The evolution of nodulation

Innovation and appropriation in mycorrhizal and rhizobial Symbioses

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

Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen-fixing clade

Nitrogen is one of the most inaccessible plant nutrients, but certain species have overcome this limitation by establishing symbiotic interactions with nitrogen-fixing bacteria in the root nodule. This root-nodule symbiosis (RNS) is restricted to species within a single clade of angiosperms, suggesting a critical, but undetermined, evolutionary event at the base of this clade. To identify putative regulatory sequences implicated in the evolution of RNS, we evaluated the genomes of 25 species capable of nodulation and identified 3091 conserved noncoding sequences (CNS) in the nitrogen-fixing clade (NFC). We show that the chromatin accessibility of 452 CNS correlates significantly with the regulation of genes responding to lipochitooligosaccharides in Medicago truncatula. These included 38 CNS in proximity to 19 known genes involved in RNS. Five such regions are upstream of MtCRE1, Cytokinin Response Element 1, required to activate a suite of downstream transcription factors necessary for nodulation in M. truncatula. Genetic complementation of an Mtcre1 mutant showed a significant decrease of nodulation in the absence of the five CNS, when they are driving the expression of a functional copy of MtCRE1. CNS identified in the NFC may harbor elements required for the regulation of genes controlling RNS in M. truncatula.

Insights into the early stages of plant-endophytic bacteria interaction

The plant holobiont is a complex entity composed of the plant and the organisms that live in and on it including its microbiota. The plant microbiota includes, among other microorganisms, bacterial endophytes, which are bacteria that can invade living plant tissues without causing symptoms of disease. The interaction between the endophytic bacterial microbiota and their plant host has profound influences on their fitness and depends on biotic and abiotic factors. For these interactions to be established, the bacteria have to be present at the right time, in the right place either colonizing the soil or the seed. In this review we summarize the current knowledge regarding the sources of the bacterial endophytic microbiome and the processes involved in the assemblage of the resulting community during the initial stages of plant development. The adaptations that allow the spatial approximation of soil- and seed-borne bacteria towards infection and colonization of the internal tissues of plants will be addressed in this review.

An SHR-SCR module specifies legume cortical cell fate to enable nodulation

Legumes, unlike other plants, have the ability to establish symbiosis with nitrogen-fixing rhizobia. It has been theorized that a unique property of legume root cortical cells enabled the initial establishment of rhizobial symbiosis^1-3. Here we show that a SHORTROOT-SCARECROW (SHR-SCR) stem cell program in cortical cells of the legume Medicago truncatula specifies their distinct fate. Regulatory elements drive the cortical expression of SCR, and stele-expressed SHR protein accumulates in cortical cells of M. truncatula but not Arabidopsis thaliana. The cortical SHR-SCR network is conserved across legume species, responds to rhizobial signals, and initiates legume-specific cortical cell division for de novo nodule organogenesis and accommodation of rhizobia. Ectopic activation of SHR and SCR in legumes is sufficient to induce root cortical cell division. Our work suggests that acquisition of the cortical SHR-SCR module enabled cell division coupled to rhizobial infection in legumes. We propose that this event was central to the evolution of rhizobial endosymbiosis.

Chemical signaling involved in plant-microbe interactions

Microorganisms are found everywhere, and they are closely associated with plants. Because the establishment of any plant-microbe association involves chemical communication, understanding crosstalk processes is fundamental to defining the type of relationship. Although several metabolites from plants and microbes have been fully characterized, their roles in the chemical interplay between these partners are not well understood in most cases, and they require further investigation. In this review, we describe different plant-microbe associations from colonization to microbial establishment processes in plants along with future prospects, including agricultural benefits.

The Symbiosome: Legume and Rhizobia Co-evolution toward a Nitrogen-Fixing Organelle?

In legume nodules, symbiosomes containing endosymbiotic rhizobial bacteria act as temporary plant organelles that are responsible for nitrogen fixation, these bacteria develop mutual metabolic dependence with the host legume. In most legumes, the rhizobia infect post-mitotic cells that have lost their ability to divide, although in some nodules cells do maintain their mitotic capacity after infection. Here, we review what is currently known about legume symbiosomes from an evolutionary and developmental perspective, and in the context of the different interactions between diazotroph bacteria and eukaryotes. As a result, it can be concluded that the symbiosome possesses organelle-like characteristics due to its metabolic behavior, the composite origin and differentiation of its membrane, the retargeting of host cell proteins, the control of microsymbiont proliferation and differentiation by the host legume, and the cytoskeletal dynamics and symbiosome segregation during the division of rhizobia-infected cells. Different degrees of symbiosome evolution can be defined, specifically in relation to rhizobial infection and to the different types of nodule. Thus, our current understanding of the symbiosome suggests that it might be considered a nitrogen-fixing link in organelle evolution and that the distinct types of legume symbiosomes could represent different evolutionary stages toward the generation of a nitrogen-fixing organelle.

Comparative analysis of the tubulin cytoskeleton organization in nodules of Medicago truncatula and Pisum sativum: bacterial release and bacteroid positioning correlate with characteristic microtubule rearrangements

In this study we analyzed and compared the organization of the tubulin cytoskeleton in nodules of Medicago truncatula and Pisum sativum. We combined antibody labeling and green fluorescent protein tagging with laser confocal microscopy to observe microtubules (MTs) in nodules of both wild-type (WT) plants and symbiotic plant mutants blocked at different steps of nodule development. The 3D MT organization of each histological nodule zone in both M. truncatula and P. sativum is correlated to specific developmental processes. Endoplasmic MTs appear to support infection thread growth, infection droplet formation and bacterial release into the host cytoplasm in nodules of both species. No differences in the organization of the MT cytoskeleton between WT and bacterial release mutants were apparent, suggesting both that the phenotype is not linked to a defect in MT organization and that the growth of hypertrophied infection threads is supported by MTs. Strikingly, bacterial release coincides with a change in the organization of cortical MTs from parallel arrays into an irregular, crisscross arrangement. After release, the organization of endoplasmic MTs is linked to the distribution of symbiosomes. The 3D MT organization of each nodule histological zone in M. truncatula and P. sativum was analyzed and linked to specific developmental processes.

