Multiclavula ichthyiformis (Fungi: Basidiomycota: Cantharellales: Clavulinaceae), a remarkable new basidiolichen from Costa Rica

The new basidiolichen Multiclavula ichthyiformis Nelsen, Lücking, Uma?a, Trest & Will-Wolf is described from Costa Rica. The new species differs from other species of Multiclavula in having a basidiocarp with tomentose stipe and flattened lamina with nonamphigenous hymenium. Molecular sequence data (ITS) confirmed its placement within Multiclavula in the Clavulinaceae (Cantharellales, Agaricomycetes). The new lichen was discovered in a Central American paramo remnant, illustrating the importance of biotic inventories of fungi and lichens to increase our knowledge of the diversity of these groups in endangered tropical ecosystems. The new species was found as part of the TICOLICHEN project in Costa Rica.     

Phylogenetic diversity of lichen-associated homobasidiomycetes

The vast majority of lichenicolous fungi are relatively host-specific, nonvirulent ascomycetes and heterobasidiomycetes. A few known lichenicolous homobasidiomycetes (mushroom-forming fungi) generally exhibit broad host ecologies and in some cases, high virulence. Many produce conspicuous sclerotia or bulbils, thought to be adaptive in dispersal and survival. To more clearly understand the evolution of these atypical behaviors in lichenicolous basidiomycetes, we isolated or acquired specimens or cultures of 23 lichenicolous homobasidiomycetes and their relatives, from which we obtained mainly nuclear and some mitochondrial rDNA sequences. Phylogenetic analyses in this study indicate that a lichenicolous habit arose in four major clades. In two of these clades the habit represents a major evolutionary theme linked to the origin of well-known basidiolichens. The phylogenetic diversity of these fungi indicates that the lichenicolous habit arose recently and independently in the mushroom-forming fungi.     

Two new species of Multiclavula (lichenized basidiomycetes) from savanna soils in Rwanda (East Africa)

Two new species of Multiclavula are described from Rwanda: M. akagerae , with a thallus consisting of turgescent glomerules, and M. rugaramae , with a thallus composed of flattened, rounded, marginate, and dispersed squamules. They grow on soil in frequently burned savannas or on lateritic soils in eastern Rwanda. The genus Lepidostroma should probably be reduced into synonymy with Multiclavula .  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 155 , 457–465.     

Trouble with lichen: the re-evaluation and re-interpretation of thallus form and fruit body types in the molecular era

Following discussions of the definition of the terms ‘lichen’ and ‘thallus’, the role of lichenization in the evolution of asco- and basidiomycetes, and divergence and convergence in fruit body types, the morphogenetic interpretation of types of thallus form in lichens is reviewed. Attention is drawn to the various morphogenetic hypotheses proposed to explain the lichen thallus, but it is concluded that it is best interpreted as a novel phenotype with no exact homologue. Similar ascomatal and thallus types are found in lichen-forming fungi of different orders and families, as now revealed by molecular phylogenetic studies. These are interpreted as examples of convergent evolution, strategies by which unrelated fungi either display captured algae to maximize photosynthetic opportunities, or to attach themselves to a substratum. Phenotypic evolution of fruit body and thallus types in the major orders and clades is summarized, and the thallus types known in each order are tabulated. An hypothesis relating the evolution of these structures to hygroscopic movements is proposed, and the critical position of lichens in developing an integrated approach to ascomycete evolution is emphasized.     

山西太行山地区铦囊蘑属两新种

铦囊蘑属Melanoleuca属于担子菌门Basidiomycota伞菌纲Agaricomycetes伞菌目Agaricales,因该属很多种类都是重要的食用菌而受到广泛关注。本文报道了在山西太行山地区发现的该属2个新种,即浅灰铦囊蘑Melanoleuca grisea和近白柄铦囊蘑M. subleucopoda。通过形态学特征、ITS和RPB2基因序列的分子系统发育分析结果,确定了其分类地位,并讨论了它们与铦囊蘑属内相关物种的形态学和系统发育关系。     

Phylogenetic relationships of ascomycetes and basidiomycetes based on comparative genomics analysis

The relationship between ascomycetes and basidiomycetes, the two main phyla of non-flagellated fungi, has rarely been investigated. In this study, we performed a comparative genomics analysis of genome sequences of 55 ascomycetes and 26 basidiomycetes species and detected 81 universal markers, 875 homologous genes and a conserved contig in the glucose-regulated protein gene. In dendrograms based on simple sequence repeat markers and homologous genes, ascomycetes and basidiomycetes formed distinct clusters, with each set of taxa having a high coefficient of relatedness. Ascomycetes and basidiomycetes also constituted distinct groups in a phylogenetic tree based on a conserved contig in the glucose-regulated protein gene. These results provide evidence that basidiomycetes may be derived from ascomycetes but are definitely genetically differentiated at the genomic level. The phylogenetic relationships of ascomycetes and basidiomycetes uncovered in this study provide new insights for future research related to fungal classification and evolution.     

