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Sample records for camillea xylariaceae ascomycota

  1. Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota).

    PubMed

    U'Ren, Jana M; Miadlikowska, Jolanta; Zimmerman, Naupaka B; Lutzoni, François; Stajich, Jason E; Arnold, A Elizabeth

    2016-05-01

    The Xylariaceae (Sordariomycetes) comprise one of the largest and most diverse families of Ascomycota, with at least 85 accepted genera and ca. 1343 accepted species. In addition to their frequent occurrence as saprotrophs, members of the family often are found as endophytes in living tissues of phylogenetically diverse plants and lichens. Many of these endophytes remain sterile in culture, precluding identification based on morphological characters. Previous studies indicate that endophytes are highly diverse and represent many xylariaceous genera; however, phylogenetic analyses at the family level generally have not included endophytes, such that their contributions to understanding phylogenetic relationships of Xylariaceae are not well known. Here we use a multi-locus, cumulative supermatrix approach to integrate 92 putative species of fungi isolated from plants and lichens into a phylogenetic framework for Xylariaceae. Our collection spans 1933 isolates from living and senescent tissues in five biomes across the continental United States, and here is analyzed in the context of previously published sequence data from described species and additional taxon sampling of type specimens from culture collections. We found that the majority of strains obtained in our surveys can be classified in the hypoxyloid and xylaroid subfamilies, although many also were found outside of these lineages (as currently circumscribed). Many endophytes were placed in lineages previously not known for endophytism. Most endophytes appear to represent novel species, but inferences are limited by potential gaps in public databases. By linking our data, publicly available sequence data, and records of ascomata, we identify many geographically widespread, host-generalist clades capable of symbiotic associations with diverse photosynthetic partners. Concomitant with such cosmopolitan host use and distributions, many xylariaceous endophytes appear to inhabit both living and non-living plant

  2. Rickenyls A-E, antioxidative terphenyls from the fungus Hypoxylon rickii (Xylariaceae, Ascomycota).

    PubMed

    Kuhnert, Eric; Surup, Frank; Herrmann, Jennifer; Huch, Volker; Müller, Rolf; Stadler, Marc

    2015-10-01

    Our screening efforts for new natural products with interesting bioactivity have revealed the neotropical ascomycete Hypoxylon rickii as a prolific source. We isolated five secondary metabolites with a p-terphenyl backbone from the mycelial extract of a fermentation of this fungus in 70 l scale by using RP-HPLC, which were named rickenyls A-E (1-5). Their structures were elucidated by X-ray crystallography and NMR spectroscopy, complemented by HRESIMS. Two of the compounds contained a quinone core structure in ortho (2) and para-position (5), respectively. We obtained 2 spontaneously and by lead tetraacetate oxidation from 1. All compounds were screened for antimicrobial, antioxidative and cytotoxic activities. Rickenyl A (1) exhibited strong antioxidative effects and moderate cytotoxic activity against various cancer cell lines. PMID:26296745

  3. A polyphasic taxonomy of Daldinia (Xylariaceae)1

    PubMed Central

    Stadler, Marc; Læssøe, Thomas; Fournier, Jacques; Decock, Cony; Schmieschek, Beata; Tichy, Hans-Volker; Peršoh, Derek

    2014-01-01

    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

  4. Polyketides from a Marine-Derived Fungus Xylariaceae sp.

    PubMed Central

    Nong, Xu-Hua; Zheng, Zhi-Hui; Zhang, Xiao-Yong; Lu, Xin-Hua; Qi, Shu-Hua

    2013-01-01

    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. PMID:23697953

  5. Polyketides from a marine-derived fungus Xylariaceae sp.

    PubMed

    Nong, Xu-Hua; Zheng, Zhi-Hui; Zhang, Xiao-Yong; Lu, Xin-Hua; Qi, Shu-Hua

    2013-05-01

    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. PMID:23697953

  6. Cytotoxic Cytochalasins and Other Metabolites from Xylariaceae sp. FL0390, a Fungal Endophyte of Spanish Moss.

    PubMed

    Xu, Ya-Ming; Bashyal, Bharat P; Liu, Mangping X; Espinosa-Artiles, Patricia; U'Ren, Jana M; Arnold, A Elizabeth; Gunatilaka, A A Leslie

    2015-10-01

    Two new metabolites, 6-oxo-12-norcytochalasin D (1) and 4,5-di-isobutyl-2(1H)-pyrimidinone (2), together with seven known metabolites, cytochalasins D (3), Q (4), and N (5), 12-hydroxyzygosporin G (6), heptelidic acid chlorohydrin (7), (+)-heptelidic acid (8), and trichoderonic acid A (9), were isolated from Xylariaceae sp. FL0390, a fungal endophyte inhabiting Spanish moss, Tillandsia usneoides. Metabolite 1 is the first example of a 12-norcytochalasin. All metabolites, except 2 and 9, showed cytotoxic activity in a panel of five human tumor cell lines with IC50S of 0.2-5.0 μM. PMID:26669096

  7. Dating the Diversification of the Major Lineages of Ascomycota (Fungi)

    PubMed Central

    Prieto, María; Wedin, Mats

    2013-01-01

    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. PMID:23799026

  8. Dating the diversification of the major lineages of Ascomycota (Fungi).

    PubMed

    Prieto, María; Wedin, Mats

    2013-01-01

    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. PMID:23799026

  9. Pupal mortality and adult emergence of western cherry fruit fly (Diptera: Tephritidae) exposed to the fungus Muscodor albus (Xylariales: Xylariaceae).

    PubMed

    Yee, Wee L; Lacey, Lawrence A; Bishop, Belinda J B

    2009-12-01

    Western cherry fruit fly, Rhagoletis indifferens Curran (Diptera: Tephritidae), is a major pest of sweet cherry, Prunus avium (L.) L. (Rosales: Rosaceae), that is conventionally controlled using insecticides. One alternative to the use of insecticides alone for fly control could be fumigation of the fly's overwintering habitat using the fungus Muscodor albus Worapong, Strobel & Hess (Xylariales: Xylariaceae) in conjunction with reduced insecticide use. The fungus produces a mixture of volatile organic compounds (VOCs) that are biocidal for a variety of organisms. In this study, the main objectives were to determine the effects of M. albus VOCs on mortality of R. indifferens pupae and on adult emergence under laboratory conditions. In fumigation chamber experiments, a 14-d exposure of pupae in soil to VOCs resulted in 61.9% control, and exposure to VOCs for 7, 10, and 14 d reduced fly emergence by 44.2, 70.0, and 86.3%, respectively, relative to controls. In an experiment using plastic covers to retain VOCs in treated soil, a concentration of 1% M. albus formulation (fungus + rye grain) did not affect pupal mortality and fly emergence, but a concentration of 5% M. albus formulation resulted in 27.4% control and reduced fly emergence by 30.1% relative to the control. Larvae of R. indifferens that were dropped onto soil with 1% M. albus formulation were not affected by the fungus. Results indicate that prolonged exposure and high concentrations of M. albus VOCs can cause significant mortality of R. indifferens pupae in soil and delay adult emergence. PMID:20069829

  10. The complete mitochondrial genome of Paecilomyces hepiali (Ascomycota, Eurotiomycetes).

    PubMed

    Wang, Linping; Xu, Jiayue; Li, Huchen; Song, Lipu; Yu, Yi; Zhang, Wensheng; Liu, Guiming; Feng, Chengqiang

    2016-01-01

    Paecilomyces hepiali, belonging to the Eurotiales order Ascomycota, is an endoparasitic fungus that commonly exists in the natural Cordyceps sinensis anamorph stage. Here, we report the complete mitochondrial DNA sequences of P. hepiali for the first time. The genome is 24,245 bp in length, encoding 15 protein-coding genes (PCGs), 2 rRNA genes, 25 tRNA genes and 3 homing endonucleases. The overall AT composition is 73.37% and the average AT content of PCG, rRNA, tRNA and non-coding region are 74.21%, 66.07%, 62.83% and 75.96%, respectively. Phylogenetic analysis with eight Ascomycota species and thirteen Basidiomycota species revealed that P. hepiali is was more closely related to Cordyceps bassiana, Cordycep smilitaris and Cordyceps brongniartii. It is confirmed that P. hepiali is a derivative of Cordyceps sinensis. This study provided valuable information on the gene contents of the mitochondrial genome and would facilitate the study of function and evolution of P. hepiali. PMID:24963769

  11. Saccharomycotina and Taphrinomycotina: the yeasts and yeast-like fungi of the Ascomycota

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The phylum Ascomycota has been resolved into three major phylogenetic lineages: the subphyla Saccharomycotina (e.g., Saccharomyces, Pichia, Candida), Taphrinomycotina (e.g., Protomyces, Taphrina, Pneumocystis), and the Pezizomycotina (e.g., Aspergillus, Neurospora, Peziza). We discuss the ecology, ...

  12. Origin and evolution of carnivorism in the Ascomycota (fungi)

    PubMed Central

    Yang, Ence; Xu, Lingling; Yang, Ying; Zhang, Xinyu; Xiang, Meichun; Wang, Chengshu; An, Zhiqiang; Liu, Xingzhong

    2012-01-01

    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

  13. Estimating the Phanerozoic history of the Ascomycota lineages: combining fossil and molecular data.

    PubMed

    Beimforde, Christina; Feldberg, Kathrin; Nylinder, Stephan; Rikkinen, Jouko; Tuovila, Hanna; Dörfelt, Heinrich; Gube, Matthias; Jackson, Daniel J; Reitner, Joachim; Seyfullah, Leyla J; Schmidt, Alexander R

    2014-09-01

    The phylum Ascomycota is by far the largest group in the fungal kingdom. Ecologically important mutualistic associations such as mycorrhizae and lichens have evolved in this group, which are regarded as key innovations that supported the evolution of land plants. Only a few attempts have been made to date the origin of Ascomycota lineages by using molecular clock methods, which is primarily due to the lack of satisfactory fossil calibration data. For this reason we have evaluated all of the oldest available ascomycete fossils from amber (Albian to Miocene) and chert (Devonian and Maastrichtian). The fossils represent five major ascomycete classes (Coniocybomycetes, Dothideomycetes, Eurotiomycetes, Laboulbeniomycetes, and Lecanoromycetes). We have assembled a multi-gene data set (18SrDNA, 28SrDNA, RPB1 and RPB2) from a total of 145 taxa representing most groups of the Ascomycota and utilized fossil calibration points solely from within the ascomycetes to estimate divergence times of Ascomycota lineages with a Bayesian approach. Our results suggest an initial diversification of the Pezizomycotina in the Ordovician, followed by repeated splits of lineages throughout the Phanerozoic, and indicate that this continuous diversification was unaffected by mass extinctions. We suggest that the ecological diversity within each lineage ensured that at least some taxa of each group were able to survive global crises and rapidly recovered. PMID:24792086

  14. Extracellular polysaccharides from Ascomycota and Basidiomycota: production conditions, biochemical characteristics, and biological properties.

    PubMed

    Osińska-Jaroszuk, Monika; Jarosz-Wilkołazka, Anna; Jaroszuk-Ściseł, Jolanta; Szałapata, Katarzyna; Nowak, Artur; Jaszek, Magdalena; Ozimek, Ewa; Majewska, Małgorzata

    2015-12-01

    Fungal polysaccharides (PSs) are the subject of research in many fields of science and industry. Many properties of PSs have already been confirmed and the list of postulated functions continues to grow. Fungal PSs are classified into different groups according to systematic affinity, structure (linear and branched), sugar composition (homo- and heteropolysaccharides), type of bonds between the monomers (β-(1 → 3), β-(1 → 6), and α-(1 → 3)) and their location in the cell (cell wall PSs, exoPSs, and endoPSs). Exopolysaccharides (EPSs) are most frequently studied fungal PSs but their definition, classification, and origin are still not clear and should be explained. Ascomycota and Basidiomycota fungi producing EPS have different ecological positions (saprotrophic and endophytic, pathogenic or symbiotic-mycorrhizae fungi); therefore, EPSs play different biological functions, for example in the protection against environmental stress factors and in interactions with other organisms. EPSs obtained from Ascomycota and Basidiomycota fungal cultures are known for their antioxidant, immunostimulating, antitumor, and antimicrobial properties. The major objective of the presented review article was to provide a detailed description of the state-of-the-art knowledge of the effectiveness of EPS production by filamentous and yeast Ascomycota and Basidiomycota fungi and techniques of derivation of EPSs, their biochemical characteristics, and biological properties allowing comprehensive analysis as well as indication of similarities and differences between these fungal groups. Understanding the role of EPSs in a variety of processes and their application in food or pharmaceutical industries requires improvement of the techniques of their derivation, purification, and characterization. The detailed analyses of data concerning the derivation and application of Ascomycota and Basidiomycota EPSs can facilitate development and trace the direction of application of these EPSs

  15. EPR investigation of some desiccated Ascomycota and Basidiomycota gamma-irradiated mushrooms

    NASA Astrophysics Data System (ADS)

    Bercu, V.; Negut, C. D.; Duliu, O. G.

    2010-12-01

    The suitability of the EPR spectroscopy for detection of γ-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.

  16. Isolation of Endohyphal Bacteria from Foliar Ascomycota and In Vitro Establishment of Their Symbiotic Associations.

    PubMed

    Arendt, Kayla R; Hockett, Kevin L; Araldi-Brondolo, Sarah J; Baltrus, David A; Arnold, A Elizabeth

    2016-05-15

    Endohyphal bacteria (EHB) can influence fungal phenotypes and shape the outcomes of plant-fungal interactions. Previous work has suggested that EHB form facultative associations with many foliar fungi in the Ascomycota. These bacteria can be isolated in culture, and fungi can be cured of EHB using antibiotics. Here, we present methods for successfully introducing EHB into axenic mycelia of strains representing two classes of Ascomycota. We first establish in vitro conditions favoring reintroduction of two strains of EHB (Luteibacter sp.) into axenic cultures of their original fungal hosts, focusing on fungi isolated from healthy plant tissue as endophytes: Microdiplodia sp. (Dothideomycetes) and Pestalotiopsis sp. (Sordariomycetes). We then demonstrate that these EHB can be introduced into a novel fungal host under the same conditions, successfully transferring EHB between fungi representing different classes. Finally, we manipulate conditions to optimize reintroduction in a focal EHB-fungal association. We show that EHB infections were initiated and maintained more often under low-nutrient culture conditions and when EHB and fungal hyphae were washed with MgCl2 prior to reassociation. Our study provides new methods for experimental assessment of the effects of EHB on fungal phenotypes and shows how the identity of the fungal host and growth conditions can define the establishment of these widespread and important symbioses. PMID:26969692

  17. Kodamaea ohmeri (Ascomycota: Saccharomycotina) presence in commercial Bombus impatiens Cresson and feral Bombus pensylvanicus DeGeer (Hymenoptera: Apidae) colonies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this study, eight commercial and three feral bumble bee (Bombus impatiens Cresson and Bombus pensylvanicus DeGeer respectively, Hymenoptera: Apidae) colonies were tested for the presence of Kodamaea ohmeri (Ascomycota: Saccharomycotina), a yeast known to attract small hive beetles (SHB) (Aethina ...

  18. Promising approaches towards biotransformation of polycyclic aromatic hydrocarbons with Ascomycota fungi.

    PubMed

    Aranda, Elisabet

    2016-04-01

    The bioremediation of hazardous aromatic pollutants such as polycyclic aromatic hydrocarbons (PAHs) has been extensively studied in recent decades, including the potential use of different phyla of fungi for this purpose. Molecular technologies are starting to reveal that the real players in polluted environments are mainly represented by the phylum Ascomycota and the subphylum Mucoromycotina and, to a lesser extent, the phylum Basidiomycota. Paradoxically, despite their key involvement, these groups of fungi are often treated as a black box, and their potential roles in the transformation of xenobiotics and catabolic pathways remain poorly understood. The complex intracellular metabolism seems to play a major role in the ability of these fungi to transform or remove PAHs, and their associated enzymes are encoded in the xenome. Functional genomics offers novel information about this enzymatic system, which is widely distributed among all phyla. PMID:26722717

  19. Saitoella coloradoensis sp. nov., a new species of the Ascomycota, subphylum Taphrinomycotina.

    PubMed

    Kurtzman, Cletus P; Robnett, Christie J

    2012-05-01

    Saitoella coloradoensis sp. nov. (NRRL YB-2330, CBS 12360, type strain, MycoBank accession number 563858) is described. This new member of the phylum Ascomycota, subphylum Taphrinomycotina was isolated from insect frass occurring in an Engelmann spruce (Picea engelmannii) that was growing in Colorado, USA. Multigene sequence analysis showed that S. coloradoensis is distinct from Saitoella complicata, the only other known species of Saitoella. The two species may be separated phenotypically from growth reactions on D: -xylose, ribitol and methyl-α-D: -glucoside. Asexual reproduction is by budding and both species produce thick-walled, spherical cells that appear morphologically similar to the ascogenous cells formed in plant host tissue by species of Protomyces and some species of Taphrina. The thick-walled cells did not form ascospores but did produce buds when placed on fresh growth media. PMID:22246589

  20. Molecular analysis reveals two new dimorphic species of Hesperomyces (Ascomycota, Laboulbeniomycetes) parasitic on the ladybird Coleomegilla maculata (Coleoptera, Coccinellidae).

    PubMed

    Goldmann, Lauren; Weir, Alex; Rossi, Walter

    2013-01-01

    Four morphotypes of Hesperomyces (Ascomycota, Laboulbeniomycetes) were found on the ladybird Coleomegilla maculata (Coleoptera, Coccinellidae) from Costa Rica and Ecuador. Partial SSU and ITS rDNA sequence analysis revealed that these belong to two phylogenetic species, each with a pair of morphotypes displaying position specificity. Confirmation of dimorphism in Laboulbeniales highlights the need for a thorough systematic revision of species concepts within the order. The theory of 'position specificity' also needs to be revisited. PMID:24295919

  1. Ascomycota Members Dominate Fungal Communities during Straw Residue Decomposition in Arable Soil

    PubMed Central

    Ma, Anzhou; Zhuang, Xuliang; Wu, Junmei; Cui, Mengmeng; Lv, Di; Liu, Chunzhao; Zhuang, Guoqiang

    2013-01-01

    This study investigated the development of fungal community composition in arable soil during the degradation of straw residue. We explored the short-term responses of the fungal community over 28 days of decomposition in soil using culture-independent polymerase chain reaction in combination with a clone library and denaturing gradient gel electrophoresis (DGGE). Fungal cellobiohydrolase I (cbhI) genes in the soil were also characterized, and their diversity suggested the existence of a different cellulose decomposer. The DGGE profiles based on fungal internal transcribed spacer analysis showed different successions of fungal populations during residue decomposition. Members of Lecythophora and Sordariales were dominant in the early succession, while Hypocrea and Engyodontium were better adapted in the late succession. The succession of fungal communities might be related to changes of residue quality during decomposition. Collectively, sequences assigned to Ascomycota members were dominant at different stages of the fungal succession during decomposition, revealing that they were key drivers responsible for residue degradation in the arable soil tested. PMID:23840414

  2. Main airborne Ascomycota spores: characterization by culture, spore morphology, ribosomal DNA sequences and enzymatic analysis.

    PubMed

    Oliveira, Manuela; Amorim, M Isabel; Ferreira, Elsa; Delgado, Luís; Abreu, Ilda

    2010-04-01

    The aim of this work was to identify the main allergy-related Ascomycetes fungal spores present in the atmosphere of Porto, using different and complementary techniques. The atmospheric sampling, performed in the atmosphere of Porto (Portugal) from August 2006 to July 2008, indicated Cladosporium, Penicillium, Aspergillus and Alternaria as the main fungal spore taxa. Alternaria and Cladosporium peaks were registered during summer. Aspergillus and Penicillium highest values were registered from late winter to early spring. Additionally, the Andersen sampler allowed the culture and isolation of the collected viable spores subsequently used for different identification approaches. The internal-transcribed spacer region of the nuclear ribosomal repeat unit sequences of airborne Ascomycetes fungi isolates revealed 11 taxonomically related fungal species. Among the identified taxa, Penicillum and Aspergillus presented the highest diversity, while only one species of Cladosporium and Alternaria, respectively, were identified. All selected fungal spore taxa possessed phosphatase, esterase, leucine arylamidase and beta-glucosidase enzymatic activity, while none had lipase, cystine arylamidase, trypsin or beta-glucuronidase activity. The association between the spore cell wall morphology, DNA-based techniques and enzymatic activity approaches allowed a more reliable identification procedure of the airborne Ascomycota fungal spores. PMID:20143229

  3. New species of Elaphomyces (Elaphomycetaceae, Eurotiales, Ascomycota) from tropical rainforests of Cameroon and Guyana.

    PubMed

    Castellano, Michael A; Dentinger, Bryn T M; Séné, Olivier; Elliott, Todd F; Truong, Camille; Henkel, Terry W

    2016-06-01

    The sequestrate false truffles Elaphomyces favosus, E. iuppitercellus, and E. labyrinthinus spp. nov. are described as new to science from the Dja Biosphere Reserve, Cameroon. Elaphomyces adamizans sp. nov. is described as new from the Pakaraima Mountains of Guyana. The Cameroonian species are the first Elaphomyces taxa to be formally described from Africa, occurring in lowland Guineo-Congolian tropical rainforests dominated by the ectomycorrhizal (ECM) canopy tree Gilbertiodendron dewevrei (Fabaceae subfam. Caesalpinioideae). The Guyanese species is the third to be discovered in lowland tropical South America, occurring in forests dominated by the ECM trees Pakaraimaea dipterocarpacea (Dipterocarpaceae) and Dicymbe jenmanii (Fabaceae subfam. Caesalpinioideae). Macromorphological, micromorphological, habitat, and DNA sequence data are provided for each new species. Molecular and morphological data place these fungi in Elaphomycetaceae (Eurotiales, Ascomycota). Unique morphological features are congruent with molecular delimitation of each of the new species based on a phylogenetic analysis of the rDNA ITS and 28S loci across the Elaphomycetaceae. The phylogenetic analysis also suggests that a common ancestor is shared between some Elaphomyces species from Africa and South America, and that species of the stalked, volvate genus Pseudotulostoma may be nested in Elaphomyces. PMID:27433441

  4. Ascomycota members dominate fungal communities during straw residue decomposition in arable soil.

    PubMed

    Ma, Anzhou; Zhuang, Xuliang; Wu, Junmei; Cui, Mengmeng; Lv, Di; Liu, Chunzhao; Zhuang, Guoqiang

    2013-01-01

    This study investigated the development of fungal community composition in arable soil during the degradation of straw residue. We explored the short-term responses of the fungal community over 28 days of decomposition in soil using culture-independent polymerase chain reaction in combination with a clone library and denaturing gradient gel electrophoresis (DGGE). Fungal cellobiohydrolase I (cbhI) genes in the soil were also characterized, and their diversity suggested the existence of a different cellulose decomposer. The DGGE profiles based on fungal internal transcribed spacer analysis showed different successions of fungal populations during residue decomposition. Members of Lecythophora and Sordariales were dominant in the early succession, while Hypocrea and Engyodontium were better adapted in the late succession. The succession of fungal communities might be related to changes of residue quality during decomposition. Collectively, sequences assigned to Ascomycota members were dominant at different stages of the fungal succession during decomposition, revealing that they were key drivers responsible for residue degradation in the arable soil tested. PMID:23840414

  5. The anamorphic genus Monotosporella (Ascomycota) from Eocene amber and from modern Agathis resin.

    PubMed

    Sadowski, Eva-Maria; Beimforde, Christina; Gube, Matthias; Rikkinen, Jouko; Singh, Hukam; Seyfullah, Leyla J; Heinrichs, Jochen; Nascimbene, Paul C; Reitner, Joachim; Schmidt, Alexander R

    2012-10-01

    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

  6. Rickia wasmannii increases the need for water in Myrmica scabrinodis (Ascomycota: Laboulbeniales; Hymenoptera: Formicidae).

    PubMed

    Báthori, Ferenc; Csata, Enikő; Tartally, András

    2015-03-01

    The order Laboulbeniales (Fungi, Ascomycota) is a little-studied group of microscopic ectoparasites of invertebrates, mostly insects. The effects of Laboulbeniales species on their hosts are mostly unknown. Rickia wasmannii Cavara, 1899 is a common Laboulbeniales fungus occurring in Europe and is currently known to be a parasite of at least eight Myrmica ant species. R.wasmannii serves as a good model organism for Laboulbeniales-host interactions, as this species covers the host in a very high density, and infected host individuals can be easily collected in high numbers. The effect of R. wasmannii on the survival rate of its most common host species, Myrmica scabrinodis Nylander 1846, was therefore investigated in a laboratory experiment on an individual level. To enhance the results, environmental stresses were simulated by depriving infected and uninfected workers of water and food. The survival of individuals was recorded hourly until the death of the last individual. Infected specimens were significantly more sensitive to the withdrawal of food and water than uninfected specimens. When we tested for water consumption, we found that infected ants spent more time consuming water than uninfected ants. Therefore, it is possible that infected ants must replace the loss of water. Based on these results, R. wasmannii substantially decreases the chances and time of survival of infected individuals, at least in resource-limited environments, which suggest that R. wasmannii has a negative effect on its host. PMID:25620725

  7. Molecular characterization and comparative virulence of Beauveria bassiana isolates (Ascomycota: Hypocreales) associated with the greenhouse shore fly, Scatella tenuicosta (Diptera: Ephydridae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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. bass...

  8. Seasonality of Laboulbenia phaeoxanthae (Ascomycota, Laboulbeniales) and its host Phaeoxantha aequinoctialis (Coleoptera, Carabidae) at a central Amazonian blackwater floodplain.

    PubMed

    Zerm, Matthias; Adis, Joachim

    2004-05-01

    Terrestrial invertebrates in central Amazonian floodplains must cope with annual long-term inundation. Parasites should be affected mainly indirectly through the specific life-cycles of their hosts. We studied the temporal structure of a beetle-fungus system at a central Amazonian blackwater floodplain (Rio Negro, Brazil). The host species Phaeoxantha aequinoctialis (Coleoptera, Carabidae, Cicindelinae) showed a seasonal, univoltine life-cycle triggered by the annual flood pulse. Infestation frequency of its fungal parasite, Laboulbenia phaeoxanthae (Ascomycota, Laboulbeniales), varied seasonally. However, the seasonality was opposed in host and parasite: the lowest infestation frequencies were observed during periods of highest beetle abundance and vice versa. Periods of lowest beetle abundance coincided with the end of the old generation, those with highest abundance with the appearance of new adults. The resulting annual patterns of a slow spread in the host population resembled the few records of temporal patterns from temperate regions. It is explicitly demonstrated that older adult female beetles are more frequently infested than younger ones. Future studies may reveal whether this is simply the result of specific host life-cycles (driven by a flood pulse, winter, or other factors), or might also be related to potentially easier infestation in older individuals. PMID:15230009

  9. Conservation and divergence of transcriptional coregulations between box C/D snoRNA and ribosomal protein genes in Ascomycota

    PubMed Central

    Diao, Li-Ting; Xiao, Zhen-Dong; Leng, Xiao-Min; Li, Bin; Li, Jun-Hao; Luo, Yu-Ping; Li, Si-Guang; Yu, Chuan-He; Zhou, Hui

    2014-01-01

    Coordinated assembly of the ribosome is essential for proper translational activity in eukaryotic cells. It is therefore critical to coordinate the expression of components of ribosomal programs with the cell's nutritional status. However, coordinating expression of these components is poorly understood. Here, by combining experimental and computational approaches, we systematically identified box C/D snoRNAs in four fission yeasts and found that the expression of box C/D snoRNA and ribosomal protein (RP) genes were orchestrated by a common Homol-D box, thereby ensuring a constant balance of these two genetic components. Interestingly, such transcriptional coregulations could be observed in most Ascomycota species and were mediated by different cis-regulatory elements. Via the reservation of cis elements, changes in spatial configuration, the substitution of cis elements, and gain or loss of cis elements, the regulatory networks of box C/D snoRNAs evolved to correspond with those of the RP genes, maintaining transcriptional coregulation between box C/D snoRNAs and RP genes. Our results indicate that coregulation via common cis elements is an important mechanism to coordinate expression of the RP and snoRNA genes, which ensures a constant balance of these two components. PMID:25002674

  10. Histopathological effects of Aspergillus clavatus (Ascomycota: Trichocomaceae) on larvae of the southern house mosquito, Culex quinquefasciatus (Diptera: Culicidae).

    PubMed

    Bawin, Thomas; Seye, Fawrou; Boukraa, Slimane; Zimmer, Jean-Yves; Raharimalala, Fara Nantenaina; Ndiaye, Mady; Compere, Philippe; Delvigne, Frank; Francis, Frédéric

    2016-04-01

    Aspergillus clavatus (Ascomycota: Trichocomaceae) was previously found to be an opportunistic pathogen of mosquitoes (Diptera: Culicidae). In the present study, the mechanism leading to its insecticidal activity was investigated regarding histological damages on Culex quinquefasciatus larvae exposed to A. clavatus spores. Multiple concentration assays using spore suspensions (0.5-2.5 × 10(8) spores ml(-1)) revealed 17.0-74.3 % corrected mortalities after 48 h exposure. Heat-deactivated spores induced a lower mortality compared to nonheated spores suggesting that insecticidal effects are actively exerted. Spore-treated and untreated larvae were prepared for light microscopy as well as for scanning and transmission electron microscopy. Spores failed to adhere to the external body surface (except the mouth parts) of these aquatic immature stages but progressively filled the digestive tract where their metabolism seemed to activate. In parallel, the internal tissues of the larvae, i.e. the midgut wall, the skeletal muscles, and the cuticle-secreting epidermis, were progressively destroyed between 8 and 24 h of exposure. These observations suggest that toxins secreted by active germinating spores of A. clavatus in the digestive tract altered the larval tissues, leading to their necrosis and causing larval death. Fungal proliferation and sporulation then occurred during a saprophytic phase. A. clavatus enzymes or toxins responsible for these pathogenic effects need to be identified in further studies before any use of this fungus in mosquito control. PMID:27020151

  11. First Detection of the Larval Chalkbrood Disease Pathogen Ascosphaera apis (Ascomycota: Eurotiomycetes: Ascosphaerales) in Adult Bumble Bees

    PubMed Central

    Maxfield-Taylor, Sarah A.; Mujic, Alija B.; Rao, Sujaya

    2015-01-01

    Fungi in the genus Ascosphaera (Ascomycota: Eurotiomycetes: Ascosphaerales) cause chalkbrood disease in larvae of bees. Here, we report the first-ever detection of the fungus in adult bumble bees that were raised in captivity for studies on colony development. Wild queens of Bombus griseocollis, B. nevadensis and B. vosnesenskii were collected and maintained for establishment of nests. Queens that died during rearing or that did not lay eggs within one month of capture were dissected, and tissues were examined microscopically for the presence of pathogens. Filamentous fungi that were detected were plated on artificial media containing broad spectrum antibiotics for isolation and identification. Based on morphological characters, the fungus was identified as Ascosphaera apis (Maasen ex Claussen) Olive and Spiltoir, a species that has been reported earlier only from larvae of the European honey bee, Apis mellifera, the Asian honey bee, Apis cerana, and the carpenter bee Xylocopa californica arizonensis. The identity of the fungus was confirmed using molecular markers and phylogenetic analysis. Ascosphaera apis was detected in queens of all three bumble bee species examined. Of 150 queens dissected, 12 (8%) contained vegetative and reproductive stages of the fungus. Both fungal stages were also detected in two workers collected from colonies with Ascosphaera-infected B. nevadensis queens. In this study, wild bees could have been infected prior to capture for rearing, or, the A. apis infection could have originated via contaminated European honey bee pollen fed to the bumble bees in captivity. Thus, the discovery of A. apis in adult bumble bees in the current study has important implications for commercial production of bumble bee colonies and highlights potential risks to native bees via pathogen spillover from infected bees and infected pollen. PMID:25885679

  12. Origin and diversification of major clades in parmelioid lichens (Parmeliaceae, Ascomycota) during the Paleogene inferred by Bayesian analysis.

    PubMed

    Amo de Paz, Guillermo; Cubas, Paloma; Divakar, Pradeep K; Lumbsch, H Thorsten; Crespo, Ana

    2011-01-01

    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

  13. First detection of the larval chalkbrood disease pathogen Ascosphaera apis (Ascomycota: Eurotiomycetes: Ascosphaerales) in adult bumble bees.

    PubMed

    Maxfield-Taylor, Sarah A; Mujic, Alija B; Rao, Sujaya

    2015-01-01

    Fungi in the genus Ascosphaera (Ascomycota: Eurotiomycetes: Ascosphaerales) cause chalkbrood disease in larvae of bees. Here, we report the first-ever detection of the fungus in adult bumble bees that were raised in captivity for studies on colony development. Wild queens of Bombus griseocollis, B. nevadensis and B. vosnesenskii were collected and maintained for establishment of nests. Queens that died during rearing or that did not lay eggs within one month of capture were dissected, and tissues were examined microscopically for the presence of pathogens. Filamentous fungi that were detected were plated on artificial media containing broad spectrum antibiotics for isolation and identification. Based on morphological characters, the fungus was identified as Ascosphaera apis (Maasen ex Claussen) Olive and Spiltoir, a species that has been reported earlier only from larvae of the European honey bee, Apis mellifera, the Asian honey bee, Apis cerana, and the carpenter bee Xylocopa californica arizonensis. The identity of the fungus was confirmed using molecular markers and phylogenetic analysis. Ascosphaera apis was detected in queens of all three bumble bee species examined. Of 150 queens dissected, 12 (8%) contained vegetative and reproductive stages of the fungus. Both fungal stages were also detected in two workers collected from colonies with Ascosphaera-infected B. nevadensis queens. In this study, wild bees could have been infected prior to capture for rearing, or, the A. apis infection could have originated via contaminated European honey bee pollen fed to the bumble bees in captivity. Thus, the discovery of A. apis in adult bumble bees in the current study has important implications for commercial production of bumble bee colonies and highlights potential risks to native bees via pathogen spillover from infected bees and infected pollen. PMID:25885679

  14. Origin and Diversification of Major Clades in Parmelioid Lichens (Parmeliaceae, Ascomycota) during the Paleogene Inferred by Bayesian Analysis

    PubMed Central

    Amo de Paz, Guillermo; Cubas, Paloma; Divakar, Pradeep K.; Lumbsch, H. Thorsten; Crespo, Ana

    2011-01-01

    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

  15. Miocene and Pliocene dominated diversification of the lichen-forming fungal genus Melanohalea (Parmeliaceae, Ascomycota) and Pleistocene population expansions

    PubMed Central

    2012-01-01

    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

  16. Multigene Molecular Phylogeny and Biogeographic Diversification of the Earth Tongue Fungi in the Genera Cudonia and Spathularia (Rhytismatales, Ascomycota)

    PubMed Central

    Ge, Zai-Wei; Yang, Zhu L.; Pfister, Donald H.; Carbone, Matteo; Bau, Tolgor; Smith, Matthew E.

    2014-01-01

    The family Cudoniaceae (Rhytismatales, Ascomycota) was erected to accommodate the “earth tongue fungi” in the genera Cudonia and Spathularia. There have been no recent taxonomic studies of these genera, and the evolutionary relationships within and among these fungi are largely unknown. Here we explore the molecular phylogenetic relationships within Cudonia and Spathularia using maximum likelihood and Bayesian inference analyses based on 111 collections from across the Northern Hemisphere. Phylogenies based on the combined data from ITS, nrLSU, rpb2 and tef-1α sequences support the monophyly of three main clades, the /flavida, /velutipes, and /cudonia clades. The genus Cudonia and the family Cudoniaceae are supported as monophyletic groups, while the genus Spathularia is not monophyletic. Although Cudoniaceae is monophyletic, our analyses agree with previous studies that this family is nested within the Rhytismataceae. Our phylogenetic analyses circumscribes 32 species-level clades, including the putative recognition of 23 undescribed phylogenetic species. Our molecular phylogeny also revealed an unexpectedly high species diversity of Cudonia and Spathularia in eastern Asia, with 16 (out of 21) species-level clades of Cudonia and 8 (out of 11) species-level clades of Spathularia. We estimate that the divergence time of the Cudoniaceae was in the Paleogene approximately 28 Million years ago (Mya) and that the ancestral area for this group of fungi was in Eastern Asia based on the current data. We hypothesize that the large-scale geological and climatic events in Oligocene (e.g. the global cooling and the uplift of the Tibetan plateau) may have triggered evolutionary radiations in this group of fungi in East Asia. This work provides a foundation for future studies on the phylogeny, diversity, and evolution of Cudonia and Spathularia and highlights the need for more molecular studies on collections from Europe and North America. PMID:25084276

  17. First record of Clonostachys rosea (Ascomycota: Hypocreales) as an entomopathogenic fungus of Oncometopia tucumana and Sonesimia grossa (Hemiptera: Cicadellidae) in Argentina.

    PubMed

    Toledo, A V; Virla, E; Humber, R A; Paradell, S L; Lastra, C C López

    2006-05-01

    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 record of C. rosea as an entomopathogenic fungus of two leafhoppers pest, Oncometopia tucumana and Sonesimia grossa (Hemiptera: Cicadellidae), in Argentina and evaluate the pathogenicity of C. rosea against them. PMID:16580016

  18. Who's getting around? Assessing species diversity and phylogeography in the widely distributed lichen-forming fungal genus Montanelia (Parmeliaceae, Ascomycota).

    PubMed

    Leavitt, Steven D; Divakar, Pradeep K; Ohmura, Yoshihito; Wang, Li-Song; Esslinger, Theodore L; Lumbsch, H Thorsten

    2015-09-01

    Brown parmelioid lichens comprise a number of distinct genera in one of the most species-rich families of lichen-forming fungi, Parmeliaceae (Ascomycota). In spite of their superficial similarity, a number of studies of brown parmelioids have provided important insight into diversification in lichen-forming fungi with cosmopolitan distributions. In this study we assess species diversity, biogeography and diversification of the genus Montanelia, which includes alpine to temperate saxicolous species. We sampled each of the five known species, four of which are known from broad, intercontinental distributions. In order to identify potential biogeographical patterns, each broadly distributed species was represented by individuals collected across their intercontinental distributions. Molecular sequence data were generated for six loci, including three nuclear protein-coding markers (MCM7, RPB1, and RPB2), two nuclear ribosomal markers (ITS and nrLSU), and a fragment of the mitochondrial small subunit. We used three sequence-based species delimitations methods to validate traditional, phenotype-based species and circumscribe previously unrecognized species-level lineages in Montanelia. Relationships among putative lineages and divergence times were estimated within a coalescent-based multi-locus species tree framework. Based on the results of the species delimitation analyses, we propose that the genus Montanelia is likely comprised of six to nine species-level lineages, including previously unrecognized species-level diversity in the nominal taxa M. panniformis and M. tominii. In contrast, molecular sequence data suggest that M. predisjuncta may be conspecific with the widespread taxon M. disjuncta in spite of distinct morphological differences. The rate-based age estimation of the most recent common ancestor of Montanelia (ca. 23.1Ma) was similar to previous estimates based on the fossil record. Furthermore, our data suggest that diversification in Montanelia occurred

  19. A monograph of Allantonectria, Nectria, and Pleonectria (Nectriaceae, Hypocreales, Ascomycota) and their pycnidial, sporodochial, and synnematous anamorphs

    PubMed Central

    Hirooka, Y.; Rossman, A.Y.; Samuels, G.J.; Lechat, C.; Chaverri, P.

    2012-01-01

    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

  20. A new species of Phyllopsora (Lecanorales, lichen-forming Ascomycota) from Dominican amber, with remarks on the fossil history of lichens.

    PubMed

    Rikkinen, Jouko; Poinar, George O

    2008-01-01

    Phyllopsora dominicanus sp. nov. (Bacidiaceae, Lecanorales, lichen-forming Ascomycota) is described and illustrated from Dominican amber. The diagnostic features of the lichen include a minute subfolious thallus of lacinulate, ascending squamules, a well-developed upper cortex, and a net-like pseudocortex on the lower surface. The algal symbionts are unicellular green algae, forming a distinct layer immediately below the upper cortex. The fossil demonstrates that distinguishing features of Phyllopsora have remained unchanged for tens of millions of years. The fossil also provides the first detailed views of mycobiont-photobiont contacts in Tertiary green algal lichens. The mycobiont hyphae formed apical and intercalary appressoria by pressing closely against the photobiont cells. This indicates that a conserved maintenance of structure is also seen in the fine details of the fungal-algal interface. PMID:18319239

  1. Fodinomyces uranophilus gen. nov. sp. nov. and Coniochaeta fodinicola sp. nov., two uranium mine-inhabiting Ascomycota fungi from northern Australia.

    PubMed

    Vázquez-Campos, Xabier; Kinsela, Andrew S; Waite, T David; Collins, Richard N; Neilan, Brett A

    2014-01-01

    Seven acidophilic/acidotolerant fungal strains were characterized from samples of process waters (raffinate) at one of Australia's largest uranium mines, the Ranger Mine in Northern Territory. They were isolated from raffinate, which typically were very acidic (pH 1.7-1.8) and contained high concentrations of total dissolved/colloidal salts (> 100 g/L). Five of the isolates correspond to two new acidotolerant Ascomycota fungi. The first is a member of a new genus, here described as Fodinomyces (Teratosphaeriaceae, Capnodiales, Dothideomycetes) and does not show clear close affiliation with any other described fungus in the scientific literature. The second belongs to the genus Coniochaeta (Coniochaetaceae, Coniochaetales, Sordariomycetes) and is closely related to Coniochaeta hansenii. PMID:25143478

  2. Multilocus phylogeny of the lichen-forming fungal genus Melanohalea (Parmeliaceae, Ascomycota): insights on diversity, distributions, and a comparison of species tree and concatenated topologies.

    PubMed

    Leavitt, Steven D; Esslinger, Theodore L; Spribille, Toby; Divakar, Pradeep K; Thorsten Lumbsch, H

    2013-01-01

    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

  3. Rapid discovery and functional characterization of terpene synthases from four endophytic xylariaceae

    DOE PAGESBeta

    Wu, Weihua; Tran, William; Taatjes, Craig A.; Alonso-Gutierrez, Jorge; Lee, Taek Soon; Gladden, John M.; Hamberger, Bjorn

    2016-02-17

    Endophytic fungi are ubiquitous plant endosymbionts that establish complex and poorly understood relationships with their host organisms. Many endophytic fungi are known to produce a wide spectrum of volatile organic compounds (VOCs) with potential energy applications, which have been described as "mycodiesel". Many of these mycodiesel hydrocarbons are terpenes, a chemically diverse class of compounds produced by many plants, fungi, and bacteria. Due to their high energy densities, terpenes, such as pinene and bisabolene, are actively being investigated as potential "drop-in" biofuels for replacing diesel and aviation fuel. In this study, we rapidly discovered and characterized 26 terpene synthases (TPSs)more » derived from four endophytic fungi known to produce mycodiesel hydrocarbons. The TPS genes were expressed in an E. coli strain harboring a heterologous mevalonate pathway designed to enhance terpene production, and their product profiles were determined using Solid Phase Micro-Extraction (SPME) and GC-MS. Lastly, out of the 26 TPS’s profiled, 12 TPS’s were functional, with the majority of them exhibiting both monoterpene and sesquiterpene synthase activity.« less

  4. Rapid Discovery and Functional Characterization of Terpene Synthases from Four Endophytic Xylariaceae

    PubMed Central

    Wu, Weihua; Tran, William; Taatjes, Craig A.; Alonso-Gutierrez, Jorge; Lee, Taek Soon; Gladden, John M.

    2016-01-01

    Endophytic fungi are ubiquitous plant endosymbionts that establish complex and poorly understood relationships with their host organisms. Many endophytic fungi are known to produce a wide spectrum of volatile organic compounds (VOCs) with potential energy applications, which have been described as "mycodiesel". Many of these mycodiesel hydrocarbons are terpenes, a chemically diverse class of compounds produced by many plants, fungi, and bacteria. Due to their high energy densities, terpenes, such as pinene and bisabolene, are actively being investigated as potential "drop-in" biofuels for replacing diesel and aviation fuel. In this study, we rapidly discovered and characterized 26 terpene synthases (TPSs) derived from four endophytic fungi known to produce mycodiesel hydrocarbons. The TPS genes were expressed in an E. coli strain harboring a heterologous mevalonate pathway designed to enhance terpene production, and their product profiles were determined using Solid Phase Micro-Extraction (SPME) and GC-MS. Out of the 26 TPS’s profiled, 12 TPS’s were functional, with the majority of them exhibiting both monoterpene and sesquiterpene synthase activity. PMID:26885833

  5. Rapid Discovery and Functional Characterization of Terpene Synthases from Four Endophytic Xylariaceae.

    PubMed

    Wu, Weihua; Tran, William; Taatjes, Craig A; Alonso-Gutierrez, Jorge; Lee, Taek Soon; Gladden, John M

    2016-01-01

    Endophytic fungi are ubiquitous plant endosymbionts that establish complex and poorly understood relationships with their host organisms. Many endophytic fungi are known to produce a wide spectrum of volatile organic compounds (VOCs) with potential energy applications, which have been described as "mycodiesel". Many of these mycodiesel hydrocarbons are terpenes, a chemically diverse class of compounds produced by many plants, fungi, and bacteria. Due to their high energy densities, terpenes, such as pinene and bisabolene, are actively being investigated as potential "drop-in" biofuels for replacing diesel and aviation fuel. In this study, we rapidly discovered and characterized 26 terpene synthases (TPSs) derived from four endophytic fungi known to produce mycodiesel hydrocarbons. The TPS genes were expressed in an E. coli strain harboring a heterologous mevalonate pathway designed to enhance terpene production, and their product profiles were determined using Solid Phase Micro-Extraction (SPME) and GC-MS. Out of the 26 TPS's profiled, 12 TPS's were functional, with the majority of them exhibiting both monoterpene and sesquiterpene synthase activity. PMID:26885833

  6. New Elaphomyces species (Elaphomycetaceae, Eurotiales, Ascomycota) from Guyana.

    PubMed

    Castellano, Michael A; Henkel, Terry W; Miller, Steven L; Smith, Matthew E; Aime, M Catherine

    2012-01-01

    Elaphomyces compleximurus sp. nov. and E. digitatus sp. nov. are described from the Pakaraima Mountains of Guyana. Macromorphological, micromorphological, habitat and DNA sequence data are provided for each new species. This is the first report of Elaphomyces ascomata associated with ectomycorrhizal members of the Fabaceae and also for the genus from the lowland South American tropics. PMID:22505430

  7. Understanding phenotypical character evolution in parmelioid lichenized fungi (Parmeliaceae, Ascomycota).

    PubMed

    Divakar, Pradeep K; Kauff, Frank; Crespo, Ana; Leavitt, Steven D; Lumbsch, H Thorsten

    2013-01-01

    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

  8. Understanding Phenotypical Character Evolution in Parmelioid Lichenized Fungi (Parmeliaceae, Ascomycota)

    PubMed Central

    Divakar, Pradeep K.; Kauff, Frank; Crespo, Ana; Leavitt, Steven D.; Lumbsch, H. Thorsten

    2013-01-01

    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

  9. Altitudinal patterns of Stereocaulon (Lichenized Ascomycota) in China

    NASA Astrophysics Data System (ADS)

    Huang, Man-Rong

    2010-03-01

    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.

  10. Cladonia peziziformis (Lichenized Ascomycota, Cladoniaceae) New to Korea.

    PubMed

    Wang, Xin Yu; Hur, Hyun; Lee, You Mi; Bae, Funny; Koh, Young Jin; Hur, Jae-Seoun

    2008-09-01

    Cladonia peziziformis (With.) J.R. Laundon was collected from Baega mountain, Jeonnam Province, Korea in 2008. It is characterized by short and slender podetia with verruculose surface, split along the sides. Apothecia large, pale brown, always growing on the top of the podetia. Primary squamules shell-like, thick, and convex. Fumarprotocetraric acid contained in thallus. This is the first record of this species in Korea. PMID:23997624

  11. Pupal Mortality and Adult Emergence of Western Cherry Fruit Fly (Diptera: Tephritidae) Exposed to the Fungus Muscodor albus (Xylariales: Xylariaceae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Western cherry fruit fly, Rhagoletis indifferens Curran, is a major pest of sweet cherry, Prunus avium (L.) L., that is conventionally controlled using insecticides. One alternative to the use of insecticides for fly control could be fumigation of the fly’s overwintering habitat using the fungus Mus...

  12. Molecular phylogenetics of Pleosporales: Melanommataceae and Lophiostomataceae re-circumscribed (Pleosporomycetidae, Dothideomycetes, Ascomycota)

    PubMed Central

    Mugambi, G.K.; Huhndorf, S.M.

    2009-01-01

    The classification of Pleosporales has posed major challenges due to the lack of clear understanding of the importance of the morphological characters used to distinguish between different groups in the order. This has resulted in varied taxonomic treatments of many families in the group including Melanommataceae and Lophiostomataceae. In this study we employ two nuclear DNA gene markers, nuclear ribosomal large subunit DNA and translation elongation factor 1-alpha in order to examine the molecular phylogenetics of Pleosporales with strong emphasis on the families Melanommataceae and Lophiostomataceae. Phylogenetic analyses recovered Melanommataceae, Lophiostomataceae, Hypsostromataceae, and a few others as strongly supported clades within the Pleosporales. Melanommataceae as currently circumscribed was found to be polyphyletic. The genera Byssosphaeria, Melanomma, and Pseudotrichia were recovered within the family, while others such as Ostropella and Xenolophium nested outside in a weakly supported group along with Platystomum compressum and Pseudotrichia guatopoensis that may correspond to the family Platystomaceae. The genus Byssosphaeria was recovered as a strongly supported group within the Melanommataceae while Melanomma was weakly supported with unclear relationships among the species. The genera Herpotrichia and Bertiella were also found to belong in the Melanommataceae. Lophiostomataceae occurs as a strongly supported group but its concept is here expanded to include a new genus Misturatosphaeria that bears morphology traditionally not known to occur in the family. The strongly supported clade of Misturatosphaeria contains nine species that have gregarious, papillate ascomata with lighter coloured apices and plugged ostioles and that vary in ascospore morphology from 1- to 3-septate to muriform. Along with a strongly supported Lophiostoma clade, also within the family are Thyridaria macrostomoides based on new sequences from Kenyan collections and Massariosphaeria triseptata, M. grandispora, Westerdykella cylindrica and Preussia terricola based on GenBank sequences. The family Hypsostromataceae was recovered as a strongly supported monophyletic group nested within the Pleosporales. PMID:20169025

  13. Seven wood-inhabiting new species of the genus Trichoderma (Fungi, Ascomycota) in Viride clade.

    PubMed

    Qin, Wen-Tao; Zhuang, Wen-Ying

    2016-01-01

    More than 200 recent collections of Trichoderma from China were examined and 16 species belonging to the Viride clade were identified based on integrated studies of phenotypic and molecular data. Among them, seven wood-inhabiting new species, T. albofulvopsis, T. densum, T. laevisporum, T. sinokoningii, T. sparsum, T. sphaerosporum and T. subviride, are found. They form trichoderma- to verticillium-like conidiophores, lageniform to subulate phialides and globose to ellipsoidal conidia, but vary greatly in colony features, growth rates, and sizes of phialides and conidia. To explore their taxonomic positions, the phylogenetic tree including all the known species of the Viride clade is constructed based on sequence analyses of the combined RNA polymerase II subunit b and translation elongation factor 1 alpha exon genes. Our results indicated that the seven new species were well-located in the Koningii, Rogersonii and Neorufum subclades as well as a few independent terminal branches. They are clearly distinguishable from any existing species. Morphological distinctions and sequence divergences between the new species and their close relatives were discussed. PMID:27245694

  14. Proposal to conserve the name Bipolaris against Cochliobolus (Ascomycota: Pleosporales: Pleosporaceae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The fungal genera Bipolaris Shoemaker and Cochliobolus Drechsler have been applied to economically important plant pathogens causing diseases of cereal crops worldwide, especially southern corn leaf blight. There are major accounts of these genera including those incorporating molecular phylogenetic...

  15. Common Microfungi of Costa Rica and Other Tropical Regions: An Illustrated Guide (Ascomycota, Pezizomycotina, Sordariomycetes)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    One hundred and sixteen common tropical pyrenomycete fungi are described and illustrated in a bilingual (Spanish/English) guide. The pyrenomycete fungi include some of the most important plant and human pathogens and also are highly significant in nutrient cycling in tropical forest ecosystems. The...

  16. Extreme phenotypic variation in Cetraria aculeata (lichenized Ascomycota): adaptation or incidental modification?

    PubMed Central

    Pérez-Ortega, Sergio; Fernández-Mendoza, Fernando; Raggio, José; Vivas, Mercedes; Ascaso, Carmen; Sancho, Leopoldo G.; Printzen, Christian; de los Ríos, Asunción

    2012-01-01

    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. PMID:22451601

  17. Assessment of ectomycorrhizal fungal communities in the natural habitats of Tuber magnatum (Ascomycota, Pezizales).

    PubMed

    Leonardi, M; Iotti, M; Oddis, M; Lalli, G; Pacioni, G; Leonardi, P; Maccherini, S; Perini, C; Salerni, E; Zambonelli, A

    2013-07-01

    The ectomycorrhizal (ECM) fungal communities of four natural Tuber magnatum truffle grounds, located in different Italian regions (Abruzzo, Emilia-Romagna, Molise, and Tuscany), were studied. The main objective of this study was to characterize and compare the ECM fungal communities in the different regions and in productive (where T. magnatum ascomata were found) and nonproductive points. More than 8,000 (8,100) colonized root tips were counted in 73 soil cores, and 129 operational taxonomic units were identified using morphological and molecular methods. Although the composition of the ECM fungal communities studied varied, we were able to highlight some common characteristics. The most plentiful ECM fungal taxa belong to the Thelephoraceae and Sebacinaceae families followed by Inocybaceae and Russulaceae. Although several ectomycorrhizas belonging to Tuber genus were identified, no T. magnatum ectomycorrhizas were found. The putative ecological significance of some species is discussed. PMID:23299664

  18. Delimitation of Neonectria and Cylindrocarpon (Nectriaceae, Hypocreales, Ascomycota) and related genera with Cylindrocarpon-like anamorphs

    PubMed Central

    Chaverri, P.; Salgado, C.; Hirooka, Y.; Rossman, A.Y.; Samuels, G.J.

    2011-01-01

    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. PMID:21523189

  19. An Integrative Approach for Understanding Diversity in the Punctelia rudecta Species Complex (Parmeliaceae, Ascomycota).

    PubMed

    Alors, David; Lumbsch, H Thorsten; Divakar, Pradeep K; Leavitt, Steven D; Crespo, Ana

    2016-01-01

    High levels of cryptic diversity have been documented in lichenized fungi, especially in Parmeliaceae, and integrating various lines of evidence, including coalescent-based species delimitation approaches, help establish more robust species circumscriptions. In this study, we used an integrative taxonomic approach to delimit species in the lichen-forming fungal genus Punctelia (Parmeliaceae), with a particular focus on the cosmopolitan species P. rudecta. Nuclear, mitochondrial ribosomal DNA and protein-coding DNA sequences were analyzed in phylogenetic and coalescence-based frameworks. Additionally, morphological, ecological and geographical features of the sampled specimens were evaluated. Five major strongly supported monophyletic clades were recognized in the genus Punctelia, and each clade could be characterized by distinct patterns in medullary chemistry. Punctelia rudecta as currently circumscribed was shown to be polyphyletic. A variety of empirical species delimitation methods provide evidence for a minimum of four geographically isolated species within the nominal taxon Punctelia rudecta, including a newly described saxicolous species, P. guanchica, and three corticolous species. In order to facilitate reliable sample identification for biodiversity, conservation, and air quality bio-monitoring research, these three species have been epitypified, in addition to the description of a new species. PMID:26863231

  20. An Integrative Approach for Understanding Diversity in the Punctelia rudecta Species Complex (Parmeliaceae, Ascomycota)

    PubMed Central

    Alors, David; Lumbsch, H. Thorsten; Divakar, Pradeep K.; Leavitt, Steven D.; Crespo, Ana

    2016-01-01

    High levels of cryptic diversity have been documented in lichenized fungi, especially in Parmeliaceae, and integrating various lines of evidence, including coalescent-based species delimitation approaches, help establish more robust species circumscriptions. In this study, we used an integrative taxonomic approach to delimit species in the lichen-forming fungal genus Punctelia (Parmeliaceae), with a particular focus on the cosmopolitan species P. rudecta. Nuclear, mitochondrial ribosomal DNA and protein-coding DNA sequences were analyzed in phylogenetic and coalescence-based frameworks. Additionally, morphological, ecological and geographical features of the sampled specimens were evaluated. Five major strongly supported monophyletic clades were recognized in the genus Punctelia, and each clade could be characterized by distinct patterns in medullary chemistry. Punctelia rudecta as currently circumscribed was shown to be polyphyletic. A variety of empirical species delimitation methods provide evidence for a minimum of four geographically isolated species within the nominal taxon Punctelia rudecta, including a newly described saxicolous species, P. guanchica, and three corticolous species. In order to facilitate reliable sample identification for biodiversity, conservation, and air quality bio-monitoring research, these three species have been epitypified, in addition to the description of a new species. PMID:26863231

  1. Upper cortex anatomy corroborates phylogenetic hypothesis in species of Physconia (Ascomycota, Lecanoromycetes).

    PubMed

    Divakar, Pradeep K; Amo De Paz, Guillermo; Del Prado, Ruth; Esslinger, Theodore L; Crespo, Ana

    2007-11-01

    A phylogenetic and taxonomic study of the Physconia distorta morphotype complex was undertaken using ITS nu-rDNA as a molecular marker to re-evaluate this group. The analysis incorporated several samples of European P. distorta and also of American and European populations, recently named as P. americana. The phylogenetic analysis revealed that P. distorta and the European population of P. americana form two monophyletic and partially sympatric species and that both are distinct from the American species P. americana. Because differences in upper cortex anatomy had been used in establishing P. americana as distinct from P. distorta, the anatomy of the upper cortex was restudied in all three of these taxa, and notable differences were revealed. Our study confirmed that the upper cortex of P. distorta is prosoplectenchymatous with thick hyphal cell walls and narrow lumina, and that American specimens of P. americana have a typical paraplectenchymatous upper cortex. The cortex anatomy of both of these looks essentially the same in both longitudinal and transverse sections. Conversely, the European specimens that have been called P. americana are different from both of these. The cells of the upper cortex are rather thin walled, and in transverse lobe sections the cortex closely resembles a paraplectenchyma. However, in longitudinal lobe sections these thin walled cells can be seen to be elongate and ramified, obviously hyphal in nature, and better meeting the criteria of a prosoplectenchyma. The results confirmed the evolutionary pattern and taxonomic assessment of the anatomy of the upper cortex in the genus Physconia and revealed a common undescribed species (P. thorstenii sp. nov.) that can be added to the North African and Southern Euro-Asiatic lichen flora. PMID:18023166

  2. Delimitation of Neonectria and Cylindrocarpon (Nectriaceae, Hypocreales, Ascomycota) and related genera with Cylindrocarpon-like anamorphs.

    PubMed

    Chaverri, P; Salgado, C; Hirooka, Y; Rossman, A Y; Samuels, G J

    2011-01-01

    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 Neonectriasensu stricto and Cylindrocarponsensu stricto are phylogenetically congeneric. In addition, morphological and molecular data accumulated over several years have indicated that Neonectria sensu lato and Cylindrocarponsensu 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 Neonectriasensu 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/Cylindrocarponsensu 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. PMID:21523189

  3. Delimitation of Neonectria and Cylindrocarpon (Nectriaceae, Hypocreales, Ascomycota) and related genera with Cylindrocarpon-like anamorphs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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. Forty years ago Booth divided Cylindrocarpon into four groups defined by p...

  4. Biogeography and Genetic Structure in Populations of a Widespread Lichen (Parmelina tiliacea, Parmeliaceae, Ascomycota).

    PubMed

    Núñez-Zapata, Jano; Cubas, Paloma; Hawksworth, David L; Crespo, Ana

    2015-01-01

    The genetic diversity and population structure of the foliose lichenized fungus Parmelina tiliacea has been analyzed through its geographical range, including samples from Macaronesia (Canary Islands), the Mediterranean, and Eurosiberia. DNA sequences from the nuclear ribosomal internal transcribed spacer, the mitochondrial large subunit ribosomal RNA gene, and the translation elongation factor 1-α were used as molecular markers. The haplotypes of the three markers and the molecular variance analyses of multilocus haplotypes showed the highest diversity in the Canary Islands, while restricted haplotypes occurred at high frequencies in Mediterranean coastal samples. The multilocus haplotypes formed three unevenly distributed clusters (clusters 1-3). In the Canary Islands all the haplotypes were present in a similar proportion, while the coastal Mediterranean sites had almost exclusively haplotypes of cluster 3; cluster 2 predominated in inland Mediterranean sites; and cluster 1 was more abundant in central and northern Europe (Eurosiberian area). The distribution of clusters is partially explained by climatic factors, and its interaction with local spatial structure, but much of the variation remains unexplained. The high frequency of individuals in the Canary Islands with haplotypes shared with other areas suggests that could be a refugium of genetic diversity, and the high frequency of individuals of the Mediterranean coastal sites with restricted haplotypes indicates that gene flow to contiguous areas may be restricted. This is significant for the selection of areas for conservation purposes, as those with most genetic variation may reflect historical factors and biological properties of the species. PMID:25961726

  5. Phylogeny and taxonomic revision of Thelonectria discophora (Ascomycota, Hypocreales, Nectriaceae) species complex

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Thelonectria discophora (Thelonectria, Nectriaceae, Hypocreales) is a conspicuous group of saprobic fungi on decaying plant material, characterized by red perithecia each with a broad mammiform (nipple-like) apex. The anamorphic state is characterized by a cylindrocarpon-like morphology, with 3–5 se...

  6. Nine new cytochalasan alkaloids from Chaetomium globosum TW1-1 (Ascomycota, Sordariales).

    PubMed

    Chen, Chunmei; Tong, Qingyi; Zhu, Hucheng; Tan, Dongdong; Zhang, Jinwen; Xue, Yongbo; Yao, Guangmin; Luo, Zengwei; Wang, Jianping; Wang, Yanyan; Zhang, Yonghui

    2016-01-01

    Chemical investigation on the methanol extract of Chaetomium globosum TW1-1, a fungus isolated from the common pillbug (Armadillidium vulgare), has resulted in the isolation of nine new highly oxygenated cytochalasan alkaloids, armochaetoglobins S-Z (1 and 3-9) and 7-O-acetylarmochaetoglobin S (2), together with eight structurally related known analogues (10-17). Their structures and absolute configurations were elucidated by spectroscopic analyses. Among them, compound 2 presents to be the first member of chaetoglobosin family with an acetyl group, and compounds 3 represents the first chaetoglobosin characterized by an 2',3'-epoxy-indole moiety. The discovery of these new compounds revealed the largely untapped chemical diversity of cytochalasans and enriched their chemical research. Compounds 1-9 were evaluated for their cytotoxic activities against five human cancer cell lines, and compounds 8 and 9 exhibited significant cytotoxic activities with IC50 values ranging from 10.45 to 30.42 μM. PMID:26739896

  7. Nine new cytochalasan alkaloids from Chaetomium globosum TW1-1 (Ascomycota, Sordariales)

    PubMed Central

    Chen, Chunmei; Tong, Qingyi; Zhu, Hucheng; Tan, Dongdong; Zhang, Jinwen; Xue, Yongbo; Yao, Guangmin; Luo, Zengwei; Wang, Jianping; Wang, Yanyan; Zhang, Yonghui

    2016-01-01

    Chemical investigation on the methanol extract of Chaetomium globosum TW1-1, a fungus isolated from the common pillbug (Armadillidium vulgare), has resulted in the isolation of nine new highly oxygenated cytochalasan alkaloids, armochaetoglobins S–Z (1 and 3–9) and 7-O-acetylarmochaetoglobin S (2), together with eight structurally related known analogues (10–17). Their structures and absolute configurations were elucidated by spectroscopic analyses. Among them, compound 2 presents to be the first member of chaetoglobosin family with an acetyl group, and compounds 3 represents the first chaetoglobosin characterized by an 2′,3′-epoxy-indole moiety. The discovery of these new compounds revealed the largely untapped chemical diversity of cytochalasans and enriched their chemical research. Compounds 1–9 were evaluated for their cytotoxic activities against five human cancer cell lines, and compounds 8 and 9 exhibited significant cytotoxic activities with IC50 values ranging from 10.45 to 30.42 μM. PMID:26739896

  8. Hypoxylon pulicicidum sp. nov. (Ascomycota, Xylariales), a Pantropical Insecticide-Producing Endophyte

    PubMed Central

    Bills, Gerald F.; González-Menéndez, Victor; Martín, Jesús; Platas, Gonzalo; Fournier, Jacques; Peršoh, Derek; Stadler, Marc

    2012-01-01

    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. PMID:23056404

  9. Taxonomic Study on the Lichen Genus Cetrelia (Lecanorales, Ascomycota) in South Korea

    PubMed Central

    Luo, Heng; Wei, Xin Li; Han, Keon Seon; Koh, Young Jin

    2007-01-01

    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. PMID:24015081

  10. Study on the ice nucleation activity of fungal spores (Ascomycota and Basidiomycota)

    NASA Astrophysics Data System (ADS)

    Pummer, B. G.; Atanasova, L.; Bauer, H.; Bernardi, J.; Druzhinina, I. S.; Grothe, H.

    2012-04-01

    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 [3] 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. [1] Kieft TL and Ruscetti T: J. Bacteriol. 172, 3519-3523, 1990. [2] Pouleur S et al.: Appl. Environ. Microbiol., 58, 2960-2964, 1992. [3] Marcolli C et al.: Atmos. Chem. Phys. 7, 5081-5091, 2007.

  11. Biogeography and Genetic Structure in Populations of a Widespread Lichen (Parmelina tiliacea, Parmeliaceae, Ascomycota)

    PubMed Central

    Hawksworth, David L.; Crespo, Ana

    2015-01-01

    The genetic diversity and population structure of the foliose lichenized fungus Parmelina tiliacea has been analyzed through its geographical range, including samples from Macaronesia (Canary Islands), the Mediterranean, and Eurosiberia. DNA sequences from the nuclear ribosomal internal transcribed spacer, the mitochondrial large subunit ribosomal RNA gene, and the translation elongation factor 1-α were used as molecular markers. The haplotypes of the three markers and the molecular variance analyses of multilocus haplotypes showed the highest diversity in the Canary Islands, while restricted haplotypes occurred at high frequencies in Mediterranean coastal samples. The multilocus haplotypes formed three unevenly distributed clusters (clusters 1-3). In the Canary Islands all the haplotypes were present in a similar proportion, while the coastal Mediterranean sites had almost exclusively haplotypes of cluster 3; cluster 2 predominated in inland Mediterranean sites; and cluster 1 was more abundant in central and northern Europe (Eurosiberian area). The distribution of clusters is partially explained by climatic factors, and its interaction with local spatial structure, but much of the variation remains unexplained. The high frequency of individuals in the Canary Islands with haplotypes shared with other areas suggests that could be a refugium of genetic diversity, and the high frequency of individuals of the Mediterranean coastal sites with restricted haplotypes indicates that gene flow to contiguous areas may be restricted. This is significant for the selection of areas for conservation purposes, as those with most genetic variation may reflect historical factors and biological properties of the species. PMID:25961726

  12. Transoceanic Dispersal and Subsequent Diversification on Separate Continents Shaped Diversity of the Xanthoparmelia pulla Group (Ascomycota)

    PubMed Central

    de Paz, Guillermo Amo; Cubas, Paloma; Crespo, Ana; Elix, John A.; Lumbsch, H. Thorsten

    2012-01-01

    In traditional morphology-based concepts many species of lichenized fungi have world-wide distributions. Molecular data have revolutionized the species delimitation in lichens and have demonstrated that we underestimated the diversity of these organisms. The aim of this study is to explore the phylogeography and the evolutionary patterns of the Xanthoparmelia pulla group, a widespread group of one of largest genera of macrolichens. We used a dated phylogeny based on nuITS and nuLSU rDNA sequences and performed an ancestral range reconstruction to understand the processes and explain their current distribution, dating the divergence of the major lineages in the group. An inferred age of radiation of parmelioid lichens and the age of a Parmelia fossil were used as the calibration points for the phylogeny. The results show that many species of the X. pulla group as currently delimited are polyphyletic and five major lineages correlate with their geographical distribution and the biosynthetic pathways of secondary metabolites. South Africa is the area where the X. pulla group radiated during the Miocene times, and currently is the region with the highest genetic, morphological and chemical diversity. From this center of radiation the different lineages migrated by long-distance dispersal to others areas, where secondary radiations developed. The ancestral range reconstruction also detected that a secondary lineage migrated from Australia to South America via long-distance dispersal and subsequent continental radiation. PMID:22745810

  13. Inoculation of coffee plants with the fungal entomopathogen Beauveria bassiana (Ascomycota: Hypocreales)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 per...

