Cellular programs for arbuscular mycorrhizal symbiosis

Integration of rice apocarotenoid profile and expression pattern of Carotenoid Cleavage Dioxygenases reveals a positive effect of β-ionone on mycorrhization

Carotenoids are susceptible to degrading processes initiated by oxidative cleavage reactions mediated by Carotenoid Cleavage Dioxygenases that break their backbone, leading to products called apocarotenoids. These carotenoid-derived metabolites include the phytohormones abscisic acid and strigolactones, and different signaling molecules and growth regulators, which are utilized by plants to coordinate many aspects of their life. Several apocarotenoids have been recruited for the communication between plants and arbuscular mycorrhizal (AM) fungi and as regulators of the establishment of AM symbiosis. However, our knowledge on their biosynthetic pathways and the regulation of their pattern during AM symbiosis is still limited. In this study, we generated a qualitative and quantitative profile of apocarotenoids in roots and shoots of rice plants exposed to high/low phosphate concentrations, and upon AM symbiosis in a time course experiment covering different stages of growth and AM development. To get deeper insights in the biology of apocarotenoids during this plant-fungal symbiosis, we complemented the metabolic profiles by determining the expression pattern of CCD genes, taking advantage of chemometric tools. This analysis revealed the specific profiles of CCD genes and apocarotenoids across different stages of AM symbiosis and phosphate supply conditions, identifying novel reliable markers at both local and systemic levels and indicating a promoting role of β-ionone in AM symbiosis establishment.

Calcium signalling components underlying NPK homeostasis: potential avenues for exploration

Plants require the major macronutrients, nitrogen (N), phosphorus (P) and potassium (K) for normal growth and development. Their deficiency in soil directly affects vital cellular processes, particularly root growth and architecture. Their perception, uptake and assimilation are regulated by complex signalling pathways. To overcome nutrient deficiencies, plants have developed certain response mechanisms that determine developmental and physiological adaptations. The signal transduction pathways underlying these responses involve a complex interplay of components such as nutrient transporters, transcription factors and others. In addition to their involvement in cross-talk with intracellular calcium signalling pathways, these components are also engaged in NPK sensing and homeostasis. The NPK sensing and homeostatic mechanisms hold the key to identify and understand the crucial players in nutrient regulatory networks in plants under both abiotic and biotic stresses. In this review, we discuss calcium signalling components/pathways underlying plant responses to NPK sensing, with a focus on the sensors, transporters and transcription factors involved in their respective signalling and homeostasis.

A glycan receptor kinase facilitates intracellular accommodation of arbuscular mycorrhiza and symbiotic rhizobia in the legume Lotus japonicus

Receptors that distinguish the multitude of microbes surrounding plants in the environment enable dynamic responses to the biotic and abiotic conditions encountered. In this study, we identify and characterise a glycan receptor kinase, EPR3a, closely related to the exopolysaccharide receptor EPR3. Epr3a is up-regulated in roots colonised by arbuscular mycorrhizal (AM) fungi and is able to bind glucans with a branching pattern characteristic of surface-exposed fungal glucans. Expression studies with cellular resolution show localised activation of the Epr3a promoter in cortical root cells containing arbuscules. Fungal infection and intracellular arbuscule formation are reduced in epr3a mutants. In vitro, the EPR3a ectodomain binds cell wall glucans in affinity gel electrophoresis assays. In microscale thermophoresis (MST) assays, rhizobial exopolysaccharide binding is detected with affinities comparable to those observed for EPR3, and both EPR3a and EPR3 bind a well-defined β-1,3/β-1,6 decasaccharide derived from exopolysaccharides of endophytic and pathogenic fungi. Both EPR3a and EPR3 function in the intracellular accommodation of microbes. However, contrasting expression patterns and divergent ligand affinities result in distinct functions in AM colonisation and rhizobial infection in Lotus japonicus. The presence of Epr3a and Epr3 genes in both eudicot and monocot plant genomes suggest a conserved function of these receptor kinases in glycan perception.

Iron in the Symbiosis of Plants and Microorganisms

Iron is an essential element for most organisms. Both plants and microorganisms have developed different mechanisms for iron uptake, transport and storage. In the symbiosis systems, such as rhizobia-legume symbiosis and arbuscular mycorrhizal (AM) symbiosis, maintaining iron homeostasis to meet the requirements for the interaction between the host plants and the symbiotic microbes is a new challenge. This intriguing topic has drawn the attention of many botanists and microbiologists, and many discoveries have been achieved so far. In this review, we discuss the current progress on iron uptake and transport in the nodules and iron homeostasis in rhizobia-legume symbiosis. The discoveries with regard to iron uptake in AM fungi, iron uptake regulation in AM plants and interactions between iron and other nutrient elements during AM symbiosis are also summarized. At the end of this review, we propose prospects for future studies in this fascinating research area.

Host- and virus-induced gene silencing of HOG1-MAPK cascade genes in Rhizophagus irregularis inhibit arbuscule development and reduce resistance of plants to drought stress

Arbuscular mycorrhizal (AM) fungi can form beneficial associations with the most terrestrial vascular plant species. AM fungi not only facilitate plant nutrient acquisition but also enhance plant tolerance to various environmental stresses such as drought stress. However, the molecular mechanisms by which AM fungal mitogen-activated protein kinase (MAPK) cascades mediate the host adaptation to drought stimulus remains to be investigated. Recently, many studies have shown that virus-induced gene silencing (VIGS) and host-induced gene silencing (HIGS) strategies are used for functional studies of AM fungi. Here, we identify the three HOG1 (High Osmolarity Glycerol 1)-MAPK cascade genes RiSte11, RiPbs2 and RiHog1 from Rhizophagus irregularis. The expression levels of the three HOG1-MAPK genes are significantly increased in mycorrhizal roots of the plant Astragalus sinicus under severe drought stress. RiHog1 protein was predominantly localized in the nucleus of yeast in response to 1 M sorbitol treatment, and RiPbs2 interacts with RiSte11 or RiHog1 directly by pull-down assay. Importantly, VIGS or HIGS of RiSte11, RiPbs2 or RiHog1 hampers arbuscule development and decreases relative water content in plants during AM symbiosis. Moreover, silencing of HOG1-MAPK cascade genes led to the decreased expression of drought-resistant genes (RiAQPs, RiTPSs, RiNTH1 and Ri14-3-3) in the AM fungal symbiont in response to drought stress. Taken together, this study demonstrates that VIGS or HIGS of AM fungal HOG1-MAPK cascade inhibits arbuscule development and expression of AM fungal drought-resistant genes under drought stress.

A transcriptional activator from Rhizophagus irregularis regulates phosphate uptake and homeostasis in AM symbiosis during phosphorous starvation

Introduction

Phosphorus (P) is one of the most important nutrient elements for plant growth and development. Under P starvation, arbuscular mycorrhizal (AM) fungi can promote phosphate (Pi) uptake and homeostasis within host plants. However, the underlying mechanisms by which AM fungal symbiont regulates the AM symbiotic Pi acquisition from soil under P starvation are largely unknown. Here, we identify a HLH domain containing transcription factor RiPho4 from Rhizophagus irregularis.

Methods

To investigate the biological functions of the RiPho4, we combined the subcellular localization and Yeast One-Hybrid (Y1H) experiments in yeasts with gene expression and virus-induced gene silencing approach during AM symbiosis.

Results

The approach during AM symbiosis. The results indicated that RiPho4 encodes a conserved transcription factor among different fungi and is induced during the in planta phase. The transcription of RiPho4 is significantly up-regulated by P starvation. The subcellular localization analysis revealed that RiPho4 is located in the nuclei of yeast cells during P starvation. Moreover, knock-down of RiPho4 inhibits the arbuscule development and mycorrhizal Pi uptake under low Pi conditions. Importantly, RiPho4 can positively regulate the downstream components of the phosphate (PHO) pathway in R. irregularis.

Discussion

In summary, these new findings reveal that RiPho4 acts as a transcriptional activator in AM fungus to maintain arbuscule development and regulate Pi uptake and homeostasis in the AM symbiosis during Pi starvation.

