A dipeptide transporter from the arbuscular mycorrhizal fungus Rhizophagus irregularis is upregulated in the intraradical phase

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.

The Root-Colonizing Endophyte Piriformospora indica Supports Nitrogen-Starved Arabidopsis thaliana Seedlings with Nitrogen Metabolites

The root-colonizing endophytic fungus Piriformospora indica promotes the root and shoot growth of its host plants. We show that the growth promotion of Arabidopsis thaliana leaves is abolished when the seedlings are grown on media with nitrogen (N) limitation. The fungus neither stimulated the total N content nor did it promote 15NO3- uptake from agar plates to the leaves of the host under N-sufficient or N-limiting conditions. However, when the roots were co-cultivated with 15N-labelled P. indica, more labels were detected in the leaves of N-starved host plants but not in plants supplied with sufficient N. Amino acid and primary metabolite profiles, as well as the expression analyses of N metabolite transporter genes suggest that the fungus alleviates the adaptation of its host from the N limitation condition. P. indica alters the expression of transporter genes, which participate in the relocation of NO3-, NH4+ and N metabolites from the roots to the leaves under N limitation. We propose that P. indica participates in the plant's metabolomic adaptation against N limitation by delivering reduced N metabolites to the host, thus alleviating metabolic N starvation responses and reprogramming the expression of N metabolism-related genes.

The Roles of Phosphorus and Nitrogen Nutrient Transporters in the Arbuscular Mycorrhizal Symbiosis

More than 80% of land plant species can form symbioses with arbuscular mycorrhizal (AM) fungi, and nutrient transfer to plants is largely mediated through this partnership. Over the last few years, great progress has been made in deciphering the molecular mechanisms underlying the AM-mediated modulation of nutrient uptake progress, and a growing number of fungal and plant genes responsible for the uptake of nutrients from soil or transfer across the fungal–root interface have been identified. In this review, we outline the current concepts of nutrient exchanges within this symbiosis (mechanisms and regulation) and focus on P and N transfer from the fungal partner to the host plant, with a highlight on a possible interplay between P and N nutrient exchanges. Transporters belonging to the plant or AM fungi can synergistically process the transmembrane transport of soil nutrients to the symbiotic interface for further plant acquisition. Although much progress has been made to elucidate the complex mechanism for the integrated roles of nutrient transfers in AM symbiosis, questions still remain to be answered; for example, P and N transporters are less studied in different species of AM fungi; the involvement of AM fungi in plant N uptake is not as clearly defined as that of P; coordinated utilization of N and P is unknown; transporters of cultivated plants inoculated with AM fungi and transcriptomic and metabolomic networks at both the soil–fungi interface and fungi–plant interface have been insufficiently studied. These findings open new perspectives for fundamental research and application of AM fungi in agriculture.

The potential role of Mucoromycotina 'fine root endophytes' in plant nitrogen nutrition

Mycorrhizal associations between fungi and plant roots have globally significant impacts on nutrient cycling. Mucoromycotina 'fine root endophytes' (MFRE) are a distinct and recently characterised group of mycorrhiza-forming fungi that associate with the roots of a range of host plant species. Given their previous misidentification and assignment as arbuscular mycorrhizal fungi (AMF) of the Glomeromycotina, it is now important to untangle the specific form and function of MFRE symbioses. In particular, relatively little is known about the nature of MFRE colonisation and its role in N uptake and transfer to host plants. Even less is known about the mechanisms by which MFRE access and assimilate N, and how this N is processed and subsequently exchanged with host plants for photosynthates. Here, we summarise and contrast the structures formed by MFRE and arbuscular mycorrhizal fungi in host plants as well as compare the N source preference of each mycorrhizal fungal group with what is currently known for MFRE N uptake. We compare the mechanisms of N assimilation and transfer to host plants utilised by the main groups of mycorrhizal fungi and hypothesise potential mechanisms for MFRE N assimilation and transfer, outlining directions for future research.

