Science.gov

Sample records for conserve fungal diversity

  1. The contribution of DNA metabarcoding to fungal conservation: diversity assessment, habitat partitioning and mapping red-listed fungi in protected coastal Salix repens communities in the Netherlands.

    PubMed

    Geml, József; Gravendeel, Barbara; van der Gaag, Kristiaan J; Neilen, Manon; Lammers, Youri; Raes, Niels; Semenova, Tatiana A; de Knijff, Peter; Noordeloos, Machiel E

    2014-01-01

    Western European coastal sand dunes are highly important for nature conservation. Communities of the creeping willow (Salix repens) represent one of the most characteristic and diverse vegetation types in the dunes. We report here the results of the first kingdom-wide fungal diversity assessment in S. repens coastal dune vegetation. We carried out massively parallel pyrosequencing of ITS rDNA from soil samples taken at ten sites in an extended area of joined nature reserves located along the North Sea coast of the Netherlands, representing habitats with varying soil pH and moisture levels. Fungal communities in Salix repens beds are highly diverse and we detected 1211 non-singleton fungal 97% sequence similarity OTUs after analyzing 688,434 ITS2 rDNA sequences. Our comparison along a north-south transect indicated strong correlation between soil pH and fungal community composition. The total fungal richness and the number OTUs of most fungal taxonomic groups negatively correlated with higher soil pH, with some exceptions. With regard to ecological groups, dark-septate endophytic fungi were more diverse in acidic soils, ectomycorrhizal fungi were represented by more OTUs in calcareous sites, while detected arbuscular mycorrhizal genera fungi showed opposing trends regarding pH. Furthermore, we detected numerous red listed species in our samples often from previously unknown locations, indicating that some of the fungal species currently considered rare may be more abundant in Dutch S. repens communities than previously thought.

  2. Topographic diversity of fungal and bacterial communities in human skin.

    PubMed

    Findley, Keisha; Oh, Julia; Yang, Joy; Conlan, Sean; Deming, Clayton; Meyer, Jennifer A; Schoenfeld, Deborah; Nomicos, Effie; Park, Morgan; Kong, Heidi H; Segre, Julia A

    2013-06-20

    Traditional culture-based methods have incompletely defined the microbial landscape of common recalcitrant human fungal skin diseases, including athlete's foot and toenail infections. Skin protects humans from invasion by pathogenic microorganisms and provides a home for diverse commensal microbiota. Bacterial genomic sequence data have generated novel hypotheses about species and community structures underlying human disorders. However, microbial diversity is not limited to bacteria; microorganisms such as fungi also have major roles in microbial community stability, human health and disease. Genomic methodologies to identify fungal species and communities have been limited compared with those that are available for bacteria. Fungal evolution can be reconstructed with phylogenetic markers, including ribosomal RNA gene regions and other highly conserved genes. Here we sequenced and analysed fungal communities of 14 skin sites in 10 healthy adults. Eleven core-body and arm sites were dominated by fungi of the genus Malassezia, with only species-level classifications revealing fungal-community composition differences between sites. By contrast, three foot sites--plantar heel, toenail and toe web--showed high fungal diversity. Concurrent analysis of bacterial and fungal communities demonstrated that physiologic attributes and topography of skin differentially shape these two microbial communities. These results provide a framework for future investigation of the contribution of interactions between pathogenic and commensal fungal and bacterial communities to the maintainenace of human health and to disease pathogenesis.

  3. Resource availability controls fungal diversity across a plant diversity gradient

    USGS Publications Warehouse

    Waldrop, M.P.; Zak, D.R.; Blackwood, C.B.; Curtis, C.D.; Tilman, D.

    2006-01-01

    Despite decades of research, the ecological determinants of microbial diversity remain poorly understood. Here, we test two alternative hypotheses concerning the factors regulating fungal diversity in soil. The first states that higher levels of plant detritus production increase the supply of limiting resources (i.e. organic substrates) thereby increasing fungal diversity. Alternatively, greater plant diversity increases the range of organic substrates entering soil, thereby increasing the number of niches to be filled by a greater array of heterotrophic fungi. These two hypotheses were simultaneously examined in experimental plant communities consisting of one to 16 species that have been maintained for a decade. We used ribosomal intergenic spacer analysis (RISA), in combination with cloning and sequencing, to quantify fungal community composition and diversity within the experimental plant communities. We used soil microbial biomass as a temporally integrated measure of resource supply. Plant diversity was unrelated to fungal diversity, but fungal diversity was a unimodal function of resource supply. Canonical correspondence analysis (CCA) indicated that plant diversity showed a relationship to fungal community composition, although the occurrence of RISA bands and operational taxonomic units (OTUs) did not differ among the treatments. The relationship between fungal diversity and resource availability parallels similar relationships reported for grasslands, tropical forests, coral reefs, and other biotic communities, strongly suggesting that the same underlying mechanisms determine the diversity of organisms at multiple scales. ?? 2006 Blackwell Publishing Ltd/CNRS.

  4. 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 ...

  5. Fungal endophyte diversity in Sarracenia.

    PubMed

    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.

  6. Serpentine soils promote ectomycorrhizal fungal diversity.

    PubMed

    Branco, Sara

    2010-12-01

    Serpentine soils impose physiological stresses that limit plant establishment and diversity. The degree to which serpentine soils entail constraints on other organisms is, however, poorly understood. Here, I investigate the effect of serpentine soils on ectomycorrhizal (ECM) fungi by conducting a reciprocal transplant experiment, where serpentine and nonserpentine ECM fungal communities were cultured in both their native and non-native soils. Contrary to expectation, serpentine soils hosted higher fungal richness compared to nonserpentine, and most species were recovered from serpentine soil, suggesting ECM fungi are not overall specialized or strongly affected by serpentine edaphic constraints.

  7. A fungal perspective on conservation biology.

    PubMed

    Heilmann-Clausen, Jacob; Barron, Elizabeth S; Boddy, Lynne; Dahlberg, Anders; Griffith, Gareth W; Nordén, Jenni; Ovaskainen, Otso; Perini, Claudia; Senn-Irlet, Beatrice; Halme, Panu

    2015-02-01

    Hitherto fungi have rarely been considered in conservation biology, but this is changing as the field moves from addressing single species issues to an integrative ecosystem-based approach. The current emphasis on biodiversity as a provider of ecosystem services throws the spotlight on the vast diversity of fungi, their crucial roles in terrestrial ecosystems, and the benefits of considering fungi in concert with animals and plants. We reviewed the role of fungi in ecosystems and composed an overview of the current state of conservation of fungi. There are 5 areas in which fungi can be readily integrated into conservation: as providers of habitats and processes important for other organisms; as indicators of desired or undesired trends in ecosystem functioning; as indicators of habitats of conservation value; as providers of powerful links between human societies and the natural world because of their value as food, medicine, and biotechnological tools; and as sources of novel tools and approaches for conservation of megadiverse organism groups. We hope conservation professionals will value the potential of fungi, engage mycologists in their work, and appreciate the crucial role of fungi in nature.

  8. Fungal biogeography. Global diversity and geography of soil fungi.

    PubMed

    Tedersoo, Leho; Bahram, Mohammad; Põlme, Sergei; Kõljalg, Urmas; Yorou, Nourou S; Wijesundera, Ravi; Villarreal Ruiz, Luis; Vasco-Palacios, Aída M; Thu, Pham Quang; Suija, Ave; Smith, Matthew E; Sharp, Cathy; Saluveer, Erki; Saitta, Alessandro; Rosas, Miguel; Riit, Taavi; Ratkowsky, David; Pritsch, Karin; Põldmaa, Kadri; Piepenbring, Meike; Phosri, Cherdchai; Peterson, Marko; Parts, Kaarin; Pärtel, Kadri; Otsing, Eveli; Nouhra, Eduardo; Njouonkou, André L; Nilsson, R Henrik; Morgado, Luis N; Mayor, Jordan; May, Tom W; Majuakim, Luiza; Lodge, D Jean; Lee, Su See; Larsson, Karl-Henrik; Kohout, Petr; Hosaka, Kentaro; Hiiesalu, Indrek; Henkel, Terry W; Harend, Helery; Guo, Liang-dong; Greslebin, Alina; Grelet, Gwen; Geml, Jozsef; Gates, Genevieve; Dunstan, William; Dunk, Chris; Drenkhan, Rein; Dearnaley, John; De Kesel, André; Dang, Tan; Chen, Xin; Buegger, Franz; Brearley, Francis Q; Bonito, Gregory; Anslan, Sten; Abell, Sandra; Abarenkov, Kessy

    2014-11-28

    Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially toward the poles. Climatic factors, followed by edaphic and spatial variables, constitute the best predictors of fungal richness and community composition at the global scale. Fungi show similar latitudinal diversity gradients to other organisms, with several notable exceptions. These findings advance our understanding of global fungal diversity patterns and permit integration of fungi into a general macroecological framework. PMID:25430773

  9. Fungal biogeography. Global diversity and geography of soil fungi.

    PubMed

    Tedersoo, Leho; Bahram, Mohammad; Põlme, Sergei; Kõljalg, Urmas; Yorou, Nourou S; Wijesundera, Ravi; Villarreal Ruiz, Luis; Vasco-Palacios, Aída M; Thu, Pham Quang; Suija, Ave; Smith, Matthew E; Sharp, Cathy; Saluveer, Erki; Saitta, Alessandro; Rosas, Miguel; Riit, Taavi; Ratkowsky, David; Pritsch, Karin; Põldmaa, Kadri; Piepenbring, Meike; Phosri, Cherdchai; Peterson, Marko; Parts, Kaarin; Pärtel, Kadri; Otsing, Eveli; Nouhra, Eduardo; Njouonkou, André L; Nilsson, R Henrik; Morgado, Luis N; Mayor, Jordan; May, Tom W; Majuakim, Luiza; Lodge, D Jean; Lee, Su See; Larsson, Karl-Henrik; Kohout, Petr; Hosaka, Kentaro; Hiiesalu, Indrek; Henkel, Terry W; Harend, Helery; Guo, Liang-dong; Greslebin, Alina; Grelet, Gwen; Geml, Jozsef; Gates, Genevieve; Dunstan, William; Dunk, Chris; Drenkhan, Rein; Dearnaley, John; De Kesel, André; Dang, Tan; Chen, Xin; Buegger, Franz; Brearley, Francis Q; Bonito, Gregory; Anslan, Sten; Abell, Sandra; Abarenkov, Kessy

    2014-11-28

    Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially toward the poles. Climatic factors, followed by edaphic and spatial variables, constitute the best predictors of fungal richness and community composition at the global scale. Fungi show similar latitudinal diversity gradients to other organisms, with several notable exceptions. These findings advance our understanding of global fungal diversity patterns and permit integration of fungi into a general macroecological framework.

  10. 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

  11. 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

  12. 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

  13. 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.

  14. Fungal diversity on fallen leaves of Ficus in northern Thailand.

    PubMed

    Wang, Hong-Kai; Hyde, Kevin D; Soytong, Kasem; Lin, Fu-Cheng

    2008-10-01

    Fallen leaves of Ficus altissima, F. virens, F. benjamina, F. fistulosa and F. semicordata, were collected in Chiang Mai Province in northern Thailand and examined for fungi. Eighty taxa were identified, comprising 56 anamorphic taxa, 23 ascomycetes and 1 basidiomycete. Common fungal species occurring on five host species with high frequency of occurrence were Beltraniella nilgirica, Lasiodiplodia theobromae, Ophioceras leptosporum, Periconia byssoides and Septonema harknessi. Colletotrichum and Stachybotrys were also common genera. The leaves of different Ficus species supported diverse fungal taxa, and the fungal assemblages on the different hosts showed varying overlap. The fungal diversity of saprobes at the host species level is discussed. PMID:18837113

  15. Patterns of fungal diversity and composition along a salinity gradient

    PubMed Central

    Mohamed, Devon J; Martiny, Jennifer BH

    2011-01-01

    Estuarine salinity gradients are known to influence plant, bacterial and archaeal community structure. We sequenced 18S rRNA genes to investigate patterns in sediment fungal diversity (richness and evenness of taxa) and composition (taxonomic and phylogenetic) along an estuarine salinity gradient. We sampled three marshes—a salt, brackish and freshwater marsh—in Rhode Island. To compare the relative effect of the salinity gradient with that of plants, we sampled fungi in plots with Spartina patens and in plots from which plants were removed 2 years prior to sampling. The fungal sediment community was unique compared with previously sampled fungal communities; we detected more Ascomycota (78%), fewer Basidiomycota (6%) and more fungi from basal lineages (16%) (Chytridiomycota, Glomeromycota and four additional groups) than typically found in soil. Across marshes, fungal composition changed substantially, whereas fungal diversity differed only at the finest level of genetic resolution, and was highest in the intermediate, brackish marsh. In contrast, the presence of plants had a highly significant effect on fungal diversity at all levels of genetic resolution, but less of an effect on fungal composition. These results suggest that salinity (or other covarying parameters) selects for a distinctive fungal composition, and plants provide additional niches upon which taxa within these communities can specialize and coexist. Given the number of sequences from basal fungal lineages, the study also suggests that further sampling of estuarine sediments may help in understanding early fungal evolution. PMID:20882058

  16. First genomic survey of human skin fungal diversity

    Cancer.gov

    Fungal infections of the skin affect 29 million people in the United States. In the first study of human fungal skin diversity, National Institutes of Health researchers sequenced the DNA of fungi that thrive at different skin sites of healthy adults to d

  17. 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

  18. 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

  19. 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.

  20. Conservative ecological and evolutionary patterns in liverwort–fungal symbioses

    PubMed Central

    Bidartondo, Martin I.; Duckett, Jeffrey G.

    2010-01-01

    Liverworts, the most ancient group of land plants, form a range of intimate associations with fungi that may be analogous to the mycorrhizas of vascular plants. Most thalloid liverworts contain arbuscular mycorrhizal glomeromycete fungi similar to most vascular plants. In contrast, a range of leafy liverwort genera and one simple thalloid liverwort family (the Aneuraceae) have switched to basidiomycete fungi. These liverwort switches away from glomeromycete fungi may be expected to parallel switches undergone by vascular plants that target diverse lineages of basidiomycete fungi to form ectomycorrhizas. To test this hypothesis, we used a cultivation-independent approach to examine the basidiomycete fungi associated with liverworts in varied worldwide locations by generating fungal DNA sequence data from over 200 field collections of over 30 species. Here we show that eight leafy liverwort genera predominantly and consistently associate with members of the Sebacina vermifera species complex and that Aneuraceae thalloid liverworts associate nearly exclusively with Tulasnella species. Furthermore, within sites where multiple liverwort species co-occur, they almost never share the same fungi. Our analyses reveal a strikingly conservative ecological and evolutionary pattern of liverwort symbioses with basidiomycete fungi that is unlike that of vascular plant mycorrhizas. PMID:19812075

  1. Conservative ecological and evolutionary patterns in liverwort-fungal symbioses.

    PubMed

    Bidartondo, Martin I; Duckett, Jeffrey G

    2010-02-01

    Liverworts, the most ancient group of land plants, form a range of intimate associations with fungi that may be analogous to the mycorrhizas of vascular plants. Most thalloid liverworts contain arbuscular mycorrhizal glomeromycete fungi similar to most vascular plants. In contrast, a range of leafy liverwort genera and one simple thalloid liverwort family (the Aneuraceae) have switched to basidiomycete fungi. These liverwort switches away from glomeromycete fungi may be expected to parallel switches undergone by vascular plants that target diverse lineages of basidiomycete fungi to form ectomycorrhizas. To test this hypothesis, we used a cultivation-independent approach to examine the basidiomycete fungi associated with liverworts in varied worldwide locations by generating fungal DNA sequence data from over 200 field collections of over 30 species. Here we show that eight leafy liverwort genera predominantly and consistently associate with members of the Sebacina vermifera species complex and that Aneuraceae thalloid liverworts associate nearly exclusively with Tulasnella species. Furthermore, within sites where multiple liverwort species co-occur, they almost never share the same fungi. Our analyses reveal a strikingly conservative ecological and evolutionary pattern of liverwort symbioses with basidiomycete fungi that is unlike that of vascular plant mycorrhizas.

  2. Conservation businesses and conservation planning in a biological diversity hotspot.

    PubMed

    Di Minin, Enrico; Macmillan, Douglas Craig; Goodman, Peter Styan; Escott, Boyd; Slotow, Rob; Moilanen, Atte

    2013-08-01

    The allocation of land to biological diversity conservation competes with other land uses and the needs of society for development, food, and extraction of natural resources. Trade-offs between biological diversity conservation and alternative land uses are unavoidable, given the realities of limited conservation resources and the competing demands of society. We developed a conservation-planning assessment for the South African province of KwaZulu-Natal, which forms the central component of the Maputaland-Pondoland-Albany biological diversity hotspot. Our objective was to enhance biological diversity protection while promoting sustainable development and providing spatial guidance in the resolution of potential policy conflicts over priority areas for conservation at risk of transformation. The conservation-planning assessment combined spatial-distribution models for 646 conservation features, spatial economic-return models for 28 alternative land uses, and spatial maps for 4 threats. Nature-based tourism businesses were competitive with other land uses and could provide revenues of >US$60 million/year to local stakeholders and simultaneously help meeting conservation goals for almost half the conservation features in the planning region. Accounting for opportunity costs substantially decreased conflicts between biological diversity, agricultural use, commercial forestry, and mining. Accounting for economic benefits arising from conservation and reducing potential policy conflicts with alternative plans for development can provide opportunities for successful strategies that combine conservation and sustainable development and facilitate conservation action. PMID:23565917

  3. Conservation businesses and conservation planning in a biological diversity hotspot.

    PubMed

    Di Minin, Enrico; Macmillan, Douglas Craig; Goodman, Peter Styan; Escott, Boyd; Slotow, Rob; Moilanen, Atte

    2013-08-01

    The allocation of land to biological diversity conservation competes with other land uses and the needs of society for development, food, and extraction of natural resources. Trade-offs between biological diversity conservation and alternative land uses are unavoidable, given the realities of limited conservation resources and the competing demands of society. We developed a conservation-planning assessment for the South African province of KwaZulu-Natal, which forms the central component of the Maputaland-Pondoland-Albany biological diversity hotspot. Our objective was to enhance biological diversity protection while promoting sustainable development and providing spatial guidance in the resolution of potential policy conflicts over priority areas for conservation at risk of transformation. The conservation-planning assessment combined spatial-distribution models for 646 conservation features, spatial economic-return models for 28 alternative land uses, and spatial maps for 4 threats. Nature-based tourism businesses were competitive with other land uses and could provide revenues of >US$60 million/year to local stakeholders and simultaneously help meeting conservation goals for almost half the conservation features in the planning region. Accounting for opportunity costs substantially decreased conflicts between biological diversity, agricultural use, commercial forestry, and mining. Accounting for economic benefits arising from conservation and reducing potential policy conflicts with alternative plans for development can provide opportunities for successful strategies that combine conservation and sustainable development and facilitate conservation action.

  4. Multi-stressor impacts on fungal diversity and ecosystem functions in streams: natural vs. anthropogenic stress.

    PubMed

    Tolkkinen, M; Mykrä, H; Annala, M; Markkola, A M; Vuori, K M; Muotka, T

    2015-03-01

    Biological assemblages are often subjected to multiple stressors emerging from both anthropogenic activities and naturally stressful conditions, and species' responses to simultaneous stressors may differ from those predicted based on the individual effects of each stressor alone. We studied the influence of land-use disturbance (forest drainage) on fungal decomposer assemblages and leaf decomposition rates in naturally harsh (low pH caused by black-shale dominated geology) vs. circumneutral streams. We used pyrosequencing to determine fungal richness and assemblage structure. Decomposition rates did not differ between circumneutral and naturally acidic reference sites. However, the effect of forest drainage on microbial decomposition was more pronounced in the naturally acidic streams than in circumneutral streams. Single-effect responses of fungal assemblages were mainly related to geology. Community similarity was significantly higher in the naturally acidic disturbed sites than in corresponding reference sites, suggesting that land-use disturbance simplifies fungal assemblages in naturally stressful conditions. Naturally acidic streams supported distinct fungal assemblages with many OTUs (operational taxonomic unit) unique to these streams. Our results indicate that fungal assemblages in streams are sensitive to both structural and functional impairment in response to multiple stressors. Anthropogenic degradation of naturally acidic streams may decrease regional fungal diversity and impair ecosystem functions, and these globally occurring environments therefore deserve special attention in conservation planning. PMID:26236864

  5. Multi-stressor impacts on fungal diversity and ecosystem functions in streams: natural vs. anthropogenic stress.

    PubMed

    Tolkkinen, M; Mykrä, H; Annala, M; Markkola, A M; Vuori, K M; Muotka, T

    2015-03-01

    Biological assemblages are often subjected to multiple stressors emerging from both anthropogenic activities and naturally stressful conditions, and species' responses to simultaneous stressors may differ from those predicted based on the individual effects of each stressor alone. We studied the influence of land-use disturbance (forest drainage) on fungal decomposer assemblages and leaf decomposition rates in naturally harsh (low pH caused by black-shale dominated geology) vs. circumneutral streams. We used pyrosequencing to determine fungal richness and assemblage structure. Decomposition rates did not differ between circumneutral and naturally acidic reference sites. However, the effect of forest drainage on microbial decomposition was more pronounced in the naturally acidic streams than in circumneutral streams. Single-effect responses of fungal assemblages were mainly related to geology. Community similarity was significantly higher in the naturally acidic disturbed sites than in corresponding reference sites, suggesting that land-use disturbance simplifies fungal assemblages in naturally stressful conditions. Naturally acidic streams supported distinct fungal assemblages with many OTUs (operational taxonomic unit) unique to these streams. Our results indicate that fungal assemblages in streams are sensitive to both structural and functional impairment in response to multiple stressors. Anthropogenic degradation of naturally acidic streams may decrease regional fungal diversity and impair ecosystem functions, and these globally occurring environments therefore deserve special attention in conservation planning.

  6. Diverse honeydew-consuming fungal communities associated with scale insects.

    PubMed

    Dhami, Manpreet K; Weir, Bevan S; Taylor, Michael W; Beggs, Jacqueline R

    2013-01-01

    Sooty mould fungi are ubiquitous, abundant consumers of insect-honeydew that have been little-studied. They form a complex of unrelated fungi that coexist and compete for honeydew, which is a chemically complex resource. In this study, we used scanning electron microscopy in combination with T-RFLP community profiling and ITS-based tag-pyrosequencing to extensively describe the sooty mould community associated with the honeydews of two ecologically important New Zealand coelostomidiid scale insects, Coelostomidia wairoensis and Ultracoelostoma brittini. We tested the influence of host plant on the community composition of associated sooty moulds, and undertook limited analyses to examine the influence of scale insect species and geographic location. We report here a previously unknown degree of fungal diversity present in this complex, with pyrosequencing detecting on average 243 operational taxonomic units across the different sooty mould samples. In contrast, T-RFLP detected only a total of 24 different "species" (unique peaks). Nevertheless, both techniques identified similar patterns of diversity suggesting that either method is appropriate for community profiling. The composition of the microbial community associated with individual scale insect species varied although the differences may in part reflect variation in host preference and site. Scanning electron microscopy visualised an intertwined mass of fungal hyphae and fruiting bodies in near-intact physical condition, but was unable to distinguish between the different fungal communities on a morphological level, highlighting the need for molecular research. The substantial diversity revealed for the first time by pyrosequencing and our inability to identify two-thirds of the diversity to further than the fungal division highlights the significant gap in our knowledge of these fungal groups. This study provides a first extensive look at the community diversity of the fungal community closely associated

  7. Diversity and distribution of fungal communities in lakes of Antarctica.

    PubMed

    Gonçalves, Vívian N; Vaz, Aline B M; Rosa, Carlos A; Rosa, Luiz H

    2012-11-01

    This study assessed the diversity and distribution of filamentous fungi obtained from water sampled from six lakes in the Antarctic Peninsula. One hundred and twenty-eight fungal isolates were purified and identified by analysis of nuclear rDNA ITS region sequences as belonging to 31 fungal different operational taxonomic units (OTUs). The most frequently isolated fungi were Geomyces pannorum and Mortierella sp.; these species occurred in six and three of the lakes sampled, respectively, and displayed the highest total colony-forming unit per L. Different species that have not been found to these lakes and/or had adapted to cold conditions were found. In general, the fungal community displayed low richness and high dominance indices. The species Cadophora cf. luteo-olivacea, Cadophora malorum, Davidiella tassiana, G. pannorum, Mortierella cf. alpina and Thelebolus cf. microsporus that were found in the lakes in question were also previously found in other cold ecosystems, such as Arctic, temperate and Alpine regions. The results of this study suggest the presence of an interesting aquatic fungal web, including symbionts, weak and strong saprophytes and parasite/pathogen fungal species. This aquatic web fungal may be a useful community model for further ecological and evolutionary studies of extreme habitats.

  8. Application of species richness estimators for the assessment of fungal diversity.

    PubMed

    Unterseher, Martin; Schnittler, Martin; Dormann, Carsten; Sickert, Andreas

    2008-05-01

    Species richness and distribution patterns of wood-inhabiting fungi and mycetozoans (slime moulds) were investigated in the canopy of a Central European temperate mixed deciduous forest. Species richness was described with diversity indices and species-accumulation curves. Nonmetrical multidimensional scaling was used to assess fungal species composition on different tree species. Different species richness estimators were used to extrapolate species richness beyond our own data. The reliability of the abundance-based coverage estimator, Chao, Jackknife and other estimators of species richness was evaluated for mycological surveys. While the species-accumulation curve of mycetozoans came close to saturation, that of wood-inhabiting fungi was continuously rising. The Chao 2 richness estimator was considered most appropriate to predict the number of species at the investigation site if sampling were continued. Gray's predictor of species richness should be used if statements of the number of species in larger areas are required. Multivariate analysis revealed the importance of different tree species for the conservation and maintenance of fungal diversity within forests, because each tree species possessed a characteristic fungal community. The described mathematical approaches of estimating species richness possess great potential to address fungal diversity on a regional, national, and global scale. PMID:18355274

  9. Application of species richness estimators for the assessment of fungal diversity.

    PubMed

    Unterseher, Martin; Schnittler, Martin; Dormann, Carsten; Sickert, Andreas

    2008-05-01

    Species richness and distribution patterns of wood-inhabiting fungi and mycetozoans (slime moulds) were investigated in the canopy of a Central European temperate mixed deciduous forest. Species richness was described with diversity indices and species-accumulation curves. Nonmetrical multidimensional scaling was used to assess fungal species composition on different tree species. Different species richness estimators were used to extrapolate species richness beyond our own data. The reliability of the abundance-based coverage estimator, Chao, Jackknife and other estimators of species richness was evaluated for mycological surveys. While the species-accumulation curve of mycetozoans came close to saturation, that of wood-inhabiting fungi was continuously rising. The Chao 2 richness estimator was considered most appropriate to predict the number of species at the investigation site if sampling were continued. Gray's predictor of species richness should be used if statements of the number of species in larger areas are required. Multivariate analysis revealed the importance of different tree species for the conservation and maintenance of fungal diversity within forests, because each tree species possessed a characteristic fungal community. The described mathematical approaches of estimating species richness possess great potential to address fungal diversity on a regional, national, and global scale.

  10. Ectomycorrhizal fungal diversity and saprotrophic fungal diversity are linked to different tree community attributes in a field-based tree experiment.

    PubMed

    Nguyen, Nhu H; Williams, Laura J; Vincent, John B; Stefanski, Artur; Cavender-Bares, Jeannine; Messier, Christian; Paquette, Alain; Gravel, Dominique; Reich, Peter B; Kennedy, Peter G

    2016-08-01

    Exploring the link between above- and belowground biodiversity has been a major theme of recent ecological research, due in large part to the increasingly well-recognized role that soil microorganisms play in driving plant community processes. In this study, we utilized a field-based tree experiment in Minnesota, USA, to assess the effect of changes in plant species richness and phylogenetic diversity on the richness and composition of both ectomycorrhizal and saprotrophic fungal communities. We found that ectomycorrhizal fungal species richness was significantly positively influenced by increasing plant phylogenetic diversity, while saprotrophic fungal species richness was significantly affected by plant leaf nitrogen content, specific root length and standing biomass. The increasing ectomycorrhizal fungal richness associated with increasing plant phylogenetic diversity was driven by the combined presence of ectomycorrhizal fungal specialists in plots with both gymnosperm and angiosperm hosts. Although the species composition of both the ectomycorrhizal and saprotrophic fungal communities changed significantly in response to changes in plant species composition, the effect was much greater for ectomycorrhizal fungi. In addition, ectomycorrhizal but not saprotrophic fungal species composition was significantly influenced by both plant phylum (angiosperm, gymnosperm, both) and origin (Europe, America, both). The phylum effect was caused by differences in ectomycorrhizal fungal community composition, while the origin effect was attributable to differences in community heterogeneity. Taken together, this study emphasizes that plant-associated effects on soil fungal communities are largely guild-specific and provides a mechanistic basis for the positive link between plant phylogenetic diversity and ectomycorrhizal fungal richness. PMID:27284759

  11. Conservation of diversity in forest trees

    SciTech Connect

    Ledig, F.T.

    1988-07-01

    This article discusses the threat to forest from population growth and concomitant poverty. Deforestation, pollution, and climatic change threaten forest diversity; and because forests are the habitats for diverse organisms, the threat extends to all flora and fauna associated with forests. Three different objectives included under the rubric of gene conservation are discussed: protection, particularly of domesticated plants, from genetic vulnerability; protection of endangered species; and preservation of genes for future use.

  12. Plant functional diversity enhances associations of soil fungal diversity with vegetation and soil in the restoration of semiarid sandy grassland.

    PubMed

    Zuo, Xiaoan; Wang, Shaokun; Lv, Peng; Zhou, Xin; Zhao, Xueyong; Zhang, Tonghui; Zhang, Jing

    2016-01-01

    The trait-based approach shows that plant functional diversity strongly affects ecosystem properties. However, few empirical studies show the relationship between soil fungal diversity and plant functional diversity in natural ecosystems. We investigated soil fungal diversity along a restoration gradient of sandy grassland (mobile dune, semifixed dune, fixed dune, and grassland) in Horqin Sand Land, northern China, using the denaturing gradient gel electrophoresis of 18S rRNA and gene sequencing. We also examined associations of soil fungal diversity with plant functional diversity reflected by the dominant species' traits in community (community-weighted mean, CWM) and the dispersion of functional trait values (FD is). We further used the structure equation model (SEM) to evaluate how plant richness, biomass, functional diversity, and soil properties affect soil fungal diversity in sandy grassland restoration. Soil fungal richness in mobile dune and semifixed dune was markedly lower than those of fixed dune and grassland (P < 0.05). Soil fungal richness was positively associated with plant richness, biomass, CWM plant height, and soil gradient aggregated from the principal component analysis, but SEM results showed that plant richness and CWM plant height determined by soil properties were the main factors exerting direct effects. Soil gradient increased fungal richness through indirect effect on vegetation rather than direct effect. The negative indirect effect of FDis on soil fungal richness was through its effect on plant biomass. Our final SEM model based on plant functional diversity explained nearly 70% variances of soil fungal richness. Strong association of soil fungal richness with the dominant species in the community supported the mass ratio hypothesis. Our results clearly highlight the role of plant functional diversity in enhancing associations of soil fungal diversity with community structure and soil properties in sandy grassland ecosystems.

  13. Loss of diversity in wood-inhabiting fungal communities affects decomposition activity in Norway spruce wood.

    PubMed

    Valentín, Lara; Rajala, Tiina; Peltoniemi, Mikko; Heinonsalo, Jussi; Pennanen, Taina; Mäkipää, Raisa

    2014-01-01

    Hundreds of wood-inhabiting fungal species are now threatened, principally due to a lack of dead wood in intensively managed forests, but the consequences of reduced fungal diversity on ecosystem functioning are not known. Several experiments have shown that primary productivity is negatively affected by a loss of species, but the effects of microbial diversity on decomposition are less studied. We studied the relationship between fungal diversity and the in vitro decomposition rate of slightly, moderately and heavily decayed Picea abies wood with indigenous fungal communities that were diluted to examine the influence of diversity. Respiration rate, wood-degrading hydrolytic enzymes and fungal community structure were assessed during a 16-week incubation. The number of observed OTUs in DGGE was used as a measure of fungal diversity. Respiration rate increased between early- and late-decay stages. Reduced fungal diversity was associated with lower respiration rates during intermediate stages of decay, but no effects were detected at later stages. The activity of hydrolytic enzymes varied among decay stages and fungal dilutions. Our results suggest that functioning of highly diverse communities of the late-decay stage were more resistant to the loss of diversity than less diverse communities of early decomposers. This indicates the accumulation of functional redundancy during the succession of the fungal community in decomposing substrates. PMID:24904544

  14. Diversity and bioprospection of fungal community present in oligotrophic soil of continental Antarctica

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The diversity of fungal communities from different substrates in Antarctica were studied and their capability to produce bioactive compounds. A one hundred and one fungal isolates were identified by molecular analysis in 35 different fungal taxa from 20 genera. Pseudogymnoascus sp. 3, Pseudogymnoasc...

  15. Conservation, duplication, and loss of the Tor signaling pathway in the fungal kingdom

    PubMed Central

    2010-01-01

    Background The nutrient-sensing Tor pathway governs cell growth and is conserved in nearly all eukaryotic organisms from unicellular yeasts to multicellular organisms, including humans. Tor is the target of the immunosuppressive drug rapamycin, which in complex with the prolyl isomerase FKBP12 inhibits Tor functions. Rapamycin is a gold standard drug for organ transplant recipients that was approved by the FDA in 1999 and is finding additional clinical indications as a chemotherapeutic and antiproliferative agent. Capitalizing on the plethora of recently sequenced genomes we have conducted comparative genomic studies to annotate the Tor pathway throughout the fungal kingdom and related unicellular opisthokonts, including Monosiga brevicollis, Salpingoeca rosetta, and Capsaspora owczarzaki. Results Interestingly, the Tor signaling cascade is absent in three microsporidian species with available genome sequences, the only known instance of a eukaryotic group lacking this conserved pathway. The microsporidia are obligate intracellular pathogens with highly reduced genomes, and we hypothesize that they lost the Tor pathway as they adapted and streamlined their genomes for intracellular growth in a nutrient-rich environment. Two TOR paralogs are present in several fungal species as a result of either a whole genome duplication or independent gene/segmental duplication events. One such event was identified in the amphibian pathogen Batrachochytrium dendrobatidis, a chytrid responsible for worldwide global amphibian declines and extinctions. Conclusions The repeated independent duplications of the TOR gene in the fungal kingdom might reflect selective pressure acting upon this kinase that populates two proteinaceous complexes with different cellular roles. These comparative genomic analyses illustrate the evolutionary trajectory of a central nutrient-sensing cascade that enables diverse eukaryotic organisms to respond to their natural environments. PMID:20863387

  16. 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.

  17. 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.

  18. Evolutionary Conserved Positions Define Protein Conformational Diversity.

    PubMed

    Saldaño, Tadeo E; Monzon, Alexander M; Parisi, Gustavo; Fernandez-Alberti, Sebastian

    2016-03-01

    Conformational diversity of the native state plays a central role in modulating protein function. The selection paradigm sustains that different ligands shift the conformational equilibrium through their binding to highest-affinity conformers. Intramolecular vibrational dynamics associated to each conformation should guarantee conformational transitions, which due to its importance, could possibly be associated with evolutionary conserved traits. Normal mode analysis, based on a coarse-grained model of the protein, can provide the required information to explore these features. Herein, we present a novel procedure to identify key positions sustaining the conformational diversity associated to ligand binding. The method is applied to an adequate refined dataset of 188 paired protein structures in their bound and unbound forms. Firstly, normal modes most involved in the conformational change are selected according to their corresponding overlap with structural distortions introduced by ligand binding. The subspace defined by these modes is used to analyze the effect of simulated point mutations on preserving the conformational diversity of the protein. We find a negative correlation between the effects of mutations on these normal mode subspaces associated to ligand-binding and position-specific evolutionary conservations obtained from multiple sequence-structure alignments. Positions whose mutations are found to alter the most these subspaces are defined as key positions, that is, dynamically important residues that mediate the ligand-binding conformational change. These positions are shown to be evolutionary conserved, mostly buried aliphatic residues localized in regular structural regions of the protein like β-sheets and α-helix. PMID:27008419

  19. Evolutionary Conserved Positions Define Protein Conformational Diversity

    PubMed Central

    Saldaño, Tadeo E.; Monzon, Alexander M.; Parisi, Gustavo; Fernandez-Alberti, Sebastian

    2016-01-01

    Conformational diversity of the native state plays a central role in modulating protein function. The selection paradigm sustains that different ligands shift the conformational equilibrium through their binding to highest-affinity conformers. Intramolecular vibrational dynamics associated to each conformation should guarantee conformational transitions, which due to its importance, could possibly be associated with evolutionary conserved traits. Normal mode analysis, based on a coarse-grained model of the protein, can provide the required information to explore these features. Herein, we present a novel procedure to identify key positions sustaining the conformational diversity associated to ligand binding. The method is applied to an adequate refined dataset of 188 paired protein structures in their bound and unbound forms. Firstly, normal modes most involved in the conformational change are selected according to their corresponding overlap with structural distortions introduced by ligand binding. The subspace defined by these modes is used to analyze the effect of simulated point mutations on preserving the conformational diversity of the protein. We find a negative correlation between the effects of mutations on these normal mode subspaces associated to ligand-binding and position-specific evolutionary conservations obtained from multiple sequence-structure alignments. Positions whose mutations are found to alter the most these subspaces are defined as key positions, that is, dynamically important residues that mediate the ligand-binding conformational change. These positions are shown to be evolutionary conserved, mostly buried aliphatic residues localized in regular structural regions of the protein like β-sheets and α-helix. PMID:27008419

  20. Alternative Splicing and Subfunctionalization Generates Functional Diversity in Fungal Proteomes

    PubMed Central

    Jiménez-López, Claudia; Lorenz, Michael C.; van Hoof, Ambro

    2013-01-01

    Alternative splicing is commonly used by the Metazoa to generate more than one protein from a gene. However, such diversification of the proteome by alternative splicing is much rarer in fungi. We describe here an ancient fungal alternative splicing event in which these two proteins are generated from a single alternatively spliced ancestral SKI7/HBS1 gene retained in many species in both the Ascomycota and Basidiomycota. While the ability to express two proteins from a single SKI7/HBS1 gene is conserved in many fungi, the exact mechanism by which they achieve this varies. The alternative splicing was lost in Saccharomyces cerevisiae following the whole-genome duplication event as these two genes subfunctionalized into the present functionally distinct HBS1 and SKI7 genes. When expressed in yeast, the single gene from Lachancea kluyveri generates two functionally distinct proteins. Expression of one of these proteins complements hbs1, but not ski7 mutations, while the other protein complements ski7, but not hbs1. This is the first known case of subfunctionalization by loss of alternative splicing in yeast. By coincidence, the ancestral alternatively spliced gene was also duplicated in Schizosaccharomyces pombe with subsequent subfunctionalization and loss of splicing. Similar subfunctionalization by loss of alternative splicing in fungi also explains the presence of two PTC7 genes in the budding yeast Tetrapisispora blattae, suggesting that this is a common mechanism to preserve duplicate alternatively spliced genes. PMID:23516382

  1. Fungal community composition in neotropical rain forests: the influence of tree diversity and precipitation.

    PubMed

    McGuire, Krista L; Fierer, Noah; Bateman, Carling; Treseder, Kathleen K; Turner, Benjamin L

    2012-05-01

    Plant diversity is considered one factor structuring soil fungal communities because the diversity of compounds in leaf litter might determine the extent of resource heterogeneity for decomposer communities. Lowland tropical rain forests have the highest plant diversity per area of any biome. Since fungi are responsible for much of the decomposition occurring in forest soils, understanding the factors that structure fungi in tropical forests may provide valuable insight for predicting changes in global carbon and nitrogen fluxes. To test the role of plant diversity in shaping fungal community structure and function, soil (0-20 cm) and leaf litter (O horizons) were collected from six established 1-ha forest census plots across a natural plant diversity gradient on the Isthmus of Panama. We used 454 pyrosequencing and phospholipid fatty acid analysis to evaluate correlations between microbial community composition, precipitation, soil nutrients, and plant richness. In soil, the number of fungal taxa increased significantly with increasing mean annual precipitation, but not with plant richness. There were no correlations between fungal communities in leaf litter and plant diversity or precipitation, and fungal communities were found to be compositionally distinct between soil and leaf litter. To directly test for effects of plant species richness on fungal diversity and function, we experimentally re-created litter diversity gradients in litter bags with 1, 25, and 50 species of litter. After 6 months, we found a significant effect of litter diversity on decomposition rate between one and 25 species of leaf litter. However, fungal richness did not track plant species richness. Although studies in a broader range of sites is required, these results suggest that precipitation may be a more important factor than plant diversity or soil nutrient status in structuring tropical forest soil fungal communities.

  2. Fungal community composition in neotropical rain forests: the influence of tree diversity and precipitation.

    PubMed

    McGuire, Krista L; Fierer, Noah; Bateman, Carling; Treseder, Kathleen K; Turner, Benjamin L

    2012-05-01

    Plant diversity is considered one factor structuring soil fungal communities because the diversity of compounds in leaf litter might determine the extent of resource heterogeneity for decomposer communities. Lowland tropical rain forests have the highest plant diversity per area of any biome. Since fungi are responsible for much of the decomposition occurring in forest soils, understanding the factors that structure fungi in tropical forests may provide valuable insight for predicting changes in global carbon and nitrogen fluxes. To test the role of plant diversity in shaping fungal community structure and function, soil (0-20 cm) and leaf litter (O horizons) were collected from six established 1-ha forest census plots across a natural plant diversity gradient on the Isthmus of Panama. We used 454 pyrosequencing and phospholipid fatty acid analysis to evaluate correlations between microbial community composition, precipitation, soil nutrients, and plant richness. In soil, the number of fungal taxa increased significantly with increasing mean annual precipitation, but not with plant richness. There were no correlations between fungal communities in leaf litter and plant diversity or precipitation, and fungal communities were found to be compositionally distinct between soil and leaf litter. To directly test for effects of plant species richness on fungal diversity and function, we experimentally re-created litter diversity gradients in litter bags with 1, 25, and 50 species of litter. After 6 months, we found a significant effect of litter diversity on decomposition rate between one and 25 species of leaf litter. However, fungal richness did not track plant species richness. Although studies in a broader range of sites is required, these results suggest that precipitation may be a more important factor than plant diversity or soil nutrient status in structuring tropical forest soil fungal communities. PMID:22080256

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

    PubMed Central

    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

  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. 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

  6. Diversity and bioprospecting of fungal communities associated with endemic and cold-adapted macroalgae in Antarctica

    PubMed Central

    Godinho, Valéria M; Furbino, Laura E; Santiago, Iara F; Pellizzari, Franciane M; Yokoya, Nair S; Pupo, Diclá; Alves, Tânia MA; S Junior, Policarpo A; Romanha, Alvaro J; Zani, Carlos L; Cantrell, Charles L; Rosa, Carlos A; Rosa, Luiz H

    2013-01-01

    We surveyed the distribution and diversity of fungi associated with eight macroalgae from Antarctica and their capability to produce bioactive compounds. The collections yielded 148 fungal isolates, which were identified using molecular methods as belonging to 21 genera and 50 taxa. The most frequent taxa were Geomyces species (sp.), Penicillium sp. and Metschnikowia australis. Seven fungal isolates associated with the endemic Antarctic macroalgae Monostroma hariotii (Chlorophyte) displayed high internal transcribed spacer sequences similarities with the psychrophilic pathogenic fungus Geomyces destructans. Thirty-three fungal singletons (66%) were identified, representing rare components of the fungal communities. The fungal communities displayed high diversity, richness and dominance indices; however, rarefaction curves indicated that not all of the fungal diversity present was recovered. Penicillium sp. UFMGCB 6034 and Penicillium sp. UFMGCB 6120, recovered from the endemic species Palmaria decipiens (Rhodophyte) and M. hariotii, respectively, yielded extracts with high and selective antifungal and/or trypanocidal activities, in which a preliminary spectral analysis using proton nuclear magnetic resonance spectroscopy indicated the presence of highly functionalised aromatic compounds. These results suggest that the endemic and cold-adapted macroalgae of Antarctica shelter a rich, diversity and complex fungal communities consisting of a few dominant indigenous or mesophilic cold-adapted species, and a large number of rare and/or endemic taxa, which may provide an interesting model of algal–fungal interactions under extreme conditions as well as a potential source of bioactive compounds. PMID:23702515

  7. Genetic selection and conservation of genetic diversity*.

    PubMed

    Blackburn, H D

    2012-08-01

    For 100s of years, livestock producers have employed various types of selection to alter livestock populations. Current selection strategies are little different, except our technologies for selection have become more powerful. Genetic resources at the breed level have been in and out of favour over time. These resources are the raw materials used to manipulate populations, and therefore, they are critical to the past and future success of the livestock sector. With increasing ability to rapidly change genetic composition of livestock populations, the conservation of these genetic resources becomes more critical. Globally, awareness of the need to steward genetic resources has increased. A growing number of countries have embarked on large scale conservation efforts by using in situ, ex situ (gene banking), or both approaches. Gene banking efforts have substantially increased and data suggest that gene banks are successfully capturing genetic diversity for research or industry use. It is also noteworthy that both industry and the research community are utilizing gene bank holdings. As pressures grow to meet consumer demands and potential changes in production systems, the linkage between selection goals and genetic conservation will increase as a mechanism to facilitate continued livestock sector development. PMID:22827378

  8. Genetic selection and conservation of genetic diversity*.

    PubMed

    Blackburn, H D

    2012-08-01

    For 100s of years, livestock producers have employed various types of selection to alter livestock populations. Current selection strategies are little different, except our technologies for selection have become more powerful. Genetic resources at the breed level have been in and out of favour over time. These resources are the raw materials used to manipulate populations, and therefore, they are critical to the past and future success of the livestock sector. With increasing ability to rapidly change genetic composition of livestock populations, the conservation of these genetic resources becomes more critical. Globally, awareness of the need to steward genetic resources has increased. A growing number of countries have embarked on large scale conservation efforts by using in situ, ex situ (gene banking), or both approaches. Gene banking efforts have substantially increased and data suggest that gene banks are successfully capturing genetic diversity for research or industry use. It is also noteworthy that both industry and the research community are utilizing gene bank holdings. As pressures grow to meet consumer demands and potential changes in production systems, the linkage between selection goals and genetic conservation will increase as a mechanism to facilitate continued livestock sector development.

  9. FUNGAL BIOGEOGRAPHY. Comment on "Global diversity and geography of soil fungi".

    PubMed

    Schadt, Christopher W; Rosling, Anna

    2015-06-26

    Tedersoo et al. (Research Article, 28 November 2014, p. 1078) present a compelling study regarding patterns of biodiversity of fungi, carried out at a scale unprecedented to date for fungal biogeographical studies. The study demonstrates strong global biogeographic patterns in richness and community composition of soil fungi. What concerns us with the study is what we do not see. Unfortunately, this study underestimates the fungal diversity of one key group of soil fungi due to reliance on a single primer with known flaws.

  10. 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.

  11. 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

  12. How Should Beta-Diversity Inform Biodiversity Conservation?

    PubMed

    Socolar, Jacob B; Gilroy, James J; Kunin, William E; Edwards, David P

    2016-01-01

    To design robust protected area networks, accurately measure species losses, or understand the processes that maintain species diversity, conservation science must consider the organization of biodiversity in space. Central is beta-diversity--the component of regional diversity that accumulates from compositional differences between local species assemblages. We review how beta-diversity is impacted by human activities, including farming, selective logging, urbanization, species invasions, overhunting, and climate change. Beta-diversity increases, decreases, or remains unchanged by these impacts, depending on the balance of processes that cause species composition to become more different (biotic heterogenization) or more similar (biotic homogenization) between sites. While maintaining high beta-diversity is not always a desirable conservation outcome, understanding beta-diversity is essential for protecting regional diversity and can directly assist conservation planning. PMID:26701706

  13. Relationship between soil fungal diversity and temperature in the maritime Antarctic

    NASA Astrophysics Data System (ADS)

    Newsham, Kevin K.; Hopkins, David W.; Carvalhais, Lilia C.; Fretwell, Peter T.; Rushton, Steven P.; O'Donnell, Anthony G.; Dennis, Paul G.

    2016-02-01

    Soil fungi have pivotal ecological roles as decomposers, pathogens and symbionts. Alterations to their diversity arising from climate change could have substantial effects on ecosystems, particularly those undergoing rapid warming that contain few species. Here, we report a study using pyrosequencing to assess fungal diversity in 29 soils sampled from a 1,650 km climatic gradient through the maritime Antarctic, the most rapidly warming region in the Southern Hemisphere. Using a `space-for-time’ substitution approach, we show that soil fungal diversity is higher in warmer habitats, with increases of 4.7 (observed) and 11.3 (predicted) fungal taxa per degree Celsius rise in surface temperature along the transect. Among 22 predictor variables, air temperature was the strongest and most consistent predictor of diversity. We propose that the current rapid warming in the maritime Antarctic (0.34 °C per decade) will facilitate the colonization of soil by a wider diversity of fungi than at present, with data from regression models suggesting 20-27% increases in fungal species richness in the southernmost soils by 2100. Such increases in diversity, which provide a sentinel for changes at lower latitudes, are likely to have substantial effects on nutrient cycling and, ultimately, productivity in the species-poor soils of maritime Antarctica.

  14. The fungal community structure of barley malts from diverse geographical regions correlates with malt quality parameters.

    PubMed

    Kaur, Mandeep; Bowman, John P; Stewart, Doug C; Evans, David E

    2015-12-23

    Malt is a preferred base for fermentations that produce beer or whisky. Barley for malt is grown under diverse environments in different geographical locations. Malt provides an ecological niche for a varied range of microorganisms with both positive and negative effects on its quality for brewing. Little information exists in the literature on the microbial community structure of Australian malt as well as broader global geographical differences in the associated fungal and bacterial communities. The aims of the present study were to compare the bacterial and fungal community structures of Australian commercial malt with its international counterparts originating from different geographical regions using terminal restriction fragment length polymorphism (TRFLP) fingerprinting and clone library analyses of ribosomal RNA genes. Further, the relationship between malt associated microbial communities and conventional malt quality parameters was also compared. Results showed that differences in fungal communities of malts from different geographical location were more pronounced than bacterial communities. TRFLP analysis discriminated high quality commercial malts with low fungal loads from malts deliberately infected with fungal inocula (Fusarium/Penicillium). Malt moisture, beta-amylase, α-amylase and limit dextrinase contents showed significant correlations with fungal community structure. This investigation concluded that fungal community structure was more important to subsequent malt quality outcomes than bacteria.

  15. The fungal community structure of barley malts from diverse geographical regions correlates with malt quality parameters.

    PubMed

    Kaur, Mandeep; Bowman, John P; Stewart, Doug C; Evans, David E

    2015-12-23

    Malt is a preferred base for fermentations that produce beer or whisky. Barley for malt is grown under diverse environments in different geographical locations. Malt provides an ecological niche for a varied range of microorganisms with both positive and negative effects on its quality for brewing. Little information exists in the literature on the microbial community structure of Australian malt as well as broader global geographical differences in the associated fungal and bacterial communities. The aims of the present study were to compare the bacterial and fungal community structures of Australian commercial malt with its international counterparts originating from different geographical regions using terminal restriction fragment length polymorphism (TRFLP) fingerprinting and clone library analyses of ribosomal RNA genes. Further, the relationship between malt associated microbial communities and conventional malt quality parameters was also compared. Results showed that differences in fungal communities of malts from different geographical location were more pronounced than bacterial communities. TRFLP analysis discriminated high quality commercial malts with low fungal loads from malts deliberately infected with fungal inocula (Fusarium/Penicillium). Malt moisture, beta-amylase, α-amylase and limit dextrinase contents showed significant correlations with fungal community structure. This investigation concluded that fungal community structure was more important to subsequent malt quality outcomes than bacteria. PMID:26340674

  16. Fungal disease incidence along tree diversity gradients depends on latitude in European forests.

    PubMed

    Nguyen, Diem; Castagneyrol, Bastien; Bruelheide, Helge; Bussotti, Filippo; Guyot, Virginie; Jactel, Hervé; Jaroszewicz, Bogdan; Valladares, Fernando; Stenlid, Jan; Boberg, Johanna

    2016-04-01

    European forests host a diversity of tree species that are increasingly threatened by fungal pathogens, which may have cascading consequences for forest ecosystems and their functioning. Previous experimental studies suggest that foliar and root pathogen abundance and disease severity decrease with increasing tree species diversity, but evidences from natural forests are rare. Here, we tested whether foliar fungal disease incidence was negatively affected by tree species diversity in different forest types across Europe. We measured the foliar fungal disease incidence on 16 different tree species in 209 plots in six European countries, representing a forest-type gradient from the Mediterranean to boreal forests. Forest plots of single species (monoculture plots) and those with different combinations of two to five tree species (mixed species plots) were compared. Specifically, we analyzed the influence of tree species richness, functional type (conifer vs. broadleaved) and phylogenetic diversity on overall fungal disease incidence. The effect of tree species richness on disease incidence varied with latitude and functional type. Disease incidence tended to increase with tree diversity, in particular in northern latitudes. Disease incidence decreased with tree species richness in conifers, but not in broadleaved trees. However, for specific damage symptoms, no tree species richness effects were observed. Although the patterns were weak, susceptibility of forests to disease appears to depend on the forest site and tree type. PMID:27066232

  17. Fungal disease incidence along tree diversity gradients depends on latitude in European forests.

    PubMed

    Nguyen, Diem; Castagneyrol, Bastien; Bruelheide, Helge; Bussotti, Filippo; Guyot, Virginie; Jactel, Hervé; Jaroszewicz, Bogdan; Valladares, Fernando; Stenlid, Jan; Boberg, Johanna

    2016-04-01

    European forests host a diversity of tree species that are increasingly threatened by fungal pathogens, which may have cascading consequences for forest ecosystems and their functioning. Previous experimental studies suggest that foliar and root pathogen abundance and disease severity decrease with increasing tree species diversity, but evidences from natural forests are rare. Here, we tested whether foliar fungal disease incidence was negatively affected by tree species diversity in different forest types across Europe. We measured the foliar fungal disease incidence on 16 different tree species in 209 plots in six European countries, representing a forest-type gradient from the Mediterranean to boreal forests. Forest plots of single species (monoculture plots) and those with different combinations of two to five tree species (mixed species plots) were compared. Specifically, we analyzed the influence of tree species richness, functional type (conifer vs. broadleaved) and phylogenetic diversity on overall fungal disease incidence. The effect of tree species richness on disease incidence varied with latitude and functional type. Disease incidence tended to increase with tree diversity, in particular in northern latitudes. Disease incidence decreased with tree species richness in conifers, but not in broadleaved trees. However, for specific damage symptoms, no tree species richness effects were observed. Although the patterns were weak, susceptibility of forests to disease appears to depend on the forest site and tree type.

  18. Methylated glycans as conserved targets of animal and fungal innate defense.

    PubMed

    Wohlschlager, Therese; Butschi, Alex; Grassi, Paola; Sutov, Grigorij; Gauss, Robert; Hauck, Dirk; Schmieder, Stefanie S; Knobel, Martin; Titz, Alexander; Dell, Anne; Haslam, Stuart M; Hengartner, Michael O; Aebi, Markus; Künzler, Markus

    2014-07-01

    Effector proteins of innate immune systems recognize specific non-self epitopes. Tectonins are a family of β-propeller lectins conserved from bacteria to mammals that have been shown to bind bacterial lipopolysaccharide (LPS). We present experimental evidence that two Tectonins of fungal and animal origin have a specificity for O-methylated glycans. We show that Tectonin 2 of the mushroom Laccaria bicolor (Lb-Tec2) agglutinates Gram-negative bacteria and exerts toxicity toward the model nematode Caenorhabditis elegans, suggesting a role in fungal defense against bacteria and nematodes. Biochemical and genetic analysis of these interactions revealed that both bacterial agglutination and nematotoxicity of Lb-Tec2 depend on the recognition of methylated glycans, namely O-methylated mannose and fucose residues, as part of bacterial LPS and nematode cell-surface glycans. In addition, a C. elegans gene, termed samt-1, coding for a candidate membrane transport protein for the presumptive donor substrate of glycan methylation, S-adenosyl-methionine, from the cytoplasm to the Golgi was identified. Intriguingly, limulus lectin L6, a structurally related antibacterial protein of the Japanese horseshoe crab Tachypleus tridentatus, showed properties identical to the mushroom lectin. These results suggest that O-methylated glycans constitute a conserved target of the fungal and animal innate immune system. The broad phylogenetic distribution of O-methylated glycans increases the spectrum of potential antagonists recognized by Tectonins, rendering this conserved protein family a universal defense armor. PMID:24879441

  19. Methylated glycans as conserved targets of animal and fungal innate defense

    PubMed Central

    Wohlschlager, Therese; Butschi, Alex; Grassi, Paola; Sutov, Grigorij; Gauss, Robert; Hauck, Dirk; Schmieder, Stefanie S.; Knobel, Martin; Titz, Alexander; Dell, Anne; Haslam, Stuart M.; Hengartner, Michael O.; Aebi, Markus; Künzler, Markus

    2014-01-01

    Effector proteins of innate immune systems recognize specific non-self epitopes. Tectonins are a family of β-propeller lectins conserved from bacteria to mammals that have been shown to bind bacterial lipopolysaccharide (LPS). We present experimental evidence that two Tectonins of fungal and animal origin have a specificity for O-methylated glycans. We show that Tectonin 2 of the mushroom Laccaria bicolor (Lb-Tec2) agglutinates Gram-negative bacteria and exerts toxicity toward the model nematode Caenorhabditis elegans, suggesting a role in fungal defense against bacteria and nematodes. Biochemical and genetic analysis of these interactions revealed that both bacterial agglutination and nematotoxicity of Lb-Tec2 depend on the recognition of methylated glycans, namely O-methylated mannose and fucose residues, as part of bacterial LPS and nematode cell-surface glycans. In addition, a C. elegans gene, termed samt-1, coding for a candidate membrane transport protein for the presumptive donor substrate of glycan methylation, S-adenosyl-methionine, from the cytoplasm to the Golgi was identified. Intriguingly, limulus lectin L6, a structurally related antibacterial protein of the Japanese horseshoe crab Tachypleus tridentatus, showed properties identical to the mushroom lectin. These results suggest that O-methylated glycans constitute a conserved target of the fungal and animal innate immune system. The broad phylogenetic distribution of O-methylated glycans increases the spectrum of potential antagonists recognized by Tectonins, rendering this conserved protein family a universal defense armor. PMID:24879441

  20. Leaf and Root-Associated Fungal Assemblages Do Not Follow Similar Elevational Diversity Patterns

    PubMed Central

    Coince, Aurore; Cordier, Tristan; Lengellé, Juliette; Defossez, Emmanuel; Vacher, Corinne; Robin, Cécile

    2014-01-01

    The diversity of fungi along environmental gradients has been little explored in contrast to plants and animals. Consequently, environmental factors influencing the composition of fungal assemblages are poorly understood. The aim of this study was to determine whether the diversity and composition of leaf and root-associated fungal assemblages vary with elevation and to investigate potential explanatory variables. High-throughput sequencing of the Internal Transcribed Spacer 1 region was used to explore fungal assemblages along three elevation gradients, located in French mountainous regions. Beech forest was selected as a study system to minimise the host effect. The variation in species richness and specific composition was investigated for ascomycetes and basidiomycetes assemblages with a particular focus on root-associated ectomycorrhizal fungi. The richness of fungal communities associated with leaves or roots did not significantly relate to any of the tested environmental drivers, i.e. elevation, mean temperature, precipitation or edaphic variables such as soil pH or the ratio carbon∶nitrogen. Nevertheless, the ascomycete species richness peaked at mid-temperature, illustrating a mid-domain effect model. We found that leaf and root-associated fungal assemblages did not follow similar patterns of composition with elevation. While the composition of the leaf-associated fungal assemblage correlated primarily with the mean annual temperature, the composition of root-associated fungal assemblage was explained equally by soil pH and by temperature. The ectomycorrhizal composition was also related to these variables. Our results therefore suggest that above and below-ground fungal assemblages are not controlled by the same main environmental variables. This may be due to the larger amplitude of climatic variables in the tree foliage compared to the soil environment. PMID:24971637

  1. Unexpectedly High Beta-Diversity of Root-Associated Fungal Communities in the Bolivian Andes.

    PubMed

    Barnes, Christopher J; Maldonado, Carla; Frøslev, Tobias G; Antonelli, Alexandre; Rønsted, Nina

    2016-01-01

    Bolivia is one of the most biologically diverse countries on the planet. Between the Andes and the Amazon drainage basin spans the Yungas, a vast forested region shown to be extremely species rich in macro-organisms. However, it remains unclear whether this high diversity is also reflected in microbial diversity. Here we assess the genetic, taxonomic and functional diversity of root-associated fungi surrounding Cinchona calisaya trees, a typical element of the intermediate altitudes of the Bolivian Yungas. We determine the relative effects of edaphic properties, climate, and geography in regulating fungal community assembly. We show that α-diversity for these fungal communities was similar to temperate and arid ecosystems, averaging 90.1 operational taxonomic units (OTUs) per sample, with reads predominantly assigned to the Ascomycota phylum and with a saprotrophic lifestyle. ß-diversity was calculated as the distance-decay rate, and in contrast to α-diversity, was exceptionally high with a rate of -0.407. Soil properties (pH and P) principally regulated fungal community assembly in an analogous manner to temperate environments, with pH and phosphorus explaining 7.8 and 7.2% of community variation respectively. Surprisingly, altitude does not influence community formation, and there is limited evidence that climate (precipitation and temperature) play a role. Our results suggest that sampling should be performed over a wide geographical and environmental range in order to capture the full root-associated fungal diversity in subtropical regions. This study sheds further light on the diversity and distribution of the world's "hidden biodiversity." PMID:27630629

  2. Unexpectedly High Beta-Diversity of Root-Associated Fungal Communities in the Bolivian Andes

    PubMed Central

    Barnes, Christopher J.; Maldonado, Carla; Frøslev, Tobias G.; Antonelli, Alexandre; Rønsted, Nina

    2016-01-01

    Bolivia is one of the most biologically diverse countries on the planet. Between the Andes and the Amazon drainage basin spans the Yungas, a vast forested region shown to be extremely species rich in macro-organisms. However, it remains unclear whether this high diversity is also reflected in microbial diversity. Here we assess the genetic, taxonomic and functional diversity of root-associated fungi surrounding Cinchona calisaya trees, a typical element of the intermediate altitudes of the Bolivian Yungas. We determine the relative effects of edaphic properties, climate, and geography in regulating fungal community assembly. We show that α-diversity for these fungal communities was similar to temperate and arid ecosystems, averaging 90.1 operational taxonomic units (OTUs) per sample, with reads predominantly assigned to the Ascomycota phylum and with a saprotrophic lifestyle. ß-diversity was calculated as the distance-decay rate, and in contrast to α-diversity, was exceptionally high with a rate of −0.407. Soil properties (pH and P) principally regulated fungal community assembly in an analogous manner to temperate environments, with pH and phosphorus explaining 7.8 and 7.2% of community variation respectively. Surprisingly, altitude does not influence community formation, and there is limited evidence that climate (precipitation and temperature) play a role. Our results suggest that sampling should be performed over a wide geographical and environmental range in order to capture the full root-associated fungal diversity in subtropical regions. This study sheds further light on the diversity and distribution of the world's “hidden biodiversity.” PMID:27630629

  3. Unexpectedly High Beta-Diversity of Root-Associated Fungal Communities in the Bolivian Andes.

    PubMed

    Barnes, Christopher J; Maldonado, Carla; Frøslev, Tobias G; Antonelli, Alexandre; Rønsted, Nina

    2016-01-01

    Bolivia is one of the most biologically diverse countries on the planet. Between the Andes and the Amazon drainage basin spans the Yungas, a vast forested region shown to be extremely species rich in macro-organisms. However, it remains unclear whether this high diversity is also reflected in microbial diversity. Here we assess the genetic, taxonomic and functional diversity of root-associated fungi surrounding Cinchona calisaya trees, a typical element of the intermediate altitudes of the Bolivian Yungas. We determine the relative effects of edaphic properties, climate, and geography in regulating fungal community assembly. We show that α-diversity for these fungal communities was similar to temperate and arid ecosystems, averaging 90.1 operational taxonomic units (OTUs) per sample, with reads predominantly assigned to the Ascomycota phylum and with a saprotrophic lifestyle. ß-diversity was calculated as the distance-decay rate, and in contrast to α-diversity, was exceptionally high with a rate of -0.407. Soil properties (pH and P) principally regulated fungal community assembly in an analogous manner to temperate environments, with pH and phosphorus explaining 7.8 and 7.2% of community variation respectively. Surprisingly, altitude does not influence community formation, and there is limited evidence that climate (precipitation and temperature) play a role. Our results suggest that sampling should be performed over a wide geographical and environmental range in order to capture the full root-associated fungal diversity in subtropical regions. This study sheds further light on the diversity and distribution of the world's "hidden biodiversity."

