Dating in the dark: how roots respond to fungal signals to establish arbuscular mycorrhizal symbiosis

Nonbinary fungal signals and calcium-mediated transduction in plant immunity and symbiosis

Chitin oligomers (COs) are among the most common and active fungal elicitors of plant responses. Short-chain COs from symbiotic arbuscular mycorrhizal fungi activate accommodation responses in the host root, while long-chain COs from pathogenic fungi are acknowledged to trigger defence responses. The modulation of intracellular calcium concentration - a common second messenger in a wide variety of plant signal transduction processes - plays a central role in both signalling pathways with distinct signature features. Nevertheless, mounting evidence suggests that plant immunity and symbiosis signalling partially overlap at multiple levels. Here, we elaborate on recent findings on this topic, highlighting the nonbinary nature of chitin-based fungal signals, their perception and their interpretation through Ca2+ -mediated intracellular signals. Based on this, we propose that plant perception of symbiotic and pathogenic fungi is less clear-cut than previously described and involves a more complex scenario in which partially overlapping and blurred signalling mechanisms act upstream of the unambiguous regulation of gene expression driving accommodation or defence responses.

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.

Harnessing root exudates for plant microbiome engineering and stress resistance in plants

A wide range of abiotic and biotic stresses adversely affect plant's growth and production. Under stress, one of the main responses of plants is the modulation of exudates excreted in the rhizosphere, which consequently leads to alterations in the resident microbiota. Thus, the exudates discharged into the rhizospheric environment play a preponderant role in the association and formation of plant-microbe interactions. In this review, we aimed to provide a synthesis of the latest and most pertinent literature on the diverse biochemical and structural compositions of plant root exudates. Also, this work investigates into their multifaceted role in microbial nutrition and intricate signaling processes within the rhizosphere, which includes quorum-sensing molecules. Specifically, it explores the contributions of low molecular weight compounds, such as carbohydrates, phenolics, organic acids, amino acids, and secondary metabolites, as well as the significance of high molecular weight compounds, including proteins and polysaccharides. It also discusses the state-of-the-art omics strategies that unveil the vital role of root exudates in plant-microbiome interactions, including defense against pathogens like nematodes and fungi. We propose multiple challenges and perspectives, including exploiting plant root exudates for host-mediated microbiome engineering. In this discourse, root exudates and their derived interactions with the rhizospheric microbiota should receive greater attention due to their positive influence on plant health and stress mitigation.

Molecular and Systems Biology Approaches for Harnessing the Symbiotic Interaction in Mycorrhizal Symbiosis for Grain and Oil Crop Cultivation

Mycorrhizal symbiosis, the mutually beneficial association between plants and fungi, has gained significant attention in recent years due to its widespread significance in agricultural productivity. Specifically, arbuscular mycorrhizal fungi (AMF) provide a range of benefits to grain and oil crops, including improved nutrient uptake, growth, and resistance to (a)biotic stressors. Harnessing this symbiotic interaction using molecular and systems biology approaches presents promising opportunities for sustainable and economically-viable agricultural practices. Research in this area aims to identify and manipulate specific genes and pathways involved in the symbiotic interaction, leading to improved cereal and oilseed crop yields and nutrient acquisition. This review provides an overview of the research frontier on utilizing molecular and systems biology approaches for harnessing the symbiotic interaction in mycorrhizal symbiosis for grain and oil crop cultivation. Moreover, we address the mechanistic insights and molecular determinants underpinning this exchange. We conclude with an overview of current efforts to harness mycorrhizal diversity to improve cereal and oilseed health through systems biology.

Spatially and temporally distinct Ca2+ changes in Lotus japonicus roots orient fungal-triggered signalling pathways towards symbiosis or immunity

Plants activate an immune or symbiotic response depending on the detection of distinct signals from root-interacting microbes. Both signalling cascades involve Ca2+ as a central mediator of early signal transduction. In this study, we combined aequorin- and cameleon-based methods to dissect the changes in cytosolic and nuclear Ca2+ concentration caused by different chitin-derived fungal elicitors in Lotus japonicus roots. Our quantitative analyses highlighted the dual character of the evoked Ca2+ responses taking advantage of the comparison between different genetic backgrounds: an initial Ca2+ influx, dependent on the LysM receptor CERK6 and independent of the common symbiotic signalling pathway (CSSP), is followed by a second CSSP-dependent and CERK6-independent phase, that corresponds to the well-known perinuclear/nuclear Ca2+ spiking. We show that the expression of immunity marker genes correlates with the amplitude of the first Ca2+ change, depends on elicitor concentration, and is controlled by Ca2+ storage in the vacuole. Our findings provide an insight into the Ca2+-mediated signalling mechanisms discriminating plant immunity- and symbiosis-related pathways in the context of their simultaneous activation by single fungal elicitors.

Comparative RNA sequencing-based transcriptome profiling of ten grapevine rootstocks: shared and specific sets of genes respond to mycorrhizal symbiosis

Arbuscular mycorrhizal symbiosis improves water and nutrient uptake by plants and provides them other ecosystem services. Grapevine is one of the major crops in the world. Vitis vinifera scions generally are grafted onto a variety of rootstocks that confer different levels of resistance against different pests, tolerance to environmental stress, and influence the physiology of the scions. Arbuscular mycorrhizal fungi are involved in the root architecture and in the immune response to soil-borne pathogens. However, the fine-tuned regulation and the transcriptomic plasticity of rootstocks in response to mycorrhization are still unknown. We compared the responses of 10 different grapevine rootstocks to arbuscular mycorrhizal symbiosis (AMS) formed with Rhizophagus irregularis DAOM197198 using RNA sequencing-based transcriptome profiling. We have highlighted a few shared regulation mechanisms, but also specific rootstock responses to R. irregularis colonization. A set of 353 genes was regulated by AMS in all ten rootstocks. We also compared the expression level of this set of genes to more than 2000 transcriptome profiles from various grapevine varieties and tissues to identify a class of transcripts related to mycorrhizal associations in these 10 rootstocks. Then, we compared the response of the 351 genes upregulated by mycorrhiza in grapevine to their Medicago truncatula homologs in response to mycorrhizal colonization based on available transcriptomic studies. More than 97% of the 351 M. truncatula-homologous grapevine genes were expressed in at least one mycorrhizal transcriptomic study, and 64% in every single RNAseq dataset. At the intra-specific level, we described, for the first time, shared and specific grapevine rootstock genes in response to R. irregularis symbiosis. At the inter-specific level, we defined a shared subset of mycorrhiza-responsive genes.

Long-lasting impact of chitooligosaccharide application on strigolactone biosynthesis and fungal accommodation promotes arbuscular mycorrhiza in Medicago truncatula

The establishment of arbuscular mycorrhiza (AM) between plants and Glomeromycotina fungi is preceded by the exchange of chemical signals: fungal released Myc-factors, including chitooligosaccharides (CO) and lipo-chitooligosaccharides (LCO), activate plant symbiotic responses, while root-exuded strigolactones stimulate hyphal branching and boost CO release. Furthermore, fungal signaling reinforcement through CO application was shown to promote AM development in Medicago truncatula, but the cellular and molecular bases of this effect remained unclear. Here, we focused on long-term M. truncatula responses to CO treatment, demonstrating its impact on the transcriptome of both mycorrhizal and nonmycorrhizal roots over several weeks and providing an insight into the mechanistic bases of the CO-dependent promotion of AM colonization. CO treatment caused the long-lasting regulation of strigolactone biosynthesis and fungal accommodation-related genes. This was mirrored by an increase in root didehydro-orobanchol content, and the promotion of accommodation responses to AM fungi in root epidermal cells. Lastly, an advanced downregulation of AM symbiosis marker genes was observed at the latest time point in CO-treated plants, in line with an increased number of senescent arbuscules. Overall, CO treatment triggered molecular, metabolic, and cellular responses underpinning a protracted acceleration of AM development.

