Pierre-Arthur Moreau

Species diversity and drivers of spread of alien fungi (sensu lato) in Europe with a particular focus on France

A first comprehensive inventory of alien fungi and fungal-like organisms (in Stramenopila) recorded in France since 1800 was established, comprising 227 species, with 64.7% plant pathogens, 29.5% saprotrophic species, 3.5% ectomycorrhizal fungi, 1.3% animal parasites and 0.9% mycopathogenic fungi. Using this and a previously built European dataset, correlates of invasion success in fungi (sensu lato) were investigated, especially for pathogenic species occurring in wild environments (mostly forest tree pathogens). Several common features were demonstrated at the two spatial scales. Some taxonomic/phylogenetic orders were shown to be over-represented in alien fungi and Stramenopila pseudo-fungi, e.g. Peronosporales and to have faster spread, e.g. Erysiphales. Residence time and economic variables, especially imports, were important explaining variables of the levels of invasion. The influence of climatic factors was also suggested.

Comparative phylogenies and host specialization in the alder ectomycorrhizal fungi Alnicola , Alpova and Lactarius (Basidiomycota) in Europe

BackgroundMycorrhizal fungi form intimate associations with their host plants that constitute their carbon resource and habitat. Alnus spp. (Betulaceae) are known to host an exceptional species-poor and specialized ectomycorrhizal (ECM) fungal community compared to other tree species, but the host-specificity pattern and its significance in terms of fungal diversification and speciation remain poorly documented. The degree of parallel speciation, host switching, and patterns of biogeography were explored in the historical associations between alders and three ECM taxa of Basidiomycetes: Alnicola (Agaricales), Alpova (Boletales), and Lactarius (Russulales). The aim was to develop an evolutionary framework on host specificity and diversification of Basidiomycetes in this highly specialized plant-fungus symbiosis.ResultsSporocarps of Alnicola (220), Lactarius (61) and Alpova (29) were collected from stands of the four European alder species (A. alnobetula including the endemic subsp. suaveolens in Corsica, A. cordata, A. glutinosa, A. incana) in Western Europe (mainly in France and Austria), from 1995 to 2009. Specimens were morphologically identified to the species level. From these, 402 sequences of four DNA regions (ITS, rpb2, gpd, and the V9 domain of the mit-SSU rDNA) were successfully obtained and analyzed in addition with 89 sequences available in GenBank and UNITE databases. Phylogenetic analyses were conducted on all sequence data sets (individual and combined) using maximum likelihood reconstruction and Bayesian inference. Fungal phylogenies are compared and discussed in relation to the host, with a focus on species boundaries by associating taxonomic, systematic and molecular information.ConclusionsPatterns of host specificity and phylogenies of Alnicola and Lactarius suggest coevolution as a basal factor of speciation in relation with the subgeneric diversification of Alnus, possibly due to the very selective pressure of the host. A second element of the historical associations between Alnus and its fungal symbionts is a host-dependent speciation (radiation without host change), here observed in Alnicola and Alpova in relation with Alnus subgen. Alnus. Finally host shifts from Alnus subgen. Alnus to A. alnobetula are found in most lineages of Alnicola (at least four times), Alpova (twice) and Lactarius (once), but they do not represent such a common event as could be expected by geographic proximity of trees from the two subgenera. However, active or very recent host extensions clearly occurred in Corsica, where some fungi usually associated with Alnus glutinosa on mainland Europe locally extend there to A. alnobetula subsp. suaveolens without significant genetic or morphological deviation.

Phylogenetic species delimitation in ectomycorrhizal fungi and implications for barcoding: the case of the Tricholoma scalpturatum complex (Basidiomycota).

Population studies have revealed that the fungal ectomycorrhizal morphospecies Tricholoma scalpturatum consists of at least two genetically distinct groups that occur sympatrically in several geographical areas. This discovery prompted us to examine species boundaries and relationships between members formerly assigned to T. scalpturatum and allied taxa using phylogenetic analyses. Sequence data were obtained from three nuclear DNA regions [internal transcribed spacer (ITS), gpd and tef], from 101 carpophores collected over a large geographical range in Western Europe, and some reference sequences from public databases. The ITS was also tested for its applicability as DNA barcode for species delimitation. Four highly supported phylogenetic clades were detected. The two previously detected genetic groups of T. scalpturatum were assigned to the phylospecies Tricholoma argyraceum and T. scalpturatum. The two remaining clades were referred to as Tricholoma cingulatum and Tricholoma inocybeoides. Unexpectedly, T. cingulatum showed an accelerated rate of evolution that we attributed to narrow host specialization. This study also reveals recombinant ITS sequences in T. inocybeoides, suggesting a hybrid origin. The ITS was a useful tool for the determination of species boundaries: the mean value of intraspecific genetic distances in the entire ITS region (including 5.8S rDNA) was <0.2%, whereas interspecific divergence estimates ranged from 1.78% to 4.22%. Apart from giving insights into the evolution of the T. scalpturatum complex, this study contributes to the establishment of a library of taxonomically verified voucher specimens, an a posteriori correlation between phenotype and genotype, and DNA barcoding of ectomycorrhizal fungi.