  4. Unexpectedly High Beta-Diversity of Root-Associated Fungal Communities in the Bolivian Andes

    PubMed Central

    Barnes, Christopher J.; Maldonado, Carla; Frøslev, Tobias G.; Antonelli, Alexandre; Rønsted, Nina

    2016-01-01

    Bolivia is one of the most biologically diverse countries on the planet. Between the Andes and the Amazon drainage basin spans the Yungas, a vast forested region shown to be extremely species rich in macro-organisms. However, it remains unclear whether this high diversity is also reflected in microbial diversity. Here we assess the genetic, taxonomic and functional diversity of root-associated fungi surrounding Cinchona calisaya trees, a typical element of the intermediate altitudes of the Bolivian Yungas. We determine the relative effects of edaphic properties, climate, and geography in regulating fungal community assembly. We show that α-diversity for these fungal communities was similar to temperate and arid ecosystems, averaging 90.1 operational taxonomic units (OTUs) per sample, with reads predominantly assigned to the Ascomycota phylum and with a saprotrophic lifestyle. ß-diversity was calculated as the distance-decay rate, and in contrast to α-diversity, was exceptionally high with a rate of −0.407. Soil properties (pH and P) principally regulated fungal community assembly in an analogous manner to temperate environments, with pH and phosphorus explaining 7.8 and 7.2% of community variation respectively. Surprisingly, altitude does not influence community formation, and there is limited evidence that climate (precipitation and temperature) play a role. Our results suggest that sampling should be performed over a wide geographical and environmental range in order to capture the full root-associated fungal diversity in subtropical regions. This study sheds further light on the diversity and distribution of the world's “hidden biodiversity.”

  5. 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

  6. 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

  7. 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.

  8. 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

  9. Book review: Black bass diversity: Multidisciplinary science for conservation

    USGS Publications Warehouse

    Jelks, Howard

    2016-01-01

    Review info: Black bass diversity: Multidisciplinary science for conservation. Edited by Michael D. Tringali, James M. Long, Timothy W. Birdsong, and Michael S. Allen, 2015. ISBN: 978-1-934874-40-0, 685 pp.

  10. Fungal diversity is not determined by mineral and chemical differences in serpentine substrates.

    PubMed

    Daghino, Stefania; Murat, Claude; Sizzano, Elisa; Girlanda, Mariangela; Perotto, Silvia

    2012-01-01

    The physico-chemical properties of serpentine soils lead to strong selection of plant species. Whereas many studies have described the serpentine flora, little information is available on the fungal communities dwelling in these sites. Asbestos minerals, often associated with serpentine rocks, can be weathered by serpentine-isolated fungi, suggesting an adaptation to this substrate. In this study, we have investigated whether serpentine substrates characterized by the presence of rocks with distinct mineral composition could select for different fungal communities. Both fungal isolation and 454 pyrosequencing of amplicons obtained from serpentine samples following direct DNA extraction revealed some fungal taxa shared by the four ophiolitic substrates, but also highlighted several substrate-specific taxa. Bootstrap analysis of 454 OTU abundances indicated weak clustering of fungal assemblages from the different substrates, which did not match substrate classification based on exchangeable macronutrients and metals. Intra-substrate variability, as assessed by DGGE profiles, was similar across the four serpentine substrates, and comparable to inter-substrate variability. These findings indicate the absence of a correlation between the substrate (mineral composition and available cations) and the diversity of the fungal community. Comparison of culture-based and culture-independent methods supports the higher taxonomic precision of the former, as complementation of the better performance of the latter.

  11. High fungal diversity and abundance recovered in the deep-sea sediments of the Pacific Ocean.

    PubMed

    Xu, Wei; Pang, Ka-Lai; Luo, Zhu-Hua

    2014-11-01

    Knowledge about the presence and ecological significance of bacteria and archaea in the deep-sea environments has been well recognized, but the eukaryotic microorganisms, such as fungi, have rarely been reported. The present study investigated the composition and abundance of fungal community in the deep-sea sediments of the Pacific Ocean. In this study, a total of 1,947 internal transcribed spacer (ITS) regions of fungal rRNA gene clones were recovered from five sediment samples at the Pacific Ocean (water depths ranging from 5,017 to 6,986 m) using three different PCR primer sets. There were 16, 17, and 15 different operational taxonomic units (OTUs) identified from fungal-universal, Ascomycota-, and Basidiomycota-specific clone libraries, respectively. Majority of the recovered sequences belonged to diverse phylotypes of Ascomycota (25 phylotypes) and Basidiomycota (18 phylotypes). The multiple primer approach totally recovered 27 phylotypes which showed low similarities (≤97 %) with available fungal sequences in the GenBank, suggesting possible new fungal taxa occurring in the deep-sea environments or belonging to taxa not represented in the GenBank. Our results also recovered high fungal LSU rRNA gene copy numbers (3.52 × 10(6) to 5.23 × 10(7)copies/g wet sediment) from the Pacific Ocean sediment samples, suggesting that the fungi might be involved in important ecological functions in the deep-sea environments.

  12. Fungal diversity from deep marine subsurface sediments (IODP 317, Canterbury Basin, New Zealand)

    NASA Astrophysics Data System (ADS)

    Redou, V.; Arzur, D.; Burgaud, G.; Barbier, G.

    2012-12-01

    Recent years have seen a growing interest regarding micro-eukaryotic communities in extreme environments as a third microbial domain after Bacteria and Archaea. However, knowledge is still scarce and the diversity of micro-eukaryotes in such environments remains hidden and their ecological role unknown. Our research program is based on the deep sedimentary layers of the Canterbury Basin in New Zealand (IODP 317) from the subsurface to the record depth of 1884 meters below seafloor. The objectives of our study are (i) to assess the genetic diversity of fungi in deep-sea sediments and (ii) identify the functional part in order to better understand the origin and the ecological role of fungal communities in this extreme ecosystem. Fingerprinting-based methods using capillary electrophoresis single-strand conformation polymorphism and denaturing high-performance liquid chromatography were used as a first step to raise our objectives. Molecular fungal diversity was assessed using amplification of ITS1 (Internal Transcribed Spacer 1) as a biomarker on 11 samples sediments from 3.76 to 1884 meters below seafloor. Fungal molecular signatures were detected throughout the sediment core. The phyla Ascomycota and Basidiomycota were revealed with DNA as well as cDNA. Most of the phylotypes are affiliated to environmental sequences and some to common fungal cultured species. The discovery of a present and metabolically active fungal component in this unique ecosystem allows some interesting first hypotheses that will be further combined to culture-based methods and deeper molecular methods (454 pyrosequencing) to highlight essential informations regarding physiology and ecological role of fungal communities in deep marine sediments.

  13. Biogeography in the Air: Fungal Diversity over Land and Oceans

    EPA Science Inventory

    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...

  14. Low multifunctional redundancy of soil fungal diversity at multiple scales.

    PubMed

    Mori, Akira S; Isbell, Forest; Fujii, Saori; Makoto, Kobayashi; Matsuoka, Shunsuke; Osono, Takashi

    2016-03-01

    Theory suggests that biodiversity might help sustain multiple ecosystem functions. To evaluate possible biodiversity-multifunctionality relationships in a natural setting, we considered different spatial scales of diversity metrics for soil fungi in the northern forests of Japan. We found that multifunctionality increased with increasing local species richness, suggesting a limited degree of multifunctional redundancy. This diversity-multifunctionality relationship was independent of the compositional uniqueness of each community. However, we still found the importance of community composition, because there was a positive correlation between community dissimilarity and multifunctional dissimilarity across the landscape. This result suggests that functional redundancy can further decrease when spatial variations in identities of both species and functions are simultaneously considered at larger spatial scales. We speculate that different scales of diversity could provide multiple levels of insurance against the loss of functioning if high-levels of local species diversity and compositional variation across locations are both maintained. Alternatively, making species assemblages depauperate may result in the loss of multifunctionality. PMID:26689733

  15. Leaf-associated fungal diversity in acidified streams: insights from combining traditional and molecular approaches.

    PubMed

    Clivot, Hugues; Cornut, Julien; Chauvet, Eric; Elger, Arnaud; Poupin, Pascal; Guérold, François; Pagnout, Christophe

    2014-07-01

    We combined microscopic and molecular methods to investigate fungal assemblages on alder leaf litter exposed in the benthic and hyporheic zones of five streams across a gradient of increasing acidification for 4 weeks. The results showed that acidification and elevated Al concentrations strongly depressed sporulating aquatic hyphomycetes diversity in both zones of streams, while fungal diversity assessed by denaturing gradient gel electrophoresis (DGGE) appeared unaffected. Clone library analyses revealed that fungal communities on leaves were dominated by members of Ascomycetes and to a lesser extent by Basidiomycetes and Chytridiomycetes. An important contribution of terrestrial fungi was observed in both zones of the most acidified stream and in the hyporheic zone of the reference circumneutral stream. The highest leaf breakdown rate was observed in the circumneutral stream and occurred in the presence of both the highest diversity of sporulating aquatic hyphomycetes and the highest contribution to clone libraries of sequences affiliated with aquatic hyphomycetes. Both methods underline the major role played by aquatic hyphomycetes in leaf decomposition process. Our findings also bring out new highlights on the identity of leaf-associated fungal communities and their responses to anthropogenic alteration of running water ecosystems.

  16. Daldionin, an Unprecedented Binaphthyl Derivative, and Diverse Polyketide Congeners from a Fungal Orchid Endophyte.

    PubMed

    Barnes, Emma C; Jumpathong, Juangjun; Lumyong, Saisamorn; Voigt, Kerstin; Hertweck, Christian

    2016-03-18

    Thailand possesses a rich diversity of orchid species that, in turn, live in symbiosis with a wide variety of fungi. Such endophytes have the potential to produce secondary metabolites with bioactivity against orchid and/or human pathogens. The orchid-associated fungal strain Daldinia eschscholtzii was found to produce a diverse range of aromatic polyketides including the new naphthalene derivatives daldionin, nodulones B and C, and daldinones F and G along with eight known compounds. Daldionin possesses an unprecedented oxane-linked binaphthyl ring system. These compounds demonstrate the high diversity of structural variations that are constructed during fungal biosynthesis, and the results include important observations concerning the biosynthesis of binaphthyl derivatives. Daldionin was found to have weak antiproliferative activity against HUVEC and K-562 cell lines. All but one of the isolated compounds showed moderate antimicrobial activity towards at least one of the four tested microbial strains. PMID:26880363

  17. Daldionin, an Unprecedented Binaphthyl Derivative, and Diverse Polyketide Congeners from a Fungal Orchid Endophyte.

    PubMed

    Barnes, Emma C; Jumpathong, Juangjun; Lumyong, Saisamorn; Voigt, Kerstin; Hertweck, Christian

    2016-03-18

    Thailand possesses a rich diversity of orchid species that, in turn, live in symbiosis with a wide variety of fungi. Such endophytes have the potential to produce secondary metabolites with bioactivity against orchid and/or human pathogens. The orchid-associated fungal strain Daldinia eschscholtzii was found to produce a diverse range of aromatic polyketides including the new naphthalene derivatives daldionin, nodulones B and C, and daldinones F and G along with eight known compounds. Daldionin possesses an unprecedented oxane-linked binaphthyl ring system. These compounds demonstrate the high diversity of structural variations that are constructed during fungal biosynthesis, and the results include important observations concerning the biosynthesis of binaphthyl derivatives. Daldionin was found to have weak antiproliferative activity against HUVEC and K-562 cell lines. All but one of the isolated compounds showed moderate antimicrobial activity towards at least one of the four tested microbial strains.

  18. Evolution of genomic diversity and sex at extreme environments: Fungal life under hypersaline Dead Sea stress

    PubMed Central

    Kis-Papo, Tamar; Kirzhner, Valery; Wasser, Solomon P.; Nevo, Eviatar

    2003-01-01

    We have found that genomic diversity is generally positively correlated with abiotic and biotic stress levels (1–3). However, beyond a high-threshold level of stress, the diversity declines to a few adapted genotypes. The Dead Sea is the harshest planetary hypersaline environment (340 g·liter–1 total dissolved salts, ≈10 times sea water). Hence, the Dead Sea is an excellent natural laboratory for testing the “rise and fall” pattern of genetic diversity with stress proposed in this article. Here, we examined genomic diversity of the ascomycete fungus Aspergillus versicolor from saline, nonsaline, and hypersaline Dead Sea environments. We screened the coding and noncoding genomes of A. versicolor isolates by using >600 AFLP (amplified fragment length polymorphism) markers (equal to loci). Genomic diversity was positively correlated with stress, culminating in the Dead Sea surface but dropped drastically in 50- to 280-m-deep seawater. The genomic diversity pattern paralleled the pattern of sexual reproduction of fungal species across the same southward gradient of increasing stress in Israel. This parallel may suggest that diversity and sex are intertwined intimately according to the rise and fall pattern and adaptively selected by natural selection in fungal genome evolution. Future large-scale verification in micromycetes will define further the trajectories of diversity and sex in the rise and fall pattern. PMID:14645702

  19. Severe plant invasions can increase mycorrhizal fungal abundance and diversity.

    PubMed

    Lekberg, Ylva; Gibbons, Sean M; Rosendahl, Søren; Ramsey, Philip W

    2013-07-01

    Invasions by non-native plants can alter ecosystem functions and reduce native plant diversity, but relatively little is known about their effect on belowground microbial communities. We show that invasions by knapweed (Centaurea stoebe) and leafy spurge (Euphorbia esula, hereafter spurge)--but not cheatgrass (Bromus tectorum)--support a higher abundance and diversity of symbiotic arbuscular mycorrhizal fungi (AMF) than multi-species native plant communities. The higher AMF richness associated with knapweed and spurge is unlikely due to a co-invasion by AMF, because a separate sampling showed that individual native forbs hosted a similar AMF abundance and richness as exotic forbs. Native grasses associated with fewer AMF taxa, which could explain the reduced AMF richness in native, grass-dominated communities. The three invasive plant species harbored distinct AMF communities, and analyses of co-occurring native and invasive plants indicate that differences were partly driven by the invasive plants and were not the result of pre-invasion conditions. Our results suggest that invasions by mycotrophic plants that replace poorer hosts can increase AMF abundance and richness. The high AMF richness in monodominant plant invasions also indicates that the proposed positive relationship between above and belowground diversity is not always strong. Finally, the disparate responses among exotic plants and consistent results between grasses and forbs suggest that AMF respond more to plant functional group than plant provenance.

  20. Biological diversity conservation: A public policy perspective

    NASA Astrophysics Data System (ADS)

    Pipkin, James

    1996-11-01

    While extinctions of individual species are part of a normal cycle, the current rate of extinctions should be a concern to us all. The maintenance of biological diversity is important for utilitarian reasons, quality of life considerations, and because biodiversity is important to sustainable regional economies. Single-species approaches are too limited to protect biodiversity at the landscape, habitat, and watershed levels. New approaches are necessary to deal with the complexity of biological diversity. The administration is using provisions in the Endangered Species Act to bring about broader multispecies habitat protection. The ecosystem approach provides a framework for ensuring that ecological considerations are taken into account, along with economic and social factors, and that all interested parties are able to participate in the decision-making process.

  1. Long-term phosphorus fertilization impacts soil fungal and bacterial diversity but not AM fungal community in alfalfa.

    PubMed

    Beauregard, M S; Hamel, C; Atul-Nayyar; St-Arnaud, M

    2010-02-01

    Soil function may be affected by cropping practices impacting the soil microbial community. The effect of different phosphorus (P) fertilization rates (0, 20, or 40 kg P(2)O(5) ha(-1)) on soil microbial diversity was studied in 8-year-old alfalfa monocultures. The hypothesis that P fertilization modifies soil microbial community was tested using denaturing gradient gel electrophoresis and phospholipids fatty acid (PLFA) profiling to describe soil bacteria, fungi, and arbuscular mycorrhizal (AM) fungi diversity. Soil parameters related to fertility (soil phosphate flux, soluble P, moisture, phosphatase and dehydrogenase assays, and carbon and nitrogen content of the light fraction of soil organic matter) were also monitored and related to soil microbial ribotype profiles. Change in soil P fertility with the application of fertilizer had no effect on crop yield in 8 years, but on the year of this study was associated with shifts in the composition of fungal and bacterial communities without affecting their richness, as evidenced by the absence of effect on the average number of ribotypes detected. However, variation in soil P level created by a history of differential fertilization did not significantly influence AM fungi ribotype assemblages nor AM fungi biomass measured with the PLFA 16:1omega5. Fertilization increased P flux and soil soluble P level but reduced soil moisture and soil microbial activity, as revealed by dehydrogenase assay. Results suggest that soil P fertility management could influence soil processes involving soil microorganisms. Seasonal variations were also recorded in microbial activity, soil soluble P level as well as in the abundance of specific bacterial and fungal PLFA indicators of soil microbial biomass.

  2. Tree diversity and the role of non-host neighbour tree species in reducing fungal pathogen infestation

    PubMed Central

    Hantsch, Lydia; Bien, Steffen; Radatz, Stine; Braun, Uwe; Auge, Harald; Bruelheide, Helge

    2014-01-01

    The degree to which plant pathogen infestation occurs in a host plant is expected to be strongly influenced by the level of species diversity among neighbouring host and non-host plant species. Since pathogen infestation can negatively affect host plant performance, it can mediate the effects of local biodiversity on ecosystem functioning. We tested the effects of tree diversity and the proportion of neighbouring host and non-host species with respect to the foliar fungal pathogens of Tilia cordata and Quercus petraea in the Kreinitz tree diversity experiment in Germany. We hypothesized that fungal pathogen richness increases while infestation decreases with increasing local tree diversity. In addition, we tested whether fungal pathogen richness and infestation are dependent on the proportion of host plant species present or on the proportion of particular non-host neighbouring tree species. Leaves of the two target species were sampled across three consecutive years with visible foliar fungal pathogens on the leaf surface being identified macro- and microscopically. Effects of diversity among neighbouring trees were analysed: (i) for total fungal species richness and fungal infestation on host trees and (ii) for infestation by individual fungal species. We detected four and five fungal species on T. cordata and Q. petraea, respectively. High local tree diversity reduced (i) total fungal species richness and infestation of T. cordata and fungal infestation of Q. petraea and (ii) infestation by three host-specialized fungal pathogen species. These effects were brought about by local tree diversity and were independent of host species proportion. In general, host species proportion had almost no effect on fungal species richness and infestation. Strong effects associated with the proportion of particular non-host neighbouring tree species on fungal species richness and infestation were, however, recorded. Synthesis. For the first time, we experimentally

  3. Exploring fungal diversity in deep-sea sediments from Okinawa Trough using high-throughput Illumina sequencing

    NASA Astrophysics Data System (ADS)

    Zhang, Xiao-Yong; Wang, Guang-Hua; Xu, Xin-Ya; Nong, Xu-Hua; Wang, Jie; Amin, Muhammad; Qi, Shu-Hua

    2016-10-01

    The present study investigated the fungal diversity in four different deep-sea sediments from Okinawa Trough using high-throughput Illumina sequencing of the nuclear ribosomal internal transcribed spacer-1 (ITS1). A total of 40,297 fungal ITS1 sequences clustered into 420 operational taxonomic units (OTUs) with 97% sequence similarity and 170 taxa were recovered from these sediments. Most ITS1 sequences (78%) belonged to the phylum Ascomycota, followed by Basidiomycota (17.3%), Zygomycota (1.5%) and Chytridiomycota (0.8%), and a small proportion (2.4%) belonged to unassigned fungal phyla. Compared with previous studies on fungal diversity of sediments from deep-sea environments by culture-dependent approach and clone library analysis, the present result suggested that Illumina sequencing had been dramatically accelerating the discovery of fungal community of deep-sea sediments. Furthermore, our results revealed that Sordariomycetes was the most diverse and abundant fungal class in this study, challenging the traditional view that the diversity of Sordariomycetes phylotypes was low in the deep-sea environments. In addition, more than 12 taxa accounted for 21.5% sequences were found to be rarely reported as deep-sea fungi, suggesting the deep-sea sediments from Okinawa Trough harbored a plethora of different fungal communities compared with other deep-sea environments. To our knowledge, this study is the first exploration of the fungal diversity in deep-sea sediments from Okinawa Trough using high-throughput Illumina sequencing.

  4. Distribution and diversity of fungal species in and adjacent to the Los Alamos National Laboratory

    SciTech Connect

    Balice, R.G.; Jarmie, N.; Rogers, F.J.

    1997-12-01

    Fungi have demonstrated their ability to diversify and specialize to take advantage of new environments (Murphy 1996). These species are essential to the normal functioning of ecosystems and the impacts of human activities may be harmful to fungi. There is a need to inventory fungi throughout the range of their environments. Previously archived information representing 43 sample locations was used to perform a preliminary evaluation of the distributions and diversity of fungal species at the Los Alamos National Laboratory and in adjacent environments. Presence-absence data for 71 species of fungi in five habitats, pinon-juniper, canyon-bottom ponderosa pine, ponderosa pine, canyon-bottom mixed conifer, and mixed conifer were analyzed. The results indicate that even though fungi occur in each of the habitats, fungal species are not distributed evenly among these habitats. The richness of fungal species is greater in the canyon-bottom mixed conifer and mixed conifer habitats than in the pinon-juniper, canyon-bottom ponderosa pine or ponderosa pine habitats. All but three of the fungal species were recorded in either the canyon-bottom mixed conifer or the mixed conifer habitats, and all but seven of the fungal species were found in the mixed conifer habitat.

  5. Host associations and beta diversity of fungal endophyte communities in New Guinea rainforest trees.

    PubMed

    Vincent, J B; Weiblen, G D; May, G

    2016-02-01

    Processes shaping the distribution of foliar fungal endophyte species remain poorly understood. Despite increasing evidence that these cryptic fungal symbionts of plants mediate interactions with pathogens and herbivores, there remain basic questions regarding the extent to which dispersal limitation and host specificity might shape fungal endophyte community composition in rainforests. To assess the relative importance of spatial pattern and host specificity, we isolated fungi from a sample of mapped trees in lowland Papua New Guinea. Sequences of the internal transcribed spacer (ITS) region were obtained for 2079 fungal endophytes from three sites and clustered into molecular operational taxonomic units (MOTUs) at 95% similarity. Multivariate analyses suggest that host affinity plays a significant role in structuring endophyte community composition whereas there was no evidence of endophyte spatial pattern at the scale of tens to hundreds of metres. Differences in endophyte communities between sampled trees were weakly correlated with variation in foliar traits but not with tree species relatedness. The dominance of relatively few generalist endophytes and the presence of a large number of rare MOTUs was a consistent observation at three sites separated by hundreds of kilometres and regional turnover was low. Host specificity appears to play a relatively weak but more important role than dispersal limitation in shaping the distribution of fungal endophyte communities in New Guinea forests. Our results suggest that in the absence of strong ecological gradients and host turnover, beta diversity of endophyte communities could be low in large areas of contiguous forest.

  6. Host associations and beta diversity of fungal endophyte communities in New Guinea rainforest trees.

    PubMed

    Vincent, J B; Weiblen, G D; May, G

    2016-02-01

    Processes shaping the distribution of foliar fungal endophyte species remain poorly understood. Despite increasing evidence that these cryptic fungal symbionts of plants mediate interactions with pathogens and herbivores, there remain basic questions regarding the extent to which dispersal limitation and host specificity might shape fungal endophyte community composition in rainforests. To assess the relative importance of spatial pattern and host specificity, we isolated fungi from a sample of mapped trees in lowland Papua New Guinea. Sequences of the internal transcribed spacer (ITS) region were obtained for 2079 fungal endophytes from three sites and clustered into molecular operational taxonomic units (MOTUs) at 95% similarity. Multivariate analyses suggest that host affinity plays a significant role in structuring endophyte community composition whereas there was no evidence of endophyte spatial pattern at the scale of tens to hundreds of metres. Differences in endophyte communities between sampled trees were weakly correlated with variation in foliar traits but not with tree species relatedness. The dominance of relatively few generalist endophytes and the presence of a large number of rare MOTUs was a consistent observation at three sites separated by hundreds of kilometres and regional turnover was low. Host specificity appears to play a relatively weak but more important role than dispersal limitation in shaping the distribution of fungal endophyte communities in New Guinea forests. Our results suggest that in the absence of strong ecological gradients and host turnover, beta diversity of endophyte communities could be low in large areas of contiguous forest. PMID:26661903

  7. Effects of species diversity on establishment and coexistence: a phylloplane fungal community model system.

    PubMed

    Stohr, S N; Dighton, J

    2004-10-01

    A model system was devised, evaluating the influence that species diversity (species richness) has on fungal establishment and coexistence. Seven members of the fungal phylloplane community of Vaccinium macrocarpon (American cranberry) were selected to assess how species diversity affected development and coexistence of another community member, Pestalotia vaccinii. Pestalotia was engaged in competitive interactions on 1% Malt Extract Agar (MEA) petri dishes with each of the seven individual saprotrophs (two-way interaction), in random combinations with three of the seven saprotrophs (four-way interaction), and in random combinations with five of the seven saprotrophs (six-way interaction). The saprotrophic fungi used in this study were Aspergillus sp., Alternaria alternata, Cladosporium cladosporoides, Curvularia lunata, Epicoccum purpuracens, Penicillium sp., and Pithomyces chartarum. We hypothesized that species diversity would have a significant impact on the establishment and coexistence of Pestalotia vaccinii in culture. In an effort to minimize density-dependent effects, the number of viable spores employed in the three types of interactions was kept constant. Target spore concentrations of 50 viable spores of P. vaccinii and 50 saprotroph spores were used, regardless of the number of species involved in the interaction. This proved to be a very important factor in the experiment. As our results show, species diversity had little or no effect on the establishment and coexistence of Pestalotia vaccinii; however, spore density played an extremely important role in the establishment and development of fungal propagules in our model. PMID:15692863

  8. Effects of species diversity on establishment and coexistence: a phylloplane fungal community model system.

    PubMed

    Stohr, S N; Dighton, J

    2004-10-01

    A model system was devised, evaluating the influence that species diversity (species richness) has on fungal establishment and coexistence. Seven members of the fungal phylloplane community of Vaccinium macrocarpon (American cranberry) were selected to assess how species diversity affected development and coexistence of another community member, Pestalotia vaccinii. Pestalotia was engaged in competitive interactions on 1% Malt Extract Agar (MEA) petri dishes with each of the seven individual saprotrophs (two-way interaction), in random combinations with three of the seven saprotrophs (four-way interaction), and in random combinations with five of the seven saprotrophs (six-way interaction). The saprotrophic fungi used in this study were Aspergillus sp., Alternaria alternata, Cladosporium cladosporoides, Curvularia lunata, Epicoccum purpuracens, Penicillium sp., and Pithomyces chartarum. We hypothesized that species diversity would have a significant impact on the establishment and coexistence of Pestalotia vaccinii in culture. In an effort to minimize density-dependent effects, the number of viable spores employed in the three types of interactions was kept constant. Target spore concentrations of 50 viable spores of P. vaccinii and 50 saprotroph spores were used, regardless of the number of species involved in the interaction. This proved to be a very important factor in the experiment. As our results show, species diversity had little or no effect on the establishment and coexistence of Pestalotia vaccinii; however, spore density played an extremely important role in the establishment and development of fungal propagules in our model.

  9. The Distant Siblings-A Phylogenomic Roadmap Illuminates the Origins of Extant Diversity in Fungal Aromatic Polyketide Biosynthesis.

    PubMed

    Koczyk, Grzegorz; Dawidziuk, Adam; Popiel, Delfina

    2015-11-01

    In recent years, the influx of newly sequenced fungal genomes has enabled sampling of secondary metabolite biosynthesis on an unprecedented scale. However, explanations of extant diversity which take into account both large-scale phylogeny reconstructions and knowledge gained from multiple genome projects are still lacking. We analyzed the evolutionary sources of genetic diversity in aromatic polyketide biosynthesis in over 100 model fungal genomes. By reconciling the history of over 400 nonreducing polyketide synthases (NR-PKSs) with corresponding species history, we demonstrate that extant fungal NR-PKSs are clades of distant siblings, originating from a burst of duplications in early Pezizomycotina and thinned by extensive losses. The capability of higher fungi to biosynthesize the simplest precursor molecule (orsellinic acid) is highlighted as an ancestral trait underlying biosynthesis of aromatic compounds. This base activity was modified during early evolution of filamentous fungi, toward divergent reaction schemes associated with biosynthesis of, for example, aflatoxins and fusarubins (C4-C9 cyclization) or various anthraquinone derivatives (C6-C11 cyclization). The functional plasticity is further shown to have been supplemented by modularization of domain architecture into discrete pieces (conserved splice junctions within product template domain), as well as tight linkage of key accessory enzyme families and divergence in employed transcriptional factors. Although the majority of discord between species and gene history is explained by ancient duplications, this landscape has been altered by more recent duplications, as well as multiple horizontal gene transfers. The 25 detected transfers include previously undescribed events leading to emergence of, for example, fusarubin biosynthesis in Fusarium genus. Both the underlying data and the results of present analysis (including alternative scenarios revealed by sampling multiple reconciliation optima) are

  10. Bacterial and fungal diversity in the starter production process of Fen liquor, a traditional Chinese liquor.

    PubMed

    Li, Xiao-Ran; Ma, En-Bo; Yan, Liang-Zhen; Meng, Han; Du, Xiao-Wei; Quan, Zhe-Xue

    2013-08-01

    Fermented foods and beverages are important parts of human diet. Fen liquor, a Chinese liquor is a fermented beverage that uses a traditional fermentation process. Starters are the main microbial source and also provide nutrients for microorganisms during fermentation. In this study, starters of Fen liquor were produced through a complex traditional fermentation process. To investigate the community structure and the composition of microorganisms in the starter production process, bacterial 16S rRNA and fungal internal transcribed spacer (ITS) regions were sequenced using clone libraries and pyrosequencing, respectively. There was much higher diversity among the bacteria than among the fungi in the starter production process. Bacteria on the surface of the starters belonged mostly to the Lactobacillaceae family, while members of the Bacillacae family were dominant in the interior of the samples that lacked access to air and water. In the fungi population, diversity was high only in the raw material. In all other samples, nearly all of the fungal sequences were from Pichia kudriavzevii, a member of the Saccharomycetaceae family. Nearly all samples showed similar fungal community structures, indicating that there was little change in the fungal community. To the best of our knowledge, this is the first report to reveal the whole process of the starter production of Chinese traditional liquor. The findings obtained in this study provide new insights into understanding the composition of the microbial community during the traditional Chinese liquor starter production process and information about the production process control and monitoring. PMID:23990293

  11. Diversity and bioprospection of fungal community present in oligotrophic soil of continental Antarctica.

    PubMed

    Godinho, Valéria M; Gonçalves, Vívian N; Santiago, Iara F; Figueredo, Hebert M; Vitoreli, Gislaine A; Schaefer, Carlos E G R; Barbosa, Emerson C; Oliveira, Jaquelline G; Alves, Tânia M A; Zani, Carlos L; Junior, Policarpo A S; Murta, Silvane M F; Romanha, Alvaro J; Kroon, Erna Geessien; Cantrell, Charles L; Wedge, David E; Duke, Stephen O; Ali, Abbas; Rosa, Carlos A; Rosa, Luiz H

    2015-05-01

    We surveyed the diversity and capability of producing bioactive compounds from a cultivable fungal community isolated from oligotrophic soil of continental Antarctica. A total of 115 fungal isolates were obtained and identified in 11 taxa of Aspergillus, Debaryomyces, Cladosporium, Pseudogymnoascus, Penicillium and Hypocreales. The fungal community showed low diversity and richness, and high dominance indices. The extracts of Aspergillus sydowii, Penicillium allii-sativi, Penicillium brevicompactum, Penicillium chrysogenum and Penicillium rubens possess antiviral, antibacterial, antifungal, antitumoral, herbicidal and antiprotozoal activities. Bioactive extracts were examined using (1)H NMR spectroscopy and detected the presence of secondary metabolites with chemical shifts. Our results show that the fungi present in cold-oligotrophic soil from Antarctica included few dominant species, which may have important implications for understanding eukaryotic survival in cold-arid oligotrophic soils. We hypothesize that detailed further investigations may provide a greater understanding of the evolution of Antarctic fungi and their relationships with other organisms described in that region. Additionally, different wild pristine bioactive fungal isolates found in continental Antarctic soil may represent a unique source to discover prototype molecules for use in drug and biopesticide discovery studies.

  12. Global Diversity Hotspots and Conservation Priorities for Sharks

    PubMed Central

    Lucifora, Luis O.; García, Verónica B.; Worm, Boris

    2011-01-01

    Sharks are one of the most threatened groups of marine animals, as high exploitation rates coupled with low resilience to fishing pressure have resulted in population declines worldwide. Designing conservation strategies for this group depends on basic knowledge of the geographic distribution and diversity of known species. So far, this information has been fragmented and incomplete. Here, we have synthesized the first global shark diversity pattern from a new database of published sources, including all 507 species described at present, and have identified hotspots of shark species richness, functional diversity and endemicity from these data. We have evaluated the congruence of these diversity measures and demonstrate their potential use in setting priority areas for shark conservation. Our results show that shark diversity across all species peaks on the continental shelves and at mid-latitudes (30–40 degrees N and S). Global hotspots of species richness, functional diversity and endemicity were found off Japan, Taiwan, the East and West coasts of Australia, Southeast Africa, Southeast Brazil and Southeast USA. Moreover, some areas with low to moderate species richness such as Southern Australia, Angola, North Chile and Western Continental Europe stood out as places of high functional diversity. Finally, species affected by shark finning showed different patterns of diversity, with peaks closer to the Equator and a more oceanic distribution overall. Our results show that the global pattern of shark diversity is uniquely different from land, and other well-studied marine taxa, and may provide guidance for spatial approaches to shark conservation. However, similar to terrestrial ecosystems, protected areas based on hotspots of diversity and endemism alone would provide insufficient means for safeguarding the diverse functional roles that sharks play in marine ecosystems. PMID:21573162

  13. Global diversity hotspots and conservation priorities for sharks.

    PubMed

    Lucifora, Luis O; García, Verónica B; Worm, Boris

    2011-01-01

    Sharks are one of the most threatened groups of marine animals, as high exploitation rates coupled with low resilience to fishing pressure have resulted in population declines worldwide. Designing conservation strategies for this group depends on basic knowledge of the geographic distribution and diversity of known species. So far, this information has been fragmented and incomplete. Here, we have synthesized the first global shark diversity pattern from a new database of published sources, including all 507 species described at present, and have identified hotspots of shark species richness, functional diversity and endemicity from these data. We have evaluated the congruence of these diversity measures and demonstrate their potential use in setting priority areas for shark conservation. Our results show that shark diversity across all species peaks on the continental shelves and at mid-latitudes (30-40 degrees N and S). Global hotspots of species richness, functional diversity and endemicity were found off Japan, Taiwan, the East and West coasts of Australia, Southeast Africa, Southeast Brazil and Southeast USA. Moreover, some areas with low to moderate species richness such as Southern Australia, Angola, North Chile and Western Continental Europe stood out as places of high functional diversity. Finally, species affected by shark finning showed different patterns of diversity, with peaks closer to the Equator and a more oceanic distribution overall. Our results show that the global pattern of shark diversity is uniquely different from land, and other well-studied marine taxa, and may provide guidance for spatial approaches to shark conservation. However, similar to terrestrial ecosystems, protected areas based on hotspots of diversity and endemism alone would provide insufficient means for safeguarding the diverse functional roles that sharks play in marine ecosystems.

  14. 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.

  15. Detection and diversity of fungal nitric oxide reductase genes (p450nor) in agricultural soils

    DOE PAGES

    Higgins, Steven A.; Welsh, Allana; Orellana, Luis H.; Konstantinidis, Konstantinos T.; Chee-Sanford, Joanne C.; Sanford, Robert A.; Schadt, Christopher W.; Löffler, Frank E.

    2016-03-11

    Members of the Fungi convert nitrate (NO3-) and nitrite (NO2-) to gaseous nitrous oxide (N2O) (denitrification), but the fungal contributions to N-loss from soil remain uncertain. Cultivation-based methodologies that include antibiotics to selectively assess fungal activities have limitations and complementary molecular approaches to assign denitrification potential to fungi are desirable. Microcosms established with soils from two representative U.S. Midwest agricultural regions produced N2O from added NO3- or NO2- in the presence of antibiotics to inhibit bacteria. Cultivation efforts yielded 214 fungal isolates belonging to at least 15 distinct morphological groups, of which 151 produced N2O from NO2-. Novel PCR primersmore » targeting the p450nor gene that encodes the nitric oxide (NO) reductase responsible for N2O production in fungi yielded 26 novel p450nor amplicons from DNA of 37 isolates and 23 amplicons from environmental DNA obtained from two agricultural soils. The sequences shared 54-98% amino acid identity to reference P450nor sequences within the phylum Ascomycota, and expand the known fungal P450nor sequence diversity. p450nor was detected in all fungal isolates that produced N2O from nitrite, whereas nirK (encoding the NO-forming nitrite reductase) was amplified in only 13-74% of the N2O-forming isolates using two separate nirK primer sets. Altogether, our findings demonstrate the value of p450nor-targeted PCR to complement existing approaches to assess the fungal contributions to denitrification and N2O formation.« less

  16. Diversity of fungal endophytes in non-native Phragmites australis in the Great Lakes

    USGS Publications Warehouse

    Clay, Keith; Shearin, Zachery; Bourke, Kimberly; Bickford, Wesley A.; Kowalski, Kurt P.

    2016-01-01

    Plant–microbial interactions may play a key role in plant invasions. One common microbial interaction takes place between plants and fungal endophytes when fungi asymptomatically colonize host plant tissues. The objectives of this study were to isolate and sequence fungal endophytes colonizing non-native Phragmites australis in the Great Lakes region to evaluate variation in endophyte community composition among three host tissue types and three geographical regions. We collected entire ramets from multiple clones and populations, surface sterilized plant tissues, and plated replicate tissue samples from leaves, stems, and rhizomes on corn meal agar plates to culture and isolate fungal endophytes. Isolates were then subjected to Sanger sequencing of the ITS region of the nuclear ribosomal DNA. Sequences were compared to fungal databases to define operational taxonomic units (OTUs) that were analyzed statistically for community composition. In total, we obtained 173 endophyte isolates corresponding to 55 OTUs, 39 of which were isolated only a single time. The most common OTU corresponded most closely to Sarocladium strictum and comprised 25 % of all fungal isolates. More OTUs were found in stem tissues, but endophyte diversity was greatest in rhizome tissues. PERMANOVA analyses indicated significant differences in endophyte communities among tissue types, geographical regions, and the interaction between those factors, but no differences among individual ramets were detected. The functional role of the isolated endophytes is not yet known, but one genus isolated here (Stagonospora) has been reported to enhance Phragmites growth. Understanding the diversity and functions of Phragmites endophytes may provide targets for control measures based on disrupting host plant/endophyte interactions.

  17. 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

  18. 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

  19. Fungal diversity in oxygen-depleted regions of the Arabian Sea revealed by targeted environmental sequencing combined with cultivation.

    PubMed

    Jebaraj, Cathrine S; Raghukumar, Chandralata; Behnke, Anke; Stoeck, Thorsten

    2010-03-01

    In order to study fungal diversity in oxygen minimum zones of the Arabian Sea, we analyzed 1440 cloned small subunit rRNA gene (18S rRNA gene) sequences obtained from environmental samples using three different PCR primer sets. Restriction fragment length polymorphism (RFLP) analyses yielded 549 distinct RFLP patterns, 268 of which could be assigned to fungi (Dikarya and zygomycetes) after sequence analyses. The remaining 281 RFLP patterns represented a variety of nonfungal taxa, even when using putatively fungal-specific primers. A substantial number of fungal sequences were closely related to environmental sequences from a range of other anoxic marine habitats, but distantly related to known sequences of described fungi. Community similarity analyses suggested distinctively different structures of fungal communities from normoxic sites, seasonally anoxic sites and permanently anoxic sites, suggesting different adaptation strategies of fungal communities to prevailing oxygen conditions. Additionally, we obtained 26 fungal cultures from the study sites, most of which were closely related (>97% sequence similarity) to well-described Dikarya. This indicates that standard cultivation mainly produces more of what is already known. However, two of these cultures were highly divergent to known sequences and seem to represent novel fungal groups on high taxonomic levels. Interestingly, none of the cultured isolates is identical to any of the environmental sequences obtained. Our study demonstrates the importance of a multiple-primer approach combined with cultivation to obtain deeper insights into the true fungal diversity in environmental samples and to enable adequate intersample comparisons of fungal communities.

  20. The Diversity of Anti-Microbial Secondary Metabolites Produced by Fungal Endophytes: An Interdisciplinary Perspective

    PubMed Central

    Mousa, Walaa Kamel; Raizada, Manish N.

    2013-01-01

    Endophytes are microbes that inhabit host plants without causing disease and are reported to be reservoirs of metabolites that combat microbes and other pathogens. Here we review diverse classes of secondary metabolites, focusing on anti-microbial compounds, synthesized by fungal endophytes including terpenoids, alkaloids, phenylpropanoids, aliphatic compounds, polyketides, and peptides from the interdisciplinary perspectives of biochemistry, genetics, fungal biology, host plant biology, human and plant pathology. Several trends were apparent. First, host plants are often investigated for endophytes when there is prior indigenous knowledge concerning human medicinal uses (e.g., Chinese herbs). However, within their native ecosystems, and where investigated, endophytes were shown to produce compounds that target pathogens of the host plant. In a few examples, both fungal endophytes and their hosts were reported to produce the same compounds. Terpenoids and polyketides are the most purified anti-microbial secondary metabolites from endophytes, while flavonoids and lignans are rare. Examples are provided where fungal genes encoding anti-microbial compounds are clustered on chromosomes. As different genera of fungi can produce the same metabolite, genetic clustering may facilitate sharing of anti-microbial secondary metabolites between fungi. We discuss gaps in the literature and how more interdisciplinary research may lead to new opportunities to develop bio-based commercial products to combat global crop and human pathogens. PMID:23543048

  1. Diversity of Marine-Derived Fungal Cultures Exposed by DNA Barcodes: The Algorithm Matters

    PubMed Central

    Andreakis, Nikos; Høj, Lone; Kearns, Philip; Hall, Michael R.; Ericson, Gavin; Cobb, Rose E.; Gordon, Benjamin R.; Evans-Illidge, Elizabeth

    2015-01-01

    Marine fungi are an understudied group of eukaryotic microorganisms characterized by unresolved genealogies and unstable classification. Whereas DNA barcoding via the nuclear ribosomal internal transcribed spacer (ITS) provides a robust and rapid tool for fungal species delineation, accurate classification of fungi is often arduous given the large number of partial or unknown barcodes and misidentified isolates deposited in public databases. This situation is perpetuated by a paucity of cultivable fungal strains available for phylogenetic research linked to these data sets. We analyze ITS barcodes produced from a subsample (290) of 1781 cultured isolates of marine-derived fungi in the Bioresources Library located at the Australian Institute of Marine Science (AIMS). Our analysis revealed high levels of under-explored fungal diversity. The majority of isolates were ascomycetes including representatives of the subclasses Eurotiomycetidae, Hypocreomycetidae, Sordariomycetidae, Pleosporomycetidae, Dothideomycetidae, Xylariomycetidae and Saccharomycetidae. The phylum Basidiomycota was represented by isolates affiliated with the genera Tritirachium and Tilletiopsis. BLAST searches revealed 26 unknown OTUs and 50 isolates corresponding to previously uncultured, unidentified fungal clones. This study makes a significant addition to the availability of barcoded, culturable marine-derived fungi for detailed future genomic and physiological studies. We also demonstrate the influence of commonly used alignment algorithms and genetic distance measures on the accuracy and comparability of estimating Operational Taxonomic Units (OTUs) by the automatic barcode gap finder (ABGD) method. Large scale biodiversity screening programs that combine datasets using algorithmic OTU delineation pipelines need to ensure compatible algorithms have been used because the algorithm matters. PMID:26308620

  2. Fire regime, not time-since-fire, affects soil fungal community diversity and composition in temperate grasslands.

    PubMed

    Egidi, Eleonora; McMullan-Fisher, Sapphire; Morgan, John W; May, Tom; Zeeman, Ben; Franks, Ashley E

    2016-09-01

    Frequent burning is commonly undertaken to maintain diversity in temperate grasslands of southern Australia. How burning affects below-ground fungal community diversity remains unknown. We show, using a fungal rDNA metabarcoding approach (Illumina MiSeq), that the fungal community composition was influenced by fire regime (frequency) but not time-since-fire. Fungal community composition was resilient to direct fire effects, most likely because grassland fires transfer little heat to the soil. Differences in the fungal community composition due to fire regime was likely due to associated changes that occur in vegetation with recurrent fire, via the break up of obligate symbiotic relationships. However, fire history only partially explains the observed dissimilarity in composition among the soil samples, suggesting a distinctiveness in composition in each grassland site. The importance of considering changes in soil microbe communities when managing vegetation with fire is highlighted.

  3. Effects on diversity of soil fungal community and fate of an artificially applied Beauveria bassiana strain assessed through 454 pyrosequencing.

    PubMed

    Hirsch, Jacqueline; Galidevara, Sandhya; Strohmeier, Stephan; Devi, K Uma; Reineke, Annette

    2013-10-01

    The entomopathogenic fungus Beauveria bassiana is widely used as a biological control agent (BCA) for insect pest control, with fungal propagules being either incorporated into the potting media or soil or sprayed directly onto the foliage or soil. To gain a better understanding of entomopathogenic fungal ecology when applied as a BCA to the soil environment, a case study using tag-encoded 454 pyrosequencing of fungal ITS sequences was performed to assess the fate and potential effect of an artificially applied B. bassiana strain on the diversity of soil fungal communities in an agricultural field in India. Results show that the overall fungal diversity was not influenced by application of B. bassiana during the 7 weeks of investigation. Strain-specific microsatellite markers indicated both an establishment of the applied B. bassiana strain in the treated plot and its spread to the neighboring nontreated control plot. These results might be important for proper risk assessment of entomopathogenic fungi-based BCAs.

  4. Fire regime, not time-since-fire, affects soil fungal community diversity and composition in temperate grasslands.

    PubMed

    Egidi, Eleonora; McMullan-Fisher, Sapphire; Morgan, John W; May, Tom; Zeeman, Ben; Franks, Ashley E

    2016-09-01

    Frequent burning is commonly undertaken to maintain diversity in temperate grasslands of southern Australia. How burning affects below-ground fungal community diversity remains unknown. We show, using a fungal rDNA metabarcoding approach (Illumina MiSeq), that the fungal community composition was influenced by fire regime (frequency) but not time-since-fire. Fungal community composition was resilient to direct fire effects, most likely because grassland fires transfer little heat to the soil. Differences in the fungal community composition due to fire regime was likely due to associated changes that occur in vegetation with recurrent fire, via the break up of obligate symbiotic relationships. However, fire history only partially explains the observed dissimilarity in composition among the soil samples, suggesting a distinctiveness in composition in each grassland site. The importance of considering changes in soil microbe communities when managing vegetation with fire is highlighted. PMID:27528692

  5. Systematic Conservation Planning for Groundwater Ecosystems Using Phylogenetic Diversity

    PubMed Central

    Asmyhr, Maria G.; Linke, Simon; Hose, Grant; Nipperess, David A.

    2014-01-01

    Aquifer ecosystems provide a range of important services including clean drinking water. These ecosystems, which are largely inaccessible to humans, comprise a distinct invertebrate fauna (stygofauna), which is characterized by narrow distributions, high levels of endemism and cryptic species. Although being under enormous anthropogenic pressure, aquifers have rarely been included in conservation planning because of the general lack of knowledge of species diversity and distribution. Here we use molecular sequence data and phylogenetic diversity as surrogates for stygofauna diversity in aquifers of New South Wales, Australia. We demonstrate how to incorporate these data as conservation features in the systematic conservation planning software Marxan. We designated each branch of the phylogenetic tree as a conservation feature, with the branch length as a surrogate for the number of distinct characters represented by each branch. Two molecular markers (nuclear 18S ribosomal DNA and mitochondrial cytochrome oxidase subunit I) were used to evaluate how marker variability and the resulting tree topology affected the site-selection process. We found that the sites containing the deepest phylogenetic branches were deemed the most irreplaceable by Marxan. By integrating phylogenetic data, we provide a method for including taxonomically undescribed groundwater fauna in systematic conservation planning. PMID:25514422

  6. Systematic conservation planning for groundwater ecosystems using phylogenetic diversity.

    PubMed

    Asmyhr, Maria G; Linke, Simon; Hose, Grant; Nipperess, David A

    2014-01-01

    Aquifer ecosystems provide a range of important services including clean drinking water. These ecosystems, which are largely inaccessible to humans, comprise a distinct invertebrate fauna (stygofauna), which is characterized by narrow distributions, high levels of endemism and cryptic species. Although being under enormous anthropogenic pressure, aquifers have rarely been included in conservation planning because of the general lack of knowledge of species diversity and distribution. Here we use molecular sequence data and phylogenetic diversity as surrogates for stygofauna diversity in aquifers of New South Wales, Australia. We demonstrate how to incorporate these data as conservation features in the systematic conservation planning software Marxan. We designated each branch of the phylogenetic tree as a conservation feature, with the branch length as a surrogate for the number of distinct characters represented by each branch. Two molecular markers (nuclear 18S ribosomal DNA and mitochondrial cytochrome oxidase subunit I) were used to evaluate how marker variability and the resulting tree topology affected the site-selection process. We found that the sites containing the deepest phylogenetic branches were deemed the most irreplaceable by Marxan. By integrating phylogenetic data, we provide a method for including taxonomically undescribed groundwater fauna in systematic conservation planning.

  7. 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

  8. 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.

  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. Differentiating between effects of invasion and diversity: impacts of aboveground plant communities on belowground fungal communities.

    PubMed

    Kivlin, Stephanie N; Hawkes, Christine V

    2011-01-01

    Exotic plant species can affect soil microbial communities with the potential for community and ecosystem feedbacks. Yet, separating the effects of exotics from confounded changes in plant community diversity still remains a challenge. We focused on how plant diversity and native or exotic life history affected root fungi because of their significant roles in community and ecosystem processes. Specifically, we examined how fungi colonizing plant roots were affected by plant richness (one, two or four species) replicated across a range of plant community mixtures (natives, exotics, native-exotic mixtures). Fungal biomass inside roots was affected independently by plant richness and mixture, while root fungal community composition was affected only by plant richness. Extraradical networks also increased in size with plant richness. By contrast, plant biomass was a function of plant mixture, with natives consistently smaller than exotics and native-exotic mixtures intermediate. Plant invasions may have an impact on the belowground community primarily through their effects on diversity, at least in the short-term. Disentangling the effects of diversity and invasion on belowground microbial communities can help us to understand both the controllers of belowground resilience and mechanisms of successful colonization and spread of exotic plants.

  11. FUNGAL SYMBIONTS. Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism.

    PubMed

    Davison, J; Moora, M; Öpik, M; Adholeya, A; Ainsaar, L; Bâ, A; Burla, S; Diedhiou, A G; Hiiesalu, I; Jairus, T; Johnson, N C; Kane, A; Koorem, K; Kochar, M; Ndiaye, C; Pärtel, M; Reier, Ü; Saks, Ü; Singh, R; Vasar, M; Zobel, M

    2015-08-28

    The global biogeography of microorganisms remains largely unknown, in contrast to the well-studied diversity patterns of macroorganisms. We used arbuscular mycorrhizal (AM) fungus DNA from 1014 plant-root samples collected worldwide to determine the global distribution of these plant symbionts. We found that AM fungal communities reflected local environmental conditions and the spatial distance between sites. However, despite AM fungi apparently possessing limited dispersal ability, we found 93% of taxa on multiple continents and 34% on all six continents surveyed. This contrasts with the high spatial turnover of other fungal taxa and with the endemism displayed by plants at the global scale. We suggest that the biogeography of AM fungi is driven by unexpectedly efficient dispersal, probably via both abiotic and biotic vectors, including humans. PMID:26315436

  12. Diversity of endophytic fungal and bacterial communities in Ilex paraguariensis grown under field conditions.

    PubMed

    Pérez, María Laura; Collavino, Mónica Mariana; Sansberro, Pedro Alfonso; Mroginski, Luis Amado; Galdeano, Ernestina

    2016-04-01

    The composition and diversity of the endophytic community associated with yerba mate (Ilex paraguariensis) was investigated using culture-depending methods. Fungi were identified based on their micromorphological characteristics and internal transcribed spacer rDNA sequence analysis; for bacteria 16S rDNA sequence analysis was used. Fungal and bacterial diversity did not show significant differences between organ age. The highest fungal diversity was registered during fall season and the lowest in winter. Bacterial diversity was higher in stems and increased from summer to winter, in contrast with leaves, which decreased. The most frequently isolated fungus was Fusarium, followed by Colletotrichum; they were both present in all the sampling seasons and organ types assayed. Actinobacteria represented 57.5 % of all bacterial isolates. The most dominant bacterial taxa were Curtobacterium and Microbacterium. Other bacteria frequently found were Methylobacterium, Sphingomonas, Herbiconiux and Bacillus. Nitrogen fixation and phosphate solubilization activity, ACC deaminase production and antagonism against plant fungal pathogens were assayed in endophytic bacterial strains. In the case of fungi, strains of Trichoderma, Penicillium and Aspergillus were assayed for antagonism against pathogenic Fusarium sp. All microbial isolates assayed showed at least one growth promoting activity. Strains of Bacillus, Pantoea, Curtobacterium, Methylobacterium, Brevundimonas and Paenibacillus had at least two growth-promoting activities, and Bacillus, Paenibacillus and the three endophytic fungi showed high antagonistic activity against Fusarium sp. In this work we have made a wide study of the culturable endophytic community within yerba mate plants and found that several microbial isolates could be considered as potential inoculants useful for improving yerba mate production. PMID:26925623

  13. Metabarcoding Analysis of Fungal Diversity in the Phyllosphere and Carposphere of Olive (Olea europaea).

    PubMed

    Abdelfattah, Ahmed; Li Destri Nicosia, Maria Giulia; Cacciola, Santa Olga; Droby, Samir; Schena, Leonardo

    2015-01-01

    The fungal diversity associated with leaves, flowers and fruits of olive (Olea europaea) was investigated in different phenological stages (May, June, October and December) using an implemented metabarcoding approach. It consisted of the 454 pyrosequencing of the fungal ITS2 region and the subsequent phylogenetic analysis of relevant genera along with validated reference sequences. Most sequences were identified up to the species level or were associated with a restricted number of related taxa enabling supported speculations regarding their biological role. Analyses revealed a rich fungal community with 195 different OTUs. Ascomycota was the dominating phyla representing 93.6% of the total number of detected sequences followed by unidentified fungi (3.6%) and Basidiomycota (2.8%). A higher level of diversity was revealed for leaves compared to flowers and fruits. Among plant pathogens the genus Colletotrichum represented by three species (C. godetiae syn. C. clavatum, C. acutatum s.s and C. karstii) was the most abundant on ripe fruits but it was also detected in other organs. Pseudocercospora cladosporioides was detected with a high frequency in all leaf samples and to a less extent in ripe fruits. A much lower relative frequency was revealed for Spilocaea oleagina and for other putative pathogens including Fusarium spp., Neofusicoccum spp., and Alternaria spp. Among non-pathogen taxa, Aureobasidium pullulans, the species complex of Cladosporium cladosporioides and Devriesia spp. were the most represented. This study highlights the existence of a complex fungal consortium including both phytopathogenic and potentially antagonistic microorganisms that can have a significant impact on olive productions. PMID:26132745

  14. Metabarcoding Analysis of Fungal Diversity in the Phyllosphere and Carposphere of Olive (Olea europaea)

    PubMed Central

    Abdelfattah, Ahmed; Li Destri Nicosia, Maria Giulia; Cacciola, Santa Olga; Droby, Samir; Schena, Leonardo

    2015-01-01

    The fungal diversity associated with leaves, flowers and fruits of olive (Olea europaea) was investigated in different phenological stages (May, June, October and December) using an implemented metabarcoding approach. It consisted of the 454 pyrosequencing of the fungal ITS2 region and the subsequent phylogenetic analysis of relevant genera along with validated reference sequences. Most sequences were identified up to the species level or were associated with a restricted number of related taxa enabling supported speculations regarding their biological role. Analyses revealed a rich fungal community with 195 different OTUs. Ascomycota was the dominating phyla representing 93.6% of the total number of detected sequences followed by unidentified fungi (3.6%) and Basidiomycota (2.8%). A higher level of diversity was revealed for leaves compared to flowers and fruits. Among plant pathogens the genus Colletotrichum represented by three species (C. godetiae syn. C. clavatum, C. acutatum s.s and C. karstii) was the most abundant on ripe fruits but it was also detected in other organs. Pseudocercospora cladosporioides was detected with a high frequency in all leaf samples and to a less extent in ripe fruits. A much lower relative frequency was revealed for Spilocaea oleagina and for other putative pathogens including Fusarium spp., Neofusicoccum spp., and Alternaria spp. Among non-pathogen taxa, Aureobasidium pullulans, the species complex of Cladosporium cladosporioides and Devriesia spp. were the most represented. This study highlights the existence of a complex fungal consortium including both phytopathogenic and potentially antagonistic microorganisms that can have a significant impact on olive productions. PMID:26132745

  15. Metabarcoding Analysis of Fungal Diversity in the Phyllosphere and Carposphere of Olive (Olea europaea).

    PubMed

    Abdelfattah, Ahmed; Li Destri Nicosia, Maria Giulia; Cacciola, Santa Olga; Droby, Samir; Schena, Leonardo

    2015-01-01

    The fungal diversity associated with leaves, flowers and fruits of olive (Olea europaea) was investigated in different phenological stages (May, June, October and December) using an implemented metabarcoding approach. It consisted of the 454 pyrosequencing of the fungal ITS2 region and the subsequent phylogenetic analysis of relevant genera along with validated reference sequences. Most sequences were identified up to the species level or were associated with a restricted number of related taxa enabling supported speculations regarding their biological role. Analyses revealed a rich fungal community with 195 different OTUs. Ascomycota was the dominating phyla representing 93.6% of the total number of detected sequences followed by unidentified fungi (3.6%) and Basidiomycota (2.8%). A higher level of diversity was revealed for leaves compared to flowers and fruits. Among plant pathogens the genus Colletotrichum represented by three species (C. godetiae syn. C. clavatum, C. acutatum s.s and C. karstii) was the most abundant on ripe fruits but it was also detected in other organs. Pseudocercospora cladosporioides was detected with a high frequency in all leaf samples and to a less extent in ripe fruits. A much lower relative frequency was revealed for Spilocaea oleagina and for other putative pathogens including Fusarium spp., Neofusicoccum spp., and Alternaria spp. Among non-pathogen taxa, Aureobasidium pullulans, the species complex of Cladosporium cladosporioides and Devriesia spp. were the most represented. This study highlights the existence of a complex fungal consortium including both phytopathogenic and potentially antagonistic microorganisms that can have a significant impact on olive productions.