Reconstructing the evolution of agarics from nuclear gene sequences and basidiospore ultrastructure

Traditional classifications of agaric fungi involve gross morphology of their fruit bodies and meiospore print-colour. However, the phylogeny of these fungi and the evolution of their morphological and ecological traits are poorly understood. Phylogenetic analyses have already demonstrated that characters used in traditional classifications of basidiomycetes may be heavily affected by homoplasy, and that non-gilled taxa evolved within the agarics several times. By integrating molecular phylogenetic analyses including domains D1–D3 and D7–D8 of nucLSU rDNA and domains A–C of the RPB1 gene with morphological and chemical data from representative species of 88 genera, we were able to resolve higher groups of agarics. We found that the species with thick-walled and pigmented basidiospores constitute a derived group, and hypothesize that this specific combination of characters represents an evolutionary advantage by increasing the tolerance of the basidiospores to dehydration and solar radiation and so opened up new ecological niches, e.g. the colonization of dung substrates by enabling basidiospores to survive gut passages through herbivores. Our results confirm the validity of basidiospore morphology as a phylogenetic marker in the agarics.     

PHYLOGENETIC DIVERSITY OF TRENTEPOHLIALEAN ALGAE ASSOCIATED WITH LICHEN‐FORMING FUNGI1

Nearly one‐fourth of the lichen‐forming fungi associate with trentepohlialean algae, yet their genetic diversity remains unknown. Recent work focusing on free‐living trentepohlialean algae has provided a phylogenetic context within which questions regarding the lichenization of these algae can be asked. Here, we concentrated our sampling on trentepohlialean algae from lichens producing a diversity of growth forms (fruticose and crustose) over a broad geographic substratum, ecological, and phylogenetic range. We have demonstrated that there is no evidence for a single clade of strictly lichenized algae; rather, a wide range demonstrated the ability to associate with lichenized fungi. Variation was also observed among trentepohlialean algae in lichens from a single geographic area and tree, suggesting that fungi in close proximity can associate with different trentepohlialean algae, consistent with the findings of trebouxiophycean algae and cyanobacteria.     

Detection and Identification of Decay Fungi in Spruce Wood by Restriction Fragment Length Polymorphism Analysis of Amplified Genes Encoding rRNA

We have developed a DNA-based assay to reliably detect brown rot and white rot fungi in wood at different stages of decay. DNA, isolated by a series of CTAB (cetyltrimethylammonium bromide) and organic extractions, was amplified by the PCR using published universal primers and basidiomycete-specific primers derived from ribosomal DNA sequences. We surveyed 14 species of wood-decaying basidiomycetes (brown-rot and white-rot fungi), as well as 25 species of wood-inhabiting ascomycetes (pathogens, endophytes, and saprophytes). DNA was isolated from pure cultures of these fungi and also from spruce wood blocks colonized by individual isolates of wood decay basidiomycetes or wood-inhabiting ascomycetes. The primer pair ITS1-F (specific for higher fungi) and ITS4 (universal primer) amplified the internal transcribed spacer region from both ascomycetes and basidiomycetes from both pure culture and wood, as expected. The primer pair ITS1-F (specific for higher fungi) and ITS4-B (specific for basidiomycetes) was shown to reliably detect the presence of wood decay basidiomycetes in both pure culture and wood; ascomycetes were not detected by this primer pair. We detected the presence of decay fungi in wood by PCR before measurable weight loss had occurred to the wood. Basidiomycetes were identified to the species level by restriction fragment length polymorphisms of the internal transcribed spacer region.     

