Lumbsch, H. T. and S.M. Huhndorf (ed.) 2007. Outline of Ascomycota - 2007. Myconet 13: 1 - 58. The present classification contains all accepted genera and higher taxa above the generic level in phylum Ascomycota.
H. Thorsten Lumbsch; Sabine M. Huhndorf
For a monograph based on a polythetic concept, several thousands of herbarium specimens, and several hundreds of freshly collected and cultured specimens of Daldinia and allied Xylariaceae, originating from around the world, were studied for morphological traits, including by SEM, and chemically by HPLC profiles using UV-visible and mass spectrometric detection. Emphasis was given to tropical material, and importantly, ancient specimens, including as many types as possible, were tracked and studied to review earlier taxonomic concepts. An epitype of D. eschscholtzii was selected as representative of the morphochemotype that is most widely distributed in the tropics. Six new species of Daldinia from the tropics and the southern Hemisphere are described. Daldinia asphalatum is resurrected, and D. cudonia is regarded as its synonym. In addition, the following binomials are epi-, iso-, neo- and/or lectotypified: Daldinia asphalatum, D. caldariorum, D. clavata, D. cuprea, D. durissima, D. eschscholtzii, D. grandis, D. loculata, and D. vernicosa. Annellosporium and Versiomyces are regarded as synonyms of Daldinia. Many new synonymies in Daldinia are proposed, and some previously published names are rejected. In total, 47 taxa in Daldinia are recognised and a key is provided. Their biogeography, chorology, and ecology, as well as the importance of their secondary metabolites, are also discussed. The previous definition of the genus is emended. The species concept is based mainly on morphological and other phenotype-derived characters because, despite diligent search, no molecular data or cultures of several of the accepted species could be obtained. Daldinia is segregated into five major groups, based on phenotypic characteristics. Some unnamed but aberrant specimens were not found in good condition and are therefore not formally described as new species. However, they are illustrated in detail in a hope that this will facilitate the discovery of fresh material in future. A preliminary molecular phylogeny based on 5.8S/ITS nrDNA including numerous representatives of all hitherto described taxa for which cultures are extant, was found basically in agreement with the above mentioned segregation of the genus, based on morphological and chemotaxonomic evidence. In the rDNA based phylogenetic tree, Daldinia appears clearly distinct from members of the genera Annulohypoxylon and Hypoxylon; nevertheless, representatives of small genera of predominantly tropical origin (Entonaema, Phylacia, Ruwenzoria, Rhopalostroma, Thamnomyces) appear to have evolved from daldinioid ancestors and are nested inside the Daldinia clade. Interestingly, these findings correlate with chemotaxonomic characters to a great extent, especially regarding the distribution of marker metabolites in their mycelial cultures. Hence, the current study revealed for the first time that fungal secondary metabolite profiles can have taxonomic value beyond the species rank and even coincide with phylogenetic data. Taxonomic novelties: Daldinia andina sp. nov., D. australis sp. nov., D. hausknechtii sp. nov., D. rehmii sp. nov., D. starbaeckii sp. nov., D. theissenii sp. nov., D. cahuchosa comb. nov., D. nemorosa comb. nov.
Stadler, Marc; Laess?e, Thomas; Fournier, Jacques; Decock, Cony; Schmieschek, Beata; Tichy, Hans-Volker; Persoh, Derek
Eighteen polyketides (1–18) including six citrinin derivatives, two phenol derivatives, one cyclopentenone, two naphthol derivatives, and seven tetralone derivatives were isolated from the culture broth of a marine-derived fungal strain Xylariaceae sp. SCSGAF0086. Five of these compounds (1, 2, 8, 9, and 10) were new, and their structures were determined by spectroscopic methods. Compounds 4, 6, 7, and 17 showed enzyme-inhibitory activities towards several tested enzymes, and 6 and 7 showed strong antifouling activity against Bugula neritina larvae settlement. This is the first time that the antifouling and enzyme-inhibitory activities of these compounds has been reported.
Nong, Xu-Hua; Zheng, Zhi-Hui; Zhang, Xiao-Yong; Lu, Xin-Hua; Qi, Shu-Hua
A new pyridine derivative, 5-(2'-hydroxypropyl)pyridin-3-ol (1), with seven known alkaloids, 3-hydroxy-5-methyl-5,6-dihydro-7H-cyclopenta[b]pyridin-7-one (2), penicillenol A1 (3), penicillenol A2 (4), a mixture of quinolactacin AI (5a) and quinolactacin A2 (5b), and a mixture of quinolactacin C1 (6a) and quinolactacin C2 (6b), were isolated from the culture broth of a marine-derived fungus Xylariaceae sp. SCSGAF0086. Their structures were elucidated by spectroscopic methods. Compound 2 showed weak antimicrobial activity against Bacillus subtilis, and a mixture of 6a and 6b exhibited strong antifouling activity toward Bugula neritina larval settlement. PMID:24868856
Nong, Xu-Hua; Zhang, Xiao-Yong; Xu, Xin-Ya; Sun, Yun-Lin; Qi, Shu-Hua
What makes a fungus pathogenic? In this review, phylogenetic inference is used to speculate on the evolution of plant and animal pathogens in the fungal Phylum Ascomycota. A phylogeny is presented using 297 18S ribosomal DNA sequences from GenBank and it is shown that most known plant pathogens are concentrated in four classes in the Ascomycota. Animal pathogens are also
Mary L. Berbee
Establishing the dates for the origin and main diversification events in the phylogeny of Ascomycota is among the most crucial remaining goals in understanding the evolution of Fungi. There have been several analyses of divergence times in the fungal tree of life in the last two decades, but most have yielded contrasting results for the origin of the major lineages. Moreover, very few studies have provided temporal estimates for a large set of clades within Ascomycota. We performed molecular dating to estimate the divergence times of most of the major groups of Ascomycota. To account for paleontological uncertainty, we included alternative fossil constraints as different scenarios to enable a discussion of the effect of selection of fossils. We used data from 6 molecular markers and 121 extant taxa within Ascomycota. Our various ‘relaxed clock’ scenarios suggest that the origin and diversification of the Pezizomycotina occurred in the Cambrian. The main lineages of lichen–forming Ascomycota originated at least as early as the Carboniferous, with successive radiations in the Jurassic and Cretaceous generating the diversity of the main modern groups. Our study provides new information about the timing of the main diversification events in Ascomycota, including estimates for classes, orders and families of both lichenized and non–lichenized Ascomycota, many of which had not been previously dated.
Prieto, Maria; Wedin, Mats
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
Philipp Pagel; Hans-Werner Mewes; Dmitrij Frishman
The early diverging Ascomycota lineage, detected primarily from nSSU rDNA sequence-based phylogenetic analyses, includes enigmatic key taxa important to an understanding of the phylogeny and evolution of higher fungi. At the moment six representative genera of early diverging ascomycetes (i.e. Taphrina, Protomyces, Saitoella, Schizosaccharo- myces, Pneumocystis and Neolecta) have been assigned to ''Archiascomycetes'' sensu Nishida and Sugiyama (1994) or the
Junta Sugiyama; Kentaro Hosaka; Sung-Oui Suh
For phylogenetic analysis of the higher fungi, we sequenced the nuclear small subunit rRNA (18S rRNA) gene fromTaphrina populina, the type species of the genusTaphrina, andProtomyces lactucae-debilis. The molecular phylogeny inferred from these 2 sequences and 75 sequences from the DNA data bank divided the Ascomycota into three major lineages: the hemiascomycetes, the euascomycetes, and the archiascomycetes, newly described herein.
Hiromi Nishida; Junta Sugiyama
Carnivorism is one of the basic life strategies of fungi. Carnivorous fungi possess the ability to trap and digest their preys by sophisticated trapping devices. However, the origin and development of fungal carnivorism remains a gap in evolution biology. In this study, five protein-encoding genes were used to construct the phylogeny of the carnivorous fungi in the phylum Ascomycota; these fungi prey on nematodes by means of specialized trapping structures such as constricting rings and adhesive traps. Our analysis revealed a definitive pattern of evolutionary development for these trapping structures. Molecular clock calibration based on two fossil records revealed that fungal carnivorism diverged from saprophytism about 419 Mya, which was after the origin of nematodes about 550-600 Mya. Active carnivorism (fungi with constricting rings) and passive carnivorism (fungi with adhesive traps) diverged from each other around 246 Mya, shortly after the occurrence of the Permian-Triassic extinction event about 251.4 Mya. The major adhesive traps evolved around 198-208 Mya, which was within the time frame of the Triassic-Jurassic extinction event about 201.4 Mya. However, no major carnivorous ascomycetes divergence was correlated to the Cretaceous-Tertiary extinction event, which occurred more recently (about 65.5 Mya). Therefore, a causal relationship between mass extinction events and fungal carnivorism evolution is not validated in this study. More evidence including additional fossil records is needed to establish if fungal carnivorism evolution was a response to mass extinction events. PMID:22715289
Yang, Ence; Xu, Lingling; Yang, Ying; Zhang, Xinyu; Xiang, Meichun; Wang, Chengshu; An, Zhiqiang; Liu, Xingzhong
The family Parmeliaceae (Lecanorales, Ascomycota) is possibly the largest, best known and most thoroughly studied lichen family within its order. Despite this fact the relationship between Parmeliaceae and other groups in Lecanorales is still poorly known. The aim of the present study is to contribute to finding the sister group of Parmeliaceae as an aid in future studies on the phylogeny and character evolution of the group. We do this by sampling all potential relatives to the Parmeliaceae that we have identified, i.e. Gypsoplaca, Japewia, Mycoblastus, Protoparmelia, and Tephromela, a good representation of the major groups within the Parmeliaceae s. lat. and a good representation of other taxa in the core Lecanorales. We use molecular data from two genes, the large subunit of the nuclear ribosomal RNA gene (nrLSU) and the small subunit of the mitochondrial ribosomal RNA gene (mrSSU), and a Bayesian analysis of the combined data. The results show that the closest relatives to Parmeliaceae are the two genera Protoparmelia and Gypsoplaca, which are crustose lichens. Parmeliaceae in our sense is a well supported group, including also the family segregates Alectoriaceae, Hypogymniaceae, Usneaceae and Anziaceae. PMID:17663122
Arup, Ulf; Ekman, Stefan; Grube, Martin; Mattsson, Jan-Eric; Wedin, Mats
Carnivorism is one of the basic life strategies of fungi. Carnivorous fungi possess the ability to trap and digest their preys by sophisticated trapping devices. However, the origin and development of fungal carnivorism remains a gap in evolution biology. In this study, five protein-encoding genes were used to construct the phylogeny of the carnivorous fungi in the phylum Ascomycota; these fungi prey on nematodes by means of specialized trapping structures such as constricting rings and adhesive traps. Our analysis revealed a definitive pattern of evolutionary development for these trapping structures. Molecular clock calibration based on two fossil records revealed that fungal carnivorism diverged from saprophytism about 419 Mya, which was after the origin of nematodes about 550–600 Mya. Active carnivorism (fungi with constricting rings) and passive carnivorism (fungi with adhesive traps) diverged from each other around 246 Mya, shortly after the occurrence of the Permian–Triassic extinction event about 251.4 Mya. The major adhesive traps evolved around 198–208 Mya, which was within the time frame of the Triassic–Jurassic extinction event about 201.4 Mya. However, no major carnivorous ascomycetes divergence was correlated to the Cretaceous–Tertiary extinction event, which occurred more recently (about 65.5 Mya). Therefore, a causal relationship between mass extinction events and fungal carnivorism evolution is not validated in this study. More evidence including additional fossil records is needed to establish if fungal carnivorism evolution was a response to mass extinction events.
Yang, Ence; Xu, Lingling; Yang, Ying; Zhang, Xinyu; Xiang, Meichun; Wang, Chengshu; An, Zhiqiang; Liu, Xingzhong
Cinto, I. E. & Dokmetzian, D. A. 2006. Iodophanus granulipolaris (Ascomycota -Pezizales): first record from Argentina. A morphological and physiological study. Hickenia 3(62): 277-284. In this paper, Iodophanus granulipolaris is recorded for the first time for Argentina. It's life cycle, development, cytology and physiology were studied. Culture studies showed that I. granulipolaris is homothallic and cellulolitic. Light plays an important
ISABEL E. CINTO; DIANA A. DOKMETZIAN
The lichen-forming genus Porpidia (Porpidiaceae, Ascomycota) provides excellent opportunities for evolutionary, reproductive, and ecological studies of crustose epilithic lichen symbioses. However, despite the fact that the genus itself seemed to be clearly delimited, the group was thought to be a hopeless case with regard to intrageneric relationships and species delimitations due to apparently rampant homoplasy throughout most character systems. Contrary
Jutta Buschbom; Gregory Mueller
Powdery mildew fungi (Erysiphales, Ascomycota) are obligate biotrophs that infect a wide range of angiosperms. Phylogenetic analyses based on the nucleotide sequences of the nuclear ribosomal DNA revealed that the powdery mildew fungi are divided into five major lineages. The respective lineage was well defined by the morphology of conidial stage, but not of ascomata. In this fungal group, tree-parasitic
Molecular phylogenies for the fungi in the Ascomycota rely heavily on 18S rRNA gene sequences but this gene alone does not answer all questions about relationships. Particularly problematical are the relationships among the first ascomycetes to diverge, the Archiascomycetes, and the branching order among the basal filamentous ascomycetes, the Euascomycetes. Would more data resolve branching order? We used the jackknife
Mary L. Berbee; David A. Carmean; Katarina Winka
Phyllactinia is a unique genus within the Erysiphales (Ascomycota) having a partly endo-parasitic nature of the mycelium within the host plant tissues. We constructed phylogenetic trees for the genus Phyllactinia and its allied genera based on a total of 120 nucleotide sequences of the 28S rDNA and ITS regions to discuss their phylogenetic relationships with special references to host plants,
Susumu Takamatsu; Mihoko Inagaki; Seiko Niinomi; Seyed Akbar Khodaparast; Hyeon-Dong Shin; Banga Grigaliunaite; Maria Havrylenko
(?)-Galiellalactone is a hexaketide metabolite with interesting pharmacological activities which was detected in four strains of Galiella rufa (Sarcosomataceae, Ascomycota) and in two unidentified fungi shown by their 18S rDNA sequences also to belong to the Sarcosomataceae. These were a wood-inhabiting apothecial species from Chile and an endophytic isolate from Cistus salviifolius (Sardinia). Other members of the family (Urnula helvelloides,
Bärbel Köpcke; Roland W. S. Weber; Heidrun Anke
Nonribosomal peptides (NRPs) and polyketides (PKs) are ecologically important secondary metabolites produced by bacteria and fungi using multidomain enzymes called nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), respectively. Previous phylogenetic analyses of fungal NRPSs and PKSs have suggested that a few of these genes were acquired by fungi via horizontal gene transfer (HGT) from bacteria, including a hybrid NPS/PKS found in Cochliobolus heterostrophus (Dothideomycetes, Ascomycota). Here, we identify this hybrid gene in fungi representing two additional classes of Ascomycota (Aspergillus spp., Microsporum canis, Arthroderma spp., and Trichophyton spp., Eurotiomycetes; Chaetomium spp. and Metarhizium spp., Sordariomycetes) and use phylogenetic analyses of the most highly conserved domains from NRPSs (adenylation (A) domain) and PKSs (ketoacyl synthase (KS) domain) to examine the hypothesis that the hybrid NPS7/PKS24 was acquired by fungi from bacteria via HGT relatively early in the evolution of the Pezizomycotina. Our results reveal a unique ancestry of the A domain and KS domain in the hybrid gene relative to known fungal NRPSs and PKSs, provide strong evidence for HGT of the hybrid gene from a putative bacterial donor in the Burkholderiales, and suggest the HGT event occurred early in the evolution of the filamentous Ascomycota.
Lawrence, Daniel P.; Kroken, Scott; Pryor, Barry M.; Arnold, A. Elizabeth
Despite various morphological and anatomical similarities, the two orders Gyalectales (lichenized ascomycetes) and Ostropales (lichenized and non-lichenized ascomycetes) have been considered to be distantly related to each other and their position within the Ascomycota was unsettled. To estimate relationships within these groups and their respective phylogenenetic placement within the Ascomycota, we analyzed DNA sequences from the nuclear small and large
Frank Kauff; François Lutzoni
The suitability of the EPR spectroscopy for detection of ?-irradiation in five species of dried mushroom, currently used in gastronomy: yellow morel— Morchella esculenta, (L.) Pers. (Phylum Ascomycota), button mushroom— Agaricus bisporus (J.E.Lange), Agaricus haemorrhoidarius Fr., golden chantarelle— Cantharellus cibarius Fr., as well as oyster mushroom— Pleurotus ostreatus (Jacq. ex Fr.) (Phylum Basidiomycota) is presented and discussed. Although after irradiation at doses up to 11 kGy, all specimens presented well defined EPR spectra, only A. bisporus EPR signal was enough stable to make detection possible after 18 months.
Bercu, V.; Negut, C. D.; Duliu, O. G.
Geosmithia spp. (Ascomycota: Hypocreales) are dry-spored fungi that occur in galleries built by many phloeophagous bark beetles. This study mapped the diversity, host spectrum and area of distribution of Geosmithia spp. occurring in galleries of bark beetle species with a Mediterranean distribution. Eighty-six wood samples of 19 tree species infested by 18 subcortical insect species were collected from across the
Miroslav Kola?ík; Martin Kostov?ík; Sylvie Pažoutová
We present the first and southernmost records of the fungi Hirsutella strigosa Petch, H. citriformis Speare (Ascomycota: Hypocreales), and Pandora nouryi (Remaudière & Hennebert) Humber (Zygomycota: Entomophthorales) infecting Doru lineare (Eschscholtz) (Dermaptera: Forficulidae), Ectopsocus californicus (Banks) (Psocodea: Ectopsocidae), and Heterocaecilius sp. (Psocodea: Pseudocaeciliidae), respectively. This is the first report of naturally occurring pathogenic fungi infecting Psocoptera, and it is also
A. V. Toledo; R. A. Humber; C. C. López Lastra
(Thallus structure and isidium development in two Parmeliaceae species (lichenized Ascomycota)). Conventional techniques for structural studies under light microscope and scanning electron microscope were employed to describe and compare the histology of thallus and isidia development in Parmotrema tinctorum and Parmelinopsis minarum. Although presenting layers typical of the heteromerous structure of Parmeliaceae lichens, the studied species have very distinct anatomical details including: the type of upper cortex, medulla thickness, hyphal orientation pattern and distinct strata in this layer, variations of crystal shape, color, location and degree of association with medullary hyphae, rhizines thickness and covering by a cortical layer. Isidium formation starts with cortical cell proliferation, which results in a small protuberance on the thallus surface, followed by the photobiont cell proliferation. Medullary hyphal intrusions occur only after the formation of this protuberance. In this stage medullary hyphae grow, ramifying or not inside the protuberance. In a posterior stage, the isidium base becomes constricted, which facilitates its detachment from the thallus. PMID:19419880
Barbosa, Suzana Bissacot; Machado, Silvia Rodrigues; Marcelli, Marcelo Pinto
The resolving power and statistical support provided by two protein-coding (RPB1 and RPB2) and three ribosomal RNA-coding (nucSSU, nucLSU, and mitSSU) genes individually and in various combinations were investigated based on maximum likelihood bootstrap analyses on lichen-forming fungi from the class Lecanoromycetes (Ascomycota). Our results indicate that the optimal loci (single and combined) to use for molecular systematics of lichen-forming
Valérie Hofstetter; Jolanta Miadlikowska; Frank Kauff; François Lutzoni
Multi-gene phylogenetic analyses were conducted to address the evolution of Clavicipitaceae (Ascomycota). Data are presented here for approximately 5900 base pairs from portions of seven loci: the nuclear ribosomal small and large subunit DNA (nrSSU and nrLSU), ?-tubulin, elongation factor 1? (EF-1?), the largest and second largest subunits of RNA polymerase II (RPB1 and RPB2), and mitochondrial ATP Synthase subunit
Gi-Ho Sung; Jae-Mo Sung; Nigel L. Hywel-Jones; Joseph W. Spatafora
The anamorphic fungal genus Monotosporella (Ascomycota, Sordariomycetes) has been reco-vered from a piece of Early Eocene Indian amber, as well as from the surface of extant resin flows in New Caledonia. The fossil fungus was obtained from the Tarkeshwar Lignite Mine of Gujarat State, western India, and was part of the biota of an early tropical angiosperm rainforest. The amber inclusion represents the second fossil record of Sordariomycetes, as well as the first fossil of its particular order (either Savoryellales or Chaetosphaeriales). The fossil fungus is distinguished from extant representatives by possessing both short conidiophores and small two-septate pyriform conidia, and is described as Monotosporella doerfeltii sp. nov. Inside the amber, the anamorph is attached to its substrate, which is likely the degraded thallus of a cladoniform lichen. The extant New Caledonian species is assigned to Monotosporella setosa. It was found growing on semi-solidified resin flows of Agathis ovata (Araucariaceae), and is the first record of Monotosporella from modern resin substrates. PMID:23063189
Sadowski, Eva-Maria; Beimforde, Christina; Gube, Matthias; Rikkinen, Jouko; Singh, Hukam; Seyfullah, Leyla J; Heinrichs, Jochen; Nascimbene, Paul C; Reitner, Joachim; Schmidt, Alexander R
Relationships among ascomycetous yeast genera (subphylum Saccharomycotina, phylum Ascomycota) have been uncertain. In the present study, type species of 70 currently recognized genera are compared from divergence in the nearly entire nuclear gene sequences for large subunit rRNA, small subunit (SSU) rRNA, translation elongation factor-1?, and RNA polymerase II, subunits 1 (RPB1) and 2 (RPB2). The analysis substantiates earlier proposals that all known ascomycetous yeast genera now assigned to the Saccharomycotina represent a single clade. Maximum likelihood analysis resolved the taxa into eight large multigenus clades and four-one- and two-genus clades. Maximum parsimony and neighbor-joining analyses gave similar results. Genera of the family Saccharomycetaceae remain as one large clade as previously demonstrated, to which the genus Cyniclomyces is now assigned. Pichia, Saturnispora, Kregervanrija, Dekkera, Ogataea and Ambrosiozyma are members of a single large clade, which is separate from the clade that includes Barnettozyma, Cyberlindnera, Phaffomyces, Starmera and Wickerhamomyces. Other clades include Kodamaea, Metschnikowia, Debaryomyces, Cephaloascus and related genera, which are separate from the clade that includes Zygoascus, Trichomonascus, Yarrowia and others. This study once again demonstrates that there is limited congruence between a system of classification based on phenotype and a system determined from DNA sequences. PMID:22978764
Kurtzman, Cletus P; Robnett, Christie J
Fungi Evolution Revisited: Application of the Penalized Likelihood Method to a Bayesian Fungal Phylogeny Provides a New Perspective on Phylogenetic Relationships and Divergence Dates of Ascomycota Groups
The depiction of evolutionary relationships within phylum Ascomycota is still controversial because of unresolved branching orders in the radiation of major taxa. Here we generated a dataset of 166 small subunit (18S) rDNA sequences, representative of all groups of Fungi and used as input in a Bayesian phylogenetic analysis. This phylogeny suggests that Discomycetes are a basal group of filamentous
Ana Carolina B. Padovan; Gerdine F. O. Sanson; Adriana Brunstein; Marcelo R. S. Briones
Peltigera (Peltigerineae, lichenized Ascomycota) is one of the most widespread lichen genera incorporating bi- and trimembered associations involving fungi, green algae (cf. Coccomyxa), and cyanobacteria (cf. Nostoc). A wide range of morphological and chemical (secondary compounds) variation at both the intra- and inter- specific levels is present in this genus. Compared to many other genera of macrolichens, its taxonomy, including
Jolanta Miadlikowska; Francois Lutzoni
The Ascomycota species Phaeomoniella chlamydospora, in concert with other fungi, is a causal agent for grapevine trunk diseases. Here, we present the first draft of the P. chlamydospora genome sequence, which comprises 355 scaffolds, with a total length of 26.59 Mb and 7,279 predicted protein-coding genes. PMID:24723699
Antonielli, Livio; Compant, Stéphane; Strauss, Joseph; Sessitsch, Angela; Berger, Harald
Reports of natural infections of the insect pathogenic fungus Beauveria bassiana (Bals.) Vuill. (Ascomycota: Hypocreales) in greenhouses and laboratory colonies of Scatella tenuicosta Collin (Diptera: Ephydridae), a nuisance pest and vector of plant pathogens, suggest the potential for using B. bassiana for microbial control of this pest. In this study we assessed the diversity of B. bassiana isolates found associated
Louela A. Castrillo; Todd A. Ugine; Melanie J. Filotas; John P. Sanderson; John D. Vandenberg; Stephen P. Wraight
Clonostachys rosea (Link: Fries) Schroers, Samuels, Seifert, and Gams (Ascomycota: Hypocreales) has been reported as a mycoparasite of fungi and nematodes and as saprobe in soils, but this fungus has not been reported previously to be entomopathogenic. Many species of cicadellid leafhoppers cause economic damage to crops as vectors of plant pathogens. In the present work, we report the first
A. V. Toledo; E. Virla; R. A. Humber; S. L. Paradell; C. C. López Lastra
We present the first and southernmost records of the fungi Hirsutella strigosa Petch, H. citriformis Speare (Ascomycota: Hypocreales), and Pandora nouryi (Remaudière & Hennebert) Humber (Zygomycota: Entomophthorales) infecting Doru lineare (Eschscholtz) (Dermaptera: Forficulidae), Ectopsocus californicus (Banks) (Psocodea: Ectopsocidae), and Heterocaecilius sp. (Psocodea: Pseudocaeciliidae), respectively. This is the first report of naturally occurring pathogenic fungi infecting Psocoptera, and it is also the first report of P. nouryi from any host outside of the Aphididae. The three fungal species were morphologically described from their host insects and from microscopic preparations. Attempts to obtain pure fungal isolates were unsuccessful but slides and photographs of these fungi were preserved and deposited in mycological collections as herbarium material. PMID:17949742
Toledo, A V; Humber, R A; Lastra, C C López
We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene
C. L. Schoch; G.-H. Sung; F. López-Giráldez; J. P. Townsend; J. Miadlikowska; V. Hofstetter; B. Robbertse; P. Brandon Matheny; F. Kauff; Z. Wang; C. Gueidan; R. M. Andrie; K. Trippe; L. M. Ciufetti; A. Wynns; E. Fraker; B. P. Hodkinson; G. Bonito; J. Z. Groenewald; M. Arzanlou; Hoog de G. S; P. W. Crous; D. Hewitt; D. H. Pfister; K. Peterson; M. Gryzenhout; M. J. Wingfield; A. Aptroot; S.-O. Suh; M. Blackwell; D. M. Hillis; G. W. Griffith; L. A. Castlebury; A. Y. Rossman; H. T. Lumbsch; R. Lücking; B. Büdel; A. Rauhut; P. Diederich; D. Ertz; D. M. Geiser; K. Hosaka; P. Inderbitzin; J. Kohlmeyer; B. Volkmann-Kohlmeyer; L. Mostert; K. O'Donnell; H. Sipman; J. D. Rogers; R. A. Shoemaker; J. Sugiyama; R. C. Summerbell; W. Untereiner; P. R. Johnston; S. Stenroos; A. Zuccaro; P. S. Dyer; P. D. Crittenden; M. S. Cole; K. Hansen; J. M. Trappe; R. Yahr; F. Lutzoni; J. W. Spatafora
The phylogeny of Lecanoromycetes (Ascomycota, Fungi) is investigated utilizing parsimony and Bayesian Markov Chain Monte Carlo analyses, of combined nLSU rDNA and mtSSU rDNA sequence datasets. The results suggest that Acarosporaceae, Candelariaceae, Phlyctis and Pycnora are not members of the monophyletic Lecanorales, and that Timdalia and Pleopsidium are members of a monophyletic Acarosporaceae. Pycnora, Candelariaceae and Acarosporaceae form a monophyletic
Mats Wedin; Elisabeth Wiklund; Anna Crewe; Heidi Döring; Stefan Ekman; Åsa Nyberg; Imke Schmitt; H. Thorsten Lumbsch
The ultrastructural and cytochemical characterization of the brown soft scale, Coccus hesperidum L. (Hemiptera: Coccidae) infected by the hyphomycete Lecanicillium lecanii (Zimmermann) Gams & Zare, belonging to the phylum Ascomycota and order Hypocreales, was investigated by light, scanning and transmission electron microscopy. Gold cytochemistry was used to label chitin in the cuticle of the scale insect. The results revealed that the pathogenic fungus, L. lecanii generally infected by penetrating the integument, especially at anus, vulva, spiracles, stigmatic furrow, body margin, and the areas of cuticle with grooves, fissures and rugoses areas. The conidia became attached to the host body surface and germinated into hyphae that established colonies by branching repeatedly. Hyphae penetrated the integument by means of their penetration pegs using mechanical force and extracellular enzymes. During integument penetration, the hyphae extended vertically or parallel along the cuticle. Labeling with the WGA/Ovo-G complex showed disruption of the parallel sheets of chitin and a decrease in the density of the gold particles surrounding the penetrated hyphae. Hyphal invasion also separated the cuticle and epidermis from each other. Once in the haemocoele, blastospores of the fungus infected the haemocytes and internal organs. After some time, the nutritive value of the haemocoele decreased and the insect's internal organs disappeared. The hyphae then produced conidiophores and released them through the cuticle of the scale insect cadaver. PMID:20863711
Liu, Weimin; Xie, Yingping; Xue, Jiaoliang; Zhang, Yanfeng; Zhang, Xiaomin
Hirsutella thompsonii (Fischer) (Ascomycota: Ophiocordycipitaceae), a fungal pathogen, often causes high mortality in populations of Calacarus heveae Feres (Acari: Eriophyidae), an important pest mite in rubber tree plantations (Hevea brasiliensis Muell. Arg., Euphorbiaceae). However, the ecological and climatic factors regulating this host-pathogen system are poorly known. We compared fungal infections in agroforestry and traditional rubber plantations to evaluate the role of native vegetation and climatic factors on infection rates of C. heveae by H. thompsonii. While the prevalence of H. thompsonii was higher in managed rubber tree plantations, the abundance of C. heveae was about three times higher in traditional plantations. Abundance of C. heveae, agroecosystem management type and microclimatic variables were responsible for driving the infection rates of H. thompsonii. Native vegetation was a source for H. thompsonii and also modified the crop's microclimate, which contributed to its maintenance in the crop fields. Therefore, appropriate management practices may enhance the effects of entomopathogens on conservative biological control of pest mites in agroforestry systems. PMID:24509786
Nuvoloni, Felipe Micali; de Castro, Elizeu Barbosa; Feres, Reinaldo José Fazzio
Background RNA secondary structure is highly conserved throughout evolution. The higher order structure is fundamental in establishing important structure-function relationships. Nucleotide sequences from ribosomal RNA (rRNA) genes have made a great contribution to our understanding of Ascomycota phylogeny. However, filling the gaps between molecular phylogeny and morphological assumptions based on ascus dehiscence modes and type of fruitbodies at the higher level classification of the phylum remains an unfulfilled task faced by mycologists. Methodology/Principal Findings We selected some major groups of Ascomycota to view their phylogenetic relationships based on analyses of rRNA secondary structure. Using rRNA secondary structural information, here, we converted nucleotide sequences into the structure ones over a 20-symbol code. Our structural analyses together with ancestral character state reconstruction produced reasonable phylogenetic position for the class Geoglossomycetes as opposed to the classic nucleotide analyses. Judging from the secondary structure analyses with consideration of mode of ascus dehiscence and the ability of forming fruitbodies, we draw a clear picture of a possible evolutionary route for fungal asci and some major groups of fungi in Ascomycota. The secondary structure trees show a more reasonable phylogenetic position for the class Geoglossomycetes. Conclusions Our results illustrate that asci lacking of any dehiscence mechanism represent the most primitive type. Passing through the operculate and Orbilia-type asci, bitunicate asci occurred. The evolution came to the most advanced inoperculate type. The ascus-producing fungi might be derived from groups lacking of the capacity to form fruitbodies, and then evolved multiple times. The apothecial type of fruitbodies represents the ancestral state, and the ostiolar type is advanced. The class Geoglossomycetes is closely related to Leotiomycetes and Sordariomycetes having a similar ascus type other than it was originally placed based on nucleotide sequence analyses.
Zhuang, Wen-Ying; Liu, Chao-Yang
Background Factors promoting diversification in lichen symbioses remain largely unexplored. While Pleistocene events have been important for driving diversification and affecting distributions in many groups, recent estimates suggest that major radiations within some genera in the largest clade of macrolichens (Parmeliaceae, Ascomycota) vastly predate the Pleistocene. To better understand the temporal placement and sequence of diversification events in lichens, we estimated divergence times in a common lichen-forming fungal genus, Melanohalea, in the Northern Hemisphere. Divergence times were estimated using both concatenated gene tree and coalescent-based multilocus species tree approaches to assess the temporal context of major radiation events within Melanohalea. In order to complement our understanding of processes impacting genetic differentiation, we also evaluated the effects of Pleistocene glacial cycles on population demographics of distinct Melanohalea lineages, differing in reproductive strategies. Results We found that divergence estimates, from both concatenated gene tree and coalescent-based multilocus species tree approaches, suggest that diversification within Melanohalea occurred predominantly during the Miocene and Pliocene, although estimated of divergence times differed by up to 8.3 million years between the two methods. These results indicate that, in some cases, taxonomically diagnostic characters may be maintained among divergent lineages for millions of years. In other cases, similar phenotypic characters among non-sister taxa, including reproductive strategies, suggest the potential for convergent evolution due to similar selective pressures among distinct lineages. Our analyses provide evidence of population expansions predating the last glacial maximum in the sampled lineages. These results suggest that Pleistocene glaciations were not inherently unfavorable or restrictive for some Melanohalea species, albeit with apparently different demographic histories between sexually and vegetatively reproducing lineages. Conclusions Our results contribute to the understanding of how major changes during the Miocene and Pliocene have been important in promoting diversification within common lichen-forming fungi in the northern Hemisphere. Additionally, we provide evidence that glacial oscillations have influenced current population structure of broadly distributed lichenized fungal species throughout the Holarctic.
There is a long-standing debate on the extent of vicariance and long-distance dispersal events to explain the current distribution of organisms, especially in those with small diaspores potentially prone to long-distance dispersal. Age estimates of clades play a crucial role in evaluating the impact of these processes. The aim of this study is to understand the evolutionary history of the largest clade of macrolichens, the parmelioid lichens (Parmeliaceae, Lecanoromycetes, Ascomycota) by dating the origin of the group and its major lineages. They have a worldwide distribution with centers of distribution in the Neo- and Paleotropics, and semi-arid subtropical regions of the Southern Hemisphere. Phylogenetic analyses were performed using DNA sequences of nuLSU and mtSSU rDNA, and the protein-coding RPB1 gene. The three DNA regions had different evolutionary rates: RPB1 gave a rate two to four times higher than nuLSU and mtSSU. Divergence times of the major clades were estimated with partitioned BEAST analyses allowing different rates for each DNA region and using a relaxed clock model. Three calibrations points were used to date the tree: an inferred age at the stem of Lecanoromycetes, and two dated fossils: Parmelia in the parmelioid group, and Alectoria. Palaeoclimatic conditions and the palaeogeological area cladogram were compared to the dated phylogeny of parmelioid. The parmelioid group diversified around the K/T boundary, and the major clades diverged during the Eocene and Oligocene. The radiation of the genera occurred through globally changing climatic condition of the early Oligocene, Miocene and early Pliocene. The estimated divergence times are consistent with long-distance dispersal events being the major factor to explain the biogeographical distribution patterns of Southern Hemisphere parmelioids, especially for Africa-Australia disjunctions, because the sequential break-up of Gondwana started much earlier than the origin of these clades. However, our data cannot reject vicariance to explain South America-Australia disjunctions. PMID:22174775
Amo de Paz, Guillermo; Cubas, Paloma; Divakar, Pradeep K; Lumbsch, H Thorsten; Crespo, Ana
Although Nectria is the type genus of Nectriaceae (Hypocreales, Sordariomycetes, Pezizomycotina, Ascomycota), the systematics of the teleomorphic and anamorphic state of Nectria sensu Rossman has not been studied in detail. The objectives of this study are to 1) provide a phylogenetic overview to determine if species of Nectria with Gyrostroma, Tubercularia, and Zythiostroma anamorphs form a monophyletic group; 2) define Nectria, segregate genera, and their species using morphologically informative characters of teleomorphic and anamorphic states; and 3) provide descriptions and illustrations of these genera and species. To accomplish these objectives, results of phylogenetic analyses of DNA sequence data from six loci (act, ITS, LSU, rpb1, tef1 and tub), were integrated with morphological characterisations of anamorphs and teleomorphs. Results from the phylogenetic analyses demonstrate that species previously regarded as the genus Nectria having Gyrostroma, Tubercularia, and Zythiostroma anamorphs belong in two major paraphyletic clades. The first major clade regarded as the genus Pleonectria contains 26 species with ascoconidia produced by ascospores in asci, perithecial walls having bright yellow scurf, and immersed or superficial pycnidial anamorphs (Zythiostroma = Gyrostroma). A lineage basal to the Pleonectria clade includes Nectria miltina having very small, aseptate ascospores, and trichoderma-like conidiophores and occurring on monocotyledonous plants. These characteristics are unusual in Pleonectria, thus we recognise the monotypic genus Allantonectria with Allantonectria miltina. The second major clade comprises the genus Nectria sensu stricto including the type species, N. cinnabarina, and 28 additional species. Within the genus Nectria, four subclades exist. One subclade includes species with sporodochial anamorphs and another with synnematous anamorphs. The other two paraphyletic subclades include species that produce abundant stromata in which the large perithecia are immersed, large ascospores, and peculiar anamorphs that form pycnidia or sporodochia either on their natural substrate or in culture. In this study the evolution of species, morphology, and ecology of the three genera, Allantonectria, Nectria, and Pleonectria, are discussed based on the phylogenetic analyses. In addition, descriptions, illustrations, and keys for identification are presented for the 56 species in Allantonectria, Nectria, and Pleonectria. Taxonomic novelties: New species: Nectria argentinensis Hirooka, Rossman & P. Chaverri, Nectria berberidicola Hirooka, Lechat, Rossman, & P. Chaverri, Nectria himalayensis Hirooka, Rossman, & P. Chaverri, Nectria magnispora Hirooka, Rossman, & P. Chaverri, Nectria mariae Hirooka, Fournier, Lechat, Rossman, & P. Chaverri, Nectria pyriformis Hirooka, Rossman & P. Chaverri, Pleonectria boothii Hirooka, Rossman & Chaverri, Pleonectria clavatispora Hirooka, Rossman & P. Chaverri, Pleonectria ilicicola Hirooka, Rossman & P. Chaverri, Pleonectria okinawensis Hirooka, Rossman & P. Chaverri, Pleonectria pseudomissouriensis Hirooka, Rossman & P. Chaverri, Pleonectria quercicola Hirooka, Checa, Areual, Rossman & P. Chaverri, Pleonectria strobi Hirooka, Rossman & P. Chaverri. New combinations: Cosmospora proteae (Marinc., M.J. Wingf. & Crous) Hirooka, Rossman & P. Chaverri, Nectricladiella viticola (Berk. & M.A. Curtis) Hirooka, Rossman & P. Chaverri, Neocosmospora guarapiensis (Speg.) Hirooka, Samuels, Rossman & P. Chaverri, Neocosmospora rehmiana (Kirschstein) Hirooka, Samuels, Rossman & P. Chaverri, Pleonectria aquifolii (Fr.) Hirooka, Rossman & P. Chaverri, Pleonectria aurigera (Berk. & Rav.) Hirooka, Rossman & P. Chaverri, Pleonectria chlorinella (Cooke) Hirooka, Rossman & P. Chaverri, Pleonectria coryli (Fuckel) Hirooka, Rossman & P. Chaverri, Pleonectria cucurbitula (Tode: Fr.) Hirooka, Rossman & P. Chaverri, Pleonectria lonicerae (Seeler) Hirooka, Rossman & P. Chaverri, Pleonectria rosellinii (Carestia) Hirooka, Rossman & P. Chaverri, Pleonectria rubicarpa (Cooke) Hirooka, Rossman & P. Chaverri,
Hirooka, Y.; Rossman, A.Y.; Samuels, G.J.; Lechat, C.; Chaverri, P.
Interactions between the entomopathogenic fungi Beauveria bassiana (Ascomycota: Hypocreales) and the aphid parasitoid Diaeretiella rapae (Hymenoptera: Braconidae) on Myzus persicae (Hemiptera: Aphididae).
The interactions between the entomopathogenic fungus Beauveria bassiana (Balsamo-Crivelli) Vuillemin (Ascomycota: Hypocreales) and the aphid parasitoid Diaeretiella rapae McIntoch (Hymenoptera: Braconidae) were evaluated under laboratory conditions. Nymphs of Myzus persicae Sulzer (Hemiptera: Aphididae) were first exposed to parasitoid females for 24 h and then 0, 24, and 48 h afterwards sprayed with a solution of B. bassiana. Likewise, aphids were also sprayed with B. bassiana and then exposed to parasitoids at 0, 24, and 48 h afterwards. Parasitism rate varied from 13 to 66.5%, and were significantly lower in treatments where the two agents were exposed within a 0-24 h time interval compared with the control (without B. bassiana). Parasitoid emergence was negatively affected in treatments with B. bassiana spraying and subsequent exposure to D. rapae. Decreases in longevity of adult females of the D. rapae F1 generation were observed in treatments with B. bassiana spraying. The application of these two biological control agents can be used in combination on the control of M. persicae, wherein this use requires effective time management to avoid antagonistic interactions. PMID:25026650
Silva, R J; Alencar, J R D C C; Silva, K P; Cividanes, F J; Duarte, R T; Agostini, L T; Polanczyk, R A
Accurate species circumscriptions are central for many biological disciplines and have critical implications for ecological and conservation studies. An increasing body of evidence suggests that in some cases traditional morphology-based taxonomy have underestimated diversity in lichen-forming fungi. Therefore, genetic data play an increasing role for recognizing distinct lineages of lichenized fungi that it would otherwise be improbable to recognize using classical phenotypic characters. Melanohalea (Parmeliaceae, Ascomycota) is one of the most widespread and common lichen-forming genera in the northern Hemisphere. In this study, we assess traditional phenotype-based species boundaries, identify previously unrecognized species-level lineages and discuss biogeographic patterns in Melanohalea. We sampled 487 individuals worldwide, representing 18 of the 22 described Melanohalea species, and generated DNA sequence data from mitochondrial, nuclear ribosomal, and protein-coding markers. Diversity previously hidden within traditional species was identified using a genealogical concordance approach. We inferred relationships among sampled species-level lineages within Melanohalea using both concatenated phylogenetic methods and a coalescent-based multilocus species tree approach. Although lineages identified from genetic data are largely congruent with traditional taxonomy, we found strong evidence supporting the presence of previously unrecognized species in six of the 18 sampled taxa. Strong nodal support and overall congruence among independent loci suggest long-term reproductive isolation among most species-level lineages. While some Melanohalea taxa are truly widespread, a limited number of clades appear to have much more restricted distributional ranges. In most instances the concatenated gene tree and multilocus species tree approaches provided similar estimates of relationships. However, nodal support was generally higher in the phylogeny estimated from concatenated data, and relationships among taxa within one major clade were largely unresolved in the species tree. This study contributes to our understanding of diversity and evolution in common lichen-forming fungi by incorporating multiple locus sequence data to circumscribe morphologicallly cryptic lineages and infer relationships within a coalescent-based species tree approach. PMID:23017822
Leavitt, Steven D; Esslinger, Theodore L; Spribille, Toby; Divakar, Pradeep K; Thorsten Lumbsch, H
Pyrenophora tritici-repentis requires the production of host-selective toxins (HSTs) to cause the disease tan spot of wheat, including Ptr ToxA, Ptr ToxB, and Ptr ToxC. Pyrenophora bromi, the species most closely related to P. tritici-repentis, is the causal agent of brown leaf spot of bromegrass. Because of the relatedness of P. bromi and P. tritici-repentis, we investigated the possibility that P. bromi contains sequences homologous to ToxA and/or ToxB, the products of which may be involved in its interaction with bromegrass. Multiplex polymerase chain reaction (PCR) revealed the presence of ToxB-like sequences in P. bromi and high-fidelity PCR was used to clone several of these loci, which were subsequently confirmed to be homologous to ToxB. Additionally, Southern analysis revealed ToxB from P. bromi to have a multicopy nature similar to ToxB from P. tritici-repentis. A combination of phylogenetic and Southern analyses revealed that the distribution of ToxB extends further into the Pleosporaceae, and a search of available fungal genomes identified a distant putative homolog in Magnaporthe grisea, causal agent of rice blast. Thus, unlike most described HSTs, ToxB homologs are present across a broad range of plant pathogenic ascomycetes, suggesting that it may have arose in an early ancestor of the Ascomycota. PMID:18226934
Andrie, Rachael M; Schoch, Conrad L; Hedges, Rebecca; Spatafora, Joseph W; Ciuffetti, Lynda M
We tested the decay abilities of 28 isolates from 28 lignicolous fungal species (Basidiomycota, Ascomycota and Zygomycota) with the pure culture test. We used beech wood powder in varying moisture conditions and decay stages (nondecayed, intermediately decayed and well decayed) as substrates. The weight loss in wood powder was -0.2-17.8%. Five isolates of Basidiomycota (Bjerkandera adusta, Mycena haematopus, Omphalotus guepiniformis, Trametes hirsuta, Trametes versicolor) caused high weight losses in nondecayed wood. We detected significant effects of decay stage on weight loss in wood in most isolates tested, whereas moisture content rarely had an effect on weight loss. Among Basidiomycota and Xylariaceae in Ascomycota weight loss was greater for nondecayed wood than for intermediately and well decayed wood. In contrast four isolates in Ascomycota (Scytalidium lignicola, Trichoderma hamatum, T. harzianum, T. koningii) caused substantial weight loss in intermediately and well decayed wood, although they rarely caused weight loss in nondecayed wood. Zygomycota caused low weight loss in wood. Wood decay stages also affected decomposition of wood chemical components. Acid-unhydrolyzable residue (AUR) decomposition was reduced, whereas holocellulose decomposition was stimulated by some strains of Basidiomycota and Ascomycota in well decayed wood. T. harzianum in particular caused significant weight loss of holocellulose in well decayed wood, although this fungus caused negligible weight loss of both AUR and holocellulose in nondecayed wood. We discuss these changes in the decay patterns of AUR and holocellulose with varying wood decay stages in relation to the role of fungal decomposition of woody debris in forests. PMID:21262989
Fukasawa, Yu; Osono, Takashi; Takeda, Hiroshi
An automated procedure was developed to extract orthologous sequences from fungal genomes and incorporate them into phylogenomic analyses in a timely and efficient manner. This approach involves parsing an all versus all BLASTP search of 17 proteomes and creating a similarity matrix from e-values, which is then used to cluster proteins into related groups by means of a Markov Clustering
Barbara Robbertse; John B. Reeves; Conrad L. Schoch; Joseph W. Spatafora
Parmotrema is one of the larger genera segregated from Parmelia s. lat. Additional genera recently have been segregated from this large genus based mainly on morphological and chemical fea- tures. We have employed molecular data from three genes to continue a revision of the generic concept within the parmelioid lichens. A Bayesian analysis of nuclear ITS, LSU rDNA and mitochondrial
Oscar Blanco; Ana Crespo; Pradeep K. Divakar; John A. Elix; H. Thorsten Lumbsch
Abstract:Lecanora demissa (Körb.) Zahlbr. is a crustose, lobate lichen that produces soredia and conidiomata but no apothecia. Its placement in Lecanora has long been questioned but nothing better has been proposed. We have studied the nuclear rDNA of the ITS regions and the SSU of L. demissa. In an alignment of the ITS regions of several representatives of Lecanora s.
Ulf Arup; Martin Grube
Parmotrema is one of the larger genera segregated from Parmelia s. lat. Additional genera recently have been segregated from this large genus based mainly on morphological and chemical features. We have employed molecular data from three genes to continue a revision of the generic concept within the parmelioid lichens. A Bayesian analysis of nuclear ITS, LSU rDNA and mitochondrial SSU rDNA sequences was performed. The genera Canomaculina, Concamerella, Parmelaria and Rimelia appear nested within Parmotrema. Alternative hypotheses to maintain the independence of Canomaculina, Concamerella and Rimelia are shown to be highly unlikely and are rejected. As a consequence these three genera are reduced to synonymy with Parmotrema. An alternative topology segregating Parmelaria from Parmotrema s. lat. cannot be rejected with the dataset at hand. However we have established that this genus is closely related to Parmotrema rather than to cetrarioid species as was considered previously. The revised genus Parmotrema includes species that have an upper cortex consisting of a palisade plectenchyma or rarely paraplectenchyma with vaults, have a pored or fenestrated epicortex, lack pseudocyphellae, have or lack cilia, have laminal, perforate or eperforate apothecia, usually have simple rhizines and filiform, cylindrical, bacilliform or sublageniform conidia. It is closely related to Flavoparmelia but the status of these genera requires further investigation. Nineteen new combinations are made. PMID:16389966
Blanco, Oscar; Crespol, Ana; Divakar, Pradeep K; Elix, John A; Lumbsch, H Thorsten
Species of Sarawakus are rarely encountered. Their teleomorphs resemble sexual stages of Trichoderma, formerly called Hypocrea, but differ from that genus by unicellular ascospores. The two green-spored species S. britannicus and the type species of Sarawakus, S. lycogaloides, recently were collected, compared with their types and cultured. We redescribe and illustrate these species and transfer them to Trichoderma, based on phylogenetic analysis of the translation elongation factor 1-alpha encoding gene (tef1), containing the two last introns and exon, and a part of the rpb2 gene, encoding the second largest RNA polymerase subunit. Trichoderma lycogaloides, was found to cluster with Hypocrea sulawesensis, an unusual species of Trichoderma, while T. britannicum is closely related to T. aerugineum of the Spinulosa clade. The anamorphs of the two examined species are characterized by (odd) verticillium-like conidiophores, large cylindrical phialides and conidia, which belong to the largest of those species forming green conidia, oval to subglobose in T. lycogaloides and oblong in T. britannicum. All species currently recognized in Sarawakus are transferred to Trichoderma, introducing the new combinations T. fragile, T. hexasporum, T. izawae, T. sordidum, T. subtrachycarpum, T. succisum and T. trachycarpum and the new name T. rosellum. Trichoderma trachycarpum is redescribed and illustrated from an isotype. PMID:24603837
Jaklitsch, Walter M; Lechat, Christian; Voglmayr, Hermann
We document here for the first time ultrastructural details of the cellular interaction of Asteridiella callista and its host Stachytarpheta mutabilis var. violacea from Costa Rica. A. callista attaches to the host with appressoria, invades the epidermal cell wall and forms an apoplastic complex cisternal net, presumably for nutrient uptake from its host. This unique structure, called an interaction apparatus (Ia), consists of cisternae surrounded by a membrane continuous with the fungal cytoplasmic membrane. Subsequently the apoplastic trunk of the Ia extends into the host epidermal cell wall and contacts the host cytoplasmic membrane. Electron-opaque material, probably of fungal origin appears at the host cytoplasmic membrane. Finally these electron-opaque deposits are encased by host material. Functional and systematical aspects of this interaction scenario are discussed. PMID:24782491
Justavino, Délfida Rodríguez; Velásquez, Julieta Carranza; Morales Sánchez, Carlos O; Rincón, Rafael; Oberwinkler, Franz; Bauer, Robert
A taxonomic study of Peltigera in South Korea was performed. The phylogenetic analysis based on nr DNA internal transcribed spacer sequences suggests that Peltigera is a well-supported monophyletic group. Important characteristics are the phycobiont type of thallus and the vein type at the lower cortex (wide and flat, or narrow and ridged). The vertical or horizontal arrangement of the apothecia is also important in distinguishing species in this genus. Eleven species of Peltigera were revealed and confirmed, which included one new record, P. elisabethae. A description of each species is presented with morphological, anatomic, and chemical characteristics, and comparisons between similar species are made. A key to the species is also presented.
Wei, Xin Li; Wang, Xin Yu; Koh, Young Jin
Results of molecular studies regarding the phylogenetic placement of the order Ostropales and related taxa within Lecanoromycetes were thus far inconclusive. Some analyses placed the order as sister to the rest of Lecanoromycetes, while others inferred a position nested within Lecanoromycetes. We assembled a data set of 101 species including sequences from nuLSU rDNA, mtSSU rDNA, and the nuclear protein-coding
H. Thorsten Lumbsch; Imke Schmitt; Robert Lücking; Elisabeth Wiklund; Mats Wedin
Partial sequences of nuLSU rDNA were obtained to investigate the phylogenetic relationships of Pyronemataceae, the largest and least studied family of Pezizales. The dataset includes sequences for 162 species from 51 genera of Pyronemataceae, and 39 species from an additional 13 families of Pezizales. Parsimony, ML, and Bayesian analyses suggest that Pyronemataceae is not monophyletic as it is currently circumscribed.
Brian A. Perry; Karen Hansen; Donald H. Pfister
The taxonomic status of the genera Lignincola and Nais was re-evaluated by phylogenetic analysis of the partial large subunit ribosomal DNA sequence. Both Lignincola and Nais are inferred to be polyphyletic genera. Lignincola laevis and L. longirostris are phylogenetically related taxa but they are not monophyletic. Nais inornata, the type species of the genus, has a close relationship with Aniptodera
Ka-Lai Pang; Lilian L. P. Vrijmoed; Richard Y. C. Kong; E. B. Gareth Jones
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
Joseph W. Spatafora; Brigitte Volkmann-Kohlmeyer; Jan Kohlmeyer
Based on herbarium collections, the altitudinal distribution patterns of six species of the lichen genus Stereocaulon in China were analyzed. Species are elevation-dependent: normal distributions and corresponding empirical formulae were detected for the genus and S. japonicum and S. paschale, the species distributed in low elevation areas, and log-normal distributions detected for S. sorediiferum and S. tomentosum, the species in medium elevation areas, while S. pomiferum and S. myriocarpum, the species in high elevation areas, appear to be irregularly distributed according to altitude. Such formulae should prove valuable for biological conservation practices.
Background The rate of nucleotide substitutions is not constant across the Tree of Life, and departures from a molecular clock have been commonly reported. Within parmelioid lichens, the largest group of macrolichens, large discrepancies in branch lengths between clades were found in previous studies. Using an extended taxon sampling, we test for presence of significant rate discrepancies within and between these clades and test our a priori hypothesis that such rate discrepancies may be explained by shifts in moisture regime or other environmental conditions. Results In this paper, the first statistical evidence for accelerated evolutionary rate in lichenized ascomycetes is presented. Our results give clear evidence for a faster rate of evolution in two Hypotrachyna clades that includes species occurring in tropical and oceanic habitats in comparison with clades consisting of species occurring in semi-arid and temperate habitats. Further we explore potential links between evolutionary rates and shifts in habitat by comparing alternative Ornstein-Uhlenbeck models. Conclusion Although there was only weak support for a shift at the base of a second tropical clade, where the observed nucleotide substitution rate is high, overall support for a shift in environmental conditions at cladogenesis is very strong. This suggests that speciation in some lichen clades has proceeded by dispersal into a novel environment, followed by radiation within that environment. We found moderate support for a shift in moisture regime at the base of one tropical clade and a clade occurring in semi-arid regions and a shift in minimum temperature at the base of a boreal-temperate clade.
