A reassessment of cleistothecia as a taxonomic character

A new lineage of mazaediate fungi in the Eurotiomycetes: Cryptocaliciomycetidae subclass. nov., based on the new species Cryptocalicium blascoi and the revision of the ascoma evolution

The class Eurotiomycetes (Ascomycota, Pezizomycotina) comprises important fungi used for medical, agricultural, industrial and scientific purposes. Eurotiomycetes is a morphologically and ecologically diverse monophyletic group. Within the Eurotiomycetes, different ascoma morphologies are found including cleistothecia and perithecia but also apothecia or stromatic forms. Mazaediate representatives (with a distinct structure in which loose masses of ascospores accumulate to be passively disseminated) have evolved independently several times. Here we describe a new mazaediate species belonging to the Eurotiomycetes. The multigene phylogeny produced (7 gene regions: nuLSU, nuSSU, 5.8S nuITS, mtSSU, RPB1, RPB2 and MCM7) placed the new species in a lineage sister to Eurotiomycetidae. Based on the evolutionary relationships and morphology, a new subclass, a new order, family and genus are described to place the new species: Cryptocalicium blascoi. This calicioid species occurs on the inner side of loose bark strips of Cupressaceae (Cupressus, Juniperus). Morphologically, C. blascoi is characterized by having minute apothecioid stalked ascomata producing mazaedia, clavate bitunicate asci with hemiamyloid reaction, presence of hamathecium and an apothecial external surface with dark violet granules that becomes turquoise green in KOH. The ancestral state reconstruction analyses support a common ancestor with open ascomata for all deep nodes in Eurotiomycetes and the evolution of closed ascomata (cleistothecioid in Eurotiomycetidae and perithecioid in Chaetothyriomycetidae) from apothecioid ancestors. The appropriateness of the description of a new subclass for this fungus is also discussed.

Phylogenetic analysis of Monascus and new species from honey, pollen and nests of stingless bees

The genus Monascus was described by van Tieghem (1884) to accommodate M. ruber and M. mucoroides, two species with non-ostiolate ascomata. Species delimitation in the genus is still mainly based on phenotypic characters, and taxonomic studies that include sequence data are limited. The genus is of economic importance. Species are used in fermented Asian foods as food colourants (e.g. ‘red rice’ (ang-kak, angka)) and found as spoilage organisms, and recently Monascus was found to be essential in the lifecycle of stingless bees. In this study, a polyphasic approach was applied combining morphological characters, ITS, LSU, β-tubulin, calmodulin and RNA polymerase II second largest subunit sequences and extrolite data, to delimit species and to study phylogenetic relationships in Monascus. Furthermore, 30 Monascus isolates from honey, pollen and nests of stingless bees in Brazil were included. Based on this polyphasic approach, the genus Monascus is resolved in nine species, including three new species associated with stingless bees (M. flavipigmentosus sp. nov., M. mellicola sp. nov., M. recifensis sp. nov., M. argentinensis, M. floridanus, M. lunisporas, M. pallens, M. purpureus, M. ruber), and split in two new sections (section Floridani sect. nov., section Rubri sect. nov.). Phylogenetic analysis showed that the xerophile Monascus eremophilus does not belong in Monascus and monophyly in Monascus is restored with the transfer of M. eremophilus to Penicillium (P. eremophilum comb. nov.). A list of accepted and excluded Monascus and Basipetospora species is given, together with information on (ex-)types cultures and barcode sequence data.

New fungal cephalothecoid-like fructifications from central European Neogene deposits

Fragments of cephalothecoid fructifications (peridia) were encountered during palynological investigations of Neogene deposits in Mizerna-Nowa/Poland and Adendorf/Germany. Isolated plates of cephalothecoid ascoma in shape and cellular structure similar to the extant members of the family Cephalothecaceae are described as Cephalothecoidomyces neogenicus fossil gen. et sp. nov. while remnants of fungal sporocarps with cephalothecoid walls with indistinct lines of dehiscence, similar in structure to peridia with cephalothecoid morphology of extant representatives the family Chaetomiaceae (mainly genus Chaetomidium) are assigned to Adendorfia miocenica fossil gen. et sp. nov. We also propose a new interpretation of some previously described fossil fungal taxa that we consider to be remnants of cephalothecoid ascomata.