Plant nitrogen nutrition: The roles of arbuscular mycorrhizal fungi

Nitrogen (N) is the most abundant mineral nutrient required by plants, and crop productivity depends heavily on N fertilization in many soils. Production and application of N fertilizers consume huge amounts of energy and substantially increase the costs of agricultural production. Excess N compounds released from agricultural systems are also detrimental to the environment. Thus, increasing plant N uptake efficiency is essential for the development of sustainable agriculture. Arbuscular mycorrhizal (AM) fungi are beneficial symbionts of most terrestrial plants that facilitate plant nutrient uptake and increase host resistance to diverse environmental stresses. AM association is an endosymbiotic process that relies on the differentiation of both host plant roots and AM fungi to create novel contact interfaces within the cells of plant roots. AM plants have two pathways for nutrient uptake: either direct uptake via the root hairs and root epidermis, or indirectly through AM fungal hyphae into root cortical cells. Over the last few years, great progress has been made in deciphering the molecular mechanisms underlying the AM-mediated modulation of nutrient uptake processes, and a growing number of fungal and plant genes responsible for the uptake of nutrients from soil or transfer across the fungi-root interface have been identified. Here, we mainly summarize the recent advances in N uptake, assimilation, and translocation in AM symbiosis, and also discuss how N interplays with C and P in modulating AM development, as well as the synergies between AM fungi and soil microbial communities in N uptake.

Genome-Scale Modeling Specifies the Metabolic Capabilities of Rhizophagus irregularis

Rhizophagus irregularis is one of the most extensively studied arbuscular mycorrhizal fungi (AMF) that forms symbioses with and improves the performance of many crops. Lack of transformation protocol for R. irregularis renders it challenging to investigate molecular mechanisms that shape the physiology and interactions of this AMF with plants. Here, we used all published genomics, transcriptomics, and metabolomics resources to gain insights into the metabolic functionalities of R. irregularis by reconstructing its high-quality genome-scale metabolic network that considers enzyme constraints. Extensive validation tests with the enzyme-constrained metabolic model demonstrated that it can be used to (i) accurately predict increased growth of R. irregularis on myristate with minimal medium; (ii) integrate enzyme abundances and carbon source concentrations that yield growth predictions with high and significant Spearman correlation (ρS = 0.74) to measured hyphal dry weight; and (iii) simulate growth rate increases with tighter association of this AMF with the host plant across three fungal structures. Based on the validated model and system-level analyses that integrate data from transcriptomics studies, we predicted that differences in flux distributions between intraradical mycelium and arbuscles are linked to changes in amino acid and cofactor biosynthesis. Therefore, our results demonstrated that the enzyme-constrained metabolic model can be employed to pinpoint mechanisms driving developmental and physiological responses of R. irregularis to different environmental cues. In conclusion, this model can serve as a template for other AMF and paves the way to identify metabolic engineering strategies to modulate fungal metabolic traits that directly affect plant performance.

IMPORTANCE Mounting evidence points to the benefits of the symbiotic interactions between the arbuscular mycorrhiza fungus Rhizophagus irregularis and crops; however, the molecular mechanisms underlying the physiological responses of this fungus to different host plants and environments remain largely unknown. We present a manually curated, enzyme-constrained, genome-scale metabolic model of R. irregularis that can accurately predict experimentally observed phenotypes. We show that this high-quality model provides an entry point into better understanding the metabolic and physiological responses of this fungus to changing environments due to the availability of different nutrients. The model can be used to design metabolic engineering strategies to tailor R. irregularis metabolism toward improving the performance of host plants.

