PhD thesis : Understanding the link between the tolerance to drought and to Diplodia sapinea in pine species

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The French National Research Institute for Agriculture, Food, and Environment (INRAE) is a major player in research and innovation. It is a community of 12,000 people with 272 research, experimental research, and support units located in 18 regional centres throughout France. Internationally, INRAE is among the top research organisations in the agricultural and food sciences, plant and animal sciences, as well as in ecology and environmental science. It is the world’s leading research organisation specialising in agriculture, food and the environment. INRAE’s goal is to be a key player in the transitions necessary to address major global challenges. Faced with a growing world population, climate change, resource scarcity, and declining biodiversity, the Institute has a major role to play in building solutions and supporting the necessary acceleration of agricultural, food and environmental transitions.

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Keywords

Diplodia sapinea, Pinus spp., proline, drought tolerance, multirisk, water stress 

Summary of thesis project 

Drought-induced forest diseases are increasing in frequency and severity in Europe due to climate change. The Diplodia tip blight disease is one example. The causal agent of this disease, the ascomycete Diplodia sapinea, is one of the most important pathogens of pine species worldwide. It is present asymptomatically in the host tissues, and the disease symptoms are triggered by abiotic stress, particularly drought. The mechanism by which latent infections can progress to pathogenic colonisation and tissue necrosis is not yet well understood. 

Different pine species show varying degrees of susceptibility to D. sapinea in the field. Often, pine species that are highly tolerant to drought are also less susceptible to the disease. Two key factors have been identified to play a role in the onset of the disease. On the one hand, more negative water potentials are associated with more severe necrotic lesions, but the absolute values vary depending on the host species. On the other hand, drought-induced biochemical changes have been associated with the colonisation by drought-induced pathogens. In particular, the accumulation of proline in the host promotes infection by D. sapinea. In addition, altered carbon metabolism has also been associated with infection, as it 

can lead to reduced defence responses. Consequently, specific proline profiles and non-structural carbohydrates (NSC) in each host species, resulting from water stress, could explain the different sensitivity of hosts to D. sapinea. 

This thesis aims at better understanding the link between these drought-induced biochemical and physiological changes and infection by D. sapinea. Our working hypothesis is that the drought-response traits of pines are specific and determine the susceptibility to D. sapinea. 

This study will be developed in three axes of research. 

(1) First, we propose to study two pine species with contrasting sensitivity to drought and D. sapinea: Pinus sylvestris and Pinus halepensis. A greenhouse experiment with artificial inoculations and drought treatments will allow us to study the effect of changes in water potential, proline concentration and NSC on the development of the pathogen. 

(2) The main selected traits will then be studied in a wider range of pine species according to a susceptibility gradient to D. sapinea. 

(3) The level of inoculum that each pine species is capable of sustaining in the field will be studied following two strategies: (i) sampling of healthy-looking twigs in stands comprising two or more mixed pine species under natural conditions, to assess the intrinsic susceptibility of each pine species to latent infections by the fungus; as well as (ii) systematically on plots within the pin-dominated plots of the large-scale forest condition monitoring network (Level I, 16 × 16 km), which will enable an assessment of whether climatic conditions underlie different intensities of twig colonisation. These two strategies will therefore allow to assess whether there is species-specific variability in pines’ ability to sustain latent infections, or whether the climatic niche of each pine species is more or less favourable to such latent infections. 

Thématique de recherche 

This thesis focuses on the interactions between drought and pathogens in forests. These interactions are becoming increasingly significant in French and European forests, leading to episodes of tree decline that have grown in severity and frequency over recent decades. The occurrence of drought affects trees, in some cases increasing their vulnerability to pathogens. The mechanisms underlying this vulnerability are poorly understood, and this thesis addresses this knowledge gap. The study of interactions between biotic and abiotic stress requires a multidisciplinary approach. On the one hand, ecophysiology helps to understand the response to and impact of drought on trees. On the other hand, this impact produces biochemical and hydraulic changes that could either promote or prevent infection by pathogens.