Root acid phosphatases and rhizobacteria synergistically enhance white lupin and rice phosphorus acquisition

The rhizosheath is a belowground area that acts as a communication hub at the root-soil interface to promote water and nutrient acquisition. Certain crops, such as white lupin (Lupinus albus), acquire large amounts of phosphorus (P), owing partially to exudation of acid phosphatases (APases). Plant growth-promoting rhizobacteria also increase soil P availability. However, potential synergistic effects of root APases and rhizosheath-associated microbiota on P acquisition require further research. In this study, we investigated the roles of root purple APases (PAPs) and plant growth-promoting rhizobacteria in rhizosheath formation and P acquisition under conditions of soil drying (SD) and P treatment (+P: soil with P fertilizer; -P: soil without fertilizer). We expressed purple acid phosphatase12 (LaPAP12) in white lupin and rice (Oryza sativa) plants and analyzed the rhizosheath-associated microbiome. Increased or heterologous LaPAP12 expression promoted APase activity and rhizosheath formation, resulting in increased P acquisition mainly under SD-P conditions. It also increased the abundance of members of the genus Bacillus in the rhizosheath-associated microbial communities of white lupin and rice. We isolated a phosphate-solubilizing, auxin-producing Bacillus megaterium strain from the rhizosheath of white lupin and used this to inoculate white lupin and rice plants. Inoculation promoted rhizosheath formation and P acquisition, especially in plants with increased LaPAP12 expression and under SD-P conditions, suggesting a functional role of the bacteria in alleviating P deficit stress via rhizosheath formation. Together, our results suggest a synergistic enhancing effect of LaPAP12 and plant growth-promoting rhizobacteria on rhizosheath formation and P acquisition under SD-P conditions.

Plant-microbe interactions that have impacted plant terrestrializations

Plants display a tremendous diversity of developmental and physiological features, resulting from gains and losses of functional innovations across the plant phylogeny. Among those, the most impactful have been undoubtedly the ones that allowed plant terrestrializations, the transitions from an aquatic to a terrestrial environment. Although the embryophyte terrestrialization has been particularly scrutinized, others occurred across the plant phylogeny with the involvement of mutualistic symbioses as a common theme. Here, we review the current pieces of evidence supporting that the repeated colonization of land by plants has been facilitated by interactions with mutualistic symbionts. In that context, we detail two of these mutualistic symbioses: the arbuscular mycorrhizal symbiosis in embryophytes and the lichen symbiosis in chlorophyte algae. We suggest that associations with bacteria should be revisited in that context, and we propose that overlooked symbioses might have facilitated the emergence of other land plant clades.

Expression and roles of GRAS gene family in plant growth, signal transduction, biotic and abiotic stress resistance and symbiosis formation-a review

The GRAS (derived from GAI, RGA and SCR) gene family consists of plant-specific genes, works as a transcriptional regulator and plays a key part in the regulation of plant growth and development. The past decade has witnessed significant progress in understanding and advances on GRAS transcription factors in various plants. A notable concern is to what extent the mechanisms found in plants, particularly crops, are shared by other species, and what other characteristics are dependent on GRAS transcription factor (TFS)-mediated gene expression. GRAS are involved in many processes that are intimately linked to plant growth regulation. However, GRAS also perform additional roles against environmental stresses, allowing plants to function more efficiently. GRAS increase plant growth and development by improving several physiological processes, such as phytohormone, biosynthetic and signalling pathways. Furthermore, the GRAS gene family plays an important role in response to abiotic stresses, e.g. photooxidative stress. Moreover, evidence shows the involvement of GRAS in arbuscule development during plant-mycorrhiza associations. In this review, the diverse roles of GRAS in plant systems are highlighted that could be useful in enhancing crop productivity through genetic modification, especially of crops. This is the first review to report the role and function of the GRAS gene family in plant systems. Furthermore, a large number of studies are reviewed, and several limitations and research gaps identified that must be addressed in future studies.

Plant immunity suppression via PHR1-RALF-FERONIA shapes the root microbiome to alleviate phosphate starvation

The microbiome plays an important role in shaping plant growth and immunity, but few plant genes and pathways impacting plant microbiome composition have been reported. In Arabidopsis thaliana, the phosphate starvation response (PSR) was recently found to modulate the root microbiome upon phosphate (Pi) starvation through the transcriptional regulator PHR1. Here, we report that A. thaliana PHR1 directly binds to the promoters of rapid alkalinization factor (RALF) genes, and activates their expression under phosphate-starvation conditions. RALFs in turn suppress complex formation of pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) receptor through FERONIA, a previously-identified PTI modulator that increases resistance to certain detrimental microorganisms. Suppression of immunity via the PHR1-RALF-FERONIA axis allows colonization by specialized root microbiota that help to alleviate phosphate starvation by upregulating the expression of PSR genes. These findings provide a new paradigm for coordination of host-microbe homeostasis through modulating plant innate immunity after environmental perturbations.

Fifteen compelling open questions in plant cell biology

As scientists, we are at least as excited about the open questions-the things we do not know-as the discoveries. Here, we asked 15 experts to describe the most compelling open questions in plant cell biology. These are their questions: How are organelle identity, domains, and boundaries maintained under the continuous flux of vesicle trafficking and membrane remodeling? Is the plant cortical microtubule cytoskeleton a mechanosensory apparatus? How are the cellular pathways of cell wall synthesis, assembly, modification, and integrity sensing linked in plants? Why do plasmodesmata open and close? Is there retrograde signaling from vacuoles to the nucleus? How do root cells accommodate fungal endosymbionts? What is the role of cell edges in plant morphogenesis? How is the cell division site determined? What are the emergent effects of polyploidy on the biology of the cell, and how are any such "rules" conditioned by cell type? Can mechanical forces trigger new cell fates in plants? How does a single differentiated somatic cell reprogram and gain pluripotency? How does polarity develop de-novo in isolated plant cells? What is the spectrum of cellular functions for membraneless organelles and intrinsically disordered proteins? How do plants deal with internal noise? How does order emerge in cells and propagate to organs and organisms from complex dynamical processes? We hope you find the discussions of these questions thought provoking and inspiring.

Phosphate Suppression of Arbuscular Mycorrhizal Symbiosis Involves Gibberellic Acid Signaling

Most land plants entertain a mutualistic symbiosis known as arbuscular mycorrhiza with fungi (Glomeromycota) that provide them with essential mineral nutrients, in particular phosphate (Pi), and protect them from biotic and abiotic stress. Arbuscular mycorrhizal (AM) symbiosis increases plant productivity and biodiversity and is therefore relevant for both natural plant communities and crop production. However, AM fungal populations suffer from intense farming practices in agricultural soils, in particular Pi fertilization. The dilemma between natural fertilization from AM symbiosis and chemical fertilization has raised major concern and emphasizes the need to better understand the mechanisms by which Pi suppresses AM symbiosis. Here, we test the hypothesis that Pi may interfere with AM symbiosis via the phytohormone gibberellic acid (GA) in the Solanaceous model systems Petunia hybrida and Nicotiana tabacum. Indeed, we find that GA is inhibitory to AM symbiosis and that Pi may cause GA levels to increase in mycorrhizal roots. Consistent with a role of endogenous GA as an inhibitor of AM development, GA-defective N. tabacum lines expressing a GA-metabolizing enzyme (GA methyltransferase-GAMT) are colonized more quickly by the AM fungus Rhizoglomus irregulare, and exogenous Pi is less effective in inhibiting AM colonization in these lines. Systematic gene expression analysis of GA-related genes reveals a complex picture, in which GA degradation by GA2 oxidase plays a prominent role. These findings reveal potential targets for crop breeding that could reduce Pi suppression of AM symbiosis, thereby reconciling the advantages of Pi fertilization with the diverse benefits of AM symbiosis.

Silencing MdGH3-2/12 in apple reduces drought resistance by regulating AM colonization

Drought leads to reductions in plant growth and crop yields. Arbuscular mycorrhizal fungi (AMF), which form symbioses with the roots of the most important crop species, alleviate drought stress in plants. In the present work, we identified 14 GH3 genes in apple (Malus domestica) and provided evidence that MdGH3-2 and MdGH3-12 play important roles during AM symbiosis. The expression of both MdGH3-2 and MdGH3-12 was upregulated during mycorrhization, and the silencing of MdGH3-2/12 had a negative impact on AM colonization. MdGH3-2/12 silencing resulted in the downregulation of five genes involved in strigolactone synthesis, and there was a corresponding change in root strigolactone content. Furthermore, we observed lower root dry weights in RNAi lines under AM inoculation conditions. Mycorrhizal transgenic plants showed greater sensitivity to drought stress than WT, as indicated by their higher relative electrolytic leakage and lower relative water contents, osmotic adjustment ability, ROS scavenging ability, photosynthetic capacity, chlorophyll fluorescence values, and abscisic acid contents. Taken together, these data demonstrate that MdGH3-2/12 plays an important role in AM symbiosis and drought stress tolerance in apple.