Identification of Effector Metabolites Using Exometabolite Profiling of Diverse Microalgae

Dissolved exometabolites mediate algal interactions in aquatic ecosystems, but microalgal exometabolomes remain understudied. We conducted an untargeted metabolomic analysis of nonpolar exometabolites exuded from four phylogenetically and ecologically diverse eukaryotic microalgal strains grown in the laboratory, freshwater Chlamydomonas reinhardtii, brackish Desmodesmus sp., marine Phaeodactylum tricornutum, and marine Microchloropsis salina, to identify released metabolites based on relative enrichment in the exometabolomes compared to cell pellet metabolomes. Exudates from the different taxa were distinct, but we did not observe clear phylogenetic patterns. We used feature-based molecular networking to explore the identities of these metabolites, revealing several distinct di- and tripeptides secreted by each of the algae, lumichrome, a compound that is known to be involved in plant growth and bacterial quorum sensing, and novel prostaglandin-like compounds. We further investigated the impacts of exogenous additions of eight compounds selected based on exometabolome enrichment on algal growth. Of these compounds, five (lumichrome, 5′-S-methyl-5′-thioadenosine, 17-phenyl trinor prostaglandin A2, dodecanedioic acid, and aleuritic acid) impacted growth in at least one of the algal cultures. Two of these compounds (dodecanedioic acid and aleuritic acid) produced contrasting results, increasing growth in some algae and decreasing growth in others. Together, our results reveal new groups of microalgal exometabolites, some of which could alter algal growth when provided exogenously, suggesting potential roles in allelopathy and algal interactions.

IMPORTANCE Microalgae are responsible for nearly half of primary production on earth and play an important role in global biogeochemical cycling as well as in a range of industrial applications. Algal exometabolites are important mediators of algal-algal and algal-bacterial interactions that ultimately affect algal growth and physiology. In this study, we characterize exometabolomes across marine and freshwater algae to gain insights into the diverse metabolites they release into their environments (“exudates”). We observe that while phylogeny can play a role in exometabolome content, environmental conditions or habitat origin (freshwater versus marine) are also important. We also find that several of these compounds can influence algal growth (as measured by chlorophyll production) when provided exogenously, highlighting the importance of characterization of these novel compounds and their role in microalgal ecophysiology.

Arbuscular mycorrhizal fungi-induced mitigation of heavy metal phytotoxicity in metal contaminated soils: A critical review

The heavy metal pollution is a worldwide problem and has received a serious concern for the ecosystem and human health. In the last decade, remediation of the agricultural polluted soil has attracted great attention. Phytoremediation is one of the technologies that effectively alleviate heavy metal toxicity, however, this technique is limited to many factors contributing to low plant growth rate and nature of metal toxicities. Arbuscular mycorrhizal fungi (AMF) assisted alleviation of heavy metal phytotoxicity is a cost-effective and environment-friendly strategy. AMF have a symbiotic relationship with the host plant. The bidirectional exchange of resources is a hallmark and also a functional necessity in mycorrhizal symbiosis. During the last few years, a significant progress in both physiological and molecular mechanisms regarding roles of AMF in the alleviation of heavy metals (HMs) toxicities in plants, acquisition of nutrients, and improving plant performance under toxic conditions of HMs has been well studied. This review summarized the current knowledge regarding AMF assisted remediation of heavy metals and some of the strategies used by mycorrhizal fungi to cope with stressful environments. Moreover, this review provides the information of both molecular and physiological responses of mycorrhizal plants as well as AMF to heavy metal stress which could be helpful for exploring new insight into the mechanisms of HMs remediation by utilizing AMF.

