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Unité Mixte de Recherche Inra-Univ. Bordeaux "Biodiversité Gènes et Communautés" - Biogeco

Unité mixte de recherche (Inra, Univ. Bordeaux 1) Biodiversité, gènes et communautés (Biogeco)


INRA Bordeaux-Aquitaine
Site de Recherches Forêt-Bois
69 route d'Arcachon
33612 CESTAS Cedex - FRANCE

Thèses en cours

Retrouvez ci-dessous le résumé des thèses en cours à l'UMR Biogeco.

Juliette ARCHAMBEAU. Modélisation statistique sur le rôle de l'environnement et de la différenciation génétique des populations dans le Pinus sylvestris L. et Pinus pinater Ait. au changement climatique à l'échelle de leur aire de répartition.université de Bordeaux. Dir. GONZALEZ-MARTINEZ Santiago

Alexandre CHANGENET. Ecological and economical evaluation of the mediterraneisation of the French forests. Université de Bordeaux. Dir. PORTE Annabel

Thomas DAMESTOY. Effects of genetic and specific diversity of forest stands on oak resistance at processionary caterpillar, Thaumetopoea processionea. Université de Bordeaux. Dir. CASTAGNEYROL, PLOMION Christophe

The oak processionary moth (OPM, Thaumetopoea processionea) is a specialist herbivore of deciduous oaks in Central Europe and Middle East. It is responsible of major defoliations reducing growth of defoliated trees. Caterpillars are also highly urticating, threatening health of foresters, walkers and animals present in forest stands. How to reduce OPM attacks is therefore a critical issue. Associational resistance theory predicts that tree inter- and intraspecific diversity reduces attacks and damage caused by OPM. We will associational resistance hypothesis and explore underlying mechanisms. Specifically, we will address the effects of tree diversity on OPM preferences and performances and search for underlying oak traits by combining field observations and laboratory experiments, focusing and Quercus robur, Quercus petraea and their hybrids. We will determine oak foliar traits reducing OPM consumption, and the causes of variability in the expression of these traits, in particular the tree genotype effect and neighbour identity. The research program involves a close collaboration between entomologists, ecologists, geneticists and forest managers belonging to different institutes (INRA, ONF, and DSF). Ultimately, we aim to proposing management options allowing to efficiently reduce the negative impact of this pest on oaks, forests and forest users.

Mots clés : Thaumetopoea processionea, Quercus, Diversity, Genetic, Foliar traits

Arthur DEMENE. Évolution des génomes de champignons phytopathogènes après une introduction : l'exemple de Cryphonectria parasitica, l'agent causal du chancre du châtaignier en Europe. Université de Bordeaux. Dir. DUTECH Cyril

Tania FORT. Plant-microbiota interactions: influence of microclimate on leaf microbiota and feedback effects on leaf physiology and phenology. Université de Bordeaux. Dir. VACHER Corinne.

Homero GARATE ESCAMILLA. Modeling forest tree community turnover based on speices' phenotypic variability and response to climate change. Université de Bordeaux. Dir. BENITO Marta, HAMPE Arndt.

Myriam GARROUJ. Restaurer des zones humides alluviales en contexte péri-urbain : mécanismes locaux et approche paysagère. Université de Bordeaux. Dir. ALARD Didier, BENOT Marie-Lise.

In a national and global wetland regression context, the conservation and restoration challenges have to be supported by in-depth knowledge of these systems, at entire territory scales. Wetland restoration set in the French National Strategy for the biodiversity, launched by the Ministry of Ecology, Sustainable development and Environment in 2011. One of its goals is to restore 15% of degraded ecosystems in France by 2020. These restoration operations aim at both functional restoration and ecological continuity restoration.

The thesis project aims at identifying the ecological processes at stake in the dynamic of floodplains of Garonne river basin and characterizing the potential restoration trajectories. It will enable to put forward restoration-rehabilitation solutions for degraded floodplain ecosystems. The thesis project will concern three sites within the floodplain along the Garonne river: the “Olive” site at Parempuyre, the “Bois de Bordeaux” site at Bordeaux and the “Île de Raymond” site at Paillet.

The thesis project will pursue the understanding of effects of 1) the initial conditions of a restoration-aimed site, and 2) the restoration management applied on restored site in the restoration operation success.

The thesis is defined on three hinge points. As a first step, an analysis of ecological restoration experiments already carried out on wetlands will be performed. Then, a study of ecological processes at stake (initial conditions and management modalities effects) will be lead thanks to experimentations on two of the three studied sites. Lastly, the final point will aim at defining floodplain monitoring and assessment protocols in order to bring the best restoration follow-up program.

Mots clés : Ecological restoration; Restoration trajectory; Floodplain; Grassland management

Agathe HUREL. Génomique écologique de l'adaptation. Université de Bordeaux. Dir. GONZALEZ Santiago.

This PhD project is placed deep in the concern of the ongoing climate change: it was predicted that the climate change will be the cause of an expected value loss for the European forest of 21-50% by 2071-2100 (Hanewinkel et al, 2012).

The main objective of this PhD is to investigate the geographical and temporal scales of genetic adaptation, in particular whether rapid genetic change can take place in long lived trees in response to environmental changes and with a focus on polygenic adaptation. A study of resistance to biotic stresses will also be conducted.
The first task will be to measure adaptive traits related to growth, bud phenology and resistance to water deficit in two common gardens, so as to be able to develop association studies to identify genes and polymorphisms underlying those traits, using molecular data obtained by genotyping. Then we will develop methods to study polygenic adaptation, based either on pairwise population comparison of allele frequencies, but also by the construction of a compound statistic correlated to environmental values. In parallel, we aim to study the short term evolutionary response in maritime pine with an experimental setting: we will plant seeds of different families of European lineages and phenotype saplings for growth and resistance to water deficit to compute genetic selection gradients.