Lineage-Specific Genes and Cryptic Sex: Parallels and Differences between Arbuscular Mycorrhizal Fungi and Fungal Pathogens

Arbuscular mycorrhizal fungi (AMF) live as obligate root symbionts on almost all land plants. They have long been regarded as ancient asexuals that have propagated clonally for millions of years. However, genomic studies in Rhizophagus irregularis and other AMF revealed many features indicative of sex. Surprisingly, comparative genomics of conspecific isolates of R. irregularis revealed an unexpected interstrain diversity, suggesting that AMF carry a high number of lineage-specific (LS) genes. Intriguingly, cryptic sex and LS genomic regions have previously been reported in a number of fungal pathogens of plants and humans. Here, we discuss these genomic similarities and highlight their potential relevance for AMF adaptation to the environment and for symbiotic functioning.

Overexpression of MdIAA24 improves apple drought resistance by positively regulating strigolactone biosynthesis and mycorrhization

Most land plant species have the ability to establish a symbiosis with arbuscular mycorrhizal (AM) fungi. These fungi penetrate into root cortical cells and form branched structures (known as arbuscules) for nutrient exchange. We cloned the MdIAA24 from apple (Malus domestica) following its up-regulation during AM symbiosis. Results demonstrate the positive impact of the overexpression (OE) of MdIAA24 in apple on AM colonization. We observed the strigolactone (SL) synthesis genes, including MdD27, MdCCD7, MdCCD8a, MdCCD8b and MdMAXa, to be up-regulated in the OE lines. Thus, the OE lines exhibited both a higher SL content and colonization rate. Furthermore, we observed that the OE lines were able to maintain better growth parameters under AM inoculation conditions. Under drought stress with the AM inoculation, the OE lines were less damaged, which was demonstrated by a higher relative water content, a lower relative electrolytic leakage, a greater osmotic adjustment, a higher reactive oxygen species scavenging ability, an improved gas exchange capacity and an increased chlorophyll fluorescence performance. Our findings demonstrate that the OE of MdIAA24 in apple positively regulates the synthesis of SL and the formation of arbuscules as a drought stress coping mechanism.

Mycorrhizal Interventions for Sustainable Potato Production in Africa

The potato (Solanum tuberosum L.) is an important tuber crop with high dietary value that could potentially help to alleviate malnutrition and hunger in Africa. However, production is expensive, with high fertilizer and pesticide demands that lead to environmental pollution, and tillage practices that negatively affect soil structure. Microorganisms of different types have increasingly been found to be useful as biofertilizers, and arbuscular mycorrhizal (AM) fungi are an important crop symbiont. AM fungi have been shown to increase tolerance of crop plants to drought, salinity and disease by facilitating water and nutrient acquisition and by improving overall soil structure. However, the establishment and maintenance of the symbioses are greatly affected by agricultural practices. Here, we review the benefits that AM fungi confer in potato production, discuss the role and importance of mycorrhiza helper bacteria, and focus on how AM fungal diversity and abundance can be affected by conventional agricultural practices, such as those used in potato production. We suggest approaches for maintaining AM fungal abundance in potato production by highlighting the potential of conservation tillage practices augmented with cover crops and crop rotations. An approach that balances weed control, nutrient provision, and AM fungal helper bacterial populations, whilst promoting functional AM fungal populations for varying potato genotypes, will stimulate efficient mycorrhizal interventions.

Responses of Arbuscular Mycorrhizal Symbiosis to Abiotic Stress: A Lipid-Centric Perspective

Arbuscular mycorrhizal (AM) fungi are one of the most important soil microbial resources that help host plants cope with various abiotic stresses. Although a tremendous number of studies have revealed the responses of AM fungi to abiotic stress and their beneficial effects transferred to host plants, little work has focused on the role of lipid metabolism in AM fungi under abiotic stress conditions. AM fungi contain a large amount of lipids in their biomass, including phospholipids (PLs) in their hyphal membranes and neutral lipids (NLs) in their storage structures (e.g., vesicles and spores). Recently, lipid transfer from plants to AM fungi has been suggested to be indispensable for the establishment of AM symbiosis, and extraradical hyphae are capable of directly taking up lipids from the environment. This experimental evidence highlights the importance of lipids in AM symbiosis. Moreover, abiotic stress reduces lipid transfer to AM fungi and promotes arbuscule collapse as well as the hydrolysis and conversion of PLs to NLs in collapsed arbuscules. Overall, this knowledge encourages us to rethink the responses of AM symbiosis to abiotic stress from a lipid-centric perspective. The present review provides current and comprehensive knowledge on lipid metabolism in AM fungi, especially in response to various abiotic stresses. A regulatory role of abscisic acid (ABA), which is considered a "stress hormone," in lipid metabolism and in the resulting consequences is also proposed.

The interactions of Trichoderma at multiple trophic levels: inter-kingdom communication

Trichoderma spp. are universal saprotrophic fungi in terrestrial ecosystems, and as rhizosphere inhabitants, they mediate interactions with other soil microorganisms, plants, and arthropods at multiple trophic levels. In the rhizosphere, Trichoderma can reduce the abundance of phytopathogenic microorganisms, which involves the action of potent inhibitory molecules, such as gliovirin and siderophores, whereas endophytic associations between Trichoderma and the seeds and roots of host plants can result in enhanced plant growth and crop productivity, as well as the alleviation of abiotic stress. Such beneficial effects are mediated via the activation of endogenous mechanisms controlled by phytohormones such as auxins and abscisic acid, as well as by alterations in host plant metabolism. During either root colonization or in the absence of physical contact, Trichoderma can trigger early defense responses mediated by Ca²⁺ and reactive oxygen species, and subsequently stimulate plant immunity by enhancing resistance mechanisms regulated by the phytohormones salicylic acid, jasmonic acid, and ethylene. In addition, Trichoderma release volatile organic compounds and nitrogen or oxygen heterocyclic compounds that serve as signaling molecules, which have effects on plant growth, phytopathogen levels, herbivorous insects, and at the third trophic level, play roles in attracting the natural enemies (predators and parasitoids) of herbivores. In this paper, we review some of the most recent advances in our understanding of the environmental influences of Trichoderma spp., with particular emphasis on their multiple interactions at different trophic levels.

Gibberellin Promotes Fungal Entry and Colonization during Paris-Type Arbuscular Mycorrhizal Symbiosis in Eustoma grandiflorum

Arbuscular mycorrhizas (AMs) are divided into two types according to morphology: Arum- and Paris-type AMs. Gibberellins (GAs) mainly inhibit the establishment of Arum-type AM symbiosis in most model plants, whereas the effects of GAs on Paris-type AM symbiosis are unclear. To provide insight into the mechanism underlying this type of symbiosis, the roles of GAs were investigated in Eustoma grandiflorum when used as the host plant for Paris-type AM establishment. Eustoma grandiflorum seedlings were inoculated with the model AM fungus, Rhizophagus irregularis, and the effects of GA and the GA biosynthesis inhibitor uniconazole-P on the symbiosis were quantitatively evaluated. Exogenous GA significantly increased hyphopodium formation at the epidermis, thus leading to the promotion of fungal colonization and arbuscule formation in the root cortex. By contrast, the suppression of GA biosynthesis and signaling attenuated fungal entry to E. grandiflorum roots. Moreover, the exudates from GA-treated roots strongly induced the hyphal branching of R. irregularis. Our results show that GA has an contrasting effect on Paris-type AM symbiosis in E. grandiflorum compared with Arum-type AM symbiosis. This finding could be explained by the differential regulation of the early colonization stage, where fungal hyphae make contact with and penetrate the epidermis.