Parmelioid lichens form a species-rich group of predominantly foliose and fruticose lichenized fungi encompassing a broad range of morphological and chemical diversity. Using a multilocus approach, we reconstructed a phylogeny including 323 OTUs of parmelioid lichens and employed ancestral character reconstruction methods to understand the phenotypical evolution within this speciose group of lichen-forming fungi. Specifically, we were interested in the evolution of growth form, epicortex structure, and cortical chemistry. Since previous studies have shown that results may differ depending on the reconstruction method used, here we employed both maximum-parsimony and maximum-likelihood approaches to reconstruct ancestral character states. We have also implemented binary and multistate coding of characters and performed parallel analyses with both coding types to assess for potential coding-based biases. We reconstructed the ancestral states for nine well-supported major clades in the parmelioid group, two higher-level sister groups and the ancestral character state for all parmelioid lichens. We found that different methods for coding phenotypical characters and different ancestral character state reconstruction methods mostly resulted in identical reconstructions but yield conflicting inferences of ancestral states, in some cases. However, we found support for the ancestor of parmelioid lichens having been a foliose lichen with a non-pored epicortex and pseudocyphellae. Our data suggest that some traits exhibit patterns of evolution consistent with adaptive radiation. PMID:24312438
Divakar, Pradeep K; Kauff, Frank; Crespo, Ana; Leavitt, Steven D; Lumbsch, H Thorsten
Pseudotulostoma volvata (O. K. Mill. and T. W. Henkel) is a morphologically unusual member of the otherwise hypogeous Elaphomycetaceae due to its epigeous habit and exposed gleba borne on an elevated stalk at maturity. Field observations in Guyana indicated that P. volvata was restricted to rain forests dominated by ectomycorrhizal (EM) Dicymbe corymbosa (Caesalpiniaceae), suggesting an EM nutritional mode for the fungus. In this paper, we confirm the EM status of P. volvata with a combination of morphological, molecular, and mycosociological data. The EM status for P. volvata corroborates its placement in the ectotrophic Elaphomycetaceae. PMID:16547736
Henkel, Terry W; James, Timothy Y; Miller, Steven L; Aime, M Catherine; Miller, Orson K
To infer the phylogenetic relationships of Xylaria species associated with termite nests within the genus Xylaria and among genera of the subfamily Xylarioideae, beta-tubulin, RPB2, and alpha-actin sequences of 131 cultures of 114 species from Xylaria and 11 other genera of the subfamily were analyzed. These 11 genera included Astrocystis, Amphirosellinia, Discoxylaria, Entoleuca, Euepixylon, Kretzschmaria, Nemania, Podosordaria, Poronia, Rosellinia, and Stilbohypoxylon. We showed that Xylaria species were distributed among three major clades, TE, HY, and PO, with clade TE-an equivalent of the subgenus Pseudoxylaria-encompassing exclusively those species associated with termite nests and the other two clades containing those associated with substrates other than termite nests. Xylaria appears to be a paraphyletic genus, with most of the 11 genera submerged within it. Podosordaria and Poronia, which formed a distinct clade, apparently diverged from Xylaria and the other genera early. Species of Entoleuca, Euepixylon, Nemania, and Rosellinia constituted clade NR, a major clade sister to clade PO, while those of Kretzschmaria were inserted within clade HY and those of Astrocystis, Amphirosellinia, Discoxylaria, and Stilbohypoxylon were within clade PO. PMID:20035889
Hsieh, Huei-Mei; Lin, Chun-Ru; Fang, Mei-Jane; Rogers, Jack D; Fournier, Jacques; Lechat, Christian; Ju, Yu-Ming
The new corticolous species Arthonia isidiata is described from the Pacific lowlands of Costa Rica. A. isidiata is characterized by minute, cylindrical to coralloid isidia produced on the thallus surface. The species currently is known only from the type locality in Corcovado National Park, where it occurs abundantly in the coastal rainforest around Sirena Biological Station. PMID:21148936
Grube, Martin; Lücking, Robert; Umaña-Tenorio, Loengrin
The new corticolous species Arthonia isi- diata is described from the Pacific lowlands of Costa Rica. A. isidiata is characterized by minute, cylindri- cal to coralloid isidia produced on the thallus sur- face. The species currently is known only from the type locality in Corcovado National Park, where it oc- curs abundantly in the coastal rainforest around Sir- ena Biological
The molecular phylogeny of Acarosporaceae with a focus on the recently proposed genus Polysporinopsis was investigated using maximum parsimony and Bayesian analyses, using nuITS-LSU and mtSSU rDNA sequence datasets. A well-supported monophyletic clade corresponding to Acarospora (including the type species A. schleicheri, A. fuscata, A. nitrophila, A. rugulosa, A. bullata, A. sinopica, A molybdina and A. peliscypha) was present in all analyses. Acarospora as currently delimited is not monophyletic; neither A. smaragdula nor A. badiofusca belongs to the genus in the restricted sense. Polysporinopsis, which comprises three species previously classified in Acarospora (P. sinopica-type species, P. smaragdula, and P. rugulosa) is not a monophyletic group separate from Acarospora s. str. Acarospora sinopica and A. smaragdula are not closely related; A. sinopica belongs to Acarospora s. str., but A. smaragdula is one of the most basal taxa currently known in Acarosporaceae. PMID:16616841
Crewe, Anna T; Purvis, O William; Wedin, Mats
The earliest pre-Linnaean fungal genera are briefly discussed here with special emphasis on the nomenclatural connection with the genus Cordyceps Fr. Since its valid publication under the basidiomycetous genus Clavaria Vaill. ex L. (Clavaria militaris L. Sp. Pl. 2:1182, 1753), the genus Cordyceps has undergone nomenclatural changes in the post-Linnaean era, but has stood firmly for approximately 200 years. Synonyms of Cordyceps were collected from different literature sources and analyzed based on the species they represent. True synonyms of Cordyceps Fr. were defined as genera that represented species of Cordyceps Fr. emend. G. H. Sung, J. M. Sung, Hywel-Jones & Spatafora. The most common synonyms of Cordyceps observed were Clavaria and Sphaeria Hall, reported in the 18th and in the first half of the 19th century, respectively. Cordyceps, the oldest genus in the Cordyceps s. s. clade of Cordycipitaceae, is the most preferred name under the "One Fungus = One Name" principle on priority bases.
Tanaka, Eiji; Han, Jae-Gu; Oh, Junsang; Han, Sang-Kuk; Lee, Kang-Hyo
The pigeon tick Argas reflexus is a pathogen-transmitting soft tick that typically feeds on pigeons, but can also attack humans causing local and systemic reactions. Chemical control is made difficult due to environmental contamination and resistance development. As a result, there is much interest in increasing the role of other strategies like biological control. In this study, the efficacy of three strains (V245, 685 and 715C) of entomopathogenic fungus Metarhizium anisopliae for biological control of three life stages of pigeon tick A. reflexus including eggs, larvae, engorged and unfed adults was investigated under laboratory conditions. Five concentrations of different strains of M. anisopliae ranging from 103 to 107 conidia/ml were used. All fungal strains significantly decreased hatchability of A. reflexus eggs. Strain V245 was the most effective strain on the mortality of larval stage with nearly 100% mortality at the lowest concentration (103 conidia/ml) at 10 days post-inoculation. The mortality rate of both engorged and unfed adult ticks were also increased significantly exposed to different conidial concentrations compared to the control groups (P < 0.05) making this fungus a potential biological control agent of pigeon tick reducing the use of chemical acaricides.
Tavassoli, Mosa; Pourseyed, Seyed Hassan; Ownagh, Abdulghaffar; Bernousi, Iraj; Mardani, Karim
Biogenic ice nucleation (IN) in the atmosphere is a topic of growing interest, as, according to IPCC, the impact of IN on global climate is crucial to perform reliable climate model calculations. About 20 years ago IN activity of a few lichen and Fusarium species [1,2] was reported, while all other investigated fungi were IN-negative. However, as the fungal kingdom is vast, many abundant species, especially the Basidiomycota (most mushrooms), were not tested before. Furthermore, the focus of the past studies was on the IN activity of the mycelium as a cryoprotective mechanism, and not on the airborne spores. We carried out oil immersion measurements  with spores from 17 different fungal species of ecological, economical or sanitary importance. Most of these species have not been investigated before, like exponents of Aspergillus, Trichoderma and Agaricales (most mushrooms). Apart from F. avenaceum, spores of all measured species showed moderate or no IN activity, supporting the hypothesis that significant IN activity is a rather exclusive property of only a few species within the fungal kingdom.  Kieft TL and Ruscetti T: J. Bacteriol. 172, 3519-3523, 1990.  Pouleur S et al.: Appl. Environ. Microbiol., 58, 2960-2964, 1992.  Marcolli C et al.: Atmos. Chem. Phys. 7, 5081-5091, 2007.
Pummer, B. G.; Atanasova, L.; Bauer, H.; Bernardi, J.; Druzhinina, I. S.; Grothe, H.
The two diaporthalean fungi Anisogramma virgultorum and A. anomala are biotrophic parasites. A. virgultorum causes stromatal cankers on young shoots of birch whereas A. anomala infects young branches of Corylus avellana. Although previous classifications based on morphological characteristics placed both species in the Gnomoniaceae, Diaporthales, their taxonomic position within the order and their relationship to each other required further clarification. We determined the nucleotide sequences of the ITS and partial LSU nu-rDNA regions of both species. A putative second teleomorph form of A. virgultorum, described in the literature as the 'single perithecial form', was also included in the analysis. Based on phylogenetic analyses of LSU sequences, the stromatal forms of A. virgultorum and A. anomala were part of a well-supported monophyletic sister clade to the Gnomoniaceae. The single perithecial form was placed within a clade containing representative members of the Gnomoniaceae, separate from species of Anisogramma. These results indicate that the single perithecial form of A. virgultorum actually represents an unrelated and as yet unidentified species of Gnomoniaceae. A morphological description of asci and ascospores of the three species is given. A Wilcoxon two sample test revealed that asci of the stromatal form of A. virgultorum were significantly shorter than those of the single perithecial species. Ascospores of the stromatal form of A. virgultorum were significantly shorter and wider than those of the single perithecial species. PMID:18824098
De Silva, Heike; Castlebury, Lisa A; Green, Sarah; Stone, Jeffrey K
Heterodermia squamulosa (Degel.) W.L. Culb. was found in the mountain of Gariwang, Gangwon province, in 2008. It is characterized by numerous squamules along the margin, decorticate and white lower surface, rhizines along the margin, black and densely squarrosely branched, usually forming a dense mat under the thallus. Apothecia margins densely squamulose, ascospores 12~15 × 25~30 µm. Atranorin and zeorin contained in thallus. This is the first record of this species in South Korea. PMID:23997623
Wang, Xin Yu; Hur, Hyun; Lee, You Mi; Koh, Young Jin; Hur, Jae-Seoun
Heterodermia squamulosa (Degel.) W.L. Culb. was found in the mountain of Gariwang, Gangwon province, in 2008. It is characterized by numerous squamules along the margin, decorticate and white lower surface, rhizines along the margin, black and densely squarrosely branched, usually forming a dense mat under the thallus. Apothecia margins densely squamulose, ascospores 12~15 × 25~30 µm. Atranorin and zeorin contained in thallus. This is the first record of this species in South Korea.
Wang, Xin Yu; Hur, Hyun; Lee, You Mi; Koh, Young Jin
Leptogium (Ach.) Gray is distributed throughout South Korea; however, for nearly two decades no detailed taxonomic or revisionary research on this lichen genus has been conducted. This study examined the specimens deposited in the lichen herbarium at the Korean Lichen Research Institute, and samples were identified using descriptions recently published in the scientific literature. In this revisionary study, a total of fourteen species of Leptogium were documented, including new records of Leptogium delavayi Hue, Leptogium denticulatum Nyl., and Leptogium trichophoroides P. M. Jørg. & A. K. Wallace. Detailed descriptions of each species are given, including their morphological, anatomical, and chemical characteristics. A key to all Leptogium species known to occur in South Korea is also presented.
Jayalal, Udeni; Jang, Seol Hwa; Yu, Nan Hee; Oh, Soon Ok
Beauveria bassiana , an entomogenous fungus used for the biological control of pest insects, comprises a globally-distributed species complex of regionally endemic lineages. In order to study the population genetics of B. bassiana , detail species boundaries, conduct ecolog- ical studies of natural populations and track fates of experimentally-released strains, sen- sitive genetic markers are required. We describe the isolation
S. A. Rehner; E. P. Buckley
Verrucariaceae are a family of mostly crustose lichenized ascomycetes colonizing various habitats ranging from marine and fresh water to arid environments. Phylogenetic relationships among members of the Verrucariaceae are mostly unknown and the current morphology-based classification has never been confronted to molecular data. A multilocus phylogeny (nuLSU, nuSSU and RPB1) was reconstructed for 83 taxa representing all main genera of
Cécile Gueidan; Claude Roux; François Lutzoni
Golovinomyces is a strictly herb-parasitic genus in the Erysiphaceae. Host–parasite co-speciation was reported recently between the genus Golovinomyces and Asteraceae from molecular phylogenetic analyses. The Asteraceae originated in South America and latterly expanded their geographic distribution into the Northern Hemisphere. If the co-speciation between Golovinomyces and Asteraceae originated in South America, the geographic origin of Golovinomyces could be assumed to
Susumu TAKAMATSU; Sanae MATSUDA; Seiko NIINOMI; Maria HAVRYLENKO
The phylogeny of Agyriaceae was investigated using MP and Bayesian approaches based on a combined dataset of nuLSU rDNA, mtSSU rDNA, and RPB1 sequences of 78 ascomycetes. The type genus of the family is shown to be a strongly supported sister to Coccotremataceae+Pertusariaceae, whereas the remaining species currently classified in Agyriaceae have a well-supported sister-group relationship with Baeomycetales. Monophyly of
H. Thorsten Lumbsch; Imke Schmitt; Armin Mangold; Mats Wedin
Lichen-forming ascomycetes exhibit often complex morphologies of the vegetative thallus that are usually not found in non-lichenized fungi. This includes the thallus organization and appendical structures associated with the main thallus, such as cilia and rhizines. Such morphological characters are widely employed in the taxonomy of parmelioid lichens, especially at generic level. Within parmelioid lichens, several monophyletic groups can be
Pradeep K. Divakar; Ana Crespo; Oscar Blanco; H. Thorsten Lumbsch
Lichenized fungi synthesize a great variety of secondary metabolites. These are typically crystalline compounds, which are deposited extracellularly on the fungal hyphae. While we know a lot about the chemical properties and structures of these substances, we have very little information on the molecular background of their biosynthesis. In the current study we analyze the diversity of non-reducing polyketide synthase
Imke Schmitt; María P. Martín; Stefanie Kautz; H. Thorsten Lumbsch
A checklist and keys are given for the 16 genera in the lichen family Graphidaceae found in the Solomon Islands. A total of 75 species in the family Graphidaceae were identified, distributed as follows: Acanthothecis two species, Anomomorpha one species, Carbacanthographis three species, Diorygma six species, Dyplolabia one species, Fissurina 11 species, Graphis 17 species, Hemithecium four species, Leiorreuma four
Alan W. Archer
Abstract: The genus Skyttea is characterized by urceolate ascomata, with a narrow pore when young, a greenish or brownish, rarely reddish exciple of conglutinate hyphae with subglobose to ±cylindrical lumina, bordered near the margin by hyaline to greenish or brownish, usually smooth, straight hairs, the absence of periphyses, rarely branched and apically hardly thickened paraphyses, asci and a hymenium that
Paul Diederich; Javier ETAYOJ
Parmelioid lichens comprise about 1500 species and have a worldwide distribution. Numerous species are widely distributed and well known, including important bioindicators for atmospheric pollution. The phylogeny and classification of parmelioid lichens has been a matter of debate for several decades. Previous studies using molecular data have helped to establish hypotheses of the phylogeny of certain clades within this group.
Oscar Blanco; Ana Crespo; Richard H. Ree; H. Thorsten Lumbsch
A phylogenetic analysis of the 5.8S rDNA and internal transcribed spacer (ITS1 and ITS2) sequences from some entomogenous Paecilomyces species supports the polyphyly of the genus and showed the existence of cryptic spe- cies. In the Eurotiales, anamorphs Paecilomyces variotii and Paecilomyces leycettanus were related to the teleomorphs Talaromyces and Thermoascus. In the Hypocreales, three major ITS subgroups were found,
Peter W. Inglis; Myrian S. Tigano
The evolutionary history of gains and losses of vegetative reproductive propagules (soredia) in Porpidia s.l., a group of lichen-forming ascomycetes, was clarified using Bayesian Markov chain Monte Carlo (MCMC) approaches to monophyly tests and a combined MCMC and maximum likelihood approach to ancestral character state reconstructions. The MCMC framework provided confidence estimates for the reconstructions of relationships and ancestral character
Jutta Buschbom; Daniel Barker
The entomopathogenic fungus Beauveria bassiana was established in coffee seedlings after fungal spore suspensions were applied as foliar sprays, stem injections, or soil drenches. Direct injection yielded the highest post-inoculation recovery of endophytic B. bassiana. Establishment, based on percent recovery of B. bassiana, decreased as time post-inoculation increased in all treatments. Several other endophytes were isolated from the seedlings and
Francisco Posada; M. Catherine Aime; Stephen W. Peterson; Stephen A. Rehner; Fernando E. Vega
A phylogenetic study of the lichen family Graphidaceae is presented. Most genera of the family, as well as selected representatives of the closely related Thelotremataceae, are included. The results of the Bayesian analysis of combined mt SSU and nuLSU rDNA sequence data were compared with recently introduced concepts of genera. Species of Fissurina and Dyplolabia form a monophyletic group in
Bettina Staiger; Klaus Kalb; Martin Grube
Fulgensia Massal. & De Not. is a widespread genus with considerable morphological and ecological heterogeneity across species. For this reason, the taxonomic delimitation of this genus has been controversial. Relationships among species of Fulgensia, Caloplaca Th. Fr., and Xanthoria (Fr.) Th. Fr. (Lecanorales) were investigated based on a comprehensive phylogenetic analysis of 62 DNA sequences from the nuclear ribosomal internal
ESTER GAYA; F. Lutzoni; STEFAN ZOLLER; P. Navarro-Rosines
To provide a comprehensive molecular phylogeny for peltigeralean fungi and to establish a classification based on monophyly, phylogenetic analyses were carried out on sequences from the nuclear ribosomal large (LSU) and small (SSU) subunits obtained from 113 individuals that represent virtually all main lineages of ascomycetes. Analyses were also conducted on a subset of 77 individuals in which the ingroup
JOLANTA MIADLIKOWSKA; F. Lutzoni
The phylogeny of the lichen family Candelariaceae was investigated using nucleotide sequences from the ITS region of the nu-rDNA. Twenty-three species of Candelariella, six species of Candelaria, two species of Candelina and two species of Placomaronea were included in the study. Acarospora cervina and Pleopsidium chlorophanum were used as outgroup species. The phylogenetic analyses were performed using MP and Bayesian
Martin Westberg; Ulf Arup; Ingvar Kärnefelt
Pentachlorophenol (PCP) bioremediation by the fungal strains amongst the cork-colonising community has not yet been analysed.\\u000a In this paper, the co- and direct metabolism of PCP by each of the 17 fungal species selected from this community were studied.\\u000a Using hierarchical data analysis, the isolates were ranked by their PCP bioremediation potential. Fifteen isolates were able\\u000a to degrade PCP under
Mariana B. Carvalho; Isabel Martins; Maria C. Leitão; Helga Garcia; Cátia Rodrigues; Vitória San Romão; Iain McLellan; Andrew Hursthouse; Cristina Silva Pereira
Pentachlorophenol (PCP) bioremediation by the fungal strains amongst the cork-colonising community has not yet been analysed. In this paper, the co- and direct metabolism of PCP by each of the 17 fungal species selected from this community were studied. Using hierarchical data analysis, the isolates were ranked by their PCP bioremediation potential. Fifteen isolates were able to degrade PCP under co-metabolic conditions, and surprisingly Chrysonilia sitophila, Trichoderma longibrachiatum, Mucor plumbeus, Penicillium janczewskii and P. glandicola were able to directly metabolise PCP, leading to its complete depletion from media. PCP degradation intermediates are preliminarily discussed. Data emphasise the significance of these fungi to have an interesting potential to be used in PCP bioremediation processes. PMID:19543759
Carvalho, Mariana B; Martins, Isabel; Leitão, Maria C; Garcia, Helga; Rodrigues, Cátia; San Romão, Vitória; McLellan, Iain; Hursthouse, Andrew; Silva Pereira, Cristina
Neonectria is a cosmopolitan genus and it is, in part, defined by its link to the anamorph genus Cylindrocarpon. Neonectria has been divided into informal groups on the basis of combined morphology of anamorph and teleomorph. Previously, Cylindrocarpon was divided into four groups defined by presence or absence of microconidia and chlamydospores. Molecular phylogenetic analyses have indicated that Neonectria sensu stricto and Cylindrocarpon sensu stricto are phylogenetically congeneric. In addition, morphological and molecular data accumulated over several years have indicated that Neonectria sensu lato and Cylindrocarpon sensu lato do not form a monophyletic group and that the respective informal groups may represent distinct genera. In the present work, a multilocus analysis (act, ITS, LSU, rpb1, tef1, tub) was applied to representatives of the informal groups to determine their level of phylogenetic support as a first step towards taxonomic revision of Neonectria sensu lato. Results show five distinct highly supported clades that correspond to some extent with the informal Neonectria and Cylindrocarpon groups that are here recognised as genera: (1) N. coccinea-group and Cylindrocarpon groups 1 & 4 (Neonectria/Cylindrocarpon sensu stricto); (2) N. rugulosa-group (Rugonectria gen. nov.); (3) N. mammoidea/N. veuillotiana-groups and Cylindrocarpon group 2 (Thelonectria gen. nov.); (4) N. radicicola-group and Cylindrocarpon group 3 (Ilyonectria gen. nov.); and (5) anamorph genus Campylocarpon. Characteristics of the anamorphs and teleomorphs correlate with the five genera, three of which are newly described. New combinations are made for species where their classification is confirmed by phylogenetic data.
Chaverri, P.; Salgado, C.; Hirooka, Y.; Rossman, A.Y.; Samuels, G.J.
Parmelioid lichens comprise about 1500 species and have a worldwide distribution. Numerous species are widely distributed and well known, including important bioindicators for atmospheric pollution. The phylogeny and classification of parmelioid lichens has been a matter of debate for several decades. Previous studies using molecular data have helped to establish hypotheses of the phylogeny of certain clades within this group. In this study, we infer the phylogeny of major clades of parmelioid lichens using DNA sequence data from two nuclear loci and one mitochondrial locus from 145 specimens (117 species) that represent the morphological and chemical diversity in these taxa. Parmelioid lichens are not monophyletic; however, a core group is strongly supported as monophyletic, excluding Arctoparmelia and Melanelia s. str., and including Parmeliopsis and Parmelaria. Within this group, seven well-supported clades are found, but the relationships among them remain unresolved. Stochastic mapping on a MC/MCMC tree sampling was employed to infer the evolution of two morphological and two chemical traits believed to be important for the evolutionary success of these lichens, and have also been used as major characters for classification. The results suggest that these characters have been gained and lost multiple times during the diversification of parmelioid lichens. PMID:16481204
Blanco, Oscar; Crespo, Ana; Ree, Richard H; Lumbsch, H Thorsten
Anatomical information on most lichen species, including Parmeliaceae species, is scarce and superficial. This is partially due to the technical difficulties found during the preparation of samples and sections suitable for optical microscopy analysis. There is a lack of pictures of anatomical sections as well as detailed anatomical protocols related to the sample processing made by specialized plant anatomists in literature. This work aimed to look for a standardized histological technique and to develop a protocol for histological studies of foliose Parmeliaceae under light microscopy. Four common pantropical species of Parmeliaceae, abundant in the Brazilian cerrado vegetation, were processed in several ways in relation to fixing and inclusion media, sectioning thicknesses, and staining, including both fresh and 2-year-old herbarium specimens. The best technique found for anatomical studies of Parmeliaceae under light microscopy is represented by 2 or 3 microm thick sections of fresh or herbarium samples, desiccated and fixed in FAA 50, infiltrated and embedded in glycol-methacrylate resin (Leica), and stained by Toluidine Blue or Methylene Blue. PMID:18977150
Barbosa, Suzana Bissacot; Marcelli, Marcelo Pinto; Machado, Silvia Rodrigues
Background and Aims Phenotypic variability is a successful strategy in lichens for colonizing different habitats. Vagrancy has been reported as a specific adaptation for lichens living in steppe habitats around the world. Among the facultatively vagrant species, the cosmopolitan Cetraria aculeata apparently forms extremely modified vagrant thalli in steppe habitats of Central Spain. The aim of this study was to investigate whether these changes are phenotypic plasticity (a single genotype producing different phenotypes), by characterizing the anatomical and ultrastructural changes observed in vagrant morphs, and measuring differences in ecophysiological performance. Methods Specimens of vagrant and attached populations of C. aculeata were collected on the steppes of Central Spain. The fungal internal transcribed spacer (ITS), glyceraldehyde-3-phosphate dehydrogenase (GPD) and the large sub-unit of the mitochondrial ribosomal DNA (mtLSUm), and the algal ITS and actin were studied within a population genetics framework. Semi-thin and ultrathin sections were analysed by means of optical, scanning electron and transmission electron microscopy. Gas exchange and chlorophyll fluorescence were used to compare the physiological performance of both morphs. Key Results and Conclusions Vagrant and attached morphs share multilocus haplotypes which may indicate that they belong to the same species in spite of their completely different anatomy. However, differentiation tests suggested that vagrant specimens do not represent a random sub-set of the surrounding population. The morphological differences were related to anatomical and ultrastructural differences. Large intercalary growth rates of thalli after the loss of the basal–apical thallus polarity may be the cause of the increased growth shown by vagrant specimens. The anatomical and morphological changes lead to greater duration of ecophysiological activity in vagrant specimens. Although the anatomical and physiological changes could be chance effects, the genetic differentiation between vagrant and attached sub-populations and the higher biomass of the former show fitness effects and adaptation to dry environmental conditions in steppe habitats.
Perez-Ortega, Sergio; Fernandez-Mendoza, Fernando; Raggio, Jose; Vivas, Mercedes; Ascaso, Carmen; Sancho, Leopoldo G.; Printzen, Christian; de los Rios, Asuncion
Lichen-forming ascomycetes exhibit often complex morphologies of the vegetative thallus that are usually not found in non-lichenized fungi. This includes the thallus organization and appendical structures associated with the main thallus, such as cilia and rhizines. Such morphological characters are widely employed in the taxonomy of parmelioid lichens, especially at generic level. Within parmelioid lichens, several monophyletic groups can be distinguished, the Hypotrachyna clade being one of them, which includes mostly tropical taxa. In this first molecular study focused specifically on the Hypotrachyna clade, we used maximum parsimony and Bayesian analyses of a combined data set of nuclear ITS and mitochondrial SSU rDNA sequences to (1) test the monophyly of genera presently accepted within the clade and (2) evaluate the phylogenetic value of the morphological characters used to circumscribe genera in parmelioid lichens. Out of the 89 mtSSU and 88 nuITS sequences included in the present study, 121 sequences were newly obtained. Our results show that the taxa within the clade fall into two major groups and that the genus Hypotrachyna is polyphyletic. Everniastrum and Parmelinopsis are nested within Hypotrachyna sensu stricto, the latter being also polyphyletic. Bulbothrix is paraphyletic with Parmelinella nested within and is basal to the second major Hypotrachyna clade. Monophylies of Bulbothrix and Hypotrachyna are significantly rejected. The phylogenetic analysis demonstrates that morphological characters currently used to circumscribe genera in parmelioid lichens, such as cortical anatomy, lobe configuration, cilia, and rhizines have been overestimated and have only minor value in identifying monophyletic groups. PMID:16647864
Divakar, Pradeep K; Crespo, Ana; Blanco, Oscar; Lumbsch, H Thorsten
We performed a taxonomic study on two species of the genus Bryoria from the Sino-Himalayas, SW-China. B. nadvornikiana is new to China and B. furcellata is new to Yunnan and Sichuan provinces in the Sino-Himalayas. Morphology, habitat, distributions and chemistry of the two species are discussed.
Wang, Li-song; Harada, Hiroshi; Koh, Young Jin
Seventy-two lichen specimens of Cetrelia collected in South Korea since 2003 were examined by both phenotypic and phylogenetic analyses. The phenotypic analysis was based on morphological and chemical characters, and the phylogenetic analysis was based on nrDNA ITS sequences. The result suggested that the presence and absence of isidia, soredia, lobules and medullar reaction C+ or C- are the important characters in the taxonomy of this genus. Four species of Cetrelia, C. chicitae, C. braunsiana, C. japonica, and C. pseudolivetorum have been identified in this study. Description of each species is presented with morphological and chemical characters. A key to the Cetrelia species is also presented.
Luo, Heng; Wei, Xin Li; Han, Keon Seon; Koh, Young Jin
We performed a taxonomic study on two species of the genus Bryoria from the Sino-Himalayas, SW-China. B. nadvornikiana is new to China and B. furcellata is new to Yunnan and Sichuan provinces in the Sino-Himalayas. Morphology, habitat, distributions and chemistry of the two species are discussed. PMID:24049496
Wang, Li-Song; Harada, Hiroshi; Koh, Young Jin; Hur, Jae-Seoun
Conventional techniques for structural studies under light microscope were employed to describe and compare the upper cortex anatomy in three species groups of Parmotrema sensu lato. This study indicates that there is a pattern in the structure of the upper cortex in all the three groups of Parmotrema species studied here, and this pattern can be used to place each species group separately within the genus Parmotrema. Although the species of Parmotrema studied have palisade prosoplectenchymatous upper cortex, there are clear differences between the analyzed groups. The upper cortex of Parmotrema s. str. can be characterized by more elongated cells and very compressed hyphae with small interstices between them; the upper cortex of the species with reticular maculae is characterized by the presence of maculae produced by the organization of hyphae that rise towards to the upper cortex and that are not so compressed, while the upper cortex of the species with dimorphic rhizinae has less elongated almost-rounded cells without interstices or cracks but is generally accompanied by aeroplectenchyma. Besides, the first cell layer of the upper cortex presents differential staining by toluidine blue and the epicortex is tightly attached to it. PMID:20542705
Barbosa, Suzana Bissacot; Marcelli, Marcelo Pinto
Three species of Coccocarpia have been reported from Korean Peninsular. However, there was no revisional study on this genus before. After careful examination of the specimens deposited in the Korean Lichen Research Institute (KoLRI) and collected from main mountain areas of Korea, two species of Coccocarpia, C. palmicola and C. erythroxyli, have been revealed to occur and confirmed in South Korea. The presence and absence of isidia and apothecia are the most important characters for the South Korean species. We provide the detailed description and illustration of the available two species. A key to the species is also provided.
Wang, Xin Yu; Wei, Xin Li; Han, Keon Seon; Koh, Young Jin
in this issue; and Bidartondo et al.: High root concentration and uneven ectomycorrhizal diversity near Sarcodes sanguinea(Ericaceae): a cheater that stimulates its victims?, 87/12/1783"">pp. 17831788 in this issue. Photo credit: Dirk Redecker.
Mohamed A. Abdel-Wahab (City University of Hong Kong, Department of Biology and Chemistry ADR;POSTAL); Patrik Inderbitzen (University of British Columbia;Department of Botany ADR;POSTAL)
Background Nodulisporic acids (NAs) are indole diterpene fungal metabolites exhibiting potent systemic efficacy against blood-feeding arthropods, e.g., bedbugs, fleas and ticks, via binding to arthropod specific glutamate-gated chloride channels. Intensive medicinal chemistry efforts employing a nodulisporic acid A template have led to the development of N-tert-butyl nodulisporamide as a product candidate for a once monthly treatment of fleas and ticks on companion animals. The source of the NAs is a monophyletic lineage of asexual endophytic fungal strains that is widely distributed in the tropics, tentatively identified as a Nodulisporium species and hypothesized to be the asexual state of a Hypoxylon species. Methods and Results Inferences from GenBank sequences indicated that multiple researchers have encountered similar Nodulisporium endophytes in tropical plants and in air samples. Ascomata-derived cultures from a wood-inhabiting fungus, from Martinique and closely resembling Hypoxylon investiens, belonged to the same monophyletic clade as the NAs-producing endophytes. The hypothesis that the Martinique Hypoxylon collections were the sexual state of the NAs-producing endophytes was tested by mass spectrometric analysis of NAs, multi-gene phylogenetic analysis, and phenotypic comparisons of the conidial states. We established that the Martinique Hypoxylon strains produced an ample spectrum of NAs and were conspecific with the pantropical Nodulisporium endophytes, yet were distinct from H. investiens. A new species, H. pulicicidum, is proposed to accommodate this widespread organism. Conclusions and Significance Knowledge of the life cycle of H. pulicicidum will facilitate an understanding of the role of insecticidal compounds produced by the fungus, the significance of its infections in living plants and how it colonizes dead wood. The case of H. pulicicidum exemplifies how life cycle studies can consolidate disparate observations of a fungal organism, whether from environmental sequences, vegetative mycelia or field specimens, resulting in holistic species concepts critical to the assessment of the dimensions of fungal diversity.
Bills, Gerald F.; Gonzalez-Menendez, Victor; Martin, Jesus; Platas, Gonzalo; Fournier, Jacques; Persoh, Derek; Stadler, Marc
Mycosphaerella punctiformis, the type species of the genus Mycosphaerella, is epitypified by material collected on Quercus robur in The Netherlands. The teleomorph is described in planta, and the Ramularia anamorph, for which the new name R. endophylla is proposed, and the Asteromella spermatial state are characterized in vitro. Sequence data of the nuclear ribosomal DNA are presented and analyzed together with other Mycosphaerella spp. with Ramularia and several other anamorphs. Several strains originating from Quercus, Acer and Tilia showed diverging ITS sequences, indicating that the M. punctiformis complex may comprise more than a single phylogenetic species, but this could not be confirmed by the analysis of our dataset. An endophytic phase is established for the first time in the life-cycle of M. punctiformis, as the species was repeatedly isolated from surface sterilized green healthy leaves of Quercus robur in summer at the epitype locality. PMID:15587478
Verkley, Gerard J M; Crous, Pedro W; Groenewald, J Z; Braun, Uwe; Aptroot, André
The Cladia aggregata complex is one of the phenotypically most variable groups in lichenized fungi, making species determination difficult and resulting in different classifications accepting between one to eight species. Multi-locus DNA sequence data provide an avenue to test species delimitation scenarios using genealogical and coalescent methods, employing gene and species trees. Here we tested species delimitation in the complex using molecular data of four loci (nuITS and IGS rDNA, protein-coding GAPDH and Mcm-7), including 474 newly generated sequences. Using a combination of ML and Bayesian gene tree topologies, species tree inferences, coalescent-based species delimitation, and examination of phenotypic variation we assessed the circumscription of lineages. We propose that results from our analyses support a 12 species delimitation scenario, suggesting that there is a high level of species diversity in the complex. Morphological and chemical characters often do not characterize lineages but show some degree of plasticity within at least some of the clades. However, clades can often be characterized by a combination of several phenotypical characters. In contrast to the amount of homoplasy in the morphological characters, the data set exhibits some geographical patterns with putative species having distribution patterns, such as austral, Australasian or being endemic to Australia, New Zealand or Tasmania.
Parnmen, Sittiporn; Rangsiruji, Achariya; Mongkolsuk, Pachara; Boonpragob, Kansri; Nutakki, Aparna; Lumbsch, H. Thorsten
Historical and contemporary geographical distribution ranges with their associated gene flow patterns interact to produce the genetic diversity observed today. Often it is not possible to separate out the impacts of historical events, e.g. past fragmentation, and contemporary gene flow, e.g. long-distance dispersal. Porpidia flavicunda is a lichen-forming ascomycete occurring circumpolar in the boreal to arctic zones for which vegetation history suggests that its distribution pattern has stayed broadly the same over the past millennia. DNA-sequence diversity in P. flavicunda can, thus, be expected to predominantly represent geographical population differentiation and its contemporary migration rates. The population sample consists of 110 specimens collected in Northern Québec, Baffin Island, Western Greenland and Northern Scandinavia. DNA-sequence data sets of three nuclear gene fragments (LSU, RPB2 and beta-tubulin) were analysed for genetic diversity within, and differentiation between, geographical regions. Tests of population subdivision employing analyses of molecular variance and exact tests of haplotype frequency distributions showed significant structure between the geographical regions. However, the lack of fixed nucleotide polymorphisms and the wide sharing of identical haplotypes between geographical regions suggest recurrent long-distance gene flow of propagules. Still, the means by which propagules are dispersed remain to be discovered. Inference of migration rates shows that in many cases a sufficiently high amount of migrants is exchanged between geographical regions to prevent drastic population differentiation through genetic drift. The observed haplotype distributions and migration rates point to a gene flow model of isolation by distance. PMID:17444896
Previous genealogical analyses of population structure in Coccidioides immitis revealed the presence of two cryptic and sexual species in this pathogenic fungus but did not clarify their origin and relationships with respect to other taxa. By combining the C. immitis data with those of two of its closest relatives, the free-living saprophytes Auxarthron zuffianumand Uncinocarpus reesii, we show that the
Vassiliki Koufopanou; Austin Burt; Timothy Szaro; John W. Taylor
Fraxinus excelsior, common ash native to Europe, is threatened by a recently identified pathogenic fungus Chalara fraxinea, which causes extensive damage on ash trees across Europe. In Denmark, most stands are severely affected leaving many trees with dead crowns. However, single trees show notably fewer symptoms. In this study, the impact of the emerging infectious disease on native Danish ash trees is assessed by estimating presence of inherent resistance in natural populations. Disease symptoms were assessed from 2007 to 2009 at two different sites with grafted ramets of 39 selected clones representing native F. excelsior trees. A strong genetic variation in susceptibility to C. fraxinea infections was observed. No genetic or geographic structure can explain the differences, but strong genetic correlations to leaf senescence were observed. The results suggest that a small fraction of trees in the Danish population of ash possess substantial resistance against the damage. Though this fraction is probably too low to avoid population collapse in most natural or managed ash forests, the observed presence of putative resistance against the emerging infectious disease in natural stands is likely to be of evolutionary importance. This provides prospects of future maintenance of the species through natural or artificial selection in favour of remaining healthy individuals.
McKinney, L V; Nielsen, L R; Hansen, J K; Kjaer, E D
The minisatellite locus, BbMin1, was isolated from a partial Beauveria bassiana genomic library that con- sisted of poly(GA) flanked inserts. Polymerase chain reaction (PCR) of the BbMin1 repeat demonstrated allele size variation among 95 B. bassiana isolates. Amplification was also observed from single isolates of Beauveria amorpha, Beauveria brongniartii, and Beauveria caledonica. Eight alleles were identified at the haploid locus,
Brad S. Coates; Richard L. Hellmich; Leslie C. Lewis
During 2002–2006, nymph bands of Locusta migratoria manilensis (Meyen) were treated by ground and aerial applications in 6000ha of grasslands and the nearby beach of Yellow river using a soybean oil miscible suspension ULV formulation of Metarhizium anisopliae var. acridum isolate CQMa102. The formulation was also applied in Tianjin, Henan, Hebei, Shandong and Shanxi provinces of Northern China by ground
Guoxiong Peng; Zhongkang Wang; Youping Yin; Dengyu Zeng; Yuxian Xia
Ancestral state reconstructions of morphological or ecological traits on molecular phylogenies are becoming in- creasingly frequent. They rely on constancy of character state change rates over trees, a correlation between neutral genetic change and phenotypic change, as well as on adequate likelihood models and (for Bayesian methods) prior distributions. This investigation explored the outcomes of a variety of methods for
S TEFAN EKMAN; HEIDI L. ANDERSEN; MATS WEDIN
The fungal entomopathogen Beauveria bassiana became established as an endophyte in coffee seedlings grown in vitro and inoculated with B. bassiana suspensions in the radicle. The fungus was recovered as an endophyte 30 and 60 days postinoculation, from stems, leaves,\\u000a and roots, and at 60 days postinoculation one of the isolates was also recovered as an epiphyte. Fusarium sp., Rhodotorula
Francisco Posada; Fernando E. Vega
A molecular phylogenetic analysis of rDNA was performed for seven Caloplaca, seven Xanthoria, one Fulgensia and five outgroup species. Phylogenetic hypotheses are constructed based on nuclear small and large subunit rDNA, separately and in combination. Three strongly supported major monophyletic groups were revealed within the Teloschistaceae. One group represents the Xanthoria fallax-group. The second group includes three subgroups: (1) X.
Ulrik Søchting; François Lutzoni
The fungal entomopathogen Beauveria bassiana became established as an endophyte in in vitro-grown cocoa seedlings tested for up to 2 mo after inoculation to the radicle with B. bassiana suspensions. The fungus was recovered in culture from stems, leaves and roots. B. bassiana also was detected as an epiphyte 1 and 2 mo postinoculation. Penicillium oxalicum and five bacterial morphospecies
Francisco Posada; Fernando E. Vega
Laboulbenia littoralis is described from the halobiont Cafius xantholoma (Coleoptera, Staphylinidae); it previously was misidentified and not properly documented. Morphologically the new species belongs to a group of carabidicolous taxa similar to Laboulbenia pedicellata and especially Laboulbenia slackensis. It is generally accepted that the specificity of Laboulbeniales is based on their need for substances from the host. In this relatively strict context, shifts between unrelated hosts are difficult to explain. We present morphological and ecological evidence supporting the hypothesis that these fungi are capable of shifting between unrelated hosts as long as they share the same habitat. Adaptation to a particular environment, combined with a reduced dependence from specific nutrients of the host, explains the proposed interfamilial host shift. PMID:24871602
De Kesel, André; Haelewaters, Danny
A multi-locus phylogenetic study of the order Arthoniales is presented here using the nuclear ribosomal large subunit (nuLSU), the second largest subunit of RNA polymerase II (RPB2) and the mitochondrial ribosomal small subunit (mtSSU). These genes were sequenced from 43 specimens or culture isolates representing 33 species from this order, 16 of which were from the second largest genus, Opegrapha.
Damien Ertz; Jolanta Miadlikowska; François Lutzoni; Steven Dessein; Olivier Raspé; Nathalie Vigneron; Valérie Hofstetter; Paul Diederich
Mycosphaerella punctiformis, the type species of the genus Mycosphaerella, is epitypified by material collected on Quercus robur in The Netherlands. The teleomorph is described in planta, and the Ramularia anamorph, for which the new name R. endophylla is proposed, and the Asteromella spermatial state are characterized in vitro. Sequence data of the nuclear ribosomal DNA are presented and analyzed together
Gerard J. M. Verkley; Pedro W. Crous; Uwe Braun; André Aptroot
Leaves of oak trees are often infected by various pathogenic fungi. As it is difficult to remove such organisms quantitatively from the leaf surface and as it is often impossible to grow these organisms independently from their host, there are almost no molecular data available from these oak leaf specific pathogens. For the quantitative removal of the microorganisms a procedure
Thomas Heuser; Wolfgang Zimmer
The purpose of this study was to investigate the natural relationships within the large bitunicate order Pleosporales, with special focus on the coprophilous families Delitschiaceae, Phaeotrichaceae and Sporormiaceae. Parsimony and Bayesian analyses were performed using nSSU, nLSU and mtSSU rDNA sequence data. We also investigated the placement of a number of taxa with uncertain position. Our results showed that Pleosporales,
Åsa Kruys; Ove E. Eriksson; Mats Wedin
Biogeographical studies of lichens used to be complicated because of the large distribution ranges of many species. Molecular systematics has revitalized lichen biogeography by improving species delimitation and providing better information about species range limitations. This study focuses on the major clade of tropical parmelioid lichens, which share a chemical feature, the presence of isolichenan in the cell wall, and a morphological feature, microscopic pores in the uppermost layer. Our previous phylogenetic studies revealed that the largest genus in this clade, Hypotrachyna, is polyphyletic with a clade mainly distributed in South and East Asia clustering distant from the core of the genus. To divide the Hypotrachyna clade into monophyletic groups and to reevaluate morphological and chemical characters in a phylogenetic context, we sampled ITS, nuclear large subunit (nuLSU) and mitochondrial small subunit (mtSSU) rDNA sequences from 77 species. We are erecting the new genus Remototrachyna for a core group of 15 former Hypotrachyna species. The segregation of Remototrachyna from Hypotrachyna receives support from morphological and chemical data, as well from maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses of the DNA. We used a likelihood approach to study the geographic range evolution of Remototrachyna and Bulbothrix, which are sister groups. This analysis suggests that the ancestral range of Remototrachyna was restricted to India and that subsequent long-distance dispersal is responsible for the pantropical occurrence of two species of Remototrachyna. PMID:21622420
Divakar, Pradeep K; Lumbsch, H Thorsten; Ferencova, Zuzana; Del Prado, Ruth; Crespo, Ana
Lichens are a prominent feature of northern conifer forests and a large number of species are thought to be circumboreal. Whether or not circumboreal lichen species really constitute monophyletic groups has seldom been tested. We investigated molecular phylogenetic patterns in the mycobiont of Mycoblastus sanguinarius, a well known epiphytic lichen species of the boreal forest, based on material collected from across the high latitude northern hemisphere. A three-locus dataset of internal transcribed spacer rDNA, translation elongation factor 1-? and replication licensing factor Mcm7 DNA sequences revealed that material treated until now as belonging to M. sanguinarius does indeed form a monophyletic group within the genus and is distinct from a strongly supported Mycoblastus affinis. The M. sanguinarius complex appears closely related to the rare Mycoblastus glabrescens, which is currently known only from the Pacific Northwest and was rediscovered during the present study. However, within M. sanguinarius s.lat. in the northern hemisphere, two deeply divergent and morphologically coherent species can be recovered, one of which matches the southern hemisphere species Mycoblastus sanguinarioides and turns out to be widespread in North America and Asia, and one of which corresponds to M. sanguinarius s.str. Both M. sanguinarius and M. sanguinarioides exhibit additional low-level genetic differentiation into geographically structured clades, the most prominent of which are distributed in East Asia/eastern North America and western North America/Europe, respectively. Individuals from these lowest-level clades are morphologically indistinguishable but chemical analyses by thin layer chromatography revealed that each clade possesses its own fatty acid profile, suggesting that chemical differentiation precedes morphological differentiation and may be a precursor to speciation.
Spribille, Toby; Klug, Barbara; Mayrhofer, Helmut
The species delimitation in fungi is currently in flux. A growing body of evidence shows that the morphology-based species circumscription underestimates the number of existing species. The large and ever growing number of DNA sequence data of fungi makes it possible to use these to identify potential cases of hidden species, which then need to be studied with extensive taxon samplings. We used Parmeliaceae, one of the largest families of lichenized fungi as a model. Intra- and interspecific distances derived from maximum-likelihood phylogenetic trees inferred from 491 nuclear ITS rDNA sequences were examined for five major clades of parmelioid lichens. The intra- and interspecific distances were well separated in most cases allowing the calculation of a threshold, with exceptions of highly deviating distances in a few cases. These situations are shown to be taxa in which the current delimitation needs revision. Thus the analysis of the distance distributions is shown to be a powerful tool for identifying species complexes. PMID:20399873
Del-Prado, Ruth; Cubas, Paloma; Lumbsch, H Thorsten; Divakar, Pradeep K; Blanco, Oscar; de Paz, Guillermo Amo; Molina, M Carmen; Crespo, Ana
Parmeliaceae is the largest family of lichen-forming fungi. In spite of its importance for fungal diversity, its relationships with other families in Lecanorales remain poorly known. To better understand the evolutionary history of the diversification of lineages and species richness in Parmeliaceae it is important to know the phylogenetic relationships of the closest relatives of the family. A recent study based on two molecular loci suggested that either Protoparmelia s. str. or a group consisting of Gypsoplaca and Protoparmelia s. str. were the possible sister-group candidates of Parmeliaceae, but that study could not distinguish between these two alternatives. Here, we used a four-locus phylogeny (nuLSU, ITS, RPB1, MCM7) to reveal relationships of Parmeliaceae with other potential relatives in Lecanorales. Maximum likelihood and Bayesian analyses showed that Protoparmelia is polyphyletic, with Protoparmelia s. str. (including Protoparmelia badia and Protoparmelia picea) being most closely related to Parmeliaceae s. str., while the Protoparmelia atriseda-group formed the sister-group to Miriquidica. Gypsoplaca formed the sister-group to the Parmeliaceae s. str. + Protoparmelia s. str. clade. Monophyly of Protoparmelia as currently circumscribed, and Gypsoplaca as sister-group to Parmeliaceae s. str. were both significantly rejected by alternative hypothesis testing. PMID:24119410
Singh, Garima; Divakar, Pradeep K; Dal Grande, Francesco; Otte, Jürgen; Parnmen, Sittiporn; Wedin, Mats; Crespo, Ana; Lumbsch, H Thorsten; Schmitt, Imke
Three new genera are established in the Sordariomycetidae based on morphological and molecular data (SSU and LSU nrDNA) to accommodate five ascomycete species collected from submerged woody debris in freshwater habitats from Costa Rica. The genus Bullimyces contains three new species, B. communis, B. costaricensis and B. aurisporus. Bullimyces is characterized by globose to subglobose, membranous, black, ostiolate ascomata; deliquescent, hyaline, globose cells that fill the center of the centrum; unitunicate asci that deliquesce early in some species; and septate, thick-walled ascospores with or without gelatinous sheaths or appendages. Bullimyces species form a well supported clade with 100% bootstrap support, but the position of the genus in the Sordariomycetidae remains unclear. The second genus, Riomyces, is represented by a single species, R. rotundus. Riomyces is characterized by globose to subglobose, membranous, black, ostiolate ascomata, unitunicate, cylindrical asci, hyaline, globose cells that fill the hamathecium and septate, thick-walled ascospores with a gelatinous sheath. Although Riomyces is morphologically similar to Bullimyces, the two genera did not group together with support in any analysis. The third genus, Hydromelitis, is represented by a single species, H. pulchella. Hydromelitis is characterized by pyriform, membranous, black, ostiolate ascomata, unitunicate asci lacking an apical structure, simple, thin-walled, septate paraphyses and hyaline to golden yellow, multiseptate, thick-walled ascospores with a gelatinous sheath. Bullimyces, Riomyces and Hydromelitis were nested within an unsupported clade consisting of members of the Ophiostomatales, Magnaporthales and freshwater Annulatacaceae sensu lato and sensu stricto. PMID:22453118
Ferrer, Astrid; Miller, Andrew N; Sarmiento, Carolina; Shearer, Carol A
Entomopathogenic fungi (EPF) are commonly found in diverse habitats and are known to cause mycoses in many different taxa of arthropods. Various unexpected roles have been recently reported for fungal entomopathogens, including their presence as fungal endophytes, plant disease antagonists, rhizosphere colonizers and plant growth promoting fungi. In Tunisia, a wide range of indigenous EPF isolates from different species, such as Beauveria bassiana and Bionectria ochroleuca, were found to occur in the soil, and to be pathogenic against the artichoke aphid Capitophorus elaeagni (Hemiptera: Aphididae). Since endophytic fungi are recently regarded as plant-defending mutualists and their presence in internal plant tissue has been discussed as an adaptive protection against insects, we were interested on elucidating the possible endophytic behavior of B. bassiana and B. ochroleuca on artichoke, Cynara scolymus, after foliar spraying tehcnique. The leaf spray inoculation method was effective in introducing the inoculated fungi into the plant tissues and showed, then, an endophytic activity on artichoke even 10days later. According S-N-K test, there was significant differences between the two fungal treatments, B. ochroleuca (84% a) and B. bassiana (78% a), and controls (0% b). Likewise, the inoculated entomopathogenic fungi were also isolated from new leaves even though with significant differences respectively between controls (0% c), B. bassiana (56% b) and B. ochroleuca (78% a). These results reveals significant new data on the interaction of inoculated fungi with artichoke plant as ecological roles that can be exploited for the protection of plants. PMID:24681358
Guesmi-Jouini, J; Garrido-Jurado, I; López-Díaz, C; Ben Halima-Kamel, M; Quesada-Moraga, E
The Basidiomycota Agrocybe aegerita (Aa) mitochondrial cox1 gene (6790 nucleotides), encoding a protein of 527aa (58?377Da), is split by four large subgroup IB introns possessing site-specific endonucleases assumed to be involved in intron mobility. When compared to other fungal COX1 proteins, the Aa protein is closely related to the COX1 one of the Basidiomycota Schizophyllum commune (Sc). This clade reveals
Patrice Gonzalez; Gérard Barroso; Jacques Labarère
Bark and ambrosia beetles are ecologically and economically important phloeophagous insects that often have complex symbiotic relationships with fungi and mites. These systems are greatly understudied in Africa. In the present study we identified bark and ambrosia beetles, their phoretic mites and their main fungal associates from native Virgilia trees in the Cape Floristic Region (CFR) of South Africa. In addition, we tested the ability of mites to feed on the associated fungi. Four species of scolytine beetles were collected from various Virgilia hosts and from across the CFR. All were consistently associated with various Geosmithia species, fungi known from phloeophagous beetles in many parts of the world, but not yet reported as Scolytinae associates in South Africa. Four beetle species, a single mite species and five Geosmithia species were recovered. The beetles, Hapalogenius fuscipennis, Cryphalini sp. 1, and Scolytoplatypus fasciatus were associated with a single species of Elattoma phoretic mite that commonly carried spores of Geosmithia species. Liparthrum sp. 1 did not carry phoretic mites. Similar to European studies, Geosmithia associates of beetles from Virgilia were constant over extended geographic ranges, and species that share the same host plant individual had similar Geosmithia communities. Phoretic mites were unable to feed on their Geosmithia associates, but were observed to feed on bark beetle larvae within tunnels. This study forms the first African-centred base for ongoing global studies on the associations between arthropods and Geosmithia species. It strengthens hypotheses that the association between Scolytinae beetles and dry-spored Geosmithia species may be more ubiquitous than commonly recognised. PMID:24863476
Machingambi, Netsai M; Roux, Jolanda; Dreyer, Léanne L; Roets, Francois
Within the last decade, molecular methods have revealed the relationships in many groups of lichenized Ascomycetes. However,\\u000a the published phylogenies were often contradictory with respect to higher taxonomic levels. To achieve a more convincing overall\\u000a picture of phylogenetic relationships of and within the Lecanoromycetes, we set up an alignment of all publicly available\\u000a SSU nrDNA sequences of the Pezizomycotina, discarded
Derek Peršoh; Andreas Beck; Gerhard Rambold
Pathogenicity of fungal isolates (Ascomycota: Hypocreales) against Peregrinus maidis , Delphacodes kuscheli (Hemiptera: Delphacidae), and Dalbulus maidis (Hemiptera: Cicadellidae), vectors of corn diseases
Preliminary screening assays were carried out on 17 isolates from five fungal species Beauveria bassiana, Lecanicillium muscarium, Metarhizium anisopliae, Isaria farinosa, and I. fumosorosea. The three most effective isolates against Peregrinus maidis (Hemiptera: Delphacidae) were B. bassiana CEP 147, CEP 150, and CEP 189. There were no consistent differences found in males and females regarding fungal susceptibility.\\u000a However, more females
Andrea Vanesa Toledo; Ana M. Marino de Remes Lenicov; Claudia C. López Lastra
Species of the Neuropogon group in the lichen genus Usnea have their centre of distribution in polar regions of the Southern Hemisphere. Their morphological and chemical variability is poorly understood and several asexual taxa with uncertain relationships to fertile taxa occur in the group. The species concept is controversial. A phylogenetic analysis revealed three related complexes of mainly asexual lineages
Nora Wirtz; Christian Printzen; H. Thorsten Lumbsch
Parmeliaceae is the largest family of lichen-forming fungi with more than 2000 species and includes taxa with different growth forms. Morphology was widely employed to distinguish groups within this large, cosmopolitan family. In this study we test these morphology-based groupings using DNA sequence data from three nuclear and one mitochondrial marker from 120 taxa that include 59 genera and represent
Ana Crespo; H. Thorsten Lumbsch; Jan-Eric Mattsson; Oscar Blanco; Pradeep K. Divakar; Kristina Articus; Elisabeth Wiklund; Paulina A. Bawingan; Mats Wedin
A survey for entomopathogenic fungi of the Chagas disease vector Triatoma infestans was conducted in two provinces of Argentina from March–December 2003. Field-collected insects that died in the laboratory\\u000a were individually maintained in moist chamber and incubated at 22 °C. Triatominae adults infected with the fungus Paecilomyces lilacinus were found at El Quebracho (27°34?S–64°31?W), Santiago del Estero province, Argentina, in December
Gerardo A. Marti; Claudia C. López Lastra; Sebastian A. Pelizza; Juan J. García
Accurate monitoring of an introduced, mass-released microbial control agent is essential in evaluating its persistence and in designing application strategies for insect pest control. As part of our multi-year study on the development and use of the entomopathogenic fungus Beauveria bassiana against the emerald ash borer, a major invasive pest of ash trees, we are determining persistence of the fungus
Louela A. Castrillo; Michael H. Griggs; John D. Vandenberg
In lichen-forming fungi, traditional taxonomical concepts are frequently in conflict with molecular data, and identifying appropriate taxonomic characters to describe phylogenetic clades remains challenging in many groups. The selection of suitable markers for the reconstruction of solid phylogenetic hypotheses is therefore fundamental. The lichen genus Usnea is highly diverse, with more than 350 estimated species, distributed in polar, temperate and tropical regions. The phylogeny and classification of Usnea have been a matter of debate, given the lack of phenotypic characters to describe phylogenetic clades and the low degree of resolution of phylogenetic trees. In this study, we investigated the phylogenetic relationships of 52 Usnea species from across the genus, based on ITS rDNA, nuLSU, and two protein-coding genes RPB1 and MCM7. ITS comprised several highly variable regions, containing substantial genetic signal, but also susceptible to causing bias in the generation of the alignment. We compared several methods of alignment of ITS and found that a simultaneous optimization of alignment and phylogeny (using BAli-phy) improved significantly both the topology and the resolution of the phylogenetic tree. However the resolution was even better when using protein-coding genes, especially RPB1 although it is less variable. The phylogeny based on the concatenated dataset revealed that the genus Usnea is subdivided into four highly-supported clades, corresponding to the traditionally circumscribed subgenera Eumitria, Dolichousnea, Neuropogon and Usnea. However, characters that have been used to describe these clades are often homoplasious within the phylogeny and their parallel evolution is suggested. On the other hand, most of the species were reconstructed as monophyletic, indicating that combinations of phenotypic characters are suitable discriminators for delimitating species, but are inadequate to describe generic subdivisions. PMID:23603312
Truong, Camille; Divakar, Pradeep K; Yahr, Rebecca; Crespo, Ana; Clerc, Philippe
Parmeliaceae is the largest family of lichen-forming fungi with more than 2000 species and includes taxa with different growth forms. Morphology was widely employed to distinguish groups within this large, cosmopolitan family. In this study we test these morphology-based groupings using DNA sequence data from three nuclear and one mitochondrial marker from 120 taxa that include 59 genera and represent the morphological and chemical diversity in this lineage. Parmeliaceae is strongly supported as monophyletic and six well-supported main clades can be distinguished within the family. The relationships among them remain unresolved. The clades largely agree with the morphology-based groupings and only the placement of four of the genera studied is rejected by molecular data, while four other genera belong to clades previously unrecognised. The classification of these previously misplaced genera, however, has already been questioned by some authors based on morphological evidence. These results support morphological characters as important for the identification of monophyletic clades within Parmeliaceae. PMID:17276700
Crespo, Ana; Lumbsch, H Thorsten; Mattsson, Jan-Eric; Blanco, Oscar; Divakar, Pradeep K; Articus, Kristina; Wiklund, Elisabeth; Bawingan, Paulina A; Wedin, Mats
The present taxonomic revision deals with Neotropical species of three entomopathogenic genera that were once included in Hypocrella s. l.: Hypocrella s. str. (anamorph Aschersonia), Moelleriella (anamorph aschersonia-like), and Samuelsia gen. nov (anamorph aschersonia-like). Species of Hypocrella, Moelleriella, and Samuelsia are pathogens of scale insects (Coccidae and Lecaniidae, Homoptera) and whiteflies (Aleyrodidae, Homoptera) and are common in tropical regions. Phylogenetic analyses of DNA sequences from nuclear ribosomal large subunit (28S), translation elongation factor 1-alpha (TEF 1-alpha), and RNA polymerase II subunit 1 (RPB1) and analyses of multiple morphological characters demonstrate that the three segregated genera can be distinguished by the disarticulation of the ascospores and shape and size of conidia. Moelleriella has filiform multi-septate ascospores that disarticulate at the septa within the ascus and aschersonia-like anamorphs with fusoid conidia. Hypocrella s. str. has filiform to long-fusiform ascospores that do not disarticulate and Aschersonia s. str. anamorphs with fusoid conidia. The new genus proposed here, Samuelsia, has filiform to long-fusiform ascospores that do not disarticulate and aschersonia-like anamorphs with small allantoid conidia. In addition, the present study presents and discusses the evolution of species, morphology, and ecology in Hypocrella, Moelleriella, and Samuelsia based on multigene phylogenetic analyses. PMID:18490956
Chaverri, P; Liu, M; Hodge, K T
Species of the Neuropogon group in the lichen genus Usnea have their centre of distribution in polar regions of the Southern Hemisphere. Their morphological and chemical variability is poorly understood and several asexual taxa with uncertain relationships to fertile taxa occur in the group. The species concept is controversial. A phylogenetic analysis revealed three related complexes of mainly asexual lineages arranged around three fertile Usnea species: U. aurantiaco-atra, U. trachycarpa and U. perpusilla. In this study a dataset of 80 specimens was used to resolve species circumscriptions in the U. perpusilla complex. We used a phylogenetic and a haplotype network approach based on three gene fragments (ITS, IGS and RPB1) to detect distinct lineages. To support the hypothesis that these lineages represent different species, we tested for correlation of morphological and chemical characters with hierarchical nested haplotype groups, employing statistical tests of contingency tables and analysis of variance (ANOVA). This cohesion species recognition method detected three fertile U. perpusilla lineages. We could also delimit an undescribed fertile species with yellow apothecia and a new asexual species from the High Andes. Interestingly, there is an additional bipolar species, U. lambii, which was formerly confused with U. sphacelata. The fact that U. lambii shows a geographically disjunct distribution pattern, but the genetic distances among specimens are low, points to recent long-distance dispersal. PMID:18314319
Wirtz, Nora; Printzen, Christian; Lumbsch, H Thorsten
The present taxonomic revision deals with Neotropical species of three entomopathogenic genera that were once included in Hypocrella s. l.: Hypocrella s. str. (anamorph Aschersonia), Moelleriella (anamorph aschersonia-like), and Samuelsia gen. nov (anamorph aschersonia-like). Species of Hypocrella, Moelleriella, and Samuelsia are pathogens of scale insects (Coccidae and Lecaniidae, Homoptera) and whiteflies (Aleyrodidae, Homoptera) and are common in tropical regions. Phylogenetic analyses of DNA sequences from nuclear ribosomal large subunit (28S), translation elongation factor 1-? (TEF 1-?), and RNA polymerase II subunit 1 (RPB1) and analyses of multiple morphological characters demonstrate that the three segregated genera can be distinguished by the disarticulation of the ascospores and shape and size of conidia. Moelleriella has filiform multi-septate ascospores that disarticulate at the septa within the ascus and aschersonia-like anamorphs with fusoid conidia. Hypocrella s. str. has filiform to long-fusiform ascospores that do not disarticulate and Aschersonia s. str. anamorphs with fusoid conidia. The new genus proposed here, Samuelsia, has filiform to long-fusiform ascospores that do not disarticulate and aschersonia-like anamorphs with small allantoid conidia. In addition, the present study presents and discusses the evolution of species, morphology, and ecology in Hypocrella, Moelleriella, and Samuelsia based on multigene phylogenetic analyses.
