Phylogeny and Ecophysiology of Opportunistic “Snow Molds” from a Subalpine Forest Ecosystem

Mats of coenocytic “snow molds” are commonly observed covering the soil and litter of alpine and subalpine areas immediately following snow melt. Here, we describe the phylogenetic placement, growth rates, and metabolic potential of cold-adapted fungi from under-snow mats in the subalpine forests of Colorado. SSU rDNA sequencing revealed that these fungi belong to the zygomycete orders Mucorales and Mortierellales. All of the isolates could grow at temperatures observed under the snow at our sites (0°C and −2°C) but were unable to grow at temperatures above 25°C and were unable to grow anaerobically. Growth rates for these fungi were very high at −2°C, approximately an order of magnitude faster than previously studied cold-tolerant fungi from Antarctic soils. Given the rapid aerobic growth of these fungi at low temperatures, we propose that they are uniquely adapted to take advantage of the flush of nutrient that occurs at the soil–snow interface beneath late winter snow packs. In addition, extracellular enzyme production was relatively high for the Mucorales, but quite low for the Mortierellales, perhaps indicating some niche separation between these fungi beneath the late winter snow pack.     

Detecting morphological convergence in true fungi, using 18S rRNA gene sequence data.

For the true fungi, phylogenetic relationships inferred from 18S ribosomal DNA sequence data agree with morphology when (1) the fungi exhibit diagnostic morphological characters, (2) the sequence-based phylogenetic groups are statistically supported, and (3) the ribosomal DNA evolves at roughly the same rate in the lineages being compared. 18S ribosomal RNA gene sequence data and biochemical data provide a congruent definition of true fungi. Sequence data support the traditional fungal subdivisions Ascomycotina and Basidiomycotina. In conflict with morphology, some zygomycetes group with chytrid water molds rather than with other terrestrial fungi, possibly owing to unequal rates of nucleotide substitutions among zygomycete lineages. Within the ascomycetes, the taxonomic consequence of simple or reduced morphology has been a proliferation of mutually incongruent classification systems. Sequence data provide plausible resolution of relationships for some cases where reduced morphology has created confusion. For example, phylogenetic trees from rDNA indicate that those morphologically simple ascomycetes classified as yeasts are polyphyletic and that forcible spore discharge was lost convergently from three lineages of ascomycetes producing flask-like fruiting bodies.     

Diversity of fungi in creosote-treated crosstie wastes and their resistance to polycyclic aromatic hydrocarbons

This study was conducted to generate information regarding the diversity of fungi inhabiting creosote-treated wood in a storage yard for crosstie wastes in Gwangmyeong, Korea. Additionally, the resistance to polycyclic aromatic hydrocarbons (PAHs) of indigenous fungi that mainly occupy creosote-treated wood was evaluated. We isolated fungi from the surface and inner area of crosstie wastes and identified them using a combination of traditional methods and molecular techniques. Overall, 179 isolates including 47 different species were isolated from 240 sampling sites. The identified fungal species included 23 ascomycetes, 19 basidiomycetes, and 5 zygomycetes. Three species, Alternaria alternata, Irpex lacteus, and Rhizomucor variabilis, were the most frequently isolated ascomycetes, basidiomycetes, and zygomycetes, respectively. The results of this study showed that there was a large difference in the fungal diversity between the surface and the inner area. Additionally, zygomycetes and ascomycetes were found to have a greater tolerance to PAHs than basidiomycetes. However, two basidiomycetes, Heterobasidion annosum and Schizophyllum commune, showed very high resistance to PAHs, even in response to the highest concentration (1,000 ppm), which indicates that these species may play a role in the degradation of PAHs.     

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.      

