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PubMed1999

Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi.

In the past, molecular clocks have been used to estimate divergence times among animal phyla, but those time estimates have varied widely (1200-670 million years ago, Ma). In order to obtain time estimates that are more robust, we have analysed a larger number of genes for divergences among three well-represented animal phyla, and among plants, animals and fungi. The time estimate for the chordate-arthropod divergence, using 50 genes, is 993 +/- 46 Ma. Nematodes were found to have diverged from the lineage leading to arthropods and chordates at 1177 +/- 79 Ma. Phylogenetic analyses also show that a basal position of nematodes has strong support (p > 99%) and is not the result of rate biases. The three-way split (relationships unresolved) of plants, animals and fungi was estimated at 1576 +/- 88 Ma. By inference, the basal animal phyla (Porifera, Cnidaria, Ctenophora) diverged between about 1200-1500 Ma. This suggests that at least six animal phyla originated deep in the Precambrian, more than 400 million years earlier than their first appearance in the fossil record.

Animals↗
PubMed2006

Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi.

The claim that eukaryotic micro-organisms have global geographic ranges, constituting a significant departure from the situation with macro-organisms, has been supported by studies of morphological species from protistan kingdoms. Here, we examine this claim by reviewing examples from another kingdom of eukaryotic microbes, the Fungi. We show that inferred geographic range of a fungal species depends upon the method of species recognition. While some fungal species defined by morphology show global geographic ranges, when fungal species are defined by phylogenetic species recognition they are typically shown to harbour several to many endemic species. We advance two non-exclusive reasons to explain the perceived difference between the size of geographic ranges of microscopic and macroscopic eukaryotic species when morphological methods of species recognition are used. These reasons are that microbial organisms generally have fewer morphological characters, and that the rate of morphological change will be slower for organisms with less elaborate development and fewer cells. Both of these reasons result in fewer discriminatory morphological differences between recently diverged lineages. The rate of genetic change, moreover, is similar for both large and small organisms, which helps to explain why phylogenetic species of large and small organisms show a more similar distribution of geographic ranges. As a consequence of the different rates in fungi of genetic and morphological changes, genetic isolation precedes a recognizable morphological change. The final step in speciation, reproductive isolation, also follows genetic isolation and may precede morphological change.

Classification↗
PubMed1978

Resistance of selected saprobic and zoopathogenic fungi to cycloheximide.

Spore germination was used as an assay to measure the sensitivities of selected fungi (Achlya bisexualis, Cladosporium sp., Trichophyton mentagrophytes and Microsporum gypseum) to cyclohexamide and to determine their abilities to adapt to the drug. Two patterns of response were noted. The saprobes, A. bisexualis and Cladosporium sp., demonstrated acquired resistance. Spores from hyphae previously exposed to cycloheximide either germinated in the presence of concentrations of the drug that completely inhibited spores from unexposed hyphae (Achlya), or germinates with a shorter lag and to a greater extent in the presence of the antibiotic than did spores from unexposed hyphae (Cladosporium). Hyphae of Achlya adapted at concentrations of cycloheximide in which spores did not germinate and hyphae of Cladosporium adapted more rapidly than spores. Achlya adapted to only 12 muM-cycloheximide whereas Cladosporium acquired resistance to 18 mM-cycloheximide. These fungi lost this acquired resistance after a single transfer to media lacking cycloheximide. The zoopathogens, T. mentagrophytes and M. gypseum, had a contrasting response, indicating constitutive resistance. Conidia from unexposed hyphae showed 90 to 100% germination on media containing up to 18 mM-cycloheximide; prior exposure to the drug did not affect their response.

Adaptation, Physiological↗
PubMed1981

Isolation of cellulolytic phycomycete fungi from the caecum of the horse.

Microscopic examination of horse caecum contents revealed vegetative growth of phycomycete fungi on particles of digesta, and uniflagellated cells similar to fungal zoospores in the liquid phase. Three morphologically distinct isolates of strictly anaerobic phycomycete fungi were obtained from the caecum contents and cultured in vitro. Two of the isolates were able to utilize a wide range of plant carbohydrates for growth, including alpha-cellulose, xylan and particulate starch, and extensively digested water-insoluble plant tissues.