Chaverri, P.; Liu, M.; Hodge, K.T.
Muscodor albus strain GBA is a newly isolated endophytic fungus from Ginko biloba (family Ginkoaceae) collected in Newport, RI, USA. The cultural characteristics (color, growth pattern) and mycelial\\/hyphal characteristics resemble many isolates of Muscodor albus. The ITS rDNA sequence of the strain has at least 98% similarity with other isolates of M. albus and M. crispans. This xylariaceaous species effectively
Debdulal Banerjee; Gary Strobel; Brad Geary; Joe Sears; David Ezra; Orna Liarzi; James Coombs
Summary The catalogue is based on a comprehensive evaluation of 152 published sources. It includes 624 species (with 4 subspecies and 13 varieties) of lichenized and 17 species of lichenicolous Ascomycota, as well as 9 non-lichenized Ascomycota traditionally included in lichenological literature.
Bilovitz, Peter O.; Mayrhofer, Helmut
Pyrenophora tritici-repentis requires the production of host-selective toxins (HSTs) to cause the disease tan spot of wheat, including Ptr ToxA, Ptr ToxB, and Ptr ToxC. Pyrenophora bromi, the species most closely related to P. tritici-repentis, is the causal agent of brown leaf spot of bromegrass. Because of the relatedness of P. bromi and P. tritici-repentis, we investigated the possibility that
Rachael M. Andrie; Conrad L. Schoch; Rebecca Hedges; Joseph W. Spatafora; Lynda M. Ciuffetti
\\u000a Dual biological control, of both insect pests and plant pathogens, has been reported for the fungal entomopathogens, Beauveria bassiana (Bals.-Criv.) Vuill. (Ascomycota: Hypocreales) and Lecanicillium spp. (Ascomycota: Hypocreales). However, the primary mechanisms of plant disease suppression are different for these fungi.\\u000a Beauveria spp. produce an array of bioactive metabolites, and have been reported to limit growth of fungal plant pathogens
Bonnie H. OwnleyKimberly; Kimberly D. Gwinn; Fernando E. Vega
Dual biological control, of both insect pests and plant pathogens, has been reported for the fungal entomopathogens, Beauveria bassiana (Bals.-Criv.) Vuill. (Ascomycota: Hypocreales) and Lecanicillium spp. (Ascomycota: Hypocreales). However, the primary mechanisms of plant disease suppression are different for these fungi.\\u000a Beauveria spp. produce an array of bioactive metabolites, and have been reported to limit growth of fungal plant pathogens
Bonnie H. OwnleyKimberly; Kimberly D. Gwinn; Fernando E. Vega
Samples of Xylaria humosa, a rare species of Xylariaceae, were collected during an investigation into the diversity of the fungus in the Phu Khieo Wildlife Sanctuary, Thailand. Nine compounds were isolated from the species and their structures elucidated by spectroscopic methods. The compounds were ergosterol (1), ergosterol peroxide (2), two meroterpenoids, chevalone B and C (3-4), together with five indole alkaloids, tryptoquivaline L (5), tryptoquivaline M (6), fiscalin A (7), epi-fiscalin A (8) and epi-fiscalin C (9). Compounds 2-9 exhibited variable cytotoxic activity against KB, NCI-H187 and MCF-7 cell lines. PMID:24689278
Sodngam, Sirirath; Sawadsitang, Sasiphimol; Suwannasai, Nuttika; Mongkolthanaruk, Wiyada
Manganese-containing superoxide dismutases (MnSODs) are ubiquitous metalloenzymes involved in cell defence against endogenous and exogenous reactive oxygen species. In fungi, using this essential enzyme for phylogenetic analysis of Pneumocystis and Ganoderma genera, and of species selected among Ascomycota, Basidiomycota and Zygomycota, provided interesting results in taxonomy and evolution. The role of mitochondrial and cytosolic MnSODs was explored in some pathogenic Basidiomycota yeasts (Cryptococcus neoformans var. grubii, Cryptococcus neoformans var. gattii, Malassezia sympodialis), Ascomycota filamentous fungi (Aspergillus fumigatus), and Ascomycota yeasts (Candida albicans). MnSOD-based phylogenetic and pathogenic data are confronted in order to evaluate the roles of fungal MnSODs in pathophysiological mechanisms. PMID:16055318
Fréalle, Emilie; Noël, Christophe; Viscogliosi, Eric; Camus, Daniel; Dei-Cas, Eduardo; Delhaes, Laurence
Introduction: Botrytis cinerea (teleomorph: Botryotinia fuckeliana) is an airborne plant pathogen with a necrotrophic lifestyle attacking over 200 crop hosts worldwide. Although there are fungicides for its control, many classes of fungicides have failed due to its genetic plasticity. It has become an important model for molecular study of necrotrophic fungi. Taxonomy: Kingdom: Fungi, phylum: Ascomycota, subphylum: Pezizomycotina, class: Leotiomycetes,
BRIAN WILLIAMSON; BETTINA TUDZYNSKI; PAUL TUDZYNSKI; Kan van J. A. L
Laboratory bioassays were conducted to determine host plant effect on pathogenicity of the entomopathogenic fungus Beauveria bassiana (Balsamo) Vuill. (Ascomycota: Hypocreales) to the sweetpotato whitefly, Bemisia tabaci (Gennadius) (Homoptera: Aleyrodidae). Fourth instar B. tabaci reared on cucumber, tomato, melon, green pepper, potato, eggplant, marrow, cabbage, bean or cotton, were treated with 1 × 107 conidia\\/ml B. bassiana EABb 93\\/14-Tp isolate.
Cándido Santiago-Álvarez; Elizabeth Araujo Maranhão; Eduardo Maranhão; Enrique Quesada-Moraga
The ambrosia beetle, Platypus koryoensis, is a serious pest of oak trees in Korea. In this study we investigated filamentous fungi present in the body of the beetle. Fourteen genera of filamentous fungi belonging to Ascomycota and Basidiomycota were isolated. Among the isolated fungi, some were able to produce wood degrading enzymes. This is first report of fungi associated with P. koryoensis.
Suh, Dong Yeon; Hyun, Min Woo; Seo, Sang Tae; Kim, Kyung Hee
Distribution of a polemic in Baltic countries forest disease - snow blight and its agent Phacidium infestans Karst. (Phacidiales, Ascomycota ) are discussed on the base of the investigations carried out during several decades. Baltic countries lie in the zone of southern border of the huge natural distribution area of this fungus. Only occasional damages to the forest nurseries and
Fungi are one of the most diverse groups of Eukarya and play essential roles in terrestrial ecosystems as decomposers, pathogens and mutualists. This study unifies disparate reports of unclassified fungal sequences from soils of diverse origins and anchors many of them in a well-supported clade of the Ascomycota equivalent to a subphylum. We refer to this clade as Soil Clone
Terri M. Porter; Christopher Warren Schadt; L. Rizvi; Andrew P. Martin; Steven K. Schmidt; Laura Scott-Denton; Rytas Vilgalys; Jean-Marc Moncalvo
Ascomycete yeasts (phylum Ascomycota: subphylum Saccharomycotina: class Saccharomycetes: order Saccharomycetales) comprise a monophyletic lineage with a single order of about 1000 known species. These yeasts live as saprobes, often in association with plants, animals and their interfaces. A few species account for most human mycotic infections, and fewer than 10 species are plant pathogens. Yeasts are responsible for important industrial
Sung-Oui Suh; Meredith Blackwell; Cletus P. Kurtzman; M.-A. Lachance
Horizontally transmitted fungal endophytes are an ecological group of fungi, mostly belonging to the Ascomycota, that reside in the aerial tissues and roots of plants without inducing any visual symptoms of their presence. These fungi appear to have a capacity to produce an array of secondary metabolites exhibiting a variety of biological activity. Although the ability of fungi to produce
T. S. Suryanarayanan; N. Thirunavukkarasu; M. B. Govindarajulu; F. Sasse; R. Jansen; T. S. Murali
BACKGROUND: At present, there is not a widely accepted consensus view regarding the phylogenetic structure of kingdom Fungi although two major phyla, Ascomycota and Basidiomycota, are clearly delineated. Regarding the lower fungi, Zygomycota and Chytridiomycota, a variety of proposals have been advanced. Microsporidia may or may not be fungi; the Glomales (vesicular-arbuscular mycorrhizal fungi) may or may not constitute a
Yajuan J Liu; Matthew C Hodson; Benjamin D Hall
Fungal pathogens are the most important pathogens of aphids (Homoptera: Aphididae), and epizootics, particularly those caused by Entomophthorales (Zygomycota), are frequently observed and often rapidly reduce aphid populations. Fungi in the Hypocreales (Ascomycota) are less commonly found infecting aphids but can be important. The transmission of aphid fungal pathogens is affected by many factors, including: host biology and structure, pathogen
Donald C. Steinkraus
Background: A variety of spore discharge processes have evolved among the fungi. Those with the longest ranges are powered by hydrostatic pressure and include ''squirt guns'' that are most common in the Ascomycota and Zygomycota. In these fungi, fluid-filled stalks that support single spores or spore-filled sporangia, or cells called asci that contain multiple spores, are pressurized by osmosis. Because
Levi Yafetto; Loran Carroll; Yunluan Cui; Diana J. Davis; Mark W. F. Fischer; Andrew C. Henterly; Jordan D. Kessler; Hayley A. Kilroy; Jacob B. Shidler; Jessica L. Stolze-Rybczynski; Zachary Sugawara; Nicholas P. Money
The new species Stenocybe fragmenta (Ascomycota, Mycocaliciaceae) is described from western North America. The species was collected from twigs of Cercocarpus montanus and Rhamnus purshiana. Stenocybe fragmenta is characterized by 5-7 septate, 18-30 I?m long ascospores that fragment at maturity. This is the first report of spore fragmentation among the Mycocaliciaceae.
Peterson, E. B.; Rikkinen, Jouko
The study aims to investigate fungal community structures and dynamic changes in forest soil lignocellulose-degrading process. rRNA gene clone libraries for the samples collected in different stages of lignocellulose degradation process were constructed and analyzed. A total of 26 representative RFLP types were obtained from original soil clone library, including Mucoromycotina (29.5%), unclassified Zygomycetes (33.5%), Ascomycota (32.4%), and Basidiomycota (4.6%). When soil accumulated with natural lignocellulose, 16 RFLP types were identified from 8-day clone library, including Basidiomycota (62.5%), Ascomycota (36.1%), and Fungi incertae sedis (1.4%). After enrichment for 15 days, identified 11 RFLP types were placed in 3 fungal groups: Basidiomycota (86.9%), Ascomycota (11.5%), and Fungi incertae sedis (1.6%). The results showed richer, more diversity and abundance fungal groups in original forest soil. With the degradation of lignocellulose, fungal groups Mucoromycotina and Ascomycota decreased gradually, and wood-rotting fungi Basidiomycota increased and replaced the opportunist fungi to become predominant group. Most of the fungal clones identified in sample were related to the reported lignocellulose-decomposing strains. Understanding of the microbial community structure and dynamic change during natural lignocellulose-degrading process will provide us with an idea and a basis to construct available commercial lignocellulosic enzymes or microbial complex. PMID:24574925
Tian, Baoyu; Wang, Chunxiang; Lv, Ruirui; Zhou, Junxiong; Li, Xin; Zheng, Yi; Jin, Xiangyu; Wang, Mengli; Ye, Yongxia; Huang, Xinyi; Liu, Ping
An Asian powdery mildew fungus Erysiphe (Uncinula) kenjiana (Erysiphales, Ascomycota) has been found in Ukraine. This is the first record of this fungus in Europe. In 2007, E. kenjiana was collected on four Ulmus species in Kiev. All locations adjoined railways or an airport. Development of E. kenjiana was epiphytotic. This species was not found on elms surveyed at towns
Vasyl Heluta; Susumu Takamatsu; Svitlana Voytyuk; Yoshiaki Shiroya
BACKGROUND: The mitosporic fungus Trichoderma harzianum (Hypocrea, Ascomycota, Hypocreales, Hypocreaceae) is an ubiquitous species in the environment with some strains commercially exploited for the biological control of plant pathogenic fungi. Although T. harzianum is asexual (or anamorphic), its sexual stage (or teleomorph) has been described as Hypocrea lixii. Since recombination would be an important issue for the efficacy of an
Irina S Druzhinina; Christian P Kubicek; Monika Komo?-Zelazowska; Temesgen Belayneh Mulaw; John Bissett
Muscodor albus MOW12, an endophytic fungus isolated from Piper nigrum in Mawlong, Meghalaya, India, resembles some cultural and hyphal characteristics of previous isolates of Muscodor sp. In addition, it possesses about 99 % similarity in its ITS rDNA with other M. albus isolates and thus is nicely centered within the genetic tree to other Muscodor spp. This xylariaceae fungus effectively inhibits and kills certain plant pathogenic fungi by virtue of a mixture of volatile compounds that it produces. The majority of these compounds were identified by gas chromatography/mass spectrometry as small molecular weight esters, alcohols, and acids. The main ester components of this isolate of M. albus in its volatile mixture are acetic acid, ethyl ester; propanoic acid, 2-methyl-, methyl ester and acetic acid, 2-methylpropyl ester. This appears to be the first report of any M. albus strain from India. PMID:24426163
Banerjee, Debdulal; Pandey, Akhil; Jana, Maloy; Strobel, Gary
Two new fungal pigments named schweinitzins A and B (1-2), together with (S)-torosachrysone-8-O-methyl ether (3) and emodin-6,8-di-O-methyl ether (4) have been isolated from the methanolic extract of the fruit bodies of Xylaria schweinitzii (Xylariaceae) collected in Cuc Phuong national park, Ninh Binh province, Vietnam, by silica gel column chromatography and preparative HPLC. Their structures were elucidated by spectroscopic analysis such as IR, UV-Vis, 2D NMR and FT-ICR-MS. In addition, two compounds (1 and 3) showed strong cytotoxicity against all four cancer cell lines, KB (a human epidermal carcinoma), MCF7 (human breast carcinoma), SK-LU-I (human lung carcinoma) and HepG2 (hepatocellular carcinoma). PMID:25026714
Linh, Doan Thi Phuong; Hien, Bui Thi Thu; Que, Do Duc; Lam, Duong Minh; Arnold, Norbert; Schmidt, Jürgen; Porzel, Andrea; Quang, Dang Ngoc
The Wood Rot Ascomycete Xylaria polymorpha Produces a Novel GH78 Glycoside Hydrolase That Exhibits ?-l-Rhamnosidase and Feruloyl Esterase Activities and Releases Hydroxycinnamic Acids from Lignocelluloses
Soft rot (type II) fungi belonging to the family Xylariaceae are known to substantially degrade hardwood by means of their poorly understood lignocellulolytic system, which comprises various hydrolases, including feruloyl esterases and laccase. In the present study, several members of the Xylariaceae were found to exhibit high feruloyl esterase activity during growth on lignocellulosic materials such as wheat straw (up to 1,675 mU g?1) or beech wood (up to 80 mU g?1). Following the ester-cleaving activity toward methyl ferulate, a hydrolase of Xylaria polymorpha was produced in solid-state culture on wheat straw and purified by different steps of anion-exchange and size-exclusion chromatography to apparent homogeneity (specific activity, 2.2 U mg?1). The peptide sequence of the purified protein deduced from the gene sequence and verified by de novo peptide sequencing shows high similarity to putative ?-l-rhamnosidase sequences belonging to the glycoside hydrolase family 78 (GH78; classified under EC 188.8.131.52). The purified enzyme (98 kDa by SDS-PAGE, 103 kDa by size-exclusion chromatography; pI 3.7) converted diverse glycosides (e.g., ?-l-rhamnopyranoside and ?-l-arabinofuranoside) but also natural and synthetic esters (e.g., chlorogenic acid, hydroxycinnamic acid glycoside esters, veratric acid esters, or p-nitrophenyl acetate) and released free hydroxycinnamic acids (ferulic and coumaric acid) from arabinoxylan and milled wheat straw. These catalytic properties strongly suggest that X. polymorpha GH78 is a multifunctional enzyme. It is the first fungal enzyme that combines glycosyl hydrolase with esterase activities and may help this soft rot fungus to degrade lignocelluloses.
Nghi, Do Huu; Bittner, Britta; Kellner, Harald; Jehmlich, Nico; Ullrich, Rene; Pecyna, Marek J.; Nousiainen, Paula; Sipila, Jussi; Huong, Le Mai; Hofrichter, Martin
The wood rot ascomycete Xylaria polymorpha produces a novel GH78 glycoside hydrolase that exhibits ?-L-rhamnosidase and feruloyl esterase activities and releases hydroxycinnamic acids from lignocelluloses.
Soft rot (type II) fungi belonging to the family Xylariaceae are known to substantially degrade hardwood by means of their poorly understood lignocellulolytic system, which comprises various hydrolases, including feruloyl esterases and laccase. In the present study, several members of the Xylariaceae were found to exhibit high feruloyl esterase activity during growth on lignocellulosic materials such as wheat straw (up to 1,675 mU g(-1)) or beech wood (up to 80 mU g(-1)). Following the ester-cleaving activity toward methyl ferulate, a hydrolase of Xylaria polymorpha was produced in solid-state culture on wheat straw and purified by different steps of anion-exchange and size-exclusion chromatography to apparent homogeneity (specific activity, 2.2 U mg(-1)). The peptide sequence of the purified protein deduced from the gene sequence and verified by de novo peptide sequencing shows high similarity to putative ?-L-rhamnosidase sequences belonging to the glycoside hydrolase family 78 (GH78; classified under EC 184.108.40.206). The purified enzyme (98 kDa by SDS-PAGE, 103 kDa by size-exclusion chromatography; pI 3.7) converted diverse glycosides (e.g., ?-L-rhamnopyranoside and ?-L-arabinofuranoside) but also natural and synthetic esters (e.g., chlorogenic acid, hydroxycinnamic acid glycoside esters, veratric acid esters, or p-nitrophenyl acetate) and released free hydroxycinnamic acids (ferulic and coumaric acid) from arabinoxylan and milled wheat straw. These catalytic properties strongly suggest that X. polymorpha GH78 is a multifunctional enzyme. It is the first fungal enzyme that combines glycosyl hydrolase with esterase activities and may help this soft rot fungus to degrade lignocelluloses. PMID:22544251
Nghi, Do Huu; Bittner, Britta; Kellner, Harald; Jehmlich, Nico; Ullrich, René; Pecyna, Marek J; Nousiainen, Paula; Sipilä, Jussi; Huong, Le Mai; Hofrichter, Martin; Liers, Christiane
The viability, growth and morphology of 48 strains of Ascomycota (including 17 yeasts) and 20 strains of Zygomycota were determined after a 2-d and then after 1-year storage in liquid nitrogen using a new cryopreservation method with perlite as a particulate solid carrier. In case of Ascomycota, 45 strains (94 %) out of 48 survived both 2-d and 1-year storage in liquid nitrogen, respectively. In case of Zygomycota, all 20 strains survived both storage. In addition, 3 strains of Basidiomycota counted among yeasts were tested and all survived the 1 year storage. In all surviving cultures no negative effects of cryopreservation by this method have been observed after 1-year of storage in liquid nitrogen. The results indicate that the perlite protocol can be successfully used for cryopreservation of taxonomically different groups of fungi and also for fungi which failed to survive other routinely used preservation procedures. PMID:17575914
Homolka, L; Lisá, L; Kubatová, A; Valqová, M; Janderová, B; Nerud, F
Fungi display a large diversity in genome size and complexity, variation that is often considered to be adaptive. But because nonadaptive processes can also have important consequences on the features of genomes, we investigated the relationship of genetic drift and genome size in the phylum Ascomycota using multiple indicators of genetic drift. We detected a complex relationship between genetic drift and genome size in fungi: genetic drift is associated with genome expansion on broad evolutionary timescales, as hypothesized for other eukaryotes; but within subphyla over smaller timescales, the opposite trend is observed. Moreover, fungi and bacteria display similar patterns of genome degradation that are associated with initial effects of genetic drift. We conclude that changes in genome size within Ascomycota have occurred using two different routes: large-scale genome expansions are catalyzed by increasing drift as predicted by the mutation-hazard model of genome evolution and small-scale modifications in genome size are independent of drift.
Kelkar, Yogeshwar D.; Ochman, Howard
The Sphaerophorus globosus complex (Lecanorales, lichenized Ascomycota) shows a large morphological variation, and three relatively distinct morphotypes can be distinguished in parts of the distribution area. Here, we utilize a multigene-based maximum-parsimony approach (nITS+LSU rDNA, mtSSU rDNA, ?-tubulin, and actin) to investigate whether these morphotypes constitute distinct species. The results show that there are at least two well-supported monophyletic groups
Filip Högnabba; Mats Wedin
\\u000a A broad range of fungi were isolated from different geographic regions and substrates and identified according to traditional\\u000a and modern methods. A total of 120 different isolates were assigned to the phyla, Basidiomycota with 8 isolates, Ascomycota\\u000a with 75 isolates, and “Zygomycota” with 37 isolates. Although morphological characters were able to differentiate the isolates\\u000a to their phyla and in most
Youssuf Gherbawy; Claudia Kesselboth; Hesham Elhariry; Kerstin Hoffmann
AMONG the Eukaryota, the true fungi comprise four divisions (Chytridiomycota, Zymogomycota, Ascomycota and Basidio-mycota) that constitute a natural group which is thought to have diverged about 1 billion (109) years ago, believed also to be the time of divergence between metaphyta and metazoa lineages1. The endosymbionts responsible for the most prevalent plant root symbiosis, the vesicular-arbuscular mycorrhizae (VAM) or, more
Luc Simon; Jean Bousquet; Roger C. Lévesque; Maurice Lalonde
Fungal communities in decaying sapwood and heartwood of K. evelyniana were demonstrated through construction of four 18 S rRNA gene libraries. The 210 sequenced clones were clustered into 11\\u000a subgroups, belonging to Basidiomycota (71.9%) and to Ascomycota (22.4%) and unclassified (1 subgroup; 5.7%). The heartwood\\u000a displayed higher species richness than the sapwood. Basidiomycota were dominant in either the heartwood or the
Han-Bo Zhang; Ming-Xia Yang; Ran Tu; Lei Gao; Zhi-Wei Zhao
Pezizomycotina is the largest subphylum of Ascomycota and includes the vast majority of filamen- tous, ascoma-producing species. Here we report the results from weighted parsimony, maximum likelihood and Bayesian phylogenetic analyses of five nuclear loci (SSU rDNA, LSU rDNA, RPB1, RPB2 and EF-1a) from 191 taxa. Nine of the 10 Pezizomycotina classes currently recognized were represented in the sam- pling.
Joseph W. Spatafora; Gi-Ho Sung; Desiree Johnson; Cedar Hesse; Benjamin O'Rourke; Maryna Serdani; Robert Spotts; Francois Lutzoni; Valerie Hofstetter; Jolanta Miadlikowska; Valerie Reeb; Cecile Gueidan; E. Fraker; T. Lumbsch; R. Lucking; I. Schmitt; K. Hosaka; A. Aptroot; C. Roux; A. N. Miller; D. M. Geiser; J. Hafellner; G. Hestmark; A. E. Arnold; B. Budel; A. Rauhut; D. Hewitt; W. A. Untereiner; M. S. Cole; C. Scheidegger; M. Schultz; H. Sipman; C. L. Schoch
\\u000a The increased availability of molecular data has had a major impact on phylogenetic studies in general, and on the study of\\u000a fungal phylogeny in particular. To date, more than 60 fungal genomes have been completely sequenced, ranging from the Chytridiomycota\\u000a to the Ascomycota. There have been several attempts to reconstruct aspects of the fungal Tree of Life, using a variety
David A. Fitzpatrick; Geraldine Butler
During a survey of insect gut micro-organisms, we consistently isolated Pichia stipitis-like yeasts (Fungi: Ascomycota, Saccharomycetes) from the wood-ingesting beetles, Odonto- taenius disjunctus and Verres stembergianus (Coleóptera: Passalidae). The yeasts were iso- lated from passalid beetles over a wide area, including the eastern and midwestern USA and Panama. Phylogenetic analyses of the nuclear encoded small and large subunit rRNA gene
SUNG-OUI SUH; CHRISTOPHER J. MARSHALL; MEREDITH BLACKWELL
Adverse conditions, including low humidity, UV irradiation, and high temperature, appreciably affect the efficacy of mycoinsecticides.\\u000a Oil formulation increased the virulence of Metarhizium\\u000a anisopliae var. acridum (Ascomycota: Hypocreales) against locusts and grasshoppers by reducing the dependence on saturated water. A mycoinsecticide\\u000a diluent (a water-in-oil emulsion) has been widely used to dilute the oil formulation of M. anisopliae in China. The
Guoxiong Peng; Yuxian Xia
Traditional techniques for studying the fungal community composition in streams favour the detection and identification of\\u000a aquatic hyphomycetes. Our objective was to use molecular techniques to determine the presence and contributions of other fungal\\u000a groups. We designed primers specific for the ITS regions in Ascomycota, Basidiomycota, Chytridiomycota, Zygomycota and Oomycota.\\u000a The primers were used to amplify DNA from linden, maple,
Liliya G. Nikolcheva; Felix Bärlocher
Changes in litter quality resulting from pretreatment of leaf litter by phyllosphere fungi may affect its subsequent decomposition\\u000a by succeeding fungi. The purpose of this study is to clarify the effect of prior decomposition of leaf litter by two phyllosphere\\u000a fungi of beech, Xylaria sp. and Ascochyta sp., on substrate utilization of 12 fungal species in the Basidiomycota, the Ascomycota,
Extracts of 14 filamentous fungi were examined regarding their potential for production of (R)-phenylacetylcarbinol [(R)-PAC], which is the chiral precursor in the manufacture of the pharmaceuticals ephedrine and pseudoephedrine. Benzaldehyde and pyruvate were transformed at a scale of 1.2 ml into PAC by cell-free extracts of all selected strains, covering the broad taxonomic spectrum of Ascomycota, Zygomycota and Basidiomycota. Highest
B. Rosche; V. Sandford; M. Breuer; B. Hauer; P. Rogers
Fungal pathogens are the most important pathogens of aphids (Homoptera: Aphididae), and epizootics, particularly those caused by Entomophthorales (Zygomycota), are frequently observed and often rapidly reduce aphid populations. Fungi in the Hypocreales (Ascomycota) are less commonly found infecting aphids but can be important. The transmission of aphid fungal pathogens is affected by many factors, including: host biology and structure, pathogen characteristics, host-plant characteristics, and environmental factors. This paper is an overview of selected factors affecting transmission of aphid pathogens. PMID:16780867
Steinkraus, Donald C
. The origins of fungal group I introns within nuclear small-subunit (nSSU) rDNA are enigmatic. This is partly because they\\u000a have never been reported in basal fungal phyla (Zygomycota and Chytridiomycota), which are hypothesized to be ancestral to\\u000a derived phyla (Ascomycota and Basidiomycota). Here we report group I introns from the nSSU rDNA of two zygomycete fungi, Zoophagus insidians (Zoopagales)
Yuuhiko Tanabe; Akira Yokota; Junta Sugiyama
In this study, we sequenced 18S rRNA genes (rDNA) from 49 fungal strains representing 31 species from 15 genera. Most of these species are common airborne fungi and pathogens that may cause various public health concerns. Sequence analysis revealed distinct divergence between Zygomycota and Ascomycota. Within Ascomy- cota, several strongly supported clades were identified that facilitate the taxonomic placement of
Zhihong Wu; Yoshihiko Tsumura; Goran Blomquist; Xiao-Ru Wang
Endophytic fungi were isolated from healthy tissues of Lippia sidoides Cham. (Verbenaceae), a medicinal plant used as an antiseptic in the northeast of Brazil. From 480 fragments of leaves (240)\\u000a and stems (240), a total of 203 endophytic fungi were isolated, representing 14 species belonging to the groups Ascomycota, Coelomycetes and Hyphomycetes. Endophytic colonization was greater in leaves (50.4%) than
Virginia Medeiros de Siqueira; Raphael Conti; Janete Magali de Araújo; Cristina Maria Souza-Motta
A new naphthopyrone derivative, lasionectrin (1), was isolated from fermentations of an Acremonium-like fungus provisionally identified as a Lasionectria sp. (Ascomycota, Hypocreales) and isolated from forest leaf litter from Equatorial Guinea. Its structure was determined by a combination of spectroscopic techniques, including UV, (+)-HRESIMS, and 1D and 2D NMR spectroscopy, and comparison with published data for related fungal metabolites. Compound 1 inhibited the growth of Plasmodium falciparum with an IC(50) value of 11 ?M. PMID:22694295
El Aouad, Noureddine; Pérez-Moreno, Guiomar; Sánchez, Paula; Cantizani, Juan; Ortiz-López, Francisco Javier; Martín, Jesús; González-Menéndez, Víctor; Ruiz-Pérez, Luis M; González-Pacanowska, Dolores; Vicente, Francisca; Bills, Gerald; Reyes, Fernando
A phylogenetic analysis of the Erysiphe with uncinuloid ascoma appendages (Erysiphe section Uncinula, Erysiphales, Ascomycota) on Carpinus spp. was done using sequences of the rDNA ITS regions and the D1\\/D2 domains of the 28S rDNA. These results, combined with morphological data, revealed a complex consisting of several distinct taxa. These included the already described Erysiphe\\u000a carpinicola on C. japonica distinguishable
Uwe Braun; Susumu Takamatsu; Vasyl Heluta; Saranya Limkaisang; Rangsi Divarangkoon; Roger Cook; Herbert Boyle
Gargas, A., and Taylor, J. W. 1995. Phylogeny of discomycetes and early radiations of the apothecial Ascomycotina inferred from SSU rDNA sequence data. Experimental Mycology 19, 7-15. We used nucleotide sequences of the small subunit ribosomal genes (SSU rDNA) to examine evolutionary relationships of apothecial ascomycetes (division Ascomycota; class Discomycetes sensu ), commonly known as the cup fungi. The apothecial
Andrea Gargas; John W. Taylor
Compared to traditional methods of fungal exposure assessment, molecular methods have provided new insight into the richness of fungal communities present in both indoor and outdoor environments. In this study, we describe the diversity of fungi in the homes of asthmatic children located in Kansas City. Fungal diversity was determined by sequencing the internal transcribed spacer (ITS) regions of ribosomal RNA derived from fungi collected in air and dust samples from 31 homes participating in the Kansas City Safe and Healthy Homes Program (KCSHHP). Sequencing results were then compared to data obtained using viable and non-viable fungal exposure assessment methods. ITS clone libraries were predominantly derived from the phylum Ascomycota in both air (68%) and dust (92%) samples and followed by the Basidiomycota and Zygomycota. The majority of Ascomycota clones belonged to four orders including the Pleosporales, Eurotiales, Capnodiales, and Dothideales. ITS sequencing revealed the presence of a number of rarely documented fungal species placed in the Pleosporales. Several species placed in the Basidiomycota were detected in ITS clone libraries but not by viable or non-viable methods. The prevalence of organizational taxonomic units (OTUs) was significantly higher in air than in dust samples (p < 0.0001); however, no differences between OTUs in air samples collected in the subjects' room and basement were observed. These sequencing results demonstrate a much broader diversity of Ascomycota and Basidiomycota communities in KCSHHP indoor environments than previously estimated using traditional methods of assessment. PMID:24258337
Rittenour, William R; Ciaccio, Christina E; Barnes, Charles S; Kashon, Michael L; Lemons, Angela R; Beezhold, Donald H; Green, Brett J
Fungal spores are widespread and common in the atmosphere. In this study, we use a metagenomic approach to study the fungal diversity in six total air samples collected from April to May 2012 in Seoul, Korea. This springtime period is important in Korea because of the peak in fungal spore concentration and Asian dust storms, although the year of this study (2012) was unique in that were no major Asian dust events. Clustering sequences for operational taxonomic unit (OTU) identification recovered 1,266 unique OTUs in the combined dataset, with between 223?96 OTUs present in individual samples. OTUs from three fungal phyla were identified. For Ascomycota, Davidiella (anamorph: Cladosporium) was the most common genus in all samples, often accounting for more than 50% of all sequences in a sample. Other common Ascomycota genera identified were Alternaria, Didymella, Khuskia, Geosmitha, Penicillium, and Aspergillus. While several Basidiomycota genera were observed, Chytridiomycota OTUs were only present in one sample. Consistency was observed within sampling days, but there was a large shift in species composition from Ascomycota dominant to Basidiomycota dominant in the middle of the sampling period. This marked change may have been caused by meteorological events. A potential set of 40 allergyinducing genera were identified, accounting for a large proportion of the diversity present (22.5?7.2%). Our study identifies high fungal diversity and potentially high levels of fungal allergens in springtime air of Korea, and provides a good baseline for future comparisons with Asian dust storms. PMID:24723107
Oh, Seung-Yoon; Fong, Jonathan J; Park, Myung Soo; Chang, Limseok; Lim, Young Woon
Dendrobium spp. are traditional Chinese medicinal plants, and the main effective ingredients (polysaccharides and alkaloids) have pharmacologic effects on gastritis infection, cancer, and anti-aging. Previously, we confirmed endophytic xylariaceous fungi as the dominant fungi in several Dendrobium species of tropical regions from China. In the present study, the diversity, taxonomy, and distribution of culturable endophytic xylariaceous fungi associated with seven medicinal species of Dendrobium (Orchidaceae) were investigated. Among the 961 endophytes newly isolated, 217 xylariaceous fungi (morphotaxa) were identified using morphological and molecular methods. The phylogenetic tree constructed using nuclear ribosomal internal transcribed spacer (ITS), large subunit of ribosomal DNA (LSU), and beta-tubulin sequences divided these anamorphic xylariaceous isolates into at least 18 operational taxonomic units (OTUs). The diversity of the endophytic xylariaceous fungi in these seven Dendrobium species was estimated using Shannon and evenness indices, with the results indicating that the dominant Xylariaceae taxa in each Dendrobium species were greatly different, though common xylariaceous fungi were found in several Dendrobium species. These findings implied that different host plants in the same habitats exhibit a preference and selectivity for their fungal partners. Using culture-dependent approaches, these xylariaceous isolates may be important sources for the future screening of new natural products and drug discovery.
Chen, Juan; Zhang, Li-Chun; Xing, Yong-Mei; Wang, Yun-Qiang; Xing, Xiao-Ke; Zhang, Da-Wei; Liang, Han-Qiao; Guo, Shun-Xing
Based on an overview of progress in molecular systematics of the true fungi (Fungi/Eumycota) since 1990, little overlap was found among single-locus data matrices, which explains why no large-scale multilocus phylogenetic analysis had been undertaken to reveal deep relationships among fungi. As part of the project "Assembling the Fungal Tree of Life" (AFTOL), results of four Bayesian analyses are reported with complementary bootstrap assessment of phylogenetic confidence based on (1) a combined two-locus data set (nucSSU and nucLSU rDNA) with 558 species representing all traditionally recognized fungal phyla (Ascomycota, Basidiomycota, Chytridiomycota, Zygomycota) and the Glomeromycota, (2) a combined three-locus data set (nucSSU, nucLSU, and mitSSU rDNA) with 236 species, (3) a combined three-locus data set (nucSSU, nucLSU rDNA, and RPB2) with 157 species, and (4) a combined four-locus data set (nucSSU, nucLSU, mitSSU rDNA, and RPB2) with 103 species. Because of the lack of complementarity among single-locus data sets, the last three analyses included only members of the Ascomycota and Basidiomycota. The four-locus analysis resolved multiple deep relationships within the Ascomycota and Basidiomycota that were not revealed previously or that received only weak support in previous studies. The impact of this newly discovered phylogenetic structure on supraordinal classifications is discussed. Based on these results and reanalysis of subcellular data, current knowledge of the evolution of septal features of fungal hyphae is synthesized, and a preliminary reassessment of ascomal evolution is presented. Based on previously unpublished data and sequences from GenBank, this study provides a phylogenetic synthesis for the Fungi and a framework for future phylogenetic studies on fungi. PMID:21652303
Lutzoni, François; Kauff, Frank; Cox, Cymon J; McLaughlin, David; Celio, Gail; Dentinger, Bryn; Padamsee, Mahajabeen; Hibbett, David; James, Timothy Y; Baloch, Elisabeth; Grube, Martin; Reeb, Valérie; Hofstetter, Valérie; Schoch, Conrad; Arnold, A Elizabeth; Miadlikowska, Jolanta; Spatafora, Joseph; Johnson, Desiree; Hambleton, Sarah; Crockett, Michael; Shoemaker, Robert; Sung, Gi-Ho; Lücking, Robert; Lumbsch, Thorsten; O'Donnell, Kerry; Binder, Manfred; Diederich, Paul; Ertz, Damien; Gueidan, Cécile; Hansen, Karen; Harris, Richard C; Hosaka, Kentaro; Lim, Young-Woon; Matheny, Brandon; Nishida, Hiromi; Pfister, Don; Rogers, Jack; Rossman, Amy; Schmitt, Imke; Sipman, Harrie; Stone, Jeffrey; Sugiyama, Junta; Yahr, Rebecca; Vilgalys, Rytas
This article documents the addition of 142 microsatellite marker loci to the Molecular Ecology Resources database. Loci were developed for the following species: Agriophyllum squarrosum, Amazilia cyanocephala, Batillaria attramentaria, Fungal strain CTeY1 (Ascomycota), Gadopsis marmoratus, Juniperus phoenicea subsp. turbinata, Liriomyza sativae, Lupinus polyphyllus, Metschnikowia reukaufii, Puccinia striiformis and Xylocopa grisescens. These loci were cross-tested on the following species: Amazilia beryllina, Amazilia candida, Amazilia rutila, Amazilia tzacatl, Amazilia violiceps, Amazilia yucatanensis, Campylopterus curvipennis, Cynanthus sordidus, Hylocharis leucotis, Juniperus brevifolia, Juniperus cedrus, Juniperus osteosperma, Juniperus oxycedrus, Juniperus thurifera, Liriomyza bryoniae, Liriomyza chinensis, Liriomyza huidobrensis and Liriomyza trifolii. PMID:23693143
Arias, M C; Atteke, Christiane; Augusto, S C; Bailey, J; Bazaga, Pilar; Beheregaray, Luciano B; Benoit, Laure; Blatrix, Rumsaïs; Born, Céline; Brito, R M; Chen, Hai-kui; Covarrubias, Sara; de Vega, Clara; Djiéto-Lordon, Champlain; Dubois, Marie-Pierre; Francisco, F O; García, Cristina; Gonçalves, P H P; González, Clementina; Gutiérrez-Rodríguez, Carla; Hammer, Michael P; Herrera, Carlos M; Itoh, H; Kamimura, S; Karaoglu, H; Kojima, S; Li, Shou-Li; Ling, Hannah J; Matos-Maraví, Pável F; McKey, Doyle; Mezui-M'Eko, Judicaël; Ornelas, Juan Francisco; Park, R F; Pozo, María I; Ramula, Satu; Rigueiro, Cristina; Sandoval-Castillo, Jonathan; Santiago, L R; Seino, Miyuki M; Song, Chang-Bing; Takeshima, H; Vasemägi, Anti; Wellings, C R; Yan, Ji; Yu-Zhou, Du; Zhang, Chang-Rong; Zhang, Tian-Yun
Fifty Beauveria bassiana (Balsamo) Vuillemin (Ascomycota: Hypocreales) strains isolated from the coffee berry borer were used to develop a novel screening method aimed at selecting strains with the highest biocontrol potential. The screening method is based on percent insect mortality, average survival time, mortality distribution, percent spore germination, fungal life cycle duration, and spore production on the insect. Based on these parameters, only 11 strains merited further study. The use of a sound scientific protocol for the selection of promising fungal entomopathogens should lead to more efficient use of time, labor, and financial resources in biological control programs.
Posada, Francisco J.; Vega, Fernando E.
We summarized experimental data on species diversity of fungi decomposing synthetic polymeric materials. Most of the fungi were anamorphs of the phylum Ascomycota, class Ascomycetes (231 species and 85 genera). Teleomorphs of ascomycetes were represented by 18 species and 7 genera. We revealed a smaller number of fungi belonging to the phylum Zygomycota, class Zygomycetes (31 species and 15 genera), or the phylum Basidiomycota, class Basidiomycetes (5 species and 5 genera). The specific composition of fungi was assessed on polymeric materials of various classes. PMID:18669268
Kurakov, A B; Gevorkian, S A; Goginian, V B; Ozeskaia, S M
A new 12-membered macrolide, balticolid (1) was isolated from the EtOAc extract of the culture broth of fungal strain 222 belonging to the Ascomycota, which was found on driftwood collected from the coast of the Greifswalder Bodden, Baltic Sea, Germany. The structure of balticolid was determined to be (3R,11R), (4E,8E)-3-hydroxy-11-methyloxacyclododeca-4,8-diene-1,7-dione using extensive spectral data as well as the modified Mosher ester method. Balticolid (1) displayed anti-HSV-1 activity with an IC50 value of 0.45 ?M.
Shushni, Muftah A. M.; Singh, Rajinder; Mentel, Renate; Lindequist, Ulrike
The phylogenetic position of the fission yeast Schizosaccharomyces pombe in the fungal Tree of Life is still controversial. Three alternative phylogenetic positions have been proposed in the literature, namely (1) a position basal to the Hemiascomycetes and Euascomycetes, (2) a position as a sister group to the Euascomycetes with the Hemiascomycetes as a basal branch, or (3) a sister group to the Hemiascomycetes with Euascomycetes as a basal branch. Here we compared 91 clusters of orthologous proteins containing a single orthologue that are shared by 19 eukaryote genomes. The major part of these 91 orthologues supports a phylogenetic position of S. pombe as a basal lineage among the Ascomycota, thus supporting the second proposition. Interestingly, part of the orthologous proteins supported a fourth, not yet described alternative, in which S. pombe is basal to both Basidiomycota and Ascomycota. Both topologies of phylogenetic trees are well supported. We believe that both reflect correctly the phylogenetic history of the species concerned. This apparent paradox may point to a heterogeneous nuclear genome of the fungi. Importantly, this needs to be taken in consideration for a correct understanding of the fungal Tree of Life. PMID:16904286
Kuramae, Eiko E; Robert, Vincent; Snel, Berend; Boekhout, Teun
Studies on the molecular diversity of the micro-eukaryotic community have shown that fungi occupy a central position in a large number of marine habitats. Environmental surveys using molecular tools have shown the presence of fungi from a large number of marine habitats such as deep-sea habitats, pelagic waters, coastal regions, hydrothermal vent ecosystem, anoxic habitats, and ice-cold regions. This is of interest to a variety of research disciplines like ecology, evolution, biogeochemistry, and biotechnology. In this review, we have summarized how molecular tools have helped to broaden our understanding of the fungal diversity in various marine habitats. Majority of the environmental phylotypes could be grouped as novel clades within Ascomycota, Basidiomycota, and Chytridiomycota or as basal fungal lineages. Deep-branching novel environmental clusters could be grouped within Ascomycota as the Pezizomycotina clone group, deep-sea fungal group-I, and soil clone group-I, within Basidiomycota as the hydrothermal and/or anaerobic fungal group, and within Chytridiomycota as Cryptomycota or the Rozella clade. However, a basal true marine environmental cluster is still to be identified as most of the clusters include representatives from terrestrial regions. The challenge for future research is to explore the true marine fungi using molecular techniques. PMID:23363246
Manohar, Cathrine Sumathi; Raghukumar, Chandralata
The known enzymes that open the s-triazine ring, the cyanuric acid hydrolases, have been confined almost exclusively to the kingdom Bacteria and are all homologous members of the rare cyanuric acid hydrolase/barbiturase protein family. In the present study, a filamentous fungus, Sarocladium sp. strain CA, was isolated from soil by enrichment culturing using cyanuric acid as the sole source of nitrogen. A reverse-genetic approach identified a fungal cyanuric acid hydrolase gene composed of two exons and one intron. The translated spliced sequence was 39 to 53% identical to previously characterized bacterial cyanuric acid hydrolases. The sequence was used to generate a gene optimized for expression in Escherichia coli and encoding an N-terminally histidine-tagged protein. The protein was purified by nickel affinity and anion-exchange chromatography. The purified protein was shown by 13C nuclear magnetic resonance (13C-NMR) to produce carboxybiuret as the product, which spontaneously decarboxylated to yield biuret and carbon dioxide. The protein was very narrow in substrate specificity, showing activity only with cyanuric acid and N-methyl cyanuric acid. Barbituric acid was an inhibitor of enzyme activity. Sequence analysis identified genes with introns in other fungi from the Ascomycota that, if spliced, are predicted to encode proteins with cyanuric acid hydrolase activity. The Ascomycota cyanuric acid hydrolase homologs are most closely related to cyanuric acid hydrolases from Actinobacteria.
Dodge, Anthony G.; Preiner, Chelsea S.