  14. Lichen-Associated Fungal Community in Hypogymnia hypotrypa (Parmeliaceae, Ascomycota) Affected by Geographic Distribution and Altitude

    PubMed Central

    Wang, Yanyan; Zheng, Yong; Wang, Xinyu; Wei, Xinli; Wei, Jiangchun

    2016-01-01

    Lichen-associated fungal species have already been investigated in almost all the main growth forms of lichens, however, whether or not they are homogeneous and constant within each lichen species are still inconclusive. Moreover, the related ecological factors to affect and structure the fungal composition have been poorly studied. In order to answer these questions, we took Hypogymnia hypotrypa as a model to study the relationship between the lichen-associated fungal composition and two ecological factors, i.e., site and altitude, using the method of IlluminaMiSeq sequencing. Four different sites and two levels of altitude were included in this study, and the effects of site and altitude on fungal community composition were assessed at three levels, i.e., operational taxonomic unit (OTU), class and phylum. The results showed that a total of 50 OTUs were identified and distributed in 4 phyla, 13 classes, and 20 orders. The lichen-associated fungal composition within H. hypotrypa were significantly affected by both site and altitude at OTU and class levels, while at the phylum level, it was only affected by altitude. While the lichen associated fungal communities were reported to be similar with endophytic fungi of the moss, our results indicated the opposite results in some degree. But whether there exist specific OTUs within this lichen species corresponding to different sites and altitudes is still open. More lichen species and ecological factors would be taken into the integrated analyses to address these knowledge gaps in the near future. PMID:27547204

  15. Screening pentachlorophenol degradation ability by environmental fungal strains belonging to the phyla Ascomycota and Zygomycota.

    PubMed

    Carvalho, Mariana B; Martins, Isabel; Leitão, Maria C; Garcia, Helga; Rodrigues, Cátia; San Romão, Vitória; McLellan, Iain; Hursthouse, Andrew; Silva Pereira, Cristina

    2009-10-01

    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

  16. A note on the lichen genus ramalina (ramalinaceae, ascomycota) in the hengduan mountains in china.

    PubMed

    Oh, Soon-Ok; Wang, Xin Yu; Wang, Li Song; Liu, Pei Gui; Hur, Jae-Seoun

    2014-09-01

    On the basis of extensive field investigation and a series of herbarium specimen identifications, we present and discuss the descriptions and distribution of 22 species of Ramalina found in the Hengduan Mountains of southwestern China. In this revisionary study, representatives of the Ramalina genus, including R. americana, R. confirmata, R. dendriscoides, R. obtusata, R. pacifica, R. pentecostii, R. peruviana, R. shinanoana, and R. subcomplanata are found for the first time in this area. In addition, R. holstii is reported for the first time China. Finally, a newly described species identified as Ramalina hengduanshanensis S. O. Oh & L. S. Wang is reported. It is characterized as growing from a narrow holdfast, solid, sparsely or richly and irregularly dichotomously branched, palmate and flattened lobes with distinctly dorsiventral appearance, surface rugose to reticulate, surface rugosely cracked, dense chondroid tissue, helmet shaped soralia at the tip. The species grows on rock and tree at the highest elevations in this area. Although very few lichen species belonging to the genus Ramalina have been collected above 4,000 m, this new species is found at this elevation. We present detailed morphological, anatomical, and chemical descriptions of this species along with molecular phylogenetic analysis of the internal transcribed spacer rDNA sequences. PMID:25346599

  17. Lichen-Associated Fungal Community in Hypogymnia hypotrypa (Parmeliaceae, Ascomycota) Affected by Geographic Distribution and Altitude.

    PubMed

    Wang, Yanyan; Zheng, Yong; Wang, Xinyu; Wei, Xinli; Wei, Jiangchun

    2016-01-01

    Lichen-associated fungal species have already been investigated in almost all the main growth forms of lichens, however, whether or not they are homogeneous and constant within each lichen species are still inconclusive. Moreover, the related ecological factors to affect and structure the fungal composition have been poorly studied. In order to answer these questions, we took Hypogymnia hypotrypa as a model to study the relationship between the lichen-associated fungal composition and two ecological factors, i.e., site and altitude, using the method of IlluminaMiSeq sequencing. Four different sites and two levels of altitude were included in this study, and the effects of site and altitude on fungal community composition were assessed at three levels, i.e., operational taxonomic unit (OTU), class and phylum. The results showed that a total of 50 OTUs were identified and distributed in 4 phyla, 13 classes, and 20 orders. The lichen-associated fungal composition within H. hypotrypa were significantly affected by both site and altitude at OTU and class levels, while at the phylum level, it was only affected by altitude. While the lichen associated fungal communities were reported to be similar with endophytic fungi of the moss, our results indicated the opposite results in some degree. But whether there exist specific OTUs within this lichen species corresponding to different sites and altitudes is still open. More lichen species and ecological factors would be taken into the integrated analyses to address these knowledge gaps in the near future. PMID:27547204

  18. Biocontrol of pigeon tick Argas reflexus (Acari: Argasidae) by entomopathogenic fungus Metarhizium Anisopliae (Ascomycota: Hypocreales)

    PubMed Central

    Tavassoli, Mosa; Pourseyed, Seyed Hassan; Ownagh, Abdulghaffar; Bernousi, Iraj; Mardani, Karim

    2011-01-01

    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. PMID:24031777

  19. Sublethal Effects of Beauveria bassiana (Ascomycota: Hypocreales) on Life Table Parameters of Frankliniella occidentalis (Thysanoptera: Thripidae).

    PubMed

    Zhang, Tao; Reitz, Stuart R; Wang, Haihong; Lei, Zhongren

    2015-06-01

    We assessed effects of parental exposure to Beauveria bassiana on life history traits of subsequent generations of western flower thrips, Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae). Progeny from individuals that survived fungal exposure as second instars had significantly shorter egg stages, but longer prepupal development times than corresponding untreated controls. However, survivorship to adulthood of these progeny groups did not differ. Although fecundities of the parental types did not differ, the sex ratio of progeny from fungal-treated parents was male-biased, whereas sex ratio of progeny from untreated control parents was even. We calculated life table parameters for the progeny and found that all parameters, except for generation time, were significantly less for the progeny of fungal-treated parents than for progeny of untreated parents. The intrinsic rate of increase, finite rate of increase, net reproductive rate, mean generation time, and gross reproductive rate were 0.199 d(-1), 1.229 d(-1), 21.84, 15.48 d, and 27.273, respectively, for progeny of treated thrips, and 0.266 d(-1), 1.316 d(-1), 52.540, 14.92 d, and 70.64, respectively, for progeny of control thrips. Consequently, population projections demonstrated that offspring of parents exposed to B. bassiana would increase their population more slowly than those from untreated parents. These results demonstrate that B. bassiana has sublethal effects that reduce the reproductive success of F. occidentalis and these effects should be taken into account when evaluating its use in management programs for F. occidentalis. PMID:26470219

  20. New molecular markers for fungal phylogenetics: Two genes for species level systematics in the Sordariomycetes (Ascomycota)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although significant progress has been made resolving deep branches of the fungal tree of life in recent works, many fungal systematists are interested in species-level questions to both define species and to assess fungal biodiversity. Fungal genome sequences are a useful resource to systematic bio...

  1. Novel aspects in the life cycle and biotrophic interactions in Pezizomycetes (Ascomycota, Fungi).

    PubMed

    Tedersoo, Leho; Arnold, A Elizabeth; Hansen, Karen

    2013-03-01

    The ascomycete class Pezizomycetes (single order Pezizales)is known for its cup-shaped fruit bodies and the evolution of edible truffles and morels, but little is known about the ontogeny and ecology of this large and ecologically diverse fungal group. In this issue of Molecular Ecology, Healy et al. (2013) make a great leap forward by describing and identifying asexual, anamorphic structures that produce mitotic spores in many ectomycorrhiza-forming truffle and nontruffle species on soil surfaces worldwide(Fig. 1). Although such anamorphic forms have been reported sporadically from certain ectomycorrhizal and saprotrophic Pezizomycetes (e.g. Warcup 1990), Healy et al. (2013) demonstrate that these terricolous asexual forms are both taxonomically and geographically more widespread and, in fact, much more common than previously understood. We anticipate that deeper insight into other substrates, provided by molecular analyses of materials such as dead wood and seeds, is likely to reveal numerous anamorphs of saprotrophic and pathogenic Pezizomycetes as well (see Marek et al. 2009). PMID:23599958

  2. Seven wood-inhabiting new species of the genus Trichoderma (Fungi, Ascomycota) in Viride clade

    PubMed Central

    Qin, Wen-Tao; Zhuang, Wen-Ying

    2016-01-01

    More than 200 recent collections of Trichoderma from China were examined and 16 species belonging to the Viride clade were identified based on integrated studies of phenotypic and molecular data. Among them, seven wood-inhabiting new species, T. albofulvopsis, T. densum, T. laevisporum, T. sinokoningii, T. sparsum, T. sphaerosporum and T. subviride, are found. They form trichoderma- to verticillium-like conidiophores, lageniform to subulate phialides and globose to ellipsoidal conidia, but vary greatly in colony features, growth rates, and sizes of phialides and conidia. To explore their taxonomic positions, the phylogenetic tree including all the known species of the Viride clade is constructed based on sequence analyses of the combined RNA polymerase II subunit b and translation elongation factor 1 alpha exon genes. Our results indicated that the seven new species were well-located in the Koningii, Rogersonii and Neorufum subclades as well as a few independent terminal branches. They are clearly distinguishable from any existing species. Morphological distinctions and sequence divergences between the new species and their close relatives were discussed. PMID:27245694

  3. Proposal to conserve the name Diaporthe eres against all other competing names (Ascomycota, Diaporthales, Diaporthaceae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    With the change to one scientific name for pleomorphic fungi based on relative priority, Diaporthe represents the generic name that is older than the synonym Phomopsis. At present Diaporthe includes over 800 names while the number of names described in Phomopsis exceeds 1,000, thus merging these two...

  4. Phylogenetic overview of the genus Genea (Pezizales, Ascomycota) with an emphasis on European taxa.

    PubMed

    Alvarado, Pablo; Cabero, Julio; Moreno, Gabriel; Bratek, Zoltán; van Vooren, Nicolas; Kaounas, Vasileios; Konstantinidis, Giorgos; Agnello, Carlo; Merényi, Zsolt; Smith, Matthew E; Vizzini, Alfredo; Trappe, James M

    2016-01-01

    We constructed a comprehensive phylogeny of the genus Genea, with new molecular data from samples collected in several countries in temperate and Mediterranean Europe, as well as North America. Type specimens and authentic material of most species were examined to support identifications. The molecular identity of the most common species in Genea was compared with nuc rDNA internal transcribed spacer (ITS), D1-D2 domains of 28S nuc rDNA (28S rDNA) and translation elongation factor 1-α ene (TEF1) profiles of 10 recently proposed taxa, G. brunneocarpa, G. compressa, G. dentata, G. fageticola, G. lobulata, G. oxygala, G. pinicola, G. pseudobalsleyi, G. pseudoverrucosa and G. tuberculata, supporting their status as distinct species. Genea mexicana and G. thaxteri on the one hand and G. sphaerica and G. lespiaultii on the other are closely related. Multiple lineages were recorded for G. verrucosa and G. fragrans, but we found no morphological traits to discriminate among them, so we tentatively interpreted them as cryptic species. A key to species of the genus Genea is provided to facilitate identification. We provide macroscopic images of fresh specimens and of representative spores of most species. Finally, we conducted a molecular analysis of the divergence time for Genea and discuss the implications of our results. PMID:26740538

  5. Saitoella coloradoensis sp. nov., a new species of the Ascomycota, subphylum Taphrinomycotina

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Saitoella coloradoensis sp. nov. (NRRL YB-2330, CBS 12360, type strain) is described. This new member of the phylum Ascomycotina, subphylum Taphrinomycotina was isolated from insect frass occurring in an Engelmann spruce (Picea engelmannii) that was growing in Colorado, USA. Multigene sequence analy...

  6. Inoculation of coffee plants with the fungal entomopathogen Beauveria bassiana (Ascomycota: Hypocreales).

    PubMed

    Posada, Francisco; Aime, M Catherine; Peterson, Stephen W; Rehner, Stephen A; Vega, Fernando E

    2007-06-01

    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 could have negatively influenced establishment of B. bassiana. The recovery of B. bassiana from sites distant from the point of inoculation indicates that the fungus has the potential to move throughout the plant. PMID:17604149

  7. (2049-2050) Proposals to conserve the name Wickerhamomyces against Hansenula and to reject the name Saccharomyces sphaericus (Ascomycota: Saccharomycotina)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The International Rules of Botanical Nomenclature, under which fungi are also classified, require a preserved specimen, the type specimen, for all described species. The yeast Wickerhamomyces anomalus, which is common in nature and widely used for the biocontrol of spoilage fungi that contaminate en...

  8. Distribution of the myrmecoparasitic fungus Rickia wasmannii (Ascomycota: Laboulbeniales) across colonies, individuals, and body parts of Myrmica scabrinodis.

    PubMed

    Markó, Bálint; Csata, Enikő; Erős, Katalin; Német, Enikő; Czekes, Zsolt; Rózsa, Lajos

    2016-05-01

    The ant species Myrmica scabrinodis plays a markedly important ecological role through much of the humid grasslands of Eurasia. It hosts a species-rich community of pathogens and parasites, including Rickia wasmannii, an enigmatic member of entomoparasitic laboulbenialean fungi. This study provides a descriptive ecology of R. wasmannii by characterizing its prevalence and distribution across several hierarchical levels: colonies, individuals, and anatomic body parts. Infections were restricted to a single ant species, M. scabrinodis, and infected colonies occurred predominantly in wet habitats. Infections tended to be highly prevalent within infected colonies, often reaching 100% sample prevalence among workers. Individual infections exhibited an aggregated distribution typical to host-parasite systems. Workers from the aboveground part of nests (presumably older ones acting as foragers) were more infected than those from the belowground part. Fungal thalli could be found all over the body of the hosts, the head and the abdomen being the most infected parts of the body. The fungi's distribution among host body parts statistically differed between low versus high-intensity infections: the initial dominance of the head decreased with advancing infection. These findings may provide baseline data for future comparative or monitoring studies. PMID:26970261

  9. Remototrachyna, a newly recognized tropical lineage of lichens in the Hypotrachyna clade (Parmeliaceae, Ascomycota), originated in the Indian subcontinent.

    PubMed

    Divakar, Pradeep K; Lumbsch, H Thorsten; Ferencova, Zuzana; Del Prado, Ruth; Crespo, Ana

    2010-04-01

    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

  10. Genetic distances within and among species in monophyletic lineages of Parmeliaceae (Ascomycota) as a tool for taxon delimitation.

    PubMed

    Del-Prado, Ruth; Cubas, Paloma; Lumbsch, H Thorsten; Divakar, Pradeep K; Blanco, Oscar; de Paz, Guillermo Amo; Molina, M Carmen; Crespo, Ana

    2010-07-01

    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

  11. The sister-group relationships of the largest family of lichenized fungi, Parmeliaceae (Lecanorales, Ascomycota).

    PubMed

    Singh, Garima; Divakar, Pradeep K; Dal Grande, Francesco; Otte, Jürgen; Parnmen, Sittiporn; Wedin, Mats; Crespo, Ana; Lumbsch, H Thorsten; Schmitt, Imke

    2013-10-01

    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

  12. (2289) Proposal to conserve the name Morchella semilibera against Phallus crassipes, P. gigas and P. undosus (Ascomycota)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    True morels (Morchella) are among the most highly prized and easily recognized edible mushrooms collected during spring throughout the Northern Hemisphere. To help ensure that commercial harvests are sustainable and species diversity is preserved, management practices and conservation policies need...

  13. Efficacy of the Biofumigant Fungus Muscodor albus (Ascomycota: Xylariales) for Control of Codling Moth (Lepidoptera: Tortricidae) in Simulated Storage Conditions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Codling moth CM, Cydia pomonella, (L.), a serious pest of pome fruit, is a threat to exportation of apples because of the possibility of shipping infested fruit. Broad spectrum fumigants have been used as the principle method for the protection of exported fruit from insect infestations. Some of th...

  14. Phylogenetic placement, species delimitation, and cyanobiont identity of endangered aquatic Peltigera species (lichen-forming Ascomycota, Lecanoromycetes).

    PubMed

    Miadlikowska, Jolanta; Richardson, David; Magain, Nicolas; Ball, Bernard; Anderson, Frances; Cameron, Robert; Lendemer, James; Truong, Camille; Lutzoni, François

    2014-07-11

    • Premise of this study: Aquatic cyanolichens from the genus Peltigera section Hydrothyriae are subject to anthropogenic threats and, therefore, are considered endangered. In this study we addressed the phylogenetic placement of section Hydrothyriae within Peltigera. We delimited species within the section and identified their symbiotic cyanobacteria.• Methods: Species delimitation and population structure were explored using monophyly as a grouping criterion (RAxML) and Structurama based on three protein-coding genes in combination with two nuclear ribosomal loci. The 16S and rbcLX sequences for the cyanobionts were analyzed in the broad phylogenetic context of free-living and symbiotic cyanobacteria.• Key results: We confirm with high confidence the placement of section Hydrothyriae within the monophyletic genus Peltigera; however, its phylogenetic position within the genus remains unsettled. We recovered three distinct monophyletic groups corresponding to three species: P. hydrothyria, P. gowardii s.s., and P. aquatica Miadl. & Lendemer, the latter being formally introduced here. Each species was associated with an exclusive set of Nostoc haplotypes.• Conclusions: The ITS region alone provides sufficient genetic information to distinguish the three morphologically cryptic species within section Hydrothyriae. Section Hydrothyriae seems to be associated with a monophyletic lineage of Nostoc, that has not been found in symbiotic association with other members of Peltigera. Capsosira lowei should be transferred to the genus Nostoc. Potential threats to P. aquatica should be re-examined based on the recognition of two aquatic species in western North America. PMID:25016011

  15. Presence of natural genetic resistance in Fraxinus excelsior (Oleraceae) to Chalara fraxinea (Ascomycota): an emerging infectious disease

    PubMed Central

    McKinney, L V; Nielsen, L R; Hansen, J K; Kjær, E D

    2011-01-01

    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. PMID:20823903

  16. A phylogenetic analysis of the boreal lichen Mycoblastus sanguinarius (Mycoblastaceae, lichenized Ascomycota) reveals cryptic clades correlated with fatty acid profiles

    PubMed Central

    Spribille, Toby; Klug, Barbara; Mayrhofer, Helmut

    2011-01-01

    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-α 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. PMID:21443957

  17. A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families

    PubMed Central

    Miadlikowska, Jolanta; Kauff, Frank; Högnabba, Filip; Oliver, Jeffrey C.; Molnár, Katalin; Fraker, Emily; Gaya, Ester; Hafellner, Josef; Hofstetter, Valérie; Gueidan, Cécile; Otálora, Mónica A.G.; Hodkinson, Brendan; Kukwa, Martin; Lücking, Robert; Björk, Curtis; Sipman, Harrie J.M.; Burgaz, Ana Rosa; Thell, Arne; Passo, Alfredo; Myllys, Leena; Goward, Trevor; Fernández-Brime, Samantha; Hestmark, Geir; Lendemer, James; Lumbsch, H. Thorsten; Schmull, Michaela; Schoch, Conrad; Sérusiaux, Emmanuël; Maddison, David R.; Arnold, A. Elizabeth; Lutzoni, François; Stenroos, Soili

    2014-01-01

    The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 642 newly generated and 3329 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, ‘Candelariomycetidae’). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed relatively stable relationships for many families and orders. However, the increasing number of taxa without the addition of more loci also resulted in an expected substantial loss of phylogenetic resolving power and support (especially for deep phylogenetic relationships), potentially including the misplacements of several taxa. Future phylogenetic analyses should include additional single copy protein-coding markers in order to improve the tree of the Lecanoromycetes. As part of this study, a new module (“Hypha”) of the freely available Mesquite software was developed to compare and display the internodal support values derived from this cumulative supermatrix approach. PMID:24747130

  18. Establishment of fungal entomopathogens Beauveria bassiana and Bionectria ochroleuca (Ascomycota: Hypocreales) as endophytes on artichoke Cynara scolymus.

    PubMed

    Guesmi-Jouini, J; Garrido-Jurado, I; López-Díaz, C; Ben Halima-Kamel, M; Quesada-Moraga, E

    2014-06-01

    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 10 days 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

  19. Position specificity in Chitonomyces (Ascomycota, Laboulbeniomycetes) on Laccophilus (Coleoptera, Dytiscidae): a molecular approach resolves a century-old debate.

    PubMed

    Goldmann, Lauren; Weir, Alex

    2012-01-01

    The occurrence of Laboulbeniomycete species consistently on a precise portion of beetle integument was investigated in 13 species of Chitonomyces ectoparasitic on the aquatic diving beetle Laccophilus maculosus (Coleoptera, Dytiscidae). The phenomenon was called "position specificity" by Roland Thaxter in 1896, yet the mechanism has remained unknown. By using molecular analysis of the nucSSU rRNA gene and the 5.8S and partial ITS1 rRNA regions, 13 species of Chitonomyces reported to exhibit position specificity on Laccophilus maculosus were placed neatly into pairs of morphotypes, resulting in synonomies and recognition of six phylogenetic species (one species is a triplet). Each phylogenetic species was located at corresponding positions on male and female beetles that make contact during mating. In addition, ecological data and video footage of the mating behaviors of Laccophilus confirmed that sexual transmission is the mechanism behind this enigmatic phenomenon. PMID:22684291

  20. Using Phylogenetic and Coalescent Methods to Understand the Species Diversity in the Cladia aggregata Complex (Ascomycota, Lecanorales)

    PubMed Central

    Parnmen, Sittiporn; Rangsiruji, Achariya; Mongkolsuk, Pachara; Boonpragob, Kansri; Nutakki, Aparna; Lumbsch, H. Thorsten

    2012-01-01

    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. PMID:23272229

  1. A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families.

    PubMed

    Miadlikowska, Jolanta; Kauff, Frank; Högnabba, Filip; Oliver, Jeffrey C; Molnár, Katalin; Fraker, Emily; Gaya, Ester; Hafellner, Josef; Hofstetter, Valérie; Gueidan, Cécile; Otálora, Mónica A G; Hodkinson, Brendan; Kukwa, Martin; Lücking, Robert; Björk, Curtis; Sipman, Harrie J M; Burgaz, Ana Rosa; Thell, Arne; Passo, Alfredo; Myllys, Leena; Goward, Trevor; Fernández-Brime, Samantha; Hestmark, Geir; Lendemer, James; Lumbsch, H Thorsten; Schmull, Michaela; Schoch, Conrad L; Sérusiaux, Emmanuël; Maddison, David R; Arnold, A Elizabeth; Lutzoni, François; Stenroos, Soili

    2014-10-01

    The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 642 newly generated and 3329 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, 'Candelariomycetidae'). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed relatively stable relationships for many families and orders. However, the increasing number of taxa without the addition of more loci also resulted in an expected substantial loss of phylogenetic resolving power and support (especially for deep phylogenetic relationships), potentially including the misplacements of several taxa. Future phylogenetic analyses should include additional single copy protein-coding markers in order to improve the tree of the Lecanoromycetes. As part of this study, a new module ("Hypha") of the freely available Mesquite software was developed to compare and display the internodal support values derived from this cumulative supermatrix approach. PMID:24747130

  2. Cuticle Fatty Acid Composition and Differential Susceptibility of Three Species of Cockroaches to the Entomopathogenic Fungi Metarhizium anisopliae (Ascomycota, Hypocreales).

    PubMed

    Gutierrez, Alejandra C; Gołębiowski, Marek; Pennisi, Mariana; Peterson, Graciela; García, Juan J; Manfrino, Romina G; López Lastra, Claudia C

    2015-04-01

    Differences in free fatty acids (FFAs) chemical composition of insects may be responsible for susceptibility or resistance to fungal infection. Determination of FFAs found in cuticular lipids can effectively contribute to the knowledge concerning insect defense mechanisms. In this study, we have evaluated the susceptibility of three species of cockroaches to the entomopathogenic fungi Metarhizium anisopliae (Metschnikoff) Sorokin by topical application. Mortality due to M. anisopliae was highly significant on adults and nymphs of Blattella germanica L. (Blattodea: Blattellidae). However, mortality was faster in adults than in nymphs. Adults of Blatta orientalis L. (Blattodea: Blattidae) were not susceptible to the fungus, and nymphs of Blaptica dubia Serville (Blattodea: Blaberidae) were more susceptible to the fungus than adults. The composition of cuticular FFAs in the three species of cockroaches was also studied. The analysis indicated that all of the fatty acids were mostly straight-chain, long-chain, saturated or unsaturated. Cuticular lipids of three species of cockroaches contained 19 FFAs, ranging from C14:0 to C24:0. The predominant fatty acids found in the three studied species of cockroaches were oleic, linoleic, palmitic, and stearic acid. Only in adults of Bl. orientalis, myristoleic acid, γ-linolenic acid, arachidic acid, dihomolinoleic acid, and behenic acid were identified. Lignoceric acid was detected only in nymphs of Bl. orientalis. Heneicosylic acid and docosahexaenoic acid were identified in adults of Ba. dubia. PMID:26470187

  3. Pathogenic and enzyme activities of the entomopathogenic fungus Tolypocladium cylindrosporum (Ascomycota: Hypocreales) from Tierra del Fuego, Argentina.

    PubMed

    Scorsetti, Ana C; Elíades, Lorena A; Stenglein, Sebastián A; Cabello, Marta N; Pelizza, Sebastián A; Saparrat, Mario C N

    2012-06-01

    Tolypocladium cylindrosporum is an entomopathogenic fungi that has been studied as a biological control agent against insects of several orders. The fungus has been isolated from the soil as well as from insects of the orders Coleoptera, Lepidoptera, Diptera and Hymenoptera. In this study, we analyzed the ability of a strain of T cylindrosporum, isolated from soil samples taken in Tierra del Fuego, Argentina, to produce hydrolytic enzymes, and to study the relationship of those activities to the fungus pathogenicity against pest aphids. We have made the traditional and molecular characterization of this strain of T cylindrosporum. The expression of hydrolase activity in the fungal strain was estimated at three incubation temperatures (4 degreeC, 12 degreeC and 24 degreeC), on different agar media supplemented with the following specific substrates: chitin azure, Tween 20, casein, and urea for chitinase, lipase, protease, and urease activity, respectively. The hydrolytic-enzyme activity was estimated qualitatively according to the presence of a halo of clarification through hydrolase action, besides was expressed semi-quantitatively as the ratio between the hydrolytic-halo and colony diameters. The pathogenicity of the fungus was tested on adults of the aphid Rhopalosiphum padi at three temperatures of incubation (4 degree C, 12 degree C and 24 degree C). The suspension was adjusted to a concentration of 1x10(7) conidia/ml. In pathogenicity assays at seven days post-inoculation, the fungus caused the mortality of adults of Ropalosiphum padi at different temperatures also showed a broad ability to grow on several agar-culture media, supplemented with different carbon sources at the three incubation temperatures tested. Although, the growth was greater with higher incubation temperatures (with maximum levels at 24 degreeC), the fungus reached similar colony diameters after 15 days of incubation on the medium supplemented with Tween 20 at the lower two incubation temperatures of 4 degreeC or 12 degreeC. In accordance with the results on colony diameters, the fungus revealed an ability to degrade casein, chitin derivatives, Tween 20, and urea as evidenced by the appearance of a halo around the fungal colony. Because of its origin and temperature tolerance, this Argentine strain has great potential for use as a biocontrol agent for insect pest control in cold and temperate environments. PMID:23894949

  4. Retention of genes in a secondary metabolite gene cluster that has degenerated in multiple lineages of the Ascomycota

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fungal secondary metabolite (SM) gene clusters encode proteins involved in SM biosynthesis, protection against SMs, and regulation of cluster gene transcription. RNA-Seq analysis of Fusarium langsethiae (class Sordariomycetes) revealed a cluster of six genes that were highly expressed during growth...

  5. Paecilomyces niveus Stolk & Samson, 1971 (Ascomycota: Thermoascaceae) as a pathogen of Nasonovia ribisnigri (Mosley, 1841) (Hemiptera, Aphididae) in Brazil.

    PubMed

    Zawadneak, M A C; Pimentel, I C; Robl, D; Dalzoto, P; Vicente, V; Sosa-Gómez, D R; Porsani, M; Cuquel, F L

    2015-11-01

    Nasonovia ribisnigri is a key pest of lettuce (Lactuca sativa L.) in Brazil that requires alternative control methods to synthetic pesticides. We report, for the first time, the occurrence of Paecilomyces niveus as an entomopathogen of the aphid Nasonovia ribisnigri in Pinhais, Paraná, Brazil. Samples of mummified aphids were collected from lettuce crops. The fungus P. niveus (PaePR) was isolated from the insect bodies and identified by macro and micromorphology. The species was confirmed by sequencing Internal Transcribed Spacer (ITS) rDNA. We obtained a sequence of 528 bp (accession number HQ441751), which aligned with Byssochlamys nivea strains (100% identities). In a bioassay, 120 h after inoculation of N. ribisnigri with pathogenic P. niveus had an average mortality of 74%. The presence of P. niveus as a natural pathogen of N. ribisnigri in Brazil suggests that it may be possible to employ P. niveus to minimize the use of chemical insecticides. PMID:26602345

  6. Alloascoidea hylecoeti gen. nov., comb. nov., Alloascoidea africana comb. nov., Ascoidea tarda sp. nov. and Nadsonia starkeyi-henricii comb. nov., new members of the Saccharomycotina (Ascomycota)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phylogenetic analysis of concatenated nuclear gene sequences for large and small subunit rRNAs, translation elongation factor 1-a and the two large subunits of RNA polymerase II (RPB1, RPB2) demonstrated that species assigned to the yeast genus Ascoidea represent two separate and distantly related c...

  7. Effect of plant extracts and a disinfectant on biological parameters and pathogenicity of the fungus Beauveria bassiana (Bals.) Vuill. (Ascomycota: Cordycipitaceae).

    PubMed

    Martins, C C; Alves, L F A; Mamprim, A P

    2016-06-01

    The fungus Beauveria bassiana is naturally found in poultry houses and causes high rates of mortality in Alphitobius diaperinus. Laboratory and field experiments have shown the potential of this fungus as an insect control agent. However, in poultry houses, bacteria as Salmonella, can be found and have been studied alternative control methods for this pathogen. Thus, this study aimed to evaluate the effect of plant extracts and a disinfectant on the fungus Beauveria bassiana (strain Unioeste 4). Conidial viability, colony-forming unit (CFU) counts, vegetative growth, conidia production, insecticidal activity of the fungus and compatibility were used as parameters in the evaluation of the effect of these products on the fungus. Alcoholic and aqueous extracts of jabuticaba (Myrciaria cauliflora (Mart.), guava (Psidium guajava (L.)), and jambolan (Syzygium cumini (L.), at concentrations of 10% as well as the commercial disinfectant, Peroxitane® 1512 AL, were evaluated at the recommended concentrations (RC), 1:200 (RC), 0.5 RC and 2 RC. There was a negative influence of alcoholic and aqueous extracts of jabuticaba, guava and three dilutions of Peroxitane on the viability of conidia. The CFUs and vegetative growth of the fungus were affected only by the Peroxitane (all dilutions). For conidial production, the aqueous extract of guava had a positive effect, increasing production, while the Peroxitane at the R and RC concentrations resulted in a negative influence. The mortality of A. diaperinus, caused by the fungus after exposure to these products, was 60% for the peracetic acid at 0.5 RC, and above 80% for the extracts. Thus, the results showed that all the extracts and Peroxitane at RC 0.5 are compatible with the fungus B. bassiana Unioeste 4, however only the extracts had a low impact on inoculum potential. PMID:27143049

  8. Fungal specificity and selectivity for algae play a major role in determining lichen partnerships across diverse ecogeographic regions in the lichen-forming family Parmeliaceae (Ascomycota).

    PubMed

    Leavitt, Steven D; Kraichak, Ekaphan; Nelsen, Matthew P; Altermann, Susanne; Divakar, Pradeep K; Alors, David; Esslinger, Theodore L; Crespo, Ana; Lumbsch, Thorsten

    2015-07-01

    Microbial symbionts are instrumental to the ecological and long-term evolutionary success of their hosts, and the central role of symbiotic interactions is increasingly recognized across the vast majority of life. Lichens provide an iconic group for investigating patterns in species interactions; however, relationships among lichen symbionts are often masked by uncertain species boundaries or an inability to reliably identify symbionts. The species-rich lichen-forming fungal family Parmeliaceae provides a diverse group for assessing patterns of interactions of algal symbionts, and our study addresses patterns of lichen symbiont interactions at the largest geographic and taxonomic scales attempted to date. We analysed a total of 2356 algal internal transcribed spacer (ITS) region sequences collected from lichens representing ten mycobiont genera in Parmeliaceae, two genera in Lecanoraceae and 26 cultured Trebouxia strains. Algal ITS sequences were grouped into operational taxonomic units (OTUs); we attempted to validate the evolutionary independence of a subset of the inferred OTUs using chloroplast and mitochondrial loci. We explored the patterns of symbiont interactions in these lichens based on ecogeographic distributions and mycobiont taxonomy. We found high levels of undescribed diversity in Trebouxia, broad distributions across distinct ecoregions for many photobiont OTUs and varying levels of mycobiont selectivity and specificity towards the photobiont. Based on these results, we conclude that fungal specificity and selectivity for algal partners play a major role in determining lichen partnerships, potentially superseding ecology, at least at the ecogeographic scale investigated here. To facilitate effective communication and consistency across future studies, we propose a provisional naming system for Trebouxia photobionts and provide representative sequences for each OTU circumscribed in this study. PMID:26073165

  9. Coalescent-Based Species Delimitation Approach Uncovers High Cryptic Diversity in the Cosmopolitan Lichen-Forming Fungal Genus Protoparmelia (Lecanorales, Ascomycota)

    PubMed Central

    Singh, Garima; Dal Grande, Francesco; Divakar, Pradeep K.; Otte, Jürgen; Leavitt, Steven D.; Szczepanska, Katarzyna; Crespo, Ana; Rico, Víctor J.; Aptroot, André; Cáceres, Marcela Eugenia da Silva; Lumbsch, H. Thorsten; Schmitt, Imke

    2015-01-01

    Species recognition in lichen-forming fungi has been a challenge because of unsettled species concepts, few taxonomically relevant traits, and limitations of traditionally used morphological and chemical characters for identifying closely related species. Here we analyze species diversity in the cosmopolitan genus Protoparmelia s.l. The ~25 described species in this group occur across diverse habitats from the boreal -arctic/alpine to the tropics, but their relationship to each other remains unexplored. In this study, we inferred the phylogeny of 18 species currently assigned to this genus based on 160 specimens and six markers: mtSSU, nuLSU, ITS, RPB1, MCM7, and TSR1. We assessed the circumscription of species-level lineages in Protoparmelia s. str. using two coalescent-based species delimitation methods – BP&P and spedeSTEM. Our results suggest the presence of a tropical and an extra-tropical lineage, and eleven previously unrecognized distinct species-level lineages in Protoparmelia s. str. Several cryptic lineages were discovered as compared to phenotype-based species delimitation. Many of the putative species are supported by geographic evidence. PMID:25932996

  10. Testing the use of ITS rDNA and protein-coding genes in the generic and species delimitation of the lichen genus Usnea (Parmeliaceae, Ascomycota).

    PubMed

    Truong, Camille; Divakar, Pradeep K; Yahr, Rebecca; Crespo, Ana; Clerc, Philippe

    2013-08-01

    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

  11. Coalescent-based species delimitation approach uncovers high cryptic diversity in the cosmopolitan lichen-forming fungal genus Protoparmelia (Lecanorales, Ascomycota).

    PubMed

    Singh, Garima; Dal Grande, Francesco; Divakar, Pradeep K; Otte, Jürgen; Leavitt, Steven D; Szczepanska, Katarzyna; Crespo, Ana; Rico, Víctor J; Aptroot, André; Cáceres, Marcela Eugenia da Silva; Lumbsch, H Thorsten; Schmitt, Imke

    2015-01-01

    Species recognition in lichen-forming fungi has been a challenge because of unsettled species concepts, few taxonomically relevant traits, and limitations of traditionally used morphological and chemical characters for identifying closely related species. Here we analyze species diversity in the cosmopolitan genus Protoparmelia s.l. The ~25 described species in this group occur across diverse habitats from the boreal-arctic/alpine to the tropics, but their relationship to each other remains unexplored. In this study, we inferred the phylogeny of 18 species currently assigned to this genus based on 160 specimens and six markers: mtSSU, nuLSU, ITS, RPB1, MCM7, and TSR1. We assessed the circumscription of species-level lineages in Protoparmelia s. str. using two coalescent-based species delimitation methods--BP&P and spedeSTEM. Our results suggest the presence of a tropical and an extra-tropical lineage, and eleven previously unrecognized distinct species-level lineages in Protoparmelia s. str. Several cryptic lineages were discovered as compared to phenotype-based species delimitation. Many of the putative species are supported by geographic evidence. PMID:25932996

  12. Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria-rich microbiome.

    PubMed

    Quandt, C Alisha; Kohler, Annegret; Hesse, Cedar N; Sharpton, Thomas J; Martin, Francis; Spatafora, Joseph W

    2015-08-01

    Many obligate symbiotic fungi are difficult to maintain in culture, and there is a growing need for alternative approaches to obtaining tissue and subsequent genomic assemblies from such species. In this study, the genome of Elaphomyces granulatus was sequenced from sporocarp tissue. The genome assembly remains on many contigs, but gene space is estimated to be mostly complete. Phylogenetic analyses revealed that the Elaphomyces lineage is most closely related to Talaromyces and Trichocomaceae s.s. The genome of E. granulatus is reduced in carbohydrate-active enzymes, despite a large expansion in genome size, both of which are consistent with what is seen in Tuber melanosporum, the other sequenced ectomycorrhizal ascomycete. A large number of transposable elements are predicted in the E. granulatus genome, especially Gypsy-like long terminal repeats, and there has also been an expansion in helicases. The metagenome is a complex community dominated by bacteria in Bradyrhizobiaceae, and there is evidence to suggest that the community may be reduced in functional capacity as estimated by KEGG pathways. Through the sequencing of sporocarp tissue, this study has provided insights into Elaphomyces phylogenetics, genomics, metagenomics and the evolution of the ectomycorrhizal association. PMID:25753751

  13. Quantitative detection of Beauveria bassiana GHA (Ascomycota: Hypocreales), a potential microbial control agent of the emerald ash borer, by use of real-time PCR

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 agains...

  14. Proposal to conserve the name Helminthosporium maydis Y. Nisik. & C. Miyake (Bipolaris maydis) against H. maydis Brond. and Ophiobolus heterostrophus (Ascomycota: Pleosporales: Pleosporaceae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The name Bipolaris maydis (Y. Nisik. & C. Miyake) Shoemaker is the type of the genus Bipolaris Shoemaker, while Cochliobolus heterostrophus (Drechsler) Drechsler is the type of the genus Cochliobolus Drechsler. Initially described as Helminthosporium maydis Y. Nisik. & C. Miyake, Bipolaris maydis is...

  15. Virulence of Beauveria bassiana and Metarhizium anisopliae (Ascomycota: Hypocreales) commercial strains against adult Xylosandrus germanus (Coleoptera: Scolytidae) and impact on brood

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The ambrosia beetle Xylosandrus germanus is an invasive pest with a wide host range and is a serious pest of orchards and nurseries in the eastern US. In this study we evaluated the potential of entomopathogenic fungi Beauveria bassiana and Metarhizium anisopliae as control agents against this beet...

  16. Not as Ubiquitous as We Thought: Taxonomic Crypsis, Hidden Diversity and Cryptic Speciation in the Cosmopolitan Fungus Thelonectria discophora (Nectriaceae, Hypocreales, Ascomycota)

    PubMed Central

    Salgado-Salazar, Catalina; Rossman, Amy Y.; Chaverri, Priscila

    2013-01-01

    The distribution of microbial species, including fungi, has long been considered cosmopolitan. Recently, this perception has been challenged by molecular studies in historical biogeography, phylogeny and population genetics. Here we explore this issue using the fungal morphological species Thelonectria discophora, one of the most common species of fungi in the family Nectriaceae, encountered in almost all geographic regions and considered as a cosmopolitan taxon. In order to determine if T. discophora is a single cosmopolitan species or an assemblage of sibling species, we conducted various phylogenetic analyses, including standard gene concatenation, Bayesian concordance methods, and coalescent-based species tree reconstruction on isolates collected from a wide geographic range. Results show that diversity among isolates referred as T. discophora is greatly underestimated and that it represents a species complex. Within this complex, sixteen distinct highly supported lineages were recovered, each of which has a restricted geographic distribution and ecology. The taxonomic status of isolates regarded as T. discophora is reconsidered, and the assumed cosmopolitan distribution of this species is rejected. We discuss how assumptions about geographically widespread species have implications regarding their taxonomy, true diversity, biological diversity conservation, and ecological functions. PMID:24204665

  17. Assessing deposition and persistence of Beauveria bassiana GHA (Ascomycota: Hypocreales) applied for control of emerald ash borer, Agrilus planipennis (Coleoptera: Buprestidae), in a commercial tree nursery

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Determining the deposition and field persistence of mycoinsecticides is essential in the development of effective and economical application strategies, including specifically the timing and frequency of spray applications. In this study we used three methods to evaluate the persistence of Beauveri...

  18. Characterization and phylogeny of entomopathogenic Isaria spp. (Ascomycota: Hypocreales) using ITS1-5.8X-ITS2 and elongation factor 1-alpha sequences

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The elongation factor 1-alpha (EF1-a) and the internal transcribed spacer regions ITS1 and ITS2 (ITS1-5.8S-ITS2) sequences were used to characterize and identify Isaria isolates from Argentina and Brazil, as well as to study the phylogenetic relationships among these isolates and other related fungi...

  19. Not as ubiquitous as we thought: taxonomic crypsis, hidden diversity and cryptic speciation in the cosmopolitan fungus Thelonectria discophora (Nectriaceae, Hypocreales, Ascomycota)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The distribution of microbial species, including fungi, has long been considered cosmopolitan. Recently, this perception has been challenged by molecular studies in historical biogeography, phylogeny and population genetics. Here we explore this issue using the fungal morphological species Thelonect...

  20. Neoerysiphe kerribeeensis sp. nov. (Ascomycota: Erysiphales), a new species of Neoerysiphe on native and introduced species of Senecio (Asteraceae) in Australia.

    PubMed

    Beilharz, Vyrna; Cunnington, James H; Pascoe, Ian G

    2010-04-01

    Anamorphic powdery mildew fungi on introduced taxa of Senecio and Pericallis × hybrida in Australia have previously been identified as Neoerysiphe cumminsiana on the basis of a combination of Euoidium-type conidiophores and lobed mycelial and germ tube appressoria. But, two specimens with chasmothecia on the indigenous Senecio glossanthus did not agree with published descriptions of N. cumminsiana. The teleomorph of the S. glossanthus mildew differed from that of N. cumminsiana in the morphology of its peridial cells, the pigmentation of its appendages, and the morphology and pigmentation of some secondary hyphae. Ribosomal DNA ITS sequences from the two S. glossanthus mildew specimens and five other specimens of Senecio mildews from south-eastern Australia demonstrated that all Australian Senecio mildews are conspecific and distinct from the northern hemisphere Senecio mildew (N. cumminsiana) and from other Neoerysiphe taxa. Based on morphological characters and rDNA sequence data, the Australian Senecio mildew is described as a new species, Neoerysiphe kerribeeensis. This is the first native teleomorphic powdery mildew described from Australia. PMID:20943143

  1. Complex patterns of speciation in cosmopolitan "rock posy" lichens--discovering and delimiting cryptic fungal species in the lichen-forming Rhizoplaca melanophthalma species-complex (Lecanoraceae, Ascomycota).

    PubMed

    Leavitt, Steven D; Fankhauser, Johnathon D; Leavitt, Dean H; Porter, Lyndon D; Johnson, Leigh A; St Clair, Larry L

    2011-06-01

    A growing body of evidence indicates that in some cases morphology-based species circumscription of lichenized fungi misrepresents the number of existing species. The cosmopolitan "rock posy" lichen (Rhizoplaca melanophthalma) species-complex includes a number of morphologically distinct species that are both geographically and ecologically widespread, providing a model system to evaluate speciation in lichen-forming ascomycetes. In this study, we assembled multiple lines of evidence from nuclear DNA sequence data, morphology, and biochemistry for species delimitation in the R. melanophthalma species-complex. We identify a total of ten candidate species in this study, four of which were previously recognized as distinct taxa and six previously unrecognized lineages found within what has been thus far considered a single species. Candidate species are supported using inferences from multiple empirical operational criteria. Multiple instances of sympatry support the view that these lineages merit recognition as distinct taxa. Generally, we found little corroboration between morphological and chemical characters, and previously unidentified lineages were morphologically polymorphic. However, secondary metabolite data supported one cryptic saxicolous lineage, characterized by orsellinic-derived gyrophoric and lecanoric acids, which we consider to be taxonomically significant. Our study of the R. melanophthalma species-complex indicates that the genus Rhizoplaca, as presently circumscribed, is more diverse in western North American than originally perceived, and we present our analyses as a working example of species delimitation in morphologically cryptic and recently diverged lichenized fungi. PMID:21443956

  2. A monograph of the entomopathogenic genera Hypocrella, Moelleriella, and Samuelsia gen. nov. (Ascomycota, Hypocreales, Clavicipitaceae), and their aschersonia-like anamorphs in the Neotropics

    PubMed Central

    Chaverri, P.; Liu, M.; Hodge, K.T.

    2008-01-01

    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-α (TEF 1-α), 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

  3. Sporothrix chilensis sp. nov. (Ascomycota: Ophiostomatales), a soil-borne agent of human sporotrichosis with mild-pathogenic potential to mammals.

    PubMed

    Rodrigues, Anderson Messias; Cruz Choappa, Rodrigo; Fernandes, Geisa Ferreira; de Hoog, G Sybren; de Camargo, Zoilo Pires

    2016-02-01

    A combination of phylogeny, evolution, morphologies and ecologies has enabled major advances in understanding the taxonomy of Sporothrix species, including members exhibiting distinct lifestyles such as saprobes, human/animal pathogens, and insect symbionts. Phylogenetic analyses of ITS1/2 + 5.8s sequences split Sporothrix genus in two well-defined groups with dissimilar ecologies. Species embedded in the Sporothrix schenckii complex are frequently agents of human and animal sporotrichosis, and some of these are responsible for large sapronoses and zoonoses around the warmer temperate regions of the world. At the other extreme, basal saprophytic species evolved in association with decaying wood and soil, and are rarely found to cause human disease. We propose to create a new taxa, Sporothrix chilensis sp. nov., to accommodate strains collected from a clinical case of onychomycosis as well as from environmental origins in Chile. Multigene analyses based on ITS1/2 + 5.8s region, beta-tubulin, calmodulin and translation elongation factor 1α revealed that S. chilensis is a member of the Sporothrix pallida complex, and the nearest taxon is Sporothrix mexicana, a rare soil-borne species, non-pathogenic to humans. The ITS region serves as a primary barcode marker, while each one of the protein-coding loci easily recognized species boundaries providing sufficient information for species identification. A disseminated model of murine sporotrichosis revealed a mild-pathogenic potential, with lung invasion. Although S. chilensis is not a primary pathogen, accidental infection may have an impact in the immunosuppressed population. With the introduction of distinct species with similar routes of transmission but different virulence, identification of Sporothrix agents at the species level is mandatory. PMID:26781380

  4. Isolation of Paecilomyces lilacinus (Thom) Samson (Ascomycota: Hypocreales) from the Chagas disease vector, Triatoma infestans Klug (Hemiptera: Reduviidae) in an endemic area in Argentina.

    PubMed

    Marti, Gerardo A; Lastra, Claudia C López; Pelizza, Sebastian A; García, Juan J

    2006-11-01

    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 were individually maintained in moist chamber and incubated at 22 degrees C. Triatominae adults infected with the fungus Paecilomyces lilacinus were found at El Quebracho (27 degrees 34'S-64 degrees 31'W), Santiago del Estero province, Argentina, in December 2003. Paecilomyces lilacinus was cultured and isolated from infected insects in SDAY, PYG and MEA media. Pathogenicity tests were conducted and positive results were recorded. The median survival time (MST) of T. infestans exposed to a P. lilacinus conidial suspension was 12.8 days, and 100% mortality occurred at 30 days post-treatment. This is the first record of natural infection caused by P. lilacinus in T. infestans in the world. PMID:17123036

  5. Catalogue of the Lichenized and Lichenicolous Fungi of Bosnia and Herzegovina

    PubMed Central

    Bilovitz, Peter O.; Mayrhofer, Helmut

    2011-01-01

    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. PMID:22121302

  6. Draft Genome Sequence of Microdochium bolleyi, a Dark Septate Fungal Endophyte of Beach Grass.

    PubMed

    David, Aaron S; Haridas, Sajeet; LaButti, Kurt; Lim, Joanne; Lipzen, Anna; Wang, Mei; Barry, Kerrie; Grigoriev, Igor V; Spatafora, Joseph W; May, Georgiana

    2016-01-01

    Here, we present the genome sequence of the dark septate fungal endophyte Microdochium bolleyi (Ascomycota, Sordariomycetes, Xylariales). The assembled genome size was 38.84 Mbp and consisted of 173 scaffolds and 13,177 predicted genes. PMID:27125481

  7. Draft Genome Sequence of Microdochium bolleyi, a Dark Septate Fungal Endophyte of Beach Grass

    PubMed Central

    Haridas, Sajeet; LaButti, Kurt; Lim, Joanne; Lipzen, Anna; Wang, Mei; Barry, Kerrie; Grigoriev, Igor V.; Spatafora, Joseph W.

    2016-01-01

    Here, we present the genome sequence of the dark septate fungal endophyte Microdochium bolleyi (Ascomycota, Sordariomycetes, Xylariales). The assembled genome size was 38.84 Mbp and consisted of 173 scaffolds and 13,177 predicted genes. PMID:27125481

  8. Compatibility of the insect pathogenic fungus Beauveria bassiana with neem against sweetpotato whitefly, Bemisia tabaci, on eggplant

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A study on the compatibility of the entomopathogenic fungus Beauveria bassiana (Balsamo) Vuillemin (Ascomycota: Hypocreales) with neem was conducted against sweetpotato whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae), on eggplant. Initially, three concentrations of B. bassiana (106, 1...

  9. PHYLOGENETICS OF SACCHAROMYCETALES, THE ASCOMYCETE YEASTS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 s...

  10. Limited transmission of the ectoparasitic fungus Hesperomyces virescens between lady beetles

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The ectoparasitic fungus Hesperomyces virescens Thaxter (Ascomycota: Laboulbeniales) commonly infects the invasive lady beetle Harmonia axyridis (Pallas) and several other aphidophagous lady beetles in North America and Europe. We tested the hypothesis that bodily contact between adults of differen...

  11. Antagonistic activity of fungi of Olea europaea L. against Colletotrichum acutatum.

    PubMed

    Landum, Miguel C; Félix, Maria do Rosário; Alho, Joana; Garcia, Raquel; Cabrita, Maria João; Rei, Fernando; Varanda, Carla M R

    2016-02-01

    Fungi naturally present in olive trees were identified and tested for their antagonistic potential against Colletotrichum acutatum. A total of 14 isolates were identified, 12 belonged to genera Alternaria, Epicoccum, Fusarium, Aspergillus, Anthrinium, Chaetomium, Diaporthe, Nigrospora, one to family Xylariaceae and one was unclassified. All fungal isolates showed some inhibitory action over the growth of C. acutatum during dual culture growth, however, when agar-diffusible tests were performed only five fungal isolates caused C. acutatum growth inhibition: Alternaria sp. isolate 2 (26.8%), the fungus from Xylariaceae family (14.3%), Alternaria sp. isolate 1 (10.7%); Diaporthe sp. (10.7%), Nigrospora oryzae (3.5%). Volatile substances produced by these isolates were identified through gas-chromatography techniques, as phenylethyl alcohol, 4-methylquinazoline, benzothiazole, benzyl alcohol, lilial, galaxolide, among others. These inhibitory volatiles could play a significant role in reduction of C. acutatum expansion in olive and their study as potential biocontrol agents should be further explored. PMID:26805623

  12. Sporothriolide derivatives as chemotaxonomic markers for Hypoxylon monticulosum

    PubMed Central

    Surup, Frank; Kuhnert, Eric; Lehmann, Erik; Heitkämper, Simone; Hyde, Kevin D.; Fournier, Jacques; Stadler, Marc

    2014-01-01

    During the course of a screening for novel anti-infective agents from cultures of tropical Xylariaceae originating from French Guiana and Thailand, pronounced antifungal activity was noted in extracts of cultures of Hypoxylon monticulosum. A bioassay-guided fractionation led to the known metabolite sporothriolide as active principle. In addition, three new derivatives of sporothriolide were isolated, for which we propose the trivial names sporothric acid, isosporothric acid and dihydroisosporothric acid. Their chemical structures were elucidated by high-resolution electrospray mass spectrometry in conjunction with two-dimensional nuclear magnetic resonance (2D-NMR) spectroscopy. From earlier studies on the biogenesis of the chemically similar canadensolides, we postulate that the new compounds were shunt products, rather than biogenetic precursors of sporothriolide. Interestingly, this compound class, as well as strong antifungal activities, was only observed in multiple cultures of H. monticulosum, but not in several hundreds of Hypoxylon cultures studied previously or concurrently. Therefore, sporothriolide production may constitute a species-specific feature with respect to Hypoxylon and the Xylariaceae, although the compound was previously reported from non-related fungal taxa. PMID:25379335

  13. 18S rRNA Gene Variation among Common Airborne Fungi, and Development of Specific Oligonucleotide Probes for the Detection of Fungal Isolates

    PubMed Central

    Wu, Zhihong; Tsumura, Yoshihiko; Blomquist, Göran; Wang, Xiao-Ru

    2003-01-01

    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 Ascomycota, several strongly supported clades were identified that facilitate the taxonomic placement of several little-studied fungi. Wallemia appeared as the group most diverged from all the other Ascomycota species. Based on the 18S rDNA sequence variation, 108 oligonucleotide probes were designed for each genus and species included in this study. After homology searches and DNA hybridization evaluations, 33 probes were verified as genus or species specific. The optimal hybridization temperatures to achieve the best specificity for these 33 probes were determined. These new probes can contribute to the molecular diagnostic research for environmental monitoring. PMID:12957927

  14. Muscodor albus MOW12 an Endophyte of Piper nigrum L. (Piperaceae) Collected from North East India Produces Volatile Antimicrobials.

    PubMed

    Banerjee, Debdulal; Pandey, Akhil; Jana, Maloy; Strobel, Gary

    2014-03-01

    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

  15. Contrasting Diversity and Host Association of Ectomycorrhizal Basidiomycetes versus Root-Associated Ascomycetes in a Dipterocarp Rainforest

    PubMed Central

    Sato, Hirotoshi; Tanabe, Akifumi S.; Toju, Hirokazu

    2015-01-01

    Root-associated fungi, including ectomycorrhizal and root-endophytic fungi, are among the most diverse and important belowground plant symbionts in dipterocarp rainforests. Our study aimed to reveal the biodiversity, host association, and community structure of ectomycorrhizal Basidiomycota and root-associated Ascomycota (including root-endophytic Ascomycota) in a lowland dipterocarp rainforest in Southeast Asia. The host plant chloroplast ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) region and fungal internal transcribed spacer 2 (ITS2) region were sequenced using tag-encoded, massively parallel 454 pyrosequencing to identify host plant and root-associated fungal taxa in root samples. In total, 1245 ascomycetous and 127 putative ectomycorrhizal basidiomycetous taxa were detected from 442 root samples. The putative ectomycorrhizal Basidiomycota were likely to be associated with closely related dipterocarp taxa to greater or lesser extents, whereas host association patterns of the root-associated Ascomycota were much less distinct. The community structure of the putative ectomycorrhizal Basidiomycota was possibly more influenced by host genetic distances than was that of the root-associated Ascomycota. This study also indicated that in dipterocarp rainforests, root-associated Ascomycota were characterized by high biodiversity and indistinct host association patterns, whereas ectomycorrhizal Basidiomycota showed less biodiversity and a strong host phylogenetic preference for dipterocarp trees. Our findings lead to the working hypothesis that root-associated Ascomycota, which might be mainly represented by root-endophytic fungi, have biodiversity hotspots in the tropics, whereas biodiversity of ectomycorrhizal Basidiomycota increases with host genetic diversity. PMID:25884708

  16. Contrasting diversity and host association of ectomycorrhizal basidiomycetes versus root-associated ascomycetes in a dipterocarp rainforest.

    PubMed

    Sato, Hirotoshi; Tanabe, Akifumi S; Toju, Hirokazu

    2015-01-01

    Root-associated fungi, including ectomycorrhizal and root-endophytic fungi, are among the most diverse and important belowground plant symbionts in dipterocarp rainforests. Our study aimed to reveal the biodiversity, host association, and community structure of ectomycorrhizal Basidiomycota and root-associated Ascomycota (including root-endophytic Ascomycota) in a lowland dipterocarp rainforest in Southeast Asia. The host plant chloroplast ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) region and fungal internal transcribed spacer 2 (ITS2) region were sequenced using tag-encoded, massively parallel 454 pyrosequencing to identify host plant and root-associated fungal taxa in root samples. In total, 1245 ascomycetous and 127 putative ectomycorrhizal basidiomycetous taxa were detected from 442 root samples. The putative ectomycorrhizal Basidiomycota were likely to be associated with closely related dipterocarp taxa to greater or lesser extents, whereas host association patterns of the root-associated Ascomycota were much less distinct. The community structure of the putative ectomycorrhizal Basidiomycota was possibly more influenced by host genetic distances than was that of the root-associated Ascomycota. This study also indicated that in dipterocarp rainforests, root-associated Ascomycota were characterized by high biodiversity and indistinct host association patterns, whereas ectomycorrhizal Basidiomycota showed less biodiversity and a strong host phylogenetic preference for dipterocarp trees. Our findings lead to the working hypothesis that root-associated Ascomycota, which might be mainly represented by root-endophytic fungi, have biodiversity hotspots in the tropics, whereas biodiversity of ectomycorrhizal Basidiomycota increases with host genetic diversity. PMID:25884708

  17. The Wood Rot Ascomycete Xylaria polymorpha Produces a Novel GH78 Glycoside Hydrolase That Exhibits α-l-Rhamnosidase and Feruloyl Esterase Activities and Releases Hydroxycinnamic Acids from Lignocelluloses

    PubMed Central

    Nghi, Do Huu; Bittner, Britta; Kellner, Harald; Jehmlich, Nico; Ullrich, René; Pecyna, Marek J.; Nousiainen, Paula; Sipilä, Jussi; Huong, Le Mai; Hofrichter, Martin

    2012-01-01

    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 α-l-rhamnosidase sequences belonging to the glycoside hydrolase family 78 (GH78; classified under EC 3.2.1.40). The purified enzyme (98 kDa by SDS-PAGE, 103 kDa by size-exclusion chromatography; pI 3.7) converted diverse glycosides (e.g., α-l-rhamnopyranoside and α-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

  18. [Classification of Fungi in modern view].

    PubMed

    Agerer, R

    2003-01-01

    Fungi are a heterogeneous jumble coming together from three kingdoms of organisms. The True Fungi represent a kingdom of its own and are positioned closer to the Animalia than to the Plantae. At present the Fungi are divided into five Divisions. Species pathogenic for humans are found in the Divisions Zygomycota, Ascomycota and Basidiomycota. The Pneumocystidales are now classified in the Ascomycota. The Malasseziales are included in the Class Ustilaginomycetes. Essential characteristics for the classification of Fungi are derived from ultrastructure, chemistry, and more recently also from molecular biology of these organisms. None of these methods can stand for its own, all characteristics must be included. PMID:12955846

  19. Tubakia seoraksanensis sp. nov., a new species from Korea

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An unknown species of Tubakia (Diaporthales, Ascomycota) was collected recently from Quercus mongolica on Seoraksan Mountain, GangWon province in Korea. It was characterized with cultural, ITS region sequence, and morphologial data. After comparison with known species of Tubakia, this species is des...

  20. Phylogeny and historical biogeography of true morels (Morchella) reveals an early Cretaceous origin and high continental endemism and provincialism in the Holarctic

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Morel mushrooms (Morchella, phylum Ascomycota) are arguably the most widely recognized and highly prized of the estimated 1.5 million fungi that inhabit our planet. Although field guides treat these epicurean macrofungi as though the species have cosmopolitan distributions, this assumption has not b...

  1. Full Genome of Phialocephala scopiformis DAOMC 229536, a Fungal Endophyte of Spruce Producing the Potent Anti-Insectan Compound Rugulosin

    PubMed Central

    Frasz, Samantha L.; Seifert, Keith A.; Miller, J. David; Mondo, Stephen J.; LaButti, Kurt; Lipzen, Anna; Dockter, Rhyan B.; Kennedy, Megan C.; Grigoriev, Igor V.; Spatafora, Joseph W.

    2016-01-01

    We present the full genome of Phialocephala scopiformis DAOMC 229536 (Helotiales, Ascomycota), a foliar endophyte of white spruce from eastern Quebec. DAOMC 229536 produces the anti-insectan compound rugulosin, which inhibits a devastating forestry pest, the spruce budworm. This genome will enable fungal genotyping and host-endophyte evolutionary genomics in inoculated trees. PMID:26950333

  2. Full Genome of Phialocephala scopiformis DAOMC 229536, a Fungal Endophyte of Spruce Producing the Potent Anti-Insectan Compound Rugulosin.

    PubMed

    Walker, Allison K; Frasz, Samantha L; Seifert, Keith A; Miller, J David; Mondo, Stephen J; LaButti, Kurt; Lipzen, Anna; Dockter, Rhyan B; Kennedy, Megan C; Grigoriev, Igor V; Spatafora, Joseph W

    2016-01-01

    We present the full genome of Phialocephala scopiformis DAOMC 229536 (Helotiales, Ascomycota), a foliar endophyte of white spruce from eastern Quebec. DAOMC 229536 produces the anti-insectan compound rugulosin, which inhibits a devastating forestry pest, the spruce budworm. This genome will enable fungal genotyping and host-endophyte evolutionary genomics in inoculated trees. PMID:26950333

  3. Fungi associated with rocks of the Atacama Desert: taxonomy, distribution, diversity, ecology and bioprospection for bioactive compounds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study assessed the diversity of fungi living in rocks from different altitudes in the Atacama Desert, Chile. Eighty-one fungal isolates obtained were identified as 21 species of 12 genera from Ascomycota using molecular techniques. Cladosporium halotolerans, Penicillium chrysogenum and Penicill...

  4. Community Structure and Succession Regulation of Fungal Consortia in the Lignocellulose-Degrading Process on Natural Biomass

    PubMed Central

    Wang, Chunxiang; Lv, Ruirui; Zhou, Junxiong; Li, Xin; Zheng, Yi; Jin, Xiangyu; Wang, Mengli; Ye, Yongxia; Huang, Xinyi; Liu, Ping

    2014-01-01

    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

  5. Draft Genome Sequence of the Fungus Penicillium brasilianum MG11.

    PubMed

    Horn, Fabian; Linde, Jörg; Mattern, Derek J; Walther, Grit; Guthke, Reinhard; Brakhage, Axel A; Valiante, Vito

    2015-01-01

    The genus Penicillium belongs to the phylum Ascomycota and includes a variety of fungal species important for food and drug production. We report the draft genome sequence of Penicillium brasilianum MG11. This strain was isolated from soil, and it was reported to produce different secondary metabolites. PMID:26337871

  6. Cyberlindnera xylolytica sp. nov., a xylitol-producing yeast species isolated from lignocellulosic materials

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Independent surveys of yeasts associated with lignocellulosic-related materials led to the discovery of a novel yeast species belonging to the Cyberlindnera clade (Saccharomycotina, Ascomycota). Analysis of the sequences of the internal transcribed spacer (ITS) region and the D1/D2 domains of the la...

  7. Microsatellite loci for the fungus, Ascosphaera apis, cause of honey bee chalkbrood disease

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The fungus Ascosphaera apis (Ascomycota:Ascosphaeriaceae) is a worldwide fungal pathogen of honey bees. To provide tools for understanding the dispersal history of this pathogen, strain differences in virulence, and host-pathogen interactions, we developed and tested microsatellite loci for this sp...

  8. Contribution of Ergot Alkaloids to Suppression of a Grass-Feeding Caterpillar Assessed with Gene-Knockout Endophytes in Perennial Rygrass

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Neotyphodium and Epichloë species (Ascomycota: Clavicipitaceae) are fungal symbionts (endophytes) of grasses. Many of these endophytes produce alkaloids that enhance their hosts' resistance to insects or are toxic to grazing mammals. The goals of eliminating from forage grasses factors such as ergot...

  9. Saccharomycotina and Taphrinomycotina – progress in circumscription of genera

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Much progress has been made in understanding relationships among the yeasts. DNA barcoding (D1/D2, ITS) has provided a rapid means for species identification and phylogenetic analysis of gene sequences has shown that the Ascomycota is comprised of three major lineages, i.e, Saccharomycotina (buddin...

  10. Fungi associated with rocks of the Atacama Desert: Taxonomy, distribution, diversity, ecology and bioprospection for bioactive compounds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study assessed the diversity of fungi living in rocks from different altitudes in the Atacama Desert, Chile. Eighty-one fungal isolates obtained were identified as 21 species of 12 genera from Ascomycota using molecular techniques. Cladosporium halotolerans, Penicillium chrysogenum and Penicill...

  11. Recommendations of generic names in Diaporthales competing for protection or use

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In advancing to one name for fungi, this paper treats generic names competing for use in the order Diaporthales (Ascomycota, Sordariomycetes) and makes a recommendation for the use or protection of one generic name among synonymous names that may be either sexua...

  12. Discussion of teleomorphic and anamorphic Ascomycetous yeasts and yeast-like taxa

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The relationship of ascomycetous yeasts with other members of the ascomycete fungi (Ascomycota) has been controversial for over 100 years. Because yeasts are morphologically simple, it was proposed that they represent primitive forms of ascomycetes (e.g., Guilliermond 1912). Alternatively, the ide...

  13. Trichoderma amazonicum, a new endophytic species on Hevea brasiliensis and H. guianensis from the Amazon basin

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A new species of Trichoderma (teleomorph Hypocrea, Ascomycota, Sordariomycetes, Hypocreales, Hypocreaceae), T. amazonicum, endophytic on the living sapwood and leaves of Hevea spp. trees is described. Trichoderma amazonicum is distinguished from closely related species in the Harzianum clade (e.g. ...

  14. Stenocybe fragmenta, a new species of Mycocaliciaceae with fragmenting spores

    USGS Publications Warehouse

    Peterson, E.B.; Rikkinen, Jouko

    1998-01-01

    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.

  15. Trypsin-like Proteins of the Fungi as Possible Markers of Phytopathogenicity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 74 fungal genomes, 30 species of parasitic Ascomycota contained...

  16. Molecular Systematics of Entomopathogenic Fungi

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Insect parasitism has multiple and diverse origins within the Kingdom Fungi, with shifts to trophic specialization on insects having evolved one or more times in each of the four traditionally recognized phyla of fungi, the Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. The rich legacy ...

  17. Fungal endophyte diversity in Sarracenia

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fungal endophytes were isolated from four species of the carnivorous pitcher plant genus Sarracenia: S. minor, S. oreophila, S. purpurea, and S. psittacina. Twelve taxa of fungi, eight within the Ascomycota and four within the Basidiomycota, were identified based on PCR amplification and sequencing ...

  18. Detrimental and neutral effects of a wild grass-fungal endophyte symbiotum on insect preference and performance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The presence of seed-borne Epichloë/Neotyphodium (Ascomycota: Clavicipitaceae) fungal endophytes in temperate grasses can influence the outcome of grass–insect interactions. For example, the expression of endophyte-mediated resistance to insects depends on the insect species involved. The behavior...

  19. Population genetics of Eutypa lata in the major grape-growing regions of the world and historical patterns of viticulture.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The causal agent of Eutypa dieback of grape, Eutypa lata (Ascomycota), is a destructive disease worldwide. The pathogen has a broad host range, but causes severe symptoms on only a few cultivated hosts (e.g., apricot & grape). To decipher its cosmopolitan distribution, we examined the population gen...

  20. Two members of the Ustilago maydis velvet family influence teliospore development and virulence on maize seedlings

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 disea...

  1. Sexual reproduction and recombination in the aflatoxin-producing fungus Aspergillus parasiticus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The fungal phylum Ascomycota comprises a large proportion of species with no known sexual stage, despite high genetic variability in field populations. One such asexual species, Aspergillus parasiticus, is a potent producer of carcinogenic and hepatotoxic aflatoxins, polyketide-derived secondary me...

  2. What is Scirrhia?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The ascomycete genus Scirrhia is presently treated as a member of the Dothideomycetidae, though uncertainty remains to which family it belongs in the Capnodiales within the Ascomycota. Recent collections on stems of a fern, Pteridium aquilinum (Dennstaedtiaceae) in Brazil, led to the discovery of a ...

  3. Glucosylation and other biotransformations of T-2 toxin by yeasts of the Trichomonascus clade

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Twenty-five yeasts assigned to the Trichomonascus clade (Saccharomycotina, Ascomycota), including three Trichomonascus species and 22 anamorphic species presently classified in Blastobotrys, were tested for their ability to convert T-2 toxin, a Fusarium trichothecene mycotoxin, to less toxic product...