To be or noot to be: evolutionary tinkering for symbiotic organ identity

Legume plants develop symbiosis specific organs on their roots as a result of their interaction with rhizobia. These organs, called nodules, house the nitrogen fixing bacteria. The molecular mechanisms governing the identity and maintenance of this organ are still poorly understood, but it is supposed that root and nodule development share common features. We have identified the Medicago truncatula nodule root (NOOT) and Pisum sativum cochleata (COCH) orthologous genes as necessary for the robust maintenance of nodule identity throughout the nodule developmental program. NOOT and COCH are Arabidopsis blade-on-petiole (BOP) orthologs and NOOT and COCH show functions in leaf and flower development in M. truncatula and P. sativum respectively that are conserved with the functions of BOP in Arabidopsis. The characterization of the noot and coch mutants highlights the root evolutionary origin of nodule vascular strands and suggests that the NOOT and COCH genes were recruited to repress root identity in the legume symbiotic organ.

Matching roots to their environment

BACKGROUND

Plants form the base of the terrestrial food chain and provide medicines, fuel, fibre and industrial materials to humans. Vascular land plants rely on their roots to acquire the water and mineral elements necessary for their survival in nature or their yield and nutritional quality in agriculture. Major biogeochemical fluxes of all elements occur through plant roots, and the roots of agricultural crops have a significant role to play in soil sustainability, carbon sequestration, reducing emissions of greenhouse gasses, and in preventing the eutrophication of water bodies associated with the application of mineral fertilizers.

SCOPE

This article provides the context for a Special Issue of Annals of Botany on 'Matching Roots to Their Environment'. It first examines how land plants and their roots evolved, describes how the ecology of roots and their rhizospheres contributes to the acquisition of soil resources, and discusses the influence of plant roots on biogeochemical cycles. It then describes the role of roots in overcoming the constraints to crop production imposed by hostile or infertile soils, illustrates root phenotypes that improve the acquisition of mineral elements and water, and discusses high-throughput methods to screen for these traits in the laboratory, glasshouse and field. Finally, it considers whether knowledge of adaptations improving the acquisition of resources in natural environments can be used to develop root systems for sustainable agriculture in the future.

Rhizobial infection is associated with the development of peripheral vasculature in nodules of Medicago truncatula

Nodulation in legumes involves the coordination of epidermal infection by rhizobia with cell divisions in the underlying cortex. During nodulation, rhizobia are entrapped within curled root hairs to form an infection pocket. Transcellular tubes called infection threads then develop from the pocket and become colonized by rhizobia. The infection thread grows toward the developing nodule primordia and rhizobia are taken up into the nodule cells, where they eventually fix nitrogen. The epidermal and cortical developmental programs are synchronized by a yet-to-be-identified signal that is transmitted from the outer to the inner cell layers of the root. Using a new allele of the Medicago truncatula mutant Lumpy Infections, lin-4, which forms normal infection pockets but cannot initiate infection threads, we show that infection thread initiation is required for normal nodule development. lin-4 forms nodules with centrally located vascular bundles similar to that found in lateral roots rather than the peripheral vasculature characteristic of legume nodules. The same phenomenon was observed in M. truncatula plants inoculated with the Sinorhizobium meliloti exoY mutant, and the M. truncatula vapyrin-2 mutant, all cases where infections arrest. Nodules on lin-4 have reduced expression of the nodule meristem marker MtCRE1 and do not express root-tip markers. In addition, these mutant nodules have altered patterns of gene expression for the cytokinin and auxin markers CRE1 and DR5. Our work highlights the coordinating role that bacterial infection exerts on the developing nodule and allows us to draw comparisons with primitive actinorhizal nodules and rhizobia-induced nodules on the nonlegume Parasponia andersonii.

The evolution of land plant hemoglobins

This review discusses the evolution of land plant hemoglobins within the broader context of eukaryote hemoglobins and the three families of bacterial globins. Most eukaryote hemoglobins, including metazoan globins and the symbiotic and non-symbiotic plant hemoglobins, are homologous to the bacterial 3/3-fold flavohemoglobins. The remaining plant hemoglobins are homologous to the bacterial 2/2-fold group 2 hemoglobins. We have proposed that all eukaryote globins were acquired via horizontal gene transfer concomitant with the endosymbiotic events responsible for the origin of mitochondria and chloroplasts. Although the 3/3 hemoglobins originated in the ancestor of green algae and plants prior to the emergence of embryophytes at about 450 mya, the 2/2 hemoglobins appear to have originated via horizontal gene transfer from a bacterium ancestral to present day Chloroflexi. Unlike the 2/2 hemoglobins, the evolution of the 3/3 hemoglobins was accompanied by duplication, diversification, and functional adaptations. Duplication of the ancestral plant nshb gene into the nshb-1 and nshb-2 lineages occurred prior to the monocot-dicot divergence at ca. 140 mya. It was followed by the emergence of symbiotic hemoglobins from a non-symbiotic hemoglobin precursor and further specialization, leading to leghemoglobins in N₂-fixing legume nodules concomitant with the origin of nodulation at ca. 60 mya. The transition of non-symbiotic to symbiotic hemoglobins (including to leghemoglobins) was accompanied by the alteration of heme-Fe coordination from hexa- to penta-coordination. Additional genomic information about Charophyte algae, the sister group to land plants, is required for the further clarification of plant globin phylogeny.

