Quantitative and Evolutionary Ecology of Communities Group

Members

Our research activities, focused on interspecific interactions (community ecology), aim to better understand the ecological and evolutionary processes structuring species assemblages and biodiversity at different temporal and spatial scales. Our team addresses these major issues using contrasting biological models (communities of large African mammals, insects, microbiota, plants) from 3 complementary angles:

  • Our work is strongly anchored in the conceptual framework of evolutionary biology by studying (i) the diversity of adaptive responses implemented by organisms to selective pressures in their environment, (ii) their consequences on population demography and ultimately (iii) the dynamics and composition of species communities.
  • Our research is closely linked to societal issues of biodiversity conservation and management by integrating both the functioning of socio-ecological systems and the context of climate change. We conduct experimental studies, manage and ensure the long-term monitoring of several community observation networks.
  • Methodological issues also occupy a central place in our team, with the development of new tools for statistical processing and modeling of ecological data. This activity leads to the development of methods and software that we develop and distribute freely.

 

Research programs

 

hwange

Functioning of African savanna communities

The Hwange LTSER (Long-Term Socio-Ecological Research site in Zimbabwe hosts a long-term interdisciplinary research program that focuses on the functioning of plant and animal communities within the Hwange National Park and the interactions between this protected area and humans living in its periphery. Based on this program, three axes are developed: (1) studying the population dynamics of elephants, exploring their impact and that of management policies on the socio-ecosystem functioning; (2) Understanding the extent to which interactions within and between trophic levels are sensitive to management actions (e.g. sport hunting, water management) and climate change; (3) Decoding human ecology and human-wildlife coexistence mechanisms towards integrated conservation and sustainable functioning of the socio-ecosystem. This research is complemented by more recent works in the Hluhluwe-iMfolozi Park and in the Madikwe reserve in South Africa, which focus on the role of environmental conditions on the hunting success of large African carnivores. We work in close collaboration with the IRL (International Research Lab) Rehabs.

Involved group members : Alice Bernard, Laura Lacomme, Aïssa Morin, Lisa Nicvert, Elie Pedarros, Yolan Richard, Marion Valeix*

 

Masting and the community dynamics of seed consumers

Masting is a reproductive strategy often encountered in perennial plants, characterized by fructifications highly fluctuating in time and being synchronized at the population level. The seeds produced that way constitute a pulsed resource with a strong impact on the eco-evolutionary dynamics of seed-consuming communities and forest regeneration. Our lack of knowledge of this system still impedes our understanding of the dynamics of temperate forest ecosystems and its future in the context of climate change. Our work carried out on oak forests aims to better understand (i) the proximal causes of masting, (ii) the mechanisms underlying the coexistence of species competing for such highly fluctuating resource and (iii) the co-evolution of consumer exploitation strategies for the fluctuating resource and forest tree fruiting strategies. On the basis of the results obtained, scenarii will be proposed on the future of forest regeneration under climate change, that may serve forest management.

Involved group members : Marie-Claude Bel-Venner*, Emilie Fleurot, Léa Keurinck, Jean Lobry, Samuel Venner

 

image_antibioresitance

The spread of antibiotic resistance genes in bacteria

Antibiotic resistance is recognized as one of the greatest current threats to human health, and the mobile genetic elements (MGEs) that circulate in bacterial populations and communities are the main vehicles. To understand the dynamics and diversity of MGEs in bacterial pangenomes and the emergence of antibiotic resistance genes, we propose to go beyond the framework of conventional genomics by considering pangenomes as complex ecological communities. In the Ab-One program, we mobilize the concepts and tools developed in community ecology based on an integrative approach (monitoring of bacterial populations/communities evolving in contrasting environments -One-Health approaches-, pan-genomic analyses, experimentation in molecular and cellular microbiology, mathematical modelling). This program is currently focused on the dynamics of MGEs in Acinetobacter baumannii, an antibiotic-resistant microorganism classified as a priority by the WHO. Other more general approaches will illustrate the relevance of this new conceptual framework to understand the dynamics and diversity of MGEs in bacterial pangenomes. This program, co-piloted by our team and a team from CIRI (Horigene) involves the participation of 9 organizations (6 from Lyon -LBBE, CIRI, MMSB, HCL, LEM, VetAgro Sup-, Institut Pasteur (Paris), LMGM (Toulouse ), Robert Koch Institute (Germany)).

Involved group members : Stéphane Dray, Rémi Tuffet, Samuel Venner*

 

Statistical analysis of ecological data

Understanding the structure and dynamics of species assemblages, and the processes behind them, requires collecting data that are becoming increasingly complex owing to the sophisticated technological developments made available for their acquisition (e.g. GPS, loggers, satellite imagery, molecular data). We are developing new methods for analysing such data, that provide new insights into the ecological processes at work in communities. Multivariate analysis methods allow the analysis of spatial structures, accounting for various information on species (functional traits, morphology, phylogeny), the spatio-temporal variation of species-environment relationships or the multifaceted perception of the protected human-environment relationship. We also model multi-'omics' dose-response data within communities in order to better understand the Adverse Outcome Pathway (AOP) and to better appreciate the risks to the environment. These methodological innovations are made available to the scientific community through the development, distribution and maintenance of software (libraries for the R language: ade4, adegraphics, adephylo, ade4TkGUI, nlstools, fitdistrplus, DRomics, seqinr).