  16. Use of a biosynthetic intermediate to explore the chemical diversity of pseudo-natural fungal polyketides

    NASA Astrophysics Data System (ADS)

    Asai, Teigo; Tsukada, Kento; Ise, Satomi; Shirata, Naoki; Hashimoto, Makoto; Fujii, Isao; Gomi, Katsuya; Nakagawara, Kosuke; Kodama, Eiichi N.; Oshima, Yoshiteru

    2015-09-01

    The structural complexity and diversity of natural products make them attractive sources for potential drug discovery, with their characteristics being derived from the multi-step combination of enzymatic and non-enzymatic conversions of intermediates in each biosynthetic pathway. Intermediates that exhibit multipotent behaviour have great potential for use as starting points in diversity-oriented synthesis. Inspired by the biosynthetic pathways that form complex metabolites from simple intermediates, we developed a semi-synthetic process that combines heterologous biosynthesis and artificial diversification. The heterologous biosynthesis of fungal polyketide intermediates led to the isolation of novel oligomers and provided evidence for ortho-quinonemethide equivalency in their isochromene form. The intrinsic reactivity of the isochromene polyketide enabled us to access various new chemical entities by modifying and remodelling the polyketide core and through coupling with indole molecules. We thus succeeded in generating exceptionally diverse pseudo-natural polyketides through this process and demonstrated an advanced method of using biosynthetic intermediates.

  17. Early fungal infection in an aortic prosthesis with probable cerebral metastasis: the success of a conservative strategy.

    PubMed

    Guedes, Anabela Malho; de Macedo, Teresa Anastácio; Rocha, Carla; Neves, José; Mapril, Joana

    2013-02-01

    Infection of an aortic prosthesis presents a diagnostic and therapeutic challenge. Fungal infections are rarely described and among these Candida spp. are the most prevalent agents. Although the therapeutic approach to prosthetic bacterial infection may be conservative, in the case of fungal etiology, surgery, such as the removal and substitution of the device, debridement and repair of the infected prosthesis is usually warranted. The authors describe the case of a 48-year-old man, with a thoraco-abdominal aneurysm of the aorta, submitted to surgery for insertion of a prosthetic aortic duct. The procedure was made difficult by Candida albicans empyema associated with an aortic prosthesis infection that was complicated by probable cerebral metastasis. Antifungal therapy was the initial option, as the steady clinical, laboratory and radiological improvement deferred a surgical intervention. This case demonstrates the success of a conservative approach in a very serious fungal infection of a thoraco-abdominal aorta prosthesis.

  18. Split diversity in constrained conservation prioritization using integer linear programming

    PubMed Central

    Chernomor, Olga; Minh, Bui Quang; Forest, Félix; Klaere, Steffen; Ingram, Travis; Henzinger, Monika; von Haeseler, Arndt

    2015-01-01

    Phylogenetic diversity (PD) is a measure of biodiversity based on the evolutionary history of species. Here, we discuss several optimization problems related to the use of PD, and the more general measure split diversity (SD), in conservation prioritization. Depending on the conservation goal and the information available about species, one can construct optimization routines that incorporate various conservation constraints. We demonstrate how this information can be used to select sets of species for conservation action. Specifically, we discuss the use of species' geographic distributions, the choice of candidates under economic pressure, and the use of predator–prey interactions between the species in a community to define viability constraints. Despite such optimization problems falling into the area of NP hard problems, it is possible to solve them in a reasonable amount of time using integer programming. We apply integer linear programming to a variety of models for conservation prioritization that incorporate the SD measure. We exemplarily show the results for two data sets: the Cape region of South Africa and a Caribbean coral reef community. Finally, we provide user-friendly software at http://www.cibiv.at/software/pda. PMID:25893087

  19. Fungal endophytes of aquatic macrophytes: diverse host-generalists characterized by tissue preferences and geographic structure

    PubMed Central

    Sandberg, Dustin C.; Battista, Lorna J.; Arnold, A. Elizabeth

    2014-01-01

    Most studies of endophytic symbionts have focused on terrestrial plants, neglecting the ecologically and economically important plants present in aquatic ecosystems. We evaluated the diversity, composition, host- and tissue affiliations, and geographic structure of fungal endophytes associated with common aquatic plants in northern Arizona, USA. Endophytes were isolated in culture from roots and photosynthetic tissues during two growing seasons. A total of 226 isolates representing 60 putative species was recovered from 9,600 plant tissue segments. Although isolation frequency was low, endophytes were phylogenetically diverse and species-rich. Comparisons among the most thoroughly sampled species and reservoirs revealed that isolation frequency and diversity did not differ significantly between collection periods, among species, among reservoirs, or as a function of depth. However, community structure differed significantly among reservoirs and tissue types. Phylogenetic analyses of a focal genus (Penicillium) corroborated estimates of species boundaries and informed community analyses, highlighting clade- and genotype-level affiliations of aquatic endophytes with both sediment- and waterborne fungi, and endophytes of proximate terrestrial plants. Together these analyses provide a first quantitative examination of endophytic associations in roots and foliage of aquatic plants and can be used to optimize survey strategies for efficiently capturing fungal biodiversity at local and regional scales. PMID:24402358

  20. Soil bacterial and fungal community responses across a conservation reserve program chronosequence in Texas high plains region

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We investigated changes in soil bacterial and fungal communities with increasing restoration time across a Conservation Reserve Program chronosequence (CRP) on fine sandy loam soils in the Texas high plains region. Soil samples (0-10cm) were collected in 2012 and 2014 from seven dryland croplands (0...

  1. Conservation priority of global Galliformes species based on phylogenetic diversity.

    PubMed

    Chen, Youhua

    2014-06-01

    In this study, based on phylogenetic diversity (PD), I develop a conservation strategy for Galliformes species around the world. A cladogram of 197 Galliformes species derived from a previous study was used for calculating PD metrics. Branch length is an important aspect of the phylogenetic information a tree can convey, but 2 traditionally-used metrics, the number of phylogenetic groups to which a taxon belongs (I) and the proportion that each taxon contributes to the total diversity of the group (W), are fully node-based and do not take branch length into account. Therefore, to measure PD more appropriately, I combined a branch-related metric, pendant edge (P), in addition to I and W. A final combined rank for Galliformes species was obtained by summing the ranks of the 3 metrics. My results showed that the 5% top priority species for conserving evolutionary potential were Galloperdix lunulata, Haematortyx sanguiniceps, Margaroperdix madagarensis, Syrmaticus soemmerringii, Coturnix pectoralis, Polyplectron napoleonis, Alectoris melanocephala, Xenoperdix udzungwensis, Afropavo congensis and Syrmaticus reevesii. The current species priority ranking based on pylogenetic diversity and the official International Union for Conservation of Nature (IUCN) ranking of Galliformes species was significantly correlated when considering the 5 categories of IUCN (critical endangered, endangered, vulnerable, near threatened and least concern). This indicated the feasibility of introducing the PD index into the network of IUCN regional Red List assessment. The 5% top priority countries selected using the complementarity principle possessing diversified Galliformes genetic resources were China, Indonesia, Mexico, India, Colombia, Australia, Brazil, Angola, Congo and Japan (in descending order). China, Indonesia, Mexico, Brazil, India and Colombia are consistently selected among the 4 top priority sets of richness, rarity, endemicity and PD. This result indicated that the priority

  2. Structure Analysis Uncovers a Highly Diverse but Structurally Conserved Effector Family in Phytopathogenic Fungi

    PubMed Central

    Gracy, Jérome; Fournier, Elisabeth; Kroj, Thomas; Padilla, André

    2015-01-01

    Phytopathogenic ascomycete fungi possess huge effector repertoires that are dominated by hundreds of sequence-unrelated small secreted proteins. The molecular function of these effectors and the evolutionary mechanisms that generate this tremendous number of singleton genes are largely unknown. To get a deeper understanding of fungal effectors, we determined by NMR spectroscopy the 3-dimensional structures of the Magnaporthe oryzae effectors AVR1-CO39 and AVR-Pia. Despite a lack of sequence similarity, both proteins have very similar 6 β-sandwich structures that are stabilized in both cases by a disulfide bridge between 2 conserved cysteins located in similar positions of the proteins. Structural similarity searches revealed that AvrPiz-t, another effector from M. oryzae, and ToxB, an effector of the wheat tan spot pathogen Pyrenophora tritici-repentis have the same structures suggesting the existence of a family of sequence-unrelated but structurally conserved fungal effectors that we named MAX-effectors (Magnaporthe Avrs and ToxB like). Structure-informed pattern searches strengthened this hypothesis by identifying MAX-effector candidates in a broad range of ascomycete phytopathogens. Strong expansion of the MAX-effector family was detected in M. oryzae and M. grisea where they seem to be particularly important since they account for 5–10% of the effector repertoire and 50% of the cloned avirulence effectors. Expression analysis indicated that the majority of M. oryzae MAX-effectors are expressed specifically during early infection suggesting important functions during biotrophic host colonization. We hypothesize that the scenario observed for MAX-effectors can serve as a paradigm for ascomycete effector diversity and that the enormous number of sequence-unrelated ascomycete effectors may in fact belong to a restricted set of structurally conserved effector families. PMID:26506000

  3. Fungal diversity in the rhizosphere of endemic plant species of Tenerife (Canary Islands): relationship to vegetation zones and environmental factors.

    PubMed

    Zachow, Christin; Berg, Christian; Müller, Henry; Meincke, Remo; Komon-Zelazowska, Monika; Druzhinina, Irina S; Kubicek, Christian P; Berg, Gabriele

    2009-01-01

    Knowledge about fungal diversity scaling relationships relative to that of plants is important to understand ecosystem functioning. Tenerife Island, a natural laboratory to study terrestrial biodiversity, is represented by six different vegetation zones characterized by specific abiotic conditions and plant communities with a high proportion of endemic plants. Little is known about the biodiversity of associated fungi. To understand the relationship between plant and fungal communities, we analysed soil/rhizosphere fungi from all vegetation zones. From 12 sampling points dispersed on the whole island, molecular analysis of fungal communities was determined by single-strand conformation polymorphism (SSCP) analysis using universal and specific primers for Trichoderma. The highly diverse fungal communities were mainly characterized by ectomycorrhiza-forming Basidiomycota and a high proportion of yet-unidentified species. Besides, Trichoderma-specific SSCP resulted in low diversity of mainly cosmopolitan species, for example Hypocrea lixii/T. harzianum. The dominance of T. harzianum was confirmed by cultivation. All Trichoderma isolates show an extraordinarily high antagonistic potential towards different groups of plant pathogens, supporting the hypothesis of extensive colonization by highly competitive Trichoderma species from the continent. In contrast, biodiversity patterns of the whole fungal and plant communities follow the same ecological rules. Furthermore, a high statistical correlation between fungal communities and the main environmental factors, temperature and precipitation, was found.

  4. Elevated atmospheric CO2 stimulates soil fungal diversity through increased fine root production in a semiarid shrubland ecosystem.

    PubMed

    Lipson, David A; Kuske, Cheryl R; Gallegos-Graves, La Verne; Oechel, Walter C

    2014-08-01

    Soil fungal communities are likely to be central in mediating microbial feedbacks to climate change through their effects on soil carbon (C) storage, nutrient cycling, and plant health. Plants often produce increased fine root biomass in response to elevated atmospheric carbon dioxide (CO2 ), but the responses of soil microbial communities are variable and uncertain, particularly in terms of species diversity. In this study, we describe the responses of the soil fungal community to free air CO2 enrichment (FACE) in a semiarid chaparral shrubland in Southern California (dominated by Adenomstoma fasciculatum) using large subunit rRNA gene sequencing. Community composition varied greatly over the landscape and responses to FACE were subtle, involving a few specific groups. Increased frequency of Sordariomycetes and Leotiomycetes, the latter including the Helotiales, a group that includes many dark septate endophytes known to associate positively with roots, was observed in the FACE plots. Fungal diversity, both in terms of richness and evenness, increased consistently in the FACE treatment, and was relatively high compared to other studies that used similar methods. Increases in diversity were observed across multiple phylogenetic levels, from genus to class, and were distributed broadly across fungal lineages. Diversity was also higher in samples collected close to (5 cm) plants compared to samples in canopy gaps (30 cm away from plants). Fungal biomass correlated well with soil organic matter (SOM) content, but patterns of diversity were correlated with fine root production rather than SOM. We conclude that the fungal community in this ecosystem is tightly linked to plant fine root production, and that future changes in the fungal community in response to elevated CO2 and other climatic changes will be primarily driven by changes in plant belowground allocation. Potential feedbacks mediated by soil fungi, such as soil C sequestration, nutrient cycling, and

  5. Fungal Endophyte Diversity and Bioactivity in the Indian Medicinal Plant Ocimum sanctum Linn.

    PubMed

    Chowdhary, Kanika; Kaushik, Nutan

    2015-01-01

    Endophytic mycopopulation isolated from India's Queen of herbs Tulsi (Ocimum sanctum) were explored and investigated for their diversity and antiphytopathogenic activity against widespread plant pathogens Botrytis cinerea, Sclerotinia sclerotiorum, Rhizoctonia solani and Fusarium oxysporum. 90 fungal isolates, representing 17 genera were recovered from 313 disease-free and surface sterilised plant segments (leaf and stem tissues) from three different geographic locations (Delhi, Hyderabad and Mukteshwar) during distinct sampling times in consequent years 2010 and 2011 in India. Fungal endophytes were subjected to molecular identification based on rDNA ITS sequence analysis. Plant pathogens such as F. verticillioides, B. maydis, C. coarctatum, R. bataticola, Hypoxylon sp., Diaporthe phaseolorum, Alternaria tenuissima and A. alternata have occurred as endophyte only during second sampling (second sampling in 2011) in the present study. Bi-plot generated by principal component analysis suggested tissue specificity of certain fungal endophytes. Dendrogram revealed species abundance as a function of mean temperature of the location at the time of sampling. Shannon diversity in the first collection is highest in Hyderabad leaf tissues (H' = 1.907) whereas in second collection it was highest from leaf tissues of Delhi (H' = 1.846). Mukteshwar (altitude: 7500 feet) reported least isolation rate in second collection. Nearly 23% of the total fungal isolates were considered as potent biocontrol agent. Hexane extract of M. phaseolina recovered from Hyderabad in first collection demonstrated highest activity against S. sclerotiorum with IC50 value of 0.38 mg/ml. Additionally, its components 2H-pyran-2-one, 5,6-dihydro-6-pentyl and palmitic acid, methyl ester as reported by GC-MS Chromatogram upon evaluation for their antiphytopathogenic activity exhibited IC50 value of 1.002 and 0.662 against respectively S. sclerotiorum indicating their significant role in antiphytopathogenic

  6. Fungal Endophyte Diversity and Bioactivity in the Indian Medicinal Plant Ocimum sanctum Linn

    PubMed Central

    Chowdhary, Kanika; Kaushik, Nutan

    2015-01-01

    Endophytic mycopopulation isolated from India’s Queen of herbs Tulsi (Ocimum sanctum) were explored and investigated for their diversity and antiphytopathogenic activity against widespread plant pathogens Botrytis cinerea, Sclerotinia sclerotiorum, Rhizoctonia solani and Fusarium oxysporum. 90 fungal isolates, representing 17 genera were recovered from 313 disease-free and surface sterilised plant segments (leaf and stem tissues) from three different geographic locations (Delhi, Hyderabad and Mukteshwar) during distinct sampling times in consequent years 2010 and 2011 in India. Fungal endophytes were subjected to molecular identification based on rDNA ITS sequence analysis. Plant pathogens such as F. verticillioides, B. maydis, C. coarctatum, R. bataticola, Hypoxylon sp., Diaporthe phaseolorum, Alternaria tenuissima and A. alternata have occurred as endophyte only during second sampling (second sampling in 2011) in the present study. Bi-plot generated by principal component analysis suggested tissue specificity of certain fungal endophytes. Dendrogram revealed species abundance as a function of mean temperature of the location at the time of sampling. Shannon diversity in the first collection is highest in Hyderabad leaf tissues (H' = 1.907) whereas in second collection it was highest from leaf tissues of Delhi (H' = 1.846). Mukteshwar (altitude: 7500 feet) reported least isolation rate in second collection. Nearly 23% of the total fungal isolates were considered as potent biocontrol agent. Hexane extract of M. phaseolina recovered from Hyderabad in first collection demonstrated highest activity against S. sclerotiorum with IC50 value of 0.38 mg/ml. Additionally, its components 2H-pyran-2-one, 5,6-dihydro-6-pentyl and palmitic acid, methyl ester as reported by GC-MS Chromatogram upon evaluation for their antiphytopathogenic activity exhibited IC50 value of 1.002 and 0.662 against respectively S. sclerotiorum indicating their significant role in

  7. Evolutionarily conserved recognition and innate immunity to fungal pathogens by the scavenger receptors SCARF1 and CD36

    PubMed Central

    Mylonakis, Eleftherios; Tampakakis, Emmanouil; Colvin, Richard A.; Seung, Edward; Puckett, Lindsay; Tai, Melissa F.; Stewart, Cameron R.; Pukkila-Worley, Read; Hickman, Suzanne E.; Moore, Kathryn J.; Calderwood, Stephen B.; Hacohen, Nir; Luster, Andrew D.; El Khoury, Joseph

    2009-01-01

    Receptors involved in innate immunity to fungal pathogens have not been fully elucidated. We show that the Caenorhabditis elegans receptors CED-1 and C03F11.3, and their mammalian orthologues, the scavenger receptors SCARF1 and CD36, mediate host defense against two prototypic fungal pathogens, Cryptococcus neoformans and Candida albicans. CED-1 and C03F11.1 mediated antimicrobial peptide production and were necessary for nematode survival after C. neoformans infection. SCARF1 and CD36 mediated cytokine production and were required for macrophage binding to C. neoformans, and control of the infection in mice. Binding of these pathogens to SCARF1 and CD36 was β-glucan dependent. Thus, CED-1/SCARF1 and C03F11.3/CD36 are β-glucan binding receptors and define an evolutionarily conserved pathway for the innate sensing of fungal pathogens. PMID:19237602

  8. Bird diversity and conservation of Alto Balsas (southwestern Puebla), Mexico.

    PubMed

    Ramírez-Albores, Jorge E

    2007-03-01

    Knowledge of the composition of the bird community in Alto Balsas (southwestern Puebla, Central Mexico) is needed for management programs aiming at protection and conservation of bird species and their habitats I studied sites with tropical deciduous forest. Data were obtained during 1666 hours of field work in 238 days from March 1998 to September 2000. Six permanent transect (3.5 km long and 100 m wide; 30 to 40 ha in each transect) were used to determine species richness in the study sites. The Shannon-Wiener diversity index was calculated for each site and Sorensen's index was used to assess similarity between sites. One-way analysis of variance was used to test for differences between sites in species richness and diversity values. A total of 128 species were recorded, Tepexco (n=75, H' = 3.76) and Puente Márquez (n=61, H' = 3.62) were the sites that showed the greatest specific richness and diversity. However, species richness and diversity seasonally patterns were similar among sites (ANOVA p > 0.05), with highest diversity during the rainy season. Most species were resident; 42 were migrants. The avifauna was represented by 30 species associated with tropical deciduous forest and 12 from open habitats or heavily altered habitats. Insectivores were the best represented trophic category, followed by carnivores and omnivores.

  9. Understanding the diversity of public interests in wildlife conservation.

    PubMed

    Teel, Tara L; Manfredo, Michael J

    2010-02-01

    North American state wildlife agencies are increasingly faced with the challenge of effectively representing a diverse public. With increasing social conflict over wildlife issues, the future of wildlife conservation hinges on preparedness of the profession to respond to this challenge. In the interest of finding ways to improve response, 19 agencies in the western U.S. joined forces to initiate an investigation that would provide a better understanding of the diversity of wildlife-related interests in the region. Specific objectives, accomplished through use of a mail survey administered in 2004, were to categorize people on the basis of their value orientations toward wildlife and explore how different groups were distributed across states and to examine differences on sociodemographic characteristics and attitudes toward wildlife-related topics among groups. The focus was on two orientations: domination (view of wildlife that prioritizes human well-being over wildlife and treats wildlife in utilitarian terms); and mutualism (view of wildlife as capable of relationships of trust with humans and defined by a desire for companionship with wildlife). Four types of people were identified on the basis of these orientations. Types differed in their geographic distribution and wildlife-related attitudes and behaviors, revealing how value orientations can form the foundation for conflict on wildlife issues. Our characterizations of stakeholder groups offer a framework that can be applied over time and across geographic scales to improve conservation planning efforts and inform broader thinking about the social aspects of wildlife conservation.

  10. Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges

    PubMed Central

    Faith, Daniel P.; Baker, Andrew M.

    2007-01-01

    Biodiversity conservation addresses information challenges through estimations encapsulated in measures of diversity. A quantitative measure of phylogenetic diversity, “PD”, has been defined as the minimum total length of all the phylogenetic branches required to span a given set of taxa on the phylogenetic tree (Faith 1992a). While a recent paper incorrectly characterizes PD as not including information about deeper phylogenetic branches, PD applications over the past decade document the proper incorporation of shared deep branches when assessing the total PD of a set of taxa. Current PD applications to macroinvertebrate taxa in streams of New South Wales, Australia illustrate the practical importance of this definition. Phylogenetic lineages, often corresponding to new, “cryptic”, taxa, are restricted to a small number of stream localities. A recent case of human impact causing loss of taxa in one locality implies a higher PD value for another locality, because it now uniquely represents a deeper branch. This molecular-based phylogenetic pattern supports the use of DNA barcoding programs for biodiversity conservation planning. Here, PD assessments side-step the contentious use of barcoding-based “species” designations. Bio-informatics challenges include combining different phylogenetic evidence, optimization problems for conservation planning, and effective integration of phylogenetic information with environmental and socio-economic data. PMID:19455206

  11. Generating Phenotypic Diversity in a Fungal Biocatalyst to Investigate Alcohol Stress Tolerance Encountered during Microbial Cellulosic Biofuel Production

    PubMed Central

    Hennessy, Rosanna C.; Doohan, Fiona; Mullins, Ewen

    2013-01-01

    Consolidated bioprocessing (CBP) of lignocellulosic biomass offers an alternative route to renewable energy. The crop pathogen Fusarium oxysporum is a promising fungal biocatalyst because of its broad host range and innate ability to co-saccharify and ferment lignocellulose to bioethanol. A major challenge for cellulolytic CBP-enabling microbes is alcohol inhibition. This research tested the hypothesis that Agrobacterium tumefaciens - mediated transformation (ATMT) could be exploited as a tool to generate phenotypic diversity in F. oxysporum to investigate alcohol stress tolerance encountered during CBP. A random mutagenesis library of gene disruption transformants (n=1,563) was constructed and screened for alcohol tolerance in order to isolate alcohol sensitive or tolerant phenotypes. Following three rounds of screening, exposure of select transformants to 6% ethanol and 0.75% n-butanol resulted respectively in increased (≥11.74%) and decreased (≤43.01%) growth compared to the wild –type (WT). Principal component analysis (PCA) quantified the level of phenotypic diversity across the population of genetically transformed individuals and isolated candidate strains for analysis. Characterisation of one strain, Tr. 259, ascertained a reduced growth phenotype under alcohol stress relative to WT and indicated the disruption of a coding region homologous to a putative sugar transporter (FOXG_09625). Quantitative PCR (RT-PCR) showed FOXG_09625 was differentially expressed in Tr. 259 compared to WT during alcohol-induced stress (P<0.05). Phylogenetic analysis of putative sugar transporters suggests diverse functional roles in F. oxysporum and other filamentous fungi compared to yeast for which sugar transporters form part of a relatively conserved family. This study has confirmed the potential of ATMT coupled with a phenotypic screening program to select for genetic variation induced in response to alcohol stress. This research represents a first step in the

  12. Generating phenotypic diversity in a fungal biocatalyst to investigate alcohol stress tolerance encountered during microbial cellulosic biofuel production.

    PubMed

    Hennessy, Rosanna C; Doohan, Fiona; Mullins, Ewen

    2013-01-01

    Consolidated bioprocessing (CBP) of lignocellulosic biomass offers an alternative route to renewable energy. The crop pathogen Fusarium oxysporum is a promising fungal biocatalyst because of its broad host range and innate ability to co-saccharify and ferment lignocellulose to bioethanol. A major challenge for cellulolytic CBP-enabling microbes is alcohol inhibition. This research tested the hypothesis that Agrobacterium tumefaciens--mediated transformation (ATMT) could be exploited as a tool to generate phenotypic diversity in F. oxysporum to investigate alcohol stress tolerance encountered during CBP. A random mutagenesis library of gene disruption transformants (n=1,563) was constructed and screened for alcohol tolerance in order to isolate alcohol sensitive or tolerant phenotypes. Following three rounds of screening, exposure of select transformants to 6% ethanol and 0.75% n-butanol resulted respectively in increased (≥ 11.74%) and decreased (≤ 43.01%) growth compared to the wild -type (WT). Principal component analysis (PCA) quantified the level of phenotypic diversity across the population of genetically transformed individuals and isolated candidate strains for analysis. Characterisation of one strain, Tr. 259, ascertained a reduced growth phenotype under alcohol stress relative to WT and indicated the disruption of a coding region homologous to a putative sugar transporter (FOXG_09625). Quantitative PCR (RT-PCR) showed FOXG_09625 was differentially expressed in Tr. 259 compared to WT during alcohol-induced stress (P<0.05). Phylogenetic analysis of putative sugar transporters suggests diverse functional roles in F. oxysporum and other filamentous fungi compared to yeast for which sugar transporters form part of a relatively conserved family. This study has confirmed the potential of ATMT coupled with a phenotypic screening program to select for genetic variation induced in response to alcohol stress. This research represents a first step in the

  13. Phylogenetic Resolution of Deep Eukaryotic and Fungal Relationships Using Highly Conserved Low-Copy Nuclear Genes.

    PubMed

    Ren, Ren; Sun, Yazhou; Zhao, Yue; Geiser, David; Ma, Hong; Zhou, Xiaofan

    2016-09-11

    A comprehensive and reliable eukaryotic tree of life is important for many aspects of biological studies from comparative developmental and physiological analyses to translational medicine and agriculture. Both gene-rich and taxon-rich approaches are effective strategies to improve phylogenetic accuracy and are greatly facilitated by marker genes that are universally distributed, well conserved, and orthologous among divergent eukaryotes. In this article, we report the identification of 943 low-copy eukaryotic genes and we show that many of these genes are promising tools in resolving eukaryotic phylogenies, despite the challenges of determining deep eukaryotic relationships. As a case study, we demonstrate that smaller subsets of ∼20 and 52 genes could resolve controversial relationships among widely divergent taxa and provide strong support for deep relationships such as the monophyly and branching order of several eukaryotic supergroups. In addition, the use of these genes resulted in fungal phylogenies that are congruent with previous phylogenomic studies that used much larger datasets, and successfully resolved several difficult relationships (e.g., forming a highly supported clade with Microsporidia, Mitosporidium and Rozella sister to other fungi). We propose that these genes are excellent for both gene-rich and taxon-rich analyses and can be applied at multiple taxonomic levels and facilitate a more complete understanding of the eukaryotic tree of life.

  14. Phylogenetic Resolution of Deep Eukaryotic and Fungal Relationships Using Highly Conserved Low-Copy Nuclear Genes.

    PubMed

    Ren, Ren; Sun, Yazhou; Zhao, Yue; Geiser, David; Ma, Hong; Zhou, Xiaofan

    2016-01-01

    A comprehensive and reliable eukaryotic tree of life is important for many aspects of biological studies from comparative developmental and physiological analyses to translational medicine and agriculture. Both gene-rich and taxon-rich approaches are effective strategies to improve phylogenetic accuracy and are greatly facilitated by marker genes that are universally distributed, well conserved, and orthologous among divergent eukaryotes. In this article, we report the identification of 943 low-copy eukaryotic genes and we show that many of these genes are promising tools in resolving eukaryotic phylogenies, despite the challenges of determining deep eukaryotic relationships. As a case study, we demonstrate that smaller subsets of ∼20 and 52 genes could resolve controversial relationships among widely divergent taxa and provide strong support for deep relationships such as the monophyly and branching order of several eukaryotic supergroups. In addition, the use of these genes resulted in fungal phylogenies that are congruent with previous phylogenomic studies that used much larger datasets, and successfully resolved several difficult relationships (e.g., forming a highly supported clade with Microsporidia, Mitosporidium and Rozella sister to other fungi). We propose that these genes are excellent for both gene-rich and taxon-rich analyses and can be applied at multiple taxonomic levels and facilitate a more complete understanding of the eukaryotic tree of life. PMID:27604879

  15. [Comparison between transgenic insect-resistant cotton expressing Cry1Ac protein and its parental variety in rhizospheric fungal diversity].

    PubMed

    Pan, Jian-Gang; Jiao, Hai-Hua; Bai, Zhi-Hui; Qi, Hong-Yan; Ma, An-Zhou; Zhuang, Guo-qiang; Zhang, Hong-xun

    2014-11-01

    The dynamics of rhizospheric fungal diversity and biomass at different sampling stages associated with two transgenic insectresistant cottons expressing Cry1Ac protein and their control varieties were studied under greenhouse conditions, followed by PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and quantitative real-time polymerase chain reaction (Q-PCR), in order to evaluate the ecological security of planting transgenic cotton expressing Cry1Ac protein. The results indicated that the fungal superior bands in rhizosphere of transgenic Bt cotton were similar with that of control cotton at four sampling stages, the more obvious difference in the blurred bands among transgenic Bt cotton, JM20 and SHIYUAN321 was detected. The rhizospheric fungal biomass of transgenic Bt cotton SGK321 was significantly lower than that of its parental control cotton at seedling stage, while the slight decrease in fungal biomass of transgenic Bt cotton XP188 was detected at boll forming stage, the ill-defined decrease, even growing tendency in two transgenic Bt cottons was detected at other stages. However, the difference of rhizospheric fungal community compositions and biomass was not only existed between transgenic cotton and its control, but also between SHIYUAN321 and JM20, and the same phenomenon was also detected between transgenic Bt cotton SGK321 and XP188. Hence, Bt protein is not the only incentive resulting in the difference in fungal community composition and diversity, the decrease in biomass between transgenic cotton and untransgenic cotton, different cotton varieties has an effect on them. PMID:25639113

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

    PubMed

    Asemaninejad, Asma; Weerasuriya, Nimalka; Gloor, Gregory B; Lindo, Zoë; Thorn, R Greg

    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

  17. 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

  18. The biological diversity conservation district: A rain forest conservation tool for the future

    SciTech Connect

    Simons, M.

    1995-12-01

    Over the next twenty years, the Earth`s rain forests may decrease by forty percent! This paper presents a revolutionary corporate entity for the protection of those forests, the biological diversity conservation district (biodistricts). The underlying cause of rain forest destruction is unfettered competition for limited resources. The competitors are many: farmers, business, local and national governments, the biotechnology and ecotourism industries, multinational companies, public utilities, and indigenous groups. To varying degrees, all compete within the marketplace. biodistricts will bring together two forces once thought to be antithetical: conservation an development. They will be set up in corporate form, owned and controlled by groups claiming access to the forest resources. Because the various groups will fight for the same resources habitats, ecosystems, and genetic diversity-each will prevent the others from destroying them. The district members will ensure that all businesses maintain sustainable development practices because the economic success of the district depends upon the area`s natural beauty and biological diversity. This paper analyzes the effects on the culture, politics, economy and conservation there. It will conclude that the comprehensive approach taken by biodistricts is the only method for solving the problem of rain forest destruction; that it is economically feasible, culturally viable, and ethically defensible. By March 1, 1995, the paper will represent not only the culmination of eighteen months of research, writing and interviews regarding biological diversity conservation, but also the impetus to push the thinking of environmentalists and business persons in a new direction, perhaps the only direction that will allow the nations of the world to protect their forests for the next twenty years and beyond.

  19. Exploring the conformational diversity of loops on conserved frameworks.

    PubMed

    Li, W; Liang, S; Wang, R; Lai, L; Han, Y

    1999-12-01

    Loops are structurally variable regions, but the secondary structural elements bracing loops are often conserved. Motifs with similar secondary structures exist in the same and different protein families. In this study, we made an all-PDB-based analysis and produced 495 motif families accessible from the Internet. Every motif family contains some variable loops spanning a common framework (a pair of secondary structures). The diversity of loops and the convergence of frameworks were examined. In addition, we also identified 119 loops with conformational changes in different PDB files. These materials can give some directions for functional loop design and flexible docking. PMID:10611401

  20. Characterizing fish community diversity across Virginia landscapes: Prerequisite for conservation

    USGS Publications Warehouse

    Angermeier, P.L.; Winston, M.R.

    1999-01-01

    The number of community types occurring within landscapes is an important, but often unprotected, component of biological diversity. Generally applicable protocols for characterizing community diversity need to be developed to facilitate conservation. We used several multivariate techniques to analyze geographic variation in the composition of fish communities in Virginia streams. We examined relationships between community composition and six landscape variables: drainage basin, physiography, stream order, elevation, channel slope, and map coordinates. We compared patterns at two scales (statewide and subdrainage-specific) to assess sensitivity of community classification to spatial scale. We also compared patterns based on characterizing communities by species composition vs. ecological composition. All landscape variables explained significant proportions of the variance in community composition. Statewide, they explained 32% of the variance in species composition and 48% of the variance in ecological composition. Typical communities in each drainage or physiography were statistically distinctive. Communities in different combinations of drainage, physiography, and stream size were even more distinctive, but composition was strongly spatially autocorrelated. Ecological similarity and species similarity of community pairs were strongly related, but replacement by ecologically similar species was common among drainage-physiography combinations. Landscape variables explained significant proportions of variance in community composition within selected subdrainages, but proportions were less than at the statewide scale, and the explanatory power of individual variables varied considerably among subdrainages. Community variation within subdrainages appeared to be much more closely related to environmental variation than to replacement among ecologically similar species. Our results suggest that taxonomic and ecological characterizations of community composition are

  1. Mycorrhizal Fungal Diversity and Community Composition in Two Closely Related Platanthera (Orchidaceae) Species

    PubMed Central

    Esposito, Fabiana; Jacquemyn, Hans; Waud, Michael; Tyteca, Daniel

    2016-01-01

    While it is generally acknowledged that orchid species rely on mycorrhizal fungi for completion of their life cycle, little is yet known about how mycorrhizal fungal diversity and community composition vary within and between closely related orchid taxa. In this study, we used 454 amplicon pyrosequencing to investigate variation in mycorrhizal communities between pure (allopatric) and mixed (sympatric) populations of two closely related Platanthera species (Platanthera bifolia and P. chlorantha) and putative hybrids. Consistent with previous research, the two species primarily associated primarily with members of the Ceratobasidiaceae and, to a lesser extent, with members of the Sebacinales and Tulasnellaceae. In addition, a large number of ectomycorrhizal fungi belonging to various families were observed. Although a considerable number of mycorrhizal fungi were common to both species, the fungal communities were significantly different between the two species. Individuals with intermediate morphology showed communities similar to P. bifolia, confirming previous results based on the genetic architecture and fragrance composition that putative hybrids essentially belonged to one of the parental species (P. bifolia). Differences in mycorrhizal communities between species were smaller in mixed populations than between pure populations, suggesting that variation in mycorrhizal communities was largely controlled by local environmental conditions. The small differences in mycorrhizal communities in mixed populations suggests that mycorrhizal fungi are most likely not directly involved in maintaining species boundaries between the two Platanthera species. However, seed germination experiments are needed to unambiguously assess the contribution of mycorrhizal divergence to reproductive isolation. PMID:27695108

  2. Ectomycorrhizal fungal diversity in orchards of cultivated pecan (Carya illinoinensis; Juglandaceae).

    PubMed

    Bonito, Gregory; Brenneman, Timothy; Vilgalys, Rytas

    2011-10-01

    Carya illinoinensis (pecan) belongs to the Juglandaceae (walnut family) and is a major economic nut crop in the southern USA. Although evidence suggests that some species in the Juglandaceae are ectomycorrhizal, investigations on their ectomycorrhizal fungal symbionts are quite limited. Here we assessed the ectomycorrhizal fungal diversity in cultivated orchards of C. illinoinensis. Five pecan orchards in southern Georgia, USA, were studied, three of which were known to fruit the native edible truffle species Tuber lyonii. We sequenced rDNA from single ectomycorrhizal root tips sampled from a total of 50 individual trees. Mycorrhizae were identified by ITS and LSU rDNA sequence-based methods. Forty-four distinct ectomycorrhizal taxa were detected. Sequestrate taxa including Tuber and Scleroderma were particularly abundant. The two most abundant sequence types belonged to T. lyonii (17%) and an undescribed Tuber species (~20%). Because of our interest in the ecology of T. lyonii, we also conducted greenhouse studies to determine whether this species would colonize and form ectomycorrhizae on roots of pecan, oak, or pine species endemic to the region. T. lyonii ectomycorrhizae were formed on pecan and oak seedlings, but not pine, when these were inoculated with spores. That oak and pecan seedling roots were receptive to truffle spores indicates that spore slurry inoculation could be a suitable method for commercial use and that, ecologically, T. lyonii may function as a pioneer ectomycorrhizal species for these hosts. PMID:21369784

  3. Fungal spore diversity of arbuscular mycorrhizal fungi associated with spring wheat: effects of tillage.

    PubMed

    Schalamuk, S; Velazquez, S; Chidichimo, H; Cabello, M

    2006-01-01

    We investigated the influence of tilling, N fertilization and crop stage on arbuscular mycorrhizae (AM) fungal species diversity in a wheat monoculture in the Pampa region of Argentina. Glomalean spores were isolated by wet sieving and decanting from conventionally tilled and nontilled soils cropped with wheat with or without N fertilization, at three phenological stages of the crop (tilling, flowering and grain filling) and fallow. Morphological characterization yielded at least 24 AM fungi taxa in the field samples, belonging to six genera of AMF: Acaulospora Archaeospora, Entrophospora, Gigaspora, Glomus and Scutellospora. Tilling and fertilization treatments did not result in decreased spore biodiversity. Wheat phenology influenced AM communities, with highest spore biodiversity during grain filling.

  4. Diversity of endophytic fungal community associated with Piper hispidum (Piperaceae) leaves.

    PubMed

    Orlandelli, R C; Alberto, R N; Rubin Filho, C J; Pamphile, J A

    2012-05-22

    Tropical and subtropical plants are rich in endophytic community diversity. Endophytes, mainly fungi and bacteria, inhabit the healthy plant tissues without causing any damage to the hosts. These fungi can be useful for biological control of pathogens and plant growth promotion. Some plants of the genus Piper are hosts of endophytic microorganisms; however, there is little information about endophytes on Piper hispidum, a medicinal shrub used as an insecticide, astringent, diuretic, stimulant, liver treatment, and for stopping hemorrhages. We isolated the fungal endophyte community associated with P. hispidum leaves from plants in a Brazilian forest remnant. The endophytic diversity was examined based on sequencing of the ITS1-5.8S-ITS2 region of rDNA. A high colonization frequency was obtained, as expected for tropical angiosperms. Isolated endophytes were divided into 66 morphogroups, demonstrating considerable diversity. We identified 21 isolates, belonging to 11 genera (Alternaria, Bipolaris, Colletotrichum, Glomerella, Guignardia, Lasiodiplodia, Marasmius, Phlebia, Phoma, Phomopsis, and Schizophyllum); one isolate was identified only to the order level (Diaporthales). Bipolaris was the most frequent genus among the identified endophytes. Phylogenetic analysis confirmed the molecular identification of some isolates to genus level while for others it was confirmed at the species level.

  5. Metagenomic analysis of fungal diversity in Korean traditional wheat-based fermentation starter nuruk.

    PubMed

    Bal, Jyotiranjan; Yun, Suk-Hyun; Yeo, Soo-Hwan; Kim, Jung-Mi; Kim, Dae-Hyuk

    2016-12-01

    Nuruk, a traditional natural starter, is extensively used in the brewing of Makgeolli, one of Korea's most popular alcoholic beverages that has been recently gaining global popularity. Thus, the quality of traditional nuruk needs to be enhanced. The nuruk mycobiome greatly influences both fermentation process as well as palatability enhancement. Limitations of culture-dependent identification restrict an accurate analysis of fungal diversity and distribution in nuruks. 454 pyrosequencing of two traditional wheat-based nuruks, prepared at two representative temperature conditions revealed a total of 153 and 53 OTUs for nuruks A and B, respectively, from a total of 33,157 ITS sequences. Phylogenetic assignments indicated that nuruk A mycobiota was dominated by the genera Aspergillus and Mucorales, whereas nuruk B by Rhizomucor. Species-level identification indicated that Mucorales sp., Aspergillus candidus, and Aspergillus cibarius predominated in nuruk A mycoflora whereas Rhizomucor pusillus, Mucorales sp., and Thermoascus crustaceus in nuruk B. The alpha diversity indices suggest nuruk A mycobiota to be more diverse than that of nuruk B at almost all time points of fermentation. Resemblances of patterns of predominant species composition and succession between culture-dependent and -independent phylogenetic analysis creates the potential to reconstruct the nuruk mycobiome in vitro, which allows the establishment of a standard inoculum for scientific comparison. PMID:27554148

  6. Molecular diversity of the entomopathogenic fungal Metarhizium community within an agroecosystem.

    PubMed

    Steinwender, Bernhardt M; Enkerli, Jürg; Widmer, Franco; Eilenberg, Jørgen; Thorup-Kristensen, Kristian; Meyling, Nicolai V

    2014-11-01

    The entomopathogenic fungal Metarhizium anisopliae lineage harbors cryptic diversity and was recently split into several species. Metarhizium spp. are frequently isolated from soil environments, but the abundance and distribution of the separate species in local communities is still largely unknown. Entomopathogenic isolates of Metarhizium spp. were obtained from 32 bulked soil samples of a single agroecosystem in Denmark using Tenebrio molitor as bait insect. To assess the Metarhizium community in soil from the agricultural field and surrounding hedgerow, 123 isolates were identified by sequence analysis of 5' end of elongation factor 1-α and their genotypic diversity characterized by multilocus simple sequence repeat (SSR) typing. Metarhizium brunneum was most frequent (78.8%) followed by M. robertsii (14.6%), while M. majus and M. flavoviride were infrequent (3.3% each) revealing co-occurrence of at least four Metarhizium species in the soil of the same agroecosystem. Based on SSR fragment length analysis five genotypes of M. brunneum and six genotypes of M. robertsii were identified among the isolates. A single genotype within M. brunneum predominated (72.3% of all genotypes) while the remaining genotypes of M. brunneum and M. robertsii were found at low frequencies throughout the investigated area indicating a diverse Metarhizium community. The results may indicate potentially favorable adaptations of the predominant M. brunneum genotype to the agricultural soil environment. PMID:25224815

  7. Diversity of endophytic fungal community associated with Piper hispidum (Piperaceae) leaves.

    PubMed

    Orlandelli, R C; Alberto, R N; Rubin Filho, C J; Pamphile, J A

    2012-01-01

    Tropical and subtropical plants are rich in endophytic community diversity. Endophytes, mainly fungi and bacteria, inhabit the healthy plant tissues without causing any damage to the hosts. These fungi can be useful for biological control of pathogens and plant growth promotion. Some plants of the genus Piper are hosts of endophytic microorganisms; however, there is little information about endophytes on Piper hispidum, a medicinal shrub used as an insecticide, astringent, diuretic, stimulant, liver treatment, and for stopping hemorrhages. We isolated the fungal endophyte community associated with P. hispidum leaves from plants in a Brazilian forest remnant. The endophytic diversity was examined based on sequencing of the ITS1-5.8S-ITS2 region of rDNA. A high colonization frequency was obtained, as expected for tropical angiosperms. Isolated endophytes were divided into 66 morphogroups, demonstrating considerable diversity. We identified 21 isolates, belonging to 11 genera (Alternaria, Bipolaris, Colletotrichum, Glomerella, Guignardia, Lasiodiplodia, Marasmius, Phlebia, Phoma, Phomopsis, and Schizophyllum); one isolate was identified only to the order level (Diaporthales). Bipolaris was the most frequent genus among the identified endophytes. Phylogenetic analysis confirmed the molecular identification of some isolates to genus level while for others it was confirmed at the species level. PMID:22653631

  8. 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

  9. Role of vermicompost chemical composition, microbial functional diversity, and fungal community structure in their microbial respiratory response to three pesticides.

    PubMed

    Fernández-Gómez, Manuel J; Nogales, Rogelio; Insam, Heribert; Romero, Esperanza; Goberna, Marta

    2011-10-01

    The relationships between vermicompost chemical features, enzyme activities, community-level physiological profiles (CLPPs), fungal community structures, and its microbial respiratory response to pesticides were investigated. Fungal community structure of vermicomposts produced from damaged tomato fruits (DT), winery wastes (WW), olive-mill waste and biosolids (OB), and cattle manure (CM) were determined by denaturing gradient gel electrophoresis of 18S rDNA. MicroResp™ was used for assessing vermicompost CLPPs and testing the microbial response to metalaxyl, imidacloprid, and diuron. Vermicompost enzyme activities and CLPPs indicated that WW, OB, and DT had higher microbial functional diversity than CM. The microbiota of the former tolerated all three pesticides whereas microbial respiration in CM was negatively affected by metalaxyl and imidacloprid. The response of vermicompost microbiota to the fungicide metalaxyl was correlated to its fungal community structure. The results suggest that vermicomposts with higher microbial functional diversity can be useful for the management of pesticide pollution in agriculture.

  10. The effects of climate change on fungal diversity patterns in the UK and Greece: Contrasting trends and ecological interpretations

    NASA Astrophysics Data System (ADS)

    Damialis, A.; Gange, A. C.; Mohammad, A. B.; Halley, J. M.

    2013-05-01

    It is well known that climate change has been affecting the ecology of living organisms. However, very little research has been done concerning alterations in fungal ecology. The changes in climate are expected to have an impact on fungal biodiversity patterns. Such changes in turn might have implications for public health since the spores of certain fungal taxa (e.g. Alternaria, Cladosporium) cause respiratory problems in sensitised individuals, with symptoms manifested even as acute respiratory failure. The objectives of this study were: a) to perform a comprehensive analysis of trends in long-term time series of fungal fruiting and sporulation variables for a wide range of fungal taxa, b) to investigate the response of fungal abundance and diversity to environmental variability. Data from two different geoclimatic areas were used: a) England, UK from more than 350 fungal species belonging to 10 different functional groups and with phenological records of fungal fruiting (start, end and duration) since 1950, b) Thessaloniki, Greece for 14 airborne fungal types with quantitative records (total annual concentration) and phenological records (start, peak, end, duration) of the atmospheric spore season since 1987. In parallel, various meteorological factors were examined in both areas in order to elucidate the relationship between climate and fungal diversity patterns. Long-term trends were found in most cases: these were particularly pronounced in the UK, where more than 300 species (~82%) displayed trends. Of these, ~77% were towards an earlier beginning and ~81% towards a later ending of the fruiting season; overall, an extension of the fruiting season seems to occur in more than 200 species. On a per-functional-group basis, except for manure, soil and mycorrhizal deciduous fungal species, all the other (137 species) exhibited earlier first fruiting dates and extended seasons. On the other hand, in Greece, although a tendency was observed towards lower yearly

  11. Ruminal bacterial, archaeal, and fungal diversity of dairy cows in response to ingestion of lauric or myristic acid

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this experiment, part of a larger study, was to investigate changes in rumen bacterial, archaeal, and fungal diversity in cows with normal and reduced protozoal populations. In the main study, 6 lactating dairy cows were dosed intraruminally with 240 g/cow per day of stearic (contr...

  12. Conservation of native Pacific trout diversity in western North America

    USGS Publications Warehouse

    Penaluna, Brooke E.; Abadía-Cardoso, Alicia; Dunham, Jason; García de León, Francisco J; Gresswell, Robert E.; Luna, Arturo Ruiz; Taylor, Eric B.; Shepard, Bradley B.; Al-Chokhachy, Robert K.; Muhlfeld, Clint C.; Bestgen, Kevin R.; Rogers, Kevin H.; Escalante, Marco A; Keeley, Ernest R; Temple, Gabriel; Williams, Jack E.; Matthews, Kathleen; Pierce, Ron; Mayden, Richard L.; Kovach, Ryan; Garza, John Carlos; Fausch, Kurt D.

    2016-01-01

    Pacific trout Oncorhynchus spp. in western North America are strongly valued in ecological, socioeconomic, and cultural views, and have been the subject of substantial research and conservation efforts. Despite this, the understanding of their evolutionary histories, overall diversity, and challenges to their conservation is incomplete. We review the state of knowledge on these important issues, focusing on Pacific trout in the genus Oncorhynchus. Although most research on salmonid fishes emphasizes Pacific salmon, we focus on Pacific trout because they share a common evolutionary history, and many taxa in western North America have not been formally described, particularly in the southern extent of their ranges. Research in recent decades has led to the revision of many hypotheses concerning the origin and diversification of Pacific trout throughout their range. Although there has been significant success at addressing past threats to Pacific trout, contemporary and future threats represented by nonnative species, land and water use activities, and climate change pose challenges and uncertainties. Ultimately, conservation of Pacific trout depends on how well these issues are understood and addressed, and on solutions that allow these species to coexist with a growing scope of human influences.

  13. Blue reflectance in tarantulas is evolutionarily conserved despite nanostructural diversity

    PubMed Central

    Hsiung, Bor-Kai; Deheyn, Dimitri D.; Shawkey, Matthew D.; Blackledge, Todd A.

    2015-01-01

    Slight shifts in arrangement within biological photonic nanostructures can produce large color differences, and sexual selection often leads to high color diversity in clades with structural colors. We use phylogenetic reconstruction, electron microscopy, spectrophotometry, and optical modeling to show an opposing pattern of nanostructural diversification accompanied by unusual conservation of blue color in tarantulas (Araneae: Theraphosidae). In contrast to other clades, blue coloration in phylogenetically distant tarantulas peaks within a narrow 20-nm region around 450 nm. Both quasi-ordered and multilayer nanostructures found in different tarantulas produce this blue color. Thus, even within monophyletic lineages, tarantulas have evolved strikingly similar blue coloration through divergent mechanisms. The poor color perception and lack of conspicuous display during courtship of tarantulas argue that these colors are not sexually selected. Therefore, our data contrast with sexual selection that typically produces a diverse array of colors with a single structural mechanism by showing that natural selection on structural color in tarantulas resulted in convergence on similar color through diverse structural mechanisms. PMID:26702433

  14. Higher fungal diversity is correlated with lower CO2 emissions from dead wood in a natural forest.

    PubMed

    Yang, Chunyan; Schaefer, Douglas A; Liu, Weijie; Popescu, Viorel D; Yang, Chenxue; Wang, Xiaoyang; Wu, Chunying; Yu, Douglas W

    2016-01-01

    Wood decomposition releases almost as much CO2 to the atmosphere as does fossil-fuel combustion, so the factors regulating wood decomposition can affect global carbon cycling. We used metabarcoding to estimate the fungal species diversities of naturally colonized decomposing wood in subtropical China and, for the first time, compared them to concurrent measures of CO2 emissions. Wood hosting more diverse fungal communities emitted less CO2, with Shannon diversity explaining 26 to 44% of emissions variation. Community analysis supports a 'pure diversity' effect of fungi on decomposition rates and thus suggests that interference competition is an underlying mechanism. Our findings extend the results of published experiments using low-diversity, laboratory-inoculated wood to a high-diversity, natural system. We hypothesize that high levels of saprotrophic fungal biodiversity could be providing globally important ecosystem services by maintaining dead-wood habitats and by slowing the atmospheric contribution of CO2 from the world's stock of decomposing wood. However, large-scale surveys and controlled experimental tests in natural settings will be needed to test this hypothesis. PMID:27553882

  15. The structure of fungal biomass and diversity of cultivated micromycetes in Antarctic soils (progress and Russkaya Stations)

    NASA Astrophysics Data System (ADS)

    Marfenina, O. E.; Nikitin, D. A.; Ivanova, A. E.

    2016-08-01

    The distribution of the fungal biomass and diversity of cultivated microscopic fungi in the profiles of some soils from East (Progress Station, valleys of the Larsemann Hills oasis) and West (Russkaya Station, the Marie Byrd Land) Antarctica regions were studied. The structure of the biomass (spore/mycelium and live cells/dead cells) was analyzed by fluorescence microscopy with staining using a set of coloring agents: calcofluor white, ethidium bromide, and fluorescein diacetate. The species composition of the cultivated microscopic fungi was determined on Czapek's medium. The fungal biomass in the soils studied is not high (on the average, 0.3 mg/g of soil); the greatest biomass (0.6 mg/g) was found in the soil samples with plant residues. The fungal biomass is mainly (to 70%) represented by small (to 2.5 μm) spores. About half of the fungal biomass is composed of living cells. There are differences in the distribution of the fungal biomass within the profiles of different primitive soils. In the soil samples taken under mosses and lichens, the maximal biomass was registered in the top soil horizons. In the soils with the peat horizon under stone pavements, the greatest fungal biomass was registered in the subsurface horizons. Thirty-eight species of cultivated microscopic fungi were isolated from the soils studied. Species of the genus Penicillium and Phoma herbarum predominated.

  16. Fungal epidemiology and diversity in cystic fibrosis patients over a 5-year period in a national reference center.

    PubMed

    Ziesing, S; Suerbaum, S; Sedlacek, L

    2016-11-01

    The knowledge on prevalence rates of yeasts and moulds in patients with cystic fibrosis (CF) in Germany is scarce. The aim of this report is to give an overview of the diversity and epidemiology of fungal species in CF patients. Over a 5-year period, all fungal isolates cultured from microbiological specimen from CF patients were recorded. Beside standard bacteriological culture media two fungal media were used for cultivation. Species were identified by microscopy, biochemical profiling, MALDI-TOF analysis or DNA sequencing methods. In sum, 25,975 clinical samples from CF patients were analyzed. About 75% of CF patients were colonized by yeasts, mainly Candida albicans (38%) and Candida dubliniensis (12%). In 35% of the patients Aspergillus spp. (Aspergillus fumigatus: 29%) were detected, followed by Exophiala dermatitidis and Scedosporium/Lomentospora complex isolates (4% each). Data for other fungal species are shown. Over a 5-year period, the epidemiology of fungal species detected in CF patients was relatively constant. Clinical microbiology laboratories should carefully monitor samples from CF patients for newly occurring fungal pathogens. PMID:27364649

  17. Effects on diversity of soil fungal community and fate of an artificially applied Beauveria bassiana strain assessed through 454 pyrosequencing.

    PubMed

    Hirsch, Jacqueline; Galidevara, Sandhya; Strohmeier, Stephan; Devi, K Uma; Reineke, Annette

    2013-10-01

    The entomopathogenic fungus Beauveria bassiana is widely used as a biological control agent (BCA) for insect pest control, with fungal propagules being either incorporated into the potting media or soil or sprayed directly onto the foliage or soil. To gain a better understanding of entomopathogenic fungal ecology when applied as a BCA to the soil environment, a case study using tag-encoded 454 pyrosequencing of fungal ITS sequences was performed to assess the fate and potential effect of an artificially applied B. bassiana strain on the diversity of soil fungal communities in an agricultural field in India. Results show that the overall fungal diversity was not influenced by application of B. bassiana during the 7 weeks of investigation. Strain-specific microsatellite markers indicated both an establishment of the applied B. bassiana strain in the treated plot and its spread to the neighboring nontreated control plot. These results might be important for proper risk assessment of entomopathogenic fungi-based BCAs. PMID:23736813

  18. [Characteristics of arbuscular mycorrhizal fungal diversity and functions in saline-alkali land].

    PubMed

    Yang, Hai-xia; Guo, Shao-xia; Liu, Run-jin

    2015-01-01

    Arbuscular mycorrhizal (AM) fungi, widely distributing in various terrestrial ecosys- tems, are one of the important functional biotic components in soil habitats and play a vital role in improving soil evolution, maintaining soil health and sustainable productivity. Saline-alkali soil is a special habitat affecting plant growth and grain yield. Under the influence of a series of factors, such as human activities on the nature, S and N deposition, ozone, greenhouse effect, climate anomalies, and alien species invasions etc., soil salinization, biodiversity and functions of saline farmlands may be greatly affected, which could consequently influence agricultural production and the sustainable development of ecosystems. Followed by an introduction of the changing characteristics of saline soil area and the secondary salinization under the background of global changes, the present review mainly discussed the changing features of diversity and functions of AM fungi in saline habitats, summarized the factors influencing AM fungal diversity and functions, and the factors' changing characters under the global changes, in order to provide new ideas and ways in further elucidating the position, role and function of AM fungi in saline soil, and in strengthening saline farmland remediation in response to global changes.

  19. [Characteristics of arbuscular mycorrhizal fungal diversity and functions in saline-alkali land].

    PubMed

    Yang, Hai-xia; Guo, Shao-xia; Liu, Run-jin

    2015-01-01

    Arbuscular mycorrhizal (AM) fungi, widely distributing in various terrestrial ecosys- tems, are one of the important functional biotic components in soil habitats and play a vital role in improving soil evolution, maintaining soil health and sustainable productivity. Saline-alkali soil is a special habitat affecting plant growth and grain yield. Under the influence of a series of factors, such as human activities on the nature, S and N deposition, ozone, greenhouse effect, climate anomalies, and alien species invasions etc., soil salinization, biodiversity and functions of saline farmlands may be greatly affected, which could consequently influence agricultural production and the sustainable development of ecosystems. Followed by an introduction of the changing characteristics of saline soil area and the secondary salinization under the background of global changes, the present review mainly discussed the changing features of diversity and functions of AM fungi in saline habitats, summarized the factors influencing AM fungal diversity and functions, and the factors' changing characters under the global changes, in order to provide new ideas and ways in further elucidating the position, role and function of AM fungi in saline soil, and in strengthening saline farmland remediation in response to global changes. PMID:25985684

  20. Fungal diversity in grape must and wine fermentation assessed by massive sequencing, quantitative PCR and DGGE.

    PubMed

    Wang, Chunxiao; García-Fernández, David; Mas, Albert; Esteve-Zarzoso, Braulio

    2015-01-01

    The diversity of fungi in grape must and during wine fermentation was investigated in this study by culture-dependent and culture-independent techniques. Carignan and Grenache grapes were harvested from three vineyards in the Priorat region (Spain) in 2012, and nine samples were selected from the grape must after crushing and during wine fermentation. From culture-dependent techniques, 362 isolates were randomly selected and identified by 5.8S-ITS-RFLP and 26S-D1/D2 sequencing. Meanwhile, genomic DNA was extracted directly from the nine samples and analyzed by qPCR, DGGE and massive sequencing. The results indicated that grape must after crushing harbored a high species richness of fungi with Aspergillus tubingensis, Aureobasidium pullulans, or Starmerella bacillaris as the dominant species. As fermentation proceeded, the species richness decreased, and yeasts such as Hanseniaspora uvarum, Starmerella bacillaris and Saccharomyces cerevisiae successively occupied the must samples. The "terroir" characteristics of the fungus population are more related to the location of the vineyard than to grape variety. Sulfur dioxide treatment caused a low effect on yeast diversity by similarity analysis. Because of the existence of large population of fungi on grape berries, massive sequencing was more appropriate to understand the fungal community in grape must after crushing than the other techniques used in this study. Suitable target sequences and databases were necessary for accurate evaluation of the community and the identification of species by the 454 pyrosequencing of amplicons. PMID:26557110

  1. Diversity-oriented combinatorial biosynthesis of benzenediol lactone scaffolds by subunit shuffling of fungal polyketide synthases.