From Soil Amendments to Controlling Autophagy: Supporting Plant Metabolism under Conditions of Water Shortage and Salinity

Crop resistance to environmental stress is a major issue. The globally increasing land degradation and desertification enhance the demand on management practices to balance both food and environmental objectives, including strategies that tighten nutrient cycles and maintain yields. Agriculture needs to provide, among other things, future additional ecosystem services, such as water quantity and quality, runoff control, soil fertility maintenance, carbon storage, climate regulation, and biodiversity. Numerous research projects have focused on the food–soil–climate nexus, and results were summarized in several reviews during the last decades. Based on this impressive piece of information, we have selected only a few aspects with the intention of studying plant–soil interactions and methods for optimization. In the short term, the use of soil amendments is currently attracting great interest to cover the current demand in agriculture. We will discuss the impact of biochar at water shortage, and plant growth promoting bacteria (PGPB) at improving nutrient supply to plants. In this review, our focus is on the interplay of both soil amendments on primary reactions of photosynthesis, plant growth conditions, and signaling during adaptation to environmental stress. Moreover, we aim at providing a general overview of how dehydration and salinity affect signaling in cells. With the use of the example of abscisic acid (ABA) and ethylene, we discuss the effects that can be observed when biochar and PGPB are used in the presence of stress. The stress response of plants is a multifactorial trait. Nevertheless, we will show that plants follow a general concept to adapt to unfavorable environmental conditions in the short and long term. However, plant species differ in the upper and lower regulatory limits of gene expression. Therefore, the presented data may help in the identification of traits for future breeding of stress-resistant crops. One target for breeding could be the removal and efficient recycling of damaged as well as needless compounds and structures. Furthermore, in this context, we will show that autophagy can be a useful goal of breeding measures, since the recycling of building blocks helps the cells to overcome a period of imbalanced substrate supply during stress adjustment.

Tandem application of endophytic fungus Serendipita indica and phosphorus synergistically recuperate arsenic induced stress in rice

In the context of eco-sustainable acquisition of food security, arsenic (As) acts as a deterring factor, which easily infiltrates our food chain via plant uptake. Therefore, devising climate-smart strategies becomes exigent for minimizing the imposed risks. Pertinently, Serendipita indica (S. indica) is well reputed for its post-symbiotic stress alleviatory and phyto-promotive potential. Management of phosphorus (P) is acclaimed for mitigating arsenic toxicity in plants by inhibiting the uptake of As molecules due to the competitive cationic exchange in the rhizosphere. The current study was designed to investigate the tandem effects of S. indica and P in combating As toxicity employing two rice genotypes, i.e., Guodao-6 (GD-6; As-sensitive genotype) and Zhongzhe You-1 (ZZY-1; As-tolerant genotype). After successful fungal colonization, alone and combined arsenic (10  μ M L^-1) and phosphorus (50  μ M L^-1) treatments were applied. Results displayed that the recuperating effects of combined S. indica and P treatment were indeed much profound than their alone treatments; however, most of the beneficial influences were harnessed by ZZY-1 in comparison with GD-6. Distinct genotypic differences were observed for antioxidant enzyme activities, which were induced slightly higher in S. indica-colonized ZZY-1 plants, with or without additional P, as compared to GD-6. Ultrastructure images of root and shoot exhibited ravages of As in the form of chloroplasts-, nuclei-and cell wall-damage with enlarged vacuole area, mellowed mostly by the combined treatment of S. indica and P in both genotypes. Gene expression of PHTs family transporters was regulated at different levels in almost all treatments across genotypes. Conclusively, the results of this study validated the promising role of S. indica and additional P in mitigating As stress, albeit corroborated that the extent of relevant benefit exploitation is highly genotype-dependent. Verily, unlocking the potential of nature-friendly solutions will mend the anthropogenic damage already been done to our environment.

A modular microfluidic bioreactor to investigate plant cell-cell interactions

Plants produce a wide variety of secondary metabolites, which often are of interest to pharmaceutical and nutraceutical industry. Plant-cell cultures allow producing these metabolites in a standardised manner, independently from various biotic and abiotic factors difficult to control during conventional cultivation. However, plant-cell fermentation proves to be very difficult, since these chemically complex compounds often result from the interaction of different biosynthetic pathways operating in different cell types. To simulate such interactions in cultured cells is a challenge. Here, we present a microfluidic bioreactor for plant-cell cultivation to mimic the cell-cell interactions occurring in real plant tissues. In a modular set-up of several microfluidic bioreactors, different cell types can connect through a flow that transports signals or metabolites from module to module. The fabrication of the chip includes hot embossing of a polycarbonate housing and subsequent integration of a porous membrane and in-plane tube fittings in a two-step ultrasonic welding process. The resulting microfluidic chip is biocompatible and transparent. Simulation of mass transfer for the nutrient sucrose predicts a sufficient nutrient supply through the membrane. We demonstrate the potential of this chip for plant cell biology in three proof-of-concept applications. First, we use the chip to show that tobacco BY-2 cells in suspension divide depending on a "quorum-sensing factor" secreted by proliferating cells. Second, we show that a combination of two Catharanthus roseus cell strains with complementary metabolic potency allows obtaining vindoline, a precursor of the anti-tumour compound vincristine. Third, we extend the approach to operationalise secretion of phytotoxins by the fungus Neofusicoccum parvum as a step towards systems to screen for interorganismal chemical signalling.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Towards a Systems Biology Approach to Understanding the Lichen Symbiosis: Opportunities and Challenges of Implementing Network Modelling

Lichen associations, a classic model for successful and sustainable interactions between micro-organisms, have been studied for many years. However, there are significant gaps in our understanding about how the lichen symbiosis operates at the molecular level. This review addresses opportunities for expanding current knowledge on signalling and metabolic interplays in the lichen symbiosis using the tools and approaches of systems biology, particularly network modelling. The largely unexplored nature of symbiont recognition and metabolic interdependency in lichens could benefit from applying a holistic approach to understand underlying molecular mechanisms and processes. Together with ‘omics’ approaches, the application of signalling and metabolic network modelling could provide predictive means to gain insights into lichen signalling and metabolic pathways. First, we review the major signalling and recognition modalities in the lichen symbioses studied to date, and then describe how modelling signalling networks could enhance our understanding of symbiont recognition, particularly leveraging omics techniques. Next, we highlight the current state of knowledge on lichen metabolism. We also discuss metabolic network modelling as a tool to simulate flux distribution in lichen metabolic pathways and to analyse the co-dependence between symbionts. This is especially important given the growing number of lichen genomes now available and improved computational tools for reconstructing such models. We highlight the benefits and possible bottlenecks for implementing different types of network models as applied to the study of lichens.