Animals↗
PubMed1984

Transhyphal electrical currents in fungi.

Representative mycelial fungi from the phycomycete, ascomycete and basidiomycete groups (Achlya bisexualis, Neurospora crassa, Aspergillus nidulans, Schizophyllum commune and Coprinus cinereus) all generated steady electrical currents around their hyphal tips; the generation of a transhyphal ion current may therefore be a universal characteristic of hyphal growth. As with all other tip growing organisms, positive current always entered apically and left distally; non-growing hyphae did not drive transcellular currents. The current density, measured approximately 30 micron from the membrane surface at the hyphal tips, varied between 0.05 and 0.06 microA cm-2 in different fungi and tended to be larger in wider, rapidly extending hyphae than in thinner, slow growing hyphae. The possibility that these currents serve to localize growth at the apex is discussed.

Electricity↗
PubMed1991

Morphology of three polycentric rumen fungi and description of a procedure for the induction of zoosporogenesis and release of zoospores in cultures.

Three polycentric rumen fungi, LL, LC2 and Ruminomyces elegans (C2), isolated from the rumen of cattle were grown in six culture media. LL and LC2 were morphologically similar. Their characteristics resembled those of Orpinomyces and Neocallimastix joyonii, and they grew well and produced sporangia after 3-4 d growth in all the media. R. elegans differed morphologically from LL and LC2, but although it also grew well in all media, abundant sporangia occurred only after 2-3 d growth in media containing cellulose. Undifferentiated sporangia were produced by all three isolates; differentiation of the sporangia did not occur in the spent growth media. However, if thalli possessing recently-formed sporangia were transferred to, or flooded with, fresh liquid medium or rumen fluid, zoosporogenesis and liberation of zoospores occurred within 17-20 min for isolates LL and LC2 and 30 min for R. elegans. Procedures for inducing zoosporogenesis by polycentric anaerobic fungi are described.

Animals↗
PubMed1991

Comparison of growth characteristics of anaerobic fungi isolated from ruminant and non-ruminant herbivores during cultivation in a defined medium.

Anaerobic fungi were isolated from rumen fluid of a domestic sheep (Ovis aries; a ruminant) and from faeces of five non-ruminants: African elephant (Loxodonta africana), black rhinoceros (Diceros bicornis), Indian rhinoceros (Rhinoceros unicornis), Indian elephant (Elephas maximus) and mara (Dolichotis patagonum). The anaerobic fungus isolated from the sheep was a Neocallimastix species and the isolates from non-ruminants were all species similar to Piromyces spp. A defined medium is described which supported growth of all the isolates, and was used to examine growth characteristics of the different strains. For each fungus the lipid phosphate content was determined after growth on cellobiose and the resulting values were used to estimate fungal biomass after growth on solid substrates. The ability of isolates from ruminants and non-ruminants to digest both wheat straw and cellulose was comparable. More than 90% and 60%, respectively, of filter paper cellulose and wheat straw were digested by most strains within 60-78 h. Growth of two fungi, isolated from rumen fluid of a sheep (Neocallimastix strain N1) and from faeces of an Indian rhinoceros (Piromyces strain R1), on cellobiose was studied in detail. Fungal growth yields on cellobiose were 64.1 g (mol substrate)-1 for N1 and 34.2 g mol-1 for R1. The major fermentation products of both strains were formate, lactate, acetate, ethanol and hydrogen.

Anaerobiosis↗
PubMed1994

Detection of a wide range of medically important fungi by the polymerase chain reaction.