Relative roles of Arbuscular Mycorrhizae in establishing a correlation between soil properties, carbohydrate utilization and yield in Cicer arietinum L. under As stress

Accumulation of As (metalloid) degrades soil by negatively affecting the activities of soil enzymes, which in turn reduce growth and yield of the inhabiting plant. Arbuscular mycorrhizal (AM) symbiosis can impart metalloid tolerance in plants by secreting glomalin-related soil protein (GRSP) which binds with As or inertly adsorb in the extraradical mycelial surface. However, profitable use of AM requires selection of the most efficient combination of host plant and fungal species. The current study, therefore designed to study the efficacy of 3 a.m. fungal species: Rhizoglomus intraradices (Ri), Funneliformis mosseae (Fm) and Claroideoglomus claroideum (Cc) in imparting arsenate As(V) and arsenite As(III) stress tolerance in Cicer arietinum (chickpea) genotypes (G) - relatively metalloid tolerant- HC 3 and sensitive- C 235. Roots were found to be more severly affected as compared to shoots which resulted into a major decline in uptake of nutrients, chlorophyll concentrations and yield with As(III) inducing more toxic effects than As(V). HC 3 established more effective mycorrhizal symbiosis and was able to extract higher nutrients from the soil than C 235. Ri was most beneficial in improving plant biomass, carbohydrate utilization and productivity followed by Fm and Cc which could be due to its capability to initiate highest percent colonization and least metalloid uptake in roots through higher glomalin production in the soil. Moreover, Ri was highly efficient in improving soil enzymes activities-phosphatases (PHAs), β-glucosidase (BGA) and invertase (INV), thereby, imparting metalloid tolerance in chickpea genotypes. The results suggested use of Ri-chickpea symbiosis as a promising strategy for ameliorating As stress in chickpea.

New insights into HcPTR2A and HcPTR2B, two high-affinity peptide transporters from the ectomycorrhizal model fungus Hebeloma cylindrosporum

While plants mainly rely on the use of inorganic nitrogen sources like ammonium and nitrate, soil-borne microorganisms like the ectomycorrhizal fungus Hebeloma cylindrosporum can also take up soil organic N in the form of amino acids and peptides that they use as nitrogen and carbon sources. Following the previous identification and functional expression in yeast of two PTR-like peptide transporters, the present study details the functions and substrates of HcPTR2A and HcPTR2B by analysing their transport kinetics in Xenopus laevis oocytes. While both transporters mediated high-affinity di- and tripeptide transport, HcPTR2A also showed low-affinity transport of several amino acids-mostly hydrophobic ones with large side chains.

Photosynthetic Traits and Nitrogen Uptake in Crops: Which Is the Role of Arbuscular Mycorrhizal Fungi?

Arbuscular mycorrhizal (AM) fungi are root symbionts that provide mineral nutrients to the host plant in exchange for carbon compounds. AM fungi positively affect several aspects of plant life, improving nutrition and leading to a better growth, stress tolerance, and disease resistance and they interact with most crop plants such as cereals, horticultural species, and fruit trees. For this reason, they receive expanding attention for the potential use in sustainable and climate-smart agriculture context. Although several positive effects have been reported on photosynthetic traits in host plants, showing improved performances under abiotic stresses such as drought, salinity and extreme temperature, the involved mechanisms are still to be fully discovered. In this review, some controversy aspects related to AM symbiosis and photosynthesis performances will be discussed, with a specific focus on nitrogen acquisition-mediated by AM fungi.

Laser Microdissection as a Useful Tool to Study Gene Expression in Plant and Fungal Partners in AM Symbiosis

Laser microdissection (LMD) technology has been widely applied to plant tissues, offering novel information on the role of different cell-type populations during plant-microbe interactions. In this chapter, protocols to apply the LMD approach to study plant and fungal transcript profiles in different cell-type populations from arbuscular mycorrhizal (AM) roots are described in detail, starting from the biological material preparation to gene expression analyses by RT-PCR and RT-qPCR.

Contrasting Nitrogen Fertilisation Rates Alter Mycorrhizal Contribution to Barley Nutrition in a Field Trial

Controlled environment studies show that arbuscular mycorrhizal fungi (AMF) may contribute to plant nitrogen (N) uptake, but the role of these near-ubiquitous symbionts in crop plant N nutrition under natural field conditions remains largely unknown. In a field trial, we tested the effects of N fertilisation and barley (Hordeum vulgare L.) cultivar identity on the contribution of AMF to barley N uptake using 15N tracers added to rhizosphere soil compartments. AMF were shown capable of significantly increasing plant 15N acquisition from root exclusion zones, and this was influenced by nitrogen addition type, N fertiliser application rate and barley cultivar identity. Our data demonstrate a previously overlooked potential route of crop plant N uptake which may be influenced substantially and rapidly in response to shifting agricultural management practices.