  4. HYPOCREA RUFA/TRICHODERMA VIRIDE: A REASSESSMENT, AND DESCRIPTION OF THREE CLOSELY RELATED SPECIES WITH AND WITHOUT WARTED CONIDIA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The type species of the genus Hypocrea (Hypocreaceae, Hypocreales, Ascomycota, Fungi), H. rufa, is re-defined and epitypified using a combination of phenotype (morphology of teleomorphs and anamorphs, and characteristics in culture) and phylogenetic analyses of the translation-elongation factor 1' g...

  5. Revision of the Genus Corallomycetella with Corallonectria gen. nov. for C. jatrophae (Nectriaceae, Hypocreales)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genus Corallomycetella (Ascomycota, Sordariomycetes, Hypocreales, Nectriaceae) has been defined to include red nectrioid fungi associated with rhizomorphs in nature and culture. With the recent collection of an unusual specimen having striated ascospores, the genus was re-examined using this and...

  6. Comparative physiology of forty-five Yarrowia lipolytica strains grown on pretreated switchgrass hydrolysate

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Yarrowia lipolytica is a well-characterized yeast of the phylum Ascomycota with established use in the biotechnology industry for production of organic acids and enzymes. In addition, the yeast is a model oleaginous organism that accumulates lipids during growth on a variety of carbon sources. The a...

  7. Phylogenetic placement of the ectomycorrhizal genus Cenococcum in Gloniaceae (Dothideomycetes).

    PubMed

    Spatafora, Joseph W; Owensby, C Alisha; Douhan, Greg W; Boehm, Eric W A; Schoch, Conrad L

    2012-01-01

    Cenococcum is a genus of ectomycorrhizal Ascomycota that has a broad host range and geographic distribution. It is not known to produce either meiotic or mitotic spores and is known to exist only in the form of hyphae, sclerotia and host-colonized ectomycorrhizal root tips. Due to its lack of sexual and asexual spores and reproductive structures, it has proven difficult to incorporate into traditional classification within Ascomycota. Molecular phylogenetic studies of ribosomal RNA placed Cenococcum in Dothideomycetes, but the definitive identification of closely related taxa remained elusive. Here we report a phylogenetic analysis of five nuclear loci (SSU, LSU, TEF1, RPB1, RPB2) of Dothideomycetes that placed Cenococcum as a close relative of the genus Glonium of Gloniaceae (Pleosporomycetidae incertae sedis) with strong statistical support. Glonium is a genus of saprobic Dothideomycetes that produces darkly pigmented, carbonaceous, hysteriate apothecia and is not known to be biotrophic. Evolution of ectomycorhizae, Cenococcum and Dothideomycetes is discussed. PMID:22453119

  8. Fireworks under the microscope: a spectacular new species of Zodiomyces from the Thaxter collection.

    PubMed

    Rossi, Walter; Haelewaters, Danny; Pfister, Donald H

    2016-01-01

    A new species of Zodiomyces (Ascomycota, Laboulbeniales) is described, Z. rhizophorus, parasitic on a hydrophilid beetle (Coleoptera, Hydrophilidae) from Trinidad. This species was discovered during the examination of the slides of Laboulbeniales made by Roland Thaxter. It is characterized by numerous long, slender, multicellular and multiseriate outgrowths at the base of the receptacle. Thaxter's outstanding illustrations have set a standard in the field of mycology; we provide a review of the methods he employed in the preparation of these illustrations. PMID:27055574

  9. Comparison of pectin-degrading fungal communities in temperate forests using glycosyl hydrolase family 28 pectinase primers targeting Ascomycete fungi.

    PubMed

    Gacura, Matthew D; Sprockett, Daniel D; Heidenreich, Bess; Blackwood, Christopher B

    2016-04-01

    Fungi have developed a wide assortment of enzymes to break down pectin, a prevalent polymer in plant cell walls that is important in plant defense and structure. One enzyme family used to degrade pectin is the glycosyl hydrolase family 28 (GH28). In this study we developed primers for the amplification of GH28 coding genes from a database of 293 GH28 sequences from 40 fungal genomes. The primers were used to successfully amplify GH28 pectinases from all Ascomycota cultures tested, but only three out of seven Basidiomycota cultures. In addition, we further tested the primers in PCRs on metagenomic DNA extracted from senesced tree leaves from different forest ecosystems, followed by cloning and sequencing. Taxonomic specificity for Ascomycota GH28 genes was tested by comparing GH28 composition in leaves to internal transcribed spacer (ITS) amplicon composition using pyrosequencing. All sequences obtained from GH28 primers were classified as Ascomycota; in contrast, ITS sequences indicated that fungal communities were up to 39% Basidiomycetes. Analysis of leaf samples indicated that both forest stand and ecosystem type were important in structuring fungal communities. However, site played the prominent role in explaining GH28 composition, whereas ecosystem type was more important for ITS composition, indicating possible genetic drift between populations of fungi. Overall, these primers will have utility in understanding relationships between fungal community composition and ecosystem processes, as well as detection of potentially pathogenic Ascomycetes. PMID:26899925

  10. Comparison of pectin-degrading fungal communities in temperate forests using glycosyl hydrolase family 28 pectinase primers targeting Ascomycete fungi

    DOE PAGESBeta

    Gacura, Matthew D.; Sprockett, Daniel D.; Heidenreich, Bess; Blackwood, Christopher B.

    2016-02-17

    Here, fungi have developed a wide assortment of enzymes to break down pectin, a prevalent polymer in plant cell walls that is important in plant defense and structure. One enzyme family used to degrade pectin is the glycosyl hydrolase family 28 (GH28). In this studywe developed primers for the amplification of GH28 coding genes from a database of 293 GH28 sequences from40 fungal genomes. The primerswere used to successfully amplify GH28 pectinases from all Ascomycota cultures tested, but only three out of seven Basidiomycota cultures. In addition, we further tested the primers in PCRs on metagenomic DNA extracted from senescedmore » tree leaves from different forest ecosystems, followed by cloning and sequencing. Taxonomic specificity for Ascomycota GH28 genes was tested by comparing GH28 composition in leaves to internal transcribed spacer (ITS) amplicon composition using pyrosequencing. All sequences obtained from GH28 primers were classified as Ascomycota; in contrast, ITS sequences indicated that fungal communitieswere up to 39% Basidiomycetes. Analysis of leaf samples indicated that both forest stand and ecosystemtype were important in structuring fungal communities. However, site played the prominent role in explaining GH28 composition, whereas ecosystem type was more important for ITS composition, indicating possible genetic drift between populations of fungi. Overall, these primers will have utility in understanding relationships between fungal community composition and ecosystem processes, as well as detection of potentially pathogenic Ascomycetes.« less

  11. Spatial and Temporal Profiling of Griseofulvin Production in Xylaria cubensis Using Mass Spectrometry Mapping

    PubMed Central

    Sica, Vincent P.; Rees, Evan R.; Tchegnon, Edem; Bardsley, Robert H.; Raja, Huzefa A.; Oberlies, Nicholas H.

    2016-01-01

    A large portion of natural products research revolves around the discovery of new, bioactive chemical entities; however, studies to probe the biological purpose of such secondary metabolites for the host organism are often limited. Mass spectrometry mapping of secondary metabolite biosynthesis in situ can be used to probe a series of ecological questions about fungi that may be lost through traditional natural products chemistry extraction protocols. A griseofulvin-producing fungal culture of the Xylariaceae family, isolated as an endophyte of the tree Asimina triloba, was analyzed through a series of spatial and temporal mapping experiments. This fungus produced unique fungal characteristics, such as guttates and stroma, both of which were explored spatially. The distribution of griseofulvin on this culture in isolation was compared to its dispersal when grown in co-culture with a competing Penicillium species via a droplet–based surface sampling system. The fungistatic properties of griseofulvin were visualized, including the consequences for biosynthesis of polyhydroxyanthraquinones in a rival culture. PMID:27199902

  12. Identification of a Fungal 1,8-Cineole Synthase from Hypoxylon sp. with Specificity Determinants in Common with the Plant Synthases*

    PubMed Central

    Shaw, Jeffrey J.; Berbasova, Tetyana; Sasaki, Tomoaki; Jefferson-George, Kyra; Spakowicz, Daniel J.; Dunican, Brian F.; Portero, Carolina E.; Narváez-Trujillo, Alexandra; Strobel, Scott A.

    2015-01-01

    Terpenes are an important and diverse class of secondary metabolites widely produced by fungi. Volatile compound screening of a fungal endophyte collection revealed a number of isolates in the family Xylariaceae, producing a series of terpene molecules, including 1,8-cineole. This compound is a commercially important component of eucalyptus oil used in pharmaceutical applications and has been explored as a potential biofuel additive. The genes that produce terpene molecules, such as 1,8-cineole, have been little explored in fungi, providing an opportunity to explore the biosynthetic origin of these compounds. Through genome sequencing of cineole-producing isolate E7406B, we were able to identify 11 new terpene synthase genes. Expressing a subset of these genes in Escherichia coli allowed identification of the hyp3 gene, responsible for 1,8-cineole biosynthesis, the first monoterpene synthase discovered in fungi. In a striking example of convergent evolution, mutational analysis of this terpene synthase revealed an active site asparagine critical for water capture and specificity during cineole synthesis, the same mechanism used in an unrelated plant homologue. These studies have provided insight into the evolutionary relationship of fungal terpene synthases to those in plants and bacteria and further established fungi as a relatively untapped source of this important and diverse class of compounds. PMID:25648891

  13. Measurement of personal exposure to outdoor aeromycota in northern New South Wales, Australia.

    PubMed

    Green, Brett James; O'Meara, Timothy; Sercombe, Jason; Tovey, Euan

    2006-01-01

    Aerobiological sampling traditionally uses a volumetric spore trap located in a fixed position to estimate personal exposure to airborne fungi. In this study, the number and identity of fungi inhaled by human subjects (n=34), wearing Intra-nasal air samplers (INASs), was measured over 2-hour periods in an outdoor community setting, and compared to fungal counts made with a Burkard spore trap and Institute of Occupational Medicine personal filter air samplers (IOMs). All sampling devices were in close proximity and located in an outdoor environment in Casino, northern New South Wales, Australia. Using INASs, the most prevalent fungi inhaled belonged to soil or vegetation borne spores of Alternaria, Arthrinium, Bipolaris, Cladosporium, Curvularia, Epicoccum, Exserohilum, Fusarium, Pithomyces, Spegazzinia and Tetraploa species, Xylariaceae ascospores, in addition to hyphal fragments. These results showed that inhaled fungal exposure in most people varied in a 2-fold range with 10-fold outliers. In addition, the INASs and personal air filters agreed more with each other than with Burkard spore trap counts (r=0.74, p < 0.0001). These findings further support a new paradigm of personal fungal exposure, which implicates the inhalation of a spectrum of fungi more closely associated with soil or vegetation borne mycoflora and hyphal fragments than what is collected by stationary spore traps in the same geographic region. PMID:17195994

  14. Diversity and Taxonomy of Endophytic Xylariaceous Fungi from Medicinal Plants of Dendrobium (Orchidaceae)

    PubMed Central

    Chen, Juan; Zhang, Li-Chun; Xing, Yong-Mei; Wang, Yun-Qiang; Xing, Xiao-Ke; Zhang, Da-Wei; Liang, Han-Qiao; Guo, Shun-Xing

    2013-01-01

    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. PMID:23472167

  15. Identification of a fungal 1,8-cineole synthase from Hypoxylon sp. with specificity determinants in common with the plant synthases.

    PubMed

    Shaw, Jeffrey J; Berbasova, Tetyana; Sasaki, Tomoaki; Jefferson-George, Kyra; Spakowicz, Daniel J; Dunican, Brian F; Portero, Carolina E; Narváez-Trujillo, Alexandra; Strobel, Scott A

    2015-03-27

    Terpenes are an important and diverse class of secondary metabolites widely produced by fungi. Volatile compound screening of a fungal endophyte collection revealed a number of isolates in the family Xylariaceae, producing a series of terpene molecules, including 1,8-cineole. This compound is a commercially important component of eucalyptus oil used in pharmaceutical applications and has been explored as a potential biofuel additive. The genes that produce terpene molecules, such as 1,8-cineole, have been little explored in fungi, providing an opportunity to explore the biosynthetic origin of these compounds. Through genome sequencing of cineole-producing isolate E7406B, we were able to identify 11 new terpene synthase genes. Expressing a subset of these genes in Escherichia coli allowed identification of the hyp3 gene, responsible for 1,8-cineole biosynthesis, the first monoterpene synthase discovered in fungi. In a striking example of convergent evolution, mutational analysis of this terpene synthase revealed an active site asparagine critical for water capture and specificity during cineole synthesis, the same mechanism used in an unrelated plant homologue. These studies have provided insight into the evolutionary relationship of fungal terpene synthases to those in plants and bacteria and further established fungi as a relatively untapped source of this important and diverse class of compounds. PMID:25648891

  16. Spatial and Temporal Profiling of Griseofulvin Production in Xylaria cubensis Using Mass Spectrometry Mapping.

    PubMed

    Sica, Vincent P; Rees, Evan R; Tchegnon, Edem; Bardsley, Robert H; Raja, Huzefa A; Oberlies, Nicholas H

    2016-01-01

    A large portion of natural products research revolves around the discovery of new, bioactive chemical entities; however, studies to probe the biological purpose of such secondary metabolites for the host organism are often limited. Mass spectrometry mapping of secondary metabolite biosynthesis in situ can be used to probe a series of ecological questions about fungi that may be lost through traditional natural products chemistry extraction protocols. A griseofulvin-producing fungal culture of the Xylariaceae family, isolated as an endophyte of the tree Asimina triloba, was analyzed through a series of spatial and temporal mapping experiments. This fungus produced unique fungal characteristics, such as guttates and stroma, both of which were explored spatially. The distribution of griseofulvin on this culture in isolation was compared to its dispersal when grown in co-culture with a competing Penicillium species via a droplet-based surface sampling system. The fungistatic properties of griseofulvin were visualized, including the consequences for biosynthesis of polyhydroxyanthraquinones in a rival culture. PMID:27199902

  17. Illumina MiSeq investigations on the changes of microbial community in the Fusarium oxysporum f.sp. cubense infected soil during and after reductive soil disinfestation.

    PubMed

    Huang, Xinqi; Liu, Liangliang; Wen, Teng; Zhu, Rui; Zhang, Jinbo; Cai, Zucong

    2015-12-01

    Although reductive soil disinfestation (RSD) is increasingly used for the control of soil-borne diseases, its impact on the soil microbial community during and after RSD remains poorly understood. MiSeq pyrosequencing, real-time PCR and denaturing gradient gel electrophoresis were performed to investigate the changes of microbial community in the Fusarium oxysporum f. sp. cubense (FOC) infected soil during RSD and at the simulative banana cultivation after RSD. The results showed that RSD significantly increased soil microbial populations and a different microbial community with the pathogenic soil was established after RSD. Specifically, the number of Firmicutes mainly containing Ruminococcus and Coprococcus followed by a small part of Clostridium which were the dominant bacterial genera significantly increased during RSD. In contrast, Symbiobacterium and Flavisolibacter were the dominant genera in the flooding soil. When the soils were recovered under aerobic condition, the relative abundances of the bacteria belonging to the phylum Bacteroidetes, Acidobacteria, Planctomycetes increased as alternatives to the reducing Firmicutes. For fungi, the population of F. oxysporum significantly decreased during RSD accompanied with the pH decline, which resulted in the significant decrease of relative abundance in the phylum Ascomycota. Alternatively, the relative abundances of some other fungal species increased, such as Chaetomium spp. and Penicillium spp. belonging to Ascomycota and the family Clavulinaceae belonging to Basidiomycota. Then, the relative abundance of Ascomycota re-increased after RSD with Podospora and Zopfiella as dominant genera, whereas the relative abundance of Fusarium further decreased. Overall, the microbial populations and community re-established by RSD made the soil more disease-suppressive and beneficial to the soil nutrient cycling and plant growth compared with the previous pathogenic soil. PMID:26640050

  18. Phytochelatin synthase is required for tolerating metal toxicity in a basidiomycete yeast and is a conserved factor involved in metal homeostasis in fungi

    PubMed Central

    Shine, Alaina M; Shakya, Viplendra PS; Idnurm, Alexander

    2015-01-01

    Background Phytochelatin synthase (PCS) is an enzyme that catalyzes the biosynthesis of phytochelatin from glutathione. Phytochelatins protect cells against the toxic effects of non-essential heavy metals, such as cadmium, and hence growth is restricted in the presence of these metals in mutants in PCS-encoding genes. PCS genes from fungi have been characterized in only two species in the Ascomycota, and these genes are considered sparsely distributed in the fungal kingdom. Results A gene encoding a putative PCS was identified in Sporobolomyces sp. strain IAM 13481, a fungus that is a member of the Pucciniomycotina subphylum of the Basidiomycota. The function of this PCS1 gene was assessed by heterologous expression in the Ascomycota yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, and by mutating the gene in Sporobolomyces. The gene is required for tolerance to toxic concentrations of non-essential cadmium as well as the essential metal copper. Pcs1 homologs in fungi and other eukaryotes have putative targeting sequences for mitochondrial localization: the S. pombe homolog was fused to green fluorescent protein and it co-localized with a mitochondrial dye. Evaluation of the presence or absence of PCS and PCS-like homologs in the genome sequences of fungi indicates that they have a wide distribution, and the absence in most Ascomycota and Basidiomycota (the Dikarya) species can be explained by a small number of gene losses. Conclusions The ecology of the species within the fungi carrying putative PCS genes, the phenotypes of phytochelatin synthase mutants in two major fungal lineages, and the presence of homologs in many non-Dikarya lineages parallel what is seen in the plant and animal kingdoms. That is, PCS is a protein present early during the evolution of the fungi and whose role is not solely dedicated to combating toxic concentrations of non-essential metals. PMID:25926993

  19. A new method to evaluate the biocontrol potential of single spore isolates of fungal entomopathogens

    PubMed Central

    Posada, Francisco J.; Vega, Fernando E.

    2005-01-01

    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. PMID:17119619

  20. Structural Diversity and Biological Activities of Indole Diketopiperazine Alkaloids from Fungi.

    PubMed

    Ma, Yang-Min; Liang, Xi-Ai; Kong, Yang; Jia, Bin

    2016-09-01

    Indole diketopiperazine alkaloids are secondary metabolites of microorganisms that are widely distributed in filamentous fungi, especially in the genera Aspergillus and Penicillium of the phylum Ascomycota or sac fungi. These alkaloids represent a group of natural products characterized by diversity in both chemical structures and biological activities. This review aims to summarize 166 indole diketopiperazine alkaloids from fungi published from 1944 to mid-2015. The emphasis is on diverse chemical structures within these alkaloids and their relevant biological activities. The aim is to assess which of these compounds merit further study for purposes of drug development. PMID:27538469

  1. New insight into biodegradation of polylactide (PLA)/clay nanocomposites using molecular ecological techniques.

    PubMed

    Sangwan, Parveen; Way, Cameron; Wu, Dong-Yang

    2009-07-01

    Novel molecular ecological techniques were used to study changes in microbial community structure and population during degradation of polylactide (PLA)/organically modified layered silicates (OMLS) nanocomposites. Cloned gene sequences belonging to members of the phyla Actinobacteria and Ascomycota comprized the most dominant groups of microorganisms during biodegradation of PLA/OMLS nanocomposites. Due to their numerical abundance, members of these microbial groups are likely to play an important role during biodegradation process. This paper presents new insights into the biodegradability of PLA/OMLS nanocomposites and highlights the importance of using novel molecular ecological techniques for in situ identification of new microorganisms involved in biodegradation of polymeric materials. PMID:19148900

  2. Permanent genetic resources added to Molecular Ecology Resources Database 1 February 2013-31 March 2013.

    PubMed

    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

    2013-07-01

    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

  3. New Primers for Discovering Fungal Diversity Using Nuclear Large Ribosomal DNA

    PubMed Central

    Gloor, Gregory B.; Lindo, Zoë

    2016-01-01

    Metabarcoding has become an important tool in the discovery of biodiversity, including fungi, which are the second most speciose group of eukaryotes, with diverse and important ecological roles in terrestrial ecosystems. We have designed and tested new PCR primers that target the D1 variable region of nuclear large subunit (LSU) ribosomal DNA; one set that targets the phylum Ascomycota and another that recovers all other fungal phyla. The primers yield amplicons compatible with the Illumina MiSeq platform, which is cost-effective and has a lower error rate than other high throughput sequencing platforms. The new primer set LSU200A-F/LSU476A-R (Ascomycota) yielded 95–98% of reads of target taxa from environmental samples, and primers LSU200-F/LSU481-R (all other fungi) yielded 72–80% of target reads. Both primer sets have fairly low rates of data loss, and together they cover a wide variety of fungal taxa. We compared our results with these primers by amplifying and sequencing a subset of samples using the previously described ITS3_KYO2/ITS4_KYO3 primers, which amplify the internal transcribed spacer 2 (ITS2) of Ascomycota and Basidiomycota. With approximately equivalent read depth, our LSU primers recovered a greater number and phylogenetic diversity of sequences than the ITS2 primers. For instance, ITS3_KYO2/ITS4_KYO3 primers failed to pick up any members of Eurotiales, Mytilinidiales, Pezizales, Saccharomycetales, or Venturiales within Ascomycota, or members of Exobasidiomycetes, Microbotryomycetes, Pucciniomycetes, or Tremellomycetes within Basidiomycota, which were retrieved in good numbers from the same samples by our LSU primers. Among the OTUs recovered using the LSU primers were 127 genera and 28 species that were not obtained using the ITS2 primers, although the ITS2 primers recovered 10 unique genera and 16 species that were not obtained using either of the LSU primers These features identify the new primer sets developed in this study as useful

  4. Analysis of the microbial diversity in faecal material of the endangered blue whale, Balaenoptera musculus.

    PubMed

    Guass, Olivia; Haapanen, Lisa Meier; Dowd, Scot E; Širović, Ana; McLaughlin, Richard William

    2016-07-01

    Using bacterial and fungal tag-encoded FLX-Titanium amplicon pyrosequencing, the microbiota of the faecal material of two blue whales living in the wild off the coast of California was investigated. In both samples the most predominant bacterial phylum was the Firmicutes with Clostridium spp. being the most dominant bacteria. The most predominant fungi were members of the phylum Ascomycota with Metschnikowia spp. being the most dominant. In this study, we also preliminarily characterised the culturable anaerobic bacteria from the faecal material, using traditional culture and 16S rRNA gene sequencing approaches. In total, three bacterial species belonging to the phylum Firmicutes were identified. PMID:27108139

  5. Fungal diversity from various marine habitats deduced through culture-independent studies.

    PubMed

    Manohar, Cathrine Sumathi; Raghukumar, Chandralata

    2013-04-01

    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

  6. Comparative Genomics and Transcriptomics Analyses Reveal Divergent Lifestyle Features of Nematode Endoparasitic Fungus Hirsutella minnesotensis

    PubMed Central

    Lai, Yiling; Liu, Keke; Zhang, Xinyu; Zhang, Xiaoling; Li, Kuan; Wang, Niuniu; Shu, Chi; Wu, Yunpeng; Wang, Chengshu; Bushley, Kathryn E.; Xiang, Meichun; Liu, Xingzhong

    2014-01-01

    Hirsutella minnesotensis [Ophiocordycipitaceae (Hypocreales, Ascomycota)] is a dominant endoparasitic fungus by using conidia that adhere to and penetrate the secondary stage juveniles of soybean cyst nematode. Its genome was de novo sequenced and compared with five entomopathogenic fungi in the Hypocreales and three nematode-trapping fungi in the Orbiliales (Ascomycota). The genome of H. minnesotensis is 51.4 Mb and encodes 12,702 genes enriched with transposable elements up to 32%. Phylogenomic analysis revealed that H. minnesotensis was diverged from entomopathogenic fungi in Hypocreales. Genome of H. minnesotensis is similar to those of entomopathogenic fungi to have fewer genes encoding lectins for adhesion and glycoside hydrolases for cellulose degradation, but is different from those of nematode-trapping fungi to possess more genes for protein degradation, signal transduction, and secondary metabolism. Those results indicate that H. minnesotensis has evolved different mechanism for nematode endoparasitism compared with nematode-trapping fungi. Transcriptomics analyses for the time-scale parasitism revealed the upregulations of lectins, secreted proteases and the genes for biosynthesis of secondary metabolites that could be putatively involved in host surface adhesion, cuticle degradation, and host manipulation. Genome and transcriptome analyses provided comprehensive understanding of the evolution and lifestyle of nematode endoparasitism. PMID:25359922

  7. Alectorioid Morphologies in Paleogene Lichens: New Evidence and Re-Evaluation of the Fossil Alectoria succini Mägdefrau.

    PubMed

    Kaasalainen, Ulla; Heinrichs, Jochen; Krings, Michael; Myllys, Leena; Grabenhorst, Heinrich; Rikkinen, Jouko; Schmidt, Alexander R

    2015-01-01

    One of the most important issues in molecular dating studies concerns the incorporation of reliable fossil taxa into the phylogenies reconstructed from DNA sequence variation in extant taxa. Lichens are symbiotic associations between fungi and algae and/or cyanobacteria. Several lichen fossils have been used as minimum age constraints in recent studies concerning the diversification of the Ascomycota. Recent evolutionary studies of Lecanoromycetes, an almost exclusively lichen-forming class in the Ascomycota, have utilized the Eocene amber inclusion Alectoria succinic as a minimum age constraint. However, a re-investigation of the type material revealed that this inclusion in fact represents poorly preserved plant remains, most probably of a root. Consequently, this fossil cannot be used as evidence of the presence of the genus Alectoria (Parmeliaceae, Lecanorales) or any other lichens in the Paleogene. However, newly discovered inclusions from Paleogene Baltic and Bitterfeld amber verify that alectorioid morphologies in lichens were in existence by the Paleogene. The new fossils represent either a lineage within the alectorioid group or belong to the genus Oropogon. PMID:26053106

  8. Traversing the fungal terpenome

    PubMed Central

    Quin, Maureen B.; Flynn, Christopher M.; Schmidt-Dannert, Claudia

    2014-01-01

    Fungi (Ascomycota and Basidiomycota) are prolific producers of structurally diverse terpenoid compounds. Classes of terpenoids identified in fungi include the sesqui-, di- and triterpenoids. Biosynthetic pathways and enzymes to terpenoids from each of these classes have been described. These typically involve the scaffold generating terpene synthases and cyclases, and scaffold tailoring enzymes such as e.g. cytochrome P450 monoxygenases, NAD(P)+ and flavin dependent oxidoreductases, and various group transferases that generate the final bioactive structures. The biosynthesis of several sesquiterpenoid mycotoxins and bioactive diterpenoids has been well-studied in Ascomycota (e.g. filamentous fungi). Little is known about the terpenoid biosynthetic pathways in Basidiomycota (e.g. mushroom forming fungi), although they produce a huge diversity of terpenoid natural products. Specifically, many trans-humulyl cation derived sesquiterpenoid natural products with potent bioactivities have been isolated. Biosynthetic gene clusters responsible for the production of trans-humulyl cation derived protoilludanes, and other sesquiterpenoids, can be rapidly identified by genome sequencing and bioinformatic methods. Genome mining combined with heterologous biosynthetic pathway refactoring has the potential to facilitate discovery and production of pharmaceutically relevant fungal terpenoids. PMID:25171145

  9. Fluid mechanical responses to nutrient depletion in fungi and biofilmsa)

    NASA Astrophysics Data System (ADS)

    Brenner, Michael P.

    2014-10-01

    In both fungi and bacterial biofilms, when nutrients are depleted, the organisms cannot physically migrate to find a new source, but instead must develop adaptations that allow them to survive. This paper reviews our work attempting to discover design principles for these adaptations. We develop fluid mechanical models, and aim to understand whether these suggest organizing principles for the observed morphological diversity. Determining whether a proposed organizing principle explains extant biological designs is fraught with difficulty: simply because a design principle predicts characteristics similar to an organism's morphology could just as well be accidental as revealing. In each of the two sets of examples, we adopt different strategies to develop understanding in spite of this difficulty. Within the fungal phylum Ascomycota, we use the large observed diversity of different morphological solutions to the fundamental fluid mechanical problem to measure how far each solution is from a design optimum, thereby measuring how far the extant designs deviate from the hypothesized optimum. This allows comparing different design principles to each other. For biofilms, we use engineering principles to make qualitative predictions of what types of adaptations might exist given the physicochemical properties of the repertoire of proteins that bacteria can create, and then find evidence for these adaptations in experiments. While on the surface this paper addresses the particular adaptations used by the fungal phylum Ascomycota and bacterial biofilms, we also aim to motivate discussion of different approaches to using design principles, fluid mechanical or otherwise, to rationalize observed engineering solutions in biology.

  10. Assessment of the fungal diversity and succession of ligninolytic endophytes in Camellia japonica leaves using clone library analysis.

    PubMed

    Hirose, Dai; Matsuoka, Shunsuke; Osono, Takashi

    2013-01-01

    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

  11. Activity of the novel fungicide SYP-Z048 against plant pathogens.

    PubMed

    Chen, Fengping; Han, Ping; Liu, Pengfei; Si, Naiguo; Liu, Junli; Liu, Xili

    2014-01-01

    In in vitro tests with 18 plant pathogens, the fungicide 3-[5-(4-chlorophenyl)-2,3-dimethyl-3-isoxazolidinyl] pyridine (SYP-Z048) was highly effective on inhibiting mycelial growth of various ascomycota and basidiomycota, with EC50 values ranging from 0.008 to 1.140 μg/ml. SYP-Z048 had much weaker activity against growth of oomycota with EC50 values > 100 μg/ml. In a second in vitro test with Monilinia fructicola isolates, SYP-Z048 inhibited mycelial growth (EC50 = 0.013 μg/ml), germ tube elongation (EC50 = 0.007 μg/ml), and sporulation but did not affect spore germination. In a detached pear fruit assay inoculated with M. fructicola isolates, SYP-Z048 showed protective and curative activity. Field tests indicated that SYP-Z048 was an efficacious fungicide for control of brown rot disease in two peach orchards. When applied to a single spot on a tomato leaflet in a compound leaf, SYP-Z048 suppressed the growth of Botrytis cinerea isolates on the rest 4 leaflets, indicating that the fungicide has systemic movement in plant tissues. These results indicate that SYP-Z048 has potential for management of brown rot causing by M. fructicola and other diseases caused by ascomycota and basidiomycota. PMID:25253681

  12. Seasonal Succession of Fungi Associated with Ips typographus Beetles and Their Phoretic Mites in an Outbreak Region of Finland

    PubMed Central

    Mahilainen, Saila; Harrington, Alison; Vanhanen, Henri; Eriksson, Miikka; Mehtätalo, Lauri; Pappinen, Ari; Wingfield, Michael J.

    2016-01-01

    The ophiostomatoid fungi (Microascales and Ophiostomatales, Ascomycota) are common associates of Ips typographus, and include tree pathogens and species responsible for blue-stain of timber. Fungal assemblages associated with I. typographus have varied considerably between studies but few investigations have attempted to explain this variation. For this reason, we assessed the overall cultivable fungal diversity associated with I. typographus in a storm-felled spruce forest in south-eastern Finland. Fungi were isolated from the individually collected beetles as well as their phoretic mites in spring, summer and autumn, including different life stages of the beetle (hibernation, dispersal flight and first generation). The internal transcribed spacer (ITS) gene region was used to identify the fungi. A total of 32 operational taxonomic units (OTUs) were found and these resided in four fungal phyla/subphyla (24 Ascomycota, 2 Basidiomycota, 5 Mucoromycotina, 1 Mortierellomycotina) in association with adult bark beetles. Ophiostomatoid species were the most commonly detected fungal associates. A generalized linear model analysis showed a clear association between fungal communities and season, indicating seasonal succession among I. typographus-associated fungi. The season of sampling appears to be an important factor that has resulted in inconsistencies between results in previous studies. Many of these fungi were also found on phoretic mites and their presence or absence could have influenced variation in patterns of association. PMID:27187192

  13. Diversity and Distribution of Aquatic Fungal Communities in the Ny-Ålesund Region, Svalbard (High Arctic) : Aquatic Fungi in the Arctic.

    PubMed

    Zhang, Tao; Wang, Neng-Fei; Zhang, Yu-Qin; Liu, Hong-Yu; Yu, Li-Yan

    2016-04-01

    We assessed the diversity and distribution of fungi in 13 water samples collected from four aquatic environments (stream, pond, melting ice water, and estuary) in the Ny-Ålesund Region, Svalbard (High Arctic) using 454 pyrosequencing with fungi-specific primers targeting the internal transcribed spacer (ITS) region of the ribosomal rRNA gene. Aquatic fungal communities in this region showed high diversity, with a total of 43,061 reads belonging to 641 operational taxonomic units (OTUs) being found. Of these OTUs, 200 belonged to Ascomycota, 196 to Chytridiomycota, 120 to Basidiomycota, 13 to Glomeromycota, and 10 to early diverging fungal lineages (traditional Zygomycota), whereas 102 belonged to unknown fungi. The major orders were Helotiales, Eurotiales, and Pleosporales in Ascomycota; Chytridiales and Rhizophydiales in Chytridiomycota; and Leucosporidiales and Sporidiobolales in Basidiomycota. The common fungal genera Penicillium, Rhodotorula, Epicoccum, Glaciozyma, Holtermanniella, Betamyces, and Phoma were identified. Interestingly, the four aquatic environments in this region harbored different aquatic fungal communities. Salinity, conductivity, and temperature were important factors in determining the aquatic fungal diversity and community composition. The results suggest the presence of diverse fungal communities and a considerable number of potentially novel fungal species in Arctic aquatic environments, which can provide reliable data for studying the ecological and evolutionary responses of fungi to climate change in the Arctic ecosystem. PMID:26492897

  14. Phylogenetic diversity of fungal communities in areas accessible and not accessible to tourists in Naracoorte Caves.

    PubMed

    Adetutu, Eric M; Thorpe, Krystal; Bourne, Steven; Cao, Xiangsheng; Shahsavari, Esmaeil; Kirby, Greg; Ball, Andrew S

    2011-01-01

    The fungal diversity in areas accessible and not accessible to tourists at UNESCO World Heritage-listed Naracoorte Caves was investigated with culture-dependent and culture-independent techniques for assistance in cave management protocol development. The caves were selected based on tourist numbers and configurations: Stick Tomato (open, high numbers), Alexandra (lockable openings, high numbers) and Strawhaven (control; no access). Culture-based survey revealed Ascomycota dominance irrespective of sampling area with Microascales (Trichurus sp.) being most frequently isolated. Some Hypocreales-like sequences belonging to Fusarium sp., Trichoderma sp. and Neonectria sp. (Stick Tomato) were cultured only from areas not accessible to tourists. These orders also were detected by DGGE assay irrespective of sampling area. The predominance of Ascomycota (especially Microascales) suggested their important ecological roles in these caves. Culture-independent analysis showed higher Shannon fungal diversity values (from ITS-based DGGE profiles) in tourist-accessible areas of these caves than in inaccessible areas with the fungal community banding patterns being substantially different in Stick Tomato Cave. Further investigations are needed to determine the cause of the differences in the fungal communities of Stick Tomato Cave, although cave-related factors such as use, configuration and sediment heterogeneity might have contributed to these differences. PMID:21642344

  15. Widespread occurrence and phylogenetic placement of a soil clone group adds a prominant new branch to the fungal tree of life

    SciTech Connect

    Porter, Terri M.; Schadt, Christopher Warren; Rizvi, L; Martin, Andrew P.; Schmidt, Steven K.; Scott-Denton, Laura; Vilgalys, Rytas; Moncalvo, Jean-Marc

    2008-01-01

    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 Group I (SCGI). We expand the breadth of environments surveyed and develop a taxon-specific primer to amplify 2.4 kbp rDNA fragments directly from soil. Our results also expand the known range of this group from North America to Europe and Australia. The ancient origin of SCGI implies that it may represent an important transitional form among the basal Ascomycota groups. SCGI is unusual because it currently represents the only major fungal lineage known only from sequence data. This is an important contribution towards building a more complete fungal phylogeny and highlights the need for further work to determine the function and biology of SCGI taxa.

  16. Mechanisms of Bacterial (Serratia marcescens) Attachment to, Migration along, and Killing of Fungal Hyphae.

    PubMed

    Hover, Tal; Maya, Tal; Ron, Sapir; Sandovsky, Hani; Shadkchan, Yana; Kijner, Nitzan; Mitiagin, Yulia; Fichtman, Boris; Harel, Amnon; Shanks, Robert M Q; Bruna, Roberto E; García-Véscovi, Eleonora; Osherov, Nir

    2016-05-01

    We have found a remarkable capacity for the ubiquitous Gram-negative rod bacteriumSerratia marcescensto migrate along and kill the mycelia of zygomycete molds. This migration was restricted to zygomycete molds and several basidiomycete species. No migration was seen on any molds of the phylum Ascomycota.S. marcescensmigration did not require fungal viability or surrounding growth medium, as bacteria migrated along aerial hyphae as well.S. marcescensdid not exhibit growth tropism toward zygomycete mycelium. Bacterial migration along hyphae proceeded only when the hyphae grew into the bacterial colony.S. marcescenscells initially migrated along the hyphae, forming attached microcolonies that grew and coalesced to generate a biofilm that covered and killed the mycelium. Flagellum-defective strains ofS. marcescenswere able to migrate along zygomycete hyphae, although they were significantly slower than the wild-type strain and were delayed in fungal killing. Bacterial attachment to the mycelium does not necessitate type 1 fimbrial adhesion, since mutants defective in this adhesin migrated equally well as or faster than the wild-type strain. Killing does not depend on the secretion ofS. marcescenschitinases, as mutants in which all three chitinase genes were deleted retained wild-type killing abilities. A better understanding of the mechanisms by whichS. marcescensbinds to, spreads on, and kills fungal hyphae might serve as an excellent model system for such interactions in general; fungal killing could be employed in agricultural fungal biocontrol. PMID:26896140

  17. Watershed-Scale Fungal Community Characterization along a pH Gradient in a Subsurface Environment Cocontaminated with Uranium and Nitrate

    PubMed Central

    Jasrotia, Puja; Green, Stefan J.; Canion, Andy; Overholt, Will A.; Prakash, Om; Wafula, Denis; Hubbard, Daniela; Watson, David B.; Schadt, Christopher W.; Brooks, Scott C.

    2014-01-01

    The objective of this study was to characterize fungal communities in a subsurface environment cocontaminated with uranium and nitrate at the watershed scale and to determine the potential contribution of fungi to contaminant transformation (nitrate attenuation). The abundance, distribution, and diversity of fungi in subsurface groundwater samples were determined using quantitative and semiquantitative molecular techniques, including quantitative PCR of eukaryotic small-subunit rRNA genes and pyrosequencing of fungal internal transcribed spacer (ITS) regions. Potential bacterial and fungal denitrification was assessed in sediment-groundwater slurries amended with antimicrobial compounds and in fungal pure cultures isolated from the subsurface. Our results demonstrate that subsurface fungal communities are dominated by members of the phylum Ascomycota, and a pronounced shift in fungal community composition occurs across the groundwater pH gradient at the field site, with lower diversity observed under acidic (pH <4.5) conditions. Fungal isolates recovered from subsurface sediments, including cultures of the genus Coniochaeta, which were detected in abundance in pyrosequence libraries of site groundwater samples, were shown to reduce nitrate to nitrous oxide. Denitrifying fungal isolates recovered from the site were classified and found to be distributed broadly within the phylum Ascomycota and within a single genus of the Basidiomycota. Potential denitrification rate assays with sediment-groundwater slurries showed the potential for subsurface fungi to reduce nitrate to nitrous oxide under in situ acidic pH conditions. PMID:24389927

  18. Watershed scale fungal community characterization along a pH gradient in a subsurface environment co-contaminated with uranium and nitrate

    SciTech Connect

    Jasrotia, Puja; Green, Stefan; Canion, Andy; Overholt, Will; Prakash, Om; Wafula, Dennis; Hubbard, Daniela; Watson, David B; Schadt, Christopher Warren; Brooks, Scott C; Kostka,

    2014-01-01

    The objective of this study was to characterize fungal communities in a subsurface environment co-contaminated with uranium and nitrate at the watershed scale, and to determine the potential contribution of fungi to contaminant transformation (nitrate attenuation). The abundance, distribution and diversity of fungi in subsurface groundwater samples were determined using quantitative and semi-quantitative molecular techniques, including quantitative PCR of eukaryotic SSU rRNA genes and pyrosequencing of fungal internal transcribed spacer (ITS) regions. Potential bacterial and fungal denitrification was assessed in sediment-groundwater slurries amended with antimicrobial compounds and in fungal pure cultures isolated from subsurface. Our results demonstrate that subsurface fungal communities are dominated by members of the phylum Ascomycota, and a pronounced shift in fungal community composition occurs across the groundwater pH gradient at the field site, with lower diversity observed under acidic (pH < 4.5) conditions. Fungal isolates recovered from subsurface sediments were shown to reduce nitrate to nitrous oxide, including cultures of the genus Coniochaeta that were detected in abundance in pyrosequence libraries of site groundwater samples. Denitrifying fungal isolates recovered from the site were classified, and found to be distributed broadly within the phylum Ascomycota, and within a single genus within the Basidiomycota. Potential denitrification rate assays with sediment-groundwater slurries showed the potential for subsurface fungi to reduce nitrate to nitrous oxide under in situ acidic pH conditions.

  19. Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing

    PubMed Central

    Mhuantong, Wuttichai; Wongwilaiwalin, Sarunyou; Laothanachareon, Thanaporn; Eurwilaichitr, Lily; Tangphatsornruang, Sithichoke; Boonchayaanant, Benjaporn; Limpiyakorn, Tawan; Pattaragulwanit, Kobchai; Punmatharith, Thantip; McEvoy, John; Khan, Eakalak; Rachakornkij, Manaskorn; Champreda, Verawat

    2015-01-01

    The Thailand flood crisis in 2011 was one of the largest recorded floods in modern history, causing enormous damage to the economy and ecological habitats of the country. In this study, bacterial and fungal diversity in sediments and waters collected from ten flood areas in Bangkok and its suburbs, covering residential and agricultural areas, were analyzed using high-throughput 454 pyrosequencing of 16S rRNA gene and internal transcribed spacer sequences. Analysis of microbial community showed differences in taxa distribution in water and sediment with variations in the diversity of saprophytic microbes and sulfate/nitrate reducers among sampling locations, suggesting differences in microbial activity in the habitats. Overall, Proteobacteria represented a major bacterial group in waters, while this group co-existed with Firmicutes, Bacteroidetes, and Actinobacteria in sediments. Anaeromyxobacter, Steroidobacter, and Geobacter were the dominant bacterial genera in sediments, while Sulfuricurvum, Thiovirga, and Hydrogenophaga predominated in waters. For fungi in sediments, Ascomycota, Glomeromycota, and Basidiomycota, particularly in genera Philipsia, Rozella, and Acaulospora, were most frequently detected. Chytridiomycota and Ascomycota were the major fungal phyla, and Rhizophlyctis and Mortierella were the most frequently detected fungal genera in water. Diversity of sulfate-reducing bacteria, related to odor problems, was further investigated using analysis of the dsrB gene which indicated the presence of sulfate-reducing bacteria of families Desulfobacteraceae, Desulfobulbaceae, Syntrobacteraceae, and Desulfoarculaceae in the flood sediments. The work provides an insight into the diversity and function of microbes related to biological processes in flood areas. PMID:26020967

  20. Seasonal Succession of Fungi Associated with Ips typographus Beetles and Their Phoretic Mites in an Outbreak Region of Finland.

    PubMed

    Linnakoski, Riikka; Mahilainen, Saila; Harrington, Alison; Vanhanen, Henri; Eriksson, Miikka; Mehtätalo, Lauri; Pappinen, Ari; Wingfield, Michael J

    2016-01-01

    The ophiostomatoid fungi (Microascales and Ophiostomatales, Ascomycota) are common associates of Ips typographus, and include tree pathogens and species responsible for blue-stain of timber. Fungal assemblages associated with I. typographus have varied considerably between studies but few investigations have attempted to explain this variation. For this reason, we assessed the overall cultivable fungal diversity associated with I. typographus in a storm-felled spruce forest in south-eastern Finland. Fungi were isolated from the individually collected beetles as well as their phoretic mites in spring, summer and autumn, including different life stages of the beetle (hibernation, dispersal flight and first generation). The internal transcribed spacer (ITS) gene region was used to identify the fungi. A total of 32 operational taxonomic units (OTUs) were found and these resided in four fungal phyla/subphyla (24 Ascomycota, 2 Basidiomycota, 5 Mucoromycotina, 1 Mortierellomycotina) in association with adult bark beetles. Ophiostomatoid species were the most commonly detected fungal associates. A generalized linear model analysis showed a clear association between fungal communities and season, indicating seasonal succession among I. typographus-associated fungi. The season of sampling appears to be an important factor that has resulted in inconsistencies between results in previous studies. Many of these fungi were also found on phoretic mites and their presence or absence could have influenced variation in patterns of association. PMID:27187192

  1. Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing.

    PubMed

    Mhuantong, Wuttichai; Wongwilaiwalin, Sarunyou; Laothanachareon, Thanaporn; Eurwilaichitr, Lily; Tangphatsornruang, Sithichoke; Boonchayaanant, Benjaporn; Limpiyakorn, Tawan; Pattaragulwanit, Kobchai; Punmatharith, Thantip; McEvoy, John; Khan, Eakalak; Rachakornkij, Manaskorn; Champreda, Verawat

    2015-01-01

    The Thailand flood crisis in 2011 was one of the largest recorded floods in modern history, causing enormous damage to the economy and ecological habitats of the country. In this study, bacterial and fungal diversity in sediments and waters collected from ten flood areas in Bangkok and its suburbs, covering residential and agricultural areas, were analyzed using high-throughput 454 pyrosequencing of 16S rRNA gene and internal transcribed spacer sequences. Analysis of microbial community showed differences in taxa distribution in water and sediment with variations in the diversity of saprophytic microbes and sulfate/nitrate reducers among sampling locations, suggesting differences in microbial activity in the habitats. Overall, Proteobacteria represented a major bacterial group in waters, while this group co-existed with Firmicutes, Bacteroidetes, and Actinobacteria in sediments. Anaeromyxobacter, Steroidobacter, and Geobacter were the dominant bacterial genera in sediments, while Sulfuricurvum, Thiovirga, and Hydrogenophaga predominated in waters. For fungi in sediments, Ascomycota, Glomeromycota, and Basidiomycota, particularly in genera Philipsia, Rozella, and Acaulospora, were most frequently detected. Chytridiomycota and Ascomycota were the major fungal phyla, and Rhizophlyctis and Mortierella were the most frequently detected fungal genera in water. Diversity of sulfate-reducing bacteria, related to odor problems, was further investigated using analysis of the dsrB gene which indicated the presence of sulfate-reducing bacteria of families Desulfobacteraceae, Desulfobulbaceae, Syntrobacteraceae, and Desulfoarculaceae in the flood sediments. The work provides an insight into the diversity and function of microbes related to biological processes in flood areas. PMID:26020967

  2. Alectorioid Morphologies in Paleogene Lichens: New Evidence and Re-Evaluation of the Fossil Alectoria succini Mägdefrau

    PubMed Central

    Kaasalainen, Ulla; Heinrichs, Jochen; Krings, Michael; Myllys, Leena; Grabenhorst, Heinrich; Rikkinen, Jouko; Schmidt, Alexander R.

    2015-01-01

    One of the most important issues in molecular dating studies concerns the incorporation of reliable fossil taxa into the phylogenies reconstructed from DNA sequence variation in extant taxa. Lichens are symbiotic associations between fungi and algae and/or cyanobacteria. Several lichen fossils have been used as minimum age constraints in recent studies concerning the diversification of the Ascomycota. Recent evolutionary studies of Lecanoromycetes, an almost exclusively lichen-forming class in the Ascomycota, have utilized the Eocene amber inclusion Alectoria succinic as a minimum age constraint. However, a re-investigation of the type material revealed that this inclusion in fact represents poorly preserved plant remains, most probably of a root. Consequently, this fossil cannot be used as evidence of the presence of the genus Alectoria (Parmeliaceae, Lecanorales) or any other lichens in the Paleogene. However, newly discovered inclusions from Paleogene Baltic and Bitterfeld amber verify that alectorioid morphologies in lichens were in existence by the Paleogene. The new fossils represent either a lineage within the alectorioid group or belong to the genus Oropogon. PMID:26053106

  3. Characterization of active and total fungal communities in the atmosphere over the Amazon rainforest

    NASA Astrophysics Data System (ADS)

    Womack, A. M.; Artaxo, P. E.; Ishida, F. Y.; Mueller, R. C.; Saleska, S. R.; Wiedemann, K. T.; Bohannan, B. J. M.; Green, J. L.

    2015-11-01

    Fungi are ubiquitous in the atmosphere and may play an important role in atmospheric processes. We investigated the composition and diversity of fungal communities over the Amazon rainforest canopy and compared these communities to fungal communities found in terrestrial environments. We characterized the total fungal community and the metabolically active portion of the community using high-throughput DNA and RNA sequencing and compared these data to predictions generated by a mass-balance model. We found that the total community was primarily comprised of fungi from the phylum Basidiomycota. In contrast, the active community was primarily composed of members of the phylum Ascomycota and included a high relative abundance of lichen fungi, which were not detected in the total community. The relative abundance of Basidiomycota and Ascomycota in the total and active communities was consistent with our model predictions, suggesting that this result was driven by the relative size and number of spores produced by these groups. When compared to other environments, fungal communities in the atmosphere were most similar to communities found in tropical soils and leaf surfaces. Our results demonstrate that there are significant differences in the composition of the total and active fungal communities in the atmosphere, and that lichen fungi, which have been shown to be efficient ice nucleators, may be abundant members of active atmospheric fungal communities over the forest canopy.

  4. High-throughput sequencing-based analysis of endogenetic fungal communities inhabiting the Chinese Cordyceps reveals unexpectedly high fungal diversity.

    PubMed

    Xia, Fei; Chen, Xin; Guo, Meng-Yuan; Bai, Xiao-Hui; Liu, Yan; Shen, Guang-Rong; Li, Yu-Ling; Lin, Juan; Zhou, Xuan-Wei

    2016-01-01

    Chinese Cordyceps, known in Chinese as "DongChong XiaCao", is a parasitic complex of a fungus (Ophiocordyceps sinensis) and a caterpillar. The current study explored the endogenetic fungal communities inhabiting Chinese Cordyceps. Samples were collected from five different geographical regions of Qinghai and Tibet, and the nuclear ribosomal internal transcribed spacer-1 sequences from each sample were obtained using Illumina high-throughput sequencing. The results showed that Ascomycota was the dominant fungal phylum in Chinese Cordyceps and its soil microhabitat from different sampling regions. Among the Ascomycota, 65 genera were identified, and the abundant operational taxonomic units showed the strongest sequence similarity to Ophiocordyceps, Verticillium, Pseudallescheria, Candida and Ilyonectria Not surprisingly, the genus Ophiocordyceps was the largest among the fungal communities identified in the fruiting bodies and external mycelial cortices of Chinese Cordyceps. In addition, fungal communities in the soil microhabitats were clustered separately from the external mycelial cortices and fruiting bodies of Chinese Cordyceps from different sampling regions. There was no significant structural difference in the fungal communities between the fruiting bodies and external mycelial cortices of Chinese Cordyceps. This study revealed an unexpectedly high diversity of fungal communities inhabiting the Chinese Cordyceps and its microhabitats. PMID:27625176

  5. Calcineurin Orchestrates Hyphal Growth, Septation, Drug Resistance and Pathogenesis of Aspergillus fumigatus: Where Do We Go from Here?

    PubMed

    Juvvadi, Praveen R; Steinbach, William J

    2015-01-01

    Studies on fungal pathogens belonging to the ascomycota phylum are critical given the ubiquity and frequency with which these fungi cause infections in humans. Among these species, Aspergillus fumigatus causes invasive aspergillosis, a leading cause of death in immunocompromised patients. Fundamental to A. fumigatus pathogenesis is hyphal growth. However, the precise mechanisms underlying hyphal growth and virulence are poorly understood. Over the past 10 years, our research towards the identification of molecular targets responsible for hyphal growth, drug resistance and virulence led to the elucidation of calcineurin as a key signaling molecule governing these processes. In this review, we summarize our salient findings on the significance of calcineurin for hyphal growth and septation in A. fumigatus and propose future perspectives on exploiting this pathway for designing new fungal-specific therapeutics. PMID:26694470

  6. The phylogenetic position of Spathulospora based on DNA sequences from dried herbarium material.

    PubMed

    Inderbitzin, Patrik; Lim, Sea Ra; Volkmann-Kohlmeyer, Brigitte; Kohlmeyer, Jan; Berbee, Mary L

    2004-07-01

    The phylogenetic position of the marine ascomycete genus Spathulospora was investigated using partial SSU and LSU DNA sequences obtained from dried herbarium specimens. Spathulospora was represented by the two species S. adelpha and S. antarctica. Phylogenetic analyses using Bayesian, parsimony, and neighbour-joining algorithms on SSU and LSU data sets agreed with the placement of Spathulospora. Both Spathulospora species are each others closest relatives, and group within the Lulworthiales (Sordariomycetes, Ascomycota) with support in all analyses. Members of the morphologically similar insect parasites in the Laboulbeniomycetes are not closely related to Spathulospora. Despite several striking morphological differences between Spathulospora and Lulworthiales, an important shared morphological character was found that until now had not been recognized. Ascospores of Spathulospora and some members of the Lulworthiales have apical chambers containing mucus believed to be involved in ascospore attachment. A closest relative to Spathulospora could not be determined. PMID:15446706

  7. Manipulation of culture conditions alters lipid content and fatty acid profiles of a wide variety of known and new oleaginous yeasts species

    PubMed Central

    Sitepu, Irnayuli R.; Sestric, Ryan; Ignatia, Laura; Levin, David; German, J. Bruce; Gillies, Laura A.; Almada, Luis A.G.; Boundy-Mills, Kyria L.

    2013-01-01

    Oleaginous yeasts have been studied for oleochemical production for over 80 years. Only a few species have been studied intensely. To expand the diversity of oleaginous yeasts available for lipid research, we surveyed a broad diversity of yeasts with indicators of oleaginicity including known oleaginous clades, and buoyancy. Sixty-nine strains representing 17 genera and 50 species were screened for lipid production. Yeasts belonged to Ascomycota families, Basidiomycota orders, and the yeast-like algal genus Prototheca. Total intracellular lipids and fatty acid composition were determined under different incubation times and nitrogen availability. Thirteen new oleaginous yeast species were discovered, representing multiple ascomycete and basidiomycete clades. Nitrogen starvation generally increased intracellular lipid content. The fatty acid profiles varied with the growth conditions regardless of taxonomic affiliation. The dominant fatty acids were oleic acid, palmitic acid, linoleic acid, and stearic acid. Yeasts and culture conditions that produced fatty acids appropriate for biodiesel were identified. PMID:23891835

  8. Endophytic Fungal Communities Associated with Vascular Plants in the High Arctic Zone Are Highly Diverse and Host-Plant Specific.

    PubMed

    Zhang, Tao; Yao, Yi-Feng

    2015-01-01

    This study assessed the diversity and distribution of endophytic fungal communities associated with the leaves and stems of four vascular plant species in the High Arctic using 454 pyrosequencing with fungal-specific primers targeting the ITS region. Endophytic fungal communities showed high diversity. The 76,691 sequences obtained belonged to 250 operational taxonomic units (OTUs). Of these OTUs, 190 belonged to Ascomycota, 50 to Basidiomycota, 1 to Chytridiomycota, and 9 to unknown fungi. The dominant orders were Helotiales, Pleosporales, Capnodiales, and Tremellales, whereas the common known fungal genera were Cryptococcus, Rhizosphaera, Mycopappus, Melampsora, Tetracladium, Phaeosphaeria, Mrakia, Venturia, and Leptosphaeria. Both the climate and host-related factors might shape the fungal communities associated with the four Arctic plant species in this region. These results suggested the presence of an interesting endophytic fungal community and could improve our understanding of fungal evolution and ecology in the Arctic terrestrial ecosystems. PMID:26067836

  9. Lichensphere: a protected natural microhabitat of the non-lichenised fungal communities living in extreme environments of Antarctica.

    PubMed

    Santiago, Iara F; Soares, Marco Aurélio; Rosa, Carlos A; Rosa, Luiz H

    2015-11-01

    We surveyed the diversity, distribution and ecology of non-lichenised fungal communities associated with the Antarctic lichens Usnea antarctica and Usnea aurantiaco-atra across Antarctica. The phylogenetic study of the 438 fungi isolates identified 74 taxa from 21 genera of Ascomycota, Basidiomycota and Zygomycota. The most abundant taxa were Pseudogymnoascus sp., Thelebolus sp., Antarctomyces psychrotrophicus and Cryptococcus victoriae, which are considered endemic and/or highly adapted to Antarctica. Thirty-five fungi may represent new and/or endemic species. The fungal communities displayed high diversity, richness and dominance indices; however, the similarity among the communities was variable. After discovering rich and diverse fungal communities composed of symbionts, decomposers, parasites and endemic and cold-adapted cosmopolitan taxa, we introduced the term "lichensphere". We hypothesised that the lichensphere may represent a protected natural microhabitat with favourable conditions able to help non-lichenised fungi and other Antarctic life forms survive and disperse in the extreme environments of Antarctica. PMID:26400492

  10. Fungal Endophyte Diversity in Sarracenia

    PubMed Central

    Glenn, Anthony; Bodri, Michael S.

    2012-01-01

    Fungal endophytes were isolated from 4 species of the carnivorous pitcher plant genus Sarracenia: S. minor, S. oreophila, S. purpurea, and S. psittacina. Twelve taxa of fungi, 8 within the Ascomycota and 4 within the Basidiomycota, were identified based on PCR amplification and sequencing of the internal transcribed spacer sequences of nuclear ribosomal DNA (ITS rDNA) with taxonomic identity assigned using the NCBI nucleotide megablast search tool. Endophytes are known to produce a large number of metabolites, some of which may contribute to the protection and survival of the host. We speculate that endophyte-infected Sarracenia may benefit from their fungal associates by their influence on nutrient availability from within pitchers and, possibly, by directly influencing the biota within pitchers. PMID:22427921

  11. Antimicrobial dihydrobenzofurans and xanthenes from a foliar endophyte of Pinus strobus.

    PubMed

    Richardson, Susan N; Nsiama, Tienabe K; Walker, Allison K; McMullin, David R; Miller, J David

    2015-09-01

    Foliar fungal endophytes of Pinus strobus (eastern white pine) were collected from different sites across south-eastern New Brunswick, Canada and screened for the production of bioactive metabolites. From one site, two fungal isolates representing a formerly unknown genus and species within the family Massarinaceae (Pleosporales, Dothideomycetes, Ascomycota) were resolved by phylogenetic analysis. These isolates produced crude organic extracts that were active against Microbotryum violaceum and Saccharomyces cerevisiae. From these strains, DAOM 242779 and 242780, four dihydrobenzofurans (1-4) and two xanthenes (5-6) were characterized. Structures were elucidated by HRMS, interpretation of NMR spectra and other spectroscopic techniques. All isolated metabolites displayed antimicrobial activity against the biotrophic fungal pathogen M. violaceum and Bacillus subtilis. PMID:26189049

  12. Subaerial biofilms on granitic historic buildings: microbial diversity and development of phototrophic multi-species cultures.

    PubMed

    Vázquez-Nion, D; Rodríguez-Castro, J; López-Rodríguez, M C; Fernández-Silva, I; Prieto, B

    2016-07-01

    Microbial communities of natural subaerial biofilms developed on granitic historic buildings of a World Heritage Site (Santiago de Compostela, NW Spain) were characterized and cultured in liquid BG11 medium. Environmental barcoding through next-generation sequencing (Pacific Biosciences) revealed that the biofilms were mainly composed of species of Chlorophyta (green algae) and Ascomycota (fungi) commonly associated with rock substrata. Richness and diversity were higher for the fungal than for the algal assemblages and fungi showed higher heterogeneity among samples. Cultures derived from natural biofilms showed the establishment of stable microbial communities mainly composed of Chlorophyta and Cyanobacteria. Although most taxa found in these cultures were not common in the original biofilms, they are likely common pioneer colonizers of building stone surfaces, including granite. Stable phototrophic multi-species cultures of known microbial diversity were thus obtained and their reliability to emulate natural colonization on granite should be confirmed in further experiments. PMID:27192622

  13. New primers for promising single-copy genes in fungal phylogenetics and systematics.

    PubMed

    Schmitt, I; Crespo, A; Divakar, P K; Fankhauser, J D; Herman-Sackett, E; Kalb, K; Nelsen, M P; Nelson, N A; Rivas-Plata, E; Shimp, A D; Widhelm, T; Lumbsch, H T

    2009-12-01

    Developing powerful phylogenetic markers is a key concern in fungal phylogenetics. Here we report degenerate primers that amplify the single-copy genes Mcm7 (MS456) and Tsr1 (MS277) across a wide range of Pezizomycotina (Ascomycota). Phylogenetic analyses of 59 taxa belonging to the Eurotiomycetes, Lecanoromycetes, Leotiomycetes, Lichinomycetes and Sordariomycetes, indicate the utility of these loci for fungal phylogenetics at taxonomic levels ranging from genus to class. We also tested the new primers in silico using sequences of Saccharomycotina, Taphrinomycotina and Basidiomycota to predict their potential of amplifying widely across the Fungi. The analyses suggest that the new primers will need no, or only minor sequence modifications to amplify Saccharomycotina, Taphrinomycotina and Basidiomycota. PMID:20198159

  14. Pyrosequencing assessment of rhizosphere fungal communities from a soybean field.

    PubMed

    Sugiyama, Akifumi; Ueda, Yoshikatsu; Takase, Hisabumi; Yazaki, Kazufumi

    2014-10-01

    Soil fungal communities play essential roles in soil ecosystems, affecting plant growth and health. Rhizosphere bacterial communities have been shown to undergo dynamic changes during plant growth. This study utilized 454 pyrosequencing to analyze rhizosphere fungal communities during soybean growth. Members of the Ascomycota and Basiodiomycota dominated in all soils. There were no statistically significant changes at the phylum level among growth stages or between bulk and rhizosphere soils. In contrast, the relative abundance of small numbers of operational taxonomic units, 4 during growth and 28 between bulk and rhizosphere soils, differed significantly. Clustering analysis revealed that rhizosphere fungal communities were different from bulk fungal communities during growth stages of soybeans. Taken together, these results suggest that in contrast to rhizosphere bacterial communities, most constituents of rhizosphere fungal communities remained stable during soybean growth. PMID:25264806

  15. Calnexin induces expansion of antigen-specific CD4(+) T cells that confer immunity to fungal ascomycetes via conserved epitopes.

    PubMed

    Wüthrich, Marcel; Brandhorst, Tristan T; Sullivan, Thomas D; Filutowicz, Hanna; Sterkel, Alana; Stewart, Douglas; Li, Mengyi; Lerksuthirat, Tassanee; LeBert, Vanessa; Shen, Zu Ting; Ostroff, Gary; Deepe, George S; Hung, Chiung Yu; Cole, Garry; Walter, Jennifer A; Jenkins, Marc K; Klein, Bruce

    2015-04-01

    Fungal infections remain a threat due to the lack of broad-spectrum fungal vaccines and protective antigens. Recent studies showed that attenuated Blastomyces dermatitidis confers protection via T cell recognition of an unknown but conserved antigen. Using transgenic CD4(+) T cells recognizing this antigen, we identify an amino acid determinant within the chaperone calnexin that is conserved across diverse fungal ascomycetes. Calnexin, typically an ER protein, also localizes to the surface of yeast, hyphae, and spores. T cell epitope mapping unveiled a 13-residue sequence conserved across Ascomycota. Infection with divergent ascomycetes, including dimorphic fungi, opportunistic molds, and the agent causing white nose syndrome in bats, induces expansion of calnexin-specific CD4(+) T cells. Vaccine delivery of calnexin in glucan particles induces fungal antigen-specific CD4(+) T cell expansion and resistance to lethal challenge with multiple fungal pathogens. Thus, the immunogenicity and conservation of calnexin make this fungal protein a promising vaccine target. PMID:25800545

  16. Calnexin induces expansion of antigen-specific CD4+ T cells that confer immunity to fungal ascomycetes via conserved epitopes

    PubMed Central

    Wüthrich, Marcel; Brandhorst, Tristan T.; Sullivan, Thomas D.; Filutowicz, Hanna; Sterkel, Alana; Stewart, Douglas; Li, Mengyi; Lerksuthirat, Tassanee; LeBert, Vanessa; Shen, Zu Ting; Ostroff, Gary; Deepe, George S.; Hung, Chiung Yu; Cole, Garry; Walter, Jennifer A.; Jenkins, Marc K.; Klein, Bruce

    2015-01-01

    Fungal infections remain a threat due to the lack of broad spectrum fungal vaccines and protective antigens. Recent studies showed that attenuated Blastomyces dermatitidis confers protection via T cell recognition of an unknown, but conserved antigen. Using transgenic CD4+ T cells recognizing this antigen, we identify an amino acid determinant within the chaperone calnexin that is conserved across diverse fungal ascomycetes. Calnexin, typically an ER protein, also localizes to the surface of yeast, hyphae and spores. T cell epitope mapping unveiled a 13-residue sequence conserved across Ascomycota. Infection with divergent ascomycetes including dimorphic fungi, opportunistic molds, and the agent causing white nose syndrome in bats induces expansion of calnexin-specific CD4+ T cells. Vaccine delivery of calnexin in glucan particles induces fungal antigen-specific CD4+ T cell expansion and resistance to lethal challenge with multiple fungal pathogens. Thus, the immunogeneticity and conservation of calnexin make this fungal protein a promising vaccine target. PMID:25800545

  17. Fungi on the Skin: Dermatophytes and Malassezia

    PubMed Central

    White, Theodore C.; Findley, Keisha; Dawson, Thomas L.; Scheynius, Annika; Boekhout, Teun; Cuomo, Christina A.; Xu, Jun; Saunders, Charles W.

    2014-01-01

    Several human skin diseases and disorders are associated with two groups of fungi, the dermatophytes and Malassezia. Although these skin-related problems are not generally life threatening, they are among the most common diseases and disorders of mankind. These fungi are phylogenetically divergent, with the dermatophytes within the Ascomycota and Malassezia within Basidiomycota. Genome analysis indicates that the adaptations to the skin environment are different in these two groups of fungi. Malassezia are dependent on host lipids and secrete lipases and phospholipases that likely release host fatty acids. The dermatophytes encode multiple enzymes with potential roles in modulating host interactions: polyketide synthases, nonribosomal peptide synthetases, LysM, proteases, kinases, and pseudokinases. These two fungal groups have maximized their interactions with the host using two very different mechanisms. PMID:25085959

  18. Isolation and Characterization of a Novel Facultative Anaerobic Filamentous Fungus from Japanese Rice Field Soil

    PubMed Central

    Tonouchi, Akio

    2009-01-01

    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. PMID:20148171

  19. Biogeography in the air: fungal diversity over land and oceans

    NASA Astrophysics Data System (ADS)

    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.

    2011-07-01

    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.

  20. Biogeography in the air: fungal diversity over land and oceans

    NASA Astrophysics Data System (ADS)

    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.

    2012-03-01

    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 find 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 understanding of global changes in biodiversity.

  1. Diversity and biochemical features of culturable fungi from the coastal waters of Southern China

    PubMed Central

    2014-01-01

    Fungi play a major role in various biogeochemical cycles of terrestrial and marine ecosystems. However, fungi in marine environments remain to be one of the most under-studied microbial groups. This study investigates the diversity of planktonic fungi from the coastal habitat off Pearl River Delta (China) using culture-dependent approach. A total of 22 fungi and 9 yeast isolates were recovered from 30 seawater and 2 sediment samples. Microscopic and ITS rRNA gene sequence analyses revealed that most of the fungi belonged to the phylum Ascomycota and Basidiomycota with a very small percentage (3%) of the subphylum Mucoromycotina of the Phylum Zygomycota. Most of these fungal isolates exhibited considerable production of extracellular enzymes, cellulase, lipase and laccase. Fungal isolates of two genera Mucor and Aspergillus sp. demonstrated pelletization capability over a wide range of pH, suggesting them as potential agents towards algae harvesting and wastewater treatment. PMID:25401065

  2. Distribution and Diversity of Planktonic Fungi in the West Pacific Warm Pool

    PubMed Central

    Wang, Xin; Singh, Purnima; Gao, Zheng; Zhang, Xiaobo; Johnson, Zackary I.; Wang, Guangyi

    2014-01-01

    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

  3. Aspergillus 6V4, a Strain Isolated from Manipueira, Produces High Amylases Levels by Using Wheat Bran as a Substrate

    PubMed Central

    Celestino, Jessyca dos Reis; Duarte, Ana Caroline; Silva, Cláudia Maria de Melo; Sena, Hellen Holanda; Ferreira, Maria do Perpétuo Socorro Borges Carriço; Mallmann, Neila Hiraishi; Lima, Natacha Pinheiro Costa; Tavares, Chanderlei de Castro; de Souza, Rodrigo Otávio Silva; Souza, Érica Simplício; Souza, João Vicente Braga

    2014-01-01

    The aim of this study was screening fungi strains, isolated from manipueira (a liquid subproduct obtained from the flour production of Manihot esculenta), for amylases production and investigating production of these enzymes by the strain Aspergillus 6V4. The fungi isolated from manipueira belonged to Ascomycota phylum. The strain Aspergillus 6V4 was the best amylase producer in the screening assay of starch hydrolysis in petri dishes (ASHPD) and in the assay in submerged fermentation (ASbF). The strain Aspergillus 6V4 produced high amylase levels (335 UI/L) using wheat bran infusion as the exclusive substrate and the supplementation of this substrate with peptone decreased the production of this enzyme. The moisture content of 70% was the best condition for the production of Aspergillus 6V4 amylases (385 IU/g) in solid state fermentation (SSF). PMID:24724017

  4. Phylogenetic Diversity and Antifungal Activity of Endophytic Fungi Associated with Tephrosia purpurea

    PubMed Central

    Luo, Ze-Ping; Lin, Hai-Yan; Ding, Wen-Bing; He, Hua-Liang

    2015-01-01

    Sixty-one endophytic fungus strains with different colony morphologies were isolated from the leaves, stems and roots of Tephrosia purpurea with colonization rates of 66.95%, 37.50%, and 26.92%, respectively. Based on internal transcribed spacer sequence analysis, 61 isolates were classified into 16 genera belonging to 3 classes under the phylum Ascomycota. Of the 61 isolates, 6 (9.84%) exhibited antifungal activity against one or more indicator plant pathogenic fungi according to the dual culture test. Isolate TPL25 had the broadest antifungal spectrum of activity, and isolate TPL35 was active against 5 plant pathogenic fungi. Furthermore, culture filtrates of TPL25 and TPL35 exhibited greater than 80% growth inhibition against Sclerotinia sclerotiorum. We conclude that the endophytic fungal strains TPL25 and TPL35 are promising sources of bioactive compounds. PMID:26839503

  5. [Peculiarities of mortmass mycobiota formation in soft-deciduous young forests on old-tillage soils of the Chernihiv Polissya].

