A5090882548- Microbial Community Ecology and Physiology
- Gut microbiota and health
- Genomics and Phylogenetic Studies
- Plant-Microbe Interactions and Immunity
- Science, Research, and Medicine
- Health and Medical Research Impacts
- Legume Nitrogen Fixing Symbiosis
- Evolution and Genetic Dynamics
- Bacteriophages and microbial interactions
- Nematode management and characterization studies
- Biofuel production and bioconversion
- Plant Pathogens and Fungal Diseases
- Bioenergy crop production and management
- Marine and coastal ecosystems
- Arsenic contamination and mitigation
- Pharmaceutical and Antibiotic Environmental Impacts
- Environmental DNA in Biodiversity Studies
- Heavy metals in environment
- Chromium effects and bioremediation
- Antibiotic Resistance in Bacteria
- Plant pathogens and resistance mechanisms
- Soil Carbon and Nitrogen Dynamics
- Species Distribution and Climate Change
- Mycorrhizal Fungi and Plant Interactions
- Metabolomics and Mass Spectrometry Studies
Université Claude Bernard Lyon 1
2023-2025
Centre National de la Recherche Scientifique
2023-2025
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2023-2025
VetAgro Sup
2023-2025
Michigan State University
2015-2024
Centre National pour la Recherche Scientifique et Technique (CNRST)
2024
National Council for Scientific Research
2024
Great Lakes Bioenergy Research Center
2016-2023
École Centrale de Lyon
2023
Laboratoire Ampère
2023
Microbial communities are at the heart of all ecosystems, and yet microbial community behavior in disturbed environments remains difficult to measure predict. Understanding drivers stability, including resistance (insensitivity disturbance) resilience (the rate recovery after is important for predicting response disturbance. Here, we provide an overview concepts stability that relevant communities. First, highlight insights from ecology useful defining measuring stability. To determine...
ABSTRACT Microbial communities typically contain many rare taxa that make up the majority of observed membership, yet contribution this microbial “rare biosphere” to community dynamics is unclear. Using 16S rRNA amplicon sequencing 3,237 samples from 42 time series nine different ecosystems (air; marine; lake; stream; adult human skin, tongue, and gut; infant brewery wastewater treatment), we introduce a new method detect occasionally become very abundant (conditionally [CRT]) then quantify...
Soil microbial communities are intricately linked to ecosystem functioning because they play important roles in carbon and nitrogen cycling. Still, we know little about how soil will be affected by disturbances expected with climate change. This is a significant gap understanding, as the stability of communities, defined community's ability resist recover from disturbances, likely has consequences for function. Here, propose framework predicting response change, based on specific functional...
Local diversity (within-sample or alpha diversity) is often implicated as a cause of success failure microbial community. However, the relationships between and emergent properties community, such its stability, productivity invasibility, are much more nuanced. I argue that without context provides limited insights into mechanisms underpinning community patterns. provide examples from traditional ecology to discuss common complications assumptions about within-sample may prevent us digging...
Between July 18(th) and 24(th) 2010, 26 leading microbial ecology, computation, bioinformatics statistics researchers came together in Snowbird, Utah (USA) to discuss the challenge of how best characterize world using next-generation sequencing technologies. The meeting was entitled "Terabase Metagenomics" sponsored by Institute for Computing Science (ICiS) summer 2010 workshop program. aim explore fundamental questions relating ecology that could be addressed advances potential....
Abstract Multiple models describe the formation and evolution of distinct microbial phylogenetic groups. These evolutionary make different predictions regarding how adaptive alleles spread through populations genetic diversity is maintained. Processes predicted by competing models, for example, genome-wide selective sweeps vs gene-specific sweeps, could be captured in natural using time-series metagenomics if approach were applied over a sufficiently long time frame. Direct observations...