True morels (Morchella, Pezizales) of Europe and North America: evolutionary relationships inferred from multilocus data and a unified taxonomy

Applying early names, with or without original material, to genealogical species is challenging. For morels this task is especially difficult because of high morphological stasis and high plasticity of apothecium color and shape. Here we propose a nomenclatural revision of true morels (Morchella, Pezizales) from Europe and North America, based on molecular phylogenetic analyses of portions of the genes for RNA polymerase II largest subunit (RPB1) and second largest subunit (RPB2), translation elongation factor-1α (TEF1), the nuc rDNA region encompassing the internal transcribed spacers 1 and 2, along with the 5.8S rDNA (ITS), and partial nuc 28S rDNA D1-D2 domains (28S). The 107 newly sequenced collections were from both continents, including 48 types, together with previously published sequences. Names are applied to 30 of the 65 currently recognized genealogical species. Results of the present study revealed that the number of Morchella species in Europe (n = 21) is nearly identical to that in North America (n = 22). Only seven species were found on both continents, consistent with previous reports of high continental endemism within the genus. Presently it is not possible to tell whether the transoceanic disjunctions were due to human activities, migration across a Bering land bridge or long-distance dispersal. In an effort to stabilize the taxonomy, due in part to the recent publication of synonyms for 11 of the species, accepted names are presented together with their corresponding later synonyms. A new subclade that includes holotypes of M. castanea and M. brunneorosea is identified in sect. Morchella (Esculenta Clade). Lectotypes for Morchella deliciosa, M. eximia and M. tridentina are designated here, as well as epitypes for M. dunalii, M. eximia, M. purpurascens and M. vulgaris. Morchella conica was determined to be illegitimate, and further research is required to determine the identity of M. elata and M. inamoena.

Mycophilic or Mycophobic? Legislation and Guidelines on Wild Mushroom Commerce Reveal Different Consumption Behaviour in European Countries

Mycophiles forage for and pick vast quantities of a wide variety of wild mushroom species. As a result, mushroom intoxications are comparatively frequent in such countries with mycophiles. Thus, national governments are forced to release guidelines or enact legislation in order to ensure the safe commerce of wild mushrooms due to food safety concerns. It is in these guidelines and laws that one can observe whether a country is indeed mycophobic or mycophilic. Furthermore, these laws and guidelines provide valuable information on mushroom preferences and on the consumption habits of each country. As such we were interested in the questions as to whether mushroom consumption behaviour was different within Europe, and if it was possible to discover the typical or distinctive culinary preferences of Slavic or Romanic speaking people, people from special geographical regions or from different zones. This work is based on the analysis of edible mushroom lists available in specific guidelines or legislation related to the consumption and commerce of mushrooms in 27 European countries. The overall diversity of edible mushrooms authorised to be commercialised in Europe is very high. However, only 60 out of a total 268 fungal species can be cultivated. This highlights the importance of guidelines or legislation for the safe commerce of wild mushrooms. The species richness and composition of the mushrooms listed for commerce is very heterogeneous within Europe. The consumption behaviour is not only language-family-related, but is strongly influenced by geographical location and neighbouring countries. Indicator species were detected for different European regions; most of them are widespread fungi, and thus prove culture-specific preferences for these mushrooms. Our results highlight tradition and external input such as trade and cultural exchange as strong factors shaping mushroom consumption behaviour.

Molecular phylogeny of Trametes and related genera, and description of a new genus Leiotrametes

A phylogenetic analysis of Trametes and related taxa is proposed, based on a wide sampling of temperate and tropical species. Concatenate sequences of ribosomal DNA (ITS1-5.8S-ITS2) and RPB2 gene from mycelia cultures were analyzed by Maximum Likelihood and Bayesian methods, whilst morphological features were documented from the corresponding herbarium vouchers. Congruent results were obtained from analyses of ribosomal LSU sequences downloaded from Genbank. The Bayesian analysis of ITS + RPB2 sequences gave the best resolution for the phylogenetic reconstructions and revealed the existence of three main lineages in the Trametes-clade: 1) a monospecific lineage represented by Artolenzites elegans 2) a lineage including the genus Pycnoporus in its traditional sense and several species usually classified in the genus Trametes (T. cingulata, T. lactinea, T. ljubarskyi, T. menziesii) & 3) a lineage corresponding to the core genus Trametes, including type species of Trametes, Coriolopsis and Lenzites. The presence of a pseudostipe, aspect and structure of the abhymenial surface, colour change with 5% aqueous solutions of potassium hydroxide and topography of pigments on skeletal hyphae gave relevant morphological support to these clades. When the structure of the hymenial surface, presence of a black line below the tomentum and color of context (except for genus Pycnoporus) usually used in traditional polypore-classifications did not reveal any phylogenetic significance. A partial systematic arrangement of the Trametes clade is proposed, with the introduction of a new genus: Leiotrametes Welti & Courtec. gen. nov.. Two new combinations: Leiotrametes lactinea (Berk.) Welti & Courtec. comb. nov. and L. menziesii (Berk.) Welti & Courtec. comb. nov. are proposed.