    PubMed

    Xu, Yuquan; Zhou, Tong; Zhang, Shuwei; Espinosa-Artiles, Patricia; Wang, Luoyi; Zhang, Wei; Lin, Min; Gunatilaka, A A Leslie; Zhan, Jixun; Molnár, István

    2014-08-26

    Combinatorial biosynthesis aspires to exploit the promiscuity of microbial anabolic pathways to engineer the synthesis of new chemical entities. Fungal benzenediol lactone (BDL) polyketides are important pharmacophores with wide-ranging bioactivities, including heat shock response and immune system modulatory effects. Their biosynthesis on a pair of sequentially acting iterative polyketide synthases (iPKSs) offers a test case for the modularization of secondary metabolic pathways into "build-couple-pair" combinatorial synthetic schemes. Expression of random pairs of iPKS subunits from four BDL model systems in a yeast heterologous host created a diverse library of BDL congeners, including a polyketide with an unnatural skeleton and heat shock response-inducing activity. Pairwise heterocombinations of the iPKS subunits also helped to illuminate the innate, idiosyncratic programming of these enzymes. Even in combinatorial contexts, these biosynthetic programs remained largely unchanged, so that the iPKSs built their cognate biosynthons, coupled these building blocks into chimeric polyketide intermediates, and catalyzed intramolecular pairing to release macrocycles or α-pyrones. However, some heterocombinations also provoked stuttering, i.e., the relaxation of iPKSs chain length control to assemble larger homologous products. The success of such a plug and play approach to biosynthesize novel chemical diversity bodes well for bioprospecting unnatural polyketides for drug discovery.

  2. Fungal diversity in grape must and wine fermentation assessed by massive sequencing, quantitative PCR and DGGE

    PubMed Central

    Wang, Chunxiao; García-Fernández, David; Mas, Albert; Esteve-Zarzoso, Braulio

    2015-01-01

    The diversity of fungi in grape must and during wine fermentation was investigated in this study by culture-dependent and culture-independent techniques. Carignan and Grenache grapes were harvested from three vineyards in the Priorat region (Spain) in 2012, and nine samples were selected from the grape must after crushing and during wine fermentation. From culture-dependent techniques, 362 isolates were randomly selected and identified by 5.8S-ITS-RFLP and 26S-D1/D2 sequencing. Meanwhile, genomic DNA was extracted directly from the nine samples and analyzed by qPCR, DGGE and massive sequencing. The results indicated that grape must after crushing harbored a high species richness of fungi with Aspergillus tubingensis, Aureobasidium pullulans, or Starmerella bacillaris as the dominant species. As fermentation proceeded, the species richness decreased, and yeasts such as Hanseniaspora uvarum, Starmerella bacillaris and Saccharomyces cerevisiae successively occupied the must samples. The “terroir” characteristics of the fungus population are more related to the location of the vineyard than to grape variety. Sulfur dioxide treatment caused a low effect on yeast diversity by similarity analysis. Because of the existence of large population of fungi on grape berries, massive sequencing was more appropriate to understand the fungal community in grape must after crushing than the other techniques used in this study. Suitable target sequences and databases were necessary for accurate evaluation of the community and the identification of species by the 454 pyrosequencing of amplicons. PMID:26557110

  3. Diversity of Fungal Endophytes in Various Tissues of Panax ginseng Meyer Cultivated in Korea.

    PubMed

    Park, Young-Hwan; Lee, Soon-Gu; Ahn, Doek Jong; Kwon, Tae Ryong; Park, Sang Un; Lim, Hyoun-Sub; Bae, Hanhong

    2012-04-01

    Endophytic fungi were isolated from various tissues (root, stem, petiole, leaf, and fl ower stalk) of 3- and 4-year-old ginseng plants (Panax ginseng Meyer) cultivated in Korea. The isolated endophytic fungi were identified based on the sequence analysis of the internal transcribed spacer (ITS), 1-5.8-ITS 2. A morphological characterization was also conducted using microscopic observations. According to the identification, 127 fungal isolates were assigned to 27 taxa. The genera of Phoma, Alternaria and Colletotrichum were the most frequent isolates, followed by Fusarium, Entrophospora and Xylaria. Although 19 of the 27 taxa were identified at the species level, the remainder were classified at the genus level (6 isolates), phylum level (Ascomycota, 1 isolate), and unknown fungal species (1 isolate). Endophytic fungi of 13 and 19 species were isolated from 3- and 4-year-old ginseng plants, respectively, and Phoma radicina and Fusarium solani were the most frequently isolated species colonizing the tissues of the 3- and 4-year-old ginseng plants, respectively. The colonization frequency (CF%) was dependant on the age and tissue examined: the CFs of the roots and stems in the 3-year-old ginseng were higher than the CF of tissues in the 4-year-old plants. In contrast, higher CFs were observed in the leaves and petioles of 4-year-old plants, and endophytic fungi in the flower stalks were only detected in the 4-year-old plants. In conclusion, we detected diverse endophytic fungi in ginseng plants, which were distributed differently depending on the age and tissue examined. PMID:23717122

  4. Pyrosequencing-derived bacterial, archaeal, and fungal diversity of spacecraft hardware destined for Mars.

    PubMed

    La Duc, Myron T; Vaishampayan, Parag; Nilsson, Henrik R; Torok, Tamas; Venkateswaran, Kasthuri

    2012-08-01

    Spacecraft hardware and assembly cleanroom surfaces (233 m(2) in total) were sampled, total genomic DNA was extracted, hypervariable regions of the 16S rRNA gene (bacteria and archaea) and ribosomal internal transcribed spacer (ITS) region (fungi) were subjected to 454 tag-encoded pyrosequencing PCR amplification, and 203,852 resulting high-quality sequences were analyzed. Bioinformatic analyses revealed correlations between operational taxonomic unit (OTU) abundance and certain sample characteristics, such as source (cleanroom floor, ground support equipment [GSE], or spacecraft hardware), cleaning regimen applied, and location about the facility or spacecraft. National Aeronautics and Space Administration (NASA) cleanroom floor and GSE surfaces gave rise to a larger number of diverse bacterial communities (619 OTU; 20 m(2)) than colocated spacecraft hardware (187 OTU; 162 m(2)). In contrast to the results of bacterial pyrosequencing, where at least some sequences were generated from each of the 31 sample sets examined, only 13 and 18 of these sample sets gave rise to archaeal and fungal sequences, respectively. As was the case for bacteria, the abundance of fungal OTU in the GSE surface samples dramatically diminished (9× less) once cleaning protocols had been applied. The presence of OTU representative of actinobacteria, deinococci, acidobacteria, firmicutes, and proteobacteria on spacecraft surfaces suggests that certain bacterial lineages persist even following rigorous quality control and cleaning practices. The majority of bacterial OTU observed as being recurrent belonged to actinobacteria and alphaproteobacteria, supporting the hypothesis that the measures of cleanliness exerted in spacecraft assembly cleanrooms (SAC) inadvertently select for the organisms which are the most fit to survive long journeys in space.

  5. Pyrosequencing-Derived Bacterial, Archaeal, and Fungal Diversity of Spacecraft Hardware Destined for Mars

    PubMed Central

    Vaishampayan, Parag; Nilsson, Henrik R.; Torok, Tamas; Venkateswaran, Kasthuri

    2012-01-01

    Spacecraft hardware and assembly cleanroom surfaces (233 m2 in total) were sampled, total genomic DNA was extracted, hypervariable regions of the 16S rRNA gene (bacteria and archaea) and ribosomal internal transcribed spacer (ITS) region (fungi) were subjected to 454 tag-encoded pyrosequencing PCR amplification, and 203,852 resulting high-quality sequences were analyzed. Bioinformatic analyses revealed correlations between operational taxonomic unit (OTU) abundance and certain sample characteristics, such as source (cleanroom floor, ground support equipment [GSE], or spacecraft hardware), cleaning regimen applied, and location about the facility or spacecraft. National Aeronautics and Space Administration (NASA) cleanroom floor and GSE surfaces gave rise to a larger number of diverse bacterial communities (619 OTU; 20 m2) than colocated spacecraft hardware (187 OTU; 162 m2). In contrast to the results of bacterial pyrosequencing, where at least some sequences were generated from each of the 31 sample sets examined, only 13 and 18 of these sample sets gave rise to archaeal and fungal sequences, respectively. As was the case for bacteria, the abundance of fungal OTU in the GSE surface samples dramatically diminished (9× less) once cleaning protocols had been applied. The presence of OTU representative of actinobacteria, deinococci, acidobacteria, firmicutes, and proteobacteria on spacecraft surfaces suggests that certain bacterial lineages persist even following rigorous quality control and cleaning practices. The majority of bacterial OTU observed as being recurrent belonged to actinobacteria and alphaproteobacteria, supporting the hypothesis that the measures of cleanliness exerted in spacecraft assembly cleanrooms (SAC) inadvertently select for the organisms which are the most fit to survive long journeys in space. PMID:22729532

  6. Higher fungal diversity is correlated with lower CO2 emissions from dead wood in a natural forest

    PubMed Central

    Yang, Chunyan; Schaefer, Douglas A.; Liu, Weijie; Popescu, Viorel D.; Yang, Chenxue; Wang, Xiaoyang; Wu, Chunying; Yu, Douglas W.

    2016-01-01

    Wood decomposition releases almost as much CO2 to the atmosphere as does fossil-fuel combustion, so the factors regulating wood decomposition can affect global carbon cycling. We used metabarcoding to estimate the fungal species diversities of naturally colonized decomposing wood in subtropical China and, for the first time, compared them to concurrent measures of CO2 emissions. Wood hosting more diverse fungal communities emitted less CO2, with Shannon diversity explaining 26 to 44% of emissions variation. Community analysis supports a ‘pure diversity’ effect of fungi on decomposition rates and thus suggests that interference competition is an underlying mechanism. Our findings extend the results of published experiments using low-diversity, laboratory-inoculated wood to a high-diversity, natural system. We hypothesize that high levels of saprotrophic fungal biodiversity could be providing globally important ecosystem services by maintaining dead-wood habitats and by slowing the atmospheric contribution of CO2 from the world’s stock of decomposing wood. However, large-scale surveys and controlled experimental tests in natural settings will be needed to test this hypothesis. PMID:27553882

  7. Mycorrhizal fungal diversity and community composition in a lithophytic and epiphytic orchid.

    PubMed

    Xing, Xiaoke; Gai, Xuege; Liu, Qiang; Hart, Miranda M; Guo, Shunxing

    2015-05-01

    Some orchid species are present as epiphytes and lithophytes in the same habitat, but little is known about the differences of their mycorrhizal fungal communities. We used Coelogyne viscosa, which occurs both as an epiphyte and a lithophyte, as a study system to investigate orchid mycorrhizal fungal communities in lithophytes and epiphytes in Xishuangbanna National Nature Reserve (Yunnan Province, China). Twenty-three fungal operational taxonomic units (OTUs) from 18 sampling sites were identified. Results indicated that mycorrhizal fungal community composition was different between epi- and lithophytes. When we analyzed the Tulasnellaceae and Sebacinales communities separately, we found that the Sebacinales fungal communities were significantly different in the two growth habitats, but the Tulasnellaceae fungal communities were not. Our results provide evidence for distinct orchid mycorrhiza fungal communities depending on the growth habitat of the orchid. Consistent with some recent investigations of mycorrhizal fungus community composition, this study suggests that for one orchid, growth habitat affects mycorrhizal symbioses.

  8. Shrines in Central Italy conserve plant diversity and large trees.

    PubMed

    Frascaroli, Fabrizio; Bhagwat, Shonil; Guarino, Riccardo; Chiarucci, Alessandro; Schmid, Bernhard

    2016-05-01

    Sacred natural sites (SNS) are instances of biocultural landscapes protected for spiritual motives. These sites frequently host important biological values in areas of Asia and Africa, where traditional resource management is still upheld by local communities. In contrast, the biodiversity value of SNS has hardly been quantitatively tested in Western contexts, where customs and traditions have relatively lost importance due to modernization and secularization. To assess whether SNS in Western contexts retain value for biodiversity, we studied plant species composition at 30 SNS in Central Italy and compared them with a paired set of similar but not sacred reference sites. We demonstrate that SNS are important for conserving stands of large trees and habitat heterogeneity across different land-cover types. Further, SNS harbor higher plant species richness and a more valuable plant species pool, and significantly contribute to diversity at the landscape scale. We suggest that these patterns are related not only to pre-existent features, but also to traditional management. Conservation of SNS should take into account these specificities, and their cultural as well as biological values, by supporting the continuation of traditional management practices.

  9. Conserved Gene Expression Programs in Developing Roots from Diverse Plants.

    PubMed

    Huang, Ling; Schiefelbein, John

    2015-08-01

    The molecular basis for the origin and diversification of morphological adaptations is a central issue in evolutionary developmental biology. Here, we defined temporal transcript accumulation in developing roots from seven vascular plants, permitting a genome-wide comparative analysis of the molecular programs used by a single organ across diverse species. The resulting gene expression maps uncover significant similarity in the genes employed in roots and their developmental expression profiles. The detailed analysis of a subset of 133 genes known to be associated with root development in Arabidopsis thaliana indicates that most of these are used in all plant species. Strikingly, this was also true for root development in a lycophyte (Selaginella moellendorffii), which forms morphologically different roots and is thought to have evolved roots independently. Thus, despite vast differences in size and anatomy of roots from diverse plants, the basic molecular mechanisms employed during root formation appear to be conserved. This suggests that roots evolved in the two major vascular plant lineages either by parallel recruitment of largely the same developmental program or by elaboration of an existing root program in the common ancestor of vascular plants.

  10. Molecular analysis of fungal diversity associated with three bryophyte species in the Fildes Region, King George Island, maritime Antarctica.

    PubMed

    Zhang, Tao; Xiang, Hai-Bo; Zhang, Yu-Qin; Liu, Hong-Yu; Wei, Yu-Zhen; Zhao, Li-Xun; Yu, Li-Yan

    2013-09-01

    The fungal communities associated with three bryophytes species (the liverwort Barbilophozia hatcheri, the mosses Chorisodontium aciphyllum and Sanionia uncinata) in the Fildes Region, King George Island, maritime Antarctica, were studied using clone library analysis. Fungal communities showed low diversity; the 680 clones belonged to 93 OTUs. Of these, 78 belonged to the phylum Ascomycota, 13 to the phylum Basidiomycota, 1 to the phylum Zygomycota, and 1 to an unknown phylum. Among the OTUs, the most common orders in the Ascomycota were Helotiales (42 OTUs) and Chaetothyriales (14 OTUs) and the most common orders in the Basidiomycota were Sebacinales (3 OTUs) and Platygloeales (3 OTUs). Most OTUs clustered within clades that contained phylotypes identified from samples in Antarctic or Arctic ecosystems or from bryophytes in other ecosystems. In addition, we found that host-related factor may shape the fungal communities associated with bryophytes in this region. This is the first systematic study of the fungal community in Antarctic bryophytes to be performed using culture-independent method and the results may improve understanding of the endophytic fungal evolution and ecology in the Antarctic ecosystem.

  11. Detection and diversity of copper containing nitrite reductase genes (nirK) in prokaryotic and fungal communities of agricultural soils.

    PubMed

    Long, Andrew; Song, Bongkeun; Fridey, Kelly; Silva, Amy

    2015-02-01

    Microorganisms are capable of producing N2 and N2O gases as the end products of denitrification. Copper-containing nitrite reductase (NirK), a key enzyme in the microbial N-cycle, has been found in bacteria, archaea and fungi. This study seeks to assess the diversity of nirK genes in the prokaryotic and fungal communities of agricultural soils in the United States. New primers targeting the nirK genes in fungi were developed, while nirK genes in archaea and bacteria were detected using previously published methods. The new primers were able to detect fungal nirK genes as well as bacterial nirK genes from a group that could not be observed with previously published primers. Based on the sequence analyses from three different primer sets, five clades of nirK genes were identified, which were associated with soil archaea, ammonium-oxidizing bacteria, denitrifying bacteria and fungi. The diversity of nirK genes in the two denitrifying bacteria clades was higher than the diversity found in other clades. Using a newly designed primer set, this study showed the detection of fungal nirK genes from environmental samples. The newly designed PCR primers in this study enhance the ability to detect the diversity of nirK-encoding microorganisms in soils.

  12. Fungal diversity in adult date palm (Phoenix dactylifera L.) revealed by culture-dependent and culture-independent approaches.

    PubMed

    Ben Chobba, Ines; Elleuch, Amine; Ayadi, Imen; Khannous, Lamia; Namsi, Ahmed; Cerqueira, Frederique; Drira, Noureddine; Gharsallah, Néji; Vallaeys, Tatiana

    2013-12-01

    Endophytic flora plays a vital role in the colonization and survival of host plants, especially in harsh environments, such as arid regions. This flora may, however, contain pathogenic species responsible for various troublesome host diseases. The present study is aimed at investigating the diversity of both cultivable and non-cultivable endophytic fungal floras in the internal tissues (roots and leaves) of Tunisian date palm trees (Phoenix dactylifera). Accordingly, 13 isolates from both root and leaf samples, exhibiting distinct colony morphology, were selected from potato dextrose agar (PDA) medium and identified by a sequence match search wherein their 18S-28S internal transcribed spacer (ITS) sequences were compared to those available in public databases. These findings revealed that the cultivable root and leaf isolates fell into two groups, namely Nectriaceae and Pleosporaceae. Additionally, total DNA from palm roots and leaves was further extracted and ITS fragments were amplified. Restriction fragment length polymorphism (RFLP) analysis of the ITS from 200 fungal clones (leaves: 100; roots: 100) using HaeIII restriction enzyme revealed 13 distinct patterns that were further sequenced and led to the identification of Alternaria, Cladosporium, Davidiella (Cladosporium teleomorph), Pythium, Curvularia, and uncharacterized fungal endophytes. Both approaches confirmed that while the roots were predominantly colonized by Fusaria (members of the Nectriaceae family), the leaves were essentially colonized by Alternaria (members of the Pleosporaceae family). Overall, the findings of the present study constitute, to the authors' knowledge, the first extensive report on the diversity of endophytic fungal flora associated with date palm trees (P. dactylifera).

  13. Taxa-area relationship and neutral dynamics influence the diversity of fungal communities on senesced tree leaves.

    PubMed

    Feinstein, Larry M; Blackwood, Christopher B

    2012-06-01

    This study utilized individual senesced sugar maple and beech leaves as natural sampling units within which to quantify saprotrophic fungal diversity. Quantifying communities in individual leaves allowed us to determine if fungi display a classic taxa-area relationship (species richness increasing with area). We found a significant taxa-area relationship for sugar maple leaves, but not beech leaves, consistent with Wright's species-energy theory. This suggests that energy availability as affected plant biochemistry is a key factor regulating the scaling relationships of fungal diversity. We also compared taxa rank abundance distributions to models associated with niche or neutral theories of community assembly, and tested the influence of leaf type as an environmental niche factor controlling fungal community composition. Among rank abundance distribution models, the zero-sum model derived from neutral theory showed the best fit to our data. Leaf type explained only 5% of the variability in community composition. Habitat (vernal pool, upland or riparian forest floor) and site of collection explained > 40%, but could be attributed to either niche or neutral processes. Hence, although niche dynamics may regulate fungal communities at the habitat scale, our evidence points towards neutral assembly of saprotrophic fungi on individual leaves, with energy availability constraining the taxa-area relationship. PMID:22489632

  14. 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

  15. Phylogenetically diverse cultivable fungal community and polyketide synthase (PKS), non-ribosomal peptide synthase (NRPS) genes associated with the South China Sea sponges.

    PubMed

    Zhou, Kang; Zhang, Xia; Zhang, Fengli; Li, Zhiyong

    2011-10-01

    Compared with sponge-associated bacteria, the phylogenetic diversity of fungi in sponge and the association of sponge fungi remain largely unknown. Meanwhile, no detection of polyketide synthase (PKS) or non-ribosomal peptide synthase (NRPS) genes in sponge-associated fungi has been attempted. In this study, diverse and novel cultivable fungi including 10 genera (Aspergillus, Ascomycete, Fusarium, Isaria, Penicillium, Plectosphaerella, Pseudonectria, Simplicillium, Trichoderma, and Volutella) in four orders (Eurotiales, Hypocreales, Microascales, and Phyllachorales) of phylum Ascomycota were isolated from 10 species marine sponges in the South China Sea. Eurotiales and Hypocreales fungi were suggested as sponge generalists. The predominant isolates were Penicillium and Aspergillus in Eurotiales followed by Volutella in Hypocreales. Based on the conserved Beta-ketosynthase of PKS and A domain of NRPS, 15 polyketide synthases, and four non-ribosomal peptides synthesis genes, including non-reducing and reducing PKSs and hybrid PKS-NRPS, were detected in these fungal isolates. A lateral gene transfer event was indicated in the comparison between the phylogenetic diversity of 18S rRNA genes and β-ketoacyl synthase domain sequences. Some fungi, especially those with PKS or NRPS genes, showed antimicrobial activity against P. fluorescens, S. aureus and B. subtilis. It was the first time to investigate PKS and NRPS genes in sponge-associated fungi. Based on the detected antibiotics biosynthesis-related PKS and NRPS genes and antimicrobial activity, the potential ecological role of sponge-associated fungi in the chemical defense for sponge host was suggested. This study extended our knowledge of sponge-associated fungal phylogenetic diversity and their potential roles in the chemical defense.

  16. Diversity of fungal endophytes in recent and ancient wheat ancestors Triticum dicoccoides and Aegilops sharonensis.

    PubMed

    Ofek-Lalzar, Maya; Gur, Yonatan; Ben-Moshe, Sapir; Sharon, Or; Kosman, Evsey; Mochli, Elad; Sharon, Amir

    2016-10-01

    Endophytes have profound impacts on plants, including beneficial effects on agriculturally important traits. We hypothesized that endophytes in wild plants include beneficial endophytes that are absent or underrepresented in domesticated crops. In this work, we studied the structure of endophyte communities in wheat-related grasses, Triticum dicoccoides and Aegilops sharonensis, and compared it to an endophyte community from wheat (T. aeastivum). Endophytes were isolated by cultivation and by cultivation-independent methods. In total, 514 intergenic spacer region sequences from single cultures were analyzed. Categorization at 97% sequence similarity resulted in 67 operational taxonomic units (OTUs) that were evenly distributed between the different plant species. A narrow core community of Alternaria spp. was found in all samples, but each plant species also contained a significant portion of unique endophytes. The cultivation-independent analysis identified a larger number of OTUs than the cultivation method, half of which were singletons or doubletons. For OTUs with a relative abundance >0.5%, similar numbers were obtained by both methods. Collectively, our data show that wild grass relatives of wheat contain a wealth of taxonomically diverse fungal endophytes that are not found in modern wheat, some of which belong to taxa with known beneficial effects. PMID:27402714

  17. Diversity of fungal endophytes in recent and ancient wheat ancestors Triticum dicoccoides and Aegilops sharonensis.

    PubMed

    Ofek-Lalzar, Maya; Gur, Yonatan; Ben-Moshe, Sapir; Sharon, Or; Kosman, Evsey; Mochli, Elad; Sharon, Amir

    2016-10-01

    Endophytes have profound impacts on plants, including beneficial effects on agriculturally important traits. We hypothesized that endophytes in wild plants include beneficial endophytes that are absent or underrepresented in domesticated crops. In this work, we studied the structure of endophyte communities in wheat-related grasses, Triticum dicoccoides and Aegilops sharonensis, and compared it to an endophyte community from wheat (T. aeastivum). Endophytes were isolated by cultivation and by cultivation-independent methods. In total, 514 intergenic spacer region sequences from single cultures were analyzed. Categorization at 97% sequence similarity resulted in 67 operational taxonomic units (OTUs) that were evenly distributed between the different plant species. A narrow core community of Alternaria spp. was found in all samples, but each plant species also contained a significant portion of unique endophytes. The cultivation-independent analysis identified a larger number of OTUs than the cultivation method, half of which were singletons or doubletons. For OTUs with a relative abundance >0.5%, similar numbers were obtained by both methods. Collectively, our data show that wild grass relatives of wheat contain a wealth of taxonomically diverse fungal endophytes that are not found in modern wheat, some of which belong to taxa with known beneficial effects.

  18. Nitrogen addition, not initial phylogenetic diversity, increases litter decomposition by fungal communities.

    PubMed

    Amend, Anthony S; Matulich, Kristin L; Martiny, Jennifer B H

    2015-01-01

    Fungi play a critical role in the degradation of organic matter. Because different combinations of fungi result in different rates of decomposition, determining how climate change will affect microbial composition and function is fundamental to predicting future environments. Fungal response to global change is patterned by genetic relatedness, resulting in communities with comparatively low phylogenetic diversity (PD). This may have important implications for the functional capacity of disturbed communities if lineages sensitive to disturbance also contain unique traits important for litter decomposition. Here we tested the relationship between PD and decomposition rates. Leaf litter fungi were isolated from the field and deployed in microcosms as mock communities along a gradient of initial PD, while species richness was held constant. Replicate communities were subject to nitrogen fertilization comparable to anthropogenic deposition levels. Carbon mineralization rates were measured over the course of 66 days. We found that nitrogen fertilization increased cumulative respiration by 24.8%, and that differences in respiration between fertilized and ambient communities diminished over the course of the experiment. Initial PD failed to predict respiration rates or their change in response to nitrogen fertilization, and there was no correlation between community similarity and respiration rates. Last, we detected no phylogenetic signal in the contributions of individual isolates to respiration rates. Our results suggest that the degree to which PD predicts ecosystem function will depend on environmental context. PMID:25741330

  19. Fungal diversity and natural occurrence of deoxynivalenol and zearalenone in freshly harvested wheat grains from Brazil.

    PubMed

    Tralamazza, Sabina Moser; Bemvenuti, Renata Heidtmann; Zorzete, Patrícia; de Souza Garcia, Fábio; Corrêa, Benedito

    2016-04-01

    This study investigated the fungal diversity and presence of deoxynivalenol and zearalenone in 150 samples of freshly harvested wheat grains collected in three regions of Brazil (Sao Paulo, Parana, and Rio Grande do Sul). Analysis of the mycobiota showed a predominance of Alternaria sp., Fusarium sp. and Epicoccum sp. Microdochium nivale (23%), a fungus rarely found in Brazilian crops, was detected in Sao Paulo. Four members of the Fusarium graminearum species complex were isolated: F. graminearum s.s. (37%), Fusarium meridionale (46%), Fusarium cortaderiae (13%), and Fusarium austroamericanum (3%). Toxin analysis revealed 99% contamination with deoxynivalenol (mean 706 μg/kg). The frequency of zearalenone varied greatly across regions: wheat grains from Rio Grande do Sul (84%) and Sao Paulo (12%) had median concentrations of 70.9 and 57.9 μg/kg, respectively. ZEA was not detected in the samples from Parana. A total of six samples were above the maximum tolerated level recommended by the European Commission for ZEA in wheat grains. This study provided new insights into the natural mycobiota of Brazilian wheat, demonstrating contamination of most samples with deoxynivalenol and high frequency of zearalenone in samples from Rio Grande do Sul.

  20. Divergence Times and Phylogenetic Patterns of Sebacinales, a Highly Diverse and Widespread Fungal Lineage

    PubMed Central

    Garnica, Sigisfredo; Riess, Kai; Schön, Max E.; Oberwinkler, Franz; Setaro, Sabrina D.

    2016-01-01

    Patterns of geographic distribution and composition of fungal communities are still poorly understood. Widespread occurrence in terrestrial ecosystems and the unique richness of interactions of Sebacinales with plants make them a target group to study evolutionary events in the light of nutritional lifestyle. We inferred diversity patterns, phylogenetic structures and divergence times of Sebacinales with respect to their nutritional lifestyles by integrating data from fossil-calibrated phylogenetic analyses. Relaxed molecular clock analyses indicated that Sebacinales originated late Permian within Basidiomycota, and their split into Sebacinaceae and Serendipitaceae nom. prov. likely occurred during the late Jurassic and the early Cretaceous, coinciding with major diversifications of land plants. In Sebacinaceae, diversification of species with ectomycorrhizal lifestyle presumably started during the Paleocene. Lineage radiations of the core group of ericoid and cavendishioid mycorrhizal Sebacinales started probably in the Eocene, coinciding with diversification events of their hosts. The diversification of Sebacinales with jungermannioid interactions started during the Oligocene, and occurred much later than the diversification of their hosts. Sebacinales communities associated either with ectomycorrhizal plants, achlorophyllous orchids, ericoid and cavendishioid Ericaceae or liverworts were phylogenetically clustered and globally distributed. Major Sebacinales lineage diversifications started after the continents had drifted apart. We also briefly discuss dispersal patterns of extant Sebacinales. PMID:26938104

  1. Divergence Times and Phylogenetic Patterns of Sebacinales, a Highly Diverse and Widespread Fungal Lineage.

    PubMed

    Garnica, Sigisfredo; Riess, Kai; Schön, Max E; Oberwinkler, Franz; Setaro, Sabrina D

    2016-01-01

    Patterns of geographic distribution and composition of fungal communities are still poorly understood. Widespread occurrence in terrestrial ecosystems and the unique richness of interactions of Sebacinales with plants make them a target group to study evolutionary events in the light of nutritional lifestyle. We inferred diversity patterns, phylogenetic structures and divergence times of Sebacinales with respect to their nutritional lifestyles by integrating data from fossil-calibrated phylogenetic analyses. Relaxed molecular clock analyses indicated that Sebacinales originated late Permian within Basidiomycota, and their split into Sebacinaceae and Serendipitaceae nom. prov. likely occurred during the late Jurassic and the early Cretaceous, coinciding with major diversifications of land plants. In Sebacinaceae, diversification of species with ectomycorrhizal lifestyle presumably started during the Paleocene. Lineage radiations of the core group of ericoid and cavendishioid mycorrhizal Sebacinales started probably in the Eocene, coinciding with diversification events of their hosts. The diversification of Sebacinales with jungermannioid interactions started during the Oligocene, and occurred much later than the diversification of their hosts. Sebacinales communities associated either with ectomycorrhizal plants, achlorophyllous orchids, ericoid and cavendishioid Ericaceae or liverworts were phylogenetically clustered and globally distributed. Major Sebacinales lineage diversifications started after the continents had drifted apart. We also briefly discuss dispersal patterns of extant Sebacinales. PMID:26938104

  2. Nitrogen addition, not initial phylogenetic diversity, increases litter decomposition by fungal communities

    PubMed Central

    Amend, Anthony S.; Matulich, Kristin L.; Martiny, Jennifer B. H.

    2015-01-01

    Fungi play a critical role in the degradation of organic matter. Because different combinations of fungi result in different rates of decomposition, determining how climate change will affect microbial composition and function is fundamental to predicting future environments. Fungal response to global change is patterned by genetic relatedness, resulting in communities with comparatively low phylogenetic diversity (PD). This may have important implications for the functional capacity of disturbed communities if lineages sensitive to disturbance also contain unique traits important for litter decomposition. Here we tested the relationship between PD and decomposition rates. Leaf litter fungi were isolated from the field and deployed in microcosms as mock communities along a gradient of initial PD, while species richness was held constant. Replicate communities were subject to nitrogen fertilization comparable to anthropogenic deposition levels. Carbon mineralization rates were measured over the course of 66 days. We found that nitrogen fertilization increased cumulative respiration by 24.8%, and that differences in respiration between fertilized and ambient communities diminished over the course of the experiment. Initial PD failed to predict respiration rates or their change in response to nitrogen fertilization, and there was no correlation between community similarity and respiration rates. Last, we detected no phylogenetic signal in the contributions of individual isolates to respiration rates. Our results suggest that the degree to which PD predicts ecosystem function will depend on environmental context. PMID:25741330

  3. Higher diversity in fungal species discriminates children with type 1 diabetes mellitus from healthy control

    PubMed Central

    Kowalewska, Beata; Zorena, Katarzyna; Szmigiero-Kawko, Małgorzata; Wąż, Piotr; Myśliwiec, Małgorzata

    2016-01-01

    Objective To conduct qualitative and quantitative assessment of yeast-like fungi in the feces of children and adolescents with type 1 diabetes mellitus (T1DM) with respect to their metabolic control and duration of the disease. Materials and methods The studied materials included samples of fresh feces collected from 53 children and adolescents with T1DM. Control group included 30 age- and sex-matched healthy individuals. Medical history was taken and physical examination was conducted in the two study arms. Prevalence of the yeast-like fungi in the feces was determined as well as their amounts, species diversity, drug susceptibility, and enzymatic activity. Results The yeast-like fungi were found in the samples of feces from 75.4% of T1DM patients and 70% controls. In the group of T1DM patients, no correlation was found between age (Rs=0.253, P=0.068), duration of diabetes (Rs=−0.038, P=0.787), or body mass index (Rs=0.150, P=0.432) and the amount of the yeast-like fungi isolated in the feces. Moreover, no correlation was seen between the amount of the yeast-like fungi and glycated hemoglobin (Rs=0.0324, P=0.823), systolic blood pressure (Rs=0.102, P=0.483), or diastolic blood pressure (Rs=0.271, P=0.345). Conclusion Our research has shown that children and adolescents with T1DM show higher species diversity of the yeast-like fungi, with Candida albicans being significantly less prevalent versus control subjects. Moreover, fungal species in patients with T1DM turn out to be more resistant to antifungal treatment. PMID:27143864

  4. [Diversity and tissue distribution of fungal endophytes in Alpinia officinarum: an important south-China medicinal plant].

    PubMed

    Zhou, Ren-Chao; Huang, Juan; Li, Ze-En; Li, Shu-Bin

    2014-08-01

    In the present study, terminal-restriction fragment length polymorphism (T-RFLP) technique was applied to assess the diversity and tissue distribution of the fungal endophyte communities of Alpinia officinarum collected from Longtang town in Xuwen county, Guangdong province, China, at which the pharmacological effect of the medicine plant is traditional considered to be the significantly higher than that in any other growth areas in China. A total of 28 distinct Terminal-Restriction Fragment (T-RFs) were detected with HhaI Mono-digestion targeted amplified fungal nuclear ribosomal internal transcribed spacer region sequences (rDNA ITS) from the root, rhizome, stem, and leaf internal tissues of A. officinarum plant, indicating that at least 28 distinct fungal species were able to colonize the internal tissue of the host plant. The rDNA ITS-T-RFLP profiles obtained from different tissues of the host plant were obvious distinct. And the numbers of total T-RFs, and the dominant T-RFs detected from various tissues were significantly different. Based on the obtained T-RFLP profiles, Shannon's diversity index and the Shannon's evenness index were calculated, which were significantly different among tissues (P < 0.05). Furthermore, two types of active chemicals, total volatile oils by water vapor distillation method and galangin by methanol extraction-HPLC method, were examined in the each tissue of the tested plant. Both of tested components were detected in all of the four tissues of the medicine plant with varying contents. And the highest was in rhizome tissue. Correlation analysis revealed there were significant negative correlations between both of the tested active components contents and calculated Shannon's diversity index, as well as the Shannon's evenness index of the fungal endophyte communities of the host plant (P = 0, Pearson correlation coefficient ≤ -0.962), and significant positive correlations between both of the tested active components contents and

  5. PCR Primers to Study the Diversity of Expressed Fungal Genes Encoding Lignocellulolytic Enzymes in Soils Using High-Throughput Sequencing

    PubMed Central

    Barbi, Florian; Bragalini, Claudia; Vallon, Laurent; Prudent, Elsa; Dubost, Audrey; Fraissinet-Tachet, Laurence; Marmeisse, Roland; Luis, Patricia

    2014-01-01

    Plant biomass degradation in soil is one of the key steps of carbon cycling in terrestrial ecosystems. Fungal saprotrophic communities play an essential role in this process by producing hydrolytic enzymes active on the main components of plant organic matter. Open questions in this field regard the diversity of the species involved, the major biochemical pathways implicated and how these are affected by external factors such as litter quality or climate changes. This can be tackled by environmental genomic approaches involving the systematic sequencing of key enzyme-coding gene families using soil-extracted RNA as material. Such an approach necessitates the design and evaluation of gene family-specific PCR primers producing sequence fragments compatible with high-throughput sequencing approaches. In the present study, we developed and evaluated PCR primers for the specific amplification of fungal CAZy Glycoside Hydrolase gene families GH5 (subfamily 5) and GH11 encoding endo-β-1,4-glucanases and endo-β-1,4-xylanases respectively as well as Basidiomycota class II peroxidases, corresponding to the CAZy Auxiliary Activity family 2 (AA2), active on lignin. These primers were experimentally validated using DNA extracted from a wide range of Ascomycota and Basidiomycota species including 27 with sequenced genomes. Along with the published primers for Glycoside Hydrolase GH7 encoding enzymes active on cellulose, the newly design primers were shown to be compatible with the Illumina MiSeq sequencing technology. Sequences obtained from RNA extracted from beech or spruce forest soils showed a high diversity and were uniformly distributed in gene trees featuring the global diversity of these gene families. This high-throughput sequencing approach using several degenerate primers constitutes a robust method, which allows the simultaneous characterization of the diversity of different fungal transcripts involved in plant organic matter degradation and may lead to the

  6. PCR primers to study the diversity of expressed fungal genes encoding lignocellulolytic enzymes in soils using high-throughput sequencing.

    PubMed

    Barbi, Florian; Bragalini, Claudia; Vallon, Laurent; Prudent, Elsa; Dubost, Audrey; Fraissinet-Tachet, Laurence; Marmeisse, Roland; Luis, Patricia

    2014-01-01

    Plant biomass degradation in soil is one of the key steps of carbon cycling in terrestrial ecosystems. Fungal saprotrophic communities play an essential role in this process by producing hydrolytic enzymes active on the main components of plant organic matter. Open questions in this field regard the diversity of the species involved, the major biochemical pathways implicated and how these are affected by external factors such as litter quality or climate changes. This can be tackled by environmental genomic approaches involving the systematic sequencing of key enzyme-coding gene families using soil-extracted RNA as material. Such an approach necessitates the design and evaluation of gene family-specific PCR primers producing sequence fragments compatible with high-throughput sequencing approaches. In the present study, we developed and evaluated PCR primers for the specific amplification of fungal CAZy Glycoside Hydrolase gene families GH5 (subfamily 5) and GH11 encoding endo-β-1,4-glucanases and endo-β-1,4-xylanases respectively as well as Basidiomycota class II peroxidases, corresponding to the CAZy Auxiliary Activity family 2 (AA2), active on lignin. These primers were experimentally validated using DNA extracted from a wide range of Ascomycota and Basidiomycota species including 27 with sequenced genomes. Along with the published primers for Glycoside Hydrolase GH7 encoding enzymes active on cellulose, the newly design primers were shown to be compatible with the Illumina MiSeq sequencing technology. Sequences obtained from RNA extracted from beech or spruce forest soils showed a high diversity and were uniformly distributed in gene trees featuring the global diversity of these gene families. This high-throughput sequencing approach using several degenerate primers constitutes a robust method, which allows the simultaneous characterization of the diversity of different fungal transcripts involved in plant organic matter degradation and may lead to the

  7. Detection and diversity of fungal nitric oxide reductase genes (p450nor) in agricultural soils

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Members of the Fungi convert nitrate (NO3-) and nitrite (NO2-) to gaseous nitrous oxide (N2O) (denitrification), but the fungal contributions to N-loss from soil remain uncertain. Cultivation-based methodologies that include antibiotics to selectively assess fungal activities have limitations and co...

  8. A comparison of the community diversity of foliar fungal endophytes between seedling and adult loblolly pines (Pinus taeda).

    PubMed

    Oono, Ryoko; Lefèvre, Emilie; Simha, Anita; Lutzoni, François

    2015-10-01

    Fungal endophytes represent one of the most ubiquitous plant symbionts on Earth and are phylogenetically diverse. The structure and diversity of endophyte communities have been shown to depend on host taxa and climate, but there have been relatively few studies exploring endophyte communities throughout host maturity. We compared foliar fungal endophyte communities between seedlings and adult trees of loblolly pines (Pinus taeda) at the same seasons and locations by culturing and culture-independent methods. We sequenced the internal transcribed spacer region and adjacent partial large subunit nuclear ribosomal RNA gene (ITS-LSU amplicon) to delimit operational taxonomic units and phylogenetically characterize the communities. Despite the lower infection frequency in seedlings compared to adult trees, seedling needles were receptive to a more diverse community of fungal endophytes. Culture-free method confirmed the presence of commonly cultured OTUs from adult needles but revealed several new OTUs from seedling needles that were not found with culturing methods. The two most commonly cultured OTUs in adults were rarely cultured from seedlings, suggesting that host age is correlated with a selective enrichment for specific endophytes. This shift in endophyte species dominance may be indicative of a functional change between these fungi and their loblolly pine hosts. PMID:26399186

  9. A comparison of the community diversity of foliar fungal endophytes between seedling and adult loblolly pines (Pinus taeda)

    PubMed Central

    Oono, Ryoko; Lefèvre, Emilie; Simha, Anita; Lutzoni, François

    2015-01-01

    Fungal endophytes represent one of the most ubiquitous plant symbionts on Earth and are phylogenetically diverse. The structure and diversity of endophyte communities have been shown to depend on host taxa and climate, but there have been relatively few studies exploring endophyte communities throughout host maturity. We compared foliar fungal endophyte communities between seedlings and adult trees of loblolly pines (Pinus taeda) at the same seasons and locations by culturing and culture-independent methods. We sequenced the internal transcribed spacer region and adjacent partial large subunit nuclear ribosomal RNA gene (ITS–LSU amplicon) to delimit operational taxonomic units and phylogenetically characterize the communities. Despite the lower infection frequency in seedlings compared to adult trees, seedling needles were receptive to a more diverse community of fungal endophytes. Culture-free method confirmed the presence of commonly cultured OTUs from adult needles but revealed several new OTUs from seedling needles that were not found with culturing methods. The two most commonly cultured OTUs in adults were rarely cultured from seedlings, suggesting that host age is correlated with a selective enrichment for specific endophytes. This shift in endophyte species dominance may be indicative of a functional change between these fungi and their loblolly pine hosts. PMID:26399186

  10. 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.

  11. 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

  12. Antibody to a conserved antigenic target is protective against diverse prokaryotic and eukaryotic pathogens.

    PubMed

    Cywes-Bentley, Colette; Skurnik, David; Zaidi, Tanweer; Roux, Damien; Deoliveira, Rosane B; Garrett, Wendy S; Lu, Xi; O'Malley, Jennifer; Kinzel, Kathryn; Zaidi, Tauqeer; Rey, Astrid; Perrin, Christophe; Fichorova, Raina N; Kayatani, Alexander K K; Maira-Litràn, Tomas; Gening, Marina L; Tsvetkov, Yury E; Nifantiev, Nikolay E; Bakaletz, Lauren O; Pelton, Stephen I; Golenbock, Douglas T; Pier, Gerald B

    2013-06-11

    Microbial capsular antigens are effective vaccines but are chemically and immunologically diverse, resulting in a major barrier to their use against multiple pathogens. A β-(1→6)-linked poly-N-acetyl-d-glucosamine (PNAG) surface capsule is synthesized by four proteins encoded in genetic loci designated intercellular adhesion in Staphylococcus aureus or polyglucosamine in selected Gram-negative bacterial pathogens. We report that many microbial pathogens lacking an identifiable intercellular adhesion or polyglucosamine locus produce PNAG, including Gram-positive, Gram-negative, and fungal pathogens, as well as protozoa, e.g., Trichomonas vaginalis, Plasmodium berghei, and sporozoites and blood-stage forms of Plasmodium falciparum. Natural antibody to PNAG is common in humans and animals and binds primarily to the highly acetylated glycoform of PNAG but is not protective against infection due to lack of deposition of complement opsonins. Polyclonal animal antibody raised to deacetylated glycoforms of PNAG and a fully human IgG1 monoclonal antibody that both bind to native and deacetylated glycoforms of PNAG mediated complement-dependent opsonic or bactericidal killing and protected mice against local and/or systemic infections by Streptococcus pyogenes, Streptococcus pneumoniae, Listeria monocytogenes, Neisseria meningitidis serogroup B, Candida albicans, and P. berghei ANKA, and against colonic pathology in a model of infectious colitis. PNAG is also a capsular polysaccharide for Neisseria gonorrhoeae and nontypable Hemophilus influenzae, and protects cells from environmental stress. Vaccination targeting PNAG could contribute to immunity against serious and diverse prokaryotic and eukaryotic pathogens, and the conserved production of PNAG suggests that it is a critical factor in microbial biology. PMID:23716675

  13. Diverse ecological roles within fungal communities in decomposing logs of Picea abies.

    PubMed

    Ottosson, Elisabet; Kubartová, Ariana; Edman, Mattias; Jönsson, Mari; Lindhe, Anders; Stenlid, Jan; Dahlberg, Anders

    2015-03-01

    Fungal communities in Norway spruce (Picea abies) logs in two forests in Sweden were investigated by 454-sequence analyses and by examining the ecological roles of the detected taxa. We also investigated the relationship between fruit bodies and mycelia in wood and whether community assembly was affected by how the dead wood was formed. Fungal communities were highly variable in terms of phylogenetic composition and ecological roles: 1910 fungal operational taxonomic units (OTUs) were detected; 21% were identified to species level. In total, 58% of the OTUs were ascomycetes and 31% basidiomycetes. Of the 231 337 reads, 38% were ascomycetes and 60% basidiomycetes. Ecological roles were assigned to 35% of the OTUs, accounting for 62% of the reads. Wood-decaying fungi were the most common group; however, other saprotrophic, mycorrhizal, lichenized, parasitic and endophytic fungi were also common. Fungal communities in logs formed by stem breakage were different to those in logs originating from butt breakage or uprooting. DNA of specific species was detected in logs many years after the last recorded fungal fruiting. Combining taxonomic identification with knowledge of ecological roles may provide valuable insights into properties of fungal communities; however, precise ecological information about many fungal species is still lacking. PMID:25764460

  14. 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.

  15. 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

  16. Fungal diversity in adult date palm (Phoenix dactylifera L.) revealed by culture-dependent and culture-independent approaches*

    PubMed Central

    Ben Chobba, Ines; Elleuch, Amine; Ayadi, Imen; Khannous, Lamia; Namsi, Ahmed; Cerqueira, Frederique; Drira, Noureddine; Gharsallah, Néji; Vallaeys, Tatiana

    2013-01-01

    Endophytic flora plays a vital role in the colonization and survival of host plants, especially in harsh environments, such as arid regions. This flora may, however, contain pathogenic species responsible for various troublesome host diseases. The present study is aimed at investigating the diversity of both cultivable and non-cultivable endophytic fungal floras in the internal tissues (roots and leaves) of Tunisian date palm trees (Phoenix dactylifera). Accordingly, 13 isolates from both root and leaf samples, exhibiting distinct colony morphology, were selected from potato dextrose agar (PDA) medium and identified by a sequence match search wherein their 18S–28S internal transcribed spacer (ITS) sequences were compared to those available in public databases. These findings revealed that the cultivable root and leaf isolates fell into two groups, namely Nectriaceae and Pleosporaceae. Additionally, total DNA from palm roots and leaves was further extracted and ITS fragments were amplified. Restriction fragment length polymorphism (RFLP) analysis of the ITS from 200 fungal clones (leaves: 100; roots: 100) using HaeIII restriction enzyme revealed 13 distinct patterns that were further sequenced and led to the identification of Alternaria, Cladosporium, Davidiella (Cladosporium teleomorph), Pythium, Curvularia, and uncharacterized fungal endophytes. Both approaches confirmed that while the roots were predominantly colonized by Fusaria (members of the Nectriaceae family), the leaves were essentially colonized by Alternaria (members of the Pleosporaceae family). Overall, the findings of the present study constitute, to the authors’ knowledge, the first extensive report on the diversity of endophytic fungal flora associated with date palm trees (P. dactylifera). PMID:24302709

  17. The conformal supercurrents in diverse dimensions and conserved superconformal currents

    NASA Astrophysics Data System (ADS)

    Korovin, Yegor; Kuzenko, Sergei M.; Theisen, Stefan

    2016-05-01

    Given a conserved and traceless energy-momentum tensor and a conformal Killing vector, one obtains a conserved current. We generalise this construction to superconformal theories in three, four, five and six dimensions with various amounts of supersymmetry by working in the appropriate superspaces.

  18. Soil fungal community development in a high Arctic glacier foreland follows a directional replacement model, with a mid-successional diversity maximum.

    PubMed

    Dong, Ke; Tripathi, Binu; Moroenyane, Itumeleng; Kim, Woosung; Li, Nan; Chu, Haiyan; Adams, Jonathan

    2016-05-31

    Directional replacement and directional non-replacement models are two alternative paradigms for community development in primary successional environments. The first model emphasizes turnover in species between early and late successional niches. The second emphasizes accumulation of additional diversity over time. To test whether the development of soil fungal communities in the foreland of an Arctic glacier conforms to either of these models, we collected samples from the Midtre Lovénbreen Glacier, Svalbard, along a soil successional series spanning >80 years. Soil DNA was extracted, and fungal ITS1 region was amplified and sequenced on an Illumina Miseq. There was a progressive change in community composition in the soil fungal community, with greatest fungal OTU richness in the Mid Stage (50-80 years). A nestedness analysis showed that the Early Stage (20-50 years) and the Late Stage (>80 years) fungal communities were nested within the Mid Stage communities. These results imply that fungal community development in this glacier succession follows a directional replacement model. Soil development processes may initially be important in facilitating arrival of additional fungal species, to give a mid-successional diversity maximum that contains both early- and late-successional fungi. Competition may then decrease the overall diversity due to the loss of early successional species.

  19. Soil fungal community development in a high Arctic glacier foreland follows a directional replacement model, with a mid-successional diversity maximum

    PubMed Central

    Dong, Ke; Tripathi, Binu; Moroenyane, Itumeleng; Kim, Woosung; Li, Nan; Chu, Haiyan; Adams, Jonathan

    2016-01-01

    Directional replacement and directional non-replacement models are two alternative paradigms for community development in primary successional environments. The first model emphasizes turnover in species between early and late successional niches. The second emphasizes accumulation of additional diversity over time. To test whether the development of soil fungal communities in the foreland of an Arctic glacier conforms to either of these models, we collected samples from the Midtre Lovénbreen Glacier, Svalbard, along a soil successional series spanning >80 years. Soil DNA was extracted, and fungal ITS1 region was amplified and sequenced on an Illumina Miseq. There was a progressive change in community composition in the soil fungal community, with greatest fungal OTU richness in the Mid Stage (50–80 years). A nestedness analysis showed that the Early Stage (20–50 years) and the Late Stage (>80 years) fungal communities were nested within the Mid Stage communities. These results imply that fungal community development in this glacier succession follows a directional replacement model. Soil development processes may initially be important in facilitating arrival of additional fungal species, to give a mid-successional diversity maximum that contains both early- and late-successional fungi. Competition may then decrease the overall diversity due to the loss of early successional species. PMID:27240660

  20. Plant and Fungal Diversity in Gut Microbiota as Revealed by Molecular and Culture Investigations

    PubMed Central

    Gouba, Nina; Raoult, Didier; Drancourt, Michel

    2013-01-01

    Background Few studies describing eukaryotic communities in the human gut microbiota have been published. The objective of this study was to investigate comprehensively the repertoire of plant and fungal species in the gut microbiota of an obese patient. Methodology/Principal Findings A stool specimen was collected from a 27-year-old Caucasian woman with a body mass index of 48.9 who was living in Marseille, France. Plant and fungal species were identified using a PCR-based method incorporating 25 primer pairs specific for each eukaryotic phylum and universal eukaryotic primers targeting 18S rRNA, internal transcribed spacer (ITS) and a chloroplast gene. The PCR products amplified using these primers were cloned and sequenced. Three different culture media were used to isolate fungi, and these cultured fungi were further identified by ITS sequencing. A total of 37 eukaryotic species were identified, including a Diatoms (Blastocystis sp.) species, 18 plant species from the Streptophyta phylum and 18 fungal species from the Ascomycota, Basidiomycota and Chytridiocomycota phyla. Cultures yielded 16 fungal species, while PCR-sequencing identified 7 fungal species. Of these 7 species of fungi, 5 were also identified by culture. Twenty-one eukaryotic species were discovered for the first time in human gut microbiota, including 8 fungi (Aspergillus flavipes, Beauveria bassiana, Isaria farinosa, Penicillium brevicompactum, Penicillium dipodomyicola, Penicillium camemberti, Climacocystis sp. and Malassezia restricta). Many fungal species apparently originated from food, as did 11 plant species. However, four plant species (Atractylodes japonica, Fibraurea tinctoria, Angelica anomala, Mitella nuda) are used as medicinal plants. Conclusions/Significance Investigating the eukaryotic components of gut microbiota may help us to understand their role in human health. PMID:23555039

  1. Investigations of fungal diversity in wooden structures and soils at historic sites on the Antarctic Peninsula.

    PubMed

    Arenz, Brett E; Blanchette, Robert A

    2009-01-01

    Investigations of microbial diversity in Antarctic are important to begin to understand ecosystem functioning and decomposition processes. This study documents fungi at 9 historic sites on the Antarctic Peninsula collected from wooden structures, other organic materials, and soils during a joint National Science Foundation and British Antarctic Survey expedition in 2007. Many of these sites had wooden structures built by the British during the World War II Operation Tabarin, but others visited included the American "East Base" on Stonington Island and the Swedish hut on Snow Hill Island. Fungi were cultured on several different media and pure cultures were obtained and identified by DNA sequencing of the internal transcribed spacer region. Cadophora species previously found to attack historic wooden structures on Ross Island, Antarctica, were found at all but 1 location sampled in the Peninsula region. Fungi causing decay in the historic wooden structures and artifacts and those causing mold problems inside the structures are of great concern, and conservation efforts are urgently needed to help preserve these important polar heritage structures. The results presented also expand our knowledge on the identity of fungi present throughout the Antarctic Peninsula region and provide insights into the organisms responsible for decomposition and nutrient recycling.

  2. AM fungal diversity and modularity reveal different trends in the mycorrhizal association with generalist and specialist plant species.

    NASA Astrophysics Data System (ADS)

    Torrecillas, Emma; del Mar Alguacil, Mª; Roldán, Antonio; Díaz, Gisela; Montesinos-Navarro, Alicia; Torres, Mª Pilar

    2013-04-01

    The plant communities present on gypsum soils include one of the most remarkable groups of edaphic "specialists", which coexist with edaphic "generalists". This study hypothesized that plant-arbuscular mycorrhizal fungi(AMF) associations can be related with specific functional plant strategies in gypsum soils.We analyzed, using network analysis, a plant-AMF mutualistic system in a gypsum environment, to characterize the plant-AMF interaction patterns according to their modularity or the tendency of species to be grouped into modules.Taking into account the total area studied (gypsum soil and marly-limestone soil), our results show that the factors determining the AM fungal community's distribution were soil type and plant species, with gypsovags harboring a different AM fungal community in gypsum and non-gypsum soils. But, there were no differences in the community diversity between specialist and generalist plants. Modularity analysis revealed that, when only gypsum soils are considered, there were some AM fungal groups with a tendency to interact differently with gypsophytes(specialists) and gypsovags (generalists).

  3. Rich and cold: diversity, distribution and drivers of fungal communities in patterned-ground ecosystems of the North American Arctic.

    PubMed

    Timling, I; Walker, D A; Nusbaum, C; Lennon, N J; Taylor, D L

    2014-07-01

    Fungi are abundant and functionally important in the Arctic, yet comprehensive studies of their diversity in relation to geography and environment are not available. We sampled soils in paired plots along the North American Arctic Transect (NAAT), which spans all five bioclimatic subzones of the Arctic. Each pair of plots contrasted relatively bare, cryoturbated patterned-ground features (PGFs) and adjacent vegetated between patterned-ground features (bPGFs). Fungal communities were analysed via sequencing of 7834 ITS-LSU clones. We recorded 1834 OTUs - nearly half the fungal richness previously reported for the entire Arctic. These OTUs spanned eight phyla, 24 classes, 75 orders and 120 families, but were dominated by Ascomycota, with one-fifth belonging to lichens. Species richness did not decline with increasing latitude, although there was a decline in mycorrhizal taxa that was offset by an increase in lichen taxa. The dominant OTUs were widespread even beyond the Arctic, demonstrating no dispersal limitation. Yet fungal communities were distinct in each subzone and were correlated with soil pH, climate and vegetation. Communities in subzone E were distinct from the other subzones, but similar to those of the boreal forest. Fungal communities on disturbed PGFs differed significantly from those of paired stable areas in bPGFs. Indicator species for PGFs included lichens and saprotrophic fungi, while bPGFs were characterized by ectomycorrhizal and pathogenic fungi. Our results suggest that the Arctic does not host a unique mycoflora, while Arctic fungi are highly sensitive to climate and vegetation, with potential to migrate rapidly as global change unfolds.

  4. Firing Range Soils Yield a Diverse Array of Fungal Isolates Capable of Organic Acid Production and Pb Mineral Solubilization

    PubMed Central

    Sullivan, Tarah S.; Gottel, Neil R.; Basta, Nicholas; Jardine, Philip M.

    2012-01-01

    Anthropogenic sources of lead contamination in soils include mining and smelting activities, effluents and wastes, agricultural pesticides, domestic garbage dumps, and shooting ranges. While Pb is typically considered relatively insoluble in the soil environment, some fungi may potentially contribute to mobilization of heavy metal cations by means of secretion of low-molecular-weight organic acids (LMWOAs). We sought to better understand the potential for metal mobilization within an indigenous fungal community at an abandoned shooting range in Oak Ridge, TN, where soil Pb contamination levels ranged from 24 to >2,700 mg Pb kg dry soil−1. We utilized culture-based assays to determine organic acid secretion and Pb-carbonate dissolution of a diverse collection of soil fungal isolates derived from the site and verified isolate distribution patterns within the community by 28S rRNA gene analysis of whole soils. The fungal isolates examined included both ascomycetes and basidiomycetes that excreted high levels (up to 27 mM) of a mixture of LMWOAs, including oxalic and citric acids, and several isolates demonstrated a marked ability to dissolve Pb-carbonate at high concentrations up to 10.5 g liter−1 (18.5 mM) in laboratory assays. Fungi within the indigenous community of these highly Pb-contaminated soils are capable of LMWOA secretion at levels greater than those of well-studied model organisms, such as Aspergillus niger. Additionally, these organisms were found in high relative abundance (>1%) in some of the most heavily contaminated soils. Our data highlight the need to understand more about autochthonous fungal communities at Pb-contaminated sites and how they may impact Pb biogeochemistry, solubility, and bioavailability, thus consequently potentially impacting human and ecosystem health. PMID:22729539

  5. Firing range soils yield a diverse array of fungal isolates capable of organic acid production and Pb mineral solubilization.

    PubMed

    Sullivan, Tarah S; Gottel, Neil R; Basta, Nicholas; Jardine, Philip M; Schadt, Christopher W

    2012-09-01

    Anthropogenic sources of lead contamination in soils include mining and smelting activities, effluents and wastes, agricultural pesticides, domestic garbage dumps, and shooting ranges. While Pb is typically considered relatively insoluble in the soil environment, some fungi may potentially contribute to mobilization of heavy metal cations by means of secretion of low-molecular-weight organic acids (LMWOAs). We sought to better understand the potential for metal mobilization within an indigenous fungal community at an abandoned shooting range in Oak Ridge, TN, where soil Pb contamination levels ranged from 24 to >2,700 mg Pb kg dry soil(-1). We utilized culture-based assays to determine organic acid secretion and Pb-carbonate dissolution of a diverse collection of soil fungal isolates derived from the site and verified isolate distribution patterns within the community by 28S rRNA gene analysis of whole soils. The fungal isolates examined included both ascomycetes and basidiomycetes that excreted high levels (up to 27 mM) of a mixture of LMWOAs, including oxalic and citric acids, and several isolates demonstrated a marked ability to dissolve Pb-carbonate at high concentrations up to 10.5 g liter(-1) (18.5 mM) in laboratory assays. Fungi within the indigenous community of these highly Pb-contaminated soils are capable of LMWOA secretion at levels greater than those of well-studied model organisms, such as Aspergillus niger. Additionally, these organisms were found in high relative abundance (>1%) in some of the most heavily contaminated soils. Our data highlight the need to understand more about autochthonous fungal communities at Pb-contaminated sites and how they may impact Pb biogeochemistry, solubility, and bioavailability, thus consequently potentially impacting human and ecosystem health.

