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This issue of Mycological Research News features: Forthcoming International Mycological Meetings.
Fifteen papers are presented. The first consider the functional assignments of Aspergillus nidulans genes, and coding and non-coding data in the model fungus Phycomyces blakesleeanus. Molecular phylogenetic studies are used to present a new classification of the lichen-forming genus Melanelia, determine the relationships of Stachybotrys chartarum, examine the phylogeny and biogeography of Amanita muscaria and A. pantherina, and re-evaluate the identity of Trichoderma isolates used in biocontrol. Mycoviruses are reported from Monilinia fructicola for the first time.
Pleurotus sajor-caju can degrade toxic juglone, and the degradation of tannic acid by black Aspergillus species is compared. The dynamics of fungi and other organisms in soil are studied with ergosterol and glomalin markers. The distribution of the dark septate endophyte Phialocephala fortinii is examined in Canada, and in a broader study found to comprise different genotypes; the melanin in the endophytic Phyllosticta capitalensis is also characterized. Influences on the solubilization of metal phosphate by ericoid mycorrhizal fungi are explored, as are the factors affecting the growth of Potebniamyces pyri.
The following new scientific names are introduced: Melanelixia, and Melanohalea gens. nov.; Melanelixia albertana (syn. Parmelia albertana) M. fuliginosa (syn. P. olivacea var. fuliginosa), M. glabra (syn. P. olivacea f. glabra), M. glabroides (syn. P. glabroides), M. huei (syn. P. huei), M. subargentifera (syn. P. subargentifera), M. subaurifera (syn. P. subaurifera), M. villosella (syn. P. villosella), Melanohalea elegantula (syn. P. olivacea var. elegantula), M. exasperata (syn. P. exasperata), M. exasperatula (syn. P. exasperatula), M. gomukhensis (syn. Melanelia gomukhensis), Melanohalea halei (syn. Parmelia halei), M. inactiva (syn. Melanelia inactiva), Melanohalea infumata (syn. P. infumata), M. laciniatula (syn. P. exasperata var. laciniatula), M. multispora (syn. P. multispora), M. olivacea (syn. Lichen olivaceus), M. olivaceoides (syn. P. olivaceoides), M. poeltii (syn. Melanelia poeltii), Melanohalea septentrionalis (syn. P. olivacea var. septentrionalis), M. subelegantula (syn. Parmelia subelegantula), M. subolivacea (syn. P. subolivacea), M. subverruculifera (syn. P. subverruculifera), M. trabeculata (syn. P. trabeculata), M. ushuaiensis (syn. P. ushuaiensis), and M. zopheroa (syn. Melanelia zopheroa) combs. nov.
Whole genome sequencing of several filamentous ascomycetes is complete or in progress; these species, such as Aspergillus nidulans, are relatives of Saccharomyces cerevisiae. However, their genomes are much larger and their gene structure more complex, with genes often containing multiple introns. Automated annotation programs can quickly identify open reading frames for hypothetical genes, many of which will be conserved across large evolutionary distances, but further information is required to confirm functional assignments. We describe a comparative and functional genomics approach using sequence alignments and gene expression data to predict the function of Aspergillus nidulans genes. By highlighting examples of discrepancies between the automated genome annotation and cDNA or EST sequencing, we demonstrate that the greater complexity of gene structure in filamentous fungi demands independent data on gene expression and the gene sequence be used to make confident functional assignments.
The zygomycete Phycomyces blakesleeanus has a 30 Mb genome with a 35% content of guanine and cytosine (GC). We determined the GC content in Phycomyces genes and fragments of genes available in public databases, the frequency of nucleotides in each codon position, and the codon usage. We observed a difference of 18% between the GC content of protein-coding and non-coding DNA. This large difference allowed the visualization of protein-coding DNA by plotting the GC content along a segment of Phycomyces DNA. We have identified a high GC DNA segment linked to the pyrG genes of the zygomycete genera Phycomyces, Mucor, and Blakeslea that corresponds to the 3′ end of the gene responsible for the protein kinase C.
Stachybotrys chartarum is an asexually reproducing fungus commonly isolated from soil and litter that is also known to occur in indoor environments and is implicated as the cause of serious illness and even death in humans. Despite its economic importance, higher level phylogenetic relationships of Stachybotrys have not been determined nor has a sexual state for S. chartarum been reported. DNA sequences from four nuclear and one mitochondrial gene were analyzed to determine the ordinal and familial placement of Stachybotrys within the Euascomycota. These data reveal that species of Stachybotrys including S. chartarum, S. albipes, for which the sexual state Melanopsamma pomiformis is reported, species of Myrothecium, and two other tropical hypocrealean species form a previously unknown monophyletic lineage within the Hypocreales. These results suggest that Stachybotrys and Myrothecium are closely related and share characteristics with other hypocrealean fungi. In addition, S. chartarum may have a sexual state in nature that consists of small, black, fleshy perithecia similar to Melanopsamma.