Fatty Acids in the Species of Several Zygomycete Taxa

The composition of fatty acids synthesized de novo by thirty strains of zygomycetes from various taxa was studied. The qualitative fatty acid compositions of the fungal lipids were found to be virtually identical, but there were significant differences in the contents of individual acids. Highly active producers of essential C₁₈ fatty acids, with their content exceeding 30–40% of total fatty acids, were discovered among the fungi of the families Mucoraceae, Pilobolaceae, and Radiomycetaceae. Linoleic acid was found to predominate in the fungi of the genera Radiomyces, Mycotypha, and Circinella, and linolenic acid (identified as its -isomer by gas-liquid chromatography), in the fungi of the genera Absidia, Circinella, Pilaira, and Hesseltinella. The total yield (mg/l) of bioactive acids (C_18:3, C_18:2, C_18:1) varied from 761.4 in Pilaira anomala to 3477.9 in Syncephalastrum racemosum; the total yield of essential acids, from 520.7 in Pilaira anomala to 1154.5 in Hesseltinella vesiculosa; of linoleic acid, from 279.7 in Pilaira anomala to 836.3 in Mycotypha indica; and of linolenic acid, from 120.8 in Mycotypha indica to 708.0 in Hesseltinella vesiculosa. The data on the efficient synthesis of these acids make the actively producing strains promising for biotechnological synthesis of commercially valuable lipids. Linderina pennispora VKM F-1219, a zygomycete of the family Kickxellaceae, which was earlier singled out into the order Kickxellales, was shown to differ from zygomycetes of the order Mucorales in having a high content of cis-9-hexadecenoic (palmitoleic) acid, reaching 37.0% of the fatty acid total.     

Cladistic analysis of 5S rRNA and 16S rRNA secondary and primary structure—The evolution of eukaryotes and their relation to archaebacteria

Summary The secondary structure of 5S rRNA has been elucidated by a cladistic analysis resulting in minimal models for eukaryotes, eubacteria, and halophilic-methanogenic archaebacteria, as well as for an ur-5S rRNA. This ancestor of all present-day 5S rRNA molecules is compared with an ur-tRNA and can be fitted into a tRNA-like structure allowing tertiary-structure interactions at the equivalent positions. A phylogenetic analysis of eukaryotic 5SrRNA and 16S rRNA sequences confirms particular monophyletic taxa: rhodophytes (red algae), chlorobionts (green algae and plants), metazoans (multicellular animals), euglenozoans (euglenids and trypanosomatids), a group of zygomycetes (excluding Kickxellales), a group of ascomycetes (excluding Protomycetales), two distinct groups of basidiomycetes, and a group consisting of phaeophyceans (brown algae) and oomycetes (water molds). The Euglenozoa show a distinct relation to the Eumycota (true fungi) and Metazoa. An analysis of archaebacterial sequences substantiates the paraphyletic nature of this third urkingdom defining the eubacteria as a sister group of the halophile-methanogens and defining the eukaryotes as a sister group of a particular lineage of the eocytes/sulfur-dependents. The latter fact implies that even the eocytes/sulfur-dependent archaebacteria are paraphyletic.Presented at the FEBS Symposium on Genome Organization and Evolution, held in Crete, Greece, September 1–5, 1986Dedicated to the memory of Erik Huysmans who died on July 8, 1986, at the age of 29.     

Two Origins for the Gene Encoding α-Isopropylmalate Synthase in Fungi

Background

The biosynthesis of leucine is a biochemical pathway common to prokaryotes, plants and fungi, but absent from humans and animals. The pathway is a proposed target for antimicrobial therapy.

Methodology/Principal Findings

Here we identified the leuA gene encoding α-isopropylmalate synthase in the zygomycete fungus Phycomyces blakesleeanus using a genetic mapping approach with crosses between wild type and leucine auxotrophic strains. To confirm the function of the gene, Phycomyces leuA was used to complement the auxotrophic phenotype exhibited by mutation of the leu3⁺ gene of the ascomycete fungus Schizosaccharomyces pombe. Phylogenetic analysis revealed that the leuA gene in Phycomyces, other zygomycetes, and the chytrids is more closely related to homologs in plants and photosynthetic bacteria than ascomycetes or basidiomycetes, and suggests that the Dikarya have acquired the gene more recently.

Conclusions/Significance

The identification of leuA in Phycomyces adds to the growing body of evidence that some primary metabolic pathways or parts of them have arisen multiple times during the evolution of fungi, probably through horizontal gene transfer events.     