The determinants of the actinorhizal symbiosis

The actinorhizal symbiosis is a major contributor to the global nitrogen budget, playing a dominant role in ecological successions following disturbances. The mechanisms involved are still poorly known but there emerges the vision that on the plant side, the kinases that transmit the symbiotic signal are conserved with those involved in the transmission of the Rhizobium Nod signal in legumes. However, on the microbial side, complementation with Frankia DNA of Rhizobium nod mutants failed to permit identification of symbiotic genes. Furthermore, analysis of three Frankia genomes failed to permit identification of canonical nod genes and revealed symbiosis-associated genes such as nif, hup, suf and shc to be spread around the genomes. The present review explores some recently published approaches aimed at identifying bacterial symbiotic determinants.

GmPep914, an eight-amino acid peptide isolated from soybean leaves, activates defense-related genes

Only a handful of endogenous peptide defense signals have been isolated from plants. Herein, we report a novel peptide from soybean (Glycine max) leaves that is capable of alkalinizing the media of soybean suspension cells, a response that is generally associated with defense peptides. The peptide, DHPRGGNY, was synthesized and found to be active at 0.25 nM and requiring only 5 to 10 min to obtain a maximal pH change. The peptide is located on the carboxy-terminal end of a 52-amino acid precursor protein (Glyma12g00990) deduced from the soybean genome project. A search of the soybean databank revealed a homolog (Glyma09g36370) that contained a similar peptide, DLPRGGNY, which was synthesized and shown to have identical activity. The peptides, designated GmPep914 (DHPRGGNY) and GmPep890 (DLPRGGNY), were capable of inducing the expression of both Glyma12g00990 (GmPROPEP914) and Glyma09g36370 (GmPROPEP890) in cultured soybean suspension cells within 1 h. Both peptides induced the expression of defense genes, including CYP93A1, a cytochrome P450 gene involved in phytoalexin synthesis, chitinaseb1-1, a chitinase involved in pathogen defense, and Glycine max chalcone synthase1 (Gmachs1), chalcone synthase, involved in phytoalexin production. Both GmPROPEP914 and GmPROPEP890 were highly expressed in the roots, relative to the aerial portions of the plant. However, treatment of the aerial portion of soybean plants with hormones involved in elicitation of defense responses revealed a significant increase in expression levels of GmPROPEP914 and GmPROPEP890. A search of gene databases revealed homologous sequences in other members of the Fabales and also in the closely related Cucurbitales but not in any other order of plants.

Function and evolution of nodulation genes in legumes

Root nodule (RN) symbiosis has a unique feature in which symbiotic bacteria fix atmospheric nitrogen. The symbiosis is established with a limited species of land plants, including legumes. How RN symbiosis evolved is still a mystery, but recent findings on legumes genes that are necessary for RN symbiosis may give us a clue.

The biodiversity of beneficial microbe-host mutualism: the case of rhizobia

Symbiotic nitrogen fixation is the main route for sustainable input of nitrogen into ecosystems. Nitrogen fixation in agriculture can be improved by inoculation of legume crops with suitable rhizobia. Knowledge of the biodiversity of rhizobia and of local populations is important for the design of successful inoculation strategies. Soybeans are major nitrogen-fixing crops in many parts of the world. Bradyrhizobial inoculants for soybean are very diverse, yet classification and characterization of strains have long been difficult. Recent genetic characterization methods permit more reliable identification and will improve our knowledge of local populations. Forage legumes form another group of agronomically important legumes. Research and extension policies valorizing rhizobial germplasm diversity and preservation, farmer training for proper inoculant use and legal enforcement of commercial inoculant quality have proved a successful approach to promoting the use of forage legumes while enhancing biological N(2) fixation. It is worth noting that taxonomically important strains may not necessarily be important reference strains for other uses such as legume inoculation and genomics due to specialization of the different fields. This article points out both current knowledge and gaps remaining to be filled for further interaction and improvement of a rhizobial commons.

Salicylic acid differentially affects suspension cell cultures of Lotus japonicus and one of its non-symbiotic mutants

Salicylic acid (SA) is known to play an important role in the interaction between plant and micro-organisms, both symbiotic and pathogen. In particular, high levels of SA block nodule formation and mycorrhizal colonization in plants. A mutant of Lotus japonicus, named Ljsym4-2, was characterized as unable to establish positive interactions with Rhizobium and fungi (NOD(-), MYC(-)); in particular, it does not recognize signal molecules released by symbiotic micro-organisms so that eventually, epidermal cells undergo PCD at the contact area. We performed a detailed characterization of wild-type and Ljsym4-2 cultured cells by taking into account several parameters characterizing cell responses to SA, a molecule strongly involved in defense signaling pathways. In the presence of 0.5 mM SA, Ljsym4-2 suspension-cultured cells reduce their growth and eventually die, whereas in order to induce the same effects in wt suspension cells, SA concentration must be raised to 1.5 mM. An early and short production of nitric oxide (NO) and reactive oxygen species (ROS) was detected in wt-treated cells. In contrast, a continuous production of NO and a double-peak ROS response, similar to that reported after a pathogenic attack, was observed in the mutant Ljsym4-2 cells. At the molecular level, a constitutive higher level of a SA-inducible pathogenesis related gene was observed. The analysis in planta revealed a strong induction of the LjPR1 gene in the Ljsym4-2 mutant inoculated with Mesorhizobium loti.

Genomic and evolutionary comparisons of diazotrophic and pathogenic bacteria of the order Rhizobiales

BACKGROUND

Species belonging to the Rhizobiales are intriguing and extensively researched for including both bacteria with the ability to fix nitrogen when in symbiosis with leguminous plants and pathogenic bacteria to animals and plants. Similarities between the strategies adopted by pathogenic and symbiotic Rhizobiales have been described, as well as high variability related to events of horizontal gene transfer. Although it is well known that chromosomal rearrangements, mutations and horizontal gene transfer influence the dynamics of bacterial genomes, in Rhizobiales, the scenario that determine pathogenic or symbiotic lifestyle are not clear and there are very few studies of comparative genomic between these classes of prokaryotic microorganisms trying to delineate the evolutionary characterization of symbiosis and pathogenesis.