The Medicago truncatula LysM receptor-like kinase LYK9 plays a dual role in immunity and the arbuscular mycorrhizal symbiosis

Plant -specific lysin-motif receptor-like kinases (LysM-RLKs) are implicated in the perception of N-acetyl glucosamine-containing compounds, some of which are important signal molecules in plant-microbe interactions. Among these, both lipo-chitooligosaccharides (LCOs) and chitooligosaccharides (COs) are proposed as arbuscular mycorrhizal (AM) fungal symbiotic signals. COs can also activate plant defence, although there are scarce data about CO production by pathogens, especially nonfungal pathogens. We tested Medicago truncatula mutants in the LysM-RLK MtLYK9 for their abilities to interact with the AM fungus Rhizophagus irregularis and the oomycete pathogen Aphanomyces euteiches. This prompted us to analyse whether A. euteiches can produce COs. Compared with wild-type plants, Mtlyk9 mutants had fewer infection events and were less colonised by the AM fungus. By contrast, Mtlyk9 mutants were more heavily infected by A. euteiches and showed more disease symptoms. Aphanomyces euteiches was also shown to produce short COs, mainly CO II, but also CO III and CO IV, and traces of CO V, both ex planta and in planta. MtLYK9 thus has a dual role in plant immunity and the AM symbiosis, which raises questions about the functioning and the ancestral origins of such a receptor protein.

Molecular dialogue between arbuscular mycorrhizal fungi and the nonhost plant Arabidopsis thaliana switches from initial detection to antagonism

Approximately 29% of all vascular plant species are unable to establish an arbuscular mycorrhizal (AM) symbiosis. Despite this, AM fungi (Rhizophagus spp.) are enriched in the root microbiome of the nonhost Arabidopsis thaliana, and Arabidopsis roots become colonized when AM networks nurtured by host plants are available. Here, we investigated the nonhost-AM fungus interaction by analyzing transcriptional changes in Rhizophagus, Arabidopsis and the host plant Medicago truncatula while growing in the same mycorrhizal network. In early interaction stages, Rhizophagus activated the Arabidopsis strigolactone biosynthesis genes CCD7 and CCD8, suggesting that detection of AM fungi is not completely impaired. However, in colonized Arabidopsis roots, fungal nutrient transporter genes GintPT, GintAMT2, GintMST2 and GintMST4, essential for AM symbiosis, were not activated. RNA-seq transcriptome analysis pointed to activation of costly defenses in colonized Arabidopsis roots. Moreover, Rhizophagus colonization caused a 50% reduction in shoot biomass, but also led to enhanced systemic immunity against Botrytis cinerea. This suggests that early signaling between AM fungi and Arabidopsis is not completely impaired and that incompatibility appears at later interaction stages. Moreover, Rhizophagus-mediated defenses coincide with reduced Arabidopsis growth, but also with systemic disease resistance, highlighting the multifunctional role of AM fungi in host and nonhost interactions.

Effector proteins of Rhizophagus proliferus: conserved protein domains may play a role in host-specific interaction with different plant species

Arbuscular mycorrhizal (AM) fungi show high promiscuity in terms of host. Effector proteins expressed by AM fungi are found important in establishing interaction with host. However, the mechanistic underlying host-specific interactions of the fungi remain unknown. The present study aimed (i) to identify effectors encoded by Rhizophagus proliferus and (ii) to understand molecular specificity encoded in effectors for interaction with specific plant species. The effectors predicted from the whole genome sequence were annotated by homology search in NCBI non-redundant protein, Interproscan, and pathogen-host interaction (PHI) databases. In total, 416 small secreted peptides (SSPs) were predicted, which were effector peptides with presence of nuclear localization signal, small cysteine-rich, and repeat-containing proteins domains. Similar to the functionally validated SP7 effectors in Rhizophagus irregularis, two proteins (RP8598 and RP23081) were identified in R. proliferus. To understand whether interaction between SP7 and the plant target protein, ERF19, is specific in nature, we examined protein-peptide interaction using in silico molecular docking. Pairwise interaction of RP8598 and RP23081 with the ethylene-responsive factors (ERF19) coded by five different plant species (Lotus japonicus, Solanum lycopersicum, Ocimum tenuiflorum, Medicago truncatula, Diospyros kaki) was investigated. Prediction of high-quality interaction of SP7 effector with ERF19 protein expressed only by specific plant species was observed in in silico molecular docking, which may reiterate the role of effectors in host specificity. The outcomes from our study indicated that sequence precision encoded in the effector peptides of AM fungi and immunomodulatory proteins of host may regulate host specificity in these fungi.

VAPYRIN Marks an Endosomal Trafficking Compartment Involved in Arbuscular Mycorrhizal Symbiosis

Arbuscular mycorrhiza (AM) is a symbiosis between plants and AM fungi that requires the intracellular accommodation of the fungal partner in the host. For reciprocal nutrient exchange, AM fungi form intracellular arbuscules that are surrounded by the peri-arbuscular membrane. This membrane, together with the fungal plasma membrane, and the space in between, constitute the symbiotic interface, over which nutrients are exchanged. Intracellular establishment of AM fungi requires the VAPYRIN protein which is induced in colonized cells, and which localizes to numerous small mobile structures of unknown identity (Vapyrin-bodies). In order to characterize the identity and function of the Vapyrin-bodies we pursued a dual strategy. First, we co-expressed fluorescently tagged VAPYRIN with a range of subcellular marker proteins, and secondly, we employed biochemical tools to identify interacting partner proteins of VAPYRIN. As an important tool for the quantitative analysis of confocal microscopic data sets from co-expression of fluorescent proteins, we developed a semi-automated image analysis pipeline that allows for precise spatio-temporal quantification of protein co-localization and of the dynamics of organelle association from movies. Taken together, these experiments revealed that Vapyrin-bodies have an endosomal identity with trans-Golgi features, and that VAPYRIN interacts with a symbiotic R-SNARE of the VAMP721 family, that localizes to the same compartment.

Integrative Analysis of the Wheat PHT1 Gene Family Reveals A Novel Member Involved in Arbuscular Mycorrhizal Phosphate Transport and Immunity

Phosphorus (P) deficiency is one of the main growth-limiting factors for plants. However, arbuscular mycorrhizal (AM) symbiosis can significantly promote P uptake. Generally, PHT1 transporters play key roles in plants' P uptake, and thus, PHT1 genes have been investigated in some plants, but the regulation and functions of these genes in wheat (TaPHT1) during AM symbiosis have not been studied in depth. Therefore, a comprehensive analysis of TaPHT1 genes was performed, including sequence, phylogeny, cis-elements, expression, subcellular localization and functions, to elucidate their roles in AM-associated phosphate transport and immunity. In total, 35 TaPHT1s were identified in the latest high-quality bread wheat genome, 34 of which were unevenly distributed on 13 chromosomes, and divided into five groups. Sequence analysis indicated that there are 11 types of motif architectures and five types of exon-intron structures in the TaPHT1 family. Duplication mode analysis indicated that the TaPHT1 family has expanded mainly through segmental and tandem duplication events, and that all duplicated gene pairs have been under purifying selection. Transcription analysis of the 35 TaPHT1s revealed that not only known the mycorrhizal-specific genes TaPht-myc, TaPT15-4B (TaPT11) and TaPT19-4D (TaPT10), but also four novel mycorrhizal-specific/inducible genes (TaPT3-2D, TaPT11-4A, TaPT29-6A, and TaPT31-7A) are highly up-regulated in AM wheat roots. Furthermore, the mycorrhizal-specific/inducible genes are significantly induced in wheat roots at different stages of infection by colonizing fungi. Transient Agrobacterium tumefaciens-mediated transformation expression in onion epidermal cells showed that TaPT29-6A is a membrane-localized protein. In contrast to other AM-specific/inducible PHT1 genes, TaPT29-6A is apparently required for the symbiotic and direct Pi pathway. TaPT29-6A-silenced lines exhibited reduced levels of AM fungal colonization and arbuscules, but increased susceptibility to biotrophic, hemi-biotrophic and necrotrophic pathogens. In conclusion, TaPT29-6A was not only essential for the AM symbiosis, but also played vital roles in immunity.

Size matters: three methods for estimating nuclear size in mycorrhizal roots of Medicago truncatula by image analysis

BACKGROUND

The intracellular accommodation of arbuscular mycorrhizal (AM) fungi involves a profound molecular reprogramming of the host cell architecture and metabolism, based on the activation of a symbiotic signaling pathway. In analogy with other plant biotrophs, AM fungi are reported to trigger cell cycle reactivation in their host tissues, possibly in support of the enhanced metabolic demand required for the symbiosis.

