Diversity of fungal DyP-type peroxidases and their potential contribution to organic matter degradation

Lignin is one of the most abundant natural polymers on earth whose resistance to degradation contributes to the mechanical strength of plant cell walls and protects plant cells from pathogen attack. Few organisms are can degrade lignin efficiently; most of them belong to the fungal Kingdom. In most cases, plant cell wall degradation results from enzymatic attack. Recent studies also underline the contribution of secreted fungal enzymes in many areas:- many of these enzymes are already in use in numerous industrial processes,- thanks to the comparison between fungal genomes, through the study of genes implicated in organic matter degradation, it becomes obvious that fungal evolution and their ecology are two tightly linked phenomena,- saprotrophic fungi degrading organic matter are the main decomposers in terrestrial ecosystems. Among others, they contribute in a decisive way to the carbon biogeochemical cycle in temperate and boreal ecosystems. The study and a better comprehension of carbon fluxes are of prime importance in the evaluation of climate change. The fungal enzymatic machinery involved in organic matter decomposition is composed of dozens of enzymes whose functions are diversely understood. The roles of several of them need to be clarified. This is the case for the DyP peroxidases, an enzyme family recently described but already well known in the field of biotechnology for their capacity of catalyzing many reactions. Their natural role in natural ecosystems is however matter of discussion. It has been suggested that they could participate in lignin degradation although a role in detoxification during biomass degradation cannot be excluded. In the course of this thesis, we highlighted the potential roles of these enzymes. The DyP gene family had been divided into different sub-families but no study specifically dealt with the phylogeny of fungal DyPs. Such an analysis revealed the unsuspected existence of both intracellular and extracellular DyPs in fungi. To better understand the potential roles of this fungal gene family we developed ecological analyses that first required the development of specific tools such as a protocol to extract RNA directly from decomposing wood. Following a molecular ecology approach, we evaluated the source and diversity of DyP-producing fungi in three distinct habitats; grassland soils, forest soils and decomposing wood. A metabarcoding analysis of the fungal communities present in these different environments has first been conducted and has revealed the beneficial impact of performing metabarcoding on both environmental DNA and RNA to accurately describe fungal communities. The study of DyPs expressed within fungal communities colonizing these different habitats has been conducted by sequence capture on environmental RNA. Preliminary results demonstrate the validity of this approach to isolate the corresponding full-length genes from all studies environmental samples. Several of these environmental DyP genes were transformed in the fungus Podospora anserina and the expression of one of them in this heterologous host was demonstrated.In conclusion, DyP peroxidases still represent a family of fungal enzymes of unclear role. We suggest that extracellular and intracellular DyPs may play complementary roles in both lignin degradation and detoxification of toxic environmental compounds, respectively. This enzyme family is more specifically present in the genomes of basidiomycete fungi capable of enzymatic deconstrustion of lignin. A restricted number of DyP genes has been isolated from each of the different studied environmental samples, thus suggesting that the corresponding enzymes are not abundantly produced although present in all environments