RESULTS

Non-symbiotic nitrogen-fixing bacteria and bacteria involved in bioremediation closer to symbionts and pathogens in study may assist in the origin and ancestry genes and the gene flow occurring in Rhizobiales. The genomic comparisons of 19 species of Rhizobiales, including nitrogen-fixing, bioremediators and pathogens resulted in 33 common clusters to biological nitrogen fixation and pathogenesis, 15 clusters exclusive to all nitrogen-fixing bacteria and bacteria involved in bioremediation, 13 clusters found in only some nitrogen-fixing and bioremediation bacteria, 01 cluster exclusive to some symbionts, and 01 cluster found only in some pathogens analyzed. In BBH performed to all strains studied, 77 common genes were obtained, 17 of which were related to biological nitrogen fixation and pathogenesis. Phylogenetic reconstructions for Fix, Nif, Nod, Vir, and Trb showed possible horizontal gene transfer events, grouping species of different phenotypes.

CONCLUSIONS

The presence of symbiotic and virulence genes in both pathogens and symbionts does not seem to be the only determinant factor for lifestyle evolution in these microorganisms, although they may act in common stages of host infection. The phylogenetic analysis for many distinct operons involved in these processes emphasizes the relevance of horizontal gene transfer events in the symbiotic and pathogenic similarity.

Common trends in mutualism revealed by model associations between invertebrates and bacteria

Mutually beneficial interactions between microorganisms and animals are a conserved and ubiquitous feature of biotic systems. In many instances animals, including humans, are dependent on their microbial associates for nutrition, defense, or development. To maintain these vital relationships, animals have evolved processes that ensure faithful transmission of specific microbial symbionts between generations. Elucidating mechanisms of transmission and symbiont specificity has been aided by the study of experimentally tractable invertebrate animals with diverse and highly evolved associations with microorganisms. Here, we review several invertebrate model systems that contribute to our current understanding of symbiont transmission, recognition, and specificity. Although the details of transmission and symbiont selection vary among associations, comparisons of diverse mutualistic associations are revealing a number of common themes, including restriction of symbiont diversity during transmission and glycan-lectin interactions during partner selection and recruitment.

The role of the plant cytoskeleton in the interaction between legumes and rhizobia

The study of the symbiotic interaction between rhizobia and legumes represents a major theme in plant biology. This interaction results in the formation of nodules, root organs in which the bacteria reduce atmospheric nitrogen into ammonia, which can subsequently be utilized by the plant. The execution of the different developmental stages observed during nodule ontogenesis involves many cellular processes with significant roles for the plant cytoskeleton. A challenging question in cell biology is how the cytoskeleton organizes itself into the dynamic arrays required for cell differentiation and functioning. Nodulation is, particularly, well qualified as an experimental system for cytoskeleton research because an early essential step of the plant/microbe interaction takes place in surface-exposed root hairs, well suited for cell biological in vivo experimentation. Moreover, the changes in the organization of the cytoskeleton can be elicited by a well-defined molecule, the Nod factor, or by bacterial inoculation, thus providing the researcher with the possibility of controlling the cytoskeletal changes in target cells. In addition, the well-known cytology of the symbiotic interaction facilitates the correlation between the changes in the organization of the plant cytoskeleton with both histological and cellular changes. In this review, the current knowledge on the role of the plant cytoskeleton during nodulation is summarized, with emphasis on the interaction between Medicago truncatula and Sinorhizobium meliloti.

Auxin: at the root of nodule development?

Root nodules are formed as a result of an orchestrated exchange of chemical signals between symbiotic nitrogen fixing bacteria and certain plants. In plants that form nodules in symbiosis with actinorhizal bacteria, nodules are derived from lateral roots. In most legumes, nodules are formed de novo from pericycle and cortical cells that are re-stimulated for division and differentiation by rhizobia. The ability of plants to nodulate has only evolved recently and it has, therefore, been suggested that nodule development is likely to have co-opted existing mechanisms for development and differentiation from lateral root formation. Auxin is an important regulator of cell division and differentiation, and changes in auxin accumulation and transport are essential for lateral root development. There is growing evidence that rhizobia alter the root auxin balance as a prerequisite for nodule formation, and that nodule numbers are regulated by shoot-to-root auxin transport. Whereas auxin requirements appear to be similar for lateral root and nodule primordium activation and organ differentiation, the major difference between the two developmental programs lies in the specification of founder cells. It is suggested that differing ratios of auxin and cytokinin are likely to specify the precursors of the different root organs.

Signaling in plant disease resistance and symbiosis

Interactions between plants and microbes result in plant disease and symbiosis. The former causes considerable economic damage in modern agriculture, while the latter has produced great beneficial effects to our agriculture system. Comparison of the two interactions has revealed that a common panel of signaling pathways might participate in the establishment of the equilibrium between plant and microbes or its break-up. Plants appear to detect both pathogenic and symbiotic microbes by a similar set of genes. All symbiotic microbes seem to produce effectors to overcome plant basal defenses and it is speculated that symbiotic effectors have functions similar to pathogenic ones. Signaling molecules, salicylic acid (SA), jasmonic acid (JA) and ethylene (ET), are involved in both plant defense and symbiosis. Switching off signals contributing to deterioration of disease symptom would establish a new equilibrium between plant and pathogenic microbes. This would facilitate the development of strategies for durable disease resistance.

