16.5G: The Legume-Root Nodule Symbiosis - Biology

16.5G: The Legume-Root Nodule Symbiosis - Biology

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Legumes have a symbiotic relationship with bacteria called rhizobia, which create ammonia from atmospheric nitrogen and help the plant.

Learning Objectives

  • Evaluate legume and nitrogen-fixing bacteria symbiosis

Key Points

  • Rhizobia normally live in the soil, but when there is limited soil nitrogen, legumes release flavonoids which signal to rhizobia that the plant is seeking symbiotic bacteria.
  • When exposed to flavonoids, the Rhizobia release nodulation factor, which stimulates the plant to create deformed root hairs. Rhizobia then form an ” infection thread” which allows them to enter the root cells through the root hairs.
  • Once the rhizobia are inside the root cells, the root cells divide rapidly, forming a nodule.
  • The rhizobia create ammonia from nitrogen in the air, which is used by the plant to create amino acids and nucleotides. The plant provides the bacteria with sugars.

Key Terms

  • Nodulation Factor: Signaling molecules produced by bacteria known as rhizobia during the initiation of nodules on the root of legumes. A symbiosis is formed when legumes take up the bacteria.

Legumes and their Nitrogen-Fixing Bacteria

Many legumes have root nodules that provide a home for symbiotic nitrogen-fixing bacteria called rhizobia. This relationship is particularly common in nitrogen-limited conditions. The Rhizobia convert nitrogen gas from the atmosphere into ammonia, which is then used in the formation of amino acids and nucleotides.

Rhizobia normally live in the soil and can exist without a host plant. However, when legume plants encounter low nitrogen conditions and want to form a symbiotic relationship with rhizobia they release flavinoids into the soil. Rhizobia respond by releasing nodulation factor (sometimes just called nod factor), which stimulates nodule formation in plant roots. Exposure to nod factor triggers the formation of deformed root hairs, which permit rhizobia to enter the plant. Rhizobia then form an infection thread, which is an intercellular tube that penetrates the cells of the host plant, and the bacteria then enter the host plants cells through the deformed root hair. Rhizobia can also enter the root by inserting themselves between cracks between root cells; this method of infection is called crack entry. Bacteria enter the root cells from the intercellular spaces, also using an infection thread to penetrate cell walls. Infection triggers rapid cell division in the root cells, forming a nodule of tissue.

The relationship between a host legume and the rhizobia is symbiotic, providing benefits to both participants. Once the rhizobia have established themselves in the root nodule, the plant provides carbohydrates in the form of malate and succinate, and the rhizobia provide ammonia for the formation of amino acids. Many legumes are popular agricultural crops specifically because they require very little fertilizer: their rhiziobia fix nitrogen for them. Used properly some legumes can even serve as fertilizer for later crops, binding nitrogen in the plant remains in the soil.

Correlations between the ascorbate-glutathione pathway and effectiveness in legume root nodules

Legume root nodules use the ascorbate-glutathione pathway to remove harmful H2O2. In the present study. effective and ineffective nodules from soybean and alfalfa were compared with regard to this pathway. Effective nodules had higher activity of all 4 enzymes (ascorbate peroxidase, EC 1. 11. 1. 11: monodehydroascorbate reductase, EC 1. 6. 5. 4: dehydroascorbate reductase, EC 1. 8. 5. 1: and glutathione reductase, EC 1. 6. 4. 2). The concentration of thiol tripeptides (primarily homoglutathione) was about 1 mM in effective nodules – a level 3–4-fold higher than in ineffective nodules. Effective nodules contained higher levels of NAD + . NADP + and NADPH. but not of NADH or ascorbate. The increased capacity for peroxide scavenging in effective nodules as compared to ineffective nodules emphasizes the important protective role that this pathway may play in processes related to nitrogen fixation.

Legume-imposed selection for more-efficient symbiotic rhizobia

Agriculture could reduce the economic and environmental costs of nitrogen (N) fertilizers by relying more on atmospheric N taken up (fixed) by rhizobia bacteria in legume root nodules. Just scaling up current N fixation might not help, however, because many nodules are occupied by rhizobia with high carbon (C) costs relative to N fixed. Given this low efficiency, greater plant investment in nodules can decrease yields ( 1 ). Even if we inoculate with more-efficient rhizobia, evolution can favor mutants that divert more resources from N fixation to their own reproduction ( 2 ). Could we instead breed legumes that preferentially support the reproduction and release into soil of only the most-efficient rhizobia in their nodules? If so, how much would this benefit future crops grown in the same soil? In PNAS, Westhoek et al. ( 3 ) present modeling and convincing results that expand our understanding of host-imposed selection among rhizobia differing in efficiency. Their methods could help plant breeders “select for legumes which are better at discriminating among strains” ( 3 ). Although their results are also relevant to broader questions about the evolution of cooperation, this commentary will focus on issues related to that suggested application.