RESULTS

We here compare the efficiency of three Fiji/ImageJ image analysis plugins in localizing and quantifying the increase in nuclear size - a hallmark of recursive events of endoreduplication - in M. truncatula roots colonized by the AM fungus Gigaspora margarita. All three approaches proved to be versatile and upgradeable, allowing the investigation of nuclear changes in a complex tissue; 3D Object Counter provided more detailed information than both TrackMate and Round Surface Detector plugins. On this base we challenged 3D Object Counter with two case studies: verifying the lack of endoreduplication-triggering responses in Medicago truncatula mutants with a known non-symbiotic phenotype; and analysing the correlation in space and time between the induction of cortical cell division and endoreduplication upon AM colonization. Both case studies revealed important biological aspects. Mutant phenotype analyses have demonstrated that the knock-out mutation of different key genes in the symbiotic signaling pathway block AM-associated endoreduplication. Furthermore, our data show that cell divisions occur during initial stages of root colonization and are followed by recursive activation of the endocycle in preparation for arbuscule accommodation.

CONCLUSIONS

In conclusion, our results indicate 3D Object Counter as the best performing Fiji/ImageJ image analysis script in plant root thick sections and its application highlighted endoreduplication as a major feature of the AM pre-penetration response in root cortical cells.

Size matters: three methods for estimating nuclear size in mycorrhizal roots of Medicago truncatula by image analysis

BACKGROUND

The intracellular accommodation of arbuscular mycorrhizal (AM) fungi involves a profound molecular reprogramming of the host cell architecture and metabolism, based on the activation of a symbiotic signaling pathway. In analogy with other plant biotrophs, AM fungi are reported to trigger cell cycle reactivation in their host tissues, possibly in support of the enhanced metabolic demand required for the symbiosis.

RESULTS

We here compare the efficiency of three Fiji/ImageJ image analysis plugins in localizing and quantifying the increase in nuclear size - a hallmark of recursive events of endoreduplication - in M. truncatula roots colonized by the AM fungus Gigaspora margarita. All three approaches proved to be versatile and upgradeable, allowing the investigation of nuclear changes in a complex tissue; 3D Object Counter provided more detailed information than both TrackMate and Round Surface Detector plugins. On this base we challenged 3D Object Counter with two case studies: verifying the lack of endoreduplication-triggering responses in Medicago truncatula mutants with a known non-symbiotic phenotype; and analysing the correlation in space and time between the induction of cortical cell division and endoreduplication upon AM colonization. Both case studies revealed important biological aspects. Mutant phenotype analyses have demonstrated that the knock-out mutation of different key genes in the symbiotic signaling pathway block AM-associated endoreduplication. Furthermore, our data show that cell divisions occur during initial stages of root colonization and are followed by recursive activation of the endocycle in preparation for arbuscule accommodation.

CONCLUSIONS

In conclusion, our results indicate 3D Object Counter as the best performing Fiji/ImageJ image analysis script in plant root thick sections and its application highlighted endoreduplication as a major feature of the AM pre-penetration response in root cortical cells.

Colonization of legumes by an endophytic Fusarium solani strain FsK reveals common features to symbionts or pathogens

Plant cellular responses to endophytic filamentous fungi are scarcely reported, with the majority of described colonization processes in plant-fungal interactions referring to either pathogens or true symbionts. Fusarium solani strain K (FsK) is a root endophyte of Solanum lycopersicum, which protects against root and foliar pathogens. Here, we investigate the association of FsK with two legumes (Lotus japonicus and Medicago truncatula) and report on colonization patterns and plant responses during the establishment of the interaction. L. japonicus plants colonized by FsK complete their life cycle and exhibit no apparent growth defects under normal conditions. We followed the growth of FsK within root-inoculated plants spatiotemporally and showed the capability of the endophyte to migrate to the stem. In a bipartite system comprising of the endophyte and either whole plants or root organ cultures, we studied the plant sub-cellular responses to FsK recognition, using optical, confocal and transmission electron microscopy. A polarized reorganization of the root cell occurs: endoplasmic reticulum/cytoplasm accumulation and nuclear placement at contact sites, occasional development of papillae underneath hyphopodia and membranous material rearrangements towards penetrating hyphae. Fungal hyphae proliferate within the vascular bundle of the plant. Plant cell death is involved in fungal colonization of the root. Our data suggest that the establishment of FsK within legume tissues requires fungal growth adaptations and plant cell-autonomous responses, known to occur during both symbiotic and pathogenic plant-fungal interactions. We highlight the overlooked plasticity of endophytic fungi upon plant colonization, and introduce a novel plant-endophyte association.

Identification and Expression Analysis of GRAS Transcription Factor Genes Involved in the Control of Arbuscular Mycorrhizal Development in Tomato

The formation and functioning of arbuscular mycorrhizal (AM) symbiosis are complex and tightly regulated processes. Transcriptional regulation mechanisms have been reported to mediate gene expression changes closely associated with arbuscule formation, where nutrients move between the plant and fungus. Numerous genes encoding transcription factors (TFs), with those belonging to the GRAS family being of particular importance, are induced upon mycorrhization. In this study, a screening for candidate transcription factor genes differentially regulated in AM tomato roots showed that more than 30% of known GRAS tomato genes are upregulated upon mycorrhization. Some AM-upregulated GRAS genes were identified as encoding for transcription factors which are putative orthologs of previously identified regulators of mycorrhization in other plant species. The symbiotic role played by other newly identified AM-upregulated GRAS genes remains unknown. Preliminary results on the involvement of tomato SlGRAS18, SlGRAS38, and SlGRAS43 from the SCL3, SCL32, and SCR clades, respectively, in mycorrhization are presented. All three showed high transcript levels in the late stages of mycorrhization, and the analysis of promoter activity demonstrated that SlGRAS18 and SlGRAS43 are significantly induced in cells containing arbuscules. When SlGRAS18 and SlGRAS38 genes were silenced using RNA interference in hairy root composite tomato plants, a delay in mycorrhizal infection was observed, while an increase in mycorrhizal colonization was observed in SlGRAS43 RNAi roots. The possible mode of action of these TFs during mycorrhization is discussed, with a particular emphasis on the potential involvement of the SHR/SCR/SCL3 module of GRAS TFs in the regulation of gibberellin signaling during mycorrhization, which is analogous to other plant developmental processes.

Structural plasticity in root-fungal symbioses: diverse interactions lead to improved plant fitness

Root-fungal symbioses such as mycorrhizas and endophytes are key components of terrestrial ecosystems. Diverse in trophy habits (obligate, facultative or hemi-biotrophs) and symbiotic relations (from mutualism to parasitism), these associations also show great variability in their root colonization and nutritional strategies. Specialized interface structures such as arbuscules and Hartig nets are formed by certain associations while others are restricted to non-specialized intercellular or intracellular hyphae in roots. In either case, there are documented examples of active nutrient exchange, reinforcing the fact that specialized structures used to define specific mycorrhizal associations are not essential for reciprocal exchange of nutrients and plant growth promotion. In feremycorrhiza (with Austroboletus occidentalis and eucalypts), the fungal partner markedly enhances plant growth and nutrient acquisition without colonizing roots, emphasizing that a conventional focus on structural form of associations may have resulted in important functional components of rhizospheres being overlooked. In support of this viewpoint, mycobiome studies using the state-of-the-art DNA sequencing technologies have unearthed much more complexity in root-fungal relationships than those discovered using the traditional morphology-based approaches. In this review, we explore the existing literature and most recent findings surrounding structure, functioning, and ecology of root-fungal symbiosis, which highlight the fact that plant fitness can be altered by taxonomically/ecologically diverse fungal symbionts regardless of root colonization and interface specialization. Furthermore, transition from saprotrophy to biotrophy seems to be a common event that occurs in diverse fungal lineages (consisting of root endophytes, soil saprotrophs, wood decayers etc.), and which may be accompanied by development of specialized interface structures and/or mycorrhiza-like effects on plant growth and nutrition.