Tissue culture, genetic transformation, interaction with beneficial microbes, and modern bio-imaging techniques in alfalfa research

Current research needs to be more focused on agronomical plants to effectively utilize the knowledge obtained from model plant species. Efforts to improve legumes have long employed common breeding tools. Recently, biotechnological approaches facilitated the development of improved legumes with new traits, allowing them to withstand climatic changes and biotic stress. Owing to its multiple uses and profits, alfalfa (Medicago sativa L.) has become a prominent forage crop worldwide. This review provides a comprehensive research summary of tissue culture-based genetic transformation methods, which could be exploited for the development of transgenic alfalfa with agronomically desirable traits. Moreover, advanced bio-imaging approaches, including cutting-edge microscopy and phenotyping, are outlined here. Finally, characterization and the employment of beneficial microbes should help to produce biotechnologically improved and sustainable alfalfa cultivars.

Similar Arbuscular Mycorrhizal Fungal Communities in 31 Durum Wheat Cultivars (Triticum turgidum L. var. durum) Under Field Conditions in Eastern Canada

Wheat is among the important crops harnessed by humans whose breeding efforts resulted in a diversity of genotypes with contrasting traits. The goal of this study was to determine whether different old and new cultivars of durum wheat (Triticum turgidum L. var. durum) recruit specific arbuscular mycorrhizal (AM) fungal communities from indigenous AM fungal populations of soil under field conditions. A historical set of five landraces and 26 durum wheat cultivars were field cultivated in a humid climate in Eastern Canada, under phosphorus-limiting conditions. To characterize the community of AMF inhabiting bulk soil, rhizosphere, and roots, MiSeq amplicon sequencing targeting the 18S rRNA gene (SSU) was performed on total DNAs using a nested PCR approach. Mycorrhizal colonization was estimated using root staining and microscope observations. A total of 317 amplicon sequence variants (ASVs) were identified as belonging to Glomeromycota. The core AM fungal community (i.e., ASVs present in > 50% of the samples) in the soil, rhizosphere, and root included 29, 30, and 29 ASVs, respectively. ASVs from the genera Funneliformis, Claroideoglomus, and Rhizophagus represented 37%, 18.6%, and 14.7% of the sequences recovered in the rarefied dataset, respectively. The two most abundant ASVs had sequence homology with the 18S sequences from well-identified herbarium cultures of Funneliformis mosseae BEG12 and Rhizophagus irregularis DAOM 197198, while the third most abundant ASV was assigned to the genus Paraglomus. Cultivars showed no significant difference of the percentage of root colonization ranging from 57.8% in Arnautka to 84.0% in AC Navigator. Cultivars were generally associated with similar soil, rhizosphere, and root communities, but the abundance of F. mosseae, R. irregularis, and Claroideoglomus sp. sequences varied in Eurostar, Golden Ball, and Wakooma. Although these results were obtained in one field trial using a non-restricted pool of durum wheat and at the time of sampling, that may have filtered the community in biotopes. The low genetic variation between durum wheat cultivars for the diversity of AM symbiosis at the species level suggests breeding resources need not be committed to leveraging plant selective influence through the use of traditional methods for genotype development.

Exploring the Relationship Among Divergence Time and Coding and Non-coding Elements in the Shaping of Fungal Mitochondrial Genomes

The order Hypocreales (Ascomycota) is composed of ubiquitous and ecologically diverse fungi such as saprobes, biotrophs, and pathogens. Despite their phylogenetic relationship, these species exhibit high variability in biomolecules production, lifestyle, and fitness. The mitochondria play an important role in the fungal biology, providing energy to the cells and regulating diverse processes, such as immune response. In spite of its importance, the mechanisms that shape fungal mitogenomes are still poorly understood. Herein, we investigated the variability and evolution of mitogenomes and its relationship with the divergence time using the order Hypocreales as a study model. We sequenced and annotated for the first time Trichoderma harzianum mitochondrial genome (mtDNA), which was compared to other 34 mtDNAs species that were publicly available. Comparative analysis revealed a substantial structural and size variation on non-coding mtDNA regions, despite the conservation of copy number, length, and structure of protein-coding elements. Interestingly, we observed a highly significant correlation between mitogenome length, and the number and size of non-coding sequences in mitochondrial genome. Among the non-coding elements, group I and II introns and homing endonucleases genes (HEGs) were the main contributors to discrepancies in mitogenomes structure and length. Several intronic sequences displayed sequence similarity among species, and some of them are conserved even at gene position, and were present in the majority of mitogenomes, indicating its origin in a common ancestor. On the other hand, we also identified species-specific introns that advocate for the origin by different mechanisms. Investigation of mitochondrial gene transfer to the nuclear genome revealed that nuclear copies of the nad5 are the most frequent while atp8, atp9, and cox3 could not be identified in any of the nuclear genomes analyzed. Moreover, we also estimated the divergence time of each species and investigated its relationship with coding and non-coding elements as well as with the length of mitogenomes. Altogether, our results demonstrated that introns and HEGs are key elements on mitogenome shaping and its presence on fast-evolving mtDNAs could be mostly explained by its divergence time, although the intron sharing profile suggests the involvement of other mechanisms on the mitochondrial genome evolution, such as horizontal transference.

Identification of the key genes involved in the regulation of symbiotic pathways induced by Metarhizium anisopliae in peanut (Arachis hypogaea) roots

We detected and compared the mRNA and protein expression levels of immunity-associated and symbiosis-associated genes in peanut (Arachis hypogaea) roots inoculated with entomopathogenic fungus M. anisopliae or the phytopathogenic fungus Fusarium oxysporum, by RT-qPCR and parallel reaction monitoring (PRM). The selected genes were mainly associated with plant-fungus interactions, signal transduction, regulation of cell death, nitrogen or iron metabolism, nutrient acquisition or transport, and compound synthesis based on previous transcriptome analysis. The results showed that the host basal defense responses were significantly inhibited by both M. anisopliae and F. oxysporum, which suggests that both fungi actively suppress the host immunity for successful colonization and infection. However, only F. oxysporum induced a strong host hypersensitivity, which indicates that the host is strongly resisting F. oxysporum but potentially allowing M. anisopliae. Additionally, the genes (SYMRK, CaM, CCaMK, FRI2, ABCC2, F6H1, SCT, NRT24 and LTP1) related to symbiosis and growth were distinctively observed with an up-regulated expression following M. anisopliae treatment, which implies that the host was actively initiating the establishment of symbiosis with the fungus. This study revealed a synergistic relationship between host immunosuppression and the promotion of symbiosis during interactions with M. anisopliae. It suggested that M. anisopliae benefited plant for symbiotic relationship, in addition to controlling herbivorous insects as an entomopathogen.

A LysM Receptor Heteromer Mediates Perception of Arbuscular Mycorrhizal Symbiotic Signal in Rice

Symbiotic microorganisms improve nutrient uptake by plants. To initiate mutualistic symbiosis with arbuscular mycorrhizal (AM) fungi, plants perceive Myc factors, including lipochitooligosaccharides (LCOs) and short-chain chitooligosaccharides (CO4/CO5), secreted by AM fungi. However, the molecular mechanism of Myc factor perception remains elusive. In this study, we identified a heteromer of LysM receptor-like kinases consisting of OsMYR1/OsLYK2 and OsCERK1 that mediates the perception of AM fungi in rice. CO4 directly binds to OsMYR1, promoting the dimerization and phosphorylation of this receptor complex. Compared with control plants, Osmyr1 and Oscerk1 mutant rice plants are less sensitive to Myc factors and show decreased AM colonization. We engineered transgenic rice by expressing chimeric receptors that respectively replaced the ectodomains of OsMYR1 and OsCERK1 with those from the homologous Nod factor receptors MtNFP and MtLYK3 of Medicago truncatula. Transgenic plants displayed increased calcium oscillations in response to Nod factors compared with control rice. Our study provides significant mechanistic insights into AM symbiotic signal perception in rice. Expression of chimeric Nod/Myc receptors achieves a potentially important step toward generating cereals that host nitrogen-fixing bacteria.