  6. Fungal Endophytes of Alpinia officinarum Rhizomes: Insights on Diversity and Variation across Growth Years, Growth Sites, and the Inner Active Chemical Concentration

    PubMed Central

    Shubin, Li; Juan, Huang; RenChao, Zhou; ShiRu, Xu; YuanXiao, Jin

    2014-01-01

    In the present study, the terminal-restriction fragment length polymorphism (T-RFLP) technique, combined with the use of a clone library, was applied to assess the baseline diversity of fungal endophyte communities associated with rhizomes of Alpinia officinarum Hance, a medicinal plant with a long history of use. A total of 46 distinct T-RFLP fragment peaks were detected using HhaI or MspI mono-digestion-targeted, amplified fungal rDNA ITS sequences from A. officinarum rhizomes. Cloning and sequencing of representative sequences resulted in the detection of members of 10 fungal genera: Pestalotiopsis, Sebacina, Penicillium, Marasmius, Fusarium, Exserohilum, Mycoleptodiscus, Colletotrichum, Meyerozyma, and Scopulariopsis. The T-RFLP profiles revealed an influence of growth year of the host plant on fungal endophyte communities in rhizomes of this plant species; whereas, the geographic location where A. officinarum was grown contributed to only limited variation in the fungal endophyte communities of the host tissue. Furthermore, non-metric multidimensional scaling (NMDS) analysis across all of the rhizome samples showed that the fungal endophyte community assemblages in the rhizome samples could be grouped according to the presence of two types of active indicator chemicals: total volatile oils and galangin. Our present results, for the first time, address a diverse fungal endophyte community is able to internally colonize the rhizome tissue of A. officinarum. The diversity of the fungal endophytes found in the A. officinarum rhizome appeared to be closely correlated with the accumulation of active chemicals in the host plant tissue. The present study also provides the first systematic overview of the fungal endophyte communities in plant rhizome tissue using a culture-independent method. PMID:25536070

  7. Fungal endophytes of Alpinia officinarum rhizomes: insights on diversity and variation across growth years, growth sites, and the inner active chemical concentration.

    PubMed

    Shubin, Li; Juan, Huang; RenChao, Zhou; ShiRu, Xu; YuanXiao, Jin

    2014-01-01

    In the present study, the terminal-restriction fragment length polymorphism (T-RFLP) technique, combined with the use of a clone library, was applied to assess the baseline diversity of fungal endophyte communities associated with rhizomes of Alpinia officinarum Hance, a medicinal plant with a long history of use. A total of 46 distinct T-RFLP fragment peaks were detected using HhaI or MspI mono-digestion-targeted, amplified fungal rDNA ITS sequences from A. officinarum rhizomes. Cloning and sequencing of representative sequences resulted in the detection of members of 10 fungal genera: Pestalotiopsis, Sebacina, Penicillium, Marasmius, Fusarium, Exserohilum, Mycoleptodiscus, Colletotrichum, Meyerozyma, and Scopulariopsis. The T-RFLP profiles revealed an influence of growth year of the host plant on fungal endophyte communities in rhizomes of this plant species; whereas, the geographic location where A. officinarum was grown contributed to only limited variation in the fungal endophyte communities of the host tissue. Furthermore, non-metric multidimensional scaling (NMDS) analysis across all of the rhizome samples showed that the fungal endophyte community assemblages in the rhizome samples could be grouped according to the presence of two types of active indicator chemicals: total volatile oils and galangin. Our present results, for the first time, address a diverse fungal endophyte community is able to internally colonize the rhizome tissue of A. officinarum. The diversity of the fungal endophytes found in the A. officinarum rhizome appeared to be closely correlated with the accumulation of active chemicals in the host plant tissue. The present study also provides the first systematic overview of the fungal endophyte communities in plant rhizome tissue using a culture-independent method.

  8. Global patterns of terrestrial vertebrate diversity and conservation.

    PubMed

    Jenkins, Clinton N; Pimm, Stuart L; Joppa, Lucas N

    2013-07-01

    Identifying priority areas for biodiversity is essential for directing conservation resources. Fundamentally, we must know where individual species live, which ones are vulnerable, where human actions threaten them, and their levels of protection. As conservation knowledge and threats change, we must reevaluate priorities. We mapped priority areas for vertebrates using newly updated data on >21,000 species of mammals, amphibians, and birds. For each taxon, we identified centers of richness for all species, small-ranged species, and threatened species listed with the International Union for the Conservation of Nature. Importantly, all analyses were at a spatial grain of 10 × 10 km, 100 times finer than previous assessments. This fine scale is a significant methodological improvement, because it brings mapping to scales comparable with regional decisions on where to place protected areas. We also mapped recent species discoveries, because they suggest where as-yet-unknown species might be living. To assess the protection of the priority areas, we calculated the percentage of priority areas within protected areas using the latest data from the World Database of Protected Areas, providing a snapshot of how well the planet's protected area system encompasses vertebrate biodiversity. Although the priority areas do have more protection than the global average, the level of protection still is insufficient given the importance of these areas for preventing vertebrate extinctions. We also found substantial differences between our identified vertebrate priorities and the leading map of global conservation priorities, the biodiversity hotspots. Our findings suggest a need to reassess the global allocation of conservation resources to reflect today's improved knowledge of biodiversity and conservation.

  9. Hidden Genetic Diversity in an Asexually Reproducing Lichen Forming Fungal Group.

    PubMed

    Del-Prado, Ruth; Divakar, Pradeep Kumar; Lumbsch, H Thorsten; Crespo, Ana M

    2016-01-01

    Asexual species with vegetative propagation of both symbiont partners (soredia) in lichens may harbor lower species diversity because they may indeed represent evolutionary dead ends or clones. In this study we aim to critically examine species boundaries in the sorediate lichen forming fungi Parmotrema reticulatum-Parmotrema pseudoreticulatum complex applying coalescent-based approaches and other recently developed DNA-based methods. To this end, we gathered 180 samples from Africa, Asia, Australasia, Europe, North and South America and generated sequences of internal transcribed spacer of nuclear ribosomal DNA (ITS) and DNA replication licensing factor MCM7 (MCM7). The dataset was analysed using different approaches such as traditional phylogeny-maximum likelihood and Bayesian-genetic distances, automatic barcode gap discovery and coalescent-based methods-PTP, GMYC, spedeSTEM and *Beast-in order to test congruence among results. Additionally, the divergence times were also estimated to elucidate diversification events. Delimitations inferred from the different analyses are comparable with only minor differences, and following a conservative approach we propose that the sampled specimens of the P. reticulatum-P. pseudoreticulatum complex belong to at least eight distinct species-level lineages. Seven are currently classified under P. reticulatum and one as P. pseudoreticulatum. In this work we discuss one of only few examples of cryptic species that have so far been found in sorediate reproducing lichen forming fungi. Additionally our estimates suggest a recent origin of the species complex-during the Miocene. Consequently, the wide distribution of several of the cryptic species has to be explained by intercontinental long-distance dispersal events.

  10. Hidden Genetic Diversity in an Asexually Reproducing Lichen Forming Fungal Group.

    PubMed

    Del-Prado, Ruth; Divakar, Pradeep Kumar; Lumbsch, H Thorsten; Crespo, Ana M

    2016-01-01

    Asexual species with vegetative propagation of both symbiont partners (soredia) in lichens may harbor lower species diversity because they may indeed represent evolutionary dead ends or clones. In this study we aim to critically examine species boundaries in the sorediate lichen forming fungi Parmotrema reticulatum-Parmotrema pseudoreticulatum complex applying coalescent-based approaches and other recently developed DNA-based methods. To this end, we gathered 180 samples from Africa, Asia, Australasia, Europe, North and South America and generated sequences of internal transcribed spacer of nuclear ribosomal DNA (ITS) and DNA replication licensing factor MCM7 (MCM7). The dataset was analysed using different approaches such as traditional phylogeny-maximum likelihood and Bayesian-genetic distances, automatic barcode gap discovery and coalescent-based methods-PTP, GMYC, spedeSTEM and *Beast-in order to test congruence among results. Additionally, the divergence times were also estimated to elucidate diversification events. Delimitations inferred from the different analyses are comparable with only minor differences, and following a conservative approach we propose that the sampled specimens of the P. reticulatum-P. pseudoreticulatum complex belong to at least eight distinct species-level lineages. Seven are currently classified under P. reticulatum and one as P. pseudoreticulatum. In this work we discuss one of only few examples of cryptic species that have so far been found in sorediate reproducing lichen forming fungi. Additionally our estimates suggest a recent origin of the species complex-during the Miocene. Consequently, the wide distribution of several of the cryptic species has to be explained by intercontinental long-distance dispersal events. PMID:27513649

  11. Hidden Genetic Diversity in an Asexually Reproducing Lichen Forming Fungal Group

    PubMed Central

    Del-Prado, Ruth; Divakar, Pradeep Kumar; Lumbsch, H. Thorsten; Crespo, Ana M.

    2016-01-01

    Asexual species with vegetative propagation of both symbiont partners (soredia) in lichens may harbor lower species diversity because they may indeed represent evolutionary dead ends or clones. In this study we aim to critically examine species boundaries in the sorediate lichen forming fungi Parmotrema reticulatum–Parmotrema pseudoreticulatum complex applying coalescent-based approaches and other recently developed DNA-based methods. To this end, we gathered 180 samples from Africa, Asia, Australasia, Europe, North and South America and generated sequences of internal transcribed spacer of nuclear ribosomal DNA (ITS) and DNA replication licensing factor MCM7 (MCM7). The dataset was analysed using different approaches such as traditional phylogeny–maximum likelihood and Bayesian–genetic distances, automatic barcode gap discovery and coalescent-based methods–PTP, GMYC, spedeSTEM and *Beast–in order to test congruence among results. Additionally, the divergence times were also estimated to elucidate diversification events. Delimitations inferred from the different analyses are comparable with only minor differences, and following a conservative approach we propose that the sampled specimens of the P. reticulatum–P. pseudoreticulatum complex belong to at least eight distinct species-level lineages. Seven are currently classified under P. reticulatum and one as P. pseudoreticulatum. In this work we discuss one of only few examples of cryptic species that have so far been found in sorediate reproducing lichen forming fungi. Additionally our estimates suggest a recent origin of the species complex–during the Miocene. Consequently, the wide distribution of several of the cryptic species has to be explained by intercontinental long-distance dispersal events. PMID:27513649

  12. Structural and functional diversity of soil bacterial and fungal communities following woody plant encroachment in the southern Great Plains

    SciTech Connect

    Hollister, Emily B; Schadt, Christopher Warren; Palumbo, Anthony Vito; Ansley, R J; Boutton, Thomas W

    2010-01-01

    In the southern Great Plains (USA), encroachment of grassland ecosystems by Prosopis glandulosa (honey mesquite) is widespread. Mesquite encroachment alters net primary productivity, enhances stores of C and N in plants and soil, and leads to increased levels of soil microbial biomass and activity. While mesquite's impact on the biogeochemistry of the region is well established, it effects on soil microbial diversity and function are unknown. In this study, soils associated with four plant types (C{sub 3} perennial grasses, C{sub 4} midgrasses, C{sub 4} shortgrasses, and mesquite) from a mesquite-encroached mixed grass prairie were surveyed to in an attempt to characterize the structure, diversity, and functional capacity of their soil microbial communities. rRNA gene cloning and sequencing were used in conjunction with the GeoChip functional gene array to evaluate these potential differences. Mesquite soil supported increased bacterial and fungal diversity and harbored a distinct fungal community relative to other plant types. Despite differences in composition and diversity, few significant differences were detected with respect to the potential functional capacity of the soil microbial communities. These results may suggest that a high level of functional redundancy exists within the bacterial portion of the soil communities; however, given the bias of the GeoChip toward bacterial functional genes, potential functional differences among soil fungi could not be addressed. The results of this study illustrate the linkages shared between above- and belowground communities and demonstrate that soil microbial communities, and in particular soil fungi, may be altered by the process of woody plant encroachment.

  13. Defining conservation priorities for freshwater fishes according to taxonomic, functional, and phylogenetic diversity

    USGS Publications Warehouse

    Strecker, A.L.; Olden, J.D.; Whittier, Joanna B.; Paukert, C.P.

    2011-01-01

    To date, the predominant use of systematic conservation planning has been to evaluate and conserve areas of high terrestrial biodiversity. Although studies in freshwater ecosystems have received recent attention, research has rarely considered the potential tradeoffs between protecting different dimensions of biodiversity and the ecological processes that maintain diversity. We provide the first systematic prioritization for freshwaters (focusing on the highly threatened and globally distinct fish fauna of the Lower Colorado River Basin, USA) simultaneously considering scenarios of: taxonomic, functional, and phylogenetic diversity;contemporary threats to biodiversity (including interactions with nonnative species);and future climate change and human population growth. There was 75% congruence between areas of highest conservation priority for different aspects of biodiversity, suggesting that conservation efforts can concurrently achieve strong complementarity among all types of diversity. However, sizable fractions of the landscape were incongruent across conservation priorities for different diversity scenarios, underscoring the importance of considering multiple dimensions of biodiversity and highlighting catchments that contribute disproportionately to taxonomic, functional, and phylogenetic diversity in the region. Regions of projected human population growth were not concordant with conservation priorities;however, higher human population abundance will likely have indirect effects on native biodiversity by increasing demand for water. This will come in direct conflict with projected reductions in precipitation and warmer temperatures, which have substantial overlap with regions of high contemporary diversity. Native and endemic fishes in arid ecosystems are critically endangered by both current and future threats, but our results highlight the use of systematic conservation planning for the optimal allocation of limited resources that incorporates multiple

  14. Defining conservation priorities for freshwater fishes according to taxonomic, functional, and phylogenetic diversity

    USGS Publications Warehouse

    Strecker, Angela; Olden, Julian D.; Whittier, Joanna B.; Paukert, Craig P.

    2011-01-01

    To date, the predominant use of systematic conservation planning has been to evaluate and conserve areas of high terrestrial biodiversity. Although studies in freshwater ecosystems have received recent attention, research has rarely considered the potential trade-offs between protecting different dimensions of biodiversity and the ecological processes that maintain diversity. We provide the first systematic prioritization for freshwaters (focusing on the highly threatened and globally distinct fish fauna of the Lower Colorado River Basin, USA) simultaneously considering scenarios of: taxonomic, functional, and phylogenetic diversity; contemporary threats to biodiversity (including interactions with nonnative species); and future climate change and human population growth. There was 75% congruence between areas of highest conservation priority for different aspects of biodiversity, suggesting that conservation efforts can concurrently achieve strong complementarity among all types of diversity. However, sizable fractions of the landscape were incongruent across conservation priorities for different diversity scenarios, underscoring the importance of considering multiple dimensions of biodiversity and highlighting catchments that contribute disproportionately to taxonomic, functional, and phylogenetic diversity in the region. Regions of projected human population growth were not concordant with conservation priorities; however, higher human population abundance will likely have indirect effects on native biodiversity by increasing demand for water. This will come in direct conflict with projected reductions in precipitation and warmer temperatures, which have substantial overlap with regions of high contemporary diversity. Native and endemic fishes in arid ecosystems are critically endangered by both current and future threats, but our results highlight the use of systematic conservation planning for the optimal allocation of limited resources that incorporates

  15. Benzenediol lactones: a class of fungal metabolites with diverse structural features and biological activities.

    PubMed

    Shen, Weiyun; Mao, Hongqiang; Huang, Qian; Dong, Jinyan

    2015-06-01

    Benzenediol lactones are a structurally variable family of fungal polyketide metabolites possessing a macrolide core structure fused into a resorcinol aromatic ring. These compounds are widespread in fungi mainly in the genera such as Aigialus, Cochliobolus, Curvularia, Fusarium, Humicola, Lasiodiplodia, Penicillium and Pochonia etc. Most of these fungal metabolites were reported to possess several interesting biological activities, such as cytotoxicities, nematicidal properties, inhibition of various kinases, receptor agonists, anti-inflammatory activities, heat shock response and immune system modulatory activities etc. This review summarizes the research on the isolation, structure elucidation, and biological activities of the benzenediol lactones, along with some available structure-activity relationships, biosynthetic studies, first syntheses, and syntheses that lead to the revision of structure or stereochemistry, published up to the year of 2014. More than 190 benzenediol lactones are described, and over 300 references cited. PMID:25559850

  16. Waterfowl populations of conservation concern: learning from diverse challenges, models, and conservation strategies

    USGS Publications Warehouse

    Austin, Jane E.; Slattery, Stuart; Clark, Robert G.

    2014-01-01

    There are 30 threatened or endangered species of waterfowl worldwide, and several sub-populations are also threatened. Some of these species occur in North America, and others there are also of conservation concern due to declining population trends and their importance to hunters. Here we review conservation initiatives being undertaken for several of these latter species, along with conservation measures in place in Europe, to seek common themes and approaches that could be useful in developing broad conservation guidelines. While focal species may vary in their life histories, population threats and geopolitical context, most conservation efforts have used a systematic approach to understand factors limiting populations and o identify possible management or policy actions. This approach generally includes a priori identification of plausible hypotheses about population declines or status, incorporation of hypotheses into conceptual or quantitative planning models, and the use of some form of structured decision making and adaptive management to develop and implement conservation actions in the face of many uncertainties. A climate of collaboration among jurisdictions sharing these birds is important to the success of a conservation or management programme. The structured conservation approach exemplified herein provides an opportunity to involve stakeholders at all planning stages, allows for all views to be examined and incorporated into model structures, and yields a format for improved communication, cooperation and learning, which may ultimately be one of the greatest benefits of this strategy.

  17. Mycophagy among Japanese macaques in Yakushima: fungal species diversity and behavioral patterns.

    PubMed

    Sawada, Akiko; Sato, Hirotoshi; Inoue, Eiji; Otani, Yosuke; Hanya, Goro

    2014-04-01

    Mycophagy (fungus-feeding) by Japanese macaques (Macaca fuscata yakui) in Yakushima has been observed by many researchers, but no detailed information is available on this behavior, including which fungal species are consumed. To provide a general description of mycophagy and to understand how and whether macaques avoid poisonous fungi, we conducted behavioral observation of wild Japanese macaques in Yakushima and used molecular techniques to identify fungal species. The results indicate that the diet of the macaques contains a large variety of fungal species (67 possible species in 31 genera), although they compose a very small portion of the total diet (2.2% of annual feeding time). Fungi which were eaten by macaques immediately after they were picked up were less likely to be poisonous than those which were examined (sniffed, nibbled, carefully handled) by macaques. However, such examining behaviors did not appear to increase the macaques' abilities to detect poisonous fungi. Fungi that were only partially consumed included more poisonous species than those fully consumed with/without examining behavior, yet this was not significant. Taste, therefore, might also play an important role in discriminating poisonous from non-poisonous.

  18. Fungal diversity of saprotrophic litter fungi in a Mediterranean maquis environment.

    PubMed

    Lunghini, D; Granito, V M; Di Lonardo, D P; Maggi, O; Persiani, A M

    2013-01-01

    Monospecific and mixed-leaf litters from plant species of Mediterranean maquis (Quercus ilex, Phillyrea angustifolia, Pistacia lentiscus, Cistus spp.) in an undisturbed area in southern Italy were studied with respect to the structure and composition of their decomposer fungal community over an incubation period of 403 d. The data matrix structure was analyzed by means of detrended correspondence analysis (DCA), while indicator species analysis (ISA) was used to determine the preferential association of species with a substrate, a succession phase and monospecific/mixed experimental conditions. The ecological nature of the gradient expressed by the DCA axes was investigated by means of experimental and main chemical leaf-litter variables. The litter mixture had non-additive effects on the decomposition process even though the fungal species richness of the mixed litter was considerably higher than that of the monospecific litter. Our findings highlight the occurrence of shifts in the fungal community during decomposition in response to changes in the substrate, such as those related to the cellulose content and lignin/N ratio. PMID:23921238

  19. Native fungal endophytes suppress an exotic dominant and increase plant diversity over small and large spatial scales.

    PubMed

    Afkhami, Michelle E; Strauss, Sharon Y

    2016-05-01

    Understanding community dynamics and processes, such as the factors that generate and maintain biodiversity, drive succession, and affect invasion susceptibility, is a central goal in ecology and evolution. While most studies of how species interactions affect communities have focused on highly visible macroorganisms, we show that mutualistic microfungal endophytes have community-level effects across their host plant's range and provide the first example of fungal endophytes enhancing plant diversity. A three-year field study in which we experimentally manipulated endophyte abundance in a native Californian grass showed that despite their minute biomass, endophytes dramatically increased plant community diversity (~110% greater increase with endophytes) by suppressing a dominant invasive grass, Bromus diandrus. This effect was also detectable, but smaller, across five additional common gardens spanning ecologically diverse habitats, different climates, and > 400 km of the host grass' range as well as at microspatial scales within gardens. Our study illustrates that mutualistic microbes, while often hidden players, can have unexpectedly large ecological impacts across a wide range of habitats and scales and may be important for promoting diverse communities and ecosystems. PMID:27349093

  20. A comparison of fungal endophytic community diversity in tree leaves of rural and urban temperate forests of Kanto district, eastern Japan.

    PubMed

    Matsumura, Emi; Fukuda, Kenji

    2013-03-01

    To clarify the effects of forest fragmentation and a change in tree species composition following urbanization on endophytic fungal communities, we isolated fungal endophytes from the foliage of nine tree species in suburban (Kashiwa City, Chiba) and rural (Mt. Wagakuni, Ibaraki; Mt. Takao, Tokyo) forests and compared the fungal communities between sites and host tree species. Host specificity was evaluated using the index of host specificity (Si), and the number of isolated species, total isolation frequency, and the diversity index were calculated. From just one to several host-specific species were recognized in all host tree species at all sites. The total isolation frequency of all fungal species on Quercus myrsinaefolia, Quercus serrata, and Chamaecyparis obtusa and the total isolation frequency of host-specific species on Q. myrsinaefolia, Q. serrata, and Eurya japonica were significantly lower in Kashiwa than in the rural forests. The similarity indices (nonmetric multidimensional scaling (NMS) and CMH) of endophytic communities among different tree species were higher in Kashiwa, as many tree species shared the same fungal species in the suburban forest. Endophytic fungi with a broad host range were grouped into four clusters suggesting their preference for conifer/broadleaves and evergreen/deciduous trees. Forest fragmentation and isolation by urbanization have been shown to cause the decline of host-specific fungal species and a decrease in β diversity of endophytic communities, i.e., endophytic communities associated with tree leaves in suburban forests were found to be depauperate. PMID:23537876

  1. A comparison of fungal endophytic community diversity in tree leaves of rural and urban temperate forests of Kanto district, eastern Japan.

    PubMed

    Matsumura, Emi; Fukuda, Kenji

    2013-03-01

    To clarify the effects of forest fragmentation and a change in tree species composition following urbanization on endophytic fungal communities, we isolated fungal endophytes from the foliage of nine tree species in suburban (Kashiwa City, Chiba) and rural (Mt. Wagakuni, Ibaraki; Mt. Takao, Tokyo) forests and compared the fungal communities between sites and host tree species. Host specificity was evaluated using the index of host specificity (Si), and the number of isolated species, total isolation frequency, and the diversity index were calculated. From just one to several host-specific species were recognized in all host tree species at all sites. The total isolation frequency of all fungal species on Quercus myrsinaefolia, Quercus serrata, and Chamaecyparis obtusa and the total isolation frequency of host-specific species on Q. myrsinaefolia, Q. serrata, and Eurya japonica were significantly lower in Kashiwa than in the rural forests. The similarity indices (nonmetric multidimensional scaling (NMS) and CMH) of endophytic communities among different tree species were higher in Kashiwa, as many tree species shared the same fungal species in the suburban forest. Endophytic fungi with a broad host range were grouped into four clusters suggesting their preference for conifer/broadleaves and evergreen/deciduous trees. Forest fragmentation and isolation by urbanization have been shown to cause the decline of host-specific fungal species and a decrease in β diversity of endophytic communities, i.e., endophytic communities associated with tree leaves in suburban forests were found to be depauperate.

  2. Phylogenetic Analysis of a Spontaneous Cocoa Bean Fermentation Metagenome Reveals New Insights into Its Bacterial and Fungal Community Diversity

    PubMed Central

    Illeghems, Koen; De Vuyst, Luc; Papalexandratou, Zoi; Weckx, Stefan

    2012-01-01

    This is the first report on the phylogenetic analysis of the community diversity of a single spontaneous cocoa bean box fermentation sample through a metagenomic approach involving 454 pyrosequencing. Several sequence-based and composition-based taxonomic profiling tools were used and evaluated to avoid software-dependent results and their outcome was validated by comparison with previously obtained culture-dependent and culture-independent data. Overall, this approach revealed a wider bacterial (mainly γ-Proteobacteria) and fungal diversity than previously found. Further, the use of a combination of different classification methods, in a software-independent way, helped to understand the actual composition of the microbial ecosystem under study. In addition, bacteriophage-related sequences were found. The bacterial diversity depended partially on the methods used, as composition-based methods predicted a wider diversity than sequence-based methods, and as classification methods based solely on phylogenetic marker genes predicted a more restricted diversity compared with methods that took all reads into account. The metagenomic sequencing analysis identified Hanseniaspora uvarum, Hanseniaspora opuntiae, Saccharomyces cerevisiae, Lactobacillus fermentum, and Acetobacter pasteurianus as the prevailing species. Also, the presence of occasional members of the cocoa bean fermentation process was revealed (such as Erwinia tasmaniensis, Lactobacillus brevis, Lactobacillus casei, Lactobacillus rhamnosus, Lactococcus lactis, Leuconostoc mesenteroides, and Oenococcus oeni). Furthermore, the sequence reads associated with viral communities were of a restricted diversity, dominated by Myoviridae and Siphoviridae, and reflecting Lactobacillus as the dominant host. To conclude, an accurate overview of all members of a cocoa bean fermentation process sample was revealed, indicating the superiority of metagenomic sequencing over previously used techniques. PMID:22666442

  3. 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

  4. Plant diversity and conservation in China: planning a strategic bioresource for a sustainable future.

    PubMed

    Huang, Hongwen

    2011-01-01

    China is one of the richest countries for plant diversity with approximately 33 000 vascular plant species, ranking second in the world. However, the plant diversity in China is increasingly threatened, with an estimated 4000–5000 plant species being threatened or on the verge of extinction, making China, proportionally, one of the highest priorities for global plant biodiversity conservation. Coming in the face of the current ecological crisis, it is timely that China has launched China's Strategy for Plant Conservation (CSPC). China has increasingly recognized the importance of plant diversity in efforts to conserve and sustainably use its plant diversity. More than 3000 nature reserves have been established, covering approximately 16% of the land surface of China. These natural reserves play important roles in plant conservation, covering more than 85% of types of terrestrial natural ecosystems, 40% of types of natural wetlands, 20% of native forests and 65% of natural communities of vascular plants. Meanwhile, the flora conserved in botanical gardens is also extensive. A recent survey shows that the 10 largest botanical gardens have living collections of 43 502 taxa, with a total of 24 667 species in ex situ conservation. These provide an important reserve of plant resources for sustainable economic and social development in China. Plant diversity is the basis for bioresources and sustainable utilization. The 21st century is predicted to be an era of bio-economy driven by advances of bioscience and biotechnology. Bio-economy may become the fourth economy form after agricultural, industrial, and information and information technology economies, having far-reaching impacts on sustainable development in agriculture, forestry, environmental protection, light industry, food supply and health care and other micro-economy aspects. Thus, a strategic and forward vision for conservation of plant diversity and sustainable use of plant resources in the 21st century is of

  5. Plant diversity and conservation in China: planning a strategic bioresource for a sustainable future.

    PubMed

    Huang, Hongwen

    2011-01-01

    China is one of the richest countries for plant diversity with approximately 33 000 vascular plant species, ranking second in the world. However, the plant diversity in China is increasingly threatened, with an estimated 4000–5000 plant species being threatened or on the verge of extinction, making China, proportionally, one of the highest priorities for global plant biodiversity conservation. Coming in the face of the current ecological crisis, it is timely that China has launched China's Strategy for Plant Conservation (CSPC). China has increasingly recognized the importance of plant diversity in efforts to conserve and sustainably use its plant diversity. More than 3000 nature reserves have been established, covering approximately 16% of the land surface of China. These natural reserves play important roles in plant conservation, covering more than 85% of types of terrestrial natural ecosystems, 40% of types of natural wetlands, 20% of native forests and 65% of natural communities of vascular plants. Meanwhile, the flora conserved in botanical gardens is also extensive. A recent survey shows that the 10 largest botanical gardens have living collections of 43 502 taxa, with a total of 24 667 species in ex situ conservation. These provide an important reserve of plant resources for sustainable economic and social development in China. Plant diversity is the basis for bioresources and sustainable utilization. The 21st century is predicted to be an era of bio-economy driven by advances of bioscience and biotechnology. Bio-economy may become the fourth economy form after agricultural, industrial, and information and information technology economies, having far-reaching impacts on sustainable development in agriculture, forestry, environmental protection, light industry, food supply and health care and other micro-economy aspects. Thus, a strategic and forward vision for conservation of plant diversity and sustainable use of plant resources in the 21st century is of

  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. 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

  8. Native arbuscular mycorrhizal fungi (AMF) from mountain grassland (Cordoba, Argentina) I. Seasonal variation of fungal spore diversity.

    PubMed

    Lugo, Mónica A; Cabello, Marta N

    2002-01-01

    Arbuscular mycorrhizal fungi (AMF) were studied in the rhizosphere of 3 Poaceae with metabolic pathway C(3) (Briza subaristata Lam., Deyeuxia hieronymi (Hack.) Türpe and Poa stuckertii (Hack.) Parodi), 2 Poaceae with C(4) metabolic type (Eragrostis lugens Nees and Sorghastrum pellitum (Hack.) Parodi.), and a Rosaceae (Alchemilla pinnata Ruíz & Pav.) from a natural mountain grassland in Central Argentina (South America). Host species, their metabolic type, seasonal changes, and grazing effects over AM fungal diversity were analyzed. Seventeen mycorrhizal fungi taxa were found, widespread in all families of Glomales. Density of endomycorrhizal fungi was found to be strongly influenced with seasons and host metabolic pathway, although biodiversity (H), richness (S) and evenness (E) did not change. In most cases grazing did not affect these variables.

  9. Nematode Hsp90: highly conserved but functionally diverse.

    PubMed

    Gillan, Victoria; Devaney, Eileen

    2014-08-01

    Nematodes are amongst the most successful and abundant organisms on the planet with approximately 30 000 species described, although the actual number of species is estimated to be one million or more. Despite sharing a relatively simple and invariant body plan, there is considerable diversity within the phylum. Nematodes have evolved to colonize most ecological niches, and can be free-living or can parasitize plants or animals to the detriment of the host organism. In this review we consider the role of heat shock protein 90 (Hsp90) in the nematode life cycle. We describe studies on Hsp90 in the free-living nematode Caenorhabditis elegans and comparative work on the parasitic species Brugia pahangi, and consider whether a dependence upon Hsp90 can be exploited for the control of parasitic species. PMID:24721950

  10. Unexplored diversity and conservation potential of neotropical hot caves.

    PubMed

    Ladle, Richard J; Firmino, João V L; Malhado, Ana C M; Rodríguez-Durán, Armando

    2012-12-01

    The term hot cave is used to describe some subterranean chambers in the Neotropics that are characterized by constantly high ambient temperatures generated by the body heat of high densities of certain bat species. Many of these species have limited geographic ranges, and some occur only in the hot-cave environment. In addition to the bats, the stable microclimate and abundant bat guano provides refuge and food for a high diversity of invertebrates. Hot caves have so far been described in the Caribbean and in a few isolated locations from Mexico to Brazil, although there is some evidence that similar caves may be present throughout the tropics. The existing literature suggests these poorly known ecosystems, with their unique combination of geomorphology and bat-generated microclimate, are particularly sensitive to disturbance and face multiple threats from urbanization, agricultural development, mining, and tourism. PMID:23003344

  11. Conservation phylogeography: does historical diversity contribute to regional vulnerability in European tree frogs (Hyla arborea)?

    PubMed

    Dufresnes, Christophe; Wassef, Jérôme; Ghali, Karim; Brelsford, Alan; Stöck, Matthias; Lymberakis, Petros; Crnobrnja-Isailovic, Jelka; Perrin, Nicolas

    2013-11-01

    Documenting and preserving the genetic diversity of populations, which conditions their long-term survival, have become a major issue in conservation biology. The loss of diversity often documented in declining populations is usually assumed to result from human disturbances; however, historical biogeographic events, otherwise known to strongly impact diversity, are rarely considered in this context. We apply a multilocus phylogeographic study to investigate the late-Quaternary history of a tree frog (Hyla arborea) with declining populations in the northern and western part of its distribution range. Mitochondrial and nuclear polymorphisms reveal high genetic diversity in the Balkan Peninsula, with a spatial structure moulded by the last glaciations. While two of the main refugial lineages remained limited to the Balkans (Adriatic coast, southern Balkans), a third one expanded to recolonize Northern and Western Europe, loosing much of its diversity in the process. Our findings show that mobile and a priori homogeneous taxa may also display substructure within glacial refugia ('refugia within refugia') and emphasize the importance of the Balkans as a major European biodiversity centre. Moreover, the distribution of diversity roughly coincides with regional conservation situations, consistent with the idea that historically impoverished genetic diversity may interact with anthropogenic disturbances, and increase the vulnerability of populations. Phylogeographic models seem important to fully appreciate the risks of local declines and inform conservation strategies. PMID:24102652

  12. Distribution, diversity and bioprospecting of bioactive compounds from cryptic fungal communities associated with endemic and cold-adapted macroalgae in Antarctica

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We surveyed the distribution and diversity of fungi associated with eight macroalgae from Antarctica and their capability to produce bioactive compounds. The collections yielded 148 fungal isolates identified using molecular methods into 21 genera and 43 species. The most frequent taxa were Geomyces...

  13. Questions of importance to the conservation of global biological diversity: answers from the past

    NASA Astrophysics Data System (ADS)

    Willis, K. J.; Bhagwat, S. A.

    2010-06-01

    Paleoecological records are replete with examples of biotic responses to past climate change and human impact but how can we use these records in the conservation of current and future biodiversity? A recently published list of One Hundred Questions of Importance to the Conservation of Global Biological Diversity (Sutherland et al., 2009) highlights a number of key research questions that need a temporal perspective. Many of these questions are related to the determination of ecological processes in order to assess ecosystem function and services, climate change-integrated conservation strategies, and ecosystem management and restoration. However, it is noticeable that not a single contributor to this list was from the paleo-research community and that extremely few paleo-records are ever used in the development of terrestrial conservation management plans. This lack of dialogue between conservationists and the paleo-community is partially driven by a perception that the data provided by paleoecological records are purely descriptive and not of relevance to the day-to-day management and conservation of biological diversity. This paper illustrates, through a series of case-studies, how long-term ecological records (>50 years) can provide a test of predictions and assumptions of ecological processes that are directly relevant to management strategies necessary in order to retain biological diversity in a changing climate. This includes information on diversity baselines, thresholds, resilience, and restoration of ecological processes.

  14. Questions of importance to the conservation of biological diversity: answers from the past

    NASA Astrophysics Data System (ADS)

    Willis, K. J.; Bhagwat, S. A.

    2010-11-01

    Paleoecological records are replete with examples of biotic responses to past climate change and human impact, but how can we use these records in the conservation of current and future biodiversity? A recently published list of (One Hundred Questions of Importance to the Conservation of Global Biological Diversity) (Sutherland et al., 2009) highlights a number of key research questions that need a temporal perspective. Many of these questions are related to the determination of ecological processes in order to assess ecosystem function and services, climate change-integrated conservation strategies, and ecosystem management and restoration. However, it is noticeable that not a single contributor to this list was from the paleo-research community and that extremely few paleo-records are ever used in the development of terrestrial conservation management plans. This lack of dialogue between conservationists and the paleo-community is partially driven by a perception that the data provided by paleoecological records are purely descriptive and not of relevance to the day-to-day management and conservation of biological diversity. This paper illustrates, through a series of case-studies, how long-term ecological records (>50 years) can provide a test of predictions and assumptions of ecological processes that are directly relevant to management strategies necessary to retain biological diversity in a changing climate. This discussion paper includes information on diversity baselines, thresholds, resilience, and restoration of ecological processes.

  15. Genome-Wide Identification of Mitogen-Activated Protein Kinase Gene Family across Fungal Lineage Shows Presence of Novel and Diverse Activation Loop Motifs

    PubMed Central

    Mohanta, Tapan Kumar; Mohanta, Nibedita; Parida, Pratap; Panda, Sujogya Kumar; Ponpandian, Lakshmi Narayanan; Bae, Hanhong

    2016-01-01

    The mitogen-activated protein kinase (MAPK) is characterized by the presence of the T-E-Y, T-D-Y, and T-G-Y motifs in its activation loop region and plays a significant role in regulating diverse cellular responses in eukaryotic organisms. Availability of large-scale genome data in the fungal kingdom encouraged us to identify and analyse the fungal MAPK gene family consisting of 173 fungal species. The analysis of the MAPK gene family resulted in the discovery of several novel activation loop motifs (T-T-Y, T-I-Y, T-N-Y, T-H-Y, T-S-Y, K-G-Y, T-Q-Y, S-E-Y and S-D-Y) in fungal MAPKs. The phylogenetic analysis suggests that fungal MAPKs are non-polymorphic, had evolved from their common ancestors around 1500 million years ago, and are distantly related to plant MAPKs. We are the first to report the presence of nine novel activation loop motifs in fungal MAPKs. The specificity of the activation loop motif plays a significant role in controlling different growth and stress related pathways in fungi. Hence, the presences of these nine novel activation loop motifs in fungi are of special interest. PMID:26918378

  16. The price of conserving avian phylogenetic diversity: a global prioritization approach

    PubMed Central

    Nunes, Laura A.; Turvey, Samuel T.; Rosindell, James

    2015-01-01

    The combination of rapid biodiversity loss and limited funds available for conservation represents a major global concern. While there are many approaches for conservation prioritization, few are framed as financial optimization problems. We use recently published avian data to conduct a global analysis of the financial resources required to conserve different quantities of phylogenetic diversity (PD). We introduce a new prioritization metric (ADEPD) that After Downlisting a species gives the Expected Phylogenetic Diversity at some future time. Unlike other metrics, ADEPD considers the benefits to future PD associated with downlisting a species (e.g. moving from Endangered to Vulnerable in the International Union for Conservation of Nature Red List). Combining ADEPD scores with data on the financial cost of downlisting different species provides a cost–benefit prioritization approach for conservation. We find that under worst-case spending $3915 can save 1 year of PD, while under optimal spending $1 can preserve over 16.7 years of PD. We find that current conservation spending patterns are only expected to preserve one quarter of the PD that optimal spending could achieve with the same total budget. Maximizing PD is only one approach within the wider goal of biodiversity conservation, but our analysis highlights more generally the danger involved in uninformed spending of limited resources. PMID:25561665

  17. The price of conserving avian phylogenetic diversity: a global prioritization approach.

    PubMed

    Nunes, Laura A; Turvey, Samuel T; Rosindell, James

    2015-02-19

    The combination of rapid biodiversity loss and limited funds available for conservation represents a major global concern. While there are many approaches for conservation prioritization, few are framed as financial optimization problems. We use recently published avian data to conduct a global analysis of the financial resources required to conserve different quantities of phylogenetic diversity (PD). We introduce a new prioritization metric (ADEPD) that After Downlisting a species gives the Expected Phylogenetic Diversity at some future time. Unlike other metrics, ADEPD considers the benefits to future PD associated with downlisting a species (e.g. moving from Endangered to Vulnerable in the International Union for Conservation of Nature Red List). Combining ADEPD scores with data on the financial cost of downlisting different species provides a cost-benefit prioritization approach for conservation. We find that under worst-case spending $3915 can save 1 year of PD, while under optimal spending $1 can preserve over 16.7 years of PD. We find that current conservation spending patterns are only expected to preserve one quarter of the PD that optimal spending could achieve with the same total budget. Maximizing PD is only one approach within the wider goal of biodiversity conservation, but our analysis highlights more generally the danger involved in uninformed spending of limited resources. PMID:25561665

  18. Benefits to poorly studied taxa of conservation of bird and mammal diversity on islands.

    PubMed

    Aslan, Clare; Holmes, Nick; Tershy, Bernie; Spatz, Dena; Croll, Donald A

    2015-02-01

    Protected area delineation and conservation action are urgently needed on marine islands, but the potential biodiversity benefits of these activities can be difficult to assess due to lack of species diversity information for lesser known taxa. We used linear mixed effects modeling and simple spatial analyses to investigate whether conservation activities based on the diversity of well-known insular taxa (birds and mammals) are likely to also capture the diversity of lesser known taxa (reptiles, amphibians, vascular land plants, ants, land snails, butterflies, and tenebrionid beetles). We assembled total, threatened, and endemic diversity data for both well-known and lesser known taxa and combined these with physical island biogeography characteristics for 1190 islands from 109 archipelagos. Among physical island biogeography factors, island area was the best indicator of diversity of both well-known and little-known taxa. Among taxonomic factors, total mammal species richness was the best indicator of total diversity of lesser known taxa, and the combination of threatened mammal and threatened bird diversity was the best indicator of lesser known endemic richness. The results of other intertaxon diversity comparisons were highly variable, however. Based on our results, we suggest that protecting islands above a certain minimum threshold area may be the most efficient use of conservation resources. For example, using our island database, if the threshold were set at 10 km(2) and the smallest 10% of islands greater than this threshold were protected, 119 islands would be protected. The islands would range in size from 10 to 29 km(2) and would include 268 lesser known species endemic to a single island, along with 11 bird and mammal species endemic to a single island. Our results suggest that for islands of equivalent size, prioritization based on total or threatened bird and mammal diversity may also capture opportunities to protect lesser known species endemic to

  19. Benefits to poorly studied taxa of conservation of bird and mammal diversity on islands.

    PubMed

    Aslan, Clare; Holmes, Nick; Tershy, Bernie; Spatz, Dena; Croll, Donald A

    2015-02-01

    Protected area delineation and conservation action are urgently needed on marine islands, but the potential biodiversity benefits of these activities can be difficult to assess due to lack of species diversity information for lesser known taxa. We used linear mixed effects modeling and simple spatial analyses to investigate whether conservation activities based on the diversity of well-known insular taxa (birds and mammals) are likely to also capture the diversity of lesser known taxa (reptiles, amphibians, vascular land plants, ants, land snails, butterflies, and tenebrionid beetles). We assembled total, threatened, and endemic diversity data for both well-known and lesser known taxa and combined these with physical island biogeography characteristics for 1190 islands from 109 archipelagos. Among physical island biogeography factors, island area was the best indicator of diversity of both well-known and little-known taxa. Among taxonomic factors, total mammal species richness was the best indicator of total diversity of lesser known taxa, and the combination of threatened mammal and threatened bird diversity was the best indicator of lesser known endemic richness. The results of other intertaxon diversity comparisons were highly variable, however. Based on our results, we suggest that protecting islands above a certain minimum threshold area may be the most efficient use of conservation resources. For example, using our island database, if the threshold were set at 10 km(2) and the smallest 10% of islands greater than this threshold were protected, 119 islands would be protected. The islands would range in size from 10 to 29 km(2) and would include 268 lesser known species endemic to a single island, along with 11 bird and mammal species endemic to a single island. Our results suggest that for islands of equivalent size, prioritization based on total or threatened bird and mammal diversity may also capture opportunities to protect lesser known species endemic to

  20. The Tree versus the Forest: The Fungal Tree of Life and the Topological Diversity within the Yeast Phylome

    PubMed Central

    Marcet-Houben, Marina; Gabaldón, Toni

    2009-01-01

    A recurrent topic in phylogenomics is the combination of various sequence alignments to reconstruct a tree that describes the evolutionary relationships within a group of species. However, such approach has been criticized for not being able to properly represent the topological diversity found among gene trees. To evaluate the representativeness of species trees based on concatenated alignments, we reconstruct several fungal species trees and compare them with the complete collection of phylogenies of genes encoded in the Saccharomyces cerevisiae genome. We found that, despite high levels of among-gene topological variation, the species trees do represent widely supported phylogenetic relationships. Most topological discrepancies between gene and species trees are concentrated in certain conflicting nodes. We propose to map such information on the species tree so that it accounts for the levels of congruence across the genome. We identified the lack of sufficient accuracy of current alignment and phylogenetic methods as an important source for the topological diversity encountered among gene trees. Finally, we discuss the implications of the high levels of topological variation for phylogeny-based orthology prediction strategies. PMID:19190756

  1. The impact of ecosystem degradation on the diversity of AM fungal communities associated to shrub species from the semiarid Spanish southeast

    NASA Astrophysics Data System (ADS)

    Barea, J. M.; Palenzuela, J.; Sánchez-Castro, I.; López-García, A.; Ferrol, M.; Azcón-Aguilar, C.

    2012-04-01

    Both the incidence of some soil environmental factors and the disturbance of natural plant communities, are often accompanied or preceded by loss of key physical-chemical and biological soil properties. In particular, plant community degradation causes disturbance of AM inoculum potential which is a critical ecological factor to help further plant developments in degraded habitats. The effect of disturbance of the vegetation cover on AM fungal population (number and diversity), is particularly relevant in the case of shrub communities, characteristics of semiarid Mediterranean ecosystems. In this context, a series of experiments have been carried out based on five representative communities of shrub species from southeast Spain. Both morphological and molecular approaches were followed for characterization of AM fungi associated to the target plant species, either as spores, extra-radical mycelia or actually colonizing their roots. The experiments can be grouped into three categories: (i) Analyzing the effect of plant cover degradation status. We demonstrated that degradation affects negatively the density and diversity of AM fungi as spores. (ii) Analyzing the community composition, and the temporal colonization dynamics, of AM fungi colonizing the roots of representative shrub species. It was found that the different co-occurring plant species are colonized by AM fungal communities of different composition, and that many AM fungal sequences detected in plant roots cannot be related to known AM fungal taxa present as spores in the rhizosphere soil. (iii) Assessing the effect of soil disturbance on AM fungal populations. It was found that, in spite of the induced perturbation, the phylotype diversity of AM fungi in receptor plants exclusively colonized by the AM propagules from the altered soil was not reduced in comparison to that of plants exclusively colonized from donor plants taken from the target ecosystem, used as inoculum source. The results will be

  2. Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A combination of Sanger and 454 sequences of small subunit rRNA loci were used to interrogate the microbial diversity in the bovine rumen of 14 pasture-fed animals. The observed bacterial species richness, based on the V1-V3 region of the 15S rRNA gene, was between 1902 to 2596 species-level operati...

  3. Broadly Conserved Fungal Effector BEC1019 Suppresses Host Cell Death and Enhances Pathogen Virulence in Powdery Mildew of Barley (Hordeum vulgare L.).

    PubMed

    Whigham, Ehren; Qi, Shan; Mistry, Divya; Surana, Priyanka; Xu, Ruo; Fuerst, Gregory; Pliego, Clara; Bindschedler, Laurence V; Spanu, Pietro D; Dickerson, Julie A; Innes, Roger W; Nettleton, Dan; Bogdanove, Adam J; Wise, Roger P

    2015-09-01

    The interaction of barley, Hordeum vulgare L., with the powdery mildew fungus Blumeria graminis f. sp. hordei is a well-developed model to investigate resistance and susceptibility to obligate biotrophic pathogens. The 130-Mb Blumeria genome encodes approximately 540 predicted effectors that are hypothesized to suppress or induce host processes to promote colonization. Blumeria effector candidate (BEC)1019, a single-copy gene encoding a putative, secreted metalloprotease, is expressed in haustorial feeding structures, and host-induced gene silencing of BEC1019 restricts haustorial development in compatible interactions. Here, we show that Barley stripe mosaic virus-induced gene silencing of BEC1019 significantly reduces fungal colonization of barley epidermal cells, demonstrating that BEC1019 plays a central role in virulence. In addition, delivery of BEC1019 to the host cytoplasm via Xanthomonas type III secretion suppresses cultivar nonspecific hypersensitive reaction (HR) induced by Xanthomonas oryzae pv. oryzicola, as well as cultivar-specific HR induced by AvrPphB from Pseudomonas syringae pv. phaseolicola. BEC1019 homologs are present in 96 of 241 sequenced fungal genomes, including plant pathogens, human pathogens, and free-living nonpathogens. Comparative analysis revealed variation at several amino acid positions that correlate with fungal lifestyle and several highly conserved, noncorrelated motifs. Site-directed mutagenesis of one of these, ETVIC, compromises the HR-suppressing activity of BEC1019. We postulate that BEC1019 represents an ancient, broadly important fungal protein family, members of which have evolved to function as effectors in plant and animal hosts.

  4. Sponsored Neo-Conservative Challenges to Diversity and Intercultural Competence in the US Undergraduate Curriculum

    ERIC Educational Resources Information Center

    Selden, Steven

    2013-01-01

    For the past six decades, conservative foundations in the United States have targeted their funding on a transformation of the public's understanding of markets, culture , and the undergraduate course of study. These foundations, and their sponsored researchers, have specifically challenged the place of diversity and intercultural competence…

  5. On the Brink of Extinction: Conserving the Diversity of Life. Worldwatch Paper 78.

    ERIC Educational Resources Information Center

    Wolf, Edward C.

    Concerns associated with biological diversity and the extinction of species are addressed in this report. Major topic areas examined include: (1) historical records of extinctions; (2) conservation biology and tropical ecology; (3) human-management regeneration potentials; (4) restoration ecology; (5) experimental restoration efforts; (6)…

  6. Conserving the Stage: Climate Change and the Geophysical Underpinnings of Species Diversity

    PubMed Central

    Anderson, Mark G.; Ferree, Charles E.

    2010-01-01

    Conservationists have proposed methods for adapting to climate change that assume species distributions are primarily explained by climate variables. The key idea is to use the understanding of species-climate relationships to map corridors and to identify regions of faunal stability or high species turnover. An alternative approach is to adopt an evolutionary timescale and ask ultimately what factors control total diversity, so that over the long run the major drivers of total species richness can be protected. Within a single climatic region, the temperate area encompassing all of the Northeastern U.S. and Maritime Canada, we hypothesized that geologic factors may take precedence over climate in explaining diversity patterns. If geophysical diversity does drive regional diversity, then conserving geophysical settings may offer an approach to conservation that protects diversity under both current and future climates. Here we tested how well geology predicts the species diversity of 14 US states and three Canadian provinces, using a comprehensive new spatial dataset. Results of linear regressions of species diversity on all possible combinations of 23 geophysical and climatic variables indicated that four geophysical factors; the number of geological classes, latitude, elevation range and the amount of calcareous bedrock, predicted species diversity with certainty (adj. R2 = 0.94). To confirm the species-geology relationships we ran an independent test using 18,700 location points for 885 rare species and found that 40% of the species were restricted to a single geology. Moreover, each geology class supported 5–95 endemic species and chi-square tests confirmed that calcareous bedrock and extreme elevations had significantly more rare species than expected by chance (P<0.0001), strongly corroborating the regression model. Our results suggest that protecting geophysical settings will conserve the stage for current and future biodiversity and may be a robust

  7. DNA barcoding applied to ex situ tropical amphibian conservation programme reveals cryptic diversity in captive populations.

    PubMed

    Crawford, Andrew J; Cruz, Catalina; Griffith, Edgardo; Ross, Heidi; Ibáñez, Roberto; Lips, Karen R; Driskell, Amy C; Bermingham, Eldredge; Crump, Paul

    2013-11-01

    Amphibians constitute a diverse yet still incompletely characterized clade of vertebrates, in which new species are still being discovered and described at a high rate. Amphibians are also increasingly endangered, due in part to disease-driven threats of extinctions. As an emergency response, conservationists have begun ex situ assurance colonies for priority species. The abundance of cryptic amphibian diversity, however, may cause problems for ex situ conservation. In this study we used a DNA barcoding approach to survey mitochondrial DNA (mtDNA) variation in captive populations of 10 species of Neotropical amphibians maintained in an ex situ assurance programme at El Valle Amphibian Conservation Center (EVACC) in the Republic of Panama. We combined these mtDNA sequences with genetic data from presumably conspecific wild populations sampled from across Panama, and applied genetic distance-based and character-based analyses to identify cryptic lineages. We found that three of ten species harboured substantial cryptic genetic diversity within EVACC, and an additional three species harboured cryptic diversity among wild populations, but not in captivity. Ex situ conservation efforts focused on amphibians are therefore vulnerable to an incomplete taxonomy leading to misidentification among cryptic species. DNA barcoding may therefore provide a simple, standardized protocol to identify cryptic diversity readily applicable to any amphibian community.

  8. Large-scale fungal diversity assessment in the Andean Yungas forests reveals strong community turnover among forest types along an altitudinal gradient.

    PubMed

    Geml, József; Pastor, Nicolás; Fernandez, Lisandro; Pacheco, Silvia; Semenova, Tatiana A; Becerra, Alejandra G; Wicaksono, Christian Y; Nouhra, Eduardo R

    2014-05-01

    The Yungas, a system of tropical and subtropical montane forests on the eastern slopes of the Andes, are extremely diverse and severely threatened by anthropogenic pressure and climate change. Previous mycological works focused on macrofungi (e.g. agarics, polypores) and mycorrhizae in Alnus acuminata forests, while fungal diversity in other parts of the Yungas has remained mostly unexplored. We carried out Ion Torrent sequencing of ITS2 rDNA from soil samples taken at 24 sites along the entire latitudinal extent of the Yungas in Argentina. The sampled sites represent the three altitudinal forest types: the piedmont (400-700 m a.s.l.), montane (700-1500 m a.s.l.) and montane cloud (1500-3000 m a.s.l.) forests. The deep sequence data presented here (i.e. 4 108 126 quality-filtered sequences) indicate that fungal community composition correlates most strongly with elevation, with many fungi showing preference for a certain altitudinal forest type. For example, ectomycorrhizal and root endophytic fungi were most diverse in the montane cloud forests, particularly at sites dominated by Alnus acuminata, while the diversity values of various saprobic groups were highest at lower elevations. Despite the strong altitudinal community turnover, fungal diversity was comparable across the different zonal forest types. Besides elevation, soil pH, N, P, and organic matter contents correlated with fungal community structure as well, although most of these variables were co-correlated with elevation. Our data provide an unprecedented insight into the high diversity and spatial distribution of fungi in the Yungas forests.

  9. Aquatic macrophyte and macroinvertebrate diversity and conservation in wetlands of the Sinos River basin.

    PubMed

    Maltchik, L; Rolon, A S; Stenert, C

    2010-12-01

    Wetlands are important sites for biological conservation because they support rich biodiversity and present high productivity. Species-area relationship is an important tool in conservation planning and it has been extensively used for wetland management. This study had as aims: (1) to analyse macrophyte and macroinvertebrate diversity in the fragmented wetlands of the Sinos River basin; and (2) to investigate whether wetland areas could work as a tool for selecting the important habitats for biodiversity conservation. Throughout the study, 56 species of macrophytes and 57 taxa of macroinvertebrates were identified. Macrophyte richness was related to the wetland area, but macroinvertebrate richness, however, was not related to the wetland area. The macrophyte and macroinvertebrate composition were not related to the wetland area. Species composition varied between the regions of the basin and the difference in the species composition occurred mainly by the distribution of macroinvertebrates. With regard to the biodiversity conservation of the Sinos River basin, the wetland area must not be a priority criterion for choosing the important wetlands for conservation. The environmental policies for biodiversity conservation must include management actions focused also on the protection of small wetlands. Moreover, other criteria should be analysed in further research such as habitat diversity, hydroperiod, geographic distribution and connectivity.

  10. Identifying priority areas for conservation and management in diverse tropical forests.

    PubMed

    Mokany, Karel; Westcott, David A; Prasad, Soumya; Ford, Andrew J; Metcalfe, Daniel J

    2014-01-01

    The high concentration of the world's species in tropical forests endows these systems with particular importance for retaining global biodiversity, yet it also presents significant challenges for ecology and conservation science. The vast number of rare and yet to be discovered species restricts the applicability of species-level modelling for tropical forests, while the capacity of community classification approaches to identify priorities for conservation and management is also limited. Here we assessed the degree to which macroecological modelling can overcome shortfalls in our knowledge of biodiversity in tropical forests and help identify priority areas for their conservation and management. We used 527 plant community survey plots in the Australian Wet Tropics to generate models and predictions of species richness, compositional dissimilarity, and community composition for all the 4,313 vascular plant species recorded across the region (>1.3 million communities (grid cells)). We then applied these predictions to identify areas of tropical forest likely to contain the greatest concentration of species, rare species, endemic species and primitive angiosperm families. Synthesising these alternative attributes of diversity into a single index of conservation value, we identified two areas within the Australian wet tropics that should be a high priority for future conservation actions: the Atherton Tablelands and Daintree rainforest. Our findings demonstrate the value of macroecological modelling in identifying priority areas for conservation and management actions within highly diverse systems, such as tropical forests.

  11. Metagenomic analysis of fungal diversity on strawberry plants and the effect of management practices on the fungal community structure of aerial organs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Metabarcoding, defined as Next Generation Sequencing (NGS) of amplicons of the ITS2 region (DNA barcode), was used to identify the composition of the fungal community on different strawberry organs i.e. leaves, flowers, and immature and mature fruits grown on a farm using disease and insect control ...

  12. Targeting climate diversity in conservation planning to build resilience to climate change

    USGS Publications Warehouse

    Heller, Nicole E.; Kreitler, Jason R.; Ackerly, David; Weiss, Stuart; Recinos, Amanda; Branciforte, Ryan; Flint, Lorraine E.; Flint, Alan L.; Micheli, Elisabeth

    2015-01-01

    Climate change is raising challenging concerns for systematic conservation planning. Are methods based on the current spatial patterns of biodiversity effective given long-term climate change? Some conservation scientists argue that planning should focus on protecting the abiotic diversity in the landscape, which drives patterns of biological diversity, rather than focusing on the distribution of focal species, which shift in response to climate change. Climate is one important abiotic driver of biodiversity patterns, as different climates host different biological communities and genetic pools. We propose conservation networks that capture the full range of climatic diversity in a region will improve the resilience of biotic communities to climate change compared to networks that do not. In this study we used historical and future hydro-climate projections from the high resolution Basin Characterization Model to explore the utility of directly targeting climatic diversity in planning. Using the spatial planning tool, Marxan, we designed conservation networks to capture the diversity of climate types, at the regional and sub-regional scale, and compared them to networks we designed to capture the diversity of vegetation types. By focusing on the Conservation Lands Network (CLN) of the San Francisco Bay Area as a real-world case study, we compared the potential resilience of networks by examining two factors: the range of climate space captured, and climatic stability to 18 future climates, reflecting different emission scenarios and global climate models. We found that the climate-based network planned at the sub-regional scale captured a greater range of climate space and showed higher climatic stability than the vegetation and regional based-networks. At the same time, differences among network scenarios are small relative to the variance in climate stability across global climate models. Across different projected futures, topographically heterogeneous areas

  13. Genetic diversity and population structure of endangered Aquilaria malaccensis revealed potential for future conservation.

    PubMed

    Singh, Pradeep; Nag, Akshay; Parmar, Rajni; Ghosh, Sneha; Bhau, Brijmohan Singh; Sharma, Ram Kumar

    2015-12-01

    The endangered Aquilaria malaccensis,is an important plant with high economic values. Characterization of genetic diversity and population structure is receiving tremendous attention for effective conservation of genetic resources. Considering important repositories of biological diversity, the genetic relationships of 127 A. malaccensis accessions from 10 home gardens of three states of northeast India were assessed using amplified fragment length polymorphism (AFLP). Of the 1153 fragments amplified with four AFLP primer combinations, 916 (79.4%) were found to be polymorphic. Polymorphic information content (PIC) and marker index (MI) of each primer combination correlate significantly with the number of genotypes resolved. Overall, a high genetic diversity (avg. 71.85%) was recorded. Further, high gene flow (Nm: 3.37), low genetic differentiation (FST: 0.069) and high within population genetic variation (93%) suggests that most of the genetic diversity is restricted within population. Neighbour joining (NJ), principal coordinate analysis (PCoA) and Bayesian-based STRUCTURE grouped all the accessions in two clusters with significant intermixing between populations, therefore, revealed that two genetically distinct gene pools are operating in the A. malaccensis populations cultivated in home gardens. Based on the various diversity inferences, five diverse populations (JOH, FN, HLF, DHM and ITN) were identified, which can be potentially exploited to develop conservation strategies for A. malaccensis.

