Damien Ertz

The ascomycota tree of life: A phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits

We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.

The Faces of Fungi database: fungal names linked with morphology, phylogeny and human impacts

Taxonomic names are key links between various databases that store information on different organisms. Several global fungal nomenclural and taxonomic databases (notably Index Fungorum, Species Fungorum and MycoBank) can be sourced to find taxonomic details about fungi, while DNA sequence data can be sourced from NCBI, EBI and UNITE databases. Although the sequence data may be linked to a name, the quality of the metadata is variable and generally there is no corresponding link to images, descriptions or herbarium material. There is generally no way to establish the accuracy of the names in these genomic databases, other than whether the submission is from a reputable source. To tackle this problem, a new database (FacesofFungi), accessible at www.facesoffungi.org (FoF) has been established. This fungal database allows deposition of taxonomic data, phenotypic details and other useful data, which will enhance our current taxonomic understanding and ultimately enable mycologists to gain better and updated insights into the current fungal classification system. In addition, the database will also allow access to comprehensive metadata including descriptions of voucher and type specimens. This database is user-friendly, providing links and easy access between taxonomic ranks, with the classification system based primarily on molecular data (from the literature and via updated web-based phylogenetic trees), and to a lesser extent on morphological data when molecular data are unavailable. In FoF species are not only linked to the closest phylogenetic representatives, but also relevant data is provided, wherever available, on various applied aspects, such as ecological, industrial, quarantine and chemical uses. The data include the three main fungal groups (Ascomycota, Basidiomycota, Basal fungi) and fungus-like organisms. The FoF webpage is an output funded by the Mushroom Research Foundation which is an NGO with seven directors with mycological expertise. The webpage has 76 curators, and with the help of these specialists, FoF will provide an updated natural classification of the fungi, with illustrated accounts of species linked to molecular data. The present paper introduces the FoF database to the scientific community and briefly reviews some of the problems associated with classification and identification of the main fungal groups. The structure and use of the database is then explained. We would like to invite all mycologists to contribute to these web pages.

The phylogeny of Arthoniales (Pezizomycotina) inferred from nucLSU and RPB2 sequences

A two-locus phylogenetic study of the order Arthoniales is presented here using the nuclear ribosomal large subunit (nucLSU) and the second largest subunit of RNA polymerase II (RPB2). This analysis is the first large phylogeny of this fungal group and includes 476 sequences and 240 specimens representing 132 species sampled from 31 genera (in their traditional circumscription). In addition to the previously recognized families (Arthoniaceae, Chrysothricaceae and Roccellaceae), three additional family-level groups are recovered, one being poorly supported. Therefore, the new family Roccellographaceae is described and the family Opegraphaceae is reinstated. Morphological characters such as growth form, fruit body type, exciple, hypothecium and ascospores colour, ascospores septation pattern, and chemistry are found to be of limited use in delimiting families and genera, which indicates an unusual level of plasticity in the Arthoniales. This high level of homoplasy might indicate that the Arthoniales is an old group with taxa having evolved in parallel for very long times. The genera Arthonia, Arthothelium, Chiodecton, Hubbsia, Ingaderia, Lecanactis, Lecanographa, Llimonaea, Opegrapha, Roccellina, Schismatomma and Sclerophyton were found paraphyletic. In order to make these genera monophyletic, the new genera Dimidiographa, Fulvophyton, Paraingaderia, Paralecanographa, Paraschismatomma and Sparria are newly described and the genera Alyxoria, Dictyographa and Zwackhia reinstated. The new species Lecanactis borbonica and Paraingaderia placodioidea are described.