Trichoderma harzianum favours the access of arbuscular mycorrhizal fungi to non-host Brassicaceae roots and increases plant productivity

The family Brassicaceae includes plants that are non-host for arbuscular mycorrhizal fungi (AMF) such as the model plant Arabidopsis thaliana (arabidopsis) and the economically important crop plant Brassica napus (rapeseed). It is well known that Trichoderma species have the ability to colonize the rhizosphere of Brassicaceae plants, promoting growth and development as well as stimulating systemic defenses. The aim of the present work is to ascertain that Brassicaceae plants increase productivity when AMF and Trichoderma are combinedly applied, and how such an effect can be ruled. This simultaneous application of a Trichoderma harzianum biocontrol strain and an AMF formulation produces a significant increase in the colonization by Trichoderma and the presence of AMF in arabidopsis and rapeseed roots, such colonization accompanied by improved productivity in both Brassicaceae species. Expression profiling of defense-related marker genes suggests that the phytohormone salicylic acid plays a key role in the modulation of the root colonization process when both fungi are jointly applied.

Local endoreduplication as a feature of intracellular fungal accommodation in arbuscular mycorrhizas

The intracellular accommodation of arbuscular mycorrhizal (AM) fungi is a paradigmatic feature of this plant symbiosis that depends on the activation of a dedicated signaling pathway and the extensive reprogramming of host cells, including striking changes in nuclear size and transcriptional activity. By combining targeted sampling of early root colonization sites, detailed confocal imaging, flow cytometry and gene expression analyses, we demonstrate that local, recursive events of endoreduplication are triggered in the Medicago truncatula root cortex during AM colonization. AM colonization induces an increase in ploidy levels and the activation of endocycle specific markers. This response anticipates the progression of fungal colonization and is limited to arbusculated and neighboring cells in the cortical tissue. Furthermore, endoreduplication is not induced in M. truncatula mutants for symbiotic signaling pathway genes. On this basis, we propose endoreduplication as part of the host cell prepenetration responses that anticipate AM fungal accommodation in the root cortex.

Root Exudation of Primary Metabolites: Mechanisms and Their Roles in Plant Responses to Environmental Stimuli

Root exudation is an important process determining plant interactions with the soil environment. Many studies have linked this process to soil nutrient mobilization. Yet, it remains unresolved how exudation is controlled and how exactly and under what circumstances plants benefit from exudation. The majority of root exudates including primary metabolites (sugars, amino acids, and organic acids) are believed to be passively lost from the root and used by rhizosphere-dwelling microbes. In this review, we synthetize recent advances in ecology and plant biology to explain and propose mechanisms by which root exudation of primary metabolites is controlled, and what role their exudation plays in plant nutrient acquisition strategies. Specifically, we propose a novel conceptual framework for root exudates. This framework is built upon two main concepts: (1) root exudation of primary metabolites is driven by diffusion, with plants and microbes both modulating concentration gradients and therefore diffusion rates to soil depending on their nutritional status; (2) exuded metabolite concentrations can be sensed at the root tip and signals are translated to modify root architecture. The flux of primary metabolites through root exudation is mostly located at the root tip, where the lack of cell differentiation favors diffusion of metabolites to the soil. We show examples of how the root tip senses concentration changes of exuded metabolites and translates that into signals to modify root growth. Plants can modify the concentration of metabolites either by controlling source/sink processes or by expressing and regulating efflux carriers, therefore challenging the idea of root exudation as a purely unregulated passive process. Through root exudate flux, plants can locally enhance concentrations of many common metabolites, which can serve as sensors and integrators of the plant nutritional status and of the nutrient availability in the surrounding environment. Plant-associated micro-organisms also constitute a strong sink for plant carbon, thereby increasing concentration gradients of metabolites and affecting root exudation. Understanding the mechanisms of and the effects that environmental stimuli have on the magnitude and type of root exudation will ultimately improve our knowledge of processes determining soil CO₂ emissions, ecosystem functioning, and how to improve the sustainability of agricultural production.

Metabolome changes are induced in the arbuscular mycorrhizal fungus Gigaspora margarita by germination and by its bacterial endosymbiont

Metabolomic profiling is becoming an increasingly important technique in the larger field of systems biology by allowing the simultaneous measurement of thousands of small molecules participating in and resulting from cellular reactions. In this way, metabolomics presents an opportunity to observe the physiological state of a system, which may provide the ability to monitor the whole of cellular metabolism as the technology progresses. The arbuscular mycorrhizal fungus Gigaspora margarita has not previously been explored with regard to metabolite composition. To develop a better understanding of G. margarita and the influences of its endosymbiont Candidatus Glomeribacter gigasporarum, a metabolomic analysis was applied to quiescent and germinated spores with and without endobacteria. Over 100 metabolites were identified and greater than 2600 unique unidentified spectral features were observed. Multivariate analysis of the metabolomes was performed, and a differentiation between all metabolic states of spores and spores hosting the endobacteria was observed. The known metabolites were recruited to many biochemical pathways, with many being involved in maintenance of the antioxidant potential, tyrosine metabolism, and melanin production. Each of the pathways had higher metabolite abundances in the presence of the endosymbiont. These metabolomics data also agree with previously reported transcriptomics results demonstrating the capability of this technique to confirm hypotheses and showing the feasibility of multi-omic approaches for the study of arbuscular mycorrhizal fungi and their endobacterial communities. Challenges still exist in metabolomic analysis, e.g., the identification of compounds is demanding due to incomplete libraries. A metabolomics technique to probe the effects of bacterial endosymbionts on fungal physiology is presented herein, and this method is useful for hypothesis generation as well as testing as noted above.

Non-Mycorrhizal Plants: The Exceptions that Prove the Rule

The widespread symbiotic interaction between plants and arbuscular mycorrhizal (AM) fungi relies on a complex molecular dialog with reciprocal benefits in terms of nutrition, growth, and protection. Approximately 29% of all vascular plant species do not host AM symbiosis, including major crops. Under certain conditions, however, presumed non-host plants can become colonized by AM fungi and develop rudimentary AM (RAM) phenotypes. Here we zoom in on the mustard family (Brassicaceae), which harbors AM hosts, non-hosts, and presumed non-host species such as Arabidopsis thaliana, for which conditional RAM colonization has been described. We advocate that RAM phenotypes and redundant genomic elements of the symbiotic 'toolkit' are missing links that can help to unravel genetic constraints that drive the evolution of symbiotic incompatibility.

Increase in Artemisia annua Plant Biomass Artemisinin Content and Guaiacol Peroxidase Activity Using the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis

The main objective of this study was to investigate Artemisia annua plant property variations in terms of plant biomass, glandular trichome numbers, artemisinin production and Guaiacol peroxidase (GPOX) activity when plants are in mutualism with AMF. According to the results, A. annua mutualism with AMF significantly increased the most important and pharmaceutically relevant factors of fresh and dry plant biomass. This increase, especially in the biomass of plant herba (leaves), was 30% higher during the vegetation period and remained high (29% higher than for control) when plants were harvested at the end of the vegetation period. Similar differences in dry biomass were also detected. Glandular trichomas numbers increased by 40%, and the artemisinin content by 17% under AMF colonization. No effects due to AMF on chlorophyll variations were detected, while GPOX enzyme concentrations increased significantly under AMF colonization. Altogether the Artemisia plant properties with high pharmaceutically importance (fresh and dry biomass of leaves and artemisinin, number of trichomes and the artemisinin content) were significantly improved by AMF, the application in Artemisia cultivation can be an effective and cheap method. The high GPOX activity under AMF colonization indicate an enhanced oxidative stress alleviation, therefore a higher resistance to water deficiency, mechanisms important under climate conditions with low water supply where Artemisia is usually cultivated.