Previous modeling showed that, without host-imposed selection, rhizobia strains that invest anything in N fixation would have lower fitness than competing strains in the same plants that allocate resources only to their own reproduction. Fixing strains would only have greater fitness if hosts impose fitness-reducing “sanctions” on less-beneficial strains ( 2 ). All legumes tested appear to reduce allocation to nonfixing nodules ( 4 ⇓ – 6 ), although decreased allocation may not always limit rhizobia reproduction ( 7 ). Most …

Legume root nodule symbiosis: An evolving story in biology and biotechnology

The evolution of biological nitrogen fixation is central to the evolution of life on earth. Nitrogen is an essential component of proteins and nucleic acids and its restricted availability to living organisms has often been a major factor limiting growth. Despite the overwhelming abundance of N2 gas in the atmosphere, di-nitrogen is chemically inaccessible to most forms of life. For their growth and metabolism, most organisms use the ‘fixed’ forms of nitrogen, either as ammonium (NH4 + ) or as nitrate (NO3 - ), or derivatives thereof. However, the major input into the global nitrogen cycle is through the reductive process of biological nitrogen fixation which converts atmospheric N2 into ammonia (NH3). This process evolved in bacteria and/or archaea over 2.5 billion years ago while the planet still had a reducing atmosphere. Today, biological nitrogen fixation is still restricted to the bacteria and archaea. The legume root nodule symbiosis allows the host plant to benefit directly by association with soil bacteria, collectively termed rhizobia, which fix nitrogen as endosymbionts.

16.5G: The Legume-Root Nodule Symbiosis - Biology

ISSN: 0973-7510

E-ISSN: 2581-690X

Symbiosis in legume plants is an ever evolving research as the factors that initiate, regulate and accomplish the complex relationship between the plant and microorganisms are very dynamic. Rhizobium is a common symbiont in legumes which throughout the process of evolution, has undergone multiple phenotypic and genotypic manifestations. Crop specificity based on the compatible combination of plant and rhizobium is, of course, the modern concept in advanced biofertilizer research. Yet, the biofertilizers are not being considered as replacement of synthetic fertilizers, but just an alternative to the chemical fertilizers. It is clearly evident from both the usage and yielding perspectives that biofertilizers are not the priority of the farming communities. A serious fundamental amendment in the research of biofertilizers is proposed in this review article in the name of Geo specificity. Exploring the natural combination of rhizobium and legume plants with respect to geography and reinoculating in the same geographical region is the central dogma of the concept. Rhizobium of one geography could be sensitive to other geographies even though the crop remains the same. Therefore a new consideration in the biofertilizer research is proposed, presented and illustrated in this review to give more insights about Bio-Geo Specificity.

Rhizobium, symbiosis, Geospecificity, legume plants

Plant interacting microbes vary in the nature of the relationship they establish with their hosts. For example, pathogenic microorganisms establish interactions that can severely impair the development/survival of the susceptible hosts. In distinction to pathogenic bacteria, symbiotic bacteria example rhizobia are beneficial to their hosts. Rhizobia, the soil bacteria interact symbiotically with the leguminous plants forming nitrogen-fixing nodules 1 . The process initiates on the root, beginning with the exchange of signal molecules between the host and microbe 2 . It then invades the plant by forming infection threads. Initiation begins from the curled root hair ends and grows towards the plant cortex 3 . Located just in front of these growing threads are the inner cortical cells. Dedifferentiation of these cells leads to the induction of primordium of the nodule. Further, the activity of the nodule meristem is initiated on the outer side of the primordium leading to the further growth of the nodule 4 .

