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 421 to 450 publications on 572 in total

Variation partitioning of species data matrices : estimation and comparaison of fractions

P.R. Peres-Neto, P. Legendre, S. Dray, D. Borcard

Ecology . 87 : 2614-2625

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, I. Chadès, Marie-Claude Venner, A. Pasquet, F. Charpillet, R. Leborgne

Journal of Theoretical Biology . : 725-733

Journal article

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Effect of temperature, water-phase salt and phenolic contents on Listeria monocytogenes growth rates on cold-smoked salmon and evaluation of secondary models.

M. Cornu, Aurélien Beaufort Beaufort, S. Rudelle, L. Laloux, H. Bergis, N. Miconnet...

International Journal of Food Microbiology . 106 ( 2 ) : 159-68

DOI: 10.1016/j.ijfoodmicro.2005.06.017

Journal article

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Serological and molecular ecology of Listeria monocytogenes isolates collected from 13 French pork meat salting–curing plants and their products

D. Thévenot, Marie Laure Delignette-Muller, S. Christieans, Sylvie Leroy, A. Kodjo, Christine Vernozy-Rozand

International Journal of Food Microbiology . 112 : 341-342

Journal article

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Growth and survival of non-O157:H7 Shiga-toxin-producing Escherichia coli in cow manure

B. Fremaux, Marie Laure Delignette-Muller, C. Prigent-Combaret, A. Gleizal, Christine Vernozy-Rozand

Journal of Applied Microbiology . 102 : 89-99

DOI: 10.1111/j.1365-2672.2006.03059.x

Journal article

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Isolation of E. coli O157:H7 and non-O157 STEC in different matrices: review of the most commonly used enrichment protocols

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

Letters in Applied Microbiology . 42 : 102-108

Journal article

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Use of Bayesian modelling in risk assessment: Application to growth of Listeria monocytogenes and food flora in cold-smoked salmon

Marie Laure Delignette-Muller, M. Cornu, R. Pouillot, J.-B. Denis

International Journal of Food Microbiology . 106 : 195-208

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)

F. Peyron, J.R. Lobry, K. Musset, J. Ferrandiz, J.E. Gómez-Marín, E. Petersen...

Microbes and Infection . 8 : 2333-2340

Journal article

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Synonymous codon usage and its potential link with optimal growth temperature in prokaryotes.

J.R. Lobry, A. Necşulea

Gene . 385 : 128-136

Journal article

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No Evidence for Tissue-Specific Adaptation of Synonymous Codon Usage in Humans

M. Sémon, J.R. Lobry, L. Duret

Molecular Biology and Evolution . 23 : 523-529

Journal article

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Revisiting the directionnal mutation pressure theory : The analysis of a particular genomic structure in Leishmania major

A. Necşulea, J.R. Lobry

Gene . 385 : 28-40

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, S. Venner

Animal Behaviour . 71 : 1315-1323

Journal article

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Resource partitioning in a grazer guild feeding on a multilayer diatom mat

L. Tall, A. Cattaneo, L. Cloutier, S. Dray, P. Legendre

Journal of the North American Benthological Society . 25 : 800-810

Journal article

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Spatial modelling : a comprehensive framework for principal coordinate analysis of neighbour matrices (PCNM)

S. Dray, P. Legendre, P.R. Peres-Neto

Ecological Modelling . -- : 483-493

Journal article

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Lavandula species as accompanying plants in Cupressus replanting strategies : Effect on plant growth mycorrhizal soil infectivity and soil microbial catabolic diversity

L. Ouahmane, M. Hafidi, C. Plenchette, M. Kisa, A. Boumezzough, J. Thioulouse...

Applied Soil Ecology . -- : 190-199

Journal article

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Identification of Genomic Species in Agrobacterium Biovar 1 by AFLP Genomic Markers

Perrine Portier, Marion Fischer-Le Saux, Christophe Mougel, Catherine Lerondelle, David Chapulliot, Jean Thioulouse...

