Species Of Ascomycota Research Articles

Trypsin-like proteins of the fungi as possible markers of pathogenicity

Sequences of peptidases with conserved motifs around the active site residues that are characteristic of trypsins (similar to trypsin peptidases, STP) were obtained from publicly-available fungal genomes and related databases. Among the 75 fungal genomes, 29 species of parasitic Ascomycota contained genes encoding STP and their homologs. Searches of non-redundant protein sequences, patented protein sequences, and expressed sequence tags resulted in another 18 STP sequences in 10 fungal species from Ascomycota, Basidiomycota, and Zygomycota. A comparison of fungi species containing STP sequences revealed that almost all are pathogens of plants, animals or fungi. A comparison of the primary structure of homologous proteins, including the residues responsible for substrate binding and specificity of the enzyme, revealed three groups of homologous sequences, all presumably from S1 family: trypsin-like peptidases, chymotrypsin-like peptidases and serine peptidases with unknown substrate specificity. Homologs that are presumably functionally inactive were predicted in all groups. The results in general support the hypothesis that the expression of trypsin-like peptidases in fungi represents a marker of fungal phytopathogenicity. A phylogenetic tree was constructed using peptidase and homolog amino acid sequences, demonstrating that all have noticeable differences and almost immediately deviate from the common root. Therefore, we conclude that the changes that occurred in STP of pathogenic fungi in the course of evolution represent specific adaptations to proteins of their respective hosts, and mutations in peptidase genes are important components of life-style changes and taxonomic divergence.

Fungal ecology catches fire

Fungal ecology catches fire

The Fungi

The Kingdom Fungi, home to molds, mushrooms, lichens, rusts, smuts and yeasts, comprises eukaryotes with remarkably diverse life histories that make essential contributions to the biosphere, human industry, medicine and research. With the aim of enticing biologists to include fungi in their research, we note that many fungi have haploid genetics, and that those in cultivation are essentially immortal, two features that make it easier to associate traits with genotype, even for complex traits, than with Drosophila or Arabidopsis. The typical fungal genome size of 30–40 Mb is small by eukaryotic standards, which is why fungi have led the way as models for eukaryote genome sequencing with over 100 assembled genome sequences available [1, 2]. For some fungi, DNA transformations, gene knockouts and knockdowns are routine. Species of Ascomycota and Basidiomycota show simple, multicellular development with differentiated tissues. In many species these tissues are large enough to support studies of transcription and translation in the lab and even in nature. About a billion years ago, give or take 500 million years [3], a population of aquatic, unicellular eukaryotes making sporangia containing zoospores each with a single posterior flagellum split into two lineages: one eventually gave rise to animals, the other to fungi. Here we shall summarize the major diversifications of the Fungi by introducing each major fungal branch in the order that it is thought to have diverged (Figure 1) and presenting salient facts about fungal modes of nutrition, reproduction, communication and interaction with other life. Our views are strongly influenced by the Fungal Tree of Life Project [4–6]. Readers interested in learning more about fungi are encouraged to consult any of a number of comprehensive texts [7, 8]. Figure 1 The fungi. Phylogenetic tree, based on [4], showing relationships of many of the fungal lineages fit to geologic time using the program r8s [73] and considering Paleopyrenomycites to be a member of the Ascomycota [3]. Arrows depict changes in morphology ... The exact order of divergence in deep regions of the eukaryotic tree is controversial. On the lineage that leads to the Fungi there are thought to be two other groups; the first to diverge are the nucleariid amoebae [9], and the next the Microsporidia. Microsporidia are either the sister group to the Fungi, or lie within the Fungi, (Figure 1), and they should be included in studies of fungi. They are unculturable, obligate parasites of animals, including humans. They have extremely reduced eukaryotic genomes — with a genome size of ~2.6 Mb and ~2000 genes [10, 11] — remnant mitochondria, and unique morphologies related to parasitism, including a very frightening polar tube used to initiate infection [10].