The process of nitrogen fixation occurs naturally by which the atmospheric nitrogen is converted into ammonia (readily available form for plants) with the help of the nitrogenase enzyme 5 . The bacteria present inside the nodules help to fix this nitrogen and the process results in a complex interaction between the host plant and the rhizobia. This mutualism has found to be advantageous for both the host in which plants provide rhizobacteria with carbon as a source and energy that is necessary for its growth and functions and the microbes, in turn, provide reduced nitrogen to the host in the form of ammonium 6 . This process of nodulation and nitrogen fixing requires several rhizobia bacteria as well as symbiotic genes for effective symbiosis between the host and the microbes. Rhizobial genes present in rhizobacteria will play an important role in nodule development and bacterioid metabolism. Some of them, “nod, nol, noe” genes involves in nodulation, “nif, fix” for nitrogen fixation, and the other plant genes that are expressed in the root tissue are nodulin genes 7 .

One conspicuous feature of legume-rhizobialsymbios is a highly specific feature that may occur both at initial and final stages like bacterial infection and nitrogen fixation respectively.

Domesticated crop species were found to have higher specificity i.e. fewer compatible symbionts than their wild counterparts 8 . Such constraints could decrease the yield in conditions where no favorable strains are available. This knowledge concerning genetic control of symbiotic specificity would help manipulate the key genetic factors controlling the interaction and improve the agronomic potential of the root nodule symbiosis. Hence the present review will give a brief overview of the various factors accounting for this to the symbiotic specificity and prove that nodules occupy a competitive niche for microbial accommodation.

Flavonoid-NodD interaction
In the early course of legume-rhizobial symbiosis, the legumes produce flavonoids, which diffuse across the bacterial membrane resulting in the activation of nodulation genes (nod). These genes encode enzymes that produce bacterial Nod factors, thereby initiating a symbiotic development for the most part of leguminous plants 9 . Once symbiosis is initiated, the process of transcription occurs furthering this mutualism. Flavonoid activates bacterial proteins (NodD) belongs to the LysR family of transcription regulators mediate this transcription of nod genes. These NodD genes bind to the nod boxes (DNA motifs), which are found in the nod genes promoter region 10 .

Broughton and Peck, et al. demonstrated that these NodDs from rhizobial groups respond differently to different flavonoids 11,12 . In view of the fact that legumes produce various types of flavonoids, nod genes that are regulated by NodD will respond to the specific flavonoids at an early stage of symbiosis. For example, mutations in the nodD from R. leguminosarumbv. trifoli results host range extension owing to the expression of nod genes with flavonoid inducers that are generally dormant in nature 13 .The role of NodD regulation by nodD gene expression of Sinorhizobiummeliloti and the mutated expression of nodD of S. meliloti was explained in Peck et al. 12 research. It is henceforth established that flavonoid induced nod gene expression depends on the source of NodD.

Determinants of specificity
Nod factors
The process of nodulation in most part of the legume plants occurs by producing Nod factors. In contrast, photosynthetic bacteria nodulate without producing Nod factors, the reason being the absence of Nod genes 14 . The Nod factors possess a backbone structure called N-acetyl glucosamine oligosaccharide with a fatty chain at the non reducing end which is similar in different rhizobia but vary in size and saturation, including supplementary additions at each ends, such as glycosylation and sulfation 15 . These modifications help us to determine if a particular Nod factor be able to perceive by a particular host 16 .

The nodABC genes usually present in all rhizobium bacteria required for the synthesis of Nod factors (NF’s) which are made up of lipo-chitooligosaccharides. A mutation occurs in nodABC genes that interrupt and abolish the entire process of symbiosis. Apart from this, any modifications in the additional genes that determine the Nod factor corealters this specificity. For instance, obliterating the nodE gene present in R. leguminosarum bv. trifolii changes the uniqueness of the fatty acyl chain attached to the Nod factor and this modification affects symbiosis with Trifolium species 17 .

Perception of signals from the Nod factor is mediated by NFRs i.e. Nod factor signals. They are basically serine/threonine receptor kinases containing LysM motifs in the extracellular component 18 . These motifs were demonstrated by molecular and genetic analyses in L. japonicas as host determinants of symbiosis specificity. It was observed that by transferring Lj-NFR1 and Lj-NFR5 receptors into a legume M. truncatula have enabled nodulation by a Mesorhizobium lotisymbiont in the L. japonicus legume plant 19 .