A polymerase chain reaction (PCR) method was developed that was capable of detecting a wide range of medically important fungi from clinical specimens. The primer pair was designed in conserved sequences of 18S-ribosomal RNA genes shared by most fungi. The lower limit of detection of this PCR technique was 1 pg of Candida albicans genomic DNA by ethidium bromide staining and 100 fg after Southern analysis. A 687-bp product was amplified successfully by PCR from all 78 strains of 25 medically important fungal species studies, including Candida spp., Hansenula spp., Saccharomyces cerevisiae, Cryptococcus neoformans, Trichosporon beigelii, Malassezia furfur, Pneumocystis carinii, Aspergillus spp., and Penicillium spp., but not from any strains of Mucor spp., Escherichia coli, or methicillin-resistant Staphylococcus aureus (MRSA), calf thymus or human placenta. This specificity was subsequently confirmed by Southern analysis. PCR analysis of blood specimens collected from mice systemically infected with C. albicans and clinical samples including blood, cerebrospinal fluid and sputum appeared to be a more sensitive diagnostic method for invasive fungal infections than a conventional blood culture technique.

Animals↗
PubMed2003

'Candidatus glomeribacter gigasporarum' gen. nov., sp. nov., an endosymbiont of arbuscular mycorrhizal fungi.

Arbuscular mycorrhizal fungi are obligate endosymbionts that colonize the roots of almost 80 % of land plants. The present paper describes morphological and molecular data on a bacterial endosymbiont living in the cytoplasm of dormant or germinating spores and symbiotic mycelia of the fungal species Gigaspora margarita, Scutellospora persica and Scutellospora castanea. PCR amplification of almost the entire 16S rRNA gene of the Gigaspora margarita BEG 34 endosymbiont, using universal bacterial primers, and subsequent sequence analysis demonstrated that this organism occupies a very distinct phylogenetic position within the beta-Proteobacteria, with the genera Burkholderia, Pandoraea and Ralstonia as its closest neighbours. Primers specific to the 16S rDNA of the endosymbiotic bacteria of BEG 34 allowed amplification of spore DNA from endosymbionts of Gigaspora margarita, Gigaspora decipiens, S. persica and S. castanea, but not from the Gigaspora gigantea endosymbiont (which was morphologically different) or from the cytoplasm of Gigaspora rosea (which did not contain endosymbiotic bacteria). These specific primers were successfully used as a probe for the in-situ hybridization of endobacteria in Gigaspora margarita spores. The overall rod-shaped morphology of the Gigaspora margarita, Gigaspora decipiens, S. persica and S. castanea endosymbionts was similar, and amplification and sequence analysis of the almost-complete 16S rRNA genes of several Gigaspora margarita, S. persica and S. castanea endosymbionts revealed over 98% sequence similarity. These morphological and genomic characteristics were used to assign the endosymbionts of these three species (five isolates) of arbuscular mycorrhizal fungi as 'Candidatus Glomeribacter gigasporarum' gen. nov., sp. nov.

Bacteria↗
PubMed2003

Species identification of medically important fungi by use of real-time LightCycler PCR.

Invasive fungal infection has become a major cause of morbidity and mortality in immunocompromised patients. Rapid identification of pathogenic fungi to species level is critical for disease treatment. A real-time LightCycler assay aiming at rapid detection and species identification of pathogenic fungi from clinical isolates was developed. Template DNAs of different species were amplified and detected in real time by employing SYBR Green fluorescent dye. The target sequences for species-level detection were located between the 18S and 28S rDNA. Seven fungal species encountered frequently in the clinical setting, Candida albicans, Candida glabrata, Candida krusei, Candida parapsilosis, Candida tropicalis, Candida guilliermondii and Cryptococcus neoformans, could be discriminated by species-specific primers and confirmed by melting-curve analyses. The range of linearity was from 1 ng to 1 pg (microl(-1) water) and the sensitivity was 1 pg fungal DNA microl(-1). Identification by this real-time PCR method matched biochemical identification for all 58 clinical strains. Therefore, the method is simple, rapid and sensitive enough for detection and identification of several fungal species.

Fungi↗
PubMed1992

Rapid quantitation by PCR of endomycorrhizal fungi colonizing roots.

