Biology subjects

Veneault-Fourrey, C.

Publications and source records attributed to Veneault-Fourrey, C..

9 recordsLinked to original sources

bioRxiv2025

Poplar CLE peptides stimulating ectomycorrhizal symbiosis uncovered by genome-wide identification of ectomycorrhizal-responsive small secreted peptides

Plants small secreted peptides (SSPs) regulate root development, immunity and symbiotic relationships in herbaceous plants. These processes are equally important for establishing functional ectomycorrhizal associations in trees. While fungal SSPs involved in ectomycorrhizal establishment have been identified, the role of plant SSPs remains largely unexplored. Although thousands of SSPs were predicted in plant genomes, their small size and high sequence divergence hinder their accurate automated annotations. To address this issue, we combined de novo gene prediction with family-specific motif search to identify 1,053 SSPs from 21 symbiosis-related families in the genomes of two ectomycorrhizal tree species: Populus trichocarpa and Quercus robur. Nearly half of these SSPs are transcriptionally regulated during ectomycorrhizal symbiosis with various fungal partners. Functional assays of selected Populus CLE peptides, a SSP family known to repress arbuscular mycorrhizal and rhizobial symbioses, revealed that five enhanced ectomycorrhizal roots formation. Unlike CLEs involved in the autoregulation of arbuscular mycorrhizal and rhizobial symbioses, these peptides belonged to clades associated with meristem activity. Their activity did not increase lateral root number but inhibited adventitious root growth, suggesting their role in promoting ectomycorrhizal root organogenesis. These findings demonstrate that CLE peptides promote, rather than repress, ectomycorrhizal symbiosis. This functional divergence from their roles in other symbioses suggests that poplar co-opted a distinct set of SSPs to support ectomycorrhizal development. Our results expand the understanding of host tree contributions to ectomycorrhizal development and identify a set of candidate SSPs for future functional studies, thereby highlighting a new layer of regulation in tree-fungal mutualism.

plant biology↗

bioRxiv2025

Comparative transcriptomics uncovers plant and fungal genetic determinants of mycorrhizal compatibility

Ectomycorrhizal symbiosis supports tree growth and is crucial for nutrient cycling and temperate and boreal ecosystems functioning. The establishment of functional ECM first requires the association of compatible partners. However, host and fungal genetic determinants governing mycorrhizal compatibility are unknown. To identify such factors in poplar and its fungal associates, we mined existing and de-novo tree and fungal transcriptional datasets. We identified core plant regulons enabling ECM symbiosis at early and mature stages of the interaction. These regulons can be divided into general fungal-sensing and ECM-specific components. We highlight the importance of fungal modulation of plant JA-related defences and the regulation of secretory pathways for ECM compatibility, including upregulation of key fungal small secreted proteins, the downregulation of plant secreted peroxidases and the downregulation of plant cell-wall remodelling proteins concomitantly with the upregulation of fungal glycosyl hydrolases acting on pectin. Not only gene-regulation, but also its temporal scale and dynamics seems to play a crucial role for mycorrhizal compatibility. The expression profile of the host Common Symbiosis Pathway was also studied, revealing constitutive levels of expression of a part of the pathway and moderate upregulation in compatible ECM interactions. Overall, these results underscore the importance of novel biological functions during the establishment of ECM symbiosis, help us gain insights into the molecular events determining mycorrhiza compatibility and serve as a data-rich transcriptomic resource to open new research questions in the field. Significance statementEctomycorrhizal symbiosis is essential for forest ecosystems, but the genetic determinants of host and fungal compatibility remain underexplored. Employing comparative transcriptomics, we identified plant general and ECM-specific gene regulons, outlining the expression profile of Common Symbiosis Pathway genes in multiple ECM interactions and highlighting fungal and plant genes associated to interkingdom crosstalk and cell wall remodelling. These findings help us gain insights into the molecular events determining mycorrhiza compatibility.

plant biology↗

bioRxiv2025

Manipulation of in planta ethylene levels modulates the metabolome of Populus tremula x tremuloides in a microbial-dependent manner.