Rhizobial surface polysaccharides & plant lectins
Added classes of bacterial components that are the key factors to interact with the host include the bacterial surface polysaccharides, reported in numerous studies as having a symbiotic role. A various group of bacterial polysaccharides such as lipopolysaccharides (LPS), cyclic glucans, Exopolysaccharides (EPS), and capsular polysaccharides is the bacterial groups of polysaccharides that interact with the host and any defect in any of these components results in the immediate failure of the early or later stages of symbiosis. It was noticed that defects in the EPS production resulted in the arrest at the infection thread stage in the S. meliloti group of microorganisms 20,21 . Furthermore, the severity of these defects had a correlation with the degree of change in the structure of EPS 22 . Likewise, an observed failure in the production or export of cyclic b-glucansled to a drastic problem of infection thread malformation or no formation during symbiosis in the host plant 23 .

Numerous strains of S. meliloti distinguished ecotypes of M. truncatula by producing a normal nodule on one and defective ones on the other 24 . It was demonstrated from the above-mentioned study that by an exchange of EPS locus the phenotype can be switched, by supporting this concept that the surface polysaccharides are the determinants of specificity in the symbiosis process of legume vs.rhizobium. At the nitrogen fixing level, bacterial polysaccharides specificity was expressed in various other legume-rhizobial interactions. For example, Exopolysaccharides mutants of M. Loti produced functional nodules on L. pedunculatus and non-functional ones on L. leucocephala 25 . In R. leguminosarum strain 3841 where some lipopolysaccharide mutants behaved normally on a pea, whereas other mutants behaved a defective mechanism in nitrogen fixation 26 .Lectins belonging to the family of carbohydrate binding proteins are normally found in the legume seeds. Their role as receptors for rhizobial polysaccharides was speculated long ago and thus acts as a determinant of host range 27 . They bind to the surface polysaccharides and promote the addition of rhizobia to root hairs, consequently, initiating nodule formation by enhancing the delivery of Nod factors towards root hairs 28,29 . An observation says that host specificity depends on the – surface polysaccharides interactions in which lectin genes would support a host range expansion 30 .

Host immunity
The plant immune system helps fight against any microbial attack by forming structural barriers preventing invasion and subsequent infection. In the initial phases, they respond to the attack by triggering pathogen-associated molecular pattern immunity (PAMP). In order to dampen this immunity and gain to the host access, gram-negative microbes use a type III secretion system (T3SS). Further, as the second line of defense, plant genes perceive the effector protein of the invading microbe to initiate effector-triggered immunity 31 . Therefore, microbe-encoded effector and plant defense act as determinants of host range for pathogens.

In the preliminary period of compatible legume-rhizobial interaction, defense responses do occur but become less pronounced as symbiosis is established 32 . Microbe-associated molecular patterns (MAMPs) i.e. nod factors plus surface polysaccharides could have played a possible role in the inhibition of defense responses during compatible legume hosts 33-36 . Contrastingly, these MAMPs can bring for the defense response in non-leguminous plants 37 . This suggests that rhizobia could have developed their specific MAMPs recognized definitive compatible legume hosts for the development of symbiosis.

Infection thread formation initiates when rhizobia get entrapped between the two root hair cells. The number of threads that are initiated with a rhizobial strain generally outnumbers the number of developing nodules 38 . Nutman documentation of infection and nodular dynamics observed that infection proceeds in two phases, First the early phase in which the higher infection rate and the second phase related to the time of nodule formation had a much lower infection rate. He furthermore noticed that the early stage of infections was not uniformly disseminated along the seedling root. There were zones that predominantly susceptible to early infection (root hairs), in which the infection occurred preceding to their occurrence in the farther zone 39 . Apart from these experiments involving split root systems and nodule excision found that nodules accountable for this decline in infection rates (40-43 . These findings indicate that the plant itself controls its infection rates and, also its numbers of infections to permit the progress of nodule developmental pathways.

Strain-specific nitrogen fixation
Legume plant naturally builds a fundamental capacity in its nodules to accommodate both the symbiotic as well as endophytic bacteria for their respective roles to perform. However co-inoculation studies revealed that symbiotic bacteria occupy a majority portion of the nodule and the endophytes remained in a small distinctive segment of the nodule 44 . This demonstrates the ability of the symbiont to adopt the nodule environment and compete with the endophytes. It also reveals the fact that symbiotic bacteria effectively perform the communication and improves its mechanical capacity with the host while infecting the rizho zone of the plant. As such no definitive rate of nitrogen fixing efficiency of plant-rhizobial combinations, it varies with a variety of combinations. In some extreme conditions though the rhizobial strains nodulate a host plant but were unable to fix nitrogen. On the other hand, the same strain could have the capacity to fix nitrogen with alternative host genotypes 45,46 .

