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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_rvb150  

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.

Hafiz Bashir Ahmad. Understanding the mechanism of cavitation resistance in plants. Université de Bordeaux. Dir. DELZON Sylvain, PORTE Annabel.

Water transport system in plants consists of xylem conduit network through which water moves under negative pressure (tension) caused by transpiration pull at the leaf level which is transmitted down to the root level through a continuous water column. This metastable liquid state is prone to cavitation, a phase change from liquid water to vapour leading to blockage of water flow (air embolism) through the conduits, thus reducing the ability of plants to move water from soil to leaf. This leads to partial or total stomatal closure and reduction in gas exchange and growth but also to desiccation and mortality. Xylem embolism is a consequence of drought and rising global temperatures linked with climate change have already enhanced drought induced tree mortality irrespective of the region of their existence affecting the global net primary productivity (Anderegg et al, 2012; Breshears et al, 2005; Zhao and Running, 2010). Previous studies indicate that the ability of woody plants to survive and recover from long drought spells is strongly associated with their ability of resistance to cavitation (Brodribb and Cochard, 2009; Kursar et al, 2009; Urli et al 2013). Understanding the phenomenon of cavitation resistance is, therefore, a trait of vital importance to understand the ability of woody species to transport water during drought events and predicting drought induced forest decline at regional and global level. 

Resistance to cavitation varies considerably among species, especially conifers. The aim of this study is to investigate the intraspecific variability in cavitation resistance in a conifer species (Pinus pinaster) as well as in several crop species such as sunflower. Vulnerability to cavitation will be assessed by constructing vulnerability curves using the Cavitron technique (Cochard, 2002) based on centrifugal force. Xylem anatomy will be studied to find out structural variation. Genetic variation in resistance to cavitation in maritime pine (Pinus pinaster)will also be assessed in situ. Quantitative Trait Locus (QTL) Analysis will be conducted to detect the genomic regions involved in cavitation resistance.   

Mots clés : Drought; climate change; cavitation resistance; hydraulic conductance; xylem

Xavier BOUTEILLER. Rôle des stratégies d’histoire de vie et de l’adaptation dans la dynamique d’invasion par Robinia pseudoacacia. Université de Bordeaux. Dir. PORTE Annabel, MARIETTE Stéphanie.

Thomas CAIGNARD. Tree population responses to climate change: monitoring reproduction into the wild. Université de Bordeaux. Dir. DELZON Sylvain, KREMER Antoine

Phenology is a sensitive biosphere indicator of climate change. Previous studies indicated that plant phenology has been advanced by 2–3 days in spring and delayed by 0.3–1.6 days in autumn per decade in the past 50 years, resulting in extension of the growing season (Vitasse et al. 2009, Menzel et al. 2006). Although changes in vegetative phenology have considerable consequences for ecosystem functioning (Keeling et al 1996), we lack information on the response of reproductive phenology in forest trees to climate change. Yet, reproduction is one of the most important traits in determining plant fitness. Because the flowering and fruiting phenology of plants is sensitive to environmental cues such as temperature and moisture (Piovesan and Adams, 2001; Richardson et al 2005), climate change is likely to alter patterns of reproductive phenology (Hedhly et al 2008). The understanding of the sensitivity of tree reproduction to temperature and its possible evolution with climate change is a key issue that could provide new insights into the adaptation of plants to environmental changes. We therefore need to characterize temperature sensitivity of reproductive phenology in natural forests in order to forecast change in reproductive success and species distribution under global warming.

The aim of this project is to investigate the relationship between reproductive capacity and temperature. Based on an altitudinal and latitudinal gradients, we will evaluate the sensitivity of reproduction to warming. Seed production of beech and oak populations will be assessed along altitudinal gradients and in a common garden experiment. Seed quantity and quality for each population will be monitored in situ to evaluate the phenotypic plasticity and in common gardens to quantify the genetic differentiation between populations (local adaptation). The monitoring was set up last year and will be completed by a larger seed collection device in each population. We hypothesize that reproductive traits are more under environmental (i.e., plasticity) than genetic control, as shown for leaf phenology (Vitasse et al. 2010).

Mots clés : Trees’ reproduction - Masting - Fitness - Gradient of selection - Climate change

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

Pilar Fernandez-Conradi. Diversité des arbres et résistance des forêts aux invasions biologiques: application au châtaigner et son complexe de bioagresseurs exotiques, chancre (Cryphonectria parasitica) et cynips (Dryocosmus kuriphilus). Université de Bordeaux. Dir. JACTEL Hervé, ROBIN Cécile

L’objectif principal de la thèse est d’analyser les relations fonctionnelles entre la diversité des essences forestières et le service écosystémique de régulation des invasions biologiques.

