Piriformospora indica colonizes roots of mono- and dicotyledonous plants, and thereby improves plant health and yield. Given the capability of P. indica to colonize a broad range of hosts, it must be anticipated that the fungus has evolved efficient strategies to overcome plant immunity and to establish a proper environment for nutrient acquisition and reproduction. Global gene expression studies in barley identified various ethylene synthesis and signaling components that were differentially regulated in P. indica-colonized roots. Based on these findings we examined the impact of ethylene in the symbiotic association. The data presented here suggest that P. indica induces ethylene synthesis in barley and Arabidopsis roots during colonization. Moreover, impaired ethylene signaling resulted in reduced root colonization, Arabidopsis mutants exhibiting constitutive ethylene signaling, -synthesis or ethylene-related defense were hyper-susceptible to P. indica. Our data suggest that ethylene signaling is required for symbiotic root colonization by P. indica.

Invasion by invitation: rhizobial infection in legumes

Nodulation of legume roots typically begins with rhizobia attaching to the tip of a growing root-hair cell. The attached rhizobia secrete Nod factors (NF), which are perceived by the plant. This initiates a series of preinfection events that include cytoskeletal rearrangements, curling at the root-hair tip, and formation of radially aligned cytoplasmic bridges called preinfection threads (PIT) in outer cortical cells. Within the root-hair curl, an infection pocket filled with bacteria forms, from which originates a tubular invagination of cell wall and membrane called an infection thread (IT). IT formation is coordinated with nodule development in the underlying root cortex tissues. The IT extends from the infection pocket down through the root hair and into the root cortex, where it passes through PIT and eventually reaches the nascent nodule. As the IT grows, it is colonized by rhizobia that are eventually released into cells within the nodule, where they fix nitrogen. NF can also induce cortical root hairs that appear to originate from PIT and can become infected like normal root hairs. Several genes involved in NF signaling and some of the downstream transcription factors required for infection have been characterized. More recently, several genes with direct roles in infection have been identified, some with roles in actin rearrangement and others with possible roles in protein turnover and secretion. This article provides an overview of the infection process, including the roles of NF signaling, actin, and calcium and the influence of the hormones ethylene and cytokinin.

Determination of symbiotic nodule occupancy in the model Vicia tetrasperma using a fluorescence scanner

BACKGROUND

Fluorescent tagging of nodule bacteria forming symbioses with legume host plants represents a tool for vital tracking of bacteria inside the symbiotic root nodules and monitoring changes in gene activity. The constitutive expression of heterologous fluorescent proteins, such as green fluorescent protein (GFP), also allows screening for nodule occupancy by a particular strain. Imaging of the fluorescence signal on a macro-scale is associated with technical problems due to the robustness of nodule tissues and a high level of autofluorescence.

SCOPE

These limitations can be reduced by the use of a model species with a fine root system, such as Vicia tetrasperma. Further increases in the sensitivity and specificity of the detection and in image resolution can be attained by the use of a fluorescence scanner. Compared with the standard CCD-type cameras, the availability of a laser source of a specified excitation wavelength decreases non-specific autofluorescence while the photomultiplier tubes in emission detection significantly increase sensitivity. The large scanning area combined with a high resolution allow us to visualize individual nodules during the scan of whole root systems. Using a fluorescence scanner with excitation wavelength of 488 nm, a band-pass specific emission channel of 532 nm and a long-pass background channel of 555 nm, it was possible to distinguish nodules occupied by a rhizobial strain marked with one copy of cycle3 GFP from nodules colonized by the wild-type strain.

CONCLUSIONS

The main limitation of the current plant model and GFP with the wild-type emission peak at 409 nm is a sharp increase in root autofluorescence below 550 nm. The selectivity of the technique can be enhanced by the use of red-shifted fluorophores and the contrasting labelling of the variants, provided that the excitation (482 nm) and emission (737 nm) maxima corresponding to root chlorophyll are respected.