In the Tibetan permafrost region, vegetation types and soil properties have been affected by permafrost degradation, but little is known about the corresponding patterns of their soil microbial communities. Thus, we analyzed the effects of vegetation types and their covariant soil properties on bacterial and fungal community structure and membership and bacterial community-level physiological patterns. Pyrosequencing and Biolog EcoPlates were used to analyze 19 permafrost-affected soil samples from four principal vegetation types: swamp meadow (SM), meadow (M), steppe (S) and desert steppe (DS). Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria dominated bacterial communities and the main fungal phyla were Ascomycota, Basidiomycota and Mucoromycotina. The ratios of Proteobacteria/Acidobacteria decreased in the order: SM>M>S>DS, whereas the Ascomycota/Basidiomycota ratios increased. The distributions of carbon and nitrogen cycling bacterial genera detected were related to soil properties. The bacterial communities in SM/M soils degraded amines/amino acids very rapidly, while polymers were degraded rapidly by S/DS communities. UniFrac analysis of bacterial communities detected differences among vegetation types. The fungal UniFrac community patterns of SM differed from the others. Redundancy analysis showed that the carbon/nitrogen ratio had the main effect on bacteria community structures and their diversity in alkaline soil, whereas soil moisture was mainly responsible for structuring fungal communities. Thus, microbial communities and their functioning are probably affected by soil environmental change in response to permafrost degradation. PMID:24463013
Zhang, Xinfang; Xu, Shijian; Li, Changming; Zhao, Lin; Feng, Huyuan; Yue, Guangyang; Ren, Zhengwei; Cheng, Guogdong
To date, the knowledge of eukaryotic communities associated with sponges remains limited compared with prokaryotic communities. In a manner similar to prokaryotes, it could be hypothesized that sponge holobionts have phylogenetically diverse eukaryotic symbionts, and the eukaryotic community structures in different sponge holobionts were probably different. In order to test this hypothesis, the communities of eukaryota associated with 11 species of South China Sea sponges were compared with the V4 region of 18S ribosomal ribonucleic acid gene using 454 pyrosequencing. Consequently, 135 and 721 unique operational taxonomic units (OTUs) of fungi and protists were obtained at 97 % sequence similarity, respectively. These sequences were assigned to 2 phyla of fungi (Ascomycota and Basidiomycota) and 9 phyla of protists including 5 algal phyla (Chlorophyta, Haptophyta, Streptophyta, Rhodophyta, and Stramenopiles) and 4 protozoal phyla (Alveolata, Cercozoa, Haplosporidia, and Radiolaria) including 47 orders (12 fungi, 35 protists). Entorrhizales of fungi and 18 orders of protists were detected in marine sponges for the first time. Particularly, Tilletiales of fungi and Chlorocystidales of protists were detected for the first time in marine habitats. Though Ascomycota, Alveolata, and Radiolaria were detected in all the 11 sponge species, sponge holobionts have different fungi and protistan communities according to OTU comparison and principal component analysis at the order level. This study provided the first insights into the fungal and protistan communities associated with different marine sponge holobionts using pyrosequencing, thus further extending the knowledge on sponge-associated eukaryotic diversity. PMID:24577740
He, Liming; Liu, Fang; Karuppiah, Valliappan; Ren, Yi; Li, Zhiyong
The known enzymes that open the s-triazine ring, the cyanuric acid hydrolases, have been confined almost exclusively to the kingdom Bacteria and are all homologous members of the rare cyanuric acid hydrolase/barbiturase protein family. In the present study, a filamentous fungus, Sarocladium sp. strain CA, was isolated from soil by enrichment culturing using cyanuric acid as the sole source of nitrogen. A reverse-genetic approach identified a fungal cyanuric acid hydrolase gene composed of two exons and one intron. The translated spliced sequence was 39 to 53% identical to previously characterized bacterial cyanuric acid hydrolases. The sequence was used to generate a gene optimized for expression in Escherichia coli and encoding an N-terminally histidine-tagged protein. The protein was purified by nickel affinity and anion-exchange chromatography. The purified protein was shown by (13)C nuclear magnetic resonance ((13)C-NMR) to produce carboxybiuret as the product, which spontaneously decarboxylated to yield biuret and carbon dioxide. The protein was very narrow in substrate specificity, showing activity only with cyanuric acid and N-methyl cyanuric acid. Barbituric acid was an inhibitor of enzyme activity. Sequence analysis identified genes with introns in other fungi from the Ascomycota that, if spliced, are predicted to encode proteins with cyanuric acid hydrolase activity. The Ascomycota cyanuric acid hydrolase homologs are most closely related to cyanuric acid hydrolases from Actinobacteria. PMID:24039269
Dodge, Anthony G; Preiner, Chelsea S; Wackett, Lawrence P
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. PMID:20960971
Dubovenko, Aleksej G; Dunaevsky, Yakov E; Belozersky, Mikhail A; Oppert, Brenda; Lord, Jeffrey C; Elpidina, Elena N
The fungal communities associated with three bryophytes species (the liverwort Barbilophozia hatcheri, the mosses Chorisodontium aciphyllum and Sanionia uncinata) in the Fildes Region, King George Island, maritime Antarctica, were studied using clone library analysis. Fungal communities showed low diversity; the 680 clones belonged to 93 OTUs. Of these, 78 belonged to the phylum Ascomycota, 13 to the phylum Basidiomycota, 1 to the phylum Zygomycota, and 1 to an unknown phylum. Among the OTUs, the most common orders in the Ascomycota were Helotiales (42 OTUs) and Chaetothyriales (14 OTUs) and the most common orders in the Basidiomycota were Sebacinales (3 OTUs) and Platygloeales (3 OTUs). Most OTUs clustered within clades that contained phylotypes identified from samples in Antarctic or Arctic ecosystems or from bryophytes in other ecosystems. In addition, we found that host-related factor may shape the fungal communities associated with bryophytes in this region. This is the first systematic study of the fungal community in Antarctic bryophytes to be performed using culture-independent method and the results may improve understanding of the endophytic fungal evolution and ecology in the Antarctic ecosystem. PMID:23818107
Zhang, Tao; Xiang, Hai-Bo; Zhang, Yu-Qin; Liu, Hong-Yu; Wei, Yu-Zhen; Zhao, Li-Xun; Yu, Li-Yan
This study evaluated the fecal microbiota of 12 healthy pet dogs and 12 pet cats using bacterial and fungal tag-encoded FLX-Titanium amplicon pyrosequencing. A total of 120,406 pyrosequencing reads for bacteria (mean 5017) and 5359 sequences (one pool each for dogs and cats) for fungi were analyzed. Additionally, group-specific 16S rRNA gene clone libraries for Bifidobacterium spp. and lactic acid-producing bacteria (LAB) were constructed. The most abundant bacterial phylum was Firmicutes, followed by Bacteroidetes in dogs and Actinobacteria in cats. The most prevalent bacterial class in dogs and cats was Clostridia, dominated by the genera Clostridium (clusters XIVa and XI) and Ruminococcus. At the genus level, 85 operational taxonomic units (OTUs) were identified in dogs and 113 OTUs in cats. Seventeen LAB and eight Bifidobacterium spp. were detected in canine feces. Ascomycota was the only fungal phylum detected in cats, while Ascomycota, Basidiomycota, Glomeromycota, and Zygomycota were identified in dogs. Nacaseomyces was the most abundant fungal genus in dogs; Saccharomyces and Aspergillus were predominant in cats. At the genus level, 33 different fungal OTUs were observed in dogs and 17 OTUs in cats. In conclusion, this study revealed a highly diverse bacterial and fungal microbiota in canine and feline feces. PMID:21261668
Handl, Stefanie; Dowd, Scot E; Garcia-Mazcorro, Jose F; Steiner, Jörg M; Suchodolski, Jan S
Fungal assemblages in live, newly shed and partly decomposed leaves of Camellia japonica were investigated with a clone library analysis to assess the fungal diversity and succession in a subtropical forest in southern Japan. Partly decomposed leaves were divided into bleached and adjacent nonbleached portions to estimate the fungi functionally associated with lignin decomposition in the bleached portions, with an emphasis on Coccomyces sinensis (Rhytismataceae, Ascomycota). From 144 cloned 28S ribosomal DNA (rDNA) sequences, 48 operational taxonomic units (OTUs) were defined based on a sequence similarity threshold of 98%. Forty-one (85%) of the 48 OTUs belonged to the Ascomycota and seven OTUs (15%) to the Basidiomycota. Twenty-six OTUs (54%) were detected only once (singletons). The number of OTUs and the diversity indices of the fungal assemblages in the different leaves were in this order: live leaves > newly shed leaves > bleached portions > nonbleached portions of partly decomposed leaves. The fungal assemblages were similar in newly shed leaves and the bleached portions of partly decomposed leaves. Ligninolytic fungi of the genera Coccomyces, Lophodermium and Xylaria were frequently detected in the bleached portions. OTU3, identified as Coccomyces sinensis, was detected in live and newly shed leaves and the bleached portions of partly decomposed leaves, suggesting that this fungus latently infects live leaves, persists after leaf fall and takes part in lignin decomposition. PMID:23709486
Hirose, Dai; Matsuoka, Shunsuke; Osono, Takashi
We investigated in vitro antioxidant activities of 49 endophytic fungi isolated from the liverwort Scapania verrucosa. Based on morphological and molecular identification, the endophytic fungi isolated were classified into seven genera (Hypocrea, Penicillium, Tolypocladium, Chaetomium, Xylaria, Nemania, and Creosphaeria), all belonging to one family (Xylariaceae). By screening with the 2,2'-azino-di(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) decolorization assay, the ethyl acetate extracts of five endophytic fungi (T7, T21, T24, T32, and T38 strains), which exhibited remarkable Trolox equivalent (TE) antioxidant capacity (ranging from 997.06 to 1248.10 ?mol TE/g extract), were selected and their antioxidant capacity was further evaluated by assays for 2,2'-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging, hydroxyl radical scavenging, reducing power, and ferrous ion chelating. The ethyl acetate extracts of two endophytic fungi (T24 and T38) were found to have comparable scavenging abilities on both DPPH-free radicals (93.9 and 88.7%, respectively, at 50 ?g/mL) and hydroxyl radicals (97.1 and 89.4%, respectively, at 2 mg/mL) when compared with those of the positive controls (ascorbic acid and butylated hydroxytoluene, respectively). Although their reducing powers were similar to that of butylated hydroxytoluene, as indicated by absorbance (0.35 and 0.30 at 50 ?g/mL, respectively), only the T38 strain's ethyl acetate extract showed ferrous ion chelating ability (92.9% at 1 mg/mL) comparable to that of the EDTA-2Na control. These endophytic fungi in S. verrucosa are a potential novel source of natural antioxidants. PMID:22194173
Zeng, P Y; Wu, J G; Liao, L M; Chen, T-Q; Wu, J Z; Wong, K-H
The DNA entry and exit points on the nucleosome core regulate the initial invasion of the nucleosome by factors requiring access to the underlying DNA. Here we describe in vivo consequences of eliminating a single protein–DNA interaction at this position through mutagenesis of histone H3 Lys 42 to alanine. This substitution has a dramatic effect on the Saccharomyces cerevisiae transcriptome in both the transcriptional output and landscape of mRNA species produced. We attribute this in part to decreased histone H3 occupancy at transcriptionally active loci, leading to enhanced elongation. Additionally we show that this lysine is methylated in vivo, and genetic studies of methyl-lysine mimics suggest that this modification may be crucial in attenuating gene expression. Interestingly, this site of methylation is unique to Ascomycota, suggesting a recent evolutionary innovation that highlights the evolvability of post-translational modifications of chromatin.
Hyland, Edel M.; Molina, Henrik; Poorey, Kunal; Jie, Chunfa; Xie, Zhi; Dai, Junbiao; Qian, Jiang; Bekiranov, Stefan; Auble, David T.; Pandey, Akhilesh; Boeke, Jef D.
Molecular methodologies were used to investigate fungal assemblages of biological soil crusts (BSCs) from arid lands in the southwestern United States. Fungal diversity of BSCs was assessed in a broad survey that included the Chihuahuan and Sonoran deserts as well as the Colorado Plateau. At selected sites samples were collected along kilometer-scale transects, and fungal community diversity and composition were assessed based on community rRNA gene fingerprinting using PCR-denaturing gradient gel electrophoresis (DGGE). Individual phylotypes were characterized through band sequencing. The results indicate that a considerable diversity of fungi is present within crusted soils, with higher diversity being recovered from more successionally mature BSCs. The overwhelming majority of crust fungi belong to the Ascomycota, with the Pleosporales being widespread and frequently dominant. Beta diversity patterns of phylotypes putatively representing dominant members of BSC fungal communities suggest that these assemblages are specific to their respective geographic regions of origin. PMID:22123652
Bates, Scott T; Nash, Thomas H; Garcia-Pichel, Ferran
To evaluate which dye is effective in a plate assay for detecting extracellular cellulase activity produced by fungi, four chromogenic dyes including remazol brilliant blue, phenol red, congo red, and tryphan blue, were compared using chromagenic media. For the comparison, 19 fungal species belonging to three phyla, ascomycota, basidiomycota, and zygomycota were inoculated onto yeast nitrogen-based media containing different carbon substrates such as cellulose (carboxylmethyl and avicel types) and cellobiose labeled with each of the four dyes. Overall, the formation of clear zone on agar media resulting from the degradation of the substrates by the enzymes secreted from the test fungi was most apparent with media containing congo red. The detection frequency of cellulase activity was also most high on congo red-supplemented media. The results of this study showed that congo red is better dye than other three dyes in a plate assay for fungal enzyme detection. PMID:24015063
Yoon, Ji Hwan; Park, Ji Eun; Suh, Dong Yeon; Hong, Seung Beom; Ko, Seung Ju; Kim, Seong Hwan
From April 2009 to October 2011, we surveyed the higher fungi in the Byeonsanbando National Park, Korea. In total, we identified 2 kingdoms, 3 divisions, 7 classes, 22 orders, 63 families, 149 genera, and 313 species (including 6 undocumented taxa: 2 families, 2 genera, and 2 species). Seventeen 17 orders, 49 families, 128 genera, and 286 species belonged to Basidiomycota; 7 orders, 9 families, 15 genera, and 21 species were of Ascomycota; and 4 orders, 5 families, 6 genera, and 6 species of primordial fungi. Among the Basidiomycota, Agaricomycetes were represented by 47 families, 126 genera, and 282 species. The most common fungi were Boletaceae (33 species), followed by Russulaceae (30), Agaricaceae (27), and Amanitaceae (24). Various species of most of the higher fungi occurred during periods with average temperatures of 23~24.9?, maximum temperatures of 28~31.9?, minimum temperatures of 22~23.9?, > 82% relative humidity, and > 200 mm precipitation. PMID:24808731
Jang, Seog-Ki; Hur, Tae-Chul
The endophytic lifestyle has played an important role in the evolution of the morphology of reproductive structures (body) in one of the most problematic groups in fungal classification, the Leotiomycetes (Ascomycota). Mapping fungal morphologies to two groups in the Leiotiomycetes, the Rhytismatales and Hemiphacidiaceae reveals significant divergence in body size, shape and complexity. Mapping ecological roles to these taxa reveals that the groups include endophytic fungi living on leaves and saprobic fungi living on duff or dead wood. Finally, mapping of the morphologies to ecological roles reveals that leaf endophytes produce small, highly reduced fruiting bodies covered with fungal tissue or dead host tissue, while saprobic species produce large and intricate fruiting bodies. Intriguingly, resemblance between asexual conidiomata and sexual ascomata in some leotiomycetes implicates some common developmental pathways for sexual and asexual development in these fungi.
Wang, Zheng; Johnston, Peter R.; Yang, Zhu L.; Townsend, Jeffrey P.
Fungi contribute substantially to biogeochemical cycles of terrestrial and marine habitats by decomposing matter and recycling nutrients. Yet, the diversity of their planktonic forms in the open ocean is poorly described. In this study, culture-independent and molecular approaches were applied to investigate fungal diversity and abundance derived from samples collected from a broad swath of the Pacific Warm Pool across major environmental gradients Our results revealed that planktonic fungi were molecularly diverse and their diversity patterns were related to major phytoplankton taxa and various nutrients including nitrate, nitrite, orthophosphate and silicic acid. Over 400 fungal phylotypes were recovered across this region and nearly half of them grouped into two major fungal lineages of Ascomycota and Basidiomycota, whose abundance varied among stations. These results suggest that planktonic fungi are a diverse and integral component of the marine microbial community and should be included in future marine microbial ecosystem models. PMID:24992154
Wang, Xin; Singh, Purnima; Gao, Zheng; Zhang, Xiaobo; Johnson, Zackary I; Wang, Guangyi
Fungi contribute substantially to biogeochemical cycles of terrestrial and marine habitats by decomposing matter and recycling nutrients. Yet, the diversity of their planktonic forms in the open ocean is poorly described. In this study, culture-independent and molecular approaches were applied to investigate fungal diversity and abundance derived from samples collected from a broad swath of the Pacific Warm Pool across major environmental gradients Our results revealed that planktonic fungi were molecularly diverse and their diversity patterns were related to major phytoplankton taxa and various nutrients including nitrate, nitrite, orthophosphate and silicic acid. Over 400 fungal phylotypes were recovered across this region and nearly half of them grouped into two major fungal lineages of Ascomycota and Basidiomycota, whose abundance varied among stations. These results suggest that planktonic fungi are a diverse and integral component of the marine microbial community and should be included in future marine microbial ecosystem models.
Wang, Xin; Singh, Purnima; Gao, Zheng; Zhang, Xiaobo; Johnson, Zackary I.; Wang, Guangyi
Laccases (EC 220.127.116.11) are phenoloxidases involved in the transformation of the recalcitrant fraction of organic matter in soil. These enzymes are also able to transform certain aromatic pollutants such as polycyclic aromatic hydrocarbons (PAHs) and are known to be inhibited by chloride ions. This study aims to test the potential of some fungal strains newly isolated from natural environments subjected to high osmotic pressure such as coastal ecosystems, to produce chloride tolerant laccases. Three strains were identified as Chaetomium sp., Xylogone sphaerospora (two Ascomycota), and Coprinopsis sp. (a Basidiomycota) and the laccases produced by these fungi were weakly inhibited by chloride ions compared with previous data from literature. Moreover, we tested their reactivity towards various PAHs which are widespread anthropic pollutants. They were able to transform anthracene to 9,10-anthraquinone and we determine 7.5 eV as the threshold of ionization potential for PAH oxidation by these laccases. PMID:23063188
Qasemian, Leila; Billette, Christophe; Guiral, Daniel; Alazard, Emilie; Moinard, Magalie; Farnet, Anne-Marie
Fungal spores can account for large proportions of air particulate matter, and they may potentially influence the hydrological cycle and climate as nuclei for water droplets and ice crystals in clouds, fog, and precipitation. Moreover, some fungi are major pathogens and allergens. The diversity of airborne fungi is, however, not well-known. By DNA analysis we found pronounced differences in the relative abundance and seasonal cycles of various groups of fungi in coarse and fine particulate matter, with more plant pathogens in the coarse fraction and more human pathogens and allergens in the respirable fine particle fraction (<3 ?m). Moreover, the ratio of Basidiomycota to Ascomycota was found to be much higher than previously assumed, which might also apply to the biosphere.
Frohlich-Nowoisky, Janine; Pickersgill, Daniel A.; Despres, Viviane R.; Poschl, Ulrich
The outbreak of fungal meningitis associated with contaminated methylprednisolone acetate has thrust the importance of fungal infections into the public consciousness. The predominant pathogen isolated from clinical specimens, Exserohilum rostratum (teleomorph: Setosphaeria rostrata), is a dematiaceous fungus that infects grasses and rarely humans. This outbreak highlights the potential for fungal pathogens to infect both plants and humans. Most crossover or trans-kingdom pathogens are soil saprophytes and include fungi in Ascomycota and Mucormycotina phyla. To establish infection, crossover fungi must overcome disparate, host-specific barriers, including protective surfaces (e.g. cuticle, skin), elevated temperature, and immune defenses. This review illuminates the underlying mechanisms used by crossover fungi to cause infection in plants and mammals, and highlights critical events that lead to human infection by these pathogens. Several genes including veA, laeA, and hapX are important in regulating biological processes in fungi important for both invasive plant and animal infections. PMID:24021881
Gauthier, Gregory M; Keller, Nancy P
Epichloë endophytes (Clavicipitaceae, Ascomycota), including asexual forms placed in Neotyphodium, are common in cool-season grasses. Here we characterize the endophytes of the European woodland grass Hordelymus europaeus based on growth characteristics, morphology of conidiophores and conidia and phylogenetic relationships. Of the six different taxa found on H. europaeus, four are new, for which we propose the species names E. hordelymi, E. disjuncta, E. danica and subspecies E. sylvatica subsp. pollinensis. The other two are assigned to previously described E. bromicola and E. sylvatica. E. hordelymi, E. disjuncta and E. danica are asexual interspecific hybrids, while the other taxa are haploid. Only E. sylvatica subsp. pollinensis was found to reproduce sexually on H. europaeus. The high diversity of endophytes may be explained by repeated host jumps to H. europaeus with and without subsequent interspecific hybridizations. PMID:23921239
Leuchtmann, Adrian; Oberhofer, Martina
Fungal community composition in composts of lignocellulosic wastes was assessed via 454-pyrosequencing of ITS1 libraries derived from the three major composting phases. Ascomycota represented most (93%) of the 27,987 fungal sequences. A total of 102 genera, 120 species, and 222 operational taxonomic units (OTUs; >97% similarity) were identified. Thirty genera predominated (ca. 94% of the sequences), and at the species level, sequences matching Chaetomium funicola and Fusarium oxysporum were the most abundant (26 and 12%, respectively). In all composts, fungal diversity in the mature phase exceeded that of the mesophilic phase, but there was no consistent pattern in diversity changes occurring in the thermophilic phase. Fifteen species of human pathogens were identified, eight of which have not been previously identified in composts. This study demonstrated that deep sequencing can elucidate fungal community diversity in composts, and that this information can have important implications for compost use and human health.
De Gannes, Vidya; Eudoxie, Gaius; Hickey, William J.
Tuber macrosporum Vittad. is a truffle with superb organoleptic properties, whose cultivation is still in its infancy. For the first time we have aimed to provide information on ectomycorrhizal communities in natural and cultivated T. macrosporum sites. Ectomycorrhizal morphotypes were identified using ITS nrDNA sequencing and sorted into molecular operational taxonomic unit (MOTU). We detected 16 MOTUs in the T. macrosporum cultivated plantation. Ascomycota were the most abundant (86.4%) with Helvellaceae, Pyronemataceae and Pezizaceae the most common. Twenty-two MOTUs were collected in the natural T. macrosporum site. Basidiomycota morphotypes were plentiful (70.6%) and Thelephoraceae dominated. Each site had different taxa belowground with only T. macrosporum in common, being more abundant in the natural (18.2%) than in the cultivated (14.4%) site. Species richness, Simpson and Shannon diversity indices, taxonomic diversity, distinctness and variation of taxonomic distinctness were lower in the cultivated than in the natural site. PMID:24232503
Benucci, Gian Maria Niccolò; Raggi, Lorenzo; Albertini, Emidio; Csorbai, Andrea Gógán; Donnini, Domizia
Ophiocordyceps unilateralis (Ascomycota: Hypocreales) is a specialized parasite that infects, manipulates and kills formicine ants, predominantly in tropical forest ecosystems. We have reported previously, based on a preliminary study in remnant Atlantic Forest in Minas Gerais (Brazil), that O. unilateralis represents a species complex. On each of the four species of infected carpenter ant (Camponotus) collected, the fungus—characterized macroscopically by a single stalk arising from the dorsal neck region on which the sexual structures (stromatal plates) are borne laterally—can readily be distinguished both microscopically and functionally. Here, we describe and discuss the biology, life cycle and infection strategies of O. unilateralis s.l. and hypothesize that there may be hundreds of species within the complex parasitizing formicine ants worldwide. We then address the diversity within related hypocrealean fungi, with particular reference to symbionts (mutualists through to parasites), and argue that the widely-quoted total of extant fungi (1.5 million species) may be grossly underestimated.
Elliot, Simon L; Hughes, David P
The first report, to our knowledge, on the occurrence of filamentous fungi in the hypersaline (340 g salt l-1) Dead Sea is presented. Three species of filamentous fungi from surface water samples of the Dead Sea were isolated: Gymnascella marismortui (Ascomycota), which is described as a new species, Ulocladium chlamydosporum and Penicillium westlingii (Deuteromycota). G. marismortui and U. chlamydosporum grew on media containing up to 50% Dead Sea water. G. marismortui was found to be an obligate halophile growing optimally in the presence of 0.5-2 M NaCl or 10 30% (by volume) of Dead Sea water. Isolated cultures did not grow on agar media without salt, but grew on agar prepared with up to 50% Dead Sea water. This suggests that they may be adapted to life in the extremely stressful hypersaline Dead Sea.
Buchalo, A S; Nevo, E; Wasser, S P; Oren, A; Molitoris, H P
The composting ecosystem is a suitable source for the discovery of novel microorganisms and secondary metabolites. This work analyzes the identity of microbial community that persists throughout lignocellulose-based composting, evaluates their metabolic activities and studies the capability of selected isolates for composting bioaugmentation. Bacterial species of the phyla Firmicutes, Actinobacteria and Proteobacteria and fungi of the phylum Ascomycota were ubiquitous throughout the composting. The species Arthrobacter russicus, Microbacterium gubbeenense, Ochrocladosporium frigidarii and Cladosporium lignicola are detected for the first time in this ecosystem. In addition, several bacterial and fungal isolates exhibited a wide range of metabolic capabilities such as polymers (lignocellulose, protein, lipids, pectin and starch) breakdown and phosphate-solubilization that may find many biotechnological applications. In particular, Streptomyces albus BM292, Gibellulopsis nigrescens FM1397 and FM1411, Bacillus licheniformis BT575, Bacillus smithii AT907 and Alternaria tenuissima FM1385 exhibited a great potential as inoculants for composting bioaugmentation. PMID:24759645
Jurado, Macarena; López, María J; Suárez-Estrella, Francisca; Vargas-García, María C; López-González, Juan A; Moreno, Joaquín
Thirty eight species of fungi were identified as a result of mycological analysis of 180 mortmass samples of Betulapendula Routh. and Populus tremula L. Mortmass mycobiota of B. pendula and P. tremula was represented by white, brown- and soft-rot species. Fungi of Ascomycota phylum were most numerous (24 species). Species of genera Aspergillus, Penicillium, Brachysporium, Cladosporium, Drechslera, Fusarium, Cylindrocarpon, Spadicesporium, Trichoderma in variants with middle and hard classes of wood degradation were identified among them. The Basidiomycota phylum was represented by 12 species; among them Armillariella mellea and Phellinus igniarius occurred most frequently. The most specific fungal complex decaying B. pendula and P tremula mortmass was observed under class III of its degradation. PMID:24450187
Bilous, A M; Voloshchuk, N M; Buzyl', M A; Kovbasa, Ia V
A wide range of fungal species in the phylum Ascomycota uses the forcible ejection of microscopic spores to disperse and to cover new territory, triggered by the breakdown of osmolytes in the sack containing the spores (the ascus). The spores experience very high aerodynamic drag due to their small size and need to attain high velocities to leave the boundary layer of still air around the fruiting body. Here we address the efficiency of conversion of osmotic pressure to the kinetic energy of the spore, and in particular its dependence on the design of the ascus and the hole (the so-called apical ring) from where the spores leave the ascus. We present a fluid mechanical model of the ejection process, which predicts that the hole the apical ring should have specific properties, in order to minimize frictional and pressure losses and maximize the ejection velocity. We compare these predictions to measurements of apical ring properties across the phylum.
Fritz, Joerg; Seminara, Agnese; Roper, Marcus; Pringle, Anne; Brenner, Michael
Biogenic aerosols are relevant for the Earth system, climate, and public health on local, regional, and global scales. Up to now, however, little is known about the diversity and biogeography of airborne microorganisms. We present the first DNA-based analysis of airborne fungi on global scales, showing pronounced geographic patterns and boundaries. In particular we found that the ratio of species richness between Basidiomycota and Ascomycota is much higher in continental air than in marine air. This may be an important difference between the "blue ocean" and "green ocean" regimes in the formation of clouds and precipitation, for which fungal spores can act as nuclei. Our findings also suggest that air flow patterns and the global atmospheric circulation are important for the evolution of microbial ecology and for the understanding of global changes in biodiversity.
Fröhlich-Nowoisky, J.; Burrows, S. M.; Xie, Z.; Engling, G.; Solomon, P. A.; Fraser, M. P.; Mayol-Bracero, O. L.; Artaxo, P.; Begerow, D.; Conrad, R.; Andreae, M. O.; Després, V. R.; Pöschl, U.
Endophytic fungi were isolated from healthy leaf and root samples of Taraxacum coreanum. Of the 72 isolates recovered, 39 were from leaves and 33 from roots with an isolation frequency of 54% and 46%, respectively. Based on ITS sequence analysis, 72 isolates were classified into 19 genera of which 17 were under the phylum Ascomycota and 2 were under Basidiomycota. Diverse genera were found and Alternaria, Cladosporium, Fusarium and Phoma were dominant. Out of 19 genera, Apodus, Ceriporia, Dothideales, Leptodontidium, Nemania, Neoplaconema, Phaeosphaeria, Plectosphaerella and Terfezia were new to Korea. Seventy two isolates were screened for antifungal activity, of which 10 isolates (14%) were found active at least against one of the tested fungi. Isolate 050603 had the widest antifungal spectra of activity, and isolates 050592 and 050611 were active against three plant pathogenic fungi.
Paul, Narayan Chandra; Kim, Won Ki; Woo, Sung Kyoon; Park, Myung Soo
Angelina rufescens is placed within the core clade of Rhytismatales (Leotiomycetes, Pezizomycotina, Ascomycota) based on analysis of LSU and mtSSU rDNA. The only species in the genus, it produces distinctive ascomata that reoccur annually on wood and on the remains of its own previous fructifications, forming dense conglomerations of interlocking longitudinally elongated apothecia with gray hymenia. Known collections and references of A. rufescens indicate that it is endemic to eastern and central United States. Morphological and cultural characters are described with notes on ascomata development. No mitospores were observed in field collections or in culture. Lectotypes are designated for Hysterium rufescens and its synonym Ascobolus conglomeratus. Angelina rufescens is illustrated here for the first time in the taxonomic literature. PMID:24603839
Karakehian, Jason M; LoBuglio, Katherine F; Pfister, Donald H
A novel filamentous fungus strain designated RB-1 was isolated into pure culture from Japanese rice field soil through an anaerobic role tube technique. The strain is a mitosporic fungus that grows in both aerobic and strict anaerobic conditions using various mono-, di-, tri-, and polysaccharides with acetate and ethanol productions. The amount of acetate produced was higher than that of ethanol in both aerobic and anaerobic cultures. The characteristic verrucose or punctuate conidia of RB-1 closely resembled those of some strains of the genus Thermomyces, a thermophilic or mesophilic anamorphic ascomycete. However, based on phylogenetic analysis with the small subunit (SSU) and large subunit (LSU) rDNA sequences, RB-1 was characterized as a member of the class Lecanoromycetes of the phylum Ascomycota. Currently, RB-1 is designated as an anamorphic ascomycete and is phylogenetically considered an incertae sedis within the class Lecanoromycetes.
From April 2009 to October 2011, we surveyed the higher fungi in the Byeonsanbando National Park, Korea. In total, we identified 2 kingdoms, 3 divisions, 7 classes, 22 orders, 63 families, 149 genera, and 313 species (including 6 undocumented taxa: 2 families, 2 genera, and 2 species). Seventeen 17 orders, 49 families, 128 genera, and 286 species belonged to Basidiomycota; 7 orders, 9 families, 15 genera, and 21 species were of Ascomycota; and 4 orders, 5 families, 6 genera, and 6 species of primordial fungi. Among the Basidiomycota, Agaricomycetes were represented by 47 families, 126 genera, and 282 species. The most common fungi were Boletaceae (33 species), followed by Russulaceae (30), Agaricaceae (27), and Amanitaceae (24). Various species of most of the higher fungi occurred during periods with average temperatures of 23~24.9?, maximum temperatures of 28~31.9?, minimum temperatures of 22~23.9?, > 82% relative humidity, and > 200 mm precipitation.
The molecular phylogeny and comparative morphological studies reported here provide evidence for the recognition of the genus Picoa, an hypogeous desert truffle, in the family Pyronemataceae (Ascomycota, Pezizales). Picoa juniperi and Picoa lefebvrei were reassigned to the genus Picoa based on large subunit (LSU) sequence (28S) rDNA and internal transcribed spacer (ITS) rDNA (including the partial 18S, ITS1, ITS2, 5.8S gene, and partial 28S of the nuclear rDNA) data. Morphological studies of spores, asci, perida, and gleba revealed high similarities between P. lefebvrei and P. juniperi, thereby confirming the membership of both species in the genus Picoa. These two species were primarily distinguishable based on ascospore ornamentation. PMID:20559873
Sbissi, Imed; Neffati, Mohamed; Boudabous, Abdellatif; Murat, Claude; Gtari, Maher
Quercus woodlands are key components of California's wild landscapes, yet little is known about ectomycorrhizal (EM) fungi in these ecosystems. We examined the EM community associated with Quercus douglasii using sporocarp surveys and by pooling EM roots and subjecting them to DNA extraction, polymerase chain reaction (PCR), cloning, restriction fragment length polymorphism (RFLP) screening and DNA sequencing. Ectomycorrhizal root symbionts were sampled four times in 2003-04. During this time, the below-ground community structure was relatively stable; we found no evidence of taxa adapted to winter or spring conditions and only one species varied widely in occurrence between years. The EM community from sporocarps and roots was diverse (161 species), rich in Ascomycota (46 species), and dominated by fungi with cryptic sporocarps. This included a large number of resupinate and hypogeous taxa, many of which were detected both above- and below-ground. PMID:17504467
Smith, Matthew E; Douhan, Greg W; Rizzo, David M
Evidence suggests that truffle-like sporocarp forms have evolved many times in the Pezizales, but primarily from epigeous ancestors within ectomycorrhizal clades. There are several ectomycorrhizal clades, however, that contain no known hypogeous species. We collected specimens of an unusual unidentified truffle from mixed oak woodlands in Iowa. Although clearly a member of the Pezizales (Ascomycota), this hypogeous species did not belong to any of the described truffle genera. Based on a combination of ecological, phylogenetic, and morphological evidence we determined that this new truffle is a hypogeous member of the genus Otidea (Pyronemataceae), a lineage with no described truffle species. We describe it here as a new species, Otidea subterranea. PMID:19422914
Smith, Matthew E; Healy, Rosanne A
Divergence in gene regulation can play a major role in evolution. Here, we used a phylogenetic framework to measure mRNA profiles in 15 yeast species from the phylum Ascomycota and reconstruct the evolution of their modular regulatory programs along a time course of growth on glucose over 300 million years. We found that modules have diverged proportionally to phylogenetic distance, with prominent changes in gene regulation accompanying changes in lifestyle and ploidy, especially in carbon metabolism. Paralogs have significantly contributed to regulatory divergence, typically within a very short window from their duplication. Paralogs from a whole genome duplication (WGD) event have a uniquely substantial contribution that extends over a longer span. Similar patterns occur when considering the evolution of the heat shock regulatory program measured in eight of the species, suggesting that these are general evolutionary principles. DOI: http://dx.doi.org/10.7554/eLife.00603.001
Thompson, Dawn A; Roy, Sushmita; Chan, Michelle; Styczynsky, Mark P; Pfiffner, Jenna; French, Courtney; Socha, Amanda; Thielke, Anne; Napolitano, Sara; Muller, Paul; Kellis, Manolis; Konieczka, Jay H; Wapinski, Ilan; Regev, Aviv
Dragmacidon reticulatum is a marine sponge of wide occurrence in the Eastern and Western Atlantic. Little is known about D. reticulatum fungal diversity. Filamentous fungi recovered from D. reticulatum were assessed in the present study using a polyphasic taxonomic approach, including classical morphology, molecular biology and MALDI-TOF ICMS. Ninety-eight fungal strains were isolated from two D. reticulatum samples by using six different culture media, which were identified up to the genus level. Sixty-four distinct fungal ribotypes were obtained, distributed among twenty-four different genera belonging to the Ascomycota and Zygomycota. Representatives of Penicillium and Trichoderma were the most diverse and abundant fungi isolated. Amongst Penicillium spp. three isolates belonged to the same ribotype can be considered as a putative new species. Data derived from the present study highlight the importance of using a polyphasic approach to get an accurate identification in order to structure a reliable culture collection. PMID:23179657
Passarini, Michel R Z; Santos, Cledir; Lima, Nelson; Berlinck, Roberto G S; Sette, Lara D
Cytochrome P450 (CYP) monooxygenase superfamily contributes a broad array of biological functions in living organisms. In fungi, CYPs play diverse and pivotal roles in versatile metabolism and fungal adaptation to specific ecological niches. In this report, CYPomes in the 47 genomes of fungi belong to the phyla Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota have been studied. The comparison of fungal CYPomes suggests that generally fungi possess abundant CYPs belonging to a variety of families with the two global families CYP51 and CYP61, indicating individuation of CYPomes during the evolution of fungi. Fungal CYPs show highly conserved characteristic motifs, but very low overall sequence similarities. The characteristic motifs of fungal CYPs are distinguishable from those of CYPs in animals, plants, and especially archaea and bacteria. The four representative motifs contribute to the general function of CYPs. Fungal CYP51s and CYP61s can be used as the models for the substrate recognition sites analysis. The CYP proteins are clustered into 15 clades and the phylogenetic analyses suggest that the wide variety of fungal CYPs has mainly arisen from gene duplication. Two large duplication events might have been associated with the booming of Ascomycota and Basidiomycota. In addition, horizontal gene transfer also contributes to the diversification of fungal CYPs. Finally, a possible evolutionary scenario for fungal CYPs along with fungal divergences is proposed. Our results provide the fundamental information for a better understanding of CYP distribution, structure and function, and new insights into the evolutionary events of fungal CYPs along with the evolution of fungi. PMID:24966179
Chen, Wanping; Lee, Mi-Kyung; Jefcoate, Colin; Kim, Sun-Chang; Chen, Fusheng; Yu, Jae-Hyuk
We utilized a series of analogs of D-V13K (a 26-residue amphipathic ?-helical antimicrobial peptide, denoted D1) to compare and contrast the role of hydrophobicity on antifungal and antibacterial activity to the results obtained previously with Pseudomonas aeruginosa strains. Antifungal activity for Zygomycota fungi decreased with increasing hydrophobicity (D-V13K/A12L/A20L/A23L, denoted D4, the most hydrophobic analog was 6-fold less active than D1, the least hydrophobic analog). In contrast, antifungal activity for Ascomycota fungi increased with increasing hydrophobicity (D4, the most hydrophobic analog was 5-fold more active than D1). Hemolytic activity is dramatically affected by increasing hydrophobicity with peptide D4 being 286-fold more hemolytic than peptide D1. The therapeutic index for peptide D1 is 1569-fold and 62-fold better for Zygomycota fungi and Ascomycota fungi, respectively, compared to peptide D4. To reduce the hemolytic activity of peptide D4 and improve/maintain the antifungal activity of D4, we substituted another lysine residue in the center of the nonpolar face (V16K) to generate D5 (D-V13K/V16K/A12L/A20L/A23L). This analog D5 decreased hemolytic activity by 13-fold, enhanced antifungal activity to Zygomycota fungi by 16-fold and improved the therapeutic index by 201-fold compared to D4 and represents a unique approach to control specificity while maintaining high hydrophobicity in the two hydrophobic segments on the nonpolar face of D5.
Jiang, Ziqing; Kullberg, Bart Jan; Lee, Hein van der; Vasil, Adriana I.; Hale, John D.; Mant, Colin T.; Hancock, Robert E. W.; Vasil, Michael L.; Netea, Mihai G.; Hodges, Robert S.
Leaf litter decomposition is the breakdown of dead plant material, a terrestrial ecosystem process of paramount importance. Nutrients released during decomposition play a key role for microbial growth and plant productivity. These processes are controlled by abiotic factors, such as climate, and by biotic factors, such as litter nutrient concentration and stoichiometry (carbon:nutrient ratio) and activity of soil organisms. Future climate change scenarios predict temperature perturbations, therefore following changes of microbial community composition and possible feedbacks on ecosystem processes are of key interest; especially as our knowledge about the microbial regulation of these processes is still scarce. Our aim was to elucidate how temperature perturbations and leaf litter stoichiometry affect the composition of the microbial decomposer community. To this end a terrestrial microcosm experiment using beech (Fagus sylvatica) litter with different stoichiometry was conducted. In a semi-quantitative metaproteomics approach (1D-SDS PAGE combined with liquid chromatography and tandem mass spectrometry; unique spectral counting) we used the intrinsic metabolic function of proteins to relate specific microbial activities to their phylogenetic origin in multispecies communities. Decomposer communities varied on litter with different stoichiometry so that microbial decomposers (fungi and bacteria) were favoured in litter with narrow C:nutrient ratios. The fungal community was dominated by Ascomycota (Eurotiomycetes, Sordariomycetes) and Basidiomycota (Agaricomycetes) and the bacterial community was dominated by Proteobacteria, Actinobacteria and Firmicutes. The extracellular enzymes we detected belonged mainly to classes of xylanases, pectinases, cellulases and proteases and were almost exclusively of fungal origin (particularly Ascomycota). Temperature stress (heat and frost) evoked strong changes in community composition, enzyme activities, dissolved organic nitrogen and litter pH. Freeze treatments resulted in increased fungal abundance and a decline in residual plant litter material, indicating slightly accelerated decomposition. Extracellular enzyme activities were especially blocked by heat treatment. Using metaproteomics enabled us to link the composition of the microbial community to its ecosystem function.
Keiblinger, K. M.; Schneider, T.; Leitner, S.; Hämmerle, I.; Riedel, K.; Zechmeister-Boltenstern, S.
We utilized a series of analogs of D-V13K (a 26-residue amphipathic alpha-helical antimicrobial peptide, denoted D1) to compare and contrast the role of hydrophobicity on antifungal and antibacterial activity to the results obtained previously with Pseudomonas aeruginosa strains. Antifungal activity for zygomycota fungi decreased with increasing hydrophobicity (D-V13K/A12L/A20L/A23L, denoted D4, the most hydrophobic analog was sixfold less active than D1, the least hydrophobic analog). In contrast, antifungal activity for ascomycota fungi increased with increasing hydrophobicity (D4, the most hydrophobic analog was fivefold more active than D1). Hemolytic activity is dramatically affected by increasing hydrophobicity with peptide D4 being 286-fold more hemolytic than peptide D1. The therapeutic index for peptide D1 is 1569-fold and 62-fold better for zygomycota fungi and ascomycota fungi, respectively, compared with peptide D4. To reduce the hemolytic activity of peptide D4 and improve/maintain the antifungal activity of D4, we substituted another lysine residue in the center of the non-polar face (V16K) to generate D5 (D-V13K/V16K/A12L/A20L/A23L). This analog D5 decreased hemolytic activity by 13-fold, enhanced antifungal activity to zygomycota fungi by 16-fold and improved the therapeutic index by 201-fold compared with D4 and represents a unique approach to control specificity while maintaining high hydrophobicity in the two hydrophobic segments on the non-polar face of D5. PMID:19090916
Jiang, Ziqing; Kullberg, Bart Jan; van der Lee, Hein; Vasil, Adriana I; Hale, John D; Mant, Colin T; Hancock, Robert E W; Vasil, Michael L; Netea, Mihai G; Hodges, Robert S
Yeasts were isolated from the phylloplane of various plant species collected from seven provinces in Thailand. A total of 114 yeast strains and 10 strains of a yeast-like fungus were obtained by enrichment isolation from 91 out of 97 leaf samples (93.8 %). On the basis of the D1/D2 domain of the large subunit rRNA gene sequence similarity, 98 strains were identified to be of 36 yeast species in 18 genera belonging to Ascomycota viz. Candida, Clavispora, Cyberlindnera, Debaryomyces, Hanseniaspora, Hyphopichia, Kazachstania, Kluyveromyces, Kodamaea, Lachancea, Metschnikowia, Meyrozyma, Pichia, Starmerella, Torulaspora and Wickerhamomyces, and to Basidiomycota viz. Sporidiobolus and Trichosporon. Three strains were found to represent two novels Candida species which were previously described as C. sirachaensis and C. sakaeoensis. Ten strains of yeast-like fungus were identified as Aureobasidium pullulans of the phylum Ascomycota. Ascomycetous yeast species accounted altogether for 98.0 % of the 98 strains. The prevalent species was Candida tropicalis with a low frequency of isolation (14.3 %). Diversity of yeasts other than ballistoconidium-forming yeast in phylloplane in a tropical country in Asia has been reported for the first time. All strains obtained were accessed for the capability to produce IAA and result revealed that 39 strains in 20 species, one strain each of an undescribed and a novel species, and two unidentified strains showed the capability of producing IAA when cultivated in yeast extract peptone dextrose broth supplemented with 0.1 % L-tryptophan. All five strains of Candida maltosa produced relatively high concentrations of IAA. PMID:22886557
Limtong, Savitree; Koowadjanakul, Nampueng
A major goal of bioinformatics is the characterization of transcription factors and the transcriptional programs they regulate. Given the speed of genome sequencing, we would like to quickly annotate regulatory sequences in newly-sequenced genomes. In such cases, it would be helpful to predict sequence motifs by using experimental data from closely related model organism. Here we present a general algorithm that allow to identify transcription factor binding sites in one newly sequenced species by performing Bayesian regression on the annotated species. First we set the rationale of our method by applying it within the same species, then we extend it to use data available in closely related species. Finally, we generalise the method to handle the case when a certain number of experiments, from several species close to the species on which to make inference, are available. In order to show the performance of the method, we analyse three functionally related networks in the Ascomycota. Two gene network case studies are related to the G2/M phase of the Ascomycota cell cycle; the third is related to morphogenesis. We also compared the method with MatrixReduce and discuss other types of validation and tests. The first network is well known and provides a biological validation test of the method. The two cell cycle case studies, where the gene network size is conserved, demonstrate an effective utility in annotating new species sequences using all the available replicas from model species. The third case, where the gene network size varies among species, shows that the combination of information is less powerful but is still informative. Our methodology is quite general and could be extended to integrate other high-throughput data from model organisms.
Lio, Pietro; Angelini, Claudia; De Feis, Italia; Nguyen, Viet-Anh
Muscodor albus (Xylariaceae, Ascomycetes) isolate CZ-620 produces antimicrobial volatile organic compounds (VOC), which appear to have potential for the control of various postharvest diseases. The effect of water activity (Aw) on the production of VOC by M. albus culture, and their inhibitory effects on the growth of three pathogens of potato tuber (Fusarium sambucinum, Helminthosporium solani, and Pectobacterium atrosepticum) and the development of diseases caused by the three pathogens (dry rot, silver scurf, and bacterial soft rot, respectively) were investigated. Rye grain culture of the fungus produced six alcohols, three aldehydes, five acids or esters, and two terpenoids. The most abundant VOC were: isobutyric acid; bulnesene, a sesquiterpene; an unidentified terpene; 2 and 3-methyl-1-butanol; and ethanol. However, the level of each of those VOC varied with Aw of the culture. Emission activity occurred mainly at Aw above 0.75 and high emission of most VOC occurred only at Aw above 0.90. The aldehydes (2-methyl-propanal and 3-methyl-butanal) were the only VOC produced in quantities below an Aw of 0.90. An Aw value of 0.96 favored maximum emission of acids, esters, and terpenoids. There was a higher production of alcohols and a decrease in aldehydes with increase in Aw. Isobutyric acid, which has been the main M. albus VOC monitored in previous studies as an indicator of antifungal activity, had a rather narrow optimum, peaking at Aw of 0.96 and declining sharply above 0.98. Results showed that substrate Aw affects the production dynamics of each group of VOC by the fungus, and suggest that VOC production can be prolonged by maintaining M. albus culture at a constant optimum Aw. The VOC was inhibitory to F. sambucinum, H. solani, and P. atrosepticum; and biofumigation with M. albus significantly reduced dry rot and soft rot development, and completely controlled silver scurf in inoculated tubers incubated at both 8°C and 22°C. The results show that Aw of grain culture affects the production of VOC by M. albus; and that the VOC inhibit the growth of the tested pathogens and the diseases caused by them in potato tubers. PMID:21354528
Corcuff, Ronan; Mercier, Julien; Tweddell, Russell; Arul, Joseph
BACKGROUND: The pattern and timing of the rise in complex multicellular life during Earth's history has not been established. Great disparity persists between the pattern suggested by the fossil record and that estimated by molecular clocks, especially for plants, animals, fungi, and the deepest branches of the eukaryote tree. Here, we used all available protein sequence data and molecular clock methods to place constraints on the increase in complexity through time. RESULTS: Our phylogenetic analyses revealed that (i) animals are more closely related to fungi than to plants, (ii) red algae are closer to plants than to animals or fungi, (iii) choanoflagellates are closer to animals than to fungi or plants, (iv) diplomonads, euglenozoans, and alveolates each are basal to plants+animals+fungi, and (v) diplomonads are basal to other eukaryotes (including alveolates and euglenozoans). Divergence times were estimated from global and local clock methods using 20-188 proteins per node, with data treated separately (multigene) and concatenated (supergene). Different time estimation methods yielded similar results (within 5%): vertebrate-arthropod (964 million years ago, Ma), Cnidaria-Bilateria (1,298 Ma), Porifera-Eumetozoa (1,351 Ma), Pyrenomycetes-Plectomycetes (551 Ma), Candida-Saccharomyces (723 Ma), Hemiascomycetes-filamentous Ascomycota (982 Ma), Basidiomycota-Ascomycota (968 Ma), Mucorales-Basidiomycota (947 Ma), Fungi-Animalia (1,513 Ma), mosses-vascular plants (707 Ma), Chlorophyta-Tracheophyta (968 Ma), Rhodophyta-Chlorophyta+Embryophyta (1,428 Ma), Plantae-Animalia (1,609 Ma), Alveolata-plants+animals+fungi (1,973 Ma), Euglenozoa-plants+animals+fungi (1,961 Ma), and Giardia-plants+animals+fungi (2,309 Ma). By extrapolation, mitochondria arose approximately 2300-1800 Ma and plastids arose 1600-1500 Ma. Estimates of the maximum number of cell types of common ancestors, combined with divergence times, showed an increase from two cell types at 2500 Ma to approximately 10 types at 1500 Ma and 50 cell types at approximately 1000 Ma. CONCLUSIONS: The results suggest that oxygen levels in the environment, and the ability of eukaryotes to extract energy from oxygen, as well as produce oxygen, were key factors in the rise of complex multicellular life. Mitochondria and organisms with more than 2-3 cell types appeared soon after the initial increase in oxygen levels at 2300 Ma. The addition of plastids at 1500 Ma, allowing eukaryotes to produce oxygen, preceded the major rise in complexity.
Hedges, S. Blair; Blair, Jaime E.; Venturi, Maria L.; Shoe, Jason L.
Background Many 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. Results We 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. Conclusion We 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.
Parrent, Jeri Lynn; James, Timothy Y; Vasaitis, Rimvydas; Taylor, Andrew FS
Trichothecenes are sesquiterpenoid toxins produced by Fusarium species. Since these mycotoxins are very stable, there is interest in microbial transformations that can remove toxins from contaminated grain or cereal products. Twenty-three yeast species assigned to the Trichomonascus clade (Saccharomycotina, Ascomycota), including four Trichomonascus species and 19 anamorphic species presently classified in Blastobotrys, were tested for their ability to convert the trichothecene T-2 toxin to less-toxic products. These species gave three types of biotransformations: acetylation to 3-acetyl T-2 toxin, glycosylation to T-2 toxin 3-glucoside, and removal of the isovaleryl group to form neosolaniol. Some species gave more than one type of biotransformation. Three Blastobotrys species converted T-2 toxin into T-2 toxin 3-glucoside, a compound that has been identified as a masked mycotoxin in Fusarium-infected grain. This is the first report of a microbial whole-cell method for producing trichothecene glycosides, and the potential large-scale availability of T-2 toxin 3-glucoside will facilitate toxicity testing and development of methods for detection of this compound in agricultural and other products.
Price, Neil P. J.; Kurtzman, Cletus P.
Ancient mariners knew that dust whipped up from deserts by strong winds travelled long distances, including over oceans. Satellite remote sensing revealed major dust sources across the Sahara. Indeed, the Bodélé Depression in the Republic of Chad has been called the dustiest place on earth. We analysed desert sand from various locations in Chad and dust that had blown to the Cape Verde Islands. High throughput sequencing techniques combined with classical microbiological methods showed that the samples contained a large variety of microbes well adapted to the harsh desert conditions. The most abundant bacterial groupings in four different phyla included: (a) Firmicutes—Bacillaceae, (b) Actinobacteria—Geodermatophilaceae, Nocardiodaceae and Solirubrobacteraceae, (c) Proteobacteria—Oxalobacteraceae, Rhizobiales and Sphingomonadaceae, and (d) Bacteroidetes—Cytophagaceae. Ascomycota was the overwhelmingly dominant fungal group followed by Basidiomycota and traces of Chytridiomycota, Microsporidia and Glomeromycota. Two freshwater algae (Trebouxiophyceae) were isolated. Most predominant taxa are widely distributed land inhabitants that are common in soil and on the surfaces of plants. Examples include Bradyrhizobium spp. that nodulate and fix nitrogen in Acacia species, the predominant trees of the Sahara as well as Herbaspirillum (Oxalobacteraceae), a group of chemoorganotrophic free-living soil inhabitants that fix nitrogen in association with Gramineae roots. Few pathogenic strains were found, suggesting that African dust is not a large threat to public health.
Favet, Jocelyne; Lapanje, Ales; Giongo, Adriana; Kennedy, Suzanne; Aung, Yin-Yin; Cattaneo, Arlette; Davis-Richardson, Austin G; Brown, Christopher T; Kort, Renate; Brumsack, Hans-Jurgen; Schnetger, Bernhard; Chappell, Adrian; Kroijenga, Jaap; Beck, Andreas; Schwibbert, Karin; Mohamed, Ahmed H; Kirchner, Timothy; de Quadros, Patricia Dorr; Triplett, Eric W; Broughton, William J; Gorbushina, Anna A
In order to investigate the diversity of endophytes, fungal endophytes in Panax ginseng Meyer cultivated in Korea were isolated and identified using internal transcribed spacer (ITS) sequences of ribosomal DNA. Three cultivars of 3-year-old ginseng roots (Chunpoong, Yunpoong, and Gumpoong) were used to isolate fungal endophytes. Surface sterilized ginseng roots were placed on potato dextrose agar plates supplemented with ampicilin and streptomycin to inhibit bacterial growth. Overall, 38 fungal endophytes were isolated from 12 ginseng roots. According to the sequence analysis of the ITS1-5.8S-ITS2, 38 fungal isolates were classified into 4 different fungal species, which were Phoma radicina, Fusarium oxysporum, Setophoma terrestris and Ascomycota sp. 2-RNK. The most dominant fungal endophyte was P. radicina in 3 cultivars. The percentage of dominant endophytes of P. radicina was 65.8%. The percentage of colonization frequency of P. radicina was 80%, 52.9%, and 75% in Chunpoong, Yunpoong, and Gumpoong, respectively. The second most dominant fungal endophyte was F. oxysporum. The diversity of the fungal endophytes was low and no ginseng cultivar specificity among endophytes was detected in this study. The identified endophytes can be potential fungi for the production of bioactive compounds and control against ginseng pathogens.
Park, Sang Un; Lim, Hyoun-Sub; Park, Kee-Choon; Park, Young-Hwan; Bae, Hanhong
Among fungi, the basic life strategies are saprophytism, parasitism, and predation. Fungi in Orbiliaceae (Ascomycota) prey on animals by means of specialized trapping structures. Five types of trapping devices are recognized, but their evolutionary origins and divergence are not well understood. Based on comprehensive phylogenetic analysis of nucleotide sequences of three protein-coding genes (RNA polymerase II subunit gene, rpb2; elongation factor 1-? gene, ef1-?; and ß tubulin gene, bt) and ribosomal DNA in the internal transcribed spacer region, we have demonstrated that the initial trapping structure evolved along two lineages yielding two distinct trapping mechanisms: one developed into constricting rings and the other developed into adhesive traps. Among adhesive trapping devices, the adhesive network separated from the others early and evolved at a steady and gentle speed. The adhesive knob evolved through stalk elongation, with a final development of nonconstricting rings. Our data suggest that the derived adhesive traps are at a highly differentiated stage. The development of trapping devices is felicitous proof of adaptive evolution.
Yang, Ying; Yang, Ence; An, Zhiqiang; Liu, Xingzhong
Five fungal genomes from the Ascomycota (sac fungi) were found to contain a gene with sequence similarity to a recently discovered small group of bacterial prenyltransferases that catalyze the C-prenylation of aromatic substrates in secondary metabolism. The genes from Aspergillus terreus NIH2624, Botryotinia fuckeliana B05.10 and Sclerotinia sclerotiorum 1980 were expressed in Escherichia coli, and the resulting His(8)-tagged proteins were purified and investigated biochemically. Their substrate specificity was found to be different from that of any other prenyltransferase investigated previously. Using 2,7-dihydroxynaphthalene (2,7-DHN) and dimethylallyl diphosphate as substrates, they catalyzed a regiospecific Friedel-Crafts alkylation of 2,7-DHN at position 3. Using the enzyme of A. terreus, the K(m) values for 2,7-DHN and dimethylallyl diphosphate were determined as 324 +/- 25 microM and 325 +/- 35 microM, respectively, and k(cat) as 0.026 +/- 0.001 s(-1). A significantly lower level of prenylation activity was found using dihydrophenazine-1-carboxylic acid as aromatic substrate, and only traces of products were detected with aspulvinone E, flaviolin, or 4-hydroxybenzoic acid. No product was formed with l-tryptophan, l-tyrosine, or 4-hydroxyphenylpyruvate. The genes for these fungal prenyltransferases are not located within recognizable secondary metabolic gene clusters. Their physiological function is yet unknown. PMID:20351110
Haug-Schifferdecker, Elisa; Arican, Deniz; Brückner, Reinhard; Heide, Lutz
Lichenization is assumed to be a very ancient mode of fungal nutrition, but fossil records are rare. Here we describe two fragments of exceptionally preserved, probably charred, lichen thalli with internal stratification. Cyanolichenomycites devonicus has a cyanobacterial and Chlorolichenomycites salopensis a unicellular, presumably green algal photobiont. Fruiting bodies are missing. Cyanolichenomycites devonicus forms asexual spores in a pycnidium. All specimens were examined with scanning electron microscopy techniques. The fossils were extracted by maceration. Extant lichens and free-living cyanobacteria were either experimentally charcoalified for comparison or conventionally prepared. Based on their septate hyphal structure, both specimens are tentatively interpreted as representatives of the Pezizomycotina (Ascomycota). Their presence in 415 million yr (Myr) old rocks from the Welsh Borderland predates existing Late Cretaceous records of pycnidial conidiomata by some 325 Myr and Triassic records of lichens with broadly similar organization by some 195 Myr. These fossils represent the oldest known record of lichens with symbionts and anatomy as typically found in morphologically advanced taxa today. The latter does not apply to Winfrenatia reticulata, the enigmatic crustose lichen fossil from the Lower Devonian, nor to presumed lichen-like organisms such as the Cambrian Farghera robusta or to the Lower Devonian Spongiophyton minutissimum. PMID:23110612
Honegger, Rosmarie; Edwards, Dianne; Axe, Lindsey
The objective of this study was 2-fold: to evaluate whether phylogenetically closely related yeasts share common antifungal susceptibility profiles (ASPs) and whether these ASPs can be predicted from phylogeny. To address this question, 9,627 yeast strains were collected and tested for their antifungal susceptibility. Isolates were reidentified by considering recent changes in taxonomy and nomenclature. A phylogenetic (PHYLO) code based on the results of multilocus sequence analyses (large-subunit rRNA, small-subunit rRNA, translation elongation factor 1?, RNA polymerase II subunits 1 and 2) and the classification of the cellular neutral sugar composition of coenzyme Q and 18S ribosomal DNA was created to group related yeasts into PHYLO groups. The ASPs were determined for fluconazole, itraconazole, and voriconazole in each PHYLO group. The majority (95%) of the yeast strains were Ascomycetes. After reclassification, a total of 23 genera and 54 species were identified, resulting in an increase of 64% of genera and a decrease of 5% of species compared with the initial identification. These taxa were assigned to 17 distinct PHYLO groups (Ascomycota, n=13; Basidiomycota, n=4). ASPs for azoles were similar among members of the same PHYLO group and different between the various PHYLO groups. Yeast phylogeny may be an additional tool to significantly enhance the assessment of MIC values and to predict antifungal susceptibility, thereby more rapidly initiating appropriate patient management. PMID:24366735
Schmalreck, A F; Lackner, M; Becker, K; Fegeler, W; Czaika, V; Ulmer, H; Lass-Flörl, C
Paleoophiocordyceps coccophagus, a fungal parasite of a scale insect from the Early Cretaceous (Upper Albian), is reported and described here. This fossil not only provides the oldest fossil evidence of animal parasitism by fungi but also contains morphological features similar to asexual states of Hirsutella and Hymenostilbe of the extant genus Ophiocordyceps (Ophiocordycipitaceae, Hypocreales, Sordariomycetes, Pezizomycotina, Ascomycota). Because species of Hypocreales collectively exhibit a broad range of nutritional modes and symbioses involving plants, animals and other fungi, we conducted ancestral host reconstruction coupled with phylogenetic dating analyses calibrated with P.coccophagus. These results support a plant-based ancestral nutritional mode for Hypocreales, which then diversified ecologically through a dynamic process of intra- and interkingdom host shifts involving fungal, higher plant and animal hosts. This is especially evident in the families Cordycipitaceae, Clavicipitaceae and Ophiocordycipitaceae, which are characterized by a high occurrence of insect pathogens. The ancestral ecologies of Clavicipitaceae and Ophiocordycipitaceae are inferred to be animal pathogens, a trait inherited from a common ancestor, whereas the ancestral host affiliation of Cordycipitaceae was not resolved. Phylogenetic dating supports both a Jurassic origin of fungal-animal symbioses within Hypocreales and parallel diversification of all three insect pathogenic families during the Cretaceous, concurrent with the diversification of insects and angiosperms. PMID:18817884
Sung, Gi-Ho; Poinar, George O; Spatafora, Joseph W
Dermatophytes are a group of closely related fungi that have keratinase and can therefore cause infections in keratinised human and animal tissues (skin, hair and nails), leading to a disease known as dermatophytosis. This group is composed by the genera Epidermophyton, Trichophyton and Microsporum, forming an approximated total of 40 species. Depending on the source of the keratin used, dermatophytes can be divided in geophilic (soil), zoophilic (animals) and anthropophilic (human), with soil, some animals and humans being their primary habitats. Many dermatophytes can be present in both anamorphic (asexual state) or imperfect and teleomorphic state (with sexual reproduction) or perfect fungi. Anamorphic states (genera Epidermophyton, Microsporum and Trichophyton ) belong to the Hyphomycetes and phylum Deuteromycota class and teleomorphic states (the majority of geophilic and zoophilic species of Microsporum and Trichophyton) are classified in the teleomorphic genus Arthroderma, order Onygenales, phylum Ascomycota, and are usually found in their anamorphic state. Dermatophytes have a worldwide distribution, being responsible for most of the skin mycoses in both healthy and immunocompromised patients. The diagnosis and treatment of dermatophytosis are well known by most microbiologists and scientists in general. However, we describe recent techniques for their diagnosis and up-to-date treatments. The main purpose of this review is to provide a detailed description of the three genera of dermatophytes, with special mention of Epidermophyton floccosum, a object of the SEIMC's mycology quality control (M-2/09). PMID:21458709
Molina de Diego, Araceli
The fungal kingdom displays a fascinating diversity of sex-determination systems. Recent advances in genomics provide insights into the molecular mechanisms of sex, mating type determination, and evolution of sexual reproduction in many fungal species in both ancient and modern phylogenetic lineages. All major fungal groups have evolved sexual differentiation and recombination pathways. However, sexuality is unknown in arbuscular mycorrhizal fungi (AMF) of the phylum Glomeromycota, an ecologically vital group of obligate plant root symbionts. AMF are commonly considered an ancient asexual lineage dating back to the Ordovician, approximately 460 M years ago. In this study, we used genomic and transcriptomic surveys of several AMF species to demonstrate the presence of conserved putative sex pheromone-sensing mitogen-activated protein (MAP) kinases, comparable to those described in Ascomycota and Basidiomycota. We also find genes for high mobility group (HMG) transcription factors, homologous to SexM and SexP genes in the Mucorales. The SexM genes show a remarkable sequence diversity among multiple copies in the genome, while only a single SexP sequence was detected in some isolates of Rhizophagus irregularis. In the Mucorales and Microsporidia, the sexM gene is flanked by genes for a triosephosphate transporter (TPT) and a RNA helicase, but we find no evidence for synteny in the vicinity of the Sex locus in AMF. Nonetheless, our results, together with previous observations on meiotic machinery, suggest that AMF could undergo a complete sexual reproduction cycle.