    PubMed

    Bilous, A M; Voloshchuk, N M; Buzyl', M A; Kovbasa, Ia V

    2013-01-01

    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

  6. Exploiting composting biodiversity: study of the persistent and biotechnologically relevant microorganisms from lignocellulose-based composting.

    PubMed

    Jurado, Macarena; López, María J; Suárez-Estrella, Francisca; Vargas-García, María C; López-González, Juan A; Moreno, Joaquín

    2014-06-01

    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

  7. Secondary metabolite profiling of Alternaria dauci, A. porri, A. solani, and A. tomatophila.

    PubMed

    Andersen, Birgitte; Dongo, Anita; Pryor, Barry M

    2008-02-01

    Chemotaxonomy (secondary metabolite profiling) has been shown to be of great value in the classification and differentiation in Ascomycota. However, few studies have investigated the use of metabolite production for classification and identification purposes of plant pathogenic Alternaria species. The purpose of the present study was to describe the methodology behind metabolite profiling in chemotaxonomy using A. dauci, A. porri, A. solani, and A. tomatophila strains as examples of the group. The results confirmed that A. dauci, A. solani, and A. tomatophila are three distinct species each with their own specific metabolite profiles, and that A. solani and A. tomatophila both produce altersolanol A, altertoxin I, and macrosporin. By using automated chemical image analysis and other multivariate statistic analyses, three sets of species-specific metabolites could be selected, one each for A. dauci, A. solani, and A. tomatophila. PMID:18262401

  8. Cercosporoid fungi (Mycosphaerellaceae) 5. Species on dicots (Anacardiaceae to Annonaceae).

    PubMed

    Braun, Uwe; Crous, Pedro W; Nakashima, Chiharu

    2016-06-01

    The present paper is a continuation of a series of comprehensive taxonomic treatments of cercosporoid fungi (formerly Cercospora s. lat.), belonging to Mycosphaerellaceae (Ascomycota). This fifth contribution of this series proceeds with treatments of cercosporoid fungi on dicots and comprises species occurring on hosts belonging to the families Anacardiaceae and Annonaceae, which are described and illustrated in alphabetical order under the particular cercosporoid genera, supplemented by keys to the species concerned. A detailed introduction, a survey of currently recognised cercosporoid genera, a key to the genera concerned, and a discussion of taxonomically relevant characters were published in the first part of this series. The following taxonomic novelties are introduced: Passalora cotini sp. nov., P. guoana nom. nov., P. rhois-aromaticae sp. nov., and Pseudocercospora rhoicola. PMID:27433446

  9. Molecular analysis of microbial diversity in corrosion samples from energy transmission towers.

    PubMed

    Oliveira, Valéria M; Lopes-Oliveira, Patrícia F; Passarini, Michel R Z; Menezes, Claudia B A; Oliveira, Walter R C; Rocha, Adriano J; Sette, Lara D

    2011-04-01

    Microbial diversity in corrosion samples from energy transmission towers was investigated using molecular methods. Ribosomal DNA fragments were used to assemble gene libraries. Sequence analysis indicated 10 bacterial genera within the phyla Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. In the two libraries generated from corroded screw-derived samples, the genus Acinetobacter was the most abundant. Acinetobacter and Clostridium spp. dominated, with similar percentages, in the libraries derived from corrosion scrapings. Fungal clones were affiliated with 14 genera belonging to the phyla Ascomycota and Basidiomycota; of these, Capnobotryella and Fellomyces were the most abundant fungi observed. Several of the microorganisms had not previously been associated with biofilms and corrosion, reinforcing the need to use molecular techniques to achieve a more comprehensive assessment of microbial diversity in environmental samples. PMID:21563009

  10. Evolution of Reproductive Morphology in Leaf Endophytes

    PubMed Central

    Wang, Zheng; Johnston, Peter R.; Yang, Zhu L.; Townsend, Jeffrey P.

    2009-01-01

    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. PMID:19158947

  11. Subcutaneous infection by Ochroconis mirabilis in an immunocompetent patient

    PubMed Central

    Shi, Dongmei; Lu, Guixia; Mei, Huan; de Hoog, G. Sybren; Samerpitak, Kittipan; Deng, Shuwen; Shen, Yongnian; Liu, Weida

    2016-01-01

    Recently, the taxonomy of Ochroconis (Ascomycota, Pezizomycotina, Venturiales, Sympoventuriaceae) has been revised with the recognition of an additional genus, Verruconis. Ochroconis comprises mesophilic saprobes that occasionally infect vertebrates which mostly are cold-blooded, while Verruconis contains thermophilic species which is a neurotrope in humans and birds. On the basis of molecular data it is noted that only a single Ochroconis species regularly infects immunocompetent human hosts. Here we report a subcutaneous infection due to Ochroconis mirabilis in a 50-year-old immunocompetent female patient. In vitro antifungal susceptibility tests revealed that terbinafine was the most effective drug. The patient was successfully cured with oral administration of terbinafine 250 mg daily in combination with 3 times of topical ALA-photodynamic therapy for 9 months. PMID:27182484

  12. The spectrum of allergic fungal diseases of the upper and lower airways.

    PubMed

    Rodrigues, Jonathan; Caruthers, Carrie; Azmeh, Roua; Dykewicz, Mark S; Slavin, Raymond G; Knutsen, Alan P

    2016-05-01

    Fungi cause a wide spectrum of fungal diseases of the upper and lower airways. There are three main phyla involved in allergic fungal disease: (1) Ascomycota (2) Basidiomycota (3) Zygomycota. Allergic fungal rhinosinusitis (AFRS) causes chronic rhinosinusitis symptoms and is caused predominantly by Aspergillus fumigatus in India and Bipolaris in the United States. The recommended treatment approach for AFRS is surgical intervention and systemic steroids. Allergic bronchopulmonary aspergillosis (APBA) is most commonly diagnosed in patients with asthma or cystic fibrosis. Long term systemic steroids are the mainstay treatment option for ABPA with the addition of an antifungal medication. Fungal sensitization or exposure increases a patient's risk of developing severe asthma and has been termed severe asthma associated with fungal sensitivity (SAFS). Investigating for triggers and causes of a patient's asthma should be sought to decrease worsening progression of the disease. PMID:26776889

  13. Endophytic Fungal Communities Associated with Vascular Plants in the High Arctic Zone Are Highly Diverse and Host-Plant Specific

    PubMed Central

    Zhang, Tao; Yao, Yi-Feng

    2015-01-01

    This study assessed the diversity and distribution of endophytic fungal communities associated with the leaves and stems of four vascular plant species in the High Arctic using 454 pyrosequencing with fungal-specific primers targeting the ITS region. Endophytic fungal communities showed high diversity. The 76,691 sequences obtained belonged to 250 operational taxonomic units (OTUs). Of these OTUs, 190 belonged to Ascomycota, 50 to Basidiomycota, 1 to Chytridiomycota, and 9 to unknown fungi. The dominant orders were Helotiales, Pleosporales, Capnodiales, and Tremellales, whereas the common known fungal genera were Cryptococcus, Rhizosphaera, Mycopappus, Melampsora, Tetracladium, Phaeosphaeria, Mrakia, Venturia, and Leptosphaeria. Both the climate and host-related factors might shape the fungal communities associated with the four Arctic plant species in this region. These results suggested the presence of an interesting endophytic fungal community and could improve our understanding of fungal evolution and ecology in the Arctic terrestrial ecosystems. PMID:26067836

  14. High-throughput Sequencing of Trace Quantities of Soil Provides Reproducible and Discriminative Fungal DNA Profiles.

    PubMed

    Young, Jennifer M; Weyrich, Laura S; Cooper, Alan

    2016-03-01

    High-throughput sequencing (HTS) offers improved resolution between forensic soil samples by characterizing individual taxa present; however, the heterogeneous distribution of taxa in soils, and limited quantity of material available, may hinder the reliability of HTS in casework. Using HTS of the internal transcribed spacer, we examined the effect of soil mass (50, 150, and 250 mg) on fungal DNA profiles, focusing on reproducibility and discriminatory power between close proximity soils, and samples with similar textural classification. The results show that reduced soil mass had no significant effect on sample differentiation and that 150 mg soil provides the most reproducible DNA profiles across different soil types. In addition, Ascomycota was identified as a robust fungal target for forensic intelligence as this phylum was detected consistently across all samples regardless of sample quantity. Overall, this study highlights the value of trace quantities of soil for use in forensic casework. PMID:27404621

  15. Assessment of ectomycorrhizal biodiversity in Tuber macrosporum productive sites.

    PubMed

    Benucci, Gian Maria Niccolò; Raggi, Lorenzo; Albertini, Emidio; Csorbai, Andrea Gógán; Donnini, Domizia

    2014-05-01

    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

  16. Biosynthetic pathways of ergot alkaloids.

    PubMed

    Gerhards, Nina; Neubauer, Lisa; Tudzynski, Paul; Li, Shu-Ming

    2014-01-01

    Ergot alkaloids are nitrogen-containing natural products belonging to indole alkaloids. The best known producers are fungi of the phylum Ascomycota, e.g., Claviceps, Epichloë, Penicillium and Aspergillus species. According to their structures, ergot alkaloids can be divided into three groups: clavines, lysergic acid amides and peptides (ergopeptines). All of them share the first biosynthetic steps, which lead to the formation of the tetracyclic ergoline ring system (except the simplest, tricyclic compound: chanoclavine). Different modifications on the ergoline ring by specific enzymes result in an abundance of bioactive natural products, which are used as pharmaceutical drugs or precursors thereof. From the 1950s through to recent years, most of the biosynthetic pathways have been elucidated. Gene clusters from several ergot alkaloid producers have been identified by genome mining and the functions of many of those genes have been demonstrated by knock-out experiments or biochemical investigations of the overproduced enzymes. PMID:25513893

  17. Insights into fungal communities in composts revealed by 454-pyrosequencing: implications for human health and safety

    PubMed Central

    De Gannes, Vidya; Eudoxie, Gaius; Hickey, William J.

    2013-01-01

    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. PMID:23785368

  18. A comprehensive model to predict mitotic division in budding yeasts

    PubMed Central

    Sutradhar, Sabyasachi; Yadav, Vikas; Sridhar, Shreyas; Sreekumar, Lakshmi; Bhattacharyya, Dibyendu; Ghosh, Santanu Kumar; Paul, Raja; Sanyal, Kaustuv

    2015-01-01

    High-fidelity chromosome segregation during cell division depends on a series of concerted interdependent interactions. Using a systems biology approach, we built a robust minimal computational model to comprehend mitotic events in dividing budding yeasts of two major phyla: Ascomycota and Basidiomycota. This model accurately reproduces experimental observations related to spindle alignment, nuclear migration, and microtubule (MT) dynamics during cell division in these yeasts. The model converges to the conclusion that biased nucleation of cytoplasmic microtubules (cMTs) is essential for directional nuclear migration. Two distinct pathways, based on the population of cMTs and cortical dyneins, differentiate nuclear migration and spindle orientation in these two phyla. In addition, the model accurately predicts the contribution of specific classes of MTs in chromosome segregation. Thus we present a model that offers a wider applicability to simulate the effects of perturbation of an event on the concerted process of the mitotic cell division. PMID:26310442

  19. Description and phylogenetic placement of Beauveria hoplocheli sp. nov. used in the biological control of the sugarcane white grub, Hoplochelus marginalis, on Reunion Island.

    PubMed

    Robène-Soustrade, Isabelle; Jouen, Emmanuel; Pastou, Didier; Payet-Hoarau, Magali; Goble, Tarryn; Linderme, Daphné; Lefeuvre, Pierre; Calmès, Cédric; Reynaud, Bernard; Nibouche, Samuel; Costet, Laurent

    2015-01-01

    On Reunion Island successful biological control of the sugarcane white grub Hoplochelus marginalis Fairmaire (Coleoptera: Melolonthidae) has been conducted for decades with strains from the entomopathogenic fungal genus Beauveria (Ascomycota: Hypocreales). A study based on morphological characters combined with a multisequence phylogenetic analysis of genes that encode the translation elongation factor 1-alpha (TEF1), RNA polymerase II largest subunit (RPB1), RNA polymerase II second largest subunit (RPB2) and the Bloc nuc intergenic region was carried out on Beauveria strains isolated on Reunion and Madagascar from H. marginalis. This study revealed that these strains, previously identified as Beauveria brongniartii, did not match that species and are closely related to but still distinct from B. malawiensis strains. Therefore we describe the Reunion Island fungus as the new species B. hoplocheli. PMID:26297783

  20. Molecular systematics of the cotton root rot pathogen, Phymatotrichopsis omnivora.

    PubMed

    Marek, S M; Hansen, K; Romanish, M; Thorn, R G

    2009-06-01

    Cotton root rot is an important soilborne disease of cotton and numerous dicot plants in the south-western United States and Mexico. The causal organism, Phymatotrichopsis omnivora (= Phymatotrichum omnivorum), is known only as an asexual, holoanamorphic (mitosporic) fungus, and produces conidia resembling those of Botrytis. Although the corticoid basidiomycetes Phanerochaete omnivora (Polyporales) and Sistotrema brinkmannii (Cantharellales; both Agaricomycetes) have been suggested as teleomorphs of Phymatotrichopsis omnivora, phylogenetic analyses of nuclear small- and large-subunit ribosomal DNA and subunit 2 of RNA polymerase II from multiple isolates indicate that it is neither a basidiomycete nor closely related to other species of Botrytis (Sclerotiniaceae, Leotiomycetes). Phymatotrichopsis omnivora is a member of the family Rhizinaceae, Pezizales (Ascomycota: Pezizomycetes) allied to Psilopezia and Rhizina. PMID:20198139

  1. Genome mining of ascomycetous fungi reveals their genetic potential for ergot alkaloid production.

    PubMed

    Gerhards, Nina; Matuschek, Marco; Wallwey, Christiane; Li, Shu-Ming

    2015-06-01

    Ergot alkaloids are important as mycotoxins or as drugs. Naturally occurring ergot alkaloids as well as their semisynthetic derivatives have been used as pharmaceuticals in modern medicine for decades. We identified 196 putative ergot alkaloid biosynthetic genes belonging to at least 31 putative gene clusters in 31 fungal species by genome mining of the 360 available genome sequences of ascomycetous fungi with known proteins. Detailed analysis showed that these fungi belong to the families Aspergillaceae, Clavicipitaceae, Arthrodermataceae, Helotiaceae and Thermoascaceae. Within the identified families, only a small number of taxa are represented. Literature search revealed a large diversity of ergot alkaloid structures in different fungi of the phylum Ascomycota. However, ergot alkaloid accumulation was only observed in 15 of the sequenced species. Therefore, this study provides genetic basis for further study on ergot alkaloid production in the sequenced strains. PMID:25796201

  2. Subcutaneous infection by Ochroconis mirabilis in an immunocompetent patient.

    PubMed

    Shi, Dongmei; Lu, Guixia; Mei, Huan; de Hoog, G Sybren; Samerpitak, Kittipan; Deng, Shuwen; Shen, Yongnian; Liu, Weida

    2016-03-01

    Recently, the taxonomy of Ochroconis (Ascomycota, Pezizomycotina, Venturiales, Sympoventuriaceae) has been revised with the recognition of an additional genus, Verruconis. Ochroconis comprises mesophilic saprobes that occasionally infect vertebrates which mostly are cold-blooded, while Verruconis contains thermophilic species which is a neurotrope in humans and birds. On the basis of molecular data it is noted that only a single Ochroconis species regularly infects immunocompetent human hosts. Here we report a subcutaneous infection due to Ochroconis mirabilis in a 50-year-old immunocompetent female patient. In vitro antifungal susceptibility tests revealed that terbinafine was the most effective drug. The patient was successfully cured with oral administration of terbinafine 250 mg daily in combination with 3 times of topical ALA-photodynamic therapy for 9 months. PMID:27182484

  3. The diversity of fungal genome.

    PubMed

    Mohanta, Tapan Kumar; Bae, Hanhong

    2015-01-01

    The genome size of an organism varies from species to species. The C-value paradox enigma is a very complex puzzle with regards to vast diversity in genome sizes in eukaryotes. Here we reported the detailed genomic information of 172 fungal species among different fungal genomes and found that fungal genomes are very diverse in nature. In fungi, the diversity of genomes varies from 8.97 Mb to 177.57 Mb. The average genome sizes of Ascomycota and Basidiomycota fungi are 36.91 and 46.48 Mb respectively. But higher genome size is observed in Oomycota (74.85 Mb) species, a lineage of fungus-like eukaryotic microorganisms. The average coding genes of Oomycota species are almost doubled than that of Acomycota and Basidiomycota fungus. PMID:25866485

  4. Zombie bugs? The fungus Purpureocillium cf. lilacinum may manipulate the behavior of its host bug Edessa rufomarginata.

    PubMed

    Eberhard, William; Pacheco-Esquivel, Jessica; Carrasco-Rueda, Farah; Christopher, Yuliana; Gonzalez, Cely; Ramos, Daniel; Urbina, Hector; Blackwell, Meredith

    2014-01-01

    Just before dying, Edessa rufomarginata (Hemiptera, Pentotomidae) individuals that are infected with the fungus Purpureocillium cf. lilacinum (Ascomycota: Ophiocordycipitaceae) move from the leaves onto the stems of their Solanum sp. host and firmly grasp the stems in ways seldom employed by uninfected bugs. These alterations in host behavior probably improve the chances that the subsequently produced fungal spores will be dispersed aerially. Purpureocillium cf. lilacinum is a member of the Ophiocordycipitaceae, a group in which other species also modify the behavior of their hosts. As in the case of newly distinguished relatives of Ophiocordyceps unilateralis associated with "zombie ants" the discovery of P. cf. lilacinum infecting bugs reveals that P. lilacinum may be more diverse than previously appreciated. PMID:25143477

  5. Phylogenetic affiliation of the desert truffles Picoa juniperi and Picoa lefebvrei.

    PubMed

    Sbissi, Imed; Neffati, Mohamed; Boudabous, Abdellatif; Murat, Claude; Gtari, Maher

    2010-11-01

    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

  6. Study on morphology, pathogenicity, and genetic variability of Beauveria bassiana isolates obtained from Boophilus microplus tick.

    PubMed

    Fernandes, Everton Kort Kamp; Costa, Gisela Lara; Moraes, Aurea Maria Lage; Zahner, Viviane; Bittencourt, Vânia Rita Elias Pinheiro

    2006-03-01

    Fifty isolates of Beauveria bassiana (Balsamo) Vuillemin, 1912 (Ascomycota: Clavicipitaceae) were analyzed by morphology, for their pathogenic potential to Boophilus microplus (Canestrini, 1887) (Acari: Ixodidae) larvae, and by Random Amplified Polymorphic DNA-Polymerase Chain Reaction technique. Morphological analysis demonstrated that isolates present characteristics compatible to those described for B. bassiana in the literature. Virulence test demonstrated that all isolates present lethal effect on larvae and that the lethal concentration varies among isolates. The most virulent isolate was the only one obtained from human infection, which was also the only isolate presenting synnemata. The study on genetic variability among the isolates allowed the identification of 23 electrophoretic profiles. The established groupings suggest that most of the isolates obtained from B. microplus of the same locality present low genetic variation. In this way, the data in the present study will contribute to a meticulous characterization of these B. bassiana isolates. PMID:16374618

  7. Biosynthetic Pathways of Ergot Alkaloids

    PubMed Central

    Gerhards, Nina; Neubauer, Lisa; Tudzynski, Paul; Li, Shu-Ming

    2014-01-01

    Ergot alkaloids are nitrogen-containing natural products belonging to indole alkaloids. The best known producers are fungi of the phylum Ascomycota, e.g., Claviceps, Epichloë, Penicillium and Aspergillus species. According to their structures, ergot alkaloids can be divided into three groups: clavines, lysergic acid amides and peptides (ergopeptines). All of them share the first biosynthetic steps, which lead to the formation of the tetracyclic ergoline ring system (except the simplest, tricyclic compound: chanoclavine). Different modifications on the ergoline ring by specific enzymes result in an abundance of bioactive natural products, which are used as pharmaceutical drugs or precursors thereof. From the 1950s through to recent years, most of the biosynthetic pathways have been elucidated. Gene clusters from several ergot alkaloid producers have been identified by genome mining and the functions of many of those genes have been demonstrated by knock-out experiments or biochemical investigations of the overproduced enzymes. PMID:25513893

  8. High diversity of fungi in air particulate matter

    PubMed Central

    Fröhlich-Nowoisky, Janine; Pickersgill, Daniel A.; Després, Viviane R.; Pöschl, Ulrich

    2009-01-01

    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 μm). Moreover, the ratio of Basidiomycota to Ascomycota was found to be much higher than previously assumed, which might also apply to the biosphere. PMID:19617562

  9. First record of Talaromyces udagawae in soil related to decomposing human remains in Argentina.

    PubMed

    Tranchida, María C; Centeno, Néstor D; Stenglein, Sebastián A; Cabello, Marta N

    2016-01-01

    The morphologic features of Talaromyces udagawae Stolk and Samson are here described and illustrated. This teleomorphic Ascomycota fungus was isolated from soil obtained in Buenos Aires province (Argentina) from beneath a human cadaver in an advanced state of decomposition. After washing and serial dilution of the soil along with moist-chamber techniques for fungal cultivation, T. udagawae formed very restricted colonies of bright yellow color on different growth media with 8-ascospored asci. The ascospores were ellipsoidal and ornamented. The anamorphic state was not observed. Molecular-genetic techniques identified the species. The present record is the first of the species in Argentina, pointing it as a tool to identify soils where cadaver decomposition occurs. PMID:26766627

  10. Liquid Culture Production of Fungal Microsclerotia.

    PubMed

    Jackson, Mark A; Payne, Angela R

    2016-01-01

    Fungal microsclerotia ("small" sclerotia) are compact hyphal aggregates, typically 50-600 μm in diameter, that are formed under unfavorable nutritional and/or environmental conditions. These structures are often melanized and desiccated to some degree containing endogenous nutritional reserves for use when favorable conditions return. Many fungi, mostly plant pathogens, produce microsclerotia as a survival structure. Liquid culture methods have been developed for producing microsclerotia of the Ascomycota Metarhizium spp, Colletotrichum truncatum, Mycoleptodiscus terrestris, and Trichoderma spp. While these fungi have varying culture conditions that optimize microsclerotia production, all share common nutritional and environmental requirements for microsclerotia formation. Described are the general liquid culture techniques, media components, and harvesting and drying methods necessary to produce stable microsclerotial granules of these fungi. PMID:27565493

  11. Assessment of epiphytic yeast diversity in rice (Oryza sativa) phyllosphere in Thailand by a culture-independent approach.

    PubMed

    Nasanit, Rujikan; Krataithong, Kultara; Tantirungkij, Manee; Limtong, Savitree

    2015-06-01

    The epiphytic yeast diversity in rice phyllosphere in Thailand was investigated by a culture-independent technique based on the RFLP pattern and the sequence of the D1/D2 domain of the large subunit rRNA gene. Forty-four samples of rice leaf were collected randomly from six provinces. The DNA was extracted from leaf washing samples and the D1/D2 domain was amplified using PCR technique. The PCR products were cloned and then screened by colony PCR. Of total 1121 clones, 451 clones (40.2 %) revealed the D1/D2 domain sequences closely related to sequences of yeasts in GenBank, and they were clustered into 45 operational taxonomic units (OTUs) at 99 % homology. Of total yeast related clones, 329 clones (72.9 %) were identified as nine known yeast species, which consisted of 314 clones (8 OTUs) in the phylum Basidiomycota including Bullera japonica, Pseudozyma antarctica, Pseudozyma aphidis, Sporobolomyces blumeae, Sporobolomyces carnicolor and Sporobolomyces oryzicola and 15 clones (6 OTUs) in the phylum Ascomycota including Metschnikowia koreensis, Meyerozyma guilliermondii and Wickerhamomyces anomalus. The D1/D2 sequences (122 clones) that could not be identified as known yeast species were closest to 3 and 14 species in Ascomycota and Basidiomycota, respectively, some of which may be new yeast species. The most predominant species detected was P. antarctica (42.6 %) followed by B. japonica (25.9 %) with 63.6 and 22.7 % frequency of occurrence, respectively. The results of OTU richness of each sampling location revealed that climate condition and sampling location could affect epiphytic yeast diversity in rice phyllosphere. PMID:25842038

  12. Evolution of Chemical Diversity in Echinocandin Lipopeptide Antifungal Metabolites

    PubMed Central

    Yue, Qun; Chen, Li; Zhang, Xiaoling; Li, Kuan; Sun, Jingzu; Liu, Xingzhong

    2015-01-01

    The echinocandins are a class of antifungal drugs that includes caspofungin, micafungin, and anidulafungin. Gene clusters encoding most of the structural complexity of the echinocandins provided a framework for hypotheses about the evolutionary history and chemical logic of echinocandin biosynthesis. Gene orthologs among echinocandin-producing fungi were identified. Pathway genes, including the nonribosomal peptide synthetases (NRPSs), were analyzed phylogenetically to address the hypothesis that these pathways represent descent from a common ancestor. The clusters share cooperative gene contents and linkages among the different strains. Individual pathway genes analyzed in the context of similar genes formed unique echinocandin-exclusive phylogenetic lineages. The echinocandin NRPSs, along with the NRPS from the inp gene cluster in Aspergillus nidulans and its orthologs, comprise a novel lineage among fungal NRPSs. NRPS adenylation domains from different species exhibited a one-to-one correspondence between modules and amino acid specificity that is consistent with models of tandem duplication and subfunctionalization. Pathway gene trees and Ascomycota phylogenies are congruent and consistent with the hypothesis that the echinocandin gene clusters have a common origin. The disjunct Eurotiomycete-Leotiomycete distribution appears to be consistent with a scenario of vertical descent accompanied by incomplete lineage sorting and loss of the clusters from most lineages of the Ascomycota. We present evidence for a single evolutionary origin of the echinocandin family of gene clusters and a progression of structural diversification in two fungal classes that diverged approximately 290 to 390 million years ago. Lineage-specific gene cluster evolution driven by selection of new chemotypes contributed to diversification of the molecular functionalities. PMID:26024901

  13. Fungal Cytochrome P450 Monooxygenases: Their Distribution, Structure, Functions, Family Expansion, and Evolutionary Origin

    PubMed Central

    Chen, Wanping; Lee, Mi-Kyung; Jefcoate, Colin; Kim, Sun-Chang; Chen, Fusheng; Yu, Jae-Hyuk

    2014-01-01

    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

  14. Metaproteome analysis of the microbial community during leaf litter decomposition - the impact of stoichiometry and temperature perturbations

    NASA Astrophysics Data System (ADS)

    Keiblinger, K. M.; Schneider, T.; Leitner, S.; Hämmerle, I.; Riedel, K.; Zechmeister-Boltenstern, S.

    2012-04-01

    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

  15. Revealing the unexplored fungal communities in deep groundwater of crystalline bedrock fracture zones in Olkiluoto, Finland

    PubMed Central

    Sohlberg, Elina; Bomberg, Malin; Miettinen, Hanna; Nyyssönen, Mari; Salavirta, Heikki; Vikman, Minna; Itävaara, Merja

    2015-01-01

    The diversity and functional role of fungi, one of the ecologically most important groups of eukaryotic microorganisms, remains largely unknown in deep biosphere environments. In this study we investigated fungal communities in packer-isolated bedrock fractures in Olkiluoto, Finland at depths ranging from 296 to 798 m below surface level. DNA- and cDNA-based high-throughput amplicon sequencing analysis of the fungal internal transcribed spacer (ITS) gene markers was used to examine the total fungal diversity and to identify the active members in deep fracture zones at different depths. Results showed that fungi were present in fracture zones at all depths and fungal diversity was higher than expected. Most of the observed fungal sequences belonged to the phylum Ascomycota. Phyla Basidiomycota and Chytridiomycota were only represented as a minor part of the fungal community. Dominating fungal classes in the deep bedrock aquifers were Sordariomycetes, Eurotiomycetes, and Dothideomycetes from the Ascomycota phylum and classes Microbotryomycetes and Tremellomycetes from the Basidiomycota phylum, which are the most frequently detected fungal taxa reported also from deep sea environments. In addition some fungal sequences represented potentially novel fungal species. Active fungi were detected in most of the fracture zones, which proves that fungi are able to maintain cellular activity in these oligotrophic conditions. Possible roles of fungi and their origin in deep bedrock groundwater can only be speculated in the light of current knowledge but some species may be specifically adapted to deep subsurface environment and may play important roles in the utilization and recycling of nutrients and thus sustaining the deep subsurface microbial community. PMID:26106376

  16. Morphological characteristics of bioaerosols from contrasting locations in southern tropical India - A case study

    NASA Astrophysics Data System (ADS)

    Valsan, Aswathy E.; Priyamvada, Hema; Ravikrishna, R.; Després, Viviane R.; Biju, C. V.; Sahu, Lokesh K.; Kumar, Ashwini; Verma, R. S.; Philip, L.; Gunthe, Sachin S.

    2015-12-01

    Bioaerosols, which are ubiquitous in the earth's atmosphere, are poorly characterized in terms of their physical and chemical properties. Improved knowledge of their physical and chemical properties is essential to have a better understanding of their dispersion and long-range transport in the atmosphere and at the same time to assess their role as potential Ice Nuclei (IN). In the present work, possibly for the first time we report the morphological characteristics of bioaerosols from marine urban and high altitude continental regions in Southern India. The samples were collected using polycarbonate filter paper and analyzed using Scanning Electron Microscope (SEM) coupled with Energy-dispersive Spectra Detector (EDX/EDS). The observed bioaerosols exhibited great variability in their morphological features over this region of the world. At these contrasting environments, we found that fungal spores constituted the major fraction of the total observed bioaerosols. Pollen grains, plant and insect fragments, and lot of other non-identified bio-particles were also observed constituting the remaining fraction. Further, the classification of fungal spores exhibited strong variability over this region. For example, fungal spores of both Ascomycota and Basidiomycota class were seen in abundance in marine environment, while Ascomycota especially Cladosporium were seen in abundance in high altitude continental environment. Our findings also suggest that increase in diversity of bioaerosol particles at marine site appeared to coincide with precipitation. It appears that vast diversity in the morphological features of bioaerosols exists over this region, which should further be studied using advanced online techniques for better quantification under contrasting environments. However, the diversity observed in morphological characteristics of bioaerosols at these two contrasting locations is limited and restricted to these two sites and season of the year, and should therefore

  17. Response of Soil Fungi Community Structure to Salt Vegetation Succession in the Yellow River Delta.

    PubMed

    Wang, Yan-Yun; Guo, Du-Fa

    2016-10-01

    High-throughput sequencing technology was used to reveal the composition and distribution of fungal community structure in the Yellow River Delta under bare land and four kinds of halophyte vegetation (saline seepweed, Angiospermae, Imperata and Apocynum venetum [A. venetum]). The results showed that the soil quality continuously improved with the succession of salt vegetation types. The soil fungi richness of mild-salt communities (Imperata and A. venetum) was relatively higher, with Shannon index values of 5.21 and 5.84, respectively. The soil fungi richness of severe-salt-tolerant communities (saline seepweed, Angiospermae) was relatively lower, with Shannon index values of 4.64 and 4.66, respectively. The UniFrac metric values ranged from 0.48 to 0.67 when the vegetation was in different succession stages. A total of 60,174 valid sequences were obtained for the five vegetation types, and they were classified into Ascomycota, Basidiomycota, Chytridiomycota, Glomeromycota and Mucoromycotina. Ascomycota had the greatest advantage among plant communities of Imperata and A. venetum, as indicated by relative abundances of 2.69 and 69.97 %, respectively. Basidiomycota had the greatest advantage among mild-salt communities of saline seepweed and Angiospermae, with relative abundances of 9.43 and 6.64 %, respectively. Soil physical and chemical properties were correlated with the distribution of the fungi, and Mucor was significantly correlated with soil moisture (r = 0.985; P < 0.01). Soil quality, salt vegetation and soil fungi were influenced by each other. PMID:27449214

  18. Determining the Pathogenic Potential of Non-sporulating Molds Isolated from Cutaneous Specimens.

    PubMed

    Jeyaprakasam, Nantha Kumar; Razak, Mohd Fuat Abdul; Ahmad, Noor Azimah Binti; Santhanam, Jacinta

    2016-06-01

    Although non-sporulating molds (NSM) are frequently isolated from patients and have been recognized as agents of pulmonary disease, their clinical significance in cutaneous specimens is relatively unknown. Therefore, this study aimed to identify NSM and to determine the keratinolytic activity of isolates from cutaneous sites. NSM isolates from clinical specimens such as skin, nail, and body fluids were identified based on their ribosomal DNA sequences. Of 17 NSM isolates (7 Ascomycota, 10 Basidiomycota), eleven were identified to species level while five were identified to the genus level. These include Schizophyllum commune, a known human pathogen, Phoma multirostrata, a plant pathogen, and Perenniporia tephropora, a saprophyte. To determine fungal pathogenicity, keratinolytic activity, a major virulence factor, was evaluated ex vivo using human nail samples by measuring dye release from keratin azure, for NSM along with pathogens (Trichophyton mentagrophytes, Trichophyton rubrum, Microsporum canis and Fusarium spp.) and nonpathogenic (endophyte) fungi for comparison. This study showed that pathogenic fungi had the highest keratinolytic activity (7.13 ± 0.552 keratinase units) while the nonpathogenic endophytes had the lowest activity (2.37 ± 0.262 keratinase units). Keratinolytic activity of two Ascomycota NSM (Guignardia mangiferae and Hypoxylon sp.) and one Basidiomycota NSM (Fomitopsis cf. meliae) was equivalent to that of pathogenic fungi, while Xylaria feejeensis showed significantly higher activity (p < 0.05) than nonpathogenic endophytes. These results indicate that the pathogenic ability of NSM is species dependent; clinical isolates, especially more frequently isolated species, may be involved in disease etiology. PMID:26847667

  19. Illumina sequencing of fungi associated with manganese oxide deposits in cave systems

    NASA Astrophysics Data System (ADS)

    Zorn, B. T.; Santelli, C. M.; Carmichael, S. K.; Pepe-Ranney, C. P.; Roble, L.; Carmichael, M.; Bräuer, S.

    2013-12-01

    The environmental cycling of manganese (Mn) remains relatively poorly characterized when compared with other metals such as iron. However, fungi have been observed to produce Mn(III/IV) oxides resembling buserite, birnessite, and todorokite on the periphery of vegetative hyphae, hyphal branching points and at the base of fruiting bodies. Recent studies indicate that some of these oxides may be generated by a two-stage reaction with soluble Mn(II) and biogenic reactive oxygen species for some groups of fungi, in particular the Ascomycota. These oxides can provide a versatile protective barrier or aid in the capture of trace metals in the environment, although the exact evolutionary function and trigger is unclear. In this study, two caves in the southern Appalachians, a pristine cave and an anthropogenically impacted cave, were compared by analyzing fungal community assemblages in manganese oxide rich deposits. Quantitative PCR data indicated that fungi are present in a low abundance (<1%) in all locations sampled within the caves. Among amplified DNA sequences retrieved in an 18S rDNA clone library, over 88% were representative of the phylum Basidiomycota (predominantly Agaricomycetes), 2.74% of Ascomycota, 2.28% of Blastocladiomycota and Chytridiomycota, 0.46% of Zygomycota, and 3.65% of Eukarya or Fungi incertae sedis. Using Illumina's MiSeq to sequence amplicons of the fungal ITS1 gene has yielded roughly 100,000-200,000 paired-end reads per sample. These data are currently being analyzed to compare fungal communities before and after induced Mn oxidation in the field. In addition, sites within the pristine cave are being compared with analogous sites in the impacted cave. Culturing efforts have thus far yielded Mn oxide producing members of the orders Glomerales and Pleosporales as well as two Genus incertae sedis (Fungal sp. YECT1, and Fungal sp. YECT3, growing on discarded electrical tape) that do not appear to be closely related to any other known Mn

  20. Diverse Bacteria Inhabit Living Hyphae of Phylogenetically Diverse Fungal Endophytes▿ †

    PubMed Central

    Hoffman, Michele T.; Arnold, A. Elizabeth

    2010-01-01

    Both the establishment and outcomes of plant-fungus symbioses can be influenced by abiotic factors, the interplay of fungal and plant genotypes, and additional microbes associated with fungal mycelia. Recently bacterial endosymbionts were documented in soilborne Glomeromycota and Mucoromycotina and in at least one species each of mycorrhizal Basidiomycota and Ascomycota. Here we show for the first time that phylogenetically diverse endohyphal bacteria occur in living hyphae of diverse foliar endophytes, including representatives of four classes of Ascomycota. We examined 414 isolates of endophytic fungi, isolated from photosynthetic tissues of six species of cupressaceous trees in five biogeographic provinces, for endohyphal bacteria using microscopy and molecular techniques. Viable bacteria were observed within living hyphae of endophytic Pezizomycetes, Dothideomycetes, Eurotiomycetes, and Sordariomycetes from all tree species and biotic regions surveyed. A focus on 29 fungus/bacterium associations revealed that bacterial and fungal phylogenies were incongruent with each other and with taxonomic relationships of host plants. Overall, eight families and 15 distinct genotypes of endohyphal bacteria were recovered; most were members of the Proteobacteria, but a small number of Bacillaceae also were found, including one that appears to occur as an endophyte of plants. Frequent loss of bacteria following subculturing suggests a facultative association. Our study recovered distinct lineages of endohyphal bacteria relative to previous studies, is the first to document their occurrence in foliar endophytes representing four of the most species-rich classes of fungi, and highlights for the first time their diversity and phylogenetic relationships with regard both to the endophytes they inhabit and the plants in which these endophyte-bacterium symbiota occur. PMID:20435775

  1. Ice Nucleation of Fungal Spores from the Classes Agaricomycetes, Ustilaginomycetes, and Eurotiomycetes, and the effect on the Atmospheric Transport of these Spores

    SciTech Connect

    Haga, D. I.; Burrows, Susannah M.; Iannone, R.; Wheeler, M. J.; Mason, R.; Chen, J.; Polishchuk, E. A.; Poschl, U.; Bertram, Allan K.

    2014-08-26

    Ice nucleation on fungal spores may affect the frequency and properties of ice and mixed-phase clouds. We studied the ice nucleation properties of 12 different species of fungal spores chosen from three classes: Agaricomycetes, Ustilagomycetes, and Eurotiomycetes. Agaricomycetes include many types of mushroom species and are cosmopolitan all over the globe. Ustilagomycetes are agricultural pathogens and have caused widespread damage to crops. Eurotiomycetes are found on all types of decaying material and include important human allergens. We focused on these classes since they are thought to be abundant in the atmosphere and because there is very little information on the ice nucleation ability of these classes of spores in the literature. All of the fungal spores investigated were found to cause freezing of water droplets at temperatures warmer than homogeneous freezing. The cumulative number of ice nuclei per spore was 0.001 at temperatures between -19 °C and -29 °C, 0.01 between -25.5 °C and -31 °C, and 0.1 between -26 °C and -36 °C. On average, the order of ice nucleating ability for these spores is Ustilagomycetes > Agaricomycetes ≅ Eurotiomycetes. We show that at temperatures below -20 °C, all of the fungal spores studied here are less efficient ice nuclei compared to Asian mineral dust on a per surface area basis. We used our new freezing results together with data in the literature to compare the freezing temperatures of spores from the phyla Basidiomycota and Ascomycota, which together make up 98 % of known fungal species found on Earth. The data show that within both phyla (Ascomycota and Basidiomycota) there is a wide range of freezing properties, and also that the variation within a phylum is greater than the variation between the average freezing properties of the phyla. Using a global chemistry-climate transport model, we investigated whether ice nucleation on the studied spores, followed by precipitation, can influence the atmospheric

  2. Molecular Tools for Monitoring the Ecological Sustainability of a Stone Bio-Consolidation Treatment at the Royal Chapel, Granada

    PubMed Central

    Jroundi, Fadwa; Gonzalez-Muñoz, Maria Teresa; Sterflinger, Katja; Piñar, Guadalupe

    2015-01-01

    Background Biomineralization processes have recently been applied in situ to protect and consolidate decayed ornamental stone of the Royal Chapel in Granada (Spain). While this promising method has demonstrated its efficacy regarding strengthening of the stone, little is known about its ecological sustainability. Methodology/Principal Findings Here, we report molecular monitoring of the stone-autochthonous microbiota before and at 5, 12 and 30 months after the bio-consolidation treatment (medium/long-term monitoring), employing the well-known molecular strategy of DGGE analyses. Before the bio-consolidation treatment, the bacterial diversity showed the exclusive dominance of Actinobacteria (100%), which decreased in the community (44.2%) after 5 months, and Gamma-proteobacteria (30.24%) and Chloroflexi (25.56%) appeared. After 12 months, Gamma-proteobacteria vanished from the community and Cyanobacteria (22.1%) appeared and remained dominant after thirty months, when the microbiota consisted of Actinobacteria (42.2%) and Cyanobacteria (57.8%) only. Fungal diversity showed that the Ascomycota phylum was dominant before treatment (100%), while, after five months, Basidiomycota (6.38%) appeared on the stone, and vanished again after twelve months. Thirty months after the treatment, the fungal population started to stabilize and Ascomycota dominated on the stone (83.33%) once again. Members of green algae (Chlorophyta, Viridiplantae) appeared on the stone at 5, 12 and 30 months after the treatment and accounted for 4.25%, 84.77% and 16.77%, respectively. Conclusions The results clearly show that, although a temporary shift in the bacterial and fungal diversity was observed during the first five months, most probably promoted by the application of the bio-consolidation treatment, the microbiota tends to regain its initial stability in a few months. Thus, the treatment does not seem to have any negative side effects on the stone-autochthonous microbiota over that time

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

    PubMed Central

    Parrent, Jeri Lynn; James, Timothy Y; Vasaitis, Rimvydas; Taylor, Andrew FS

    2009-01-01

    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

  4. A molecular timescale of eukaryote evolution and the rise of complex multicellular life

    NASA Technical Reports Server (NTRS)

    Hedges, S. Blair; Blair, Jaime E.; Venturi, Maria L.; Shoe, Jason L.

    2004-01-01

    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

  5. Unequal Recombination and Evolution of the Mating-Type (MAT) Loci in the Pathogenic Fungus Grosmannia clavigera and Relatives

    PubMed Central

    Tsui, Clement K.-M.; DiGuistini, Scott; Wang, Ye; Feau, Nicolas; Dhillon, Braham; Bohlmann, Jörg; Hamelin, Richard C.

    2013-01-01

    Sexual reproduction in fungi is regulated by the mating-type (MAT) locus where recombination is suppressed. We investigated the evolution of MAT loci in eight fungal species belonging to Grosmannia and Ophiostoma (Sordariomycetes, Ascomycota) that include conifer pathogens and beetle symbionts. The MAT1-2 idiomorph/allele was identified from the assembled and annotated Grosmannia clavigera genome, and the MAT locus is flanked by genes coding for cytoskeleton protein (SLA) and DNA lyase. The synteny of these genes is conserved and consistent with other members in Ascomycota. Using sequences from SLA and flanking regions, we characterized the MAT1-1 idiomorph from other isolates of G. clavigera and performed dotplot analysis between the two idiomorphs. Unexpectedly, the MAT1-2 idiomorph contains a truncated MAT1-1-1 gene upstream of the MAT1-2-1 gene that bears the high-mobility-group domain. The nucleotide and amino acid sequence of the truncated MAT1-1-1 gene is similar to its homologous copy in the MAT1-1 idiomorph in the opposite mating-type isolate, except that positive selection is acting on the truncated gene and the alpha(α)-box that encodes the transcription factor has been deleted. The MAT idiomorphs sharing identical gene organization were present in seven additional species in the Ophiostomatales, suggesting that the presence of truncated MAT1-1-1 gene is a general pattern in this order. We propose that an ancient unequal recombination event resulted in the ancestral MAT1-1-1 gene integrated into the MAT1-2 idiomorph and surviving as the truncated MAT1-1-1 genes. The α-box domain of MAT1-1-1 gene, located at the same MAT locus adjacent to the MAT1-2-1 gene, could have been removed by deletion after recombination due to mating signal interference. Our data confirmed a 1:1 MAT/sex ratio in two pathogen populations, and showed that all members of the Ophiostomatales studied here including those that were previously deemed asexual have the potential to

  6. Soil Microbial Community Responses to Short-term Multiple Experimental Climate Change Drivers

    NASA Astrophysics Data System (ADS)

    Li, Guanlin; Lee, Jongyeol; Lee, Sohye; Roh, Yujin; Son, Yowhan

    2016-04-01

    It is agreed that soil microbial communities are responsible for the cycling of carbon and nutrients in ecosystems; however, the response of these microbial communities to climate change has not been clearly understood. In this study, we measured the direct and interactive effects of climate change drivers on soil bacterial and fungal communities (abundance and composition) in an open-field multifactor climate change experiment. The experimental treatment system was established with two-year-old Pinus densiflora seedlings at Korea University in April 2013, and consisted of six different treatments with three replicates: two levels of air temperature warming (control and +3° C) were crossed with three levels of precipitation manipulation (control, -30% and +30%). After 2.5 years of treatments, in August, 2015, soil samples were collected from the topsoil (0-15cm) of all plots (n=18). High-throughput sequencing technology was used to assess the abundance and composition of soil bacterial and fungal community. Analysis of variance for a blocked split-plot design was used to detect the effects of climate change drivers and their interaction on the abundance and composition of soil bacterial and fungal community. Our results showed that 1) only the significant effect of warming on fungal community abundance was observed (P <0.05); 2) on average, warming decreased both bacterial and fungal community abundance by 20.90% and 32.30%, 6.69% and 45.89%, 14.71% and 19.56% in control, decreased, and increased precipitation plots, respectively; 3) however, warming increased the relative bacterium/fungus ratio on average by 14.03%, 37.03% and 14.31% in control, decreased, and increased precipitation plots, respectively; 4) the phylogenetic distribution of bacterial and fungal groups and their relative abundance varied among treatments; 5) treatments altered the relative abundance of Ascomycota and Basidiomycota, where Ascomycota decreased with a concomitant increase in the

  7. The Polyketide Synthase Gene pks4 of Trichoderma reesei Provides Pigmentation and Stress Resistance

    PubMed Central

    Atanasova, Lea; Knox, Benjamin P.; Kubicek, Christian P.; Baker, Scott E.

    2013-01-01

    Species of the fungal genus Trichoderma (Hypocreales, Ascomycota) are well-known for their production of various secondary metabolites. Nonribosomal peptides and polyketides represent a major portion of these products. In a recent phylogenomic investigation of Trichoderma polyketide synthase (PKS)-encoding genes, the pks4 from T. reesei was shown to be an orthologue of pigment-forming PKSs involved in synthesis of aurofusarin and bikaverin in Fusarium spp. In this study, we show that deletion of this gene in T. reesei results in loss of green conidial pigmentation and in pigmentation alteration of teleomorph structures. It also has an impact on conidial cell wall stability and the antagonistic abilities of T. reesei against other fungi, including formation of inhibitory metabolites. In addition, deletion of pks4 significantly influences the expression of other PKS-encoding genes of T. reesei. To our knowledge, this is the first indication that a low-molecular-weight pigment-forming PKS is involved in defense, mechanical stability, and stress resistance in fungi. PMID:24036343

  8. Assessment of microbial communities in PM1 and PM10 of Urumqi during winter.

    PubMed

    Gou, Huange; Lu, Jianjiang; Li, Shanman; Tong, Yanbin; Xie, Chunbin; Zheng, Xiaowu

    2016-07-01

    Recently, inhalable particulate matter has been reported to carry microorganisms responsible for human allergy and respiratory disease. The unique geographical environment and adverse weather conditions of Urumqi cause double pollution of dust and smog, but research on the microbial content of the atmosphere has not been commenced. In this study, 16S and 18S rRNA gene sequencing were conducted to investigate the microbial composition of Urumqi's PM1 and PM10 pollutants in winter. Results showed that the bacterial community is mainly composed of Proteobacteria, Firmicutes and Actinobacteria, Proteobacteria accounted for the most proportion which was significant difference in some aforementioned studies. Ascomycota and Basidiomycota constitute the main part of the fungal microbial community. The difference of bacterial relative abundance in sample point is greater than in particle sizes. The sequences of several pathogenic bacteria and opportunistic pathogens were also detected, such as Acinetobacter, Delftia, Serratia, Chryseobacterium, which may impact on immunocompromised populations (elderly, children and postoperative convalescence patients), and some fungal genera may cause several plant diseases. Our findings may serve an important reference value in the global air microbial propagation and air microbial research in desert. PMID:27086076

  9. Elucidating the Diversity of Aquatic Microdochium and Trichoderma Species and Their Activity against the Fish Pathogen Saprolegnia diclina.

    PubMed

    Liu, Yiying; Zachow, Christin; Raaijmakers, Jos M; de Bruijn, Irene

    2016-01-01

    Animals and plants are increasingly threatened by emerging fungal and oomycete diseases. Amongst oomycetes, Saprolegnia species cause population declines in aquatic animals, especially fish and amphibians, resulting in significant perturbation in biodiversity, ecological balance and food security. Due to the prohibition of several chemical control agents, novel sustainable measures are required to control Saprolegnia infections in aquaculture. Previously, fungal community analysis by terminal restriction fragment length polymorphism (T-RFLP) revealed that the Ascomycota, specifically the genus Microdochium, was an abundant fungal phylum associated with salmon eggs from a commercial fish farm. Here, phylogenetic analyses showed that most fungal isolates obtained from salmon eggs were closely related to Microdochium lycopodinum/Microdochium phragmitis and Trichoderma viride species. Phylogenetic and quantitative PCR analyses showed both a quantitative and qualitative difference in Trichoderma population between diseased and healthy salmon eggs, which was not the case for the Microdochium population. In vitro antagonistic activity of the fungi against Saprolegnia diclina was isolate-dependent; for most Trichoderma isolates, the typical mycoparasitic coiling around and/or formation of papilla-like structures on S. diclina hyphae were observed. These results suggest that among the fungal community associated with salmon eggs, Trichoderma species may play a role in Saprolegnia suppression in aquaculture. PMID:26805821

  10. Insight into the transcriptome of Arthrobotrys conoides using high throughput sequencing.

    PubMed

    Ramesh, Pandit; Reena, Patel; Amitbikram, Mohapatra; Chaitanya, Joshi; Anju, Kunjadia

    2015-12-01

    Arthrobotrys conoides is a nematode-trapping fungus belonging to Orbiliales, Ascomycota group, and traps prey nematodes by means of adhesive network. Fungus has a potential to be used as a biocontrol agent against plant parasitic nematodes. In the present study, we characterized the transcriptome of A. conoides using high-throughput sequencing technology and characterized its virulence unigenes. Total 7,255 cDNA contigs with an average length of 425 bp were generated and 6184 (61.81%) transcripts were functionally annotated and characterized. Majority of unigenes were found analogous to the genes of plant pathogenic fungi. A total of 1749 transcripts were found to be orthologous with eukaryotic proteins of KOG database. Several carbohydrate active enzymes and peptidases were identified. We also analyzed classically and nonclassically secreted proteins and confirmed by BLASTP against fungal secretome database. A total of 916 contigs were analogous to 556 unique proteins of Pathogen Host Interaction (PHI) database. Further, we identified 91 unigenes homologous to the database of fungal virulence factor (DFVF). A total of 104 putative protein kinases coding transcripts were identified by BLASTP against KinBase database, which are major players in signaling pathways. This study provides a comprehensive look at the transcriptome of A. conoides and the identified unigenes might have a role in catching and killing prey nematodes by A. conoides. PMID:26301953

  11. Archaeorhizomyces borealis sp. nov. and a sequence-based classification of related soil fungal species.

    PubMed

    Menkis, Audrius; Urbina, Hector; James, Timothy Y; Rosling, Anna

    2014-12-01

    The class Archaeorhizomycetes (Taphrinomycotina, Ascomycota) was introduced to accommodate an ancient lineage of soil-inhabiting fungi found in association with plant roots. Based on environmental sequencing data Archaeorhizomycetes may comprise a significant proportion of the total fungal community in soils. Yet the only species described and cultivated in this class is Archaeorhizomyces finlayi. In this paper, we describe a second species from a pure culture, Archaeorhizomyces borealis NS99-600(T) (=CBS138755(ExT)) based on morphological, physiological, and multi-locus molecular characterization. Archaeorhizomyces borealis was isolated from a root tip of a Pinus sylvestris seedling grown in a forest nursery in Lithuania. Analysis of Archaeorhizomycete species from environmental samples shows that it has a Eurasian distribution and is the most commonly observed species. Archaeorhizomyces borealis shows slow growth in culture and forms yellowish creamy colonies, characteristics that distinguish A. borealis from its closest relative A. finlayi. Here we also propose a sequence-based taxonomic classification of Archaeorhizomycetes and predict that approximately 500 species in this class remain to be isolated and described. PMID:25457942

  12. Insect peptide metchnikowin confers on barley a selective capacity for resistance to fungal ascomycetes pathogens

    PubMed Central

    Rahnamaeian, Mohammad; Langen, Gregor; Imani, Jafargholi; Khalifa, Walaa; Altincicek, Boran; von Wettstein, Diter; Kogel, Karl-Heinz; Vilcinskas, Andreas

    2009-01-01

    The potential of metchnikowin, a 26-amino acid residue proline-rich antimicrobial peptide synthesized in the fat body of Drosophila melanogaster was explored to engineer disease resistance in barley against devastating fungal plant pathogens. The synthetic peptide caused strong in vitro growth inhibition (IC50 value ∼1 μM) of the pathogenic fungus Fusarium graminearum. Transgenic barley expressing the metchnikowin gene in its 52-amino acid pre-pro-peptide form under the control of the inducible mannopine synthase (mas) gene promoter from the Ti plasmid of Agrobacterium tumefaciens displayed enhanced resistance to powdery mildew as well as Fusarium head blight and root rot. In response to these pathogens, metchnikowin accumulated in plant apoplastic space, specifying that the insect signal peptide is functional in monocotyledons. In vitro and in vivo tests revealed that the peptide is markedly effective against fungal pathogens of the phylum Ascomycota but, clearly, less active against Basidiomycota fungi. Importantly, germination of the mutualistic basidiomycete mycorrhizal fungus Piriformospora indica was affected only at concentrations beyond 50 μM. These results suggest that antifungal peptides from insects are a valuable source for crop plant improvements and their differential activities toward different phyla of fungi denote a capacity for insect peptides to be used as selective measures on specific plant diseases. PMID:19734262

  13. Several Genes Encoding Enzymes with the Same Activity Are Necessary for Aerobic Fungal Degradation of Cellulose in Nature

    PubMed Central

    Busk, Peter K.; Lange, Mette; Pilgaard, Bo; Lange, Lene

    2014-01-01

    The cellulose-degrading fungal enzymes are glycoside hydrolases of the GH families and lytic polysaccharide monooxygenases. The entanglement of glycoside hydrolase families and functions makes it difficult to predict the enzymatic activity of glycoside hydrolases based on their sequence. In the present study we further developed the method Peptide Pattern Recognition to an automatic approach not only to find all genes encoding glycoside hydrolases and lytic polysaccharide monooxygenases in fungal genomes but also to predict the function of the genes. The functional annotation is an important feature as it provides a direct route to predict function from primary sequence. Furthermore, we used Peptide Pattern Recognition to compare the cellulose-degrading enzyme activities encoded by 39 fungal genomes. The results indicated that cellobiohydrolases and AA9 lytic polysaccharide monooxygenases are hallmarks of cellulose-degrading fungi except brown rot fungi. Furthermore, a high number of AA9, endocellulase and β-glucosidase genes were identified, not in what are known to be the strongest, specialized lignocellulose degraders but in saprophytic fungi that can use a wide variety of substrates whereas only few of these genes were found in fungi that have a limited number of natural, lignocellulotic substrates. This correlation suggests that enzymes with different properties are necessary for degradation of cellulose in different complex substrates. Interestingly, clustering of the fungi based on their predicted enzymes indicated that Ascomycota and Basidiomycota use the same enzymatic activities to degrade plant cell walls. PMID:25461894

  14. Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae.

    PubMed

    Geiser, David M; Gueidan, Cécile; Miadlikowska, Jolanta; Lutzoni, François; Kauff, Frank; Hofstetter, Valérie; Fraker, Emily; Schoch, Conrad L; Tibell, Leif; Untereiner, Wendy A; Aptroot, André

    2006-01-01

    The class Eurotiomycetes (Ascomycota, Pezizomycotina) is a monophyletic group comprising two major clades of very different ascomycetous fungi: (i) the subclass Eurotiomycetidae, a clade that contains most of the fungi previously recognized as Plectomycetes because of their mostly enclosed ascomata and prototunicate asci; and (ii) the subclass Chaetothyriomycetidae, a group of fungi that produce ascomata with an opening reminiscent of those produced by Dothideomycetes or Sordariomycetes. In this paper we use phylogenetic analyses based on data available from the Assembling the Fungal Tree of Life project (AFTOL), in addition to sequences in GenBank, to outline this important group of fungi. The Eurotiomycetidae include producers of toxic and useful secondary metabolites, fermentation agents used to make food products and enzymes, xerophiles and psychrophiles, and the important genetics model Aspergillus nidulans. The Chaetothyriomycetidae include the common black yeast fungi, some of which are pathogens of humans and animals, as well as some primarily lichenized groups newly found to be phylogenetically associated with this group. The recently proposed order Mycocaliciales shows a sister relationship with Eurotiomycetes. The great majority of human pathogenic Pezizomycotina are Eurotiomycetes, particularly in Eurotiales, Onygenales and Chaetothyriales. Due to their broad importance in basic research, industry and public health, several genome projects have focused on species in Onygenales and Eurotiales. PMID:17486980

  15. Diversity and distribution of fungal communities in the marine sediments of Kongsfjorden, Svalbard (High Arctic)

    PubMed Central

    Zhang, Tao; Fei Wang, Neng; Qin Zhang, Yu; Yu Liu, Hong; Yan Yu, Li

    2015-01-01

    This study assessed the diversity and distribution of fungal communities in eight marine sediments of Kongsfjorden (Svalbard, High Arctic) using 454 pyrosequencing with fungal-specific primers targeting the internal transcribed spacer (ITS) region of the ribosomal rRNA gene. Sedimentary fungal communities showed high diversity with 42,219 reads belonging to 113 operational taxonomic units (OTUs). Of these OTUs, 62 belonged to the Ascomycota, 26 to Basidiomycota, 2 to Chytridiomycota, 1 to Zygomycota, 1 to Glomeromycota, and 21 to unknown fungi. The major known orders included Hypocreales and Saccharomycetales. The common fungal genera were Pichia, Fusarium, Alternaria, and Malassezia. Interestingly, most fungi occurring in these Arctic sediments may originate from the terrestrial habitats and different basins in Kongsfjorden (i.e., inner basin, central basin, and outer basin) harbor different sedimentary fungal communities. These results suggest the existence of diverse fungal communities in the Arctic marine sediments, which may serve as a useful community model for further ecological and evolutionary study of fungi in the Arctic. PMID:26494429

  16. Microbial Diversity in Cerrado Biome (Neotropical Savanna) Soils

    PubMed Central

    Pereira de Castro, Alinne; Sartori da Silva, Maria Regina Silveira; Quirino, Betania Ferraz; da Cunha Bustamante, Mercedes Maria; Krüger, Ricardo Henrique

    2016-01-01

    The Cerrado, the largest savanna region in South America, is located in central Brazil. Cerrado physiognomies, which range from savanna grasslands to forest formations, combined with the highly weathered, acidic clay Cerrado soils form a unique ecoregion. In this study, high-throughput sequencing of ribosomal RNA genes was combined with shotgun metagenomic analysis to explore the taxonomic composition and potential functions of soil microbial communities in four different vegetation physiognomies during both dry and rainy seasons. Our results showed that changes in bacterial, archaeal, and fungal community structures in cerrado denso, cerrado sensu stricto, campo sujo, and gallery forest soils strongly correlated with seasonal patterns of soil water uptake. The relative abundance of AD3, WPS-2, Planctomycetes, Thermoprotei, and Glomeromycota typically decreased in the rainy season, whereas the relative abundance of Proteobacteria and Ascomycota increased. In addition, analysis of shotgun metagenomic data revealed a significant increase in the relative abundance of genes associated with iron acquisition and metabolism, dormancy, and sporulation during the dry season, and an increase in the relative abundance of genes related to respiration and DNA and protein metabolism during the rainy season. These gene functional categories are associated with adaptation to water stress. Our results further the understanding of how tropical savanna soil microbial communities may be influenced by vegetation covering and temporal variations in soil moisture. PMID:26849674

  17. Long-term experimental warming alters community composition of ascomycetes in Alaskan moist and dry arctic tundra.

    PubMed

    Semenova, Tatiana A; Morgado, Luis N; Welker, Jeffrey M; Walker, Marilyn D; Smets, Erik; Geml, József

    2015-01-01

    Arctic tundra regions have been responding to global warming with visible changes in plant community composition, including expansion of shrubs and declines in lichens and bryophytes. Even though it is well known that the majority of arctic plants are associated with their symbiotic fungi, how fungal community composition will be different with climate warming remains largely unknown. In this study, we addressed the effects of long-term (18 years) experimental warming on the community composition and taxonomic richness of soil ascomycetes in dry and moist tundra types. Using deep Ion Torrent sequencing, we quantified how OTU assemblage and richness of different orders of Ascomycota changed in response to summer warming. Experimental warming significantly altered ascomycete communities with stronger responses observed in the moist tundra compared with dry tundra. The proportion of several lichenized and moss-associated fungi decreased with warming, while the proportion of several plant and insect pathogens and saprotrophic species was higher in the warming treatment. The observed alterations in both taxonomic and ecological groups of ascomycetes are discussed in relation to previously reported warming-induced shifts in arctic plant communities, including decline in lichens and bryophytes and increase in coverage and biomass of shrubs. PMID:25522194

  18. Horizontal Transfer of a Nitrate Assimilation Gene Cluster and Ecological Transitions in Fungi: A Phylogenetic Study

    PubMed Central

    Slot, Jason C.; Hibbett, David S.

    2007-01-01

    High affinity nitrate assimilation genes in fungi occur in a cluster (fHANT-AC) that can be coordinately regulated. The clustered genes include nrt2, which codes for a high affinity nitrate transporter; euknr, which codes for nitrate reductase; and NAD(P)H-nir, which codes for nitrite reductase. Homologs of genes in the fHANT-AC occur in other eukaryotes and prokaryotes, but they have only been found clustered in the oomycete Phytophthora (heterokonts). We performed independent and concatenated phylogenetic analyses of homologs of all three genes in the fHANT-AC. Phylogenetic analyses limited to fungal sequences suggest that the fHANT-AC has been transferred horizontally from a basidiomycete (mushrooms and smuts) to an ancestor of the ascomycetous mold Trichoderma reesei. Phylogenetic analyses of sequences from diverse eukaryotes and eubacteria, and cluster structure, are consistent with a hypothesis that the fHANT-AC was assembled in a lineage leading to the oomycetes and was subsequently transferred to the Dikarya (Ascomycota+Basidiomycota), which is a derived fungal clade that includes the vast majority of terrestrial fungi. We propose that the acquisition of high affinity nitrate assimilation contributed to the success of Dikarya on land by allowing exploitation of nitrate in aerobic soils, and the subsequent transfer of a complete assimilation cluster improved the fitness of T. reesei in a new niche. Horizontal transmission of this cluster of functionally integrated genes supports the “selfish operon” hypothesis for maintenance of gene clusters. PMID:17971860

  19. Intercropped Silviculture Systems, a Key to Achieving Soil Fungal Community Management in Eucalyptus Plantations

    PubMed Central

    Rachid, Caio T. C. C.; Balieiro, Fabiano C.; Fonseca, Eduardo S.; Peixoto, Raquel Silva; Chaer, Guilherme M.; Tiedje, James M.; Rosado, Alexandre S.

    2015-01-01

    Fungi are ubiquitous and important contributors to soil nutrient cycling, playing a vital role in C, N and P turnover, with many fungi having direct beneficial relationships with plants. However, the factors that modulate the soil fungal community are poorly understood. We studied the degree to which the composition of tree species affected the soil fungal community structure and diversity by pyrosequencing the 28S rRNA gene in soil DNA. We were also interested in whether intercropping (mixed plantation of two plant species) could be used to select fungal species. More than 50,000 high quality sequences were analyzed from three treatments: monoculture of Eucalyptus; monoculture of Acacia mangium; and a mixed plantation with both species sampled 2 and 3 years after planting. We found that the plant type had a major effect on the soil fungal community structure, with 75% of the sequences from the Eucalyptus soil belonging to Basidiomycota and 19% to Ascomycota, and the Acacia soil having a sequence distribution of 28% and 62%, respectively. The intercropping of Acacia mangium in a Eucalyptus plantation significantly increased the number of fungal genera and the diversity indices and introduced or increased the frequency of several genera that were not found in the monoculture cultivation samples. Our results suggest that management of soil fungi is possible by manipulating the composition of the plant community, and intercropped systems can be a means to achieve that. PMID:25706388

  20. Phylogenetic and chemical diversity of fungal endophytes isolated from Silybum marianum (L) Gaertn. (milk thistle)

    PubMed Central

    Raja, Huzefa A.; Kaur, Amninder; El-Elimat, Tamam; Figueroa, Mario; Kumar, Rahul; Deep, Gagan; Agarwal, Rajesh; Faeth, Stanley H.; Cech, Nadja B.; Oberlies, Nicholas H.

    2015-01-01

    Use of the herb milk thistle (Silybum marianum) is widespread, and its chemistry has been studied for over 50 years. However, milk thistle endophytes have not been studied previously for their fungal and chemical diversity. We examined the fungal endophytes inhabiting this medicinal herb to determine: (1) species composition and phylogenetic diversity of fungal endophytes; (2) chemical diversity of secondary metabolites produced by these organisms; and (3) cytotoxicity of the pure compounds against the human prostate carcinoma (PC-3) cell line. Forty-one fungal isolates were identified from milk thistle comprising 25 operational taxonomic units based on BLAST search via GenBank using published authentic sequences from nuclear ribosomal internal transcribed spacer sequence data. Maximum likelihood analyses of partial 28S rRNA gene showed that these endophytes had phylogenetic affinities to four major classes of Ascomycota, the Dothideomycetes, Sordariomycetes, Eurotiomycetes, and Leotiomycetes. Chemical studies of solid–substrate fermentation cultures led to the isolation of four new natural products. In addition, 58 known secondary metabolites, representing diverse biosynthetic classes, were isolated and characterized using a suite of nuclear magnetic resonance and mass spectrometry techniques. Selected pure compounds were tested against the PC-3 cell line, where six compounds displayed cytotoxicity. PMID:26000195

  1. Expanding genomics of mycorrhizal symbiosis

    PubMed Central

    Kuo, Alan; Kohler, Annegret; Martin, Francis M.; Grigoriev, Igor V.

    2014-01-01

    The mycorrhizal symbiosis between soil fungi and plant roots is a ubiquitous mutualism that plays key roles in plant nutrition, soil health, and carbon cycling. The symbiosis evolved repeatedly and independently as multiple morphotypes [e.g., arbuscular mycorrhizae (AM), ectomycorrhizal (ECM)] in multiple fungal clades (e.g., phyla Glomeromycota, Ascomycota, Basidiomycota). The accessibility and cultivability of many mycorrhizal partners make them ideal models for symbiosis studies. Alongside molecular, physiological, and ecological investigations, sequencing led to the first three mycorrhizal fungal genomes, representing two morphotypes and three phyla. The genome of the ECM basidiomycete Laccaria bicolor showed that the mycorrhizal lifestyle can evolve through loss of plant cell wall-degrading enzymes (PCWDEs) and expansion of lineage-specific gene families such as short secreted protein (SSP) effectors. The genome of the ECM ascomycete Tuber melanosporum showed that the ECM type can evolve without expansion of families as in Laccaria, and thus a different set of symbiosis genes. The genome of the AM glomeromycete Rhizophagus irregularis showed that despite enormous phylogenetic distance and morphological difference from the other two fungi, symbiosis can involve similar solutions as symbiosis-induced SSPs and loss of PCWDEs. The three genomes provide a solid base for addressing fundamental questions about the nature and role of a vital mutualism. PMID:25408690

  2. Pezizomycotina dominates the fungal communities of South China Sea sponges Theonella swinhoei and Xestospongia testudinaria.