Early action of pea symbiotic gene NOD3 is confirmed by adventitious root phenotype

A supernodulating and Nts (nitrate-tolerant symbiosis) symbiotic mutation of pea (Pisum sativum L.) line RisfixC was found to retain its expression in the distant genetic background of pea lines Afghanistan L1268, Zhodino E900, and cv. Arvika. This finding allowed for reliable scoring for the trait in mapping crosses. The RisfixC mutation was localized 8.2cM apart from SYM2 and cosegregated with molecular markers for SYM2-NOD3 region Psc923 and OA-1. Grafting experiments showed that supernodulation is root-determined, consistently with mutants in the NOD3 locus. Therefore, the mutation of RisfixC can be localized in gene NOD3. Like in other published nod3 alleles, the RisfixC mutation determines supernodulation when it is expressed in the root but not in the shoot. Supernodulated adventitious roots that are spontaneously formed in the wild-type scions on mutant rootstocks indicate that the descending systemic signal, which is inhibitory to nodule formation, is absent in this type of chimeric plants. Since the descending signal production in the wild-type shoot reflects the presence of the ascending root signal, the nod3-associated lesion must be located in the beginning of the systemic circuit regulating nodule number.

Common and not so common symbiotic entry

Great advances have been made in our understanding of the host plant's common symbiosis functions, which in legumes mediate intracellular accommodation of both nitrogen-fixing bacteria and arbuscular mycorrhiza (AM) fungi. However, it has become apparent that additional plant genes are required specifically for bacterial entry inside the host root. In this opinion article, we consider Lotus japonicus nap1 and pir1 symbiotic mutants within the context of other deleterious mutations that impair an intracellular accommodation of bacteria but have no impact on the colonization of roots by AM fungi. We highlight a clear delineation of early signaling events during bacterial versus AM symbioses while suggesting a more intricate origin of the plant's ability for intracellular accommodation of bacteria.

Mycorrhization of the notabilis and sitiens tomato mutants in relation to abscisic acid and ethylene contents

We examined whether the reduced mycorrhization of abscisic acid (ABA)-deficient tomato mutants correlates with their incapacity in ABA biosynthesis and whether this effect is dependent on ethylene production. The mycorrhization of notabilis and sitiens mutants, which have different ABA deficiencies and an excess of ethylene production, was analyzed. Comparative analysis of the ABA-deficient tomato mutants showed both quantitative and qualitative differences in the pattern of arbuscular mycorrhiza (AM) colonization between the two tomato mutant phenotypes. The sitiens mutant showed a great limitation in fungal colonization (mycorrhizal intensity and arbuscule formation) well correlated with their incapacity in ABA biosynthesis. The notabilis plants, which maintained normal ABA levels in roots under our experimental conditions, appeared to be less affected in their capacity for AM formation, and only a decrease in mycorrhizal intensity was noted at the end of the mycorrhization process. Blockage of ABA formation after tungstate application resulted in a reduction in mycorrhization of wild-type tomato plants. The transcript accumulation of the mycorrhiza-responsive LePT4 gene (tomato phosphate transporter) was clearly associated with the ABA content and mycorrhiza development in roots, as the tungstate treatment in wild-type plants and the inherent ABA deficiency in sitiens mutants led to a complete abolishment of their expression. Our results suggest that the decrease in arbuscular abundance in mycorrhizal sitiens roots is directly associated with their ABA biosynthesis deficiency, and the accumulation of ethylene, as a consequence of ABA deficiency in the mutants, primarily affects mycorrhizal intensity.

Sesbania rostrata: a case study of natural variation in legume nodulation

Legumes acquired the ability to engage in a symbiotic interaction with soil-borne bacteria and establish a nitrogen-fixing symbiosis in a novel root organ, the nodule. Most legume crops and the model legumes Medicago truncatula and Lotus japonicus are infected intracellularly in root hairs via infection threads that lead the bacteria towards a nodule primordium in the root cortex. This infection process, however, does not reflect the great diversity of infection strategies that are used by leguminous plants. An alternative, intercellular invasion occurs in the semiaquatic legume Sesbania rostrata. Bacteria colonize epidermal fissures at lateral root bases and trigger cortical cell death for infection pocket formation and subsequent intercellular and intracellular infection thread progression towards the primordium. This infection mode evolved as an adaptation to waterlogged conditions that inhibit intracellular invasion. In this review, we discuss the molecular basis for this adaptation and how insights into this process contribute to general knowledge of the rhizobial infection process.