Recent advances in the literature have led to an increased understanding of the process of nodule development however, mechanisms involving nitrogen fixation have largely been unknown. But the nodulation specificity and interaction was well understood and published in between the M. truncatula host and S. melilotisps. to achieve the identification of precise genes involved 47-49 . Genetic analysis recognized a distinct gene called “Mt-Sym6” which is a conditioned host specific gene in S. meliloti strain A145 for nitrogen fixation immediately upon inoculation into the host plant 45 . Studies performed on strains of R. leguminosarum bv. trifolii found strange results of varying compatibility with white clover plant and caucasian clover plant. One of the T. ambiguum rhizobial strains, ICC105 produced non-fixing nodules when inoculated in white clover whereas produced nodulating genes efficiently while inoculated on to the caucasian clover 50 . The above genetic experiments illustrated that non nodulation is because a unique sequence of ICC105 promoter regions prevented nifA protein which is necessary for activating nitrogenase enzyme assembly.

Bio-geo specific rhizobacteria
The Leguminosae comprising of 19,500 species and 751 genera that were populated major surface portion of land on the earth. Their respective species were adapted all most all terrestrial ecosystems including deserts, tropical rain forests and habituated to tropical as well as arctic habitats 51-53 . A papilionoid tribe having 65 native Fynbos legumes was analyzed with rhizobial diversity and their specific host preferences. For further deep analysis, sequencing of 16S rRNA, recA, atp Dchromosomal genes and nodA, nif Hsymbiosis related genes recognized and named those Mesorhizobium as alpha symbionts and Burkholderia as a betasymbiont. Though the host genotype was one of the factors influencing rhizobial diversity, environmental factors like the acidic nature of the soil and site elevation showed a positive association with genetic variations in the Mesorhizobium and Burkholderia. These genetic variations demonstrated host and environmental interactions for the distribution of Fynbosrhizobia in various locations 54 .

A study on Australian Acacia with rhizobia interactions was conducted for understanding the geographic patterns of symbiont abundance and adaptation. Among those 58 different sites were characterized like the size of symbiont population, environmental parameters, and soil chemistry. Further better understanding greenhouse soil experiments were conducted with native soils filled in pots, minimal apparent differences were found between host and seeding responses. When another species A. salicinagrew in A. stenophylla and A. salicinasoils in a similar fashion to check for the same behavior, no similar results were found as A. stenophylla yielded. This signifies that the plants of one geography have a broad adaptation to its own rhizosphere bacteria and perform the best symbiotic compatibility. The soil chemistry also plays a prominent role in nodulation and host growth 55 .

Mutualistic Relationships with Fungi and Fungivores

Members of Kingdom Fungi form ecologically beneficial mutualistic relationships with cyanobateria, plants, and animals.

Learning Objectives

Describe mutualistic relationships with fungi

Key Takeaways

Key Points

  • Mutualistic relationships are those where both members of an association benefit Fungi form these types of relationships with various other Kingdoms of life.
  • Mycorrhiza, formed from an association between plant roots and primitive fungi, help increase a plant’s nutrient uptake in return, the plant supplies the fungi with photosynthesis products for their metabolic use.
  • In lichen, fungi live in close proximity with photosynthetic cyanobateria the algae provide fungi with carbon and energy while the fungi supplies minerals and protection to the algae.
  • Mutualistic relationships between fungi and animals involves numerous insects Arthropods depend on fungi for protection, while fungi receive nutrients in return and ensure a way to disseminate the spores into new environments.

Key Terms

  • mycorrhiza: a symbiotic association between a fungus and the roots of a vascular plant
  • lichen: any of many symbiotic organisms, being associations of fungi and algae often found as white or yellow patches on old walls, etc.
  • thallus: vegetative body of a fungus

Mutualistic Relationships

Symbiosis is the ecological interaction between two organisms that live together. However, the definition does not describe the quality of the interaction. When both members of the association benefit, the symbiotic relationship is called mutualistic. Fungi form mutualistic associations with many types of organisms, including cyanobacteria, plants, and animals.