    PubMed

    Jin, Liling; Liu, Fang; Sun, Wei; Zhang, Fengli; Karuppiah, Valliappan; Li, Zhiyong

    2014-12-01

    Compared with the knowledge of sponge-associated bacterial diversity and ecological roles, the fungal diversity and ecological roles of sponges remain largely unknown. In this study, the fungal diversity and protein synthesis potential in two South China Sea sponges Theonella swinhoei and Xestospongia testudinaria were investigated by rRNA vs. rRNA gene analysis. EF4/fung5 was chosen after a series of PCR tests to target fungal 18S rRNA and 18S rRNA gene. Altogether, 283 high-quality sequences were obtained, which resulted in 26 Operational taxonomic units (OTUs) that were assigned to Ascomycota, Basidiomycota, and Blastocladiomycota. At subphylum level, 77.3% of sponge-derived sequences were affiliated with Pezizomycotina. The fungal compositions of T. swinhoei and X. testudinaria were different from that of ambient seawater. The predominant OTU shared between two sponges was rare in seawater, whereas the most abundant OTUs in seawater were not found in sponges. Additionally, the major OTUs of sponge cDNA datasets were shared in two sponges. The fungal diversity illustrated by sponge cDNA datasets correlated well with that derived from sponge DNA datasets, indicating that the major members of sponge-associated fungi had protein synthesis potential. This study highlighted the diversity of Pezizomycotina in marine sponge-fungi symbioses and the necessity of investigating ecological roles of sponge-associated fungi. PMID:25348120

  3. Microbial Diversity in Engineered Haloalkaline Environments Shaped by Shared Geochemical Drivers Observed in Natural Analogues.

    PubMed

    Santini, Talitha C; Warren, Lesley A; Kendra, Kathryn E

    2015-08-01

    Microbial communities in engineered terrestrial haloalkaline environments have been poorly characterized relative to their natural counterparts and are geologically recent in formation, offering opportunities to explore microbial diversity and assembly in dynamic, geochemically comparable contexts. In this study, the microbial community structure and geochemical characteristics of three geographically dispersed bauxite residue environments along a remediation gradient were assessed and subsequently compared with other engineered and natural haloalkaline systems. In bauxite residues, bacterial communities were similar at the phylum level (dominated by Proteobacteria and Firmicutes) to those found in soda lakes, oil sands tailings, and nuclear wastes; however, they differed at lower taxonomic levels, with only 23% of operational taxonomic units (OTUs) shared with other haloalkaline environments. Although being less diverse than natural analogues, bauxite residue harbored substantial novel bacterial taxa, with 90% of OTUs nonmatchable to cultured representative sequences. Fungal communities were dominated by Ascomycota and Basidiomycota, consistent with previous studies of hypersaline environments, and also harbored substantial novel (73% of OTUs) taxa. In bauxite residues, community structure was clearly linked to geochemical and physical environmental parameters, with 84% of variation in bacterial and 73% of variation in fungal community structures explained by environmental parameters. The major driver of bacterial community structure (salinity) was consistent across natural and engineered environments; however, drivers differed for fungal community structure between natural (pH) and engineered (total alkalinity) environments. This study demonstrates that both engineered and natural terrestrial haloalkaline environments host substantial repositories of microbial diversity, which are strongly shaped by geochemical drivers. PMID:25979895

  4. Impact of seasonal changes on fungal diversity of a semi-arid ecosystem revealed by 454 pyrosequencing.

    PubMed

    Vargas-Gastélum, Lluvia; Romero-Olivares, Adriana L; Escalante, Ana E; Rocha-Olivares, Axayácatl; Brizuela, Carlos; Riquelme, Meritxell

    2015-05-01

    Fungi play fundamental ecological roles in terrestrial ecosystems. However, their distribution and diversity remain poorly described in natural communities, particularly in arid and semi-arid ecosystems. In order to identify environmental factors determining fungal community structure in these systems, we assessed their diversity in conjunction with soil physicochemical characteristics in a semi-arid ecosystem in Baja California, Mexico, endemic for Coccidioidomycosis (Valley Fever). Two different microhabitats, burrows (influenced by rodent activity) and topsoil, were compared in winter and summer. Using a metagenomic approach, the ITS1 region of nuclear ribosomal DNA was used as barcode. A total of 1940 Operational Taxonomic Units (OTUs) were identified from 362 332 ITS1 sequences obtained by 454 pyrosequencing. Differences in fungal composition between seasons were clearly identified. Moreover, differences in composition between microhabitats were mainly correlated to significant differences in environmental factors, such as moisture and clay content in topsoil samples, and temperature and electrical conductivity in burrow samples. Overall, the fungal community structure (dominated by Ascomycota and Basidiomycota) was less variable between seasons in burrow than in topsoil samples. Coccidioides spp. went undetected by pyrosequencing. However, a nested PCR approach revealed its higher prevalence in burrows. PMID:25877341

  5. Profiling microbial communities in manganese remediation systems treating coal mine drainage.

    PubMed

    Chaput, Dominique L; Hansel, Colleen M; Burgos, William D; Santelli, Cara M

    2015-03-01

    Water discharging from abandoned coal mines can contain extremely high manganese levels. Removing this metal is an ongoing challenge. Passive Mn(II) removal beds (MRBs) contain microorganisms that oxidize soluble Mn(II) to insoluble Mn(III/IV) minerals, but system performance is unpredictable. Using amplicon pyrosequencing, we profiled the bacterial, fungal, algal, and archaeal communities in four MRBs, performing at different levels, in Pennsylvania to determine whether they differed among MRBs and from surrounding soil and to establish the relative abundance of known Mn(II) oxidizers. Archaea were not detected; PCRs with archaeal primers returned only nontarget bacterial sequences. Fungal taxonomic profiles differed starkly between sites that remove the majority of influent Mn and those that do not, with the former being dominated by Ascomycota (mostly Dothideomycetes) and the latter by Basidiomycota (almost entirely Agaricomycetes). Taxonomic profiles for the other groups did not differ significantly between MRBs, but operational taxonomic unit-based analyses showed significant clustering by MRB with all three groups (P < 0.05). Soil samples clustered separately from MRBs in all groups except fungi, whose soil samples clustered loosely with their respective MRB. Known Mn(II) oxidizers accounted for a minor proportion of bacterial sequences (up to 0.20%) but a greater proportion of fungal sequences (up to 14.78%). MRB communities are more diverse than previously thought, and more organisms may be capable of Mn(II) oxidation than are currently known. PMID:25595765

  6. Phylogenic diversity and tissue specificity of fungal endophytes associated with the pharmaceutical plant, Stellera chamaejasme L. revealed by a cultivation-independent approach.

    PubMed

    Jin, Hui; Yang, Xiaoyan; Lu, Dengxue; Li, Chunjie; Yan, Zhiqiang; Li, Xiuzhuang; Zeng, Liming; Qin, Bo

    2015-10-01

    The fungal endophytes associated with medicinal plants have been demonstrated as a reservoir with novel natural products useful in medicine and agriculture. It is desirable to explore the species composition, diversity and tissue specificity of endophytic fungi that inhabit in different tissues of medicinal plants. In this study, a culture-independent survey of fungal diversity in the rhizosphere, leaves, stems and roots of a toxic medicinal plant, Stellera chamaejasme L., was conducted by sequence analysis of clone libraries of the partial internal transcribed spacer region. Altogether, 145 fungal OTUs (operational taxonomic units), represented by 464 sequences, were found in four samples, of these 109 OTUs (75.2 %) belonging to Ascomycota, 20 (13.8 %) to Basidiomycota, 14 (9.7 %) to Zygomycota, 1 (0.7 %) to Chytridiomycota, and 1 (0.7 %) to Glomeromycota. The richness and diversity of fungal communities were strongly influenced by plant tissue environments, and the roots are associated with a surprisingly rich endophyte community. The endophyte assemblages associated with S. chamaejasme were strongly shaped by plant tissue environments, and exhibited a certain degree of tissue specificity. Our results suggested that a wide variety of fungal assemblages inhabit in S. chamaejasme, and plant tissue environments conspicuously influence endophyte community structure. PMID:26194722

  7. Ice Nucleation Activity in the Widespread Soil Fungus Mortierella alpina

    NASA Astrophysics Data System (ADS)

    Fröhlich-Nowoisky, J.; Hill, T. C. J.; Pummer, B. G.; Franc, G. D.; Pöschl, U.

    2014-08-01

    Biological residues in soil dust are a potentially strong source of atmospheric ice nuclei (IN). So far, however, the abundance, diversity, sources, seasonality, and role of biological - in particular, fungal - IN in soil dust have not been characterized. By analysis of the culturable fungi in topsoils, from a range of different land use and ecosystem types in south-east Wyoming, we found ice nucleation active (INA) fungi to be both widespread and abundant, particularly in soils with recent inputs of decomposable organic matter. Across all investigated soils, 8% of fungal isolates were INA. All INA isolates initiated freezing at -5 to -6 °C, and belonged to a single zygomycotic species, Mortierella alpina (Mortierellales, Mortierellomycotina). By contrast, the handful of fungal species so far reported as INA all belong within the Ascomycota or Basidiomycota phyla. M. alpina is known to be saprobic, widespread in soil and present in air and rain. Sequencing of the ITS region and the gene for γ-linolenic-elongase revealed four distinct clades, affiliated to different soil types. The IN produced by M. alpina seem to be proteinaceous, <300 kDa in size, and can be easily washed off the mycelium. Ice nucleating fungal mycelium will ramify topsoils and probably also release cell-free IN into it. If these IN survive decomposition or are adsorbed onto mineral surfaces, their contribution might accumulate over time, perhaps to be transported with soil dust and influencing its ice nucleating properties.

  8. Indole-3-Acetic Acid-Producing Yeasts in the Phyllosphere of the Carnivorous Plant Drosera indica L

    PubMed Central

    Shin, Li-Ying; Wei, Jyuan-Yu; Fu, Shih-Feng; Chou, Jui-Yu

    2014-01-01

    Yeasts are widely distributed in nature and exist in association with other microorganisms as normal inhabitants of soil, vegetation, and aqueous environments. In this study, 12 yeast strains were enriched and isolated from leaf samples of the carnivorous plant Drosera indica L., which is currently threatened because of restricted habitats and use in herbal industries. According to similarities in large subunit and small subunit ribosomal RNA gene sequences, we identified 2 yeast species in 2 genera of the phylum Ascomycota, and 5 yeast species in 5 genera of the phylum Basidiomycota. All of the isolated yeasts produced indole-3-acetic acid (IAA) when cultivated in YPD broth supplemented with 0.1% L-tryptophan. Growth conditions, such as the pH and temperature of the medium, influenced yeast IAA production. Our results also suggested the existence of a tryptophan-independent IAA biosynthetic pathway. We evaluated the effects of various concentrations of exogenous IAA on yeast growth and observed that IAA produced by wild yeasts modifies auxin-inducible gene expression in Arabidopsis. Our data suggest that yeasts can promote plant growth and support ongoing prospecting of yeast strains for inclusion into biofertilizer for sustainable agriculture. PMID:25464336

  9. Novel and highly diverse fungal endophytes in soybean revealed by the consortium of two different techniques.

    PubMed

    de Souza Leite, Tiago; Cnossen-Fassoni, Andréia; Pereira, Olinto Liparini; Mizubuti, Eduardo Seiti Gomide; de Araújo, Elza Fernandes; de Queiroz, Marisa Vieira

    2013-02-01

    Fungal endophytes were isolated from the leaves of soybean cultivars in Brazil using two different isolation techniques - fragment plating and the innovative dilution-to-extinction culturing - to increase the species richness, frequency of isolates and diversity. A total of 241 morphospecies were obtained corresponding to 62 taxa that were identified by analysis of the internal transcribed spacer (ITS) of the ribosomal DNA (rDNA). The Phylum Ascomycota predominated, representing 99% and 95.2% of isolates in the Monsoy and Conquista cultivars, respectively, whereas the Phylum Basidiomycota represented 1% and 4.8% of isolates, respectively. The genera Ampelomyces, Annulohypoxylon, Guignardia, Leptospora, Magnaporthe, Ophiognomonia, Paraconiothyrium, Phaeosphaeriopsis, Rhodotorula, Sporobolomyces, and Xylaria for the first time were isolated from soybean; this suggests that soybean harbours novel and highly diverse fungi. The yeasts genera Rhodotorula and Sporobolomyces (subphylum Pucciniomycotina) represent the Phylum Basidiomycota. The species richness was greater when both isolation techniques were used. The diversity of fungal endophytes was similar in both cultivars when the same isolation technique was used except for Hill's index, N1. The use of ITS region sequences allowed the isolates to be grouped according to Order, Class and Phylum. Ampelomyces, Chaetomium, and Phoma glomerata are endophytic species that may play potential roles in the biological control of soybean pathogens. This study is one of the first to apply extinction-culturing to isolate fungal endophytes in plant leaves, thus contributing to the development and improvement of this technique for future studies. PMID:23456713

  10. Communities of Cultivable Root Mycobionts of the Seagrass Posidonia oceanica in the Northwest Mediterranean Sea Are Dominated by a Hitherto Undescribed Pleosporalean Dark Septate Endophyte.

    PubMed

    Vohník, Martin; Borovec, Ondřej; Kolařík, Miroslav

    2016-02-01

    Seagrasses, a small group of submerged marine macrophytes, were reported to lack mycorrhizae, i.e., the root-fungus symbioses most terrestrial plants use for nutrient uptake. On the other hand, several authors detected fungal endophytes in seagrass leaves, shoots, rhizomes, and roots, and an anatomically and morphologically unique dark septate endophytic (DSE) association has been recently described in the roots of the Mediterranean seagrass Posidonia oceanica. Nevertheless, the global diversity of seagrass mycobionts is not well understood, and it remains unclear what fungus forms the DSE association in P. oceanica roots. We isolated and determined P. oceanica root mycobionts from 11 localities in the northwest Mediterranean Sea with documented presence of the DSE association and compared our results with recent literature. The mycobiont communities were low in diversity (only three species), were dominated by a single yet unreported marine fungal species (ca. 90 % of the total 177 isolates), and lacked common terrestrial and freshwater root mycobionts. Our phylogenetic analysis suggests that the dominating species represents a new monotypic lineage within the recently described Aigialaceae family (Pleosporales, Ascomycota), probably representing a new genus. Most of its examined colonies developed from intracellular microsclerotia occupying host hypodermis and resembling microsclerotia of terrestrial DSE fungi. Biological significance of this hitherto overlooked seagrass root mycobiont remains obscure, but its presence across the NW Mediterranean Sea and apparent root intracellular lifestyle indicate an intriguing symbiotic relationship with the dominant Mediterranean seagrass. Our microscopic observations suggest that it may form the DSE association recently described in P. oceanica roots. PMID:26093964

  11. Spatial Distribution of Fungal Communities in an Arable Soil

    PubMed Central

    Moll, Julia; Hoppe, Björn; König, Stephan; Wubet, Tesfaye; Buscot, François; Krüger, Dirk

    2016-01-01

    Fungi are prominent drivers of ecological processes in soils, so that fungal communities across different soil ecosystems have been well investigated. However, for arable soils taxonomically resolved fine-scale studies including vertical itemization of fungal communities are still missing. Here, we combined a cloning/Sanger sequencing approach of the ITS/LSU region as marker for general fungi and of the partial SSU region for arbuscular mycorrhizal fungi (AMF) to characterize the microbiome in different maize soil habitats. Four compartments were analyzed over two annual cycles 2009 and 2010: a) ploughed soil in 0–10 cm, b) rooted soil in 40–50 cm, c) root-free soil in 60–70 cm soil depth and d) maize roots. Ascomycota was the most dominant phylum across all compartments. Fungal communities including yeasts and AMF differed strongly between compartments. Inter alia, Tetracladium, the overall largest MOTU (molecular operational taxonomic unit), occurred in all compartments, whereas Trichosporon dominated all soil compartments. Sequences belonging to unclassified Helotiales were forming the most abundant MOTUs exclusively present in roots. This study gives new insights on spatial distribution of fungi and helps to link fungal communities to specific ecological properties such as varying resources, which characterize particular niches of the heterogeneous soil environment. PMID:26840453

  12. Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls

    PubMed Central

    Bendall, Matthew L.; Pérez-Losada, Marcos; Sabuncyan, Sarven; Severance, Emily G.; Dickerson, Faith B.; Schroeder, Jennifer R.; Yolken, Robert H.; Crandall, Keith A.

    2015-01-01

    The role of the human microbiome in schizophrenia remains largely unexplored. The microbiome has been shown to alter brain development and modulate behavior and cognition in animals through gut-brain connections, and research in humans suggests that it may be a modulating factor in many disorders. This study reports findings from a shotgun metagenomic analysis of the oropharyngeal microbiome in 16 individuals with schizophrenia and 16 controls. High-level differences were evident at both the phylum and genus levels, with Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria dominating both schizophrenia patients and controls, and Ascomycota being more abundant in schizophrenia patients than controls. Controls were richer in species but less even in their distributions, i.e., dominated by fewer species, as opposed to schizophrenia patients. Lactic acid bacteria were relatively more abundant in schizophrenia, including species of Lactobacilli and Bifidobacterium, which have been shown to modulate chronic inflammation. We also found Eubacterium halii, a lactate-utilizing species. Functionally, the microbiome of schizophrenia patients was characterized by an increased number of metabolic pathways related to metabolite transport systems including siderophores, glutamate, and vitamin B12. In contrast, carbohydrate and lipid pathways and energy metabolism were abundant in controls. These findings suggest that the oropharyngeal microbiome in individuals with schizophrenia is significantly different compared to controls, and that particular microbial species and metabolic pathways differentiate both groups. Confirmation of these findings in larger and more diverse samples, e.g., gut microbiome, will contribute to elucidating potential links between schizophrenia and the human microbiota. PMID:26336637

  13. Characterization of early microbial communities on volcanic deposits along a vegetation gradient on the island of Miyake, Japan.

    PubMed

    Guo, Yong; Fujimura, Reiko; Sato, Yoshinori; Suda, Wataru; Kim, Seok-won; Oshima, Kenshiro; Hattori, Masahira; Kamijo, Takashi; Narisawa, Kazuhiko; Ohta, Hiroyuki

    2014-01-01

    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. PMID:24463576

  14. Contrasting root associated fungi of three common oak-woodland plant species based on molecular identification: host specificity or non-specific amplification?

    PubMed

    Douhan, Greg W; Petersen, Carolyn; Bledsoe, Caroline S; Rizzo, David M

    2005-07-01

    An increasingly popular approach used to identify arbuscular mycorrhizal (AM) fungi in planta is to amplify a portion of AM fungal small subunit ribosomal DNA (SSU-rDNA) from whole root DNA extractions using the primer pair AM1-NS31, followed by cloning and sequencing. We used this approach to study the AM fungal community composition of three common oak-woodland plant species: a grass (Cynosurus echinatus), blue oak (Quercus douglasii), and a forb (Torilis arvensis). Significant diversity of AM fungi were found in the roots of C. echinatus, which is consistent with previous studies demonstrating a high degree of AM fungal diversity from the roots of various hosts. In contrast, clones from Q. douglasii and T. arvensis were primarily from non-AM fungi of diverse origins within the Ascomycota and Basidiomycota. This work demonstrates that caution must be taken when using this molecular approach to determine in planta AM fungal diversity if non-sequence based methods such as terminal restriction fragment length polymorphisms, denaturing gradient gel electrophoresis, or temperature gradient gel electrophoresis are used. PMID:15772816

  15. Fungal endophyte diversity and bioactivity in the Mediterranean cypress Cupressus sempervirens.

    PubMed

    Soltani, Jalal; Hosseyni Moghaddam, Mahdieh S

    2015-04-01

    Fungal endophytes were isolated from the Mediterranean cypress Cupressus sempervirens. Eleven taxa of fungi, all within the Ascomycota, were identified based on PCR amplification and sequencing of the internal transcribed spacer sequences of nuclear ribosomal DNA (ITS rDNA) with taxonomic identity assigned using the NCBI nucleotide megablast search tool. The endophytic fungi included Alternaria multiformis, Didymella sp., Phoma sp., Phoma herbarum, Pyrenochaeta sp. (Dothideomycetes), Penicillium brevicompactum, Talaromyces sp. (Eurotiomycetes), Ascorhizoctonia sp. (Pezizomycetes), Thielavia microspora, and Thielavia spp. (Sordariomycetes). Considering the former findings in US, this indicates that similar ascomycetous classes of fungi, all from Pezizomycotina, associate with the healthy Cupressaceous trees in Iran. The recovered endophytes produced antifungal and antiproliferative metabolites which may contribute to the protection and survival of the host. We speculate that endophyte-infected C. sempervirens may benefit from their fungal associates by their influence on the ecology and biotic stress tolerance of the host plant. Moreover, a novel niche for the identified fungal species is being introduced. PMID:25527365

  16. Intercropped silviculture systems, a key to achieving soil fungal community management in eucalyptus plantations

    SciTech Connect

    Caio T.C.C. Rachid; Balieiro, Fabiano C.; Fonseca, Eduardo S.; Peixoto, Raquel Silva; Chaer, Guilherme M.; Tiedje, James M.; Rosado, Alexandre S.

    2015-02-23

    Fungi are ubiquitous and important contributors to soil nutrient cycling, playing a vital role in C, N and P turnover, with many fungi having direct beneficial relationships with plants. However, the factors that modulate the soil fungal community are poorly understood. We studied the degree to which the composition of tree species affected the soil fungal community structure and diversity by pyrosequencing the 28S rRNA gene in soil DNA. We were also interested in whether intercropping (mixed plantation of two plant species) could be used to select fungal species. More than 50,000 high quality sequences were analyzed from three treatments: monoculture of Eucalyptus; monoculture of Acacia mangium; and a mixed plantation with both species sampled 2 and 3 years after planting. We found that the plant type had a major effect on the soil fungal community structure, with 75% of the sequences from the Eucalyptus soil belonging to Basidiomycota and 19% to Ascomycota, and the Acacia soil having a sequence distribution of 28% and 62%, respectively. The intercropping of Acacia mangium in a Eucalyptus plantation significantly increased the number of fungal genera and the diversity indices and introduced or increased the frequency of several genera that were not found in the monoculture cultivation samples. Our results suggest that management of soil fungi is possible by manipulating the composition of the plant community, and intercropped systems can be a means to achieve that.

  17. Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training.

    PubMed

    Ter-Hovhannisyan, Vardges; Lomsadze, Alexandre; Chernoff, Yury O; Borodovsky, Mark

    2008-12-01

    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

  18. Strain-level diversity of secondary metabolism in the biocontrol species Aneurinibacillus migulanus.

    PubMed

    Alenezi, Faizah N; Rekik, Imen; Bełka, Marta; Ibrahim, Abrar F; Luptakova, Lenka; Jaspars, Marcel; Woodward, Steve; Belbahri, Lassaad

    2016-01-01

    Aneurinibacillus migulanus strains Nagano and NCTC 7096 show potential in biocontrol against fungal and fungus-like plant pathogens, including a wide range of Ascomycota, Basidiomycota, and Oomycetes. Differences in terms of the range of pathogens that each strain inhibits, however, suggested that production of a single antibiotic cyclic peptide, gramicidin S (GS), by the two strains, is not the sole mechanism of inhibition. The availability of four sequenced genomes of Aneurinibacillus prompted us to apply genome mining techniques to identify the bioactive potential of A. migulanus and to provide insights into the secondary metabolite arsenal of the genus Aneurinibacillus. Up to eleven secondary metabolite biosynthetic gene clusters were present in the three Aneurinibacillus species. Biosynthetic gene clusters specifying bacteriocins, microcins, non-ribosomal peptides, polyketides, terpenes, phosphonates, lasso peptides and linaridins were identified. Chitinolytic potential and iron metabolism regulation were also investigated. With increasing numbers of biocontrol bacterial genomes being sequenced and mined, the use of approaches similar to those described in this paper will lead to an increase in the numbers of environmentally friendly natural products available to use against plant diseases. PMID:26686620

  19. Taxon-specific metagenomics of Trichoderma reveals a narrow community of opportunistic species that regulate each other’s development

    PubMed Central

    Friedl, Martina A.

    2012-01-01

    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. PMID:22075025

  20. Is Roesleria subterranea a primary pathogen or a minor parasite of grapevines? Risk assessment and a diagnostic decision scheme

    PubMed Central

    2011-01-01

    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. PMID:22318129

  1. The N‐acetylglucosamine catabolic gene cluster in Trichoderma reesei is controlled by the Ndt80‐like transcription factor RON1

    PubMed Central

    Kappel, Lisa; Gaderer, Romana; Flipphi, Michel

    2015-01-01

    Summary Chitin is an important structural constituent of fungal cell walls composed of N‐acetylglucosamine (GlcNAc) monosaccharides, but catabolism of GlcNAc has not been studied in filamentous fungi so far. In the yeast C andida albicans, the genes encoding the three enzymes responsible for stepwise conversion of GlcNAc to fructose‐6‐phosphate are clustered. In this work, we analysed GlcNAc catabolism in ascomycete filamentous fungi and found that the respective genes are also clustered in these fungi. In contrast to C . albicans, the cluster often contains a gene for an Ndt80‐like transcription factor, which we named RON1 (regulator of N‐acetylglucosamine catabolism 1). Further, a gene for a glycoside hydrolase 3 protein related to bacterial N‐acetylglucosaminidases can be found in the GlcNAc gene cluster in filamentous fungi. Functional analysis in T richoderma reesei showed that the transcription factor RON1 is a key activator of the GlcNAc gene cluster and essential for GlcNAc catabolism. Furthermore, we present an evolutionary analysis of Ndt80‐like proteins in Ascomycota. All GlcNAc cluster genes, as well as the GlcNAc transporter gene ngt1, and an additional transcriptional regulator gene, csp2, encoding the homolog of N eurospora crassa  CSP2/GRHL, were functionally characterised by gene expression analysis and phenotypic characterisation of knockout strains in T . reesei. PMID:26481444

  2. Familiar Stranger: Ecological Genomics of the Model Saprotroph and Industrial Enzyme Producer Trichoderma reesei Breaks the Stereotypes.

    PubMed

    Druzhinina, I S; Kubicek, C P

    2016-01-01

    The filamentous fungus Trichoderma reesei (Hypocreales, Ascomycota) has properties of an efficient cell factory for protein production that is exploited by the enzyme industry, particularly with respect to cellulase and hemicellulase formation. Under conditions of industrial fermentations it yields more than 100g secreted protein L(-1). Consequently, T. reesei has been intensively studied in the 20th century. Most of these investigations focused on the biochemical characteristics of its cellulases and hemicellulases, on the improvement of their properties by protein engineering, and on enhanced enzyme production by recombinant strategies. However, as the fungus is rare in nature, its ecology remained unknown. The breakthrough in the understanding of the fundamental biology of T. reesei only happened during 2000s-2010s. In this review, we compile the current knowledge on T. reesei ecology, physiology, and genomics to present a holistic view on the natural behavior of the organism. This is not only critical for science-driven further improvement of the biotechnological applications of this fungus, but also renders T. reesei as an attractive model of filamentous fungi with superior saprotrophic abilities. PMID:27261782

  3. Ophiocordyceps unilateralis: A keystone species for unraveling ecosystem functioning and biodiversity of fungi in tropical forests?

    PubMed

    Evans, Harry C; Elliot, Simon L; Hughes, David P

    2011-09-01

    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

  4. Morphological and molecular characterization of a fungus, Hirsutella sp., isolated from planthoppers and psocids in Argentina.

    PubMed

    Toledo, Andrea V; Simurro, María E; Balatti, Pedro A

    2013-01-01

    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

  5. Pyrosequencing Reveals Fungal Communities in the Rhizosphere of Xinjiang Jujube

    PubMed Central

    Wang, Xiao-Hui; Li, Jian-Gui; Qin, Wei; Xiao, Cheng-Ze; Zhao, Xu; Jiang, Hong-Xia; Sui, Jun-Kang; Sa, Rong-Bo; Wang, Wei-Yan; Liu, Xun-Li

    2015-01-01

    Fungi are important soil components as both decomposers and plant symbionts and play a major role in ecological and biogeochemical processes. However, little is known about the richness and structure of fungal communities. DNA sequencing technologies allow for the direct estimation of microbial community diversity, avoiding culture-based biases. We therefore used 454 pyrosequencing to investigate the fungal communities in the rhizosphere of Xinjiang jujube. We obtained no less than 40,488 internal transcribed spacer (ITS) rDNA reads, the number of each sample was 6943, 6647, 6584, 6550, 6860, and 6904, and we used bioinformatics and multivariate statistics to analyze the results. The index of diversity showed greater richness in the rhizosphere fungal community of a 3-year-old jujube than in that of an 8-year-old jujube. Most operational taxonomic units belonged to Ascomycota, and taxonomic analyses identified Hypocreales as the dominant fungal order. Our results demonstrated that the fungal orders are present in different proportions in different sampling areas. Redundancy analysis (RDA) revealed a significant correlation between soil properties and the abundance of fungal phyla. Our results indicated lower fungal diversity in the rhizosphere of Xinjiang jujube than that reported in other studies, and we hope our findings provide a reference for future research. PMID:25685820

  6. Ascomycetes associated with ectomycorrhizas: molecular diversity and ecology with particular reference to the Helotiales.

    PubMed

    Tedersoo, Leho; Pärtel, Kadri; Jairus, Teele; Gates, Genevieve; Põldmaa, Kadri; Tamm, Heidi

    2009-12-01

    Mycorrhizosphere microbes enhance functioning of the plant-soil interface, but little is known of their ecology. This study aims to characterize the ascomycete communities associated with ectomycorrhizas in two Tasmanian wet sclerophyll forests. We hypothesize that both the phyto- and mycobiont, mantle type, soil microbiotope and geographical distance affect the diversity and occurrence of the associated ascomycetes. Using the culture-independent rDNA sequence analysis, we demonstrate a high diversity of these fungi on different hosts and habitats. Plant host has the strongest effect on the occurrence of the dominant species and community composition of ectomycorrhiza-associated fungi. Root endophytes, soil saprobes, myco-, phyto- and entomopathogens contribute to the ectomycorrhiza-associated ascomycete community. Taxonomically these Ascomycota mostly belong to the orders Helotiales, Hypocreales, Chaetothyriales and Sordariales. Members of Helotiales from both Tasmania and the Northern Hemisphere are phylogenetically closely related to root endophytes and ericoid mycorrhizal fungi, suggesting their strong ecological and evolutionary links. Ectomycorrhizal mycobionts from Australia and the Northern Hemisphere are taxonomically unrelated to each other and phylogenetically distant to other helotialean root-associated fungi, indicating independent evolution. The ubiquity and diversity of the secondary root-associated fungi should be considered in studies of mycorrhizal communities to avoid overestimating the richness of true symbionts. PMID:19671076

  7. Atlas of nonribosomal peptide and polyketide biosynthetic pathways reveals common occurrence of nonmodular enzymes

    PubMed Central

    Wang, Hao; Fewer, David P.; Holm, Liisa; Rouhiainen, Leo; Sivonen, Kaarina

    2014-01-01

    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

  8. Phylogenomic analysis uncovers the evolutionary history of nutrition and infection mode in rice blast fungus and other Magnaporthales

    PubMed Central

    Luo, Jing; Qiu, Huan; Cai, Guohong; Wagner, Nicole E.; Bhattacharya, Debashish; Zhang, Ning

    2015-01-01

    The order Magnaporthales (Ascomycota, Fungi) includes devastating pathogens of cereals, such as the rice blast fungus Pyricularia (Magnaporthe) oryzae, which is a model in host-pathogen interaction studies. Magnaporthales also includes saprotrophic species associated with grass roots and submerged wood. Despite its scientific and economic importance, the phylogenetic position of Magnaporthales within Sordariomycetes and the interrelationships of its constituent taxa, remain controversial. In this study, we generated novel transcriptome data from 21 taxa that represent key Magnaporthales lineages of different infection and nutrition modes and phenotypes. Phylogenomic analysis of >200 conserved genes allowed the reconstruction of a robust Sordariomycetes tree of life that placed the monophyletic group of Magnaporthales sister to Ophiostomatales. Among Magnaporthales, three major clades were recognized: 1) an early diverging clade A comprised of saprotrophs associated with submerged woods; 2) clade B that includes the rice blast fungus and other pathogens that cause blast diseases of monocot plants. These species infect the above-ground tissues of host plants using the penetration structure, appressorium; and 3) clade C comprised primarily of root-associated species that penetrate the root tissue with hyphopodia. The well-supported phylogenies provide a robust framework for elucidating evolution of pathogenesis, nutrition modes, and phenotypic characters in Magnaporthales. PMID:25819715

  9. Blue pigment in Hypocrea caerulescens sp. nov. and two additional new species in sect. Trichoderma

    PubMed Central

    Jaklitsch, Walter M.; Stadler, Marc; Voglmayr, Hermann

    2012-01-01

    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

  10. Molecular identification and characterization of the edible and medicinal Morchellaceae germplasm collection of "mulch morels".

    PubMed

    Ondrej, Vladan; Havránek, Pavel; Kitner, Miloslav; Nemcová, Pavla

    2011-01-01

    The accessions of the morel (Morchellaceae, Ascomycota) germplasm collection were genetically analyzed, in order to determine both their inter- and intraspecific relationships. This was done as a starting point for cultivation experiments, as well as to provide a genetic description of invasive morel populations linked to mulched garden patches, as compared with outdoor morels. The phylogenetic data, which was based on the internal transcribed spacer (ITS) sequences and supported by amplified fragment length polymorphism (AFLP) analyses, divided the germplasm isolates and accessions from the sequence database into three groups of yellow morels, and three groups of black morels, involving a remarkable monotypic genus of half-free morels (Mitrophora semilibera), the groups Morchella conica and M. angusticeps. Both Morchella groups include morel samples that use mulch bark as a vector for their spread across gardens in various locations in the Czech Republic. The AFLP analysis supported the ITS-based phylogenetic data and determined the intraspecific genetic profile of these, as a rule, almost entirely unstudied isolates. PMID:22164767

  11. Superimposed Pristine Limestone Aquifers with Marked Hydrochemical Differences Exhibit Distinct Fungal Communities

    PubMed Central

    Nawaz, Ali; Purahong, Witoon; Lehmann, Robert; Herrmann, Martina; Küsel, Kirsten; Totsche, Kai U.; Buscot, François; Wubet, Tesfaye

    2016-01-01

    Fungi are one important group of eukaryotic microorganisms in a diverse range of ecosystems, but their diversity in groundwater ecosystems is largely unknown. We used DNA-based pyro-tag sequencing of the fungal internal transcribed spacer (ITS) rDNA gene to investigate the presence and community structure of fungi at different sampling sites of two superimposed limestone aquifers ranging from 8.5 to 84 m depth in the newly established Hainich Critical Zone Exploratory (Hainich CZE). We detected a diversity of fungal OTUs in groundwater samples of all sampling sites. The relative percentage abundance of Basidiomycota was higher in the upper aquifer assemblage, whilst Ascomycota dominated the lower one. In parallel to differences in the hydrochemistry we found distinct fungal communities at all sampling sites. Classification into functional groups revealed an overwhelming majority of saprotrophs. Finding taxa common to all analyzed groundwater sites, point to a groundwater specific fungal microbiome. The presence of different functional groups and, in particular plant and cattle pathogens that are not typical of subsurface habitats, suggests links between the surface and subsurface biogeosphere due to rapid transportation across the fracture networks typical of karstic regions during recharge episodes. However, further studies including sampling series extended in both time and space are necessary to confirm this hypothesis. PMID:27242696

  12. Evolution of Chemical Diversity in a Group of Non-Reduced Polyketide Gene Clusters: Using Phylogenetics to Inform the Search for Novel Fungal Natural Products.

    PubMed

    Throckmorton, Kurt; Wiemann, Philipp; Keller, Nancy P

    2015-09-01

    Fungal polyketides are a diverse class of natural products, or secondary metabolites (SMs), with a wide range of bioactivities often associated with toxicity. Here, we focus on a group of non-reducing polyketide synthases (NR-PKSs) in the fungal phylum Ascomycota that lack a thioesterase domain for product release, group V. Although widespread in ascomycete taxa, this group of NR-PKSs is notably absent in the mycotoxigenic genus Fusarium and, surprisingly, found in genera not known for their secondary metabolite production (e.g., the mycorrhizal genus Oidiodendron, the powdery mildew genus Blumeria, and the causative agent of white-nose syndrome in bats, Pseudogymnoascus destructans). This group of NR-PKSs, in association with the other enzymes encoded by their gene clusters, produces a variety of different chemical classes including naphthacenediones, anthraquinones, benzophenones, grisandienes, and diphenyl ethers. We discuss the modification of and transitions between these chemical classes, the requisite enzymes, and the evolution of the SM gene clusters that encode them. Integrating this information, we predict the likely products of related but uncharacterized SM clusters, and we speculate upon the utility of these classes of SMs as virulence factors or chemical defenses to various plant, animal, and insect pathogens, as well as mutualistic fungi. PMID:26378577

  13. Evolution of Chemical Diversity in a Group of Non-Reduced Polyketide Gene Clusters: Using Phylogenetics to Inform the Search for Novel Fungal Natural Products

    PubMed Central

    Throckmorton, Kurt; Wiemann, Philipp; Keller, Nancy P.

    2015-01-01

    Fungal polyketides are a diverse class of natural products, or secondary metabolites (SMs), with a wide range of bioactivities often associated with toxicity. Here, we focus on a group of non-reducing polyketide synthases (NR-PKSs) in the fungal phylum Ascomycota that lack a thioesterase domain for product release, group V. Although widespread in ascomycete taxa, this group of NR-PKSs is notably absent in the mycotoxigenic genus Fusarium and, surprisingly, found in genera not known for their secondary metabolite production (e.g., the mycorrhizal genus Oidiodendron, the powdery mildew genus Blumeria, and the causative agent of white-nose syndrome in bats, Pseudogymnoascus destructans). This group of NR-PKSs, in association with the other enzymes encoded by their gene clusters, produces a variety of different chemical classes including naphthacenediones, anthraquinones, benzophenones, grisandienes, and diphenyl ethers. We discuss the modification of and transitions between these chemical classes, the requisite enzymes, and the evolution of the SM gene clusters that encode them. Integrating this information, we predict the likely products of related but uncharacterized SM clusters, and we speculate upon the utility of these classes of SMs as virulence factors or chemical defenses to various plant, animal, and insect pathogens, as well as mutualistic fungi. PMID:26378577

  14. Cercosporoid fungi (Mycosphaerellaceae) 4. Species on dicots (Acanthaceae to Amaranthaceae).

    PubMed

    Braun, Uwe; Crous, Pedro W; Nakashima, Chiharu

    2015-12-01

    The present paper continues a series of comprehensive taxonomic treatments of cercosporoid fungi (formerly Cercospora s. lat.), belonging to the Mycosphaerellaceae (Ascomycota). The fourth contribution of this series initiates treatments of cercosporoid fungi on dicots and comprises species occurring on hosts belonging the the families Acanthaceae, Actinidiaceae, Adoxaceae, Aizoaceae, Altingiaceae, and Amaranthaceae. The species are described and illustrated in alphabetical order under the particular cercosporoid genera, supplemented by keys to the species concerned. A detailed introduction, a survey of currently recognised cercosporoid genera, a key to the genera concerned, and a discussion of taxonomically relevant characters were published in the first part of this series. The following taxonomic novelties are introduced: Cercospora blepharidicola nom. nov., C. celosiigena sp. nov., C. justiciae-adhatodae sp. nov., C. justiciigena nom. nov., C. sambucicola nom. nov., C. thunbergiigena nom. nov., Cercosporella pseudachyranthis comb. nov., Pseudocercospora cyathulae comb. nov., P. depazeoides comb. nov., P. varia var. viburni-sargentii var. nov., P. viburnicola sp. nov., P. viburni-erosi sp. nov., and P. viburni-nudi sp. nov. PMID:26734548

  15. Trehalose is required for stress resistance and virulence of the Basidiomycota plant pathogen Ustilago maydis.

    PubMed

    Cervantes-Chávez, José Antonio; Valdés-Santiago, Laura; Bakkeren, Guus; Hurtado-Santiago, Edda; León-Ramírez, Claudia Geraldine; Esquivel-Naranjo, Edgardo Ulises; Landeros-Jaime, Fidel; Rodríguez-Aza, Yolanda; Ruiz-Herrera, José

    2016-06-01

    Trehalose is an important disaccharide that can be found in bacteria, fungi, invertebrates and plants. In some Ascomycota fungal plant pathogens, the role of trehalose was recently studied and shown to be important for conferring protection against several environmental stresses and for virulence. In most of the fungi studied, two enzymes are involved in the synthesis of trehalose: trehalose-6-phosphate synthase (Tps1) and trehalose-6-phosphate phosphatase (Tps2). To study the role of trehalose in virulence and stress response in the Basidiomycota maize pathogen Ustilago maydis, Δtps2 deletion mutants were constructed. These mutants did not produce trehalose as confirmed by HPLC analysis, showing that the single gene disruption impaired its biosynthesis. The mutants displayed increased sensitivity to oxidative, heat, acid, ionic and osmotic stresses as compared to the wild-type strains. Virulence of Δtps2 mutants to maize plants was extremely reduced compared to wild-type strains, possibly due to reduced capability to deal with the hostile host environment. The phenotypic traits displayed by Δtps2 strains were fully restored to wild-type levels when complemented with the endogenous UmTPS2 gene, or a chimeric construct having the Saccharomyces cerevisiae TPS2 ORF. This report demonstrates the presence of a single biosynthetic pathway for trehalose, and its importance for virulence in this model Basidiomycota plant pathogen. PMID:27027300

  16. Effects of Transgenic Hybrid Aspen Overexpressing Polyphenol Oxidase on Rhizosphere Diversity▿

    PubMed Central

    Oliver, Kathryn L.; Hamelin, Richard C.; Hintz, William E.

    2008-01-01

    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

  17. Abundance and Diversity of Bacterial, Archaeal, and Fungal Communities Along an Altitudinal Gradient in Alpine Forest Soils: What Are the Driving Factors?

    PubMed

    Siles, José A; Margesin, Rosa

    2016-07-01

    Shifts in soil microbial communities over altitudinal gradients and the driving factors are poorly studied. Their elucidation is indispensable to gain a comprehensive understanding of the response of ecosystems to global climate change. Here, we investigated soil archaeal, bacterial, and fungal communities at four Alpine forest sites representing a climosequence, over an altitudinal gradient from 545 to 2000 m above sea level (asl), regarding abundance and diversity by using qPCR and Illumina sequencing, respectively. Archaeal community was dominated by Thaumarchaeota, and no significant shifts were detected in abundance or community composition with altitude. The relative bacterial abundance increased at higher altitudes, which was related to increasing levels of soil organic matter and nutrients with altitude. Shifts in bacterial richness and diversity as well as community structure (comprised basically of Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes) significantly correlated with several environmental and soil chemical factors, especially soil pH. The site at the lowest altitude harbored the highest bacterial richness and diversity, although richness/diversity community properties did not show a monotonic decrease along the gradient. The relative size of fungal community also increased with altitude and its composition comprised Ascomycota, Basidiomycota, and Zygomycota. Changes in fungal richness/diversity and community structure were mainly governed by pH and C/N, respectively. The variation of the predominant bacterial and fungal classes over the altitudinal gradient was the result of the environmental and soil chemical factors prevailing at each site. PMID:26961712

  18. Diversity and distribution of lichen-associated fungi in the Ny-Ålesund Region (Svalbard, High Arctic) as revealed by 454 pyrosequencing.

    PubMed

    Zhang, Tao; Wei, Xin-Li; Zhang, Yu-Qin; Liu, Hong-Yu; Yu, Li-Yan

    2015-01-01

    This study assessed the diversity and distribution of fungal communities associated with seven lichen species in the Ny-Ålesund Region (Svalbard, High Arctic) using Roche 454 pyrosequencing with fungal-specific primers targeting the internal transcribed spacer (ITS) region of the ribosomal rRNA gene. Lichen-associated fungal communities showed high diversity, with a total of 42,259 reads belonging to 370 operational taxonomic units (OTUs) being found. Of these OTUs, 294 belonged to Ascomycota, 54 to Basidiomycota, 2 to Zygomycota, and 20 to unknown fungi. Leotiomycetes, Dothideomycetes, and Eurotiomycetes were the major classes, whereas the dominant orders were Helotiales, Capnodiales, and Chaetothyriales. Interestingly, most fungal OTUs were closely related to fungi from various habitats (e.g., soil, rock, plant tissues) in the Arctic, Antarctic and alpine regions, which suggests that living in association with lichen thalli may be a transient stage of life cycle for these fungi and that long-distance dispersal may be important to the fungi in the Arctic. In addition, host-related factors shaped the lichen-associated fungal communities in this region. Taken together, these results suggest that lichens thalli act as reservoirs of diverse fungi from various niches, which may improve our understanding of fungal evolution and ecology in the Arctic. PMID:26463847

  19. Fungal communities in sediments of subtropical Chinese seas as estimated by DNA metabarcoding

    PubMed Central

    Li, Wei; Wang, Meng Meng; Wang, Xi Guang; Cheng, Xiao Li; Guo, Jia Jia; Bian, Xiao Meng; Cai, Lei

    2016-01-01

    Ribosomal RNA internal transcribed spacer-1 (ITS1) metabarcoding was used to investigate the distribution patterns of fungal communities and the factors influencing these patterns in subtropical Chinese seas, including the southern and northern Yellow Sea and the Bohai Sea. These seas were found to harbor high levels of fungal diversity, with 816 operational taxonomic units (OTUs) that span 130 known genera, 36 orders, 14 classes and 5 phyla. Ascomycota was the most abundant phylum, containing 72.18% and 79.61% of all OTUs and sequences, respectively, followed by Basidiomycota (19.98%, 18.64%), Zygomycota (1.10%, 0.11%), Chytridiomycota (0.25%, 0.04%) and Rozellomycota (0.12%, 0.006%). The compositions of fungal communities across these three sea regions were found to be vary, which may be attributed to sediment source, geographical distance, latitude and some environmental factors such as the temperature and salinity of bottom water, water depth, total nitrogen, and the ratio of total organic carbon to nitrogen. Among these environmental factors, the temperature of bottom water is the most important driver that governs the distribution patterns of fungal communities across the sampled seas. Our data also suggest that the cold-water mass of the Yellow Sea likely balances competitive relationships between fungal taxa rather than increasing species richness levels. PMID:27198490

  20. Unearthing microbial diversity of Taxus rhizosphere via MiSeq high-throughput amplicon sequencing and isolate characterization

    NASA Astrophysics Data System (ADS)

    Hao, Da Cheng; Song, Si Meng; Mu, Jun; Hu, Wen Li; Xiao, Pei Gen

    2016-04-01

    The species variability and potential environmental functions of Taxus rhizosphere microbial community were studied by comparative analyses of 15 16S rRNA and 15 ITS MiSeq sequencing libraries from Taxus rhizospheres in subtropical and temperate regions of China, as well as by isolating laccase-producing strains and polycyclic aromatic hydrocarbon (PAH)-degrading strains. Total reads could be assigned to 2,141 Operational Taxonomic Units (OTUs) belonging to 31 bacteria phyla and 2,904 OTUs of at least seven fungi phyla. The abundance of Planctomycetes, Actinobacteria, and Chloroflexi was higher in T. cuspidata var. nana and T. × media rhizospheres than in T. mairei rhizosphere (NF), while Acidobacteria, Proteobacteria, Nitrospirae, and unclassified bacteria were more abundant in the latter. Ascomycota and Zygomycota were predominant in NF, while two temperate Taxus rhizospheres had more unclassified fungi, Basidiomycota, and Chytridiomycota. The bacterial/fungal community richness and diversity were lower in NF than in other two. Three dye decolorizing fungal isolates were shown to be highly efficient in removing three classes of reactive dye, while two PAH-degrading fungi were able to degrade recalcitrant benzo[a]pyrene. The present studies extend the knowledge pedigree of the microbial diversity populating rhizospheres, and exemplify the method shift in research and development of resource plant rhizosphere.

  1. High Diversity of Fungi in Air Particulate Matter

    NASA Astrophysics Data System (ADS)

    Fröhlich-Nowoisky, J.; Despres, V. R.; Pöschl, U.

    2009-04-01

    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.

  2. Expanding genomics of mycorrhizal symbiosis

    SciTech Connect

    Kuo, Alan; Kohler, Annegret; Martin, Francis M.; Grigoriev, Igor V.

    2014-11-04

    The mycorrhizal symbiosis between soil fungi and plant roots is a ubiquitous mutualism that plays key roles in plant nutrition, soil health, and carbon cycling. The symbiosis evolved repeatedly and independently as multiple morphotypes [e.g., arbuscular mycorrhizae (AM), ectomycorrhizal (ECM)] in multiple fungal clades (e.g., phyla Glomeromycota, Ascomycota, Basidiomycota). The accessibility and cultivability of many mycorrhizal partners make them ideal models for symbiosis studies. Alongside molecular, physiological, and ecological investigations, sequencing led to the first three mycorrhizal fungal genomes, representing two morphotypes and three phyla. The genome of the ECM basidiomycete Laccaria bicolor showed that the mycorrhizal lifestyle can evolve through loss of plant cell wall-degrading enzymes (PCWDEs) and expansion of lineage-specific gene families such as short secreted protein (SSP) effectors. The genome of the ECM ascomycete Tuber melanosporum showed that the ECM type can evolve without expansion of families as in Laccaria, and thus a different set of symbiosis genes. The genome of the AM glomeromycete Rhizophagus irregularis showed that despite enormous phylogenetic distance and morphological difference from the other two fungi, symbiosis can involve similar solutions as symbiosis-induced SSPs and loss of PCWDEs. The three genomes provide a solid base for addressing fundamental questions about the nature and role of a vital mutualism.

  3. Expanding genomics of mycorrhizal symbiosis

    DOE PAGESBeta

    Kuo, Alan; Kohler, Annegret; Martin, Francis M.; Grigoriev, Igor V.

    2014-11-04

    The mycorrhizal symbiosis between soil fungi and plant roots is a ubiquitous mutualism that plays key roles in plant nutrition, soil health, and carbon cycling. The symbiosis evolved repeatedly and independently as multiple morphotypes [e.g., arbuscular mycorrhizae (AM), ectomycorrhizal (ECM)] in multiple fungal clades (e.g., phyla Glomeromycota, Ascomycota, Basidiomycota). The accessibility and cultivability of many mycorrhizal partners make them ideal models for symbiosis studies. Alongside molecular, physiological, and ecological investigations, sequencing led to the first three mycorrhizal fungal genomes, representing two morphotypes and three phyla. The genome of the ECM basidiomycete Laccaria bicolor showed that the mycorrhizal lifestyle can evolvemore » through loss of plant cell wall-degrading enzymes (PCWDEs) and expansion of lineage-specific gene families such as short secreted protein (SSP) effectors. The genome of the ECM ascomycete Tuber melanosporum showed that the ECM type can evolve without expansion of families as in Laccaria, and thus a different set of symbiosis genes. The genome of the AM glomeromycete Rhizophagus irregularis showed that despite enormous phylogenetic distance and morphological difference from the other two fungi, symbiosis can involve similar solutions as symbiosis-induced SSPs and loss of PCWDEs. The three genomes provide a solid base for addressing fundamental questions about the nature and role of a vital mutualism.« less

  4. Antioxidant and Antimycotic Activities of Two Native Lavandula Species from Portugal

    PubMed Central

    Baptista, Rafael; Madureira, Ana Margarida; Jorge, Rita; Adão, Rita; Duarte, Aida; Duarte, Noélia; Lopes, Maria Manuel; Teixeira, Generosa

    2015-01-01

    The antioxidant and antimycotic activities of the essential oils and extracts of two native Portuguese Lavandula species, L. stoechas subsp. luisieri and L. pedunculata, were evaluated by in vitro assays. The total phenolics and flavonoids content were also determined. The antioxidant potential was assessed through DPPH radical scavenging, inhibition of lipid peroxidation (ILP), and DNA protection assays. All samples displayed a high DPPH scavenging activity, some of them showing concentration dependence. The majority of the samples were also able to inhibit lipid peroxidation. A strong correlation was observed between the results of DPPH and ILP assays and the flavonoids content of the samples. In the DNA protection assay, all the extracts were able to preserve DNA integrity. The antimycotic activity was performed against twelve fungi belonging to Basidiomycota and Ascomycota Divisions. L. stoechas subsp. luisieri exhibited the broadest activity spectra. L. pedunculata extracts were active against five fungi. Cryptococcus neoformans was the most sensitive, being inhibited by all the extracts. Our results led to the conclusion that L. stoechas subsp. luisieri and L. pedunculata can be useful as new sources of natural antioxidants and antimycotic agents, providing a possible valorization of the existing biodiversity and resources of Portuguese flora. PMID:25922611

  5. Species Richness and Adaptation of Marine Fungi from Deep-Subseafloor Sediments

    PubMed Central

    Rédou, Vanessa; Navarri, Marion; Meslet-Cladière, Laurence; Barbier, Georges

    2015-01-01

    The fungal kingdom is replete with unique adaptive capacities that allow fungi to colonize a wide variety of habitats, ranging from marine habitats to freshwater and terrestrial habitats. The diversity, importance, and ecological roles of marine fungi have recently been highlighted in deep-subsurface sediments using molecular methods. Fungi in the deep-marine subsurface may be specifically adapted to life in the deep biosphere, but this can be demonstrated only using culture-based analyses. In this study, we investigated culturable fungal communities from a record-depth sediment core sampled from the Canterbury Basin (New Zealand) with the aim to reveal endemic or ubiquist adapted isolates playing a significant ecological role(s). About 200 filamentous fungi (68%) and yeasts (32%) were isolated. Fungal isolates were affiliated with the phyla Ascomycota and Basidiomycota, including 21 genera. Screening for genes involved in secondary metabolite synthesis also revealed their bioactive compound synthesis potential. Our results provide evidence that deep-subsurface fungal communities are able to survive, adapt, grow, and interact with other microbial communities and highlight that the deep-sediment habitat is another ecological niche for fungi. PMID:25769836

  6. Amid the possible causes of a very famous foxing: molecular and microscopic insight into Leonardo da Vinci's self‐portrait

    PubMed Central

    Tafer, Hakim; Sterflinger, Katja; Pinzari, Flavia

    2015-01-01

    Summary Leonardo da Vinci's self‐portrait is affected by foxing spots. The portrait has no fungal or bacterial infections in place, but is contaminated with airborne spores and fungal material that could play a role in its disfigurement. The knowledge of the nature of the stains is of great concern because future conservation treatments should be derived from scientific investigations. The lack of reliable scientific data, due to the non‐culturability of the microorganisms inhabiting the portrait, prompted the investigation of the drawing using non‐invasive and micro‐invasive sampling, in combination with scanning electron microscope (SEM) imaging and molecular techniques. The fungus E urotium halophilicum was found in foxing spots using SEM analyses. Oxalates of fungal origin were also documented. Both findings are consistent with the hypothesis that tonophilic fungi germinate on paper metabolizing organic acids, oligosaccharides and proteic compounds, which react chemically with the material at a low water activity, forming brown products and oxidative reactions resulting in foxing spots. Additionally, molecular techniques enabled a screening of the fungi inhabiting the portrait and showed differences when different sampling techniques were employed. Swabs samples showed a high abundance of lichenized Ascomycota, while the membrane filters showed a dominance of A cremonium sp. colonizing the drawing. PMID:26111623

  7. Amplicon pyrosequencing reveals the soil microbial diversity associated with invasive Japanese barberry (Berberis thunbergii DC.).

    PubMed

    Coats, V C; Pelletreau, K N; Rumpho, M E

    2014-03-01

    The soil microbial community acts as a reservoir of microbes that directly influences the structure and composition of the aboveground plant community, promotes plant growth, increases stress tolerance and mediates local patterns of nutrient cycling. Direct interactions between plants and rhizosphere-dwelling microorganisms occur at, or near, the surface of the root. Upon introduction and establishment, invasive plants modify the soil microbial communities and soil biochemistry affecting bioremediation efforts and future plant communities. Here, we used tag-encoded FLX amplicon 454 pyrosequencing (TEFAP) to characterize the bacterial and fungal community diversity in the rhizosphere of Berberis thunbergii DC. (Japanese barberry) from invasive stands in coastal Maine to investigate effects of soil type, soil chemistry and surrounding plant cover on the soil microbial community structure. Acidobacteria, Actinobacteria, Proteobacteria and Verrucomicrobia were the dominant bacterial phyla, whereas fungal communities were comprised mostly of Ascomycota and Basidiomycota phyla members, including Agaricomycetes and Sordariomycetes. Bulk soil chemistry had more effect on the bacterial community structure than the fungal community. An effect of geographic location was apparent in the rhizosphere microbial communities, yet it was less significant than the effect of surrounding plant cover. These data demonstrate a high degree of spatial variation in the rhizosphere microbial communities of Japanese barberry with apparent effects of soil chemistry, location and canopy cover on the microbial community structure. PMID:24118303

  8. Phylogenomic relationships between amylolytic enzymes from 85 strains of fungi.

    PubMed

    Chen, Wanping; Xie, Ting; Shao, Yanchun; Chen, Fusheng

    2012-01-01

    Fungal amylolytic enzymes, including α-amylase, gluocoamylase and α-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 α-amylases, eukaryotic α-amylases, bacterial and fungal α-amylases and GH13 α-glucosidases. Family GH15 had two branches, one for gluocoamylases, and the other with currently unknown function. GH31 α-glucosidases showed diverse branches consisting of neutral α-glucosidases, lysosomal acid α-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

  9. Curation of characterized glycoside hydrolases of fungal origin.

    PubMed

    Murphy, Caitlin; Powlowski, Justin; Wu, Min; Butler, Greg; Tsang, Adrian

    2011-01-01

    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/. PMID:21622642

  10. Ultrastructural alterations in Fusarium sambucinum and Heterobasidion annosum treated with aluminum chloride and sodium metabisulfite.

    PubMed

    Avis, T J; Rioux, D; Simard, M; Michaud, M; Tweddell, R J

    2009-02-01

    Aluminum chloride (AlCl(3)) and sodium metabisulfite (Na(2)S(2)O(5)) have received increasing attention as antifungal agents for the control of plant diseases. In an effort to understand their toxic action on fungi, ultrastructural changes and membrane damage in Fusarium sambucinum (Ascomycota) and Heterobasidion annosum (Basidiomycota) in response to salt exposure was investigated using transmission electron microscopy. Conidial membrane damage was quantified using SYTOX Green stain, which only enters altered membranes. The results showed that mortality of the conidia was generally closely associated with SYTOX stain absorption in F. sambucinum treated with Na(2)S(2)O(5) and in H. annosum treated with AlCl(3) or Na(2)S(2)O(5), suggesting that these salts cause membrane alterations. For both fungi, ultrastructural alterations in conidia treated with AlCl(3) and Na(2)S(2)O(5) included membrane retraction, undulation, and invagination. At higher concentrations or exposure periods to the salts, loss of membrane integrity, cytoplasmic leakage, and cell rupture were observed. Ultrastructural alterations and increased SYTOX stain absorption in salt-treated conidia appear consistent with a mode of action where AlCl(3) and Na(2)S(2)O(5) alter membrane integrity and permeability. PMID:19159309

  11. Phylogenetic analysis of DNA and RNA polymerases from a Moniliophthora perniciosa mitochondrial plasmid reveals probable lateral gene transfer.

    PubMed

    Andrade, B S; Góes-Neto, A

    2015-01-01

    The filamentous fungus Moniliophthora perniciosa is a hemibiotrophic basidiomycete that causes witches' broom disease of cacao (Theobroma cacao L.). Many fungal mitochondrial plasmids are DNA and RNA polymerase-encoding invertrons with terminal inverted repeats and 5'-linked proteins. The aim of this study was to carry out comparative and phylogenetic analyses of DNA and RNA polymerases for all known linear mitochondrial plasmids in fungi. We performed these analyses at both gene and protein levels and assessed differences between fungal and viral polymerases in order to test the lateral gene transfer (LGT) hypothesis. We analyzed all mitochondrial plasmids of the invertron type within the fungal clade, including five from Ascomycota, seven from Basidiomycota, and one from Chytridiomycota. All phylogenetic analyses generated similar tree topologies regardless of the methods and datasets used. It is likely that DNA and RNA polymerase genes were inserted into the mitochondrial genomes of the 13 fungal species examined in our study as a result of different LGT events. These findings are important for a better understanding of the evolutionary relationships between fungal mitochondrial plasmids. PMID:26535725

  12. Fungal communities in sediments of subtropical Chinese seas as estimated by DNA metabarcoding.

    PubMed

    Li, Wei; Wang, Meng Meng; Wang, Xi Guang; Cheng, Xiao Li; Guo, Jia Jia; Bian, Xiao Meng; Cai, Lei

    2016-01-01

    Ribosomal RNA internal transcribed spacer-1 (ITS1) metabarcoding was used to investigate the distribution patterns of fungal communities and the factors influencing these patterns in subtropical Chinese seas, including the southern and northern Yellow Sea and the Bohai Sea. These seas were found to harbor high levels of fungal diversity, with 816 operational taxonomic units (OTUs) that span 130 known genera, 36 orders, 14 classes and 5 phyla. Ascomycota was the most abundant phylum, containing 72.18% and 79.61% of all OTUs and sequences, respectively, followed by Basidiomycota (19.98%, 18.64%), Zygomycota (1.10%, 0.11%), Chytridiomycota (0.25%, 0.04%) and Rozellomycota (0.12%, 0.006%). The compositions of fungal communities across these three sea regions were found to be vary, which may be attributed to sediment source, geographical distance, latitude and some environmental factors such as the temperature and salinity of bottom water, water depth, total nitrogen, and the ratio of total organic carbon to nitrogen. Among these environmental factors, the temperature of bottom water is the most important driver that governs the distribution patterns of fungal communities across the sampled seas. Our data also suggest that the cold-water mass of the Yellow Sea likely balances competitive relationships between fungal taxa rather than increasing species richness levels. PMID:27198490

  13. Oviposition Deterrence and Immature Survival of Filth Flies (Diptera: Muscidae) When Exposed to Commercial Fungal Products

    PubMed Central

    Machtinger, E.T.; Weeks, E.N.I.; Geden, C. J.

    2016-01-01

    Filth flies are pests of livestock, and can transmit pathogens that cause disease to animals and their caretakers. Studies have shown successful infection of adult filth flies following exposure to different strains and formulations of entomopathogenic fungi. This study aimed to examine the effects of commercial formulations of Beauveria bassiana (Balsamo) (Moniliales: Moniliaceae) (i.e., BotaniGard ES, Mycotrol O, balEnce), and Metarhizium brunneum (Metsch.) (Ascomycota: Hypocreales) (i.e., Met52 EC), on filth fly oviposition and immature fly survival after exposure. House flies, Musca domestica L., laid significantly fewer eggs on Met52 EC-treated surfaces than on surfaces treated with all other products and the control. Similar numbers of eggs were laid on surfaces treated with all B. bassiana products, but egg production was half of the control. Stable flies, Stomoxys calcitrans (L.), laid the fewest eggs on Met52 EC- and Mycotrol O-treated surfaces. This species did not distinguish between the remaining products and the control. In a second experiment, house fly eggs were placed on treated cloths so that hatched larvae contacted the treatment prior to development. Met52 EC had the greatest effect on immature survival with a significant reduction in recovered pupae at the medium and high doses of fungi. Overall, Met52 EC, containing M. brunneum, had the greatest effect on house fly and stable fly oviposition deterrence and immature development of house flies. Management implications are discussed. PMID:27302955

  14. The Trichoderma harzianum demon: complex speciation history resulting in coexistence of hypothetical biological species, recent agamospecies and numerous relict lineages

    PubMed Central

    2010-01-01

    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 agent of the biological control in the field, we investigated the phylogenetic structure of the species. Results Using DNA sequence data from three unlinked loci for each of 93 strains collected worldwide, we detected a complex speciation process revealing overlapping reproductively isolated biological species, recent agamospecies and numerous relict lineages with unresolved phylogenetic positions. Genealogical concordance and recombination analyses confirm the existence of two genetically isolated agamospecies including T. harzianum sensu stricto and two hypothetical holomorphic species related to but different from H. lixii. The exact phylogenetic position of the majority of strains was not resolved and therefore attributed to a diverse network of recombining strains conventionally called 'pseudoharzianum matrix'. Since H. lixii and T. harzianum are evidently genetically isolated, the anamorph - teleomorph combination comprising H. lixii/T. harzianum in one holomorph must be rejected in favor of two separate species. Conclusions Our data illustrate a complex speciation within H. lixii - T. harzianum species group, which is based on coexistence and interaction of organisms with different evolutionary histories and on the absence of strict genetic borders between them. PMID:20359347

  15. Endohyphal Bacterium Enhances Production of Indole-3-Acetic Acid by a Foliar Fungal Endophyte

    PubMed Central

    Hoffman, Michele T.; Gunatilaka, Malkanthi K.; Wijeratne, Kithsiri; Gunatilaka, Leslie; Arnold, A. Elizabeth

    2013-01-01

    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. PMID:24086270

  16. Microbial hitchhikers on intercontinental dust: catching a lift in Chad

    PubMed Central

    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

    2013-01-01

    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

  17. Novel Introner-Like Elements in fungi Are Involved in Parallel Gains of Spliceosomal Introns

    PubMed Central

    Crous, Pedro W.; de Wit, Pierre J. G. M.; van der Burgt, Ate

    2015-01-01

    Spliceosomal introns are key components of the eukaryotic gene structure. Although they contributed to the emergence of eukaryotes, their origin remains elusive. In fungi, they might originate from the multiplication of invasive introns named Introner-Like Elements (ILEs). However, so far ILEs have been observed in six fungal species only, including Fulvia fulva and Dothistroma septosporum (Dothideomycetes), arguing against ILE insertion as a general mechanism for intron gain. Here, we identified novel ILEs in eight additional fungal species that are phylogenetically related to F. fulva and D. septosporum using PCR amplification with primers derived from previously identified ILEs. The ILE content appeared unique to each species, suggesting independent multiplication events. Interestingly, we identified four genes each containing two gained ILEs. By analysing intron positions in orthologues of these four genes in Ascomycota, we found that three ILEs had inserted within a 15 bp window that contains regular spliceosomal introns in other fungal species. These three positions are not the result of intron sliding because ILEs are newly gained introns. Furthermore, the alternative hypothesis of an inferred ancestral gain followed by independent losses contradicts the observed degeneration of ILEs. These observations clearly indicate three parallel intron gains in four genes that were randomly identified. Our findings suggest that parallel intron gain is a phenomenon that has been highly underestimated in ILE-containing fungi, and likely in the whole fungal kingdom. PMID:26046656

  18. Destructuring plant biomass: focus on fungal and extremophilic cell wall hydrolases.

    PubMed

    Guerriero, Gea; Hausman, Jean-Francois; Strauss, Joseph; Ertan, Haluk; Siddiqui, Khawar Sohail

    2015-05-01

    The use of plant biomass as feedstock for biomaterial and biofuel production is relevant in the current bio-based economy scenario of valorizing renewable resources. Fungi, which degrade complex and recalcitrant plant polymers, secrete different enzymes that hydrolyze plant cell wall polysaccharides. The present review discusses the current research trends on fungal, as well as extremophilic cell wall hydrolases that can withstand extreme physico-chemical conditions required in efficient industrial processes. Secretomes of fungi from the phyla Ascomycota, Basidiomycota, Zygomycota and Neocallimastigomycota are presented along with metabolic cues (nutrient sensing, coordination of carbon and nitrogen metabolism) affecting their composition. We conclude the review by suggesting further research avenues focused on the one hand on a comprehensive analysis of the physiology and epigenetics underlying cell wall degrading enzyme production in fungi and on the other hand on the analysis of proteins with unknown function and metagenomics of extremophilic consortia. The current advances in consolidated bioprocessing, altered secretory pathways and creation of designer plants are also examined. Furthermore, recent developments in enhancing the activity, stability and reusability of enzymes based on synergistic, proximity and entropic effects, fusion enzymes, structure-guided recombination between homologous enzymes and magnetic enzymes are considered with a view to improving saccharification. PMID:25804821

  19. Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts

    PubMed Central

    Morel, Guillaume; Sterck, Lieven; Swennen, Dominique; Marcet-Houben, Marina; Onesime, Djamila; Levasseur, Anthony; Jacques, Noémie; Mallet, Sandrine; Couloux, Arnaux; Labadie, Karine; Amselem, Joëlle; Beckerich, Jean-Marie; Henrissat, Bernard; Van de Peer, Yves; Wincker, Patrick; Souciet, Jean-Luc; Gabaldón, Toni; Tinsley, Colin R.; Casaregola, Serge

    2015-01-01

    The evolutionary history of the characters underlying the adaptation of microorganisms to food and biotechnological uses is poorly understood. We undertook comparative genomics to investigate evolutionary relationships of the dairy yeast Geotrichum candidum within Saccharomycotina. Surprisingly, a remarkable proportion of genes showed discordant phylogenies, clustering with the filamentous fungus subphylum (Pezizomycotina), rather than the yeast subphylum (Saccharomycotina), of the Ascomycota. These genes appear not to be the result of Horizontal Gene Transfer (HGT), but to have been specifically retained by G. candidum after the filamentous fungi–yeasts split concomitant with the yeasts’ genome contraction. We refer to these genes as SRAGs (Specifically Retained Ancestral Genes), having been lost by all or nearly all other yeasts, and thus contributing to the phenotypic specificity of lineages. SRAG functions include lipases consistent with a role in cheese making and novel endoglucanases associated with degradation of plant material. Similar gene retention was observed in three other distantly related yeasts representative of this ecologically diverse subphylum. The phenomenon thus appears to be widespread in the Saccharomycotina and argues that, alongside neo-functionalization following gene duplication and HGT, specific gene retention must be recognized as an important mechanism for generation of biodiversity and adaptation in yeasts. PMID:26108467

  20. Susceptibility of Cabbage Maggot Larvae (Diptera: Anthomyiidae) to Hypocreales Entomopathogenic Fungi.

    PubMed

    Myrand, V; Buffet, J P; Guertin, C

    2015-02-01

    The pathogenicity of six Metarhizium spp., four Beauveria bassiana (Balsamo) Vuillemin, and four Tolypocladium cylindrosporum Gams (Ascomycota: Hypocreales) fungal pathogens exposed to third-instar Delia radicum L. was evaluated in laboratory bioassays. The presence of intra- and intergeneric variations concerning the pathogenicity of the isolates was investigated. Results show that all Metarhizium spp. and T. cylindrosporum isolates caused a noteworthy mortality to the third instar and consequently reduced adult eclosion. The well-known standard, F52 strain (identified as Metarhizium brunneum), resulted in up to 79% reduction in D. radicum eclosion. The other Metarhizium isolates including UAMH 9197 (Metarhizium anisopliae) and UAMH 2801 (M. brunneum), as well as T. cylindrosporum DAOM 167325 and DAOM 183952, produced a mean eclosion reduction of >50%. While the pathogenicity of Metarhizium spp. and T. cylindrosporum is similar, the B. bassiana isolates are undoubtedly less pathogenic. Based on the results obtained with the selected isolates, no intrageneric differences relative to the pathogenicity of the isolates appeared to be present. Globally, this study deepened the knowledge about D. radicum susceptibility toward Hypocreales entomopathogenic fungi, chiefly T. cylindrosporum. The implications of this study regarding the development of a biological control agent are discussed. PMID:26470101

  1. Improved PCR primers for the detection and identification of arbuscular mycorrhizal fungi.

    PubMed

    Lee, Jaikoo; Lee, Sangsun; Young, J Peter W

    2008-08-01

    A set of PCR primers that should amplify all subgroups of arbuscular mycorrhizal fungi (AMF, Glomeromycota), but exclude sequences from other organisms, was designed to facilitate rapid detection and identification directly from field-grown plant roots. The small subunit rRNA gene was targeted for the new primers (AML1 and AML2) because phylogenetic relationships among the Glomeromycota are well understood for this gene. Sequence comparisons indicate that the new primers should amplify all published AMF sequences except those from Archaeospora trappei. The specificity of the new primers was tested using 23 different AMF spore morphotypes from trap cultures and Miscanthus sinensis, Glycine max and Panax ginseng roots sampled from the field. Non-AMF DNA of 14 plants, 14 Basidiomycota and 18 Ascomycota was also tested as negative controls. Sequences amplified from roots using the new primers were compared with those obtained using the established NS31 and AM1 primer combination. The new primers have much better specificity and coverage of all known AMF groups. PMID:18631176

  2. Intercropped silviculture systems, a key to achieving soil fungal community management in eucalyptus plantations

    DOE PAGESBeta

    Caio T.C.C. Rachid; Balieiro, Fabiano C.; Fonseca, Eduardo S.; Peixoto, Raquel Silva; Chaer, Guilherme M.; Tiedje, James M.; Rosado, Alexandre S.