Despite its importance to the host, flower microbiome is poorly understood. We report a culture-independent, community-level assessment of apple microbial diversity and dynamics. collected flowers from six trees at five time points, starting before opened ending petal fall. applied streptomycin half when opened. Assessment using tag pyrosequencing 16S rRNA genes revealed that communities were rich diverse dominated by members TM7 Deinococcus-Thermus, phyla about which relatively little...
Abstract Disturbances act as powerful structuring forces on ecosystems. To ask whether environmental microbial communities have capacity to recover after a large disturbance event, we conducted whole-ecosystem manipulation, during which imposed an intense freshwater by artificially mixing temperate lake peak summer thermal stratification. We employed sensors and water chemistry analyses evaluate the physical chemical responses of lake, bar-coded 16S ribosomal RNA gene pyrosequencing...
Perennial grasses are promising feedstocks for biofuel production, with potential leveraging their native microbiomes to increase productivity and resilience environmental stress. Here, we characterize the 16S rRNA gene diversity seasonal assembly of bacterial archaeal two perennial cellulosic feedstocks, switchgrass (Panicum virgatum L.) miscanthus (Miscanthus x giganteus). We sample leaves soil every three weeks from pre-emergence through senescence consecutive growing seasons one season,...
Though we are learning more about the diversity, dynamics, and importance of phyllosphere microbiota, have only modest knowledge microorganisms that specifically inhabit flowers. Due to their ephemerality exquisite anatomy, flowers provide unique habitats microorganisms, including a range distinct microscale niches. Here, review recent literature concerning community composition diversity in flower spatial temporal interactions between microbes, plant hosts, pollinators. We conclude with...
High-throughput RNA sequencing offers broad opportunities to explore the Earth virome. Mining 5,150 diverse metatranscriptomes uncovered >2.5 million virus contigs. Analysis of >330,000 RNA-dependent polymerases (RdRPs) shows that this expansion corresponds a 5-fold increase known diversity. Gene content analysis revealed multiple protein domains previously not found in viruses and implicated virus-host interactions. Extended RdRP phylogeny supports monophyly five established phyla reveals...
Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure function microbial communities multiple habitats on a planetary scale. Here we present multi-omics analysis diverse set 880 community samples collected for Earth Microbiome Project. We include amplicon (16S, 18S, ITS) shotgun metagenomic sequence data, untargeted metabolomics data (liquid chromatography-tandem mass spectrometry gas chromatography...
We investigated patterns of intra‐ and interannual change in pelagic bacterial community composition (BCC, assessed using automated ribosomal intergenic spacer analysis) over six years eutrophic Lake Mendota, Wisconsin. A regular phenology was repeated across years, implying that freshwater communities are more predictable their dynamics than previously thought. Seasonal events, such as water column mixing trends temperature, were most strongly related to BCC variation. Communities became...
Compared to the well‐studied open water of “growing” season, under‐ice conditions in lakes are characterized by low and rather constant temperature, slow movements, limited light availability, reduced exchange with surrounding landscape. These interact ice‐cover duration shape microbial processes temperate ultimately influence phenology community ecosystem processes. We review current knowledge on microorganisms seasonally frozen lakes. Specifically, we highlight how alter lake physics ways...
Summary For lake microbes, water column mixing acts as a disturbance because it homogenizes thermal and chemical gradients known to define the distributions of microbial taxa. Our first objective was isolate hypothesized drivers bacterial response mixing. To accomplish this, we designed an enclosure experiment with three treatments independently test key biogeochemical changes induced by mixing: oxygen addition hypolimnion, nutrient epilimnion, full We used molecular fingerprinting observe...
Summary Multiple forces structure natural microbial communities, but the relative roles and interactions of these drivers are poorly understood. Gradients physical chemical parameters can be especially influential. In traditional ecological theory, variability in environmental conditions across space time represents habitat heterogeneity, which may shape communities. Here we used aquatic communities as a model to investigate relationship between heterogeneity community composition dynamics....