Biology subjects

Deveau, A.

Publications and source records attributed to Deveau, A..

6 recordsLinked to original sources

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↗

bioRxiv2024

Endophytic and ectomycorrhizal, an overlooked dual ecological niche? Insights from natural environments and Russula species

O_LIEctomycorrhizal (EcM) fungi play key roles in ecosystem functioning, in particular temperate ones. Recent findings suggest that they can endophytically colonize the roots of non-EcM plants. Here we aim at (i) providing new evidence of colonization of non-EcM hosts by EcM fungi, (ii) exploring factors driving such colonization (plant identity, site, root filter), and (iii) providing direct microscopical evidence for endophytism. C_LIO_LIUsing amplicon sequencing (ITS2), we described the root fungal communities of 42 plant species collected at nine locations in France. In two of those sites, we also compared rhizosphere and root fungal communities to identify a potential root filter. Finally, we investigated endophytism in Russula spp. at two Russula-rich sites using fluorescence in situ hybridization (FISH) paired with confocal microscopy. C_LIO_LIWe find a large but variable share of EcM sequences in roots of non-EcM plant species, in particular nearby EcM hosts, suggesting that endophytism is a secondary ecological niche. Though EcM fungi were more abundant in the rhizosphere compared to roots, their composition was similar to that of roots, suggesting a poor root filter. We observed metabolically active hyphae of Russula spp. endophytically colonizing the apoplast of two non-EcM plant species. C_LIO_LIAs shown for other EcM fungi (e.g., Tuber spp., Ascomycota) we demonstrate the dual EcM/endophyte niche for Russula (Basidiomycota). The ecological consequences of this duality still need to be addressed. The ability to colonize two ecological niches may be a trait kept by EcM fungi which evolved from endophytic fungi, as stipulated by the "waiting room hypothesis". C_LI

microbiology↗

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↗

bioRxiv2020

Geographical based variations in white truffle Tuber magnatum truffle aroma is explained by quantitative differences in key volatile compounds

O_LIThe factors that vary the aroma of Tuber magnatum fruiting bodies are poorly understood. The study determined the headspace aroma composition, sensory aroma profiles, maturity, and microbiome composition from T. magnatum originating from Italy, Croatia, Hungary, and Serbia, and tested if truffle aroma is dependent on provenance and if fruiting body volatiles are explained by maturity and/or microbiome composition. C_LIO_LIHeadspace volatile profiles were determined by gas chromatography-mass spectrometry-olfactometry (GC-MS-O) and aroma of fruiting body extracts were sensorially assessed. Fruiting body maturity were estimated through spore melanisation. Bacterial community was determined using 16S rRNA amplicon sequencing. C_LIO_LIMain odour active compounds were present in all truffles but varied in concentration. Aroma of truffle extracts were sensorially discriminated by sites. However, volatile profiles of individual fruiting bodies varied more within sites than across geographic area, while maturity level did not play a role. Microbiome composition varied highly and was partially explained by provenance. A few rare bacterial operational taxonomical units associated with select few non-odour active volatile compounds. C_LIO_LISpecificities of the aroma of T. magnatum truffles are more likely linked to individual properties than provenance. Some constituents of the microbiome may provide biomarkers of provenance and be linked to non-odour active volatiles. C_LI

ecology↗

bioRxiv2017

Bacterial Biofilm Formation On Soil Fungi: A Widespread Ability Under Controls

In natural environments, bacteria preferentially live in biofilms that they build on abiotic surfaces but also on living tissues. Although fungi form extensive networks of hyphae within soils and thus could provide immense surfaces for bacteria to build biofilms and to proliferate, the extent on such phenomenon and the consequences for the fitness of both microorganisms is poorly known in soils. Here, we analyzed the process of formation of biofilms by various bacteria on hyphae of soil fungi in an in vitro setting using confocal and electron microscopy. We showed that the ability to form biofilms on fungal hyphae is widely shared among soil bacteria. In contrast, some fungi, mainly belonging to the Ascomycete class, did not allow for the formation of bacterial biofilms on their surfaces. The formation of biofilms was also strongly modulated by the presence of tree roots and by the development of the ectomycorrhizal symbiosis, suggesting that biofilm formation does not occur randomly in soil but that it is highly regulated by several biotic factors. Finally, our study led to the unexpected finding that networks of filaments made of extracellular DNA were used to build the skeleton of biofilms by a large array of bacteria.

microbiology↗