Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve (1) widespread losses of degrading enzymes acting on lignin and cellulose, (2) co-option of genes present in saprotrophic ancestors to fulfill new symbiotic functions, (3) diversification of novel, lineage-specific symbiosis-induced genes, (4) proliferation of transposable elements and (5) divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.

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A number of soil-borne fungi are able to form typical ericoid mycorrhizae with plants belonging to Ericales. Together with Hymenoscyphus ericae, the first isolate from roots of ericaceous plants, other fungal species belonging to the genus Oidiodendron and many sterile mycelia have been recognized as mycorrhizal by several authors. A high genetic diversity was even found when a population of ericoid mycorrhizal fungi isolated from a single plant of Calluna vulgaris was analysed with morphological and molecular techniques. Ericoid fungi have a relevant saprotrophic potential, as they can degrade several organic polymers present in the soil matrices. Diffcrcnt cell wall degrading enzymes, which are part of this arsenal and are produced in vitro by several ericoid fungi, have been investigated biochemically. Immunocytochemical studies on the production of pectin degrading enzymes during the infection process of host and non-host plants suggest that regulation mechanisms for the production of cell wall degrading enzymes in vivo may be a crucial step for the establishment of successful mycorrhiza with host plants.RQum6 : Plusieurs champignons du sol peuvent former des mycorhizcs Cricoides typiques avec des plantes appartenant aux Ericales. Avec I'Hymenoscyphus ericae, le premier champignons isolC de racines de plantes CricacCes, d'autres champignons appartenant au genre Oidiodendron et plusieurs myctlium stCriles ont Ct C reconnus comme mycorhiziens, par plusieurs auteurs. On a m&me trouvt un forte diversite gCn6tique lorsqu'une population de champignons mycorhiziens Cricoi'des provenant d'une m&me plante hbte de Calluna vulgaris a Ct C analyste 2 I'aide de mCthodes morphologiques et molCculaires. Les champignons irico'idcs possedent un fort potentiel saprophytique puisqu'ils peuvent degrader plusieurs polymbres organiques dans les litibres des sols. Les auteurs ont examine biochimiquement, differents enzymcs capables de dCgrader les parois cellulaires et qui se retrouvent dans les milieux de culture in vitro de plusieurs champignons 6ricoi'des. Des Ctudes immuno-histochimiques conduites sur la production d'enzymes dtgradant la pectine, au cours de la colonisation de plantes hbtes ou non-hbtes, suggbrent que les mCcanismes de rtgularisation de la production d'enzymes capables de degrader les parois cellulaires in vivo pourraient constituer une Ctape determinante dans la formation de mycorhizes fonctionelles avec la plante hbte.

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The endophytic microbiota can establish mutualistic or commensalistic interactions within the host plant tissues. We investigated the bacterial endophytic microbiota in three species of Mediterranean orchids (Neottia ovata, Serapias vomeracea, and Spiranthes spiralis) by metabarcoding of the 16S rRNA gene. We examined whether the different orchid species and organs, both underground and aboveground, influenced the endophytic bacterial communities. A total of 1,930 operational taxonomic units (OTUs) were obtained, mainly Proteobacteria and Actinobacteria, whose distribution model indicated that the plant organ was the main determinant of the bacterial community structure. The co-occurrence network was not modular, suggesting a relative homogeneity of the microbiota between both plant species and organs. Moreover, the decrease in species richness and diversity in the aerial vegetative organs may indicate a filtering effect by the host plant. We identified four hub OTUs, three of them already reported as plant-associated taxa (Pseudoxanthomonas, Rhizobium, and Mitsuaria), whereas Thermus was an unusual member of the plant microbiota. Core microbiota analysis revealed a selective and systemic ascent of bacterial communities from the vegetative to the reproductive organs. The core microbiota was also maintained in the S. spiralis seeds, suggesting a potential vertical transfer of the microbiota. Surprisingly, some S. spiralis seed samples displayed a very rich endophytic microbiota, with a large number of OTUs shared with the roots, a situation that may lead to a putative restoring process of the root-associated microbiota in the progeny. Our results indicate that the bacterial community has adapted to colonize the orchid organs selectively and systemically, suggesting an active involvement in the orchid holobiont.