Comparative taxonomy of desert truffles of the Australian outback and the African Kalahari

Seven truffle species are reported from the Australian Outback—six Ascomycota (Elderia arenivaga, Mattirolomyces mulpu sp. nov., Mycoclelandia arenacea, M. bulundari, Reddelomyces westraliensis, Ulurua nonparaphysata gen. & sp. nov.) and one Basidiomycota (Horakiella watarrkana sp. nov.) Three Ascomycota species are redescribed from the African Kalahari (Eremiomyces echinulatus, Kalaharituber pfeilii and Mattirolomyces austroafricanus comb. nov.). The phylogenetic analyses of nrDNA of the Australian Ascomycota provided strong support for placement of all but one in the Pezizaceae (Reddellomyces belongs in the Tuberaceae), as is true of most, if not all, other ascomycetous desert truffles. These genetic results also highlight that the genus Mattirolomyces is more taxonomically, ecologically, and geographically diverse than previously realized.

Lack of Evolutionary Conservation at Positions Important for Thermal Stability in the Yeast ODCase Protein

Mutations destabilizing the spatial structure of proteins can persist in populations if they are fixed by drift or compensated by other mutations. The prevalence and dynamics of these processes remain largely unrecognized. A suitable target to screen for both deleterious and compensatory mutations is the URA3 gene in yeast. We identified 13 positions in which a single missense substitution causes substantially strong thermal sensitivity. We then applied mild mutagenesis resulting in roughly one base substitution per gene and found that only reversions to an original amino acid can compensate for the thermal instability. However, the 13 positions are not visibly conserved across 53 species of Ascomycota, despite that the gene product is an enzyme of stable function and high efficiency. This shows how much fitness penalties for amino acid substitutions are background dependent, underscoring the role of complex intragenic interactions in the evolution of proteins.

Friend or foe? Evolutionary history of glycoside hydrolase family 32 genes encoding for sucrolytic activity in fungi and its implications for plant-fungal symbioses

BackgroundMany fungi are obligate biotrophs of plants, growing in live plant tissues, gaining direct access to recently photosynthesized carbon. Photosynthate within plants is transported from source to sink tissues as sucrose, which is hydrolyzed by plant glycosyl hydrolase family 32 enzymes (GH32) into its constituent monosaccharides to meet plant cellular demands. A number of plant pathogenic fungi also use GH32 enzymes to access plant-derived sucrose, but less is known about the sucrose utilization ability of mutualistic and commensal plant biotrophic fungi, such as mycorrhizal and endophytic fungi. The aim of this study was to explore the distribution and abundance of GH32 genes in fungi to understand how sucrose utilization is structured within and among major ecological guilds and evolutionary lineages. Using bioinformatic and PCR-based analyses, we tested for GH32 gene presence in all available fungal genomes and an additional 149 species representing a broad phylogenetic and ecological range of biotrophic fungi.ResultsWe detected 9 lineages of GH32 genes in fungi, 4 of which we describe for the first time. GH32 gene number in fungal genomes ranged from 0–12. Ancestral state reconstruction of GH32 gene abundance showed a strong correlation with nutritional mode, and gene family expansion was observed in several clades of pathogenic filamentous Ascomycota species. GH32 gene number was negatively correlated with animal pathogenicity and positively correlated with plant biotrophy, with the notable exception of mycorrhizal taxa. Few mycorrhizal species were found to have GH32 genes as compared to other guilds of plant-associated fungi, such as pathogens, endophytes and lichen-forming fungi. GH32 genes were also more prevalent in the Ascomycota than in the Basidiomycota.ConclusionWe found a strong signature of both ecological strategy and phylogeny on GH32 gene number in fungi. These data suggest that plant biotrophic fungi exhibit a wide range of ability to access plant-synthesized sucrose. Endophytic fungi are more similar to plant pathogens in their possession of GH32 genes, whereas most genomes of mycorrhizal taxa lack GH32 genes. Reliance on plant GH32 enzyme activity for C acquisition in these symbionts supports earlier predictions of possible plant control over C allocation in the mycorrhizal symbiosis.