This paper continues a revision of generic concepts in the parmelioid lichens using molecular data in order to reach a consensus among lichenologists over which segregates proposed over the last two decades should be accepted. Here we employ data from three gene portions to provide a basis for a revised generic concept of the brown parmelioid lichens hitherto classified in Melanelia. The phylogeny was studied using a Bayesian analysis of a combined data set of nuclear ITS, LSU rDNA and mitochondrial SSU rDNA sequences. 173 new sequences were obtained from 38 specimens of 15 Melanelia species, 37 related parmelioid species, and eight non-parmelioid species. The results indicate that Melanelia is not monophyletic but falls into four different clades. The genus Melanelia is restricted here to a small group of saxicolous lichens related to the type species M. stygia, and with bifusiform conidia, while the remaining species, most of which are primarily corticolous and have mainly cylindrical to filiform conidia, belong to two other clades recognised as two new genera: Melanelixia and Melanohalea, to accommodate the M. exasperata and M. glabra groups, respectively. 27 new combinations are made. The epicortex of Melanelixia species have pores or special structures termed here ‘fenestrations’, while most Melanohalea species are pseudocyphellate. Pleurosticta links to the Melanohalea clade but without strong support, and the phylogenetic position of M. disjuncta and its related species remains uncertain, linking with the Xanthoparmelia (syn. Neofuscelia) clade but also without strong support.
The molecular phylogeny and biogeography of two widely distributed Amanita species, A. muscaria and A. pantherina, were studied based on specimens from diverse localities. Analyses of both a partial sequence of the ITS region of nuclear DNA and a partial sequence of the β-tubulin gene were able to resolve specimens of each species. Analyses revealed a greater divergence of the β-tubulin region than the ITS region. Based on molecular phylogeny of the combination of the ITS and β-tubulin regions, A. muscaria could be separated into at least three groups (Eurasian, Eurasian subalpine, and North American), and A. pantherina could be separated into at least two groups (North American and Eurasian). We hypothesize that the speciation of A. muscaria occurred in Eurasia with subsequent migration to North America via land bridges. However, it is impossible to determine whether A. pantherina moved from Eurasia to North America or vice versa. For both A. muscaria and A. pantherina, the intracontinental relationships of both Eurasia and North America were closer than the relationships between eastern Asia and eastern North America.
Genetic variability within 69 biocontrol isolates of Trichoderma, obtained from different geographical locations and culture collections and selected as biocontrol agents, was studied. Sequence data, obtained from the ITS1 region of rDNA and a fragment of the translation elongation factor 1 (tef1) gene, were used in a phylogenetic analysis. Phylograms showing similar topologies were generated using alignments containing the ITS1 region or a portion of the tef1 gene. 21 distinct ITS1 sequence types and 17 distinct tef1 sequence types were identified among the 69 isolates. More than 50% of the potential biocontrol strains were grouped within Trichoderma sect. Pachybasium; of these, 81% were grouped within the cluster that included the ex-type strains of T. harzianum and T. inhamatum, and 16% were grouped with T. virens. Within T. sect. Trichoderma, which included 36% of the 69 strains, 56% were grouped with T. asperellum, and 24% with T. viride, T. atroviride or T. koningii. Only 10% of the strains studied were located in T. sect. Longibrachiatum.
DsRNAs were detected in 36 of 49 Monilinia fructicola isolates from stone fruit orchards in New Zealand. The dsRNA profiles were highly variable, even between isolates from a single tree. Comparison of pathogenicity on detached fruit, in vitro growth rate, and sporulation of 14 isolates showed no obvious correlation with presence of dsRNAs. Partially purified extracts from four isolates were examined for the presence of virus-like particles by transmission electron microscopy. One isolate contained 45 nm isometric particles similar in appearance to totiviruses and partitiviruses. A second isolate contained 200–250×25 nm rigid rods similar in appearance to the plant pathogenic tobraviruses and furoviruses. This is the first report of the presence of viral-like agents in the brown rot fungus Monilinia fructicola.