The Xenorhabdus nematophila nilABC genes confer the ability of Xenorhabdus spp. to colonize Steinernema carpocapsae nematodes

Members of the Steinernema genus of nematodes are colonized mutualistically by members of the Xenorhabdus genus of bacteria. In nature, Steinernema carpocapsae nematodes are always found in association with Xenorhabdus nematophila bacteria. Thus, this interaction, like many microbe-host associations, appears to be species specific. X. nematophila requires the nilA, nilB, and nilC genes to colonize S. carpocapsae. In this work, we showed that of all the Xenorhabdus species examined, only X. nematophila has the nilA, nilB, and nilC genes. By exposing S. carpocapsae to other Xenorhabdus spp., we established that only X. nematophila is able to colonize S. carpocapsae; therefore, the S. carpocapsae-X. nematophila interaction is species specific. Further, we showed that introduction of the nilA, nilB, and nilC genes into other Xenorhabdus species enables them to colonize the same S. carpocapsae host tissue that is normally colonized by X. nematophila. Finally, sequence analysis supported the idea that the nil genes were horizontally acquired. Our findings indicate that a single genetic locus determines host specificity in this bacteria-animal mutualism and that host range expansion can occur through the acquisition of a small genetic element.

Use of RNA fingerprinting to identify fungal genes specifically expressed during ectomycorrhizal interaction

The ecosystem soil is characterized by interactions between microorganisms and plants including mycorrhiza--mutualistic interactions between fungi and plant roots. Species of the basidiomycete genus Tricholoma form ectomycorrhiza with tree roots which is characterized by morphological and metabolic changes of both partners, yet molecular mechanisms of the interaction are poorly understood. We performed differential display with arbitrarily primed RT-PCR using ectomycorrhiza between the basidiomycete Tricholoma vaccinum and its compatible host spruce (Picea abies) to isolate mycorrhiza-specific fungal gene fragments. 76 differentially expressed PCR fragments were verified and checked for plant or fungal origin and expression pattern. Of 20 fungal fragments with mycorrhiza-specific expression, sequence analyses were performed to identify homologs with known function of the encoded protein. Among the genes identified were orthologs to an aldehyde dehydrogenase, an alcohol dehydrogenase and a protein of the MATE transporter family, all with possible function in plant pathogen response. A phospholipase B, a beta-glucosidase and a binding protein of basic amino acids might play a role in nutrient exchange and growth in planta. A protein similar to inactive E2 compounds of ubiquitin-conjugating enzymes like CROC-1 and MMS2, a Ras protein and an APS kinase were placed in signal transduction and two retrotransposons of the Ty3-gypsy and the Ty1-copia family are expressed most likely due to stress.

Tracing nonlegume orthologs of legume genes required for nodulation and arbuscular mycorrhizal symbioses

Most land plants can form a root symbiosis with arbuscular mycorrhizal (AM) fungi for assimilation of inorganic phosphate from the soil. In contrast, the nitrogen-fixing root nodule symbiosis is almost completely restricted to the legumes. The finding that the two symbioses share common signaling components in legumes suggests that the evolutionarily younger nitrogen-fixing symbiosis has recruited functions from the more ancient AM symbiosis. The recent advances in cloning of the genes required for nodulation and AM symbioses from the two model legumes, Medicago truncatula and Lotus japonicus, provide a unique opportunity to address biological questions pertaining to the evolution of root symbioses in plants. Here, we report that nearly all cloned legume genes required for nodulation and AM symbioses have their putative orthologs in nonlegumes. The orthologous relationship can be clearly defined on the basis of both sequence similarity and microsyntenic relationship. The results presented here serve as a prelude to the comparative analysis of orthologous gene function between legumes and nonlegumes and facilitate our understanding of how gene functions and signaling pathways have evolved to generate species- or family-specific phenotypes.

Iron bioavailability of hemoglobin from soy root nodules using a Caco-2 cell culture model

Heme iron has been identified in many plant sources-most commonly in the root nodules of leguminous plants, such as soy. Our objective was to test the effectiveness of soy root nodule (SRN) and purified soy hemoglobin (LHb) in improving iron bioavailability using an in vitro Caco-2 cell model, with ferritin response as the bioavailability index. We assessed bioavailability of iron from LHb (either partially purified (LHbA) or purified (LHbD)) with and without food matrix and compared it with that from bovine hemoglobin (BHb), ferrous sulfate (FeSO4), or SRN. Bioavailability of each treatment was normalized to 100% of the FeSO4 treatment. When iron sources were tested alone (100 ug iron/mL), ferritin synthesis by LHbD and BHb were 19% (P > 0.05) and 113% (P < 0.001) higher than FeSO4, respectively. However, when iron sources were used for fortification of maize tortillas (50 ppm), LHbA and BHb showed similar bioavailability, being 27% (P < 0.05) and 33% (P < 0.05) higher than FeSO4. Heat treatment had no effect on heme iron but had a significant reduction on FeSO4 bioavailability. Adding heme (LHbA) iron with nonheme (FeSO4) had no enhancement on nonheme iron absorption. Our data suggest that heme iron from plant sources may be a novel value-added product that can provide highly bioavailable iron as a food fortificant.