Ectomycorrhizal fungal community in alkaline-saline soil in northeastern China

Alkaline-saline soil is widespread in arid and semiarid regions of the world and causes severe environmental and agricultural problems. To advance our understanding of the adaptation of ectomycorrhizal fungi (EMF) to alkaline-saline soil, we investigated EMF communities on Mongolian willow (Salix linearistipularis) growing in alkaline-saline soil (up to pH 9.2) in northeastern China. In total, 75 root samples were collected from 25 willow individuals over 4.7 ha. To identify fungal species in ectomycorrhizal root tips, we used terminal restriction fragment length polymorphism and sequencing analyses of the internal transcribed spacer region of ribosomal DNA. We detected 11 EMF species, including species of Inocybe, Hebeloma, and Tomentella of the Basidiomycota and three Ascomycota species. The EMF richness of the study site was estimated to be 15-17 using major estimators. The most abundant species was Geopora sp. 1, while no Geopora-dominated EMF communities have been reported so far. Phylogenetic analysis showed that the phylogroup including Geopora sp. 1 has been found mostly in alkaline soil habitats, indicating its adaptation to high soil pH. Because EMF are indispensable for host plant growth, the EMF species detected in this study may be useful for restoration of alkaline-saline areas.

Comparative genomics of the oxidative phosphorylation system in fungi

In this study, we have carried out an in silico analysis of the available mitochondrial and nuclear genomes of fungi in order to identify the oxidative phosphorylation (OXPHOS) proteome, the complete set of proteins that perform the OXPHOS in mitochondria. The presence of OXPHOS proteins has been investigated in 27 nuclear and 52 mitochondrial genomes of fungi. Comparative genomics reveals a high conservation of the OXPHOS system within each fungal phyla, and notable differences between the OXPHOS proteomes of the fungal phyla. The most striking differences concerned Complexes I and V. The absence of Complex I has been previously described in various species of Ascomycota and Microsporidia, and the NDUFB4 and NURM accessory subunits of Complex I appear to be specific of fungi belonging to the subphylum Pezizomycotina. In addition, the Complex V essential subunit ATP14 appears to be specific of two subphyla of Ascomycota: the Saccharomycotina and Pezizomycotina.

Evolution of host resistance in a toxin-producing bacterial–fungal alliance

The rice seedling blight fungus Rhizopus microsporus harbors endosymbiotic Burkholderia sp. for the production of the virulence factor, the antimitotic agent rhizoxin. Since the toxin highly efficiently blocks mitosis in most eukaryotes, it remained elusive how self-resistance emerged in the fungal host. In this study, rhizoxin sensitivity was systematically correlated with the nature of beta-tubulin sequences in the kingdom Fungi. A total of 49 new beta-tubulin sequences were generated for representative species of Ascomycota, Basidiomycota and Zygomycota. Rhizoxin sensitivity assays revealed two further amino acids at position 100 (Ser-100 and Ala-100), in addition to the known Ile-100 and Val-100, which convey rhizoxin resistance. All sensitive strains feature Asn-100. This hot spot was verified by modeling studies, which support the finding that rhizoxin preferentially interacts with the tubulin molecule in a cavity near position 100. Ancestral character state reconstructions conducted in a Bayesian framework suggest that rhizoxin sensitivity represents the ancestral character state in fungi, and that evolution of rhizoxin resistance took place in the ancestor of extant resistant Zygomycota. These findings support a model according to which endosymbiosis became possible through a parasitism--mutualism shift in insensitive fungi.