Commonalities and Differences in Controlling Multipartite Intracellular Infections of Legume Roots by Symbiotic Microbes

Legumes have the almost unique ability to establish symbiotic associations with rhizobia and arbuscular mycorrhizal fungi. Forward and reverse genetics have identified a large number of genes that are required for either or both interactions. However, and in sharp contrast to natural soils, these interactions have been almost exclusively investigated under laboratory conditions by using separate inoculation systems, whereas both symbionts are simultaneously present in the field. Considering our recent understanding of the individual symbioses, the community is now promisingly positioned to co-inoculate plants with two or more microbes in order to understand mechanistically how legumes efficiently balance, regulate and potentially separate these symbioses and other endophytic microbes within the same root. Here, we discuss a number of key control layers that should be considered when assessing tri- or multipartite beneficial interactions and that may contribute to colonization patterns in legume roots.

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.

Strigolactone Biosynthesis Genes of Rice are Required for the Punctual Entry of Arbuscular Mycorrhizal Fungi into the Roots

Arbuscular mycorrhiza (AM) is a mutualistic association between most plant species and the ancient fungal phylum Glomeromycota in roots, and it plays a key role in a plant's nutrient uptake from the soil. Roots synthesize strigolactones (SLs), derivatives of carotenoids, and exude them to induce energy metabolism and hyphal branching of AM fungi. Despite the well-documented roles of SLs in the pre-symbiotic phase, little is known about the role of SLs in the process of root colonization. Here we show that the expansion of root colonization is suppressed in the mutants of rice (Oryza sativa) SL biosynthesis genes, carotenoid cleavage dioxygenase D10 and more severely in D17. Interestingly, most of the colonization process is normal, i.e. AM fungal hyphae approach the roots and cling around them, and epidermal penetration, arbuscule size, arbuscule number per hyphopodium and metabolic activity of the intraradical mycelium are not affected in d10 and d17 mutants. In contrast, hyphopodium formation is severely attenuated. Our observations establish the requirement for SL biosynthesis genes for efficient hyphopodium formation, suggesting that SLs are required in this process. Efficient hyphopodium formation is required for the punctual internalization of hyphae into roots and maintaining the expansion of colonization.

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.

How Auxin and Cytokinin Phytohormones Modulate Root Microbe Interactions

A large range of microorganisms can associate with plants, resulting in neutral, friendly or hostile interactions. The ability of plants to recognize compatible and incompatible microorganisms and to limit or promote their colonization is therefore crucial for their survival. Elaborated communication networks determine the degree of association between the host plant and the invading microorganism. Central to these regulations of plant microbe interactions, phytohormones modulate microorganism plant associations and coordinate cellular and metabolic responses associated to the progression of microorganisms across different plant tissues. We review here hormonal regulations, focusing on auxin and cytokinin phytohormones, involved in the interactions between plant roots and soil microorganisms, including bacterial and fungi associations, either beneficial (symbiotic) or detrimental (pathogenic). The aim is to highlight similarities and differences in cytokinin/auxin functions amongst various compatible versus incompatible associations.

RiPEIP1, a gene from the arbuscular mycorrhizal fungus Rhizophagus irregularis, is preferentially expressed in planta and may be involved in root colonization

Transcriptomics and genomics data recently obtained from the arbuscular mycorrhizal (AM) fungus Rhizophagus irregularis have offered new opportunities to decipher the contribution of the fungal partner to the establishment of the symbiotic association. The large number of genes which do not show similarity to known proteins witnesses the uniqueness of this group of plant-associated fungi. In this work, we characterize a gene that was called RiPEIP1 (Preferentially Expressed In Planta). Its expression is strongly induced in the intraradical phase, including arbuscules, and follows the expression profile of the Medicago truncatula phosphate transporter MtPT4, a molecular marker of a functional symbiosis. Indeed, mtpt4 mutant plants, which exhibit low mycorrhizal colonization and an accelerated arbuscule turnover, also show a reduced RiPEIP1 mRNA abundance. To further characterize RiPEIP1, in the absence of genetic transformation protocols for AM fungi, we took advantage of two different fungal heterologous systems. When expressed as a GFP fusion in yeast cells, RiPEIP1 localizes in the endomembrane system, in particular to the endoplasmic reticulum, which is consistent with the in silico prediction of four transmembrane domains. We then generated RiPEIP1-expressing strains of the fungus Oidiodendron maius, ericoid endomycorrhizal fungus for which transformation protocols are available. Roots of Vaccinium myrtillus colonized by RiPEIP1-expressing transgenic strains showed a higher mycorrhization level compared to roots colonized by the O. maius wild-type strain, suggesting that RiPEIP1 may regulate the root colonization process.

Strigolactones: new plant hormones in action

MAIN CONCLUSION

The key step in the mode of action of strigolactones is the enzymatic detachment of the D-ring. The thus formed hydroxy butenolide induces conformational changes of the receptor pocket which trigger a cascade of reactions in the signal transduction. Strigolactones (SLs) constitute a new class of plant hormones which are of increasing importance in plant science. For the last 60 years, they have been known as germination stimulants for parasitic plants. Recently, several new bio-properties of SLs have been discovered such as the branching factor for arbuscular mycorrhizal fungi, regulation of plant architecture (inhibition of bud outgrowth and of shoot branching) and the response to abiotic factors, etc. To broaden horizons and encourage new ideas for identifying and synthesising new and structurally simple SLs, this review is focused on molecular aspects of this new class of plant hormones. Special attention has been given to structural features, the mode of action of these phytohormones in various biological actions, the design of SL analogs and their applications.

Strigolactones: new plant hormones in action

The key step in the mode of action of strigolactones is the enzymatic detachment of the D-ring. The thus formed hydroxy butenolide induces conformational changes of the receptor pocket which trigger a cascade of reactions in the signal transduction. Strigolactones (SLs) constitute a new class of plant hormones which are of increasing importance in plant science. For the last 60 years, they have been known as germination stimulants for parasitic plants. Recently, several new bio-properties of SLs have been discovered such as the branching factor for arbuscular mycorrhizal fungi, regulation of plant architecture (inhibition of bud outgrowth and of shoot branching) and the response to abiotic factors, etc. To broaden horizons and encourage new ideas for identifying and synthesising new and structurally simple SLs, this review is focused on molecular aspects of this new class of plant hormones. Special attention has been given to structural features, the mode of action of these phytohormones in various biological actions, the design of SL analogs and their applications.