Medicago AP2-Domain Transcription Factor WRI5a Is a Master Regulator of Lipid Biosynthesis and Transfer during Mycorrhizal Symbiosis

Most land plants have evolved a mutualistic symbiosis with arbuscular mycorrhiza (AM) fungi that improve nutrient acquisition from the soil. In return, up to 20% of host plant photosynthate is transferred to the mycorrhizal fungus in the form of lipids and sugar. Nutrient exchange must be regulated by both partners in order to maintain a reliable symbiotic relationship. However, the mechanisms underlying the regulation of lipid transfer from the plant to the AM fungus remain elusive. Here, we show that the Medicago truncatula AP2/EREBP transcription factor WRI5a, and likely its two homologs WRI5b/Erf1 and WRI5c, are master regulators of AM symbiosis controlling lipid transfer and periarbuscular membrane formation. We found that WRI5a binds AW-box cis-regulatory elements in the promoters of M. truncatula STR, which encodes a periarbuscular membrane-localized ABC transporter required for lipid transfer from the plant to the AM fungus, and MtPT4, which encodes a phosphate transporter required for phosphate transfer from the AM fungus to the plant. The hairy roots of the M. truncatula wri5a mutant and RNAi composite plants displayed impaired arbuscule formation, whereas overexpression of WRI5a resulted in enhanced expression of STR and MtPT4, suggesting that WRI5a regulates bidirectional symbiotic nutrient exchange. Moreover, we found that WRI5a and RAM1 (Required for Arbuscular Mycorrhization symbiosis 1), which encodes a GRAS-domain transcription factor, regulate each other at the transcriptional level, forming a positive feedback loop for regulating AM symbiosis. Collectively, our data suggest a role for WRI5a in controlling bidirectional nutrient exchange and periarbuscular membrane formation via the regulation of genes involved in the biosynthesis of fatty acids and phosphate uptake in arbuscule-containing cells.

Beneficial Services of Arbuscular Mycorrhizal Fungi - From Ecology to Application

Arbuscular mycorrhiza (AM) is the most common symbiotic association of plants with microbes. AM fungi occur in the majority of natural habitats and they provide a range of important ecological services, in particular by improving plant nutrition, stress resistance and tolerance, soil structure and fertility. AM fungi also interact with most crop plants including cereals, vegetables, and fruit trees, therefore, they receive increasing attention for their potential use in sustainable agriculture. Basic research of the past decade has revealed the existence of a dedicated recognition and signaling pathway that is required for AM. Furthermore, recent evidence provided new insight into the exchange of nutritional benefits between the symbiotic partners. The great potential for application of AM has given rise to a thriving industry for AM-related products for agriculture, horticulture, and landscaping. Here, we discuss new developments in these fields, and we highlight future potential and limits toward the use of AM fungi for plant production.

Understanding the Arbuscule at the Heart of Endomycorrhizal Symbioses in Plants

Arbuscular mycorrhizal fungi form associations with most land plants and facilitate nutrient uptake from the soil, with the plant receiving mineral nutrients from the fungus and in return providing the fungus with fixed carbon. This nutrient exchange takes place through highly branched fungal structures called arbuscules that are formed in cortical cells of the host root. Recent discoveries have highlighted the importance of fatty acids, in addition to sugars, acting as the form of fixed carbon transferred from the plant to the fungus and several studies have begun to elucidate the mechanisms that control the plant processes necessary for fungal colonisation and arbuscule development. In this review, we analyse the mechanisms that allow arbuscule development and the processes necessary for nutrient exchange between the plant and the fungus.

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.

Manipulation of Bryophyte Hosts by Pathogenic and Symbiotic Microbes

The colonization of plant tissues by pathogenic and symbiotic microbes is associated with a strong and directed effort to reprogram host cells in order to permit, promote and sustain microbial growth. In response to colonization, hosts accommodate or sequester invading microbes by activating a set of complex regulatory programs that initiate symbioses or bolster defenses. Extensive research has elucidated a suite of molecular and physiological responses occurring in plant hosts and their microbial partners; however, this information is mostly limited to model systems representing evolutionarily young plant lineages such as angiosperms. The extent to which these processes are conserved across land plants is therefore poorly understood. In this review, we outline key aspects of host reprogramming that occur during plant-microbe interactions in early diverging land plants belonging to the bryophytes (liverworts, hornworts and mosses). We discuss how further knowledge of bryophyte-microbe interactions will advance our understanding of how plants and microbes co-operated and clashed during the conquest of land.

Arbuscular Mycorrhizal Fungal 14-3-3 Proteins Are Involved in Arbuscule Formation and Responses to Abiotic Stresses During AM Symbiosis

Arbuscular mycorrhizal (AM) fungi are soil-borne fungi belonging to the ancient phylum Glomeromycota and are important symbionts of the arbuscular mycorrhiza, enhancing plant nutrient acquisition and resistance to various abiotic stresses. In contrast to their significant physiological implications, the molecular basis involved is poorly understood, largely due to their obligate biotrophism and complicated genetics. Here, we identify and characterize three genes termed Fm201, Ri14-3-3 and RiBMH2 that encode 14-3-3-like proteins in the AM fungi Funneliformis mosseae and Rhizophagus irregularis, respectively. The transcriptional levels of Fm201, Ri14-3-3 and RiBMH2 are strongly induced in the pre-symbiotic and symbiotic phases, including germinating spores, intraradical hyphae- and arbuscules-enriched roots. To functionally characterize the Fm201, Ri14-3-3 and RiBMH2 genes, we took advantage of a yeast heterologous system owing to the lack of AM fungal transformation systems. Our data suggest that all three genes can restore the lethal Saccharomyces cerevisiae bmh1 bmh2 double mutant on galactose-containing media. Importantly, yeast one-hybrid analysis suggests that the transcription factor RiMsn2 is able to recognize the STRE (CCCCT/AGGGG) element present in the promoter region of Fm201 gene. More importantly, Host-Induced Gene Silencing of both Ri14-3-3 and RiBMH2 in Rhizophagus irregularis impairs the arbuscule formation in AM symbiosis and inhibits the expression of symbiotic PT4 and MST2 genes from plant and fungal partners, respectively. We further subjected the AM fungus-Medicago truncatula association system to drought or salinity stress. Accordingly, the expression profiles in both mycorrhizal roots and extraradical hyphae reveal that these three 14-3-3-like genes are involved in response to drought or salinity stress. Collectively, our results provide new insights into molecular functions of the AM fungal 14-3-3 proteins in abiotic stress responses and arbuscule formation during AM symbiosis.

The plasma membrane proteome of Medicago truncatula roots as modified by arbuscular mycorrhizal symbiosis

In arbuscular mycorrhizal (AM) roots, the plasma membrane (PM) of the host plant is involved in all developmental stages of the symbiotic interaction, from initial recognition to intracellular accommodation of intra-radical hyphae and arbuscules. Although the role of the PM as the agent for cellular morphogenesis and nutrient exchange is especially accentuated in endosymbiosis, very little is known regarding the PM protein composition of mycorrhizal roots. To obtain a global overview at the proteome level of the host PM proteins as modified by symbiosis, we performed a comparative protein profiling of PM fractions from Medicago truncatula roots either inoculated or not with the AM fungus Rhizophagus irregularis. PM proteins were isolated from root microsomes using an optimized discontinuous sucrose gradient; their subsequent analysis by liquid chromatography followed by mass spectrometry (MS) identified 674 proteins. Cross-species sequence homology searches combined with MS-based quantification clearly confirmed enrichment in PM-associated proteins and depletion of major microsomal contaminants. Changes in protein amounts between the PM proteomes of mycorrhizal and non-mycorrhizal roots were monitored further by spectral counting. This workflow identified a set of 82 mycorrhiza-responsive proteins that provided insights into the plant PM response to mycorrhizal symbiosis. Among them, the association of one third of the mycorrhiza-responsive proteins with detergent-resistant membranes pointed at partitioning to PM microdomains. The PM-associated proteins responsive to mycorrhization also supported host plant control of sugar uptake to limit fungal colonization, and lipid turnover events in the PM fraction of symbiotic roots. Because of the depletion upon symbiosis of proteins mediating the replacement of phospholipids by phosphorus-free lipids in the plasmalemma, we propose a role of phosphate nutrition in the PM composition of mycorrhizal roots.

