Epigeous saprotrophic and ectomycorrhizal (ECM) fungal sporocarps were assessed during 7 yr in a French temperate experimental forest site with six 30-year-old mono-specific plantations (four coniferous and two hardwood plantations) and one 150-year-old native mixed deciduous forest. A total of 331 fungal species were identified. Half of the fungal species were ECM, but this proportion varied slightly by forest composition. The replacement of the native forest by mono-specific plantations, including native species such as beech and oak, considerably altered the diversity of epigeous ECM and saprotrophic fungi. Among the six mono-specific stands, fungal diversity was the highest in Nordmann fir and Norway spruce plantations and the lowest in Corsican pine and Douglas fir plantations. Several factors, connected to the mono-specificity of host trees, could be involved in regulating fungal diversity. Interestingly, this study showed a significant negative correlation between fungal species richness and nitrogen mineralisation, indicating that increases in mineral N availability are associated with decline in saprotrophic and ECM community richness. The frequency of occurrence of fruit bodies of 11 edible fungal species that naturally occur in the native forest was modified by the treatments.

-15 N and 13 C natural abundances of foliage, branches, trunks, litter, soil, fungal sporophores, mycorrhizas and mycelium were determined in two forest stands, a natural forest and a Norway spruce plantation, to obtain some insights into the role of the functional diversity of saprotrophic and ectomycorrhizal fungi in carbon and nitrogen cycles. Almost all saprotrophic fungi sporophores were enriched in 13 C relative to their substrate. In contrast, they exhibited no or very little shift of δ 15 N. Judging from the amount of C discrimination, ectomycorrhizal fungi seem to acquire carbon from their host or from dead organic matter. Some ectomycorrhizal species seem able to acquire nitrogen from dead organic matter and could be able to transfer it to their host without nitrogen fractionation, while others supply their host with 15 N-depleted nitrogen. Moreover ectomycorrhizal species displayed a significant N fractionation during sporophore differentiation, while saprotrophic fungi did not. Presque tous les champignons saprophytes présentent un enrichissement en 13 C relativement à leur substrat. Par contre, ils ne présentent pas ou ne présentent que très peu de modifications du δ 15 N. En fonction de leur taux de discrimination du carbone, les champignons ectomycorhiziens semblent pouvoir acquérir du carbone à la fois à partir de leur hôte et de la matière organique morte. Quelques espèces semblent capables d'acquérir de l'azote organique du sol et de le transférer sans fractionnement à leur hôte alors que d'autres fournissent leur hôte en azote appauvri en 15 N. De plus, les espèces ectomycorhiziennes présentent un fractionnement significatif de l'azote pendant la différenciation des carpophores, alors que les champignons saprophytes n'en présentent pas.13C / 15N / peuplements forestiers / champignons saprophytes / champignons mycorhiziens

Abstract• Liming is a forestry practice used to counteract forest decline in acidic soils. It consists of direct Ca and Mg input to forest soil, which restores tree mineral nutrition, but also modifies microbial communities in soil. The aim of this study was to assess the effects of liming on both belowground (ectomycorrhizal root tips) and aboveground (epigeous sporocarps) fungal communities.• Results showed that the modification of soil chemical properties (pH, and Ca-Mg contents versus total free Al and Fe concentrations) was a stronger factor of ECM community structuring than tree host. The species appearing in limed plots were ubiquist or known as good competitors and replaced acidophilic and stress species.• At the sporocarp level, tree host was a stronger factor of community structuring than soil chemical properties associated with liming. On the whole, there was a shift in the community composition from a typical acidophilic forest fungal community of medium altitude in the untreated plots to a less typical one, with the reduced dominance of acidophilic fungi while many late-stage forest species appeared.• We finally suggest a marker species (Russula ochroleuca) to assess both above and belowground effects of liming on ectomycorrhizal communities. Mots-clés : mycorhize / management des écosystèmesRésumé -Le chaulage forestier influence durablement les communautés d'ectomycorrhizes et de carpophores épigés.• Le chaulage est une pratique forestière utilisée pour restaurer la nutrition minérale des arbres apparaissant sur sol acide. Il consiste en un apport direct de Ca et Mg au sol forestier, ce qui restaure la nutrition minérale de l'arbre, mais aussi modifie les communautés microbiennes du sol. Cette étude évalue les effets du chaulage sur les communautés fongiques hypogées (apex ectomycorrhiziens : « ECM ») et épigées (carpophores).• Les résultats montrent que la modification des des propriétés chimiques du sol (pH et concentrations en Ca-Mg échangeables versus concentrations en Al et Fe échangeables) est un facteur de structuration de la communauté d'ECMs plus fort que l'arbre hôte. Les espèces qui sont apparues dans les placeaux chaulés sont ubiquistes ou compétitrices et ont remplacé des espèces acidophiles ou connues pour être associées à des conditions de stress.• Concernant les carpophores, l'arbre hôte est un facteur de structuration de la communauté plus fort que les propriétés chimiques du sol associées au chaulage. Dans l'ensemble, on a observé une modification de la communauté fongique, passant d'une communauté typique de forêt acide de moyenne altitude dans les placeaux témoins vers une autre moins spécifique, caractérisée par une moindre dominance d'espèces acidophiles et l'apparition de nombreuses espèces de forêt mature.• Nous suggérons enfin une espèce marqueur (Russula ochroleuca) qui permet d'évaluer facilement les effets du chaulage sur les communautés de champignons mycorrhiziens, aussi bien du point de vue des apex mycorrhiziens que des carpophores.

