Marc Buée

Marc Buée
French National Institute for Agriculture, Food, and Environment (INRAE) | INRAE · Interactions Arbres/Micro-organismes (IAM)

PhD

About

134
Publications
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Publications

Publications (134)
Article
Full-text available
High-throughput RNA sequencing offers broad opportunities to explore the Earth RNA virome. Mining 5,150 diverse metatranscriptomes uncovered >2.5 million RNA virus contigs. Analysis of >330,000 RNA-dependent RNA polymerases (RdRPs) shows that this expansion corresponds to a 5-fold increase of the known RNA virus diversity. Gene content analysis rev...
Article
Plant-associated microorganisms have been shown to aid plants in coping with drought. However, the underlying mechanisms are poorly understood and there is uncertainty regarding which microbial taxa and functions are mostly involved. We explored these issues in Neotropical rainforests and identified foliar microorganisms that may play a role in dro...
Article
Full-text available
Replacement of primary old-growth forests by secondary woodlands in threatened subtropical biomes drives important changes at the level of the overstory, understory and forest floor, but the impact on belowground microbial biodiversity is yet poorly documented. In the present study, we surveyed by metabarcoding sequencing, the diversity and composi...
Article
Soil fungi play a fundamental role in the cycling of nutrients and tree nutrition in forests. As mycorrhizal fungi are closely associated with their host trees and provide them essential base cations and phosphorus, we hypothesize that they actively mine soil minerals and transfer their nutritive content to their host. Therefore, mycorrhizal fungi...
Article
In forests, bacteria and fungi are key players in wood degradation. Still, studies focusing on bacterial and fungal successions during the decomposition process depending on the wood types (i.e. sapwood and heartwood) remain scarce. This study aimed to understand the effect of wood type on the dynamics of microbial ecological guilds in wood decompo...
Article
Full-text available
Recent studies have highlighted that dead fungal mycelium represents an important fraction of soil carbon (C) and nitrogen (N) inputs and stocks. Consequently, identifying the microbial communities and the ecological factors that govern the decomposition of fungal necromass will provide critical insight into how fungal organic matter (OM) affects f...
Article
Wood decay is an important process in forest ecosystems, which relies on wood chemical properties and the action of a complex community of decomposers. While the important role of fungi in this process is recognized, our knowledge concerning the colonization of decaying wood by bacteria, their relative distribution as well as their potential functi...
Chapter
Full-text available
Forest soil fungal communities are extremely complex and diverse, and show a range of different lifestyles from saprotrophs, endophytes, pathogens, and mycorrhizal species. These belowground communities are differently distributed through space and time scales, and they are involved in key ecosystem processes such as plant community dynamics, below...
Article
Environmental DNA contains information on the species interaction networks that support ecosystem functions and services. Next‐Generation Biomonitoring proposes the use of this data to reconstruct ecological networks in real‐time and then compute network‐level properties to assess ecosystem change. We investigated the relevance of this proposal by...
Article
Full-text available
Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucor-omycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present...
Article
Full-text available
Fire is a major disturbance linked to the evolutionary history and climate of Mediterranean ecosystems, where the vegetation has evolved fire‐adaptive traits (e.g., serotiny in pines). In Mediterranean forests, mutualistic feedbacks between trees and ectomycorrhizal (ECM) fungi, essential for ecosystem dynamics, might be shaped by recurrent fires....
Article
Full-text available
The genus Phytophthora represents a group of plant pathogens with broad global distribution. The majority of them causes collar and root‐rot of diverse plant species. Little is known about Phytophthora communities in forest ecosystems, especially in Neotropical forests where natural enemies could maintain the huge plant diversity via negative densi...
Article
Fungal communities associated with plants and soil influence plant fitness and ecosystem functioning. They are frequently studied by metabarcoding approaches targeting the ribosomal internal transcribed spacer (ITS), but there is no consensus concerning the most appropriate bioinformatic approach for the analysis of these data. We sequenced an arti...
Preprint
Full-text available
Microbial interaction networks support many ecosystem services, including the regulation of crop diseases. One of the current challenges is automatically reconstructing these networks from metabarcoding data and monitoring their responses to environmental change. Here, we evaluated the ability of network inference methods to detect changes in crop-...
Article
Full-text available
1.Plant genetic variation, through its phenotypic display, can determine the composition of belowground microbial communities. Variation within a species is increasingly acknowledged to have substantial ecological consequences, particularly through trophic cascades. We hypothesised that the intraspecific genotypic variation of the tree host might i...
Article
Oomycetes are eukaryotic plant pathogens that require health monitoring. High-throughput sequencing (HTS) methods replace progressively cultivation-based approaches in soil surveys of Oomycetes, but very little control has been done from synthetic communities. Indeed, several potential biases do exist and need to be assessed for Oomycetes communiti...
Article
A growing demand for renewable carbon (C) has led to intensified forest management resulting in the use of forest residues (e.g. canopy, bark or litter layer) as energy sources with potential modifications of soil properties and tree productivity. Because microbes mediate the recycling of C and nutrients sequestered in organic matter, we investigat...