Detection and identification of decay fungi in spruce wood by restriction fragment length polymorphism analysis of amplified genes encoding rRNA

We have developed a DNA-based assay to reliably detect brown rot and white rot fungi in wood at different stages of decay. DNA, isolated by a series of CTAB (cetyltrimethylammonium bromide) and organic extractions, was amplified by the PCR using published universal primers and basidiomycete-specific primers derived from ribosomal DNA sequences. We surveyed 14 species of wood-decaying basidiomycetes (brown-rot and white-rot fungi), as well as 25 species of wood-inhabiting ascomycetes (pathogens, endophytes, and saprophytes). DNA was isolated from pure cultures of these fungi and also from spruce wood blocks colonized by individual isolates of wood decay basidiomycetes or wood-inhabiting ascomycetes. The primer pair ITS1-F (specific for higher fungi) and ITS4 (universal primer) amplified the internal transcribed spacer region from both ascomycetes and basidiomycetes from both pure culture and wood, as expected. The primer pair ITS1-F (specific for higher fungi) and ITS4-B (specific for basidiomycetes) was shown to reliably detect the presence of wood decay basidiomycetes in both pure culture and wood; ascomycetes were not detected by this primer pair. We detected the presence of decay fungi in wood by PCR before measurable weight loss had occurred to the wood. Basidiomycetes were identified to the species level by restriction fragment length polymorphisms of the internal transcribed spacer region.     

Phylogenetic relationships among Taphrina, Saitoella, and other higher fungi

To determine the phylogenetic placement of the major groups of higher fungi, we sequenced the DNA sequences from the small-subunit ribosomal RNA (18S rRNA) coding regions from Taphrina wiesneri (synonym: T. cerasi) and Saitoella complicata and compared them to 18S rRNA sequences from the oomycetes, chytridiomycetes, zygomycetes, ascomycetes, and basidiomycetes. Here we demonstrate that the ascomycetes have at least two major evolutionary lineages. Taphrina wiesneri and Saitoella complicata form a monophyletic branch that diverged prior to the separation of other ascomycetes. The same treatment could be accorded to Schizosaccharomyces pombe.      

Dual-histidine kinases in basidiomycete fungi

Dual-histidine kinases (HKs) are complex hybrid HKs containing in a single polypeptide two HK transmitter modules (T) and two-response regulator received domains (R) that are combined in a TRTR geometry. In fungi, this protein family is limited to some particular species of the phylum Basidiomycota and absent in the other phyla. This study extends the investigation of dual-HKs to 80 fully sequenced genomes of basidiomycetes, analyzing their distribution, domain architecture and phylogenetic relationships. Moreover, similarly to dual-HKs of basidiomycetes, several species of bacteria were found that contain hybrid HKs with a TRTR domain architecture encoded in a single gene.     

Plant-Polysaccharide-Degrading Enzymes from Basidiomycetes

SUMMARY

Basidiomycete fungi subsist on various types of plant material in diverse environments, from living and dead trees and forest litter to crops and grasses and to decaying plant matter in soils. Due to the variation in their natural carbon sources, basidiomycetes have highly varied plant-polysaccharide-degrading capabilities. This topic is not as well studied for basidiomycetes as for ascomycete fungi, which are the main sources of knowledge on fungal plant polysaccharide degradation. Research on plant-biomass-decaying fungi has focused on isolating enzymes for current and future applications, such as for the production of fuels, the food industry, and waste treatment. More recently, genomic studies of basidiomycete fungi have provided a profound view of the plant-biomass-degrading potential of wood-rotting, litter-decomposing, plant-pathogenic, and ectomycorrhizal (ECM) basidiomycetes. This review summarizes the current knowledge on plant polysaccharide depolymerization by basidiomycete species from diverse habitats. In addition, these data are compared to those for the most broadly studied ascomycete genus, Aspergillus, to provide insight into specific features of basidiomycetes with respect to plant polysaccharide degradation.     