BackgroundThe assembly of tree microbiota is a dynamic process that varies across space and time, influenced by both biotic and abiotic factors. Plants have developed defence strategies, mediated by phytohormones such as ethylene, to manage its interactions with pathogens and, in certain non-perennials, interactions with the commensal microbiota. However, whether and how ethylene regulation affects the assembly of tree microbiota is unknown. ResultsWe investigated the assembly of fungal and bacterial communities in poplars (P. tremula x. P. tremuloides T89), altered either in ethylene biosynthesis (ACO1), or in ethylene perception (etr1.1), by combining high-throughput amplicon sequencing with confocal microscopy. In parallel, we characterised root exudates, as well as root and shoot metabolomes of the different poplar lines grown on sterile soil and in the presence of microbiota using GC-MS. Alteration of ethylene levels had little impact on the metabolome of sterile poplars, but led to differential primary and secondary metabolic responses in the root and shoots of poplars colonised by microorganisms. These metabolomic changes were associated with a decrease in fungal colonisation of shoots, particularly by saprophytes in the early stages, whereas reduced ethylene stimulated root colonisation by fungi. Conversely, arbuscular mycorrhizal fungal and bacterial communities, as well as root exudation, were little affected by changes in ethylene production. ConclusionThe findings of this study suggest a potential dual role for ethylene in poplar, whereby its levels may either promote or inhibit microbial growth and activity, depending on the concentration, microbial trophic guild, and poplar organ.

plant biology↗

bioRxiv2024

Microbe tree metabolite interactions in the soil - phyllosphere continuum of poplar tree: when microbes rewire poplar root exudate and metabolome

O_LITrees are associated with a broad range of microorganisms colonising the diverse tissues of their host. However, the early dynamics of the assembly of the microbiota from the root to shoot axis and how it is linked to root exudates and metabolite contents of tissues remain unclear. C_LIO_LIHere, we characterized how fungal and bacterial communities are altering root exudates as well as root and shoot metabolomes in parallel with their establishment in poplar cuttings (Populus tremula x tremuloides clone T89) over 30 days of growth. Sterile poplar cuttings were planted in natural or gamma-irradiated soils. Bulk and rhizospheric soils, root and shoot tissues were collected from day 1 to day 30 to track the dynamic changes of fungal and bacterial communities in the different habitats by DNA metabarcoding. Root exudates and root and shoot metabolites were analysed in parallel by gas chromatography-mass spectrometry. C_LIO_LIOur study reveals that microbial colonization triggered rapid and substantial alterations in both the composition and quantity of root exudates, with over 70 metabolites exclusively identified in remarkably high abundances in the absence of microorganisms. Noteworthy among these were lipid-related metabolites and defence compounds. The microbial colonization of both roots and shoots exhibited a similar dynamic response, initially involving saprophytic microorganisms and later transitioning to endophytes and symbionts. Key constituents of the shoot microbiota were also discernible at earlier time points in the rhizosphere and roots, indicating that the soil constituted a primary source for shoot microbiota. C_LIO_LIFurthermore, the microbial colonization of belowground and aerial compartments induced a reconfiguration of plant metabolism. Specifically, microbial colonization predominantly instigated alterations in primary metabolism in roots, while in shoots, it primarily influenced defence metabolism. This highlighted the profound impact of microbial interactions on metabolic pathways of plants, shedding light on the intricate interplay between plants and their associated microbial communities. C_LI

plant biology↗

bioRxiv2022

The establishment of Populus x Laccaria bicolor ectomycorrhiza requires the inactivation of MYC2 coordinated defense response with a key role for root terpene synthases