  14. Conservation priorities of genetic diversity in domesticated metapopulations: a study in taurine cattle breeds

    PubMed Central

    Medugorac, Ivica; Veit-Kensch, Claudia E; Ramljak, Jelena; Brka, Muhamed; Marković, Božidarka; Stojanović, Srđan; Bytyqi, Hysen; Kochoski, Ljupche; Kume, Kristaq; Grünenfelder, Hans-Peter; Bennewitz, Jörn; Förster, Martin

    2011-01-01

    We estimated neutral diversity of 21 European cattle breeds with 105 microsatellites. Nine of them resembled unselected Balkan Buša strains with diffuse breeding barriers and the 12 others were strongly differentiated, isolated breeds. Because of the impact of neutral genetic diversity on long-term population adaptive capacity, we discuss the long-term outcome of different conservation priorities in a subdivided metapopulation of the investigated cattle breeds. The optimal contribution to a pool of total genetic diversity allocated more than 95% of long-term relevant neutral diversity to virtually unselected strains of the Balkan Buša, while the maximization of total variance preferred inbred breeds. Current artificial selection methods, such as genomic selection sped up and a recovery of underestimated traits becomes quickly impossible. We emphasize that currently neutral and even deleterious alleles might be required for future genotypes in sustainable and efficient livestock breeding and production systems of a 21st century. We provide cumulative evidences that long-term survival relies on genetic complexity and complexity relies on allelic diversity. Our results suggest that virtually unselected, nonuniform strains harbor a crucial proportion of neutral diversity and should be conserved with high global priority. As one example, we suggest a cooperative maintenance of the nondifferentiated, highly fragmented, and fast vanishing metapopulation of Balkan Buša. PMID:22393510

  15. Mycobiome of the Bat White Nose Syndrome Affected Caves and Mines Reveals Diversity of Fungi and Local Adaptation by the Fungal Pathogen Pseudogymnoascus (Geomyces) destructans

    PubMed Central

    Rajkumar, Sunanda S.; Li, Xiaojiang; Okoniewski, Joseph C.; Hicks, Alan C.; Davis, April D.; Broussard, Kelly; LaDeau, Shannon L.; Chaturvedi, Sudha; Chaturvedi, Vishnu

    2014-01-01

    Current investigations of bat White Nose Syndrome (WNS) and the causative fungus Pseudogymnoascus (Geomyces) destructans (Pd) are intensely focused on the reasons for the appearance of the disease in the Northeast and its rapid spread in the US and Canada. Urgent steps are still needed for the mitigation or control of Pd to save bats. We hypothesized that a focus on fungal community would advance the understanding of ecology and ecosystem processes that are crucial in the disease transmission cycle. This study was conducted in 2010–2011 in New York and Vermont using 90 samples from four mines and two caves situated within the epicenter of WNS. We used culture-dependent (CD) and culture-independent (CI) methods to catalogue all fungi (‘mycobiome’). CD methods included fungal isolations followed by phenotypic and molecular identifications. CI methods included amplification of DNA extracted from environmental samples with universal fungal primers followed by cloning and sequencing. CD methods yielded 675 fungal isolates and CI method yielded 594 fungal environmental nucleic acid sequences (FENAS). The core mycobiome of WNS comprised of 136 operational taxonomic units (OTUs) recovered in culture and 248 OTUs recovered in clone libraries. The fungal community was diverse across the sites, although a subgroup of dominant cosmopolitan fungi was present. The frequent recovery of Pd (18% of samples positive by culture) even in the presence of dominant, cosmopolitan fungal genera suggests some level of local adaptation in WNS-afflicted habitats, while the extensive distribution of Pd (48% of samples positive by real-time PCR) suggests an active reservoir of the pathogen at these sites. These findings underscore the need for integrated disease control measures that target both bats and Pd in the hibernacula for the control of WNS. PMID:25264864

  16. Mycobiome of the bat white nose syndrome affected caves and mines reveals diversity of fungi and local adaptation by the fungal pathogen Pseudogymnoascus (Geomyces) destructans.

    PubMed

    Zhang, Tao; Victor, Tanya R; Rajkumar, Sunanda S; Li, Xiaojiang; Okoniewski, Joseph C; Hicks, Alan C; Davis, April D; Broussard, Kelly; LaDeau, Shannon L; Chaturvedi, Sudha; Chaturvedi, Vishnu

    2014-01-01

    Current investigations of bat White Nose Syndrome (WNS) and the causative fungus Pseudogymnoascus (Geomyces) destructans (Pd) are intensely focused on the reasons for the appearance of the disease in the Northeast and its rapid spread in the US and Canada. Urgent steps are still needed for the mitigation or control of Pd to save bats. We hypothesized that a focus on fungal community would advance the understanding of ecology and ecosystem processes that are crucial in the disease transmission cycle. This study was conducted in 2010-2011 in New York and Vermont using 90 samples from four mines and two caves situated within the epicenter of WNS. We used culture-dependent (CD) and culture-independent (CI) methods to catalogue all fungi ('mycobiome'). CD methods included fungal isolations followed by phenotypic and molecular identifications. CI methods included amplification of DNA extracted from environmental samples with universal fungal primers followed by cloning and sequencing. CD methods yielded 675 fungal isolates and CI method yielded 594 fungal environmental nucleic acid sequences (FENAS). The core mycobiome of WNS comprised of 136 operational taxonomic units (OTUs) recovered in culture and 248 OTUs recovered in clone libraries. The fungal community was diverse across the sites, although a subgroup of dominant cosmopolitan fungi was present. The frequent recovery of Pd (18% of samples positive by culture) even in the presence of dominant, cosmopolitan fungal genera suggests some level of local adaptation in WNS-afflicted habitats, while the extensive distribution of Pd (48% of samples positive by real-time PCR) suggests an active reservoir of the pathogen at these sites. These findings underscore the need for integrated disease control measures that target both bats and Pd in the hibernacula for the control of WNS. PMID:25264864

  17. Effect of trophic status in lakes on fungal species diversity and abundance.

    PubMed

    Pietryczuk, A; Cudowski, A; Hauschild, T

    2014-11-01

    The objective of this study was to determine the species diversity and abundance of fungi in relation to the hydrochemical conditions, with special emphasis on the trophic status and degree of pollution of lakes. The study was conducted in 14 lakes of the Augustów Lakeland (central Europe, NE Poland) with different hydrological conditions, type of stratification and trophic status. The analyses were performed in the hydrological year 2013. In the waters of the studied lakes, the mean abundance of fungi was 5600±3600 CFU/mL. The minimum value (800 CFU/mL) was recorded for the mesotrophic Płaskie Lake, and the maximum value (14,000 CFU/mL) was recorded for the eutrophic Pobojno Lake. A total of 38 species of fungi were identified, including 11 belonging to the aquatic hyphomycetes; up to 14 species were potentially pathogenic fungi. The potentially pathogenic fungi, particularly Candida albicans and Scopulariopsis fusca, were found in lakes with increased concentrations of chloride and sulphate(VI) ions and may thus serve as indicators of the degree of water pollution. This paper illustrates that the species diversity and abundance of fungi in limnic waters depend on the concentration of organic matter, chlorophyll a concentration, and the degree of water pollution. The results suggest that aquatic fungi can be a valuable indicator of the degree of pollution and the sanitary quality of the water. PMID:25145569

  18. Massive parallel 16S rRNA gene pyrosequencing reveals highly diverse fecal bacterial and fungal communities in healthy dogs and cats.

    PubMed

    Handl, Stefanie; Dowd, Scot E; Garcia-Mazcorro, Jose F; Steiner, Jörg M; Suchodolski, Jan S

    2011-05-01

    This study evaluated the fecal microbiota of 12 healthy pet dogs and 12 pet cats using bacterial and fungal tag-encoded FLX-Titanium amplicon pyrosequencing. A total of 120,406 pyrosequencing reads for bacteria (mean 5017) and 5359 sequences (one pool each for dogs and cats) for fungi were analyzed. Additionally, group-specific 16S rRNA gene clone libraries for Bifidobacterium spp. and lactic acid-producing bacteria (LAB) were constructed. The most abundant bacterial phylum was Firmicutes, followed by Bacteroidetes in dogs and Actinobacteria in cats. The most prevalent bacterial class in dogs and cats was Clostridia, dominated by the genera Clostridium (clusters XIVa and XI) and Ruminococcus. At the genus level, 85 operational taxonomic units (OTUs) were identified in dogs and 113 OTUs in cats. Seventeen LAB and eight Bifidobacterium spp. were detected in canine feces. Ascomycota was the only fungal phylum detected in cats, while Ascomycota, Basidiomycota, Glomeromycota, and Zygomycota were identified in dogs. Nacaseomyces was the most abundant fungal genus in dogs; Saccharomyces and Aspergillus were predominant in cats. At the genus level, 33 different fungal OTUs were observed in dogs and 17 OTUs in cats. In conclusion, this study revealed a highly diverse bacterial and fungal microbiota in canine and feline feces.

  19. Bird diversity and the conservation value of a new Ramsar site: Guangdong Haifeng Wetlands, China.

    PubMed

    Hu, Junhua; Jiang, Zhigang; Zhang, Chunlan; Xiao, Feng; Hu, Huijian

    2011-09-01

    Wetlands are critical habitats for birds. However, wetlands are being degraded at an accelerating rate due to global human activity, and a disproportionate fraction of wetland-dependent bird species are in decline. We evaluated the conservation value of a new Ramsar site, Guangdong Haifeng Wetlands, China, for birds, by comparing bird communities (using line transect data) in 3 different districts: Gongping, Dongguan Lian'anwei and Dahu. We recorded 139 species of birds, including 26 species that are protected at a national level. Dahu had the highest species richness and diversity, whereas Dongguan Lian'anwei had the highest abundance of birds and the lowest species diversity. Finally, Gongping had both the lowest species richness and the lowest abundance. The endemism of constituent species differed among districts, and the bird communities were complementary. There were significant seasonal differences in the species richness and the number of individuals. Spring had the highest species richness and diversity. The present study identifies the high conservation value of Haifeng Wetlands for both waterbirds and terrestrial birds. Our findings suggest that conservation efforts in Haifeng Wetlands and other wetlands should focus not only on wintering migratory birds, but also on resident birds. To accomplish effective conservation, we should consider the reserve and surrounding wetlands as a whole, incorporating ecological research, education and local economic development. PMID:21910846

  20. Bird diversity and the conservation value of a new Ramsar site: Guangdong Haifeng Wetlands, China.

    PubMed

    Hu, Junhua; Jiang, Zhigang; Zhang, Chunlan; Xiao, Feng; Hu, Huijian

    2011-09-01

    Wetlands are critical habitats for birds. However, wetlands are being degraded at an accelerating rate due to global human activity, and a disproportionate fraction of wetland-dependent bird species are in decline. We evaluated the conservation value of a new Ramsar site, Guangdong Haifeng Wetlands, China, for birds, by comparing bird communities (using line transect data) in 3 different districts: Gongping, Dongguan Lian'anwei and Dahu. We recorded 139 species of birds, including 26 species that are protected at a national level. Dahu had the highest species richness and diversity, whereas Dongguan Lian'anwei had the highest abundance of birds and the lowest species diversity. Finally, Gongping had both the lowest species richness and the lowest abundance. The endemism of constituent species differed among districts, and the bird communities were complementary. There were significant seasonal differences in the species richness and the number of individuals. Spring had the highest species richness and diversity. The present study identifies the high conservation value of Haifeng Wetlands for both waterbirds and terrestrial birds. Our findings suggest that conservation efforts in Haifeng Wetlands and other wetlands should focus not only on wintering migratory birds, but also on resident birds. To accomplish effective conservation, we should consider the reserve and surrounding wetlands as a whole, incorporating ecological research, education and local economic development.

  1. Soil moisture and chemistry influence diversity of ectomycorrhizal fungal communities associating with willow along an hydrologic gradient.

    PubMed

    Erlandson, Sonya R; Savage, Jessica A; Cavender-Bares, Jeannine M; Peay, Kabir G

    2016-01-01

    Influences of soil environment and willow host species on ectomycorrhizal fungi communities was studied across an hydrologic gradient in temperate North America. Soil moisture, organic matter and pH strongly predicted changes in fungal community composition. In contrast, increased fungal richness strongly correlated with higher plant-available phosphorus. The 93 willow trees sampled for ectomycorrhizal fungi included seven willow species. Host identity did not influence fungal richness or community composition, nor was there strong evidence of willow host preference for fungal species. Network analysis suggests that these mutualist interaction networks are not significantly nested or modular. Across a strong environmental gradient, fungal abiotic niche determined the fungal species available to associate with host plants within a habitat.

  2. Assessment of genetic diversity and distribution of endophytic fungal communities of Alternaria solani isolates associated with the dominant Karanja plants in Sanganer Region of Rajasthan.

    PubMed

    Tiwari, Kartikeya; Chittora, Manish

    2013-12-01

    Higher plants are ubiquitously colonized with fungal endophytes that often lack readily detectable structures. Current study examines the distribution of endophytic fungal communities within Karanja plants and diversity of novel fungal endophyte Alternaria solani isolates collected from different locations of Sanganer region of Rajasthan. Results confirmed that A. solani is a major fungal endophyte consortium associated with Karanja plants. PCR Amplified fragments using random amplified polymorphic DNA (RAPD) primers were subjected to unweighted pair group method analysis (UPGMA), which clearly distinguished twelve ecologically diverse A. solani isolates. A total of 58 RAPD loci were amplified, out of which 35 (60.34%) were polymorphic and 23 were monomorphic (39.66%) in nature. These polymorphic loci were identified with an average of 2.92 bands per primer. The efficacy of RAPD markers proved as an efficient marker system with respect to detection of polymorphism and number of loci scored and can be used for the identification of a particular isolates, thereby defining core collections and strengthening their exploitation in acquiring novel products produced by them. PMID:23888281

  3. Long-lasting modification of soil fungal diversity associated with the introduction of rabbits to a remote sub-Antarctic archipelago.

    PubMed

    Pansu, Johan; Winkworth, Richard C; Hennion, Françoise; Gielly, Ludovic; Taberlet, Pierre; Choler, Philippe

    2015-09-01

    During the late nineteenth century, Europeans introduced rabbits to many of the sub-Antarctic islands, environments that prior to this had been devoid of mammalian herbivores. The impacts of rabbits on indigenous ecosystems are well studied; notably, they cause dramatic changes in plant communities and promote soil erosion. However, the responses of fungal communities to such biotic disturbances remain unexplored. We used metabarcoding of soil extracellular DNA to assess the diversity of plant and fungal communities at sites on the sub-Antarctic Kerguelen Islands with contrasting histories of disturbance by rabbits. Our results suggest that on these islands, the simplification of plant communities and increased erosion resulting from the introduction of rabbits have driven compositional changes, including diversity reductions, in indigenous soil fungal communities. Moreover, there is no indication of recovery at sites from which rabbits were removed 20 years ago. These results imply that introduced herbivores have long-lasting and multifaceted effects on fungal biodiversity as well as highlight the low resiliency of sub-Antarctic ecosystems.

  4. Meta-barcoded evaluation of the ISO standard 11063 DNA extraction procedure to characterize soil bacterial and fungal community diversity and composition.

    PubMed

    Terrat, Sebastien; Plassart, Pierre; Bourgeois, Emilie; Ferreira, Stéphanie; Dequiedt, Samuel; Adele-Dit-De-Renseville, Nathalie; Lemanceau, Philippe; Bispo, Antonio; Chabbi, Abad; Maron, Pierre-Alain; Ranjard, Lionel

    2015-01-01

    This study was designed to assess the influence of three soil DNA extraction procedures, namely the International Organization for Standardization (ISO-11063, GnS-GII and modified ISO procedure (ISOm), on the taxonomic diversity and composition of soil bacterial and fungal communities. The efficacy of each soil DNA extraction method was assessed on five soils, differing in their physico-chemical characteristics and land use. A meta-barcoded pyrosequencing approach targeting 16S and 18S rRNA genes was applied to characterize soil microbial communities. We first observed that the GnS-GII introduced some heterogeneity in bacterial composition between replicates. Then, although no major difference was observed between extraction procedures for soil bacterial diversity, we saw that the number of fungal genera could be underestimated by the ISO-11063. In particular, this procedure underestimated the detection in several soils of the genera Cryptococcus, Pseudallescheria, Hypocrea and Plectosphaerella, which are of ecological interest. Based on these results, we recommend using the ISOm method for studies focusing on both the bacterial and fungal communities. Indeed, the ISOm procedure provides a better evaluation of bacterial and fungal communities and is limited to the modification of the mechanical lysis step of the existing ISO-11063 standard.

  5. Comparison of ITS and 18S rDNA for estimating fungal diversity using PCR-DGGE.

    PubMed

    Liu, Jie; Yu, Yaoyao; Cai, Zhang; Bartlam, Mark; Wang, Yingying

    2015-09-01

    Both the internal transcribed spacer (ITS) region and 18S rRNA genes are broadly applied in molecular fingerprinting studies of fungi. However, the differences in those two ribosomal RNA regions are still largely unknown. In the current study, three sets of most suitable subunit ribosomes in ITS and 18S rRNA were compared using denaturing gradient gel electrophoresis (DGGE) under the optimum experimental conditions. Ten samples from both aquatic and soil environments were tested. The results revealed that the ITS region produced range-weighted richness in the range 36-361, which was significantly higher than that produced by 18S rDNA. There was a similar tendency in terms of the Shannon-Weaver diversity index and community dynamics in both water and soil samples. Samples from water and soil were better separated using ITS than 18S rDNA in principal component analysis of DGGE bands. Our study suggests that the ITS region is more precise and has more potential than 18S rRNA genes in fungal community analysis.

  6. Changes in ectomycorrhizal fungal community composition and declining diversity along a 2-million-year soil chronosequence.

    PubMed

    Albornoz, Felipe E; Teste, François P; Lambers, Hans; Bunce, Michael; Murray, Dáithí C; White, Nicole E; Laliberté, Etienne

    2016-10-01

    Ectomycorrhizal (ECM) fungal communities covary with host plant communities along soil fertility gradients, yet it is unclear whether this reflects changes in host composition, fungal edaphic specialization or priority effects during fungal community establishment. We grew two co-occurring ECM plant species (to control for host identity) in soils collected along a 2-million-year chronosequence representing a strong soil fertility gradient and used soil manipulations to disentangle the effects of edaphic properties from those due to fungal inoculum. Ectomycorrhizal fungal community composition changed and richness declined with increasing soil age; these changes were linked to pedogenesis-driven shifts in edaphic properties, particularly pH and resin-exchangeable and organic phosphorus. However, when differences in inoculum potential or soil abiotic properties among soil ages were removed while host identity was held constant, differences in ECM fungal communities and richness among chronosequence stages disappeared. Our results show that ECM fungal communities strongly vary during long-term ecosystem development, even within the same hosts. However, these changes could not be attributed to short-term fungal edaphic specialization or differences in fungal inoculum (i.e. density and composition) alone. Rather, they must reflect longer-term ecosystem-level feedback between soil, vegetation and ECM fungi during pedogenesis. PMID:27480679

  7. Use of inverse spatial conservation prioritization to avoid biological diversity loss outside protected areas.

    PubMed

    Kareksela, Santtu; Moilanen, Atte; Tuominen, Seppo; Kotiaho, Janne S

    2013-12-01

    Globally expanding human land use sets constantly increasing pressure for maintenance of biological diversity and functioning ecosystems. To fight the decline of biological diversity, conservation science has broken ground with methods such as the operational model of systematic conservation planning (SCP), which focuses on design and on-the-ground implementation of conservation areas. The most commonly used method in SCP is reserve selection that focuses on the spatial design of reserve networks and their expansion. We expanded these methods by introducing another form of spatial allocation of conservation effort relevant for land-use zoning at the landscape scale that avoids negative ecological effects of human land use outside protected areas. We call our method inverse spatial conservation prioritization. It can be used to identify areas suitable for economic development while simultaneously limiting total ecological and environmental effects of that development at the landscape level by identifying areas with highest economic but lowest ecological value. Our method is not based on a priori targets, and as such it is applicable to cases where the effects of land use on, for example, individual species or ecosystem types are relatively small and would not lead to violation of regional or national conservation targets. We applied our method to land-use allocation to peat mining. Our method identified a combination of profitable production areas that provides the needed area for peat production while retaining most of the landscape-level ecological value of the ecosystem. The results of this inverse spatial conservation prioritization are being used in land-use zoning in the province of Central Finland.

  8. Use of inverse spatial conservation prioritization to avoid biological diversity loss outside protected areas.

    PubMed

    Kareksela, Santtu; Moilanen, Atte; Tuominen, Seppo; Kotiaho, Janne S

    2013-12-01

    Globally expanding human land use sets constantly increasing pressure for maintenance of biological diversity and functioning ecosystems. To fight the decline of biological diversity, conservation science has broken ground with methods such as the operational model of systematic conservation planning (SCP), which focuses on design and on-the-ground implementation of conservation areas. The most commonly used method in SCP is reserve selection that focuses on the spatial design of reserve networks and their expansion. We expanded these methods by introducing another form of spatial allocation of conservation effort relevant for land-use zoning at the landscape scale that avoids negative ecological effects of human land use outside protected areas. We call our method inverse spatial conservation prioritization. It can be used to identify areas suitable for economic development while simultaneously limiting total ecological and environmental effects of that development at the landscape level by identifying areas with highest economic but lowest ecological value. Our method is not based on a priori targets, and as such it is applicable to cases where the effects of land use on, for example, individual species or ecosystem types are relatively small and would not lead to violation of regional or national conservation targets. We applied our method to land-use allocation to peat mining. Our method identified a combination of profitable production areas that provides the needed area for peat production while retaining most of the landscape-level ecological value of the ecosystem. The results of this inverse spatial conservation prioritization are being used in land-use zoning in the province of Central Finland. PMID:24033397

  9. Genetic Diversity and Association Characters of Bacteria Isolated from Arbuscular Mycorrhizal Fungal Spore Walls.

    PubMed

    Selvakumar, Gopal; Krishnamoorthy, Ramasamy; Kim, Kiyoon; Sa, Tong-Min

    2016-01-01

    Association between arbuscular mycorrhizal fungi (AMF) and bacteria has long been studied. However, the factors influencing their association in the natural environment is still unknown. This study aimed to isolate bacteria associated with spore walls of AMF and identify their potential characters for association. Spores collected from coastal reclamation land were differentiated based on their morphology and identified by 18S rDNA sequencing as Funneliformis caledonium, Racocetra alborosea and Funneliformis mosseae. Bacteria associated with AMF spore walls were isolated after treating them with disinfection solution at different time intervals. After 0, 10 and 20 min of spore disinfection, 86, 24 and 10 spore associated bacteria (SAB) were isolated, respectively. BOX-PCR fingerprinting analysis showed that diverse bacterial communities were associated to AMF spores. Bacteria belonging to the same genera could associate with different AMF spores. Gram positive bacteria were more closely associated with AMF spores. Isolated SAB were characterized and tested for spore association characters such as chitinase, protease, cellulase enzymes and exopolysaccharide production (EPS). Among the 120 SAB, 113 SAB were able to show one or more characters for association and seven SAB did not show any association characters. The 16S rDNA sequence of SAB revealed that bacteria belonging to the phyla Firmicutes, Proteobacteria, Actinobacteria and Bactereiodes were associated with AMF spore walls. PMID:27479250

  10. Genetic Diversity and Association Characters of Bacteria Isolated from Arbuscular Mycorrhizal Fungal Spore Walls

    PubMed Central

    Selvakumar, Gopal; Krishnamoorthy, Ramasamy; Kim, Kiyoon; Sa, Tong-Min

    2016-01-01

    Association between arbuscular mycorrhizal fungi (AMF) and bacteria has long been studied. However, the factors influencing their association in the natural environment is still unknown. This study aimed to isolate bacteria associated with spore walls of AMF and identify their potential characters for association. Spores collected from coastal reclamation land were differentiated based on their morphology and identified by 18S rDNA sequencing as Funneliformis caledonium, Racocetra alborosea and Funneliformis mosseae. Bacteria associated with AMF spore walls were isolated after treating them with disinfection solution at different time intervals. After 0, 10 and 20 min of spore disinfection, 86, 24 and 10 spore associated bacteria (SAB) were isolated, respectively. BOX-PCR fingerprinting analysis showed that diverse bacterial communities were associated to AMF spores. Bacteria belonging to the same genera could associate with different AMF spores. Gram positive bacteria were more closely associated with AMF spores. Isolated SAB were characterized and tested for spore association characters such as chitinase, protease, cellulase enzymes and exopolysaccharide production (EPS). Among the 120 SAB, 113 SAB were able to show one or more characters for association and seven SAB did not show any association characters. The 16S rDNA sequence of SAB revealed that bacteria belonging to the phyla Firmicutes, Proteobacteria, Actinobacteria and Bactereiodes were associated with AMF spore walls. PMID:27479250

  11. Fungal Diversity in a Dark Oligotrophic Volcanic Ecosystem (DOVE) on Mount Erebus, Antarctica

    PubMed Central

    Connell, Laurie; Staudigel, Hubert

    2013-01-01

    Fumarolic Ice caves on Antarctica’s Mt. Erebus contain a dark oligotrophic volcanic ecosystem (DOVE) and represent a deep biosphere habitat that can provide insight into microbial communities that utilize energy sources other than photosynthesis. The community assembly and role of fungi in these environments remains largely unknown. However, these habitats could be relatively easily contaminated during human visits. Sixty-one species of fungi were identified from soil clone libraries originating from Warren Cave, a DOVE on Mt. Erebus. The species diversity was greater than has been found in the nearby McMurdo Dry Valleys oligotrophic soil. A relatively large proportion of the clones represented Malassezia species (37% of Basidomycota identified). These fungi are associated with skin surfaces of animals and require high lipid content for growth, indicating that contamination may have occurred through the few and episodic human visits in this particular cave. These findings highlight the importance of fungi to DOVE environments as well as their potential use for identifying contamination by humans. The latter offers compelling evidence suggesting more strict management of these valuable research areas. PMID:24832809

  12. Penicillium arizonense, a new, genome sequenced fungal species, reveals a high chemical diversity in secreted metabolites

    PubMed Central

    Grijseels, Sietske; Nielsen, Jens Christian; Randelovic, Milica; Nielsen, Jens; Nielsen, Kristian Fog; Workman, Mhairi; Frisvad, Jens Christian

    2016-01-01

    A new soil-borne species belonging to the Penicillium section Canescentia is described, Penicillium arizonense sp. nov. (type strain CBS 141311T = IBT 12289T). The genome was sequenced and assembled into 33.7 Mb containing 12,502 predicted genes. A phylogenetic assessment based on marker genes confirmed the grouping of P. arizonense within section Canescentia. Compared to related species, P. arizonense proved to encode a high number of proteins involved in carbohydrate metabolism, in particular hemicellulases. Mining the genome for genes involved in secondary metabolite biosynthesis resulted in the identification of 62 putative biosynthetic gene clusters. Extracts of P. arizonense were analysed for secondary metabolites and austalides, pyripyropenes, tryptoquivalines, fumagillin, pseurotin A, curvulinic acid and xanthoepocin were detected. A comparative analysis against known pathways enabled the proposal of biosynthetic gene clusters in P. arizonense responsible for the synthesis of all detected compounds except curvulinic acid. The capacity to produce biomass degrading enzymes and the identification of a high chemical diversity in secreted bioactive secondary metabolites, offers a broad range of potential industrial applications for the new species P. arizonense. The description and availability of the genome sequence of P. arizonense, further provides the basis for biotechnological exploitation of this species. PMID:27739446

  13. Soil Microbial Functional and Fungal Diversity as Influenced by Municipal Sewage Sludge Accumulation

    PubMed Central

    Frąc, Magdalena; Oszust, Karolina; Lipiec, Jerzy; Jezierska-Tys, Stefania; Nwaichi, Eucharia Oluchi

    2014-01-01

    Safe disposal of municipal sewage sludge is a challenging global environmental concern. The aim of this study was to assess the response of soil microbial functional diversity to the accumulation of municipal sewage sludge during landfill storage. Soil samples of a municipal sewage sludge (SS) and from a sewage sludge landfill that was 3 m from a SS landfill (SS3) were analyzed relative to an undisturbed reference soil. Biolog EcoPlatesTM were inoculated with a soil suspension, and the Average Well Color Development (AWCD), Richness (R) and Shannon-Weaver index (H) were calculated to interpret the results. The fungi isolated from the sewage sludge were identified using comparative rDNA sequencing of the LSU D2 region. The MicroSEQ® ID software was used to assess the raw sequence files, perform sequence matching to the MicroSEQ® ID-validated reference database and create Neighbor-Joining trees. Moreover, the genera of fungi isolated from the soil were identified using microscopic methods. Municipal sewage sludge can serve as a habitat for plant pathogens and as a source of pathogen strains for biotechnological applications. PMID:25170681

  14. Soil microbial functional and fungal diversity as influenced by municipal sewage sludge accumulation.

    PubMed

    Frąc, Magdalena; Oszust, Karolina; Lipiec, Jerzy; Jezierska-Tys, Stefania; Nwaichi, Eucharia Oluchi

    2014-09-01

    Safe disposal of municipal sewage sludge is a challenging global environmental concern. The aim of this study was to assess the response of soil microbial functional diversity to the accumulation of municipal sewage sludge during landfill storage. Soil samples of a municipal sewage sludge (SS) and from a sewage sludge landfill that was 3 m from a SS landfill (SS3) were analyzed relative to an undisturbed reference soil. Biolog EcoPlatesTM were inoculated with a soil suspension, and the Average Well Color Development (AWCD), Richness (R) and Shannon-Weaver index (H) were calculated to interpret the results. The fungi isolated from the sewage sludge were identified using comparative rDNA sequencing of the LSU D2 region. The MicroSEQ® ID software was used to assess the raw sequence files, perform sequence matching to the MicroSEQ® ID-validated reference database and create Neighbor-Joining trees. Moreover, the genera of fungi isolated from the soil were identified using microscopic methods. Municipal sewage sludge can serve as a habitat for plant pathogens and as a source of pathogen strains for biotechnological applications. PMID:25170681

  15. Fungal compositions and diversities on indoor surfaces with visible mold growths in residential buildings in the Seoul Capital Area of South Korea.

    PubMed

    An, C; Yamamoto, N

    2016-10-01

    Indoor visible mold growths are known to be associated with allergies and respiratory illnesses. However, a question remains of their compositions and diversities. Using swab sampling and high-throughput DNA sequencing, this study analyzed taxonomic compositions and diversities of fungi on indoor surfaces laden with visible mold growths in residential apartments in South Korea. The sequencing results showed low species diversities with Shannon indices ranging from 0.14 to 2.29 (mean = 1.11). Several allergy-related genera were detected on the same surface, where the most abundant Cladosporium with a mean relative abundance of 41% co-occurred with less abundant Aspergillus (0.094%), Rhodotorula (6.3%), Cryptococcus (3.7%), Alternaria (4.1%), and Crivellia (17%). β diversity analyses showed significant differences in the fungal communities between enclosed balconies and other indoor areas (P < 0.05, ANOSIM), emphasizing a need to sample at multiple indoor locations when assessments are made for indoor visible mold growths. High-throughput sequencing is powerful in characterizing compositions and diversities of fungal communities. Future studies should examine the relationships between taxonomic compositions and diversities of indoor visible molds and health outcomes of allergies and respiratory illnesses in residential buildings.

  16. A Functionally Conserved Gene Regulatory Network Module Governing Olfactory Neuron Diversity

    PubMed Central

    Okuwa, Sumie; Maciejewski, Abigail; Brandt, Alicia T.; Reinhold, Dominik; Jones, Corbin D.; Volkan, Pelin Cayirlioglu

    2016-01-01

    Sensory neuron diversity is required for organisms to decipher complex environmental cues. In Drosophila, the olfactory environment is detected by 50 different olfactory receptor neuron (ORN) classes that are clustered in combinations within distinct sensilla subtypes. Each sensilla subtype houses stereotypically clustered 1–4 ORN identities that arise through asymmetric divisions from a single multipotent sensory organ precursor (SOP). How each class of SOPs acquires a unique differentiation potential that accounts for ORN diversity is unknown. Previously, we reported a critical component of SOP diversification program, Rotund (Rn), increases ORN diversity by generating novel developmental trajectories from existing precursors within each independent sensilla type lineages. Here, we show that Rn, along with BarH1/H2 (Bar), Bric-à-brac (Bab), Apterous (Ap) and Dachshund (Dac), constitutes a transcription factor (TF) network that patterns the developing olfactory tissue. This network was previously shown to pattern the segmentation of the leg, which suggests that this network is functionally conserved. In antennal imaginal discs, precursors with diverse ORN differentiation potentials are selected from concentric rings defined by unique combinations of these TFs along the proximodistal axis of the developing antennal disc. The combinatorial code that demarcates each precursor field is set up by cross-regulatory interactions among different factors within the network. Modifications of this network lead to predictable changes in the diversity of sensilla subtypes and ORN pools. In light of our data, we propose a molecular map that defines each unique SOP fate. Our results highlight the importance of the early prepatterning gene regulatory network as a modulator of SOP and terminally differentiated ORN diversity. Finally, our model illustrates how conserved developmental strategies are used to generate neuronal diversity. PMID:26765103

  17. A Functionally Conserved Gene Regulatory Network Module Governing Olfactory Neuron Diversity.

    PubMed

    Li, Qingyun; Barish, Scott; Okuwa, Sumie; Maciejewski, Abigail; Brandt, Alicia T; Reinhold, Dominik; Jones, Corbin D; Volkan, Pelin Cayirlioglu

    2016-01-01

    Sensory neuron diversity is required for organisms to decipher complex environmental cues. In Drosophila, the olfactory environment is detected by 50 different olfactory receptor neuron (ORN) classes that are clustered in combinations within distinct sensilla subtypes. Each sensilla subtype houses stereotypically clustered 1-4 ORN identities that arise through asymmetric divisions from a single multipotent sensory organ precursor (SOP). How each class of SOPs acquires a unique differentiation potential that accounts for ORN diversity is unknown. Previously, we reported a critical component of SOP diversification program, Rotund (Rn), increases ORN diversity by generating novel developmental trajectories from existing precursors within each independent sensilla type lineages. Here, we show that Rn, along with BarH1/H2 (Bar), Bric-à-brac (Bab), Apterous (Ap) and Dachshund (Dac), constitutes a transcription factor (TF) network that patterns the developing olfactory tissue. This network was previously shown to pattern the segmentation of the leg, which suggests that this network is functionally conserved. In antennal imaginal discs, precursors with diverse ORN differentiation potentials are selected from concentric rings defined by unique combinations of these TFs along the proximodistal axis of the developing antennal disc. The combinatorial code that demarcates each precursor field is set up by cross-regulatory interactions among different factors within the network. Modifications of this network lead to predictable changes in the diversity of sensilla subtypes and ORN pools. In light of our data, we propose a molecular map that defines each unique SOP fate. Our results highlight the importance of the early prepatterning gene regulatory network as a modulator of SOP and terminally differentiated ORN diversity. Finally, our model illustrates how conserved developmental strategies are used to generate neuronal diversity. PMID:26765103

  18. A Functionally Conserved Gene Regulatory Network Module Governing Olfactory Neuron Diversity.

    PubMed

    Li, Qingyun; Barish, Scott; Okuwa, Sumie; Maciejewski, Abigail; Brandt, Alicia T; Reinhold, Dominik; Jones, Corbin D; Volkan, Pelin Cayirlioglu

    2016-01-01

    Sensory neuron diversity is required for organisms to decipher complex environmental cues. In Drosophila, the olfactory environment is detected by 50 different olfactory receptor neuron (ORN) classes that are clustered in combinations within distinct sensilla subtypes. Each sensilla subtype houses stereotypically clustered 1-4 ORN identities that arise through asymmetric divisions from a single multipotent sensory organ precursor (SOP). How each class of SOPs acquires a unique differentiation potential that accounts for ORN diversity is unknown. Previously, we reported a critical component of SOP diversification program, Rotund (Rn), increases ORN diversity by generating novel developmental trajectories from existing precursors within each independent sensilla type lineages. Here, we show that Rn, along with BarH1/H2 (Bar), Bric-à-brac (Bab), Apterous (Ap) and Dachshund (Dac), constitutes a transcription factor (TF) network that patterns the developing olfactory tissue. This network was previously shown to pattern the segmentation of the leg, which suggests that this network is functionally conserved. In antennal imaginal discs, precursors with diverse ORN differentiation potentials are selected from concentric rings defined by unique combinations of these TFs along the proximodistal axis of the developing antennal disc. The combinatorial code that demarcates each precursor field is set up by cross-regulatory interactions among different factors within the network. Modifications of this network lead to predictable changes in the diversity of sensilla subtypes and ORN pools. In light of our data, we propose a molecular map that defines each unique SOP fate. Our results highlight the importance of the early prepatterning gene regulatory network as a modulator of SOP and terminally differentiated ORN diversity. Finally, our model illustrates how conserved developmental strategies are used to generate neuronal diversity.

  19. Ranking Mammal Species for Conservation and the Loss of Both Phylogenetic and Trait Diversity

    PubMed Central

    Redding, David W.; Mooers, Arne O.

    2015-01-01

    The 'edge of existence' (EDGE) prioritisation scheme is a new approach to rank species for conservation attention that aims to identify species that are both isolated on the tree of life and at imminent risk of extinction as defined by the World Conservation Union (IUCN). The self-stated benefit of the EDGE system is that it effectively captures unusual 'unique' species, and doing so will preserve the total evolutionary history of a group into the future. Given the EDGE metric was not designed to capture total evolutionary history, we tested this claim. Our analyses show that the total evolutionary history of mammals preserved is indeed much higher if EDGE species are protected than if at-risk species are chosen randomly. More of the total tree is also protected by EDGE species than if solely threat status or solely evolutionary distinctiveness were used for prioritisation. When considering how much trait diversity is captured by IUCN and EDGE prioritisation rankings, interestingly, preserving the highest-ranked EDGE species, or indeed just the most threatened species, captures more total trait diversity compared to sets of randomly-selected at-risk species. These results suggest that, as advertised, EDGE mammal species contribute evolutionary history to the evolutionary tree of mammals non-randomly, and EDGE-style rankings among endangered species can also capture important trait diversity. If this pattern holds for other groups, the EDGE prioritisation scheme has greater potential to be an efficient method to allocate scarce conservation effort. PMID:26630179

  20. Ranking Mammal Species for Conservation and the Loss of Both Phylogenetic and Trait Diversity.

    PubMed

    Redding, David W; Mooers, Arne O

    2015-01-01

    The 'edge of existence' (EDGE) prioritisation scheme is a new approach to rank species for conservation attention that aims to identify species that are both isolated on the tree of life and at imminent risk of extinction as defined by the World Conservation Union (IUCN). The self-stated benefit of the EDGE system is that it effectively captures unusual 'unique' species, and doing so will preserve the total evolutionary history of a group into the future. Given the EDGE metric was not designed to capture total evolutionary history, we tested this claim. Our analyses show that the total evolutionary history of mammals preserved is indeed much higher if EDGE species are protected than if at-risk species are chosen randomly. More of the total tree is also protected by EDGE species than if solely threat status or solely evolutionary distinctiveness were used for prioritisation. When considering how much trait diversity is captured by IUCN and EDGE prioritisation rankings, interestingly, preserving the highest-ranked EDGE species, or indeed just the most threatened species, captures more total trait diversity compared to sets of randomly-selected at-risk species. These results suggest that, as advertised, EDGE mammal species contribute evolutionary history to the evolutionary tree of mammals non-randomly, and EDGE-style rankings among endangered species can also capture important trait diversity. If this pattern holds for other groups, the EDGE prioritisation scheme has greater potential to be an efficient method to allocate scarce conservation effort.

  1. The alternate role of direct and environmental transmission in fungal infectious disease in wildlife: threats for biodiversity conservation.

    PubMed

    Al-Shorbaji, Farah N; Gozlan, Rodolphe E; Roche, Benjamin; Britton, J Robert; Andreou, Demetra

    2015-05-20

    Emerging fungal pathogens have substantial consequences for infected hosts, as revealed by the global decline of amphibian species from the chytrid fungus. According to the "curse of the Pharaoh" hypothesis, free-living infectious stages typical of fungal pathogens lengthen the timespan of transmission. Free-living infectious stages whose lifespan exceeds the infection time of their hosts are not constrained by virulence, enabling them to persist at high levels and continue transmitting to further sensitive hosts. Using the only Mesomycetozoea fungal species that can be cultured, Sphaerothecum destruens, we obtained tractable data on infectivity and pathogen life cycle for the first time. Here, based on the outcomes of a set of infectious trials and combined with an epidemiological model, we show a high level of dependence on direct transmission in crowded, confined environments and establish that incubation rate and length of infection dictate the epidemic dynamics of fungal disease. The spread of Mesomycetozoea in the wild raise ecological concerns for a range of susceptible species including birds, amphibians and mammals. Our results shed light on the risks associated with farming conditions and highlight the additional risk posed by invasive species that are highly abundant and can act as infectious reservoir hosts.

  2. The alternate role of direct and environmental transmission in fungal infectious disease in wildlife: threats for biodiversity conservation.

    PubMed

    Al-Shorbaji, Farah N; Gozlan, Rodolphe E; Roche, Benjamin; Britton, J Robert; Andreou, Demetra

    2015-01-01

    Emerging fungal pathogens have substantial consequences for infected hosts, as revealed by the global decline of amphibian species from the chytrid fungus. According to the "curse of the Pharaoh" hypothesis, free-living infectious stages typical of fungal pathogens lengthen the timespan of transmission. Free-living infectious stages whose lifespan exceeds the infection time of their hosts are not constrained by virulence, enabling them to persist at high levels and continue transmitting to further sensitive hosts. Using the only Mesomycetozoea fungal species that can be cultured, Sphaerothecum destruens, we obtained tractable data on infectivity and pathogen life cycle for the first time. Here, based on the outcomes of a set of infectious trials and combined with an epidemiological model, we show a high level of dependence on direct transmission in crowded, confined environments and establish that incubation rate and length of infection dictate the epidemic dynamics of fungal disease. The spread of Mesomycetozoea in the wild raise ecological concerns for a range of susceptible species including birds, amphibians and mammals. Our results shed light on the risks associated with farming conditions and highlight the additional risk posed by invasive species that are highly abundant and can act as infectious reservoir hosts. PMID:25992836

  3. The alternate role of direct and environmental transmission in fungal infectious disease in wildlife: threats for biodiversity conservation

    PubMed Central

    Al-Shorbaji, Farah N.; Gozlan, Rodolphe E.; Roche, Benjamin; Robert Britton, J.; Andreou, Demetra

    2015-01-01

    Emerging fungal pathogens have substantial consequences for infected hosts, as revealed by the global decline of amphibian species from the chytrid fungus. According to the “curse of the Pharaoh” hypothesis, free-living infectious stages typical of fungal pathogens lengthen the timespan of transmission. Free-living infectious stages whose lifespan exceeds the infection time of their hosts are not constrained by virulence, enabling them to persist at high levels and continue transmitting to further sensitive hosts. Using the only Mesomycetozoea fungal species that can be cultured, Sphaerothecum destruens, we obtained tractable data on infectivity and pathogen life cycle for the first time. Here, based on the outcomes of a set of infectious trials and combined with an epidemiological model, we show a high level of dependence on direct transmission in crowded, confined environments and establish that incubation rate and length of infection dictate the epidemic dynamics of fungal disease. The spread of Mesomycetozoea in the wild raise ecological concerns for a range of susceptible species including birds, amphibians and mammals. Our results shed light on the risks associated with farming conditions and highlight the additional risk posed by invasive species that are highly abundant and can act as infectious reservoir hosts. PMID:25992836

  4. Broadly Conserved Fungal Effector BEC1019 Suppresses Host Cell Death and Enhances Pathogen Virulence in Powdery Mildew of Barley (Hordeum vulgare L.).

    PubMed

    Whigham, Ehren; Qi, Shan; Mistry, Divya; Surana, Priyanka; Xu, Ruo; Fuerst, Gregory; Pliego, Clara; Bindschedler, Laurence V; Spanu, Pietro D; Dickerson, Julie A; Innes, Roger W; Nettleton, Dan; Bogdanove, Adam J; Wise, Roger P

    2015-09-01

    The interaction of barley, Hordeum vulgare L., with the powdery mildew fungus Blumeria graminis f. sp. hordei is a well-developed model to investigate resistance and susceptibility to obligate biotrophic pathogens. The 130-Mb Blumeria genome encodes approximately 540 predicted effectors that are hypothesized to suppress or induce host processes to promote colonization. Blumeria effector candidate (BEC)1019, a single-copy gene encoding a putative, secreted metalloprotease, is expressed in haustorial feeding structures, and host-induced gene silencing of BEC1019 restricts haustorial development in compatible interactions. Here, we show that Barley stripe mosaic virus-induced gene silencing of BEC1019 significantly reduces fungal colonization of barley epidermal cells, demonstrating that BEC1019 plays a central role in virulence. In addition, delivery of BEC1019 to the host cytoplasm via Xanthomonas type III secretion suppresses cultivar nonspecific hypersensitive reaction (HR) induced by Xanthomonas oryzae pv. oryzicola, as well as cultivar-specific HR induced by AvrPphB from Pseudomonas syringae pv. phaseolicola. BEC1019 homologs are present in 96 of 241 sequenced fungal genomes, including plant pathogens, human pathogens, and free-living nonpathogens. Comparative analysis revealed variation at several amino acid positions that correlate with fungal lifestyle and several highly conserved, noncorrelated motifs. Site-directed mutagenesis of one of these, ETVIC, compromises the HR-suppressing activity of BEC1019. We postulate that BEC1019 represents an ancient, broadly important fungal protein family, members of which have evolved to function as effectors in plant and animal hosts. PMID:25938194

  5. Genetic diversity in Napier grass (Pennisetum purpureum) cultivars: implications for breeding and conservation.

    PubMed

    Wanjala, Bramwel W; Obonyo, Meshack; Wachira, Francis N; Muchugi, Alice; Mulaa, Margaret; Harvey, Jagger; Skilton, Robert A; Proud, Janice; Hanson, Jean

    2013-01-01

    Napier grass is an important forage crop for dairy production in the tropics; as such, its existing genetic diversity needs to be assessed for conservation. The current study assessed the genetic variation of Napier grass collections from selected regions in Eastern Africa and the International Livestock Research Institute Forage Germplasm-Ethiopia. The diversity of 281 cultivars was investigated using five selective amplified fragment length polymorphism (AFLP) markers and classical population genetic parameters analysed using various software. The number of bands generated was 216 with fragments per primer set ranging from 50 to 115. Mean percentage polymorphic loci was 63.40. Genetic diversity coefficients based on Nei's genetic diversity ranged from 0.0783 to 0.2142 and Shannon's information index ranged from 0.1293 to 0.3445. The Fst value obtained was moderately significant (Fst = 0.1688). Neighbour-joining analysis gave two distinct clusters which did not reflect geographical locations. Analysis of molecular variance showed all variance components to be highly significant (P < 0.001), indicating more variation within (91 %) than between populations (9 %). Results suggested moderate genetic differentiation among Napier grass populations sampled, which could imply a high germplasm exchange within the region. The AFLP markers used in this study efficiently discriminate among cultivars and could be useful in identification and germplasm conservation.

  6. [Butterfly species diversity and its conservation in Wuyunjie National Nature Reserve, Hunan Province of China].

    PubMed

    Li, Mi; Zhou, Hong-Chun; Tan, Ji-Cai; Wang, Peng; Liu, Guo-Hua

    2011-06-01

    By using line-transect method, an investigation was conducted on the species diversity of butterfly in Wuyunjie National Nature Reserve, Changde City of Hunan Province from June 2008 to September 2010. Aiming at the main factors including plant species richness (D) , mean elevation (E) , average distance from stream/river (F), and human interference level (K) that affecting the species richness of butterfly in 31 segment-level transects in 4 line-transects, multiple regression analysis was made, and the diversity and similarity of the butterfly communities in the experimental zone, buffer zone, and core zone of the Reserve were compared. A total of 147 butterfly species were collected, belonging to 94 genera and 10 families, among which, 4 species was nationally conserved species. Multiple regression analysis showed that D, E, and K were the three most major factors affecting the distribution of butterfly. The species richness of butterfly had significant positive correlation with D (P < 0.01), and negative correlations with E and K (P < 0.05). The species diversity and evenness index of butterfly were higher in core zone than in experimental zone and buffer zone, dominance index was the highest in experimental zone, and a higher similarity index (0.526) was observed between buffer zone and core zone. To conserve the species diversity of butterfly in the Reserve, efforts should be made to protect the plant species richness, keep the natural forest succession, decrease the human interference properly, and tighten up the management of butterfly habitat.

  7. [Butterfly species diversity and its conservation in Wuyunjie National Nature Reserve, Hunan Province of China].

    PubMed

    Li, Mi; Zhou, Hong-Chun; Tan, Ji-Cai; Wang, Peng; Liu, Guo-Hua

    2011-06-01

    By using line-transect method, an investigation was conducted on the species diversity of butterfly in Wuyunjie National Nature Reserve, Changde City of Hunan Province from June 2008 to September 2010. Aiming at the main factors including plant species richness (D) , mean elevation (E) , average distance from stream/river (F), and human interference level (K) that affecting the species richness of butterfly in 31 segment-level transects in 4 line-transects, multiple regression analysis was made, and the diversity and similarity of the butterfly communities in the experimental zone, buffer zone, and core zone of the Reserve were compared. A total of 147 butterfly species were collected, belonging to 94 genera and 10 families, among which, 4 species was nationally conserved species. Multiple regression analysis showed that D, E, and K were the three most major factors affecting the distribution of butterfly. The species richness of butterfly had significant positive correlation with D (P < 0.01), and negative correlations with E and K (P < 0.05). The species diversity and evenness index of butterfly were higher in core zone than in experimental zone and buffer zone, dominance index was the highest in experimental zone, and a higher similarity index (0.526) was observed between buffer zone and core zone. To conserve the species diversity of butterfly in the Reserve, efforts should be made to protect the plant species richness, keep the natural forest succession, decrease the human interference properly, and tighten up the management of butterfly habitat. PMID:21941763

  8. Genetic diversity in Napier grass (Pennisetum purpureum) cultivars: implications for breeding and conservation

    PubMed Central

    Wanjala, Bramwel W.; Obonyo, Meshack; Wachira, Francis N.; Muchugi, Alice; Mulaa, Margaret; Harvey, Jagger; Skilton, Robert A.; Proud, Janice; Hanson, Jean

    2013-01-01

    Napier grass is an important forage crop for dairy production in the tropics; as such, its existing genetic diversity needs to be assessed for conservation. The current study assessed the genetic variation of Napier grass collections from selected regions in Eastern Africa and the International Livestock Research Institute Forage Germplasm-Ethiopia. The diversity of 281 cultivars was investigated using five selective amplified fragment length polymorphism (AFLP) markers and classical population genetic parameters analysed using various software. The number of bands generated was 216 with fragments per primer set ranging from 50 to 115. Mean percentage polymorphic loci was 63.40. Genetic diversity coefficients based on Nei's genetic diversity ranged from 0.0783 to 0.2142 and Shannon's information index ranged from 0.1293 to 0.3445. The Fst value obtained was moderately significant (Fst = 0.1688). Neighbour-joining analysis gave two distinct clusters which did not reflect geographical locations. Analysis of molecular variance showed all variance components to be highly significant (P < 0.001), indicating more variation within (91 %) than between populations (9 %). Results suggested moderate genetic differentiation among Napier grass populations sampled, which could imply a high germplasm exchange within the region. The AFLP markers used in this study efficiently discriminate among cultivars and could be useful in identification and germplasm conservation. PMID:23671788

  9. Conservation of eelgrass (Zostera marina) genetic diversity in a mesocosm-based restoration experiment.

    PubMed

    Ort, Brian S; Cohen, C Sarah; Boyer, Katharyn E; Reynolds, Laura K; Tam, Sheh May; Wyllie-Echeverria, Sandy

    2014-01-01

    Eelgrass (Zostera marina) forms the foundation of an important shallow coastal community in protected estuaries and bays. Widespread population declines have stimulated restoration efforts, but these have often overlooked the importance of maintaining the evolutionary potential of restored populations by minimizing the reduction in genetic diversity that typically accompanies restoration. In an experiment simulating a small-scale restoration, we tested the effectiveness of a buoy-deployed seeding technique to maintain genetic diversity comparable to the seed source populations. Seeds from three extant source populations in San Francisco Bay were introduced into eighteen flow-through baywater mesocosms. Following seedling establishment, we used seven polymorphic microsatellite loci to compare genetic diversity indices from 128 shoots to those found in the source populations. Importantly, allelic richness and expected heterozygosity were not significantly reduced in the mesocosms, which also preserved the strong population differentiation present among source populations. However, the inbreeding coefficient F IS was elevated in two of the three sets of mesocosms when they were grouped according to their source population. This is probably a Wahlund effect from confining all half-siblings within each spathe to a single mesocosm, elevating F IS when the mesocosms were considered together. The conservation of most alleles and preservation of expected heterozygosity suggests that this seeding technique is an improvement over whole-shoot transplantation in the conservation of genetic diversity in eelgrass restoration efforts.

  10. Genetic diversity in Napier grass (Pennisetum purpureum) cultivars: implications for breeding and conservation.

    PubMed

    Wanjala, Bramwel W; Obonyo, Meshack; Wachira, Francis N; Muchugi, Alice; Mulaa, Margaret; Harvey, Jagger; Skilton, Robert A; Proud, Janice; Hanson, Jean

    2013-01-01

    Napier grass is an important forage crop for dairy production in the tropics; as such, its existing genetic diversity needs to be assessed for conservation. The current study assessed the genetic variation of Napier grass collections from selected regions in Eastern Africa and the International Livestock Research Institute Forage Germplasm-Ethiopia. The diversity of 281 cultivars was investigated using five selective amplified fragment length polymorphism (AFLP) markers and classical population genetic parameters analysed using various software. The number of bands generated was 216 with fragments per primer set ranging from 50 to 115. Mean percentage polymorphic loci was 63.40. Genetic diversity coefficients based on Nei's genetic diversity ranged from 0.0783 to 0.2142 and Shannon's information index ranged from 0.1293 to 0.3445. The Fst value obtained was moderately significant (Fst = 0.1688). Neighbour-joining analysis gave two distinct clusters which did not reflect geographical locations. Analysis of molecular variance showed all variance components to be highly significant (P < 0.001), indicating more variation within (91 %) than between populations (9 %). Results suggested moderate genetic differentiation among Napier grass populations sampled, which could imply a high germplasm exchange within the region. The AFLP markers used in this study efficiently discriminate among cultivars and could be useful in identification and germplasm conservation. PMID:23671788

  11. Conservation tillage affects species composition but not species diversity: a comparative study in Northern Italy.

    PubMed

    Boscutti, Francesco; Sigura, Maurizia; Gambon, Nadia; Lagazio, Corrado; Krüsi, Bertil O; Bonfanti, Pierluigi

    2015-02-01

    Conservation tillage (CT) is widely considered to be a practice aimed at preserving several ecosystem functions. In the literature, however, there seems to be no clear pattern with regard to its benefits on species diversity and species composition. In Northern Italy, we compared species composition and diversity of both vascular plants and Carabids under two contrasting tillage systems, i.e., CT and conventional tillage, respectively. We hypothesized a significant positive impact of CT on both species diversity and composition. We also considered the potential influence of crop type. The tillage systems were studied under open field conditions with three types of annual crops (i.e., maize, soybean, and winter cereals), using a split-plot design on pairs of adjacent fields. Linear mixed models were applied to test tillage system, crop, and interaction effects on diversity indices. Plant and Carabids communities were analyzed by multivariate methods (CCA). On the whole, 136 plant and 51 carabid taxa were recorded. The two tillage systems studied did not differ in floristic or carabid diversity. Species composition, by contrast, proved to be characteristic for each combination of tillage system and crop type. In particular, CT fields were characterized by nutrient demanding weeds and the associated Carabids. The differences were especially pronounced in fields with winter cereals. The same was true for the flora and Carabids along the field boundaries. For studying the effects of CT practices on the sustainability of agro-ecosystems, therefore, the focus should be on species composition rather than on diversity measures.

  12. Conservation Tillage Affects Species Composition But Not Species Diversity: A Comparative Study in Northern Italy

    NASA Astrophysics Data System (ADS)

    Boscutti, Francesco; Sigura, Maurizia; Gambon, Nadia; Lagazio, Corrado; Krüsi, Bertil O.; Bonfanti, Pierluigi

    2015-02-01

    Conservation tillage (CT) is widely considered to be a practice aimed at preserving several ecosystem functions. In the literature, however, there seems to be no clear pattern with regard to its benefits on species diversity and species composition. In Northern Italy, we compared species composition and diversity of both vascular plants and Carabids under two contrasting tillage systems, i.e., CT and conventional tillage, respectively. We hypothesized a significant positive impact of CT on both species diversity and composition. We also considered the potential influence of crop type. The tillage systems were studied under open field conditions with three types of annual crops (i.e., maize, soybean, and winter cereals), using a split-plot design on pairs of adjacent fields. Linear mixed models were applied to test tillage system, crop, and interaction effects on diversity indices. Plant and Carabids communities were analyzed by multivariate methods (CCA). On the whole, 136 plant and 51 carabid taxa were recorded. The two tillage systems studied did not differ in floristic or carabid diversity. Species composition, by contrast, proved to be characteristic for each combination of tillage system and crop type. In particular, CT fields were characterized by nutrient demanding weeds and the associated Carabids. The differences were especially pronounced in fields with winter cereals. The same was true for the flora and Carabids along the field boundaries. For studying the effects of CT practices on the sustainability of agro-ecosystems, therefore, the focus should be on species composition rather than on diversity measures.

  13. Habitat fragmentation is associated to gut microbiota diversity of an endangered primate: implications for conservation.

    PubMed

    Barelli, Claudia; Albanese, Davide; Donati, Claudio; Pindo, Massimo; Dallago, Chiara; Rovero, Francesco; Cavalieri, Duccio; Tuohy, Kieran Michael; Hauffe, Heidi Christine; De Filippo, Carlotta

    2015-01-01

    The expansion of agriculture is shrinking pristine forest areas worldwide, jeopardizing the persistence of their wild inhabitants. The Udzungwa red colobus monkey (Procolobus gordonorum) is among the most threatened primate species in Africa. Primarily arboreal and highly sensitive to hunting and habitat destruction, they provide a critical model to understanding whether anthropogenic disturbance impacts gut microbiota diversity. We sampled seven social groups inhabiting two forests (disturbed vs. undisturbed) in the Udzungwa Mountains of Tanzania. While Ruminococcaceae and Lachnospiraceae dominated in all individuals, reflecting their role in extracting energy from folivorous diets, analysis of genus composition showed a marked diversification across habitats, with gut microbiota α-diversity significantly higher in the undisturbed forest. Functional analysis suggests that such variation may be associated with food plant diversity in natural versus human-modified habitats, requiring metabolic pathways to digest xenobiotics. Thus, the effects of changes in gut microbiota should not be ignored to conserve endangered populations. PMID:26445280

  14. Habitat fragmentation is associated to gut microbiota diversity of an endangered primate: implications for conservation

    PubMed Central

    Barelli, Claudia; Albanese, Davide; Donati, Claudio; Pindo, Massimo; Dallago, Chiara; Rovero, Francesco; Cavalieri, Duccio; Michael Tuohy, Kieran; Christine Hauffe, Heidi; De Filippo, Carlotta

    2015-01-01

    The expansion of agriculture is shrinking pristine forest areas worldwide, jeopardizing the persistence of their wild inhabitants. The Udzungwa red colobus monkey (Procolobus gordonorum) is among the most threatened primate species in Africa. Primarily arboreal and highly sensitive to hunting and habitat destruction, they provide a critical model to understanding whether anthropogenic disturbance impacts gut microbiota diversity. We sampled seven social groups inhabiting two forests (disturbed vs. undisturbed) in the Udzungwa Mountains of Tanzania. While Ruminococcaceae and Lachnospiraceae dominated in all individuals, reflecting their role in extracting energy from folivorous diets, analysis of genus composition showed a marked diversification across habitats, with gut microbiota α-diversity significantly higher in the undisturbed forest. Functional analysis suggests that such variation may be associated with food plant diversity in natural versus human-modified habitats, requiring metabolic pathways to digest xenobiotics. Thus, the effects of changes in gut microbiota should not be ignored to conserve endangered populations. PMID:26445280

  15. Habitat fragmentation is associated to gut microbiota diversity of an endangered primate: implications for conservation.

    PubMed

    Barelli, Claudia; Albanese, Davide; Donati, Claudio; Pindo, Massimo; Dallago, Chiara; Rovero, Francesco; Cavalieri, Duccio; Tuohy, Kieran Michael; Hauffe, Heidi Christine; De Filippo, Carlotta

    2015-10-07

    The expansion of agriculture is shrinking pristine forest areas worldwide, jeopardizing the persistence of their wild inhabitants. The Udzungwa red colobus monkey (Procolobus gordonorum) is among the most threatened primate species in Africa. Primarily arboreal and highly sensitive to hunting and habitat destruction, they provide a critical model to understanding whether anthropogenic disturbance impacts gut microbiota diversity. We sampled seven social groups inhabiting two forests (disturbed vs. undisturbed) in the Udzungwa Mountains of Tanzania. While Ruminococcaceae and Lachnospiraceae dominated in all individuals, reflecting their role in extracting energy from folivorous diets, analysis of genus composition showed a marked diversification across habitats, with gut microbiota α-diversity significantly higher in the undisturbed forest. Functional analysis suggests that such variation may be associated with food plant diversity in natural versus human-modified habitats, requiring metabolic pathways to digest xenobiotics. Thus, the effects of changes in gut microbiota should not be ignored to conserve endangered populations.

  16. Marine fungal diversity: a comparison of natural and created salt marshes of the north-central Gulf of Mexico.

    PubMed

    Walker, Allison K; Campbell, Jinx

    2010-01-01

    Marine fungal communities of created salt marshes of differing ages were compared with those of two reference natural salt marshes. Marine fungi occurring on the lower 30 cm of salt marsh plants Spartina alterniflora and Juncus roemerianus were inventoried with morphological and molecular methods (ITS T-RFLP analysis) to determine fungal species richness, relative frequency of occurrence and ascomata density. The resulting profiles revealed similar fungal communities in natural salt marshes and created salt marshes 3 y old and older with a 1.5 y old created marsh showing less fungal colonization. A 26 y old created salt marsh consistently exhibited the highest fungal species richness. Ascomata density of the dominant fungal species on each host was significantly higher in natural marshes than in created marshes at all three sampling dates. This study indicates marine fungal saprotroph communities are present in these manmade coastal salt marshes as early as 1 y after marsh creation. The lower regions of both plant hosts were dominated by a small number of marine ascomycete species consistent with those species previously reported from salt marshes of the East Coast of USA. PMID:20524584

  17. Marine fungal diversity: a comparison of natural and created salt marshes of the north-central Gulf of Mexico.

    PubMed

    Walker, Allison K; Campbell, Jinx

    2010-01-01

    Marine fungal communities of created salt marshes of differing ages were compared with those of two reference natural salt marshes. Marine fungi occurring on the lower 30 cm of salt marsh plants Spartina alterniflora and Juncus roemerianus were inventoried with morphological and molecular methods (ITS T-RFLP analysis) to determine fungal species richness, relative frequency of occurrence and ascomata density. The resulting profiles revealed similar fungal communities in natural salt marshes and created salt marshes 3 y old and older with a 1.5 y old created marsh showing less fungal colonization. A 26 y old created salt marsh consistently exhibited the highest fungal species richness. Ascomata density of the dominant fungal species on each host was significantly higher in natural marshes than in created marshes at all three sampling dates. This study indicates marine fungal saprotroph communities are present in these manmade coastal salt marshes as early as 1 y after marsh creation. The lower regions of both plant hosts were dominated by a small number of marine ascomycete species consistent with those species previously reported from salt marshes of the East Coast of USA.