Article
Harvest residue management is a key issue for the sustainability of Eucalyptus plantations established on poor soils. Soil microbial communities contribute to soil fertility by the decomposition of the organic matter (OM), but little is known about the effect of whole-tree harvesting (WTH) in comparison to stem only harvesting (SOH) on soil microbi...
Article
Fungal succession in rotting wood shows a surprising abundance of ectomycorrhizal (EM) fungi during the late decomposition stages. To better understand the links between EM fungi and saprotrophic fungi, we investigated the potential capacities of the EM fungus Paxillus involutus to mobilize nutrients from necromass of Postia placenta, a wood rot fu...
Article
Full-text available
In forests, intraspecific genetic variation in trees can affect the entire ecosystem, which in turn, depends on the different processes occurring through space and time in soil. We hypothesized that, in addition to the effect of the local site, tree genotype and season would have an effect on the properties and functions of the edaphic environment....
Chapter
Sequencing of a high number of fungal genomes has become possible due to the development of next generation sequencing techniques (NGS). The most recent developments aim to sequence single-molecule long-reads in order to improve genome assemblies, but consequently needs higher quality (minimum >20 kbp) DNA as starting material. However, environment...
Article
Full-text available
Understanding how soil pedogenesis affects microbial communities and their in situ activities according to ecosystem functioning is a central issue in soil microbial ecology, as soils represent essential nutrient reservoirs and habitats for the biosphere. To address this question, soil chronosequences developed from a single, shared mineralogical p...
Article
Chitin is one of the most abundant nitrogen-containing polymers in forest soil. Ability of ectomycorrhizal (EM) fungi to utilize chitin may play a key role in the EM symbiosis nutrition and soil carbon cycle. In forest, EM fungi exhibit high diversity, which could be based on function partitioning and trait complementarity. Although it has long bee...
Book
Sequencing of a high number of fungal genomes has become possible due to the development of next generation sequencing techniques (NGS).The most recent developments aim to sequence single-molecule long-reads in order to improve genome assemblies, but consequently needs higher quality (minimum >20 kbp) DNA as starting material.However, environmental...
Poster
Full-text available
Forests produce a huge quantity of leaf litter and woody debris, which supply, with fungal and other telluric organisms necromass, a large proportion of stored soil carbon. Interestingly, fungi have been shown to constitute a major portion of belowground biomass in forest soils and fungal hyphal tissue is particularly resistant to biodegradation. I...
Article
Full-text available
In molecular ecology, the development of efficient molecular markers for fungi remains an important research domain. Nuclear ribosomal internal transcribed spacer (ITS) region was proposed as universal DNA barcode marker for Fungi, but this marker was criticized for idel-induced alignment problems and its potential lack of phylogenetic resolution....
Article
Fungi provide relevant ecosystem services contributing to primary productivity and the cycling of nutrients in forests. These fungal inputs can be decisive for the resilience of Mediterranean forests under global change scenarios, making necessary an in-deep knowledge about how fungal communities operate in these ecosystems. By using high-throughpu...
Article
Full-text available
Soil organisms have an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems. However, most studies have considered soil biota as a black box or focussed on specific groups, whereas little is known about entire soil networks. Here we show that during the course of nature restoration on abandoned arable...
Data
Supplementary Figures, Supplementary Tables, Supplementary Methods, and Supplementary References
Article
Full-text available
The patterns of the distribution of fungal species and their potential interactions with trees remain understudied in Neotropical rainforests, which harbor more than 16,000 tree species, mostly dominated by endomycorrhizal trees. Our hypothesis was that tree species shape the non-mycorrhizal fun- gal assemblages in soil and litter and that the dive...
Article
Full-text available
Fungi provide relevant ecosystem services contributing to primary productivity and the cycling of nutrients in forests. These fungal inputs can be decisive for the resilience of Mediterranean forests under global change scenarios, making necessary an in-deep knowledge about how fungal communities operate in these ecosystems. By using high-throughpu...
Article
Endophytic fungi and ectomycorrhizal fungi co-exist in the mycorrhizal root tips of boreal forest trees. However, very little is known about the functional role they play in their host’s biology. The activity of enzymes responsible for important biochemical processes is used to determine the functional role of root-associated mycorrhizal fungi. How...
Conference Paper
Full-text available
Fire is a major disturbance of Mediterranean forests. Predicted wildfire frequency increases associated with global change may alter soil fungal communities with important consequences for the functioning of forest ecosystems. Forests with low/high fire recurrence regimes of two representative Mediterranean pines, Pinus pinaster and Pinus halepensi...
Conference Paper
Full-text available
Fungi are key actors in forest ecosystems involved in nutrient biogeochemical cycling and tree’s productivity. However, to what extend the surrounding environment affects fungal communities is still poorly understood. This work aimed to study the impact of biotic (tree genotype) and abiotic (season, site) factors on the diversity and assemblage of...
Article