The jasmonic acid (JA) signaling pathway plays an important role in the establishment of the ectomycorrhizal symbiosis (ECM) between Laccaria bicolor and poplar. We previously showed that the L. bicolor effector MiSSP7 induces the stabilization of the poplar JAZ6, a JA co-repressor protein that binds to Populus MYC2.1 and MYC2.2, orthologs of the Arabidopsis MYC2 transcription factor (TF), blocking their activity. Here we showed that both TFs play a central role in root colonization by L. bicolor mycelium, since their overexpression decreased the formation of the Hartig net, the hyphal network involved in symbiotic nutrient exchanges. By combining RNA sequencing and DNA Affinity Purification sequencing (DAP-seq) analysis, we identified a core set of JA-responsive genes directly activated by poplar MYC2.1 and MYC2.2, that need to be bypassed by the fungi to colonize root apoplastic spaces. These genes encode for other TFs, receptor-like kinases and many defense-related proteins, including terpene synthases (TPS). Monoterpenes produced by some of these TPS impact L. bicolor growth and ECM formation, suggesting a role for poplar root monoterpenes as negative regulators of in planta fungal growth and ECM symbiosis. Significance statementThe ectomycorrhizal symbiosis is a predominant mutualistic plant-fungus interaction occurring in forests, sustaining tree health. Ectomycorrhizal fungi colonize the root intercellularly establishing the symbiotic interface required for bidirectional nutrients exchanges, the Hartig net. During root colonization, the fungus L. bicolor produces the effector protein MiSSP7 that binds to the jasmonate co-receptor PtJAZ6, maintaining the repression of MYC2-targeted genes. Here we showed that defensive genes are major targets of MYC2, suggesting that their strict control is required to allow fungal colonization, with special emphasis on the host root monoterpene synthesis. Future research will focus on how root terpene defenses mediate belowground mutualistic interactions and how they can be manipulated to engineer plants with enhanced disease resistance but stable mutualistic interactions.

plant biology↗

bioRxiv2021

The ectomycorrhizal basidiomycete Laccaria bicolor releases a GH28 polygalacturonase that plays a key role in symbiosis establishment

O_LIIn ectomycorrhiza, root penetration and colonization of the intercellular space by symbiotic hyphae is thought to rely on the mechanical force that results from hyphal tip growth, enhanced by the activity of secreted cell-wall-degrading enzymes. C_LIO_LIHere, we characterize the biochemical properties of the symbiosis-induced polygalacturonase LbGH28A from the ectomycorrhizal fungus Laccaria bicolor. The transcriptional regulation of LbGH28A was measured by qPCR. The biological relevance of LbGH28A was confirmed by generating RNAi-silenced LbGH28A mutants. We localized the LbGH28A protein by immunofluorescence confocal and immunogold cytochemical microscopy in poplar ectomycorrhizal roots. C_LIO_LIqPCR confirmed the induced expression of LbGH28A during ectomycorrhiza formation. L. bicolor RNAi mutants have a lower ability to establish ectomycorrhiza confirming the key role of this enzyme in symbiosis. The purified recombinant LbGH28A has its highest activity towards pectin and polygalacturonic acid. In situ localization of LbGH28A indicates that this endopolygalacturonase is located in both fungal and plant cell walls at the symbiotic hyphal front. C_LIO_LIThe present findings suggest that the symbiosis-induced pectinase LbGH28A is involved in the Hartig net formation and is an important determinant for successful symbiotic colonization. C_LI

plant biology↗

bioRxiv2020

Colonization of naïve roots from Populus tremula x alba involves successive waves of fungi andbacteria with different trophic abilities