  18. Microbial Pathogens in the Fungal Kingdom

    PubMed Central

    Heitman, Joseph

    2011-01-01

    The fungal kingdom is vast, spanning ~1.5 to as many as 5 million species diverse as unicellular yeasts, filamentous fungi, mushrooms, lichens, and both plant and animal pathogens. The fungi are closely aligned with animals in one of the six to eight supergroups of eukaryotes, the opisthokonts. The animal and fungal kingdoms last shared a common ancestor ~1 billion years ago, more recently than other groups of eukaryotes. As a consequence of their close evolutionary history and shared cellular machinery with metazoans, fungi are exceptional models for mammalian biology, but prove more difficult to treat in infected animals. The last common ancestor to the fungal/metazoan lineages is thought to have been unicellular, aquatic, and motile with a posterior flagellum, and certain extant species closely resemble this hypothesized ancestor. Species within the fungal kingdom were traditionally assigned to four phyla, including the basal fungi (Chytridiomycota, Zygomycota) and the more recently derived monophyletic lineage, the dikarya (Ascomycota, Basidiomycota). The fungal tree of life project has revealed that the basal lineages are polyphyletic, and thus there are as many as eight to ten fungal phyla. Fungi that infect vertebrates are found in all of the major lineages, and virulence arose multiple times independently. A sobering recent development involves the species Batrachochytrium dendrobatidis from the basal fungal phylum, the Chytridiomycota, which has emerged to cause global amphibian declines and extinctions. Genomics is revolutionizing our view of the fungal kingdom, and genome sequences for zygomycete pathogens (Rhizopus, Mucor), skin-associated fungi (dermatophytes, Malassezia), and the Candida pathogenic species clade promise to provide insights into the origins of virulence. Here we survey the diversity of fungal pathogens and illustrate key principles revealed by genomics involving sexual reproduction and sex determination, loss of conserved pathways in

  19. Fungal Diagnostics

    PubMed Central

    Kozel, Thomas R.; Wickes, Brian

    2014-01-01

    Early diagnosis of fungal infection is critical to effective treatment. There are many impediments to diagnosis such as a diminishing number of clinical mycologists, cost, time to result, and requirements for sensitivity and specificity. In addition, fungal diagnostics must meet the contrasting needs presented by the increasing diversity of fungi found in association with the use of immunosuppressive agents in countries with high levels of medical care and the need for diagnostics in resource-limited countries where large numbers of opportunistic infections occur in patients with AIDS. Traditional approaches to diagnosis include direct microscopic examination of clinical samples, histopathology, culture, and serology. Emerging technologies include molecular diagnostics and antigen detection in clinical samples. Innovative new technologies that use molecular and immunoassay platforms have the potential to meet the needs of both resource-rich and resource-limited clinical environments. PMID:24692193

  20. Genetic Diversity and Population Structure of Mesoamerican Jaguars (Panthera onca): Implications for Conservation and Management

    PubMed Central

    Wultsch, Claudia; Caragiulo, Anthony; Dias-Freedman, Isabela; Quigley, Howard; Rabinowitz, Salisa; Amato, George

    2016-01-01

    Mesoamerican jaguars (Panthera onca) have been extirpated from over 77% of their historic range, inhabiting fragmented landscapes at potentially reduced population sizes. Maintaining and restoring genetic diversity and connectivity across human-altered landscapes has become a major conservation priority; nonetheless large-scale genetic monitoring of natural populations is rare. This is the first regional conservation genetic study of jaguars to primarily use fecal samples collected in the wild across five Mesoamerican countries: Belize, Costa Rica, Guatemala, Honduras, and Mexico. We genotyped 445 jaguar fecal samples and examined patterns of genetic diversity and connectivity among 115 individual jaguars using data from 12 microsatellite loci. Overall, moderate levels of genetic variation were detected (NA = 4.50 ± 1.05, AR = 3.43 ± 0.22, HE = 0.59 ± 0.04), with Mexico having the lowest genetic diversity, followed by Honduras, Guatemala, Belize, and Costa Rica. Population-based gene flow measures (FST = 0.09 to 0.15, Dest = 0.09 to 0.21), principal component analysis, and Bayesian clustering applied in a hierarchical framework revealed significant genetic structure in Mesoamerican jaguars, roughly grouping individuals into four genetic clusters with varying levels of admixture. Gene flow was highest among Selva Maya jaguars (northern Guatemala and central Belize), whereas genetic differentiation among all other sampling sites was moderate. Genetic subdivision was most pronounced between Selva Maya and Honduran jaguars, suggesting limited jaguar movement between these close geographic regions and ultimately refuting the hypothesis of contemporary panmixia. To maintain a critical linkage for jaguars dispersing through the Mesoamerican landscape and ensure long-term viability of this near threatened species, we recommend continued management and maintenance of jaguar corridors. The baseline genetic data provided by this study underscores the importance of

  1. Evolution and Phylogenetic Diversity of Yam Species (Dioscorea spp.): Implication for Conservation and Agricultural Practices.

    PubMed

    Ngo Ngwe, Marie Florence Sandrine; Omokolo, Denis Ndoumou; Joly, Simon

    2015-01-01

    Yams (Dioscorea spp.) consist of approximately 600 species. Presently, these species are threatened by genetic erosion due to many factors such as pest attacks and farming practices. In parallel, complex taxonomic boundaries in this genus makes it more challenging to properly address the genetic diversity of yam and manage its germplasm. As a first step toward evaluating and preserving the genetic diversity yam species, we use a phylogenetic diversity (PD) approach that has the advantage to investigate phylogenetic relationships and test hypotheses of species monophyly while alleviating to the problem of ploidy variation within and among species. The Bayesian phylogenetic analysis of 62 accessions from 7 species from three regions of Cameroon showed that most Dioscorea sections were monophyletic, but species within sections were generally non-monophyletic. The wild species D. praehensilis and cultivated D. cayenensis were the species with the highest PD. At the opposite, D. esculenta has a low PD and future studies should focus on this species to properly address its conservation status. We also show that wild species show a stronger genetic structure than cultivated species, which potentially reflects the management of the yam germplasm by farmers. These findings show that phylogenetic diversity is a promising approach for an initial investigation of genetic diversity in a crop consisting of closely related species.

  2. Evolution and Phylogenetic Diversity of Yam Species (Dioscorea spp.): Implication for Conservation and Agricultural Practices

    PubMed Central

    Ngo Ngwe, Marie Florence Sandrine; Omokolo, Denis Ndoumou; Joly, Simon

    2015-01-01

    Yams (Dioscorea spp.) consist of approximately 600 species. Presently, these species are threatened by genetic erosion due to many factors such as pest attacks and farming practices. In parallel, complex taxonomic boundaries in this genus makes it more challenging to properly address the genetic diversity of yam and manage its germplasm. As a first step toward evaluating and preserving the genetic diversity yam species, we use a phylogenetic diversity (PD) approach that has the advantage to investigate phylogenetic relationships and test hypotheses of species monophyly while alleviating to the problem of ploidy variation within and among species. The Bayesian phylogenetic analysis of 62 accessions from 7 species from three regions of Cameroon showed that most Dioscorea sections were monophyletic, but species within sections were generally non-monophyletic. The wild species D. praehensilis and cultivated D. cayenensis were the species with the highest PD. At the opposite, D. esculenta has a low PD and future studies should focus on this species to properly address its conservation status. We also show that wild species show a stronger genetic structure than cultivated species, which potentially reflects the management of the yam germplasm by farmers. These findings show that phylogenetic diversity is a promising approach for an initial investigation of genetic diversity in a crop consisting of closely related species. PMID:26691919

  3. Prunus persica crop management as step toward AMF diversity conservation for the sustainable soil management

    NASA Astrophysics Data System (ADS)

    Alguacil, M. M.; Torrecillas, E.; Lozano, Z.; Garcia-Orenes, F.; Roldan, A.

    2012-04-01

    We investigated the diversity of arbuscular mycorrhizal fungi (AMF) in roots of Prunus persica under two fertilization treatments (CF: consisted of application of chicken manure (1400 kg.ha-1), urea (140 kg.ha-1), complex fertilizer 12-12-17/2 (280 kg.ha-1), and potassium sulfate (40 kg.ha-1) and IF: consisted of application of urea (140 kg.ha-1), complex fertilizer 12-12-17/2 (400 kg.ha-1) and potassium sulfate (70 kg.ha-1)) combined with integrated pest management (IM) or chemical pest management (CM), in a tropical agroecosystem in the north of Venezuela. Our goal was to ascertain how different fertilizers/pest management can modify the AMF diversity colonizing P. persica roots as an important step towards sustainable soil use and therefore protection of biodiversity. The AM fungal small-subunit (SSU) rRNA genes were subjected to PCR, cloning, sequencing and phylogenetic analyses. Twenty-one different phylotypes were identified, which were grouped in five families: Glomeraceae, Paraglomeraceae, Acaulosporaceae, Gigasporaceae and Archaeosporaceae. Sixteen of these sequence groups belonged to the genus Glomus, two to Paraglomus, one to Acaulospora, one to Scutellospora and one to Archaeospora. A different distribution of the AMF phylotypes as consequence of the difference between treatments was observed. Thus, the AMF communities of tree roots in the (IF+CM) treatment had the lowest diversity (H'=1.78) with the lowest total number of AMF sequence types (9). The trees from both (CF+IM) and (IF+IM) treatments had similar AMF diversity (H'?2.00); while the treatment (CF+CM) yielded the highest number of different AMF sequence types (17) and showed the highest diversity index (H'=2.69). In conclusion, the crop management including combination of organic and inorganic fertilization and chemical pest control appears to be the most suitable strategy with respect to reactivate the AMF diversity in the roots of this crop and thus, the agricultural and environmental

  4. Reptiles of Chubut province, Argentina: richness, diversity, conservation status and geographic distribution maps

    PubMed Central

    Minoli, Ignacio; Morando, Mariana; Avila, Luciano Javier

    2015-01-01

    Abstract An accurate estimation of species and population geographic ranges is essential for species-focused studies and conservation and management plans. Knowledge of the geographic distributions of reptiles from Patagonian Argentina is in general limited and dispersed over manuscripts from a wide variety of topics. We completed an extensive review of reptile species of central Patagonia (Argentina) based on information from a wide variety of sources. We compiled and checked geographic distribution records from published literature and museum records, including extensive new data from the LJAMM-CNP (CENPAT-CONICET) herpetological collection. Our results show that there are 52 taxa recorded for this region and the highest species richness was seen in the families Liolaemidae and Dipsadidae with 31 and 10 species, respectively. The Patagónica was the phytogeographic province most diverse in species and Phymaturus was the genus of conservation concern most strongly associated with it. We present a detailed species list with geographical information, richness species, diversity analyses with comparisons across phytogeographical provinces, conservation status, taxonomic comments and distribution maps for all of these taxa. PMID:25931966

  5. Diversity, endemism and conservation of the freshwater crabs of China (Brachyura: Potamidae and Gecarcinucidae).

    PubMed

    Cumberlidge, Neil; Ng, Peter K L; Yeo, Darren C J; Naruse, Tohru; Meyer, Kirstin S; Esser, Lara J

    2011-03-01

    China lies at the heart of the global center of freshwater crab diversity in tropical Asia, where the 2 most diverse families occur: Potamidae (505 species, 95 genera) and Gecarcinucidae (344 species, 59 genera). China stands out as the country with the highest species richness of freshwater crabs globally. Its fauna comprises 243 species in 37 genera and in 2 families, and species discovery is still progressing at a rapid pace. The vast majority of the species are distributed in southwest, south central and eastern China in the Oriental zoogeographical region. China also stands out as having a highly endemic freshwater crab fauna at the species level (96%) and at the genus level (78%). Although the recent International Union for the Conservation of Nature (IUCN) red list conservation assessment found only 6 out of 228 species (2%) to be threatened (5 potamids and 1 gecarcinucid), the majority (more than 75%) of Chinese species are regarded as data deficient, so the number of threatened species is likely to be a serious underestimate. Threats from increasing habitat destruction and pollution are a major concern due to the rapidly growing economy and massive developments taking place in China. There is therefore an urgent need for increased species exploration and for the development of a conservation strategy for China's threatened (and potentially threatened) endemic freshwater crab species.

  6. Diversity distribution patterns of Chinese endemic seed plant species and their implications for conservation planning

    PubMed Central

    Huang, Jihong; Huang, Jianhua; Lu, Xinghui; Ma, Keping

    2016-01-01

    Endemism is an important concept in biogeography and biodiversity conservation. China is one of the richest countries in biodiversity, with very high levels of plant endemism. In this study, we analysed the distribution patterns of diversity, the degree of differentiation, and the endemicity of Chinese endemic seed plants using the floristic unit as a basic spatial analysis unit and 11 indices. The analysis was based on distribution data of 24,951 native seed plant species (excluding subspecies and varieties) and 12,980 Chinese endemic seed plant species, which were sourced from both specimen records and published references. The distribution patterns of Chinese endemic flora were generally consistent but disproportionate across China for diversity, degree of differentiation and endemicity. The South Hengduan Mountains Subregion had the highest values for all indices. At the regional level, both the Hengduan Mountains and the Central China regions were highest in diversity and degrees of differentiation. However, both the rate of local endemic to native species and the rate of local to Chinese endemic species were highest in the Taiwan Region and the South Taiwan Region. The Hengduan Mountains Region and the Central China Region are two key conservation priority areas for Chinese endemic seed plants. PMID:27658845

  7. Predictive habitat suitability models to aid conservation of elasmobranch diversity in the central Mediterranean Sea.

    PubMed

    Lauria, V; Gristina, M; Attrill, M J; Fiorentino, F; Garofalo, G

    2015-08-14

    Commercial fisheries have dramatically impacted elasmobranch populations worldwide. With high capture and bycatch rates, the abundance of many species is rapidly declining and around a quarter of the world's sharks and rays are threatened with extinction. At a regional scale this negative trend has also been evidenced in the central Mediterranean Sea, where bottom-trawl fisheries have affected the biomass of certain rays (e.g. Raja clavata) and sharks (e.g. Mustelus spp.). Detailed knowledge of elasmobranch habitat requirements is essential for biodiversity conservation and fisheries management, but this is often hampered by a poor understanding of their spatial ecology. Habitat suitability models were used to investigate the habitat preference of nine elasmobranch species and their overall diversity (number of species) in relation to five environmental predictors (i.e. depth, sea surface temperature, surface salinity, slope and rugosity) in the central Mediterranean Sea. Results showed that depth, seafloor morphology and sea surface temperature were the main drivers for elasmobranch habitat suitability. Predictive distribution maps revealed different species-specific patterns of suitable habitat while high assemblage diversity was predicted in deeper offshore waters (400-800 m depth). This study helps to identify priority conservation areas and diversity hot-spots for rare and endangered elasmobranchs in the Mediterranean Sea.

  8. Predictive habitat suitability models to aid conservation of elasmobranch diversity in the central Mediterranean Sea

    PubMed Central

    Lauria, V.; Gristina, M.; Attrill, M. J.; Fiorentino, F.; Garofalo, G.

    2015-01-01

    Commercial fisheries have dramatically impacted elasmobranch populations worldwide. With high capture and bycatch rates, the abundance of many species is rapidly declining and around a quarter of the world’s sharks and rays are threatened with extinction. At a regional scale this negative trend has also been evidenced in the central Mediterranean Sea, where bottom-trawl fisheries have affected the biomass of certain rays (e.g. Raja clavata) and sharks (e.g. Mustelus spp.). Detailed knowledge of elasmobranch habitat requirements is essential for biodiversity conservation and fisheries management, but this is often hampered by a poor understanding of their spatial ecology. Habitat suitability models were used to investigate the habitat preference of nine elasmobranch species and their overall diversity (number of species) in relation to five environmental predictors (i.e. depth, sea surface temperature, surface salinity, slope and rugosity) in the central Mediterranean Sea. Results showed that depth, seafloor morphology and sea surface temperature were the main drivers for elasmobranch habitat suitability. Predictive distribution maps revealed different species-specific patterns of suitable habitat while high assemblage diversity was predicted in deeper offshore waters (400–800 m depth). This study helps to identify priority conservation areas and diversity hot-spots for rare and endangered elasmobranchs in the Mediterranean Sea. PMID:26272502

  9. Impacts of early viability selection on management of inbreeding and genetic diversity in conservation.

    PubMed

    Grueber, Catherine E; Hogg, Carolyn J; Ivy, Jamie A; Belov, Katherine

    2015-04-01

    Maintaining genetic diversity is a crucial goal of intensive management of threatened species, particularly for those populations that act as sources for translocation or re-introduction programmes. Most captive genetic management is based on pedigrees and a neutral theory of inheritance, an assumption that may be violated by selective forces operating in captivity. Here, we explore the conservation consequences of early viability selection: differential offspring survival that occurs prior to management or research observations, such as embryo deaths in utero. If early viability selection produces genotypic deviations from Mendelian predictions, it may undermine management strategies intended to minimize inbreeding and maintain genetic diversity. We use empirical examples to demonstrate that straightforward approaches, such as comparing litter sizes of inbred vs. noninbred breeding pairs, can be used to test whether early viability selection likely impacts estimates of inbreeding depression. We also show that comparing multilocus genotype data to pedigree predictions can reveal whether early viability selection drives systematic biases in genetic diversity, patterns that would not be detected using pedigree-based statistics alone. More sophisticated analysis combining genomewide molecular data with pedigree information will enable conservation scientists to test whether early viability selection drives deviations from neutrality across wide stretches of the genome, revealing whether this form of selection biases the pedigree-based statistics and inference upon which intensive management is based.

  10. Fengshui forests conserve genetic diversity: a case study of Phoebe bournei (Hemsl.) Yang in southern China.

    PubMed

    Ge, Y J; Liu, Y J; Shen, A H; Lin, X C

    2015-03-20

    Fengshui forests (sacred groves) are important in traditional Chinese culture and home to many endangered species. These forests may provide protection for some endangered plant species outside the nature reserves, but little is known about their role in genetic conservation. Using inter-simple sequence repeat (ISSR) markers, we compared the genetic diversity of 6 populations of Phoebe bournei (Hemsl.) Yang, a commercially important woody species, which is under second-class national protection and endemic to China. Samples were collected from the nature reserves and Fengshui forests in southern China. Herein, we show that Fengshui forest populations are capable of maintaining some level of genetic diversity. For nature reserve populations, the average NA and NE were 1.58 and 1.39, respectively; and for Fengshui forests, they were 1.39 and 1.12, respectively. For nature reserve populations, Nei's gene diversity (H) and Shannon's index (I) were 0.32 and 0.11, respectively; and for Fengshui forests, they were 0.22 and 0.07, respectively. We discuss the reasons for the genetic differences between populations of the Fengshui forests and nature reserves and propose conservation strategies for the Fengshui forest.

  11. Predictive habitat suitability models to aid conservation of elasmobranch diversity in the central Mediterranean Sea

    NASA Astrophysics Data System (ADS)

    Lauria, V.; Gristina, M.; Attrill, M. J.; Fiorentino, F.; Garofalo, G.

    2015-08-01

    Commercial fisheries have dramatically impacted elasmobranch populations worldwide. With high capture and bycatch rates, the abundance of many species is rapidly declining and around a quarter of the world’s sharks and rays are threatened with extinction. At a regional scale this negative trend has also been evidenced in the central Mediterranean Sea, where bottom-trawl fisheries have affected the biomass of certain rays (e.g. Raja clavata) and sharks (e.g. Mustelus spp.). Detailed knowledge of elasmobranch habitat requirements is essential for biodiversity conservation and fisheries management, but this is often hampered by a poor understanding of their spatial ecology. Habitat suitability models were used to investigate the habitat preference of nine elasmobranch species and their overall diversity (number of species) in relation to five environmental predictors (i.e. depth, sea surface temperature, surface salinity, slope and rugosity) in the central Mediterranean Sea. Results showed that depth, seafloor morphology and sea surface temperature were the main drivers for elasmobranch habitat suitability. Predictive distribution maps revealed different species-specific patterns of suitable habitat while high assemblage diversity was predicted in deeper offshore waters (400-800 m depth). This study helps to identify priority conservation areas and diversity hot-spots for rare and endangered elasmobranchs in the Mediterranean Sea.

  12. Predictive habitat suitability models to aid conservation of elasmobranch diversity in the central Mediterranean Sea.

    PubMed

    Lauria, V; Gristina, M; Attrill, M J; Fiorentino, F; Garofalo, G

    2015-01-01

    Commercial fisheries have dramatically impacted elasmobranch populations worldwide. With high capture and bycatch rates, the abundance of many species is rapidly declining and around a quarter of the world's sharks and rays are threatened with extinction. At a regional scale this negative trend has also been evidenced in the central Mediterranean Sea, where bottom-trawl fisheries have affected the biomass of certain rays (e.g. Raja clavata) and sharks (e.g. Mustelus spp.). Detailed knowledge of elasmobranch habitat requirements is essential for biodiversity conservation and fisheries management, but this is often hampered by a poor understanding of their spatial ecology. Habitat suitability models were used to investigate the habitat preference of nine elasmobranch species and their overall diversity (number of species) in relation to five environmental predictors (i.e. depth, sea surface temperature, surface salinity, slope and rugosity) in the central Mediterranean Sea. Results showed that depth, seafloor morphology and sea surface temperature were the main drivers for elasmobranch habitat suitability. Predictive distribution maps revealed different species-specific patterns of suitable habitat while high assemblage diversity was predicted in deeper offshore waters (400-800 m depth). This study helps to identify priority conservation areas and diversity hot-spots for rare and endangered elasmobranchs in the Mediterranean Sea. PMID:26272502

  13. A regional perspective on the diversity and conservation of tropical Andean fishes.

    PubMed

    Anderson, Elizabeth P; Maldonado-Ocampo, Javier A

    2011-02-01

    The tropical Andes harbor an extraordinarily varied concentration of species in a landscape under increasing pressure from human activities. Conservation of the region's native plants and animals has received considerable international attention, but the focus has been on terrestrial biota. The conservation of freshwater fauna, particularly the conservation of fishes, has not been emphasized. Tropical Andean fishes are among the most understudied vertebrates in the world. We estimate that between 400 and 600 fish species inhabit the diverse aquatic environments in the region. Nearly 40% of these species are endemic. Tropical Andean fishes are vulnerable to ongoing environmental changes related to deforestation, water withdrawals, water pollution, species introductions, and hydropower development. Additionally, their distributions and population dynamics may be affected by hydrologic alterations and warmer water temperatures associated with projected climate change. Presently, at least three species are considered extinct, some populations are endangered, and some species are likely to decline or disappear. The long-term persistence of tropical Andean fishes will depend on greater consideration of freshwater systems in regional conservation initiatives.

  14. Conservation implications of changes in endemic Hawaiian Drosophilidae diversity across land use gradients.

    PubMed

    Leblanc, Luc; Rubinoff, Daniel; Wright, Mark G

    2013-01-01

    Endemic Hawaiian Drosophilidae, a radiation of nearly 1000 species including 13 federally listed as endangered, occur mostly in intact native forest, 500-1500 m above sea level. But their persistence in disturbed forest and agricultural areas has not been documented. Thus, control efforts for agricultural pests may impact endemic species if previously undocumented refugia in agricultural areas may play a role in their conservation. To quantify whether invasive plants and agriculture habitats may harbor endemic Drosophilidae, we established standardized trapping arrays, with traps typically designed to control invasive fruit flies (Tephritidae), with 81 sites across native, disturbed and agricultural land use gradients on the islands of Hawai'i and Maui. We collected and identified, to species level, over 22,000 specimens. We found 121 of the possible 292 species expected to occur in the sampled areas, and the majority (91%) of the captured specimens belonged to 24 common species. Species diversity and numbers were greatest in the native forest, but 55% of the species occurred in the invasive strawberry guava belt and plantation forest, adjacent to and almost 500 m from native forest, and 22 species were collected in orchards and nonnative forest as far as 10 km from native habitats. Their persistence outside of native forest suggests that more careful management of disturbed forest and a reassessment of its conservation value are in order. Conservation efforts and assessments of native forest integrity should include the subset of species restricted to intact native forest, since these species are highly localized and particularly sensitive. Additionally, future efforts to control invasive pest fruit flies should consider the nontarget impacts of maintaining traps in and near native forest. This survey project demonstrates the utility of thorough biotic surveys and taxonomic expertise in developing both sensitive species lists and baseline diversity indices for

  15. Conservation Implications of Changes in Endemic Hawaiian Drosophilidae Diversity across Land Use Gradients

    PubMed Central

    Leblanc, Luc; Rubinoff, Daniel; Wright, Mark G.

    2013-01-01

    Endemic Hawaiian Drosophilidae, a radiation of nearly 1000 species including 13 federally listed as endangered, occur mostly in intact native forest, 500–1500 m above sea level. But their persistence in disturbed forest and agricultural areas has not been documented. Thus, control efforts for agricultural pests may impact endemic species if previously undocumented refugia in agricultural areas may play a role in their conservation. To quantify whether invasive plants and agriculture habitats may harbor endemic Drosophilidae, we established standardized trapping arrays, with traps typically designed to control invasive fruit flies (Tephritidae), with 81 sites across native, disturbed and agricultural land use gradients on the islands of Hawai’i and Maui. We collected and identified, to species level, over 22,000 specimens. We found 121 of the possible 292 species expected to occur in the sampled areas, and the majority (91%) of the captured specimens belonged to 24 common species. Species diversity and numbers were greatest in the native forest, but 55% of the species occurred in the invasive strawberry guava belt and plantation forest, adjacent to and almost 500 m from native forest, and 22 species were collected in orchards and nonnative forest as far as 10 km from native habitats. Their persistence outside of native forest suggests that more careful management of disturbed forest and a reassessment of its conservation value are in order. Conservation efforts and assessments of native forest integrity should include the subset of species restricted to intact native forest, since these species are highly localized and particularly sensitive. Additionally, future efforts to control invasive pest fruit flies should consider the nontarget impacts of maintaining traps in and near native forest. This survey project demonstrates the utility of thorough biotic surveys and taxonomic expertise in developing both sensitive species lists and baseline diversity indices for

  16. Tropical rain forest conservation and the twin challenges of diversity and rarity.

    PubMed

    Hubbell, Stephen P

    2013-09-01

    Data from a global network of large, permanent plots in lowland tropical forests demonstrate (1) that the phenomenon of tropical tree rarity is real and (2) that almost all the species diversity in such forests is due to rare species. Theoretical and empirically based reasoning suggests that many of these rare species are not as geographically widespread as previously thought. These findings suggest that successful strategies for conserving global tree diversity in lowland tropical forests must pay much more attention to the biogeography of rarity, as well as to the impact of climate change on the distribution and abundance of rare species. Because the biogeography of many tropical tree species is poorly known, a high priority should be given to documenting the distribution and abundance of rare tropical tree species, particularly in Amazonia, the largest remaining tropical forested region in the world.

  17. Tropical rain forest conservation and the twin challenges of diversity and rarity

    PubMed Central

    Hubbell, Stephen P

    2013-01-01

    Data from a global network of large, permanent plots in lowland tropical forests demonstrate (1) that the phenomenon of tropical tree rarity is real and (2) that almost all the species diversity in such forests is due to rare species. Theoretical and empirically based reasoning suggests that many of these rare species are not as geographically widespread as previously thought. These findings suggest that successful strategies for conserving global tree diversity in lowland tropical forests must pay much more attention to the biogeography of rarity, as well as to the impact of climate change on the distribution and abundance of rare species. Because the biogeography of many tropical tree species is poorly known, a high priority should be given to documenting the distribution and abundance of rare tropical tree species, particularly in Amazonia, the largest remaining tropical forested region in the world. PMID:24223266

  18. Putting the Plants Back into Plant Ecology: Six Pragmatic Models for Understanding and Conserving Plant Diversity

    PubMed Central

    KEDDY, PAUL

    2005-01-01

    • Background There is a compelling need to protect natural plant communities and restore them in degraded landscapes. Activities must be guided by sound scientific principles, practical conservation tools, and clear priorities. With perhaps one-third of the world's flora facing extinction, scientists and conservation managers will need to work rapidly and collaboratively, recognizing each other's strengths and limitations. As a guide to assist managers in maintaining plant diversity, six pragmatic models are introduced that are already available. Although theoretical models continue to receive far more space and headlines in scientific journals, more managers need to understand that pragmatic, rather than theoretical, models have the most promise for yielding results that can be applied immediately to plant communities. • Six Pragmatic Models For each model, key citations and an array of examples are provided, with particular emphasis on wetlands, since ‘wet and wild’ was my assigned theme for the Botanical Society of America in 2003. My own work may seem rather prominent, but the application and refinement of these models has been a theme for me and my many students over decades. The following models are reviewed: (1) species–area: larger areas usually contain more species; (2) species–biomass: plant diversity is maximized at intermediate levels of biomass; (3) centrifugal organization: multiple intersecting environmental gradients maintain regional landscape biodiversity; (4) species–frequency: a few species are frequent while most are infrequent; (5) competitive hierarchies: in the absence of constraints, large canopy-forming species dominate patches of landscape, reducing biological diversity; and (6) intermediate disturbance: perturbations such as water level fluctuations, fire and grazing are essential for maintaining plant diversity. • Conclusions The good news is that managers faced with protecting or restoring landscapes already have this

  19. Using genomic tools to maintain diversity and fitness in conservation programmes.

    PubMed

    de Cara, María Ángeles Rodríguez; Villanueva, Beatriz; Toro, Miguel Ángel; Fernández, Jesús

    2013-12-01

    Conservation programmes aim at maximizing the survival probability of populations, by minimizing the loss of genetic diversity, which allows populations to adapt to changes, and controlling inbreeding increases. The best known strategy to achieve these goals is optimizing the contributions of the parents to minimize global coancestry in their offspring. Results on neutral scenarios showed that management based on molecular coancestry could maintain more diversity than management based on genealogical coancestry when a large number of markers were available. However, if the population has deleterious mutations, managing using optimal contributions can lead to a decrease in fitness, especially using molecular coancestry, because both beneficial and harmful alleles are maintained, compromising the long-term viability of the population. We introduce here two strategies to avoid this problem: The first one uses molecular coancestry calculated removing markers with low minor allele frequencies, as they could be linked to selected loci. The second one uses a coancestry based on segments of identity by descent, which measures the proportion of genome segments shared by two individuals because of a common ancestor. We compare these strategies under two contrasting mutational models of fitness effects, one assuming many mutations of small effect and another with few mutations of large effect. Using markers at intermediate frequencies maintains a larger fitness than using all markers, but leads to maintaining less diversity. Using the segment-based coancestry provides a compromise solution between maintaining diversity and fitness, especially when the population has some inbreeding load.

  20. Analysis of tomato plasma membrane H(+)-ATPase gene family suggests a mycorrhiza-mediated regulatory mechanism conserved in diverse plant species.

    PubMed

    Liu, Junli; Liu, Jianjian; Chen, Aiqun; Ji, Minjie; Chen, Jiadong; Yang, Xiaofeng; Gu, Mian; Qu, Hongye; Xu, Guohua

    2016-10-01

    In plants, the plasma membrane H(+)-ATPase (HA) is considered to play a crucial role in regulating plant growth and respoding to environment stresses. Multiple paralogous genes encoding different isozymes of HA have been identified and characterized in several model plants, while limited information of the HA gene family is available to date for tomato. Here, we describe the molecular and expression features of eight HA-encoding genes (SlHA1-8) from tomato. All these genes are interrupted by multiple introns with conserved positions. SlHA1, 2, and 4 were widely expressed in all tissues, while SlHA5, 6, and 7 were almost only expressed in flowers. SlHA8, the transcripts of which were barely detectable under normal or nutrient-/salt-stress growth conditions, was strongly activated in arbuscular mycorrhizal (AM) fungal-colonized roots. Extreme lack of SlHA8 expression in M161, a mutant defective to AM fungal colonization, provided genetic evidence towards the dependence of its expression on AM symbiosis. A 1521-bp SlHA8 promoter could direct the GUS reporter expression specifically in colonized cells of transgenic tobacco, soybean, and rice mycorrhizal roots. Promoter deletion assay revealed a 223-bp promoter fragment of SlHA8 containing a variant of AM-specific cis-element MYCS (vMYCS) sufficient to confer the AM-induced activity. Targeted deletion of this motif in the corresponding promoter region causes complete abolishment of GUS staining in mycorrhizal roots. Together, these results lend cogent evidence towards the evolutionary conservation of a potential regulatory mechanism mediating the activation of AM-responsive HA genes in diverse mycorrhizal plant species.

  1. Investigating the Perceptions of Intellectual Diversity among Socially Conservative Christian Seniors at Elite U.S. Colleges

    ERIC Educational Resources Information Center

    Brow, Mark V.

    2016-01-01

    This study investigated the perceptions of intellectual diversity at elite U.S. universities through the lens of the socially conservative Christian senior. Closely aligned with the principle of academic freedom, intellectual diversity is a foundational value putatively espoused by most if not all colleges and universities in the US. Although…

  2. Model-based conservation planning of the genetic diversity of Phellodendron amurense Rupr due to climate change

    PubMed Central

    Wan, Jizhong; Wang, Chunjing; Yu, Jinghua; Nie, Siming; Han, Shijie; Zu, Yuangang; Chen, Changmei; Yuan, Shusheng; Wang, Qinggui

    2014-01-01

    Climate change affects both habitat suitability and the genetic diversity of wild plants. Therefore, predicting and establishing the most effective and coherent conservation areas is essential for the conservation of genetic diversity in response to climate change. This is because genetic variance is a product not only of habitat suitability in conservation areas but also of efficient protection and management. Phellodendron amurense Rupr. is a tree species (family Rutaceae) that is endangered due to excessive and illegal harvesting for use in Chinese medicine. Here, we test a general computational method for the prediction of priority conservation areas (PCAs) by measuring the genetic diversity of P. amurense across the entirety of northeast China using a single strand repeat analysis of twenty microsatellite markers. Using computational modeling, we evaluated the geographical distribution of the species, both now and in different future climate change scenarios. Different populations were analyzed according to genetic diversity, and PCAs were identified using a spatial conservation prioritization framework. These conservation areas were optimized to account for the geographical distribution of P. amurense both now and in the future, to effectively promote gene flow, and to have a long period of validity. In situ and ex situ conservation, strategies for vulnerable populations were proposed. Three populations with low genetic diversity are predicted to be negatively affected by climate change, making conservation of genetic diversity challenging due to decreasing habitat suitability. Habitat suitability was important for the assessment of genetic variability in existing nature reserves, which were found to be much smaller than the proposed PCAs. Finally, a simple set of conservation measures was established through modeling. This combined molecular and computational ecology approach provides a framework for planning the protection of species endangered by climate

  3. Triazole resistance mediated by mutations of a conserved active site tyrosine in fungal lanosterol 14α-demethylase

    PubMed Central

    Sagatova, Alia A.; Keniya, Mikhail V.; Wilson, Rajni K.; Sabherwal, Manya; Tyndall, Joel D. A.; Monk, Brian C.

    2016-01-01

    Emergence of fungal strains showing resistance to triazole drugs can make treatment of fungal disease problematic. Triazole resistance can arise due to single mutations in the drug target lanosterol 14α-demethylase (Erg11p/CYP51). We have determined how commonly occurring single site mutations in pathogenic fungi affect triazole binding using Saccharomyces cerevisiae Erg11p (ScErg11p) as a target surrogate. The mutations Y140F/H were introduced into full-length hexahistidine-tagged ScErg11p. Phenotypes and high-resolution X-ray crystal structures were determined for the mutant enzymes complexed with short-tailed (fluconazole and voriconazole) or long-tailed (itraconazole and posaconazole) triazoles and wild type enzyme complexed with voriconazole. The mutations disrupted a water-mediated hydrogen bond network involved in binding of short-tailed triazoles, which contain a tertiary hydroxyl not present in long-tailed triazoles. This appears to be the mechanism by which resistance to these short chain azoles occurs. Understanding how these mutations affect drug affinity will aid the design of azoles that overcome resistance. PMID:27188873

  4. Diversity of the Bacterial and Fungal Microflora from the Midgut and Cuticle of Phlebotomine Sand Flies Collected in North-Western Iran

    PubMed Central

    Akhoundi, Mohammad; Bakhtiari, Rounak; Guillard, Thomas; Baghaei, Ahmad; Tolouei, Reza; Sereno, Denis; Toubas, Dominique; Depaquit, Jérôme; Abyaneh, Mehdi Razzaghi

    2012-01-01

    Background Phlebotomine sand flies are the vectors of the leishmaniases, parasitic diseases caused by Leishmania spp. Little is known about the prevalence and diversity of sand fly microflora colonizing the midgut or the cuticle. Particularly, there is little information on the fungal diversity. This information is important for development of vector control strategies. Methodology/Principal Findings Five sand fly species: Phlebotomus papatasi, P. sergenti, P. kandelakii, P. perfiliewi and P. halepensis were caught in Bileh Savar and Kaleybar in North-Western Iran that are located in endemic foci of visceral leishmaniasis. A total of 35 specimens were processed. Bacterial and fungal strains were identified by routine microbiological methods. We characterized 39 fungal isolates from the cuticle and/or the midgut. They belong to six different genera including Penicillium (17 isolates), Aspergillus (14), Acremonium (5), Fusarium (1), Geotrichum (1) and Candida (1). We identified 33 Gram-negative bacteria: Serratia marcescens (9 isolates), Enterobacter cloacae (6), Pseudomonas fluorescens (6), Klebsiella ozaenae (4), Acinetobacter sp. (3), Escherichia coli (3), Asaia sp. (1) and Pantoea sp. (1) as well as Gram-positive bacteria Bacillus subtilis (5) and Micrococcus luteus (5) in 10 isolates. Conclusion/Significance Our study provides new data on the microbiotic diversity of field-collected sand flies and for the first time, evidence of the presence of Asaia sp. in sand flies. We have also found a link between physiological stages (unfed, fresh fed, semi gravid and gravid) of sand flies and number of bacteria that they carry. Interestingly Pantoea sp. and Klebsiella ozaenae have been isolated in Old World sand fly species. The presence of latter species on sand fly cuticle and in the female midgut suggests a role for this arthropod in dissemination of these pathogenic bacteria in endemic areas. Further experiments are required to clearly delineate the vectorial role

  5. Genetic diversity in fragmented populations of Populus talassica inferred from microsatellites: implications for conservation.

    PubMed

    Zhu, X H; Cheng, S P; Liao, T; Kang, X Y

    2016-01-01

    Populus talassica Kom. is an ecologically important species endemic to central Asia. In China, its main distribution is restricted to the Ili region in the Xinjiang Autonomous Region. An understanding of genetic diversity and population structure is crucial for the development of a feasible conservation strategy. Twenty-six high-level simple sequence repeat (SSR) markers were screened and used to genotype 220 individuals from three native populations. A high level of genetic diversity and low population differentiation were revealed. We identified 163 alleles, with a mean of 6.269 alleles per locus. The observed and expected heterozygosities ranged from 0.472 to 0.485 (with a mean of 0.477), and from 0.548 to 0.591 (mean 0.569), respectively. Analysis of molecular variance revealed 93% variation within populations and 7% among populations. A model-based population structure analysis divided P. talassica into two groups (optimal K = 2). These genetic data provide crucial insight for conservation management. PMID:27323095

  6. Gonadal Expression of Foxo1, but Not Foxo3, Is Conserved in Diverse Mammalian Species1

    PubMed Central

    Tarnawa, Edward D.; Baker, Michael D.; Aloisio, Gina M.; Carr, Bruce R.; Castrillon, Diego H.

    2013-01-01

    ABSTRACT The Foxos are key effectors of the PI3K/Akt signaling pathway and regulate diverse physiologic processes. Two of these factors, Foxo1 and Foxo3, serve specific roles in reproduction in the mouse. Foxo3 is required for suppression of primordial follicle activation in females, while Foxo1 regulates spermatogonial stem cell maintenance in males. In the mouse ovary, Foxo1 is highly expressed in somatic cells (but not in oocytes), suggesting an important functional role for Foxo1 in these cells. Given that invertebrate model species such as Caenorhabditis elegans and Drosophila melanogaster harbor a single ancestral Foxo homolog, these observations suggest that gene duplication conferred a selective advantage by permitting the Foxos to adopt distinct roles in oogenesis and spermatogenesis. Our objective was to determine if the remarkably specific expression patterns of Foxo1 and Foxo3 in mouse gonads (and, by inference, Foxo function) are conserved in diverse mammalian species. Western blotting was used to validate isoform-specific antibodies in rodents, companion animals, farm animals, nonhuman primates, and humans. Following validation of each antibody, immunohistochemistry was performed to ascertain Foxo1 and Foxo3 gonadal expression patterns. While Foxo1 expression in spermatogonia and granulosa cells was conserved in each species evaluated, Foxo3 expression in oocytes was not. Our findings suggest that Foxo3 is not uniquely required for primordial follicle maintenance in nonrodent species and that other Foxos, particularly Foxo1, may contribute to oocyte maintenance in a functionally redundant manner. PMID:23486915

  7. Reduced genetic diversity in endemic Brazilian Lymania spp (Bromeliaceae) populations and implications for conservation.

    PubMed

    Pamponét, V C C; Alves, T F; Martinez, R A; Corrêa, R X; Gaiotto, F A

    2013-01-01

    We analyzed the genetic diversity of populations of two sympatric species of Lymania (Bromeliaceae), both endemic to the Atlantic rainforest of southern Bahia (Brazil). Lymania azurea has a restricted occurrence, while Lymania smithii has a wider distribution. Our aim was to provide genetic data to contribute to the design of more efficient conservation strategies for these bromeliads, possibly justifying inclusion in the official Brazilian list of Endangered Species. Up to now, L. azurea has been classified by the Brazilian Ministry of the Environment as "data deficient". We sampled four populations of L. azurea throughout its distribution area in southern Bahia and two populations of L. smithii in the same region. Genotyping was performed with 48 random amplified polymorphic DNA markers. Based on the Jaccard genetic similarity index, L. smithii has greater diversity than L. azurea. An analysis of molecular variation showed greater genetic variance within than between populations for both species. L. azurea was found to have 20% inbreeding, probably due to population fragmentation, with L. smithii showing only 10%. When we analyzed pairs of populations of L. azurea within a conservation unit, we found low population structure (ФST = 0.098), apparently due to a large degree of gene flow between them. In disturbed areas, we found a higher ФST (0.372). We found low genetic variability for L. azurea, probably as a consequence of habitat fragmentation, supporting the need for its inclusion in the Brazilian list of endangered flora. PMID:24222215

  8. Recovering Greater Fungal Diversity from Pristine and Diesel Fuel Contaminated Sub-Antarctic Soil Through Cultivation Using Both a High and a Low Nutrient Media Approach

    PubMed Central

    Ferrari, Belinda C.; Zhang, Chengdong; van Dorst, Josie

    2011-01-01

    Novel cultivation strategies for bacteria are widespread and well described for recovering greater diversity from the “hitherto” unculturable majority. While similar approaches have not yet been demonstrated for fungi it has been suggested that of the 1.5 million estimated species less than 5% have been recovered into pure culture. Fungi are known to be involved in many degradative processes, including the breakdown of petroleum hydrocarbons, and it has been speculated that in Polar Regions they contribute significantly to bioremediation of contaminated soils. Given the biotechnological potential of fungi there is a need to increase efforts for greater species recovery, particularly from extreme environments such as sub-Antarctic Macquarie Island. In this study, like the yet-to-be cultured bacteria, high concentrations of nutrients selected for predominantly different fungal species to that recovered using a low nutrient media. By combining both media approaches to the cultivation of fungi from contaminated and non-contaminated soils, 91 fungal species were recovered, including 63 unidentified species. A preliminary biodegradation activity assay on a selection of isolates found that a high proportion of novel and described fungal species from a range of soil samples were capable of hydrocarbon degradation and should be characterized further. PMID:22131985

  9. Whose truffle is this? Distribution patterns of ectomycorrhizal fungal diversity in Tuber melanosporum brûlés developed in multi-host Mediterranean plant communities.

    PubMed

    Taschen, Elisa; Sauve, Mathieu; Taudiere, Adrien; Parlade, Javier; Selosse, Marc-André; Richard, Franck

    2015-08-01

    In the Mediterranean region, patches of vegetation recovering from disturbance and transiently dominated by shrubs produce one of the world's most prized fungi, the black truffle (Tuber melanosporum). In these successional plant communities, we have fragmentary knowledge of the distribution of T. melanosporum in space among ectomycorrhizal (ECM) host species and in time. Molecular identification of hosts (Restriction Fragment Length Polymorphism) and fungi (Internal Transcribed Spacer sequencing) and quantification of T. melanosporum mycelium (quantitative Polymerase Chain Reaction) were employed to evaluate the presence of T. melanosporum on four dominant ECM host species (Quercus ilex, Quercus  coccifera, Arbutus unedo, Cistus albidus) and the extent to which their respective ECM communities shared fungal diversity, over the course of development of truffle grounds, from recent unproductive brûlés to senescent ones where production has stopped. We found that truffle grounds host rich communities in which multi-host fungal species dominate in frequency. When considering both ECM tips and soil mycelia, we documented a dynamic and spatially heterogeneous pattern of T. melanosporum distribution in soils and a presence of ECM tips restricted to Q. ilex roots. This study advances our knowledge of the ecology of T. melanosporum, and provides insight into the extent of ECM fungal sharing among plant species that dominate Mediterranean landscapes. PMID:25522815

  10. A small-scale land-sparing approach to conserving biological diversity in tropical agricultural landscapes.

    PubMed

    Chandler, Richard B; King, David I; Raudales, Raul; Trubey, Richard; Chandler, Carlin; Chávez, Víctor Julio Arce

    2013-08-01

    Two contrasting strategies have been proposed for conserving biological diversity while meeting the increasing demand for agricultural products: land sparing and land sharing production systems. Land sparing involves increasing yield to reduce the amount of land needed for agriculture, whereas land-sharing agricultural practices incorporate elements of native ecosystems into the production system itself. Although the conservation value of these systems has been extensively debated, empirical studies are lacking. We compared bird communities in shade coffee, a widely practiced land-sharing system in which shade trees are maintained within the coffee plantation, with bird communities in a novel, small-scale, land-sparing coffee-production system (integrated open canopy or IOC coffee) in which farmers obtain higher yields under little or no shade while conserving an area of forest equal to the area under cultivation. Species richness and diversity of forest-dependent birds were higher in the IOC coffee farms than in the shade coffee farms, and community composition was more similar between IOC coffee and primary forest than between shade coffee and primary forest. Our study represents the first empirical comparison of well-defined land sparing and land sharing production systems. Because IOC coffee farms can be established by allowing forest to regenerate on degraded land, widespread adoption of this system could lead to substantial increases in forest cover and carbon sequestration without compromising agricultural yield or threatening the livelihoods of traditional small farmers. However, we studied small farms (<5 ha); thus, our results may not generalize to large-scale land-sharing systems. Furthermore, rather than concluding that land sparing is generally superior to land sharing, we suggest that the optimal approach depends on the crop, local climate, and existing land-use patterns.

  11. Low-intensity agricultural landscapes in Transylvania support high butterfly diversity: implications for conservation.

    PubMed

    Loos, Jacqueline; Dorresteijn, Ine; Hanspach, Jan; Fust, Pascal; Rakosy, László; Fischer, Joern

    2014-01-01

    European farmland biodiversity is declining due to land use changes towards agricultural intensification or abandonment. Some Eastern European farming systems have sustained traditional forms of use, resulting in high levels of biodiversity. However, global markets and international policies now imply rapid and major changes to these systems. To effectively protect farmland biodiversity, understanding landscape features which underpin species diversity is crucial. Focusing on butterflies, we addressed this question for a cultural-historic landscape in Southern Transylvania, Romania. Following a natural experiment, we randomly selected 120 survey sites in farmland, 60 each in grassland and arable land. We surveyed butterfly species richness and abundance by walking transects with four repeats in summer 2012. We analysed species composition using Detrended Correspondence Analysis. We modelled species richness, richness of functional groups, and abundance of selected species in response to topography, woody vegetation cover and heterogeneity at three spatial scales, using generalised linear mixed effects models. Species composition widely overlapped in grassland and arable land. Composition changed along gradients of heterogeneity at local and context scales, and of woody vegetation cover at context and landscape scales. The effect of local heterogeneity on species richness was positive in arable land, but negative in grassland. Plant species richness, and structural and topographic conditions at multiple scales explained species richness, richness of functional groups and species abundances. Our study revealed high conservation value of both grassland and arable land in low-intensity Eastern European farmland. Besides grassland, also heterogeneous arable land provides important habitat for butterflies. While butterfly diversity in arable land benefits from heterogeneity by small-scale structures, grasslands should be protected from fragmentation to provide

  12. Low-Intensity Agricultural Landscapes in Transylvania Support High Butterfly Diversity: Implications for Conservation

    PubMed Central

    Loos, Jacqueline; Dorresteijn, Ine; Hanspach, Jan; Fust, Pascal; Rakosy, László; Fischer, Joern

    2014-01-01

    European farmland biodiversity is declining due to land use changes towards agricultural intensification or abandonment. Some Eastern European farming systems have sustained traditional forms of use, resulting in high levels of biodiversity. However, global markets and international policies now imply rapid and major changes to these systems. To effectively protect farmland biodiversity, understanding landscape features which underpin species diversity is crucial. Focusing on butterflies, we addressed this question for a cultural-historic landscape in Southern Transylvania, Romania. Following a natural experiment, we randomly selected 120 survey sites in farmland, 60 each in grassland and arable land. We surveyed butterfly species richness and abundance by walking transects with four repeats in summer 2012. We analysed species composition using Detrended Correspondence Analysis. We modelled species richness, richness of functional groups, and abundance of selected species in response to topography, woody vegetation cover and heterogeneity at three spatial scales, using generalised linear mixed effects models. Species composition widely overlapped in grassland and arable land. Composition changed along gradients of heterogeneity at local and context scales, and of woody vegetation cover at context and landscape scales. The effect of local heterogeneity on species richness was positive in arable land, but negative in grassland. Plant species richness, and structural and topographic conditions at multiple scales explained species richness, richness of functional groups and species abundances. Our study revealed high conservation value of both grassland and arable land in low-intensity Eastern European farmland. Besides grassland, also heterogeneous arable land provides important habitat for butterflies. While butterfly diversity in arable land benefits from heterogeneity by small-scale structures, grasslands should be protected from fragmentation to provide

  13. Phylogenetic diversity meets conservation policy: small areas are key to preserving eucalypt lineages

    PubMed Central

    Pollock, Laura J.; Rosauer, Dan F.; Thornhill, Andrew H.; Kujala, Heini; Crisp, Michael D.; Miller, Joseph T.; McCarthy, Michael A.

    2015-01-01

    Evolutionary and genetic knowledge is increasingly being valued in conservation theory, but is rarely considered in conservation planning and policy. Here, we integrate phylogenetic diversity (PD) with spatial reserve prioritization to evaluate how well the existing reserve system in Victoria, Australia captures the evolutionary lineages of eucalypts, which dominate forest canopies across the state. Forty-three per cent of remaining native woody vegetation in Victoria is located in protected areas (mostly national parks) representing 48% of the extant PD found in the state. A modest expansion in protected areas of 5% (less than 1% of the state area) would increase protected PD by 33% over current levels. In a recent policy change, portions of the national parks were opened for development. These tourism development zones hold over half the PD found in national parks with some species and clades falling entirely outside of protected zones within the national parks. This approach of using PD in spatial prioritization could be extended to any clade or area that has spatial and phylogenetic data. Our results demonstrate the relevance of PD to regional conservation policy by highlighting that small but strategically located areas disproportionally impact the preservation of evolutionary lineages. PMID:25561668

  14. Phylogenetic diversity meets conservation policy: small areas are key to preserving eucalypt lineages.

    PubMed

    Pollock, Laura J; Rosauer, Dan F; Thornhill, Andrew H; Kujala, Heini; Crisp, Michael D; Miller, Joseph T; McCarthy, Michael A

    2015-02-19

    Evolutionary and genetic knowledge is increasingly being valued in conservation theory, but is rarely considered in conservation planning and policy. Here, we integrate phylogenetic diversity (PD) with spatial reserve prioritization to evaluate how well the existing reserve system in Victoria, Australia captures the evolutionary lineages of eucalypts, which dominate forest canopies across the state. Forty-three per cent of remaining native woody vegetation in Victoria is located in protected areas (mostly national parks) representing 48% of the extant PD found in the state. A modest expansion in protected areas of 5% (less than 1% of the state area) would increase protected PD by 33% over current levels. In a recent policy change, portions of the national parks were opened for development. These tourism development zones hold over half the PD found in national parks with some species and clades falling entirely outside of protected zones within the national parks. This approach of using PD in spatial prioritization could be extended to any clade or area that has spatial and phylogenetic data. Our results demonstrate the relevance of PD to regional conservation policy by highlighting that small but strategically located areas disproportionally impact the preservation of evolutionary lineages.

  15. Comparing activated sludge fungal community population diversity using denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism.

    PubMed

    Evans, Tegan N; Watson, Garth; Rees, Gavin N; Seviour, Robert J

    2014-03-01

    We compared the relative values of denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) for profiling fungal communities in wastewater treatment plants using both ITS and 18S rRNA gene fragments as phylogenetic markers. A similar number of fungal ribotypes was obtained with both methods for the same treatment plant when the ITS primer set was used, while a greater number of ribotypes was obtained with T-RFLP compared to DGGE with the 18S rRNA primer set. Non-metric multi-dimensional scaling of presence/absence data and analysis of similarity showed that both methods could distinguish between the different plant communities at a statistically significant level (p < 0.05), regardless of which phylogenetic marker was used. The data suggest that both methods can be used preferably together to profile activated sludge fungal communities. A comparison of profiles generated with both these phylogenetic markers based on the number of ribotypes/bands, suggests that the 18S rRNA region is more discriminatory than the ITS region. Detected differences in fungal community compositions between plants probably reflect differences in their influent compositions and operational parameters.

  16. Fungal Genome Sequencing and Bioenergy

    SciTech Connect

    Baker, Scott E.; Thykaer, Jette; Adney, William S.; Brettin, T.; Brockman, Fred J.; D'haeseleer, Patrik; Martinez, Antonio D.; Miller, R. M.; Rokhsar, Daniel S.; Schadt, Christopher W.; Torok, Tamas; Tuskan, Gerald; Bennett, Joan W.; Berka, Randy; Briggs, Steve; Heitman, Joseph; Taylor, John; Turgeon, Barbara G.; Werner-Washburne, Maggie; Himmel, Michael E.

    2008-09-30

    To date, the number of ongoing filamentous fungal genome sequencing projects is almost tenfold fewer than those of bacterial and archaeal genome projects. The fungi chosen for sequencing represent narrow kingdom diversity; most are pathogens or models. We advocate an ambitious, forward-looking phylogenetic-based genome sequencing program, designed to capture metabolic diversity within the fungal kingdom, thereby enhancing research into alternative bioenergy sources, bioremediation, and fungal-environment interactions.

  17. Fungal Genome Sequencing and Bioenergy

    SciTech Connect

    Baker, Scott; Thykaer, Jette; Adney, William S; Brettin, Tom; Brockman, Fred; Dhaeseleer, Patrick; Martinez, A diego; Miller, R michael; Rokhsar, Daniel; Schadt, Christopher Warren; Torok, Tamas; Tuskan, Gerald A; Bennett, Joan; Berka, Randy; Briggs, Steven; Heitman, Joseph; Taylor, John; Turgeon, Gillian; Werner-Washburne, Maggie; Himmel, Michael E

    2008-01-01

    To date, the number of ongoing filamentous fungal genome sequencing projects is almost tenfold fewer than those of bacterial and archaeal genome projects. The fungi chosen for sequencing represent narrow kingdom diversity; most are pathogens or models. We advocate an ambitious, forward-looking phylogenetic-based genome sequencing program, designed to capture metabolic diversity within the fungal kingdom, thereby enhancing research into alternative bioenergy sources, bioremediation, and fungal-environment interactions. Published by Elsevier Ltd on behalf of The British Mycological Society.

  18. Fungal Genome Sequencing and Bioenergy

    SciTech Connect

    Schadt, Christopher Warren; Baker, Scott; Thykaer, Jette; Adney, William S; Brettin, Tom; Brockman, Fred; Dhaeseleer, Patrick; Martinez, A diego; Miller, R michael; Rokhsar, Daniel; Torok, Tamas; Tuskan, Gerald A; Bennett, Joan; Berka, Randy; Briggs, Steven; Heitman, Joseph; Rizvi, L; Taylor, John; Turgeon, Gillian; Werner-Washburne, Maggie; Himmel, Michael

    2008-01-01

    To date, the number of ongoing filamentous fungal genome sequencing projects is almost tenfold fewer than those of bacterial and archaeal genome projects. The fungi chosen for sequencing represent narrow kingdom diversity; most are pathogens or models. We advocate an ambitious, forward-looking phylogenetic-based genome sequencing program, designed to capture metabolic diversity within the fungal kingdom, thereby enhancing research into alternative bioenergy sources, bioremediation, and fungal-environment interactions.

  19. The Key Role of Cultural Preservation in Maize Diversity Conservation in the Argentine Yungas

    PubMed Central

    Hilgert, Norma I.; Zamudio, Fernando; Cariola, Lucía

    2013-01-01

    Farmers' decisions on what to grow and why can contribute in understanding the conservation of agrobiodiversity. Culture and ethnicity are indicated as first-class factors leading preservation of heirloom cultivars but this has been little considered in studies examining factors that influence the loss or preservation of agrobiodiversity. We propose that corn's ethnotaxa of less diverse uses, which are also key partners in local cultural reproduction, are usually cultivated by a few households. We analyse if there is a relationship between uses and richness of cultivated ethnotaxa at household level and describe corn's medicinal and ritual uses. We found 25 cultivated ethnotaxa, heterogeneously distributed in the region, and we also found that ethnotaxa with less diverse uses are cultivated in fewer households. We identified that, at regional scale, richness is related with food use diversity. The most frequently cited medicinal uses were urinary and tract infections, diarrhoea, and liver disorders. Medicinal recipes involve combinations with other elements. Maize is an indispensable resource in the rituals that propitiate productive activity, to augur prosperity or misfortune according to signals. We have identified the vulnerability in preserving the richness of corn in the region and the factors that shape its cultivation at different scales. PMID:24078829

  20. The key role of cultural preservation in maize diversity conservation in the argentine yungas.

    PubMed

    Hilgert, Norma I; Zamudio, Fernando; Furlan, Violeta; Cariola, Lucía

    2013-01-01

    Farmers' decisions on what to grow and why can contribute in understanding the conservation of agrobiodiversity. Culture and ethnicity are indicated as first-class factors leading preservation of heirloom cultivars but this has been little considered in studies examining factors that influence the loss or preservation of agrobiodiversity. We propose that corn's ethnotaxa of less diverse uses, which are also key partners in local cultural reproduction, are usually cultivated by a few households. We analyse if there is a relationship between uses and richness of cultivated ethnotaxa at household level and describe corn's medicinal and ritual uses. We found 25 cultivated ethnotaxa, heterogeneously distributed in the region, and we also found that ethnotaxa with less diverse uses are cultivated in fewer households. We identified that, at regional scale, richness is related with food use diversity. The most frequently cited medicinal uses were urinary and tract infections, diarrhoea, and liver disorders. Medicinal recipes involve combinations with other elements. Maize is an indispensable resource in the rituals that propitiate productive activity, to augur prosperity or misfortune according to signals. We have identified the vulnerability in preserving the richness of corn in the region and the factors that shape its cultivation at different scales.

  1. Genetic diversity and conservation status of managed vicuña (Vicugna vicugna) populations in Argentina.

    PubMed

    Anello, M; Daverio, M S; Romero, S R; Rigalt, F; Silbestro, M B; Vidal-Rioja, L; Di Rocco, F

    2016-02-01

    The vicuña (Vicugna vicugna) was indiscriminately hunted for more than 400 years and, by the end of 1960s, it was seriously endangered. At that time, a captive breeding program was initiated in Argentina by the National Institute of Agricultural Technology (INTA) with the aim of preserving the species. Nowadays, vicuñas are managed in captivity and in the wild to obtain their valuable fiber. The current genetic status of Argentinean vicuña populations is virtually unknown. Using mitochondrial DNA and microsatellite markers, we assessed levels of genetic diversity of vicuña populations managed in the wild and compared it with a captive population from INTA. Furthermore, we examined levels of genetic structure and evidence for historical bottlenecks. Overall, all populations revealed high genetic variability with no signs of inbreeding. Levels of genetic diversity between captive and wild populations were not significantly different, although the captive population showed the lowest estimates of allelic richness, number of mitochondrial haplotypes, and haplotype diversity. Significant genetic differentiation at microsatellite markers was found between free-living populations from Jujuy and Catamarca provinces. Moreover, microsatellite data also revealed genetic structure within the Catamarca management area. Genetic signatures of past bottlenecks were detected in wild populations by the Garza Williamson test. Results from this study are discussed in relation to the conservation and management of the species.