Tomato LysM Receptor-Like Kinase SlLYK12 Is Involved in Arbuscular Mycorrhizal Symbiosis

Arbuscular mycorrhiza (AM) is a widespread symbiotic relationship between plants and fungi (Glomeromycota), which improves the supply of water and nutrients to host plants. AM symbiosis is set in motion by fungal chitooligosaccharides and lipochitooligosaccharides, which are perceived by plant-specific LysM-type receptor kinases (LYK). In rice this involves OsCERK1, a LYK also essential for chitin triggered innate immunity. In contrast in legumes, the CERK1 homologous gene experienced duplication events resulting in subfunctionalization. However, it remains unknown whether this subfunctionalization is legume-specific, or has occurred also in other dicot plant species. We identified four CERK1 homologs in tomato (SlLYK1, SlLYK11, SlLYK12, and SlLYK13) and investigated their roles in chitin signaling and AM symbiosis. We found that knockdown of SlLYK12 in tomato significantly reduced AM colonization, whereas chitin-induced responses were unaffected. In contrast, knockdown of SlLYK1 resulted in reduced responses to chitin, but did not alter responses to AM fungi. Moreover, ectopic overexpression of SlLYK1 and SlLYK13 in Nicotiana benthamiana induced cell death, whereas SlLYK12 overexpression did not. Based on our results and comparison with rice OsCERK1, we hypothesize that OsCERK1 orthologs in tomato underwent gene duplication, leading to the subfunctionalization of immunity and symbiosis.

Strigolactone Levels in Dicot Roots Are Determined by an Ancestral Symbiosis-Regulated Clade of the PHYTOENE SYNTHASE Gene Family

Strigolactones (SLs) are apocarotenoid phytohormones synthesized from carotenoid precursors. They are produced most abundantly in roots for exudation into the rhizosphere to cope with mineral nutrient starvation through support of root symbionts. Abscisic acid (ABA) is another apocarotenoid phytohormone synthesized in roots, which is involved in responses to abiotic stress. Typically low carotenoid levels in roots raise the issue of precursor supply for the biosynthesis of these two apocarotenoids in this organ. Increased ABA levels upon abiotic stress in Poaceae roots are known to be supported by a particular isoform of phytoene synthase (PSY), catalyzing the rate-limiting step in carotenogenesis. Here we report on novel PSY3 isogenes from Medicago truncatula (MtPSY3) and Solanum lycopersicum (SlPSY3) strongly expressed exclusively upon root interaction with symbiotic arbuscular mycorrhizal (AM) fungi and moderately in response to phosphate starvation. They belong to a widespread clade of conserved PSYs restricted to dicots (dPSY3) distinct from the Poaceae-PSY3s involved in ABA formation. An ancient origin of dPSY3s and a potential co-evolution with the AM symbiosis is discussed in the context of PSY evolution. Knockdown of MtPSY3 in hairy roots of M. truncatula strongly reduced SL and AM-induced C₁₃ α-ionol/C₁₄ mycorradicin apocarotenoids. Inhibition of the reaction subsequent to phytoene synthesis revealed strongly elevated levels of phytoene indicating induced flux through the carotenoid pathway in roots upon mycorrhization. dPSY3 isogenes are coregulated with upstream isogenes and downstream carotenoid cleavage steps toward SLs (D27, CCD7, CCD8) suggesting a combined carotenoid/apocarotenoid pathway, which provides "just in time"-delivery of precursors for apocarotenoid formation.

Role of the GRAS transcription factor ATA/RAM1 in the transcriptional reprogramming of arbuscular mycorrhiza in Petunia hybrida

BACKGROUND

Development of arbuscular mycorrhiza (AM) requires a fundamental reprogramming of root cells for symbiosis. This involves the induction of hundreds of genes in the host. A recently identified GRAS-type transcription factor in Petunia hybrida, ATA/RAM1, is required for the induction of host genes during AM, and for morphogenesis of the fungal endosymbiont. To better understand the role of RAM1 in symbiosis, we set out to identify all genes that depend on activation by RAM1 in mycorrhizal roots.

RESULTS

We have carried out a transcript profiling experiment by RNAseq of mycorrhizal plants vs. non-mycorrhizal controls in wild type and ram1 mutants. The results show that the expression of early genes required for AM, such as the strigolactone biosynthetic genes and the common symbiosis signalling genes, is independent of RAM1. In contrast, genes that are involved at later stages of symbiosis, for example for nutrient exchange in cortex cells, require RAM1 for induction. RAM1 itself is highly induced in mycorrhizal roots together with many other transcription factors, in particular GRAS proteins.

CONCLUSION

Since RAM1 has previously been shown to be directly activated by the common symbiosis signalling pathway through CYCLOPS, we conclude that it acts as an early transcriptional switch that induces many AM-related genes, among them genes that are essential for the development of arbuscules, such as STR, STR2, RAM2, and PT4, besides hundreds of additional RAM1-dependent genes the role of which in symbiosis remains to be explored. Taken together, these results indicate that the defect in the morphogenesis of the fungal arbuscules in ram1 mutants may be an indirect consequence of functional defects in the host, which interfere with nutrient exchange and possibly other functions on which the fungus depends.

Adapted Biotroph Manipulation of Plant Cell Ploidy

Diverse plant biotrophs that establish a sustained site of nutrient acquisition induce localized host endoreduplication. Endoreduplication is a process by which cells successively replicate their genomes without mitosis, resulting in an increase in nuclear DNA ploidy. Elevated ploidy is associated with enhanced cell size, metabolic capacity, and the capacity to differentiate. Localized host endoreduplication induced by adapted plant biotrophs promotes biotroph colonization, development, and/or proliferation. When induced host endoreduplication is limited, biotroph growth and/or development are compromised. Herein, we examine a diverse set of plant-biotroph interactions to identify (a) common host components manipulated to promote induced host endoreduplication and (b) biotroph effectors that facilitate this induced host process. Shared mechanisms to promote host endoreduplication and development of nutrient exchange/feeding sites include manipulation centered on endocycle entry at the G2-M transition as well as yet undefined roles for differentiation regulators (e.g., CLE peptides) and pectin/cell wall modification.

The rice LysM receptor-like kinase OsCERK1 is required for the perception of short-chain chitin oligomers in arbuscular mycorrhizal signaling

The rice lysin-motif (LysM) receptor-like kinase OsCERK1 is now known to have a dual role in both pathogenic and symbiotic interactions. Following the recent discovery that the Oscerk1 mutant is unable to host arbuscular mycorrhizal (AM) fungi, we have examined whether OsCERK1 is directly involved in the perception of the short-chain chitin oligomers (Myc-COs) identified in AM fungal exudates and shown to activate nuclear calcium (Ca²⁺ ) spiking in the rice root epidermis. An Oscerk1 knockout mutant expressing the cameleon NLS-YC2.60 was used to monitor nuclear Ca²⁺ signaling following root treatment with either crude fungal exudates or purified Myc-COs. Compared with wild-type rice, Ca²⁺ spiking responses to AM fungal elicitation were absent in root atrichoblasts of the Oscerk1 mutant. By contrast, rice lines mutated in OsCEBiP, encoding the LysM receptor-like protein which associates with OsCERK1 to perceive chitin elicitors of the host immune defense pathway, responded positively to Myc-COs. These findings provide direct evidence that the bi-functional OsCERK1 plays a central role in perceiving short-chain Myc-CO signals and activating the downstream conserved symbiotic signal transduction pathway.

A Transcriptional Program for Arbuscule Degeneration during AM Symbiosis Is Regulated by MYB1

During the endosymbiosis formed between plants and arbuscular mycorrhizal (AM) fungi, the root cortical cells are colonized by branched hyphae called arbuscules, which function in nutrient exchange with the plant [1]. Despite their positive function, arbuscules are ephemeral structures, and their development is followed by a degeneration phase, in which the arbuscule and surrounding periarbuscular membrane and matrix gradually disappear from the root cell [2, 3]. Currently, the root cell's role in this process and the underlying regulatory mechanisms are unknown. Here, by using a Medicago truncatula pt4 mutant in which arbuscules degenerate prematurely [4], we identified arbuscule degeneration-associated genes, of which 38% are predicted to encode secreted hydrolases, suggesting a role in disassembly of the arbuscule and interface. Through RNAi and analysis of an insertion mutant, we identified a symbiosis-specific MYB-like transcription factor (MYB1) that suppresses arbuscule degeneration in mtpt4. In myb1, expression of several degeneration-associated genes is reduced. Conversely, in roots constitutively overexpressing MYB1, expression of degeneration-associated genes is increased and subsequent development of symbiosis is impaired. MYB1-regulated gene expression is enhanced by DELLA proteins and is dependent on NSP1 [5], but not NSP2 [6]. Furthermore, MYB1 interacts with DELLA and NSP1. Our data identify a transcriptional program for arbuscule degeneration and reveal that its regulators include MYB1 in association with two transcriptional regulators, NSP1 and DELLA, both of which function in preceding phases of the symbiosis. We propose that the combinatorial use of transcription factors enables the sequential expression of transcriptional programs for arbuscule development and degeneration.