Existence of a pattern of reproductive character displacement inHomobasidiomycotabut not inAscomycota

Generally, stronger reproductive isolation is expected between sympatric than between allopatric sibling species. Such reproductive character displacement should predominantly affect premating reproductive isolation and can be due to several mechanisms, including population extinction, fusion of insufficiently isolated incipient species and reinforcement of reproductive isolation in response to low hybrid fitness. Experimental data on several taxa have confirmed these theoretical expectations on reproductive character displacement, but they are restricted to animals and a few plants. Using results reported in the literature on crossing experiments in fungi, we compared the degree and the nature of reproductive isolation between allopatric and sympatric species pairs. In accordance with theoretical expectations, we found a pattern of enhanced premating isolation among sympatric sibling species in Homobasidiomycota. By contrast, we did not find evidence for reproductive character displacement in Ascomycota at similar genetic distances. Both allopatric and sympatric species of Ascomycota had similarly low levels of reproductive isolation, being mostly post-zygotic. This suggests that some phylogeny-dependent life-history trait may strongly influence the evolution of reproductive isolation between closely related species. A significant correlation was found between degree of reproductive isolation and genetic divergence among allopatric species of Homobasidiomycota, but not among sympatric ones or among Ascomycota species.

Geographic locality and host identity shape fungal endophyte communities in cupressaceous trees

Understanding how fungal endophyte communities differ in abundance, diversity, taxonomic composition, and host affinity over the geographic ranges of their hosts is key to understanding the ecology and evolutionary context of endophyte–plant associations. We examined endophytes associated with healthy photosynthetic tissues of three closely related tree species in the Cupressaceae ( Coniferales): two native species within their natural ranges [ Juniperus virginiana in a mesic semideciduous forest, North Carolina (NC); Cupressus arizonica, under xeric conditions, Arizona (AZ)], and a non-native species planted in each site ( Platycladus orientalis). Endophytes were recovered from 229 of 960 tissue segments and represented at least 35 species of Ascomycota. Isolation frequency was more than threefold greater for plants in NC than in AZ, and was 2.5 (AZ) to four (NC) times greater for non-native Platycladus than for Cupressus or Juniperus. Analyses of ITS rDNA for 109 representative isolates showed that endophyte diversity was more than twofold greater in NC than in AZ, and that endophytes recovered in AZ were more likely to be host-generalists relative to those in NC. Different endophyte genera dominated the assemblages of each host species/locality combination, but in both localities, Platycladus harboured less diverse and more cosmopolitan endophytes than did either native host. Parsimony and Bayesian analyses for four classes of Ascomycota ( Dothideomycetes, Sordariomycetes, Pezizomycetes, Eurotiomycetes) based on LSU rDNA data ( ca 1.2 kb) showed that well-supported clades of endophytes frequently contained representatives of a single locality or host species, underscoring the importance of both geography and host identity in shaping a given plant's endophyte community. Together, our data show that not only do the abundance, diversity, and taxonomic composition of endophyte communities differ as a function of host identity and locality, but that host affinities of those communities are variable as well.

Intra-specific and intra-sporocarp ITS variation of ectomycorrhizal fungi as assessed by rDNA sequencing of sporocarps and pooled ectomycorrhizal roots from a Quercus woodland

The Internal Transcribed Spacer (ITS) regions of ribosomal DNA are widely used as markers for phylogenetic analyses and environmental sampling from a variety of organisms including fungi, plants, and animals. In theory, concerted evolution homogenizes multicopy genes so that little or no variation exists within populations or individuals. However, contrary to theory, ITS variation has been confirmed in populations and individuals from a diverse range of eukaryotes. The presence of intraspecific and intra-individual variation in multicopy genes has important implications for ecological and phylogenetic studies, yet relatively little is known about natural variation of these genes, particularly at the community level. In this study, we examined intraspecific and intra-sporocarp ITS variation by DNA sequencing from sporocarps and pooled roots from 68 species of ectomycorrhizal fungi collected at a single site in a Quercus woodland. We detected ITS variation in 27 species, roughly 40% of the taxa examined. Although intraspecific ITS variation was generally low (0.16-2.85%, mean = 0.74%), it was widespread within this fungal community. We detected ITS variation in both sporocarps and ectomycorrhizal roots, and variation was present within species of Ascomycota and Basidiomycota, two distantly related lineages within the Fungi. We discuss the implications of such widespread ITS variability with special reference to DNA-based environmental sampling from diverse fungal communities.