The effect of Frankia and Paxillus involutus on the performance of Alnus incana subsp. rugosa in mine tailings

The purpose of this study was to determine whether symbiotic nitrogen-fixing bacteria and mycorrhizal fungi act synergistically to improve plant performance when grown on heavy metal mine tailings. Seedlings were inoculated with Frankia, Paxillus involutus (Batsch) Fr., or a combination of both and grown in 100% peat, a 1:1 mix of peat and tailings, or 100% tailings for 20 weeks. Mortality of plants grown on pure tailings (15.0%) and peat–tailings (17.9%) was significantly greater than mortality of plants grown on peat (3.5%). The rate of nodulation and mycorrhizae formation decreased from 90.0% and 66.7%, respectively, on the peat, to 11.9% and 2.6% on the tailings. Frankia-inoculated plants grown on peat–tailings showed twice the mortality rate (38.5%) of any other inoculation treatment. Plants grown on media containing tailings had greater root/shoot ratios than plants grown on peat. Inoculating plants grown in the presence of tailings with either Frankia and (or) P. involutus increased root thickness. Inoculating plants with both symbionts increased colonization rates and shoot yield on the peat and peat–tailings media, suggesting that these symbionts act synergistically to improve plant performance. However, inoculating plants with Frankia decreased shoot relative growth rate in the early part of the experiment when plants were not fixing nitrogen, which, coupled with the higher mortality effect, suggests that nodule development is a stress for plants. It may be advisable that plants have fully functioning nodules before transplanting if they are to be used in revegetation programs.

Biological costs and benefits to plant-microbe interactions in the rhizosphere

This review looks briefly at plants and their rhizosphere microbes, the chemical communications that exist, and the biological processes they sustain. Primarily it is the loss of carbon compounds from roots that drives the development of enhanced microbial populations in the rhizosphere when compared with the bulk soil, or that sustains specific mycorrhizal or legume associations. The benefits to the plant from this carbon loss are discussed. Overall the general rhizosphere effect could help the plant by maintaining the recycling of nutrients, through the production of hormones, helping to provide resistance to microbial diseases and to aid tolerance to toxic compounds. When plants lack essential mineral elements such as P or N, symbiotic relationships can be beneficial and promote plant growth. However, this benefit may be lost in well-fertilized (agricultural) soils where nutrients are readily available to plants and symbionts reduce growth. Since these rhizosphere associations are commonplace and offer key benefits to plants, these interactions would appear to be essential to their overall success.

Range expansion leading to departures from neutrality in the nonsymbiotic hemoglobin gene and the cpDNA trnL–trnF intergenic spacer in Trema dielsiana (Ulmaceae)

The population genetics and phylogeography of Trema dielsiana in Taiwan were inferred from genetic diversity at the nonsymbiotic hemoglobin gene and the trnL-trnF intergenic spacer of cpDNA. Reduced genetic variation was detected in these two unlinked genes. The gene genealogy of the hemoglobin locus recovered two lineages corresponding to the western and eastern regions of Taiwan. This pattern is compatible with a past fragmentation event revealed by phylogeographical analyses. To distinguish between selective departures from neutrality (i.e., heterogeneous processes) and demographic (homogeneous) processes, Hahn et al.'s heterogeneity test was conducted on the hemoglobin gene. Lack of significant differences in Tajima's D statistics between synonymous and nonsynonymous mutations indicates that homogeneous processes may have played a key role in governing the evolution of the functional locus. Significantly negative Tajima's D estimates for both overall exons and introns of the hemoglobin gene as well as for the cpDNA intergenic spacer support a phylogeographical hypothesis of range expansion after genetic bottlenecks. High level of genetic variation and a negative Tajima's D statistic suggests a possible northern refugium that may have harbored populations during the glacial maximum.

Organogenesis of legume root nodules

The N(2)-fixing nodules elicited by rhizobia on legume roots represent a useful model for studying plant development. Nodule formation implies a complex progression of temporally and spatially regulated events of cell differentiation/dedifferentiation involving several root tissues. In this review we describe the morphogenetic events leading to the development of these histologically well-structured organs. These events include (1) root hair deformation, (2) development and growth of infection threads, (3) induction of the nodule primordium, and (4) induction, activity, and persistence of the nodular meristem and/or of foci of meristematic activities. Particular attention is given to specific aspects of the symbiosis, such as the early stages of intracellular invasion and to differentiation of the intracellular form of rhizobia, called symbiosomes. These developmental aspects were correlated with (1) the regulatory signals exchanged, (2) the plant genes expressed in specific cell types, and (3) the staining procedures that allow the recognition of some cell types. When strictly linked with morphogenesis, the nodulation phenotypes of plant and bacterial mutants such as the developmental consequence of the treatment with metabolic inhibitors, metabolic intermediates, or the variation of physical parameters are described. Finally, some aspects of nodule senescence and of regulation of nodulation are discussed.

Regulatory regions and nuclear factors involved in nodule-enhanced expression of a soybean phosphoenolpyruvate carboxylase gene: implications for molecular evolution

We have determined the genomic organization of two closely related phosphoenolpyruvate carboxylase genes in soybean, GmPEPC7, which is expressed at high levels in root nodules, and the housekeeping gene GmPEPC15. Their nucleotide sequences, including most introns and 5;-flanking regions within 600 bp upstream from the transcription start sites, are well conserved, suggesting that they were duplicated quite recently. To gain insights into the process of evolution of the tissue-specifically expressed GmPEPC7gene, we produced chimeric constructs carrying either the GmPEPC7or GmPEPC15promoter fused to the beta-glucuronidase gene. The expression patterns of the reporter observed in nodules that developed on transgenic hairy roots reflected the levels of mRNA levels produced by the genes in wild-type soybean plants, indicating that the GmPEPC7promoter directs nodule-specific expression. Loss-of-function experiments showed that the segment of GmPEPC7between -466 and -400, designated as the "switch region" (SR), was necessary for expression in nodules, although proteins that bind to SR were not detectable in a gel-retardation assay. Another gel-retardation assay indicated that putative nodule nuclear proteins bind specifically to the region of GmPEPC7between -400 and -318, designated as the "amplifier region" (AR). Both SR and AR have characteristic sequences that are not found in the GmPEPC15promoter. Furthermore, experiments using hybrid promoters derived from GmPEPC15demonstrated that AR confers high-level expression in nodules only in combination with SR. When wild-type soybean plants were subjected to prolonged darkness and subsequently illuminated, the level of GmPEPC7mRNA in nodules decreased and then recovered. This study suggests that the acquisition of two interdependent cis-acting elements resulted in molecular evolution of the nodule-enhanced GmPEPC7gene.