Root microbiota drive direct integration of phosphate stress and immunity

Plants live in biogeochemically diverse soils with diverse microbiota. Plant organs associate intimately with a subset of these microbes, and the structure of the microbial community can be altered by soil nutrient content. Plant-associated microbes can compete with the plant and with each other for nutrients, but may also carry traits that increase the productivity of the plant. It is unknown how the plant immune system coordinates microbial recognition with nutritional cues during microbiome assembly. Here we establish that a genetic network controlling the phosphate stress response influences the structure of the root microbiome community, even under non-stress phosphate conditions. We define a molecular mechanism regulating coordination between nutrition and defence in the presence of a synthetic bacterial community. We further demonstrate that the master transcriptional regulators of phosphate stress response in Arabidopsis thaliana also directly repress defence, consistent with plant prioritization of nutritional stress over defence. Our work will further efforts to define and deploy useful microbes to enhance plant performance.

The Mutualistic Interaction between Plants and Arbuscular Mycorrhizal Fungi

Mycorrhizal fungi belong to several taxa and develop mutualistic symbiotic associations with over 90% of all plant species, from liverworts to angiosperms. While descriptive approaches have dominated the initial studies of these fascinating symbioses, the advent of molecular biology, live cell imaging, and “omics” techniques have provided new and powerful tools to decipher the cellular and molecular mechanisms that rule mutualistic plant-fungus interactions. In this article we focus on the most common mycorrhizal association, arbuscular mycorrhiza (AM), which is formed by a group of soil fungi belonging to Glomeromycota. AM fungi are believed to have assisted the conquest of dry lands by early plants around 450 million years ago and are found today in most land ecosystems. AM fungi have several peculiar biological traits, including obligate biotrophy, intracellular development inside the plant tissues, coenocytic multinucleate hyphae, and spores, as well as unique genetics, such as the putative absence of a sexual cycle, and multiple ecological functions. All of these features make the study of AM fungi as intriguing as it is challenging, and their symbiotic association with most crop plants is currently raising a broad interest in agronomic contexts for the potential use of AM fungi in sustainable production under conditions of low chemical input.

Stress promotes Arabidopsis - Piriformospora indica interaction

The endophytic fungus Piriformospora indica colonizes Arabidopsis thaliana roots and promotes plant performance, growth and resistance/tolerance against abiotic and biotic stress. Here we demonstrate that the benefits for the plant increase when the two partners are co-cultivated under stress (limited access to nutrient, exposure to heavy metals and salt, light and osmotic stress, pathogen infection). Moreover, physical contact between P. indica and Arabidopsis roots is necessary for optimal growth promotion, and chemical communication cannot replace the physical contact. Lower nutrient availability down-regulates and higher nutrient availability up-regulates the plant defense system including the expression of pathogenesis-related genes in roots. High light, osmotic and salt stresses support the beneficial interaction between the plant and the fungus. P. indica reduces stomata closure and H2O2 production after Alternaria brassicae infection in leaves and suppresses the defense-related accumulation of the phytohormone jasmonic acid. Thus, shifting the growth conditions toward a stress promotes the mutualistic interaction, while optimal supply with nutrients or low stress diminishes the benefits for the plant in the symbiosis.

A CCaMK-CYCLOPS-DELLA Complex Activates Transcription of RAM1 to Regulate Arbuscule Branching

Intracellular arbuscular mycorrhiza symbiosis between plants and glomeromycotan fungi leads to formation of highly branched fungal arbuscules that release mineral nutrients to the plant host. Their development is regulated in plants by a mechanistically unresolved interplay between symbiosis, nutrient, and hormone (gibberellin) signaling. Using a positional cloning strategy and a retrotransposon insertion line, we identify two novel alleles of Lotus japonicus REDUCED ARBUSCULAR MYCORRHIZA1 (RAM1) encoding a GRAS protein. We confirm that RAM1 is a central regulator of arbuscule development: arbuscule branching is arrested in L. japonicus ram1 mutants, and ectopic expression of RAM1 activates genes critical for arbuscule development in the absence of fungal symbionts. Epistasis analysis places RAM1 downstream of CCaMK, CYCLOPS, and DELLA because ectopic expression of RAM1 restores arbuscule formation in cyclops mutants and in the presence of suppressive gibberellin. The corresponding proteins form a complex that activates RAM1 expression via binding of CYCLOPS to a cis element in the RAM1 promoter. We thus reveal a transcriptional cascade in arbuscule development that employs the promoter of RAM1 as integrator of symbiotic (transmitted via CCaMK and CYCLOPS) and hormonal (gibberellin) signals.

A Survey of the Gene Repertoire of Gigaspora rosea Unravels Conserved Features among Glomeromycota for Obligate Biotrophy

Arbuscular mycorrhizal (AM) fungi are a diverse group of soil fungi (Glomeromycota) that form the most ancient mutualistic association termed AM symbiosis with a majority of land plants, improving their nutrition uptake and resistance to stresses. In contrast to their great ecological implications, the knowledge of the molecular biological mechanisms involved is still scant, partly due to the limited genomic resources available. Here, we describe the gene repertoire of a new AM fungus Gigaspora rosea (Diversisporales). Among the 86332 non-redundant virtual transcripts assembled, 15346 presented similarities with proteins in the Refseq database and 10175 were assigned with GO terms. KOG and Interpro domain annotations clearly showed an enrichment of genes involved in signal transduction in G. rosea. KEGG pathway analysis indicates that most primary metabolic processes are active in G. rosea. However, as for Rhizophagus irregularis, several metabolic genes were not found, including the fatty acid synthase (FAS) gene. This finding supports the hypothesis that AM fungi depend on the lipids produced by their hosts. Furthermore, the presence of a large number of transporters and 100s of secreted proteins, together with the reduced number of plant cell wall degrading enzymes could be interpreted as an evolutionary adaptation to its mutualistic obligate biotrophy. The detection of meiosis-related genes suggests that G. rosea might use a cryptic sexual process. Lastly, a phylogeny of basal fungi clearly shows Glomeromycota as a sister clade to Mucoromycotina, not only to the Mucorales or Mortierellales. The characterization of the gene repertoire from an AM fungal species belonging to the order of Diversisporales and its comparison with the gene sets of R. irregularis (Glomerales) and Gigaspora margarita (Diversisporales), reveal that AM fungi share several features linked to mutualistic obligate biotrophy. This work contributes to lay the foundation for forthcoming studies into the genomics of Diversisporales, and also illuminates the utility of comparing gene repertoires of species from Diversisporales and other clades of Glomeromycota to gain more insights into the genetics and evolution of this fungal group.

DELLA proteins regulate expression of a subset of AM symbiosis-induced genes in Medicago truncatula

The majority of the vascular flowering plants form symbiotic associations with fungi from the phylum Glomeromycota through which both partners gain access to nutrients, either mineral nutrients in the case of the plant, or carbon, in the case of the fungus. (1) The association develops in the roots and requires substantial remodeling of the root cortical cells where branched fungal hyphae, called arbuscules, are housed in a new membrane-bound apoplastic compartment. (2) Nutrient exchange between the symbionts occurs over this interface and its development and maintenance is critical for symbiosis. Previously, we showed that DELLA proteins, which are well known as repressors of gibberellic acid signaling, also regulate development of AM symbiosis and are necessary to enable arbuscule development. (3) Furthermore, constitutive overexpression of a dominant DELLA protein (della1-Δ18) is sufficient to induce transcripts of several AM symbiosis-induced genes, even in the absence of the fungal symbiont. (4) Here we further extend this approach and identify AM symbiosis genes that respond transcriptionally to constitutive expression of a dominant DELLA protein and also genes that do respond to this treatment. Additionally, we demonstrate that DELLAs interact with REQUIRED FOR ARBUSCULE DEVELOPMENT 1 (RAD1) which further extends our knowledge of GRAS factor complexes that have the potential to regulate gene expression during AM symbiosis.