Polymicrobial Multi-functional Approach for Enhancement of Crop Productivity

There is an increasing global need for enhancing the food production to meet the needs of the fast-growing human population. Traditional approach to increasing agricultural productivity through high inputs of chemical nitrogen and phosphate fertilizers and pesticides is not sustainable because of high costs and concerns about global warming, environmental pollution, and safety concerns. Therefore, the use of naturally occurring soil microbes for increasing productivity of food crops is an attractive eco-friendly, cost-effective, and sustainable alternative to the use of chemical fertilizers and pesticides. There is a vast body of published literature on microbial symbiotic and nonsymbiotic nitrogen fixation, multiple beneficial mechanisms used by plant growth-promoting rhizobacteria (PGPR), the nature and significance of mycorrhiza-plant symbiosis, and the growing technology on production of efficacious microbial inoculants. These areas are briefly reviewed here. The construction of an inoculant with a consortium of microbes with multiple beneficial functions such as N(2) fixation, biocontrol, phosphate solubilization, and other plant growth-promoting properties is a positive new development in this area in that a single inoculant can be used effectively for increasing the productivity of a broad spectrum of crops including legumes, cereals, vegetables, and grasses. Such a polymicrobial inoculant containing several microorganisms for each major function involved in promoting the plant growth and productivity gives it greater stability and wider applications for a range of major crops. Intensifying research in this area leading to further advances in our understanding of biochemical/molecular mechanisms involved in plant-microbe-soil interactions coupled with rapid advances in the genomics-proteomics of beneficial microbes should lead to the design and development of inoculants with greater efficacy for increasing the productivity of a wide range of crops.

Integrated multi-omics analysis supports role of lysophosphatidylcholine and related glycerophospholipids in the Lotus japonicus-Glomus intraradices mycorrhizal symbiosis

Interaction of plant roots with arbuscular mycorrhizal fungi (AMF) is a complex trait resulting in cooperative interactions among the two symbionts including bidirectional exchange of resources. To study arbuscular mycorrhizal symbiosis (AMS) trait variation in the model plant Lotus japonicus, we performed an integrated multi-omics analysis with a focus on plant and fungal phospholipid (PL) metabolism and biological significance of lysophosphatidylcholine (LPC). Our results support the role of LPC as a bioactive compound eliciting cellular and molecular response mechanisms in Lotus. Evidence is provided for large interspecific chemical diversity of LPC species among mycorrhizae with related AMF species. Lipid, gene expression and elemental profiling emphasize the Lotus-Glomus intraradices interaction as distinct from other arbuscular mycorrhizal (AM) interactions. In G. intraradices, genes involved in fatty acid (FA) elongation and biosynthesis of unsaturated FAs were enhanced, while in Lotus, FA synthesis genes were up-regulated during AMS. Furthermore, FAS protein localization to mitochondria suggests FA biosynthesis and elongation may also occur in AMF. Our results suggest the existence of interspecific partitioning of PL resources for generation of LPC and novel candidate bioactive PLs in the Lotus-G. intraradices symbiosis. Moreover, the data advocate research with phylogenetically diverse Glomeromycota species for a broader understanding of the molecular underpinnings of AMS.

Does a Common Pathway Transduce Symbiotic Signals in Plant-Microbe Interactions?

Recent years have witnessed major advances in our knowledge of plant mutualistic symbioses such as the rhizobium-legume symbiosis (RLS) and arbuscular mycorrhizas (AM). Some of these findings caused the revision of longstanding hypotheses, but one of the most solid theories is that a conserved set of plant proteins rules the transduction of symbiotic signals from beneficial glomeromycetes and rhizobia in a so-called common symbiotic pathway (CSP). Nevertheless, the picture still misses several elements, and a few crucial points remain unclear. How does one common pathway discriminate between - at least - two symbionts? Can we exclude that microbes other than AM fungi and rhizobia also use this pathway to communicate with their host plants? We here discuss the possibility that our current view is biased by a long-lasting focus on legumes, whose ability to develop both AM and RLS is an exception among plants and a recent innovation in their evolution; investigations in non-legumes are starting to place legume symbiotic signaling in a broader perspective. Furthermore, recent studies suggest that CSP proteins act in a wider scenario of symbiotic and non-symbiotic signaling. Overall, evidence is accumulating in favor of distinct activities for CSP proteins in AM and RLS, depending on the molecular and cellular context where they act.

Effect of volatiles versus exudates released by germinating spores of Gigaspora margarita on lateral root formation

Arbuscular mycorrhizal (AM) fungi influence the root system architecture of their hosts; however, the underlying mechanisms have not been fully elucidated. Ectomycorrhizal fungi influence root architecture via volatiles. To determine whether volatiles also play a role in root system changes in response to AM fungi, spores of the AM fungus Gigaspora margarita were inoculated on the same plate as either wild type (WT) Lotus japonicus, the L. japonicus mutant Ljcastor (which lacks the symbiotic cation channel CASTOR, which is required for inducing nuclear calcium spiking, which is necessary for symbiotic partner recognition), or Arabidopsis thaliana, separated by cellophane membranes (fungal exudates experiment), or on different media but with a shared head space (fungal volatiles experiment). Root development was monitored over time. Both germinating spore exudates (GSEs) and geminated-spore-emitted volatile organic compounds (GVCs) significantly promoted lateral root formation (LRF) in WT L. japonicus. LRF in Ljcastor was significantly enhanced in the presence of GVCs. GVCs stimulated LRF in A. thaliana, whereas GSEs showed an inhibitory effect. The expression profile of the genes involved in mycorrhizal establishment and root development were investigated using quantitative reverse transcription-PCR analysis. Only the expression of the LjCCD7 gene, an important component of the strigolactone synthesis pathway, was differentially expressed following exposure to GVCs. We conclude that volatile organic compounds released by the germinating AM fungal spores may stimulate LRF in a symbiosis signaling pathway (SYM)- and host-independent way, whereas GSEs stimulate LRF in a SYM- and host-dependent way.

Pre-announcement of symbiotic guests: transcriptional reprogramming by mycorrhizal lipochitooligosaccharides shows a strict co-dependency on the GRAS transcription factors NSP1 and RAM1

BACKGROUND

More than 80 % of all terrestrial plant species establish an arbuscular mycorrhiza (AM) symbiosis with Glomeromycota fungi. This plant-microbe interaction primarily improves phosphate uptake, but also supports nitrogen, mineral, and water aquisition. During the pre-contact stage, the AM symbiosis is controled by an exchange of diffusible factors from either partner. Amongst others, fungal signals were identified as a mix of sulfated and non-sulfated lipochitooligosaccharides (LCOs), being structurally related to rhizobial nodulation (Nod)-factor LCOs that in legumes induce the formation of nitrogen-fixing root nodules. LCO signals are transduced via a common symbiotic signaling pathway (CSSP) that activates a group of GRAS transcription factors (TFs). Using complex gene expression fingerprints as molecular phenotypes, this study primarily intended to shed light on the importance of the GRAS TFs NSP1 and RAM1 for LCO-activated gene expression during pre-symbiotic signaling.

RESULTS

We investigated the genome-wide transcriptional responses in 5 days old primary roots of the Medicago truncatula wild type and four symbiotic mutants to a 6 h challenge with LCO signals supplied at 10(-7/-8) M. We were able to show that during the pre-symbiotic stage, sulfated Myc-, non-sulfated Myc-, and Nod-LCO-activated gene expression almost exclusively depends on the LysM receptor kinase NFP and is largely controled by the CSSP, although responses independent of this pathway exist. Our results show that downstream of the CSSP, gene expression activation by Myc-LCOs supplied at 10(-7/-8) M strictly required both the GRAS transcription factors RAM1 and NSP1, whereas those genes either co- or specifically activated by Nod-LCOs displayed a preferential NSP1-dependency. RAM1, a central regulator of root colonization by AM fungi, controled genes activated by non-sulfated Myc-LCOs during the pre-symbiotic stage that are also up-regulated in areas with early physical contact, e.g. hyphopodia and infecting hyphae; linking responses to externally applied LCOs with early root colonization.