Phylogenetic reassessment of the Chaetomium globosum species complex

Chaetomium globosum, the type species of the genus, is ubiquitous, occurring on a wide variety of substrates, in air and in marine environments. This species is recognised as a cellulolytic and/or endophytic fungus. It is also known as a source of secondary metabolites with various biological activities, having great potential in the agricultural, medicinal and industrial fields. On the negative side, C. globosum has been reported as an air contaminant causing adverse health effects and as causal agent of human fungal infections. However, the taxonomic status of C. globosum is still poorly understood. The contemporary species concept for this fungus includes a broadly defined morphological diversity as well as a large number of synonymies with limited phylogenetic evidence. The aim of this study is, therefore, to resolve the phylogenetic limits of C. globosum s.str. and related species. Screening of isolates in the collections of the CBS-KNAW Fungal Biodiversity Centre (The Netherlands) and the China General Microbiological Culture Collection Centre (China) resulted in recognising 80 representative isolates of the C. globosum species complex. Thirty-six species are identified based on phylogenetic inference of six loci, supported by typical morphological characters, mainly ascospore shape. Of these, 12 species are newly described here. Additionally, C. cruentum, C. mollipilium, C. rectum, C. subterraneum and two varieties of C. globosum are synonymised under C. globosum s.str., and six species are resurrected, i.e. C. angustispirale, C. coarctatum, C. cochliodes, C. olivaceum, C. spiculipilium and C. subglobosum. Chaetomium ascotrichoides is segregated from C. madrasense and the genus name Chaetomidium is rejected. Five species, including C. globosum s.str., are typified here to stabilise their taxonomic status. A further evaluation of the six loci used in this study as potential barcodes indicated that the 28S large subunit (LSU) nrDNA and the internal transcribed spacer regions and intervening 5.8S nrRNA (ITS) gene regions were unreliable to resolve species, whereas β-tubulin (tub2) and RNA polymerase II second largest subunit (rpb2) showed the greatest promise as DNA barcodes for differentiating Chaetomium species. This study provides a starting point to establish a more robust classification system for Chaetomium and for the Chaetomiaceae.

Convergent evolution of highly reduced fruiting bodies in Pezizomycotina suggests key adaptations to the bee habitat

Background

Among the understudied fungi found in nature are those living in close association with social and solitary bees. The bee-specialist genera Bettsia, Ascosphaera and Eremascus are remarkable not only for their specialized niche but also for their simple fruiting bodies or ascocarps, which are morphologically anomalous in Pezizomycotina. Bettsia and Ascosphaera are characterized by a unicellular cyst-like cleistothecium known as a spore cyst, while Eremascus is characterized by completely naked asci, or asci not formed within a protective ascocarp. Before molecular phylogenetics the placement of these genera within Pezizomycotina remained tentative; morphological characters were misleading because they do not produce multicellular ascocarps, a defining character of Pezizomycotina. Because of their unique fruiting bodies, the close relationship of these bee-specialist fungi and their monophyly appeared certain. However, recent molecular studies have shown that Bettsia is not closely related to Ascosphaera.

In this study, I isolated the very rare fungus Eremascus fertilis (Ascomycota, Pezizomycotina) from the bee bread of honey bees. These isolates represent the second report of E. fertilis both in nature and in the honey bee hive. To establish the systematic position of E. fertilis and Bettsia alvei, I performed phylogenetic analyses of nuclear ribosomal LSU + SSU DNA sequences from these species and 63 additional ascomycetes.

Results

The phylogenetic analyses revealed that Eremascus is not monophyletic. Eremascus albus is closely related to Ascosphaera in Eurotiomycetes while E. fertilis belongs in Myxotrichaceae, a putative member of Leotiomycetes. Bettsia is not closely related to Ascosphaera and like E. fertilis apparently belongs in Leotiomycetes. These results indicate that both the naked ascus and spore cyst evolved twice in the Pezizomycotina and in distantly related lineages. The new genus Skoua is described to accommodate E. fertilis.

Conclusions

The naked ascus and spore cyst are both shown to have evolved convergently within the bee habitat. The convergent evolution of these unusual ascocarps is hypothesized to be adaptive for bee-mediated dispersal. Elucidating the dispersal strategies of these fungal symbionts contributes to our understanding of their interaction with bees and provides insight into the factors which potentially drive the evolution of reduced ascocarps in Pezizomycotina.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0401-6) contains supplementary material, which is available to authorized users.