Trading on the arbuscular mycorrhiza market: from arbuscules to common mycorrhizal networks

Arbuscular mycorrhiza (AM) symbiosis occurs between obligate biotrophic fungi of the phylum Glomeromycota and most land plants. The exchange of nutrients between host plants and AM fungi (AMF) is presumed to be the main benefit for the two symbiotic partners. In this review article, we outline the current concepts of nutrient exchanges within this symbiosis (mechanisms and regulation). First, we focus on phosphorus and nitrogen transfer from the fungal partner to the host plant, and on the reciprocal transfer of carbon compounds, with a highlight on a possible interplay between nitrogen and phosphorus nutrition during AM symbiosis. We further discuss potential mechanisms of regulation of these nutrient exchanges linked to membrane dynamics. The review finally addresses the common mycorrhizal networks formed AMF, which interconnect plants from similar and/or different species. Finally the best way to integrate this knowledge and the ensuing potential benefits of AM into sustainable agriculture is discussed.

In silico analysis of fungal small RNA accumulation reveals putative plant mRNA targets in the symbiosis between an arbuscular mycorrhizal fungus and its host plant

BACKGROUND

Small RNAs (sRNAs) are short non-coding RNA molecules (20-30 nt) that regulate gene expression at transcriptional or post-transcriptional levels in many eukaryotic organisms, through a mechanism known as RNA interference (RNAi). Recent studies have highlighted that they are also involved in cross-kingdom communication: sRNAs can move across the contact surfaces from "donor" to "receiver" organisms and, once in the host cells of the receiver, they can target specific mRNAs, leading to a modulation of host metabolic pathways and defense responses. Very little is known about RNAi mechanism and sRNAs occurrence in Arbuscular Mycorrhizal Fungi (AMF), an important component of the plant root microbiota that provide several benefits to host plants, such as improved mineral uptake and tolerance to biotic and abiotic stress.

RESULTS

Taking advantage of the available genomic resources for the AMF Rhizophagus irregularis we described its putative RNAi machinery, which is characterized by a single Dicer-like (DCL) gene and an unusual expansion of Argonaute-like (AGO-like) and RNA-dependent RNA polymerase (RdRp) gene families. In silico investigations of previously published transcriptomic data and experimental assays carried out in this work provided evidence of gene expression for most of the identified sequences. Focusing on the symbiosis between R. irregularis and the model plant Medicago truncatula, we characterized the fungal sRNA population, highlighting the occurrence of an active sRNA-generating pathway and the presence of microRNA-like sequences. In silico analyses, supported by host plant degradome data, revealed that several fungal sRNAs have the potential to target M. truncatula transcripts, including some specific mRNA already shown to be modulated in roots upon AMF colonization.

CONCLUSIONS

The identification of RNAi-related genes, together with the characterization of the sRNAs population, suggest that R. irregularis is equipped with a functional sRNA-generating pathway. Moreover, the in silico analysis predicted 237 plant transcripts as putative targets of specific fungal sRNAs suggesting that cross-kingdom post-transcriptional gene silencing may occur during AMF colonization.

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.