Towards a new classification of the Arthoniales (Ascomycota) based on a three-gene phylogeny focussing on the genus Opegrapha

A multi-locus phylogenetic study of the order Arthoniales is presented here using the nuclear ribosomal large subunit (nuLSU), the second largest subunit of RNA polymerase II (RPB2) and the mitochondrial ribosomal small subunit (mtSSU). These genes were sequenced from 43 specimens or culture isolates representing 33 species from this order, 16 of which were from the second largest genus, Opegrapha. With the inclusion of sequences from GenBank, ten genera and 35 species are included in this study, representing about 18% of the genera and ca 3% of the species of this order. Our study revealed the homoplastic nature of morphological characters traditionally used to circumscribe genera within the Arthoniales, such as exciple carbonization and ascomatal structure. The genus Opegrapha appears polyphyletic, species of that genus being nested in all the major clades identified within Arthoniales. The transfer of O. atra and O. calcarea to the genus Arthonia will allow this genus and family Arthoniaceae to be recognized as monophyletic. The genus Enterographa was also found to be polyphyletic. Therefore, the following new combinations are needed: Arthonia calcarea (basionym: O. calcarea), and O. anguinella (basionym: Stigmatidium anguinellum); and the use of the names A. atra and Enterographa zonata are proposed here. The simultaneous use of a mitochondrial gene and two nuclear genes led to the detection of what seems to be a case of introgression of a mitochondrion from one species to another (mitochondrion capture; cytoplasmic gene flow) resulting from hybridization.

Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi.

We studied the evolutionary history of the Parmeliaceae (Lecanoromycetes, Ascomycota), one of the largest families of lichen-forming fungi with complex and variable morphologies, also including several lichenicolous fungi. We assembled a six-locus data set including nuclear, mitochondrial and low-copy protein-coding genes from 293 operational taxonomic units (OTUs). The lichenicolous lifestyle originated independently three times in lichenized ancestors within Parmeliaceae, and a new generic name is introduced for one of these fungi. In all cases, the independent origins occurred c. 24 million yr ago. Further, we show that the Paleocene, Eocene and Oligocene were key periods when diversification of major lineages within Parmeliaceae occurred, with subsequent radiations occurring primarily during the Oligocene and Miocene. Our phylogenetic hypothesis supports the independent origin of lichenicolous fungi associated with climatic shifts at the Oligocene-Miocene boundary. Moreover, diversification bursts at different times may be crucial factors driving the diversification of Parmeliaceae. Additionally, our study provides novel insight into evolutionary relationships in this large and diverse family of lichen-forming ascomycetes.

Briancoppinsia, a new coelomycetous genus of Arthoniaceae (Arthoniales) for the lichenicolous Phoma cytospora, with a key to this and similar taxa

Morphological, anatomical, chemical and molecular data suggest that a relatively common lichenicolous coelomycete on Lecanora conizaeoides is conspecific with Phoma cytospora, previously known only from parmelioid lichens, and that further populations on Cladonia and Pertusaria belong to the same species. This species is distinguished from Phoma by several taxonomically important characters and obviously represents a previously unrecognized genus, for which the name Briancoppinsia is introduced. Phylogenetic analyses using nuLSU and mtSSU sequences of isolates obtained in pure culture suggest that the new genus belongs to the Arthoniaceae (Arthoniales). This is the first obligate lichenicolous, non-lichenized anamorph confirmed to belong to the Arthoniales based on molecular data.

Heterotrophic bacterial diversity in aquatic microbial mat communities from Antarctica

Heterotrophic bacteria isolated from five aquatic microbial mat samples from different locations in continental Antarctica and the Antarctic Peninsula were compared to assess their biodiversity. A total of 2,225 isolates obtained on different media and at different temperatures were included. After an initial grouping by whole-genome fingerprinting, partial 16S rRNA gene sequence analysis was used for further identification. These results were compared with previously published data obtained with the same methodology from terrestrial and aquatic microbial mat samples from two additional Antarctic regions. The phylotypes recovered in all these samples belonged to five major phyla, Actinobacteria, Bacteroidetes, Proteobacteria, Firmicutes and Deinococcus-Thermus, and included several potentially new taxa. Ordination analyses were performed in order to explore the variance in the diversity of the samples at genus level. Habitat type (terrestrial vs. aquatic) and specific conductivity in the lacustrine systems significantly explained the variation in bacterial community structure. Comparison of the phylotypes with sequences from public databases showed that a considerable proportion (36.9%) is currently known only from Antarctica. This suggests that in Antarctica, both cosmopolitan taxa and taxa with limited dispersal and a history of long-term isolated evolution occur.