Nucleotide composition of nucleic acids of fungi. II. Deoxyribonucleic acids

Storck, Roger (The University of Texas, Austin). Nucleotide composition of nucleic acids from fungi. II. Deoxyribonucleic acids. J. Bacteriol. 91:227-230. 1966.-The nucleotide composition of the deoxyribonucleic acids (DNA) present in extracts of 30 species of fungi was determined. The results were analyzed, together with those in the literature. It was found that the content, in moles per cent of guanine plus cytosine (GC content), varied from 38 to 63% in a distribution composed of 9 species of zygomycetes, 14 of ascomycetes, and 9 each of deuteromycetes and basidiomycetes. The GC content ranges were: 38 to 48% for the zygomycetes, 38 to 54% for the ascomycetes, 47 to 62% for the deuteromycetes, and 44 to 63% for the basidiomycetes. The GC content ranged from 38 to 40% for four Mucor species. The base composition of fungal DNA appears, therefore, to have a taxonomic and phylogenetic significance.     

Isolation of diverse viable fungi from the larvae of the introduced chironomid <Emphasis Type="Italic">Eretmoptera murphyi</Emphasis> on Signy Island

The chironimid midge Eretmoptera murphyi has been introduced to Signy Island and has since become established at a single site. Viable propagules of a diverse range of micro-fungi were recovered from the normal intestinal tract of larvae of E. murphyi, indicating the potential for the larvae to act as vectors for fungal introductions. The fungi present in the intestines of the larvae included ascomycetes, zygomycetes and an oomycete, and this diversity highlights the potential for multiple microbial introductions from a single invertebrate introduction.     

Widespread Lichtheimia Infection in a Patient with Extensive Burns: Opportunities for Novel Antifungal Agents

Mycopathologia - The Mucorales fungi—formerly classified as the zygomycetes—are environmentally ubiquitous fungi, but generally rare causes of clinical infections. In the...     

Fatty acids in the species of several zygomycete taxa

The composition of fatty acids synthesized de novo by thirty strains of zygomycetes from various taxa was studied. The qualitative fatty acid compositions of the fungal lipids were found to be virtually identical, but there were significant differences in the contents of individual acids. Highly active producers of essential C18 fatty acids, with their content exceeding 30-40% of total fatty acids, were discovered among the fungi of the families Mucoraceae, Pilobolaceae, and Radiomycetaceae. Linoleic acid was found to predominate in the fungi of the genera Radiomyces, Mycotypha, and Circinella, and linolenic acid (identified as its gamma-isomer by gas-liquid chromatography), in the fungi of the genera Absidia, Circinella, Pilaira, and Hesseltinella. The total yield (mg/l) of bioactive acids (C18:3, C18:2, C18:1) varied from 761.4 in Pilaira anomala to 3477.9 in Syncephalastrum racemosum; the total yield of essential acids, from 520.7 in Pilaira anomala to 1154.5 in Hesseltinella vesiculosa; of linoleic acid, from 279.7 in Pilaira anomala to 836.3 in Mycotypha indica; and of linolenic acid, from 120.8 in Mycotypha indica to 708.0 in Hesseltinella vesiculosa. The data on the efficient synthesis of these acids make the actively producing strains promising for biotechnological synthesis of commercially valuable lipids. Linderina pennispora VKM F-1219, a zygomycete of the family Kickxellaceae, which was earlier singled out into the order Kickxellales [12], was shown to differ from zygomycetes of the order Mucorales in having a high content of cis-9-hexadecenoic (palmitoleic) acid, reaching 37.0% of the fatty acid total.     

Fungal endophytes from the three-leaved caper,Crataeva magna (Lour.) DC. (Capparidaceae)

Fungal endophytes were isolated from Crataeva magna, a medicinal plant growing along the streams and rivers, constituting riparian vegetation in Karnataka, southern India. Fresh bark and twig pieces were used for the isolation using standard methods. Ninety-six endophytic fungal isolates were isolated from 800 bark and twig segments. Mitosporic fungi represented as a major group (85%) followed by zygomycetes (10%) and ascomycetes (5%). Bark samples contained more endophytes than twig samples. Verticillium, Nigrospora oryzae and Fusarium verticilloides were the dominant fungal endophytes.     