Cell-specific expression of plant nutrient transporter genes in orchid mycorrhizae

Orchid mycorrhizal protocorms and roots are heterogeneous structures composed of different plant cell-types, where cells colonized by intracellular fungal coils (the pelotons) are close to non-colonized plant cells. Moreover, the fungal coils undergo rapid turnover inside the colonized cells, so that plant cells containing coils at different developmental stages can be observed in the same tissue section. Here, we have investigated by laser microdissection (LMD) the localization of specific plant gene transcripts in different cell-type populations collected from mycorrhizal protocorms and roots of the Mediterranean orchid Serapias vomeracea colonized by Tulasnella calospora. RNAs extracted from the different cell-type populations have been used to study plant gene expression, focusing on genes potentially involved in N uptake and transport and previously identified as up-regulated in symbiotic protocorms. Results clearly showed that some plant N transporters are differentially expressed in cells containing fungal coils at different developmental stages, as well as in non-colonized cells, and allowed the identification of new functional markers associated to coil-containing cells.

An in vivo whole-plant experimental system for the analysis of gene expression in extraradical mycorrhizal mycelium

Arbuscular mycorrhizal fungi (AMF) establish beneficial mutualistic symbioses with land plants, receiving carbon in exchange for mineral nutrients absorbed by the extraradical mycelium (ERM). With the aim of obtaining in vivo produced ERM for gene expression analyses, a whole-plant bi-dimensional experimental system was devised and tested with three host plants and three fungal symbionts. In such a system, Funneliformis mosseae in symbiosis with Cichorium intybus var. foliosum, Lactuca sativa, and Medicago sativa produced ERM whose lengths ranged from 9.8 ± 0.8 to 20.8 ± 1.2 m per plant. Since ERM produced in symbiosis with C. intybus showed the highest values for the different structural parameters assessed, this host was used to test the whole-plant system with F. mosseae, Rhizoglomus irregulare, and Funneliformis coronatus. The whole-plant system yielded 1-7 mg of ERM fresh biomass per plant per harvest, and continued producing new ERM for 6 months. Variable amounts of high-quality and intact total RNA, ranging from 15 to 65 μg RNA/mg ERM fresh weight, were extracted from the ERM of the three AMF isolates. Ammonium transporter gene expression was successfully determined in the cDNAs obtained from ERM of the three fungal symbionts by RT-qPCR using gene-specific primers designed on available (R. irregulare) and new (F. mosseae and F. coronatus) ammonium transporter gene sequences. The whole-plant experimental system represents a useful research tool for large production and easy collection of ERM for morphological, physiological, and biochemical analyses, suitable for a wide variety of AMF species, for a virtually limitless range of host plants and for studies involving diverse symbiotic interactions.

Fungal and plant gene expression in the Tulasnella calospora-Serapias vomeracea symbiosis provides clues about nitrogen pathways in orchid mycorrhizas

Orchids are highly dependent on their mycorrhizal fungal partners for nutrient supply, especially during early developmental stages. In addition to organic carbon, nitrogen (N) is probably a major nutrient transferred to the plant because orchid tissues are highly N-enriched. We know almost nothing about the N form preferentially transferred to the plant or about the key molecular determinants required for N uptake and transfer. We identified, in the genome of the orchid mycorrhizal fungus Tulasnella calospora, two functional ammonium transporters and several amino acid transporters but found no evidence of a nitrate assimilation system, in agreement with the N preference of the free-living mycelium grown on different N sources. Differential expression in symbiosis of a repertoire of fungal and plant genes involved in the transport and metabolism of N compounds suggested that organic N may be the main form transferred to the orchid host and that ammonium is taken up by the intracellular fungus from the apoplatic symbiotic interface. This is the first study addressing the genetic determinants of N uptake and transport in orchid mycorrhizas, and provides a model for nutrient exchanges at the symbiotic interface, which may guide future experiments.

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.

Take a Trip Through the Plant and Fungal Transportome of Mycorrhiza

Soil nutrient acquisition and exchanges through symbiotic plant-fungus interactions in the rhizosphere are key features for the current agricultural and environmental challenges. Improved crop yield and plant mineral nutrition through a fungal symbiont has been widely described. In return, the host plant supplies carbon substrates to its fungal partner. We review here recent progress on molecular players of membrane transport involved in nutritional exchanges between mycorrhizal plants and fungi. We cover the transportome, from the transport proteins involved in sugar fluxes from plants towards fungi, to the uptake from the soil and exchange of nitrogen, phosphate, potassium, sulfate, and water. Together, these advances in the comprehension of the mycorrhizal transportome will help in developing the future engineering of new agro-ecological systems.