Culturable bacterial diversity at the Princess Elisabeth Station (Utsteinen, Sør Rondane Mountains, East Antarctica) harbours many new taxa

We studied the culturable heterotrophic bacterial diversity present at the site of the new Princess Elisabeth Station at Utsteinen (Dronning Maud Land, East Antarctica) before construction. About 800 isolates were picked from two terrestrial microbial mat samples after incubation on several growth media at different temperatures. They were grouped using rep-PCR fingerprinting and partial 16S rRNA gene sequencing. Phylogenetic analysis of the complete 16S rRNA gene sequences of 93 representatives showed that the isolates belonged to five major phyla: Actinobacteria, Bacteroidetes, Proteobacteria, Firmicutes and Deinococcus-Thermus. Isolates related to the genus Arthrobacter were the most prevalent whereas the genera Hymenobacter, Deinococcus, Cryobacterium and Sphingomonas were also recovered in high numbers in both samples. A total of 35 different genera were found, the majority of which has previously been reported from Antarctica. For the genera Aeromicrobium, Aurantimonas, Rothia, Subtercola, Tessaracoccus and Xylophilus, this is the first report in Antarctica. In addition, numerous potential new species and new genera were recovered; many of them currently restricted to Antarctica, particularly in the phyla Bacteroidetes and Deinococcus-Thermus.

Phylogenetic placement of lichenicolous Phoma species in the Phaeosphaeriaceae (Pleosporales, Dothideomycetes)

More than twenty species of lichenicolous fungi have been described in Phoma, a large anamorphic genus of primarily plant-associated pathogens with broad geographic distributions. We obtained nuclear and mitochondrial rDNA sequences from 19 fungal cultures isolated from specimens representing four described and two undescribed lichenicolous species in the genus. Our multilocus phylogeny indicates that lichenicolous Phoma species represent at least two phylogenetically distinct clades in the Phaeosphaeriaceae, one including a new species, Phoma puncteliae, isolated from a specimen of Punctelia rudecta collected in Maryland, USA, and another group of primarily lichenicolous species. This latter group includes four described lichenicolous Phoma species, an unidentified melanized rock fungus, and a new lichenicolous Phoma species isolated from Xanthomendoza species collected in Canada that we are naming P. xanthomendozae. Some specimens in this clade collected from different lichen genera and species were found to be very similar genetically, which calls into question the recent practice of recognizing lichenicolous Phoma species mainly by differences in host preference.

Molecular data resolve a new order of Arthoniomycetes sister to the primarily lichenized Arthoniales and composed of black yeasts, lichenicolous and rock-inhabiting species

Lichenicolous fungi belonging to the anamorph-typified genus Phaeosporobolus and to the teleomorph-typified genus Lichenostigma were isolated in pure culture or sequenced directly, with nuLSU and mtSSU sequences obtained. Phylogenetic analyses place the species of Phaeosporobolus in a strongly supported clade with the generic type of Lichenostigma (L. maureri), the genus Phaeococcomyces and several melanized rock-inhabiting isolates. This strongly supported nonlichenized lineage is sister to the primarily lichenized Arthoniales in the Arthoniomycetes and is here described as the Lichenostigmatales. The new order is characterized by cells multiplying by budding, either representing black yeasts, or species in which conidiomata and ascomata are entirely made of an organised agglomeration of spherical yeast-like cells. This way of life is not only very different from all other Arthoniomycetes that exist only in the mycelial stage, but ascomata and conidiomata representing a dense and organised agglomeration of yeast cells might be unique amongst fungi. A further difference with the Arthoniales is the absence of paraphysoids. Phylogenetic results suggest that Phaeosporobolus usneae is the asexual stage of Lichenostigma maureri. Most species of Phaeosporobolus are transferred to the genus Lichenostigma except P. trypethelii, for which the new genus Etayoa is described. The genus Diederimyces is reduced into synonymy with Lichenostigma. Several other members of Lichenostigma are placed in the Dothideomycetes and are intermixed with Lichenothelia species.