The VANS1/NS21 primer pair is useful for specifically amplifying a 550-bp ribosomal (r) DNA fragment from arbuscular endomycorrhizal fungi, directly from colonized root extracts. A procedure to quantitate these obligatory biotrophs rapidly, based on competitive PCR, was developed by constructing a suitable internal standard to be used with these primers. A 130-bp deletion in the Glomus mossae VANS1/NS21 amplified rDNA fragment was produced by amplifying separately external portions of that fragment, followed by ligation and amplification using the original external primers. When this deleted fragment was added to G. mossae rDNA, amplification using VANS1/NS21 primers yielded the two expected products of 430 bp and 550 bp, respectively, resolved by agarose electrophoresis. This fragment was cloned into the pCL1920 plasmid, a low-copy-number vector (five copies per cell), and mixed with the roots to be analyzed. This provides for a rapid quantitative assay because both steps--extraction of DNA from colonized roots and PCR amplification--are taken into account by the same internal standard. Using this procedure, a sample of colonized leek roots (Allium porum x Glomus vesiculiferum) was shown to contain 5 x 10(4) copies of arbuscular endomycorrhizal fungi rDNA genes per milligram of fresh weight.

Allium↗
PubMed1981

Effect of treatment of soil with keratinaceous material on soil fungi.

In the early periods of soil storage, the total number of fungi almost regularly and significantly increased with the concentration of keratinaceous material (ground buffalo hooves) between 1% and 10%. A concentration of 20% was stimulative after 7 days and became toxic after 15 days and remained so through the end of the experiment. With increase in the storage period, the beneficial effect of all concentrations was lost and in the case of high concentrations (5-20%) toxic ammonia was produced. The occurrence of Scopulariopsis brevicaulis, Cephalosporium acremonium, Chrysosporium tropicum, C. indicum, and C. keratinophilum increased markedly, especially at the higher concentrations of the keratinaceous material and after long periods of incubation. With increase in the concentration of keratinaceous material, the rate of evolution of ammonia from the soil sharply increased during the second week after treatment and fell off sharply during the third and fourth weeks. In soil stored at 35 C, the rate of decline in total fungi after longer periods of incubation was sharper at 35 C than at 25 C. Also the amount of evolved ammonia during the first and the second weeks was almost always higher at 35 C than at 25 C. Fourteen species were tested for keratinolytic activity. Three of them were highly keratinolytic and five moderately so.

Animals↗
PubMed1982

Keratinolytic fungi in Egyptian soils.

The frequency of occurrence of keratinolytic fungi in seventy soil samples, collected from different sites in Upper Egypt and in the coastal area of the Mediterranean, was determined by baiting with human and animal hairs and pigeon feathers. Twenty-one species, in addition to an unidentified species, which belong to sixteen genera were collected. Chrysosporium indicum, C. Tropicum, C. keratinophilum, and Microsporum gypseum were the most frequent fungal species recovered from the baited soils. The soil samples collected from the salt marshes of the coastal Mediterranean area were completely free from any keratinolytic fungi, whereas the soil samples collected from cultivated soils contributed species, ranging from one to four species.

Egypt↗
PubMed1993

Interactions among xerophilic fungi associated with dried salted fish.

Interactions were investigated among five xerophilic fungi, Polypaecilum pisce, Basipetospora halophila, Eurotium rubrum, Aspergillus wentii and A. penicillioides, isolated from Indonesian dried salted fish. A range of water activities (aw) (0.98, 0.95, 0.90 and 0.84) and temperatures (15 degrees, 25 degrees and 30 degrees C) were studied on agar media in Petri dishes, and with dried fish as a substrate at 0.90 and 0.84 aw at 30 degrees C. Generally, the fungi exhibited one of two interaction types: mutual inhibition on contact, or inhibition of one or both species on contact, with the inhibited species continuing to grow at a significantly reduced rate. On glucose-based agar media A. wentii and E. rubrum were most competitive at all aw values and temperatures studied, while on NaCl media P. pisce and B. halophila were usually most competitive. The Petri dish system was a useful model, but did not completely simulate the interactions observed on dried fish. Polypaecilum pisce and B. halophila were able to compete more strongly on fish than on agar media, especially at 0.90 aw. This study provides some evidence that each species examined had a niche in which it was dominant, and that species interactions as well as environmental factors are important in determining the dominant fungal species on dried salted fish.

Animals↗
PubMed2006

A 'dirty' business: testing the limitations of terminal restriction fragment length polymorphism (TRFLP) analysis of soil fungi.