The toxic naphthoquinone juglone (5-hydroxy-1,4-naphthoquinone) is efficiently degraded by the ligninolytic fungus Pleurotus sajor-caju, as demonstrated by the total bleaching within 9 d of a conventional liquid culture medium supplemented with 0.6 mM juglone. The oxidative degradation involves the production of hydrogen peroxide arising from both enzymic and non-enzymic oxidation reactions, promoted by the fungus. Juglone is not directly attacked by the oxidative enzymes of the ligninolytic machinery of P. sajor-caju, such as laccase, manganese peroxidase and arylalcohol oxidase. On the other hand, this naphthoquinone is a good substrate for a reductase, which triggers an auto-oxidative process producing reactive oxygen species and leading to juglone degradation. The degradation process continues to completion by means of a direct, presumably non-catalysed reaction with hydrogen peroxide.
A set of aspergillus strains from culture collections and wild-type black aspergilli isolated on non-selective media were used to validate the use of media with 20% tannic acid for exclusive and complete selection of the black aspergilli. The 20% tannic acid medium proved useful for both quantitative and qualitative selection of all different black aspergilli, including all recognized species: A. carbonarius, A. japonicus, A. aculeatus, A foetidus, A. heteromorphus, A. niger, A. tubingensis and A. brasiliensis haplotypes. Even higher concentrations of tannic acid can be utilized by the black aspergilli suggesting a very efficient tannic acid-degrading system. Colour mutants show that the characteristic ability to grow on high tannic acid concentrations is not causally linked to the other typical feature of these aspergilli, i.e. the formation of brown-black pigments. Sequence analysis of the A. niger genome using the A. oryzae tannase gene yielded eleven tannase-like genes, far more than in related species. Therefore, a unique ecological niche in the degradation of tannic acid and connected nitrogen release seems to be reserved for these black-spored cosmopolitans.
Potebniamyces pyri (anamorph Phacidiopycnis piri) is the causal agent of Phacidiopycnis rot of apples and pears. The disease has recently been recognized in pears in the USA. Little information on the basic biology of the fungus is available. In this paper, we report the effects of culture media, temperature, water potential and pH on mycelial growth, and the effects of media and light on pycnidia production. Prune juice agar was the best for rapid mycelial growth. Pear juice agar, apple juice agar, potato dextrose agar, and oatmeal agar (OMA) also favoured mycelial growth. Czapek-Dox agar was not suitable for mycelial growth. The fungus was able to grow at temperatures from −3 to 25 °C. Optimal mycelial growth occurred between 15 and 20 °. The average radial growth rate on OMA was 3.9 mm d−1 at 15 ° and 4.4 mm d−1 at 20 °. Mycelial growth was not observed after 10 d at 30 °, but growth resumed at 20 °. The fungus failed to resume growth at 20 ° after being incubated for 10 d at 35 °. The fungus was able to grow at water potentials as low as −4 MPa but no growth took place at −7.3 MPa. Active mycelial growth was observed on OMA at pH between 3.2 and 6.1. Optimal growth was observed at pH around 4 and no growth was observed at pH 7.1. No pycnidia or very few formed on the nine media at 20 ° in the dark. Fluorescent light significantly stimulated formation of pycnidia. OMA was the best medium for production of pycnidia and macroconidia. Pycnidia that formed on 8-wk-old OMA cultures incubated at 20 ° under 12 h dark/12 h light produced abundant macroconidia and the technique is recommended for inoculum production of conidia for research.
Interrelations of fungal mycelium with other soil biota are of paramount importance in forestry and soil ecology. Here we present the results of statistical analysis of a comprehensive data set collected in the first (and the only) British fungus sanctuary over a period of four months. The variables studied included a number of soil properties, bacteria, protozoan flagellates, ciliates and amoebae, microbial and plant feeding nematodes, various microarthropods, and two fungal biomarkers – glomalin and ergosterol. One way ANOVA showed that the dynamics of the microbiota studied was influenced by seasonal changes. Superimposed on these changes, however, was variability due to biological interactions and habitat characteristics. Two fungal biomarkers, ergosterol and glomalin, were differently influenced by other biota and abiotic variables. The results indicate that the dynamics of soil fungi is influenced not only by soil microarthropods, but also by those found in forest litter. The overall outcome, therefore, is likely to be very complex and will depend upon specific conditions of any particular ecosystem.
