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Contract DE-AC02-05CH11231 - Laboratory of Excellence ARBRE (ANR-11- LABX-0002-01), Region Lorraine, European Regional Development Fund and Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forest University; International audience; As members of the plant microbiota, arbuscular mycorrhizal fungi (AMF, Glomeromycotina) symbiotically colonize plant roots. AMF also possess their own microbiota, hosting some uncultivable endobacteria. Ongoing research has revealed the genetics underlying plant responses to colonization by AMF, but the fungal side of the relationship remains in the dark. Here, we sequenced the genome of Gigaspora margarita, a member of the Gigasporaceae in an early diverging group of the Glomeromycotina. In contrast to other AMF, G. margarita may host distinct endobacterial populations and possesses the largest fungal genome so far annotated (773.104 Mbp), with more than 64% transposable elements. Other unique traits of the G. margarita genome include the expansion of genes for inorganic phosphate metabolism, the presence of genes for production of secondary metabolites and a considerable number of potential horizontal gene transfer events. The sequencing of G. margarita genome reveals the importance of its immune system, shedding light on the evolutionary pathways that allowed early diverging fungi to interact with both plants and bacteria.

The investigation of the adaptive strategies of wild plant species to extreme environments is a challenging issue, which favors the identification of new traits for plant resilience. We investigated different traits which characterize the root-soil interaction of Parietaria judaica, a wild plant species commonly known as “Pellitory-of-the-wall”. P. judaica adopts the acidification-reduction strategy (Strategy I) for iron (Fe) acquisition from soil, and it can complete its life cycle in highly calcareous environments without any symptoms of chlorosis. In a field-to-lab approach, the microbiome associated with P. judaica roots was analyzed in spontaneous plants harvested from an urban environment consisting in an extremely calcareous habitat. Also, the phenolics and carboxylates content and root plasticity and exudation were analyzed in P. judaica plants grown under three different controlled conditions mimicking the effect of calcareous environments on Fe availability: results show that P. judaica differentially modulates root plasticity under different Fe availability-impaired conditions, and that it induces, to a high extent, the exudation of caffeoylquinic acid derivatives under calcareous conditions, positively impacting Fe solubility.

RNA-seq is a powerful method for transcriptome profiling that allows the detection of total RNA present in a single cell, tissues, or organs. mRNA-seq is focused on protein-coding RNAs, and results in large datasets of reads, or portion of sequenced mRNA that can be assembled back to the original transcripts to reconstruct a virtual gene catalog. Studies on the biology of arbuscular mycorrhizal fungi (AMF) often took great advantage of mRNA-seq, and several attempts to decipher their coding potential relied on de novo transcriptome assembly. As the transcriptional profile of an organism is modulated depending on cell types, and in response to specific biological conditions, mRNA-seq is an attractive approach to study the physiology of AMF, which are axenically unculturable and genetically intractable. mRNA-seq analyses require bioinformatic workflows to manipulate the huge amount of raw data generated by the sequencing run, with several crucial steps (e.g., library trimming, reads mapping, normalization, and differential expression calculation) which can strongly affect the final results. Here, we propose a standard workflow for de novo transcriptome assembly and differential expression calculation for AMF, which considers the most common technical issues of working in the absence of reference sequences and with mixed biological samples.

RNA-seq is a powerful method for transcriptome profiling that allows the detection of total RNA present in a single cell, tissues, or organs. mRNA-seq is focused on protein-coding RNAs, and results in large datasets of reads, or portion of sequenced mRNA that can be assembled back to the original transcripts to reconstruct a virtual gene catalog. Studies on the biology of arbuscular mycorrhizal fungi (AMF) often took great advantage of mRNA-seq, and several attempts to decipher their coding potential relied on de novo transcriptome assembly. As the transcriptional profile of an organism is modulated depending on cell types, and in response to specific biological conditions, mRNA-seq is an attractive approach to study the physiology of AMF, which are axenically unculturable and genetically intractable. mRNA-seq analyses require bioinformatic workflows to manipulate the huge amount of raw data generated by the sequencing run, with several crucial steps (e.g., library trimming, reads mapping, normalization, and differential expression calculation) which can strongly affect the final results. Here, we propose a standard workflow for de novo transcriptome assembly and differential expression calculation for AMF, which considers the most common technical issues of working in the absence of reference sequences and with mixed biological samples.

Climate changes include the intensification of drought in many parts of the world, increasing its frequency, severity and duration. However, under natural conditions, environmental stresses do not occur alone, and, in addition, more stressed plants may become more susceptible to attacks by pests and pathogens. Studies on the impact of the arbuscular mycorrhizal (AM) symbiosis on tomato response to water deficit showed that several drought-responsive genes are differentially regulated in AM-colonized tomato plants (roots and leaves) during water deficit. To date, global changes in mycorrhizal tomato root transcripts under water stress conditions have not been yet investigated. Here, changes in root transcriptome in the presence of an AM fungus, with or without water stress (WS) application, have been evaluated in a commercial tomato cultivar already investigated for the water stress response during AM symbiosis. Since root-knot nematodes (RKNs, Meloidogyne incognita) are obligate endoparasites and cause severe yield losses in tomato, the impact of the AM fungal colonization on RKN infection at 7 days post-inoculation was also evaluated. Results offer new information about the response to AM symbiosis, highlighting a functional redundancy for several tomato gene families, as well as on the tomato and fungal genes involved in WS response during symbiosis, underlying the role of the AM fungus. Changes in the expression of tomato genes related to nematode infection during AM symbiosis highlight a role of AM colonization in triggering defense responses against RKN in tomato. Overall, new datasets on the tomato response to an abiotic and biotic stress during AM symbiosis have been obtained, providing useful data for further researches.