Fungi & Plant Mutualism

Mycorrhiza, which comes from the Greek words “myco” meaning fungus and “rhizo” meaning root, refers to the association between vascular plant roots and their symbiotic fungi. About 90 percent of all plant species have mycorrhizal partners. In a mycorrhizal association, the fungal mycelia use their extensive network of hyphae and large surface area in contact with the soil to channel water and minerals from the soil into the plant, thereby increasing a plant’s nutrient uptake. In exchange, the plant supplies the products of photosynthesis to fuel the metabolism of the fungus.

Mycorrhizae display many characteristics of primitive fungi: they produce simple spores, show little diversification, do not have a sexual reproductive cycle, and cannot live outside of a mycorrhizal association. There are a number of types of mycorrhizae. Ectomycorrhizae (“outside” mycorrhiza) depend on fungi enveloping the roots in a sheath (called a mantle) and a Hartig net of hyphae that extends into the roots between cells. The fungal partner can belong to the Ascomycota, Basidiomycota, or Zygomycota. In a second type, the Glomeromycete fungi form vesicular–arbuscular interactions with arbuscular mycorrhiza (sometimes called endomycorrhizae). In these mycorrhiza, the fungi form arbuscules that penetrate root cells and are the site of the metabolic exchanges between the fungus and the host plant. The arbuscules (from the Latin for “little trees”) have a shrub-like appearance. Orchids rely on a third type of mycorrhiza. Orchids are epiphytes that form small seeds without much storage to sustain germination and growth. Their seeds will not germinate without a mycorrhizal partner (usually a Basidiomycete). After nutrients in the seed are depleted, fungal symbionts support the growth of the orchid by providing necessary carbohydrates and minerals. Some orchids continue to be mycorrhizal throughout their lifecycle.

Mycorrhizal fungi: (a) Ectomycorrhiza and (b) arbuscular mycorrhiza have different mechanisms for interacting with the roots of plants.


Lichens display a range of colors and textures. They can survive in the most unusual and hostile habitats. They cover rocks, gravestones, tree bark, and the ground in the tundra where plant roots cannot penetrate. Lichens can survive extended periods of drought: they become completely desiccated and then rapidly become active once water is available again. Lichens fulfill many ecological roles, including acting as indicator species, which allow scientists to track the health of a habitat because of their sensitivity to air pollution.

Lichen: fungi and cyanobateria: Lichens have many forms. They may be (a) crust-like, (b) hair-like, or (c) leaf-like.

Lichens are not a single organism, but, rather, an example of a mutualism in which a fungus (usually a member of the Ascomycota or Basidiomycota phyla) lives in close contact with a photosynthetic organism (a eukaryotic alga or a prokaryotic cyanobacterium). Generally, neither the fungus nor the photosynthetic organism can survive alone outside of the symbiotic relationship. The body of a lichen, referred to as a thallus, is formed of hyphae wrapped around the photosynthetic partner. The photosynthetic organism provides carbon and energy in the form of carbohydrates. Some cyanobacteria fix nitrogen from the atmosphere, contributing nitrogenous compounds to the association. In return, the fungus supplies minerals and protection from dryness and excessive light by encasing the algae in its mycelium. The fungus also attaches the symbiotic organism to the substrate.

Thallus of lichen: This cross-section of a lichen thallus shows the (a) upper cortex of fungal hyphae, which provides protection the (b) algal zone where photosynthesis occurs, the (c) medulla of fungal hyphae, and the (d) lower cortex, which also provides protection and may have (e) rhizines to anchor the thallus to the substrate.

The thallus of lichens grows very slowly, expanding its diameter a few millimeters per year. Both the fungus and the alga participate in the formation of dispersal units for reproduction. Lichens produce soredia, clusters of algal cells surrounded by mycelia. Soredia are dispersed by wind and water and form new lichens.

Fungi & Animal Mutualism

Fungi have evolved mutualisms with numerous insects. Arthropods (jointed, legged invertebrates, such as insects) depend on the fungus for protection from predators and pathogens, while the fungus obtains nutrients and a way to disseminate spores into new environments. The association between species of Basidiomycota and scale insects is one example. The fungal mycelium covers and protects the insect colonies. The scale insects foster a flow of nutrients from the parasitized plant to the fungus. In a second example, leaf-cutting ants of Central and South America literally farm fungi. They cut disks of leaves from plants and pile them up in gardens. Fungi are cultivated in these disk gardens, digesting the cellulose in the leaves that the ants cannot break down. Once smaller sugar molecules are produced and consumed by the fungi, the fungi in turn become a meal for the ants. The insects also patrol their garden, preying on competing fungi. Both ants and fungi benefit from the association. The fungus receives a steady supply of leaves and freedom from competition, while the ants feed on the fungi they cultivate.