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.

Resolving the 'nitrogen paradox' of arbuscular mycorrhizas: fertilization with organic matter brings considerable benefits for plant nutrition and growth

Arbuscular mycorrhizal fungi (AMF) can transfer nitrogen (N) to host plants, but the ecological relevance is debated, as total plant N and biomass do not generally increase. The extent to which the symbiosis is mutually beneficial is thought to rely on the stoichiometry of N, phosphorus (P) and carbon (C) availability. While inorganic N fertilization has been shown to elicit strong mutualism, characterized by improved plant and fungal growth and mineral nutrition, similar responses following organic N addition are lacking. Using a compartmented microcosm experiment, we determined the significance to a mycorrhizal plant of placing a (15) N-labelled, nitrogen-rich patch of organic matter in a compartment to which only AMF hyphae had access. Control microcosms denied AMF hyphal access to the patch compartment. When permitted access to the patch compartment, the fungus proliferated extensively in the patch and transferred substantial quantities of N to the plant. Moreover, our data demonstrate that allowing hyphal access to an organic matter patch enhanced total plant N and P contents, with a simultaneous and substantial increase in plant biomass. Furthermore, we demonstrate that organic matter fertilization of arbuscular mycorrhizal plants can foster a mutually beneficial symbiosis based on nitrogen transfer, a phenomenon previously thought irrelevant.

Virus-Induced Gene Silencing Using Tobacco Rattle Virus as a Tool to Study the Interaction between Nicotiana attenuata and Rhizophagus irregularis

Most land plants live in a symbiotic association with arbuscular mycorrhizal fungi (AMF) that belong to the phylum Glomeromycota. Although a number of plant genes involved in the plant-AMF interactions have been identified by analyzing mutants, the ability to rapidly manipulate gene expression to study the potential functions of new candidate genes remains unrealized. We analyzed changes in gene expression of wild tobacco roots (Nicotiana attenuata) after infection with mycorrhizal fungi (Rhizophagus irregularis) by serial analysis of gene expression (SuperSAGE) combined with next generation sequencing, and established a virus-induced gene-silencing protocol to study the function of candidate genes in the interaction. From 92,434 SuperSAGE Tag sequences, 32,808 (35%) matched with our in-house Nicotiana attenuata transcriptome database and 3,698 (4%) matched to Rhizophagus genes. In total, 11,194 Tags showed a significant change in expression (p<0.05, >2-fold change) after infection. When comparing the functions of highly up-regulated annotated Tags in this study with those of two previous large-scale gene expression studies, 18 gene functions were found to be up-regulated in all three studies mainly playing roles related to phytohormone metabolism, catabolism and defense. To validate the function of identified candidate genes, we used the technique of virus-induced gene silencing (VIGS) to silence the expression of three putative N. attenuata genes: germin-like protein, indole-3-acetic acid-amido synthetase GH3.9 and, as a proof-of-principle, calcium and calmodulin-dependent protein kinase (CCaMK). The silencing of the three plant genes in roots was successful, but only CCaMK silencing had a significant effect on the interaction with R. irregularis. Interestingly, when a highly activated inoculum was used for plant inoculation, the effect of CCaMK silencing on fungal colonization was masked, probably due to trans-complementation. This study demonstrates that large-scale gene expression studies across different species induce of a core set of genes of similar functions. However, additional factors seem to influence the overall pattern of gene expression, resulting in high variability among independent studies with different hosts. We conclude that VIGS is a powerful tool with which to investigate the function of genes involved in plant-AMF interactions but that inoculum strength can strongly influence the outcome of the interaction.