Involved group members: Marie Laure Delignette-Muller, Stéphane Dray*, Jean Lobry, Jean Thioulouse.

Publications

Display of 391 to 420 publications on 572 in total

Quantitative Risk Assessment of Listeria monocytogenes in French Cold-Smoked Salmon: I. Quantitative Exposure Assessment

R. Pouillot, N. Miconnet, A.-L. Afchain, Marie Laure Delignette-Muller, Aurélien Beaufort Beaufort, L. Rosso...

Risk Analysis . 27 : 806-819

Journal article

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Persistence of Shiga toxin-producing Escherichia coli O26 in cow slurry

B. Fremaux, C. Prigent-Combaret, Marie Laure Delignette-Muller, M. Dothal, Christine Vernozy-Rozand

Letters in Applied Microbiology . 45 ( 1 ) : 55-61

DOI: 10.1111/j.1472-765X.2007.02146.x

Journal article

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A New Method for Assessing the Effect of Replication on DNA Base Composition Asymmetry

A. Necşulea, J.R. Lobry

Molecular Biology and Evolution . 24 : 2169-2179

Journal article

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The ade4 Package: Implementing the Duality Diagram for Ecologists

S. Dray, Anne-Béatrice Dufour

Journal of Statistical Software . 22 : 1-20

Journal article

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The ade4 Package--II: Two-table and K-table Methods

S. Dray, A.B. Dufour, D. Chessel

R News . 7 : 47-52

Journal article

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Growth of Shiga-Toxin producing (STEC) and bovine feces background microflora in various enrichment protocols

A. Vimont, Christine Vernozy-Rozand, M.P. Montet, C. Bavai, B. Fremaux, Marie Laure Delignette-Muller

Veterinary Microbiology . 123 ( 1-3 ) : 274

DOI: 10.1016/j.vetmic.2007.02.003

Journal article

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Growth of Shiga-Toxin producing Escherichia coli (STEC) and bovine feces background microflora in various enrichment protocols

A. Vimont, Christine Vernozy-Rozand, M.-P. Montet, C. Bavai, B. Fremaux, Marie Laure Delignette-Muller

Veterinary Microbiology . 123 : 274-281

Journal article

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Supplementation of enrichment broths by novobiocin for detecting Shiga toxin-producing Escherichia coli from food: a controversial use

A. Vimont, Marie Laure Delignette-Muller, Christine Vernozy-Rozand

Letters in Applied Microbiology . 44 : 326-331

Journal article

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A New Method for Assessing the Effect of Replication on DNA Base Composition Asymmetry

A. Necşulea, J.R. Lobry

incollection . 7 : 379-381

Journal article

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SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis

D. Charif, J.R. Lobry

incollection . -- : 207-232

Journal article

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Interactive Multivariate Data Analysis in R with the ade4 and ade4TkGUI Packages

J. Thioulouse, S. Dray

Journal of Statistical Software . 22 : 1-14

Journal article

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Influence du type de sol et du mode d’occupation des sols sur la quantité d’ADN extraite et la densité des communautés bactériennes indigènes

Samuel Dequiedt, Mélanie M. Lelievre, Claudy C. Jolivet, Dominique D. Arrouays, Manuel Pascal Martin, Nicolas N. Saby...

AFEM (Association Francophone d'Ecologie Microbienne) . : n.p.

Poster

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Microbiogéographie à l'échelle du territoire national

Samuel S. Dequiedt, Mélanie M. Lelievre, Claudy C. Jolivet, Manuel M. Martin, Nicolas N. Saby, Dominique D. Arrouays...

AFEM (Association Francophone d'Ecologie Microbienne) . : n.p.

Conference paper

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Biological control of Striga hermontica by Cubiterms mound powder amendment in sorghum culture

Z. Andrianjaka, R. Bally, Michel Le Page, J. Thioulouse, G. Comte, M. Kisa...

Applied Soil Ecology . 37 ( 3 ) : 175-183

DOI: 10.1016/j.apsoil.2007.03.001

Journal article

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Improvement of Cupressus atlantica Gaussen growth by inoculation with native arbuscular mycorrhizal fungi

L. Ouahmane, M. Hafidi, J. Thioulouse, M. Ducousso, M. Kisa, Y. Prin...

Journal of Applied Ecology . 103 : 683-690

Journal article

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Detection of recombinant human erythropoietin in urine for doping analysis: interpretation of isoelectric profiles by discriminant analysis