Halary, Sebastien; Daubois, Laurence; Terrat, Yves; Ellenberger, Sabrina; Wostemeyer, Johannes; Hijri, Mohamed
Retrotransposons with a tyrosine recombinase (YR) have been discovered recently and lack thorough annotation in fungi. YR retrotransposons are divided into 3 groups: DIRS, Ngaro and VIPER (known only from kinetoplastida). We used comparative genomics to investigate the evolutionary patterns of retrotransposons in the fungal kingdom. The identification of both functional and remnant elements provides a unique view on both recent and past transposition activity. Our searches covering a wide range of fungal genomes allowed us to identify 2241 YR retrotransposons. Based on CLANS clustering of concatenated sequences of the reverse transcriptase (RT), RNase H (RH), DNA N-6-adenine-methyltransferase (MT) and YR protein domains we propose a revised classification of YR elements expanded by two new categories of Ngaro elements. A phylogenetic analysis of 477 representatives supports this observation and additionally demonstrates that DIRS and Ngaro abundance changed independently in Basidiomycota and Blastocladiomycota/Mucoromycotina/Kixellomycotina. Interestingly, a single remnant Ngaro element could be identified in an Ascomycota genome. Our analysis revealed also that 3 Pucciniomycotina taxa, known for their overall mobile element abundance and big genome size, encode an elevated number of Ngaro retrotransposons. Considering the presence of DIRS elements in all analyzed Mucoromycotina, Kickxellomycotina and Blastocladiomycota genomes one might assume a common origin of fungal DIRS retrotransposons with a loss in Dicarya. Ngaro elements described to date from Opisthokonta, seem to have invaded the common ancestor of Agaricomycotina and Pucciniomycotina after Ustilagomycotina divergence. Yet, most of analyzed genomes are devoid of YR elements and most identified retrotransposons are incomplete.
Muszewska, Anna; Steczkiewicz, Kamil; Ginalski, Krzysztof
Lentinan is an antitumor product that is purified from fresh Lentinula edodes fruiting bodies. It is a cell wall component, comprising ?-1,3-glucan with ?-1,6-linked branches, which becomes degraded during postharvest preservation as a result of increased glucanase activity. In this study, we used N-terminal amino acid sequence to isolate tlg1, a gene encoding a thaumatin-like (TL) protein in L. edodes. The cDNA clone was approximately 1.0 kb whereas the genomic sequence was 2.1 kb, and comparison of the two indicated that tlg1 contains 12 introns. The tlg1 gene product (TLG1) was predicted to comprise 240 amino acids, with a molecular mass of 25 kD and isoelectric point value of 3.5. The putative amino acid sequence exhibits approximately 40% identity with plant TL proteins, and a fungal genome database search revealed that these TL proteins are conserved in many fungi including the basidiomycota and ascomycota. Transcription of tlg1 was not detected in vegetative mycelium or young and fresh mushrooms. However, transcription increased following harvest. Western-blot analysis demonstrated a rise in TLG1 levels following harvest and spore diffusion. TLG1 expressed in Escherichia coli and Aspergillus oryzae exhibited ?-1,3-glucanase activity and, when purified from the L. edodes fruiting body, demonstrated lentinan degrading activity. Thus, we suggest that TLG1 is involved in lentinan and cell wall degradation during senescence following harvest and spore diffusion.
Sakamoto, Yuichi; Watanabe, Hisayuki; Nagai, Masaru; Nakade, Keiko; Takahashi, Machiko; Sato, Toshitsugu
A mycosed planthopper, Oliarus dimidiatus Berg (Hemiptera: Cixiidae), and two psocids, Heterocaecilius sp. (Psocodea: Pseudocaeciliidae) and Ectopsocus sp. (Ectopsocidae), were collected from Los Hornos and La Plata, Buenos Aires, Argentina between February and September 2007. Observations of mycelia growing on the host revealed that the putative fungal parasite had synnemata supporting monophialidic conidiogenous cells. Likewise, in vitro fungal cultures presented characteristics typical of the fungus Hirsutella citriformis Speare (Ascomycota: Hypocreales: Clavicipitaceae). The identity of the isolated fungi characterized based on morphological aspects was complemented by means of the internal transcribed spacer sequences. The sequences of both isolates were highly homologous to those of Cordyceps sp. (Fries) Link and Ophiocordyceps sinensis (Berkely) G.H. Sung, J.M. Sung, Hywel-Jones, and Spatafora (Ophiocordycipitaceae). We additionally confirmed that both isolates had the ability to infect and kill adults of Delphacodes kuscheli Fennah (Hemiptera: Delphacidae) after 10 days. Therefore, based on the morphology of the isolated fungi, their ribosomal internal transcribed spacer sequence, and their ability to parasite insects, we conclude that the fungi isolated belong to the genus Hirsutella and might have biotechnological potential. PMID:23885970
Toledo, Andrea V; Simurro, María E; Balatti, Pedro A
Ancient mariners knew that dust whipped up from deserts by strong winds travelled long distances, including over oceans. Satellite remote sensing revealed major dust sources across the Sahara. Indeed, the Bodélé Depression in the Republic of Chad has been called the dustiest place on earth. We analysed desert sand from various locations in Chad and dust that had blown to the Cape Verde Islands. High throughput sequencing techniques combined with classical microbiological methods showed that the samples contained a large variety of microbes well adapted to the harsh desert conditions. The most abundant bacterial groupings in four different phyla included: (a) Firmicutes-Bacillaceae, (b) Actinobacteria-Geodermatophilaceae, Nocardiodaceae and Solirubrobacteraceae, (c) Proteobacteria-Oxalobacteraceae, Rhizobiales and Sphingomonadaceae, and (d) Bacteroidetes-Cytophagaceae. Ascomycota was the overwhelmingly dominant fungal group followed by Basidiomycota and traces of Chytridiomycota, Microsporidia and Glomeromycota. Two freshwater algae (Trebouxiophyceae) were isolated. Most predominant taxa are widely distributed land inhabitants that are common in soil and on the surfaces of plants. Examples include Bradyrhizobium spp. that nodulate and fix nitrogen in Acacia species, the predominant trees of the Sahara as well as Herbaspirillum (Oxalobacteraceae), a group of chemoorganotrophic free-living soil inhabitants that fix nitrogen in association with Gramineae roots. Few pathogenic strains were found, suggesting that African dust is not a large threat to public health. PMID:23254516
Favet, Jocelyne; Lapanje, Ales; Giongo, Adriana; Kennedy, Suzanne; Aung, Yin-Yin; Cattaneo, Arlette; Davis-Richardson, Austin G; Brown, Christopher T; Kort, Renate; Brumsack, Hans-Jürgen; Schnetger, Bernhard; Chappell, Adrian; Kroijenga, Jaap; Beck, Andreas; Schwibbert, Karin; Mohamed, Ahmed H; Kirchner, Timothy; de Quadros, Patricia Dorr; Triplett, Eric W; Broughton, William J; Gorbushina, Anna A
Ozone is considered as the main factor in air pollution related to a decline of forest in North America and Europe. In the present study, the effect of changed litter quality, due to ozone stress to trees, on the microbial communities colonizing the subsequent litter was investigated. Litter bag technique using beech and spruce litter from ozone-stressed and control trees, was combined with 16S and 18S rRNA-based fingerprinting methods and cloning to characterize phylogenetic diversity. Litter bags were incubated for 2 and 8 weeks in a beech-spruce mixed forest. Differences between the structure of microbial communities colonizing control and ozone-exposed litter were evident by fingerprints of 16S and 18S rRNA RT-PCR products. RT-PCR products, from litter degraded for 8 weeks, were cloned to identify the bacterial and fungal groups. Clones similar to members of Actinobacteria dominated the bacterial libraries, whereas effects of changed litter quality were mainly observed for the Proteobacteria. Fungal libraries were dominated by clones similar to Ascomycota members. Reduced proportion of clones similar to Basidiomycota and Zygomycota in library from ozone-stressed spruce trees and Chytridiomycota from ozone-stressed beech trees was observed when compared to their control counterparts. As hypothesized, changed litter quality due to elevated O3 did influence the structure of litter-colonizing microbial communities. However, these differences were not as pronounced as those between the two plant species. PMID:17364248
Aneja, Manish Kumar; Sharma, Shilpi; Fleischmann, Frank; Stich, Susanne; Heller, Werner; Bahnweg, Günther; Munch, Jean Charles; Schloter, Michael
The marine environment is characterized by high salinity and exerts a strong selective pressure on the biota, favouring the development of halo-tolerant microorganisms. Part of this microbial diversity is made up of fungi, important organisms from ecological and biotechnological points of view. In this study, for the first time, the qualitative and quantitative composition of the mycoflora associated to leaves, rhizomes, roots and matte of the seagrass Posidonia oceanica was estimated. A total of 88 fungal taxa, mainly belonging to Ascomycota, were identified by morphological and molecular methods. The most represented genera were Penicillium, Cladosporium and Acremonium. Most of the species (70) were selectively associated with one district; only two species (Penicillium chrysogenum var. chrysogenum and P. janczewskii) were isolated from all the districts. Moreover the capability to produce laccases, peroxidases and tannases by 107 fungal isolated by the different districts of P. oceanica was carried out. These results show that the mycoflora associated to P. oceanica is very rich and characterized by fungi able to produce ligninolytic enzymes and tannases useful to degrade and detoxify lignocellulose residues in presence of high salt concentrations. These fungi, hence, may play important ecological roles in marine environments but can also be very useful in different biotechnological areas. PMID:23410985
Panno, Luigi; Bruno, Maurizio; Voyron, Samuele; Anastasi, Antonella; Gnavi, Giorgio; Miserere, Luca; Varese, Giovanna Cristina
Diet influences health as a source of nutrients and toxins, and by shaping the composition of resident microbial populations. Previous studies have begun to map out associations between diet and the bacteria and viruses of the human gut microbiome. Here we investigate associations of diet with fungal and archaeal populations, taking advantage of samples from 98 well-characterized individuals. Diet was quantified using inventories scoring both long-term and recent diet, and archaea and fungi were characterized by deep sequencing of marker genes in DNA purified from stool. For fungi, we found 66 genera, with generally mutually exclusive presence of either the phyla Ascomycota or Basiodiomycota. For archaea, Methanobrevibacter was the most prevalent genus, present in 30% of samples. Several other archaeal genera were detected in lower abundance and frequency. Myriad associations were detected for fungi and archaea with diet, with each other, and with bacterial lineages. Methanobrevibacter and Candida were positively associated with diets high in carbohydrates, but negatively with diets high in amino acids, protein, and fatty acids. A previous study emphasized that bacterial population structure was associated primarily with long-term diet, but high Candida abundance was most strongly associated with the recent consumption of carbohydrates. Methobrevibacter abundance was associated with both long term and recent consumption of carbohydrates. These results confirm earlier targeted studies and provide a host of new associations to consider in modeling the effects of diet on the gut microbiome and human health. PMID:23799070
Hoffmann, Christian; Dollive, Serena; Grunberg, Stephanie; Chen, Jun; Li, Hongzhe; Wu, Gary D; Lewis, James D; Bushman, Frederic D
We describe a new ab initio algorithm, GeneMark-ES version 2, that identifies protein-coding genes in fungal genomes. The algorithm does not require a predetermined training set to estimate parameters of the underlying hidden Markov model (HMM). Instead, the anonymous genomic sequence in question is used as an input for iterative unsupervised training. The algorithm extends our previously developed method tested on genomes of Arabidopsis thaliana, Caenorhabditis elegans, and Drosophila melanogaster. To better reflect features of fungal gene organization, we enhanced the intron submodel to accommodate sequences with and without branch point sites. This design enables the algorithm to work equally well for species with the kinds of variations in splicing mechanisms seen in the fungal phyla Ascomycota, Basidiomycota, and Zygomycota. Upon self-training, the intron submodel switches on in several steps to reach its full complexity. We demonstrate that the algorithm accuracy, both at the exon and the whole gene level, is favorably compared to the accuracy of gene finders that employ supervised training. Application of the new method to known fungal genomes indicates substantial improvement over existing annotations. By eliminating the effort necessary to build comprehensive training sets, the new algorithm can streamline and accelerate the process of annotation in a large number of fungal genome sequencing projects. PMID:18757608
Ter-Hovhannisyan, Vardges; Lomsadze, Alexandre; Chernoff, Yury O; Borodovsky, Mark
Chemical and microbial characterisations of particle-size fractions (PSFs) from a rice paddy soil subjected to long-term heavy metal pollution (P) and nonpolluted (NP) soil were performed to investigate whether the distribution of heavy metals (Cd, Cu, Pb and Zn) regulates microbial community activity, abundance and diversity at the microenvironment scale. The soils were physically fractionated into coarse sand, fine sand, silt and clay fractions. Long-term heavy metal pollution notably decreased soil basal respiration (a measurement of the total activity of the soil microbial community) and microbial biomass carbon (MBC) across the fractions by 3-45% and 21-53%, respectively. The coarse sand fraction was more affected by pollution than the clay fraction and displayed a significantly lower MBC content and respiration and dehydrogenase activity compared with the nonpolluted soils. The abundances and diversities of bacteria were less affected within the PSFs under pollution. However, significant decreases in the abundances and diversities of fungi were noted, which may have strongly contributed to the decrease in MBC. Sequencing of denaturing gradient gel electrophoresis bands revealed that the groups Acidobacteria, Ascomycota and Chytridiomycota were clearly inhibited under pollution. Our findings suggest that long-term heavy metal pollution decreased the microbial biomass, activity and diversity in PSFs, particularly in the large-size fractions. PMID:24020402
Chen, Junhui; He, Feng; Zhang, Xuhui; Sun, Xuan; Zheng, Jufeng; Zheng, Jinwei
Mutualisms, or interactions between species that lead to net fitness benefits for each species involved, are stable and ubiquitous in nature mostly due to "byproduct benefits" stemming from the intrinsic traits of one partner that generate an indirect and positive outcome for the other. Here we verify if myrmecotrophy (where plants obtain nutrients from the refuse of their associated ants) can explain the stability of the tripartite association between the myrmecophyte Hirtella physophora, the ant Allomerus decemarticulatus and an Ascomycota fungus. The plant shelters and provides the ants with extrafloral nectar. The ants protect the plant from herbivores and integrate the fungus into the construction of a trap that they use to capture prey; they also provide the fungus and their host plant with nutrients. During a 9-month field study, we over-provisioned experimental ant colonies with insects, enhancing colony fitness (i.e., more winged females were produced). The rate of partial castration of the host plant, previously demonstrated, was not influenced by the experiment. Experimental plants showed higher ?(15)N values (confirming myrmecotrophy), plus enhanced vegetative growth (e.g., more leaves produced increased the possibility of lodging ants in leaf pouches) and fitness (i.e., more fruits produced and more flowers that matured into fruit). This study highlights the importance of myrmecotrophy on host plant fitness and the stability of ant-myrmecophyte mutualisms. PMID:23516632
Dejean, Alain; Orivel, Jérôme; Rossi, Vivien; Roux, Olivier; Lauth, Jérémie; Malé, Pierre-Jean G; Céréghino, Régis; Leroy, Céline
To get a comprehensive view of fungal M35 family (deuterolysin) and M36 family (fungalysin) genes, we conducted genome-wide investigations and phylogenetic analyses of genes in these two families from 50 sequenced Ascomycota fungi with different life styles. Large variations in the number of M35 family and M36 family genes were found among different fungal genomes, indicating that these two gene families have been highly dynamic through fungal evolution. Moreover, we found obvious expansions of Meps in two families of Onygenales: Onygenaceae and Arthodermataceae, whereas species in family Ajellomycetace did not show expansion of these genes. The strikingly different gene duplication and loss patterns in Onygenales may be associated with the different pathogenicity of these species. Interestingly, likelihood ratio tests (LRT) of both M35 family and M36 family genes suggested that several branches leading to the duplicated genes in dermatophytic and Coccidioides fungi had signatures of positive selection, indicating that the duplicated Mep genes have likely diverged functionally to play important roles during the evolution of pathogenicity of dermatophytic and Coccidioides fungi. The potentially positively selected residues discovered by our analysis may have contributed to the development of new physiological functions of the duplicated Mep genes in dermatophytic fungi and Coccidioides species. Our study adds to the current knowledge of the evolution of Meps in fungi and also establishes a theoretical foundation for future experimental investigations. PMID:24587291
Li, Juan; Zhang, Ke-Qin
A particular fungal population is present in the main stages of the manufacturing process of cork discs. Its diversity was studied using both dependent (isolation) and independent culture methods (denaturing gel gradient electrophoresis and cloning of the ITS1-5.8S-ITS2 region). The mycobiota in the samples taken in the stages before and after the first boiling seems to be distinct from the population in the subsequent manufacturing stages. Most isolated fungi belong to the genera Penicillium, Eurotium and Cladosporium. The presence of uncultivable fungi, Ascomycota and endophytes in raw cork was confirmed by sequencing. The samples taken after the first boiling contained uncultivable fungi, but in a few samples some isolated fungi were also detected. The main taxa present in the following stages were Chrysonilia sitophila, Penicillium glabrum and Penicillium spp. All applied techniques had complementary outcomes. The main factors driving the shift in cork fungal colonization seem to be the high levels of humidity and temperature to which the slabs are subjected during the boiling process. PMID:22630140
Barreto, Maria C; Houbraken, Jos; Samson, Robert A; Brito, Dulce; Gadanho, Mário; San Romão, Maria V
Invasive plants have caused great economic losses and environmental problems worldwide. Eupatorium adenophorum is one of the most invasive weeds in China. To better understand its invasive mechanisms, in the present paper, the microbial communities of healthy and diseased leaves of E. adenophorum were obtained using both culture-independent and -dependent methods and their diversities were compared. The bacteria obtained from culture-independent method belong to Proteobacteria (95.8%), Actinobacteria (2.1%), and Firmicutes (2.1%) and fungi belong to Ascomycota (65.2%) and Basidiomycota (34.8%). Very few overlapped microbial species were found by culture-dependent and -independent methods. Healthy leaves display higher bacterial diversity than diseased leaves. Phylogenetic structures are very different between healthy and diseased phyllosphere microbial communities. Bacteria close to Acinetobacter and Pseudomonas were dominant on healthy leaves, whereas those close to Shigella were dominant on diseased leaves. 52.9% of fungal clones from healthy leaves were Ustilaginomycetes, close to Rhodotorula phylloplana and uncultured basidomycete; by contrast, 60% of clones from diseased leaves were Lecanoromycetes, close to Umbilicaria muehlenbergii. No bacteria but four fungal strains phylogenetically close to Myrothecium sp. and Alternaria alternate were pathogenic to seedlings and detached leaves of the invasive plant. Therefore, this plant may be resistant to pathogens from bacteria but not fungi in its introduced range. PMID:20437143
Zhou, Zhen-Xin; Jiang, Huan; Yang, Chen; Yang, Ming-Zhi; Zhang, Han-Bo
Nonribosomal peptides and polyketides are a diverse group of natural products with complex chemical structures and enormous pharmaceutical potential. They are synthesized on modular nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) enzyme complexes by a conserved thiotemplate mechanism. Here, we report the widespread occurrence of NRPS and PKS genetic machinery across the three domains of life with the discovery of 3,339 gene clusters from 991 organisms, by examining a total of 2,699 genomes. These gene clusters display extraordinarily diverse organizations, and a total of 1,147 hybrid NRPS/PKS clusters were found. Surprisingly, 10% of bacterial gene clusters lacked modular organization, and instead catalytic domains were mostly encoded as separate proteins. The finding of common occurrence of nonmodular NRPS differs substantially from the current classification. Sequence analysis indicates that the evolution of NRPS machineries was driven by a combination of common descent and horizontal gene transfer. We identified related siderophore NRPS gene clusters that encoded modular and nonmodular NRPS enzymes organized in a gradient. A higher frequency of the NRPS and PKS gene clusters was detected from bacteria compared with archaea or eukarya. They commonly occurred in the phyla of Proteobacteria, Actinobacteria, Firmicutes, and Cyanobacteria in bacteria and the phylum of Ascomycota in fungi. The majority of these NRPS and PKS gene clusters have unknown end products highlighting the power of genome mining in identifying novel genetic machinery for the biosynthesis of secondary metabolites. PMID:24927540
Wang, Hao; Fewer, David P; Holm, Liisa; Rouhiainen, Leo; Sivonen, Kaarina
Diet influences health as a source of nutrients and toxins, and by shaping the composition of resident microbial populations. Previous studies have begun to map out associations between diet and the bacteria and viruses of the human gut microbiome. Here we investigate associations of diet with fungal and archaeal populations, taking advantage of samples from 98 well-characterized individuals. Diet was quantified using inventories scoring both long-term and recent diet, and archaea and fungi were characterized by deep sequencing of marker genes in DNA purified from stool. For fungi, we found 66 genera, with generally mutually exclusive presence of either the phyla Ascomycota or Basiodiomycota. For archaea, Methanobrevibacter was the most prevalent genus, present in 30% of samples. Several other archaeal genera were detected in lower abundance and frequency. Myriad associations were detected for fungi and archaea with diet, with each other, and with bacterial lineages. Methanobrevibacter and Candida were positively associated with diets high in carbohydrates, but negatively with diets high in amino acids, protein, and fatty acids. A previous study emphasized that bacterial population structure was associated primarily with long-term diet, but high Candida abundance was most strongly associated with the recent consumption of carbohydrates. Methobrevibacter abundance was associated with both long term and recent consumption of carbohydrates. These results confirm earlier targeted studies and provide a host of new associations to consider in modeling the effects of diet on the gut microbiome and human health.
Hoffmann, Christian; Dollive, Serena; Grunberg, Stephanie; Chen, Jun; Li, Hongzhe; Wu, Gary D.; Lewis, James D.; Bushman, Frederic D.
Corynespora Leaf Fall (CLF) is a major disease of rubber tree (Hevea brasiliensis) caused by the Ascomycota Corynespora cassiicola. Here we describe the cloning and characterization of a gene encoding cassiicolin (Cas), a glycosylated cystein-rich small secreted protein (SSP) identified as a potential CLF disease effector in rubber tree. Three isolates with contrasted levels of aggressiveness were analyzed comparatively. The cassiicolin gene was detected - and the toxin successfully purified - from the isolates with high and medium aggressiveness (CCP and CCAM3 respectively) but not from the isolate with the lowest aggressiveness (CCAM1), suggesting the existence of a different disease effector in the later. CCP and CCAM3 carried strictly identical cassiicolin genes and produced toxins of identical mass, as evidence by mass spectrometry analysis, thus suggesting conserved post-translational modifications in addition to sequence identity. The differences in aggressiveness between CCP and CCAM3 may be attributed to differences in cassiicolin transcript levels rather than qualitative variations in cassiicolin structure. Cassiicolin may play an important role in the early phase of infection since a peak of cassiicolin transcripts occurred in 1 or 2 days after inoculation (before the occurrence of the first symptoms), in both the tolerant and the susceptible cultivars. PMID:22325885
Déon, Marine; Bourré, Yanice; Gimenez, Stéphanie; Berger, Angélique; Bieysse, Daniel; de Lamotte, Frédéric; Poncet, Joël; Roussel, Véronique; Bonnot, François; Oliver, Gérald; Franchel, Jérôme; Seguin, Marc; Leroy, Thierry; Roeckel-Drevet, Patricia; Pujade-Renaud, Valérie
Approximately 60 fungal isolates from Zijin Mountain (Nanjing, China) were screened to determine their algicidal ability. The results show that 8 fungi belonging to Ascomycota and 5 belonging to Basidiomycota have algicidal ability. Of these fungi, Irpex lacteus T2b, Trametes hirsuta T24, Trametes versicolor F21a, and Bjerkandera adusta T1 showed strong algicidal ability. The order of fungal chlorophyll-a removal efficiency was as follows: T. versicolor F21a > I. lacteus T2b > B. adusta T1 > T. hirsuta T24. In particular, T. versicolor F21a completely removed algal cells within 30 h, showing the strongest algicidal ability. The results also show that all 4 fungal species degraded algal cells through direct attack. In addition, most of the tested fungi from the order Polyporales of Basidiomycota exhibited strong algicidal activity, suggesting that most fungi that belong to this order have algicidal ability. The findings of this work could direct the search for terrestrial fungi for bloom control. PMID:21887638
Han, Guomin; Feng, Xiaoguang; Jia, Yong; Wang, Congyan; He, Xingbing; Zhou, Qiyou; Tian, Xingjun
The waters of the Dead Sea currently contain about 348 g/l salts (2 M Mg(2+), 0.5 M Ca(2+), 1.5 M Na(+), 0.2 M K(+), 6.5 M Cl(-), 0.1 M Br(-)). The pH is about 6.0. After rainy winters the surface waters become diluted, triggering development of microbial blooms. The 1980 and 1992 blooms were dominated by the unicellular green alga Dunaliella and red Archaea. At least 70 species (in 26 genera) of Oomycota (Chromista), Mucoromycotina, Ascomycota, and Basidiomycota (Fungi) were isolated from near-shore localities and offshore stations, including from deep waters. Aspergillus and Eurotium were most often recovered. Aspergillus terreus, A. sydowii, A. versicolor, Eurotium herbariorum, Penicillium westlingii, Cladosporium cladosporioides, C. sphaerospermum, C. ramnotellum, and C. halotolerans probably form the stable core of the community. The species Gymnascella marismortui may be endemic. Mycelia of Dead Sea isolates of A. versicolor and Chaetomium globosum remained viable for up to 8 weeks in Dead Sea water; mycelia of other species survived for many weeks in 50% Dead Sea water. Many isolates showed a very high tolerance to magnesium salts. There is no direct proof that fungi contribute to the heterotrophic activity in the Dead Sea, but fungi may be present at least locally and temporarily, and their enzymatic activities such as amylase, protease, and cellulase may play a role in the lake's ecosystem. PMID:22222829
Oren, Aharon; Gunde-Cimerman, Nina
Ferns are an ancient and diverse lineage of vascular plants that differ morphologically, chemically and in growth habits from the angiosperms with which they co-occur. We used a culture-based approach coupled with phylogenetic analyses to characterize the incidence, diversity and composition of fungal endophyte assemblages in ferns, with a focus on healthy aboveground tissues of seven species of eupolypods at La Selva, Costa Rica. Endophytes were isolated from every individual plant and were similarly abundant and diverse in frond blades and stalks, in different vegetation types, in epiphytic vs. terrestrial species, and between sampling years. However, abundance, diversity and community structure differed significantly among fern species, and composition differed markedly between sampling years. Phylogenetic classification using separate and combined datasets revealed that as for many Neotropical angiosperms, the majority (95%) of endophyte taxa were Ascomycota, with particular dominance by Sordariomycetes, Eurotiomycetes and Dothideomycetes. However, our data suggest higher phylogenetic richness and stronger host affinities in fern associated endophytes relative to those studied in angiosperms thus far. PMID:24459121
Del Olmo-Ruiz, Mariana; Arnold, A Elizabeth
Very few studies have addressed the phylogenetic diversity of fungi from Northeast India under the Eastern Himalayan range. In the present study, an attempt has been made to study the phylogenetic diversity of culturable soil fungi along the altitudinal gradients of eastern Himalayas. Soil samples from 24 m above sea level to 2,000 m above sea level altitudes of North-East India were collected to investigate soil micro-fungal community structure and diversity. Molecular characterization of the isolates was done by PCR amplification of 18S rDNA using universal primers. Phylogenetic analysis using BLAST revealed variation in the distribution and richness of different fungal biodiversity over a wide range of altitudes. A total of 107 isolates were characterized belonging to the phyla Ascomycota and Zygomycota, corresponding to seven orders (Eurotiales, Hypocreales, Calosphaeriales, Capnodiales, Pleosporales, Mucorales, and Mortierellales) and Incertae sedis. The characterized isolates were analysed for richness, evenness and diversity indices. Fungal diversity had significant correlation with soil physico-chemical parameters and the altitude. Eurotiales and Hypocreales were most diverse and abundant group of fungi along the entire altitudinal stretch. Species of Penicillium (D = 1.44) and Aspergillus (D = 1.288) were found to have highest diversity index followed by Talaromyces (D = 1.26) and Fusarium (D = 1.26). Fungal distribution showed negative correlation with altitude and soil moisture content. Soil temperature, pH, humidity and ambient temperature showed positive correlation with fungal distribution.
Devi, Lamabam Sophiya; Khaund, Polashree; Nongkhlaw, Fenella M. W.
In the past the root rot pathogen Roesleria subterranea (Ascomycota) was generally considered as a minor parasite, a view with which we were often confronted during field work in German wine-growing regions where this ascomycete recently caused serious problems in established vineyards and at replant sites. To irrevocably demonstrate that R. subterranea is not a minor, but a primary pathogen of grapevines (and fruit trees) a pest risk analysis was carried out according to the guidelines defined by EPPO standard series PM 5, which defines the information needed, and contains standardised, detailed key questions and a decision support scheme for risk analysis. Following the provided decision scheme, it becomes apparent that R. subterranea must be considered as a serious, primary pathogen for grapevines and fruit trees that can cause massive economic losses. Based on the literature, the pathogen seems to be ubiquitous in wine growing regions in cool climates of the northern hemisphere. It is likely that because of its growth below ground, the small fruiting bodies, and ambiguous symptoms above ground, R. subterranea has been overlooked in the past and therefore, has not been considered as primary pathogen for grapevine. Available published information together with experience from field trials was implemented into a diagnostic decision scheme which will, together with the comprehensive literature provided, be the basis (a) to implement quick and efficient diagnosis of this pathogen in the field and (b) to conduct risk analysis and management in areas where R. subterranea has not established yet.
In this paper, we report on the in situ diversity of the mycotrophic fungus Trichoderma (teleomorph Hypocrea, Ascomycota, Dikarya) revealed by a taxon-specific metagenomic approach. We designed a set of genus-specific internal transcribed spacer (ITS)1 and ITS2 rRNA primers and constructed a clone library containing 411 molecular operational taxonomic units (MOTUs). The overall species composition in the soil of the two distinct ecosystems in the Danube floodplain consisted of 15 known species and two potentially novel taxa. The latter taxa accounted for only 1.5?% of all MOTUs, suggesting that almost no hidden or uncultivable Hypocrea/Trichoderma species are present at least in these temperate forest soils. The species were unevenly distributed in vertical soil profiles although no universal factors controlling the distribution of all of them (chemical soil properties, vegetation type and affinity to rhizosphere) were revealed. In vitro experiments simulating infrageneric interactions between the pairs of species that were detected in the same soil horizon showed a broad spectrum of reactions from very strong competition over neutral coexistence to the pronounced synergism. Our data suggest that only a relatively small portion of Hypocrea/Trichoderma species is adapted to soil as a habitat and that the interaction between these species should be considered in a screening for Hypocrea/Trichoderma as an agent(s) of biological control of pests.
Friedl, Martina A.
Alternative splicing (AS) is a cellular process that increases a cell's coding capacity from a limited set of genes. Although AS is common in higher plants and animals, its prevalence in other eukaryotes is mostly unknown. In fungi the involvement of AS in gene expression and its effect on multi-cellularity and virulence is of great medical and economic interest. We present a genome-wide comparative study of AS in 23 informative fungi of different taxa, based on alignments of public transcript sequences. Random sampling of expressed sequence tags allows for robust and comparable estimations of AS rates. We find that a greater fraction of fungal genes than previously expected is associated with AS. We estimate that on average, 6.4% of the annotated genes are affected by AS, with Cryptococcus neoformans showing an extraordinary rate of 18%. The investigated Basidiomycota show higher average AS rates (8.6%) than the Ascomycota (6.0%), although not significant. We find that multi-cellular complexity and younger evolutionary age associate with higher AS rates. Furthermore, AS affects genes involved in pathogenic lifestyle, particularly in functions of stress response and dimorphic switching. Together, our analysis strongly supports the view that AS is a rather common phenomenon in fungi and associates with higher multi-cellular complexity. PMID:24122896
Grützmann, Konrad; Szafranski, Karol; Pohl, Martin; Voigt, Kerstin; Petzold, Andreas; Schuster, Stefan
The combination of ecological diversity with genetic and experimental tractability makes Drosophila a powerful model for the study of animal-associated microbial communities. Despite the known importance of yeasts in Drosophila physiology, behavior, and fitness, most recent work has focused on Drosophila-bacterial interactions. In order to get a more complete understanding of the Drosophila microbiome, we characterized the yeast communities associated with different Drosophila species collected around the world. We focused on the phylum Ascomycota because it constitutes the vast majority of the Drosophila-associated yeasts. Our sampling strategy allowed us to compare the distribution and structure of the yeast and bacterial communities in the same host populations. We show that yeast communities are dominated by a small number of abundant taxa, that the same yeast lineages are associated with different host species and populations, and that host diet has a greater effect than host species on yeast community composition. These patterns closely parallel those observed in Drosophila bacterial communities. However, we do not detect a significant correlation between the yeast and bacterial communities of the same host populations. Comparative analysis of different symbiont groups provides a more comprehensive picture of host-microbe interactions. Future work on the role of symbiont communities in animal physiology, ecological adaptation, and evolution would benefit from a similarly holistic approach.
Eisen, Jonathan A.; Kopp, Artyom
Members of the fungal-specific velvet protein family regulate sexual and asexual spore production in the Ascomycota. We predicted, therefore, that velvet homologs in the basidiomycetous plant pathogen Ustilago maydis would regulate sexual spore development, which is also associated with plant disease progression in this fungus. To test this hypothesis, we studied the function of three U. maydis velvet genes, umv1, umv2 and umv3. Using a gene replacement strategy, deletion mutants were made in all three genes in compatible haploid strains, and additionally for umv1 and umv2 in the solopathogenic strain, SG200. None of the mutants showed novel morphological phenotypes during yeast-like, in vitro growth. However, the ?umv1 mutants failed to induce galls or teliospores in maize. Chlorazol black E staining of leaves infected with ?umv1 dikaryons revealed that the ?umv1 hyphae did not proliferate normally and were blocked developmentally before teliospore formation. The ?umv2 mutants were able to induce galls and teliospores in maize, but were slow to do so and thus reduced in virulence. The ?umv3 mutants were not affected in teliospore formation or disease progression. Complementation of the ?umv1 and ?umv2 mutations in the SG200 background produced disease indices similar to those of SG200. These results indicate that two U. maydis velvet family members, umv1 and umv2, are important for normal teliospore development and disease progression in maize seedlings. PMID:24064149
Karakkat, Brijesh B; Gold, Scott E; Covert, Sarah F
Parasites are able to evolve rapidly and overcome host defense mechanisms, but the molecular basis of this adaptation is poorly understood. Powdery mildew fungi (Erysiphales, Ascomycota) are obligate biotrophic parasites infecting nearly 10,000 plant genera. They obtain their nutrients from host plants through specialized feeding structures known as haustoria. We previously identified the AVRk1 powdery mildew-specific gene family encoding effectors that contribute to the successful establishment of haustoria. Here, we report the extensive proliferation of the AVRk1 gene family throughout the genome of B. graminis, with sequences diverging in formae speciales adapted to infect different hosts. Also, importantly, we have discovered that the effectors have coevolved with a particular family of LINE-1 retrotransposons, named TE1a. The coevolution of these two entities indicates a mutual benefit to the association, which could ultimately contribute to parasite adaptation and success. We propose that the association would benefit 1) the powdery mildew fungus, by providing a mechanism for amplifying and diversifying effectors and 2) the associated retrotransposons, by providing a basis for their maintenance through selection in the fungal genome.
Pedersen, Carsten; Skamnioti, Pari; Thordal-Christensen, Hans; Micali, Cristina; Brown, James K. M.; Ridout, Christopher J.
The human scalp harbors a vast community of microbial mutualists, the composition of which is difficult to elucidate as many of the microorganisms are not culturable using current culture techniques. Dandruff, a common scalp disorder, is known as a causative factor of a mild seborrheic dermatitis as well as pityriasis versicolor, seborrheic dermatitis, and atopic dermatitis. Lipophilic yeast Malassezia is widely accepted to play a role in dandruff, but relatively few comprehensive studies have been reported. In order to investigate fungal biota and genetic resources of dandruff, we amplified the 26S rRNA gene from samples of healthy scalps and dandruff-afflicted scalps. The sequences were analyzed by a high throughput method using a GS-FLX 454 pyrosequencer. Of the 74,811 total sequence reads, Basidiomycota (Filobasidium spp.) was the most common phylum associated with dandruff. In contrast, Ascomycota (Acremonium spp.) was common in the healthy scalps. Our results elucidate the distribution of fungal communities associated with dandruff and provide new avenues for the potential prevention and treatment of dandruff.
Park, Hee Kuk; Ha, Myung-Ho; Park, Sang-Gue; Kim, Myeung Nam; Kim, Beom Joon; Kim, Wonyong
Fungal diversity and community composition are mainly related to soil and vegetation factors. However, the relative contribution of the different drivers remains largely unexplored, especially in subtropical forest ecosystems. We studied the fungal diversity and community composition of soils sampled from 12 comparative study plots representing three forest age classes (Young: 10–40 yrs; Medium: 40–80 yrs; Old: ?80 yrs) in Gutianshan National Nature Reserve in South-eastern China. Soil fungal communities were assessed employing ITS rDNA pyrotag sequencing. Members of Basidiomycota and Ascomycota dominated the fungal community, with 22 putative ectomycorrhizal fungal families, where Russulaceae and Thelephoraceae were the most abundant taxa. Analysis of similarity showed that the fungal community composition significantly differed among the three forest age classes. Forest age class, elevation of the study plots, and soil organic carbon (SOC) were the most important factors shaping the fungal community composition. We found a significant correlation between plant and fungal communities at different taxonomic and functional group levels, including a strong relationship between ectomycorrhizal fungal and non-ectomycorrhizal plant communities. Our results suggest that in subtropical forests, plant species community composition is the main driver of the soil fungal diversity and community composition.
Trogisch, Stefan; Both, Sabine; Scholten, Thomas; Bruelheide, Helge; Buscot, Francois
Numerous ?12-, ?15- and multifunctional membrane fatty acid desaturases (FADs) have been identified in fungi, revealing great variability in the enzymatic specificities of FADs involved in biosynthesis of polyunsaturated fatty acids (PUFAs). Here, we report gene isolation and characterization of novel ?12/?15- and ?15-FADs named CpFad2 and CpFad3, respectively, from the opportunistic pathogenic yeast Candida parapsilosis. Overexpression of CpFad3 in Saccharomyces cerevisiae strains supplemented with linoleic acid (?9,?12-18:2) and hexadecadienoic acid (?9,?12-16:2) leads to accumulation of ?15-PUFAs, i.e., ?-linolenic acid (?9,?12,?15-18:3) and hexadecatrienoic acid with an unusual terminal double bond (?9,?12,?15-16:3). CpFad2 produces a range of ?12- and ?15-PUFAs. The major products of CpFad2 are linoleic and hexadecadienoic acid (?9,?12-16:2), accompanied by ?-linolenic acid and hexadecatrienoic acid (?9,?12,?15-16:3). Using GC/MS analysis of trimethylsilyl derivatives, we identified ricinoleic acid (12-hydroxy-9-octadecenoic acid) as an additional product of CpFad2. These results demonstrate that CpFAD2 is a multifunctional FAD and indicate that detailed analysis of fatty acid derivatives might uncover a range of enzymatic selectivities in other ?12-FADs from budding yeasts (Ascomycota: Saccharomycotina). PMID:24681902
Bu?ek, Aleš; Matoušková, Petra; Sychrová, Hana; Pichová, Iva; Hrušková-Heidingsfeldová, Olga
The microbial decomposition of plant residue is a central part of the carbon cycle in soil ecosystems. Here, we explored the microeukaryotic community responsible for the uptake of plant residue carbon in a rice field soil through DNA-based stable-isotope probing (SIP) using dried rice callus labelled with (13) C as a model substrate. Molecular fingerprinting with PCR-DGGE showed that the total eukaryotic community in soil under drained (upland) conditions distinctly changed within 3 days after the callus was applied and stable thereafter. The predominant group of eukaryotes that incorporated callus carbon were fungi affiliated with the Mucoromycotina (Mortierella), Ascomycota (Galactomyces, Eleutherascus, Gibberella and Fusarium) and Zoopagomycotina (Syncephalis). 'Fungus-like' protists such as Pythium (stramenopiles) and Polymyxa (Cercozoa) were also involved in carbon flow from the callus. Some of these fungi and 'fungus-like' protists took up soil organic matter with time, which suggested a priming effect of the callus on the eukaryotic community. Our results demonstrated the usefulness of SIP not only to trace the carbon flow from fresh organic matter but also to study the effect of fresh organic matter on the utilization of soil organic matter by the microbial community. PMID:22092599
Murase, Jun; Shibata, Manami; Lee, Chol Gyu; Watanabe, Takeshi; Asakawa, Susumu; Kimura, Makoto
Saccharomycotina and Taphrinomycotina lack intron in their histone genes, except for an intron in one of histone H4 genes of Yarrowia lipolytica. On the other hand, Basidiomycota and Perizomycotina have introns in their histone genes. We compared the distributions of 81, 47, 79, and 98 introns in the fungal histone H2A, H2B, H3, and H4 genes, respectively. Based on the multiple alignments of the amino acid sequences of histones, we identified 19, 13, 31, and 22 intron insertion sites in the histone H2A, H2B, H3, and H4 genes, respectively. Surprisingly only one hot spot of introns in the histone H2A gene is shared between Basidiomycota and Perizomycotina, suggesting that most of introns of Basidiomycota and Perizomycotina were acquired independently. Our findings suggest that the common ancestor of Ascomycota and Basidiomycota maybe had a few introns in the histone genes. In the course of fungal evolution, Saccharomycotina and Taphrinomycotina lost the histone introns; Basidiomycota and Perizomycotina acquired other introns independently. In addition, most of the introns have sequence similarity among introns of phylogenetically close species, strongly suggesting that horizontal intron transfer events between phylogenetically distant species have not occurred recently in the fungal histone genes.
Yun, Choong-Soo; Nishida, Hiromi
Fusarium verticillioides (Saccardo) Nirenberg (Ascomycota: Hypocreales) is the most common fungus reported on infected corn kernels and vegetative tissues, but has not yet been documented as being entomopathogenic for grasshoppers. Grasshoppers and locusts represent a large group of insects that cause economic damage to forage and crops. Tropidacris collaris (Stoll) (Orthoptera: Acridoidea: Romaleidae) is a large and voracious grasshopper that in recent years has become an increasingly recurrent and widespread pest in progressively more greatly extended areas of some of in Argentina's northern provinces, with chemical insecticides being currently the only means of control. During February and March of 2008–09, nymphs and adults of T. collaris were collected with sweep nets in dense woodland vegetation at a site near Tres Estacas in western Chaco Province, Argentina, and kept in screened cages. F. verticillioides was isolated from insects that died within 10 days and was cultured in PGA medium. Pathogenicity tests were conducted and positive results recorded. Using traditional and molecular-biological methods, an isolate of F. verticillioides was obtained from T. collaris, and its pathogenecity in the laboratory was shown against another harmful grasshopper, Ronderosia bergi (Stål) (Acridoidea: Acrididae: Melanoplinae). The mortality caused by F. verticillioides on R. bergi reached 58 ± 6.53% by 10 days after inoculation. This is the first record of natural infection caused by F. verticillioides in grasshoppers.
Pelizza, SA; Stenglein, SA; Cabello, MN; Dinolfo, MI; Lange, CE
Ophiocordyceps unilateralis (Ascomycota: Hypocreales) is a specialized parasite that infects, manipulates and kills formicine ants, predominantly in tropical forest ecosystems. We have reported previously, based on a preliminary study in remnant Atlantic Forest in Minas Gerais (Brazil), that O. unilateralis represents a species complex. On each of the four species of infected carpenter ant (Camponotus) collected, the fungus-characterized macroscopically by a single stalk arising from the dorsal neck region on which the sexual structures (stromatal plates) are borne laterally-can readily be distinguished both microscopically and functionally. Here, we describe and discuss the biology, life cycle and infection strategies of O. unilateralis s.l. and hypothesize that there may be hundreds of species within the complex parasitizing formicine ants worldwide. We then address the diversity within related hypocrealean fungi, with particular reference to symbionts (mutualists through to parasites), and argue that the widely-quoted total of extant fungi (1.5 million species) may be grossly underestimated. PMID:22046474
Evans, Harry C; Elliot, Simon L; Hughes, David P
Lu et al. (2002) described a method for identifying Hericium species by PCR, using the primers HT-U1 and HT-L1 which they specifically designed for this purpose. In our hands these primers do not appear to discriminate between tooth fungi and other wood decay species. Therefore PCR primers were designed that discriminated Creolophus cirrhatus from other species (HER2F/HER3R), and which discriminate Hericium alpestre, H. coralloides and H. erinaceus from other wood decay Ascomycota and Basidiomycota but not from each other (HER2F/HER2R). Using the HER2F/HER3R primers together with traditional isolation and direct incubation procedures, the location of C. cirrhatus in Turkey oak logs was mapped. The PCR approach often detected C. cirrhatus in locations where it was suspected to be, based on patterns of staining and decay, but where it was not revealed by isolation onto agar media, emphasising the value of adopting several approaches to unravel fungal community structure in wood. PMID:16279412
Parfitt, David; Hynes, Juliet; Rogers, Hilary J; Boddy, Lynne
Ascomycete yeasts (phylum Ascomycota: subphylum Saccharomycotina: class Saccharomycetes: order Saccharomycetales) comprise a monophyletic lineage with a single order of about 1000 known species. These yeasts live as saprobes, often in association with plants, animals and their interfaces. A few species account for most human mycotic infections, and fewer than 10 species are plant pathogens. Yeasts are responsible for important industrial and biotechnological processes, including baking, brewing and synthesis of recombinant proteins. Species such as Saccharomyces cerevisiae are model organisms in research, some of which led to a Nobel Prize. Yeasts usually reproduce asexually by budding, and their sexual states are not enclosed in a fruiting body. The group also is well defined by synapomorphies visible at the ultrastructural level. Yeast identification and classification changed dramatically with the availability of DNA sequencing. Species identification now benefits from a constantly updated sequence database and no longer relies on ambiguous growth tests. A phylogeny based on single gene analyses has shown the order to be remarkably divergent despite morphological similarities among members. The limits of many previously described genera are not supported by sequence comparisons, and multigene phylogenetic studies are under way to provide a stable circumscription of genera, families and orders. One recent multigene study has resolved species of the Saccharomycetaceae into genera that differ markedly from those defined by analysis of morphology and growth responses, and similar changes are likely to occur in other branches of the yeast tree as additional sequences become available. PMID:17486976
Suh, Sung-Oui; Blackwell, Meredith; Kurtzman, Cletus P; Lachance, Marc-André
Sexual reproduction in fungi is governed by a specialized genomic region, the mating type (MAT) locus, whose gene identity, organization, and complexity are diverse. We identified the MAT locus of five dermatophyte fungal pathogens (Microsporum gypseum, Microsporum canis, Trichophyton equinum, Trichophyton rubrum, and Trichophyton tonsurans) and a dimorphic fungus, Paracoccidioides brasiliensis, and performed phylogenetic analyses. The identified MAT locus idiomorphs of M. gypseum control cell type identity in mating assays, and recombinant progeny were produced. Virulence tests in Galleria mellonella larvae suggest the two mating types of M. gypseum may have equivalent virulence. Synteny analysis revealed common features of the MAT locus shared among these five dermatophytes: namely, a small size ( approximately 3 kb) and a novel gene arrangement. The SLA2, COX13, and APN2 genes, which flank the MAT locus in other Ascomycota are instead linked on one side of the dermatophyte MAT locus. In addition, the transcriptional orientations of the APN2 and COX13 genes are reversed compared to the dimorphic fungi Histoplasma capsulatum, Coccidioides immitis, and Coccidioides posadasii. A putative transposable element, pogo, was found to have inserted in the MAT1-2 idiomorph of one P. brasiliensis strain but not others. In conclusion, the evolution of the MAT locus of the dermatophytes and dimorphic fungi from the last common ancestor has been punctuated by both gene acquisition and expansion, and asymmetric gene loss. These studies further support a foundation to develop molecular and genetic tools for dermatophyte and dimorphic human fungal pathogens. PMID:19880755
Li, Wenjun; Metin, Banu; White, Theodore C; Heitman, Joseph
Sexual reproduction in fungi is governed by a specialized genomic region, the mating type (MAT) locus, whose gene identity, organization, and complexity are diverse. We identified the MAT locus of five dermatophyte fungal pathogens (Microsporum gypseum, Microsporum canis, Trichophyton equinum, Trichophyton rubrum, and Trichophyton tonsurans) and a dimorphic fungus, Paracoccidioides brasiliensis, and performed phylogenetic analyses. The identified MAT locus idiomorphs of M. gypseum control cell type identity in mating assays, and recombinant progeny were produced. Virulence tests in Galleria mellonella larvae suggest the two mating types of M. gypseum may have equivalent virulence. Synteny analysis revealed common features of the MAT locus shared among these five dermatophytes: namely, a small size (?3 kb) and a novel gene arrangement. The SLA2, COX13, and APN2 genes, which flank the MAT locus in other Ascomycota are instead linked on one side of the dermatophyte MAT locus. In addition, the transcriptional orientations of the APN2 and COX13 genes are reversed compared to the dimorphic fungi Histoplasma capsulatum, Coccidioides immitis, and Coccidioides posadasii. A putative transposable element, pogo, was found to have inserted in the MAT1-2 idiomorph of one P. brasiliensis strain but not others. In conclusion, the evolution of the MAT locus of the dermatophytes and dimorphic fungi from the last common ancestor has been punctuated by both gene acquisition and expansion, and asymmetric gene loss. These studies further support a foundation to develop molecular and genetic tools for dermatophyte and dimorphic human fungal pathogens.
Li, Wenjun; Metin, Banu; White, Theodore C.; Heitman, Joseph
Fungi cause opportunistic, nosocomial, and community-acquired infections. Among fungal infections (mycoses) zygomycoses are exceptionally severe, with a mortality rate exceeding 50 %. Immunocompromised hosts, transplant recipients, and diabetic patients with uncontrolled keto-acidosis and high iron serum levels are at risk. Zygomycota are capable of infecting hosts immune to other filamentous fungi. The infection often follows a progressive pattern, with angioinvasion and metastases. Moreover, current antifungal therapy frequently has an unfavorable outcome. Zygomycota are resistant to some of the routinely used antifungals, among them azoles (except posaconazole) and echinocandins. The typical treatment consists of surgical debridement of the infected tissues accompanied by amphotericin B administration. The latter has strong nephrotoxic side effects, which make it unsuitable for prophylaxis. Delayed administration of amphotericin and excision of mycelium-containing tissues worsens survival prognoses. More than 30 species of Zygomycota are involved in human infections, among them Mucorales is the most abundant. Prognosis and treatment suggestions differ for each species, which makes fast and reliable diagnosis essential. Serum sample PCR-based identification often gives false-negative results; culture-based identification is time-consuming and not always feasible. With the dawn of Zygomycota sequencing projects significant advancement is expected, as in the case of treatment of Ascomycota infections. PMID:24615580
Muszewska, A; Paw?owska, J; Krzy?ciak, P
The use of wood in construction has had a long history and Chile has a rich cultural heritage of using native woods for building churches and other important structures. In 2000, UNESCO designated a number of the historic churches of Chiloé, built entirely of native woods, as World Heritage Sites. These unique churches were built in the late 1700 s and throughout the 1800 s, and because of their age and exposure to the environment, they have been found to have serious deterioration problems. Efforts are underway to better understand these decay processes and to carryout conservation efforts for the long-term preservation of these important structures. This study characterized the types of degradation taking place and identified the wood decay fungi obtained from eight historic churches in Chiloé, seven of them designated as UNESCO World Heritage sites. Micromorphological observations identified white, brown and soft rot in the structural woods and isolations provided pure cultures of fungi that were identified by sequencing of the internal transcribed region of rDNA. Twenty-nine Basidiomycota and 18 Ascomycota were found. These diverse groups of fungi represent several genera and species not previously reported from Chile and demonstrates a varied microflora is causing decay in these historic buildings. PMID:24407313
Ortiz, Rodrigo; Párraga, Mario; Navarrete, José; Carrasco, Ivo; de la Vega, Eduardo; Ortiz, Manuel; Herrera, Paula; Jurgens, Joel A; Held, Benjamin W; Blanchette, Robert A
This study assessed the potential effects of transgenic aspen overexpressing a polyphenol oxidase gene on diversity in rhizosphere communities. Cultivation-independent methods were used to better delineate bacterial and fungal populations associated with transgenic and nontransgenic trees. Gene libraries for the bacterial component of the rhizosphere were established using 16S rRNA and chaperonin-60 (CPN-60) gene sequences, while the fungal community was characterized using 18S rRNA gene sequences. The 16S rRNA gene libraries were dominated by alphaproteobacterial sequences, while the CPN-60 gene libraries were dominated by members of the Bacteroidetes/Chlorobi group. In both the CPN-60 and 16S rRNA libraries, there were differences in only minor components of the bacterial community between transgenic and unmodified trees, and no significant differences in species diversity were observed. Compared to the bacterial gene libraries, greater coverage of the underlying population was achieved with the fungal 18S rRNA libraries. Members of the Zygomycota, Chytridiomycota, Ascomycota, and Basidiomycota were recovered from both libraries. The dominant groups of fungi associated with each tree type were very similar, although there were some qualitative differences in the recovery of less-abundant fungi, likely as a result of the underlying heterogeneity of the fungal population. The methods employed revealed only minor differences between the bacterial and fungal communities associated with transgenic and unmodified trees.