    2015-02-23

    Fungi are ubiquitous and important contributors to soil nutrient cycling, playing a vital role in C, N and P turnover, with many fungi having direct beneficial relationships with plants. However, the factors that modulate the soil fungal community are poorly understood. We studied the degree to which the composition of tree species affected the soil fungal community structure and diversity by pyrosequencing the 28S rRNA gene in soil DNA. We were also interested in whether intercropping (mixed plantation of two plant species) could be used to select fungal species. More than 50,000 high quality sequences were analyzed from three treatments:more » monoculture of Eucalyptus; monoculture of Acacia mangium; and a mixed plantation with both species sampled 2 and 3 years after planting. We found that the plant type had a major effect on the soil fungal community structure, with 75% of the sequences from the Eucalyptus soil belonging to Basidiomycota and 19% to Ascomycota, and the Acacia soil having a sequence distribution of 28% and 62%, respectively. The intercropping of Acacia mangium in a Eucalyptus plantation significantly increased the number of fungal genera and the diversity indices and introduced or increased the frequency of several genera that were not found in the monoculture cultivation samples. Our results suggest that management of soil fungi is possible by manipulating the composition of the plant community, and intercropped systems can be a means to achieve that.« less

  3. 454-Pyrosequencing Reveals Variable Fungal Diversity Across Farming Systems

    PubMed Central

    Kazeeroni, Elham A.; Al-Sadi, Abdullah M.

    2016-01-01

    Oasis farming system is common in some parts of the world, especially in the Arabian Peninsula and several African countries. In Oman, the farming system in the majority of farms follows a semi-oasis farming (SOF) system, which is characterized by growing multiple crops mainly for home consumption, but also for local market. This study was conducted to investigate fungal diversity using pyrosequencing approach in soils from a farm utilizing a SOF system which is cultivated with date palms, acid limes and cucumbers. Fungal diversity from this farm was compared to that from an organic farm (OR) growing cucumbers and tomatoes. Fungal diversity was found to be variable among different crops in the same farm. The observed OTUs, Chao1 richness estimates and Shannon diversity values indicated that soils from date palms and acid limes have higher fungal diversity compared to soil from cucumbers (SOF). In addition, they also indicated that the level of fungal diversity is higher in the rhizosphere of cucumbers grown in OR compared to SOF. Ascomycota was the most dominant phylum in most of the samples from the OR and SOF farms. Other dominant phyla are Microsporidia, Chytridiomycota, and Basidiomycota. The differential level of fungal diversity within the SOF could be related to the variation in the cultural practices employed for each crop. PMID:27014331

  4. Dust Rains Deliver Diverse Assemblages of Microorganisms to the Eastern Mediterranean

    PubMed Central

    Itani, Ghida Nouhad; Smith, Colin Andrew

    2016-01-01

    Dust rains may be particularly effective at delivering microorganisms, yet their biodiversities have been seldom examined. During 2011 and 2012 in Beirut, Lebanon, 16 of 21 collected rainfalls appeared dusty. Trajectory modelling of air mass origins was consistent with North African sources and at least one Southwest Asian source. As much as ~4 g particulate matter, ~20 μg DNA, and 50 million colony forming units were found deposited per square meter during rainfalls each lasting less than one day. Sequencing of 93 bacteria and 25 fungi cultured from rain samples revealed diverse bacterial phyla, both Gram positive and negative, and Ascomycota fungi. Denaturing Gradient Gel Electrophoresis of amplified 16S rDNA of 13 rains revealed distinct and diverse assemblages of bacteria. Dust rain 16S libraries yielded 131 sequences matching, in decreasing order of abundance, Betaproteobacteria, Alphaproteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Cyanobacteria, Epsilonproteobacteria, Gammaproteobacteria, and Deltaproteobacteria. Clean rain 16S libraries yielded 33 sequences matching only Betaproteobacteria family Oxalobacteraceae. Microbial composition varied between dust rains, and more diverse and different microbes were found in dust rains than clean rains. These results show that dust rains deliver diverse communities of microorganisms that may be complex products of revived desert soil species and fertilized cloud species. PMID:26939571

  5. Three European species of Hypocrea with reddish brown stromata and green ascospores

    PubMed Central

    Jaklitsch, Walter M.; Kubicek, Christian P.; Druzhinina, Irina S.

    2011-01-01

    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. PMID:18959165

  6. Colonization of roots of cultivated Solanum lycopersicum by dark septate and other ascomycetous endophytes.

    PubMed

    Andrade-Linares, Diana Rocio; Grosch, Rita; Franken, Philipp; Rexer, Karl-Heinz; Kost, Gerhard; Restrepo, Silvia; de Garcia, Maria Caridad Cepero; Maximova, Eugenia

    2011-01-01

    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

  7. Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls.

    PubMed

    Castro-Nallar, Eduardo; Bendall, Matthew L; Pérez-Losada, Marcos; Sabuncyan, Sarven; Severance, Emily G; Dickerson, Faith B; Schroeder, Jennifer R; Yolken, Robert H; Crandall, Keith A

    2015-01-01

    The role of the human microbiome in schizophrenia remains largely unexplored. The microbiome has been shown to alter brain development and modulate behavior and cognition in animals through gut-brain connections, and research in humans suggests that it may be a modulating factor in many disorders. This study reports findings from a shotgun metagenomic analysis of the oropharyngeal microbiome in 16 individuals with schizophrenia and 16 controls. High-level differences were evident at both the phylum and genus levels, with Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria dominating both schizophrenia patients and controls, and Ascomycota being more abundant in schizophrenia patients than controls. Controls were richer in species but less even in their distributions, i.e., dominated by fewer species, as opposed to schizophrenia patients. Lactic acid bacteria were relatively more abundant in schizophrenia, including species of Lactobacilli and Bifidobacterium, which have been shown to modulate chronic inflammation. We also found Eubacterium halii, a lactate-utilizing species. Functionally, the microbiome of schizophrenia patients was characterized by an increased number of metabolic pathways related to metabolite transport systems including siderophores, glutamate, and vitamin B12. In contrast, carbohydrate and lipid pathways and energy metabolism were abundant in controls. These findings suggest that the oropharyngeal microbiome in individuals with schizophrenia is significantly different compared to controls, and that particular microbial species and metabolic pathways differentiate both groups. Confirmation of these findings in larger and more diverse samples, e.g., gut microbiome, will contribute to elucidating potential links between schizophrenia and the human microbiota. PMID:26336637

  8. Fungi associated with rocks of the Atacama Desert: taxonomy, distribution, diversity, ecology and bioprospection for bioactive compounds.

    PubMed

    Gonçalves, Vívian N; Cantrell, Charles L; Wedge, David E; Ferreira, Mariana C; Soares, Marco Aurélio; Jacob, Melissa R; Oliveira, Fabio S; Galante, Douglas; Rodrigues, Fabio; Alves, Tânia M A; Zani, Carlos L; Junior, Policarpo A S; Murta, Silvane; Romanha, Alvaro J; Barbosa, Emerson C; Kroon, Erna G; Oliveira, Jaquelline G; Gomez-Silva, Benito; Galetovic, Alexandra; Rosa, Carlos A; Rosa, Luiz H

    2016-01-01

    This study assessed the diversity of cultivable rock-associated fungi from Atacama Desert. A total of 81 fungal isolates obtained were identified as 29 Ascomycota taxa by sequencing different regions of DNA. Cladosporium halotolerans, Penicillium chrysogenum and Penicillium cf. citrinum were the most frequent species, which occur at least in four different altitudes. The diversity and similarity indices ranged in the fungal communities across the latitudinal gradient. The Fisher-α index displayed the higher values for the fungal communities obtained from the siltstone and fine matrix of pyroclastic rocks with finer grain size, which are more degraded. A total of 23 fungal extracts displayed activity against the different targets screened. The extract of P. chrysogenum afforded the compounds α-linolenic acid and ergosterol endoperoxide, which were active against Cryptococcus neoformans and methicillin-resistance Staphylococcus aureus respectively. Our study represents the first report of a new habitat of fungi associated with rocks of the Atacama Desert and indicated the presence of interesting fungal community, including species related with saprobes, parasite/pathogen and mycotoxigenic taxa. The geological characteristics of the rocks, associated with the presence of rich resident/resilient fungal communities suggests that the rocks may provide a favourable microenvironment fungal colonization, survival and dispersal in extreme conditions. PMID:26235221

  9. PCR-denaturing gradient gel electrophoresis analysis of microbial community in soy-daddawa, a Nigerian fermented soybean (Glycine max (L.) Merr.) condiment.

    PubMed

    Ezeokoli, Obinna T; Gupta, Arvind K; Mienie, Charlotte; Popoola, Temitope O S; Bezuidenhout, Cornelius C

    2016-03-01

    Soy-daddawa, a fermented soybean (Glycine max (L.) Merr.) condiment, plays a significant role in the culinary practice of West Africa. It is essential to understand the microbial community of soy-daddawa for a successful starter culture application. This study investigated the microbial community structure of soy-daddawa samples collected from Nigerian markets, by PCR-denaturing gradient gel electrophoresis (DGGE) targeting the V3-V5 region of the 16S rRNA gene of bacteria and internal transcribed spacer 2 (ITS2) region of fungi. Six bacterial and 16 fungal (nine yeasts and seven molds) operational taxonomic units (OTUs)/species were obtained at 97% sequence similarity. Taxonomic assignments revealed that bacterial OTUs belonged to the phyla Firmicutes and Actinobacteria, and included species from the genera Atopostipes, Bacillus, Brevibacterium and Nosocomiicoccus. Densitometric analysis of DGGE image/bands revealed that Bacillus spp. were the dominant OTU/species in terms of population numbers. Fungal OTUs belonged to the phyla Ascomycota and Zygomycota, and included species from the genera, Alternaria, Aspergillus, Candida, Cladosporium, Dokmaia, Issatchenkia, Kodamaea, Lecythophora, Phoma, Pichia, Rhizopus, Saccharomyces and Starmerella. The majority of fungal species have not been previously reported in soy-daddawa. Potential opportunistic human pathogens such as Atopostipes suicloacalis, Candida rugosa, Candida tropicalis, and Kodamaea ohmeri were detected. Variation in soy-daddawa microbial communities amongst samples and presence of potential opportunistic pathogens emphasises the need for starter culture employment and good handling practices in soy-daddawa processing. PMID:26796580

  10. Fungal spore content of the atmosphere of the Cave of Nerja (southern Spain): diversity and origin.

    PubMed

    Docampo, Silvia; Trigo, M Mar; Recio, Marta; Melgar, Marta; García-Sánchez, José; Cabezudo, Baltasar

    2011-01-15

    Fungal spores are of great interest in aerobiology and allergy due to their high incidence in both outdoor and indoor environments and their widely recognized ability to cause respiratory diseases and other pathologies. In this work, we study the spore content of the atmosphere of the Cave of Nerja, a karstic cavity and an important tourist attraction situated on the eastern coast of Malaga (southern Spain), which receives more than half a million visitors every year. This study was carried out over an uninterrupted period of 4 years (2002-2005) with the aid of two Hirst-type volumetric pollen traps (Lanzoni VPPS 2000) situated in different halls of the cave. In the atmosphere of the Cave of Nerja, 72 different spore types were detected during the studied period and daily mean concentrations of up to 282,195 spores/m(3) were reached. Thirty-five of the spore types detected are included within Ascomycota and Basidiomycota (19 and 16 types, respectively). Of the remaining spore types, 32 were categorized within the group of so-called imperfect fungi, while Oomycota and Myxomycota were represented by 2 and 3 spore types, respectively. Aspergillus/Penicillium was the most abundant spore type with a yearly mean percentage that represented 50% of the total, followed by Cladosporium. Finally, the origin of the fungal spores found inside the cave is discussed on the basis of the indoor/outdoor concentrations and the seasonal behaviour observed. PMID:21138779

  11. Diversity and distribution of lichen-associated fungi in the Ny-Ålesund Region (Svalbard, High Arctic) as revealed by 454 pyrosequencing

    PubMed Central

    Zhang, Tao; Wei, Xin-Li; Zhang, Yu-Qin; Liu, Hong-Yu; Yu, Li-Yan

    2015-01-01

    This study assessed the diversity and distribution of fungal communities associated with seven lichen species in the Ny-Ålesund Region (Svalbard, High Arctic) using Roche 454 pyrosequencing with fungal-specific primers targeting the internal transcribed spacer (ITS) region of the ribosomal rRNA gene. Lichen-associated fungal communities showed high diversity, with a total of 42,259 reads belonging to 370 operational taxonomic units (OTUs) being found. Of these OTUs, 294 belonged to Ascomycota, 54 to Basidiomycota, 2 to Zygomycota, and 20 to unknown fungi. Leotiomycetes, Dothideomycetes, and Eurotiomycetes were the major classes, whereas the dominant orders were Helotiales, Capnodiales, and Chaetothyriales. Interestingly, most fungal OTUs were closely related to fungi from various habitats (e.g., soil, rock, plant tissues) in the Arctic, Antarctic and alpine regions, which suggests that living in association with lichen thalli may be a transient stage of life cycle for these fungi and that long-distance dispersal may be important to the fungi in the Arctic. In addition, host-related factors shaped the lichen-associated fungal communities in this region. Taken together, these results suggest that lichens thalli act as reservoirs of diverse fungi from various niches, which may improve our understanding of fungal evolution and ecology in the Arctic. PMID:26463847

  12. Fungi Sailing the Arctic Ocean: Speciose Communities in North Atlantic Driftwood as Revealed by High-Throughput Amplicon Sequencing.

    PubMed

    Rämä, Teppo; Davey, Marie L; Nordén, Jenni; Halvorsen, Rune; Blaalid, Rakel; Mathiassen, Geir H; Alsos, Inger G; Kauserud, Håvard

    2016-08-01

    High amounts of driftwood sail across the oceans and provide habitat for organisms tolerating the rough and saline environment. Fungi have adapted to the extremely cold and saline conditions which driftwood faces in the high north. For the first time, we applied high-throughput sequencing to fungi residing in driftwood to reveal their taxonomic richness, community composition, and ecology in the North Atlantic. Using pyrosequencing of ITS2 amplicons obtained from 49 marine logs, we found 807 fungal operational taxonomic units (OTUs) based on clustering at 97 % sequence similarity cut-off level. The phylum Ascomycota comprised 74 % of the OTUs and 20 % belonged to Basidiomycota. The richness of basidiomycetes decreased with prolonged submersion in the sea, supporting the general view of ascomycetes being more extremotolerant. However, more than one fourth of the fungal OTUs remained unassigned to any fungal class, emphasising the need for better DNA reference data from the marine habitat. Different fungal communities were detected in coniferous and deciduous logs. Our results highlight that driftwood hosts a considerably higher fungal diversity than currently known. The driftwood fungal community is not a terrestrial relic but a speciose assemblage of fungi adapted to the stressful marine environment and different kinds of wooden substrates found in it. PMID:27147245

  13. Culturable endophytic microbial communities in the circumpolar grass, Deschampsia flexuosa in a sub-Arctic inland primary succession are habitat and growth stage specific.

    PubMed

    Poosakkannu, Anbu; Nissinen, Riitta; Kytöviita, Minna-Maarit

    2015-02-01

    Little is known about endophytic microbes in cold climate plants and how their communities are formed.We compared culturable putative endophytic bacteria and fungi in the ecologically important circumpolargrass, Deschampsia flexuosa growing in two successional stages of subarctic sand dune (68°29′N).Sequence analyses of partial 16S rRNA and internal transcribed spacer (ITS) sequences of culturable endophytes showed that diverse bacteria and fungi inhabit different tissues of D. flexuosa. A total of 178 bacterial isolates representing seven taxonomic divisions, Alpha, Beta and Gammaproteobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Acidobacteria, and 30 fungal isolates representing the phylum Ascomycota were identified. Several endophytes were affiliated with specific plant tissues or successional stages. This first report of bacterial endophytes in D. flexuosa revealed that the genus Pseudomonas is tightly associated with D. flexuosa, and encompassed 39% of the bacterial isolates, and 58% of seed isolates. Based on 16S rRNA and ITS sequence data, most of the D. flexuosa endophytes were closely related to microbes from other cold environments. The majority of seed endophytic bacterial isolates were able to solubilize organic form of phosphate suggesting that these endophytes could play a role in resource mobilization in germinating seeds in nutrient-poor habitat. PMID:25721603

  14. Microbial hitchhikers on intercontinental dust: catching a lift in Chad.

    PubMed

    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

    2013-04-01

    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

  15. Plant Tissue Preparation for the Detection of an Endophytic Fungus In Planta.

    PubMed

    McKinnon, Aimee C

    2016-01-01

    The identification of fungal endophytes often relies on culturing isolates from surface-sterilized plant tissue. However, molecular techniques have enabled the rapid detection and identification of targeted endophyte species, and next-generation sequencing technology provides an opportunity to obtain comprehensive information on endophytic communities, directly from plant tissue. In order to achieve accurate detection from internal tissues, surface microbes and associated deoxyribonucleic acid (DNA) must be eliminated, with particular consideration for the type of plant tissue and the efficacy of the surface sterilization procedure used. The methodology described later was developed specifically for detection of DNA from the entomopathogenic fungal endophyte Beauveria bassiana (Vuillemin) (Ascomycota: Hypocreales) in various tissues of Zea mays (L.). However, the protocol may be easily applied to other fungi and bacterial endophytes. Included is a stringent sodium hypochlorite-based surface sterilization protocol for plant material in preparation for polymerase chain reaction (PCR) to detect target DNA within plant tissue. Included are a treatment for dealing with surface DNA contamination and a novel procedure for assessing the efficacy of surface sterilization using PCR. PMID:27565499

  16. Unravelling the diversity of grapevine microbiome.

    PubMed

    Pinto, Cátia; Pinho, Diogo; Sousa, Susana; Pinheiro, Miguel; Egas, Conceição; Gomes, Ana C

    2014-01-01

    Vitis vinifera is one of the most widely cultivated fruit crops with a great economic impact on the global industry. As a plant, it is naturally colonised by a wide variety of both prokaryotic and eukaryotic microorganisms that interact with grapevine, having either beneficial or phytopathogenic effects, who play a major role in fruit yield, grape quality and, ultimately, in the evolution of grape fermentation and wine production. Therefore, the objective of this study was to extensively characterize the natural microbiome of grapevine. Considering that the majority of microorganisms are uncultivable, we have deeply studied the microflora of grapevine leaves using massive parallel rDNA sequencing, along its vegetative cycle. Among eukaryotic population the most abundant microorganisms belonged to the early diverging fungi lineages and Ascomycota phylum, whereas the Basidiomycota were the least abundant. Regarding prokaryotes, a high diversity of Proteobacteria, Firmicutes and Actinobacteria was unveiled. Indeed, the microbial communities present in the vineyard during its vegetative cycle were shown to be highly structured and dynamic. In all cases, the major abundant microorganisms were the yeast-like fungus Aureobasidium and the prokaryotic Enterobacteriaceae. Herein, we report the first complete microbiome landscape of the vineyard, through a metagenomic approach, and highlight the analysis of the microbial interactions within the vineyard and its importance for the equilibrium of the microecosystem of grapevines. PMID:24454903

  17. Characterization and virulence of Beauveria bassiana associated with auger beetle (Sinoxylon anale) infesting allspice (Pimenta dioica).

    PubMed

    Senthil Kumar, C M; Jacob, T K; Devasahayam, S; D'Silva, Sharon; Nandeesh, P G

    2016-09-01

    The incidence of auger beetle, Sinoxylon anale Lesne (Bostrichidae: Coleoptera), a destructive pest of cosmopolitan occurrence is reported for the first time on allspice trees, Pimenta dioica (L.) Merr. in Kerala, India. The insects bored through the basal region of fresh twigs resulting in dieback symptoms. Morphological characterization and sequencing of a partially amplified fragment of the mitochondrial CO1 gene (696bp) revealed the insect to be Sinoxylon anale. An entomopathogenic fungus was isolated from infected cadavers of S. anale that was identified as Beauveria bassiana (Bals.-Criv.) Vuill., sensu stricto (s.s.) (Ascomycota: Hypocreales) based on morphological and molecular studies. The partial sequences of the ITS, TUB, TEF and Bloc gene regions were sequenced. The fungus grew well in ambient room temperature conditions (28-32±2°C; 60-70% relative humidity) and the infection process on the insect was documented by scanning electron microscopy. Bioassay studies with the isolate indicated that the fungus was virulent against adult beetles as evidenced by the LC50 (3.6×10(6)conidia/ml) and ST50 values (6.8days at a dose of 1×10(7)conidia/ml and 5.8days at a dose of 1×10(8)conidia/ml, respectively). This is the first record of B. bassiana naturally infecting S. anale and the fungus holds promise to be developed as a mycoinsecticide. PMID:27480402

  18. Novel chytrid lineages dominate fungal sequences in diverse marine and freshwater habitats

    PubMed Central

    Comeau, André M.; Vincent, Warwick F.; Bernier, Louis; Lovejoy, Connie

    2016-01-01

    In aquatic environments, fungal communities remain little studied despite their taxonomic and functional diversity. To extend the ecological coverage of this group, we conducted an in-depth analysis of fungal sequences within our collection of 3.6 million V4 18S rRNA pyrosequences originating from 319 individual marine (including sea-ice) and freshwater samples from libraries generated within diverse projects studying Arctic and temperate biomes in the past decade. Among the ~1.7 million post-filtered reads of highest taxonomic and phylogenetic quality, 23,263 fungal sequences were identified. The overall mean proportion was 1.35%, but with large variability; for example, from 0.01 to 59% of total sequences for Arctic seawater samples. Almost all sample types were dominated by Chytridiomycota-like sequences, followed by moderate-to-minor contributions of Ascomycota, Cryptomycota and Basidiomycota. Species and/or strain richness was high, with many novel sequences and high niche separation. The affinity of the most common reads to phytoplankton parasites suggests that aquatic fungi deserve renewed attention for their role in algal succession and carbon cycling. PMID:27444055

  19. Interannual variation and host affiliations of endophytic fungi associated with ferns at La Selva, Costa Rica.

    PubMed

    Del Olmo-Ruiz, Mariana; Arnold, A Elizabeth

    2014-01-01

    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

  20. Woody plant encroachment, and its removal, impact bacterial and fungal communities across stream and terrestrial habitats in a tallgrass prairie ecosystem.

    PubMed

    Veach, Allison M; Dodds, Walter K; Jumpponen, Ari

    2015-10-01

    Woody plant encroachment has become a global threat to grasslands and has caused declines in aboveground richness and changes in ecosystem function; yet we have a limited understanding on the effects of these phenomena on belowground microbial communities. We completed riparian woody plant removals at Konza Prairie Biological Station, Kansas and collected soils spanning land-water interfaces in removal and woody vegetation impacted areas. We measured stream sediments and soils for edaphic variables (C and N pools, soil water content, pH) and bacterial (16S rRNA genes) and fungal (ITS2 rRNA gene repeat) communities using Illumina MiSeq metabarcoding. Bacterial richness and diversity decreased with distance from streams. Fungal richness decreased with distance from the stream in wooded areas, but was similar across landscape position while Planctomycetes and Basidiomycota relative abundance was lower in removal areas. Cyanobacteria, Ascomycota, Chytridiomycota and Glomeromycota relative abundance was greater in removal areas. Ordination analyses indicated that bacterial community composition shifted more across land-water interfaces than fungi yet both were marginally influenced by treatment. This study highlights the impacts of woody encroachment restoration on grassland bacterial and fungal communities which likely subsequently affects belowground processes and plant health in this ecosystem. PMID:26347079

  1. Several genes encoding enzymes with the same activity are necessary for aerobic fungal degradation of cellulose in nature.

    PubMed

    Busk, Peter K; Lange, Mette; Pilgaard, Bo; Lange, Lene

    2014-01-01

    The cellulose-degrading fungal enzymes are glycoside hydrolases of the GH families and lytic polysaccharide monooxygenases. The entanglement of glycoside hydrolase families and functions makes it difficult to predict the enzymatic activity of glycoside hydrolases based on their sequence. In the present study we further developed the method Peptide Pattern Recognition to an automatic approach not only to find all genes encoding glycoside hydrolases and lytic polysaccharide monooxygenases in fungal genomes but also to predict the function of the genes. The functional annotation is an important feature as it provides a direct route to predict function from primary sequence. Furthermore, we used Peptide Pattern Recognition to compare the cellulose-degrading enzyme activities encoded by 39 fungal genomes. The results indicated that cellobiohydrolases and AA9 lytic polysaccharide monooxygenases are hallmarks of cellulose-degrading fungi except brown rot fungi. Furthermore, a high number of AA9, endocellulase and β-glucosidase genes were identified, not in what are known to be the strongest, specialized lignocellulose degraders but in saprophytic fungi that can use a wide variety of substrates whereas only few of these genes were found in fungi that have a limited number of natural, lignocellulotic substrates. This correlation suggests that enzymes with different properties are necessary for degradation of cellulose in different complex substrates. Interestingly, clustering of the fungi based on their predicted enzymes indicated that Ascomycota and Basidiomycota use the same enzymatic activities to degrade plant cell walls. PMID:25461894

  2. Superimposed Pristine Limestone Aquifers with Marked Hydrochemical Differences Exhibit Distinct Fungal Communities.

    PubMed

    Nawaz, Ali; Purahong, Witoon; Lehmann, Robert; Herrmann, Martina; Küsel, Kirsten; Totsche, Kai U; Buscot, François; Wubet, Tesfaye

    2016-01-01

    Fungi are one important group of eukaryotic microorganisms in a diverse range of ecosystems, but their diversity in groundwater ecosystems is largely unknown. We used DNA-based pyro-tag sequencing of the fungal internal transcribed spacer (ITS) rDNA gene to investigate the presence and community structure of fungi at different sampling sites of two superimposed limestone aquifers ranging from 8.5 to 84 m depth in the newly established Hainich Critical Zone Exploratory (Hainich CZE). We detected a diversity of fungal OTUs in groundwater samples of all sampling sites. The relative percentage abundance of Basidiomycota was higher in the upper aquifer assemblage, whilst Ascomycota dominated the lower one. In parallel to differences in the hydrochemistry we found distinct fungal communities at all sampling sites. Classification into functional groups revealed an overwhelming majority of saprotrophs. Finding taxa common to all analyzed groundwater sites, point to a groundwater specific fungal microbiome. The presence of different functional groups and, in particular plant and cattle pathogens that are not typical of subsurface habitats, suggests links between the surface and subsurface biogeosphere due to rapid transportation across the fracture networks typical of karstic regions during recharge episodes. However, further studies including sampling series extended in both time and space are necessary to confirm this hypothesis. PMID:27242696

  3. A dehydration-inducible gene in the truffle Tuber borchii identifies a novel group of dehydrins

    PubMed Central

    Abba', Simona; Ghignone, Stefano; Bonfante, Paola

    2006-01-01

    Background The expressed sequence tag M6G10 was originally isolated from a screening for differentially expressed transcripts during the reproductive stage of the white truffle Tuber borchii. mRNA levels for M6G10 increased dramatically during fruiting body maturation compared to the vegetative mycelial stage. Results Bioinformatics tools, phylogenetic analysis and expression studies were used to support the hypothesis that this sequence, named TbDHN1, is the first dehydrin (DHN)-like coding gene isolated in fungi. Homologs of this gene, all defined as "coding for hypothetical proteins" in public databases, were exclusively found in ascomycetous fungi and in plants. Although complete (or almost complete) fungal genomes and EST collections of some Basidiomycota and Glomeromycota are already available, DHN-like proteins appear to be represented only in Ascomycota. A new and previously uncharacterized conserved signature pattern was identified and proposed to Uniprot database as the main distinguishing feature of this new group of DHNs. Expression studies provide experimental evidence of a transcript induction of TbDHN1 during cellular dehydration. Conclusion Expression pattern and sequence similarities to known plant DHNs indicate that TbDHN1 is the first characterized DHN-like protein in fungi. The high similarity of TbDHN1 with homolog coding sequences implies the existence of a novel fungal/plant group of LEA Class II proteins characterized by a previously undescribed signature pattern. PMID:16512918

  4. Investigations of biodeterioration by fungi in historic wooden churches of Chiloé, Chile.

    PubMed

    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

    2014-04-01

    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

  5. Spatial Distribution of Fungal Communities in an Arable Soil.

    PubMed

    Moll, Julia; Hoppe, Björn; König, Stephan; Wubet, Tesfaye; Buscot, François; Krüger, Dirk

    2016-01-01

    Fungi are prominent drivers of ecological processes in soils, so that fungal communities across different soil ecosystems have been well investigated. However, for arable soils taxonomically resolved fine-scale studies including vertical itemization of fungal communities are still missing. Here, we combined a cloning/Sanger sequencing approach of the ITS/LSU region as marker for general fungi and of the partial SSU region for arbuscular mycorrhizal fungi (AMF) to characterize the microbiome in different maize soil habitats. Four compartments were analyzed over two annual cycles 2009 and 2010: a) ploughed soil in 0-10 cm, b) rooted soil in 40-50 cm, c) root-free soil in 60-70 cm soil depth and d) maize roots. Ascomycota was the most dominant phylum across all compartments. Fungal communities including yeasts and AMF differed strongly between compartments. Inter alia, Tetracladium, the overall largest MOTU (molecular operational taxonomic unit), occurred in all compartments, whereas Trichosporon dominated all soil compartments. Sequences belonging to unclassified Helotiales were forming the most abundant MOTUs exclusively present in roots. This study gives new insights on spatial distribution of fungi and helps to link fungal communities to specific ecological properties such as varying resources, which characterize particular niches of the heterogeneous soil environment. PMID:26840453

  6. Molecular Phylogenetic Analysis Reveals the New Genus Hemisphaericaspora of the Family Debaryomycetaceae

    PubMed Central

    Hui, Fengli; Ren, Yongcheng; Chen, Liang; Li, Ying; Zhang, Lin; Niu, Qiuhong

    2014-01-01

    Four strains of a novel ascomycetous yeast species were recovered from the frass of wood-boring beetles collected from the Baotianman Nature Reserve and the Laojieling Nature Reserve in Henan Province, China. This species produced unconjugated and deliquescent asci with hemispheroid or helmet-shaped ascospores. Analysis of gene sequences for the D1/D2 domain of the large subunit (LSU) rRNA, as well as analysis of concatenated gene sequences for the nearly complete small subunit (SSU) rRNA and D1/D2 domain of the large subunit (LSU) rRNA placed the novel species in a small clade including only one recognised species, Candida insectamans, in the family Debaryomycetaceae (Saccharomycotina, Ascomycota). DNA sequence analyses demonstrated that the novel species was distinct from all currently recognised teleomorphic yeast genus. The name Hemisphaericaspora nanyangensis gen nov., sp. nov. is proposed to accommodate the novel genus and species. The new genus can be distinguished from closely related teleomorphic genera Lodderomyces and Spathaspora through sequence comparison and ascospore morphology. The ex-type strain of H. nanyangensis is CBS 13020T ( = CICC 33021 = NYNU 13717). Furthermore, based on phenotypic and genotypic characteristics, C. insectamans is transferred to the newly described genus as Hemisphaericaspora insectamans comb. nov., in accordance with the changes in the International Code of Nomenclature for algae, fungi and plants. PMID:25075963

  7. Yeast tolerance to the ionic liquid 1-ethyl-3-methylimidazolium acetate.

    PubMed

    Sitepu, Irnayuli R; Shi, Shuang; Simmons, Blake A; Singer, Steven W; Boundy-Mills, Kyria; Simmons, Christopher W

    2014-12-01

    Lignocellulosic plant biomass is the target feedstock for production of second-generation biofuels. Ionic liquid (IL) pretreatment can enhance deconstruction of lignocellulosic biomass into sugars that can be fermented to ethanol. Although biomass is typically washed following IL pretreatment, small quantities of residual IL can inhibit fermentative microorganisms downstream, such as the widely used ethanologenic yeast, Saccharomyces cerevisiae. The aim of this study was to identify yeasts tolerant to the IL 1-ethyl-3-methylimidazolium acetate, one of the top performing ILs known for biomass pretreatment. One hundred and sixty eight strains spanning the Ascomycota and Basidiomycota phyla were selected for screening, with emphasis on yeasts within or closely related to the Saccharomyces genus and those tolerant to saline environments. Based on growth in media containing 1-ethyl-3-methylimidazolium acetate, tolerance to IL levels ranging 1-5% was observed for 80 strains. The effect of 1-ethyl-3-methylimidazolium acetate concentration on maximum cell density and growth rate was quantified to rank tolerance. The most tolerant yeasts included strains from the genera Clavispora, Debaryomyces, Galactomyces, Hyphopichia, Kazachstania, Meyerozyma, Naumovozyma, Wickerhamomyces, Yarrowia, and Zygoascus. These yeasts included species known to degrade plant cell wall polysaccharides and those capable of ethanol fermentation. These yeasts warrant further investigation for use in saccharification and fermentation of IL-pretreated lignocellulosic biomass to ethanol or other products. PMID:25348480

  8. Indole-3-acetic acid-producing yeasts in the phyllosphere of the carnivorous plant Drosera indica L.

    PubMed

    Sun, Pei-Feng; Fang, Wei-Ta; Shin, Li-Ying; Wei, Jyuan-Yu; Fu, Shih-Feng; Chou, Jui-Yu

    2014-01-01

    Yeasts are widely distributed in nature and exist in association with other microorganisms as normal inhabitants of soil, vegetation, and aqueous environments. In this study, 12 yeast strains were enriched and isolated from leaf samples of the carnivorous plant Drosera indica L., which is currently threatened because of restricted habitats and use in herbal industries. According to similarities in large subunit and small subunit ribosomal RNA gene sequences, we identified 2 yeast species in 2 genera of the phylum Ascomycota, and 5 yeast species in 5 genera of the phylum Basidiomycota. All of the isolated yeasts produced indole-3-acetic acid (IAA) when cultivated in YPD broth supplemented with 0.1% L-tryptophan. Growth conditions, such as the pH and temperature of the medium, influenced yeast IAA production. Our results also suggested the existence of a tryptophan-independent IAA biosynthetic pathway. We evaluated the effects of various concentrations of exogenous IAA on yeast growth and observed that IAA produced by wild yeasts modifies auxin-inducible gene expression in Arabidopsis. Our data suggest that yeasts can promote plant growth and support ongoing prospecting of yeast strains for inclusion into biofertilizer for sustainable agriculture. PMID:25464336

  9. The Distribution and Identity of Edaphic Fungi in the McMurdo Dry Valleys

    PubMed Central

    Dreesens, Lisa L.; Lee, Charles K.; Cary, S. Craig

    2014-01-01

    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

  10. The earliest records of internally stratified cyanobacterial and algal lichens from the Lower Devonian of the Welsh Borderland.

    PubMed

    Honegger, Rosmarie; Edwards, Dianne; Axe, Lindsey

    2013-01-01

    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

  11. 454-Pyrosequencing Reveals Variable Fungal Diversity Across Farming Systems.

    PubMed

    Kazeeroni, Elham A; Al-Sadi, Abdullah M

    2016-01-01

    Oasis farming system is common in some parts of the world, especially in the Arabian Peninsula and several African countries. In Oman, the farming system in the majority of farms follows a semi-oasis farming (SOF) system, which is characterized by growing multiple crops mainly for home consumption, but also for local market. This study was conducted to investigate fungal diversity using pyrosequencing approach in soils from a farm utilizing a SOF system which is cultivated with date palms, acid limes and cucumbers. Fungal diversity from this farm was compared to that from an organic farm (OR) growing cucumbers and tomatoes. Fungal diversity was found to be variable among different crops in the same farm. The observed OTUs, Chao1 richness estimates and Shannon diversity values indicated that soils from date palms and acid limes have higher fungal diversity compared to soil from cucumbers (SOF). In addition, they also indicated that the level of fungal diversity is higher in the rhizosphere of cucumbers grown in OR compared to SOF. Ascomycota was the most dominant phylum in most of the samples from the OR and SOF farms. Other dominant phyla are Microsporidia, Chytridiomycota, and Basidiomycota. The differential level of fungal diversity within the SOF could be related to the variation in the cultural practices employed for each crop. PMID:27014331

  12. Truffles contain endocannabinoid metabolic enzymes and anandamide.

    PubMed

    Pacioni, Giovanni; Rapino, Cinzia; Zarivi, Osvaldo; Falconi, Anastasia; Leonardi, Marco; Battista, Natalia; Colafarina, Sabrina; Sergi, Manuel; Bonfigli, Antonella; Miranda, Michele; Barsacchi, Daniela; Maccarrone, Mauro

    2015-02-01

    Truffles are the fruiting body of fungi, members of the Ascomycota phylum endowed with major gastronomic and commercial value. The development and maturation of their reproductive structure are dependent on melanin synthesis. Since anandamide, a prominent member of the endocannabinoid system (ECS), is responsible for melanin synthesis in normal human epidermal melanocytes, we thought that ECS might be present also in truffles. Here, we show the expression, at the transcriptional and translational levels, of most ECS components in the black truffle Tuber melanosporum Vittad. at maturation stage VI. Indeed, by means of molecular biology and immunochemical techniques, we found that truffles contain the major metabolic enzymes of the ECS, while they do not express the most relevant endocannabinoid-binding receptors. In addition, we measured anandamide content in truffles, at different maturation stages (from III to VI), through liquid chromatography-mass spectrometric analysis, whereas the other relevant endocannabinoid 2-arachidonoylglycerol was below the detection limit. Overall, our unprecedented results suggest that anandamide and ECS metabolic enzymes have evolved earlier than endocannabinoid-binding receptors, and that anandamide might be an ancient attractant to truffle eaters, that are well-equipped with endocannabinoid-binding receptors. PMID:25433633

  13. Bringing Laboulbeniales into the 21st century: enhanced techniques for extraction and PCR amplification of DNA from minute ectoparasitic fungi.

    PubMed

    Haelewaters, Danny; Gorczak, Michał; Pfliegler, Walter P; Tartally, András; Tischer, Marta; Wrzosek, Marta; Pfister, Donald H

    2015-12-01

    Laboulbeniales is one of the most peculiar orders of Ascomycota. These fungi are characterized by an ectoparasitic life-style on arthropods, determinate growth, lack of an asexual stage, high species richness, and intractability to culture. The order Laboulbeniales, sister to Pyxidiophorales, has only recently been assigned a separate class, the Laboulbeniomycetes, based on very few ribosomal DNA sequences. So far, DNA isolations and PCR amplifications have proven difficult. Here, we provide details of isolation techniques and the application of commercially available kits that enable efficient and reliable genetic analyses of these fungi. We provide 43 newly generated Laboulbeniales ribosomal DNA sequences, among which are the first published sequences for species in the genera Gloeandromyces, Herpomyces, Laboulbenia, Monoicomyces, and Polyandromyces. DNA extractions were possible using from 1 to 30 thalli from hosts preserved in ethanol (70-100 %). In two cases, we successfully isolated DNA from thalli on dried insect collections. Laboulbeniales molecular systematics could be substantially enhanced through these improved methods by allowing more complete sampling of both taxa and gene regions. PMID:26734547

  14. The agricultural pathology of ant fungus gardens

    PubMed Central

    Currie, Cameron R.; Mueller, Ulrich G.; Malloch, David

    1999-01-01

    Gardens of fungus-growing ants (Formicidae: Attini) traditionally have been thought to be free of microbial parasites, with the fungal mutualist maintained in nearly pure “monocultures.” We conducted extensive isolations of “alien” (nonmutualistic) fungi from ant gardens of a phylogenetically representative collection of attine ants. Contrary to the long-standing assumption that gardens are maintained free of microbial pathogens and parasites, they are in fact host to specialized parasites that are only known from attine gardens and that are found in most attine nests. These specialized garden parasites, belonging to the microfungus genus Escovopsis (Ascomycota: anamorphic Hypocreales), are horizontally transmitted between colonies. Consistent with theory of virulence evolution under this mode of pathogen transmission, Escovopsis is highly virulent and has the potential for rapid devastation of ant gardens, leading to colony mortality. The specialized parasite Escovopsis is more prevalent in gardens of the more derived ant lineages than in gardens of the more “primitive” (basal) ant lineages. Because fungal cultivars of derived attine lineages are asexual clones of apparently ancient origin whereas cultivars of primitive ant lineages were domesticated relatively recently from free-living sexual stocks, the increased virulence of pathogens associated with ancient asexual cultivars suggests an evolutionary cost to cultivar clonality, perhaps resulting from slower evolutionary rates of cultivars in the coevolutionary race with their pathogens. PMID:10393936

  15. Profiling Microbial Communities in Manganese Remediation Systems Treating Coal Mine Drainage

    PubMed Central

    Hansel, Colleen M.; Burgos, William D.

    2015-01-01

    Water discharging from abandoned coal mines can contain extremely high manganese levels. Removing this metal is an ongoing challenge. Passive Mn(II) removal beds (MRBs) contain microorganisms that oxidize soluble Mn(II) to insoluble Mn(III/IV) minerals, but system performance is unpredictable. Using amplicon pyrosequencing, we profiled the bacterial, fungal, algal, and archaeal communities in four MRBs, performing at different levels, in Pennsylvania to determine whether they differed among MRBs and from surrounding soil and to establish the relative abundance of known Mn(II) oxidizers. Archaea were not detected; PCRs with archaeal primers returned only nontarget bacterial sequences. Fungal taxonomic profiles differed starkly between sites that remove the majority of influent Mn and those that do not, with the former being dominated by Ascomycota (mostly Dothideomycetes) and the latter by Basidiomycota (almost entirely Agaricomycetes). Taxonomic profiles for the other groups did not differ significantly between MRBs, but operational taxonomic unit-based analyses showed significant clustering by MRB with all three groups (P < 0.05). Soil samples clustered separately from MRBs in all groups except fungi, whose soil samples clustered loosely with their respective MRB. Known Mn(II) oxidizers accounted for a minor proportion of bacterial sequences (up to 0.20%) but a greater proportion of fungal sequences (up to 14.78%). MRB communities are more diverse than previously thought, and more organisms may be capable of Mn(II) oxidation than are currently known. PMID:25595765

  16. Yeast and yeast-like fungi associated with dry indehiscent fruits of Nothofagus nervosa in Patagonia, Argentina.

    PubMed

    Fernández, Natalia V; Mestre, M Cecilia; Marchelli, Paula; Fontenla, Sonia B

    2012-04-01

    Nothofagus nervosa (Raulí) is a native tree species that yields valuable timber. It was overexploited in the past and is currently included in domestication and conservation programs. Several research programs have focused on the characterization of epiphytic microorganisms because it has been demonstrated that they can affect plant-pathogen interactions and/or promote plant growth. Although the microbial ecology of leaves has been well studied, less is known about microorganisms occurring on seeds and noncommercial fruits. In this work, we analyzed the yeast and yeast-like fungi present on N. nervosa fruits destined for the propagation of this species, as well as the effects of fruit preservation and seed dormancy-breaking processes on fungal diversity. Morphological and molecular methods were used, and differences between fungal communities were analyzed using a similarity index. A total of 171 isolates corresponding to 17 species were recovered, most of which belong to the phylum Ascomycota. The majority of the species develop mycelia, produce pigments and mycosporines, and these adaptation strategies are discussed. It was observed that the preservation process considerably reduced yeast and yeast-like fungal diversity. This is the first study concerning microbial communities associated with this ecologically and economically important species, and the information presented is relevant to domestication programs. PMID:22224476

  17. Dust Rains Deliver Diverse Assemblages of Microorganisms to the Eastern Mediterranean

    NASA Astrophysics Data System (ADS)

    Itani, Ghida Nouhad; Smith, Colin Andrew

    2016-03-01

    Dust rains may be particularly effective at delivering microorganisms, yet their biodiversities have been seldom examined. During 2011 and 2012 in Beirut, Lebanon, 16 of 21 collected rainfalls appeared dusty. Trajectory modelling of air mass origins was consistent with North African sources and at least one Southwest Asian source. As much as ~4 g particulate matter, ~20 μg DNA, and 50 million colony forming units were found deposited per square meter during rainfalls each lasting less than one day. Sequencing of 93 bacteria and 25 fungi cultured from rain samples revealed diverse bacterial phyla, both Gram positive and negative, and Ascomycota fungi. Denaturing Gradient Gel Electrophoresis of amplified 16S rDNA of 13 rains revealed distinct and diverse assemblages of bacteria. Dust rain 16S libraries yielded 131 sequences matching, in decreasing order of abundance, Betaproteobacteria, Alphaproteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Cyanobacteria, Epsilonproteobacteria, Gammaproteobacteria, and Deltaproteobacteria. Clean rain 16S libraries yielded 33 sequences matching only Betaproteobacteria family Oxalobacteraceae. Microbial composition varied between dust rains, and more diverse and different microbes were found in dust rains than clean rains. These results show that dust rains deliver diverse communities of microorganisms that may be complex products of revived desert soil species and fertilized cloud species.

  18. Application of temperature gradient gel electrophoresis to the study of yeast diversity in the estuary of the Tagus river, Portugal.

    PubMed

    Gadanho, Mário; Sampaio, José Paulo

    2004-12-01

    Temperature gradient gel electrophoresis (TGGE) was employed for the assessment of yeast diversity in the estuary of the Tagus river (Portugal). The molecular detection of yeasts was carried out directly from water samples and, in parallel, a cultivation approach by means of an enrichment step was employed. A nested PCR was employed to obtain a fungal amplicon containing the D2 domain of the 26S rRNA gene. For identification the TGGE bands were extracted, re-amplified, and sequenced. Fourteen fungal taxa were detected and all except one were yeasts. Most yeast sequences corresponded to members of the Ascomycota and only three belonged to the Basidiomycota. Five yeasts (four ascomycetes and one basidiomycete) could not be identified to the species level due to the uniqueness of their sequences. The number of species detected after enrichment was higher than the number of taxa found using the direct detection method. This suggests that some yeast populations are present in densities that are below the detection threshold of the method. With respect to the analysis of the yeast community structure, our results indicate that the dominant populations belong to Debaryomyces hansenii, Rhodotorula mucilaginosa, Cryptococcus longus, and to an uncultured basidiomycetous yeast phylogenetically close to Cr. longus. The combined analysis of direct detection and cultivation approaches indicates a similar community structure at the two sampled sites since nine species were present at both localities. PMID:15556087

  19. Degradation of oil by fungi isolated from Gulf of Mexico beaches.

    PubMed

    Simister, R L; Poutasse, C M; Thurston, A M; Reeve, J L; Baker, M C; White, H K

    2015-11-15

    Fungi of the Ascomycota phylum were isolated from oil-soaked sand patties collected from beaches following the Deepwater Horizon oil spill. To examine their ability to degrade oil, fungal isolates were grown on oiled quartz at 20°C, 30°C and 40°C. Consistent trends in oil degradation were not related to fungal species or temperature and all isolates degraded variable quantities of oil (32-65%). Fungal isolates preferentially degraded short (

  20. Polycyclic aromatic hydrocarbons degradation and microbial community shifts during co-composting of creosote-treated wood.

    PubMed

    Covino, Stefano; Fabianová, Tereza; Křesinová, Zdena; Čvančarová, Monika; Burianová, Eva; Filipová, Alena; Vořísková, Jana; Baldrian, Petr; Cajthaml, Tomáš

    2016-01-15

    The feasibility of decontaminating creosote-treated wood (CTW) by co-composting with agricultural wastes was investigated using two bulking agents, grass cuttings (GC) and broiler litter (BL), each employed at a 1:1 ratio with the matrix. The initial concentration of total polycyclic aromatic hydrocarbons (PAHs) in CTW (26,500 mg kg(-1)) was reduced to 3 and 19% after 240 d in GC and BL compost, respectively. PAH degradation exceeded the predicted bioaccesible threshold, estimated through sequential supercritical CO2 extraction, together with significant detoxification, assessed by contact tests using Vibrio fisheri and Hordeum vulgare. GC composting was characterized by high microbial biomass growth in the early phases, as suggested by phospholipid fatty acid analyses. Based on the 454-pyrosequencing results, fungi (mostly Saccharomycetales) constituted an important portion of the microbial community, and bacteria were characterized by rapid shifts (from Firmicutes (Bacilli) and Actinobacteria to Proteobacteria). However, during BL composting, larger amounts of prokaryotic and eukaryotic PLFA markers were observed during the cooling and maturation phases, which were dominated by Proteobacteria and fungi belonging to the Ascomycota and those putatively related to the Glomeromycota. This work reports the first in-depth analysis of the chemical and microbiological processes that occur during the co-composting of a PAH-contaminated matrix. PMID:26342147

  1. Blackpatch of Clover, Cause of Slobbers Syndrome: A Review of the Disease and the Pathogen, Rhizoctonia leguminicola.

    PubMed

    Kagan, Isabelle A

    2016-01-01

    Rhizoctonia leguminicola Gough and Elliott is a widely used name for the causal agent of blackpatch disease of red clover (Trifolium pratense L.). This fungal pathogen produces alkaloids (slaframine and swainsonine) that affect grazing mammals. Slaframine causes livestock to salivate profusely, and swainsonine causes neurological problems. Although the blackpatch fungus was classified as a Rhizoctonia species (phylum Basidiomycota), morphological studies have indicated that it is in the phylum Ascomycota, and sequencing data have indicated that it may be a new genus of ascomycete. The effects of the alkaloids on grazing mammals and their biosynthetic pathways have been extensively studied. In contrast, few studies have been done on management of the disease, which requires a greater understanding of the pathogen. Methods of disease management have included seed treatments and fungicides, but these have not been investigated since the 1950s. Searches for resistant cultivars have been limited. This review summarizes the biological effects and biosynthetic precursors of slaframine and swainsonine. Emphasis is placed on current knowledge about the epidemiology of blackpatch disease and the ecology and taxonomy of the pathogen. Possibilities for future research and disease management efforts are suggested. PMID:26858953

  2. Phylogenetic Diversity of Sponge-Associated Fungi from the Caribbean and the Pacific of Panama and Their In Vitro Effect on Angiotensin and Endothelin Receptors.

    PubMed

    Bolaños, Jessica; De León, Luis Fernando; Ochoa, Edgardo; Darias, José; Raja, Huzefa A; Shearer, Carol A; Miller, Andrew N; Vanderheyden, Patrick; Porras-Alfaro, Andrea; Caballero-George, Catherina

    2015-10-01

    Fungi occupy an important ecological niche in the marine environment, and marine fungi possess an immense biotechnological potential. This study documents the fungal diversity associated with 39 species of sponges and determines their potential to produce secondary metabolites capable of interacting with mammalian G-protein-coupled receptors involved in blood pressure regulation. Total genomic DNA was extracted from 563 representative fungal strains obtained from marine sponges collected by SCUBA from the Caribbean and the Pacific regions of Panama. A total of 194 operational taxonomic units were found with 58% represented by singletons based on the internal transcribed spacer (ITS) and partial large subunit (LSU) rDNA regions. Marine sponges were highly dominated by Ascomycota fungi (95.6%) and represented by two major classes, Sordariomycetes and Dothideomycetes. Rarefaction curves showed no saturation, indicating that further efforts are needed to reveal the entire diversity at this site. Several unique clades were found during phylogenetic analysis with the highest diversity of unique clades in the order Pleosporales. From the 65 cultures tested to determine their in vitro effect on angiotensin and endothelin receptors, the extracts of Fusarium sp. and Phoma sp. blocked the activation of these receptors by more than 50% of the control and seven others inhibited between 30 and 45%. Our results indicate that marine sponges from Panama are a "hot spot" of fungal diversity as well as a rich resource for capturing, cataloguing, and assessing the pharmacological potential of substances present in previously undiscovered fungi associated with marine sponges. PMID:26026948

  3. Epipolythiodiketopiperazines from the Marine Derived Fungus Dichotomomyces cejpii with NF-κB Inhibitory Potential

    PubMed Central

    Harms, Henrik; Orlikova, Barbora; Ji, Seungwon; Nesaei-Mosaferan, Damun; König, Gabriele M.; Diederich, Marc

    2015-01-01

    The Ascomycota Dichotomomyces cejpii was isolated from the marine sponge Callyspongia cf. C. flammea. A new gliotoxin derivative, 6-acetylmonodethiogliotoxin (1) was obtained from fungal extracts. Compounds 2 and 3, methylthio-gliotoxin derivatives were formerly only known as semi-synthetic compounds and are here described as natural products. Additionally the polyketide heveadride (4) was isolated. Compounds 1, 2 and 4 dose-dependently down-regulated TNFα-induced NF-κB activity in human chronic myeloid leukemia cells with IC50s of 38.5 ± 1.2 µM, 65.7 ± 2.0 µM and 82.7 ± 11.3 µM, respectively. The molecular mechanism was studied with the most potent compound 1 and results indicate downstream inhibitory effects targeting binding of NF-κB to DNA. Compound 1 thus demonstrates potential of epimonothiodiketopiperazine-derived compounds for the development of NF-κB inhibitors. PMID:26258781

  4. Novel chytrid lineages dominate fungal sequences in diverse marine and freshwater habitats

    NASA Astrophysics Data System (ADS)

    Comeau, André M.; Vincent, Warwick F.; Bernier, Louis; Lovejoy, Connie

    2016-07-01

    In aquatic environments, fungal communities remain little studied despite their taxonomic and functional diversity. To extend the ecological coverage of this group, we conducted an in-depth analysis of fungal sequences within our collection of 3.6 million V4 18S rRNA pyrosequences originating from 319 individual marine (including sea-ice) and freshwater samples from libraries generated within diverse projects studying Arctic and temperate biomes in the past decade. Among the ~1.7 million post-filtered reads of highest taxonomic and phylogenetic quality, 23,263 fungal sequences were identified. The overall mean proportion was 1.35%, but with large variability; for example, from 0.01 to 59% of total sequences for Arctic seawater samples. Almost all sample types were dominated by Chytridiomycota-like sequences, followed by moderate-to-minor contributions of Ascomycota, Cryptomycota and Basidiomycota. Species and/or strain richness was high, with many novel sequences and high niche separation. The affinity of the most common reads to phytoplankton parasites suggests that aquatic fungi deserve renewed attention for their role in algal succession and carbon cycling.

  5. Yucatán in black and red: Linking edaphic analysis and pyrosequencing-based assessment of bacterial and fungal community structures in the two main kinds of soil of Yucatán State.

    PubMed

    Estrada-Medina, Héctor; Canto-Canché, Blondy B; De Los Santos-Briones, César; O'Connor-Sánchez, Aileen

    2016-01-01

    Yucatán State is dominated by two kinds of soil, named "Black Leptosol" and "Red Leptosol", which are interwoven across the State. In this work, we analyzed the relation between the edaphic characteristics and the bacterial and fungal community structures in these two kinds of Leptosol. The results revealed that Black Leptosol (BlaS) had a higher content of calcium carbonates, organic matter, nitrogen, and phosphorus than Red Leptosol (RedS). The most outstanding difference in the bacterial community structure between BlaS and RedS was that while in BlaS Actinobacteria was the most abundant phylum (43.7%), followed by Acidobacteria (26.9%) and Proteobacteria (23.6%), in RedS the bacterial community was strongly dominated by Acidobacteria (83%). Two fungal phyla were identified in both kinds of soil; Ascomycota, with 77% in BlaS and 56% in RedS, and Basidiomycota, with 22% in RedS and only 0.67% in BlaS. The most relevant difference between the two fungal communities was that excepting for Fusarium sp., all the species they had were different. Thus, in contrast with bacterial communities, where most of the major OTUs were present in both kinds of soil, fungal communities appeared to be unique to each kind of Leptosol. PMID:27296959

  6. Curation of characterized glycoside hydrolases of Fungal origin

    PubMed Central

    Murphy, Caitlin; Powlowski, Justin; Wu, Min; Butler, Greg; Tsang, Adrian

    2011-01-01

    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/ PMID:21622642

  7. Metagenomic Analysis of Fungal Diversity on Strawberry Plants and the Effect of Management Practices on the Fungal Community Structure of Aerial Organs.

    PubMed

    Abdelfattah, Ahmed; Wisniewski, Michael; Li Destri Nicosia, Maria Giulia; Cacciola, Santa Olga; Schena, Leonardo

    2016-01-01

    An amplicon metagenomic approach based on the ITS2 region of fungal rDNA was used to identify the composition of fungal communities associated with different strawberry organs (leaves, flowers, immature and mature fruits), grown on a farm using management practices that entailed the routine use of various chemical pesticides. ITS2 sequences clustered into 316 OTUs and Ascomycota was the dominant phyla (95.6%) followed by Basidiomycota (3.9%). Strawberry plants supported a high diversity of microbial organisms, but two genera, Botrytis and Cladosporium, were the most abundant, representing 70-99% of the relative abundance (RA) of all detected sequences. According to alpha and beta diversity analyses, strawberry organs displayed significantly different fungal communities with leaves having the most diverse fungal community, followed by flowers, and fruit. The interruption of chemical treatments for one month resulted in a significant modification in the structure of the fungal community of leaves and flowers while immature and mature fruit were not significantly affected. Several plant pathogens of other plant species, that would not be intuitively expected to be present on strawberry plants such as Erysiphe, were detected, while some common strawberry pathogens, such as Rhizoctonia, were less evident or absent. PMID:27490110

  8. Large and variable genome size unrelated to serpentine adaptation but supportive of cryptic sexuality in Cenococcum geophilum.

    PubMed

    Bourne, Elizabeth C; Mina, Diogo; Gonçalves, Susana C; Loureiro, João; Freitas, Helena; Muller, Ludo A H

    2014-01-01

    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

  9. Moth outbreaks alter root-associated fungal communities in subarctic mountain birch forests.

    PubMed

    Saravesi, Karita; Aikio, Sami; Wäli, Piippa R; Ruotsalainen, Anna Liisa; Kaukonen, Maarit; Huusko, Karoliina; Suokas, Marko; Brown, Shawn P; Jumpponen, Ari; Tuomi, Juha; Markkola, Annamari

    2015-05-01

    Climate change has important implications on the abundance and range of insect pests in forest ecosystems. We studied responses of root-associated fungal communities to defoliation of mountain birch hosts by a massive geometrid moth outbreak through 454 pyrosequencing of tagged amplicons of the ITS2 rDNA region. We compared fungal diversity and community composition at three levels of moth defoliation (intact control, full defoliation in one season, full defoliation in two or more seasons), replicated in three localities. Defoliation caused dramatic shifts in functional and taxonomic community composition of root-associated fungi. Differentially defoliated mountain birch roots harbored distinct fungal communities, which correlated with increasing soil nutrients and decreasing amount of host trees with green foliar mass. Ectomycorrhizal fungi (EMF) abundance and richness declined by 70-80 % with increasing defoliation intensity, while saprotrophic and endophytic fungi seemed to benefit from defoliation. Moth herbivory also reduced dominance of Basidiomycota in the roots due to loss of basidiomycete EMF and increases in functionally unknown Ascomycota. Our results demonstrate the top-down control of belowground fungal communities by aboveground herbivory and suggest a marked reduction in the carbon flow from plants to soil fungi following defoliation. These results are among the first to provide evidence on cascading effects of natural herbivory on tree root-associated fungi at an ecosystem scale. PMID:25687127

  10. Fungal Community Analysis by Large-Scale Sequencing of Environmental Samples†

    PubMed Central

    O'Brien, Heath E.; Parrent, Jeri Lynn; Jackson, Jason A.; Moncalvo, Jean-Marc; Vilgalys, Rytas

    2005-01-01

    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. PMID:16151147

  11. Characterization of Early Microbial Communities on Volcanic Deposits along a Vegetation Gradient on the Island of Miyake, Japan

    PubMed Central

    Guo, Yong; Fujimura, Reiko; Sato, Yoshinori; Suda, Wataru; Kim, Seok-won; Oshima, Kenshiro; Hattori, Masahira; Kamijo, Takashi; Narisawa, Kazuhiko; Ohta, Hiroyuki

    2014-01-01

    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. PMID:24463576

  12. Hybrid histidine kinases in pathogenic fungi.

    PubMed

    Defosse, Tatiana A; Sharma, Anupam; Mondal, Alok K; Dugé de Bernonville, Thomas; Latgé, Jean-Paul; Calderone, Richard; Giglioli-Guivarc'h, Nathalie; Courdavault, Vincent; Clastre, Marc; Papon, Nicolas

    2015-03-01

    Histidine kinases (HK) sense and transduce via phosphorylation events many intra- and extracellular signals in bacteria, archaea, slime moulds and plants. HK are also widespread in the fungal kingdom, but their precise roles in the regulation of physiological processes remain largely obscure. Expanding genomic resources have recently given the opportunity to identify uncharacterised HK family members in yeasts and moulds and now allow proposing a complex classification of Basidiomycota, Ascomycota and lower fungi HK. A growing number of genetic approaches have progressively provided new insight into the role of several groups of HK in prominent fungal pathogens. In particular, a series of studies have revealed that members of group III HK, which occur in the highest number of fungal species and contain a unique N-terminus region consisting of multiple HAMP domain repeats, regulate morphogenesis and virulence in various human, plant and insect pathogenic fungi. This research field is further supported by recent shape-function studies providing clear correlation between structural properties and signalling states in group III HK. Since HK are absent in mammals, these represent interesting fungal target for the discovery of new antifungal drugs. PMID:25560420

  13. Phylogenetic position of the yeast-like symbiotes of Tagosodes orizicolus (Homoptera: Delphacidae) based on 18S ribosomal DNA partial sequences.

    PubMed

    Xet-Mull, Ana M; Quesada, Tania; Espinoza, Ana M

    2004-09-01

    Tagosodes orizicolus Muir (Homoptera: Delphacidae), the endemic delphacid species of tropical America carries yeast-like symbiotes (YLS) in the abdominal fat bodies and the ovarial tissues, like other rice planthoppers of Asia. These YLS are obligate symbiotes, which are transmitted transovarially, and maintain a mutualistic relationship with the insect host. This characteristic has made in vitro culture and classification of YLS rather difficult using conventional methods. Nevertheless, microorganisms of similar characteristics have been successfully classified by using molecular taxonomy. In the present work, the YLS of Tagosodes orizicolus (YLSTo) were purified on Percoll gradients, and specific segments of 18S rDNA were amplified by PCR, cloned and sequenced. Sequences were aligned by means of the CLUSTAL V (DNASTAR) program; phylogenetic trees were constructed with the Phylogeny Inference Package (PHYLIP), showing that YLSTo belong to the fungi class Pyrenomycetes, phylum Ascomycota. Similarities between 98% and 100% were observed among YLS of the rice delphacids Tagosodes orizicolus, Nilaparvata lugens, Laodelphax striatellus and Sogatella fur cifera, and between 89.8% and 90.8% when comparing the above to YLS of the aphid Hamiltonaphis styraci. These comparisons revealed that delphacid YLS are a highly conserved monophyletic group within the Pyrenomycetes and are closely related to Hypomyces chrysospermus. PMID:17361570

  14. Diversity of fungal isolates from three Hawaiian marine sponges.

    PubMed

    Li, Quanzi; Wang, Guangyi

    2009-01-01

    Sponges harbor diverse prokaryotic and eukaryotic microbes. However, the nature of sponge-fungal association and diversity of sponge-derived fungi have barely been addressed. In this study, the cultivation-dependent approach was applied to study fungal diversity in the Hawaiian sponges Gelliodes fibrosa, Haliclona caerulea, and Mycale armata. The cultivated fungal isolates were representatives of 8 taxonomic orders, belonging to at least 25 genera of Ascomycota and 1 of Basidiomycota. A portion of these isolates (n=15, 17%) were closely affiliated with fungal isolates isolated from other marine habitats; the rest of the isolates had affiliation with terrestrial fungal strains. Cultivated fungal isolates were classified into 3 groups: 'sponge-generalists'-found in all sponge species, 'sponge-associates'-found in more than one sponge species, and 'sponge-specialists'-found only in one sponge species. Individuals of G. fibrosa collected at two different locations shared the same group of 'sponge-specialists'. Also, representatives of 15 genera were identified for the first time in marine sponges. Large-scale phylogenetic analysis of sponge-derived fungi may provide critical information to distinguish between 'resident fungi' and 'transient fungi' in sponges as it has been done in other marine microbial groups. This is the first report of the host specificity analysis of culturable fungal communities in marine sponges. PMID:17681460

  15. Marine Drugs from Sponge-Microbe Association—A Review

    PubMed Central

    Thomas, Tresa Remya A.; Kavlekar, Devanand P.; LokaBharathi, Ponnapakkam A.

    2010-01-01

    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. PMID:20479984

  16. Genetics, Genomics and Evolution of Ergot Alkaloid Diversity

    PubMed Central

    Young, Carolyn A.; Schardl, Christopher L.; Panaccione, Daniel G.; Florea, Simona; Takach, Johanna E.; Charlton, Nikki D.; Moore, Neil; Webb, Jennifer S.; Jaromczyk, Jolanta

    2015-01-01

    The ergot alkaloid biosynthesis system has become an excellent model to study evolutionary diversification of specialized (secondary) metabolites. This is a very diverse class of alkaloids with various neurotropic activities, produced by fungi in several orders of the phylum Ascomycota, including plant pathogens and protective plant symbionts in the family Clavicipitaceae. Results of comparative genomics and phylogenomic analyses reveal multiple examples of three evolutionary processes that have generated ergot-alkaloid diversity: gene gains, gene losses, and gene sequence changes that have led to altered substrates or product specificities of the enzymes that they encode (neofunctionalization). The chromosome ends appear to be particularly effective engines for gene gains, losses and rearrangements, but not necessarily for neofunctionalization. Changes in gene expression could lead to accumulation of various pathway intermediates and affect levels of different ergot alkaloids. Genetic alterations associated with interspecific hybrids of Epichloë species suggest that such variation is also selectively favored. The huge structural diversity of ergot alkaloids probably represents adaptations to a wide variety of ecological situations by affecting the biological spectra and mechanisms of defense against herbivores, as evidenced by the diverse pharmacological effects of ergot alkaloids used in medicine. PMID:25875294

  17. Diversity and community structure of fungi through a permafrost core profile from the Qinghai-Tibet Plateau of China.