CONCLUSIONS

Since both RAM1 and NSP1 were essential for the pre-symbiotic transcriptional reprogramming by Myc-LCOs, we propose that downstream of the CSSP, these GRAS transcription factors act synergistically in the transduction of those diffusible signals that pre-announce the presence of symbiotic fungi.

Combined genetic and transcriptomic analysis reveals three major signalling pathways activated by Myc-LCOs in Medicago truncatula

Myc-LCOs are newly identified symbiotic signals produced by arbuscular mycorrhizal (AM) fungi. Like rhizobial Nod factors, they are lipo-chitooligosaccharides that activate the common symbiotic signalling pathway (CSSP) in plants. To increase our limited understanding of the roles of Myc-LCOs we aimed to analyse Myc-LCO-induced transcriptional changes and their genetic control. Whole genome RNA sequencing (RNA-seq) was performed on roots of Medicago truncatula wild-type plants, and dmi3 and nsp1 symbiotic mutants affected in nodulation and mycorrhizal signalling. Plants were treated separately with the two major types of Myc-LCOs, sulphated and nonsulphated. Generalized linear model analysis identified 2201 differentially expressed genes and classified them according to genotype and/or treatment effects. Three genetic pathways for Myc-LCO-regulation of transcriptomic reprogramming were highlighted: DMI3- and NSP1-dependent; DMI3-dependent and NSP1-independent; and DMI3- and NSP1-independent. Comprehensive analysis revealed overlaps with previous AM studies, and highlighted certain functions, especially signalling components and transcription factors. These data provide new insights into mycorrhizal signalling mechanisms, supporting a role for NSP1, and specialisation for NSP1-dependent and -independent pathways downstream of DMI3. Our data also indicate significant Myc-LCO-activated signalling upstream of DMI3 and/or parallel to the CSSP and some constitutive activity of the CSSP.

Host and non-host roots in rice: cellular and molecular approaches reveal differential responses to arbuscular mycorrhizal fungi

Oryza sativa, a model plant for Arbuscular Mycorrhizal (AM) symbiosis, has both host and non-host roots. Large lateral (LLR) and fine lateral (FLR) roots display opposite responses: LLR support AM colonization, but FLR do not. Our research aimed to study the molecular, morphological and physiological aspects related to the non-host behavior of FLR. RNA-seq analysis revealed that LLR and FLR displayed divergent expression profiles, including changes in many metabolic pathways. Compared with LLR, FLR showed down-regulation of genes instrumental for AM establishment and gibberellin signaling, and a higher expression of nutrient transporters. Consistent with the transcriptomic data, FLR had higher phosphorus content. Light and electron microscopy demonstrated that, surprisingly, in the Selenio cultivar, FLR have a two-layered cortex, which is theoretically compatible with AM colonization. According to RNA-seq, a gibberellin inhibitor treatment increased anticlinal divisions leading to a higher number of cortex cells in FLR. We propose that some of the differentially regulated genes that lead to the anatomical and physiological properties of the two root types also function as genetic factors regulating fungal colonization. The rice root apparatus offers a unique tool to study AM symbiosis, allowing direct comparisons of host and non-host roots in the same individual plant.

Role of gibberellins during arbuscular mycorrhizal formation in tomato: new insights revealed by endogenous quantification and genetic analysis of their metabolism in mycorrhizal roots

Gibberellins (GAs) are key regulators of plant growth and development and recent studies suggest also a role during arbuscular mycorrhizal (AM) formation. Here, complementary approaches have been used to obtain a clearer picture that correlates AM fungal development inside roots with GA metabolism. An extensive analysis of genes associated with GA metabolism as well as a quantification of GA content in roots was made. Application of GA3 and its biosynthesis inhibitor prohexadione calcium (PrCa) combined with a GA-constitutive response mutant (procera) were used to determine whether fungal colonization is altered by the level of these hormones or by changes in the GA-signaling pathway. The increased levels of specific GAs from the 13-hydroxylation pathway in mycorrhizal roots correlate closely with the increased expression of genes coding enzymes from the GA biosynthetic trail. The imbalance of GAs in tomato roots caused by exogenous applications of GA3 or PrCa affects arbuscules in both negative and positive ways, respectively. In addition, procera plants were adversely affected by the mycorrhization process. Our findings demonstrate that an imbalance in favor of an increased amount of GAs negatively affects the frequency of mycorrhization and particularly the arbuscular abundance in tomato mycorrhizal roots and the results point out that AM formation is associated with a change in the 13-hydroxylation pathway of GAs.

Discoveries and advances in plant and animal genomics

Plant and animal genomics is a broad area of research with respect to the biological issues covered because it continues to deal with the structure and function of genetic material underpinning all organisms. This mini-review utilizes the plenary lectures from the Plant and Animal Genome Conference as a basis for summarizing the trends in the genome-level studies of organisms.

Inter-organismal signaling and management of the phytomicrobiome

The organisms of the phytomicrobiome use signal compounds to regulate aspects of each other's behavior. Legumes use signals (flavonoids) to regulate rhizobial nod gene expression during establishment of the legume-rhizobia N2-fixation symbiosis. Lipochitooligosaccharides (LCOs) produced by rhizobia act as return signals to the host plant and are recognized by specific lysine motif receptor like kinases, which triggers a signal cascade leading to nodulation of legume roots. LCOs also enhance plant growth, particularly when plants are stressed. Chitooligosaccharides activate plant immune responses, providing enhanced resistance against diseases. Co-inoculation of rhizobia with other plant growth promoting rhizobacteria (PGPR) can improve nodulation and crop growth. PGPR also alleviate plant stress by secreting signal compounds including phytohormones and antibiotics. Thuricin 17, a small bacteriocin produced by a phytomicrobiome member promotes plant growth. Lumichrome synthesized by soil rhizobacteria function as stress-sensing cues. Inter-organismal signaling can be used to manage/engineer the phytomicrobiome to enhance crop productivity, particularly in the face of stress. Stressful conditions are likely to become more frequent and more severe because of climate change.

Through the doors of perception to function in arbuscular mycorrhizal symbioses

The formation of an arbuscular mycorrhizal (AM) symbiosis is initiated by the bidirectional exchange of diffusible molecules. While strigolactone hormones, secreted from plant roots,stimulate hyphal branching and fungal metabolism, fungal short-chain chitin oligomers as well assulfated and nonsulfated lipochitooligosaccharides (s/nsMyc-LCOs) elicit pre-symbiosis responses in the host. Fungal LCO signals are structurally related to rhizobial Nod-factor LCOs. Genome-wide expression studies demonstrated that defined sets of genes were induced by Nod-, sMyc- and nsMyc-LCOs, indicating LCO-specific perception in the pre-symbiosis phase. During hyphopodium formation and the subsequent root colonization, cross-talk between plant roots and AM fungi also involves phytohormones. Notably, gibberellins control arbuscule formation via DELLA proteins, which themselves serve as positive regulators of arbuscule formation. The establishment of arbuscules is accompanied by a substantial transcriptional and post-transcriptional reprogramming of host roots, ultimately defining the unique protein composition of arbuscule-containing cells. Based on cellular expression profiles, key check points of AM development as well as candidate genes encoding transcriptional regulators and regulatory microRNAs were identified. Detailed functional analyses of promoters specified short motifs sufficient for cell-autonomous gene regulation in cells harboring arbuscules, and suggested simultaneous, multi-level regulation of the mycorrhizal phosphate uptake pathway by integrating AM symbiosis and phosphate starvation response signaling.