A phylogenetic overview of the Agaricomycotina

The Agaricomycotina contains about one-third of the described species of Fungi, including mushrooms, jelly fungi and basidiomycetous yeasts. Recent phylogenetic analyses by P. Matheny and colleagues combining nuclear rRNA genes with the protein-coding genes rpb1, rpb2 and tef1 support the division of Agaricomycotina into Tremellomycetes, Dacrymycetes and Agaricomycetes. There is strong support for the monophyly of the Tremellomycetes, and its position as the sister group of the rest of the Agaricomycotina. Dacrymycetes and Agaricomycetes also are supported strongly, and together they form a clade that is equivalent to the Hymenomycetidae of Swann and Taylor. The deepest nodes in the Agaricomycetes, which are supported only by Bayesian measures of confidence, suggest that the Sebacinales, Cantharellales and Auriculariales are among the most ancient lineages. For the first time, the Polyporales are strongly supported as monophyletic and are placed as the sister group of the Thelephorales. The Agaricales, Boletales and Atheliales are united as the Agaricomycetidae, and the Russulales might be its sister group. There are still some problematical nodes that will require more loci to be resolved. Phylogenomics has promise for reconstructing these difficult backbone nodes, but current genome projects are limited mostly to the Agaricales, Boletales and Polyporales. Genome sequences from other major lineages, especially the early diverging clades, are needed to resolve the most ancient nodes and to assess deep homology in ecological characters in the Agaricomycotina.     

The conservation of polyol transporter proteins and their involvement in lichenized Ascomycota

In lichen symbiosis, polyol transfer from green algae is important for acquiring the fungal carbon source. However, the existence of polyol transporter genes and their correlation with lichenization remain unclear. Here, we report candidate polyol transporter genes selected from the genome of the lichen-forming fungus (LFF) Ramalina conduplicans. A phylogenetic analysis using characterized polyol and monosaccharide transporter proteins and hypothetical polyol transporter proteins of R. conduplicans and various ascomycetous fungi suggested that the characterized yeast’ polyol transporters form multiple clades with the polyol transporter-like proteins selected from the diverse ascomycetous taxa. Thus, polyol transporter genes are widely conserved among Ascomycota, regardless of lichen-forming status. In addition, the phylogenetic clusters suggested that LFFs belonging to Lecanoromycetes have duplicated proteins in each cluster. Consequently, the number of sequences similar to characterized yeast’ polyol transporters were evaluated using the genomes of 472 species or strains of Ascomycota. Among these, LFFs belonging to Lecanoromycetes had greater numbers of deduced polyol transporter proteins. Thus, various polyol transporters are conserved in Ascomycota and polyol transporter genes appear to have expanded during the evolution of Lecanoromycetes.     

Atractiellomycetes belonging to the ‘rust’ lineage (Pucciniomycotina) form mycorrhizae with terrestrial and epiphytic neotropical orchids

Distinctive groups of fungi are involved in the diverse mycorrhizal associations of land plants. All previously known mycorrhiza-forming Basidiomycota associated with trees, ericads, liverworts or orchids are hosted in Agaricomycetes, Agaricomycotina. Here we demonstrate for the first time that Atractiellomycetes, members of the ‘rust’ lineage (Pucciniomycotina), are mycobionts of orchids. The mycobionts of 103 terrestrial and epiphytic orchid individuals, sampled in the tropical mountain rainforest of Southern Ecuador, were identified by sequencing the whole ITS1-5.8S-ITS2 region and part of 28S rDNA. Mycorrhizae of 13 orchid individuals were investigated by transmission electron microscopy. Simple septal pores and symplechosomes in the hyphal coils of mycorrhizae from four orchid individuals indicated members of Atractiellomycetes. Molecular phylogeny of sequences from mycobionts of 32 orchid individuals out of 103 samples confirmed Atractiellomycetes and the placement in Pucciniomycotina, previously known to comprise only parasitic and saprophytic fungi. Thus, our finding reveals these fungi, frequently associated to neotropical orchids, as the most basal living basidiomycetes involved in mycorrhizal associations of land plants.     

Allergenicity of airborne basidiospores and ascospores: need for further studies

Many known fungal species are grouped among basidiomycetes and ascomycetes. Active mechanisms of spore release into air currents are among the main features of these fungi. Aerobiological studies have described their presence in many regions worldwide. In some areas, fungi have been described as the predominant outdoor airborne biological particulate with much higher concentrations than pollen. Other studies have determined that among the fungal aerospora, the highest concentrations belong to basidiospores and ascospores. Nevertheless, the allergenic potential of spores from basidiomycetes and meiotic forms of ascomycetes has not been studied to the extent of mitosporic fungi and allergens from other sources. The need to further evaluate the role of basidiomycetes and meiotic ascomycetes in allergies is evidenced by the few genera with characterized allergens and limited studies that had demonstrated levels of sensitization similar or higher to that of mitosporic fungi and other allergens. In this review, based on the existing aerobiological, epidemiological, immunological, and molecular biology studies, we provide evidence that the role of basidiomycetes and ascomycetes deserves more attention with respect to their roles as potential aeroallergens.     