Author information


National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai, China

Wentao Dong, Yayun Zhu, Huizhong Chang, Jun Yang, Jincai Shi, Jinpeng Gao, Weibing Yang, Liying Lan, Yuru Wang, Xiaowei Zhang, Huiling Dai, Lin Xu, Zuhua He & Ertao Wang

University of Chinese Academy of Sciences, Beijing, China

Wentao Dong, Jincai Shi, Liying Lan & Yuru Wang

Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China

Yayun Zhu, Huizhong Chang & Nan Yu

College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China

Collaborative Innovation Center of Crop Stress Biology, Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, China

Jinpeng Gao, Yuchen Miao & Chunpeng Song

Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA

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W.D. and E.W. directed the research. W.D., Y.Z., H.C., J.Y., J.S., J.G. and W.Y. performed most of the experiments. C.W., L.L., Y.W., X.Z., H.D., Y.M., L.X., Z.H., C.S., S.W. and N.Y. contributed to the analytical, molecular cloning, and transformation work. E.W. oversaw the entire study. W.D., D.W. and E.W. wrote the manuscript.

Corresponding author

Unraveling new molecular players involved in the autoregulation of nodulation in Medicago truncatula

The number of legume root nodules resulting from a symbiosis with rhizobia is tightly controlled by the plant. Certain members of the CLAVATA3/Embryo Surrounding Region (CLE) peptide family, specifically MtCLE12 and MtCLE13 in Medicago truncatula, act in the systemic autoregulation of nodulation (AON) pathway that negatively regulates the number of nodules. Little is known about the molecular pathways that operate downstream of the AON-related CLE peptides. Here, by means of a transcriptome analysis, we show that roots ectopically expressing MtCLE13 deregulate only a limited number of genes, including three down-regulated genes encoding lysin motif receptor-like kinases (LysM-RLKs), among which are the nodulation factor (NF) receptor NF Perception gene (NFP) and two up-regulated genes, MtTML1 and MtTML2, encoding Too Much Love (TML)-related Kelch-repeat containing F-box proteins. The observed deregulation was specific for the ectopic expression of nodulation-related MtCLE genes and depended on the Super Numeric Nodules (SUNN) AON RLK. Moreover, overexpression and silencing of these two MtTML genes demonstrated that they play a role in the negative regulation of nodule numbers. Hence, the identified MtTML genes are the functional counterpart of the Lotus japonicus TML gene shown to be central in the AON pathway. Additionally, we propose that the down-regulation of a subset of LysM-RLK-encoding genes, among which is NFP, might contribute to the restriction of further nodulation once the first nodules have been formed.

Keywords: Autoregulation of nodulation (AON) CLAVATA signaling peptide F-box protein Nod factor perception (NFP) rhizobia symbiotic nodulation.

© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Experimental Biology.


qRT–PCR validation of genes differentially…

qRT–PCR validation of genes differentially expressed in 35S:MtCLE13 roots. Expression analysis by qRT–PCR…

Expression of the M. truncatula…

Expression of the M. truncatula NFP , TML1 , and TML2 genes in…

Expression of the M. truncatula…

Expression of the M. truncatula NFP , TML1 , and TML2 genes in…

Down-regulated expression of a p…

Down-regulated expression of a p NFP:GUS transcriptional fusion in roots overexpressing MtCLE13 .…

Expression analysis of the two…

Expression analysis of the two M. truncatula genes, MtTML1 and MtTML2 , during…

Reduced nodule formation of roots…

Reduced nodule formation of roots ectopically expressing MtTML1 and MtTML2. (A) Expression analysis…

Increased nodule number in M.…

Increased nodule number in M. truncatula roots silenced for MtTML1 and MtTML2 .…

Nitrogen-fixing symbiosis is crucial for legume plant microbiome assembly

New findings from a study of legumes have identified an unknown role of nitrogen fixation symbiosis on plant root-associated microbiome, which agriculture may benefit from in the future.

