Corinne Vacher

Corinne Vacher
French National Institute for Agriculture, Food, and Environment (INRAE) | INRAE · Biodiversité, Gènes et Communautés (BioGeCo)

PhD

About

93
Publications
34,618
Reads
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2,794
Citations
Additional affiliations
January 2005 - present
INRA - Institut National de la Recherche Agronomique
September 2001 - October 2004
Université de Montpellier
September 2000 - August 2004
French National Centre for Scientific Research
Position
  • PhD Student

Publications

Publications (93)
Article
Plant-associated microorganisms have 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 drought...
Article
The fungal pathogen Zymoseptoria tritici is the causal agent of Septoria tritici blotch (STB), a major wheat disease in Western Europe. Microorganisms inhabiting wheat leaves might act as beneficial, biocontrol or facilitating agents that could limit or stimulate the development of Z. tritici. Improving our understanding of microbial communities in...
Preprint
Bacterial phyllosphere communities play a key role in the fitness of plants. Understanding the factors and mechanisms shaping them is necessary to predict how trees would respond to a variety of stresses or disturbances. In tropical forests, the steep vertical gradients in light, rainfall or temperature within the canopy are likely to drive the ass...
Chapter
Interaction between species in microbial communities plays an important role in the functioning of all ecosystems, from cropland soils to human gut microbiota. Many statistical approaches have been proposed to infer these interactions from microbial abundance information. However, these statistical approaches have no general mechanisms for incorpor...
Article
Biomonitoring ecosystems is necessary in order to evaluate risks and to efficiently manage ecosystems and their associated services. Agrosystems are the target of multiple stressors that can affect many species through effects cascading along food webs. However, classic biomonitoring, focused on species diversity or indicator species, might be a po...
Article
Full-text available
Purpose of Review Forest research has shown for a long time that microorganisms influence tree-insect interactions, but the complexity of microbial communities, as well as the holobiont nature of both trees and insect herbivores, has only recently been taken fully into account by forest entomologists and ecologists. In this article, we review recen...
Article
Full-text available
Leaves interact with a wealth of microorganisms. Among these, fungi are highly diverse, and are known to contribute to plant health, leaf senescence and early decomposition. However, patterns and drivers of the seasonal dynamics of foliar fungal communities are poorly understood. We used a multi-factorial experiment to investigate the influence of...
Article
Full-text available
Plants are colonized by diverse fungal and viral communities that influence their growth and survival as well as ecosystem functioning. Viruses interact with both plants and the fungi they host. Our understanding of plant–fungi–virus interactions is very limited, especially in wild plants. Combining metagenomic and culturomic approaches, we assesse...
Preprint
Purpose of review Forest research has shown for a long time that microorganisms influence tree-insect interactions, but the complexity of microbial communities, as well as the holobiont nature of both trees and insect herbivores, have only recently been taken fully into account by forest entomologists and ecologists. In this article, we review rece...
Article
The tree seed mycobiome has received little attention despite its potential role in forest regeneration and health. The aim of our study was to analyze the processes shaping the composition of seed fungal communities in natural forests as seeds transition from the mother plant to the ground for establishment. We used metabarcoding approaches and co...
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
The plant endosphere is colonized by complex microbial communities and microorganisms, which colonize the plant interior at least part of their lifetime and are termed endophytes. Their functions range from mutualism to pathogenicity. All plant organs and tissues are generally colonized by bacterial endophytes and their diversity and composition de...
Preprint
Full-text available
Interactions between plant pathogens and other plant-associated microorganisms regulate disease. Deciphering the networks formed by these interactions, termed pathobiomes, is crucial to disease management. Our aim was to investigate whether microbial association networks inferred from metabarcoding data give relevant insights into pathobiomes, by t...
Article
Full-text available
Classical biomonitoring techniques have focused primarily on measures linked to various biodiversity metrics and indicator species. Next-generation biomonitoring (NGB) describes a suite of tools and approaches that allow the examination of a broader spectrum of organizational levels—from genes to entire ecosystems. Here, we frame 10 key questions t...
Preprint
Full-text available
Trees, as foundation species, play a pivotal role in the species interaction networks that constitute forest ecosystems. From the seed stage, they interact with microbial communities that affect their growth, health and fitness. Despite their eco-evolutionary importance, the processes shaping seed microbial communities in natural forests have recei...