A multi-gene phylogeny of Lactifluus (Basidiomycota, Russulales) translated into a new infrageneric classification of the genus

Infrageneric relations of the genetically diverse milkcap genus Lactifluus (Russulales, Basidiomycota) are poorly known. Currently used classification systems still largely reflect the traditional, mainly morphological, characters used for infrageneric delimitations of milkcaps. Increased sampling, combined with small-scale molecular studies, show that this genus is underexplored and in need of revision. For this study, we assembled an extensive dataset of the genus Lactifluus, comprising 80 % of all known species and 30 % of the type collections. To unravel the infrageneric relationships within this genus, we combined a multi-gene molecular phylogeny, based on nuclear ITS, LSU, RPB2 and RPB1, with a morphological study, focussing on five important characteristics (fruit body type, presence of a secondary velum, colour reaction of the latex/context, pileipellis type and presence of true cystidia). Lactifluus comprises four supported subgenera, each containing several supported clades. With extensive sampling, ten new clades and at least 17 new species were discovered, which highlight the high diversity in this genus. The traditional infrageneric classification is only partly maintained and nomenclatural changes are proposed. Our morphological study shows that the five featured characteristics are important at different evolutionary levels, but further characteristics need to be studied to find morphological support for each clade. This study paves the way for a more detailed investigation of biogeographical history and character evolution within Lactifluus.

Plunging hands into the mushroom jar: a phylogenetic framework for Lyophyllaceae (Agaricales, Basidiomycota)

During the last two decades, the unprecedented development of molecular phylogenetic tools has propelled an opportunity to revisit the fungal kingdom under an evolutionary perspective. Mycology has been profoundly changed but a sustained effort to elucidate large sections of the astonishing fungal diversity is still needed. Here we fill this gap in the case of Lyophyllaceae, a species-rich and ecologically diversified family of mushrooms. Assembly and genealogical concordance multigene phylogenetic analysis of a large dataset that includes original, vouchered material from expert field mycologists reveal the phylogenetic topology of the family, from higher (generic) to lower (species) levels. A comparative analysis of the most widely used phylogenetic markers in Fungi indicates that the nuc rDNA region encompassing the internal transcribed spacers 1 and 2, along with the 5.8S rDNA (ITS) and portions of the genes for RNA polymerase II second largest subunit (RPB2) is the most performing combination to resolve the broadest range of taxa within Lyophyllaceae. Eleven distinct evolutionary lineages are identified, that display partial overlap with traditional genera as well as with the phylogenetic framework previously proposed for the family. Eighty phylogenetic species are delineated, which shed light on a large number of morphological concepts, including rare and poorly documented ones. Probing these novel phylogenetic species to the barcoding method of species limit delineation, indicates that the latter method fully resolves Lyophyllaceae species, except in one clade. This case study provides the first comprehensive phylogenetic overview of Lyophyllaceae, a necessary step towards a taxonomical, ecological and nomenclatural revision of this family of mushrooms. It also proposes a set of methodological guidelines that may be of relevance for future taxonomic works in other groups of Fungi.

Cantharellus coccolobae sp. nov. and Cantharellus garnieri, Two Tropical Members of Cantharellus subg. Cinnabarinus

Abstract This paper attributes two more species to Cantharellus subg. Cinnabarinus: the here newly described C. coccolobae, a strict associate of Coccoloba species in subtropical and tropical America, and the New Caledonian C. garnieri. A multigene analysis places both species in a genus phylogeny and their macro- and microscopic features are illustrated and discussed.

Beyond ectomycorrhizal bipartite networks: projected networks demonstrate contrasted patterns between early- and late-successional plants in Corsica

The ectomycorrhizal (ECM) symbiosis connects mutualistic plants and fungal species into bipartite networks. While links between one focal ECM plant and its fungal symbionts have been widely documented, systemic views of ECM networks are lacking, in particular, concerning the ability of fungal species to mediate indirect ecological interactions between ECM plant species (projected-ECM networks). We assembled a large dataset of plant–fungi associations at the species level and at the scale of Corsica using molecular data and unambiguously host-assigned records to: (i) examine the correlation between the number of fungal symbionts of a plant species and the average specialization of these fungal species, (ii) explore the structure of the plant–plant projected network and (iii) compare plant association patterns in regard to their position along the ecological succession. Our analysis reveals no trade-off between specialization of plants and specialization of their partners and a saturation of the plant projected network. Moreover, there is a significantly lower-than-expected sharing of partners between early- and late-successional plant species, with fewer fungal partners for early-successional ones and similar average specialization of symbionts of early- and late-successional plants. Our work paves the way for ecological readings of Mediterranean landscapes that include the astonishing diversity of below-ground interactions.