Dynamics of 15N natural abundance in wood-decomposing fungi and their ecophysiological implications

Nine species of basidiomycota and one species of ascomycota were grown in an ammonium sulphate media and on beech wood; and the general 15N dynamic patterns of the hyphae were examined. The fungal body initially became depleted in 15N in both the types of incubation. However, the underlying mechanisms were quite different, that is, significant fungal 15N drop on the beech wood is associated with the fungal N reallocation and the uptake of atmospheric ammonia and/or NOx, in addition to isotope fractionation during assimilation. Although the 15N values of the wood-decomposing basidiocarps were generally close to the 15N values of the wood, it does not always indicate that the wood derived N was the sole N source for the fungi throughout the growth periods as shown in our wood-decomposing experiment.

Fungos filamentosos isolados do solo em municípios na região Xingó, Brasil

O solo é considerado um dos principais hábitats para a população de microrganismos, dentre os quais estão os fungos. A região de Xingó é caracterizada por apresentar ecossistema típico de Caatinga. Com objetivo de isolar e identificar fungos filamentosos na região Xingó, utilizou-se amostras de solo coletadas nos municípios de Canindé de São Francisco (SE), Olho D'água do Casado (AL) e Piranhas (AL), durante o período chuvoso (maio e julho/2000) e de estiagem (março/2001), tanto na superfície do solo quanto a 20 cm de profundidade. Foram identificados 96 táxons pertencentes a oito espécies de Ascomycota, oito espécies de Zygomycota e 80 anamorfos, sendo uma espécie de Coelomycetes e 79 espécies de Hyphomycetes. Penicillium e Aspergillus foram os gêneros mais diversos com 31 e 17 espécies, respectivamente.

Conservation of protein–protein interactions – lessons from ascomycota

Interacting proteins from Saccharomyces cerevisiae are evolutionarily conserved and their likelihood of having an ortholog in other ascomycota species correlates with the number of interaction partners. Moreover, interacting proteins show a clear preference to be conserved as a pair, indicating that nature maintains selection pressure on the interaction links between proteins. The conservation of interacting protein pairs between different organisms does not exhibit any bias with respect to protein functional roles.

Major fungal lineages are derived from lichen symbiotic ancestors.

About one-fifth of all known extant fungal species form obligate symbiotic associations with green algae, cyanobacteria or with both photobionts. These symbioses, known as lichens, are one way for fungi to meet their requirement for carbohydrates. Lichens are widely believed to have arisen independently on several occasions, accounting for the high diversity and mixed occurrence of lichenized and non-lichenized (42 and 58%, respectively) fungal species within the Ascomycota. Depending on the taxonomic classification chosen, 15-18 orders of the Ascomycota include lichen-forming taxa, and 8-11 of these orders (representing about 60% of the Ascomycota species) contain both lichenized and non-lichenized species. Here we report a phylogenetic comparative analysis of the Ascomycota, a phylum that includes greater than 98% of known lichenized fungal species. Using a Bayesian phylogenetic tree sampling methodology combined with a statistical model of trait evolution, we take into account uncertainty about the phylogenetic tree and ancestral state reconstructions. Our results show that lichens evolved earlier than believed, and that gains of lichenization have been infrequent during Ascomycota evolution, but have been followed by multiple independent losses of the lichen symbiosis. As a consequence, major Ascomycota lineages of exclusively non-lichen-forming species are derived from lichen-forming ancestors. These species include taxa with important benefits and detriments to humans, such as Penicillium and Aspergillus.