Four ericoid mycobionts (two isolates of Hymenoscyphus ericae, and two dark, sterile ericoid mycobionts isolated from metal-contaminated mine sites) were grown on solid agar plates supplemented with zinc phosphate (0.25%) containing different forms of nitrogen (nitrate, ammonium or alanine) and different concentrations of carbon (glucose) and phosphorus (K2HPO4). The influence of nutrient variation on solubilizing ability of the fungi was assessed by measuring the zones of solubilization appearing beneath the growing colonies. All four mycobionts were capable of zinc phosphate solubilization in the presence of all three nitrogen sources and in media containing no nitrogen. No solubilization was observed at 0 mM glucose-C but was observed with increasing glucose concentration from 300 to 600 mM C. Increasing phosphorus concentration (0–5 mM P) had no effect on the solubilizing ability of the isolates. All but one of the mycobionts were capable of solubilizing calcium phosphate (CaHPO4), while no solubilization was observed in media containing aluminium phosphate (AlPO4), iron phosphate (FePO4.4H2O) or copper phosphate (Cu3O8P2.2H2O) under conditions which were found to be optimal for zinc phosphate solubilization. Under conditions of glucose at 300 mM C and alanine as the N source in the zinc phosphate-amended agar medium, one of the mycobionts produced new crystals, which were morphologically distinct from the original zinc phosphate crystals. It is concluded that medium composition influences the metal-phosphate solubilizing ability of ericoid mycobionts. The results are discussed in relation to the possible mechanisms involved in solubilization and the potential benefits of metal-phosphate solubilization to ericoid mycobionts and their host plants.
Dark septate root endophytes (DSE) are an artificial assemblage of fungi that have darkly pigmented, septate hyphae and that are frequent or distinctive intracellular associates of roots of apparently healthy plants. Based on isolates obtained from the roots of Salix spp., the distribution of a common DSE fungus, Phialocephala fortinii, was examined along a latitudinal transect in Canada running from the high arctic to the 49° N parallel. Non-sporulating isolates were provisionally identified as P. fortinii through analysis of DNA sequence data of the ITS2 region of rDNA. P. fortinii was isolated frequently from boreal and arctic habitats, but rarely from grassland habitats. Patterns of genetic variation were examined through analysis of amplified fragment length polymorphisms (AFLP). All AFLP profiles were unique with the majority of genetic variation occurring among individuals within the collecting sites at each latitude. Neighbour-joining analysis of genetic distances yielded eight well-supported clusters, three of which included individuals from more than one latitude. Some linkage disequilibrium, possibly due to partial clonality, was detected.
The aim of the present work was to determine the identity and molecular relationships between 127 strains of dark septate (DS) fungi isolated from healthy root tips, decayed coarse roots, live healthy-looking stems, coarse (stumps, snags and logs) and fine (tree branches and tops) woody debris in temperate-boreal forests in Sweden and Lithuania. Sequence analysis of ITS rDNA was used to identify the fungi. In a neighbour-joining similarity tree, all sequences were grouped into five distinct clusters. Within each of these, ITS rDNA sequence variation consisted of 2–18 nucleotides, corresponding to 1–3% of their total length. The four least variable clusters were supported with high bootstrap values of 86–100%. Comparisons with the sequences in the GenBank database showed that all our strains had a 95–100% homology with identified Phialocephala species, and they were thus assigned to this genus. The representatives of two clusters were identified, as P. fortinii and P. dimorphospora. The representatives of three remaining clusters were defined as Phialocephala sp. 35, Phialocephala sp. 6 and Phialocephala sp. 18. Within each of these clusters, ITS rDNA sequence uniformity was higher than that observed within P. fortinii and P. dimorphospora. Consequently, their clusters were most discrete, supported with bootstrap values of 100%. Genetic variation in the five distinguished Phialocephala species and their possible ecological roles are discussed. Phialocephala sp. 6 was confined to healthy root tips of conifers. P. dimorphospora was only associated with dead woody tissue of P. abies. P. fortinii, Phialocephala sp. 18 and sp. 35 were isolated from both dead and living conifers and Betula pendula. In conclusion, the present study revealed the ability of fungi from the genus Phialocephala to colonise and persist in live and dead trees under strikingly different ecological conditions.
Phyllosticta capitalensis (teleomorph Guignardia mangiferae) occurs as a foliar endophyte in woody trees belonging to different families of both temperate and tropical regions. We isolated this endophyte from plants in different habitats, such as mangroves, dry deciduous forest, moist deciduous forest and semi-evergreen forest. This endophyte was found to produce a black pigment that was characterized to be melanin based on UV-visible, IR and ESR spectra and chemical tests. Tricyclazole, a specific inhibitor of pentaketide melanin biosynthesis, inhibited synthesis of the pigment indicating it is a 1-8, dihydroxynaphthalene. This appears to be the first report of such a melanin in Phyllosticta or other foliar endophytes. Melanin in the hyphae of P. capitalensis may be responsible for the success of this fungus as a cosmopolitan endophyte, since melanin is known to enhance the survival capability of fungi in stressful environments.