Oliver, Kathryn L.; Hamelin, Richard C.; Hintz, William E.
The basic Helix-Loop-Helix (bHLH) domain is an essential highly conserved DNA-binding domain found in many transcription factors in all eukaryotic organisms. The bHLH domain has been well studied in the Animal and Plant Kingdoms but has yet to be characterized within Fungi. Herein, we obtained and evaluated the phylogenetic relationship of 490 fungal-specific bHLH containing proteins from 55 whole genome projects composed of 49 Ascomycota and 6 Basidiomycota organisms. We identified 12 major groupings within Fungi (F1–F12); identifying conserved motifs and functions specific to each group. Several classification models were built to distinguish the 12 groups and elucidate the most discerning sites in the domain. Performance testing on these models, for correct group classification, resulted in a maximum sensitivity and specificity of 98.5% and 99.8%, respectively. We identified 12 highly discerning sites and incorporated those into a set of rules (simplified model) to classify sequences into the correct group. Conservation of amino acid sites and phylogenetic analyses established that like plant bHLH proteins, fungal bHLH–containing proteins are most closely related to animal Group B. The models used in these analyses were incorporated into a software package, the source code for which is available at www.fungalgenomics.ncsu.edu.
Sailsbery, Joshua K.; Atchley, William R.; Dean, Ralph A.
Eukaryotic organisms employ a variety of mechanisms during meiosis to assess and ensure the quality of their gametes. Defects or delays in successful meiotic recombination activate conserved mechanisms to delay the meiotic divisions, but many multicellular eukaryotes also induce cell death programs to eliminate gametes deemed to have failed during meiosis. It is generally thought that yeasts lack such mechanisms. Here, we show that in the fission yeast Schizosaccharomyces pombe, defects in meiotic recombination lead to the activation of a checkpoint that is linked to ascus wall endolysis – the process by which spores are released in response to nutritional cues for subsequent germination. Defects in meiotic recombination are sensed as unrepaired DNA damage through the canonical ATM and ATR DNA damage response kinases, and this information is communicated to the machinery that stimulates ascus wall breakdown. Viability of spores that undergo endolysis spontaneously is significantly higher than that seen upon chemical endolysis, demonstrating that this checkpoint contributes to a selective mechanism for the germination of high quality progeny. These results provide the first evidence for the existence of a checkpoint linking germination to meiosis and suggest that analysis solely based on artificial, enzymatic endolysis bypasses an important quality control mechanism in this organism and potentially other ascomycota, which are models widely used to study meiosis.
Guo, Haiyan; King, Megan C.
To get a comprehensive view of fungal M35 family (deuterolysin) and M36 family (fungalysin) genes, we conducted genome-wide investigations and phylogenetic analyses of genes in these two families from 50 sequenced Ascomycota fungi with different life styles. Large variations in the number of M35 family and M36 family genes were found among different fungal genomes, indicating that these two gene families have been highly dynamic through fungal evolution. Moreover, we found obvious expansions of Meps in two families of Onygenales: Onygenaceae and Arthodermataceae, whereas species in family Ajellomycetace did not show expansion of these genes. The strikingly different gene duplication and loss patterns in Onygenales may be associated with the different pathogenicity of these species. Interestingly, likelihood ratio tests (LRT) of both M35 family and M36 family genes suggested that several branches leading to the duplicated genes in dermatophytic and Coccidioides fungi had signatures of positive selection, indicating that the duplicated Mep genes have likely diverged functionally to play important roles during the evolution of pathogenicity of dermatophytic and Coccidioides fungi. The potentially positively selected residues discovered by our analysis may have contributed to the development of new physiological functions of the duplicated Mep genes in dermatophytic fungi and Coccidioides species. Our study adds to the current knowledge of the evolution of Meps in fungi and also establishes a theoretical foundation for future experimental investigations.
Li, Juan; Zhang, Ke-Qin
Endophytic fungi associated with three bryophyte species in the Fildes Region, King George Island, maritime Antarctica, that is, the liverwort Barbilophozia hatcheri, the mosses Chorisodontium aciphyllum and Sanionia uncinata, were studied by culture-dependent method. A total of 128 endophytic fungi were isolated from 1329 tissue segments of 14 samples. The colonization rate of endophytic fungi in three bryophytes species were 12.3%, 12.1%, and 8.7%, respectively. These isolates were identified to 21 taxa, with 15 Ascomycota, 5 Basidiomycota, and 1 unidentified fungus, based on morphological characteristics and sequence analyses of ITS region and D1/D2 domain. The dominant fungal endophyte was Hyaloscyphaceae sp. in B. hatcheri, Rhizoscyphus sp. in C. aciphyllum, and one unidentified fungus in S. uncinata; and their relative frequencies were 33.3%, 32.1%, and 80.0%, respectively. Furthermore, different Shannon-Weiner diversity indices (0.91-1.99) for endophytic fungi and low endophytic fungal composition similarities (0.19-0.40) were found in three bryophyte species. Growth temperature tests indicated that 21 taxa belong to psychrophiles (9), psychrotrophs (11), and mesophile (1). The results herein demonstrate that the Antarctic bryophytes are an interesting source of fungal endophytes and the endophytic fungal composition is different among the bryophyte species, and suggest that these fungal endophytes are adapted to cold stress in Antarctica. PMID:23350605
Zhang, Tao; Zhang, Yu-Qin; Liu, Hong-Yu; Wei, Yu-Zhen; Li, Hai-Long; Su, Jing; Zhao, Li-Xun; Yu, Li-Yan
The endophytic fungus Aciculosporium take (Ascomycota; Clavicipitaceae) causes continuous shoot growth in bamboo. The colonized shoot eventually results in witches' broom formation but maintains normal leaf arrangement and branching pattern. To analyze the mechanism of well-regulated symptom development, the location of the fungal endophytic hyphae in host tissues was visualized. A colorimetric in situ hybridization technique using a species-specific oligonucleotide probe targeting the 18S rRNA of A. take was used. In situ hybridization was performed on tissue sections of diseased shoots with or without external signs of fungal colonization. Specific signals were detected in intercellular spaces of the bamboo tissues. Most signals were detected in the shoot apical meristem and the leaf primordia. In addition, fewer signals were detected in the lateral buds, juvenile leaves, and stems. These results indicate that A. take grows endophytically, particularly in the shoot apical meristem of the host. The location of A. take hyphae suggests that the mechanism of symptom development can be explained by the action of exogenous fungal auxin, which continuously induces primordium initiation within the host. PMID:19465522
Fungi are known to have an important role in the composting process as degraders of recalcitrant materials such as cellulose and lignin. Previous attempts to study the diversity and succession of fungi in compost systems have relied on the use of culture-dependent analyses and low-resolution DNA-fingerprinting techniques, lacking the necessary depth to analyse such a rich ecosystem. In this study, 454 pyrosequencing was used to characterize the fungal community composition at the different stages of an in-vessel composting process. A complex succession of fungi was revealed, with 251 fungal OTUs identified throughout the monitoring period. The Ascomycota were the dominant phylum (82.5% of all sequences recovered), followed by the Basidiomycota (10.4%) and the subphylum Mucoromycotina (4.9%). In the starting materials and early stages of the process, yeast species from the Saccharomycetales were abundant, while in latter stages and in the high temperature regions of the pile, fungi from the orders Eurotiales, Sordariales, Mucorales, Agaricales and Microascales were the most prominent. This study provides an improved understanding of the fungal diversity occurring during the composting of municipal solid waste, and this knowledge can lead to the development of more efficient composting practices and a better evaluation of the end-product quality. PMID:24490666
Langarica-Fuentes, Adrian; Zafar, Urooj; Heyworth, Alan; Brown, Thomas; Fox, Graeme; Robson, Geoffrey D
Contrary to earlier assumptions, molecular evidence has demonstrated the presence of diverse and localized soil bacterial communities in the McMurdo Dry Valleys of Antarctica. Meanwhile, it remains unclear whether fungal signals so far detected in Dry Valley soils using both culture-based and molecular techniques represent adapted and ecologically active biomass or spores transported by wind. Through a systematic and quantitative molecular survey, we identified significant heterogeneities in soil fungal communities across the Dry Valleys that robustly correlate with heterogeneities in soil physicochemical properties. Community fingerprinting analysis and 454 pyrosequencing of the fungal ribosomal intergenic spacer region revealed different levels of heterogeneity in fungal diversity within individual Dry Valleys and a surprising abundance of Chytridiomycota species, whereas previous studies suggested that Dry Valley soils were dominated by Ascomycota and Basidiomycota. Critically, we identified significant differences in fungal community composition and structure of adjacent sites with no obvious barrier to aeolian transport between them. These findings suggest that edaphic fungi of the Antarctic Dry Valleys are adapted to local environments and represent an ecologically relevant (and possibly important) heterotrophic component of the ecosystem. PMID:25079129
Dreesens, Lisa L; Lee, Charles K; Cary, S Craig
The recently recognised protein-coding genes MCM7 and TSR1 have shown significant promise for phylogenetic resolution within the Ascomycota and Basidiomycota, but have remained unexamined within other fungal groups (except for Mucorales). We designed and tested primers to amplify these genes across early-diverging fungal clades, with emphasis on the Kickxellomycotina, zygomycetous fungi with characteristic flared septal walls forming pores with lenticular plugs. Phylogenetic tree resolution and congruence with MCM7 and TSR1 were compared against those inferred with nuclear small (SSU) and large subunit (LSU) rRNA genes. We also combined MCM7 and TSR1 data with the rDNA data to create 3- and 4-gene trees of the Kickxellomycotina that help to resolve evolutionary relationships among and within the core clades of this subphylum. Phylogenetic inference suggests that Barbatospora, Orphella, Ramicandelaber and Spiromyces may represent unique lineages. It is suggested that these markers may be more broadly useful for phylogenetic studies among other groups of early-diverging fungi. PMID:24027350
Tretter, E D; Johnson, E M; Wang, Y; Kandel, P; White, M M
The Mediterranean basin has been identified as a biodiversity hotspot, about whose soil microbial diversity little is known. Intensive land use and aggressive management practices are degrading the soil, with a consequent loss of fertility. The use of organic amendments such as dry olive residue (DOR), a waste produced by a two-phase olive-oil extraction system, has been proposed as an effective way to improve soil properties. However, before its application to soil, DOR needs a pre-treatment, such as by a ligninolytic fungal transformation, e.g. Coriolopsis floccosa. The present study aimed to describe the bacterial and fungal diversity in a Mediterranean soil and to assess the impact of raw DOR (DOR) and C. floccosa-transformed DOR (CORDOR) on function and phylogeny of soil microbial communities after 0, 30 and 60 days. Pyrosequencing of the 16S rRNA gene demonstrated that bacterial diversity was dominated by the phyla Proteobacteria, Acidobacteria, and Actinobacteria, while 28S-rRNA gene data revealed that Ascomycota and Basidiomycota accounted for the majority of phyla in the fungal community. A Biolog EcoPlate experiment showed that DOR and CORDOR amendments decreased functional diversity and altered microbial functional structures. These changes in soil functionality occurred in parallel with those in phylogenetic bacterial and fungal community structures. Some bacterial and fungal groups increased while others decreased depending on the relative abundance of beneficial and toxic substances incorporated with each amendment. In general, DOR was observed to be more disruptive than CORDOR.
Siles, Jose A.; Rachid, Caio T. C. C.; Sampedro, Inmaculada; Garcia-Romera, Inmaculada; Tiedje, James M.
Estuarine salinity gradients are known to influence plant, bacterial and archaeal community structure. We sequenced 18S rRNA genes to investigate patterns in sediment fungal diversity (richness and evenness of taxa) and composition (taxonomic and phylogenetic) along an estuarine salinity gradient. We sampled three marshes—a salt, brackish and freshwater marsh—in Rhode Island. To compare the relative effect of the salinity gradient with that of plants, we sampled fungi in plots with Spartina patens and in plots from which plants were removed 2 years prior to sampling. The fungal sediment community was unique compared with previously sampled fungal communities; we detected more Ascomycota (78%), fewer Basidiomycota (6%) and more fungi from basal lineages (16%) (Chytridiomycota, Glomeromycota and four additional groups) than typically found in soil. Across marshes, fungal composition changed substantially, whereas fungal diversity differed only at the finest level of genetic resolution, and was highest in the intermediate, brackish marsh. In contrast, the presence of plants had a highly significant effect on fungal diversity at all levels of genetic resolution, but less of an effect on fungal composition. These results suggest that salinity (or other covarying parameters) selects for a distinctive fungal composition, and plants provide additional niches upon which taxa within these communities can specialize and coexist. Given the number of sequences from basal fungal lineages, the study also suggests that further sampling of estuarine sediments may help in understanding early fungal evolution.
Mohamed, Devon J; Martiny, Jennifer BH
Bioaerosols are emerging as important yet poorly understood players in atmospheric processes. Microorganisms in the atmosphere have great potential to impact chemical and physical processes that influence global climateby participating in both ice nucleation and cloud droplet formation. The role of microorganisms in atmospheric processes is thought to be species-specific and, potentially, dependent on the viability of the cell; however, few simultaneous measurements of both parameters exist. Using a coastal pier monitoring site as a sampling platform to investigate the exchange of airborne microorganisms at the air-sea interface, culture independent (i.e. DNA clone libraries from filters) and culture dependent approaches (i.e. agar plates) were combined with 18S rRNA and 16S rRNA gene targeting to determine the microbial diversity. The results indicate that in these coastal air samples two fungal phyla, Basidiomycota and Ascomycota, predominate among eukaryotes while Firmicutes and Proteobacteria predominate among bacteria. Furthermore, our culture dependent study verifies the viability of microbes from all four phyla detected through our culture independent study. Contrary to our expectations and despite oceanic air mass sources, common marine planktonic bacteria and phytoplankton were not abundantly found in our air samples indicating the potential importance of bioaerosols derived from beaches and/or coastal erosion processes.
Urbano, R.; Palenik, B.; Gaston, C. J.; Prather, K. A.
Fungal spores account for large proportions of air particulate matter, and they influence the hydrological cycle and climate as nuclei for water droplets and ice crystals in clouds, fog and precipitation. Moreover, some fungi are major pathogens and allergens. The diversity of airborne fungi is, however, hardly known. By DNA analysis we found pronounced differences in the relative abundance and seasonal cycles of various groups of fungi in coarse and fine particulate matter, with more plant pathogens in the coarse and more human pathogens and allergens in the respirable fine particle fraction (< 3 µm). Moreover, the ratio of Basidiomycota to Ascomycota was found to be much higher than previously assumed, which might also apply to the biosphere. References: Després, V.R., J.F. Nowoisky, M. Klose, R. Conrad, M.O. Andreae, U. Pöschl, Characterization of primary biogenic aerosol particles in urban, rural, and high-alpine air by DNA sequence and restriction fragment analysis of ribosomal RNA genes, Biogeosciences, 4, 1127-1141, 2007. Elbert, W., P. E. Taylor, M. O. Andreae, U. Pöschl, Contribution of fungi to primary biogenic aerosols in the atmosphere: wet and dry discharged spores, carbohydrates, and inorganic ions, Atmospheric Chemistry and Physics, 7, 4569-4588, 2007. Fröhlich-Nowoisky, J. Despres, V.R., Pöschl, U.: High diversity of fungi in air particulate matter, Proceedings of the National Academy of Sciences, submitted, 2008.
Fröhlich-Nowoisky, J.; Despres, V. R.; Pöschl, U.
Bioaerosols are emerging as important yet poorly understood players in atmospheric processes. Microorganisms can impact atmospheric chemistry through metabolic reactions and can potentially influence physical processes by participating in ice nucleation and cloud droplet formation. Microbial roles in atmospheric processes are thought to be species-specific and potentially dependent on cell viability. Using a coastal pier monitoring site as a sampling platform, culture-dependent (i.e. agar plates) and culture-independent (i.e. DNA clone libraries from filters) approaches were combined with 18S rRNA and 16S rRNA gene targeting to obtain insight into the local atmospheric microbial composition. From 13 microbial isolates and 42 DNA library clones, a total of 55 sequences were obtained representing four independent sampling events. Sequence analysis revealed that in these coastal samples two fungal phyla, Ascomycota and Basidiomycota, predominate among eukaryotes while Firmicutes and Proteobacteria predominate among bacteria. Furthermore, our culture-dependent study verifies the viability of microbes from all four phyla detected through our culture-independent study. Contrary to our expectations and despite oceanic air mass sources, common marine planktonic bacteria and phytoplankton were not typically found. The abundance of terrestrial and marine sediment-associated microorganisms suggests a potential importance for bioaerosols derived from beaches and/or coastal erosion processes.
Urbano, R.; Palenik, B.; Gaston, C. J.; Prather, K. A.
Up to now, most studies on polychlorinated biphenyl (PCB) bioremediation have examined the ability of model fungal strains to biodegrade PCBs. Yet, there is limited information concerning the potential of autochthonous filamentous fungal strains in the biodegradation of PCBs and their possible use in the environmental technologies. In this study, we investigated the capacity of autochthonous fungal strains in the biodegradation of PCBs by isolating 24 taxa from former industrial sites highly contaminated by PCBs. Microscopic and molecular analyses using the internal transcribed spacer (ITS) region revealed that the fungal strains belonged to the phyla Ascomycota (19 strains) and Zygomycota (five strains). The chromatography gas analysis revealed evidence of degradation of seven PCB congeners. With the exception of Circinella muscae which presented no degradation potential, the other fungal strains exhibited a rate of biodegradation ranging from 29 to 85 % after 7 d of incubation in liquid medium. Among these strains, Doratomyces nanus, Doratomyces purpureofuscus, Doratomyces verrucisporus, Myceliophthora thermophila, Phoma eupyrena, and Thermoascus crustaceus showed remarkable degradation ability (>70 %) regardless of the number of chlorine substituents on the biphenyl nucleus and a high tolerance towards PCBs. To our knowledge, this is the first study that demonstrates the ability of PCB degradation by these species and indicates the potential effectiveness of some autochthonous fungal strains in bioremediation systems. PMID:23622721
Mouhamadou, Bello; Faure, Mathieu; Sage, Lucile; Marçais, Johanna; Souard, Florence; Geremia, Roberto A
This study assessed the potential effects of transgenic aspen overexpressing a polyphenol oxidase gene on diversity in rhizosphere communities. Cultivation-independent methods were used to better delineate bacterial and fungal populations associated with transgenic and nontransgenic trees. Gene libraries for the bacterial component of the rhizosphere were established using 16S rRNA and chaperonin-60 (CPN-60) gene sequences, while the fungal community was characterized using 18S rRNA gene sequences. The 16S rRNA gene libraries were dominated by alphaproteobacterial sequences, while the CPN-60 gene libraries were dominated by members of the Bacteroidetes/Chlorobi group. In both the CPN-60 and 16S rRNA libraries, there were differences in only minor components of the bacterial community between transgenic and unmodified trees, and no significant differences in species diversity were observed. Compared to the bacterial gene libraries, greater coverage of the underlying population was achieved with the fungal 18S rRNA libraries. Members of the Zygomycota, Chytridiomycota, Ascomycota, and Basidiomycota were recovered from both libraries. The dominant groups of fungi associated with each tree type were very similar, although there were some qualitative differences in the recovery of less-abundant fungi, likely as a result of the underlying heterogeneity of the fungal population. The methods employed revealed only minor differences between the bacterial and fungal communities associated with transgenic and unmodified trees. PMID:18552195
Oliver, Kathryn L; Hamelin, Richard C; Hintz, William E
High throughput sequencing methods are widely used in analyses of microbial diversity, but are generally applied to small numbers of samples, which precludes characterization of patterns of microbial diversity across space and time. We have designed a primer-tagging approach that allows pooling and subsequent sorting of numerous samples, which is directed to amplification of a region spanning the nuclear ribosomal internal transcribed spacers and partial large subunit from fungi in environmental samples. To test the method for phylogenetic biases, we constructed a controlled mixture of four taxa representing the Chytridiomycota, Zygomycota, Ascomycota and Basidiomycota. Following cloning and colony restriction fragment length polymorphism analysis, we found no significant difference in representation in 19 of the 23 tested primers. We also generated a clone library from two soil DNA extracts using two primers for each extract and compared 456 clone sequences. Community diversity statistics and contingency table tests applied to counts of operational taxonomic units revealed that the two DNA extracts differed significantly, while the pairs of tagged primers from each extract were indistinguishable. Similar results were obtained using UniFrac phylogenetic comparisons. Together, these results suggest that the pig-tagged primers can be used to increase ecological inference in high throughput sequencing projects on fungi. PMID:21585882
Taylor, D Lee; Booth, Michael G; McFarland, Jack W; Herriott, Ian C; Lennon, Niall J; Nusbaum, Chad; Marr, Thomas G
The Zygomycota is an ecologically heterogenous assemblage of nonzoosporic fungi comprising two classes, Zygomycetes and Trichomycetes. Phylogenetic analyses have suggested that the phylum is polyphyletic; two of four orders of Trichomycetes are related to the Mesomycetozoa (protists) that diverged near the fungal/animal split. Current circumscription of the Zygomycota includes only orders with representatives that produce zygospores. We present a molecular-based phylogeny including recognized representatives of the Zygomycetes and Trichomycetes with a combined dataset for nuclear rRNA 18S (SSU), 5.8S and 28S (LSU) genes. Tree reconstruction by Bayesian analyses suggests the Zygomycota is paraphyletic. Although 12 clades were identified only some of these correspond to the nine orders of Zygomycota currently recognized. A large superordinal clade, comprising the Dimargaritales, Harpellales, Kickxellales and Zoopagales, grouping together many symbiotic fungi, also is identified in part by a unique septal structure. Although Harpellales and Kickxellales are not monophyletic, these lineages are distinct from the Mucorales, Endogonales and Mortierellales, which appear more closely related to the Ascomycota + Basidiomycota + Glomeromycota. The final major group, the insect-associated Entomophthorales, appears to be polyphyletic. In the present analyses Basidiobolus and Neozygites group within Zygomycota but not with the Entomophthorales. Clades are discussed with special reference to traditional classifications, mapping morphological characters and ecology, where possible, as a snapshot of our current phylogenetic perspective of the Zygomycota. PMID:17486964
White, Merlin M; James, Timothy Y; O'Donnell, Kerry; Cafaro, Matías J; Tanabe, Yuuhiko; Sugiyama, Junta
Soil fungal communities were studied using 18S rDNA-based molecular techniques. Soil DNA was analyzed using temperature gradient gel electrophoresis (TGGE), single-stranded conformational polymorphism (SSCP), cloning and sequencing methods, following community DNA extraction and polymerase chain reaction (PCR). The extracted community DNA was successfully amplified using the primer pair of EF4f-Fung5r which produced ca. 550bp 18S rDNA fragments. TGGE screening of the PCR products showed some differences in band position and intensity between two soil samples in adjacent natural forest (YNF) and hoop pine plantation (YHP) ecosystems at Yarraman in subtropical Australia. TGGE and SSCP could be used for screening PCR products. However, care must be exercised when interpreting the TGGE and SSCP results with respect to microbial diversity, because one band may not necessarily represent one species. It is recommended that the PCR products should be purified before TGGE or SSCP screening. SSCP screening of the clone sequences revealed differences among the clones. Sequence and phylogenetic analyses revealed that all obtained clones were affiliated to the kingdom Fungi, including three phyla, i.e., Zygomycota, Ascomycota and Basidiomycota. Our results suggested that community DNA extraction, PCR, cloning, SSCP screening of clones, sequencing of selected clones and phylogentic analyses could be a good strategy in investigation of soil fungal community and diversity. PMID:15927752
He, Jizheng; Xu, Zhihong; Hughes, Jane
Fungal and bacterial community structure in tussock, intertussock and shrub organic and mineral soils at Toolik Lake, Alaska were evaluated. Community structure was examined by constructing clone libraries of partial 16S and 18S rRNA genes. The soil communities were sampled at the end of the growing season in August 2004 and just after the soils thawed in June 2005. The communities differed greatly between vegetation types, although tussock and intertussock soil communities were very similar at the phyla level. The communities were relatively stable between sample dates at the phyla and subphyla levels, but differed significantly at finer phylogenetic scales. Tussock and intertussock bacterial communities were dominated by Acidobacteria, while shrub soils were dominated by Proteobacteria. These results appear consistent with previous work demonstrating that shrub soils contain an active, bioavailable C fraction, while tussock soils are dominated by more recalcitrant substrates. Tussock fungi communities had higher proportions of Ascomycota than shrub soils, while Zygomycota were more abundant in shrub soils. Recent documentation of increasing shrub abundance in the Arctic suggests that soil microbial communities and their functioning are likely to be altered by climate change. PMID:17313585
Wallenstein, Matthew David; McMahon, Shawna; Schimel, Joshua
Very few studies have addressed the phylogenetic diversity of fungi from Northeast India under the Eastern Himalayan range. In the present study, an attempt has been made to study the phylogenetic diversity of culturable soil fungi along the altitudinal gradients of eastern Himalayas. Soil samples from 24 m above sea level to 2,000 m above sea level altitudes of North-East India were collected to investigate soil micro-fungal community structure and diversity. Molecular characterization of the isolates was done by PCR amplification of 18S rDNA using universal primers. Phylogenetic analysis using BLAST revealed variation in the distribution and richness of different fungal biodiversity over a wide range of altitudes. A total of 107 isolates were characterized belonging to the phyla Ascomycota and Zygomycota, corresponding to seven orders (Eurotiales, Hypocreales, Calosphaeriales, Capnodiales, Pleosporales, Mucorales, and Mortierellales) and Incertae sedis. The characterized isolates were analysed for richness, evenness and diversity indices. Fungal diversity had significant correlation with soil physico-chemical parameters and the altitude. Eurotiales and Hypocreales were most diverse and abundant group of fungi along the entire altitudinal stretch. Species of Penicillium (D = 1.44) and Aspergillus (D = 1.288) were found to have highest diversity index followed by Talaromyces (D = 1.26) and Fusarium (D = 1.26). Fungal distribution showed negative correlation with altitude and soil moisture content. Soil temperature, pH, humidity and ambient temperature showed positive correlation with fungal distribution. PMID:23115506
Devi, Lamabam Sophiya; Khaund, Polashree; Nongkhlaw, Fenella M W; Joshi, S R
Endophytc fungi were collected from the barks, branches and leaves of Taxus chinensis var. mairei from the Jiangxi, Zhejiang and Chongqing regions of China and their influences on geographic and tissue investigated. A total of 145 fungal taxa were identified based on molecular techniques, of these 125 taxa (86.2 %) belonging to Ascomycota, 14 (9.7 %) to Basidiomycota, 5 (3.4 %) to Zygomycota, and 1 (0.7 %) to undefined fungi. The species richness and diversity of endophytic fungi were significantly affected by tissue, and were 1.2-2.5-fold higher in the branches and barks when compared to the leaves. The locality affected the species richness per tree and the shannon diversity index per tree by longitude. The endophyte assemblages were strongly shaped by locality and tissue according to partial least squares discriminant analysis. In addition, the distributions of dominant fungi at orders and genera levels differed as a function of locality and tissue. Most of the dominant taxa showed spatial heterogeneity and tissue specificity or preference and many fungal taxa with low frequency were special to one locality or one tissue. PMID:23053484
Wu, Lingshang; Han, Ting; Li, Wenchao; Jia, Min; Xue, Liming; Rahman, Khalid; Qin, Luping
The soil dilution plate method was used to determine the influences of perennial shrubs on the species diversity and density of cultivable microfungal communities inhabiting the root zones of two perennial shrubs, Zygophyllum dumosum and Hammada scoparia, in the northern Negev Desert, Israel. Soil samples were collected under the canopies of shrubs and the open spaces between them (serving as control) from five depths (0-10, 10-20, 20-30, 30-40, and 40-50 cm) during the wet and dry seasons of 2010. Fifty-one species belonging to 31 genera were identified from Zygomycota, teleomorphic and anamorphic Ascomycota, including Coelomycetes. During the wet and dry seasons, 4-10 and 2-6 species were identified at different soil depths beneath perennial shrubs and in the open spaces, while the corresponding colony-forming units (CFUs) varied from 3071 to 27687 and from 3201 to 15247 g(-1) dry soil. More diverse microfungal communities were collected in the vicinity of perennial shrubs compared to the open spaces during the wet season, while a reverse trend was observed during the dry season. Further study is needed to provide insights into the correlation between compounds of litter and root exudates of perennial shrubs and microfungal-community structure by a combination of molecular and physiological tools. PMID:22736431
Yu, Jun; Grishkan, Isabella; Steinberger, Yosef
Little is known about the microbial diversity associated with marine macroorganisms, despite the vital role microorganisms may play in marine ecosystems. The aim of the present study was to investigate the diversity of bacteria and fungi isolated from eight marine invertebrate and one algae samples. Data derived from ARDRA and sequencing analyses allowed the identification of marine-derived microorganisms isolated from those samples. Microbial strains identified up to the genus level revealed 144 distinct ribotypes out of 256 fungal strains and 158 distinct ribotypes out of 181 bacterial strains. Filamentous fungi were distributed among 24 different genera belonging to Ascomycota, Zygomycota and Basidiomycota, some of which had never been reported in the literature as marine invertebrate-inhabiting fungi (Pestalotiopsis, Xylaria, Botrysphaeria and Cunnninghamella). Bacterial isolates were affiliated to 41 different genera, being Bacillus, Ruegeria, Micrococcus, Pseudovibrio and Staphylococcus the most abundant ones. Results revealed an unexpected high microbial diversity associated to the macroorganisms which have been collected and suggested the selection of certain microbial taxonomic groups according to the host. The combined data gathered from this investigation contribute to broaden the knowledge of microbial diversity associated to marine macroorganisms, including as a promising source for the discovery of new natural products. PMID:19879115
Menezes, Cláudia B A; Bonugli-Santos, Rafaella C; Miqueletto, Paula B; Passarini, Michel R Z; Silva, Carlos H D; Justo, Mariana R; Leal, Rebeca R; Fantinatti-Garboggini, Fabiana; Oliveira, Valéria M; Berlinck, Roberto G S; Sette, Lara D
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. PMID:18309361
Schmitt, Imke; Partida-Martinez, Laila P; Winkler, Robert; Voigt, Kerstin; Einax, Esra; Dölz, Franziska; Telle, Sabine; Wöstemeyer, Johannes; Hertweck, Christian
The fungal cell wall is a coherent structure formed by microfibrillar polysaccharides and amorphous material made of other polysaccharides and proteins. We performed a phylogenetic analysis of covalent proteins and enzymes that synthesize fungal wall polysaccharides to determine the possible evolution of the wall structure. It is suggested that the components that made up the archaic walls were structural ones, forming a primitive girdle that retained noncovalently bound proteins in the periplasm and allowed cell growth in hypotonic media. The following hypothetical series of events in fungal wall evolution is suggested: (1) Construction of a primitive wall made of chitin and chitosan by division 2 chitin synthases and chitin deacetylases, respectively. (2) Appearance of class II chitin synthase genes (CHS) after separation of Microsporidia. (3) Capture of a gene encoding beta-1,3-glucan synthase from an organism related to Plantae or Chromista by horizontal transfer after separation of Chytridiomycota. (4) Appearance or horizontal capture from Chromista of genes involved in beta-1,6-glucan synthesis after separation of Zygomycota. (5). Appearance of class III CHS genes. (6) After split of Dikarya phyla, appearance in Ascomycota of class I CHS genes and the capacity to synthesize covalently bound wall proteins. PMID:19891730
Ruiz-Herrera, José; Ortiz-Castellanos, Lucila
We explored the potential of the cox1 gene in the species resolution of soil fungi and compared it with the nuclear internal transcribed spacer (ITS) and small subunit (SSU)-rDNA. Conserved primers allowing the amplification of the fungal cox1 gene were designed, and a total of 47 isolates of Zygomycota and Ascomycota were investigated. The analysis revealed a lack of introns in >90% of the isolates. Comparison of the species of each of the six studied genera showed high interspecific sequence polymorphisms. Indeed, the average of nucleotide variations (4.2-11%) according to the genus, due mainly to the nucleotide substitutions, led to the taxonomic resolution of all the species studied regarding both ITS and SSU-rDNA, in which <88% were discriminated. The phylogenetic analysis performed after alignment of the cox1 gene across distant fungal species was in accordance with the well-known taxonomic position of the species studied and no overlap was observed between intra- and interspecific variations. These results clearly demonstrated that the cox1 sequences could provide good molecular markers for the determination of the species composition of environmental samples and constitute an important advance to study soil fungal biodiversity. PMID:19909345
Molitor, Claire; Inthavong, Beatrice; Sage, Lucile; Geremia, Roberto A; Mouhamadou, Bello
Fungal amylolytic enzymes, including ?-amylase, gluocoamylase and ?-glucosidase, have been extensively exploited in diverse industrial applications such as high fructose syrup production, paper making, food processing and ethanol production. In this paper, amylolytic genes of 85 strains of fungi from the phyla Ascomycota, Basidiomycota, Chytridiomycota and Zygomycota were annotated on the genomic scale according to the classification of glycoside hydrolase (GH) from the Carbohydrate-Active enZymes (CAZy) Database. Comparisons of gene abundance in the fungi suggested that the repertoire of amylolytic genes adapted to their respective lifestyles. Amylolytic enzymes in family GH13 were divided into four distinct clades identified as heterologous ?-amylases, eukaryotic ?-amylases, bacterial and fungal ?-amylases and GH13 ?-glucosidases. Family GH15 had two branches, one for gluocoamylases, and the other with currently unknown function. GH31 ?-glucosidases showed diverse branches consisting of neutral ?-glucosidases, lysosomal acid ?-glucosidases and a new clade phylogenetically related to the bacterial counterparts. Distribution of starch-binding domains in above fungal amylolytic enzymes was related to the enzyme source and phylogeny. Finally, likely scenarios for the evolution of amylolytic enzymes in fungi based on phylogenetic analyses were proposed. Our results provide new insights into evolutionary relationships among subgroups of fungal amylolytic enzymes and fungal evolutionary adaptation to ecological conditions. PMID:23166747
Chen, Wanping; Xie, Ting; Shao, Yanchun; Chen, Fusheng
Parasites are able to evolve rapidly and overcome host defense mechanisms, but the molecular basis of this adaptation is poorly understood. Powdery mildew fungi (Erysiphales, Ascomycota) are obligate biotrophic parasites infecting nearly 10,000 plant genera. They obtain their nutrients from host plants through specialized feeding structures known as haustoria. We previously identified the AVR(k1) powdery mildew-specific gene family encoding effectors that contribute to the successful establishment of haustoria. Here, we report the extensive proliferation of the AVR(k1) gene family throughout the genome of B. graminis, with sequences diverging in formae speciales adapted to infect different hosts. Also, importantly, we have discovered that the effectors have coevolved with a particular family of LINE-1 retrotransposons, named TE1a. The coevolution of these two entities indicates a mutual benefit to the association, which could ultimately contribute to parasite adaptation and success. We propose that the association would benefit 1) the powdery mildew fungus, by providing a mechanism for amplifying and diversifying effectors and 2) the associated retrotransposons, by providing a basis for their maintenance through selection in the fungal genome. PMID:19829700
Sacristán, Soledad; Vigouroux, Marielle; Pedersen, Carsten; Skamnioti, Pari; Thordal-Christensen, Hans; Micali, Cristina; Brown, James K M; Ridout, Christopher J
The shorter reads generated by high-throughput sequencing has led to a focus on either the ITS1 or the ITS2 sublocus in fungal diversity analyses. Our study aimed to determine how making this choice would influence the datasets obtained and our vision of environmental fungal diversity. DNA was extracted from different environmental samples (water, sediments and soil) and the total internal transcribed spacer (ITS) locus was amplified. 454-sequencing was performed targeting both ITS1 and ITS2. No significant differences in the number of sequences, operational taxonomic units (OTUs) and in the dominant OTUs were detected but less diversity was observed in the ITS2 dataset. In the soil samples, differences in the fungal taxonomic identification were observed, with more Basidiomycota in the ITS1 dataset and more Ascomycota in the ITS2 dataset. Only one-third of the OTUs were detected in both datasets which could be due to (1) more short sequences removed in the ITS2 dataset, (2) different taxonomic affiliation depending on the sublocus used as BLASTn query and/or (3) selectivity in how a primer amplifies the true community. Although ITS1 and ITS2 datasets led to similar results at the fungal community level, for further in-depth diversity analysis this study suggests the analysis of both ITS regions, as they provided different information and were complementary. PMID:23176677
Monard, Cécile; Gantner, Stephan; Stenlid, Jan
Aspergillus terreus is a filamentous ascomycota, which is prominent for its production of lovastatin, an antihypercholesterolemic drug. The commercial importance of lovastatin with annual sales of billions of dollars made us to focus on lovastatin biosynthetic cluster proteins. The analysis of these lovastatin biosynthetic cluster proteins with different perspectives such as physicochemical property, structure based analysis and functional studies were done to find out the role and function of every protein involved in the lovastatin biosynthesis pathway. Several computational tools are used to predict the physicochemical properties, secondary structural features, topology, patterns, domains and cellular location. There are 8 unidentified proteins in lovastatin biosynthetic cluster, in which 6 proteins have homologous partners, and annotation transfer is done based on the closely related homologous genes, and their structures are also modeled. The two other proteins that do not have homologous partners are predicted as PQ loop repeat protein that may be involved in glycosylation machinery and as thiolase-acyl activity by the integrated functional analysis approach.
Subazini, Thankaswamy Kosalai; Kumar, Gopal Ramesh
Mounting evidence indicates that changes in the transcriptome contribute significantly to the phenotypic differentiation of closely related species. Nonetheless, further genome-wide studies, spanning a broad range of organisms, are needed to decipher the factors driving transcriptome evolution. The model Neurospora (Ascomycota) comprises a simple system for empirically studying the evolutionary dynamics of the transcriptome. Here, we studied the evolution of gene expression in Neurospora crassa and Neurospora tetrasperma and show that patterns of transcriptome evolution are connected to genome evolution, tissue type and sexual identity (mating types, mat A and mat a) in these eukaryotes. Based on the comparisons of inter- and intraspecies expression divergence, our data reveal that rapid expression divergence is more apt to occur in sexual/female (SF) than vegetative/male (VM) tissues. In addition, interspecies gene expression and protein sequence divergence were strongly correlated for SF, but not VM, tissue. A correlation between transcriptome and protein evolution parallels findings from certain animals, but not yeast, and add support for the theory that expression evolution differs fundamentally among multicellular and unicellular eukaryotes. Finally, we found that sexual identity in these hermaphroditic Neurospora species is connected to interspecies expression divergence in a tissue-dependent manner: rapid divergence occurred for mat A- and mat a-biased genes from SF and VM tissues, respectively. Based on these findings, it is hypothesized that rapid interspecies transcriptome evolution is shifting the mating types of Neurospora towards distinct female and male phenotypes, that is, sexual dimorphism. PMID:24848562
Whittle, C A; Sun, Y; Johannesson, H
In order to understand the biodeterioration process occurring on stone monuments, we analyzed the microbial communities involved in these processes and studied their ability to colonize stones under controlled laboratory experiments. In this study, a natural green biofilm from a limestone monument was cultivated, inoculated on stone probes of the same lithotype and incubated in a laboratory chamber. This incubation system, which exposes stone samples to intermittently sprinkling water, allowed the development of photosynthetic biofilms similar to those occurring on stone monuments. Denaturing gradient gel electrophoresis (DGGE) analysis was used to evaluate the major microbial components of the laboratory biofilms. Cyanobacteria, green microalgae, bacteria and fungi were identified by DNA-based molecular analysis targeting the 16S and 18S ribosomal RNA genes. The natural green biofilm was mainly composed by the Chlorophyta Chlorella, Stichococcus, and Trebouxia, and by Cyanobacteria belonging to the genera Leptolyngbya and Pleurocapsa. A number of bacteria belonging to Alphaproteobacteria, Bacteroidetes and Verrucomicrobia were identified, as well as fungi from the Ascomycota. The laboratory colonization experiment on stone probes showed a colonization pattern similar to that occurring on stone monuments. The methodology described in this paper allowed to reproduce a colonization equivalent to the natural biodeteriorating process. PMID:18768211
Miller, Ana Zélia; Laiz, Leonila; Gonzalez, Juan Miguel; Dionísio, Amélia; Macedo, Maria Filomena; Saiz-Jimenez, Cesareo
The investigations on air pollution in industrial cities of Lithuania: Vilnius, Alytus, Kaunas, Marijampole and Elektrenai were aimed at detecting the presence of fungi and aerosol particles during different seasons of the year. Sampling of fungal spores was carried out at 20 sampling sites. Active air sampling was performed simultaneously with the use of passive sedimentation plates. Data on the spread of various micromycete species in the air of cities contaminated with various pollutants are presented. Micromycetes of 430 species belonging to 165 genera, 19 families, 13 orders, 4 classes, and 3 phylla were isolated and identified. We found 21 species, 11 genera, 7 families from Ascomycota, 6 species, 1 genus, 1 family from Oomycota, 45 species, 15 genera, 8 families from Zygomycota. Mitosporic fungi comprised 138 genera, 358 species, and comprised the vast majority of identified species: 358 out of 430 (83.25 %). Conditionally pathogenic species were also isolated. It was concluded that the abundance of such fungi as Aspergillus niger, A. fumigatus, Cladosporium herbarum, Alternaria alternata, Aureobasidium pullulans in the air can be a significant criterion for the evaluation of air pollution. PMID:14677918
Lugauskas, Albinas; Sveistyte, Laima; Ulevicius, Vidmantas
Understanding pathogen transmission could illuminate new methods for disease prevention. A case in point is chalkbrood in the alfalfa leafcutting bee [Megachile rotundata (F.)]. Propagation of this solitary bee is severely hampered by chalkbrood, a larval disease caused by Ascosphaera aggregata (Ascomycota). Alfalfa leafcutting bees nest in existing cavities in wood or hollow reeds and overwinter as larvae. In the early summer, emerging adults frequently must chew through dead, diseased siblings that block their exit, becoming contaminated with chalkbrood spores in the process. When alfalfa leafcutting bees are used as a commercial pollinator, the cocoons are removed from nesting boards to reduce chalkbrood transmission, but the disease is still common. To determine if these removed cocoons (called loose cells) are an important source of disease transmission, they were disinfected with a fungicide before bees were incubated, and released in the field. Chalkbrood prevalence among the progeny of the treated bees was reduced up to 50% in one field trial, but not significantly when tested in an on-farm trial. Thus, substantial disease transmission still occurred when the loose cells were disinfected, and even when clean nesting materials were used. In conclusion, pathogen transmission must still be occurring from another source that has yet to be identified. Another possible source of transmission could arise from bees that emerge midsummer in populations with a high percent of multivoltinism, but dirty nesting boards and feral bees also may be minor sources of transmission. PMID:22251678
James, R R
The Black Pine, Pinus thunbergii, is widely distributed along the eastern coast of Korea and its importance as a shelterbelt was highlighted after tsunamis in Indonesia and Japan. The root endophytic diversity of P. thunbergii was investigated in three coastal regions; Goseong, Uljin, and Busan. Fungi were isolated from the root tips, and growth rates of pure cultures were measured and compared between PDA with and without 3% NaCl to determine their saline resistance. A total of 259 isolates were divided into 136 morphotypes, of which internal transcribed spacer region sequences identified 58 species. Representatives of each major fungi phylum were present: 44 Ascomycota, 8 Zygomycota, and 6 Basidiomycota. Eighteen species exhibited saline resistance, many of which were Penicillium and Trichoderma species. Shoreline habitats harbored higher saline-tolerant endophytic diversity compared with inland sites. This investigation indicates that endophytes of P. thunbergii living closer to the coast may have higher resistance to salinity and potentially have specific relationships with P. thunbergii. PMID:24317482
Min, Young Ju; Park, Myung Soo; Fong, Jonathan J; Quan, Ying; Jung, Sungcheol; Lim, Young Woon
Abstract We report the identification, cloning, heterologous expression and functional characterization of a novel antifungal peptide named lucimycin from the common green bottle fly Lucilia sericata. The lucimycin cDNA was isolated from a library of genes induced during the innate immune response in L. sericata larvae, which are used as therapeutic maggots. The peptide comprises 77 amino acid residues with a molecular mass of 8.2 kDa and a pI of 6.6. It is predicted to contain a zinc-binding motif and to form a random coil, lacking ?-sheets or other secondary structures. Lucimycin was active against fungi from the phyla Ascomycota, Basidiomycota and Zygomycota, in addition to the oomycete Phytophtora parasitica, but it was inactive against bacteria. A mutant version of lucimycin, lacking the four C-terminal amino acid residues, displayed 40-fold lower activity. The activity of lucimycin against a number of highly-destructive plant pathogens could be exploited to produce transgenic crops that are resistant against fungal diseases. PMID:24622788
Pöppel, Anne-Kathrin; Koch, Aline; Kogel, Karl-Heinz; Vogel, Heiko; Kollewe, Christian; Wiesner, Jochen; Vilcinskas, Andreas
Growth Inhibition of Beauveria bassiana by Bacteria Isolated from the Cuticular Surface of the Corn Leafhopper, Dalbulus maidis and the Planthopper, Delphacodes kuscheli, Two Important Vectors of Maize Pathogens
The phytosanitary importance of the corn leafhopper, Dalbulus maidis (De Long and Wolcott) (Hemiptera: Cicadellidae) and the planthopper, Delphacodes kuscheli Fennah (Hemiptera: Delphacidae) lies in their ability to transmit phloem-associated plant pathogens, mainly viruses and mollicutes, and to cause considerable mechanical damage to corn plants during feeding and oviposition. Fungi, particularly some members of the Ascomycota, are likely candidates for biocontrol agents against these insect pests, but several studies revealed their failure to invade the insect cuticle possibly because of the presence of inhibitory compounds such as phenols, quinones, and lipids and also by the antibiosis effect of the microbiota living on the cuticular surface of the host. The present work aims to understand interactions between the entomopathogenic fungus Beauveria bassiana (Balsamao-Crivelli) Vuillemin (Hypocreales: Cordycipitaceae) and bacterial antagonists isolated from the cuticular surface of D. maidis and D. kuscheli. A total of 155 bacterial isolates were recovered from the insect's cuticle and tested against B. bassiana. Ninety-one out of 155 strains inhibited the growth of B. bassiana. Bacterial strains isolated from D. maidis were significantly more antagonistic against B. bassiana than those isolates from D. kuscheli. Among the most effective antagonistic strains, six isolates of Bacillus thuringiensis Berliner (Bacillales: Bacillaeae (after B. subtilis)), one isolate of B. mycoides Flügge, eight isolates of B. megaterium de Bary, five isolates of B.pumilus Meyer and Gottheil, one isolate of B. licheniformis (Weigmann) Chester, and four isolates of B. subtilis (Ehrenberg) Cohn were identified.
Toledo, A.V.; Alippi, A.M.; de Remes Lenicov, A.M.M.
An abundance of novel fungal lineages have been indicated by DNA sequencing of the nuclear ribosomal ITS region from environmental samples such as soil and wood. Although phylogenetic analysis of these novel lineages is a key component of unveiling the structure and diversity of complex communities, such analyses are rare for environmental ITS data due to the difficulties of aligning this locus across significantly divergent taxa. One potential approach to this issue is simultaneous alignment and tree estimation. We targeted divergent ITS sequences of the earth tongue fungi (Geoglossomycetes), a basal class in the Ascomycota, to assess the performance of SATé, recent software that combines progressive alignment and tree building. We found that SATé performed well in generating high-quality alignments and in accurately estimating the phylogeny of earth tongue fungi. Drawing from a data set of 300 sequences of earth tongues and progressively more distant fungal lineages, 30 insufficiently identified ITS sequences from the public sequence databases were assigned to the Geoglossomycetes. The association between earth tongues and plants has been hypothesized for a long time, but hard evidence is yet to be collected. The ITS phylogeny showed that four ectomycorrhizal isolates shared a clade with Geoglossum but not with Trichoglossum earth tongues, pointing to the significant potential inherent to ecological data mining of environmental samples. Environmental sampling holds the key to many focal questions in mycology, and simultaneous alignment and tree estimation, as performed by SATé, can be a highly efficient companion in that pursuit.
Wang, Zheng; Nilsson, R. Henrik; Lopez-Giraldez, Francesc; Zhuang, Wen-ying; Dai, Yu-cheng; Johnston, Peter R.; Townsend, Jeffrey P.
Functional environmental genomics has the potential to identify novel biological functions that the systematic sequencing of microbial genomes or environmental DNA may fail to uncover. We targeted the functions expressed by soil eukaryotes using a metatranscriptomic approach based on the use of soil-extracted polyadenylated messenger RNA to construct environmental complementary DNA expression libraries. Functional complementation of a yeast mutant defective in di/tripeptide uptake identified a novel family of oligopeptide transporters expressed by fungi. This family has a patchy distribution in the Basidiomycota and Ascomycota and is present in the genome of a Saccharomyces cerevisiae wine strain. High throughput phenotyping of yeast mutants expressing two environmental transporters showed that they both displayed broad substrate specificity and could transport more than 60–80 dipeptides. When expressed in Xenopus oocytes one environmental transporter induced currents upon dipeptide addition, suggesting proton-coupled co-transport of dipeptides. This transporter was also able to transport specifically cysteine. Deletion of the two copies of the corresponding gene family members in the genome of the wine yeast strain severely reduced the number of dipeptides that it could assimilate. These results demonstrate that these genes are functional and can be used by fungi to efficiently scavenge the numerous, low concentration, oligopeptides continuously generated in soils by proteolysis.
Damon, Coralie; Vallon, Laurent; Zimmermann, Sabine; Haider, Muhammad Z; Galeote, Virginie; Dequin, Sylvie; Luis, Patricia; Fraissinet-Tachet, Laurence; Marmeisse, Roland
A mycosed planthopper, Oliarus dimidiatus Berg (Hemiptera: Cixiidae), and two psocids, Heterocaecilius sp. (Psocodea: Pseudocaeciliidae) and Ectopsocus sp. (Ectopsocidae), were collected from Los Hornos and La Plata, Buenos Aires, Argentina between February and September 2007. Observations of mycelia growing on the host revealed that the putative fungal parasite had synnemata supporting monophialidic conidiogenous cells. Likewise, in vitro fungal cultures presented characteristics typical of the fungus Hirsutella citriformis Speare (Ascomycota: Hypocreales: Clavicipitaceae). The identity of the isolated fungi characterized based on morphological aspects was complemented by means of the internal transcribed spacer sequences. The sequences of both isolates were highly homologous to those of Cordyceps sp. (Fries) Link and Ophiocordyceps sinensis (Berkely) G.H. Sung, J.M. Sung, Hywel-Jones, and Spatafora (Ophiocordycipitaceae). We additionally confirmed that both isolates had the ability to infect and kill adults of Delphacodes kuscheli Fennah (Hemiptera: Delphacidae) after 10 days. Therefore, based on the morphology of the isolated fungi, their ribosomal internal transcribed spacer sequence, and their ability to parasite insects, we conclude that the fungi isolated belong to the genus Hirsutella and might have biotechnological potential.
Toledo, Andrea V.; Simurro, Maria E.; Balatti, Pedro A.
Fungi comprise a vast group of microorganisms including the Ascomycota (majority of all described fungi), the Basidiomycota (mushrooms or higher fungi), and the Zygomycota and Chytridiomycota (basal or lower fungi) that produce industrially interesting secondary metabolites, such as ?-lactam antibiotics. These compounds are one of the most commonly prescribed drugs world-wide. Since Fleming's initial discovery of Penicillium notatum 80 years ago, the role of Penicillium as an antimicrobial source became patent. After the isolation of Penicillium chrysogenum NRRL 1951 six decades ago, classical mutagenesis and screening programs led to the development of industrial strains with increased productivity (at least three orders of magnitude). The new “omics” era has provided the key to understand the underlying mechanisms of the industrial strain improvement process. The review of different proteomics methods applied to P. chrysogenum has revealed that industrial modification of this microorganism was a consequence of a careful rebalancing of several metabolic pathways. In addition, the secretome analysis of P. chrysogenum has opened the door to new industrial applications for this versatile filamentous fungus.
Barreiro, Carlos; Martin, Juan F.; Garcia-Estrada, Carlos
The subject of this review is the biodiversity of marine sponges and associated microbes which have been reported to produce therapeutically important compounds, along with the contextual information on their geographic distribution. Class Demospongiae and the orders Halichondrida, Poecilosclerida and Dictyoceratida are the richest sources of these compounds. Among the microbial associates, members of the bacterial phylum Actinobacteria and fungal division Ascomycota have been identified to be the dominant producers of therapeutics. Though the number of bacterial associates outnumber the fungal associates, the documented potential of fungi to produce clinically active compounds is currently more important than that of bacteria. Interestingly, production of a few identical compounds by entirely different host-microbial associations has been detected in both terrestrial and marine environments. In the Demospongiae, microbial association is highly specific and so to the production of compounds. Besides, persistent production of bioactive compounds has also been encountered in highly specific host-symbiont associations. Though spatial and temporal variations are known to have a marked effect on the quality and quantity of bioactive compounds, only a few studies have covered these dimensions. The need to augment production of these compounds through tissue culture and mariculture has also been stressed. The reviewed database of these compounds is available at www.niobioinformatics.in/drug.php.
Thomas, Tresa Remya A.; Kavlekar, Devanand P.; LokaBharathi, Ponnapakkam A.
The 2000 eruption of Mount Oyama on the island of Miyake (Miyake-jima) created a unique opportunity to study the early ecosystem development on newly exposed terrestrial substrates. In this study, bacterial and fungal communities on 9- and 11-year-old volcanic deposits at poorly to fully vegetation-recovered sites in Miyake-jima, Japan, were characterized by conventional culture-based methods and pyrosequencing of 16S rRNA and 18S rRNA genes. Despite the differences in the vegetation cover, the upper volcanic deposit layer samples displayed low among-site variation for chemical properties (pH, total organic carbon, and total nitrogen) and microbial population densities (total direct count and culturable count). Statistical analyses of pyrosequencing data revealed that the microbial communities of volcanic deposit samples were phylogenetically diverse, in spite of very low-carbon environmental conditions, and their diversity was comparable to that in the lower soil layer (buried soil) samples. Comparing with the microbial communities in buried soil, the volcanic deposit communities were characterized by the presence of Betaproteobacteria and Gammaproteobacteria as the main bacterial class, Deinococcus- Thermus as the minor bacterial phyla, and Ascomycota as the major fungal phyla. Multivariate analysis revealed that several bacterial families and fungal classes correlated positively or negatively with plant species.
Guo, Yong; Fujimura, Reiko; Sato, Yoshinori; Suda, Wataru; Kim, Seok-won; Oshima, Kenshiro; Hattori, Masahira; Kamijo, Takashi; Narisawa, Kazuhiko; Ohta, Hiroyuki
Many bacteria and fungi are known to degrade cellulose in culture, but their combined response to cellulose in different soils is unknown. Replicate soil microcosms amended with [13C]cellulose were used to identify bacterial and fungal communities responsive to cellulose in five geographically and edaphically different soils. The diversity and composition of the cellulose-responsive communities were assessed by DNA-stable isotope probing combined with Sanger sequencing of small-subunit and large-subunit rRNA genes for the bacterial and fungal communities, respectively. In each soil, the 13C-enriched, cellulose-responsive communities were of distinct composition compared to the original soil community or 12C-nonenriched communities. The composition of cellulose-responsive taxa, as identified by sequence operational taxonomic unit (OTU) similarity, differed in each soil. When OTUs were grouped at the bacterial order level, we found that members of the Burkholderiales, Caulobacteriales, Rhizobiales, Sphingobacteriales, Xanthomonadales, and the subdivision 1 Acidobacteria were prevalent in the 13C-enriched DNA in at least three of the soils. The cellulose-responsive fungi were identified as members of the Trichocladium, Chaetomium, Dactylaria, and Arthrobotrys genera, along with two novel Ascomycota clusters, unique to one soil. Although similarities were identified in higher-level taxa among some soils, the composition of cellulose-responsive bacteria and fungi was generally unique to a certain soil type, suggesting a strong potential influence of multiple edaphic factors in shaping the community.