Molecular analysis of legume nodule development and autoregulation

Legumes are highly important food, feed and biofuel crops. With few exceptions, they can enter into an intricate symbiotic relationship with specific soil bacteria called rhizobia. This interaction results in the formation of a new root organ called the nodule in which the rhizobia convert atmospheric nitrogen gas into forms of nitrogen that are useable by the plant. The plant tightly controls the number of nodules it forms, via a complex root-to-shoot-to-root signaling loop called autoregulation of nodulation (AON). This regulatory process involves peptide hormones, receptor kinases and small metabolites. Using modern genetic and genomic techniques, many of the components required for nodule formation and AON have now been isolated. This review addresses these recent findings, presents detailed models of the nodulation and AON processes, and identifies gaps in our understanding of these process that have yet to be fully explained.

Strigolactones, signals for parasitic plants and arbuscular mycorrhizal fungi

Although strigolactones play a critical role as rhizospheric signaling molecules for the establishment of arbuscular mycorrhizal (AM) symbiosis and for seed germination of parasitic weeds, scarce data are available about interactions between AM fungi and strigolactones. In the present work, we present background data on strigolactones from studies on their seed germination activity on the parasitic weeds Orobanche and Striga, the importance of nitrogen and phosphorus for this seed germination activity, and what this could mean for AM fungi. We also present results on the susceptibility of plants to AM fungi and the possible involvement of strigolactones in this AM susceptibility and discuss the role of strigolactones for the formation and the regulation of the AM symbiosis as well as the possible implication of these compounds as plant signals in other soil-borne plant-microbe interactions.

1-aminocyclopropane-1-carboxylate (ACC) deaminase genes in rhizobia from southern Saskatchewan

A collection of 233 rhizobia strains from 30 different sites across Saskatchewan, Canada was assayed for 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, with 27 of the strains displaying activity. When all 27 strains were characterized based on 16S rRNA gene sequences, it was noted that 26 strains are close to Rhizobium leguminosarum and one strain is close to Rhizobium gallicum. Polymerase chain reaction (PCR) was used to rapidly isolate ACC deaminase structural genes from the above-mentioned 27 strains; 17 of them have 99% identities with the previously characterized ACC deaminase structural gene (acdS) from R. leguminosarum bv. viciae 128C53K, whereas the other ten strains are 84% identical (864-866/1,020 bp) compared to the acdS from strain 128C53K. Southern hybridization showed that each strain has only one ACC deaminase gene. Using inverse PCR, the region upstream of the ACC deaminase structural genes was characterized for all 27 strains, and 17 of these strains were shown to encode a leucine-responsive regulatory protein. The results are discussed in the context of a previously proposed model for the regulation of bacterial ACC deaminase in R. leguminosarum 128C53K.

Evolution of root endosymbiosis with bacteria: How novel are nodules?

Plants form diverse symbioses with nitrogen-fixing bacteria to gain access to ammonium, a product of the prokaryote-exclusive enzyme nitrogenase. Improving the symbiotic effectiveness of crop plants like maize, wheat or rice is a highly topical challenge and could help reduce the need for energy-intense nitrogen fertilizer in staple food production. Root nodule symbiosis (RNS) constitutes one of the most productive nitrogen-fixing systems, but it is restricted to a small group of related angiosperms. Here, we review the genetic regulation of RNS and its interconnections with other plant symbiosis or plant developmental programs. Since RNS uses genetic programs that are widely conserved in land plants, we evaluate the prospects for a transfer to plants that are currently non-nodulating.

Rhizosphere bacteria containing 1-aminocyclopropane-1-carboxylate deaminase increase yield of plants grown in drying soil via both local and systemic hormone signalling

Decreased soil water availability can stimulate production of the plant hormone ethylene and inhibit plant growth. Strategies aimed at decreasing stress ethylene evolution might attenuate its negative effects. An environmentally benign (nonchemical) method of modifying crop ethylene relations - soil inoculation with a natural root-associated bacterium Variovorax paradoxus 5C-2 (containing the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase that degrades the ethylene precursor ACC), was assessed with pea (Pisum sativum) plants grown in drying soil. Inoculation with V. paradoxus 5C-2, but not with a transposome mutant with massively decreased ACC deaminase activity, improved growth, yield and water-use efficiency of droughted peas. Systemic effects of V. paradoxus 5C-2 included an amplified soil drying-induced increase of xylem abscisic acid (ABA) concentration, but an attenuated soil drying-induced increase of xylem ACC concentration. A local bacterial effect was increased nodulation by symbiotic nitrogen-fixing bacteria, which prevented a drought-induced decrease in nodulation and seed nitrogen content. Successfully deploying a single bacterial gene in the rhizosphere increased yield and nutritive value of plants grown in drying soil, via both local and systemic hormone signalling. Such bacteria may provide an easily realized, economic means of sustaining crop yields and using irrigation water more efficiently in dryland agriculture.