The patterns of the distribution of fungal species and their potential interactions with trees remain understudied in Neotropical rainforests, which harbor more than 16,000 tree species, mostly dominated by endomycorrhizal trees. Our hypothesis was that tree species shape the non-mycorrhizal fungal assemblages in soil and litter and that the divers...
Article
1. Characterizing the ecological processes driving the assembly and functional composition of ectomycorrhizal (ECM) fungal communities is an area of active research. 2. Here, we applied a trait-based framework to address whether and how environmental filtering and niche differentiation influence the diversity of ECM fungal enzymatic activities in...
Chapter
The ecology of fungi, and the sub-field of community ecology of ectomycorrhizal (ECM) fungi, has changed significantly since the introduction of PCR and its application to fungal species identification. This chapter discusses recent progress and pitfalls in molecular technologies, and new highlights and future research domains in the ecology of ECM...
Article
Key messageNear- and mid-infrared spectroscopy allows for the detection of local patterns of forest soil properties. In combination with dendrometric data, it may be used as a prospective tool for determining soil heterogeneity before setting up long-term forest monitoring experiments. ContextForest soils and stands generally exhibit higher spatial...
Article
Full-text available
The impacts of plant species on the microbial communities and physico-chemical characteristics of soil are well documented for many herbs, grasses and legumes but much less so for tree species. Here, we investigate by rRNA and ITS amplicon sequencing the diversity of microorganisms from the three domains of life (Archaea, Bacteria and Eukaryota:Fun...
Article
Full-text available
Soil and climatic conditions as well as land cover and land management have been shown to strongly impact the structure and diversity of the soil bacterial communities. Here, we addressed under a same land cover the potential effect of the edaphic parameters on the soil bacterial communities, excluding potential confounding factors as climate. To d...
Article
Soil organisms are considered drivers of soil ecosystem services (primary productivity, nutrient cycling, carbon cycling, water regulation) associated with sustainable agricultural production. Soil biodiversity was highlighted in the soil thematic strategy as a key component of soil quality. The lack of quantitative standardised data at a large sca...
Article
Intensive land use practices necessary for providing food and raw materials are known to have a deleterious effect on soil. However, the effects that such practices have on soil microbes are less well understood. To investigate the effects of land use intensification on soil microbial communities we used a combined T-RFLP and pyrosequencing approac...
Article
Fungi are principal actors of forest soils implied in many ecosystem services and the mediation of tree's responses. Forecasting fungal responses to environmental changes is necessary for maintaining forest productivity, although our partial understanding of how abiotic and biotic factors affect fungal communities is restricting the predictions. We...
Article
Fungi are principal actors of forest soils implied in many ecosystem services and the mediation of tree’s responses. Forecasting fungal responses to environmental changes is necessary for maintaining forest productivity, although our partial understanding of how abiotic and biotic factors affect fungal communities is restricting the predictions. We...
Article
Full-text available
Appréhender le cortège d’organismes des sols forestiers est essentiel, que ce soit pour recenser ces communautés, comprendre leur rôle, ou déterminer leur comportement face à des perturbations. Cette caractérisation se révèle être un réel défi scientifique du fait de la diversité de ces organismes et du nombre important d’espèces encore inconnues....
Article
Full-text available
Determining the identity and function of forest soil organisms is essential to understand their relative roles, but also to determine their resilience after environmental perturbations. These characteristics are scientific challenges because of the high biological diversity of forest soil organisms, but also because many of them currently remain un...
Conference Paper
Full-text available
Fungi are a key component of forest ecosystems, involved in nutrient biogeochemical cycling and plant productivity. Symbiotic ectomycorrhizal fungal communities can be particularly relevant under harsh environmental conditions, such as those imposed by the Mediterranean climate. We examined the influence of the soil properties and the host tree on...
Article
Full-text available
The diversity of fungi along environmental gradients has been little explored in contrast to plants and animals. Consequently, environmental factors influencing the composition of fungal assemblages are poorly understood. The aim of this study was to determine whether the diversity and composition of leaf and root-associated fungal assemblages vary...
Article
One of the main objectives of sustainable forestry policies is to phase out, if possible, the use of chemical agents in forestry. The saprotrophic fungus Phlebiopsis gigantea has for several years been used as a biocontrol agent against the pathogen Heterobasidion annosum sensu lato. This pathogen is the major cause of root rot disease in conifers...
Conference Paper
Studying the fungal communities in the wood, in particular during the first events of the colonization, and the factors that underlie the dynamics of fungal species assemblages remain a challenge in ecology, because of the absence of fructification during the pioneer steps of wood degradation. The use of Next-generation DNA sequencing methods, whic...
Article
The use of next-generation DNA sequencing methods, which produce massive volumes of data, has transformed fungal molecular ecology. These technologies offer the opportunity to describe microbial communities in depth and to investigate fungal diversity at a large geographical scale. In particular, due to the emergence of studies conducted at a large...