Eichorst, Stephanie A.
Estimations of genome size and its variation can provide valuable information regarding the genetic diversity of organisms and their adaptation potential to heterogeneous environments. We used flow cytometry to characterize the variation in genome size among 40 isolates of Cenococcum geophilum, an ectomycorrhizal fungus with a wide ecological and geographical distribution, obtained from two serpentine and two non-serpentine sites in Portugal. Besides determining the genome size and its intraspecies variation, we wanted to assess whether a relationship exists between genome size and the edaphic background of the C. geophilum isolates. Our results reveal C. geophilum to have one of the largest genome sizes so far measured in the Ascomycota, with a mean haploid genome size estimate of 0.208 pg (203 Mbp). However, no relationship was found between genome size and the edaphic background of the sampled isolates, indicating genetic and demographic processes to be more important for shaping the genome size variation in this species than environmental selection. The detection of variation in ploidy level among our isolates, including a single individual with both presumed haploid and diploid nuclei, provides supportive evidence for a possible cryptic sexual or parasexual cycle in C. geophilum (although other mechanisms may have caused this variation). The existence of such a cycle would have wide significance, explaining the high levels of genetic diversity and likelihood of recombination previously reported in this species, and adds to the increasing number of studies suggesting sexual cycles in previously assumed asexual fungi. PMID:23754539
Bourne, Elizabeth C; Mina, Diogo; Gonçalves, Susana C; Loureiro, João; Freitas, Helena; Muller, Ludo A H
• The aim of this study was to gain understanding of the carbon flow from the roots of a genetically modified (GM) amylopectin-accumulating potato (Solanum tuberosum) cultivar and its parental isoline to the soil fungal community using stable isotope probing (SIP). • The microbes receiving (13)C from the plant were assessed through RNA/phospholipid fatty acid analysis with stable isotope probing (PLFA-SIP) at three time-points (1, 5 and 12 d after the start of labeling). The communities of Ascomycota, Basidiomycota and Glomeromycota were analysed separately with RT-qPCR and terminal restriction fragment length polymorphism (T-RFLP). • Ascomycetes and glomeromycetes received carbon from the plant as early as 1 and 5 d after labeling, while basidiomycetes were slower in accumulating the labeled carbon. The rate of carbon allocation in the GM variety differed from that in its parental variety, thereby affecting soil fungal communities. • We conclude that both saprotrophic and mycorrhizal fungi rapidly metabolize organic substrates flowing from the root into the rhizosphere, that there are large differences in utilization of root-derived compounds at a lower phylogenetic level within investigated fungal phyla, and that active communities in the rhizosphere differ between the GM plant and its parental cultivar through effects of differential carbon flow from the plant. PMID:22413848
Hannula, S E; Boschker, H T S; de Boer, W; van Veen, J A
Tomato (Solanum lycopersicum L.) roots from four different crop sites in Colombia were surface sterilized and 51 fungal isolates were obtained and conserved for further analysis. Based on microscopical observations and growth characteristics, 20 fungal isolates corresponded to genus Fusarium, six presented asexual conidia different from Fusarium, eight were sterile mycelia, seven of which had dark septate hyphae and 17 did not continue to grow on plates after being recovered from conservation. Growth on different media, detailed morphological characterization and ITS region sequencing of the six sporulating and eight sterile isolates revealed that they belonged to different orders of Ascomycota and that the sterile dark septate endophytes did not correspond to the well known Phialocephala group. Interactions of nine isolates with tomato plantlets were assessed in vitro. No effect on shoot development was revealed, but three isolates caused brown spots in roots. Colonization patterns as analyzed by confocal microscopy differed among the isolates and ranged from epidermal to cortical penetration. Altogether 11 new isolates from root endophytic fungi were obtained, seven of which showed features of dark septate endophytes. Four known morphotypes were represented by five isolates, while six isolates belonged to five morphotypes of putative new unknown species. PMID:21307164
Andrade-Linares, Diana Rocio; Grosch, Rita; Franken, Philipp; Rexer, Karl-Heinz; Kost, Gerhard; Restrepo, Silvia; de Garcia, Maria Caridad Cepero; Maximova, Eugenia
Numerous plant pathogens, rhizosphere symbionts, and endophytic bacteria and yeasts produce the important phytohormone indole-3-acetic acid (IAA), often with profound effects on host plants. However, to date IAA production has not been documented among foliar endophytes -- the diverse guild of primarily filamentous Ascomycota that live within healthy, above-ground tissues of all plant species studied thus far. Recently bacteria that live within hyphae of endophytes (endohyphal bacteria) have been detected, but their effects have not been studied previously. Here we show not only that IAA is produced in vitro by a foliar endophyte (here identified as Pestalotiopsis aff. neglecta, Xylariales), but that IAA production is enhanced significantly when the endophyte hosts an endohyphal bacterium (here identified as Luteibacter sp., Xanthomonadales). Both the endophyte and the endophyte/bacterium complex appear to rely on an L-tryptophan dependent pathway for IAA synthesis. The bacterium can be isolated from the fungus when the symbiotic complex is cultivated at 36°C. In pure culture the bacterium does not produce IAA. Culture filtrate from the endophyte-bacterium complex significantly enhances growth of tomato in vitro relative to controls and to filtrate from the endophyte alone. Together these results speak to a facultative symbiosis between an endophyte and endohyphal bacterium that strongly influences IAA production, providing a new framework in which to explore endophyte-plant interactions.
Hoffman, Michele T.; Gunatilaka, Malkanthi K.; Wijeratne, Kithsiri; Gunatilaka, Leslie; Arnold, A. Elizabeth
The European species Hypocrea epimyces (Hypocreales, Ascomycota, Fungi) is redescribed based on the holotype including the drawing on its envelope by Saccardo and freshly collected material. The holomorphs of two closely related species, H. alni and H. brunneoviridis, are described as new species of the genus. They are characterized with morphological and molecular methods, including culture studies and phylogenetic analyses with internal transcribed spacers 1 and 2 as a part of the ribosomal RNA gene cluster, calmodulin, endochitinase, intron 4 of the translation elongation factor 1-alpha gene, and a part of the RNA polymerase II subunit B gene as phylogenetic markers. All species described here have green ascospores. Although phylogenetically closely related to H. lixii, they form reddish brown instead of green to black stromata. Except for H. brunneoviridis, forming nearly gliocladium-like conidiophores, the anamorphs of these species are similar to each other but vary in the angles of conidiophore branches and phialides, in phenotypic arrangement of conidiation on growth plates and in growth rates of cultures.
Jaklitsch, Walter M.; Kubicek, Christian P.; Druzhinina, Irina S.
We used nucleotide sequences of the small subunit ribosomal genes (SSU rDNA) to examine evolutionary relationships of apothecial ascomycetes (division Ascomycota; class Discomycetes sensu), commonly known as the cup fungi. The apothecial ascomycetes include both lichen-forming and free-living fungi. We sequenced the SSU rDNA from representatives of 10 fungal genera from four orders: Pezizales (Ascobolus lineolatus, Morchella elata agg., Peziza badia); Leotiales (Leotia lubrica, Sclerotinia sclerotiorum); Caliciales (Calicium tricolor, Mycocalicium albonigrum, Sphaerophorus globosus); and Lecanorales (Lecanora dispersa, Porpidia crustulata). Of these, C. tricolor, S. globosus, L. dispersa, and P. crustulata are lichen-forming fungi. Based on parsimony analyses of approximately 1750 aligned nucleotides of their SSU rDNA, we determined a most parsimonious tree (MPT). This hypothesis suggests that the apothecial ascomycetes are a paraphyletic assemblage, basal to other groups of filamentous ascomycetes including representatives of the perithecial fungi and cleistothecial fungi. The most parsimonious tree produced using this dataset supported the monophyly of the orders Pezizales, Leotiales, and Lecanorales. However, there was no support for monophyly of the representative Caliciales; S. globosus had affinities with members of the Lecanorales. This phylogenetic hypothesis recognizes Pezizales as basal and supports Nannfeldt's hypothesis (1932) of a primitive apothecial ascomata with subsequent evolution of perithecial and cleistothecial forms. This MPT provides a foundation for understanding evolution of the ascomycetous fungi. PMID:7614369
Gargas, A; Taylor, J W
Fungi, in comparison with other pathogenic factors, have high pathogenicity. The number of fungal species which are able to infect people is over 500. The upper respiratory tract and ear have permanent contact with external environment which makes their ontocenoses open to continuous exchange of microorganisms of which they consist. In etiology of inflammatory processes 21 species which belonging to 3 genera (Zygomycota, Ascomycota, Basidiomycota) of fungi play important role. Administration of antifungal drugs can be: prophylactic, empiric preemptive and therapeutic. Physicians may prescribe antibiotics (mainly pollens: amphotericin B, natamycin and nystatin) and chemiotherapeutics (mainly azoles and fluorpirymidins, pigments, chlorhexidine and chlorquinaldol). In ENT practice topical and systemic drugs can be administrated. Topical lozenges include amphotericin B, clotrimazole, chlorhexidine or chlorquinaldol and oral gels: nystatin and miconazole. Some of drugs are in the form of suspension/solution, which can be used for inhalation, into the sinus, for swabbing or for lavage: amphotericin B, natamycin, nystatin, clotrimazol, flucytosine, miconazole, fluconazole, vorykonazole, caspofungin. It should be underlined that only a few of dugs can be absorbed from the digestive tract: flucytosine, fluconazole, itraconazole, ketoconazole, miconazole, vorykonazole. PMID:17847781
Kurnatowski, Piotr; Kurnatowska, Agnieszka K
Mycorrhizal fungi that form hypogeous sporocarps are an important component of the temperate forest soil community. In many regions, such as the Nothofagus forest in the Patagonian Andes, this group of fungi has been poorly studied. Here we examined the spring and autumn community composition of "sequestrate fungi", based on sporocarp production in pure forests of Nothofagus dombeyi (evergreen) and N. pumilio (deciduous). We investigated the possible relationships between these communities and environmental factors over 2 y. The rarefaction curves and the minimal richness estimates converged at nearly the same level for each forest type, and the asymptotes suggested that the sampling effort was sufficient to capture most of the hypogeous sporocarp richness in these forest stands. In total 27 species were recovered. Basidiomycota, Ascomycota and Glomeromycota respectively accounted for nine, two and one genera. Species richness of hypogeous sporocarps varied in relation to forest type but not to season (fall and spring), whereas sporocarp biomass varied according to an interaction between season and forest type. Species richness and sporocarp biomass were positively correlated with rainfall and negatively correlated with altitude. In addition sporocarp species richness was positively related to number of trees per transect. We found that two different forest stands, each dominated by different species of Nothofagus, exhibited different hypogeous sporocarp communities. PMID:21914828
Nouhra, Eduardo R; Urcelay, Carlos; Longo, M Silvana; Fontenla, Sonia
Fungi are an important and diverse component of soil communities, but these communities have proven difficult to study in conventional biotic surveys. We evaluated soil fungal diversity at two sites in a temperate forest using direct isolation of small-subunit and internal transcribed spacer (ITS) rRNA genes by PCR and high-throughput sequencing of cloned fragments. We identified 412 sequence types from 863 fungal ITS sequences, as well as 112 ITS sequences from other eukaryotic microorganisms. Equal proportions of Basidiomycota and Ascomycota sequences were present in both the ITS and small-subunit libraries, while members of other fungal phyla were recovered at much lower frequencies. Many sequences closely matched sequences from mycorrhizal, plant-pathogenic, and saprophytic fungi. Compositional differences were observed among samples from different soil depths, with mycorrhizal species predominating deeper in the soil profile and saprophytic species predominating in the litter layer. Richness was consistently lowest in the deepest soil horizon samples. Comparable levels of fungal richness have been observed following traditional specimen-based collecting and culturing surveys, but only after much more extensive sampling. The high rate at which new sequence types were recovered even after sampling 863 fungal ITS sequences and the dominance of fungi in our libraries relative to other eukaryotes suggest that the abundance and diversity of fungi in forest soils may be much higher than previously hypothesized.
O'Brien, Heath E.; Parrent, Jeri Lynn; Jackson, Jason A.; Moncalvo, Jean-Marc; Vilgalys, Rytas
Numerous ?12-, ?15- and multifunctional membrane fatty acid desaturases (FADs) have been identified in fungi, revealing great variability in the enzymatic specificities of FADs involved in biosynthesis of polyunsaturated fatty acids (PUFAs). Here, we report gene isolation and characterization of novel ?12/?15- and ?15-FADs named CpFad2 and CpFad3, respectively, from the opportunistic pathogenic yeast Candida parapsilosis. Overexpression of CpFad3 in Saccharomyces cerevisiae strains supplemented with linoleic acid (?9,?12-18:2) and hexadecadienoic acid (?9,?12-16:2) leads to accumulation of ?15-PUFAs, i.e., ?-linolenic acid (?9,?12,?15-18:3) and hexadecatrienoic acid with an unusual terminal double bond (?9,?12,?15-16:3). CpFad2 produces a range of ?12- and ?15-PUFAs. The major products of CpFad2 are linoleic and hexadecadienoic acid (?9,?12-16:2), accompanied by ?-linolenic acid and hexadecatrienoic acid (?9,?12,?15-16:3). Using GC/MS analysis of trimethylsilyl derivatives, we identified ricinoleic acid (12-hydroxy-9-octadecenoic acid) as an additional product of CpFad2. These results demonstrate that CpFAD2 is a multifunctional FAD and indicate that detailed analysis of fatty acid derivatives might uncover a range of enzymatic selectivities in other ?12-FADs from budding yeasts (Ascomycota: Saccharomycotina).
Bucek, Ales; Matouskova, Petra; Sychrova, Hana; Pichova, Iva; Hruskova-Heidingsfeldova, Olga
Mutualisms, or interactions between species that lead to net fitness benefits for each species involved, are stable and ubiquitous in nature mostly due to “byproduct benefits” stemming from the intrinsic traits of one partner that generate an indirect and positive outcome for the other. Here we verify if myrmecotrophy (where plants obtain nutrients from the refuse of their associated ants) can explain the stability of the tripartite association between the myrmecophyte Hirtella physophora, the ant Allomerus decemarticulatus and an Ascomycota fungus. The plant shelters and provides the ants with extrafloral nectar. The ants protect the plant from herbivores and integrate the fungus into the construction of a trap that they use to capture prey; they also provide the fungus and their host plant with nutrients. During a 9-month field study, we over-provisioned experimental ant colonies with insects, enhancing colony fitness (i.e., more winged females were produced). The rate of partial castration of the host plant, previously demonstrated, was not influenced by the experiment. Experimental plants showed higher ?15N values (confirming myrmecotrophy), plus enhanced vegetative growth (e.g., more leaves produced increased the possibility of lodging ants in leaf pouches) and fitness (i.e., more fruits produced and more flowers that matured into fruit). This study highlights the importance of myrmecotrophy on host plant fitness and the stability of ant-myrmecophyte mutualisms.
Dejean, Alain; Orivel, Jerome; Rossi, Vivien; Roux, Olivier; Lauth, Jeremie; Male, Pierre-Jean G.; Cereghino, Regis; Leroy, Celine
The diversity of endophytic filamentous fungi from leaves of transgenic imidazolinone-tolerant sugarcane plants and its isoline was evaluated by cultivation followed by amplified rDNA restriction analysis (ARDRA) of randomly selected strains. Transgenic and non-transgenic cultivars and their crop management (herbicide application or manual weed control) were used to assess the possible non-target effects of genetically modified sugarcane on the fungal endophytic community. A total of 14 ARDRA haplotypes were identified in the endophytic community of sugarcane. Internal transcribed spacer (ITS) sequencing revealed a rich community represented by 12 different families from the Ascomycota phylum. Some isolates had a high sequence similarity with genera that are common endophytes in tropical climates, such as Cladosporium, Epicoccum, Fusarium, Guignardia, Pestalotiopsis and Xylaria. Analysis of molecular variance indicated that fluctuations in fungal population were related to both transgenic plants and herbicide application. While herbicide applications quickly induced transient changes in the fungal community, transgenic plants induced slower changes that were maintained over time. These results represent the first draft on composition of endophytic filamentous fungi associated with sugarcane plants. They are an important step in understanding the possible effects of transgenic plants and their crop management on the fungal endophytic community. PMID:20191263
Stuart, Rodrigo Makowiecky; Romão, Aline Silva; Pizzirani-Kleiner, Aline Aparecida; Azevedo, João Lúcio; Araújo, Welington Luiz
White rot fungi (Ascomycota and Basidiomycota) were collected on fallen trunks with different decay stages, in a subandean forest (La Montaña del Ocaso nature reserve), and it was evaluated their ligninolitic activity. They were cultured on malt extract agar. Then it was performed semiquantitative tests for laccase and cellobiose dehydrogenase (CDH) activity using ABTS and DCPIP as enzymatic inducers. Based on the results of these tests, the fungi with higher activities from trunks with different decay stages were selected: Cookeina sulcipes (for stage 1), a fungus from the family Corticiaceae (for stage 2), Xylaria polymorpha (for stage 3) and Earliella sp. (for stage 4). A fermentation was performed at 28 degrees C, during 11 days, in a rotatory shaker at 150 rpm. Biomass, glucose, proteins and enzyme activities measurements were performed daily. The fungi that were in the trunks with decay states from 1 to 3, showed higher laccase activity as the state of decay increased. A higher DCH activity was also associated with a higher. Also, there was a positive relationship between both enzymes' activities. Erliella was the fungus which presented the highest biomass production (1140,19 g/l), laccase activity (157 UL(-1)) and CDH activity (43,50 UL(-1)). This work is the first report of laccase and CDH activity for Cookeina sulcipes and Earliella sp. Moreover, it gives basis for the use of these native fungi in biotechnological applications and the acknowledgment of their function in the wood decay process in native forest. PMID:19796977
Chaparro, Deisy Fernanda; Rosas, Diana Carolina; Varela, Amanda
Three new species of Hypocrea/Trichoderma sect. Trichoderma (Hypocreaceae, Hypocreales, Ascomycota, Fungi) are described from recent collections in southern Europe and the Canary Islands. They have been characterized by morphological and molecular methods, including microscopic examination of the teleomorph in thin sections, the anamorph, growth rate experiments and phylogenetic analyses based on a part of the translation elongation factor 1-alpha encoding gene (tef1) containing the two last introns and a part of the rpb2 gene, encoding the second largest RNA polymerase subunit. Analyses involving tef1 did not unequivocally resolve the sister clade relationship of Hypocrea caerulescens relative to the Koningii and Viride clades, while analyses based on rpb2 clearly suggest a close relationship with the former, although the phenotype of H. caerulescens is similar to H. viridescens, particularly by its warted conidia and a coconut-like odor in CMD culture. Hypocrea hispanica and T. samuelsii however are clearly related to the Viride clade by both phylogenetic markers, despite their morphological similarity to H. koningii and its relatives. An apparently specific blue pigment is formed in CMD cultures by Hypocrea caerulescens but could not be obtained by extraction with organic solvents. PMID:22453122
Jaklitsch, Walter M; Stadler, Marc; Voglmayr, Hermann
Fungi produce a wide range of extracellular enzymes to break down plant cell walls, which are composed mainly of cellulose, lignin and hemicellulose. Among them are the glycoside hydrolases (GH), the largest and most diverse family of enzymes active on these substrates. To facilitate research and development of enzymes for the conversion of cell-wall polysaccharides into fermentable sugars, we have manually curated a comprehensive set of characterized fungal glycoside hydrolases. Characterized glycoside hydrolases were retrieved from protein and enzyme databases, as well as literature repositories. A total of 453 characterized glycoside hydrolases have been cataloged. They come from 131 different fungal species, most of which belong to the phylum Ascomycota. These enzymes represent 46 different GH activities and cover 44 of the 115 CAZy GH families. In addition to enzyme source and enzyme family, available biochemical properties such as temperature and pH optima, specific activity, kinetic parameters and substrate specificities were recorded. To simplify comparative studies, enzyme and species abbreviations have been standardized, Gene Ontology terms assigned and reference to supporting evidence provided. The annotated genes have been organized in a searchable, online database called mycoCLAP (Characterized Lignocellulose-Active Proteins of fungal origin). It is anticipated that this manually curated collection of biochemically characterized fungal proteins will be used to enhance functional annotation of novel GH genes. Database URL: http://mycoCLAP.fungalgenomics.ca/
Murphy, Caitlin; Powlowski, Justin; Wu, Min; Butler, Greg; Tsang, Adrian
The ability of pathogenic microorganisms to assimilate essential nutrients from their hosts is critical for pathogenesis. Here we report endothelial zinc sequestration by the major human fungal pathogen, Candida albicans. We hypothesised that, analogous to siderophore-mediated iron acquisition, C. albicans utilises an extracellular zinc scavenger for acquiring this essential metal. We postulated that such a “zincophore” system would consist of a secreted factor with zinc-binding properties, which can specifically reassociate with the fungal cell surface. In silico analysis of the C. albicans secretome for proteins with zinc binding motifs identified the pH-regulated antigen 1 (Pra1). Three-dimensional modelling of Pra1 indicated the presence of at least two zinc coordination sites. Indeed, recombinantly expressed Pra1 exhibited zinc binding properties in vitro. Deletion of PRA1 in C. albicans prevented fungal sequestration and utilisation of host zinc, and specifically blocked host cell damage in the absence of exogenous zinc. Phylogenetic analysis revealed that PRA1 arose in an ancient fungal lineage and developed synteny with ZRT1 (encoding a zinc transporter) before divergence of the Ascomycota and Basidiomycota. Structural modelling indicated physical interaction between Pra1 and Zrt1 and we confirmed this experimentally by demonstrating that Zrt1 was essential for binding of soluble Pra1 to the cell surface of C. albicans. Therefore, we have identified a novel metal acquisition system consisting of a secreted zinc scavenger (“zincophore”), which reassociates with the fungal cell. Furthermore, functional similarities with phylogenetically unrelated prokaryotic systems indicate that syntenic zinc acquisition loci have been independently selected during evolution.
Citiulo, Francesco; Jacobsen, Ilse D.; Miramon, Pedro; Schild, Lydia; Brunke, Sascha; Zipfel, Peter; Brock, Matthias; Hube, Bernhard; Wilson, Duncan
Comparative genomics revealed in the last decade a scenario of rampant horizontal gene transfer (HGT) among prokaryotes, but for fungi a clearly dominant pattern of vertical inheritance still stands, punctuated however by an increasing number of exceptions. In the present work, we studied the phylogenetic distribution and pattern of inheritance of a fungal gene encoding a fructose transporter (FSY1) with unique substrate selectivity. 109 FSY1 homologues were identified in two sub-phyla of the Ascomycota, in a survey that included 241 available fungal genomes. At least 10 independent inter-species instances of horizontal gene transfer (HGT) involving FSY1 were identified, supported by strong phylogenetic evidence and synteny analyses. The acquisition of FSY1 through HGT was sometimes suggestive of xenolog gene displacement, but several cases of pseudoparalogy were also uncovered. Moreover, evidence was found for successive HGT events, possibly including those responsible for transmission of the gene among yeast lineages. These occurrences do not seem to be driven by functional diversification of the Fsy1 proteins because Fsy1 homologues from widely distant lineages, including at least one acquired by HGT, appear to have similar biochemical properties. In summary, retracing the evolutionary path of the FSY1 gene brought to light an unparalleled number of independent HGT events involving a single fungal gene. We propose that the turbulent evolutionary history of the gene may be linked to the unique biochemical properties of the encoded transporter, whose predictable effect on fitness may be highly variable. In general, our results support the most recent views suggesting that inter-species HGT may have contributed much more substantially to shape fungal genomes than heretofore assumed.
Coelho, Marco A.; Goncalves, Carla; Sampaio, Jose Paulo; Goncalves, Paula
There is growing evidence that root-associated fungi have important roles in Arctic ecosystems. Here, we assess the diversity of fungal communities associated with roots of the ectomycorrhizal perennial herb Bistorta vivipara on the Arctic archipelago of Svalbard and investigate whether spatial separation and bioclimatic variation are important structuring factors of fungal community composition. We sampled 160 plants of B. vivipara from 32 localities across Svalbard. DNA was extracted from entire root systems, and 454 pyrosequencing of ITS1 amplicons was used to profile the fungal communities. The fungal communities were predominantly composed of Basidiomycota (55% of reads) and Ascomycota (35%), with the orders Thelephorales (24%), Agaricales (13.8%), Pezizales (12.6%) and Sebacinales (11.3%) accounting for most of the reads. Plants from the same site or region had more similar fungal communities to one another than plants from other sites or regions, and sites clustered together along a weak latitudinal gradient. Furthermore, a decrease in per-plant OTU richness with increasing latitude was observed. However, no statistically significant spatial autocorrelation between sites was detected, suggesting that environmental filtering, not dispersal limitation, causes the observed patterns. Our analyses suggest that while latitudinal patterns in community composition and richness might reflect bioclimatic influences at global spatial scales, at the smaller spatial scale of the Svalbard archipelago, these changes more likely reflect varied bedrock composition and associated edaphic factors. The need for further studies focusing on identifying those specific bioclimatic and edaphic factors structuring root-associated fungal community composition at both global and local scales is emphasized. PMID:24320873
Blaalid, Rakel; Davey, Marie L; Kauserud, Håvard; Carlsen, Tor; Halvorsen, Rune; Høiland, Klaus; Eidesen, Pernille B
Endophytic fungi play an important role in terrestrial ecosystem, while little is known about those in hemi-parasitic plants, a group of special plants which absorb nutrients from its hosts by haustoria. The relationship of the endophytes in the two parts of the bipartite systems (hemiparasites together with their hosts) is also poorly understood. Endophytic fungi of a hemi-parasitic plant Macrosolen tricolor, and its host plant Camellia oleifera were investigated and compared in this study. M. tricolor contained rich and diversified endophytic fungi (H' = 2.829), which consisted mainly of ascomycetes, distributed in more than ten orders of four classes (Sordariomycetes, Dothideomycetes, Leotiomycetes and Eurotiomycetes) besides Incertae sedis strains (23.2 % of total). In addition, 2.2 % of isolates were identified to be Basidiomycota, all of which belonged to Agaricomycetes. Obvious differences were observed between the endophytic fungal assembles in the leaves and those in the branches of M. tricolor. The endophytic fungi isolated from C. oleifera distributed in nearly same orders of the four classes of Ascomycota and one class (Agaricomycetes) of Basidiomycota as those from M. tricolor with similar proportion. For both M. tricolor and C. oleifera, Valsa sp. was the dominant endophyte species in the leaves, Torula sp. 1 and Fusarium sp. 1 were the dominant endophytic fungi in the branches. The similarity coefficient of the endophyte assembles in the two host was 64.4 %. Canonical correspondence analysis showed that the endophyte assembles of M. tricolor and C. oleifera were significantly different (p < 0.01). PMID:24442818
Sheng-Liang, Zhou; Shu-Zhen, Yan; Zhen-Ying, Wu; Shuang-Lin, Chen
The post-cytokinetic separation of cells in cell-walled organisms involves enzymic processes that degrade a specific layer of the division septum and the region of the mother cell wall that edges the septum. In the fission yeast Schizosaccharomyces pombe, the 1,3-?-glucanase Agn1p, originally identified as a mutanase-like glycoside hydrolase family 71 (GH71) enzyme, dissolves the mother cell wall around the septum edge. Our search in the genomes of completely sequenced fungi identified GH71 hydrolases in Basidiomycota, Taphrinomycotina and Pezizomycotina, but not in Saccharomycotina. The most likely Agn1p orthologues in Pezizomycotina species are not mutanases having mutanase-binding domains, but experimentally non-characterized hypothetical proteins that have no carbohydrate-binding domains. The analysis of the GH71 domains corroborated the phylogenetic relationships of the Schizosaccharomyces species determined by previous studies, but suggested a closer relationship to the Basidiomycota proteins than to the Ascomycota proteins. In the Schizosaccharomyces genus, the Agn1p proteins are structurally conserved: their GH71 domains are flanked by N-terminal secretion signals and C-terminal sequences containing the conserved block YNFNA(Y)/HTG. The inactivation of the agn1(Sj) gene in Schizosaccharomyces japonicus, the only true dimorphic member of the genus, caused a severe cell-separation defect in its yeast phase, but had no effect on the hyphal growth and yeast-to-mycelium transition. It did not affect the mycelium-to-yeast transition either, only delaying the separation of the yeast cells arising from the fragmenting hyphae. The heterologous expression of agn1(Sj) partially rescued the separation defect of the agn1? cells of Schizosaccharomyces pombe. The results presented indicate that the fission yeast Agn1p 1,3-?-glucanases of Schizosaccharomyces japonicus and Schizosaccharomyces pombe share conserved functions in the yeast phase. PMID:24699070
Sipiczki, Matthias; Balazs, Anita; Monus, Aniko; Papp, Laszlo; Horvath, Anna; Sveiczer, Akos; Miklos, Ida
Across eukaryotes, Hsp70-based chaperone machineries display an underlying unity in their sequence, structure, and biochemical mechanism of action, while working in a myriad of cellular processes. In good part, this extraordinary functional versatility is derived from the ability of a single Hsp70 to interact with an array of J-protein cochaperones to form a functional chaperone network. Among J-proteins, the DnaJ-type is the most prevalent, being present in all three kingdoms and in several different compartments of eukaryotic cells. However, because these ancient DnaJ-type proteins diverged at the base of the eukaryotic phylogeny, little is understood about the evolutionary basis of their diversification and thus the functional expansion of the chaperone network. Here, we report results of evolutionary and experimental analyses of two more recent members of the cytosolic DnaJ family of Saccharomyces cerevisiae, Xdj1 and Apj1, which emerged by sequential duplications of the ancient YDJ1 in Ascomycota. Sequence comparison and molecular modeling revealed that both Xdj1 and Apj1 maintained a domain organization similar to that of multifunctional Ydj1. However, despite these similarities, both Xdj1 and Apj1 evolved highly specialized functions. Xdj1 plays a unique role in the translocation of proteins from the cytosol into mitochondria. Apj1’s specialized role is related to degradation of sumolyated proteins. Together these data provide the first clear example of cochaperone duplicates that evolved specialized functions, allowing expansion of the chaperone functional network, while maintaining the overall structural organization of their parental gene.
Yu, Hyun Young; Baranowski, Maciej; Marszalek, Jaroslaw; Craig, Elizabeth A.
Experimental research on beetle responses to removal of logging residues following clearcut harvesting in the boreal balsam fir forest of Quebec revealed several abundant rove beetle (Staphylinidae) species potentially important for long-term monitoring. To understand the trophic affiliations of these species in forest ecosystems, it was necessary to analyze their gut contents. We used microscopic and molecular (DNA) methods to identify the gut contents of the following rove beetles: Atheta capsularis Klimaszewski, Atheta klagesi Bernhauer, Oxypoda grandipennis (Casey), Bryophacis smetanai Campbell, Ischnosoma longicorne (Mäklin), Mycetoporus montanus Luze, Tachinus frigidus Erichson, Tachinus fumipennis (Say), Tachinus quebecensis Robert, and Pseudopsis subulata Herman. We found no apparent arthropod fragments within the guts; however, a number of fungi were identified by DNA sequences, including filamentous fungi and budding yeasts [Ascomycota: Candida derodonti Suh & Blackwell (accession number FJ623605), Candida mesenterica (Geiger) Diddens & Lodder (accession number FM178362), Candida railenensis Ramirez and Gonzáles (accession number JX455763), Candida sophie-reginae Ramirez & González (accession number HQ652073), Candida sp. (accession number AY498864), Pichia delftensis Beech (accession number AY923246), Pichia membranifaciens Hansen (accession number JQ26345), Pichia misumaiensis Y. Sasaki and Tak. Yoshida ex Kurtzman 2000 (accession number U73581), Pichia sp. (accession number AM261630), Cladosporium sp. (accession number KF367501), Acremoniumpsammosporum W. Gams (accession number GU566287), Alternaria sp. (accession number GU584946), Aspergillus versicolor Bubak (accession number AJ937750), and Aspergillusamstelodami (L. Mangin) Thom and Church (accession number HQ728257)]. In addition, two species of bacteria [Bradyrhizobium japonicum (Kirchner) Jordan (accession number BA000040) and Serratia marcescens Bizio accession number CP003942] were found in the guts. These results not only provide evidence of the consumer-resource relations of these beetles but also clarify the relationship between rove beetles, woody debris and fungi. Predominance of yeast-feeding by abundant rove beetles suggests that it may play an important role in their dietary requirements. PMID:24294095
Klimaszewski, Jan; Morency, Marie-Josee; Labrie, Philippe; Séguin, Armand; Langor, David; Work, Timothy; Bourdon, Caroline; Thiffault, Evelyne; Paré, David; Newton, Alfred F; Thayer, Margaret K
The sexual stage of pathogens governs recombination patterns and often also provides means of surviving the off-season. Despite its importance for evolutionary potential and between-season epidemiology, sexual systems have not been carefully investigated for many important pathogens, and what generates variation in successful sexual reproduction of pathogens remains unexplored. We surveyed the sexually produced resting structures (chasmothecia) across 86 natural populations of fungal pathogen Podosphaera plantaginis (Ascomycota) naturally infecting Plantago lanceolata in the Åland archipelago, southwestern Finland. For this pathosystem, these resting structures are a key life-history stage, as more than half of the local pathogen populations go extinct every winter. We uncovered substantial variation in the level of chasmothecia produced among populations, ranging from complete absence to presence on all infected leaves. We found that chasmothecia developed within clonal isolates (single-strain cultures). Additionally, these clonal isolates all contained both MAT1-1-1 and MAT1-2-1 genes that characterize mating types in Ascomycetes. Hence, contrary to expectations, we conclude that this species is capable of haploid selfing. In controlled inoculations, we discovered that pathogen genotypes varied in their tendency to produce chasmothecia. Production of chasmothecia was also affected by ambient temperature (E) and by the interaction between temperature and pathogen genotype (G × E). These G, E and G × E effects found both at a European scale and within the Åland archipelago may partly explain the high variability observed among populations in chasmothecia levels. Consequently, they may be key drivers of the evolutionary potential and epidemiology of this highly dynamic pathosystem. PMID:23701131
Tollenaere, C; Laine, A-L
In temperate ecosystems, acidic forest soils are among the most nutrient-poor terrestrial environments. In this context, the long-term differentiation of the forest soils into horizons may impact the assembly and the functions of the soil microbial communities. To gain a more comprehensive understanding of the ecology and functional potentials of these microbial communities, a suite of analyses including comparative metagenomics was applied on independent soil samples from a spruce plantation (Breuil-Chenue, France). The objectives were to assess whether the decreasing nutrient bioavailability and pH variations that naturally occurs between the organic and mineral horizons affects the soil microbial functional biodiversity. The 14 Gbp of pyrosequencing and Illumina sequences generated in this study revealed complex microbial communities dominated by bacteria. Detailed analyses showed that the organic soil horizon was significantly enriched in sequences related to Bacteria, Chordata, Arthropoda and Ascomycota. On the contrary the mineral horizon was significantly enriched in sequences related to Archaea. Our analyses also highlighted that the microbial communities inhabiting the two soil horizons differed significantly in their functional potentials according to functional assays and MG-RAST analyses, suggesting a functional specialisation of these microbial communities. Consistent with this specialisation, our shotgun metagenomic approach revealed a significant increase in the relative abundance of sequences related glycoside hydrolases in the organic horizon compared to the mineral horizon that was significantly enriched in glycoside transferases. This functional stratification according to the soil horizon was also confirmed by a significant correlation between the functional assays performed in this study and the functional metagenomic analyses. Together, our results suggest that the soil stratification and particularly the soil resource availability impact the functional diversity and to a lesser extent the taxonomic diversity of the bacterial communities.
Uroz, Stephane; Ioannidis, Panos; Lengelle, Juliette; Cebron, Aurelie; Morin, Emmanuelle; Buee, Marc; Martin, Francis
TET/JBP dioxygenases oxidize methylpyrimidines in nucleic acids and are implicated in generation of epigenetic marks and potential intermediates for DNA demethylation. We show that TET/JBP genes are lineage-specifically expanded in all major clades of basidiomycete fungi, with the majority of copies predicted to encode catalytically active proteins. This pattern differs starkly from the situation in most other organisms that possess just a single or a few copies of the TET/JBP family. In most basidiomycetes, TET/JBP genes are frequently linked to a unique class of transposons, KDZ (Kyakuja, Dileera, and Zisupton) and appear to have dispersed across chromosomes along with them. Several of these elements typically encode additional proteins, including a divergent version of the HMG domain. Analysis of their transposases shows that they contain a previously uncharacterized version of the RNase H fold with multiple distinctive Zn-chelating motifs and a unique insert, which are predicted to play roles in structural stabilization and target sequence recognition, respectively. We reconstruct the complex evolutionary history of TET/JBPs and associated transposons as involving multiple rounds of expansion with concomitant lineage sorting and loss, along with several capture events of TET/JBP genes by different transposon clades. On a few occasions, these TET/JBP genes were also laterally transferred to certain Ascomycota, Glomeromycota, Viridiplantae, and Amoebozoa. One such is an inactive version, calnexin-independence factor 1 (Cif1), from Schizosaccharomyces pombe, which has been implicated in inducing an epigenetically transmitted prion state. We argue that this unique transposon-TET/JBP association is likely to play important roles in speciation during evolution and epigenetic regulation. PMID:24398522
Iyer, Lakshminarayan M; Zhang, Dapeng; de Souza, Robson F; Pukkila, Patricia J; Rao, Anjana; Aravind, L
The insecticide chlordecone is a contaminant found in most of the banana plantations in the French West Indies. This study aims to search for fungal populations able to grow on it. An Andosol heavily contaminated with chlordecone, perfused for 1 year in a soil-charcoal system, was used to conduct enrichment cultures. A total of 103 fungal strains able to grow on chlordecone-mineral salt medium were isolated, purified, and deposited in the MIAE collection (Microorganismes d'Intérêt Agro-Environnemental, UMR Agroécologie, Institut National de la Recherche Agronomique, Dijon, France). Internal transcribed spacer sequencing revealed that all isolated strains belonged to the Ascomycota phylum and gathered in 11 genera: Metacordyceps, Cordyceps, Pochonia, Acremonium, Fusarium, Paecilomyces, Ophiocordyceps, Purpureocillium, Bionectria, Penicillium, and Aspergillus. Among predominant species, only one isolate, Fusarium oxysporum MIAE01197, was able to grow in a liquid culture medium that contained chlordecone as sole carbon source. Chlordecone increased F. oxysporum MIAE01197 growth rate, attesting for its tolerance to this organochlorine. Moreover, F. oxysporum MIAE01197 exhibited a higher EC50 value than the reference strain F. oxysporum MIAE00047. This further suggests its adaptation to chlordecone tolerance up to 29.2 mg l(-1). Gas chromatography-mass spectrometry (GC-MS) analysis revealed that 40 % of chlordecone was dissipated in F. oxysporum MIAE01197 suspension culture. No chlordecone metabolite was detected by GC-MS. However, weak amount of (14)CO2 evolved from (14)C10-chlordecone and (14)C10-metabolites were observed. Sorption of (14)C10-chlordecone onto fungal biomass followed a linear relationship (r (2) = 0.99) suggesting that it may also account for chlordecone dissipation in F. oxysporum MIAE01197 culture. PMID:23872892
Merlin, Chloé; Devers, Marion; Crouzet, Olivier; Heraud, Cécile; Steinberg, Christian; Mougin, Christian; Martin-Laurent, Fabrice
The present study was conducted to investigate the effect of decomposition site and plant litter species on the colonizing microbial communities. For this, litter bag technique using beech and spruce litter was combined with RNA-based fingerprinting and cloning. Litter bags were incubated for 2 and 8 weeks in the Ah horizon of beech and beech-spruce mixed forest sites. Although sugars and starch were rapidly lost, lignin content increased by more than 40% for beech and more than doubled for spruce litter at both soil sites at the end of the experiment. Denaturing gradient gel electrophoresis analysis of 16S and 18S rRNA RT-PCR products was used for screening of differences between bacterial and fungal communities colonizing the two litter types. Development of the microbial community over time was observed to be specific for each litter type and decomposition site. RT-PCR products from both litter types incubated in beech-spruce mixed forest site were also cloned to identify the bacterial and fungal colonizers. The 16S rRNA clone libraries of beech litter were dominated by gamma-proteobacterial members, whereas spruce libraries were mainly composed of alpha-, beta-, and gamma-proteobacterial members. Ascomycota members dominated the 18S rRNA clone libraries. Clones similar to Zygomycota were absent from spruce, whereas those similar to Basidiomycota and Glomeromycota were absent from beech libraries. Selective effects of litter quality were observed after 8 weeks. The study provides an insight into the bacterial and fungal communities colonizing beech and spruce litter, and the importance of litter quality and decomposition site as key factors in their development and succession. PMID:16691328
Aneja, Manish Kumar; Sharma, Shilpi; Fleischmann, Frank; Stich, Susanne; Heller, Werner; Bahnweg, Günther; Munch, Jean Charles; Schloter, Michael
Cytochrome P450 monooxygenases (P450s) are heme-thiolate proteins distributed across the biological kingdoms. P450s are catalytically versatile and play key roles in organisms primary and secondary metabolism. Identification of P450s across the biological kingdoms depends largely on the identification of two P450 signature motifs, EXXR and CXG, in the protein sequence. Once a putative protein has been identified as P450, it will be assigned to a family and subfamily based on the criteria that P450s within a family share more than 40% homology and members of subfamilies share more than 55% homology. However, to date, no evidence has been presented that can distinguish members of a P450 family. Here, for the first time we report the identification of EXXR- and CXG-motifs-based amino acid patterns that are characteristic of the P450 family. Analysis of P450 signature motifs in the under-explored fungal P450s from four different phyla, ascomycota, basidiomycota, zygomycota and chytridiomycota, indicated that the EXXR motif is highly variable and the CXG motif is somewhat variable. The amino acids threonine and leucine are preferred as second and third amino acids in the EXXR motif and proline and glycine are preferred as second and third amino acids in the CXG motif in fungal P450s. Analysis of 67 P450 families from biological kingdoms such as plants, animals, bacteria and fungi showed conservation of a set of amino acid patterns characteristic of a particular P450 family in EXXR and CXG motifs. This suggests that during the divergence of P450 families from a common ancestor these amino acids patterns evolve and are retained in each P450 family as a signature of that family. The role of amino acid patterns characteristic of a P450 family in the structural and/or functional aspects of members of the P450 family is a topic for future research.
Syed, Khajamohiddin; Mashele, Samson Sitheni
Accurate species identification is essential for effective plant disease management, but is challenging in fungi including Verticillium sensu stricto (Ascomycota, Sordariomycetes, Plectosphaerellaceae), a small genus of ten species that includes important plant pathogens. Here we present fifteen PCR assays for the identification of all recognized Verticillium species and the three lineages of the diploid hybrid V. longisporum. The assays were based on DNA sequence data from the ribosomal internal transcribed spacer region, and coding and non-coding regions of actin, elongation factor 1-alpha, glyceraldehyde-3-phosphate dehydrogenase and tryptophan synthase genes. The eleven single target (simplex) PCR assays resulted in amplicons of diagnostic size for V. alfalfae, V. albo-atrum, V. dahliae including V. longisporum lineage A1/D3, V. isaacii, V. klebahnii, V. nonalfalfae, V. nubilum, V. tricorpus, V. zaregamsianum, and Species A1 and Species D1, the two undescribed ancestors of V. longisporum. The four multiple target (multiplex) PCR assays simultaneously differentiated the species or lineages within the following four groups: Verticillium albo-atrum, V. alfalfae and V. nonalfalfae; Verticillium dahliae and V. longisporum lineages A1/D1, A1/D2 and A1/D3; Verticillium dahliae including V. longisporum lineage A1/D3, V. isaacii, V. klebahnii and V. tricorpus; Verticillium isaacii, V. klebahnii and V. tricorpus. Since V. dahliae is a parent of two of the three lineages of the diploid hybrid V. longisporum, no simplex PCR assay is able to differentiate V. dahliae from all V. longisporum lineages. PCR assays were tested with fungal DNA extracts from pure cultures, and were not evaluated for detection and quantification of Verticillium species from plant or soil samples. The DNA sequence alignments are provided and can be used for the design of additional primers.
Inderbitzin, Patrik; Davis, R. Michael; Bostock, Richard M.; Subbarao, Krishna V.
Fungi are abundant and functionally important in the Arctic, yet comprehensive studies of their diversity in relation to geography and environment are not available. We sampled soils in paired plots along the North American Arctic Transect (NAAT), which spans all five bioclimatic subzones of the Arctic. Each pair of plots contrasted relatively bare, cryoturbated patterned-ground features (PGFs) and adjacent vegetated between patterned-ground features (bPGFs). Fungal communities were analysed via sequencing of 7834 ITS-LSU clones. We recorded 1834 OTUs - nearly half the fungal richness previously reported for the entire Arctic. These OTUs spanned eight phyla, 24 classes, 75 orders and 120 families, but were dominated by Ascomycota, with one-fifth belonging to lichens. Species richness did not decline with increasing latitude, although there was a decline in mycorrhizal taxa that was offset by an increase in lichen taxa. The dominant OTUs were widespread even beyond the Arctic, demonstrating no dispersal limitation. Yet fungal communities were distinct in each subzone and were correlated with soil pH, climate and vegetation. Communities in subzone E were distinct from the other subzones, but similar to those of the boreal forest. Fungal communities on disturbed PGFs differed significantly from those of paired stable areas in bPGFs. Indicator species for PGFs included lichens and saprotrophic fungi, while bPGFs were characterized by ectomycorrhizal and pathogenic fungi. Our results suggest that the Arctic does not host a unique mycoflora, while Arctic fungi are highly sensitive to climate and vegetation, with potential to migrate rapidly as global change unfolds. PMID:24689939
Timling, I; Walker, D A; Nusbaum, C; Lennon, N J; Taylor, D L
Bamboos, regarded as therapeutic agents in ethnomedicine, have been used to inhibit inflammation and enhance natural immunity for a long time in Asia, and there are many bamboo associated fungi with medical and edible value. In the present study, a total of 350 fungal strains were isolated from the uncommon moso bamboo (Phyllostachys edulis) seeds for the first time. The molecular diversity of these endophytic fungi was investigated and bioactive compound producers were screened for the first time. All the fungal endophytes were categorized into 69 morphotypes according to culturable characteristics and their internal transcriber spacer (ITS) regions were analyzed by BLAST search with the NCBI database. The fungal isolates showed high diversity and were divided in Ascomycota (98.0%) and Basidiomycota (2.0%), including at least 19 genera in nine orders. Four particular genera were considered to be newly recorded bambusicolous fungi, including Leptosphaerulina, Simplicillium, Sebacina and an unknown genus in Basidiomycetes. Furthermore, inhibitory effects against clinical pathogens and phytopathogens were screened preliminarily and strains B09 (Cladosporium sp.), B34 (Curvularia sp.), B35 (undefined genus 1), B38 (Penicillium sp.) and zzz816 (Shiraia sp.) displayed broad-spectrum activity against clinical bacteria and yeasts by the agar diffusion method. The crude extracts of isolates B09, B34, B35, B38 and zzz816 under submerged fermentation, also demonstrated various levels of bioactivities against bambusicolous pathogenic fungi. This study is the first report on the antimicrobial activity of endophytic fungi associated with moso bamboo seeds, and the results show that they could be exploited as a potential source of bioactive compounds and plant defense activators. In addition, it is the first time that strains of Shiraia sp. have been isolated and cultured from moso bamboo seeds, and one of them (zzz816) could produce hypocrellin A at high yield, which is significantly different from the other strains published.
Cai, Chun-Ju; Fan, Li; Gao, Jian; Hou, Cheng-Lin
The etiologic agents of the dermatophytoses (ringworm) are classified in three anamorphic (asexual or imperfect) genera, Epidermophyton, Microsporum, and Trichophyton. Species capable of reproducing sexually belong in the teleomorphic genus, Arthroderma, of the Ascomycota. On the basis of primary habitat association, they may be grouped as geophilic (soil associated), zoophilic, and anthropophilic. Adaptation to growth on humans by most geophilic species resulted in diminished loss of sporulation, sexuality, and other soil-associated characteristics. The dermatophytes have the ability to invade keratinized tissue (skin, hair, and nails) but are usually restricted to the nonliving cornified layer of the epidermis because of their inability to penetrate viable tissue of an immunocompetent host. However, invasion does elicit a host response ranging from mild to severe. Acid proteinases, elastase, keratinases, and other proteinases reportedly act as virulence factors. The development of cell-mediated immunity correlated with delayed hypersensitivity and an inflammatory response is associated with clinical cure, whereas the lack of or a defective cell-mediated immunity predisposes the host to chronic or recurrent dermatophyte infection. Chronic dermatophytosis is mostly caused by Trichophyton rubrum, and there is some evidence that mannan produced by this fungus suppresses or diminishes the inflammatory response. Since dermatophytes cause a communicable disease, modes of transmission and control are discussed as well as a survey of recent trends in therapy. Collection of specimens, culture media, and tests for identification are also presented. Genetic studies have led to an understanding of incompatibility mechanisms, pleomorphism and variation, resistance to griseofulvin, and virulence. Molecular biology has contributed to our knowledge of the taxonomy and phylogenetic relationships of dermatophytes.
Weitzman, I; Summerbell, R C
Potassium, a widely accepted macronutrient, is vital for many physiological processes such as regulation of cell volume, maintenance of intracellular pH, synthesis of proteins and activation of enzymes in filamentous fungi. Another cation, calcium, plays an essential role in many signaling processes from lower to higher eukaryotes. Imbalance in the intracellular ionic levels of potassium or calcium causes adverse effects on cell growth, morphology and development, and eventually death. Previous studies on the adaptation of Aspergillus nidulans to salt and osmotic stress conditions have revealed the role of SltA, a C?H? zinc finger transcription factor in cation homeostasis. SltA is highly conserved in the Ascomycota phylum with no identifiable homolog in S. cerevisiae and other yeast-like fungi, and prevents toxicity by the cations Na?, K?, Li?, Cs? and Mg²?, but not by Ca²?. However its role in morphology and biosynthesis of natural products such as mycotoxins remained unknown. This study shows the first characterization of the role of calcium and SltA fungal homologs in morphogenesis using the model system A. nidulans. Addition of potassium to sltA deletion mutants resulted in decreased levels of sterigmatocystin production. A similar phenotype was observed for both types of mutants in veA1 and veA? genetic background. Expression of the sterigmatocystin genes aflR and stcU was strongly reduced in sltA deletion mutant when K? was added. Additionally, increased concentrations of K? drastically reduced sexual and asexual development, as well as radial growth in deletion sltA colonies. This reduction was accompanied by lower expression of the morphology related genes nsdD, steA and brlA. Interestingly, addition of calcium was able to stimulate asexual and sexual development and remediate the deletion sltA phenotype, including defects in morphology and toxin production. PMID:23840895
Shantappa, Sourabha; Dhingra, Sourabh; Hernández-Ortiz, Patricia; Espeso, Eduardo A; Calvo, Ana M
Potassium, a widely accepted macronutrient, is vital for many physiological processes such as regulation of cell volume, maintenance of intracellular pH, synthesis of proteins and activation of enzymes in filamentous fungi. Another cation, calcium, plays an essential role in many signaling processes from lower to higher eukaryotes. Imbalance in the intracellular ionic levels of potassium or calcium causes adverse effects on cell growth, morphology and development, and eventually death. Previous studies on the adaptation of Aspergillus nidulans to salt and osmotic stress conditions have revealed the role of SltA, a C2H2 zinc finger transcription factor in cation homeostasis. SltA is highly conserved in the Ascomycota phylum with no identifiable homolog in S. cerevisiae and other yeast-like fungi, and prevents toxicity by the cations Na+, K+, Li+, Cs+ and Mg2+, but not by Ca2+. However its role in morphology and biosynthesis of natural products such as mycotoxins remained unknown. This study shows the first characterization of the role of calcium and SltA fungal homologs in morphogenesis using the model system A. nidulans. Addition of potassium to sltA deletion mutants resulted in decreased levels of sterigmatocystin production. A similar phenotype was observed for both types of mutants in veA1 and veA+ genetic background. Expression of the sterigmatocystin genes aflR and stcU was strongly reduced in sltA deletion mutant when K+ was added. Additionally, increased concentrations of K+ drastically reduced sexual and asexual development, as well as radial growth in deletion sltA colonies. This reduction was accompanied by lower expression of the morphology related genes nsdD, steA and brlA. Interestingly, addition of calcium was able to stimulate asexual and sexual development and remediate the deletion sltA phenotype, including defects in morphology and toxin production.
Shantappa, Sourabha; Dhingra, Sourabh; Hernandez-Ortiz, Patricia; Espeso, Eduardo A.; Calvo, Ana M.
The packaging of eukaryotic genomes into nuclesomes plays critical roles in chromatin organization and gene regulation. Studies in Saccharomyces cerevisiae indicate that nucleosome occupancy is partially encoded by intrinsic antinucleosomal DNA sequences, such as poly(A) sequences, as well as by binding sites for trans-acting factors that can evict nucleosomes, such as Reb1 and the Rsc3/30 complex. Here, we use genome-wide nucleosome occupancy maps in 13 Ascomycota fungi to discover large-scale evolutionary reprogramming of both intrinsic and trans determinants of chromatin structure. We find that poly(G)s act as intrinsic antinucleosomal sequences, comparable to the known function of poly(A)s, but that the abundance of poly(G)s has diverged greatly between species, obscuring their antinucleosomal effect in low-poly(G) species such as S. cerevisiae. We also develop a computational method that uses nucleosome occupancy maps for discovering trans-acting general regulatory factor (GRF) binding sites. Our approach reveals that the specific sequences bound by GRFs have diverged substantially across evolution, corresponding to a number of major evolutionary transitions in the repertoire of GRFs. We experimentally validate a proposed evolutionary transition from Cbf1 as a major GRF in pre-whole-genome duplication (WGD) yeasts to Reb1 in post-WGD yeasts. We further show that the mating type switch-activating protein Sap1 is a GRF in S. pombe, demonstrating the general applicability of our approach. Our results reveal that the underlying mechanisms that determine in vivo chromatin organization have diverged and that comparative genomics can help discover new determinants of chromatin organization.
Tsankov, Alex; Yanagisawa, Yoshimi; Rhind, Nicholas; Regev, Aviv; Rando, Oliver J.
Across eukaryotes, Hsp70-based chaperone machineries display an underlying unity in their sequence, structure, and biochemical mechanism of action, while working in a myriad of cellular processes. In good part, this extraordinary functional versatility is derived from the ability of a single Hsp70 to interact with an array of J-protein cochaperones to form a functional chaperone network. Among J-proteins, the DnaJ-type is the most prevalent, being present in all three kingdoms and in several different compartments of eukaryotic cells. However, because these ancient DnaJ-type proteins diverged at the base of the eukaryotic phylogeny, little is understood about the evolutionary basis of their diversification and thus the functional expansion of the chaperone network. Here, we report results of evolutionary and experimental analyses of two more recent members of the cytosolic DnaJ family of Saccharomyces cerevisiae, Xdj1 and Apj1, which emerged by sequential duplications of the ancient YDJ1 in Ascomycota. Sequence comparison and molecular modeling revealed that both Xdj1 and Apj1 maintained a domain organization similar to that of multifunctional Ydj1. However, despite these similarities, both Xdj1 and Apj1 evolved highly specialized functions. Xdj1 plays a unique role in the translocation of proteins from the cytosol into mitochondria. Apj1's specialized role is related to degradation of sumolyated proteins. Together these data provide the first clear example of cochaperone duplicates that evolved specialized functions, allowing expansion of the chaperone functional network, while maintaining the overall structural organization of their parental gene. PMID:23329686
Sahi, Chandan; Kominek, Jacek; Ziegelhoffer, Thomas; Yu, Hyun Young; Baranowski, Maciej; Marszalek, Jaroslaw; Craig, Elizabeth A
Background A variety of spore discharge processes have evolved among the fungi. Those with the longest ranges are powered by hydrostatic pressure and include “squirt guns” that are most common in the Ascomycota and Zygomycota. In these fungi, fluid-filled stalks that support single spores or spore-filled sporangia, or cells called asci that contain multiple spores, are pressurized by osmosis. Because spores are discharged at such high speeds, most of the information on launch processes from previous studies has been inferred from mathematical models and is subject to a number of errors. Methodology/Principal Findings In this study, we have used ultra-high-speed video cameras running at maximum frame rates of 250,000 fps to analyze the entire launch process in four species of fungi that grow on the dung of herbivores. For the first time we have direct measurements of launch speeds and empirical estimates of acceleration in these fungi. Launch speeds ranged from 2 to 25 m s?1 and corresponding accelerations of 20,000 to 180,000 g propelled spores over distances of up to 2.5 meters. In addition, quantitative spectroscopic methods were used to identify the organic and inorganic osmolytes responsible for generating the turgor pressures that drive spore discharge. Conclusions/Significance The new video data allowed us to test different models for the effect of viscous drag and identify errors in the previous approaches to modeling spore motion. The spectroscopic data show that high speed spore discharge mechanisms in fungi are powered by the same levels of turgor pressure that are characteristic of fungal hyphae and do not require any special mechanisms of osmolyte accumulation.
