Ecology of Forest Pathogenic Fungi team

Our team is studying the ecology, the epidemiology and the evolutionary biology of emerging forest tree diseases. Our research focuses on several important tree diseases (poplar rust, ash dieback, Phytophthora alder decline, oak powdery mildew, Dothistroma needle blight, Diplodia shoot blight). Since these pathogens are complementary in their phylogenetic position (Basidiomycetes, Ascomycetes, Oomycetes), their etiology (root, shoot and leaf pathogens) and their biology (biotrophic, hemibiotrophic or necrotrophic), they allow us to tackle different questions. The main objectives are (i) to disentangle the causes of the emergence of several diseases, (ii) to monitor and model the dispersal of diseases and assess their genetic consequences, (iii) to study how pathogen populations adapt to their hosts, and (iv) to assess the effects of diseases on forest stands.

Our research is therefore organized in four research actions:

Action 1: Emergence of forest tree diseases and its causes

Actors: B. Marçais, C. Husson, O. Caël, A. Gillet

Emerging tree diseases, i.e. diseases that increase either in geographical range or host range or in severity within their range, are a major issue throughout the world. These diseases greatly impact natural or semi-natural ecosystems including forests, they affect the productivity of managed stands and threaten biodiversity. Four causes of forest disease emergence are usually recognized: climate change, evolution of host populations due to forestry, introduction of invasive pathogens, and evolutionary changes of the pathogen populations. Disentangling these causes remains a major scientific challenge. The availability of a reliable source of data on the occurrence of forest tree diseases since 1989 in France (French Forest Health Department, DSF database) gives us a unique opportunity to study the causes of emergences. The introduction and spread of ash dieback in France since 2008 offers us the opportunity to study an on-going biological invasion by an exotic pathogen. The effect of climate change is studied on oak mildew, Phytophthora alder decline and ash dieback. In particular, mechanism such as phenological synchrony will be studied in the case of oak mildew. The hypothesis of a climatic limitation of the distribution range of ash dieback and of Phytophthora xalni in Southern France will be tested. The evolution of pathogen populations, namely through interspecific hybridization, will be further studied on Phytophthora species.



Action 2: Dispersal of pathogens and its genetic consequences

Actors: F. Halkett, S. De Mita, B. Marçais, P. Frey, C. Husson, B. Fabre, A. Andrieux, O. Caël, J. Pétrowski, A. Gillet, M. Grosdidier

We aimed to gather the complementary expertise of all the members of the team to characterize the dispersal of pathogens and unravel the evolutionary consequences of dispersal. In particular, the wide spectrum of our disciplinary skills around population biology, from epidemiology to evolutionary biology including population genomics and modelling, allows us to address questions related to (i) monitoring and modelling the spread of an invasive pathogen, (ii) disentangling the effect of both demographic and selection events accompanying disease spread, and (iii) assessing the evolution of life history traits during disease spread. These questions are tackled on two disease models. First, Hymenoscyphus fraxineus is an exotic pathogen that strongly impacts the European ash population. Its progressive spread in France is well documented and provides a good model to study biological invasions. Second, the poplar rust fungus Melampsora larici-populina is monitored in a particular ecological situation, the Durance River valley, which allows the monitoring of recurrent annual epidemics.



Action 3: Adaptation of pathogens to their hosts

Actors: P. Frey, F. Halkett, S. De Mita, B. Fabre, A. Andrieux, J. Pétrowski, A. Maupetit

The breakdown of host resistance to plant pathogens is of critical concern in agriculture, forestry, and the management of natural systems. The aim of this action is to study the genetic architecture of life history traits related to pathogenicity in the poplar rust fungus, M. larici-populina. The main hypothesis is that the aggressiveness of M. larici-populina could increase following the deployment of new poplar cultivars with quantitative resistance. We plan to study the genetic architecture of qualitative (virulence factors) and quantitative (aggressiveness components) traits in the poplar rust fungus. To this aim, whole-genome re-sequencing techniques will be used in two complementary approaches: (i) mapping avirulence loci and aggressiveness QTLs through whole-genome re-sequencing of progenies obtained from controlled crosses of M. larici-populina, and (ii) mapping the same qualitative and quantitative traits through an approach of Genome-Wide Association Study (GWAS) in natural populations of M. larici-populina. Furthermore, we will assess the potential trade-offs between those traits, which can condition the adaptation of the pathogen to the resistance of the host. The long-term objective of this action is to better understand the potential evolution of aggressiveness in pathogens, in order to guide breeding strategies towards durable resistance, especially in poplar.



Action 4: Consequences of diseases on forest stands

Actors: B. Marçais, C. Husson, O. Caël, J. Legeay

One of the important issues raised in ecology is that of the impact of pathogens on the structure of host populations. This question is studied on Phytophthora alder decline and ash dieback. The impact of Phytophthora xalni on alder riparian stands is studied by a dual approach of monitoring the demography of alders on a portion of the Sarre River and using a SIS model developed in our team. This enables us to assess the possible effect of climate change on the impact of P. xalni on alder stands. The impact of H. fraxineus on ash demography and mortality is studied taking into account the stand age and the environment. In particular, the question of the frequency and level of disease tolerance in ash stands, and its ability to mitigate the disease impact in different environments, will be investigated in collaboration with tree geneticists. This work should have applied results in terms of ecosystem management and breeding for resistance.

The impact of pathogens on the tree community structure is also studied in the case of endemic pathogens (outside any invasion context). To this aim, we look at the oomycete communities affecting forests of the Amazonian basin, within the ANR Nebediv project. The aim will be to document whether Janzen-Connell effects (i.e. the maintenance of tree species biodiversity through pest pressure) may shape the spatial pattern of some tree species selected for their aggregative pattern.


The team participates in several research programs:

COST Action FP1102 DIAROD (Determining invasiveness and risk of Dothistroma, 2011-2016)

ANR CLONIX (Revisiting the population genetics and genomics of partially clonal organisms, 2012-2016)

COST Action FP1103 FRAXBACK (Fraxinus dieback in Europe: elaborating guidelines and strategies for sustainable management, 2012-2016)

ANR GANDALF (Genomic and adaptation of fungal life traits involved in host-pathogen interactions, 2013-2016)

ANR FUNFIT (A trait-based approach linking individual fitness of fungal plant pathogens to ecological strategies, 2013-2017)

ANR NEBEDIV (An integrated test of natural-enemy mediated tree beta-diversity across South American rain forests, 2013-2017)

RESIPATH (Responses of European forests and society to invasive pathogens, BIODIVERSA, 2014-2017)


See the group photo of the permanent staff here

Contact us: Contact