Mechanism of infection thread elongation in root hairs of Medicago truncatula and dynamic interplay with associated rhizobial colonization

In temperate legumes, endosymbiotic nitrogen-fixing rhizobia gain access to inner root tissues via a specialized transcellular apoplastic compartment known as the infection thread (IT). To study IT development in living root hairs, a protocol has been established for Medicago truncatula that allows confocal microscopic observations of the intracellular dynamics associated with IT growth. Fluorescent labeling of both the IT envelope (AtPIP2;1-green fluorescent protein) and the host endoplasmic reticulum (green fluorescent protein-HDEL) has revealed that IT growth is a fundamentally discontinuous process and that the variable rate of root hair invagination is reflected in changes in the host cell cytoarchitecture. The concomitant use of fluorescently labeled Sinorhizobium meliloti has further revealed that a bacteria-free zone is frequently present at the growing tip of the IT, thus indicating that bacterial contact is not essential for thread progression. Finally, these in vivo studies have shown that gaps within the bacterial file are a common feature during the early stages of IT development, and that segments of the file are able to slide collectively down the thread. Taken together, these observations lead us to propose that (1) IT growth involves a host-driven cellular mechanism analogous to that described for intracellular infection by arbuscular mycorrhizal fungi; (2) the non-regular growth of the thread is a consequence of the rate-limiting colonization by the infecting rhizobia; and (3) bacterial colonization involves a combination of bacterial cell division and sliding movement within the extracellular matrix of the apoplastic compartment.

Unraveling the network: Novel developments in the understanding of signaling and nutrient exchange mechanisms in the arbuscular mycorrhizal symbiosis

The arbuscular mycorrhhiza (AM) symbiosis involves an intricate network of signaling and biochemical pathways designed to ensure that a beneficial relationship is established between the plant and fungal partners as a result of a mutual nutrient exchange. Emerging data has been recently published to explain why the relationship is not always fair, as observed in prevalent parasitic AM relationships in which the plant host receives no phosphorus (P) in exchange for carbon (C) delivered to the fungus. The theory behind this unorthodox view of the AM relationship, together with the description of other recent developments in nutrient mobilization as well as in key aspects of the bi-directional signaling that culminates in the symbiotic association, is the subject of this review.

api, A novel Medicago truncatula symbiotic mutant impaired in nodule primordium invasion

Genetic approaches have proved to be extremely useful in dissecting the complex nitrogen-fixing Rhizobium-legume endosymbiotic association. Here we describe a novel Medicago truncatula mutant called api, whose primary phenotype is the blockage of rhizobial infection just prior to nodule primordium invasion, leading to the formation of large infection pockets within the cortex of noninvaded root outgrowths. The mutant api originally was identified as a double symbiotic mutant associated with a new allele (nip-3) of the NIP/LATD gene, following the screening of an ethylmethane sulphonate-mutagenized population. Detailed characterization of the segregating single api mutant showed that rhizobial infection is also defective at the earlier stage of infection thread (IT) initiation in root hairs, as well as later during IT growth in the small percentage of nodules which overcome the primordium invasion block. Neither modulating ethylene biosynthesis (with L-alpha-(2-aminoethoxyvinylglycine or 1-aminocyclopropane-1-carboxylic acid) nor reducing ethylene sensitivity in a skl genetic background alters the basic api phenotype, suggesting that API function is not closely linked to ethylene metabolism or signaling. Genetic mapping places the API gene on the upper arm of the M. truncatula linkage group 4, and epistasis analyses show that API functions downstream of BIT1/ERN1 and LIN and upstream of NIP/LATD and the DNF genes.