    PubMed

    Hu, Weigang; Zhang, Qi; Li, Dingyao; Cheng, Gang; Mu, Jing; Wu, Qingbai; Niu, Fujun; An, Lizhe; Feng, Huyuan

    2014-12-01

    While a vast number of studies have addressed the prokaryotic diversity in permafrost, characterized by subzero temperatures, low water activity, and extremely low rates of nutrient and metabolite transfer, fungal patterns have received surprisingly limited attention. Here, the fungal diversity and community structure were investigated by culture-dependent technique combined with cloning-restriction fragment length polymorphism (RFLP) analysis of sediments in a 10-m-long permafrost core from the Qinghai-Tibet Plateau of China. A total of 62 fungal phylotypes related to 10 distinct classes representing three phyla were recovered from 5031 clones generated in 13 environmental gene libraries. A large proportion of the phylotypes (25/62) that were distantly related to described fungal species appeared to be novel diversity. Ascomycota was the predominant group of fungi, with respect to both clone and phylotype number. Our results suggested there was the existence of cosmopolitan psychrophilic or psychrotolerant fungi in permafrost sediments, the community composition of fungi varied with increasing depth, while these communities largely distributed according to core layers. PMID:24920339

  18. Assembly, Annotation, and Analysis of Multiple Mycorrhizal Fungal Genomes

    SciTech Connect

    Initiative Consortium, Mycorrhizal Genomics; Kuo, Alan; Grigoriev, Igor; Kohler, Annegret; Martin, Francis

    2013-03-08

    Mycorrhizal fungi play critical roles in host plant health, soil community structure and chemistry, and carbon and nutrient cycling, all areas of intense interest to the US Dept. of Energy (DOE) Joint Genome Institute (JGI). To this end we are building on our earlier sequencing of the Laccaria bicolor genome by partnering with INRA-Nancy and the mycorrhizal research community in the MGI to sequence and analyze dozens of mycorrhizal genomes of all Basidiomycota and Ascomycota orders and multiple ecological types (ericoid, orchid, and ectomycorrhizal). JGI has developed and deployed high-throughput sequencing techniques, and Assembly, RNASeq, and Annotation Pipelines. In 2012 alone we sequenced, assembled, and annotated 12 draft or improved genomes of mycorrhizae, and predicted ~;;232831 genes and ~;;15011 multigene families, All of this data is publicly available on JGI MycoCosm (http://jgi.doe.gov/fungi/), which provides access to both the genome data and tools with which to analyze the data. Preliminary comparisons of the current total of 14 public mycorrhizal genomes suggest that 1) short secreted proteins potentially involved in symbiosis are more enriched in some orders than in others amongst the mycorrhizal Agaricomycetes, 2) there are wide ranges of numbers of genes involved in certain functional categories, such as signal transduction and post-translational modification, and 3) novel gene families are specific to some ecological types.

  19. The N-acetylglucosamine catabolic gene cluster in Trichoderma reesei is controlled by the Ndt80-like transcription factor RON1.

    PubMed

    Kappel, Lisa; Gaderer, Romana; Flipphi, Michel; Seidl-Seiboth, Verena

    2016-02-01

    Chitin is an important structural constituent of fungal cell walls composed of N-acetylglucosamine (GlcNAc) monosaccharides, but catabolism of GlcNAc has not been studied in filamentous fungi so far. In the yeast Candida albicans, the genes encoding the three enzymes responsible for stepwise conversion of GlcNAc to fructose-6-phosphate are clustered. In this work, we analysed GlcNAc catabolism in ascomycete filamentous fungi and found that the respective genes are also clustered in these fungi. In contrast to C. albicans, the cluster often contains a gene for an Ndt80-like transcription factor, which we named RON1 (regulator of N-acetylglucosamine catabolism 1). Further, a gene for a glycoside hydrolase 3 protein related to bacterial N-acetylglucosaminidases can be found in the GlcNAc gene cluster in filamentous fungi. Functional analysis in Trichoderma reesei showed that the transcription factor RON1 is a key activator of the GlcNAc gene cluster and essential for GlcNAc catabolism. Furthermore, we present an evolutionary analysis of Ndt80-like proteins in Ascomycota. All GlcNAc cluster genes, as well as the GlcNAc transporter gene ngt1, and an additional transcriptional regulator gene, csp2, encoding the homolog of Neurospora crassa CSP2/GRHL, were functionally characterised by gene expression analysis and phenotypic characterisation of knockout strains in T. reesei. PMID:26481444

  20. Spores of many common airborne fungi reveal no ice nucleation activity in oil immersion freezing experiments

    NASA Astrophysics Data System (ADS)

    Pummer, B. G.; Atanasova, L.; Bauer, H.; Bernardi, J.; Druzhinina, I. S.; Fröhlich-Nowoisky, J.; Grothe, H.

    2013-12-01

    Fungal spores are ubiquitous biological aerosols, which are considered to act as ice nuclei. In this study the ice nucleation (IN) activity of spores harvested from 29 fungal strains belonging to 21 different species was tested in the immersion freezing mode by microscopic observation of water-in-oil emulsions. Spores of 8 of these strains were also investigated in a microdroplet freezing array instrument. The focus was laid on species of economical, ecological or sanitary significance. Besides common molds (Ascomycota), some representatives of the widespread group of mushrooms (Basidiomycota) were also investigated. Fusarium avenaceum was the only sample showing IN activity at relatively high temperatures (about 264 K), while the other investigated fungal spores showed no freezing above 248 K. Many of the samples indeed froze at homogeneous ice nucleation temperatures (about 237 K). In combination with other studies, this suggests that only a limited number of species may act as atmospheric ice nuclei. This would be analogous to what is already known for the bacterial ice nuclei. Apart from that, we selected a set of fungal strains from different sites and exposed them to occasional freezing stress during their cultivation. This was in order to test if the exposure to a cold environment encourages the expression of ice nuclei during growth as a way of adaptation. Although the total protein expression was altered by this treatment, it had no significant impact on the IN activity.

  1. Diversity and distribution of fungal communities in the marine sediments of Kongsfjorden, Svalbard (High Arctic)

    NASA Astrophysics Data System (ADS)

    Zhang, Tao; Fei Wang, Neng; Qin Zhang, Yu; Yu Liu, Hong; Yan Yu, Li

    2015-10-01

    This study assessed the diversity and distribution of fungal communities in eight marine sediments of Kongsfjorden (Svalbard, High Arctic) using 454 pyrosequencing with fungal-specific primers targeting the internal transcribed spacer (ITS) region of the ribosomal rRNA gene. Sedimentary fungal communities showed high diversity with 42,219 reads belonging to 113 operational taxonomic units (OTUs). Of these OTUs, 62 belonged to the Ascomycota, 26 to Basidiomycota, 2 to Chytridiomycota, 1 to Zygomycota, 1 to Glomeromycota, and 21 to unknown fungi. The major known orders included Hypocreales and Saccharomycetales. The common fungal genera were Pichia, Fusarium, Alternaria, and Malassezia. Interestingly, most fungi occurring in these Arctic sediments may originate from the terrestrial habitats and different basins in Kongsfjorden (i.e., inner basin, central basin, and outer basin) harbor different sedimentary fungal communities. These results suggest the existence of diverse fungal communities in the Arctic marine sediments, which may serve as a useful community model for further ecological and evolutionary study of fungi in the Arctic.

  2. Dysbiosis of Fungal Microbiota in the Intestinal Mucosa of Patients with Colorectal Adenomas

    PubMed Central

    Luan, Chunguang; Xie, Lingling; Yang, Xi; Miao, Huifang; Lv, Na; Zhang, Ruifen; Xiao, Xue; Hu, Yongfei; Liu, Yulan; Wu, Na; Zhu, Yuanmin; Zhu, Baoli

    2015-01-01

    The fungal microbiota is an important component of the human gut microbiome and may be linked to gastrointestinal disease. In this study, the fungal microbiota of biopsy samples from adenomas and adjacent tissues was characterized by deep sequencing. Ascomycota, Glomeromycota and Basidiomycota were identified as the dominant phyla in both adenomas and adjacent tissues from all subjects. Among the 60 genera identified, the opportunist pathogens Phoma and Candida represented an average of 45% of the fungal microbiota. When analyzed at the operational taxonomic unit (OTU) level, however, a decreased diversity in adenomas was observed, and three OTUs differed significantly from the adjacent tissues. Principal Component Analysis (PCA) revealed that the core OTUs formed separate clusters for advanced and non-advanced adenomas for which the abundance of four OTUs differed significantly. Moreover, the size of adenomas and the disease stage were closely related to changes in the fungal microbiota in subjects with adenomas. This study characterized the fungal microbiota profile of subjects with adenomas and identified potential diagnostic biomarkers closely related to different stages of adenomas. PMID:25613490

  3. Infection with a Shoot-Specific Fungal Endophyte (Epichloë) Alters Tall Fescue Soil Microbial Communities.

    PubMed

    Rojas, Xavier; Guo, Jingqi; Leff, Jonathan W; McNear, David H; Fierer, Noah; McCulley, Rebecca L

    2016-07-01

    Tall fescue (Schedonorus arundinaceus) is a widespread grass that can form a symbiotic relationship with a shoot-specific fungal endophyte (Epichloë coenophiala). While the effects of fungal endophyte infection on fescue physiology and ecology have been relatively well studied, less attention has been given to how this relationship may impact the soil microbial community. We used high-throughput DNA sequencing and phospholipid fatty acid analysis to determine the structure and biomass of microbial communities in both bulk and rhizosphere soils from tall fescue stands that were either uninfected with E. coenophiala or were infected with the common toxic strain or one of several novel strains of the endophyte. We found that rhizosphere and bulk soils harbored distinct microbial communities. Endophyte presence, regardless of strain, significantly influenced soil fungal communities, but endophyte effects were less pronounced in prokaryotic communities. E. coenophiala presence did not change total fungal biomass but caused a shift in soil and rhizosphere fungal community composition, increasing the relative abundance of taxa within the Glomeromycota phylum and decreasing the relative abundance of genera in the Ascomycota phylum, including Lecanicillium, Volutella, Lipomyces, Pochonia, and Rhizoctonia. Our data suggests that tripartite interactions exist between the shoot endophyte E. coenophiala, tall fescue, and soil fungi that may have important implications for the functioning of soils, such as carbon storage, in fescue-dominated grasslands. PMID:26992401

  4. Taxon-specific metagenomics of Trichoderma reveals a narrow community of opportunistic species that regulate each other's development.

    PubMed

    Friedl, Martina A; Druzhinina, Irina S

    2012-01-01

    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. PMID:22075025

  5. Metagenomic analysis of soil fungal communities on Ulleungdo and Dokdo Islands.

    PubMed

    Nam, Yoon-Jong; Kim, Hyun; Lee, Jin-Hyung; Yoon, Hyeokjun; Kim, Jong-Guk

    2015-01-01

    Ulleungdo and Dokdo are volcanic islands that experience a characteristic marine climate, influenced by warm currents. The richness and diversity of the plant species, particularly vascular plants, are higher on Ulleungdo than on Dokdo. In contrast to the native plant life, little is known about the diversity of soil fungi living in the rhizosphere of these two islands. In this study, we utilized the barcoded pyrosequencing method to analyze rhizosphere soil fungi on Ulleungdo and Dokdo. In total, 768 operational taxonomic units (OTUs) were analyzed from the Ulleungdo samples, while 640 OTUs and 382 OTUs were analyzed from the Dongdo and Seodo (islets of Dokdo) samples, respectively. Species richness was considerably higher in the Ulleungdo samples than in the Dongdo and Seodo samples, while there was little difference in species diversity between the samples. The taxonomic composition analyses demonstrated that members of the phylum Basidiomycota dominated the Ulleungdo samples, whereas members of the phylum Ascomycota were predominant in the Dokdo samples. Ectomycorrhizal fungi belonging to the phylum Basidiomycota, in particular, were more abundant in the Ulleungdo samples. This finding suggests that the difference in the abundance of the ectomycorrhizal fungi in the rhizospheres of Ulleungdo and Dokdo may have been affected by species richness and diversity of the vascular plants. Our study is the first detailed report of the composition of soil fungal communities on the Ulleungdo and Dokdo islands. In addition, our findings provide a basis for understanding the ecological interactions between plants and fungi. PMID:26227909

  6. gfsA encodes a novel galactofuranosyltransferase involved in biosynthesis of galactofuranose antigen of O-glycan in Aspergillus nidulans and A. fumigatus

    PubMed Central

    Futagami, Taiki; Kizjakina, Karina; Sobrado, Pablo; Ekino, Keisuke; Takegawa, Kaoru; Goto, Masatoshi; Nomura, Yoshiyuki; Oka, Takuji

    2013-01-01

    The cell walls of filamentous fungi in the genus Aspergillus have galactofuranose-containing polysaccharides and glycoconjugates, including O-glycans, N-glycans, fungal-type galactomannan, and glycosylinositolphosphoceramide, which are important for cell wall integrity. Here, we attempted to identify galactofuranosyltransferases that couple galactofuranose monomers onto other wall components in Aspergillus nidulans. Using reverse-genetic and biochemical approaches, we identified that the AN8677 gene encoded a galactofuranosyltransferase, which we called GfsA, involved in galactofuranose (Galf) antigen biosynthesis. Disruption of gfsA reduced binding of β-Galf-specific antibody EB-A2 to O-glycosylated WscA protein and galactomannoproteins. The results of an in-vitro galactofuranose antigen synthase assay revealed that GfsA has β1,5- or β1,6- galactofuranosyltransferase activity for O-glycans in glycoproteins, uses UDP-D-galactofuranose as a sugar donor, and requires a divalent manganese cation for activity. GfsA was found to be localized at the Golgi apparatus based on cellular fractionation experiments. ΔgfsA cells exhibited an abnormal morphology characterized by poor hyphal extension, hyphal curvature, and limited formation of conidia. Several gfsA orthologs were identified in members of the Pezizomycotina subphylum of Ascomycota, including the human pathogen Aspergillus fumigatus. To our knowledge, this is the first characterization of a fungal β-galactofuranosyltransferase, which was shown to be involved in galactofuranose antigen biosynthesis of O-glycans in the Golgi. PMID:24118544

  7. Ancestral state reconstruction infers phytopathogenic origins of sooty blotch and flyspeck fungi on apple.

    PubMed

    Ismail, Siti Izera; Batzer, Jean Carlson; Harrington, Thomas C; Crous, Pedro W; Lavrov, Dennis V; Li, Huanyu; Gleason, Mark L

    2016-01-01

    Members of the sooty blotch and flyspeck (SBFS) complex are epiphytic fungi in the Ascomycota that cause economically damaging blemishes of apples worldwide. SBFS fungi are polyphyletic, but approx. 96% of SBFS species are in the Capnodiales. Evolutionary origins of SBFS fungi remain unclear, so we attempted to infer their origins by means of ancestral state reconstruction on a phylogenetic tree built utilizing genes for the nuc 28S rDNA (approx. 830 bp from near the 59 end) and the second largest subunit of RNA polymerase II (RPB2). The analyzed taxa included the well-known genera of SBFS as well as non-SBFS fungi from seven families within the Capnodiales. The non-SBFS taxa were selected based on their distinct ecological niches, including plant-parasitic and saprophytic species. The phylogenetic analyses revealed that most SBFS species in the Capnodiales are closely related to plant-parasitic fungi. Ancestral state reconstruction provided strong evidence that plant-parasitic fungi were the ancestors of the major SBFS lineages. Knowledge gained from this study may help to better understand the ecology and evolution of epiphytic fungi. PMID:26740537

  8. Genetics, genomics and evolution of ergot alkaloid diversity.

    PubMed

    Young, Carolyn A; Schardl, Christopher L; Panaccione, Daniel G; Florea, Simona; Takach, Johanna E; Charlton, Nikki D; Moore, Neil; Webb, Jennifer S; Jaromczyk, Jolanta

    2015-04-01

    The ergot alkaloid biosynthesis system has become an excellent model to study evolutionary diversification of specialized (secondary) metabolites. This is a very diverse class of alkaloids with various neurotropic activities, produced by fungi in several orders of the phylum Ascomycota, including plant pathogens and protective plant symbionts in the family Clavicipitaceae. Results of comparative genomics and phylogenomic analyses reveal multiple examples of three evolutionary processes that have generated ergot-alkaloid diversity: gene gains, gene losses, and gene sequence changes that have led to altered substrates or product specificities of the enzymes that they encode (neofunctionalization). The chromosome ends appear to be particularly effective engines for gene gains, losses and rearrangements, but not necessarily for neofunctionalization. Changes in gene expression could lead to accumulation of various pathway intermediates and affect levels of different ergot alkaloids. Genetic alterations associated with interspecific hybrids of Epichloë species suggest that such variation is also selectively favored. The huge structural diversity of ergot alkaloids probably represents adaptations to a wide variety of ecological situations by affecting the biological spectra and mechanisms of defense against herbivores, as evidenced by the diverse pharmacological effects of ergot alkaloids used in medicine. PMID:25875294

  9. Cyberlindnera xylosilytica sp. nov., a xylitol-producing yeast species isolated from lignocellulosic materials.

    PubMed

    Cadete, Raquel M; Cheab, Monaliza A M; Santos, Renata O; Safar, Silvana V B; Zilli, Jerri E; Vital, Marcos J S; Basso, Luiz C; Lee, Ching-Fu; Kurtzman, Cletus P; Lachance, Marc-André; Rosa, Carlos A

    2015-09-01

    Independent surveys of yeasts associated with lignocellulosic-related materials led to the discovery of a novel yeast species belonging to the Cyberlindnera clade (Saccharomycotina, Ascomycota). Analysis of the sequences of the internal transcribed spacer (ITS) region and the D1/D2 domains of the large subunit rRNA gene showed that this species is related to C. japonica, C. maesa and C. easanensis. Six isolates were obtained from different sources, including rotting wood, tree bark and sugar cane filter cake in Brazil, frass from white oak in the USA and decayed leaf in Taiwan. A novel species is suggested to accommodate these isolates, for which the name C. xylosilytica sp. nov. is proposed. The type strain of C. xylosilytica sp. nov. is NRRL YB-2097(T) ( = CBS 13984(T) = UFMG-CM-Y347(T)) and the allotype is UFMG-CM-Y409 ( = CBS 14083). The novel species is heterothallic and complementary mating types are represented by the type and allotype strains. The MycoBank number is MB 811428. PMID:26025941

  10. Metabarcoding-based fungal diversity on coarse and fine particulate organic matter in a first-order stream in Nova Scotia, Canada

    PubMed Central

    Wurzbacher, Christian; Grimmett, Ivan J.; Bärlocher, Felix

    2016-01-01

    Most streams receive substantial inputs of allochthonous organic material in the form of leaves and twigs (CPOM , coarse particulate organic matter). Mechanical and biological processing converts this into fine particulate organic matter (FPOM). Other sources of particles include flocculated dissolved matter and soil particles. Fungi are known to play a role in the CPOM conversion process, but the taxonomic affiliations of these fungi remain poorly studied. The present study seeks to shed light on the composition of fungal communities on FPOM and CPOM as assessed in a natural stream in Nova Scotia, Canada. Maple leaves were exposed in a stream for four weeks and their fungal community evaluated through pyrosequencing. Over the same period, four FPOM size fractions were collected by filtration and assessed. Particles had much lower ergosterol contents than leaves, suggesting major differences in the extent of fungal colonization. Pyrosequencing documented a total of 821 fungal operational taxonomic units (OTU), of which 726 were exclusive to particles and 47 to leaf samples. Most fungal phyla were represented, including yeast lineages (e.g., Taphrinaceae and Saccharomycotina), Basidiomycota, Chytridiomycota and Cryptomycota, but several classes of Pezizomycontina (Ascomycota) dominated. Cluster dendrograms clearly separated fungal communities from leaves and from particles. Characterizing fungal communities may shed some light on the processing pathways of fine particles in streams and broadens our view of the phylogenetic composition of fungi in freshwater ecosystems. PMID:26918122

  11. Unravelling the Diversity of Grapevine Microbiome

    PubMed Central

    Pinto, Cátia; Pinho, Diogo; Sousa, Susana; Pinheiro, Miguel; Egas, Conceição; C. Gomes, Ana

    2014-01-01

    Vitis vinifera is one of the most widely cultivated fruit crops with a great economic impact on the global industry. As a plant, it is naturally colonised by a wide variety of both prokaryotic and eukaryotic microorganisms that interact with grapevine, having either beneficial or phytopathogenic effects, who play a major role in fruit yield, grape quality and, ultimately, in the evolution of grape fermentation and wine production. Therefore, the objective of this study was to extensively characterize the natural microbiome of grapevine. Considering that the majority of microorganisms are uncultivable, we have deeply studied the microflora of grapevine leaves using massive parallel rDNA sequencing, along its vegetative cycle. Among eukaryotic population the most abundant microorganisms belonged to the early diverging fungi lineages and Ascomycota phylum, whereas the Basidiomycota were the least abundant. Regarding prokaryotes, a high diversity of Proteobacteria, Firmicutes and Actinobacteria was unveiled. Indeed, the microbial communities present in the vineyard during its vegetative cycle were shown to be highly structured and dynamic. In all cases, the major abundant microorganisms were the yeast-like fungus Aureobasidium and the prokaryotic Enterobacteriaceae. Herein, we report the first complete microbiome landscape of the vineyard, through a metagenomic approach, and highlight the analysis of the microbial interactions within the vineyard and its importance for the equilibrium of the microecosystem of grapevines. PMID:24454903

  12. DIRS and Ngaro Retrotransposons in Fungi

    PubMed Central

    Muszewska, Anna; Steczkiewicz, Kamil; Ginalski, Krzysztof

    2013-01-01

    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. PMID:24086727

  13. Identification of Cellulose-Responsive Bacterial and Fungal Communities in Geographically and Edaphically Different Soils by Using Stable Isotope Probing

    PubMed Central

    Eichorst, Stephanie A.

    2012-01-01

    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. PMID:22287013

  14. A higher-level phylogenetic classification of the Fungi.

    PubMed

    Hibbett, David S; Binder, Manfred; Bischoff, Joseph F; Blackwell, Meredith; Cannon, Paul F; Eriksson, Ove E; Huhndorf, Sabine; James, Timothy; Kirk, Paul M; Lücking, Robert; Thorsten Lumbsch, H; Lutzoni, François; Matheny, P Brandon; McLaughlin, David J; Powell, Martha J; Redhead, Scott; Schoch, Conrad L; Spatafora, Joseph W; Stalpers, Joost A; Vilgalys, Rytas; Aime, M Catherine; Aptroot, André; Bauer, Robert; Begerow, Dominik; Benny, Gerald L; Castlebury, Lisa A; Crous, Pedro W; Dai, Yu-Cheng; Gams, Walter; Geiser, David M; Griffith, Gareth W; Gueidan, Cécile; Hawksworth, David L; Hestmark, Geir; Hosaka, Kentaro; Humber, Richard A; Hyde, Kevin D; Ironside, Joseph E; Kõljalg, Urmas; Kurtzman, Cletus P; Larsson, Karl-Henrik; Lichtwardt, Robert; Longcore, Joyce; Miadlikowska, Jolanta; Miller, Andrew; Moncalvo, Jean-Marc; Mozley-Standridge, Sharon; Oberwinkler, Franz; Parmasto, Erast; Reeb, Valérie; Rogers, Jack D; Roux, Claude; Ryvarden, Leif; Sampaio, José Paulo; Schüssler, Arthur; Sugiyama, Junta; Thorn, R Greg; Tibell, Leif; Untereiner, Wendy A; Walker, Christopher; Wang, Zheng; Weir, Alex; Weiss, Michael; White, Merlin M; Winka, Katarina; Yao, Yi-Jian; Zhang, Ning

    2007-05-01

    A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community. The classification includes 195 taxa, down to the level of order, of which 16 are described or validated here: Dikarya subkingdom nov.; Chytridiomycota, Neocallimastigomycota phyla nov.; Monoblepharidomycetes, Neocallimastigomycetes class. nov.; Eurotiomycetidae, Lecanoromycetidae, Mycocaliciomycetidae subclass. nov.; Acarosporales, Corticiales, Baeomycetales, Candelariales, Gloeophyllales, Melanosporales, Trechisporales, Umbilicariales ords. nov. The clade containing Ascomycota and Basidiomycota is classified as subkingdom Dikarya, reflecting the putative synapomorphy of dikaryotic hyphae. The most dramatic shifts in the classification relative to previous works concern the groups that have traditionally been included in the Chytridiomycota and Zygomycota. The Chytridiomycota is retained in a restricted sense, with Blastocladiomycota and Neocallimastigomycota representing segregate phyla of flagellated Fungi. Taxa traditionally placed in Zygomycota are distributed among Glomeromycota and several subphyla incertae sedis, including Mucoromycotina, Entomophthoromycotina, Kickxellomycotina, and Zoopagomycotina. Microsporidia are included in the Fungi, but no further subdivision of the group is proposed. Several genera of 'basal' Fungi of uncertain position are not placed in any higher taxa, including Basidiobolus, Caulochytrium, Olpidium, and Rozella. PMID:17572334

  15. DIRS and Ngaro Retrotransposons in Fungi.

    PubMed

    Muszewska, Anna; Steczkiewicz, Kamil; Ginalski, Krzysztof

    2013-01-01

    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. PMID:24086727

  16. Mating Type Gene Homologues and Putative Sex Pheromone-Sensing Pathway in Arbuscular Mycorrhizal Fungi, a Presumably Asexual Plant Root Symbiont

    PubMed Central

    Halary, Sébastien; Daubois, Laurence; Terrat, Yves; Ellenberger, Sabrina; Wöstemeyer, Johannes; Hijri, Mohamed

    2013-01-01

    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. PMID:24260466

  17. Forest Age and Plant Species Composition Determine the Soil Fungal Community Composition in a Chinese Subtropical Forest

    PubMed Central

    Trogisch, Stefan; Both, Sabine; Scholten, Thomas; Bruelheide, Helge; Buscot, François

    2013-01-01

    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. PMID:23826151

  18. Endophytic Fungi from Lycium chinense Mill and Characterization of Two New Korean Records of Colletotrichum

    PubMed Central

    Paul, Narayan Chandra; Lee, Hyang Burm; Lee, Ji Hye; Shin, Kyu Seop; Ryu, Tae Hee; Kwon, Hye Ri; Kim, Yeong Kuk; Youn, Young Nam; Yu, Seung Hun

    2014-01-01

    Chinese boxthorn or matrimony vine (Lycium chinense Mill) is found primarily in southeastern Europe and Asia, including Korea. The dried ripe fruits are commonly used as oriental medicinal purposes. Endophytic fungi were isolated from surface sterilized tissues and fruits of the medicinal plant in 2013 to identify the new or unreported species in Korea. Among 14 isolates, 10 morphospecies were selected for molecular identification with the internal transcribed spacer (ITS) gene. Phylogenetic analysis revealed that all isolates belonged to Ascomycota including the genera Acremonium, Colletotrichum, Cochliobolus, Fusarium, Hypocrea and Nemania. Two Colletotrichum species were identified at the species level, using three genes including internal transcribed spacer (ITS), glycerol-3-phosphate dehydrogenase (GAPDH) and Actin (ACT) for PCR and molecular data analysis along with morphological observations. The fungal isolates, CNU122031 and CNU122032 were identified as Colletotrichum fructicola and C. brevisporum, respectively. Morphological observations also well supported the molecular identification. C. brevisporum is represented unrecorded species in Korea and C. fructicola is the first record from the host plant. PMID:25170812

  19. A novel sponge disease caused by a consortium of micro-organisms

    NASA Astrophysics Data System (ADS)

    Sweet, Michael; Bulling, Mark; Cerrano, Carlo

    2015-09-01

    In healthy sponges, microbes have been shown to account for up to 40 % of tissues. The majority of these are thought to originate from survivors evading digestion and immune responses of the sponge and growing and residing in the microenvironments of the mesophyll. Although a large percentage of these microbes are likely commensals, they may also include potentially pathogenic agents, which under specific conditions, such as temperature stress, may cause disease. Here we report a novel disease (sponge necrosis syndrome) that is severely affecting populations of the sponge Callyspongia ( Euplacella) aff biru. Both ITS fungal and 16S rDNA bacterial diversities were assessed in healthy and diseased individuals, highlighting six potential primary causal agents for this new disease: two bacteria, a Rhodobacteraceae sp. and a cyanobacterium, Hormoscilla spongeliae (formally identified as Oscillatoria spongeliae), and four fungi, a Ascomycota sp., a Pleosporales sp., a Rhabdocline sp., and a Clasosporium sp. Furthermore, histological analysis showed the dominance of fungal hyphae rather than bacteria throughout the disease lesion, which was absent or rare in healthy tissues. Inoculation trails showed that only a combination of one bacterium and one fungus could replicate the disease, fulfilling Henle-Koch's postulates and showing that this sponge disease is caused by a poly-microbial consortium.

  20. Fungal Community Successions in Rhizosphere Sediment of Seagrasses Enhalus acoroides under PAHs Stress.

    PubMed

    Ling, Juan; Zhang, Yanying; Wu, Meilin; Wang, Youshao; Dong, Junde; Jiang, Yufeng; Yang, Qingsong; Zeng, Siquan

    2015-01-01

    Seagrass meadows represent one of the highest productive marine ecosystems and are of great ecological and economic values. Recently, they have been confronted with worldwide decline. Fungi play important roles in sustaining the ecosystem health as degraders of polycyclic aromatic hydrocarbons (PAHs), but fewer studies have been conducted in seagrass ecosystems. Hence, we investigated the dynamic variations of the fungal community succession under PAH stress in rhizosphere sediment of seagrasses Enhalus acoroides in this study. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), quantitative PCR (qPCR) and a clone library have been employed to analyze the fungal community's shifts. Sequencing results of DGGE and the clone library showed that the predominant species belong to phyla Ascomycota and Basidiomycota. The abundance of three groups decreased sharply over the incubation period, whereas they demonstrated different fungal diversity patterns. Both the exposure time and the PAH concentrations affected the microbial diversity as assessed by PCR-DGGE analysis. Redundancy analysis (RDA) indicated that significant factors driving community shifts were ammonium and pH (p < 0.05). Significant amounts of the variations (31.1%) were explained by pH and ammonium, illustrating that those two parameters were the most likely ones to influence or be influenced by the fungal communities' changes. Investigation results also indicated that fungal communities in seagrass meadow were very sensitive to PAH-induced stress and may be used as potential indicators for the PAH contamination. PMID:26096007

  1. Diversity, ecological role and potential biotechnological applications of marine fungi associated to the seagrass Posidonia oceanica.

    PubMed

    Panno, Luigi; Bruno, Maurizio; Voyron, Samuele; Anastasi, Antonella; Gnavi, Giorgio; Miserere, Luca; Varese, Giovanna Cristina

    2013-09-25

    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

  2. Metagenomic Analysis of Fungal Diversity on Strawberry Plants and the Effect of Management Practices on the Fungal Community Structure of Aerial Organs

    PubMed Central

    Abdelfattah, Ahmed; Wisniewski, Michael; Li Destri Nicosia, Maria Giulia; Cacciola, Santa Olga

    2016-01-01

    An amplicon metagenomic approach based on the ITS2 region of fungal rDNA was used to identify the composition of fungal communities associated with different strawberry organs (leaves, flowers, immature and mature fruits), grown on a farm using management practices that entailed the routine use of various chemical pesticides. ITS2 sequences clustered into 316 OTUs and Ascomycota was the dominant phyla (95.6%) followed by Basidiomycota (3.9%). Strawberry plants supported a high diversity of microbial organisms, but two genera, Botrytis and Cladosporium, were the most abundant, representing 70–99% of the relative abundance (RA) of all detected sequences. According to alpha and beta diversity analyses, strawberry organs displayed significantly different fungal communities with leaves having the most diverse fungal community, followed by flowers, and fruit. The interruption of chemical treatments for one month resulted in a significant modification in the structure of the fungal community of leaves and flowers while immature and mature fruit were not significantly affected. Several plant pathogens of other plant species, that would not be intuitively expected to be present on strawberry plants such as Erysiphe, were detected, while some common strawberry pathogens, such as Rhizoctonia, were less evident or absent. PMID:27490110

  3. Characterization of rhizosphere and endophytic fungal communities from roots of Stipa purpurea in alpine steppe around Qinghai Lake.

    PubMed

    Lu, Dengxue; Jin, Hui; Yang, Xiaoyan; Zhang, Denghong; Yan, Zhiqiang; Li, Xiuzhuang; Zhao, Yuhui; Han, Rongbing; Qin, Bo

    2016-08-01

    Stipa purpurea is among constructive endemic species in the alpine steppe on the Qinghai-Xizang Plateau. To reveal the fungal community structure and diversity in the rhizosphere and roots of this important grass and to analyze the potential influence of different habitats on the structure of fungal communities, we explored the root endophyte and the directly associated rhizosphere communities of S. purpurea by using internal transcribed spacer rRNA cloning and sequencing methods. We found that the roots of S. purpurea are associated with a diverse consortium of Basidiomycota (59.8%) and Ascomycota (38.5%). Most fungi obtained from rhizosphere soil in S. purpurea have been identified as Ascomycetes, while the high proportion detected in roots were basidiomycetous endophytes. The species richness, diversity, and evenness of fungal assemblages were higher in roots than in the rhizosphere soil. Fungi inhabiting the rhizosphere and roots of S. purpurea are significantly different, and the rhizosphere and endophyte communities are largely independent with little overlap in the dominant phyla or operational taxonomic units. Taken together, these results suggested that a wide variety of fungal communities are associated with the roots and rhizosphere soil of S. purpurea and that the fungal assemblages are strongly influenced by different habitats. PMID:27348421

  4. Root-associated fungi of Vaccinium carlesii in subtropical forests of China: intra- and inter-annual variability and impacts of human disturbances

    PubMed Central

    Zhang, Yanhua; Ni, Jian; Tang, Fangping; Pei, Kequan; Luo, Yiqi; Jiang, Lifen; Sun, Lifu; Liang, Yu

    2016-01-01

    Ericoid mycorrhiza (ERM) are expected to facilitate establishment of ericaceous plants in harsh habitats. However, diversity and driving factors of the root-associated fungi of ericaceous plants are poorly understood. In this study, hair-root samples of Vaccinium carlesii were taken from four forest types: old growth forests (OGF), secondary forests with once or twice cutting (SEC I and SEC II), and Cunninghamia lanceolata plantation (PLF). Fungal communities were determined using high-throughput sequencing, and impacts of human disturbances and the intra- and inter-annual variability of root-associated fungal community were evaluated. Diverse fungal taxa were observed and our results showed that (1) Intra- and inter-annual changes in root-associated fungal community were found, and the Basidiomycota to Ascomycota ratio was related to mean temperature of the sampling month; (2) Human disturbances significantly affected structure of root-associated fungal community of V. carlesii, and two secondary forest types were similar in root-associated fungal community and were closer to that of the old growth forest; (3) Plant community composition, edaphic parameters, and geographic factors significantly affected root-associated fungal communities of V. carlesii. These results may be helpful in better understanding the maintenance mechanisms of fungal diversity associated with hair roots of ERM plants under human disturbances. PMID:26928608

  5. Algal and fungal diversity in Antarctic lichens.

    PubMed

    Park, Chae Haeng; Kim, Kyung Mo; Elvebakk, Arve; Kim, Ok-Sun; Jeong, Gajin; Hong, Soon Gyu

    2015-01-01

    The composition of lichen ecosystems except mycobiont and photobiont has not been evaluated intensively. In addition, recent studies to identify algal genotypes have raised questions about the specific relationship between mycobiont and photobiont. In the current study, we analyzed algal and fungal community structures in lichen species from King George Island, Antarctica, by pyrosequencing of eukaryotic large subunit (LSU) and algal internal transcribed spacer (ITS) domains of the nuclear rRNA gene. The sequencing results of LSU and ITS regions indicated that each lichen thallus contained diverse algal species. The major algal operational taxonomic unit (OTU) defined at a 99% similarity cutoff of LSU sequences accounted for 78.7-100% of the total algal community in each sample. In several cases, the major OTUs defined by LSU sequences were represented by two closely related OTUs defined by 98% sequence similarity of ITS domain. The results of LSU sequences indicated that lichen-associated fungi belonged to the Arthoniomycetes, Eurotiomycetes, Lecanoromycetes, Leotiomycetes, and Sordariomycetes of the Ascomycota, and Tremellomycetes and Cystobasidiomycetes of the Basidiomycota. The composition of major photobiont species and lichen-associated fungal community were mostly related to the mycobiont species. The contribution of growth forms or substrates on composition of photobiont and lichen-associated fungi was not evident. PMID:25105247

  6. Phylogenetic analyses and nitrate-reducing activity of fungal cultures isolated from the permanent, oceanic oxygen minimum zone of the Arabian Sea.

    PubMed

    Manohar, Cathrine Sumathi; Menezes, Larissa Danielle; Ramasamy, Kesava Priyan; Meena, Ram M

    2015-03-01

    Reports on the active role of fungi as denitrifiers in terrestrial ecosystems have stimulated an interest in the study of the role of fungi in oxygen-deficient marine systems. In this study, the culturable diversity of fungi was investigated from 4 stations within the permanent, oceanic, oxygen minimum zone of the Arabian Sea. The isolated cultures grouped within the 2 major fungal phyla Ascomycota and Basidiomycota; diversity estimates in the stations sampled indicated that the diversity of the oxygen-depleted environments is less than that of mangrove regions and deep-sea habitats. Phylogenetic analyses of 18S rRNA sequences revealed a few divergent isolates that clustered with environmental sequences previously obtained by others. This is significant, as these isolates represent phylotypes that so far were known only from metagenomic studies and are of phylogenetic importance. Nitrate reduction activity, the first step in the denitrification process, was recorded for isolates under simulated anoxic, deep-sea conditions showing ecological significance of fungi in the oxygen-depleted habitats. This report increases our understanding of fungal diversity in unique, poorly studied habitats and underlines the importance of fungi in the oxygen-depleted environments. PMID:25688692

  7. Microbial Diversity in Cerrado Biome (Neotropical Savanna) Soils.

    PubMed

    de Castro, Alinne Pereira; Sartori da Silva, Maria Regina Silveira; Quirino, Betania Ferraz; da Cunha Bustamante, Mercedes Maria; Krüger, Ricardo Henrique

    2016-01-01

    The Cerrado, the largest savanna region in South America, is located in central Brazil. Cerrado physiognomies, which range from savanna grasslands to forest formations, combined with the highly weathered, acidic clay Cerrado soils form a unique ecoregion. In this study, high-throughput sequencing of ribosomal RNA genes was combined with shotgun metagenomic analysis to explore the taxonomic composition and potential functions of soil microbial communities in four different vegetation physiognomies during both dry and rainy seasons. Our results showed that changes in bacterial, archaeal, and fungal community structures in cerrado denso, cerrado sensu stricto, campo sujo, and gallery forest soils strongly correlated with seasonal patterns of soil water uptake. The relative abundance of AD3, WPS-2, Planctomycetes, Thermoprotei, and Glomeromycota typically decreased in the rainy season, whereas the relative abundance of Proteobacteria and Ascomycota increased. In addition, analysis of shotgun metagenomic data revealed a significant increase in the relative abundance of genes associated with iron acquisition and metabolism, dormancy, and sporulation during the dry season, and an increase in the relative abundance of genes related to respiration and DNA and protein metabolism during the rainy season. These gene functional categories are associated with adaptation to water stress. Our results further the understanding of how tropical savanna soil microbial communities may be influenced by vegetation covering and temporal variations in soil moisture. PMID:26849674

  8. Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi.

    PubMed

    Divakar, Pradeep K; Crespo, Ana; Wedin, Mats; Leavitt, Steven D; Hawksworth, David L; Myllys, Leena; McCune, Bruce; Randlane, Tiina; Bjerke, Jarle W; Ohmura, Yoshihito; Schmitt, Imke; Boluda, Carlos G; Alors, David; Roca-Valiente, Beatriz; Del-Prado, Ruth; Ruibal, Constantino; Buaruang, Kawinnat; Núñez-Zapata, Jano; Amo de Paz, Guillermo; Rico, Víctor J; Molina, M Carmen; Elix, John A; Esslinger, Theodore L; Tronstad, Inger Kristin K; Lindgren, Hanna; Ertz, Damien; Gueidan, Cécile; Saag, Lauri; Mark, Kristiina; Singh, Garima; Dal Grande, Francesco; Parnmen, Sittiporn; Beck, Andreas; Benatti, Michel Navarro; Blanchon, Dan; Candan, Mehmet; Clerc, Philippe; Goward, Trevor; Grube, Martin; Hodkinson, Brendan P; Hur, Jae-Seoun; Kantvilas, Gintaras; Kirika, Paul M; Lendemer, James; Mattsson, Jan-Eric; Messuti, María Inés; Miadlikowska, Jolanta; Nelsen, Matthew; Ohlson, Jan I; Pérez-Ortega, Sergio; Saag, Andres; Sipman, Harrie J M; Sohrabi, Mohammad; Thell, Arne; Thor, Göran; Truong, Camille; Yahr, Rebecca; Upreti, Dalip K; Cubas, Paloma; Lumbsch, H Thorsten

    2015-12-01

    We studied the evolutionary history of the Parmeliaceae (Lecanoromycetes, Ascomycota), one of the largest families of lichen-forming fungi with complex and variable morphologies, also including several lichenicolous fungi. We assembled a six-locus data set including nuclear, mitochondrial and low-copy protein-coding genes from 293 operational taxonomic units (OTUs). The lichenicolous lifestyle originated independently three times in lichenized ancestors within Parmeliaceae, and a new generic name is introduced for one of these fungi. In all cases, the independent origins occurred c. 24 million yr ago. Further, we show that the Paleocene, Eocene and Oligocene were key periods when diversification of major lineages within Parmeliaceae occurred, with subsequent radiations occurring primarily during the Oligocene and Miocene. Our phylogenetic hypothesis supports the independent origin of lichenicolous fungi associated with climatic shifts at the Oligocene-Miocene boundary. Moreover, diversification bursts at different times may be crucial factors driving the diversification of Parmeliaceae. Additionally, our study provides novel insight into evolutionary relationships in this large and diverse family of lichen-forming ascomycetes. PMID:26299211

  9. Novel chytrid lineages dominate fungal sequences in diverse marine and freshwater habitats.

    PubMed

    Comeau, André M; Vincent, Warwick F; Bernier, Louis; Lovejoy, Connie

    2016-01-01

    In aquatic environments, fungal communities remain little studied despite their taxonomic and functional diversity. To extend the ecological coverage of this group, we conducted an in-depth analysis of fungal sequences within our collection of 3.6 million V4 18S rRNA pyrosequences originating from 319 individual marine (including sea-ice) and freshwater samples from libraries generated within diverse projects studying Arctic and temperate biomes in the past decade. Among the ~1.7 million post-filtered reads of highest taxonomic and phylogenetic quality, 23,263 fungal sequences were identified. The overall mean proportion was 1.35%, but with large variability; for example, from 0.01 to 59% of total sequences for Arctic seawater samples. Almost all sample types were dominated by Chytridiomycota-like sequences, followed by moderate-to-minor contributions of Ascomycota, Cryptomycota and Basidiomycota. Species and/or strain richness was high, with many novel sequences and high niche separation. The affinity of the most common reads to phytoplankton parasites suggests that aquatic fungi deserve renewed attention for their role in algal succession and carbon cycling. PMID:27444055

  10. Taxonomy of Allergenic Fungi.

    PubMed

    Levetin, Estelle; Horner, W Elliott; Scott, James A

    2016-01-01

    The Kingdom Fungi contains diverse eukaryotic organisms including yeasts, molds, mushrooms, bracket fungi, plant rusts, smuts, and puffballs. Fungi have a complex metabolism that differs from animals and plants. They secrete enzymes into their surroundings and absorb the breakdown products of enzyme action. Some of these enzymes are well-known allergens. The phylogenetic relationships among fungi were unclear until recently because classification was based on the sexual state morphology. Fungi lacking an obvious sexual stage were assigned to the artificial, now-obsolete category, "Deuteromycetes" or "Fungi Imperfecti." During the last 20 years, DNA sequencing has resolved 8 fungal phyla, 3 of which contain most genera associated with important aeroallergens: Zygomycota, Ascomycota, and Basidiomycota. Advances in fungal classification have required name changes for some familiar taxa. Because of regulatory constraints, many fungal allergen extracts retain obsolete names. A major benefit from this reorganization is that specific immunoglobulin E (IgE) levels in individuals sensitized to fungi appear to closely match fungal phylogenetic relationships. This close relationship between molecular fungal systematics and IgE sensitization provides an opportunity to systematically look at cross-reactivity and permits representatives from each taxon to serve as a proxy for IgE to the group. PMID:26725152

  11. 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

    PubMed Central

    Toledo, A.V.; Alippi, A.M.; de Remes Lenicov, A.M.M.

    2011-01-01

    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. PMID:21529147

  12. [Isolation of wood-decaying fungi and evaluation of their enzymatic activity (Quindío, Colombia)].

    PubMed

    Chaparro, Deisy Fernanda; Rosas, Diana Carolina; Varela, Amanda

    2009-12-31

    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

  13. Psychrophilic fungi from the world's roof.

    PubMed

    Wang, M; Jiang, X; Wu, W; Hao, Y; Su, Y; Cai, L; Xiang, M; Liu, X

    2015-06-01

    During a survey of cold-adapted fungi in alpine glaciers on the Qinghai-Tibet Plateau, 1 428 fungal isolates were obtained of which 150 species were preliminary identified. Phoma sclerotioides and Pseudogymnoascus pannorum were the most dominant species. Psychrotolerant species in Helotiales (Leotiomycetes, Ascomycota) were studied in more detail as they represented the most commonly encountered group during this investigation. Two phylogenetic trees were constructed based on the partial large subunit nrDNA (LSU) to infer the taxonomic placements of these strains. Our strains nested in two well-supported major clades, which represented Tetracladium and a previously unknown lineage. The unknown lineage is distant to any other currently known genera in Helotiales. Psychrophila gen. nov. was therefore established to accommodate these strains which are characterised by globose or subglobose conidia formed from phialides on short or reduced conidiophores. Our analysis also showed that an LSU-based phylogeny is insufficient in differentiating strains at species level. Additional analyses using combined sequences of ITS+TEF1+TUB regions were employed to further investigate the phylogenetic relationships of these strains. Together with the recognisable morphological distinctions, six new species (i.e. P. antarctica, P. lutea, P. olivacea, T. ellipsoideum, T. globosum and T. psychrophilum) were described. Our preliminary investigation indicates a high diversity of cold-adapted species in nature, and many of them may represent unknown species. PMID:26240448

  14. Endophytic fungi: expanding the arsenal of industrial enzyme producers.

    PubMed

    Corrêa, Rúbia Carvalho Gomes; Rhoden, Sandro Augusto; Mota, Thatiane Rodrigues; Azevedo, João Lúcio; Pamphile, João Alencar; de Souza, Cristina Giatti Marques; Polizeli, Maria de Lourdes Teixeira de Moraes; Bracht, Adelar; Peralta, Rosane Marina

    2014-10-01

    Endophytic fungi, mostly belonging to the Ascomycota, are found in the intercellular spaces of the aerial plant parts, particularly in leaf sheaths, sometimes even within the bark and root system without inducing any visual symptoms of their presence. These fungi appear to have a capacity to produce a wide range of enzymes and secondary metabolites exhibiting a variety of biological activities. However, they have been only barely exploited as sources of enzymes of industrial interest. This review emphasizes the suitability and possible advantages of including the endophytic fungi in the screening of new enzyme producing organisms as well as in studies aiming to optimize the production of enzymes through well-known culture processes. Apparently endophytic fungi possess the two types of extracellular enzymatic systems necessary to degrade the vegetal biomass: (1) the hydrolytic system responsible for polysaccharide degradation consisting mainly in xylanases and cellulases; and (2) the unique oxidative ligninolytic system, which degrades lignin and opens phenyl rings, comprises mainly laccases, ligninases and peroxidases. The obvious ability of endophytic fungi to degrade the complex structure of lignocellulose makes them useful in the exploration of the lignocellulosic biomass for the production of fuel ethanol and other value-added commodity chemicals. In addition to this, endophytic fungi may become new sources of industrially useful enzymes such as lipases, amylases and proteases. PMID:25117531

  15. Dynamics of the diversity of fungal and Fusarium communities during continuous cropping of cucumber in the greenhouse.

    PubMed

    Zhou, Xingang; Wu, Fengzhi

    2012-05-01

    The continuous cropping of cucumber in the same potting soils may result in a reduction of yield and quality of the crop, a phenomenon described as soil sickness. The changes of soil microbial communities as affected by continuous cropping and the link between these changes and soil sickness of cucumber are still not clear. In the present study, cucumber was cropped in pots under greenhouse conditions for nine successive cropping cycles. Structures and sizes of rhizosphere fungal and Fusarium (Ascomycota, Fungi) communities, both ubiquitous and ecologically important in soils, were analysed with PCR-denaturing gradient gel electrophoresis and quantitative reverse transcription PCR, respectively. Cucumber showed retarded growth in the seventh cropping cycle. The RNA- and DNA-based fungal community structures derived from the same sample differed from each other, and the active soil fungal communities were more sensitive to continuous cropping. The RNA-based fungal and Fusarium community sizes were larger in the seventh cropping cycle than in the other cropping cycles. Overall, the findings of this study indicate that the population sizes rather than the diversity of fungi and Fusarium communities are linked to the soil sickness associated with cucumber cultivation. PMID:22273443

  16. Elucidating the Diversity of Aquatic Microdochium and Trichoderma Species and Their Activity against the Fish Pathogen Saprolegnia diclina

    PubMed Central

    Liu, Yiying; Zachow, Christin; Raaijmakers, Jos M.; de Bruijn, Irene

    2016-01-01

    Animals and plants are increasingly threatened by emerging fungal and oomycete diseases. Amongst oomycetes, Saprolegnia species cause population declines in aquatic animals, especially fish and amphibians, resulting in significant perturbation in biodiversity, ecological balance and food security. Due to the prohibition of several chemical control agents, novel sustainable measures are required to control Saprolegnia infections in aquaculture. Previously, fungal community analysis by terminal restriction fragment length polymorphism (T-RFLP) revealed that the Ascomycota, specifically the genus Microdochium, was an abundant fungal phylum associated with salmon eggs from a commercial fish farm. Here, phylogenetic analyses showed that most fungal isolates obtained from salmon eggs were closely related to Microdochium lycopodinum/Microdochium phragmitis and Trichoderma viride species. Phylogenetic and quantitative PCR analyses showed both a quantitative and qualitative difference in Trichoderma population between diseased and healthy salmon eggs, which was not the case for the Microdochium population. In vitro antagonistic activity of the fungi against Saprolegnia diclina was isolate-dependent; for most Trichoderma isolates, the typical mycoparasitic coiling around and/or formation of papilla-like structures on S. diclina hyphae were observed. These results suggest that among the fungal community associated with salmon eggs, Trichoderma species may play a role in Saprolegnia suppression in aquaculture. PMID:26805821

  17. Phylogenomic Relationships between Amylolytic Enzymes from 85 Strains of Fungi

    PubMed Central

    Chen, Wanping; Xie, Ting; Shao, Yanchun; Chen, Fusheng

    2012-01-01

    Fungal amylolytic enzymes, including α-amylase, gluocoamylase and α-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 α- amylases, eukaryotic α-amylases, bacterial and fungal α-amylases and GH13 α-glucosidases. Family GH15 had two branches, one for gluocoamylases, and the other with currently unknown function. GH31 α-glucosidases showed diverse branches consisting of neutral α-glucosidases, lysosomal acid α-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

  18. Molecular characterization of microbial communities in bioaerosols of a coal mine by 454 pyrosequencing and real-time PCR.

    PubMed

    Wei, Min; Yu, Zhisheng; Zhang, Hongxun

    2015-04-01

    Microbial diversity and abundance in bioaerosols of a coal mine were analyzed based on 454 pyrosequencing and real-time polymerase chain reaction (PCR). A total of 37,191 high quality sequences were obtained and could be classified into 531, 1730 and 448 operational taxonomic units respectively for archaea, bacteria and fungi at 97% sequence similarity. The Shannon diversity index for archaea, bacteria and fungi was respectively 4.71, 6.29 and 3.86, indicating a high diversity in coal mine bioaerosols. Crenarchaeota, Proteobacteria and Ascomycota were the dominant phyla for archaea, bacteria and fungi, respectively. The concentrations of total archaea, bacteria and fungi were 1.44×10(8), 1.02×10(8) and 9.60×10(4) cells/m3, respectively. Methanotrophs observed in bioaerosols suggested possible methane oxidation in the coal mine. The identified potential pathogens to coal miners, such as Acinetobacter schindleri, Aeromonas cavernicola, Alternaria alternata, Aspergillus penicillioides, Cladosporium cladosporioides, and Penicillium brevicompactum were also observed. This was the first investigation of microbial diversity and abundance in coal mine bioaerosols. The investigation of microbial communities would be favorable in promoting the progress of methane control based on microbial technique and concern on coal miners' health. PMID:25872733

  19. Taxonomic and phylogenetic re-evaluation of Microdochium, Monographella and Idriella.

    PubMed

    Hernández-Restrepo, M; Groenewald, J Z; Crous, P W

    2016-06-01

    Based on morphology and DNA sequence data the taxonomic relationships of Microdochium, Monographella and Idriella were reassessed. Microdochium is morphologically and phylogenetically circumscribed, and the sexual genus Monographella treated as synonym on the basis that Microdochium has more species, is more commonly encountered, and more frequently used in literature. An epitype is designated for Microdochium phragmites, and several well-known species are redefined based on their morphology and DNA sequence data (LSU, ITS, BTUB and RPB2). Furthermore, the revision of Microdochium led to six new combinations (M. albescens, M. consociatum, M. fusariisporum, M. maydis, M. opuntiae and M. stevensonii) and six new species (M. citrinidiscum, M. colombiense, M. fisheri, M. neoqueenslandicum, M. seminicola and M. trichocladiopsis) being proposed. Microdochium s.str. belongs to a monophyletic clade, together with Idriella lunata and Selenodriella, representing a new family, Microdochiaceae, in Xylariales. Other species previously accommodated in Microdochium belong to different orders in the Ascomycota. Microdochium gracile belongs to Sordariomycetes (incertae sedis) and Paramicrodochium is proposed to accommodate this species. Microdochium tripsaci belongs to Ephelis in Clavicipitaceae, while M. fusarioides belongs to a new genus, Microdochiella in Orbiliales. Idriella s.str. is a monotypic genus phylogenetically closely related to Microdochium. Idriella s.l. separates into different genera in Xylariales (incertae sedis) including Castanediella, Selenodriella, Idriellopsis, Neoidriella and Paraidriella, the last three proposed here as new genera. PMID:27616788

  20. Molecular Diversity of Fungal Phylotypes Co-Amplified Alongside Nematodes from Coastal and Deep-Sea Marine Environments

    PubMed Central

    Lambshead, John D.; Austen, Melanie C.; Smerdon, Gary R.; Rogers, Alex D.

    2011-01-01

    Nematodes and fungi are both ubiquitous in marine environments, yet few studies have investigated relationships between these two groups. Microbial species share many well-documented interactions with both free-living and parasitic nematode species, and limited data from previous studies have suggested ecological associations between fungi and nematodes in benthic marine habitats. This study aimed to further document the taxonomy and distribution of fungal taxa often co-amplified from nematode specimens. A total of 15 fungal 18S rRNA phylotypes were isolated from nematode specimens representing both deep-sea and shallow water habitats; all fungal isolates displayed high pairwise sequence identities with published data in Genbank (99–100%) and unpublished high-throughput 454 environmental datasets (>95%). BLAST matches indicate marine fungal sequences amplified in this study broadly represent taxa within the phyla Ascomycota and Basidiomycota, and several phylotypes showed robust groupings with known taxa in phylogenetic topologies. In addition, some fungal phylotypes appeared to be present in disparate geographic habitats, suggesting cosmopolitan distributions or closely related species complexes in at least some marine fungi. The present study was only able to isolate fungal DNA from a restricted set of nematode taxa; further work is needed to fully investigate the taxonomic scope and function of nematode-fungal interactions. PMID:22046287

  1. Unearthing microbial diversity of Taxus rhizosphere via MiSeq high-throughput amplicon sequencing and isolate characterization.

    PubMed

    Hao, Da Cheng; Song, Si Meng; Mu, Jun; Hu, Wen Li; Xiao, Pei Gen

    2016-01-01

    The species variability and potential environmental functions of Taxus rhizosphere microbial community were studied by comparative analyses of 15 16S rRNA and 15 ITS MiSeq sequencing libraries from Taxus rhizospheres in subtropical and temperate regions of China, as well as by isolating laccase-producing strains and polycyclic aromatic hydrocarbon (PAH)-degrading strains. Total reads could be assigned to 2,141 Operational Taxonomic Units (OTUs) belonging to 31 bacteria phyla and 2,904 OTUs of at least seven fungi phyla. The abundance of Planctomycetes, Actinobacteria, and Chloroflexi was higher in T. cuspidata var. nana and T. × media rhizospheres than in T. mairei rhizosphere (NF), while Acidobacteria, Proteobacteria, Nitrospirae, and unclassified bacteria were more abundant in the latter. Ascomycota and Zygomycota were predominant in NF, while two temperate Taxus rhizospheres had more unclassified fungi, Basidiomycota, and Chytridiomycota. The bacterial/fungal community richness and diversity were lower in NF than in other two. Three dye decolorizing fungal isolates were shown to be highly efficient in removing three classes of reactive dye, while two PAH-degrading fungi were able to degrade recalcitrant benzo[a]pyrene. The present studies extend the knowledge pedigree of the microbial diversity populating rhizospheres, and exemplify the method shift in research and development of resource plant rhizosphere. PMID:27080869

  2. Fungal community analysis in the deep-sea sediments of the Pacific Ocean assessed by comparison of ITS, 18S and 28S ribosomal DNA regions

    NASA Astrophysics Data System (ADS)

    Xu, Wei; Luo, Zhu-Hua; Guo, Shuangshuang; Pang, Ka-Lai

    2016-03-01

    We investigated the diversity of fungal communities in 6 different deep-sea sediment samples of the Pacific Ocean based on three different types of clone libraries, including internal transcribed spacer (ITS), 18S rDNA, and 28S rDNA regions. A total of 1978 clones were generated from 18 environmental clone libraries, resulting in 140 fungal operational taxonomic units (OTUs), including 18 OTUs from ITS, 44 OTUs from 18S rDNA, and 78 OTUs from 28S rDNA gene primer sets. The majority of the recovered sequences belonged to diverse phylotypes of the Ascomycota and Basidiomycota. Additionally, our study revealed a total of 46 novel fungal phylotypes, which showed low similarities (<97%) with available fungal sequences in the GenBank, including a novel Zygomycete lineage, suggesting possible new fungal taxa occurring in the deep-sea sediments. The results suggested that 28S rDNA is an efficient target gene to describe fungal community in deep-sea environment.

  3. Microbiota Characterization of Compost Using Omics Approaches Opens New Perspectives for Phytophthora Root Rot Control

    PubMed Central

    Blaya, Josefa; Marhuenda, Frutos C.; Pascual, Jose A.; Ros, Margarita

    2016-01-01

    Phytophthora root rot caused by Phytophthora nicotianae is an economically important disease in pepper crops. The use of suppressive composts is a low environmental impact method for its control. Although attempts have been made to reveal the relationship between microbiota and compost suppressiveness, little is known about the microorganisms associated with disease suppression. Here, an Ion Torrent platform was used to assess the microbial composition of composts made of different agro-industrial waste and with different levels of suppressiveness against P. nicotianae. Both bacterial and fungal populations responded differently depending on the chemical heterogeneity of materials used during the composting process. High proportions (67–75%) of vineyard pruning waste were used in the most suppressive composts, COM-A and COM-B. This material may have promoted the presence of higher relative abundance of Ascomycota as well as higher microbial activity, which have proved to be essential for controlling the disease. Although no unique fungi or bacteria have been detected in neither suppressive nor conducive composts, relatively high abundance of Fusarium and Zopfiella were found in compost COM-B and COM-A, respectively. To the best of our knowledge, this is the first work that studies compost metabolome. Surprisingly, composts and peat clustered together in principal component analysis of the metabolic data according to their levels of suppressiveness achieved. This study demonstrated the need for combining the information provided by different techniques, including metagenomics and metametabolomics, to better understand the ability of compost to control plant diseases. PMID:27490955

  4. Blackpatch of Clover, Cause of Slobbers Syndrome: A Review of the Disease and the Pathogen, Rhizoctonia leguminicola

    PubMed Central

    Kagan, Isabelle A.

    2016-01-01

    Rhizoctonia leguminicola Gough and Elliott is a widely used name for the causal agent of blackpatch disease of red clover (Trifolium pratense L.). This fungal pathogen produces alkaloids (slaframine and swainsonine) that affect grazing mammals. Slaframine causes livestock to salivate profusely, and swainsonine causes neurological problems. Although the blackpatch fungus was classified as a Rhizoctonia species (phylum Basidiomycota), morphological studies have indicated that it is in the phylum Ascomycota, and sequencing data have indicated that it may be a new genus of ascomycete. The effects of the alkaloids on grazing mammals and their biosynthetic pathways have been extensively studied. In contrast, few studies have been done on management of the disease, which requires a greater understanding of the pathogen. Methods of disease management have included seed treatments and fungicides, but these have not been investigated since the 1950s. Searches for resistant cultivars have been limited. This review summarizes the biological effects and biosynthetic precursors of slaframine and swainsonine. Emphasis is placed on current knowledge about the epidemiology of blackpatch disease and the ecology and taxonomy of the pathogen. Possibilities for future research and disease management efforts are suggested. PMID:26858953

  5. Fungal Community Successions in Rhizosphere Sediment of Seagrasses Enhalus acoroides under PAHs Stress

    PubMed Central

    Ling, Juan; Zhang, Yanying; Wu, Meilin; Wang, Youshao; Dong, Junde; Jiang, Yufeng; Yang, Qingsong; Zeng, Siquan

    2015-01-01

    Seagrass meadows represent one of the highest productive marine ecosystems and are of great ecological and economic values. Recently, they have been confronted with worldwide decline. Fungi play important roles in sustaining the ecosystem health as degraders of polycyclic aromatic hydrocarbons (PAHs), but fewer studies have been conducted in seagrass ecosystems. Hence, we investigated the dynamic variations of the fungal community succession under PAH stress in rhizosphere sediment of seagrasses Enhalus acoroides in this study. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), quantitative PCR (qPCR) and a clone library have been employed to analyze the fungal community’s shifts. Sequencing results of DGGE and the clone library showed that the predominant species belong to phyla Ascomycota and Basidiomycota. The abundance of three groups decreased sharply over the incubation period, whereas they demonstrated different fungal diversity patterns. Both the exposure time and the PAH concentrations affected the microbial diversity as assessed by PCR-DGGE analysis. Redundancy analysis (RDA) indicated that significant factors driving community shifts were ammonium and pH (p < 0.05). Significant amounts of the variations (31.1%) were explained by pH and ammonium, illustrating that those two parameters were the most likely ones to influence or be influenced by the fungal communities’ changes. Investigation results also indicated that fungal communities in seagrass meadow were very sensitive to PAH-induced stress and may be used as potential indicators for the PAH contamination. PMID:26096007

  6. Diversity and distribution of cultured endolichenic fungi in the Ny-Ålesund Region, Svalbard (High Arctic).

    PubMed

    Zhang, Tao; Wei, Xin-Li; Wei, Yu-Zhen; Liu, Hong-Yu; Yu, Li-Yan

    2016-07-01

    Endolichenic fungi within 17 lichen species in the area near Ny-Ålesund (Svalbard, High Arctic) were studied by a culture-based method. The 247 fungal isolates were obtained from 2712 lichen thallus segments. The colonization rate of endolichenic fungi ranged from 1.6 to 26.5 %, respectively. These isolates were identified to 40 fungal taxa, including 35 Ascomycota (10 orders), 4 Basidiomycota (3 orders), and 1 unidentified fungus. Thelebolales was the most abundant order, while Sordariales were the most diverse order. The common fungal taxa shared by more than 3 lichen species were Thelebolus microsporus (93 isolates), Coniochaeta hoffmannii (7 isolates), Sarocladium kiliense (33 isolates), Coniochaeta sp. 1 (5 isolates), Coniochaeta sp. 4 (28 isolates), and Coniochaeta sp. 2 (5 isolates). Low Sorenson's similarity coefficients were observed among different lichen species, indicating that host-related factor may shape the endolichenic fungal communities in this region. In addition, no endolichenic fungal taxa were previously found in the Antarctica and Austrian Alps, suggesting endolichenic fungal communities in this region might be also shaped by the Arctic climate. The results demonstrate the existence of specific cultured endolichenic fungal species, which may be suitable objects for further study of their possible functional roles in the lichen thalli. PMID:27240672

  7. Intercropped silviculture systems, a key to achieving soil fungal community management in eucalyptus plantations.

    PubMed

    Rachid, Caio T C C; Balieiro, Fabiano C; Fonseca, Eduardo S; Peixoto, Raquel Silva; Chaer, Guilherme M; Tiedje, James M; Rosado, Alexandre S

    2015-01-01

    Fungi are ubiquitous and important contributors to soil nutrient cycling, playing a vital role in C, N and P turnover, with many fungi having direct beneficial relationships with plants. However, the factors that modulate the soil fungal community are poorly understood. We studied the degree to which the composition of tree species affected the soil fungal community structure and diversity by pyrosequencing the 28S rRNA gene in soil DNA. We were also interested in whether intercropping (mixed plantation of two plant species) could be used to select fungal species. More than 50,000 high quality sequences were analyzed from three treatments: monoculture of Eucalyptus; monoculture of Acacia mangium; and a mixed plantation with both species sampled 2 and 3 years after planting. We found that the plant type had a major effect on the soil fungal community structure, with 75% of the sequences from the Eucalyptus soil belonging to Basidiomycota and 19% to Ascomycota, and the Acacia soil having a sequence distribution of 28% and 62%, respectively. The intercropping of Acacia mangium in a Eucalyptus plantation significantly increased the number of fungal genera and the diversity indices and introduced or increased the frequency of several genera that were not found in the monoculture cultivation samples. Our results suggest that management of soil fungi is possible by manipulating the composition of the plant community, and intercropped systems can be a means to achieve that. PMID:25706388

  8. Fungal succession in an in-vessel composting system characterized using 454 pyrosequencing.

    PubMed

    Langarica-Fuentes, Adrian; Zafar, Urooj; Heyworth, Alan; Brown, Thomas; Fox, Graeme; Robson, Geoffrey D

    2014-05-01

    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

  9. Blue pigment in Hypocrea caerulescens sp. nov. and two additional new species in sect. Trichoderma.

    PubMed

    Jaklitsch, Walter M; Stadler, Marc; Voglmayr, Hermann

    2012-01-01

    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

  10. Organization and Evolutionary Trajectory of the Mating Type (MAT) Locus in Dermatophyte and Dimorphic Fungal Pathogens▿ †

    PubMed Central

    Li, Wenjun; Metin, Banu; White, Theodore C.; Heitman, Joseph

    2010-01-01

    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. PMID:19880755

  11. DNA barcoding in Mexico: an introduction.

    PubMed

    Elías-Gutiérrez, M; León-Regagnon, V

    2013-11-01

    DNA barcoding has become an important current scientific trend to the understanding of the world biodiversity. In the case of mega-diverse hot spots like Mexico, this technique represents an important tool for taxonomists, allowing them to concentrate in highlighted species by the barcodes instead of analyzing entire sets of specimens. This tendency resulted in the creation of a national network named Mexican Barcode of Life (MEXBOL) which main goals are to train students, and to promote the interaction and collective work among researchers interested in this topic. As a result, the number of records in the Barcode of Life Database (BOLD) for some groups, such as the Mammalia, Actinopterygii, Polychaeta, Branchiopoda, Ostracoda, Maxillopoda, Nematoda, Pinophyta, Ascomycota and Basidiomycota place Mexico among the top ten countries in the generation of these data. This special number presents only few of the many interesting findings in this region of the world, after the use of this technique and its integration with other methodologies. PMID:23919390

  12. A Five-Year Survey of Dematiaceous Fungi in a Tropical Hospital Reveals Potential Opportunistic Species

    PubMed Central

    Yew, Su Mei; Chan, Chai Ling; Lee, Kok Wei; Na, Shiang Ling; Tan, Ruixin; Hoh, Chee-Choong; Yee, Wai-Yan; Ngeow, Yun Fong; Ng, Kee Peng

    2014-01-01

    Dematiaceous fungi (black fungi) are a heterogeneous group of fungi present in diverse environments worldwide. Many species in this group are known to cause allergic reactions and potentially fatal diseases in humans and animals, especially in tropical and subtropical climates. This study represents the first survey of dematiaceous fungi in Malaysia and provides observations on their diversity as well as in vitro response to antifungal drugs. Seventy-five strains isolated from various clinical specimens were identified by morphology as well as an internal transcribed spacer (ITS)-based phylogenetic analysis. The combined molecular and conventional approach enabled the identification of three classes of the Ascomycota phylum and 16 genera, the most common being Cladosporium, Cochliobolus and Neoscytalidium. Several of the species identified have not been associated before with human infections. Among 8 antifungal agents tested, the azoles posaconazole (96%), voriconazole (90.7%), ketoconazole (86.7%) and itraconazole (85.3%) showed in vitro activity (MIC ≤1 µg/mL) to the largest number of strains, followed by anidulafungin (89.3%), caspofungin (74.7%) and amphotericin B (70.7%). Fluconazole appeared to be the least effective with only 10.7% of isolates showing in vitro susceptibility. Overall, almost half (45.3%) of the isolates showed reduced susceptibility (MIC >1 µg/mL) to at least one antifungal agent, and three strains (one Pyrenochaeta unguis-hominis and two Nigrospora oryzae) showed potential multidrug resistance. PMID:25098697

  13. Microbial Diversity in Engineered Haloalkaline Environments Shaped by Shared Geochemical Drivers Observed in Natural Analogues

    PubMed Central

    Warren, Lesley A.; Kendra, Kathryn E.