Expression of the apyrase-like APY1 genes in roots of Medicago truncatula is induced rapidly and transiently by stress and not by Sinorhizobium meliloti or Nod factors

The model legume Medicago truncatula contains at least six apyrase-like genes, five of which (MtAPY1;1, MtAPY1;2, MtAPY1;3, MtAPY1;4, and MtAPY1;5) are members of a legume-specific family, whereas a single gene (MtAPY2) has closer homologs in Arabidopsis. Phylogenetic analysis has revealed that the proteins encoded by these two plant gene families are more similar to yeast (Saccharomyces cerevisiae) GDA1 and to two proteins encoded by newly described mammalian genes (ENP5 and 6) than they are to mammalian CD39- and CD39-like proteins. Northern analyses and analyses of the frequencies of expressed sequence tags (ESTs) in different cDNA libraries suggest that in roots, leaves, and flowers, the more highly expressed genes are MtAPY1;3/MtAPY2, MtAPY1;3/MtAPY1;5 and MtAPY1;2/MtAPY1;3 respectively. In roots, at least four of the MtAPY1 genes are induced transiently within 3 to 6 h by a stress response that seems to be ethylene independent because it occurs after treatment with an ethylene synthesis inhibitor and also in the skl ethylene-insensitive mutant. This response also occurs in roots of the following symbiotic mutants: dmi1, dmi2, dmi3, nsp, hcl, pdl, lin, and skl. No evidence was obtained for a rapid, transient, and specific induction of the MtAPY genes in roots in response to rhizobia or rhizobial lipochitooligosaccharidic Nod factors. Thus, our data suggest that the apyrase-like genes, which in several legumes have been implicated to play a role in the legume-rhizobia symbiosis (with some members being described as early nodulin genes), are not regulated symbiotically by rhizobia in M. truncatula.

Evolution of signal transduction in intracellular symbiosis

Plant roots form intracellular symbioses with fungi and bacteria resulting in arbuscular mycorrhiza and nitrogen-fixing root nodules, respectively. A novel receptor like-kinase has been discovered that is required for the transduction of both bacterial and fungal symbiotic signals. This kinase defines an ancient signalling pathway that probably evolved in the context of arbuscular mycorrhiza and has been recruited subsequently for endosymbiosis with bacteria. An ancestral symbiotic interaction of roots with intracellular bacteria might have emerged from such a recruitment, in the progenitor of the nodulating clade of plants. Analysis of symbiotic mutants of host plants and bacterial microsymbionts has revealed that present-day endosymbioses require the coordinated induction of more than one signalling pathway for development.

Key role of bacterial NH(4)(+) metabolism in Rhizobium-plant symbiosis

Symbiotic nitrogen fixation is carried out in specialized organs, the nodules, whose formation is induced on leguminous host plants by bacteria belonging to the family Rhizobiaceae: Nodule development is a complex multistep process, which requires continued interaction between the two partners and thus the exchange of different signals and metabolites. NH(4)(+) is not only the primary product but also the main regulator of the symbiosis: either as ammonium and after conversion into organic compounds, it regulates most stages of the interaction, from the production of nodule inducers to the growth, function, and maintenance of nodules. This review examines the adaptation of bacterial NH(4)(+) metabolism to the variable environment generated by the plant, which actively controls and restricts bacterial growth by affecting oxygen and nutrient availability, thereby allowing a proficient interaction and at the same time preventing parasitic invasion. We describe the regulatory circuitry responsible for the downregulation of bacterial genes involved in NH(4)(+) assimilation occurring early during nodule invasion. This is a key and necessary step for the differentiation of N(2)-fixing bacteroids (the endocellular symbiotic form of rhizobia) and for the development of efficient nodules.

Coevolution of roots and mycorrhizas of land plants

Here, the coevolution of mycorrhizal fungi and roots is assessed in the light of evidence now available, from palaeobotanical and morphological studies and the analysis of DNA-based phylogenies. The first bryophyte-like land plants, in the early Devonian (400 million years ago), had endophytic associations resembling vesicular-arbuscular mycorrhizas (VAM) even before roots evolved. Mycorrhizal evolution would have progressed from endophytic hyphae towards balanced associations where partners were interdependent due to the exchange of limiting energy and nutrient resources. Most mycorrhizas are mutualistic, but in some cases the trend for increasing plant control of fungi culminates in the exploitative mycorrhizas of achlorophyllous, mycoheterotrophic plants. Ectomycorrhizal, ericoid and orchid mycorrhizas, as well as nonmycorrhizal roots, evolved during the period of rapid angiosperm radiation in the Cretaceous. It is hypothesised that roots gradually evolved from rhizomes to provide more suitable habitats for mycorrhizal fungi and provide plants with complex branching and leaves with water and nutrients. Selection pressures have caused the morphological divergence of roots with different types of mycorrizas. Root cortex thickness and exodermis suberization are greatest in obllgately mycorrhizal plants, while nonmycorrhizal plants tend to have fine roots, with more roots hairs and relatively advanced chemical defences. Major coevolutionary trends and the relative success of plants with different root types are discussed. Contents Summary 275 I. Introduction 276 II. Mycorrhizal Fungi 276 III. The Dawn of Mycorrhizas 279 IV. Mycorrhizal Associations of Living and Extinct Plants 282 V. Evolution of Roots 288 VI. The Root as a Habitat for Fungi 290 VII. Mycorrhizal Evolution Trends 295 Acknowledgements 298 References 298.