Modifications in cell wall composition, which can be accompanied by changes in its structure, were already reported during plant interactions with other organisms, such as the mycorrhizal fungi. Arbuscular mycorrhizal (AM) fungi are among the most widespread soil organisms that colonize the roots of land plants, where they facilitate mineral nutrient uptake from the soil in exchange for plant-assimilated carbon. In AM symbiosis, the host plasma membrane invaginates and proliferates around all the developing intracellular fungal structures, and cell wall material is laid down between this membrane and the fungal cell surface. In addition, to improve host nutrition and tolerance/resistance to environmental stresses, AM symbiosis was shown to modulate fruit features. In this study, Comprehensive Microarray Polymer Profiling (CoMMP) technique was used to verify the impact of the AM symbiosis on the tomato cell wall composition both at local (root) and systemic level (fruit). Multivariate data analyses were performed on the obtained datasets looking for the effects of fertilization, inoculation with AM fungi, and the fruit ripening stage. Results allowed for the discernment of cell wall component modifications that were correlated with mycorrhizal colonization, showing a different tomato response to AM colonization and high fertilization, both at the root and the systemic level.

Traditionally, the most popular sentences used to describe the arbuscular mycorrhizal symbiosis sound like: “AM fungi form one of the most widespread root symbioses, associating with 80% of land plants. In this symbiosis, the fungus provides the plant host with mineral nutrients, especially phosphate, receiving in turn carbohydrates.” In the last years, the mycorrhiza research field has witnessed a big step forward in the knowledge of the physiology and the mechanisms governing this important symbiosis, that helped plants colonizing the lands more than 400 MYA. The huge expansion of the -omics studies produced the first results on the fungal side, with genomes and transcriptomes of AM fungi being published. In parallel, the need for more sustainable agricultural practices has boosted the research in the field of the plant symbioses, with the final aim of improving plant productivity employing symbiotic microbes as bioinoculants. Beside all the other (positive) effects that mycorrhizal fungi exert on plants, the nutrient exchange is considered as the keystone, and the core mechanism governing this symbiosis. This review will focus on the molecular determinants underneath this exchange, both on the fungal and the plant side. Coming back to the sentence that claims this symbiosis as based on phosphate provided to the plant in return to carbohydrate, we will find that some concepts of this view still stand, while some others have been partly revolutionized.

Several studies have investigated soil microbial biodiversity, but understanding of the mechanisms underlying plant responses to soil microbiota remains in its infancy. Here, we focused on tomato (Solanum lycopersicum), testing the hypothesis that plants grown on native soils display different responses to soil microbiotas. Using transcriptomics, proteomics, and biochemistry, we describe the responses of two tomato genotypes (susceptible or resistant toFusarium oxysporumf. sp.lycopersici) grown on an artificial growth substrate and two native soils (conducive and suppressive toFusarium). Native soils affected tomato responses by modulating pathways involved in responses to oxidative stress, phenol biosynthesis, lignin deposition, and innate immunity, particularly in the suppressive soil. In tomato plants grown on steam‐disinfected soils, total phenols and lignin decreased significantly. The inoculation of a mycorrhizal fungus partly rescued this response locally and systemically. Plants inoculated with the fungal pathogen showed reduced disease symptoms in the resistant genotype in both soils, but the susceptible genotype was partially protected from the pathogen only when grown on the suppressive soil. The ‘state of alert’ detected in tomatoes reveals novel mechanisms operating in plants in native soils and the soil microbiota appears to be one of the drivers of these plant responses.

International audience; Arbuscular mycorrhizal fungi (AMF) are widespread root symbionts that perform important ecological services, such as improving plant nutrient and water acquisition. Some AMF from the Gigasporaceae family host a population of endobacteria, Candidatus Glomeribacter gigasporarum (Cagg). The analysis of the Cagg genome identified six putative toxin-antitoxin modules (TAs), consisting of pairs of stable toxins and unstable antitoxins that affect diverse physiological functions. Sequence analysis suggested that these TA modules were acquired by horizontal transfer. Gene expression patterns of two TAs (yoeB/yefM and chpB/chpS) changed during the fungal life cycle, with the expression during the pre-symbiotic phase higher than during the symbiosis with the plant host. The heterologous expression in Escherichia coli demonstrated the functionality only for the YoeB-YefM pair. On the basis of these observations, we speculate that TA modules might help Cagg adapt to its intracellular habitat, coordinating its proliferation with the physiological state of the AMF host.