Through their roots, trees interact with a highly complex community of microorganisms belonging to various trophic guilds and contributing to tree nutrition, development and protection against stresses. Tree roots select for specific microbial species from the bulk soil communities. The root microbiome formation is a dynamic process but little is known on how the different microorganisms colonize the roots and how the selection occurs. To decipher if the final composition of the root microbiome is the product of several waves of colonization by different guilds of microorganisms, we planted sterile rooted cuttings of Gray Poplar obtained from plantlets propagated in axenic conditions in natural soil taken from a poplar stand. We analyzed the root microbiome at different time points between 2 and 50 days of culture by combining high-throughput Illumina MiSeq sequencing of fungal rDNA ITS and bacterial 16S rRNA amplicons with Confocal Laser Scanning Microscope observations. The microbial colonisation of poplar roots took place in three stages but the dynamic was different between bacteria and fungi. Root bacterial communities were clearly different from the soil after two days of culture. By contrast, if fungi were also already colonizing roots after two days, the initial communities were very close to the one of the soil and were dominated by saprotrophs. Those were slowly replaced by endophytes and ectomycorhizal fungi. The replacement of the most abundant fungal and bacterial community members observed in poplar roots along time suggest potential competition effect between microorganisms and/or a selection by the host. ImportanceThe tree root microbiome is composed of a very diverse set of bacterial and fungal communities. These microorganisms have a profound impact on tree growth, development and protection against different types of stress. They mainly originate from the bulk soil and colonize the root system which provides a unique nutrient rich-environment for a diverse assemblage of microbial communities. In order to better understand how the tree root microbiome is shaped along time, we observed the composition of root-associated microbial communities of naive plantlets of poplar transferred in natural soil. The composition of the final root microbiome rely on a series of colonization stages characterized by the dominance of different fungal guilds and bacterial community members along time. Our observations suggest an early stabilization of bacterial communities, whereas fungal communities are established following a more gradual pattern.

microbiology↗

bioRxiv2017

The hydrophobin-like OmSSP1 may be an effector in the ericoid mycorrhizal symbiosis

Mutualistic and pathogenic plant-colonizing fungi use effector molecules to manipulate the host cell metabolism to allow plant tissue invasion. Some small secreted proteins (SSPs) have been identified as fungal effectors in both ectomycorrhizal and arbuscular mycorrhizal fungi, but it is currently unknown whether SSPs also play a role as effectors in other mycorrhizal associations. Ericoid mycorrhiza is a specific endomycorrhizal type that involves symbiotic fungi mostly belonging to the Leotiomycetes (Ascomycetes) and plants in the family Ericaceae. Genomic and RNASeq data from the ericoid mycorrhizal fungus Oidiodendron maius led to the identification of several symbiosis-upregulated genes encoding putative SSPs. OmSSP1, the most highly symbiosis up-regulated SSP, was found to share some features with fungal hydrophobins, even though it lacks the Pfam hydrophobin domain. Sequence alignment with other hydrophobins and hydrophobin-like fungal proteins placed OmSSP1 within Class I hydrophobins. However, the predicted features of OmSSP1 may suggest a distinct type of hydrophobin-like proteins. The presence of a predicted signal peptide and a yeast-based signal sequence trap assay demonstrate that OmSSP1 is secreted during symbiosis. OmSSP1 null-mutants showed a reduced capacity to form ericoid mycorrhiza with Vaccinium myrtillus roots, suggesting a role as effectors in the ericoid mycorrhizal interaction.

plant biology↗

bioRxiv2017

Laccaria bicolor MiSSP8 is a small-secreted protein decisive for the establishment of the ectomycorrhizal symbiosis

The ectomycorrhizal symbiosis is a predominant tree-microbe interaction in forest ecosystems sustaining tree growth and health. Its establishment and functioning implies a long-term and intimate relationship between the soil-borne fungi and the roots of trees. Mycorrhiza-induced Small Secreted Proteins (MiSSPs) are hypothesized as keystone symbiotic proteins, required to set up the symbiosis by modifying the host metabolism and/or building the symbiotic interfaces.\n\nL. bicolor MiSSP8 is the third most highly induced MiSSPs in symbiotic tissues and it is also expressed in fruiting bodies. The MiSSP8-RNAi knockdown mutants are strongly impaired in their mycorrhization ability with Populus, with the lack of fungal mantle and Hartig net development due to a lack of hyphal aggregation. MiSSP8 C-terminus displays a repetitive motif containing a kexin cleavage site, recognized by KEX2 in vitro. This suggests MiSSP8 protein might be cleaved into small peptides. Moreover, the MiSSP8 repetitive motif is found in other proteins predicted secreted by both saprotrophic and ectomycorrhizal fungi. Thus, our data indicate that MiSSP8 is a small-secreted protein involved at early stages of ectomycorrhizal symbiosis, likely by regulating hyphal aggregation and pseudoparenchyma formation.

plant biology↗