Comparison of fungal complexes of Japanese scallop Mizuhopecten yessoensis (Jay, 1856) from different areas in the Peter the Great Bay of the Sea of Japan

Mycological investigation of the Japanese scallop Mizuhopecten yessoensis (Jay) (Bivalvia) from different areas of the Peter the Great Bay (Sea of Japan) was conducted. Isolates from internal organs of M. yessoensis scallop comprise 72 species of filamentous fungi from 30 genera of ascomycetes, anamorphic fungi, and zygomycetes. Species richness of filamentous fungi—fungi of the genera Aspergillus, Penicillium, Cladosporium, and Chaetomium—in the internal organs of bivalve mollusks increases in polluted coastal waters.     

Independent terrestrial origins of the Halosphaeriales (marine Ascomycota)

A phylogenetic study of marine ascomycetes was initiated to test and refine evolutionary hypotheses of marine-terrestrial transitions among ascomycetes. Taxon sampling focused on the Halosphaeriales, the largest order of marine ascomycetes. Approximately 1050 base pairs (bp) of the gene that codes for the nuclear small subunit (SSU) and 600 bp of the gene that codes for the nuclear large subunit (LSU) ribosomal RNAs (rDNA) were sequenced for 15 halosphaerialean taxa and integrated into a data set of homologous sequences from terrestrial ascomycetes. An initial set of phylogenetic analyses of the SSU rDNA from 38 taxa representing 15 major orders of the phylum Ascomycota confirmed a close phylogenetic relationship of the halosphaerialean species with several other orders of perithecial ascomycetes. A second set of analyses, which involved more intensive taxon sampling of perithecial ascomycetes, was performed using the SSU and LSU rDNA data in combined analyses. These second analyses included 15 halosphaerialean taxa, 26 terrestrial perithecial fungi from eight orders, and five outgroup taxa from the Pezizales. In these analyses the Halosphaeriales were polyphyletic and comprised two distinct lineages. One clade of Halosphaeriales comprised 12 taxa from 11 genera and was most closely related to terrestrial fungi of the Microascales. The second clade of halosphaerialean fungi comprised taxa from the genera Lulworthia and Lindra and was an isolated lineage among the perithecial fungi. Both the main clade of Halosphaeriales and the Lulworthia/Lindra clade are supported by the data as being independently derived from terrestrial ancestors.     

Isolation of a class IV chitin synthase gene from a zygomycete fungus, Rhizopus oligosporus

We found the presence of DNA sequence which shows sequence similarity to the class IV chitin synthase gene (CHS3) of Saccharomyces cerevisiae in the genome of 14 Rhizopus species which belong to zygomycetes. We cloned a gene (chs3), which might correspond to one of these homologous sequences, from Rhizopus oligosporus by low stringency plaque hybridization probed with CHS3. The deduced amino acid sequence of this gene showed highest similarity to the class IV chitin synthase of Neurospora crassa (46.7% identity over 1087 amino acids), showing that this gene encodes a class IV chitin synthase. Northern analysis revealed the differential expression pattern of this gene in the asexual life cycle with highest expression in the early stage of asexual spore formation. This is the first report of the isolation and analysis of a class IV chitin synthase gene from zygomycete fungi.     

Diversity of facultatively anaerobic microscopic mycelial fungi in soils

The numbers of microscopic fungi isolated from soil samples after anaerobic incubation varied from tens to several hundreds of CFU per one gram of soil; a total of 30 species was found. This group is composed primarily of mitotic fungi of the ascomycete affinity belonging to the orders Hypocreales (Fusarium solani, F. oxysporum, Fusarium sp., Clonostachys grammicospora, C. rosea. Acremonium sp., Gliocladium penicilloides, Trichoderma aureoviride, T. harzianum, T. polysporum, T. viride. T. koningii, Lecanicillum lecanii, and Tolypocladium inflatum) and Eurotiales (Aspergillus terreus, A. niger, and Paecilomyces lilacimus), as well as to the phylum Zygomycota, to the order Mucorales (Actinomucor elegans, Absidia glauca, Mucor circinelloides, M. hiemalis, M. racemosus, Mucor sp., Rhizopus oryzae, Zygorrhynchus moelleri, Z. heterogamus, and Umbelopsis isabellina) and the order Mortierellales (Mortierella sp.). As much as 10-30% of the total amount of fungal mycelium remains viable for a long time (one month) under anaerobic conditions.     