Récemment deux espèces exotiques ont progressivement envahi les peuplements de châtaigniers (Castanea sativa), une essence multi-usage jouant un rôle primordial au sein des économies locales (production fruitière, production de bois). La première est l’Ascomycète Cryphonectria parasitica, responsable de la maladie du chancre du châtaignier, introduite en France dans les annés 40. Une deuxième espèce invasive est le cynips du chatagnier (Dryocosmus kuriphilus), observé pour la première fois en France en 2007. Cet insecte gallicole est maintenant répandu sur une large proportion du territoire français et menace la production de bois, de châtaignes, voire la survie des arbres en cas de fortes infestations.

Trois hypothèses principales seront testées au cours de cette thèse :

H1 – Les deux bioagresseurs invasifs ont une action synergique négative sur la santé des châtaigniers (ex., les attaques du cynips peuvent constituer des points d’entrée pour l’infection par le champignon).

H2 – Le mélange du châtaignier avec des essences non-hôtes du chancre et du cynips (conifères) réduisent la densité et l’accessibilité des arbres hôtes, réduisant la probabilité de contamination (« host concentration hypothesis »).

H3 – Le mélange du châtaignier avec des chênes caducifoliés permet le maintien d’une ressource alimentaire de complément (les galles du chêne) pour les ennemis naturels généralistes des cynipidae, qui peuvent alors mieux contrôler les populations de l’espèce invasive (« natural enemy hypothesis »).

Ces hypothèses seront testées sur des peuplements de châtaigniers établis le long d’un gradient de mélange avec d’autres essences forestières en Italie et dans des comparaisons appariées de peuplements purs vs. mixtes de châtaigniers, par des suivis épidémiologiques et des expérimentations en conditions contrôlées et des études de laboratoire.

Mots clés : Chatagnier – Biodiversité- Cynips- Chancre

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.

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.

Adib OUAYJAN. Démographie et génétique de la régénération d’une population de hêtre (Fagus sylvatica) en marge chaude de l’aire de répartition de l’espèce. Université de Bordeaux. Dir. HAMPE Arndt, BERT Didier

Les refuges climatiques sont des zones où les populations locales d'une espèce peuvent survivre pendant des périodes de climat régional défavorable. Ces refuges pourraient être importants pour atténuer l'impact du réchauffement planétaire actuel sur la persistance de la biodiversité.

Le bassin d'Aquitaine contient onze refuges climatiques de Hêtre (Fagus sylvatica) situés à basse altitude. Notre projet est constitué par des études détaillées sur le peuplement le plus grand, qui se trouve dans la vallée du Ciron. Une combinaison des approches génétiques et dendro-écologiques permettra de mieux comprendre les mécanismes écologiques qui déterminent la vigueur et la fécondité réalisée des arbres, ainsi que les patrons spatiaux du flux de gènes.

L’objectif de cette thèse sera de mieux comprendre comment la variation individuelle du succès reproducteur et de flux de gènes influence la structure et la dynamique de régénération du peuplement. De plus, nous rechercherons les éventuels signes démographiques ou génétiques de déclin de la performance de la population.

Les principales hypothèses testées sont les suivantes :

-   La taille, la vigueur et la position à l'égard de partenaires potentiels sont les principaux prédicteurs de succès reproducteur des arbres ;

-   Le flux de gènes se produit essentiellement sur des courtes distances et plusieurs réseaux d'accouplements distincts existent à l’intérieur du peuplement ;

-   La variation climatique interannuelle et la compétition avec la végétation environnante affectent, le plus, la croissance et la mortalité des arbres en position marginale.

L’application d’outils modernes (SNP et isotopes) et des méthodes avancées d’analyse et de simulation permettront une meilleure compréhension des mécanismes écologiques influençant la régénération des arbres forestiers en situation marginale. Cette connaissance sera fondamentale pour prédire la façon dont ces populations pourraient évoluer dans un climat régional plus chaud et plus sec. Cela permettra de développer des stratégies de conservation et de gestion adaptées.

Mots clés : refuge climatique, régénération, Hêtre (Fagus sylvatica), réchauffement global, dendro-écologie, génétique.

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

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