Yafetto, Levi; Carroll, Loran; Cui, Yunluan; Davis, Diana J.; Fischer, Mark W. F.; Henterly, Andrew C.; Kessler, Jordan D.; Kilroy, Hayley A.; Shidler, Jacob B.; Stolze-Rybczynski, Jessica L.; Sugawara, Zachary; Money, Nicholas P.
Recent years have seen a growing interest regarding micro-eukaryotic communities in extreme environments as a third microbial domain after Bacteria and Archaea. However, knowledge is still scarce and the diversity of micro-eukaryotes in such environments remains hidden and their ecological role unknown. Our research program is based on the deep sedimentary layers of the Canterbury Basin in New Zealand (IODP 317) from the subsurface to the record depth of 1884 meters below seafloor. The objectives of our study are (i) to assess the genetic diversity of fungi in deep-sea sediments and (ii) identify the functional part in order to better understand the origin and the ecological role of fungal communities in this extreme ecosystem. Fingerprinting-based methods using capillary electrophoresis single-strand conformation polymorphism and denaturing high-performance liquid chromatography were used as a first step to raise our objectives. Molecular fungal diversity was assessed using amplification of ITS1 (Internal Transcribed Spacer 1) as a biomarker on 11 samples sediments from 3.76 to 1884 meters below seafloor. Fungal molecular signatures were detected throughout the sediment core. The phyla Ascomycota and Basidiomycota were revealed with DNA as well as cDNA. Most of the phylotypes are affiliated to environmental sequences and some to common fungal cultured species. The discovery of a present and metabolically active fungal component in this unique ecosystem allows some interesting first hypotheses that will be further combined to culture-based methods and deeper molecular methods (454 pyrosequencing) to highlight essential informations regarding physiology and ecological role of fungal communities in deep marine sediments.
Redou, V.; Arzur, D.; Burgaud, G.; Barbier, G.
Functionalized polyhedral carboranes, including amino acid analogs, have unique physicochemical properties and are used as experimental anticancer agents. However, our current knowledge on their effect in nonmammalian biological systems is limited. We investigated the activity spectrum in vitro of o-carboranylalanine (o-Cba), considered to be a highly lipophilic analog of phenylalanine, against representative plant pathogenic bacteria and fungi of various taxonomic position. The antibacterial effect of o-Cba against some species was comparable to that of the widely used agricultural antibiotic, streptomycin. The sensitivity of individual bacterial species to o-Cba within the same genus varied to a greater extent than the average sensitivity of various genera. In general, this carborane-containing amino acid was more toxic to Gram positive bacteria (Bacillus, Corynebacterium, Curtobacterium, Micrococcus, Rhodococcus, and Staphylococcus) than to Gram negative ones (Agrobacterium, Erwinia, Escherichia, Pseudomonas, Rhizobium, and Xanthomonas). Compared to the commercial fungicide, prochloraz, o-Cba was weakly toxic against various fungi (Zygo- and Ascomycota). It was also inferior to the commercial fungicide metalaxyl in inhibiting the vegetative growth of oomyceteous plant pathogens (Pythium irregulare, Phytophthora cryptogea and Plasmopara halstedii). Against the asexual spores of P. halstedii, o-Cba, however, was over a thousandfold more active than tridemorph, a selective zoospore inhibitor fungicide. For all taxonomic groups, the observed antimicrobial effect of o-Cba could be diminished with histidine, but not with phenylalanine. In studies on healthy and mildew-infected sunflower and tobacco plants o-Cba showed neither fungicidal nor phytotoxic effects at 500 ppm. This is the first report on the biological activity spectrum of a carborane-containing amino acid. PMID:10707765
Oros, G; Ujváry, I; Nachman, R J
SUMMARY Leptosphaeria maculans is the most ubiquitous pathogen of Brassica crops, and mainly oilseed brassicas (oilseed rape, canola), causing the devastating 'stem canker' or 'blackleg'. This review summarizes our current knowledge on the pathogen, from taxonomic issues to specific life traits. It mainly illustrates the importance of formal genetics approaches on the pathogen side to dissect the interaction with the host plants. In addition, this review presents the main current research topics on L. maculans and focuses on the L. maculans genome initiative recently begun, including its main research issues. Taxonomy: Leptosphaeria maculans (Desm.) Ces. & de Not. (anamorph Phoma lingam Tode ex Fr.). Kingdom Fungi, Phylum Ascomycota, Class Dothideomycetes (Loculoascomycetes), Order Pleosporales, Genus Leptosphaeria, Species maculans. Host range: cultivated Brassicas such as Brassica napus (oilseed rape, canola), B. rapa, B. juncea, B. oleracea, etc., along with numerous wild crucifers species. Arabidopsis thaliana was recently reported to be a potential host for L. maculans. Primary disease symptoms are greyish-green collapse of cotyledon or leaf tissue, without a visible margin, bearing tiny black spots (pycnidia). The fungus then develops an endophytic symptomless growth for many months. Secondary symptoms, at the end of the growing season, are dry necroses of the crown tissues with occasional blackening (stem canker or blackleg) causing lodging of the plants. Pseudothecia differentiate on leftover residues. Seedling damping-off and premature ripening are also reported under certain environmental conditions. Useful websites: Leptosphaeria maculans sequencing project at Genoscope: http://www.genoscope.cns.fr/externe/English/Projets/Projet_DM/organisme_DM.html; the SECURE site: http://www.secure.rothamsted.ac.uk/ the 'Blackleg' group at the University of Melbourne: http://www.botany.unimelb.edu.au/blackleg/overview.htm. PMID:20565653
Rouxel, T; Balesdent, M H
We developed two species-specific PCR assays for rapid and accurate detection of the pathogenic fungi Fusarium oxysporum f. sp. niveum and Mycosphaerella melonis in diseased plant tissues and soil. Based on differences in internal transcribed spacer (ITS) sequences of Fusarium spp. and Mycosphaerella spp., two pairs of species-specific primers, Fn-1/Fn-2 and Mn-1/Mn-2, were synthesized. After screening 24 isolates of F. oxysporum f. sp. niveum, 22 isolates of M. melonis, and 72 isolates from the Ascomycota, Basidiomycota, Deuteromycota, and Oomycota, the Fn-1/Fn-2 primers amplified only a single PCR band of approximately 320 bp from F. oxysporum f. sp.niveum, and the Mn-1/Mn-2 primers yielded a PCR product of approximately 420 bp from M. melonis. The detection sensitivity with primers Fn-1/Fn-2 and Mn-1/Mn-2 was 1fg of genomic DNA. Using ITS1/ITS4 as the first-round primers, combined with either Fn-1/Fn-2 and or Mn-1/Mn-2, two nested PCR procedures were developed, and the detection sensitivity increased 1000-fold to 1ag. The detection sensitivity for the soil pathogens was 100-microconidia/g soil. A duplex PCR method, combining primers Fn-1/Fn-2 and Mn-1/Mn-2, was used to detect F. oxysporum f. sp. niveum and M. melonis in plant tissues infected by the pathogens. Real-time fluorescent quantitative PCR assays were developed to detect and monitor the pathogens directly in soil samples. The PCR-based methods developed here could simplify both plant disease diagnosis and pathogen monitoring as well as guide plant disease management. PMID:16019161
Zhang, Zhenggang; Zhang, Jingyu; Wang, Yuanchao; Wang, Yuchao; Zheng, Xiaobo
Background Few studies describing eukaryotic communities in the human gut microbiota have been published. The objective of this study was to investigate comprehensively the repertoire of plant and fungal species in the gut microbiota of an obese patient. Methodology/Principal Findings A stool specimen was collected from a 27-year-old Caucasian woman with a body mass index of 48.9 who was living in Marseille, France. Plant and fungal species were identified using a PCR-based method incorporating 25 primer pairs specific for each eukaryotic phylum and universal eukaryotic primers targeting 18S rRNA, internal transcribed spacer (ITS) and a chloroplast gene. The PCR products amplified using these primers were cloned and sequenced. Three different culture media were used to isolate fungi, and these cultured fungi were further identified by ITS sequencing. A total of 37 eukaryotic species were identified, including a Diatoms (Blastocystis sp.) species, 18 plant species from the Streptophyta phylum and 18 fungal species from the Ascomycota, Basidiomycota and Chytridiocomycota phyla. Cultures yielded 16 fungal species, while PCR-sequencing identified 7 fungal species. Of these 7 species of fungi, 5 were also identified by culture. Twenty-one eukaryotic species were discovered for the first time in human gut microbiota, including 8 fungi (Aspergillus flavipes, Beauveria bassiana, Isaria farinosa, Penicillium brevicompactum, Penicillium dipodomyicola, Penicillium camemberti, Climacocystis sp. and Malassezia restricta). Many fungal species apparently originated from food, as did 11 plant species. However, four plant species (Atractylodes japonica, Fibraurea tinctoria, Angelica anomala, Mitella nuda) are used as medicinal plants. Conclusions/Significance Investigating the eukaryotic components of gut microbiota may help us to understand their role in human health.
Gouba, Nina; Raoult, Didier; Drancourt, Michel
The ERH gene encodes a highly conserved small nuclear protein with a unique amino acid sequence and three-dimensional structure but unknown function. The gene is present in animals, plants, and protists but to date has only been found in few fungi. Here we report that ERH homologs are also present in all four species from the genus Schizosaccharomyces, S. pombe, S. octosporus, S. cryophilus, and S. japonicus, which, however, are an exception in this respect among Ascomycota and Basidiomycota. The ERH protein sequence is moderately conserved within the genus (58% identity between S. pombe and S.japonicus), but the intron-rich genes have almost identical intron-exon organizations in all four species. In S. pombe, erh1(+) is expressed at a roughly constant level during vegetative growth and adaptation to unfavorable conditions such as nutrient limitation and hyperosmotic stress caused by sorbitol. Erh1p localizes preferentially to the nucleus with the exception of the nucleolus, but is also present in the cytoplasm. Cells lacking erh1(+) have an aberrant cell morphology and a comma-like shape when cultured to the stationary phase, and exhibit a delayed recovery from this phase followed by slower growth. Loss of erh1(+) in an auxotrophic background results in enhanced arrest in the G1 phase following nutritional stress, and also leads to hypersensitivity to agents inducing hyperosmotic stress (sorbitol), inhibiting DNA replication (hydroxyurea), and destabilizing the plasma membrane (SDS); this hypersensitivity can be abolished by expression of S. pombe erh1(+) and, to a lesser extent, S. japonicus erh1(+) or human ERH. Erh1p fails to interact with the human Ciz1 and PDIP46/SKAR proteins, known molecular partners of human ERH. Our data suggest that in Schizosaccharomyces sp. erh1(+) is non-essential for normal growth and Erh1p could play a role in response to adverse environmental conditions and in cell cycle regulation. PMID:23145069
Krzyzanowski, Marek K; Kozlowska, Ewa; Kozlowski, Piotr
Sclerotia are resting structures of ectomycorrhizal fungi and appear as a response to unfavorable environmental conditions such as desiccation. They are hard, black, comparatively smooth and mostly spherical. Sclerotia are formed in rhizosphere and the 14C ages of sclerotia from A horizons of volcanic ash soils may range from modern until ca. 100~1,200 yr B.P. Most sclerotia-forming fungal species are known to be host-specific plant pathogens and therefore their abundance may indicate the presence of their host plants. The purpose of this study was to investigate fungal communities in sclerotia with an interest in describing the existing or may have previously existed host plant community. To investigate fungal community inside of sclerotia by 16S rDNA gene clone library, several hundred of sclerotia (ca. 1g) were collected from Fagus crenata forest soil in north eastern Japan. The rDNA ITS regions were then amplified by the PCR using primer pair ITS-1F/ITS-4. Aliquots of the amplified DNA were digested with restriction endonucleases AluI, Hae III, and HhaI to obtain ITS-RFLPs. To obtain the fungal community profiles a quenching fluorescence primer was used for real-time quantitative PCR (qPCR) assay to monitor the PCR amplification and then used for T-RFLP. The predominant group determined by clone library analysis from the sclerotia was Ascomycota: Arthrinium arundinis, which has been reported to be one of the soil fungal species responsible for bamboo degradation and a pathogen for many species belonging to Poaceae family.
Fathia Amasya, Anzilni; Narisawa, Kazuhiko; Watanabe, Makiko
Sexual reproduction of fungi is governed by the mating type (MAT) locus, a specialized region of the genome encoding key transcriptional regulators that direct regulatory networks to specify cell identity and fate. Knowledge of MAT locus structure and evolution has been considerably advanced in recent years as a result of genomic analyses that enable the definition of MAT locus sequences in many species as well as provide an understanding of the evolutionary plasticity of this unique region of the genome. Here, we extend this analysis to define the mating type locus of three dimorphic primary human fungal pathogens, Histoplasma capsulatum, Coccidioides immitis, and Coccidioides posadasii, using genomic analysis, direct sequencing, and bioinformatics. These studies provide evidence that all three species possess heterothallic bipolar mating type systems, with isolates encoding either a high-mobility-group (HMG) domain or an ?-box transcriptional regulator. These genes are intact in all loci examined and have not been subject to loss or decay, providing evidence that the loss of fertility upon passage in H. capsulatum is not attributable to mutations at the MAT locus. These findings also suggest that an extant sexual cycle remains to be defined in both Coccidioides species, in accord with population genetic evidence. Based on these MAT sequences, a facile PCR test was developed that allows the mating type to be rapidly ascertained. Finally, these studies highlight the evolutionary forces shaping the MAT locus, revealing examples in which flanking genes have been inverted or subsumed and incorporated into an expanding MAT locus, allowing us to propose an expanded model for the evolution of the MAT locus in the phylum Ascomycota.
Fraser, James A.; Stajich, Jason E.; Tarcha, Eric J.; Cole, Garry T.; Inglis, Diane O.; Sil, Anita; Heitman, Joseph
Mortierella alpina is an oleaginous fungus which can produce lipids accounting for up to 50% of its dry weight in the form of triacylglycerols. It is used commercially for the production of arachidonic acid. Using a combination of high throughput sequencing and lipid profiling, we have assembled the M. alpina genome, mapped its lipogenesis pathway and determined its major lipid species. The 38.38 Mb M. alpina genome shows a high degree of gene duplications. Approximately 50% of its 12,796 gene models, and 60% of genes in the predicted lipogenesis pathway, belong to multigene families. Notably, M. alpina has 18 lipase genes, of which 11 contain the class 2 lipase domain and may share a similar function. M. alpina's fatty acid synthase is a single polypeptide containing all of the catalytic domains required for fatty acid synthesis from acetyl-CoA and malonyl-CoA, whereas in many fungi this enzyme is comprised of two polypeptides. Major lipids were profiled to confirm the products predicted in the lipogenesis pathway. M. alpina produces a complex mixture of glycerolipids, glycerophospholipids and sphingolipids. In contrast, only two major sterol lipids, desmosterol and 24(28)-methylene-cholesterol, were detected. Phylogenetic analysis based on genes involved in lipid metabolism suggests that oleaginous fungi may have acquired their lipogenic capacity during evolution after the divergence of Ascomycota, Basidiomycota, Chytridiomycota and Mucoromycota. Our study provides the first draft genome and comprehensive lipid profile for M. alpina, and lays the foundation for possible genetic engineering of M. alpina to produce higher levels and diverse contents of dietary lipids.
Feng, Yun; Ren, Yan; Gu, Zhennan; Chen, Haiqin; Wang, Hongchao; Thomas, Michael J.; Zhang, Baixi; Berquin, Isabelle M.; Li, Yang; Wu, Jiansheng; Zhang, Huanxin; Song, Yuanda; Liu, Xiang; Norris, James S.; Wang, Suriguga; Du, Peng; Shen, Junguo; Wang, Na; Yang, Yanlin; Wang, Wei; Feng, Lu; Ratledge, Colin; Zhang, Hao; Chen, Yong Q.
Soil fungal communities underneath willow canopies that had established on the forefront of a receding glacier were analyzed by cloning the polymerase chain reaction (PCR)-amplified partial small subunit (18S) of the ribosomal (rRNA) genes. Congruence between two sets of fungus-specific primers targeting the same gene region was analyzed by comparisons of inferred neighbor-joining topologies. The importance of chimeric sequences was evaluated by Chimera Check (Ribosomal Database Project) and by data reanalyses after omission of potentially chimeric regions at the 5'- and 3'-ends of the cloned amplicons. Diverse communities of fungi representing Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota were detected. Ectomycorrhizal fungi comprised a major component in the early plant communities in primary successional ecosystems, as both primer sets frequently detected basidiomycetes (Russulaceae and Thelephoraceae) forming mycorrhizal symbioses. Various ascomycetes (Ophiostomatales, Pezizales, and Sordariales) of uncertain function dominated the clone libraries amplified from the willow canopy soil with one set of primers, whereas the clone libraries of the amplicons generated with the second primer set were dominated by basidiomycetes. Accordingly, primer bias is an important factor in fungal community analyses using DNA extracted from environmental samples. A large proportion (>30%) of the cloned sequences were concluded to be chimeric based on their changing positions in inferred phylogenies after omission of possibly chimeric data. Many chimeric sequences were positioned basal to existing classes of fungi, suggesting that PCR artifacts may cause frequent discovery of new, higher level taxa (order, class) in direct PCR analyses. Longer extension times during the PCR amplification and a smaller number of PCR cycles are necessary precautions to allow collection of reliable environmental sequence data. PMID:17106807
The commercial availability of next generation sequencing (NGS) technologies facilitated the assessment of functional groups of microorganisms in the environment with high coverage, resolution, and reproducibility. Soil methylotrophs were among the first microorganisms in the environment that were assessed with molecular tools, and nowadays, as well with NGS technologies. Studies in the past years re-attracted notice to the pivotal role of methylotrophs in global conversions of methanol, which mainly originates from plants, and is involved in oxidative reactions and ozone formation in the atmosphere. Aerobic methanol utilizers belong to Bacteria, yeasts, Ascomycota, and molds. Numerous bacterial methylotrophs are facultatively aerobic, and also contribute to anaerobic methanol oxidation in the environment, whereas strict anaerobic methanol utilizers belong to methanogens and acetogens. The diversity of enzymes catalyzing the initial oxidation of methanol is considerable, and comprises at least five different enzyme types in aerobes, and one in strict anaerobes. Only the gene of the large subunit of pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH; mxaF) has been analyzed by environmental pyrosequencing. To enable a comprehensive assessment of methanol utilizers in the environment, new primers targeting genes of the PQQ MDH in Methylibium (mdh2), of the nicotinamide adenine dinucleotide-dependent MDH (mdh), of the methanol oxidoreductase of Actinobacteria (mdo), of the fungal flavin adenine nucleotide-dependent alcohol oxidase (mod1, mod2, and homologs), and of the gene of the large subunit of the methanol:corrinoid methyltransferases (mtaC) in methanogens and acetogens need to be developed. Combined stable isotope probing of nucleic acids or proteins with amplicon-based NGS are straightforward approaches to reveal insights into functions of certain methylotrophic taxa in the global methanol cycle. PMID:24046766
Kolb, Steffen; Stacheter, Astrid
Reverse-osmosis (RO) desalination is frequently used for the production of high-quality water from tertiary treated wastewater (TTWW). However, the RO desalination process is often hampered by biofouling, including membrane conditioning, microbial adhesion, and biofilm growth. The vast majority of biofilm exploration concentrated on the role of bacteria in biofouling neglecting additional microbial contributors, i.e., fungi and archaea. To better understand the RO biofouling process, bacterial, archaeal and fungal diversity was characterized in a laboratory-scale RO desalination plant exploring the TTWW (RO feed), the RO membrane and the RO feed tube biofilms. We sequenced 77,400 fragments of the ribosome small subunit-encoding gene (16S and 18S rRNA) to identify the microbial community members in these matrices. Our results suggest that the bacterial, archaeal but not fungal community significantly differ from the RO membrane biofouling layer to the feedwater and tube biofilm (P < 0.01). Moreover, the RO membrane supported a more diverse community compared to the communities monitored in the feedwater and the biofilm attached to the RO feedwater tube. The tube biofilm was dominated by Actinobacteria (91.2 ± 4.6%), while the Proteobacteria phylum dominated the feedwater and RO membrane (at relative abundance of 92.3 ± 4.4% and 71.5 ± 8.3%, respectively), albeit comprising different members. The archaea communities were dominated by Crenarchaeota (53.0 ± 6.9%, 32.5 ± 7.2% and 69%, respectively) and Euryarchaeota (43.3 ± 6.3%, 23.2 ± 4.8% and 24%, respectively) in all three matrices, though the communities' composition differed. But the fungal communities composition was similar in all matrices, dominated by Ascomycota (97.6 ± 2.7%). Our results suggest that the RO membrane is a selective surface, supporting unique bacterial, and to a lesser extent archaeal communities, yet it does not select for a fungal community. PMID:24231030
Al Ashhab, Ashraf; Herzberg, Moshe; Gillor, Osnat
We previously characterized members of the Myb protein family, MYT1 and MYT2, in Fusarium graminearum. MYT1 and MYT2 are involved in female fertility and perithecium size, respectively. To expand knowledge of Myb proteins in F. graminearum, in this study, we characterized the functions of the MYT3 gene, which encodes a putative Myb-like transcription factor containing two Myb DNA-binding domains and is conserved in the subphylum Pezizomycotina of Ascomycota. MYT3 proteins were localized in nuclei during most developmental stages, suggesting the role of MYT3 as a transcriptional regulator. Deletion of MYT3 resulted in impairment of conidiation, germination, and vegetative growth compared to the wild type, whereas complementation of MYT3 restored the wild-type phenotype. Additionally, the ?myt3 strain grew poorly on nitrogen-limited media; however, the mutant grew robustly on minimal media supplemented with ammonium. Moreover, expression level of nitrate reductase gene in the ?myt3 strain was decreased in comparison to the wild type and complemented strain. On flowering wheat heads, the ?myt3 strain exhibited reduced pathogenicity, which corresponded with significant reductions in trichothecene production and transcript levels of trichothecene biosynthetic genes. When the mutant was selfed, mated as a female, or mated as a male for sexual development, perithecia were not observed on the cultures, indicating that the ?myt3 strain lost both male and female fertility. Taken together, these results demonstrate that MYT3 is required for pathogenesis and sexual development in F. graminearum, and will provide a robust foundation to establish the regulatory networks for all Myb-like proteins in F. graminearum. PMID:24722578
Kim, Yongsoo; Kim, Hun; Son, Hokyoung; Choi, Gyung Ja; Kim, Jin-Cheol; Lee, Yin-Won
The impacts of leaf litter from genetically modified hybrid poplar accumulating high levels of condensed tannins (proanthocyanidins) were examined in soil microcosms consisting of moss growing on sieved soil. Moss preferentially proliferated in microcosms with lower tannin content; DGGE (denaturing gradient gel electrophoresis) detected increased fungal diversity in microcosms with low-tannin litter. The proportion of cloned rDNA sequences from Actinobacteria decreased with litter addition while Bacteroidetes, Chloroflexi, Cyanobacteria, and ?-Proteobacteria significantly increased. ?-Proteobacteria were proportionally more numerous at high-tannin levels. Tannins had no significant impact on overall diversity of bacterial communities analyzed with various estimators. There was an increased proportion of N-fixing bacteria corresponding to the addition of litter with low-tannin levels. The addition of litter increased the proportion of Ascomycota/Basidiomycota. Dothideomycetes, Pucciniomycetes, and Tremellomycetes also increased and Agaricomycetes decreased. Agaricomycetes and Sordariomycetes were significantly more abundant in controls, whereas Pucciniomycetes increased in soil with litter from transformed trees (P = 0.051). Richness estimators and diversity indices revealed no significant difference in the composition of fungal communities; PCoA (principal coordinate analyses) partitioned the fungal communities into three groups: (i) those with higher amounts of added tannin from both transformed and untransformed treatments, (ii) those corresponding to soils without litter, and (iii) those corresponding to microcosms with litter added from trees transformed only with a ?-glucuronidase control vector. While the litter from transformed poplars had significant effects on soil microbe communities, the observed impacts reflected known impacts on soil processes associated with tannins, and were similar to changes that would be expected from natural variation in tannin levels.
Winder, Richard S.; Lamarche, Josyanne; Constabel, C. Peter; Hamelin, Richard C.
Microbial communities play a major role in terrestrial ecosystem functioning, but the determinates of their diversity and functional interactions are not well known. In this study, we explored leaf litter fungal diversity in a diverse Panama lowland tropical forest in which a replicated factorial N, P, K and micronutrient fertilization experiment of 40 × 40 m plots had been ongoing for nine years. We extracted DNA from leaf litter samples and used fungal-specific amplification and a 454 pyrosequencing approach to sequence two loci, the nuclear ribosomal internal transcribed spacer (ITS) region and the nuclear ribosomal large subunit (LSU) D1 region. Using a 95% sequence similarity threshold for ITS1 spacer recovered a total of 2523 OTUs, and the number of unique ITS1 OTUs per 0.5-1.0 g leaf litter sample ranged from 55 to 177. Ascomycota were the dominant phylum among the leaf litter fungi (71% of the OTUs), followed by Basidiomycota (26% of the OTUs). In contrast to our expectations based on temperate ecosystems, long-term addition of nutrients increased, rather than decreased, species richness relative to controls. Effect of individual nutrients was more subtle and seen primarily as changes in community compositions especially at lower taxonomic levels, rather than as significant changes in species richness. For example, plots receiving P tended to show a greater similarity in community composition compared to the other nutrient treatments, the +PK, +NK and +NPK plots appeared to be more dominated by the Nectriaceae than other treatments, and indicator species for particular nutrient combinations were identified. PMID:23601077
Kerekes, Jennifer; Kaspari, Michael; Stevenson, Bradley; Nilsson, R Henrik; Hartmann, Martin; Amend, Anthony; Bruns, Thomas D
Hsp70 molecular chaperones are ubiquitous. By preventing aggregation, promoting folding, and regulating degradation, Hsp70s are major factors in the ability of cells to maintain proteostasis. Despite a wealth of functional information, little is understood about the evolutionary dynamics of Hsp70s. We undertook an analysis of Hsp70s in the fungal clade Ascomycota. Using the well-characterized 14 Hsp70s of Saccharomyces cerevisiae, we identified 491 orthologs from 53 genomes. Saccharomyces cerevisiae Hsp70s fall into seven subfamilies: four canonical-type Hsp70 chaperones (SSA, SSB, KAR, and SSC) and three atypical Hsp70s (SSE, SSZ, and LHS) that play regulatory roles, modulating the activity of canonical Hsp70 partners. Each of the 53 surveyed genomes harbored at least one member of each subfamily, and thus establishing these seven Hsp70s as units of function and evolution. Genomes of some species contained only one member of each subfamily that is only seven Hsp70s. Overall, members of each subfamily formed a monophyletic group, suggesting that each diversified from their corresponding ancestral gene present in the common ancestor of all surveyed species. However, the pattern of evolution varied across subfamilies. At one extreme, members of the SSB subfamily evolved under concerted evolution. At the other extreme, SSA and SSC subfamilies exhibited a high degree of copy number dynamics, consistent with a birth–death mode of evolution. KAR, SSE, SSZ, and LHS subfamilies evolved in a simple divergent mode with little copy number dynamics. Together, our data revealed that the evolutionary history of this highly conserved and ubiquitous protein family was surprising complex and dynamic.
Neuveglise, Cecile; Craig, Elizabeth A.; Williams, Barry L.
Fungal diversity in the rhizosphere of healthy and diseased clonal black spruce (Picea mariana) plants was analyzed with regard to nursery production chronosequences. The four key production stages were sampled: mother plants (MP), 8-week-old cuttings (B + 0), second-year cuttings (B + 1), and third-year cuttings (B + 2). A total of 45 fungal taxa were isolated and identified based on cultural, phenotypic, and molecular characters. Members of phylum Ascomycota dominated, followed by Basidiomycota and Zygomycota. Diagnosis characters and distance analysis of the internal transcribed spacer rDNA sequences allowed the identification of 39 ascomycetous taxa. Many belong to the order Hypocreales, families Hypocreaceae and Nectriaceae, which contain many clusters of potentially pathogenic taxa (Cylindrocladium, Fusarium, and Neonectria) and are also ecologically associated with antagonistic taxa (Chaetomium, Hypocrea, Microsphaeropsis, Penicillium, Paecilomyces, Verticillium, Trichoderma, and Sporothrix). This is also the first report of a Cylindrocladium canadense association with disease symptoms and relation with Pestalotiopsis, Fusarium, Exserochilum, Rhizoctonia, and Xenochalara fungal consortia. Both production chronosequence and plant health considerably influenced fungal taxa assemblages. Unweighted pair-group arithmetic average clustering showed that isolates from MP, B + 0, and B + 1 plant rhizospheres clustered together within healthy or diseased health classes, whereas isolates from healthy and diseased B + 2 plants clustered together. Canonical correspondence analysis revealed substantial alteration in community assemblages with regard to plant health and yielded a principal axis direction that regrouped taxa associated with diseased plant rhizosphere soil, whereas the opposite axis direction was associated with healthy plants. Two diversity indices were defined and applied to assess the fungal taxa contribution (Tc) and persistence (Pi) throughout the production. PMID:17347891
Vujanovic, V; Hamelin, R C; Bernier, L; Vujanovic, G; St-Arnaud, M
Fungal diversity and composition are still relatively unknown in many ecosystems; however, host identity and environmental conditions are hypothesized to influence fungal community assembly. To test these hypotheses, we characterized the richness, diversity, and composition of rhizosphere fungi colonizing three alpine plant species, Taraxacum ceratophorum, Taraxacum officinale, and Polemonium viscosum. Roots were collected from open meadow and willow understory habitats at treeline on Pennsylvania Mountain, Colorado, USA. Fungal small subunit ribosomal DNA was sequenced using fungal-specific primers, sample-specific DNA tags, and 454 pyrosequencing. We classified operational taxonomic units (OTUs) as arbuscular mycorrhizal (AMF) or non-arbuscular mycorrhizal (non-AMF) fungi and then tested whether habitat or host identity influenced these fungal communities. Approximately 14% of the sequences represented AMF taxa (44 OTUs) with the majority belonging to Glomus groups A and B. Non-AMF sequences represented 186 OTUs belonging to Ascomycota (58%), Basidiomycota (26%), Zygomycota (14%), and Chytridiomycota (2%) phyla. Total AMF and non-AMF richness were similar between habitats but varied among host species. AMF richness and diversity per root sample also varied among host species and were highest in T. ceratophorum compared with T. officinale and P. viscosum. In contrast, non-AMF richness and diversity per root sample were similar among host species except in the willow understory where diversity was reduced in T. officinale. Fungal community composition was influenced by host identity but not habitat. Specifically, T. officinale hosted a different AMF community than T. ceratophorum and P. viscosum while P. viscosum hosted a different non-AMF community than T. ceratophorum and T. officinale. Our results suggest that host identity has a stronger effect on rhizosphere fungi than habitat. Furthermore, although host identity influenced both AMF and non-AMF, this effect was stronger for the mutualistic AMF community. PMID:22038036
Becklin, Katie M; Hertweck, Kate L; Jumpponen, Ari
Enteric microbiota play a variety of roles in intestinal health and disease. While bacteria in the intestine have been broadly characterized, little is known about the abundance or diversity of enteric fungi. This study utilized a culture-independent method termed oligonucleotide fingerprinting of rRNA genes (OFRG) to describe the compositions of fungal and bacterial rRNA genes from small and large intestines (tissue and luminal contents) of restricted-flora and specific-pathogen-free mice. OFRG analysis identified rRNA genes from all four major fungal phyla: Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. The largest assemblages of fungal rRNA sequences were related to the genera Acremonium, Monilinia, Fusarium, Cryptococcus/Filobasidium, Scleroderma, Catenomyces, Spizellomyces, Neocallimastix, Powellomyces, Entophlyctis, Mortierella, and Smittium and the order Mucorales. The majority of bacterial rRNA gene clones were affiliated with the taxa Bacteroidetes, Firmicutes, Acinetobacter, and Lactobacillus. Sequence-selective PCR analyses also detected several of these bacterial and fungal rRNA genes in the mouse chow. Fluorescence in situ hybridization analysis with a fungal small-subunit rRNA probe revealed morphologically diverse microorganisms resident in the mucus biofilm adjacent to the cecal and proximal colonic epithelium. Hybridizing organisms comprised about 2% of the DAPI (4',6-diamidino-2-phenylindole, dihydrochloride)-positive organisms in the mucus biofilm, but their abundance in fecal material may be much lower. These data indicate that diverse fungal taxa are present in the intestinal microbial community. Their abundance suggests that they may play significant roles in enteric microbial functions. PMID:16391120
Scupham, Alexandra J; Presley, Laura L; Wei, Bo; Bent, Elizabeth; Griffith, Natasha; McPherson, Michael; Zhu, Feilin; Oluwadara, Oluwadayo; Rao, Nagesh; Braun, Jonathan; Borneman, James
Cytochrome P450 monooxygenases (P450s) are heme-thiolate proteins distributed across the biological kingdoms. P450s are catalytically versatile and play key roles in organisms primary and secondary metabolism. Identification of P450s across the biological kingdoms depends largely on the identification of two P450 signature motifs, EXXR and CXG, in the protein sequence. Once a putative protein has been identified as P450, it will be assigned to a family and subfamily based on the criteria that P450s within a family share more than 40% homology and members of subfamilies share more than 55% homology. However, to date, no evidence has been presented that can distinguish members of a P450 family. Here, for the first time we report the identification of EXXR- and CXG-motifs-based amino acid patterns that are characteristic of the P450 family. Analysis of P450 signature motifs in the under-explored fungal P450s from four different phyla, ascomycota, basidiomycota, zygomycota and chytridiomycota, indicated that the EXXR motif is highly variable and the CXG motif is somewhat variable. The amino acids threonine and leucine are preferred as second and third amino acids in the EXXR motif and proline and glycine are preferred as second and third amino acids in the CXG motif in fungal P450s. Analysis of 67 P450 families from biological kingdoms such as plants, animals, bacteria and fungi showed conservation of a set of amino acid patterns characteristic of a particular P450 family in EXXR and CXG motifs. This suggests that during the divergence of P450 families from a common ancestor these amino acids patterns evolve and are retained in each P450 family as a signature of that family. The role of amino acid patterns characteristic of a P450 family in the structural and/or functional aspects of members of the P450 family is a topic for future research. PMID:24743800
Syed, Khajamohiddin; Mashele, Samson Sitheni
This review describes biologically active natural products isolated from Aphyllophorales, many of which are known as polypores. Polypores are a large group of terrestrial fungi of the phylum Basdiomycota (basidiomycetes), and they along with certain Ascomycota are a major source of pharmacologically active substances. There are about 25 000 species of basidiomycetes, of which about 500 are members of the Aphyllophorales, a polyphyletic group that contains the polypores. Many of these fungi have circumboreal distributions in North America, Europe, and Asia and broad distributions on all inhabited continents and Africa; only a small number of the most common species with the most obvious fruiting bodies (basidiocarps) have been evaluated for biological activity. An estimated 75% of polypore fungi that have been tested show strong antimicrobial activity, and these may constitute a good source for developing new antibiotics. Numerous compounds from these fungi also display antiviral, cytotoxic, and/or antineoplastic activities. Additional important components of this vast arsenal of compounds are polysaccharides derived from the fungal cell walls. These compounds have attracted significant attention in recent years because of their immunomodulatory activities, resulting in antitumor effects. These high molecular weight compounds, often called biological response modifiers (BRM), or immunopotentiators, prevent carcinogenesis, show direct anticancer effects, and prevent tumor metastasis. Some of the protein-bound polysaccharides from polypores and other basidiomycetes have found their way to the market in Japan as anticancer drugs. Finally, numerous compounds with cardiovascular, phytotoxic, immunomodulatory, analgesic, antidiabetic, antioxidant, insecticidal, and nematocidal activities, isolated from polypores, are also presented. In fact many of the fungi mentioned in this paper have long been used in herbal medicine, including polypores such as Ganoderma lucidum (Reishi or Ling Zhi), Laetiporus sulphureus (Chicken-of-the-Woods), Trametes versicolor (Yun Zhi), Grifola umbellata (Zhu Lin), Inonotus obliquus (Chaga), and Wolfiporia cocos (Hoelen). PMID:14987072
Zjawiony, Jordan K
Group I introns are commonly reported within nuclear SSU ribosomal DNA of eukaryotic micro-organisms, especially in lichen-forming fungi. We have studied the primary and secondary structure of 70 new nuclear SSU rDNA group I introns of Parmeliaceae (Ascomycota: Lecanorales) and compared them with those available in databases, covering more than 60 species. The analyzed samples of Parmeliaceae fell into two groups, one having an intron at the 1506 site and another lacking this one but having another at the 1516 or 1521 position. Introns at the 1521 position seem to be transposed from 1516 sites. Introns at the 1516 position were similar in structure to ones previously reported at this site and known from other lecanoralean fungi, while those at the 1506 position showed structural differences and no similar introns are known from related fungi. The study of the distribution of group I introns within a large monophyletic ensemble of fungi has revealed an unexpected correlation between intron types and ecological and geographical parameters. The introns at the 1516 position occurred in mainly arctic, boreal, and temperate lichens, while those at position 1506 were present in mainly tropical and subtropical to oceanic mild-temperate taxa. Further, the 1516 introns occurred in genera with few distributed species that could represent older taxa, while the 1506 ones were mainly in species-rich genera that could be of recent speciation, as many species have wide distribution areas. The transition between two different environments has been accompanied by a change in introns gained and lost. PMID:17200806
Gutiérrez, Gabriel; Blanco, Oscar; Divakar, Pradeep K; Lumbsch, H Thorsten; Crespo, Ana
The Kingdom Fungi adds substantially to the diversity of life, but due to their cryptic morphology and lifestyle, tremendous diversity, paucity of formally described specimens, and the difficulty in isolating environmental strains into culture, fungal communities are difficult to characterize. This is especially true for endophytic communities of fungi living in healthy plant tissue. The developments in next generation sequencing technologies are, however, starting to reveal the true extent of fungal diversity. One of the promising new technologies, namely semiconductor sequencing, has thus far not been used in fungal diversity assessments. In this study we sequenced the internal transcribed spacer 1 (ITS1) nuclear encoded ribosomal RNA of the endophytic community of the economically important tree, Eucalyptus grandis, from South Africa using the Ion Torrent Personal Genome Machine (PGM). We determined the impact of various analysis parameters on the interpretation of the results, namely different sequence quality parameter settings, different sequence similarity cutoffs for clustering and filtering of databases for removal of sequences with incomplete taxonomy. Sequence similarity cutoff values only had a marginal effect on the identified family numbers, whereas different sequence quality filters had a large effect (89 vs. 48 families between least and most stringent filters). Database filtering had a small, but statistically significant, effect on the assignment of sequences to reference sequences. The community was dominated by Ascomycota, and particularly by families in the Dothidiomycetes that harbor well-known plant pathogens. The study demonstrates that semiconductor sequencing is an ideal strategy for environmental sequencing of fungal communities. It also highlights some potential pitfalls in subsequent data analyses when using a technology with relatively short read lengths.
Kemler, Martin; Garnas, Jeff; Wingfield, Michael J.; Gryzenhout, Marieka; Pillay, Kerry-Anne; Slippers, Bernard
Yeasts were isolated by the enrichment technique from the phylloplane of 94 samples of sugarcane leaf collected from seven provinces in Thailand. All sugarcane leaf samples contained yeasts and 158 yeast strains were obtained. On the basis of the D1/D2 domain of the large subunit rRNA gene sequence analysis, 144 strains were identified to 24 known species in 14 genera belonging to the Ascomycota viz. Candida akabanensis, Candida dendronema, Candida mesorugosa, Candida michaelii, Candida nivariensis, Candida rugosa, Candida orthopsilosis, Candida quercitrusa, Candida tropicalis, Candida xylopsoci, Cyberlindnera fabianii, Cyberlindnera rhodanensis, Debaryomyces nepalensis, Hannaella aff. coprosmaensis, Hanseniaspora guilliermondii, Kluyveromyces marxianus, Lachancea thermotolerans, Lodderomyces elongisporus, Metschnikowia koreensis, Meyerozyma caribbica, Millerozyma koratensis, Pichia kudriavzevii, Torulaspora delbrueckii and Wickerhamomyces edaphicus, and 12 species in six genera of the Basidiomycota viz . Cryptococcus flavescens, Cryptococcus laurentii, Cryptococcus rajasthanensis, Kwoniella heveanensis, Rhodosporidium fluviale, Rhodosporidium paludigenum, Rhodotorula mucilaginosa, Rhodotorula sesimbrana, Rhodotorula taiwanensis, Sporidiobolus ruineniae, Sporobolomyces carnicolor and Sporobolomyces nylandii. Seven strains were identical or similar to four undescribed species. Another seven strains represented four novels species in the genus Metschnikowia, Nakazawaea, Wickerhamomyces and Yamadazyma. The results revealed 69 % of the isolated strains were ascomycete yeasts and 31 % were basidiomycete yeast. The most prevalent species was M. caribbica with a 23 % frequency of occurrence followed by Rh. taiwanensis (11 %) and C. tropicalis (10 %). All strains were assessed for indole-3-acetic acid (IAA) producing capability showing that 69 strains had the capability of producing IAA when cultivated in yeast extract peptone dextrose broth supplemented with 1 g/L L-tryptophan. The highest IAA concentration of 565.1 mg/L was produced by R. fluviale DMKU-RK253. PMID:24442819
Limtong, Savitree; Kaewwichian, Rungluk; Yongmanitchai, Wichien; Kawasaki, Hiroko
Bamboos, regarded as therapeutic agents in ethnomedicine, have been used to inhibit inflammation and enhance natural immunity for a long time in Asia, and there are many bamboo associated fungi with medical and edible value. In the present study, a total of 350 fungal strains were isolated from the uncommon moso bamboo (Phyllostachys edulis) seeds for the first time. The molecular diversity of these endophytic fungi was investigated and bioactive compound producers were screened for the first time. All the fungal endophytes were categorized into 69 morphotypes according to culturable characteristics and their internal transcriber spacer (ITS) regions were analyzed by BLAST search with the NCBI database. The fungal isolates showed high diversity and were divided in Ascomycota (98.0%) and Basidiomycota (2.0%), including at least 19 genera in nine orders. Four particular genera were considered to be newly recorded bambusicolous fungi, including Leptosphaerulina, Simplicillium, Sebacina and an unknown genus in Basidiomycetes. Furthermore, inhibitory effects against clinical pathogens and phytopathogens were screened preliminarily and strains B09 (Cladosporium sp.), B34 (Curvularia sp.), B35 (undefined genus 1), B38 (Penicillium sp.) and zzz816 (Shiraia sp.) displayed broad-spectrum activity against clinical bacteria and yeasts by the agar diffusion method. The crude extracts of isolates B09, B34, B35, B38 and zzz816 under submerged fermentation, also demonstrated various levels of bioactivities against bambusicolous pathogenic fungi. This study is the first report on the antimicrobial activity of endophytic fungi associated with moso bamboo seeds, and the results show that they could be exploited as a potential source of bioactive compounds and plant defense activators. In addition, it is the first time that strains of Shiraia sp. have been isolated and cultured from moso bamboo seeds, and one of them (zzz816) could produce hypocrellin A at high yield, which is significantly different from the other strains published. PMID:24759896
Shen, Xiao-Ye; Cheng, Yan-Lin; Cai, Chun-Ju; Fan, Li; Gao, Jian; Hou, Cheng-Lin
The family Microthyriaceae sensu Lumbsch and Huhndorf 2010 is a poorly known but interesting family comprising 50 genera consisting of foliar epiphytes or saprobes on dead leaves and stems. We re-visited the family based on examinations of generic types where possible. Members are distributed in Aulographaceae, Asterinaceae, Microthyriaceae, Micropeltidaceae and Palmulariaceae and notes are provided on each of these families. Nine genera are transferred from Microthyriaceae to Asterinaceae, and two to Aulographaceae based on the splitting or dissolving nature of the thyriothecia to release ascospores. New sequence data for a number of species and genera are provided. Microthyriaceous members growing on other fungi and lichens differ from Microthyriaceae sensu stricto and the family Trichothyriaceae is reinstated to accommodate these taxa. Other genera of Microthyriaceae belong in Rhytismataceae, Stictidaceae, Venturiales incertae cedis, Dothideomyetes genera incertae cedis, Hypocreales incertae cedis and Ascomycota genera incertae cedis. The family Microthyriaceae is reduced to seven genera characterised by superficial, flattened thyriothecia, with the cells of the upper wall radiating in parallel arrangement from the distinct central ostiolar opening, while the lower peridium is generally poorly developed. Sequence data is provided for five species with thyriothecia and Paramicrothyrium and Neomicrothyrium are described as new genera and Micropeltis zingiberacicola is introduced as a new species. Our phylogenetic analysis underscores the high genetic diversity for thyriotheciate species and there is no clear clade that can be well defined as Microthyriales. Nuclear ribosomal data support multiple polyphyletic lineages within Microthyriaceae and Micropeltidaceae. Some unexpected DNA based phylogenetic relationships such as those between Muyocopron and Saccardoella will require corroboration with more complete taxon sampling as well as additional non ribosomal markers. There are few differences between Aulographaceae, Asterinaceae and Palmulariaceae and these families may need synonymising.
Wu, Hai X.; Schoch, Conrad L.; Boonmee, Saranyaphat; Bahkali, Ali H.; Chomnunti, Putarak
Previously, we investigated the effect of N-acetylglucosamine (GlcNAc) on Coccidioides posadasii chitinolytic enzymes during in vitro spherule-endospore (S/E) phase culture. During those studies, sodium dodecyl sulfatepolyacrylamide gel electrophoresis analysis of supernatants from S/E phase cultures grown in Converse medium with or without added GlcNAc revealed a ??28-kDa band (CFP28), whose abundance was increased by GlcNAc in parallel with the chitinolytic enzymes. Mass spectrometry (MS) of the CFP28 band revealed peptides that matched an open reading frame found in the tentative consensus sequence, TC20325, retrieved from the Dana Farber Cancer Institute C. posadasii Gene Index Database. The TC20325 cDNA sequence was used to design internal primers based on MS peptides and a full-length cDNA was isolated using a combination of rapid amplification of cDNA ends and reverse transcription-polymerase chain reaction. The deduced amino acid sequence of the full-length cDNA consists of 231 amino acid residues with a 19 aa signal peptide. The mature protein has a calculated molecular mass of ??24.5 kDa, a theoretical pI of 6.09, and consists of a single DOMON-like type 9 carbohydrate-binding module (CBM9-like-3) conserved domain. The protein shares the highest sequence similarity (?57%) to hypothetical proteins from fungi within the Pezizomycotina subphylum of Ascomycota. Antiserum against a recombinant version of CFP28 recognized native CFP28 in S/E phase cells and culture supernatants. CFP28 mRNA and protein expression were detectable in S/E phase in Converse medium, but were increased in the presence of added GlcNAc. Purified native CFP28 reacted with pooled sera from patients with coccidioidomycosis. PMID:25023485
Lunetta, Jennine M; Pappagianis, Demosthenes
Background All globins belong to one of three families: the F (flavohemoglobin) and S (sensor) families that exhibit the canonical 3/3 ?-helical fold, and the T (truncated 3/3 fold) globins characterized by a shortened 2/2 ?-helical fold. All eukaryote 3/3 hemoglobins are related to the bacterial single domain F globins. It is known that Fungi contain flavohemoglobins and single domain S globins. Our aims are to provide a census of fungal globins and to examine their relationships to bacterial globins. Results Examination of 165 genomes revealed that globins are present in >90% of Ascomycota and ?60% of Basidiomycota genomes. The S globins occur in Blastocladiomycota and Chytridiomycota in addition to the phyla that have FHbs. Unexpectedly, group 1 T globins were found in one Blastocladiomycota and one Chytridiomycota genome. Phylogenetic analyses were carried out on the fungal globins, alone and aligned with representative bacterial globins. The Saccharomycetes and Sordariomycetes with two FHbs form two widely divergent clusters separated by the remaining fungal sequences. One of the Saccharomycete groups represents a new subfamily of FHbs, comprising a previously unknown N-terminal and a FHb missing the C-terminal moiety of its reductase domain. The two Saccharomycete groups also form two clusters in the presence of bacterial FHbs; the surrounding bacterial sequences are dominated by Proteobacteria and Bacilli (Firmicutes). The remaining fungal FHbs cluster with Proteobacteria and Actinobacteria. The Sgbs cluster separately from their bacterial counterparts, except for the intercalation of two Planctomycetes and a Proteobacterium between the Fungi incertae sedis and the Blastocladiomycota and Chytridiomycota. Conclusion Our results are compatible with a model of globin evolution put forward earlier, which proposed that eukaryote F, S and T globins originated via horizontal gene transfer of their bacterial counterparts to the eukaryote ancestor, resulting from the endosymbiotic events responsible for the origin of mitochondria and chloroplasts.
Hoogewijs, David; Dewilde, Sylvia; Vierstraete, Andy; Moens, Luc; Vinogradov, Serge N.
In a recent study pyrosequencing of the ribosomal internal transcribed spacer-1 (ITS-1) has validated the effectiveness of such technology in the survey of soil fungal diversity. Here we compare the two ITS regions, ITS-1 and ITS-2, of the fungal populations occurring in Tuber melanosporum/Quercus pubescens truffle grounds and sampled in two areas, one devoid of vegetation ("burned", brulé in French) where T. melanosporum fruiting bodies are usually collected, and outside the brulé. TS1F/ITS2 and ITS3/ITS4 were used respectively for the amplification of the ITS-1 and ITS-2 regions. Two amplicon libraries were built, one for inside and the other for outside. A set of 15.788 reads was obtained. After the removal of low quality sequences, 3568 and 3156 sequences were obtained from inside the brulé with the ITS-1 and ITS-2 primers respectively. The sequences obtained from outside the brulé were 4490 with the ITS-1 primers and 2432 with the ITS-2 primers. Most of the sequences obtained for both ITS fragments could be attributed to fungal organisms. The pair of primers, ITS1-F/ITS2, was more selective, producing fewer non-fungal sequences (1% inside, 3% outside), in addition to a higher number of sequences, than the pair ITS3/ITS4 (6% inside, 11% outside). Although differences are present in the taxa percentages between ITS-1 and ITS-2, both reveal that Ascomycota were the dominant fungal phylum and that their number decreased moving from inside the brulé to outside, while the number of Basidiomycota increased. Taken together, both the short ITS-1 and ITS-2 reads obtained by the high throughput 454 sequencing provide adequate information for taxon assignment and are suitable to correlate the dynamics of the fungal populations to specific environments. PMID:21700633
Mello, Antonietta; Napoli, Chiara; Murat, Claude; Morin, Emmanuelle; Marceddu, Giuseppe; Bonfante, Paola
Hsp70 molecular chaperones are ubiquitous. By preventing aggregation, promoting folding, and regulating degradation, Hsp70s are major factors in the ability of cells to maintain proteostasis. Despite a wealth of functional information, little is understood about the evolutionary dynamics of Hsp70s. We undertook an analysis of Hsp70s in the fungal clade Ascomycota. Using the well-characterized 14 Hsp70s of Saccharomyces cerevisiae, we identified 491 orthologs from 53 genomes. Saccharomyces cerevisiae Hsp70s fall into seven subfamilies: four canonical-type Hsp70 chaperones (SSA, SSB, KAR, and SSC) and three atypical Hsp70s (SSE, SSZ, and LHS) that play regulatory roles, modulating the activity of canonical Hsp70 partners. Each of the 53 surveyed genomes harbored at least one member of each subfamily, and thus establishing these seven Hsp70s as units of function and evolution. Genomes of some species contained only one member of each subfamily that is only seven Hsp70s. Overall, members of each subfamily formed a monophyletic group, suggesting that each diversified from their corresponding ancestral gene present in the common ancestor of all surveyed species. However, the pattern of evolution varied across subfamilies. At one extreme, members of the SSB subfamily evolved under concerted evolution. At the other extreme, SSA and SSC subfamilies exhibited a high degree of copy number dynamics, consistent with a birth-death mode of evolution. KAR, SSE, SSZ, and LHS subfamilies evolved in a simple divergent mode with little copy number dynamics. Together, our data revealed that the evolutionary history of this highly conserved and ubiquitous protein family was surprising complex and dynamic. PMID:24277689
Kominek, Jacek; Marszalek, Jaroslaw; Neuvéglise, Cécile; Craig, Elizabeth A; Williams, Barry L
Background Bromelia pinguin (Bromeliaceae) is a terrestrial bromeliad commonly found under forest stands throughout the Neotropics that has been shown to have antifungal activity in vitro. We have hypothesized that this bromeliad would also have an effect on the fungal populations in nearby soil by decreasing fungaldiversity and negatively impacting C and N cycle-related activities. A previous study in the lowland forest of Costa Rica showed the soil beneath these bromeliads had decreased fungal ITS DNA and differences in C and N levels compared to adjacent primary forest soils. Results In this follow-up study, we found that the bromeliad soils had lower rates of C and N biomass development and lower phenol oxidase activity (suggesting less decreased fungal decomposition activity). The results of T-RFLP and cloning-based taxonomic analyses showed the community level diversity and abundance of fungal ITS DNA was less in bromeliad soils. Sequence analysis of fungal ITS DNA clones showed marked differences in fungal community structure between habitats of Basidiomycota (Tremellales, Agricales, Thelephorales), Ascomycota (Helotiales), and Zycomycota populations. Conclusions The data show there to be differences in the soil nutrient dynamics and fungal community structure and activity associated with these bromeliads, as compared to the adjacent primary forest. This suggests the possibility that the anti-fungal activity of the bromeliad extends into the soil. The bromeliad-dense regions of these primary forest habitats provide a unique natural micro-habitat within the forests and the opportunity to better identify the role of fungal communities in the C and N cycles in tropical soils.
We previously characterized members of the Myb protein family, MYT1 and MYT2, in Fusarium graminearum. MYT1 and MYT2 are involved in female fertility and perithecium size, respectively. To expand knowledge of Myb proteins in F. graminearum, in this study, we characterized the functions of the MYT3 gene, which encodes a putative Myb-like transcription factor containing two Myb DNA-binding domains and is conserved in the subphylum Pezizomycotina of Ascomycota. MYT3 proteins were localized in nuclei during most developmental stages, suggesting the role of MYT3 as a transcriptional regulator. Deletion of MYT3 resulted in impairment of conidiation, germination, and vegetative growth compared to the wild type, whereas complementation of MYT3 restored the wild-type phenotype. Additionally, the ?myt3 strain grew poorly on nitrogen-limited media; however, the mutant grew robustly on minimal media supplemented with ammonium. Moreover, expression level of nitrate reductase gene in the ?myt3 strain was decreased in comparison to the wild type and complemented strain. On flowering wheat heads, the ?myt3 strain exhibited reduced pathogenicity, which corresponded with significant reductions in trichothecene production and transcript levels of trichothecene biosynthetic genes. When the mutant was selfed, mated as a female, or mated as a male for sexual development, perithecia were not observed on the cultures, indicating that the ?myt3 strain lost both male and female fertility. Taken together, these results demonstrate that MYT3 is required for pathogenesis and sexual development in F. graminearum, and will provide a robust foundation to establish the regulatory networks for all Myb-like proteins in F. graminearum.
Son, Hokyoung; Choi, Gyung Ja; Kim, Jin-Cheol; Lee, Yin-Won
The commercial availability of next generation sequencing (NGS) technologies facilitated the assessment of functional groups of microorganisms in the environment with high coverage, resolution, and reproducibility. Soil methylotrophs were among the first microorganisms in the environment that were assessed with molecular tools, and nowadays, as well with NGS technologies. Studies in the past years re-attracted notice to the pivotal role of methylotrophs in global conversions of methanol, which mainl