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
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...
Chapter
This book gives an overview on the current knowledge about endophytic fungi and bacteria, their diversity, their relationships with plant pests and pathogens, their distribution and activities inside the plant and their (potential) applications in developing more sustainable agricultural practices. Furthermore, the identification of chemical consti...
Article
Trees, as foundation species, play a pivotal role in the species interaction networks that constitute forest Ecosystems. From the seed stage, they interact with microbial communities that affect their growth, health and fitness. Despite their eco-evolutionary importance, the processes shaping seed microbial communities in natural forests have recei...
Article
Ecological network analysis (ENA) provides a mechanistic framework for describing complex species interactions, quantifying ecosystem services, and examining the impacts of environmental change on ecosystems. In this chapter, we highlight the importance and potential of ENA in future biomonitoring programs, as current biomonitoring indicators (e.g....
Book
Full-text available
Ecological network analysis (ENA) provides a mechanistic framework for describing complex species interactions, quantifying ecosystem services, and examining the impacts of environmental change on ecosystems. In this chapter, we highlight the importance and potential of ENA in future biomonitoring programs, as current biomonitoring indicators (e.g....
Book
Full-text available
Plants are surrounded with microorganisms whose abundance is promoted by the release of plant organic compounds and by the presence of niches favourable to microbial development and activities. These microorganisms thrive in three main plant compartments, i.e., spermosphere, rhizosphere and phyllosphere, which are interconnected. They are recruited...
Chapter
Full-text available
Plants are surrounded with microorganisms whose abundance is promoted by the release of plant organic compounds and by the presence of niches favourable to microbial development and activities. These microorganisms thrive in three main plant compartments, i.e., spermosphere, rhizosphere and phyllosphere, which are interconnected. They are recruited...
Article
Full-text available
The efficacy of disease resistance genes in plants decreases over time because of the selection of virulent pathogen genotypes. A key goal of crop protection programs is to increase the durability of the resistance conferred by these genes. The spatial and temporal deployment of plant disease resistance genes is considered to be a major factor dete...
Preprint
Full-text available
Dispersal events between habitat patches in a landscape mosaic can structure ecological communities and influence the functioning of agrosystems. Here we investigated whether short-distance dispersal events between vineyard and forest patches shape foliar fungal communities. We hypothesized that these communities homogenize between habitats over th...
Preprint
Full-text available
Dispersal events between habitat patches in a landscape mosaic can structure ecological communities and influence the functioning of agrosystems. Here we investigated whether short-distance dispersal events between vineyard and forest patches shape foliar fungal communities. We hypothesized that these communities homogenize between habitats over th...
Article
Full-text available
The ecosystem services (EcoS) concept is being used increasingly to attach values to natural systems and the multiple benefits they provide to human societies. Ecosystem processes or functions only become EcoS if they are shown to have social and/or economic value. This should assure an explicit connection between the natural and social sciences, b...
Article
The efficacy of disease resistance genes in plants decreases over time because of the selection of virulent pathogen genotypes. A key goal of crop protection programs is to increase the durability of the resistance conferred by these genes. The spatial and temporal deployment of plant disease resistance genes is considered to be a major factor dete...
Book
The surface of plant leaves, or the phyllosphere, harbors hyperdiverse microbial communities. These communities ediate foliar functional traits, influence plant fitness, and contribute to several ecosystem functions, including nutrient and water cycling. In this review, we briefly recall the history of phyllosphere research and present the features...
Data
Full-text available
Embedded Figure Legend: How above- and belowground multitrophic interactions may translate into ecosystem services. Most functional guilds (herbivores, omnivores, carnivores) of the detrital soil food web (brown pathway) are mirroring those of the aboveground food web (green pathway) in this conceptual graph. Their close synergy is shown by support...
Article
Full-text available
The study of ecological services is fast becoming a cornerstone of mainstream ecology, largely because they provide a useful means of linking functioning to societal benefits in complex systems by connecting different organizational levels. In order to identify the main challenges facing current and future ecosystem service research, we analysed th...
Book