-• The development of truffles in the soil is not well understood. It is not known if a direct transfer of carbohydrates takes place between the host tree and the developing ascocarps through ectomycorrhizal structures or whether sporophores become independent from their hosts after several weeks or months and are able to use dead host tissues or soil organic matter as carbon (C) and nitrogen (N) sources.• To study saprophytic or symbiotic capacities of truffle ascocarps the natural abundance of 15 N and 13 C in foliage, wood, fine roots, mycorrhizae, fungal sporophores and soil were determined in a truffle orchard.• The processes of carbon and nitrogen allocation remained unchanged during the entire period of ascocarp development of Tuber melanosporum. From 13 C and 15 N natural abundance measurements, T. melanosporum, T. brumale and T. rufum did not exhibit saprotophic strategy during ascocarp development, which is contradictory to common statements found in handbooks regarding truffle cultivation. • Le développement des truffes dans le sol n'est pas encore bien compris. Les connaissances actuelles ne nous permettent pas de savoir s'il existe un transfert direct de sucres entre l'arbre hôte et les ascocarpes en développement via les structures ectomycorhiziennes, ou si les ascocarpes utilisent le carbone et l'azote directement issu de la matière organique du sol.• Nous avons mesuré l'abondance naturelle du 15 N et du 13 C dans le sol, les feuilles, les mycorhizes, le bois et les carpophores d'une truffière naturelle à chêne vert afin de déterminer la stratégie de la nutrition carbonée des ascocarpes.• Les processus d'allocation du carbone et de l'azote restent identiques pendant toute la phase de développement des ascocarpes de Tuber melanosporum. De ces mesures d'abondance naturelle du 15 N et du 13 C, il apparaît que T. melanosporum, T. brumale et T. rufum ne développent pas de stratégie saprophytique pendant le développement des ascocarpes, ce qui est en contradiction avec les idées habituellement véhiculées par les manuels de trufficulture 13 C / 15 N / Tuber melanosporum / ascocarpes / développement

In molecular ecology, the development of efficient molecular markers for fungi remains an important research domain. Nuclear ribosomal internal transcribed spacer (ITS) region was proposed as universal DNA barcode marker for fungi, but this marker was criticized for Indel-induced alignment problems and its potential lack of phylogenetic resolution. Our main aim was to develop a new phylogenetic gene and a putative functional marker, from single-copy gene, to describe fungal diversity. Thus, we developed a series of primers to amplify a polymorphic region of the Glycoside Hydrolase GH63 gene, encoding exo-acting α-glucosidases, in basidiomycetes. These primers were validated on 125 different fungal genomic DNAs, and GH63 amplification yield was compared with that of already published functional markers targeting genes coding for laccases, N-acetylhexosaminidases, cellobiohydrolases and class II peroxidases. Specific amplicons were recovered for 95% of the fungal species tested, and GH63 amplification success was strikingly higher than rates obtained with other functional genes. We downloaded the GH63 sequences from 483 fungal genomes publicly available at the JGI mycocosm database. GH63 was present in 461 fungal genomes belonging to all phyla, except Microsporidia and Neocallimastigomycota divisions. Moreover, the phylogenetic trees built with both GH63 and Rpb1 protein sequences revealed that GH63 is also a promising phylogenetic marker. Finally, a very high proportion of GH63 proteins was predicted to be secreted. This molecular tool could be a new phylogenetic marker of fungal species as well as potential indicator of functional diversity of basidiomycetes fungal communities in term of secretory capacities.