Reprogramming of plant cells by filamentous plant-colonizing microbes

Although phylogenetically unrelated, filamentous oomycetes and fungi establish similar structures to colonize plants and they represent economically the most important microbial threat to crop production. In mutualistic interactions established by root-colonizing fungi, clear differences to pathogens can be seen, but there is mounting evidence that their infection strategies and molecular interactions have certain common features. To infect the host, fungi and oomycetes employ similar strategies to circumvent plant innate immunity. This process involves the suppression of basal defence responses which are triggered by the perception of conserved molecular patterns. To establish biotrophy, effector proteins are secreted from mutualistic and pathogenic microbes to the host tissue, where they play central roles in the modulation of host immunity and metabolic reprogramming of colonized host tissues. This review article discusses key effector mechanisms of filamentous pathogens and mutualists, how they modulate their host targets and the fundamental differences or parallels between these different interactions. The orchestration of effector actions during plant infection and the importance of their localization within host tissues are also discussed.

Breaking down walls to live in harmony

Some of the proteins and enzymes that allow bacteria to enter living fungal cells and cause rice seedling blight have been identified.

Phytohormone signaling in arbuscular mycorhiza development

To establish arbuscular mycorhiza (AM) symbiosis glomeromycotan fungi colonize the interior of roots. This process is associated with developmental changes of root cells as well as fungal hyphae. The formation of fungal colonization-structures and the extent of root colonization are largely under plant control, depending on environmental conditions and the resulting physiological state of the host. Phytohormone signaling pathways are currently emerging as important regulators of AM development. Root exuded strigolactones activate AM fungi before colonization and a host strigolactone receptor component is required for AM development. Auxin quantitatively influences AM colonization and might perform an additional cell-autonomous function in the promotion of arbuscule development. Gibberellin signaling inhibits AM and conversely DELLA proteins are required for AM formation. Given the importance of phytohormone signaling in plant developmental responses to the environment it can be predicted that elucidating how phytohormones regulate AM development will provide a lead into understanding how plants orchestrate AM symbiosis with their physiological needs under changing environmental conditions.

Broad compatibility in fungal root symbioses

Plants associate with a wide range of beneficial fungi in their roots which facilitate plant mineral nutrient uptake in exchange for carbohydrates and other organic metabolites. These associations play a key role in shaping terrestrial ecosystems and are widely believed to have promoted the evolution of land plants. To establish compatibility with their host, root-associated fungi have evolved diverse colonization strategies with distinct morphological, functional and genomic specializations as well as different degrees of interdependence. They include obligate biotrophic arbuscular mycorrhizal (AM), and facultative biotrophic ectomycorrhizal (ECM) interactions but are not restricted to these well-characterized symbioses. There is growing evidence that root endophytic associations, which due to their inconspicuous nature have been often overlooked, can be of mutualistic nature and represent important players in natural and managed environments. Recent research into the biology and genomics of root associations revealed fascinating insight into the phenotypic and trophic plasticity of these fungi and underlined genomic traits associated with biotrophy and saprotrophy. In this review we will consider the commonalities and differences of AM and ECM associations and contrast them with root endophytes.

The intracellular delivery of TAT-aequorin reveals calcium-mediated sensing of environmental and symbiotic signals by the arbuscular mycorrhizal fungus Gigaspora margarita

Arbuscular mycorrhiza (AM) is an ecologically relevant symbiosis between most land plants and Glomeromycota fungi. The peculiar traits of AM fungi have so far limited traditional approaches such as genetic transformation. The aim of this work was to investigate whether the protein transduction domain of the HIV-1 transactivator of transcription (TAT) protein, previously shown to act as a potent nanocarrier for macromolecule delivery in both animal and plant cells, may translocate protein cargoes into AM fungi. We evaluated the internalization into germinated spores of Gigaspora margarita of two recombinant TAT fusion proteins consisting of either a fluorescent (GFP) or a luminescent (aequorin) reporter linked to the TAT peptide. Both TAT-fused proteins were found to enter AM fungal mycelia after a short incubation period (5-10 min). Ca2+ measurements in G. margarita mycelia pre-incubated with TAT-aequorin demonstrated the occurrence of changes in the intracellular free Ca2+ concentration in response to relevant stimuli, such as touch, cold, salinity, and strigolactones, symbiosis-related plant signals. These data indicate that the cell-penetrating properties of the TAT peptide can be used as an effective strategy for intracellularly delivering proteins of interest and shed new light on Ca2+ homeostasis and signalling in AM fungi.

Specificity of plant-microbe interactions in the tree mycorrhizosphere biome and consequences for soil C cycling

Mycorrhizal associations are ubiquitous and form a substantial component of the microbial biomass in forest ecosystems and fluxes of C to these belowground organisms account for a substantial portion of carbon assimilated by forest vegetation. Climate change has been predicted to alter belowground plant-allocated C which may cause compositional shifts in soil microbial communities, and it has been hypothesized that this community change will influence C mitigation in forest ecosystems. Some 10,000 species of ectomycorrhizal fungi are currently recognized, some of which are host specific and will only associate with a single tree species, for example, Suillus grevillei with larch. Mycorrhizae are a strong sink for plant C, differences in mycorrhizal anatomy, particularly the presence and extent of emanating hyphae, can affect the amount of plant C allocated to these assemblages. Mycorrhizal morphology affects not only spatial distribution of C in forests, but also differences in the longevity of these diverse structures may have important consequences for C sequestration in soil. Mycorrhizal growth form has been used to group fungi into distinctive functional groups that vary qualitatively and spatially in their foraging and nutrient acquiring potential. Through new genomic techniques we are beginning to understand the mechanisms involved in the specificity and selection of ectomycorrhizal associations though much less is known about arbuscular mycorrhizal associations. In this review we examine evidence for tree species- mycorrhizal specificity, and the mechanisms involved (e.g., signal compounds). We also explore what is known about the effects of these associations and interactions with other soil organisms on the quality and quantity of C flow into the mycorrhizosphere (the area under the influence of mycorrhizal root tips), including spatial and seasonal variations. The enormity of the mycorrhizosphere biome in forests and its potential to sequester substantial C belowground highlights the vital importance of increasing our knowledge of the dynamics of the different mycorrhizal functional groups in diverse forests.

A H+-ATPase That Energizes Nutrient Uptake during Mycorrhizal Symbioses in Rice and Medicago truncatula

Most plant species form symbioses with arbuscular mycorrhizal (AM) fungi, which facilitate the uptake of mineral nutrients such as phosphate from the soil. Several transporters, particularly proton-coupled phosphate transporters, have been identified on both the plant and fungal membranes and contribute to delivering phosphate from fungi to plants. The mechanism of nutrient exchange has been studied in plants during mycorrhizal colonization, but the source of the electrochemical proton gradient that drives nutrient exchange is not known. Here, we show that plasma membrane H+-ATPases that are specifically induced in arbuscule-containing cells are required for enhanced proton pumping activity in membrane vesicles from AM-colonized roots of rice (Oryza sativa) and Medicago truncatula. Mutation of the H+-ATPases reduced arbuscule size and impaired nutrient uptake by the host plant through the mycorrhizal symbiosis. Overexpression of the H+-ATPase Os-HA1 increased both phosphate uptake and the plasma membrane potential, suggesting that this H+-ATPase plays a key role in energizing the periarbuscular membrane, thereby facilitating nutrient exchange in arbusculated plant cells.