The study of ecological services (ESs) is fast becoming a cornerstone of mainstream ecology, largely because they provide a useful means of linking functioning to societal benefits in complex systems by connecting different organizational levels. In order to identify the main challenges facing current and future ES research, we analyzed the effects...
Article
Full-text available
Key messageThis review highlights some of the discoveries and applications made possible by “omics” technologies over the last 10 years and provides perspectives for pioneering research to increase our understanding of tree biology.ContextA decade after the first forest tree genome sequence was released into the public domain, the rapidly evolving...
Article
Key messageIncreasing human impacts on forests, including unintentional movement of pathogens, climate change, and large-scale intensive plantations, are associated with an unprecedented rate of new diseases. An evolutionary ecology perspective can help address these challenges and provide direction for sustainable forest management.ContextForest p...
Article
Network ecology has been an extraordinarily fertile field of research over the last 20 years. Its ultimate goal is to understand how the complex systems of interdependent species assemble, function and evolve. Here, we aimed to help ecologists to select the best methods for detecting subgroups of highly interacting species (usually referred to as c...
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
Full-text available
Although interfertility is the key criterion upon which Mayr's biological species concept is based, it has never been applied directly to delimit species under natural conditions. Our study fills this gap. We used the interfertility criterion to delimit two closely related oak species in a forest stand by analyzing the network of natural mating eve...
Article
Full-text available
The analysis of complex networks is a rapidly growing topic with many applications in different domains. The analysis of large graphs is often made via unsupervised classification of vertices of the graph. Community detec-tion is the main way to divide a large graph into smaller ones that can be studied separately. However another defi-nition of a...
Article
The evolution of resistance to pesticides and drugs by pests and pathogens is a textbook example of adaptation to environmental changes and a major issue in both public health and agronomy. Surprisingly, there is little consensus on how to combine selection pressures (i.e., molecules used in the treatment of pests or pathogens) over space and time...
Article
1. Pest regulation is an important ecosystem service provided by biodiversity, as plants grow-ing in species-rich communities often experience associational resistance to herbivores. How-ever, little is known about the respective influence of the quantity and identity of associated species on herbivory in focal plants. 2. Using a meta-analysis to c...
Article
Full-text available
Although interfertility is the key criterion upon which Mayr's biological species concept is based, it has never been applied directly to delimit species under natural conditions. Our study fills this gap. We used the interfertility criterion to delimit two closely related oak species in a forest stand by analyzing the network of natural mating eve...
Article
Full-text available
Despite being major drivers of the dynamics and diversity of plant populations and communities, the spatial variability of phyllosphere fungal assemblages has been seldom explored. We used CE-SSCP and 454 pyrosequencing to quantify the spatial variability of European beech phyllosphere fungal assemblages with a hierarchical sampling design includin...
Article
Full-text available
Little is known about the potential effect of climate warming on phyllosphere fungi, despite their important impact on the dynamics and diversity of plant communities. The structure of phyllosphere fungal assemblages along elevation gradients may provide information about this potential effect, because elevation gradients correspond to temperature...
Article
1. Biological invasions are a major consequence of globalization and pose a significant threat to biodiversity. Because only a small fraction of introduced species become invasive, identification of those species most likely to become invasive after introduction is highly desirable to focus management efforts. The predictive potential of species-sp...
Article
Full-text available
Like conventional crops, some GM cultivars may readily hybridize with their wild or weedy relatives. The progressive introgression of transgenes into wild or weedy populations thus appears inevitable, and we are now faced with the challenge of determining the possible evolutionary effects of these transgenes. The aim of this study was to gain insig...
Article
The mixture model is a method of choice for modeling heterogeneous random graphs, because it contains most of the known structures of heterogeneity: hubs, hierarchical structures, or community structure. One of the weaknesses of mixture models on random graphs is that, at the present time, there is no computationally feasible estimation method that...
Article
Full-text available
As more and more network-structured data sets are available, the statistical analysis of valued graphs has become common place. Looking for a latent structure is one of the many strategies used to better understand the behavior of a network. Several methods already exist for the binary case. We present a model-based strategy to uncover groups of no...