<Emphasis Type="Italic">Mucor rouxii</Emphasis> Rho1 protein; characterization and possible role in polarized growth

We have previously shown that protein kinase A of the medically important zygomycete Mucor rouxii participates in fungal morphology through cytoskeletal organization. As a first step towards finding the link between protein kinase A and cytoskeletal organization we here demonstrate the cloning of the Rho1 gene and the characterization of its protein product. The RHO1 protein primary sequence shows 70–85% identity with fungal RHO1 or mammalian RhoA. Two protein kinase A phosphorylation sequences in adequate context are predicted, Ser73 and Ser135. The peptide IRRNSQKFV, containing Ser135 proved to be a good substrate for M. rouxii protein kinase A catalytic subunit. The over-expressed Rho1 fully complements a Saccharomyces cerevisiae null mutant. The endogenous protein was identified by western blot against a developed antibody and by ADP-ribosylation. Localization in germlings was visualized by immunofluorescence; the protein was localized in patches in the mother cell surface and excluded from the germ tube. Measurement of Rho1 expression during germination indicates that Rho1, at both the mRNA and protein levels, correlates with differentiation and not with growth. Rho1 has been shown to be the regulatory protein of the β-1,3-glucan synthase complex in fungi in which β-1,3-glucans are major components of the cell wall. Even though glucans have not been detected in zygomycetes, caspofungin, an echinochandin known to be an inhibitor of β-1,3-glucan synthase complex, is shown here to have a negative effect on growth and to produce an alteration on morphology when added to M. rouxii growth culture medium. This result has an important impact on the possible participation of β-1,3-glucans on the regulation of morphology of zygomycetes.     

Screening of mycelial fungi for 7α- and 7β-hydroxylase activity towards dehydroepiandrosterone

In total, 481 fungal strains were screened for the ability to carry out 7(α/β)-hydroxylation of dehydroepiandrosterone (DHEA, 3β-hydroxy-5-androsten-17-one). Representatives of 31 genera of 15 families and nine orders of ascomycetes, 17 genera of nine families and two orders of zygomycetes, two genera of two families and two orders of basidiomycetes, and 14 genera of mitosporic fungi expressed 7(α/β)-hydroxylase activity. The majority of strains were able to introduce a hydroxyl group to position 7α. Active strains selectively producing 3β,7α-dihydroxy-5-androsten-17-one were found among Actinomucor, Backusella, Benjaminiella, Epicoccum, Fusarium, Phycomyces and Trichothecium, with the highest yield of 1.25 and 1.9 g L^?1 from 2 and 5 g L^?1 DHEA, respectively, reached with F. oxysporum. Representatives of Acremonium, Bipolaris, Conidiobolus and Curvularia formed 3β,7β-dihydroxy-5-androsten-17-one as a major product from DHEA. The structures of the major steroid products were confirmed by TLC, gas chromatography (GC), mass spectra (MS), and ¹H-NMR analyses.     

On the Diversity of the Laccase Gene: A Phylogenetic Perspective from Botryosphaeria rhodina (Ascomycota: Fungi) and Other Related Taxa

The present study is the first describing the sequencing of a fragment of the copper-oxidase domain of a laccase gene in the family Botryosphaeriaceae. The aim of this work was to assess the degree of genetic and evolutionary relationships of a laccase gene from Botryosphaeria rhodina MAMB-05 with other ascomycete and basidiomycete laccase genes. The 193-amino acid sequences of the copper-oxidase domain from several different fungi, insects, a plant, and a bacterial species were retrieved from GenBank and aligned. Phylogenetic analyses were performed using neighbor-joining, maximum parsimony, and Bayesian inference methods. The organisms studied clustered into five gene clades: fungi (ascomycetes and basidiomycetes), insects, plants, and bacteria. Also, the topologies showed that fungal laccases of the ascomycetes and basidiomycetes are clearly separated into two distinct clusters. This evidence indicated that B. rhodina MAMB-05 and other closely related ascomycetes are a new biological resource given the biotechnological potential of their laccase genes.