Phylogeny, identification and nomenclature of the genus Aspergillus

Aspergillus comprises a diverse group of species based on morphological, physiological and phylogenetic characters, which significantly impact biotechnology, food production, indoor environments and human health. Aspergillus was traditionally associated with nine teleomorph genera, but phylogenetic data suggest that together with genera such as Polypaecilum, Phialosimplex, Dichotomomyces and Cristaspora, Aspergillus forms a monophyletic clade closely related to Penicillium. Changes in the International Code of Nomenclature for algae, fungi and plants resulted in the move to one name per species, meaning that a decision had to be made whether to keep Aspergillus as one big genus or to split it into several smaller genera. The International Commission of Penicillium and Aspergillus decided to keep Aspergillus instead of using smaller genera. In this paper, we present the arguments for this decision. We introduce new combinations for accepted species presently lacking an Aspergillus name and provide an updated accepted species list for the genus, now containing 339 species. To add to the scientific value of the list, we include information about living ex-type culture collection numbers and GenBank accession numbers for available representative ITS, calmodulin, β-tubulin and RPB2 sequences. In addition, we recommend a standard working technique for Aspergillus and propose calmodulin as a secondary identification marker.

Phylogeny of Penicillium and the segregation of Trichocomaceae into three families

Species of Trichocomaceae occur commonly and are important to both industry and medicine. They are associated with food spoilage and mycotoxin production and can occur in the indoor environment, causing health hazards by the formation of β-glucans, mycotoxins and surface proteins. Some species are opportunistic pathogens, while others are exploited in biotechnology for the production of enzymes, antibiotics and other products. Penicillium belongs phylogenetically to Trichocomaceae and more than 250 species are currently accepted in this genus. In this study, we investigated the relationship of Penicillium to other genera of Trichocomaceae and studied in detail the phylogeny of the genus itself. In order to study these relationships, partial RPB1, RPB2 (RNA polymerase II genes), Tsr1 (putative ribosome biogenesis protein) and Cct8 (putative chaperonin complex component TCP-1) gene sequences were obtained. The Trichocomaceae are divided in three separate families: Aspergillaceae, Thermoascaceae and Trichocomaceae. The Aspergillaceae are characterised by the formation flask-shaped or cylindrical phialides, asci produced inside cleistothecia or surrounded by Hülle cells and mainly ascospores with a furrow or slit, while the Trichocomaceae are defined by the formation of lanceolate phialides, asci borne within a tuft or layer of loose hyphae and ascospores lacking a slit. Thermoascus and Paecilomyces, both members of Thermoascaceae, also form ascospores lacking a furrow or slit, but are differentiated from Trichocomaceae by the production of asci from croziers and their thermotolerant or thermophilic nature. Phylogenetic analysis shows that Penicillium is polyphyletic. The genus is re-defined and a monophyletic genus for both anamorphs and teleomorphs is created (Penicillium sensu stricto). The genera Thysanophora, Eupenicillium, Chromocleista, Hemicarpenteles and Torulomyces belong in Penicilliums. str. and new combinations for the species belonging to these genera are proposed. Analysis of Penicillium below genus rank revealed the presence of 25 clades. A new classification system including both anamorph and teleomorph species is proposed and these 25 clades are treated here as sections. An overview of species belonging to each section is presented.

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.

Morphology and development of Nigrosabulum globosum, a cleistothecial coprophile in the Bionectriaceae (Hypocreales)

Recent DNA sequence analyses indicated that Nigrosabulum globosum is a cleistothecial representative of the Bionectriaceae in the Hypocreales, but morphological characters supporting this relationship are unknown. Using light and electron microscopy we followed the development of the ascomata of this species, from the formation of gametangia through to the development of mature ascospores, and observed a series of characters that confirmed its hypocrealean affinities. These included the formation of a gel-filled centrum during early stages of ascoma development, the subsequent appearance of hyaline peridial tissue enclosed within a layer we interpret as representing a melanized uniloculate stroma, apically derived paraphyses, and an ascogenous system that gives rise to asci that were both cylindrical to clavate and globose. Ascospores, previously reported to be smooth, were ornamented with a honeycomb-like reticulum and were able to germinate within the ascoma. The carbonaceous outer (stromatic) walls of the mature, grit-like cleistothecia indicate possible resistance to UV radiation and desiccation. Furthermore, the complement of germinated ascospores would enable mature ascomata to function as propagules that could quickly initiate new growth when transferred to fresh substrate. Our reexamination of N. globosum also provides data that support the hypothesized close relationship with other bionectriaceous, cleistothecial coprophiles, i.e., species of Hapsidospora, and Bulbithecium in particular.

New bottles for old wine: fruit body types, phylogeny, and classification

Molecular phylogenetic studies have made it evident that similar fruit body types, formerly the cornerstone of the classification of ascomycete and basidiomycete fungi, including those that form lichens, are often a result of convergent evolution. This commentary provides an introduction to this special issue of Mycological Research, which is based on papers presented at a one-day joint meeting of the British Mycological Society and the Natural History Museum held in London on 3 December 2005. The nine papers included address this issue in relation to its impact on classification, and also draw attention to the over-emphasis in fungal classification of ascus types and, in the case of lichen fungi, thallus form.