Terminal restriction fragment length polymorphism (TRFLP) is an increasingly popular method in molecular ecology. However, several key limitations of this method have not been fully examined especially when used to study fungi. We investigated the impact of spore contamination, intracollection ribosomal DNA internal transcribed spacer (ITS) region variation, and conserved restriction enzyme recognition loci on the results produced by TRFLP to characterize soil fungal communities. We find that (i) the potential for nontarget structures such as spores to contribute DNA to target sample extractions is high; (ii) multiple fragments (i.e. 'extra peaks') per PCR primer-restriction enzyme combination can be detected that are caused by restriction enzyme inefficiency and intracollection ribosomal DNA ITS variation; and (iii) restriction enzyme digestion in conserved vs. variable gene regions leads to different characterizations of community diversity. Based on these results, we suggest that studies employing TRFLP need to include information from known, identified fungi from sites within which studies take place and not to rely only on TRFLP profiles as a short cut to fungal community description.

Base Sequence↗
PubMed1992

Pneumocystis carinii shows DNA homology with the ustomycetous red yeast fungi.

Pneumocystis carinii causes life-threatening pneumonia in T-lymphocyte-immunodeficient subjects in transplant and oncology units or with acquired immune deficiency syndrome (AIDS). Recent DNA homology studies show P. carinii to be a fungus. To investigate the biology and epidemiology of this parasite further, we elected to determine for it a more precise taxonomic assignment within the fungal kingdom. We screened a wide range of organisms representing the major orders of fungi using DNA amplification and subsequently sequenced a portion of the mitochondrial gene encoding the large subunit ribosomal RNA. Our data show that the opportunistic pulmonary pathogen P. carinii is closely related to the ustomycetous red yeast fungi, a group which includes organisms that are extensively distributed throughout the environment and which release many widely dispersed airborne spores.

Animals↗
PubMed1979

Comparative temperature-stability properties of malate dehydrogenases from some thermophilic fungi.

Temperature-activity and temperature-stability relationships of malate dehydrogenases from eight thermophilic fungi were determined. Temperature optima for maximum activity of the enzymes varied between 50 degrees and 60 degrees and the Arrhenius plots were linear between 5 degrees and 50 degrees. The energies of activation ranged from 2.1 Kcal/mol for the enzyme from Sporotrichum thermophile to 9.1 Kcal/mol for that from Penicillium duponti. Heat inactivation kinetics at 50 degrees revealed heat lability of the enzyme from most of the thermophilic fungi. The t1/2's (min) were less than 10 for the enzymes from P. duponti, S. thermophile and Thermoascus aurantiacus; less than 30 for those from Chaetomium thermophile var. coprophile, H. lanuginosa and C. thermophile var. dissitum; and greater than 30 for those from Mucor pusillus and H. insolens. Salts of Na+, K+ and NH4+, and citrate protected the enzymes from H. lanuginosa, C. thermophile var. dissitum and M. pusillus against heat inactivation.

Cations, Monovalent↗
PubMed2004

A phylogenomic approach to reconstructing the diversification of serine proteases in fungi.

Using a phylogenomic approach with 10 fungi of very different virulence and habitat, we determined that there was substantial diversification of subtilase-type proteases early in ascomycete history (with subsequent loss in many lineages) but with no comparable diversification of trypsins. Patterns of intron loss and the degree of divergence between paralogues demonstrated that the proliferation of proteinase K subtilases and subtilisin type subtilases seen in pathogenic ascomycetes (Metarhizium anisopliae, Magnaporthe grisea, Fusarium graminearum) occurred after the basidiomycete/ascomycete split but predated radiation of ascomycete lineages. This suggests that the early ascomycetes had a lifestyle that selected for multiple proteases, whereas the current disparity in gene numbers between ascomycete lineages results from retention of genes in at least some pathogens that have been lost in other lineages (yeasts, Aspergillus nidulans, Neurospora crassa). A similar prevailing trend towards lineage specific gene loss of trypsins in saprophytes and some pathogens suggests that their phylogenetic breadth will have been much wider in early fungi than currently.

Cluster Analysis↗