Applied and Environmental Microbiology . 72 ( 11 ) : 7123-7131

DOI: 10.1128/AEM.00018-06

Journal article

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Fluorescent pseudomonads occuring in Macrotermes subhyalinus mound structures decrease Cd toxicity and improve its accumulation in sorghum plants

R. Duponnois, M. Kisa, K. Assigbetse, Y. Prin, Jean Thioulouse, M. Issartel...

Science of the Total Environment . 370 : 391-400

DOI: 10.1016/j.scitotenv.2006.07.008

Journal article

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Serological and molecular ecology of Listeria monocytogenes isolates collected from 13 French pork meat salting–curing plants and their products

Delphine Thévenot, Marie-Laure Delignette-Muller, Souad Christieans, Sabine Leroy, Angeli Kodjo, Christine Vernozy-Rozand

International Journal of Food Microbiology . 112 ( 2 ) : 153-161

DOI: 10.1016/j.ijfoodmicro.2006.06.017

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, Benoit Remenant, Arnaud Dechesne, Jean 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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Lavendula species as accompanying plants in Cupressus replanting strategies: Effect on plant growth, mycorrhizal soil infectivity and soil microbial catabolic diversity

Lahcen Ouahmane, Mohamed Hadifi, Christian Plenchette, Marija Kisa, Ali Boumezzough, Jean Thioulouse...

Applied Soil Ecology . 34 ( 2-3 ) : 190-199

DOI: 10.1016/j.apsoil.2006.02.002

Journal article

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Relationships between plant-parasitic nematode community fallow duration and soil factors in the Sudano-Sahelian area of Senegal

P. Cadet, D. Masse, J. Thioulouse

Agriculture, Ecosystems & Environment . 108 : 302-317

Journal article

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The mycorrhizal fungus Glomus intraradices and rock phosphate amendment influence plant growth and microbial activity in the rhizosphere of Acacia holosericea

R. Duponnois, A. Colombet, V. Hien, J. Thioulouse

Soil Biology and Biochemistry . 37 : 1460-1468

Journal article

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Soil bacterial diversity responses to root colonization by an ectomycorrhizal fungus are not root-growth dependent

K. Assigbetse, M. Gueye, J. Thioulouse, R. Duponnois

Microbial ecology . 50 : 350-359

Journal article

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Spider webs designed for rare but life-saving catches

Samuel Venner, J. Casas

Proceedings of the Royal Society B: Biological Sciences . 272 : 1587-1592

Journal article

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Fate of Listeria monocytogenes in experimentally contaminated French sausages

D. Thévenot, Marie Laure Delignette-Muller, S. Christieansa, Christine Vernozy-Rozand

International Journal of Food Microbiology . 101 : 189-200

Journal article

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Prevalence of Listeria monocytogenes in 13 dried sausage processing plants and their products

D. Thévenot, Marie Laure Delignette-Muller, S. Christieans, Christine Vernozy-Rozand

International Journal of Food Microbiology . 102 : 85-94

Journal article

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Modelling the effect of a temperature shift on the lag phase duration of Listeria monocytogenes

Marie Laure Delignette-Muller, F. Baty, M. Cornu, H. Bergis

International Journal of Food Microbiology . 100 : 77-84

Journal article

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De la prévalence aux valeurs prédictives: L`antibiogramme face à l`évolution de la résistance aux antibiotiques

B. Lamy, G. Carret, Jean-Pierre Flandrois, Marie Laure Delignette-Muller

Annales de Biologie Clinique . 63 : 493-502

Journal article

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Online synonymous codon usage analyses with the ade4 and seqinR packages

D. Charif, J. Thioulouse, J.R. Lobry, G. Perrière

Bioinformatics . 21 : 545-547

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Forcing reversibility in the no-strand-bias substitution model allows for the theoretical and practical identifiability of its 5 parameters from pairwise DNA sequence comparisons

O. Zagordi, J.R. Lobry

Gene . 347 : 175-182

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