Objectives

The central question of this PhD thesis is to understand the link between the host’s drought tolerance and its susceptibility to the pathogenic fungus Diplodia sapinea. This question will be explored through three research axes that will combine experimental and empirical work with modelling to obtain an integrated view of the pathosystem. These three areas are: 

1. Study of the coordination of drought response traits in relation to infection by Diplodia sapinea (proline, water potential, NSC) for two pine species with contrasting susceptibilities to drought and to the disease: Pinus halepensis and Pinus sylvestris. 

2. Study of a broader panel of pine species, examining the drought response traits selected in the previous study in relation to the infection by Diplodia sapinea. 

3. Analysis of the basal inoculum levels present in asymptomatic tissues of the different pine species within natural stands, to analyse whether this determines the different susceptibilities to Diplodia sapinea. 

Scientific context 

The study of the interaction between drought and fungal tree pathogens has a long history, but its ecological relevance and renewed interest have emerged in recent decades. Research efforts have focused on the direction and magnitude of this interaction, revealing non-additive impacts (antagonistic or synergistic) on plant performance1,2. The outcome of the interaction depends on several factors, including the host tissue targeted by the pathogen, the severity of water stress and the trophic interaction2–4. Secondary pathogens, which infect trees in poor physiological conditions, are directly favoured by drought2. These pathogens not only amplify drought-related impacts on trees, but are also typically triggered by water stress3,5–8. While previous research highlights the importance of drought-pathogen interactions on forest damage, little research has been focused on the mechanisms by which this interaction takes place. Those pathogens are especially concerning because of their dual-phase life cycle: they persist as endophytes within host tissues before transitioning to a drought-driven pathogenic phase. 

One example of drought-induced forest pathogens is the ascomycete Diplodia sapinea (Fr.) Fuckel (syn. Sphaeropsis sapinea (Fr.: Fr.) Dyko and Sutton), a well-known endophyte in shoots, buds and needles of Pinus spp. that becomes pathogenic after abiotic stress such as drought and hail, leading to tree dieback and mortality5,9. The disease, so-called Diplodia tip blight, threaten Pinus spp. worldwide, and is expanding to northern Europe10. The mechanisms by which D. sapinea switches from an endophytic to a pathogenic lifestyle are not completely understood, which hinders the prediction of future disease outbreaks. 

The transition to pathogenicity of D. sapinea is triggered by abiotic stress, resulting in disease expression. This thesis will focus on water stress. Disease development by D. sapinea in this case depends on two keys factors: (i) the drought response of the tree host, and (ii) the capacity of the pathogen to thrive under water stress and on the new niches created within the host under drought. We will study the different susceptibility of pine host species to D. sapinea under drought by analysing the host traits related to water stress. Some of the traits that would be studied are proline and NSC accumulation as a response to drought11. 

Practical details of the research 

Doctoral contract with the UL (University of Lorraine), but development of the work at the ECPF team at the UMR Interactions Arbres/Microorganismes (INRAE Nancy) and in collaboration with the UMR Silva (INRAE Nancy). The INRAE Nancy centre is located at Champenoux, France. 

Fieldwork in France. 

Two greenhouse experiments involving plant inoculation and the application of water stress. 

Collaboration with the Forest Health Department in France. 

Thesis funding 

The salary is funded by the French government. The associated costs are funded by the programme PEPR FORESTT.

Training and skills

Candidate profile and competences 

Background in phytopathology, ecophysiology and forest ecology (or at least two of those three fields) is required 

Experience in data analysis and R programming 

Experience in basic molecular biology methods 

Good level of written and spoken English 

Spoken French for communication in the laboratory and the field 

INRAE's life quality

By joining our teams, you benefit from (depending on the type of contract and its duration):

- up to 30 days of annual leave + 15 days "Reduction of Working Time" (for a full time);
- parenting support: CESU childcare, leisure services;
- skills development systems: training, career advise;
- social support: advice and listening, social assistance and loans;
- holiday and leisure services: holiday vouchers, accommodation at preferential rates;
- sports and cultural activities;
- collective catering.

How to apply

I send my CV and my motivation letter