Legumes form a unique symbiotic relationship with bacteria known as rhizobia, which they allow to infect their roots. This leads to root nodule formation where bacteria are accommodated to convert nitrogen from the air into ammonia that the plant can use for growth. This symbiotic nitrogen fixation allows legumes to thrive in habitats with limited nitrogen availability.

Researchers from Denmark and Germany have now found that an intact nitrogen-fixing symbiosis in Lotus japonicus is needed for the establishment of taxonomically diverse and distinctive bacterial communities. Integrating these highly specific binary interactions into an ecological community context is critical for understanding the evolution of symbiosis and efficient use of rhizobia inoculum in agricultural systems.

Legumes are known as pioneer plants colonising marginal soils, and as enhancers of the nutritional status in cultivated soils. This beneficial activity has been explained by their capacity to engage in symbiotic relationship with nitrogen-fixing rhizobia. The beneficial effect of this symbiosis is not limited to legume hosts, but extends to subsequent or concurrent plantings with non-legumes as exemplified by ancient agricultural practices with legume cropping sequences or intercropping systems. This symbiosis likely involves a beneficial activity of legumes on the nutritional status of the soil as well as the soil biome. However, the mechanisms underpinning these symbiotic interactions in a community context and their impact on the complex microbial assemblages associated with roots remain largely unknown.

Loss of nitrogen-fixing symbiosis impacts plant growth

The research team performed a bacterial community profiling analysis of Lotus japonicus wild-type plants, grown in natural soil, and symbiotic mutants impaired at different stages of the symbiotic process. They found that the loss of nitrogen-fixing symbiosis impacts plant growth, and dramatically alters Lotus-associated community structures, affecting at least 14 bacterial orders. This growth phenotype and the altered community structure were retained under nitrogen-supplemented conditions that blocked the formation of functional nodules in wild-type.

This finding extends the role of key symbiotic genes beyond perception and selection of nitrogen-fixing rhizobia for intracellular accommodation in nodules, and reveals a major role in the establishment of bacterial communities in the root and rhizosphere of L. japonicus.

Their study raises the possibility that the influence of legumes on soil performance in agricultural and ecological contexts is mediated by the enrichment of a symbiosis-linked bacterial community rather than dinitrogen-fixing rhizobia alone. In the longer term, these bacteria alone or with rhizobia could be used as inoculum for other plants to increase their growth with minimal nutrient consumption.

The results were obtained as a collaborative effort between the groups of Simona Radutoiu from Aarhus University and Paul Schulze-Lefert from MPI Cologne, Germany. They have been published in the international journal PNAS, entitled: Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities.

Involvement of Arachis hypogaea Jasmonate ZIM domain/TIFY proteins in root nodule symbiosis

Jasmonate ZIM domain (JAZ) proteins are the key negative regulators of jasmonate signaling, an important integrator of plant–microbe relationships. Versatility of jasmonate signaling outcomes are maintained through the multiplicity of JAZ proteins and their definitive functionalities. How jasmonate signaling influences the legume-Rhizobium symbiotic relationship is still unclear. In Arachis hypogaea (peanut), a legume plant, one JAZ sub-family (JAZ1) gene and one TIFY sequence containing protein family member (TIFY8) gene show enhanced expression in the early stage and late stage of root nodule symbiosis (RNS) respectively. In plants, JAZ sub-family proteins belong to a larger TIFY family. Here, this study denotes the first attempt to reveal in planta interactions of downstream jasmonate signaling regulators through proteomics and mass spectrometry to find out the mode of jasmonate signaling participation in the RNS process of A. hypogaea. From 4-day old Bradyrhizobium-infected peanut roots, the JAZ1-protein complex shows its contribution towards the rhizobial entry, nodule development, autoregulation of nodulation and photo-morphogenesis during the early stage of symbiosis. From 30-day old Bradyrhizobium infected roots, the TIFY8-protein complex reveals repressor functionality of TIFY8, suppression of root jasmonate signaling, modulation of root circadian rhythm and nodule development. Cellular localization and expression level of the interaction partners during the nodulation process further substantiate the in planta interaction pairs. This study provides a comprehensive insight into the jasmonate functionality in RNS through modulation of nodule number and development, during the early stage and root circadian rhythm during the late stage of nodulation, through the protein complexes of JAZ1 and TIFY8 respectively in A. hypogaea.

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