Auxotrophic mutant strains of Rhizobium etli reveal new nodule development phenotypes

We report here the isolation and characterization of amino acid-requiring mutant strains of Rhizobium etli. We observe that the phenotype of most mutations, even when causing a strict auxotrophy, is overcome by cross-feeding from the host plant Phaseolus vulgaris, thereby allowing bacterial production of Nod factors and, consequently, nodule induction. Conversely, light and electron microscopy analysis reveals that the nodules induced by all mutants, including those with normal external morphology, are halted or strongly altered at intermediate or late stages of development. Moreover, some mutants induce nodules that display novel symbiotic phenotypes, such as specific alterations of the invaded cells or the presence of a reduced number of abnormally shaped uninvaded cells. Other mutants induce nodules showing an early and vast necrosis of the central tissue, a phenotype not previously observed in bean nodules, not even in nodules induced by a Fix- mutant. These observations indicate that amino acid auxotrophs represent a powerful tool to study the development of globose determinate-type nodules and emphasize the importance of establishing their histology and cytology before considerations of metabolic exchange are made.

Identification of differentially expressed genes by cDNA-AFLP technique during heat stress in cowpea nodules

Legume nodules formed by diazotrophic microorganisms are active sites for biological nitrogen fixation (BNF). In tropical regions, a significant part of N supply for soybean, peanut and bean crops is derived from BNF, which is nevertheless often limited by high temperature stress. In contrast, cowpea nodules are very resistant to high temperatures. To understand the molecular bases of thermotolerance during BNF under heat stress, we have used cDNA-amplified fragment length polymorphism experiments to identify differentially expressed transcripts from cowpea nodules subjected to heat shock treatment. The expression profiles obtained showed approximately 600 bands, 55 up-regulated and nine corresponding to genes repressed by heat stress. Twenty transcript-derived fragments were isolated, cloned and sequenced. The Vigna unguiculata nodule and stress response transcripts present similarities to those that encode low molecular weight heat shock proteins, wound-induced proteins, disease resistance protein, and xylan endohydrolase isoenzyme, as well as different housekeeping genes. The differential expression of 15 genes was confirmed by using Northern blot or reverse Northern hybridization experiments.

Developmental genetics and evolution of symbiotic structures in nitrogen-fixing nodules and arbuscular mycorrhiza

Genetic and molecular mechanisms of development are compared for two major plant-microbe endosymbioses: N(2)-fixing nodules (with rhizobia or actinomycetes Frankia) and arbuscular mycorrhiza (with Glomales fungi). Development from the primordia formed de novo in root tissues is common for all known types of N(2)-fixing nodules. However, their structure varies greatly with respect to: (i) tissue topology (location of vascular bundles is peripherical in legumes or central in non-legumes); (ii) position of nodule primordium (inner or outer cortex in legumes, pericycle in non-legumes); (iii) stability of apical meristem (persistent in the indeterminate nodules, transient in the determinate ones). In addition, legumes vary in ability to form compartments harboring endosymbiotic rhizobia and located intercellularly (infection threads) and intracellularly (symbiosomes). Using pea (Pisum sativum) symbiotic mutants, the nodule developmental program is dissected into a range of spatially and temporarily differentiated steps comprising four sub-programs (development of endosymbiotic compartments; nodule histogenesis; autoregulation of nodulation; bacteroid differentiation). The developmental mutations are suggested in some cases to reverse the endosymbiotic system into the morphologically simpler forms some of which may correspond to the ancestral stages of nodule evolution. The origin of legume-rhizobial and actinorhizal symbioses is suggested to be based on a set of preadaptations many of which had been evolved in angiosperms during coevolution with arbuscular mycorrhizal fungi (e.g., inter- and intracellular maintenance of symbionts, their control via defence-like reactions and recognition of chitin-like molecules). An analysis of parallel morphological variation in symbiotic mutants and wild-growing legume species enables us to reconstruct the major stages of evolution for N(2)-fixing symbioses.

The dalbergioid legumes (Fabaceae): delimitation of a pantropical monophyletic clade

A monophyletic pantropical group of papilionoid legumes, here referred to as the "dalbergioid" legumes, is circumscribed to include all genera previously referred to the tribes Aeschynomeneae and Adesmieae, the subtribe Bryinae of the Desmodieae, and tribe Dalbergieae except Andira, Hymenolobium, Vatairea, and Vataireopsis. This previously undetected group was discovered with phylogenetic analysis of DNA sequences from the chloroplast trnK (including matK) and trnL introns, and the nuclear ribosomal 5.8S and flanking internal transcribed spacers 1 and 2. All dalbergioids belong to one of three well-supported subclades, the Adesmia, Dalbergia, and Pterocarpus clades. The dalbergioid clade and its three main subclades are cryptic in the sense that they are genetically distinct but poorly, if at all, distinguished by nonmolecular data. Traditionally important taxonomic characters, such as arborescent habit, free stamens, and lomented pods, do not provide support for the major clades identified by the molecular analysis. Short shoots, glandular-based trichomes, bilabiate calyces, and aeschynomenoid root nodules, in contrast, are better indicators of relationship at this hierarchical level. The discovery of the dalbergioid clade prompted a re-analysis of root nodule structure and the subsequent finding that the aeschynomenoid root nodule is synapomorphic for the dalbergioids.

Perception of lipo-chitooligosaccharidic Nod factors in legumes

Lipo-chitooligosaccharides produced by rhizobia are a class of signalling molecules that mediate recognition and nodule organogenesis in the legume-rhizobia symbiosis. Their synthesis is specified by the nodulation genes of rhizobia and hence they are commonly known as Nod factors. They are amphiphilic molecules and induce a variety of responses in the roots of the legume hosts. Studies using plant and rhizobial mutants and purified molecules suggest that Nod factors are recognized by more than one receptor. In this article, we review evidence about the affinity, specificity and location of these putative receptors and describe recent studies with regard to their identification.