    2015-01-01

    Microbial communities in engineered terrestrial haloalkaline environments have been poorly characterized relative to their natural counterparts and are geologically recent in formation, offering opportunities to explore microbial diversity and assembly in dynamic, geochemically comparable contexts. In this study, the microbial community structure and geochemical characteristics of three geographically dispersed bauxite residue environments along a remediation gradient were assessed and subsequently compared with other engineered and natural haloalkaline systems. In bauxite residues, bacterial communities were similar at the phylum level (dominated by Proteobacteria and Firmicutes) to those found in soda lakes, oil sands tailings, and nuclear wastes; however, they differed at lower taxonomic levels, with only 23% of operational taxonomic units (OTUs) shared with other haloalkaline environments. Although being less diverse than natural analogues, bauxite residue harbored substantial novel bacterial taxa, with 90% of OTUs nonmatchable to cultured representative sequences. Fungal communities were dominated by Ascomycota and Basidiomycota, consistent with previous studies of hypersaline environments, and also harbored substantial novel (73% of OTUs) taxa. In bauxite residues, community structure was clearly linked to geochemical and physical environmental parameters, with 84% of variation in bacterial and 73% of variation in fungal community structures explained by environmental parameters. The major driver of bacterial community structure (salinity) was consistent across natural and engineered environments; however, drivers differed for fungal community structure between natural (pH) and engineered (total alkalinity) environments. This study demonstrates that both engineered and natural terrestrial haloalkaline environments host substantial repositories of microbial diversity, which are strongly shaped by geochemical drivers. PMID:25979895

  14. Unearthing microbial diversity of Taxus rhizosphere via MiSeq high-throughput amplicon sequencing and isolate characterization

    PubMed Central

    Hao, Da Cheng; Song, Si Meng; Mu, Jun; Hu, Wen Li; Xiao, Pei Gen

    2016-01-01

    The species variability and potential environmental functions of Taxus rhizosphere microbial community were studied by comparative analyses of 15 16S rRNA and 15 ITS MiSeq sequencing libraries from Taxus rhizospheres in subtropical and temperate regions of China, as well as by isolating laccase-producing strains and polycyclic aromatic hydrocarbon (PAH)-degrading strains. Total reads could be assigned to 2,141 Operational Taxonomic Units (OTUs) belonging to 31 bacteria phyla and 2,904 OTUs of at least seven fungi phyla. The abundance of Planctomycetes, Actinobacteria, and Chloroflexi was higher in T. cuspidata var. nana and T. × media rhizospheres than in T. mairei rhizosphere (NF), while Acidobacteria, Proteobacteria, Nitrospirae, and unclassified bacteria were more abundant in the latter. Ascomycota and Zygomycota were predominant in NF, while two temperate Taxus rhizospheres had more unclassified fungi, Basidiomycota, and Chytridiomycota. The bacterial/fungal community richness and diversity were lower in NF than in other two. Three dye decolorizing fungal isolates were shown to be highly efficient in removing three classes of reactive dye, while two PAH-degrading fungi were able to degrade recalcitrant benzo[a]pyrene. The present studies extend the knowledge pedigree of the microbial diversity populating rhizospheres, and exemplify the method shift in research and development of resource plant rhizosphere. PMID:27080869

  15. Systematic Search for Cultivatable Fungi That Best Deconstruct Cell Walls of Miscanthus and Sugarcane in the Field ▿ †

    PubMed Central

    Shrestha, Prachand; Szaro, Timothy M.; Bruns, Thomas D.; Taylor, John W.

    2011-01-01

    The goals of our project were to document the diversity and distributions of cultivable fungi associated with decaying Miscanthus and sugarcane plants in nature and to further assess biodegradation of host plant cell walls by these fungi in pure cultures. Late in 2008 and early in 2009 we collected decaying Miscanthus and Saccharum from 8 sites in Illinois and 11 sites in Louisiana, respectively. To recover fungi that truly decay plants and to recover slow-growing fungi, we washed the plant material repeatedly to remove spores and cultivated fungi from plant fragments small enough to harbor at most one mycelium. We randomly selected 950 fungal colonies out of 4,560 microwell colonies and used molecular identification to discover that the most frequently recovered fungal species resided in Hypocreales (Sordariomycetes), Pleosporales (Dothideomycetes), and Chaetothryiales (Eurotiomycetes) and that only a few weedy species were recovered. We were particularly interested in Pleosporales and Chaetothyriales, groups that have not been mined for plant decay fungi. To confirm that we had truly recovered fungi that deconstruct plant cell walls, we assayed the capacity of the fungi to consume whole, alkali-pretreated, ground Miscanthus. Solid substrate cultures of the nine most commonly encountered Ascomycota resulted in Miscanthus weight loss of 8 to 13% over 4 weeks. This is the first systematic, high-throughput, isolation and biodegradation assessment of fungi isolated from decaying bioenergy grasses. PMID:21685162

  16. Clonal Species Trichoderma parareesei sp. nov. Likely Resembles the Ancestor of the Cellulase Producer Hypocrea jecorina/T. reesei▿ †

    PubMed Central

    Atanasova, Lea; Jaklitsch, Walter M.; Komoń-Zelazowska, Monika; Kubicek, Christian P.; Druzhinina, Irina S.

    2010-01-01

    We have previously reported that the prominent industrial enzyme producer Trichoderma reesei (teleomorph Hypocrea jecorina; Hypocreales, Ascomycota, Dikarya) has a genetically isolated, sympatric sister species devoid of sexual reproduction and which is constituted by the majority of anamorphic strains previously attributed to H. jecorina/T. reesei. In this paper we present the formal taxonomic description of this new species, T. parareesei, complemented by multivariate phenotype profiling and molecular evolutionary examination. A phylogenetic analysis of relatively conserved loci, such as coding fragments of the RNA polymerase B subunit II (rpb2) and GH18 chitinase (chi18-5), showed that T. parareesei is genetically invariable and likely resembles the ancestor which gave raise to H. jecorina. This and the fact that at least one mating type gene of T. parareesei has previously been found to be essentially altered compared to the sequence of H. jecorina/T. reesei indicate that divergence probably occurred due to the impaired functionality of the mating system in the hypothetical ancestor of both species. In contrast, we show that the sexually reproducing and correspondingly more polymorphic H. jecorina/T. reesei is essentially evolutionarily derived. Phenotype microarray analyses performed at seven temperature regimens support our previous speculations that T. parareesei possesses a relatively high opportunistic potential, which probably ensured the survival of this species in ancient and sustainable environment such as tropical forests. PMID:20817800

  17. Antioxidant and antimycotic activities of two native lavandula species from portugal.

    PubMed

    Baptista, Rafael; Madureira, Ana Margarida; Jorge, Rita; Adão, Rita; Duarte, Aida; Duarte, Noélia; Lopes, Maria Manuel; Teixeira, Generosa

    2015-01-01

    The antioxidant and antimycotic activities of the essential oils and extracts of two native Portuguese Lavandula species, L. stoechas subsp. luisieri and L. pedunculata, were evaluated by in vitro assays. The total phenolics and flavonoids content were also determined. The antioxidant potential was assessed through DPPH radical scavenging, inhibition of lipid peroxidation (ILP), and DNA protection assays. All samples displayed a high DPPH scavenging activity, some of them showing concentration dependence. The majority of the samples were also able to inhibit lipid peroxidation. A strong correlation was observed between the results of DPPH and ILP assays and the flavonoids content of the samples. In the DNA protection assay, all the extracts were able to preserve DNA integrity. The antimycotic activity was performed against twelve fungi belonging to Basidiomycota and Ascomycota Divisions. L. stoechas subsp. luisieri exhibited the broadest activity spectra. L. pedunculata extracts were active against five fungi. Cryptococcus neoformans was the most sensitive, being inhibited by all the extracts. Our results led to the conclusion that L. stoechas subsp. luisieri and L. pedunculata can be useful as new sources of natural antioxidants and antimycotic agents, providing a possible valorization of the existing biodiversity and resources of Portuguese flora. PMID:25922611

  18. Microbiota Characterization of Compost Using Omics Approaches Opens New Perspectives for Phytophthora Root Rot Control.

    PubMed

    Blaya, Josefa; Marhuenda, Frutos C; Pascual, Jose A; Ros, Margarita

    2016-01-01

    Phytophthora root rot caused by Phytophthora nicotianae is an economically important disease in pepper crops. The use of suppressive composts is a low environmental impact method for its control. Although attempts have been made to reveal the relationship between microbiota and compost suppressiveness, little is known about the microorganisms associated with disease suppression. Here, an Ion Torrent platform was used to assess the microbial composition of composts made of different agro-industrial waste and with different levels of suppressiveness against P. nicotianae. Both bacterial and fungal populations responded differently depending on the chemical heterogeneity of materials used during the composting process. High proportions (67-75%) of vineyard pruning waste were used in the most suppressive composts, COM-A and COM-B. This material may have promoted the presence of higher relative abundance of Ascomycota as well as higher microbial activity, which have proved to be essential for controlling the disease. Although no unique fungi or bacteria have been detected in neither suppressive nor conducive composts, relatively high abundance of Fusarium and Zopfiella were found in compost COM-B and COM-A, respectively. To the best of our knowledge, this is the first work that studies compost metabolome. Surprisingly, composts and peat clustered together in principal component analysis of the metabolic data according to their levels of suppressiveness achieved. This study demonstrated the need for combining the information provided by different techniques, including metagenomics and metametabolomics, to better understand the ability of compost to control plant diseases. PMID:27490955

  19. Proteomics Shows New Faces for the Old Penicillin Producer Penicillium chrysogenum

    PubMed Central

    Barreiro, Carlos; Martín, Juan F.; García-Estrada, Carlos

    2012-01-01

    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 β-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. PMID:22318718

  20. Ectomycorrhizal fungi of the Seychelles: diversity patterns and host shifts from the native Vateriopsis seychellarum (Dipterocarpaceae) and Intsia bijuga (Caesalpiniaceae) to the introduced Eucalyptus robusta (Myrtaceae), but not Pinus caribea (Pinaceae).

    PubMed

    Tedersoo, Leho; Suvi, Triin; Beaver, Katy; Kõljalg, Urmas

    2007-01-01

    Ectomycorrhizal (ECM) fungi form highly diverse communities in temperate forests, but little is known about their community ecology in tropical ecosystems. Using anatomotyping and rDNA sequencing, ECM fungi were identified on root tips of the introduced Eucalyptus robusta and Pinus caribea as well as the endemic Vateriopsis seychellarum and indigenous Intsia bijuga in the Seychelles. Sequencing revealed 30 species of ECM fungi on root tips of V. seychellarum and I. bijuga, with three species overlapping. Eucalyptus robusta shared five of these taxa, whereas P. caribea hosted three unique species of ECM fungi that were likely cointroduced with containerized seedlings. The thelephoroid (including the anamorphic genus Riessiella), euagaric, boletoid and hymenochaetoid clades of basidiomycetes dominated the ECM fungal community of native trees. Two species of Annulatascaceae (Sordariales, Ascomycota) were identified and described as ECM symbionts of V. seychellarum. The low diversity of native ECM fungi is attributed to deforestation and long-term isolation of the Seychelles. Native ECM fungi associate with exotic eucalypts, whereas cointroduced ECM fungi persist in pine plantations for decades. PMID:17587380

  1. Morphological and Molecular Characterization of a Fungus, Hirsutella sp., Isolated from Planthoppers and Psocids in Argentina

    PubMed Central

    Toledo, Andrea V.; Simurro, María E.; Balatti, Pedro A.

    2013-01-01

    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

  2. Distribution and diversity of fungi in freshwater sediments on a river catchment scale

    PubMed Central

    Liu, Jie; Wang, Jianan; Gao, Guanghai; Bartlam, Mark G.; Wang, Yingying

    2015-01-01

    Fungal communities perform essential functions in biogeochemical cycles. However, knowledge of fungal community structural changes in river ecosystems is still very limited. In the present study, we combined culture-dependent and culture-independent methods to investigate fungal distribution and diversity in sediment on a regional scale in the Songhua River catchment, located in North-East Asia. A total of 147 samples over the whole river catchment were analyzed. The results showed that compared to the mainstream, the tributaries have a higher fungal community organization and culturable fungal concentration, but possess lower community dynamics as assessed by denaturing gradient gel electrophoresis (DGGE). Furthermore, phylogenetic analysis of DGGE bands showed that Ascomycota and Basidiomycota were the predominant community in the Songhua River catchment. Redundancy analysis revealed that longitude was the primary factor determining the variation of fungal community structure, and fungal biomass was mainly related to the total nutrient content. Our findings provide new insights into the characteristics of fungal community distribution in a temperate zone river at a regional scale, and demonstrate that fungal dispersal is restricted by geographical barriers in a whole river catchment. PMID:25954259

  3. Oviposition Deterrence and Immature Survival of Filth Flies (Diptera: Muscidae) When Exposed to Commercial Fungal Products.

    PubMed

    Machtinger, E T; Weeks, E N I; Geden, C J

    2016-01-01

    Filth flies are pests of livestock, and can transmit pathogens that cause disease to animals and their caretakers. Studies have shown successful infection of adult filth flies following exposure to different strains and formulations of entomopathogenic fungi. This study aimed to examine the effects of commercial formulations of Beauveria bassiana (Balsamo) (Moniliales: Moniliaceae) (i.e., BotaniGard ES, Mycotrol O, balEnce), and Metarhizium brunneum (Metsch.) (Ascomycota: Hypocreales) (i.e., Met52 EC), on filth fly oviposition and immature fly survival after exposure. House flies, Musca domestica L., laid significantly fewer eggs on Met52 EC-treated surfaces than on surfaces treated with all other products and the control. Similar numbers of eggs were laid on surfaces treated with all B. bassiana products, but egg production was half of the control. Stable flies, Stomoxys calcitrans (L.), laid the fewest eggs on Met52 EC- and Mycotrol O-treated surfaces. This species did not distinguish between the remaining products and the control. In a second experiment, house fly eggs were placed on treated cloths so that hatched larvae contacted the treatment prior to development. Met52 EC had the greatest effect on immature survival with a significant reduction in recovered pupae at the medium and high doses of fungi. Overall, Met52 EC, containing M. brunneum, had the greatest effect on house fly and stable fly oviposition deterrence and immature development of house flies. Management implications are discussed. PMID:27302955

  4. Destructuring plant biomass: Focus on fungal and extremophilic cell wall hydrolases

    PubMed Central

    Guerriero, Gea; Hausman, Jean-Francois; Strauss, Joseph; Ertan, Haluk; Siddiqui, Khawar Sohail

    2016-01-01

    The use of plant biomass as feedstock for biomaterial and biofuel production is relevant in the current bio-based economy scenario of valorizing renewable resources. Fungi, which degrade complex and recalcitrant plant polymers, secrete different enzymes that hydrolyze plant cell wall polysaccharides. The present review discusses the current research trends on fungal, as well as extremophilic cell wall hydrolases that can withstand extreme physico-chemical conditions required in efficient industrial processes. Secretomes of fungi from the phyla Ascomycota, Basidiomycota, Zygomycota and Neocalli-mastigomycota are presented along with metabolic cues (nutrient sensing, coordination of carbon and nitrogen metabolism) affecting their composition. We conclude the review by suggesting further research avenues focused on the one hand on a comprehensive analysis of the physiology and epigenetics underlying cell wall degrading enzyme production in fungi and on the other hand on the analysis of proteins with unknown function and metagenomics of extremophilic consortia. The current advances in consolidated bioprocessing, altered secretory pathways and creation of designer plants are also examined. Furthermore, recent developments in enhancing the activity, stability and reusability of enzymes based on synergistic, proximity and entropic effects, fusion enzymes, structure-guided recombination between homologous enzymes and magnetic enzymes are considered with a view to improving saccharification. PMID:25804821

  5. Multigene phylogenies and morphological characterization of five new Ophiostoma spp. associated with spruce-infesting bark beetles in China.

    PubMed

    Yin, Mingliang; Wingfield, Michael J; Zhou, Xudong; de Beer, Z Wilhelm

    2016-04-01

    Ophiostoma spp. (Ophiostomatales, Ascomycota) are well-known fungi associated with bark beetles (Coleoptera: Scolytinae). Some of these are serious tree pathogens, while the majority is blue-stain agents of timber. In recent years, various bark beetle species have been attacking spruce forests in Qinghai province, China, causing significant damage. A preliminary survey was done to explore the diversity of the ophiostomatoid fungal associates of these beetles. The aims of the present study were to identify and characterize new Ophiostoma spp. associated with spruce-infesting bark beetles in Qinghai Province, and to resolve phylogenetic relationships of Ophiostoma spp. related to the Chinese isolates, using multigene phylogenetic analyses. Results obtained from four gene regions (ribosomal internal transcribed spacer regions, β-tubulin, calmodulin, translation elongation factor-1α) revealed five new Ophiostoma spp. from Qinghai. These included O. nitidus sp. nov., O. micans sp. nov., and O. qinghaiense sp. nov. in a newly defined O. piceae complex. The other two new species, O. poligraphi sp. nov. and O. shangrilae sp. nov., grouped in the O. brunneo-ciliatum complex. Based on DNA sequence and morphological comparisons, we also show that O. arduennense and O. torulosum are synonyms of O. distortum, while O. setosum is a synonym of O. cupulatum. PMID:27020148

  6. Safeguarding saproxylic fungal biodiversity in Apennine beech forest priority habitats

    NASA Astrophysics Data System (ADS)

    Maggi, Oriana; Lunghini, Dario; Pecoraro, Lorenzo; Sabatini, Francesco Maria; Persiani, Anna Maria

    2015-04-01

    The FAGUS LIFE Project (LIFE11/NAT/IT/135) targets two European priority habitats, i.e. Habitat 9210* Apennine beech forests with Taxus and Ilex, and Habitat 9220* Apennine beech forests with Abies alba, within two National Parks: Cilento, Vallo di Diano and Alburni; Gran Sasso and Monti della Laga. The current limited distribution of the target habitats is also due to the impact of human activities on forest systems, such as harvesting and grazing. The FAGUS project aims at developing and testing management strategies able to integrate the conservation of priority forest habitats (9210* and 9220*) and the sustainable use of forest resources. In order to assess the responses to different management treatments the BACI monitoring design (Before-After, Control-Intervention) has been applied on forest structure and diversity of focus taxa before and after experimental harvesting treatments. Conventional management of Apennine beech forests impacts a wealth of taxonomic groups, such as saproxylic beetles and fungi, which are threatened throughout Europe by the lack of deadwood and of senescing trees, and by the homogeneous structure of managed forests. Deadwood has been denoted as the most important manageable habitat for biodiversity in forests not only for supporting a wide diversity of organisms, but also for playing a prominent role in several ecological processes, creating the basis for the cycling of photosynthetic energy, carbon, and nutrients stored in woody material. Especially fungi can be regarded as key group for understanding and managing biodiversity associated with decaying wood. The before-intervention field sampling was carried out in Autumn 2013 in 33 monitoring plots across the two national Parks. The occurrence at plot level of both Ascomycota and Basidiomycota sporocarps was surveyed. All standing and downed deadwood with a minimum diameter of 10 cm was sampled for sporocarps larger than 1 mm, and information on decay class and fungal morphogroups

  7. Δ12-Fatty acid desaturase from Candida parapsilosis is a multifunctional desaturase producing a range of polyunsaturated and hydroxylated fatty acids.

    PubMed

    Buček, Aleš; Matoušková, Petra; Sychrová, Hana; Pichová, Iva; Hrušková-Heidingsfeldová, Olga

    2014-01-01

    Numerous Δ12-, Δ15- 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 Δ12/Δ15- and Δ15-FADs named CpFad2 and CpFad3, respectively, from the opportunistic pathogenic yeast Candida parapsilosis. Overexpression of CpFad3 in Saccharomyces cerevisiae strains supplemented with linoleic acid (Δ9,Δ12-18:2) and hexadecadienoic acid (Δ9,Δ12-16:2) leads to accumulation of Δ15-PUFAs, i.e., α-linolenic acid (Δ9,Δ12,Δ15-18:3) and hexadecatrienoic acid with an unusual terminal double bond (Δ9,Δ12,Δ15-16:3). CpFad2 produces a range of Δ12- and Δ15-PUFAs. The major products of CpFad2 are linoleic and hexadecadienoic acid (Δ9,Δ12-16:2), accompanied by α-linolenic acid and hexadecatrienoic acid (Δ9,Δ12,Δ15-16:3). 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 Δ12-FADs from budding yeasts (Ascomycota: Saccharomycotina). PMID:24681902

  8. Diversity and Composition of Airborne Fungal Community Associated with Particulate Matters in Beijing during Haze and Non-haze Days

    PubMed Central

    Yan, Dong; Zhang, Tao; Su, Jing; Zhao, Li-Li; Wang, Hao; Fang, Xiao-Mei; Zhang, Yu-Qin; Liu, Hong-Yu; Yu, Li-Yan

    2016-01-01

    To assess the diversity and composition of airborne fungi associated with particulate matters (PMs) in Beijing, China, a total of 81 PM samples were collected, which were derived from PM2.5, PM10 fractions, and total suspended particles during haze and non-haze days. The airborne fungal community in these samples was analyzed using the Illumina Miseq platform with fungi-specific primers targeting the internal transcribed spacer 1 region of the large subunit rRNA gene. A total of 797,040 reads belonging to 1633 operational taxonomic units were observed. Of these, 1102 belonged to Ascomycota, 502 to Basidiomycota, 24 to Zygomycota, and 5 to Chytridiomycota. The dominant orders were Pleosporales (29.39%), Capnodiales (27.96%), Eurotiales (10.64%), and Hypocreales (9.01%). The dominant genera were Cladosporium, Alternaria, Fusarium, Penicillium, Sporisorium, and Aspergilus. Analysis of similarities revealed that both particulate matter sizes (R = 0.175, p = 0.001) and air quality levels (R = 0.076, p = 0.006) significantly affected the airborne fungal community composition. The relative abundance of many fungal genera was found to significantly differ among various PM types and air quality levels. Alternaria and Epicoccum were more abundant in total suspended particles samples, Aspergillus in heavy-haze days and PM2.5 samples, and Malassezia in PM2.5 samples and heavy-haze days. Canonical correspondence analysis and permutation tests showed that temperature (p < 0.01), NO2 (p < 0.01), PM10 (p < 0.01), SO2(p < 0.01), CO (p < 0.01), and relative humidity (p < 0.05) were significant factors that determine airborne fungal community composition. The results suggest that diverse airborne fungal communities are associated with particulate matters and may provide reliable data for studying the responses of human body to the increasing level of air pollution in Beijing. PMID:27148180

  9. Revisiting phylogenetic diversity and cryptic species of Cenococcum geophilum sensu lato.

    PubMed

    Obase, Keisuke; Douhan, Greg W; Matsuda, Yosuke; Smith, Matthew E

    2016-08-01

    The fungus Cenococcum geophilum Fr. (Dothideomycetes, Ascomycota) is one of the most common ectomycorrhizal fungi in boreal to temperate regions. A series of molecular studies has demonstrated that C. geophilum is monophyletic but a heterogeneous species or a species complex. Here, we revisit the phylogenetic diversity of C. geophilum sensu lato from a regional to intercontinental scale by using new data from Florida (USA) along with existing data in GenBank from Japan, Europe, and North America. The combination of internal transcribed spacer (ITS) ribosomal DNA and the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene resolved six well-supported lineages (87-100 % bootstrap values) that are closely related to each other and a seventh lineage that is phylogenetically distinct. A multi-locus analysis (small subunit (SSU), large subunit (LSU), translational elongation factor (TEF), and the largest and second-largest subunits of RNA polymerase II (RPB1 and RPB2)) revealed that the divergent lineage is the sister group to all other known Cenococcum isolates. Isolates of the divergent lineage grow fast on nutrient media and do not form ectomycorrhizas on seedlings of several pine and oak species. Our results indicate that C. geophilum sensu lato includes more phylogenetically distinct cryptic species than have previously been reported. Furthermore, the divergent lineage appears to be a non-mycorrhizal sister group. We discuss the phylogenetic diversity of C. geophilum sensu lato and argue in favor of species recognition based on phylogenetic and ecological information in addition to morphological characteristics. A new genus and species (Pseudocenococcum floridanum gen. et sp. nov.) is proposed to accommodate a divergent and putatively non-mycorrhizal lineage. PMID:26968743

  10. Changes in Bacterial and Fungal Communities across Compost Recipes, Preparation Methods, and Composting Times

    PubMed Central

    Neher, Deborah A.; Weicht, Thomas R.; Bates, Scott T.; Leff, Jonathan W.; Fierer, Noah

    2013-01-01

    Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and fungal communities in compost produced at a commercial-scale. Bacterial and fungal communities responded to both compost recipe and composting method. Specifically, bacterial communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and fungal communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed by Ascomycota and finally Basidiomycota. Zygomycota were associated more with manure-silage and hay than hardwood composts. Most commercial composters focus on the thermophilic phase as an economic means to insure sanitation of compost from pathogens. However, the community succeeding the thermophilic phase begs further investigation to determine how the microbial dynamics observed here can be best managed

  11. Phylogenetic analyses of eurotiomycetous endophytes reveal their close affinities to Chaetothyriales, Eurotiales, and a new order - Phaeomoniellales.

    PubMed

    Chen, Ko-Hsuan; Miadlikowska, Jolanta; Molnár, Katalin; Arnold, A Elizabeth; U'Ren, Jana M; Gaya, Ester; Gueidan, Cécile; Lutzoni, François

    2015-04-01

    Symbiotic fungi living in plants as endophytes, and in lichens as endolichenic fungi, cause no apparent symptoms to their hosts. They are ubiquitous, ecologically important, hyperdiverse, and represent a rich source of secondary compounds for new pharmaceutical and biocontrol products. Due in part to the lack of visible reproductive structures and other distinctive phenotypic traits for many species, the diversity and phylogenetic affiliations of these cryptic fungi are often poorly known. The goal of this study was to determine the phylogenetic placement of representative endophytes within the Eurotiomycetes (Pezizomycotina, Ascomycota), one of the most diverse and evolutionarily dynamic fungal classes, and to use that information to infer processes of macroevolution in trophic modes. Sequences of a single locus marker spanning the nuclear ribosomal internal transcribed spacer region (nrITS) and 600 base pairs at the 5' end of the nuclear ribosomal large subunit (nrLSU) were obtained from previous studies of >6000 endophytic and endolichenic fungi from diverse biogeographic locations and hosts. We conducted phylum-wide phylogenetic searches using this marker to determine which fungal strains belonged to Eurotiomycetes and the results were used as the basis for a class-wide, seven-locus phylogenetic study focusing on endophytic and endolichenic Eurotiomycetes. Our cumulative supermatrix-based analyses revealed that representative endophytes within Eurotiomycetes are distributed in three main clades: Eurotiales, Chaetothyriales and Phaeomoniellales ord. nov., a clade that had not yet been described formally. This new order, described herein, is sister to the clade including Verrucariales and Chaetothyriales. It appears to consist mainly of endophytes and plant pathogens. Morphological characters of endophytic Phaeomoniellales resemble those of the pathogenic genus Phaeomoniella. This study highlights the capacity of endophytic and endolichenic fungi to expand our

  12. Deacetylation of Fungal Exopolysaccharide Mediates Adhesion and Biofilm Formation

    PubMed Central

    Lee, Mark J.; Geller, Alexander M.; Bamford, Natalie C.; Liu, Hong; Gravelat, Fabrice N.; Snarr, Brendan D.; Le Mauff, François; Chabot, Joseé; Ralph, Benjamin; Ostapska, Hanna; Lehoux, Mélanie; Cerone, Robert P.; Baptista, Stephanie D.; Vinogradov, Evgeny; Filler, Scott G.; Howell, P. Lynne

    2016-01-01

    ABSTRACT The mold Aspergillus fumigatus causes invasive infection in immunocompromised patients. Recently, galactosaminogalactan (GAG), an exopolysaccharide composed of galactose and N-acetylgalactosamine (GalNAc), was identified as a virulence factor required for biofilm formation. The molecular mechanisms underlying GAG biosynthesis and GAG-mediated biofilm formation were unknown. We identified a cluster of five coregulated genes that were dysregulated in GAG-deficient mutants and whose gene products share functional similarity with proteins that mediate the synthesis of the bacterial biofilm exopolysaccharide poly-(β1-6)-N-acetyl-d-glucosamine (PNAG). Bioinformatic analyses suggested that the GAG cluster gene agd3 encodes a protein containing a deacetylase domain. Because deacetylation of N-acetylglucosamine residues is critical for the function of PNAG, we investigated the role of GAG deacetylation in fungal biofilm formation. Agd3 was found to mediate deacetylation of GalNAc residues within GAG and render the polysaccharide polycationic. As with PNAG, deacetylation is required for the adherence of GAG to hyphae and for biofilm formation. Growth of the Δagd3 mutant in the presence of culture supernatants of the GAG-deficient Δuge3 mutant rescued the biofilm defect of the Δagd3 mutant and restored the adhesive properties of GAG, suggesting that deacetylation is an extracellular process. The GAG biosynthetic gene cluster is present in the genomes of members of the Pezizomycotina subphylum of the Ascomycota including a number of plant-pathogenic fungi and a single basidiomycete species, Trichosporon asahii, likely a result of recent horizontal gene transfer. The current study demonstrates that the production of cationic, deacetylated exopolysaccharides is a strategy used by both fungi and bacteria for biofilm formation. PMID:27048799

  13. Arbuscular Mycorrhizal Fungal Communities in the Roots of Maize Lines Contrasting for Al Tolerance Grown in Limed and Non-Limed Brazilian Oxisoil.

    PubMed

    Gomes, Eliane A; Oliveira, Christiane A; Lana, Ubiraci G P; Noda, Roberto W; Marriel, Ivanildo E; de Souza, Francisco A

    2015-07-01

    Aluminum (Al) toxicity is one of the greatest limitations to agriculture in acid soils, particularly in tropical regions. Arbuscular mycorrhizal fungi (AMF) can supply plants with nutrients and give protection against Al toxicity. The aim of this work was to evaluate the effects of soil liming (i.e., reducing Al saturation) on the AMF community composition and structure in the roots of maize lines contrasting for Al tolerance. To this end, we constructed four 18S rDNA cloning libraries from L3 (Al tolerant) and L22 (Al sensitive) maize lines grown in limed and non-limed soils. A total of 790 clones were sequenced, 69% belonging to the Glomeromycota phylum. The remaining sequences were from Ascomycota, which were more prominent in the limed soil, mainly in the L3 line. The most abundant AM fungal clones were related to the family Glomeraceae represented by the genera uncultured Glomus followed by Rhizophagus and Funneliformis. However, the most abundant operational taxonomic units with 27% of the Glomeromycota clones was affiliated to genus Racocetra. This genus was present in all the four libraries, but it was predominant in the non-limed soils, suggesting that Racocetra is tolerant to Al toxicity. Similarly, Acaulospora and Rhizophagus were also present mostly in both lines in non-limed soils. The community richness of AMF in the non-limed soils was higher than the limed soil for both lines. The results suggest that the soil Al saturation was the parameter that mostly influences the AMF species composition in the soils in this study. PMID:25674805

  14. Fungal communities respond to long-term CO2 elevation by community reassembly.

    PubMed

    Tu, Qichao; Yuan, Mengting; He, Zhili; Deng, Ye; Xue, Kai; Wu, Liyou; Hobbie, Sarah E; Reich, Peter B; Zhou, Jizhong

    2015-04-01

    Fungal communities play a major role as decomposers in the Earth's ecosystems. Their community-level responses to elevated CO2 (eCO2), one of the major global change factors impacting ecosystems, are not well understood. Using 28S rRNA gene amplicon sequencing and co-occurrence ecological network approaches, we analyzed the response of soil fungal communities in the BioCON (biodiversity, CO2, and N deposition) experimental site in Minnesota, USA, in which a grassland ecosystem has been exposed to eCO2 for 12 years. Long-term eCO2 did not significantly change the overall fungal community structure and species richness, but significantly increased community evenness and diversity. The relative abundances of 119 operational taxonomic units (OTU; ∼27% of the total captured sequences) were changed significantly. Significantly changed OTU under eCO2 were associated with decreased overall relative abundance of Ascomycota, but increased relative abundance of Basidiomycota. Co-occurrence ecological network analysis indicated that eCO2 increased fungal community network complexity, as evidenced by higher intermodular and intramodular connectivity and shorter geodesic distance. In contrast, decreased connections for dominant fungal species were observed in the eCO2 network. Community reassembly of unrelated fungal species into highly connected dense modules was observed. Such changes in the co-occurrence network topology were significantly associated with altered soil and plant properties under eCO2, especially with increased plant biomass and NH4 (+) availability. This study provided novel insights into how eCO2 shapes soil fungal communities in grassland ecosystems. PMID:25616796

  15. Ice nucleation activity in the widespread soil fungus Mortierella alpina

    NASA Astrophysics Data System (ADS)

    Fröhlich-Nowoisky, J.; Hill, T. C. J.; Pummer, B. G.; Yordanova, P.; Franc, G. D.; Pöschl, U.

    2015-02-01

    Biological residues in soil dust are a potentially strong source of atmospheric ice nuclei (IN). So far, however, the abundance, diversity, sources, seasonality, and role of biological - in particular, fungal - IN in soil dust have not been characterized. By analysis of the culturable fungi in topsoils, from a range of different land use and ecosystem types in southeast Wyoming, we found ice-nucleation-active (INA) fungi to be both widespread and abundant, particularly in soils with recent inputs of decomposable organic matter. Across all investigated soils, 8% of fungal isolates were INA. All INA isolates initiated freezing at -5 to -6 °C, and belonged to a single zygomycotic species, Mortierella alpina (Mortierellales, Mortierellomycotina). To our knowledge this is the first report of ice nucleation activity in a zygomycotic fungi because the few known INA fungi all belong to the phyla Ascomycota and Basidiomycota. M. alpina is known to be saprobic and widespread in soil, and Mortierella spores are present in air and rain. Sequencing of the ITS region and the gene for γ-linolenic elongase revealed four distinct clades, affiliated to different soil types. The IN produced by M. alpina seem to be proteinaceous, < 300 kDa in size, and can be easily washed off the mycelium. Ice nucleating fungal mycelium will ramify topsoils and probably also release cell-free IN into it. If these IN survive decomposition or are adsorbed onto mineral surfaces, their contribution might accumulate over time, perhaps to be transported with soil dust and influencing its ice nucleating properties.

  16. Chitin Mixed in Potting Soil Alters Lettuce Growth, the Survival of Zoonotic Bacteria on the Leaves and Associated Rhizosphere Microbiology

    PubMed Central

    Debode, Jane; De Tender, Caroline; Soltaninejad, Saman; Van Malderghem, Cinzia; Haegeman, Annelies; Van der Linden, Inge; Cottyn, Bart; Heyndrickx, Marc; Maes, Martine

    2016-01-01

    Chitin is a promising soil amendment for improving soil quality, plant growth, and plant resilience. The objectives of this study were twofold. First, to study the effect of chitin mixed in potting soil on lettuce growth and on the survival of two zoonotic bacterial pathogens, Escherichia coli O157:H7 and Salmonella enterica on the lettuce leaves. Second, to assess the related changes in the microbial lettuce rhizosphere, using phospholipid fatty acid (PLFA) analysis and amplicon sequencing of a bacterial 16S rRNA gene fragment and the fungal ITS2. As a result of chitin addition, lettuce fresh yield weight was significantly increased. S. enterica survival in the lettuce phyllosphere was significantly reduced. The E. coli O157:H7 survival was also lowered, but not significantly. Moreover, significant changes were observed in the bacterial and fungal community of the lettuce rhizosphere. PLFA analysis showed a significant increase in fungal and bacterial biomass. Amplicon sequencing showed no increase in fungal and bacterial biodiversity, but relative abundances of the bacterial phyla Acidobacteria, Verrucomicrobia, Actinobacteria, Bacteroidetes, and Proteobacteria and the fungal phyla Ascomycota, Basidiomycota, and Zygomycota were significantly changed. More specifically, a more than 10-fold increase was observed for operational taxonomic units belonging to the bacterial genera Cellvibrio, Pedobacter, Dyadobacter, and Streptomyces and to the fungal genera Lecanicillium and Mortierella. These genera include several species previously reported to be involved in biocontrol, plant growth promotion, the nitrogen cycle and chitin degradation. These results enhance the understanding of the response of the rhizosphere microbiome to chitin amendment. Moreover, this is the first study to investigate the use of soil amendments to control the survival of S. enterica on plant leaves. PMID:27148242

  17. Biological low pH Mn(II) oxidation in a manganese deposit influenced by metal-rich groundwater

    USGS Publications Warehouse

    Bohu, Tsing; Akob, Denise M.; Abratis, Michael; Lazar, Cassandre S.; Küsel, Kirsten

    2016-01-01

    The mechanisms, key organisms, and geochemical significance of biological low-pH Mn(II) oxidation are largely unexplored. Here, we investigated the structure of indigenous Mn(II)-oxidizing microbial communities in a secondary subsurface Mn oxide deposit influenced by acidic (pH 4.8) metal-rich groundwater in a former uranium mining area. Microbial diversity was highest in the Mn deposit compared to the adjacent soil layers and included the majority of known Mn(II)-oxidizing bacteria (MOB) and two genera of known Mn(II)-oxidizing fungi (MOF). Electron X-ray microanalysis showed that romanechite [(Ba,H2O)2(Mn4+,Mn3+)5O10] was conspicuously enriched in the deposit. Canonical correspondence analysis revealed that certain fungal, bacterial, and archaeal groups were firmly associated with the autochthonous Mn oxides. Eight MOB within the Proteobacteria, Actinobacteria, and Bacteroidetes and one MOF strain belonging to Ascomycota were isolated at pH 5.5 or 7.2 from the acidic Mn deposit. Soil-groundwater microcosms demonstrated 2.5-fold-faster Mn(II) depletion in the Mn deposit than adjacent soil layers. No depletion was observed in the abiotic controls, suggesting that biological contribution is the main driver for Mn(II) oxidation at low pH. The composition and species specificity of the native low-pH Mn(II) oxidizers were highly adapted to in situ conditions, and these organisms may play a central role in the fundamental biogeochemical processes (e.g., metal natural attenuation) occurring in the acidic, oligotrophic, and metalliferous subsoil ecosystems.

  18. Species-specific ITS primers for the identification of Picoa juniperi and Picoa lefebvrei and using nested-PCR for detection of P. juniperi in planta.

    PubMed

    Jamali, Samad; Banihashemi, Zia

    2013-10-01

    Desert truffles, hypogeous Pezizales (Ascomycota), are difficult to identify due to evolutionary convergence of morphological characters among taxa that share a similar habitat and mode of spore dispersal. Also, during their symbiotic phase, these are barely distinguishable morphologically, and molecular probes are needed for their identification. We have developed a PCR-based method for the identification of Picoa juniperi and Picoa lefebvrei based on internal transcribed spacers of rDNA. Two PCR primers specific for P. lefebvrei (FLE/RLE) and two specific for P. juniperi (FJU/RJU) were designed. A collection of samples from different geographical areas representing diversity of these species were examined for unique regions of internal transcribed spacers 1, 2 and 5.8S gene of rDNA (ITS) compared to other closely related species. Annealing temperatures and extension times were optimized for each set of primers for maximum specificity and efficiency. They proved to be efficient to specifically detect the presence of P. juniperi and P. lefebvrei by PCR and neither set amplified purified DNA from other truffle species as well as some ascomycetous fungi. The partial small subunit of ribosomal DNA genes of P. juniperi were amplified with the genomic DNA extracted from Helianthemum ledifolium var. ledifolium roots by nested polymerase chain reaction (PCR) using the universal fungal primer pair ITS1/ITS4 and specific primer pair FTC/RTC, which was designed based on internal transcribed spacer 1, 2 and 5.8S gene of rDNA sequences of P juniperi. The nested-PCR was sensitive enough to re-amplify the direct-PCR product, resulting in a DNA fragment of 426 bp. The efficacy of nested-PCR showed that it could re-amplify the direct-PCR product and detect 200 fg genomic DNA. PMID:24065525

  19. Evolutionary Dynamics of hAT DNA Transposon Families in Saccharomycetaceae

    PubMed Central

    Sarilar, Véronique; Bleykasten-Grosshans, Claudine; Neuvéglise, Cécile

    2015-01-01

    Transposable elements (TEs) are widespread in eukaryotes but uncommon in yeasts of the Saccharomycotina subphylum, in terms of both host species and genome fraction. The class II elements are especially scarce, but the hAT element Rover is a noteworthy exception that deserves further investigation. Here, we conducted a genome-wide analysis of hAT elements in 40 ascomycota. A novel family, Roamer, was found in three species, whereas Rover was detected in 15 preduplicated species from Kluyveromyces, Eremothecium, and Lachancea genera, with up to 41 copies per genome. Rover acquisition seems to have occurred by horizontal transfer in a common ancestor of these genera. The detection of remote Rover copies in Naumovozyma dairenensis and in the sole Saccharomyces cerevisiae strain AWRI1631, without synteny, suggests that two additional independent horizontal transfers took place toward these genomes. Such patchy distribution of elements prevents any anticipation of TE presence in incoming sequenced genomes, even closely related ones. The presence of both putative autonomous and defective Rover copies, as well as their diversification into five families, indicate particular dynamics of Rover elements in the Lachancea genus. Especially, we discovered the first miniature inverted-repeat transposable elements (MITEs) to be described in yeasts, together with their parental autonomous copies. Evidence of MITE insertion polymorphism among Lachancea waltii strains suggests their recent activity. Moreover, 40% of Rover copies appeared to be involved in chromosome rearrangements, showing the large structural impact of TEs on yeast genome and opening the door to further investigations to understand their functional and evolutionary consequences. PMID:25532815

  20. Diversity and Antimicrobial Activity of Culturable Endophytic Fungi Isolated from Moso Bamboo Seeds

    PubMed Central

    Cai, Chun-Ju; Fan, Li; Gao, Jian; Hou, Cheng-Lin

    2014-01-01

    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

  1. Effects of Bromelia pinguin (Bromeliaceae) on soil ecosystem function and fungal diversity in the lowland forests of Costa Rica

    PubMed Central

    2014-01-01

    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. PMID:24885984

  2. Fungal community on decomposing leaf litter undergoes rapid successional changes

    PubMed Central

    Voříšková, Jana; Baldrian, Petr

    2013-01-01

    Fungi are considered the primary decomposers of dead plant biomass in terrestrial ecosystems. However, current knowledge regarding the successive changes in fungal communities during litter decomposition is limited. Here we explored the development of the fungal community over 24 months of litter decomposition in a temperate forest with dominant Quercus petraea using 454-pyrosequencing of the fungal internal transcribed spacer (ITS) region and cellobiohydrolase I (cbhI) genes, which encode exocellulases, to specifically address cellulose decomposers. To quantify the involvement of phyllosphere fungi in litter decomposition, the fungal communities in live leaves and leaves immediately before abscission were also analysed. The results showed rapid succession of fungi with dramatic changes in the composition of the fungal community. Furthermore, most of the abundant taxa only temporarily dominated in the substrate. Fungal diversity was lowest at leaf senescence, increased until month 4 and did not significantly change during subsequent decomposition. Highly diverse community of phyllosphere fungi inhabits live oak leaves 2 months before abscission, and these phyllosphere taxa comprise a significant share of the fungal community during early decomposition up to the fourth month. Sequences assigned to the Ascomycota showed highest relative abundances in live leaves and during the early stages of decomposition. In contrast, the relative abundance of sequences assigned to the Basidiomycota phylum, particularly basidiomycetous yeasts, increased with time. Although cellulose was available in the litter during all stages of decomposition, the community of cellulolytic fungi changed substantially over time. The results indicate that litter decomposition is a highly complex process mediated by various fungal taxa. PMID:23051693

  3. Germination and seedling establishment in orchids: a complex of requirements

    PubMed Central

    Rasmussen, Hanne N.; Dixon, Kingsley W.; Jersáková, Jana; Těšitelová, Tamara

    2015-01-01

    Background Seedling recruitment is essential to the sustainability of any plant population. Due to the minute nature of seeds and early-stage seedlings, orchid germination in situ was for a long time practically impossible to observe, creating an obstacle towards understanding seedling site requirements and fluctuations in orchid populations. The introduction of seed packet techniques for sowing and retrieval in natural sites has brought with it important insights, but many aspects of orchid seed and germination biology remain largely unexplored. Key Considerations The germination niche for orchids is extremely complex, because it is defined by requirements not only for seed lodging and germination, but also for presence of a fungal host and its substrate. A mycobiont that the seedling can parasitize is considered an essential element, and a great diversity of Basidiomycota and Ascomycota have now been identified for their role in orchid seed germination, with fungi identifiable as imperfect Rhizoctonia species predominating. Specificity patterns vary from orchid species employing a single fungal lineage to species associating individually with a limited selection of distantly related fungi. A suitable organic carbon source for the mycobiont constitutes another key requirement. Orchid germination also relies on factors that generally influence the success of plant seeds, both abiotic, such as light/shade, moisture, substrate chemistry and texture, and biotic, such as competitors and antagonists. Complexity is furthermore increased when these factors influence seeds/seedling, fungi and fungal substrate differentially. Conclusions A better understanding of germination and seedling establishment is needed for conservation of orchid populations. Due to the obligate association with a mycobiont, the germination niches in orchid species are extremely complex and varied. Microsites suitable for germination can be small and transient, and direct observation is difficult

  4. Changes in the soil microbial community after reductive soil disinfestation and cucumber seedling cultivation.

    PubMed

    Huang, Xinqi; Liu, Liangliang; Wen, Teng; Zhang, Jinbo; Wang, Fenghe; Cai, Zucong

    2016-06-01

    Reductive soil disinfestation (RSD) has been proven to be an effective and environmentally friendly way to control many soilborne pathogens and diseases. In this study, the RSDs using ethanol (Et-RSD) and alfalfa (Al-RSD) as organic carbons were performed in a Rhizoctonia solani-infected soil, and the dissimilarities of microbial communities during the RSDs and after planting two seasons of cucumber seedlings in the RSDs-treated soil were respectively investigated by MiSeq pyrosequencing. The results showed that, as for bacteria, Coprococcus, Flavisolibacter, Rhodanobacter, Symbiobacterium, and UC-Ruminococcaceae became the dominant bacterial genera at the end of Al-RSD. In contrast, Et-RSD soil involved more bacteria belonging to Firmicutes, such as Sedimentibacter, UC-Gracilibacteraceae, and Desulfosporosinus. For fungi, Chaetomium significantly increased at the end of RSDs, while Rhizoctonia and Aspergillus significantly decreased. After planting two seasons of cucumber seedlings, those bacteria belonging to Firmicutes significantly decreased, but Lysobacter and Rhodanobacter belonging to the phylum Proteobacteria as well as UC-Sordariales and Humicola belonging to Ascomycota alternatively increased in Al- and Et-RSD-treated soils. Besides, some nitrification, denitrification, and nitrogen fixation genes were apparently increased in the RSD-treated soils, but the effect was more profound in Al-RSD than Et-RSD. Overall, Et-RSD could induced more antagonists belonging to Firmicutes under anaerobic condition, whereas Al-RSD could continuously stimulate some functional microorganisms (Lysobacter and Rhodanobacter) and further improve nitrogen transformation activities in the soil at the coming cropping season. PMID:26875875

  5. The effects of high-tannin leaf litter from transgenic poplars on microbial communities in microcosm soils

    PubMed Central

    Winder, Richard S.; Lamarche, Josyanne; Constabel, C. Peter; Hamelin, Richard C.

    2013-01-01

    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 α-Proteobacteria significantly increased. β-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 β-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

  6. Characterization of chlordecone-tolerant fungal populations isolated from long-term polluted tropical volcanic soil in the French West Indies.

    PubMed

    Merlin, Chloé; Devers, Marion; Crouzet, Olivier; Heraud, Cécile; Steinberg, Christian; Mougin, Christian; Martin-Laurent, Fabrice

    2014-04-01

    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

  7. De Novo Transcriptome Assembly in Shiraia bambusicola to Investigate Putative Genes Involved in the Biosynthesis of Hypocrellin A

    PubMed Central

    Zhao, Ning; Lin, Xi; Qi, Shan-Shan; Luo, Zhi-Mei; Chen, Shuang-Lin; Yan, Shu-Zhen

    2016-01-01

    Shiraia bambusicola is a species of the monotypic genus Shiraia in the phylum Ascomycota. In China, it is known for its pharmacological properties that are used to treat rheumatic arthritis, sciatica, pertussis, tracheitis and so forth. Its major medicinal active metabolite is hypocrellin A, which exhibits excellent antiviral and antitumor properties. However, the genes involved in the hypocrellin A anabolic pathways were still unknown due to the lack of genomic information for this species. To investigate putative genes that are involved in the biosynthesis of hypocrellin A and determine the pathway, we performed transcriptome sequencing for Shiraia bambusicola S4201-W and the mutant S4201-D1 for the first time. S4201-W has excellent hypocrellin A production, while the mutant S4201-D1 does not. Then, we obtained 38,056,034 and 39,086,896 clean reads from S4201-W and S4201-D1, respectively. In all, 17,923 unigenes were de novo assembled, and the N50 length was 1970 bp. Based on the negative binomial distribution test, 716 unigenes were found to be upregulated, and 188 genes were downregulated in S4201-D1, compared with S4201-W. We have found seven unigenes involved in the biosynthesis of hypocrellin A and proposed a putative hypocrellin A biosynthetic pathway. These data will provide a valuable resource and theoretical basis for future molecular studies of hypocrellin A, help identify the genes involved in the biosynthesis of hypocrellin A and help facilitate functional studies for enhancing hypocrellin A production. PMID:26927096

  8. Prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment

    PubMed Central

    Kolb, Steffen; Stacheter, Astrid

    2013-01-01

    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

  9. Multi-year assessment of coastal planktonic fungi reveals environmental drivers of diversity and abundance.

    PubMed

    Taylor, Joe D; Cunliffe, Michael

    2016-09-01

    Mycoplankton have so far been a neglected component of pelagic marine ecosystems, having been poorly studied relative to other plankton groups. Currently, there is a lack of understanding of how mycoplankton diversity changes through time, and the identity of controlling environmental drivers. Using Fungi-specific high-throughput sequencing and quantitative PCR analysis of plankton DNA samples collected over 6 years from the coastal biodiversity time series site Station L4 situated off Plymouth (UK), we have assessed changes in the temporal variability of mycoplankton diversity and abundance in relation to co-occurring environmental variables. Mycoplankton diversity at Station L4 was dominated by Ascomycota, Basidiomycota and Chytridiomycota, with several orders within these phyla frequently abundant and dominant in multiple years. Repeating interannual mycoplankton blooms were linked to potential controlling environmental drivers, including nitrogen availability and temperature. Specific relationships between mycoplankton and other plankton groups were also identified, with seasonal chytrid blooms matching diatom blooms in consecutive years. Mycoplankton α-diversity was greatest during periods of reduced salinity at Station L4, indicative of riverine input to the ecosystem. Mycoplankton abundance also increased during periods of reduced salinity, and when potential substrate availability was increased, including particulate organic matter. This study has identified possible controlling environmental drivers of mycoplankton diversity and abundance in a coastal sea ecosystem, and therefore sheds new light on the biology and ecology of an enigmatic marine plankton group. Mycoplankton have several potential functional roles, including saprotrophs and parasites, that should now be considered within the consensus view of pelagic ecosystem functioning and services. PMID:26943623

  10. Molecular characterization of a heterothallic mating system in Pseudogymnoascus destructans, the Fungus causing white-nose syndrome of bats.

    PubMed

    Palmer, Jonathan M; Kubatova, Alena; Novakova, Alena; Minnis, Andrew M; Kolarik, Miroslav; Lindner, Daniel L

    2014-09-01

    White-nose syndrome (WNS) of bats has devastated bat populations in eastern North America since its discovery in 2006. WNS, caused by the fungus Pseudogymnoascus destructans, has spread quickly in North America and has become one of the most severe wildlife epidemics of our time. While P. destructans is spreading rapidly in North America, nothing is known about the sexual capacity of this fungus. To gain insight into the genes involved in sexual reproduction, we characterized the mating-type locus (MAT) of two Pseudogymnoascus spp. that are closely related to P. destructans and homothallic (self-fertile). As with other homothallic Ascomycota, the MAT locus of these two species encodes a conserved α-box protein (MAT1-1-1) as well as two high-mobility group (HMG) box proteins (MAT1-1-3 and MAT1-2-1). Comparisons with the MAT locus of the North American isolate of P. destructans (the ex-type isolate) revealed that this isolate of P. destructans was missing a clear homolog of the conserved HMG box protein (MAT1-2-1). These data prompted the discovery and molecular characterization of a heterothallic mating system in isolates of P. destructans from the Czech Republic. Both mating types of P. destructans were found to coexist within hibernacula, suggesting the presence of mating populations in Europe. Although populations of P. destructans in North America are thought to be clonal and of one mating type, the potential for sexual recombination indicates that continued vigilance is needed regarding introductions of additional isolates of this pathogen. PMID:25053709

  11. Phylogenetic diversity of culturable fungi in the Heshang Cave, central China

    PubMed Central

    Man, Baiying; Wang, Hongmei; Xiang, Xing; Wang, Ruicheng; Yun, Yuan; Gong, Linfeng

    2015-01-01

    Caves are nutrient-limited and dark subterranean ecosystems. To date, attention has been focused on geological research of caves in China, whilst indigenous microbial diversity has been insufficiently characterized. Here, we report the fungal diversity in the pristine, oligotrophic, karst Heshang Cave, central China, using a culture-dependent method coupled with the analysis of the fungal rRNA-ITS gene sequences. A total of 194 isolates were obtained with six different media from 14 sampling sites of sediments, weathered rocks, and bat guanos. Phylogenetic analysis clustered the 194 sequenced isolates into 33 genera within 15 orders of three phyla, Ascomycota, Basidiomycota, and Zygomycota, indicating a high degree of fungal diversity in the Heshang Cave. Notably, 16 out of the 36 fungal genera were also frequently observed in solution caves around the world and 23 genera were previously found in carbonate cave, indicating potential similarities among fungal communities in cave ecosystems. However, 10 genera in this study were not reported previously in any solution caves, thus expanding our knowledge about fungal diversity in cave ecosystems. Moreover, culturable fungal diversity varied from one habitat to another within the cave, being the highest in sediments, followed by weathered rocks and bat guanos as indicated by α-diversity indexes. At the genus level, Penicillium accounted for 40, 54, and 52% in three habitats of sediments, weathered rocks, and bat guanos, respectively. Trichoderma, Paecilomyces, and Aspergillus accounted for 9, 22, and 37% in the above habitats, correspondingly. Despite of the dominance of Penicillium in all samples, β-diversity index indicated significant differences between each two fungal communities in the three habitats in view of both the composition and abundance. Our study is the first report on fungal communities in a natural pristine solution cave system in central China and sheds light on fungal diversity and functions in

  12. Molecular Characterization of a Heterothallic Mating System in Pseudogymnoascus destructans, the Fungus Causing White-Nose Syndrome of Bats

    PubMed Central

    Palmer, Jonathan M.; Kubatova, Alena; Novakova, Alena; Minnis, Andrew M.; Kolarik, Miroslav; Lindner, Daniel L.

    2014-01-01

    White-nose syndrome (WNS) of bats has devastated bat populations in eastern North America since its discovery in 2006. WNS, caused by the fungus Pseudogymnoascus destructans, has spread quickly in North America and has become one of the most severe wildlife epidemics of our time. While P. destructans is spreading rapidly in North America, nothing is known about the sexual capacity of this fungus. To gain insight into the genes involved in sexual reproduction, we characterized the mating-type locus (MAT) of two Pseudogymnoascus spp. that are closely related to P. destructans and homothallic (self-fertile). As with other homothallic Ascomycota, the MAT locus of these two species encodes a conserved α-box protein (MAT1-1-1) as well as two high-mobility group (HMG) box proteins (MAT1-1-3 and MAT1-2-1). Comparisons with the MAT locus of the North American isolate of P. destructans (the ex-type isolate) revealed that this isolate of P. destructans was missing a clear homolog of the conserved HMG box protein (MAT1-2-1). These data prompted the discovery and molecular characterization of a heterothallic mating system in isolates of P. destructans from the Czech Republic. Both mating types of P. destructans were found to coexist within hibernacula, suggesting the presence of mating populations in Europe. Although populations of P. destructans in North America are thought to be clonal and of one mating type, the potential for sexual recombination indicates that continued vigilance is needed regarding introductions of additional isolates of this pathogen. PMID:25053709

  13. Ice nucleation activity in the widespread soil fungus Mortierella alpina

    NASA Astrophysics Data System (ADS)

    Fröhlich-Nowoisky, Janine; Hill, Thomas C. J.; Pummer, Bernhard G.; Yordanova, Petya; Franc, Gary D.; Pöschl, Ulrich

    2015-04-01

    Biological residues in soil dust are a potentially strong source of atmospheric ice nucleators (IN). However, the sources and characteristics of biological - in particular, fungal - IN in soil dust have not been characterized. By analysis of the culturable fungi in topsoils, from a range of different land use and ecosystem types in south-east Wyoming, we found ice nucleation active (INA, i.e., inducing ice formation in the probed range of temperature and concentration) fungi to be both widespread and abundant, particularly in soils with recent inputs of decomposable organic matter. For example, in harvested and ploughed sugar beet and potato fields, and in the organic horizon beneath Lodgepole pine forest, their relative abundances and concentrations among the cultivable fungi were 25% (8 x 103 CFU g-1), 17% (4.8 x 103 CFU g-1) and 17% (4 x 103 CFU g-1), respectively. Across all investigated soils, 8% (2.9 x 103 CFU g-1) of fungal isolates were INA. All INA isolates initiated freezing at -5° C to -6° C and all belonged to a single zygomycotic species, Mortierella alpina (Mortierellales, Mortierellomycotina). By contrast, the handful of fungal species so far reported as INA all belong within the Ascomycota or Basidiomycota phyla. Mortierella alpina is known to be saprobic (utilizing non-living organic matter), widespread in soil and present in air and rain. Sequencing of the ITS region and the gene for γ-linolenic elongase revealed four distinct clades, affiliated to different soil types. The IN produced by M. alpina seem to be extracellular proteins of 100-300 kDa in size which are not anchored in the fungal cell wall. Ice nucleating fungal mycelium will ramify topsoils and probably also release cell-free IN into it. If these IN survive decomposition or are adsorbed onto mineral surfaces, these small cell-free IN might contribute to the as yet uncharacterized pool of atmospheric IN released by soils as dusts.

  14. Plant Invasions Associated with Change in Root-Zone Microbial Community Structure and Diversity.

    PubMed

    Rodrigues, Richard R; Pineda, Rosana P; Barney, Jacob N; Nilsen, Erik T; Barrett, John E; Williams, Mark A

    2015-01-01

    The importance of plant-microbe associations for the invasion of plant species have not been often tested under field conditions. The research sought to determine patterns of change in microbial communities associated with the establishment of invasive plants with different taxonomic and phenetic traits. Three independent locations in Virginia, USA were selected. One site was invaded by a grass (Microstegium vimineum), another by a shrub (Rhamnus davurica), and the third by a tree (Ailanthus altissima). The native vegetation from these sites was used as reference. 16S rRNA and ITS regions were sequenced to study root-zone bacterial and fungal communities, respectively, in invaded and non-invaded samples and analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Though root-zone microbial community structure initially differed across locations, plant invasion shifted communities in similar ways. Indicator species analysis revealed that Operational Taxonomic Units (OTUs) closely related to Proteobacteria, Acidobacteria, Actinobacteria, and Ascomycota increased in abundance due to plant invasions. The Hyphomonadaceae family in the Rhodobacterales order and ammonia-oxidizing Nitrospirae phylum showed greater relative abundance in the invaded root-zone soils. Hyphomicrobiaceae, another bacterial family within the phyla Proteobacteria increased as a result of plant invasion, but the effect associated most strongly with root-zones of M. vimineum and R. davurica. Functional analysis using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) showed bacteria responsible for nitrogen cycling in soil increased in relative abundance in association with plant invasion. In agreement with phylogenetic and functional analyses, greater turnover of ammonium and nitrate was associated with plant invasion. Overall, bacterial and fungal communities changed congruently across plant invaders, and support the hypothesis that nitrogen

  15. Ion Torrent PGM as Tool for Fungal Community Analysis: A Case Study of Endophytes in Eucalyptus grandis Reveals High Taxonomic Diversity

    PubMed Central

    Kemler, Martin; Garnas, Jeff; Wingfield, Michael J.; Gryzenhout, Marieka; Pillay, Kerry-Anne; Slippers, Bernard

    2013-01-01

    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. PMID:24358124

  16. Ibuprofen removal in horizontal subsurface flow constructed wetlands: treatment performance and fungal community dynamics.

    PubMed

    Zhang, Dongqing; Luo, Jinxue; Lee, Zarraz May Ping; Gersberg, Richard M; Liu, Yu; Tan, Soon Keat; Ng, Wun Jern

    2016-06-01

    The treatment performance of ibuprofen (IBP)-enriched wastewater by horizontal subsurface flow constructed wetlands planted with cattail (Typha angustifolia) and unplanted control mesocosms was investigated. Removal efficiencies of IBP were significantly (p < .05) enhanced in the planted mesocosms (78.5%) compared to those in the unplanted beds (57.9%). An 18S rRNA gene high-throughput pyrosequencing approach was used to investigate the effects of IBP on the structure of the fungal community in these wetland systems. The overall diversity of the fungal community was reduced under the IBP exposure. Taxonomic analysis revealed that 62.2% of the fungal sequences were affiliated with Basidiomycota, followed by Ascomycota (37.4%) at the phylum level. Uncultured fungus (48.2%), Chaetomium sp. (14.2%), Aspergillus sp. (12.4%), Trichoderma sp. (5.7%), Cladosporium sp. (5.4%), and Emericellopsis sp. (5.2%) were identified as dominant genera. At the genus level, a distinct profile of the fungal community in the IBP-enriched mesocosms was observed as compared to the control beds, and as well specific fungal genera were enhanced in the planted beds, regardless of IBP enrichment. However, despite these differences, the composition of the fungal community (as measured by Bray-Curtis similarity) was mostly unaffected by the significant IBP enrichment. On the other hand, a consistent similarity pattern of fungal community structure in the planted mesocosms suggests that the presence of higher macrophytes in the wetland systems may well help shape the fungal community structure. PMID:26581707

  17. Sloth hair as a novel source of fungi with potent anti-parasitic, anti-cancer and anti-bacterial bioactivity.

    PubMed

    Higginbotham, Sarah; Wong, Weng Ruh; Linington, Roger G; Spadafora, Carmenza; Iturrado, Liliana; Arnold, A Elizabeth

    2014-01-01

    The extraordinary biological diversity of tropical forests harbors a rich chemical diversity with enormous potential as a source of novel bioactive compounds. Of particular interest are new environments for microbial discovery. Sloths--arboreal mammals commonly found in the lowland forests of Panama--carry a wide variety of micro- and macro-organisms on their coarse outer hair. Here we report for the first time the isolation of diverse and bioactive strains of fungi from sloth hair, and their taxonomic placement. Eighty-four isolates of fungi were obtained in culture from the surface of hair that was collected from living three-toed sloths (Bradypus variegatus, Bradypodidae) in Soberanía National Park, Republic of Panama. Phylogenetic analyses revealed a diverse group of Ascomycota belonging to 28 distinct operational taxonomic units (OTUs), several of which are divergent from previously known taxa. Seventy-four isolates were cultivated in liquid broth and crude extracts were tested for bioactivity in vitro. We found a broad range of activities against strains of the parasites that cause malaria (Plasmodium falciparum) and Chagas disease (Trypanosoma cruzi), and against the human breast cancer cell line MCF-7. Fifty fungal extracts were tested for antibacterial activity in a new antibiotic profile screen called BioMAP; of these, 20 were active against at least one bacterial strain, and one had an unusual pattern of bioactivity against Gram-negative bacteria that suggests a potentially new mode of action. Together our results reveal the importance of exploring novel environments for bioactive fungi, and demonstrate for the first time the taxonomic composition and bioactivity of fungi from sloth hair. PMID:24454729

  18. Diversity and Composition of Airborne Fungal Community Associated with Particulate Matters in Beijing during Haze and Non-haze Days.

    PubMed

    Yan, Dong; Zhang, Tao; Su, Jing; Zhao, Li-Li; Wang, Hao; Fang, Xiao-Mei; Zhang, Yu-Qin; Liu, Hong-Yu; Yu, Li-Yan

    2016-01-01

    To assess the diversity and composition of airborne fungi associated with particulate matters (PMs) in Beijing, China, a total of 81 PM samples were collected, which were derived from PM2.5, PM10 fractions, and total suspended particles during haze and non-haze days. The airborne fungal community in these samples was analyzed using the Illumina Miseq platform with fungi-specific primers targeting the internal transcribed spacer 1 region of the large subunit rRNA gene. A total of 797,040 reads belonging to 1633 operational taxonomic units were observed. Of these, 1102 belonged to Ascomycota, 502 to Basidiomycota, 24 to Zygomycota, and 5 to Chytridiomycota. The dominant orders were Pleosporales (29.39%), Capnodiales (27.96%), Eurotiales (10.64%), and Hypocreales (9.01%). The dominant genera were Cladosporium, Alternaria, Fusarium, Penicillium, Sporisorium, and Aspergilus. Analysis of similarities revealed that both particulate matter sizes (R = 0.175, p = 0.001) and air quality levels (R = 0.076, p = 0.006) significantly affected the airborne fungal community composition. The relative abundance of many fungal genera was found to significantly differ among various PM types and air quality levels. Alternaria and Epicoccum were more abundant in total suspended particles samples, Aspergillus in heavy-haze days and PM2.5 samples, and Malassezia in PM2.5 samples and heavy-haze days. Canonical correspondence analysis and permutation tests showed that temperature (p < 0.01), NO2 (p < 0.01), PM10 (p < 0.01), SO2(p < 0.01), CO (p < 0.01), and relative humidity (p < 0.05) were significant factors that determine airborne fungal community composition. The results suggest that diverse airborne fungal communities are associated with particulate matters and may provide reliable data for studying the responses of human body to the increasing level of air pollution in Beijing. PMID:27148180

  19. Microbial Community Structure and Activity Linked to Contrasting Biogeochemical Gradients in Bog and Fen Environments of the Glacial Lake Agassiz Peatland

    PubMed Central

    Lin, X.; Green, S.; Tfaily, M. M.; Prakash, O.; Konstantinidis, K. T.; Corbett, J. E.; Chanton, J. P.; Cooper, W. T.

    2012-01-01

    The abundances, compositions, and activities of microbial communities were investigated at bog and fen sites in the Glacial Lake Agassiz Peatland of northwestern Minnesota. These sites contrast in the reactivity of dissolved organic matter (DOM) and the presence or absence of groundwater inputs. Microbial community composition was characterized using pyrosequencing and clone library construction of phylogenetic marker genes. Microbial distribution patterns were linked to pH, concentrations of dissolved organic carbon and nitrogen, C/N ratios, optical properties of DOM, and activities of laccase and peroxidase enzymes. Both bacterial and archaeal richness and rRNA gene abundance were >2 times higher on average in the fen than in the bog, in agreement with a higher pH, labile DOM content, and enhanced enzyme activities in the fen. Fungi were equivalent to an average of 1.4% of total prokaryotes in gene abundance assayed by quantitative PCR. Results revealed statistically distinct spatial patterns between bacterial and fungal communities. Fungal distribution did not covary with pH and DOM optical properties and was vertically stratified, with a prevalence of Ascomycota and Basidiomycota near the surface and much higher representation of Zygomycota in the subsurface. In contrast, bacterial community composition largely varied between environments, with the bog dominated by Acidobacteria (61% of total sequences), while the Firmicutes (52%) dominated in the fen. Acetoclastic Methanosarcinales showed a much higher relative abundance in the bog, in contrast to the dominance of diverse hydrogenotrophic methanogens in the fen. This is the first quantitative and compositional analysis of three microbial domains in peatlands and demonstrates that the microbial abundance, diversity, and activity parallel with the pronounced differences in environmental variables between bog and fen sites. PMID:22843538

  20. Microbial Diversity of a Mediterranean Soil and Its Changes after Biotransformed Dry Olive Residue Amendment

    PubMed Central

    Siles, José A.; Rachid, Caio T. C. C.; Sampedro, Inmaculada; García-Romera, Inmaculada; Tiedje, James M.

    2014-01-01

    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. PMID:25058610