Phylogeny of lichen- and non-lichen-forming omphalinoid mushrooms and the utility of testing for combinability among multiple data sets

As an initial step toward developing a model system to study requirements for and consequences of transitions to mutualism, the phylogeny of a group of closely related lichenized and nonlichenized basidiomycetes (Omphalina) was reconstructed. The phylogenetic analyses are based on four data sets representing different regions of the nuclear ribosomal repeat unit (ITS1, 5.8S, ITS2, and 25S) obtained from 30 species of Omphalina and related genera. The resulting phylogenetic trees from each of these four data sets, when analyzed separately, were not identical. Testing for the combinability of these four data sets suggested that they could not be combined in their entirety. The removal of ambiguous alignments and saturated sites was sufficient, after reapplying the combinability test on the pruned data sets, to explain the topological discrepancies. In this process, the first of two complementary tests developed by Rodrigo et al. (1993, N.Z. J. Bot. 31:257-268) to assess whether two data sets are the result of the same phylogenetic history was found to be biased, rejecting the combinability of two data sets even when they are samples of the same phylogenetic history. Combining the four pruned data sets yielded phylogenies that suggest the five lichen-forming species of Omphalina form a monophyletic group. The sister group to this symbiotic clade consists mostly of dark brown Omphalina species intermixed with species from the genera Arrhenia and Phaeothellus. The genera Omphalina and Gerronema are shown to be polyphyletic. The lichen-forming species O. ericetorum and the nonmutualistic species O. velutipes, O. epichysium, and O. sphagnicola are the best candidates for experimental work designed to gain a better understanding of mechanisms involved in symbiotic interactions and the role symbiosis has played in the evolution of fungi.     

A molecular phylogeny for the frog genus Limnodynastes (Anura: myobatrachidae)

Members of the genus Limnodynastes are a prominent and widespread feature of the Australian frog fauna. Yet despite their potential to be informative about biogeographic history and mechanisms of speciation, the relationships among these taxa are not well known. We investigated phylogenetic relationships within the genus Limnodynastes via sequencing of mitochondrial (mt)DNA from current members of the genus Limnodynastes and the monotypic genus Megistolotis. a 450-bp fragment of the 16S rRNA gene and a 370-bp fragment of the protein-coding gene ND4 were used to infer a molecular phylogeny. We revise traditional species groupings and now recognize four species groups within Limnodynastes: the L. ornatus group (L. ornatus and L. spenceri), the L. peronii group (L. peronii, L. tasmaniensis, L. fletcheri, the L. depressus), the L. salmini group (L. salmini, L. convexiusculus, and L. lignarius), and the L. dorsalis group (L. dorsalis, L. terraereginae, L. dumerilii and L. interioris). The L. ornatus species group forms a highly distinctive clade that is a sister group to the other Limnodynastes groups. Pending broader phylogenetic studies it could be removed from the genus Limnodynastes. Our results concur with previous suggestions that Megistolotis lignarius is nested within Limnodynastes, and we therefore reclassify this species as Limnodynastes lignarius. Furthermore, specimens identified as L. depressus form a mtDNA lineage distinct from other species in the genus, confirming the validity of the species. Specimens of species from the L. dorsalis group (L. dorsalis, L. dumerilii, L. interioris, and L. terraereginae) are closely related such that L. dumerilii is paraphyletic with two other species. Finally, our study provides broad support for previous phylogenies based on microcomplement fixation.     

How many fungi make sclerotia?

Most fungi produce some type of durable microscopic structure such as a spore that is important for dispersal and/or survival under adverse conditions, but many species also produce dense aggregations of tissue called sclerotia. These structures help fungi to survive challenging conditions such as freezing, desiccation, microbial attack, or the absence of a host. During studies of hypogeous fungi we encountered morphologically distinct sclerotia in nature that were not linked with a known fungus. These observations suggested that many unrelated fungi with diverse trophic modes may form sclerotia, but that these structures have been overlooked. To identify the phylogenetic affiliations and trophic modes of sclerotium-forming fungi, we conducted a literature review and sequenced DNA from fresh sclerotium collections. We found that sclerotium-forming fungi are ecologically diverse and phylogenetically dispersed among 85 genera in 20 orders of Dikarya, suggesting that the ability to form sclerotia probably evolved ≥14 different times in fungi.