F. Lasne, J. Thioulouse, L. Martin, J. de Ceaurriz

Electrophoresis . 28 ( 12 ) : 1875-1881

DOI: 10.1002/elps.200600363

Journal article

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Arbuscular mycorrhizal symbiosis can counterbalance the negative influence of the exotic tree species Eucalyptus camaldulensis on the structure and functioning of soil microbial communities in a sahelian soil

M. Kisa, A. Sanon, J. Thioulouse, K. Assigbetse, S. Sylla, Rodolphe Spichiger...

FEMS Microbiology Ecology . 62 ( 1 ) : 32-44

DOI: 10.1111/j.1574-6941.2007.00363.x

Journal article

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Quantitative risk assessment of listeria monocytogenes in french cold-smoked salmon: I. quantitative exposure assessment

Regis Pouillot, Nicolas Miconnet, Anne-Laure Afchain, Marie Laure Delignette-Muller, Annie Beaufort, Laurent Rosso...

Risk Analysis . 27 ( 3 ) : 683-700

DOI: 10.1111/j.1539-6924.2007.00921.x

Journal article

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Potential of a 16S rRNA-based taxonomic microarray for analyzing the rhizosphere effects of maize on Agrobacterium spp. and bacterial communities

Hervé Sanguin, B. Remenant, Arnaud Dechesne, J. Thioulouse, Timothy M. Vogel, Xavier Nesme...

Applied and Environmental Microbiology . 72 ( 6 ) : 4302-4312

DOI: 10.1128/AEM.02686-05

Journal article

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Biological effects of native and exotic plant residues on plant growth microbial biomass and N availability under controlled conditions

M.D. Diallo, R. Duponnois, A. Guisse, S. Sall, J.-L. Chotte, J. Thioulouse

European Journal of Soil Biology . 42 : 238-246

Journal article

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Litter-forager termite mounds enhance the ectomycorrhizal symbiosis between Acacia holosericea A. Cunn. Ex G. Don and Scleroderma dictyosporum isolates

R. Duponnois, K. Assigbetse, H. Ramanankierana, M. Kisa, Jean Thioulouse, Michel Le Page

FEMS Microbiology Ecology . 56 : 292-303

DOI: 10.1111/j.1574-6941.2006.00089.x

Journal article

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A multivariate approach to integrating Datasets using made4 and ade4

A.C. Culhane, J. Thioulouse

R News . -- : 1-15

Journal article

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Displacement of an herbaceous plant species community by mycorrhizal and non-mycorrhizal Gmelina arborea, an exotic tree, grown in a microcosm experiment

A. Sanon, P. Martin, Jean Thioulouse, Christian Plenchette, Rodolphe Spichiger, Michel Le Page...

Mycorrhiza . 16 ( 2 ) : 125-132

DOI: 10.1007/s00572-005-0024-7

Journal article

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The Ectomycorrhizosphere Effect Influences Functional Diversity of Soil Microflora

N. Ramanankierana, N. Rakotoarimanga, J. Thioulouse, K. Marija, E. Randrianjohany, L. Ramaroson...

International Journal of Soil Science . 1 : 8-19

Journal article

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Development of cellular immune responses to Plasmodium falciparum blood stage antigens from birth to 36 months of age in Cameroon

J.Y. Le Hesran, N. Fievet, J. Thioulouse, P. Personne, B. Maubert, S. M'Bidias...

Acta Tropica . 98 : 261-269

Journal article

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Mate-guarding strategies and male competitive ability: results from a field study in an orb-weaving spider

Marie-Claude Bel-Venner, Samuel Venner

Animal Behaviour . 71 : 1315-1322

Journal article

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Dynamic optimization over infinite-time horizon: Web-building strategy in an orb-weaving spider as a case study

Samuel Venner, Iadine Chadès, Marie-Claude Bel-Venner, Alain Pasquet, François Charpillet, Raymond Leborgne

Journal of Theoretical Biology . Volume 241 ( Issue 4 ) : Pages 725-733

DOI: 10.1016/j.jtbi.2006.01.008

Journal article

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Modeling and Predicting the Simultaneous Growth of Escherichia coli O157:H7 and Ground Beef Background Microflora for Various Enrichment Protocols

A. Vimont, Christine Vernozy-Rozand, M.-P. Montet, C. Lazizzera, C. Bavai, Marie Laure Delignette-Muller

Applied and Environmental Microbiology . 72 : 261-268

Journal article

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Serotyping of Toxoplasma gondii in chronically infected pregnant women: predominance of type II in Europe and types I and III in Colombia (South America).

François Peyron, Jean R Lobry, Karine Musset, Josette Ferrandiz, Jorge Enrique Gomez-Marin, Eskild Petersen...

Microbes and Infection . 8 ( 9-10 ) : 2333-40

DOI: 10.1016/j.micinf.2006.03.023

Journal article

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UV-Targeted Dinucleotides Are Not Depleted in Light-Exposed Prokaryotic Genomes

L. Palmeira, Laurent Guéguen, J.R. Lobry

Molecular Biology and Evolution . 23 : 2214-2219

Journal article

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