Succession of terrestrial macrofungi along a deglaciation gradient at Glacier Blåisen, South Norway

A survey of terrestrial macrofungi along a deglaciation gradient from the glacier forefront to the established vegetation has been performed. The study was accomplished along a transect from Lake Finsevann to Glacier Blåisen, South Norway. Fortysix 6 m × 6 m plots divided into 9 subplots were positioned along this transect. The frequency of fruit bodies of each species in each plot was given on a 0–9 scale reflecting their occurrence in the subplots. Biotic and abiotic environmental variables for the plots were also recorded. The numerical methods used include principal component analysis (PCA), detrended correspondence analysis (DCA), and canonical correspondence analysis (CCA). Totally 99 species of macrofungi were recorded; 80.8 % of the species belonged to the Basidiomycota and 19.2 % to the Ascomycota. About one third of the species was only found once. In general, the species richness was highest on the glacier forefront, lowest in the most established vegetation. The proportion of species of Ascomycota was highest close to the glacier front. The main gradient in the data set was shown related to the primary ecological succession following the retreat of glaciers. The second gradient was possibly related to fine scale variation due to local moisture, microtopography, and secondary distribution. Of the variation in composition of species, 3 % can be ascribed to abiotic variance, 10 % to vascular plant variance, and 16 % to the combination of the abiotic and vascular plant component of variation. The results are discussed in the light of the time since deglaciation and the influence of certain biotic and abiotic environmental factors.

Recovery of fungi after storage for over a quarter of a century

This paper discusses the recovery of a sample of strains originally preserved on silica gel over the period 1970–1973. Fifty-three strains were tested of which 18 recovered, demonstrating survival for more than 20 years. The recovery of 26 of the strains is directly compared with that of replicates from oil storage and freeze-drying. A summary of storage of 421 strains by the silica gel technique is given, reporting survival of 64% for a quarter of a century or more. The technique is ideal for preserving sporulating fungi of the Ascomycota and many species of mitotic fungi for laboratories of limited facilities.

Macrofungi on uranium mill tailings — Associations and metal content

Sporocarps of three species of Ascomycota and ten species of Basidiomycota were collected from abandoned uranium mill tailings. On these sites some natural colonisation by vegetation had occurred in the last 20 years. The existing vegetation provides some circumstantial evidence for mycorrhizal associations with Pinus strobus, Populus balsamifera, P. tremuliodes, and Salix sp. A new record for Helvella corium in Ontario requires confirmation. For twelve fungal collections, representing three different tailings sites, analysis of elemental composition by neutron activation was carried out, Al, Ba, Ca, Mg, Mn and Na. Fungal concentrations of these elements were for the most part much higher than previously published values; however, the respective substrate values were also higher than values for most soils. Concentration factors rarely exceeded unity. When collections were compared, concentration factors (c.f.) for Mn were consistently higher than c.f.'s for Ba, Al or Mg, with the single exception of Ba in the ascomycete Sepultaria on Madawaska site which had a concentration factor of 1.3. The possible significance of the findings for revegetation of uranium tailings, and for fungal tolerance of high mineral substrates is considered.

STUDIES OF COPROPHILOUS ASCOMYCETES VII. PREUSSIA

The Plectascales and Perisporiales are both artificial taxa each consisting of a miscellaneous assemblage of unrelated genera. The generic name Perisporium is not valid for species of Ascomycota (Ascomycetes). The valid name for those species which produce ascocarps is Preussia Fuckel. The ascocarps are non-ostiolate (cleistothecia) and their development is the same as that in the Loculo-ascomycetes (producing a pseudothecium). The ascocarp of Preussia is thus a cleistothecial pseudothecium. The genus most closely related to Preussia is Sporormia and the two may be included in the same family Sporormiaceae. Preussia is not included in the Phaeotrichaceae on account of the elongated germinal slit and lack of hairs on the peridium of the ascocarp. Twelve species are included with descriptions and illustrations. The type species of Preussia is P. funiculata Fuckel. Three species are transferred to this genus from Perisporium. These are P. punctata (Auersw.) Sacc., P. typharum Sacc, and P. vulgare Corda. One species is transferred from each of the following genera: Sporormia (Sp. fleischhakii Auersw.), Muellerella (M. nigra Routien), Pycnidiophora (P. dispersa Clum), Anixiopsis (A. multispora Saito and Minoura), and Thielavia (T. indica Chattop. and Das Gupta). The following three species are described as new: P. isomera, P. terricola, and P. purpurea.