For the biotic stresses, we selected two pathogens, armillaria (roots) and rust (branches). The ongoing experiments on the armillaria aim to determine if the effect of different strands of pathogen are similar when inoculated on excised branch. For the rust, we plan to inoculate one of our common gardens that was genotyped to study the relation between genotype and resistance.

Thanks to this work, genetic resources of forest trees can be well managed through climate change, and forestry throughout Europe greatly improved.

Mots clés : climate change, polygenic adaptation, genome-capture, pathogen resistance

Séverin JOUVEAU. Effets de la diversité biologique des forêts sur la diversité fonctionnelle des prédateurs carabiques. Université de Bordeaux. Dir. JACTEL Hervé et CASTAGNEYROL Bastien.

Ludovic LACOMBE. Importance des interactions végétales et de l'utilisation des terres dans la dynamique et la restauration de communautés de hêtres en marge d'aire de répartition. Université de Bordeaux. Dir. CORCKET Emmanuel

Clément LARUE. Pollinisation et production fruitière chez le châtaignier. Invenio. Dir. PETIT Rémy

Marylise MARCHAND. Barrières écologiques à la dissémination de la maladie de l'encre dans les châtaigneraies françaises. Université de Bordeaux. Dir. ROBIN Cécile

Charlie PAUVERT. Learning microbial networks from NGS data : application to biocontrol. Université de Bordeaux. Dir. VACHER Corinne.

Ecological interactions underpin ecosystem services, including those of disease regulation. The microbial interactions that regulate disease are usually identified by using co-culture experiments. This is a tedious and time-consuming process that cannot, therefore, be extended to the whole microbial community with which a pathogen interacts.

A current challenge is to reconstruct microbial interaction networks directly from environmental DNA1. This reconstruction will give us a deeper insight into the biotic environment of pathogen species -- i.e. the pathobiome2 -- and might allow us to identify potential biocontrol agents cost-effectively, by screening automatically whole microbial communities. It will also improve our understanding of the relationship between microbial diversity and ecosystem services, and pave the way to the large-scale bio-monitoring of microbial interactions.

The purpose of the PhD thesis is:

  1. to review existing knowledge on the methods of microbial networks inference and highlight their potential application to disease control (chapter to be submitted to Advances in Ecological Research by September 2017)
  2. to participate to the development of statistical graphical models3 and logic-based machine-learning algorithms4 for reconstructing microbial interaction networks from metabarcoding data and environmental covariates. Several metabarcoding approaches will also be compared to identify those retrieving the most accurately microbial species abundances.
  3. to test these methods by reconstructing microbial interaction networks of the phyllosphere of model plant species (oak for UMR Biogeco and grapevine for UMR Save) and validating some of these interactions using expert knowledge and experimental approaches.
  4. to assess the impact of plant genotype, climate and agricultural practices on the structure phyllosphere microbial networks. Preliminary results suggest that there is a significant effect of agricultural practices (organic versus integrated management) on the composition of phyllosphere microbial communities. Microbial networks will be inferred in the next couple months.

Mots clés : phyllosphere, microbial networks, disease regulation, metabarcoding, network inference

Clément SAINT CAST. Modélisation du développement architectural, de l'acclimatation au vent dominant et de l'ancrage du système racinaire du pin maritime. Université de Bordeaux. Dir. DANJON Frédéric, DEFOSSEZ Pauline.

Storms are responsible for 56% of dieback and mortality in European forest. Therefore, anchorage is a vital function for trees. However, this function is complex and not well described. The predominant factor that determines anchorage is root architecture. We hypothesized that the main structural root components that govern tree anchorage change with tree development and environment (wind and soil). A modeling approach is used to describe the root system development and its mechanical resistance to uprooting. This generic approach will be developed for Pinus pinaster in a sandy spodosol. This project comprises three parts:

- calibrate a growth model of tree root system from germination to mature stage based on experimental chronosequences of 3D digitized root systems;

- simulate root system development over the years with the calibrated root architectural model "Root Typ". Two modules for acclimation to prevailing winds and to soil constraints (hardpan and water table) will be included;

- simulate mechanical resistance of the root system with the biomechanical model "RootAnchor". Numerical experiments will be conducted to identify the main structural root components involved in anchorage and their change with developmental stages.

The different growth processes of the architectural model “Root Typ” were parametrized, by defining a classification of root types. The first simulations of root system growth were obtained. The mechanical resistance of root systems including their possible acclimation to wind was modeled by considering ovality of root segments in the prevailing wind direction. Simulations showed that this ovality induced an increase of root anchorage. This work aims at providing a model for structural root growth to be included in models for the biomechanics of the whole plant.

Mots clés : 3D root architecture growth, acclimation, stability, biomechanics, modelling

Sylvain SCHMITT. Génomique écologique de l’exploitation de niche et la performance individuelle chez les arbres forestiers tropicaux. Université de Bordeaux. Dir. HEUERTZ & HERAULT Bruno

Elena VALDES. Effects of the genetic structure of spontaneously established oak stands on the strcuture of insect communities and  herbivory. Université de Bordeaux. Dir. Arndt HAMPE & Bastien CASTAGNEYROL

Marion WALBOTT. Rôle des facteurs locaux dans la distribution et la persistence des communautés à hêtre (Fagus sylvatica) en marge d'aire de répartition. Université de Bordeaux. Dir. Emmanuel CORCKET