  2. Host and habitat filtering in seedling root-associated fungal communities: taxonomic and functional diversity are altered in 'novel' soils.

    PubMed

    Pickles, Brian J; Gorzelak, Monika A; Green, D Scott; Egger, Keith N; Massicotte, Hugues B

    2015-10-01

    Climatic and land use changes have significant consequences for the distribution of tree species, both through natural dispersal processes and following management prescriptions. Responses to these changes will be expressed most strongly in seedlings near current species range boundaries. In northern temperate forest ecosystems, where changes are already being observed, ectomycorrhizal fungi contribute significantly to successful tree establishment. We hypothesised that communities of fungal symbionts might therefore play a role in facilitating, or limiting, host seedling range expansion. To test this hypothesis, ectomycorrhizal communities of interior Douglas-fir and interior lodgepole pine seedlings were analysed in a common greenhouse environment following growth in five soils collected along an ecosystem gradient. Currently, Douglas-fir's natural distribution encompasses three of the five soils, whereas lodgepole pine's extends much further north. Host filtering was evident amongst the 29 fungal species encountered: 7 were shared, 9 exclusive to Douglas-fir and 13 exclusive to lodgepole pine. Seedlings of both host species formed symbioses with each soil fungal community, thus Douglas-fir did so even where those soils came from outside its current distribution. However, these latter communities displayed significant taxonomic and functional differences to those found within the host distribution, indicative of habitat filtering. In contrast, lodgepole pine fungal communities displayed high functional similarity across the soil gradient. Taxonomic and/or functional shifts in Douglas-fir fungal communities may prove ecologically significant during the predicted northward migration of this species; especially in combination with changes in climate and management operations, such as seed transfer across geographical regions for forestry purposes. PMID:25694036

  3. Conservation and diversity of seed associated endophytes in Zea across boundaries of evolution, ethnography and ecology.

    PubMed

    Johnston-Monje, David; Raizada, Manish N

    2011-01-01

    , Enterobacter asburiae, was able to exit the root and colonize the rhizosphere. Conservation and diversity in Zea-microbe relationships are discussed in the context of ecology, crop domestication, selection and migration.

  4. Conservation and Diversity of Seed Associated Endophytes in Zea across Boundaries of Evolution, Ethnography and Ecology

    PubMed Central

    Johnston-Monje, David; Raizada, Manish N.

    2011-01-01

    , Enterobacter asburiae, was able to exit the root and colonize the rhizosphere. Conservation and diversity in Zea-microbe relationships are discussed in the context of ecology, crop domestication, selection and migration. PMID:21673982

  5. High risks of losing genetic diversity in an endemic Mauritian gecko: implications for conservation.

    PubMed

    Buckland, Steeves; Cole, Nik C; Groombridge, Jim J; Küpper, Clemens; Burke, Terry; Dawson, Deborah A; Gallagher, Laura E; Harris, Stephen

    2014-01-01

    Genetic structure can be a consequence of recent population fragmentation and isolation, or a remnant of historical localised adaptation. This poses a challenge for conservationists since misinterpreting patterns of genetic structure may lead to inappropriate management. Of 17 species of reptile originally found in Mauritius, only five survive on the main island. One of these, Phelsuma guimbeaui (lowland forest day gecko), is now restricted to 30 small isolated subpopulations following severe forest fragmentation and isolation due to human colonisation. We used 20 microsatellites in ten subpopulations and two mitochondrial DNA (mtDNA) markers in 13 subpopulations to: (i) assess genetic diversity, population structure and genetic differentiation of subpopulations; (ii) estimate effective population sizes and migration rates of subpopulations; and (iii) examine the phylogenetic relationships of haplotypes found in different subpopulations. Microsatellite data revealed significant population structure with high levels of genetic diversity and isolation by distance, substantial genetic differentiation and no migration between most subpopulations. MtDNA, however, showed no evidence of population structure, indicating that there was once a genetically panmictic population. Effective population sizes of ten subpopulations, based on microsatellite markers, were small, ranging from 44 to 167. Simulations suggested that the chance of survival and allelic diversity of some subpopulations will decrease dramatically over the next 50 years if no migration occurs. Our DNA-based evidence reveals an urgent need for a management plan for the conservation of P. guimbeaui. We identified 18 threatened and 12 viable subpopulations and discuss a range of management options that include translocation of threatened subpopulations to retain maximum allelic diversity, and habitat restoration and assisted migration to decrease genetic erosion and inbreeding for the viable subpopulations.

  6. High risks of losing genetic diversity in an endemic Mauritian gecko: implications for conservation.

    PubMed

    Buckland, Steeves; Cole, Nik C; Groombridge, Jim J; Küpper, Clemens; Burke, Terry; Dawson, Deborah A; Gallagher, Laura E; Harris, Stephen

    2014-01-01

    Genetic structure can be a consequence of recent population fragmentation and isolation, or a remnant of historical localised adaptation. This poses a challenge for conservationists since misinterpreting patterns of genetic structure may lead to inappropriate management. Of 17 species of reptile originally found in Mauritius, only five survive on the main island. One of these, Phelsuma guimbeaui (lowland forest day gecko), is now restricted to 30 small isolated subpopulations following severe forest fragmentation and isolation due to human colonisation. We used 20 microsatellites in ten subpopulations and two mitochondrial DNA (mtDNA) markers in 13 subpopulations to: (i) assess genetic diversity, population structure and genetic differentiation of subpopulations; (ii) estimate effective population sizes and migration rates of subpopulations; and (iii) examine the phylogenetic relationships of haplotypes found in different subpopulations. Microsatellite data revealed significant population structure with high levels of genetic diversity and isolation by distance, substantial genetic differentiation and no migration between most subpopulations. MtDNA, however, showed no evidence of population structure, indicating that there was once a genetically panmictic population. Effective population sizes of ten subpopulations, based on microsatellite markers, were small, ranging from 44 to 167. Simulations suggested that the chance of survival and allelic diversity of some subpopulations will decrease dramatically over the next 50 years if no migration occurs. Our DNA-based evidence reveals an urgent need for a management plan for the conservation of P. guimbeaui. We identified 18 threatened and 12 viable subpopulations and discuss a range of management options that include translocation of threatened subpopulations to retain maximum allelic diversity, and habitat restoration and assisted migration to decrease genetic erosion and inbreeding for the viable subpopulations. PMID

  7. Fungal endophytes: modifiers of plant disease.

    PubMed

    Busby, Posy E; Ridout, Mary; Newcombe, George

    2016-04-01

    Many recent studies have demonstrated that non-pathogenic fungi within plant microbiomes, i.e., endophytes ("endo" = within, "phyte" = plant), can significantly modify the expression of host plant disease. The rapid pace of advancement in endophyte ecology warrants a pause to synthesize our understanding of endophyte disease modification and to discuss future research directions. We reviewed recent literature on fungal endophyte disease modification, and here report on several emergent themes: (1) Fungal endophyte effects on plant disease span the full spectrum from pathogen antagonism to pathogen facilitation, with pathogen antagonism most commonly reported. (2) Agricultural plant pathosystems are the focus of research on endophyte disease modification. (3) A taxonomically diverse group of fungal endophytes can influence plant disease severity. And (4) Fungal endophyte effects on plant disease severity are context-dependent. Our review highlights the importance of fungal endophytes for plant disease across a broad range of plant pathosystems, yet simultaneously reveals that complexity within plant microbiomes presents a significant challenge to disentangling the biotic environmental factors affecting plant disease severity. Manipulative studies integrating eco-evolutionary approaches with emerging molecular tools will be poised to elucidate the functional importance of endophytes in natural plant pathosystems that are fundamental to biodiversity and conservation.

  8. Fungal endophytes: modifiers of plant disease.

    PubMed

    Busby, Posy E; Ridout, Mary; Newcombe, George

    2016-04-01

    Many recent studies have demonstrated that non-pathogenic fungi within plant microbiomes, i.e., endophytes ("endo" = within, "phyte" = plant), can significantly modify the expression of host plant disease. The rapid pace of advancement in endophyte ecology warrants a pause to synthesize our understanding of endophyte disease modification and to discuss future research directions. We reviewed recent literature on fungal endophyte disease modification, and here report on several emergent themes: (1) Fungal endophyte effects on plant disease span the full spectrum from pathogen antagonism to pathogen facilitation, with pathogen antagonism most commonly reported. (2) Agricultural plant pathosystems are the focus of research on endophyte disease modification. (3) A taxonomically diverse group of fungal endophytes can influence plant disease severity. And (4) Fungal endophyte effects on plant disease severity are context-dependent. Our review highlights the importance of fungal endophytes for plant disease across a broad range of plant pathosystems, yet simultaneously reveals that complexity within plant microbiomes presents a significant challenge to disentangling the biotic environmental factors affecting plant disease severity. Manipulative studies integrating eco-evolutionary approaches with emerging molecular tools will be poised to elucidate the functional importance of endophytes in natural plant pathosystems that are fundamental to biodiversity and conservation. PMID:26646287

  9. Conserved factors Ryp2 and Ryp3 control cell morphology and infectious spore formation in the fungal pathogen Histoplasma capsulatum.

    PubMed

    Webster, Rachael Hanby; Sil, Anita

    2008-09-23

    The human fungal pathogen Histoplasma capsulatum grows in a sporulating filamentous form in the soil and, after inhalation of infectious spores, converts to a pathogenic yeast form inside host macrophages in response to temperature. Here we report the identification of two genes (RYP2 and RYP3) required for yeast-phase growth. Ryp2 and Ryp3 are homologous to each other and to the Velvet A family of regulatory proteins in Aspergillus species and other filamentous fungi. Wild-type H. capsulatum grows as filaments at room temperature and as yeast cells at 37 degrees C, but ryp2 and ryp3 mutants constitutively grow as filaments independent of temperature. RYP2 and RYP3 transcripts accumulate to higher levels at 37 degrees C than at room temperature. This differential expression is similar to the previously identified RYP1 transcript, which encodes a transcriptional regulator required for the yeast-phase expression program. Ryp1 associates with the upstream region of RYP2, and each of the three RYP genes is required for the differential expression of the others at 37 degrees C. In addition to responding to the elevated temperature of the mammalian host, RYP2 and RYP3 are essential for viable spore production and regulation of sporulation at room temperature. This regulatory function is strikingly similar to the role of the Aspergillus Velvet A protein family in spore development in response to light, with the notable distinction that the H. capsulatum circuit responds to temperature. PMID:18791067

  10. Regulatory Circuitry Governing Fungal Development, Drug Resistance, and Disease

    PubMed Central

    Shapiro, Rebecca S.; Robbins, Nicole; Cowen, Leah E.

    2011-01-01

    Summary: Pathogenic fungi have become a leading cause of human mortality due to the increasing frequency of fungal infections in immunocompromised populations and the limited armamentarium of clinically useful antifungal drugs. Candida albicans, Cryptococcus neoformans, and Aspergillus fumigatus are the leading causes of opportunistic fungal infections. In these diverse pathogenic fungi, complex signal transduction cascades are critical for sensing environmental changes and mediating appropriate cellular responses. For C. albicans, several environmental cues regulate a morphogenetic switch from yeast to filamentous growth, a reversible transition important for virulence. Many of the signaling cascades regulating morphogenesis are also required for cells to adapt and survive the cellular stresses imposed by antifungal drugs. Many of these signaling networks are conserved in C. neoformans and A. fumigatus, which undergo distinct morphogenetic programs during specific phases of their life cycles. Furthermore, the key mechanisms of fungal drug resistance, including alterations of the drug target, overexpression of drug efflux transporters, and alteration of cellular stress responses, are conserved between these species. This review focuses on the circuitry regulating fungal morphogenesis and drug resistance and the impact of these pathways on virulence. Although the three human-pathogenic fungi highlighted in this review are those most frequently encountered in the clinic, they represent a minute fraction of fungal diversity. Exploration of the conservation and divergence of core signal transduction pathways across C. albicans, C. neoformans, and A. fumigatus provides a foundation for the study of a broader diversity of pathogenic fungi and a platform for the development of new therapeutic strategies for fungal disease. PMID:21646428

  11. Coral-Associated Bacterial Diversity Is Conserved across Two Deep-Sea Anthothela Species.

    PubMed

    Lawler, Stephanie N; Kellogg, Christina A; France, Scott C; Clostio, Rachel W; Brooke, Sandra D; Ross, Steve W

    2016-01-01

    Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4-V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont. PMID:27092120

  12. Coral-associated bacterial diversity is conserved across two deep-sea Anthothela species

    USGS Publications Warehouse

    Lawler, Stephanie N.; Kellogg, Christina A.; France, Scott C; Clostio, Rachel W; Brooke, Sandra D.; Ross, Steve W.

    2016-01-01

    Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4-V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont.

  13. Conservation of avian diversity in the Sierra Nevada: moving beyond a single-species management focus

    USGS Publications Warehouse

    White, Angela M.; Zipkin, Elise F.; Manley, Patricia N.; Schlesinger, Matthew D.

    2013-01-01

    Background: As a result of past practices, many of the dry coniferous forests of the western United States contain dense, even-aged stands with uncharacteristically high levels of litter and downed woody debris. These changes to the forest have received considerable attention as they elevate concerns regarding the outcome of wildland fire. However, attempts to reduce biomass through fuel reduction (i.e., thinning of trees) are often opposed by public interest groups whose objectives include maintaining habitat for species of concern such as the spotted owl, Strix occidentalis, the northern goshawk, Accipiter gentilis, and the Pacific fisher, Martes pennanti. Whether protection of these upper-trophic level species confers adequate conservation of avian forest diversity is unknown. Methodology and Principal Findings: We use a multi-species occurrence model to estimate the habitat associations of 47 avian species detected at 742 sampling locations within an 880-km2 area in the Sierra Nevada. Our approach, which accounts for variations in detectability of species, estimates occurrence probabilities of all species in a community by linking species occurrence models into one hierarchical community model, thus improving inferences on all species, especially those that are rare or observed infrequently. We address how the avian community is influenced by covariates related to canopy cover, tree size and shrub cover while accounting for the impacts of abiotic variables known to affect species distributions. Conclusions and Significance: Environmental parameters estimated through our approach emphasize the importance of within and between stand-level heterogeneity in meeting biodiversity objectives and suggests that many avian species would increase under more open canopy habitat conditions than those favored by umbrella species of high conservation concern. Our results suggest that a more integrated approach that emphasizes maintaining a diversity of habitats across

  14. Assessing the effectiveness of specially protected areas for conservation of Antarctica's botanical diversity.

    PubMed

    Hughes, Kevin A; Ireland, Louise C; Convey, Peter; Fleming, Andrew H

    2016-02-01

    Vegetation is sparsely distributed over Antarctica's ice-free ground, and distinct plant communities are present in each of the continent's 15 recently identified Antarctic Conservation Biogeographic Regions (ACBRs). With rapidly increasing human activity in Antarctica, terrestrial plant communities are at risk of damage or destruction by trampling, overland transport, and infrastructure construction and from the impacts of anthropogenically introduced species, as well as uncontrollable pressures such as fur seal (Arctocephalus gazella) activity and climate change. Under the Protocol on Environmental Protection to the Antarctic Treaty, the conservation of plant communities can be enacted and facilitated through the designation of Antarctic Specially Protected Areas (ASPAs). We examined the distribution within the 15 ACBRs of the 33 ASPAs whose explicit purpose includes protecting macroscopic terrestrial flora. We completed the first survey using normalized difference vegetation index (NDVI) satellite remote sensing to provide baseline data on the extent of vegetation cover in all ASPAs designated for plant protection in Antarctica. Large omissions in the protection of Antarctic botanical diversity were found. There was no protection of plant communities in 6 ACBRs, and in another 6, <0.4% of the ACBR area was included in an ASPA that protected vegetation. Protected vegetation cover within the 33 ASPAs totaled 16.1 km(2) for the entire Antarctic continent; over half was within a single protected area. Over 96% of the protected vegetation was contained in 2 ACBRs, which together contributed only 7.8% of the continent's ice-free ground. We conclude that Antarctic botanical diversity is clearly inadequately protected and call for systematic designation of ASPAs protecting plant communities by the Antarctic Treaty Consultative Parties, the members of the governing body of the continent.

  15. Assessing the effectiveness of specially protected areas for conservation of Antarctica's botanical diversity.

    PubMed

    Hughes, Kevin A; Ireland, Louise C; Convey, Peter; Fleming, Andrew H

    2016-02-01

    Vegetation is sparsely distributed over Antarctica's ice-free ground, and distinct plant communities are present in each of the continent's 15 recently identified Antarctic Conservation Biogeographic Regions (ACBRs). With rapidly increasing human activity in Antarctica, terrestrial plant communities are at risk of damage or destruction by trampling, overland transport, and infrastructure construction and from the impacts of anthropogenically introduced species, as well as uncontrollable pressures such as fur seal (Arctocephalus gazella) activity and climate change. Under the Protocol on Environmental Protection to the Antarctic Treaty, the conservation of plant communities can be enacted and facilitated through the designation of Antarctic Specially Protected Areas (ASPAs). We examined the distribution within the 15 ACBRs of the 33 ASPAs whose explicit purpose includes protecting macroscopic terrestrial flora. We completed the first survey using normalized difference vegetation index (NDVI) satellite remote sensing to provide baseline data on the extent of vegetation cover in all ASPAs designated for plant protection in Antarctica. Large omissions in the protection of Antarctic botanical diversity were found. There was no protection of plant communities in 6 ACBRs, and in another 6, <0.4% of the ACBR area was included in an ASPA that protected vegetation. Protected vegetation cover within the 33 ASPAs totaled 16.1 km(2) for the entire Antarctic continent; over half was within a single protected area. Over 96% of the protected vegetation was contained in 2 ACBRs, which together contributed only 7.8% of the continent's ice-free ground. We conclude that Antarctic botanical diversity is clearly inadequately protected and call for systematic designation of ASPAs protecting plant communities by the Antarctic Treaty Consultative Parties, the members of the governing body of the continent. PMID:26205208

  16. Coral-Associated Bacterial Diversity Is Conserved across Two Deep-Sea Anthothela Species

    PubMed Central

    Lawler, Stephanie N.; Kellogg, Christina A.; France, Scott C.; Clostio, Rachel W.; Brooke, Sandra D.; Ross, Steve W.

    2016-01-01

    Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4–V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont. PMID:27092120

  17. Coral-Associated Bacterial Diversity Is Conserved across Two Deep-Sea Anthothela Species.

    PubMed

    Lawler, Stephanie N; Kellogg, Christina A; France, Scott C; Clostio, Rachel W; Brooke, Sandra D; Ross, Steve W

    2016-01-01

    Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4-V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont.

  18. Conservation implications of the evolutionary history and genetic diversity hotspots of the snowshoe hare.

    PubMed

    Cheng, Ellen; Hodges, Karen E; Melo-Ferreira, José; Alves, Paulo C; Mills, L Scott

    2014-06-01

    With climate warming, the ranges of many boreal species are expected to shift northward and to fragment in southern peripheral ranges. To understand the conservation implications of losing southern populations, we examined range-wide genetic diversity of the snowshoe hare (Lepus americanus), an important prey species that drives boreal ecosystem dynamics. We analysed microsatellite (8 loci) and mitochondrial DNA sequence (cytochrome b and control region) variation in almost 1000 snowshoe hares. A hierarchical structure analysis of the microsatellite data suggests initial subdivision in two groups, Boreal and southwestern. The southwestern group further splits into Greater Pacific Northwest and U.S. Rockies. The genealogical information retrieved from mtDNA is congruent with the three highly differentiated and divergent groups of snowshoe hares. These groups can correspond with evolutionarily significant units that might have evolved in separate refugia south and east of the Pleistocene ice sheets. Genetic diversity was highest at mid-latitudes of the species' range, and genetic uniqueness was greatest in southern populations, consistent with substructuring inferred from both mtDNA and microsatellite analyses at finer levels of analysis. Surprisingly, snowshoe hares in the Greater Pacific Northwest mtDNA lineage were more closely related to black-tailed jackrabbits (Lepus californicus) than to other snowshoe hares, which may result from secondary introgression or shared ancestral polymorphism. Given the genetic distinctiveness of southern populations and minimal gene flow with their northern neighbours, fragmentation and loss of southern boreal habitats could mean loss of many unique alleles and reduced evolutionary potential.

  19. Mapping Genetic Diversity of Cherimoya (Annona cherimola Mill.): Application of Spatial Analysis for Conservation and Use of Plant Genetic Resources

    PubMed Central

    van Zonneveld, Maarten; Scheldeman, Xavier; Escribano, Pilar; Viruel, María A.; Van Damme, Patrick; Garcia, Willman; Tapia, César; Romero, José; Sigueñas, Manuel; Hormaza, José I.

    2012-01-01

    There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at

  20. Seed plant phylogenetic diversity and species richness in conservation planning within a global biodiversity hotspot in eastern Asia.

    PubMed

    Li, Rong; Kraft, Nathan J B; Yu, Haiying; Li, Heng

    2015-12-01

    One of the main goals of conservation biology is to understand the factors shaping variation in biodiversity across the planet. This understanding is critical for conservation planners to be able to develop effective conservation strategies. Although many studies have focused on species richness and the protection of rare and endemic species, less attention has been paid to the protection of the phylogenetic dimension of biodiversity. We explored how phylogenetic diversity, species richness, and phylogenetic community structure vary in seed plant communities along an elevational gradient in a relatively understudied high mountain region, the Dulong Valley, in southeastern Tibet, China. As expected, phylogenetic diversity was well correlated with species richness among the elevational bands and among communities. At the community level, evergreen broad-leaved forests had the highest levels of species richness and phylogenetic diversity. Using null model analyses, we found evidence of nonrandom phylogenetic structure across the region. Evergreen broad-leaved forests were phylogenetically overdispersed, whereas other vegetation types tended to be phylogenetically clustered. We suggest that communities with high species richness or overdispersed phylogenetic structure should be a focus for biodiversity conservation within the Dulong Valley because these areas may help maximize the potential of this flora to respond to future global change. In biodiversity hotspots worldwide, we suggest that the phylogenetic structure of a community may serve as a useful measure of phylogenetic diversity in the context of conservation planning.

  1. Conservation and population genetic diversity of Curcuma wenyujin (Zingiberaceae), a multifunctional medicinal herb.

    PubMed

    Zheng, W H; Zhuo, Y; Liang, L; Ding, W Y; Liang, L Y; Wang, X F

    2015-09-08

    Curcuma wenyujin is an important multifunctional medicinal herb in China. Currently, populations of C. wenyujin are decreasing, and wild individuals have almost disappeared from their natural habitats. Moreover, little is known regarding the molecular characteristics of this plant. In this study, we investigated the genetic diversity and variation of five populations of C. wenyujin, using ran-dom amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. We found that the percentages of polymorphic loci (PPL) at the species level (98.25% by RAPD and 100% by ISSR) were significantly higher than those at the population level (66.32% by RAPD and 67.14% by ISSR). The highest values of PPL, expected heterozygosity, and Shannon's information index were in Pop1, while the lowest values were in Pop2. Both DNA markers revealed a short genetic distance between Pop1 and Pop2 (0.1424 by RAPD and 0.1904 by ISSR). Phylogenetic trees produced similar results, with Pop1, Pop2, and Pop5 in one group and Pop3 and Pop4 in another. There were no significant correlations between their genetic distances and their geographical distances. The highest genetic diversity was in Pop1 and the lowest was in Pop2, and genetic diversity at the species level was relatively low, but much higher than that at the population level. We recommended the establishment of a germplasm bank, in situ con-servation, and propagation of wild individuals. The present study will improve the evaluation, protection, and utilization of the population resources of C. wenyujin.

  2. A conserved structural module regulates transcriptional responses to diverse stress signals in bacteria

    SciTech Connect

    Campbell, Elizabeth A.; Greenwell, Roger S.; Anthony, Jennifer R.; Wang, Sheng; Lim, Lee; Das, Kakoli; Sofia, Heidi J.; Donohue, Timothy J.; Darst, Seth A.

    2007-09-07

    In Rhodbacter sphaeroides, transcriptional response to singlet oxygen is controlled by the ECF (extracytoplasmic function) transcription factor, σΕ. ECF σ’s comprise the largest and most divergent group of the σ70-family members and are negatively regulated by their cognate anti-σ factor. Here, we determine the crystal structure of the Rhodobacter sphaeroides ECF σ factor, σE, in an inhibitory complex with its anti-σ, ChrR. The structure reveals that ChrR is composed of two structural domains separated by a flexible linker. The N-terminal domain sterically occludes the two primary binding determinants on σE for core RNA polymerase and is thus referred to as the ASD (anti-σ domain). Genetic and biochemical characterization of the two domains show that the ASD is sufficient to inhibit σE dependant transcription and the C-terminal domain is required for response to singlet oxygen and the release of σE from the ASD. In addition, structural and sequence analyses of the ASD of ChrR and other ECF anti-σ’s, reveal that the N-terminal domain of different groups of ECF anti-σ’s share a common structural fold with some sequence similarity. Bioinformatics studies show that the ASD occurs in as many as one third of ECF anti-σ’s, many of which have diverse C-terminal domains. The conserved ASD are sometimes fused to diverse C-terminal domains. These studies reveal that the ASD class of anti-σ’s are extraordinarily diverse, based on the type of σΕ factors they are associated with and the C-terminal domains to which they are linked.

  3. Conservation and population genetic diversity of Curcuma wenyujin (Zingiberaceae), a multifunctional medicinal herb.

    PubMed

    Zheng, W H; Zhuo, Y; Liang, L; Ding, W Y; Liang, L Y; Wang, X F

    2015-01-01

    Curcuma wenyujin is an important multifunctional medicinal herb in China. Currently, populations of C. wenyujin are decreasing, and wild individuals have almost disappeared from their natural habitats. Moreover, little is known regarding the molecular characteristics of this plant. In this study, we investigated the genetic diversity and variation of five populations of C. wenyujin, using ran-dom amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. We found that the percentages of polymorphic loci (PPL) at the species level (98.25% by RAPD and 100% by ISSR) were significantly higher than those at the population level (66.32% by RAPD and 67.14% by ISSR). The highest values of PPL, expected heterozygosity, and Shannon's information index were in Pop1, while the lowest values were in Pop2. Both DNA markers revealed a short genetic distance between Pop1 and Pop2 (0.1424 by RAPD and 0.1904 by ISSR). Phylogenetic trees produced similar results, with Pop1, Pop2, and Pop5 in one group and Pop3 and Pop4 in another. There were no significant correlations between their genetic distances and their geographical distances. The highest genetic diversity was in Pop1 and the lowest was in Pop2, and genetic diversity at the species level was relatively low, but much higher than that at the population level. We recommended the establishment of a germplasm bank, in situ con-servation, and propagation of wild individuals. The present study will improve the evaluation, protection, and utilization of the population resources of C. wenyujin. PMID:26400273

  4. Genetic diversity in the gypsy moth fungal pathogen Entomophaga maimaiga from founder populations in North America and source populations in Asia.

    PubMed

    Nielsen, Charlotte; Milgroom, Michael G; Hajek, Ann E

    2005-08-01

    Entomophaga maimaiga is a naturally occurring fungal pathogen specific to larvae of the gypsy moth, Lymantria dispar. E. maimaiga is thought to be native to Asia where its epizootics can suppress gypsy moth outbreaks. However, in the USA this beneficial fungal pathogen was not observed until 1989, although an isolate of E. maimaiga from Tokyo was released in Massachusetts to control gypsy moths as early as in 1910-1911, and another isolate from Ishikawa Prefecture in Japan was later released in 1985 and 1986 in New York and Virginia. Our objectives were to: (1) test the hypothesis that E. maimaiga populations in the USA have reduced genetic variability due to founder effects compared to the putative ancestral populations in Asia; (2) track the origin of the North American populations of this fungus; and (3) assess whether genetic differences among E. maimaiga isolates are correlated to morphological differences. We compared genetic diversity among 30 E. maimaiga isolates originating from seven states in the USA, five prefectures in Japan, one province of China and one region of far eastern Russia by AFLPs. Among 14 USA isolates, only ten polymorphic AFLP loci were found, whereas 56 polymorphic loci were found among 16 Asian isolates; 29 loci were polymorphic among 12 isolates from Japan alone. Average gene diversity (h) for the polymorphic loci was 0.223 +/- 0.005 for Asia (including Japan), 0.131 +/- 0.006 for Japan only, and 0.041 +/- 0.004 for the USA. Thus, native populations from Asia were more diverse than the USA populations. These results are consistent with the expectation of a population founded from a source population by a small number of individuals. Distance and parsimony analyses of AFLP data showed that the isolates from the USA formed one distinct clade that was most closely related to Japanese isolates collected outside the Tokyo area. No morphological variation of E. maimaiga from different geographical locations was detected.

  5. Fungal Genomics Program

    SciTech Connect

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  6. Conservation.

    ERIC Educational Resources Information Center

    National Audubon Society, New York, NY.

    This set of teaching aids consists of seven Audubon Nature Bulletins, providing the teacher and student with informational reading on various topics in conservation. The bulletins have these titles: Plants as Makers of Soil, Water Pollution Control, The Ground Water Table, Conservation--To Keep This Earth Habitable, Our Threatened Air Supply,…

  7. Burkholderia terrae BS001 migrates proficiently with diverse fungal hosts through soil and provides protection from antifungal agents

    PubMed Central

    Nazir, Rashid; Tazetdinova, Diana I.; van Elsas, Jan Dirk

    2014-01-01

    Soil bacteria can benefit from co-occurring soil fungi in respect of the acquisition of carbonaceous nutrients released by fungal hyphae and the access to novel territories in soil. Here, we investigated the capacity of the mycosphere-isolated bacterium Burkholderia terrae BS001 to comigrate through soil along with hyphae of the soil fungi Trichoderma asperellum, Rhizoctonia solani, Fusarium oxysporum, F. oxysporum pv lini, Coniochaeta ligniaria, Phanerochaete velutina, and Phallus impudicus. We used Lyophyllum sp. strain Karsten as the reference migration-inciting fungus. Bacterial migration through presterilized soil on the extending fungal hyphae was detected with six of the seven test fungi, with only Phallus impudicus not showing any bacterial transport. Much like with Lyophyllum sp. strain Karsten, intermediate (106–108 CFU g-1 dry soil) to high (>108 CFU g-1 dry soil) strain BS001 cell population sizes were found at the hyphal migration fronts of four fungi, i.e., T. asperellum, Rhizoctonia solani, F. oxysporum and F. oxysporum pv lini, whereas for two fungi, Coniochaeta ligniaria and Phanerochaete velutina, the migration responses were retarded and population sizes were lower (103–106 CFU g-1 dry soil). Consistent with previous data obtained with the reference fungus, migration with the migration-inciting fungi occurred only in the direction of the hyphal growth front. Remarkably, Burkholderia terrae BS001 provided protection from several antifungal agents to the canonical host Lyophyllum sp. strain Karsten. Specifically, this host was protected from Pseudomonas fluorescens strain CHA0 metabolites, as well as from the anti-fungal agent cycloheximide. Similar protection by strain BS001was observed for T. asperellum, and, to a lower extent, F. oxysporum and Rhizoctonia solani. The protective effect may be related to the consistent occurrence of biofilm-like cell layers or agglomerates at the surfaces of the protected fungi. The current study represents

  8. Host species-specific conservation of a family of repeated DNA sequences in the genome of a fungal plant pathogen.

    PubMed Central

    Hamer, J E; Farrall, L; Orbach, M J; Valent, B; Chumley, F G

    1989-01-01

    We have identified a family of dispersed repetitive DNA sequences in the genome of Magnaporthe grisea, the fungus that causes rice blast disease. We have named this family of DNA sequences "MGR" for M. grisea repeat. Analysis of five MGR clones demonstrates that MGR sequences are highly polymorphic. The segregation of MGR sequences in genetic crosses and hybridization of MGR probes to separated, chromosome-size DNA molecules of M. grisea shows that this family of sequences is distributed among the M. grisea chromosomes. MGR sequences also hybridize to discrete poly(A)+ RNAs. Southern blot analysis using a MGR probe can distinguish rice pathogens from various sources. However, MGR sequences are not highly conserved in the genomes of M. grisea field isolates that do not infect rice. These results suggest that host selection for a specific pathogen genotype has occurred during the breeding and cultivation of rice. Images PMID:2602385

  9. 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

  10. 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

  11. Fungal Tests

    MedlinePlus

    ... effectiveness of treatment. For many superficial skin and yeast infections, a clinical examination of the affected person ... the chemical solution dissolves non-fungal elements; reveals yeast cells and fungal hyphae (branching filaments) on a ...

  12. Fungal arthritis

    MedlinePlus

    Mycotic arthritis; Infectious arthritis - fungal ... Marquez J, Espinoza LR. Infectious arthritis II: mycobacterial, brucellar, fungal, and parasitic arthritis. In: Hochberg MC, Silman AJ, Smolen JS, Weinblatt ME, Weisman MH, eds. Rheumatology . ...

  13. 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

  14. 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.

  15. Conserved Patterns of Microbial Immune Escape: Pathogenic Microbes of Diverse Origin Target the Human Terminal Complement Inhibitor Vitronectin via a Single Common Motif

    PubMed Central

    Kraiczy, Peter; Hammerschmidt, Sven; Skerka, Christine; Zipfel, Peter F.; Riesbeck, Kristian

    2016-01-01

    Pathogenicity of many microbes relies on their capacity to resist innate immunity, and to survive and persist in an immunocompetent human host microbes have developed highly efficient and sophisticated complement evasion strategies. Here we show that different human pathogens including Gram-negative and Gram-positive bacteria, as well as the fungal pathogen Candida albicans, acquire the human terminal complement regulator vitronectin to their surface. By using truncated vitronectin fragments we found that all analyzed microbial pathogens (n = 13) bound human vitronectin via the same C-terminal heparin-binding domain (amino acids 352–374). This specific interaction leaves the terminal complement complex (TCC) regulatory region of vitronectin accessible, allowing inhibition of C5b-7 membrane insertion and C9 polymerization. Vitronectin complexed with the various microbes and corresponding proteins was thus functionally active and inhibited complement-mediated C5b-9 deposition. Taken together, diverse microbial pathogens expressing different structurally unrelated vitronectin-binding molecules interact with host vitronectin via the same conserved region to allow versatile control of the host innate immune response. PMID:26808444

  16. Establishment of Orchards with Black Polyethylene Film Mulching: Effect on Nematode and Fungal Pathogens, Water Conservation, and Tree Growth

    PubMed Central

    Duncan, R. A.; Stapleton, J. J.; McKenry, M. V.

    1992-01-01

    Placement of a 3-m-wide, black, polyethylene film mulch down rows of peach (Prunus persica 'Red Haven' on 'Lovell' rootstock) and almond (Prunus dulcis 'Nonpareil' on 'Lovell') trees in the San Joaquin Valley of California resulted in irrigation water conservation of 75%, higher soil temperature in the surface 30 cm, a tendency toward greater root mass, elimination of weeds, and a greater abundance of Meloidogyne incognita second-stage juveniles in soil but reduced root galling when compared to the nonmulched control. Population levels of Pratylenchus hexincisus, a nematode found within tree roots, were reduced by mulching, as were those of Tylenchulus semipenetrans, which survived on old grape roots remaining from a previously planted vineyard, and Paratrichodorus minor, which probably fed on roots of various weed species growing in the nonmulched soil. Populations of Pythium ultimum were not significantly changed, probably also due to the biological refuge of the old grape roots and moderate soil heating level. Trunk diameters of peach trees were increased by mulching, but those of almond trees were reduced by the treatment. Leaf petiole analysis indicated that concentrations of mineral nutrients were inconsistent, except for a significant increase in Ca in both tree species. PMID:19283045

  17. Conserving tropical tree diversity and forest structure: the value of small rainforest patches in moderately-managed landscapes.

    PubMed

    Hernández-Ruedas, Manuel A; Arroyo-Rodríguez, Víctor; Meave, Jorge A; Martínez-Ramos, Miguel; Ibarra-Manríquez, Guillermo; Martínez, Esteban; Jamangapé, Gilberto; Melo, Felipe P L; Santos, Bráulio A

    2014-01-01

    Rainforests are undergoing severe deforestation and fragmentation worldwide. A huge amount of small forest patches are being created, but their value in conserving biodiversity and forest structure is still controversial. Here, we demonstrate that in a species-rich and moderately-managed Mexican tropical landscape small rainforest patches (<100 ha) can be highly valuable for the conservation of tree diversity and forest structure. These patches showed diverse communities of native plants, including endangered species, and a new record for the country. Although the number of logged trees increased in smaller patches, patch size was a poor indicator of basal area, stem density, number of species, genera and families, and community evenness. Cumulative species-area curves indicated that all patches had a similar contribution to the regional species diversity. This idea also was supported by the fact that patches strongly differed in floristic composition (high β-diversity), independently of patch size. Thus, in agreement with the land-sharing approach, our findings support that small forest patches in moderately-managed landscapes should be included in conservation initiatives to maintain landscape heterogeneity, species diversity, and ecosystem services. PMID:24901954

  18. Conserving Tropical Tree Diversity and Forest Structure: The Value of Small Rainforest Patches in Moderately-Managed Landscapes

    PubMed Central

    Hernández-Ruedas, Manuel A.; Arroyo-Rodríguez, Víctor; Meave, Jorge A.; Martínez-Ramos, Miguel; Ibarra-Manríquez, Guillermo; Martínez, Esteban; Jamangapé, Gilberto; Melo, Felipe P. L.; Santos, Bráulio A.

    2014-01-01

    Rainforests are undergoing severe deforestation and fragmentation worldwide. A huge amount of small forest patches are being created, but their value in conserving biodiversity and forest structure is still controversial. Here, we demonstrate that in a species-rich and moderately-managed Mexican tropical landscape small rainforest patches (<100 ha) can be highly valuable for the conservation of tree diversity and forest structure. These patches showed diverse communities of native plants, including endangered species, and a new record for the country. Although the number of logged trees increased in smaller patches, patch size was a poor indicator of basal area, stem density, number of species, genera and families, and community evenness. Cumulative species-area curves indicated that all patches had a similar contribution to the regional species diversity. This idea also was supported by the fact that patches strongly differed in floristic composition (high β-diversity), independently of patch size. Thus, in agreement with the land-sharing approach, our findings support that small forest patches in moderately-managed landscapes should be included in conservation initiatives to maintain landscape heterogeneity, species diversity, and ecosystem services. PMID:24901954

  19. Conserving tropical tree diversity and forest structure: the value of small rainforest patches in moderately-managed landscapes.

    PubMed

    Hernández-Ruedas, Manuel A; Arroyo-Rodríguez, Víctor; Meave, Jorge A; Martínez-Ramos, Miguel; Ibarra-Manríquez, Guillermo; Martínez, Esteban; Jamangapé, Gilberto; Melo, Felipe P L; Santos, Bráulio A

    2014-01-01

    Rainforests are undergoing severe deforestation and fragmentation worldwide. A huge amount of small forest patches are being created, but their value in conserving biodiversity and forest structure is still controversial. Here, we demonstrate that in a species-rich and moderately-managed Mexican tropical landscape small rainforest patches (<100 ha) can be highly valuable for the conservation of tree diversity and forest structure. These patches showed diverse communities of native plants, including endangered species, and a new record for the country. Although the number of logged trees increased in smaller patches, patch size was a poor indicator of basal area, stem density, number of species, genera and families, and community evenness. Cumulative species-area curves indicated that all patches had a similar contribution to the regional species diversity. This idea also was supported by the fact that patches strongly differed in floristic composition (high β-diversity), independently of patch size. Thus, in agreement with the land-sharing approach, our findings support that small forest patches in moderately-managed landscapes should be included in conservation initiatives to maintain landscape heterogeneity, species diversity, and ecosystem services.

  20. Designing conservation strategies to preserve the genetic diversity of Astragalus edulis Bunge, an endangered species from western Mediterranean region.

    PubMed

    Peñas, Julio; Barrios, Sara; Bobo-Pinilla, Javier; Lorite, Juan; Martínez-Ortega, M Montserrat

    2016-01-01

    Astragalus edulis (Fabaceae) is an endangered annual species from the western Mediterranean region that colonized the SE Iberian Peninsula, NE and SW Morocco, and the easternmost Macaronesian islands (Lanzarote and Fuerteventura). Although in Spain some conservation measures have been adopted, it is still necessary to develop an appropriate management plan to preserve genetic diversity across the entire distribution area of the species. Our main objective was to use population genetics as well as ecological and phylogeographic data to select Relevant Genetic Units for Conservation (RGUCs) as the first step in designing conservation plans for A. edulis. We identified six RGUCs for in situ conservation, based on estimations of population genetic structure and probabilities of loss of rare alleles. Additionally, further population parameters, i.e. occupation area, population size, vulnerability, legal status of the population areas, and the historical haplotype distribution, were considered in order to establish which populations deserve conservation priority. Three populations from the Iberian Peninsula, two from Morocco, and one from the Canary Islands represent the total genetic diversity of the species and the rarest allelic variation. Ex situ conservation is recommended to complement the preservation of A. edulis, given that effective in situ population protection is not feasible in all cases. The consideration of complementary phylogeographic and ecological data is useful for management efforts to preserve the evolutionary potential of the species. PMID:26844014

  1. Designing conservation strategies to preserve the genetic diversity of Astragalus edulis Bunge, an endangered species from western Mediterranean region

    PubMed Central

    Barrios, Sara; Bobo-Pinilla, Javier; Lorite, Juan; Martínez-Ortega, M. Montserrat

    2016-01-01

    Astragalus edulis (Fabaceae) is an endangered annual species from the western Mediterranean region that colonized the SE Iberian Peninsula, NE and SW Morocco, and the easternmost Macaronesian islands (Lanzarote and Fuerteventura). Although in Spain some conservation measures have been adopted, it is still necessary to develop an appropriate management plan to preserve genetic diversity across the entire distribution area of the species. Our main objective was to use population genetics as well as ecological and phylogeographic data to select Relevant Genetic Units for Conservation (RGUCs) as the first step in designing conservation plans for A. edulis. We identified six RGUCs for in situ conservation, based on estimations of population genetic structure and probabilities of loss of rare alleles. Additionally, further population parameters, i.e. occupation area, population size, vulnerability, legal status of the population areas, and the historical haplotype distribution, were considered in order to establish which populations deserve conservation priority. Three populations from the Iberian Peninsula, two from Morocco, and one from the Canary Islands represent the total genetic diversity of the species and the rarest allelic variation. Ex situ conservation is recommended to complement the preservation of A. edulis, given that effective in situ population protection is not feasible in all cases. The consideration of complementary phylogeographic and ecological data is useful for management efforts to preserve the evolutionary potential of the species. PMID:26844014

  2. Designing conservation strategies to preserve the genetic diversity of Astragalus edulis Bunge, an endangered species from western Mediterranean region.

    PubMed

    Peñas, Julio; Barrios, Sara; Bobo-Pinilla, Javier; Lorite, Juan; Martínez-Ortega, M Montserrat

    2016-01-01

    Astragalus edulis (Fabaceae) is an endangered annual species from the western Mediterranean region that colonized the SE Iberian Peninsula, NE and SW Morocco, and the easternmost Macaronesian islands (Lanzarote and Fuerteventura). Although in Spain some conservation measures have been adopted, it is still necessary to develop an appropriate management plan to preserve genetic diversity across the entire distribution area of the species. Our main objective was to use population genetics as well as ecological and phylogeographic data to select Relevant Genetic Units for Conservation (RGUCs) as the first step in designing conservation plans for A. edulis. We identified six RGUCs for in situ conservation, based on estimations of population genetic structure and probabilities of loss of rare alleles. Additionally, further population parameters, i.e. occupation area, population size, vulnerability, legal status of the population areas, and the historical haplotype distribution, were considered in order to establish which populations deserve conservation priority. Three populations from the Iberian Peninsula, two from Morocco, and one from the Canary Islands represent the total genetic diversity of the species and the rarest allelic variation. Ex situ conservation is recommended to complement the preservation of A. edulis, given that effective in situ population protection is not feasible in all cases. The consideration of complementary phylogeographic and ecological data is useful for management efforts to preserve the evolutionary potential of the species.

  3. Mycorrhizal status and diversity of fungal endophytes in roots of common buckwheat (Fagopyrum esculentum) and tartary buckwheat (F. tataricum).

    PubMed

    Likar, Matevz; Bukovnik, Urska; Kreft, Ivan; Chrungoo, Nikhil K; Regvar, Marjana

    2008-09-01

    To determine the mycorrhizal status and to identify the fungi colonising the roots of the plants, common buckwheat (Fagopyrum esculentum) and tartary buckwheat (F. tataricum) were inoculated with an indigenous fungal mixture from a buckwheat field. Root colonisation was characterised by the hyphae and distinct microsclerotia of dark septate endophytes, with occasional arbuscules and vesicles of arbuscular mycorrhizal fungi. Sequences of arbuscular mycorrhizal fungi colonising tartary buckwheat clustered close to the Glomus species group A. Sequences with similarity to the Ceratobasidium/Rhizoctonia complex, a putative dark septate endophyte fungus, were amplified from the roots of both common and tartary buckwheat. To the best of our knowledge, this is the first report of arbuscular mycorrhizal colonisation in tartary buckwheat and the first molecular characterisation of these fungi that can colonise both of these economically important plant species.

  4. Arbuscular mycorrhizal fungal diversity, root colonization, and soil alkaline phosphatase activity in response to maize-wheat rotation and no-tillage in North China.

    PubMed

    Hu, Junli; Yang, Anna; Zhu, Anning; Wang, Junhua; Dai, Jue; Wong, Ming Hung; Lin, Xiangui

    2015-07-01

    Monitoring the effects of no-tillage (NT) in comparison with conventional tillage (CT) on soil microbes could improve our understanding of soil biochemical processes and thus help us to develop sound management strategies. The objective of this study was to compare the species composition and ecological function of soil arbuscular mycorrhizal (AM) fungi during the growth and rotation of crops under NT and CT. From late June 2009 to early June 2010, 32 topsoil (0-15 cm) samples from four individual plots per treatment (CT and NT) were collected at both the jointing and maturation stages of maize (Zea mays L.) and wheat (Triticum aestivum L.) from a long-term experimental field that was established in an Aquic Inceptisol in North China in June 2006. The AM fungal spores were isolated and identified and then used to calculate species diversity indices, including the Shannon- Wiener index (H'), Evenness (E), and Simpson's index (D). The root mycorrhizal colonization and soil alkaline phosphatase activity were also determined. A total of 34 species of AM fungi within nine genera were recorded. Compared with NT, CT negatively affected the soil AM fungal community at the maize sowing stage, leading to decreases in the average diversity indices (from 2.12, 0.79, and 0.82 to 1.79, 0.72, and 0.74 for H', E, and D, respectively), root mycorrhizal colonization (from 28% to 20%), soil alkaline phosphatase activity (from 0.24 to 0.19 mg/g/24 h) and available phosphorus concentration (from 17.4 to 10.5 mg/kg) at the maize jointing stage. However, reductions in diversity indices of H', E, and D were restored to 2.20, 0.81, and 0.84, respectively, at the maize maturation stage. CT should affect the community again at the wheat sowing stage; however, a similar restoration in the species diversity of AM fungi was completed before the wheat jointing stage, and the highest Jaccard index (0.800) for similarity in the species composition of soil AM fungi between CT and NT was recorded at

  5. Arbuscular mycorrhizal fungal diversity, root colonization, and soil alkaline phosphatase activity in response to maize-wheat rotation and no-tillage in North China.

    PubMed

    Hu, Junli; Yang, Anna; Zhu, Anning; Wang, Junhua; Dai, Jue; Wong, Ming Hung; Lin, Xiangui

    2015-07-01

    Monitoring the effects of no-tillage (NT) in comparison with conventional tillage (CT) on soil microbes could improve our understanding of soil biochemical processes and thus help us to develop sound management strategies. The objective of this study was to compare the species composition and ecological function of soil arbuscular mycorrhizal (AM) fungi during the growth and rotation of crops under NT and CT. From late June 2009 to early June 2010, 32 topsoil (0-15 cm) samples from four individual plots per treatment (CT and NT) were collected at both the jointing and maturation stages of maize (Zea mays L.) and wheat (Triticum aestivum L.) from a long-term experimental field that was established in an Aquic Inceptisol in North China in June 2006. The AM fungal spores were isolated and identified and then used to calculate species diversity indices, including the Shannon- Wiener index (H'), Evenness (E), and Simpson's index (D). The root mycorrhizal colonization and soil alkaline phosphatase activity were also determined. A total of 34 species of AM fungi within nine genera were recorded. Compared with NT, CT negatively affected the soil AM fungal community at the maize sowing stage, leading to decreases in the average diversity indices (from 2.12, 0.79, and 0.82 to 1.79, 0.72, and 0.74 for H', E, and D, respectively), root mycorrhizal colonization (from 28% to 20%), soil alkaline phosphatase activity (from 0.24 to 0.19 mg/g/24 h) and available phosphorus concentration (from 17.4 to 10.5 mg/kg) at the maize jointing stage. However, reductions in diversity indices of H', E, and D were restored to 2.20, 0.81, and 0.84, respectively, at the maize maturation stage. CT should affect the community again at the wheat sowing stage; however, a similar restoration in the species diversity of AM fungi was completed before the wheat jointing stage, and the highest Jaccard index (0.800) for similarity in the species composition of soil AM fungi between CT and NT was recorded at

  6. Spider Diversity on the Oceanic Island of Fernando De Noronha, Brazil, and Implications for Species Conservation

    PubMed Central

    Freitas, Gilson Carlos da Conceição; Brescovit, Antonio Domingos; Vasconceloslc, Simao Dias

    2013-01-01

    Fernando de Noronha is an oceanic archipelago in Brazil that has been subjected to major alterations in its natural habitat, as it is exposed to increasing rates of tourism. This research aimed at performing the first survey of spider species on the main island, focusing on the environmental occupation and conservation status of local species. Spiders were sampled through pitfall traps, beating sheets, and active collection in the dry (October 2005) and rainy (April 2006) seasons in several parts of the island, such as urban and protected areas. A total of 1,532 adult spiders from 44 species distributed in 20 families were collected. Forty-two species are newly recorded on the archipelago, of which 10 appear to be native. Theridiidae and Salticidae were the richest families, with seven and five species respectively. Hogna sp., probably an endemic Lycosidae species, had the highest abundance throughout the study (17%). Several non-native species were found, especially in the surroundings of human habitations. Areas exposed to human settlements had higher diversity indices and evenness values when compared to preserved areas. Most species were classified as being diurnal space web-weavers. The results suggest that non-native species seemed to be established on the island, due mainly to the traffic of people and goods from the continent.

  7. Identification of Conserved and Diverse Metabolic Shifts during Rice Grain Development

    PubMed Central

    Hu, Chaoyang; Tohge, Takayuki; Chan, Shen-An; Song, Yue; Rao, Jun; Cui, Bo; Lin, Hong; Wang, Lei; Fernie, Alisdair R.; Zhang, Dabing; Shi, Jianxin

    2016-01-01

    Seed development dedicates to reserve synthesis and accumulation and uncovering its genetic and biochemical mechanisms has been a major research focus. Although proteomic and transcriptomic analyses revealed dynamic changes of genes and enzymes involved, the information regarding concomitant metabolic changes is missing. Here we investigated the dynamic metabolic changes along the rice grain development of two japonica and two indica cultivars using non-targeted metabolomics approach, in which we successfully identified 214 metabolites. Statistical analyses revealed both cultivar and developmental stage dependent metabolic changes in rice grains. Generally, the stage specific metabolic kinetics corresponded well to the physiological status of the developing grains, and metabolic changes in developing rice grain are similar to those of dicot Arabidopsis and tomato at reserve accumulation stage but are different from those of dicots at seed desiccation stage. The remarkable difference in metabolite abundances between japonica and indica rice grain was observed at the reserve accumulation stage. Metabolite-metabolite correlation analysis uncovered potential new pathways for several metabolites. Taken together, this study uncovered both conserved and diverse development associated metabolic kinetics of rice grains, which facilitates further study to explore fundamental questions regarding the evolution of seed metabolic capabilities as well as their potential applications in crop improvement. PMID:26860358

  8. Diversity, distribution, and conservation status of the native freshwater fishes of the southern United States

    USGS Publications Warehouse

    Warren, Melvin L., Jr.; Burr, Brooks M.; Walsh, Stephen J.; Bart, Henry L., Jr.; Cashner, Robert C.; Etnier, David A.; Freeman, Byron J.; Kuhajda, Bernard R.; Mayden, Richard L.; Robison, Henry W.; Ross, Stephen T.; Starnes, Wayne C.

    2000-01-01

    The Southeastern Fishes Council Technical Advisory Committee reviewed the diversity, distribution, and status of all native freshwater and diadromous fishes across 51 major drainage units of the southern United States. The southern United States supports more native fishes than any area of comparable size on the North American continent north of Mexico, but also has a high proportion of its fishes in need of conservation action. The review included 662 native freshwater and diadromous fishes and 24 marine fishes that are significant components of freshwater ecosystems. Of this total, 560 described, freshwater fish species are documented, and 49 undescribed species are included provisionally pending formal description. Described subspecies (86) are recognized within 43 species, 6 fishes have undescribed subspecies, and 9 others are recognized as complexes of undescribed taxa. Extinct, endangered, threatened, or vulnerable status is recognized for 28% (187 taxa) of southern freshwater and diadromous fishes. To date, 3 southern fishes are known to be extinct throughout their ranges, 2 are extirpated from the study region, and 2 others may be extinct. Of the extant southern fishes, 41 (6%) are regarded as endangered, 46 (7%) are regarded as threatened, and 101 (15%) are regarded as vulnerable. Five marine fishes that frequent fresh water are regarded as vulnerable. Our assessment represents a 75% increase in jeopardized southern fishes since 1989 and a 125% increase in 20 years. The trend for fishes in the southern United States is clear; jeopardized fishes are successively being moved from the vulnerable category to that of imminent threat of extinction.

  9. Relationships, origin, and diversity of Galapagos tomatoes: implications for the conservation of natural populations.

    PubMed

    Nuez, Fernando; Prohens, Jaume; Blanca, José M

    2004-01-01

    Endemic Galápagos tomatoes (Lycopersicon cheesmanii) are of great value for cultivated tomato (L. esculentum) breeding, and therefore their conservation is of significance. Although within L. cheesmanii there is heterogeneity for many traits and formal infraspecific classification is not justified, here we distinguish three forms, without taxonomic significance, of L. cheesmanii that are of interest to breeders because of their distinctive morphology and habitat preferences: L. cheesmanii 'short' (one- to two-pinnate leaves, short internodes, and coastal habitats), L. cheesmanii 'long' (one- to two-pinnate leaves, long internodes, and inland habitats), and L. cheesmanii forma minor (three- to four-pinnate leaves, short internodes, and coastal habitats). In a recent survey of tomato populations in the Galápagos Islands, we found that several populations of L. cheesmanii reported 30-50 years earlier had disappeared, mostly as a consequence of human activity. In addition, a previously unreported invasive wild red-fruited form, which we named L. esculentum 'Gal cer,' was found on the island of Santa Cruz. The total diversity (estimated with amplified fragment length polymorphisms [AFLPs]) within L. cheesmanii (H(T) = 0.051) is almost as high as that for the mainland wild species L. pimpinellifolium (H(T) = 0.072). Lycopersicon esculentum 'Gal cer,' on the other hand, has a much lower diversity (H(T) = 0.014). Comparison of AFLP fragments shared by L. esculentum 'Gal cer' with other species showed that it is closely related to weedy tomato L. esculentum var. cerasiforme and, therefore, likely of recent origin. Genetic differentiation among the three native L. cheesmanii forms is low (G(ST) = 0.235), indicating that they share a common genetic background. Nonetheless, L. cheesmanii 'short' is about twice as diverse as L. cheesmanii 'long' or L. cheesmanii f. minor. UPGMA cluster and principal components analysis distinguish four groups within Eulycopersicon: L

  10. JGI Fungal Genomics Program

    SciTech Connect

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  11. What Makes Grassroots Conservation Organizations Resilient? An Empirical Analysis of Diversity, Organizational Memory, and the Number of Leaders

    NASA Astrophysics Data System (ADS)

    Baral, Nabin

    2013-03-01

    Conservation Area Management Committees (CAMCs)—the functional decision-making units consisting entirely of local villagers—are grassroots organizations legally established to manage the Annapurna Conservation Area (ACA) in Nepal. These committees suffered due to the decade-long Maoist insurgency, but they survived. The paper attempts to test what factors contributed to their resiliency. For this, I surveyed 30 CAMCs during the summer of 2007 and conducted semi-structured interviews of 190 executive members of the CAMCs and 13 park officials who closely monitor the CAMCs. Regression results showed that the number of leaders ( b = 0.44, t = 2.38, P = .027) was the most critical variable for building the resilience of CAMCs to the Maoist insurgency, i.e., retaining the same function, structure, and identity of the committees. As there were no reported conflicts among leaders and they were involved in negotiations and devising contingency plans, CAMCs actually benefited from having more leaders. Of the three diversity indices, the quadratic terms of age diversity ( b = -5.42, t = 1.95, P = .064) and ethnic diversity ( b = -4.05, t = 1.78, P = .075) had a negative impact on the CAMCs' resilience. Skill diversity and organizational memory had no significant influence on the CAMCs' resilience ( t < 1.48, P > .10). These results have important implications for building resilience in community-based conservation.

  12. A conserved supergene locus controls colour pattern diversity in Heliconius butterflies.

    PubMed

    Joron, Mathieu; Papa, Riccardo; Beltrán, Margarita; Chamberlain, Nicola; Mavárez, Jesús; Baxter, Simon; Abanto, Moisés; Bermingham, Eldredge; Humphray, Sean J; Rogers, Jane; Beasley, Helen; Barlow, Karen; ffrench-Constant, Richard H; Mallet, James; McMillan, W Owen; Jiggins, Chris D

    2006-10-01

    We studied whether similar developmental genetic mechanisms are involved in both convergent and divergent evolution. Mimetic insects are known for their diversity of patterns as well as their remarkable evolutionary convergence, and they have played an important role in controversies over the respective roles of selection and constraints in adaptive evolution. Here we contrast three butterfly species, all classic examples of Müllerian mimicry. We used a genetic linkage map to show that a locus, Yb, which controls the presence of a yellow band in geographic races of Heliconius melpomene, maps precisely to the same location as the locus Cr, which has very similar phenotypic effects in its co-mimic H. erato. Furthermore, the same genomic location acts as a "supergene", determining multiple sympatric morphs in a third species, H. numata. H. numata is a species with a very different phenotypic appearance, whose many forms mimic different unrelated ithomiine butterflies in the genus Melinaea. Other unlinked colour pattern loci map to a homologous linkage group in the co-mimics H. melpomene and H. erato, but they are not involved in mimetic polymorphism in H. numata. Hence, a single region from the multilocus colour pattern architecture of H. melpomene and H. erato appears to have gained control of the entire wing-pattern variability in H. numata, presumably as a result of selection for mimetic "supergene" polymorphism without intermediates. Although we cannot at this stage confirm the homology of the loci segregating in the three species, our results imply that a conserved yet relatively unconstrained mechanism underlying pattern switching can affect mimicry in radically different ways. We also show that adaptive evolution, both convergent and diversifying, can occur by the repeated involvement of the same genomic regions.

  13. Endophytic fungal diversity in Theobroma cacao (cacao) and T. grandiflorum (cupuaçu) trees and their potential for growth promotion and biocontrol of black-pod disease.

    PubMed

    Hanada, Rogério Eiji; Pomella, Alan William V; Costa, Heron Salazar; Bezerra, José Luiz; Loguercio, Leandro L; Pereira, José O

    2010-01-01

    The endophytic niches of plants are a rich source of microbes that can directly and indirectly promote plant protection, growth and development. The diversity of culturable endophytic fungi from stems and branches of Theobroma cacao (cacao) and Theobroma grandiflorum (cupuaçu) trees growing in the Amazon region of Brazil was assessed. The collection of fungal endophytic isolates obtained was applied in field experiments to evaluate their potential as biocontrol agents against Phytophthora palmivora, the causal agent of the black-pod rot disease of cacao, one of the most important pathogens in cocoa-producing regions worldwide. The isolated endophytic fungi from 60 traditional, farmer-planted, healthy cacao and 10 cupuaçu plants were cultured in PDA under conditions inducing sporulation. Isolates were classified based upon the morphological characteristics of their cultures and reproductive structures. Spore suspensions from a total of 103 isolates that could be classified at least up to genus level were tested against P. palmivora in pods attached to cacao trees in the field. Results indicated that ∼70% of isolates showed biocontrol effects to a certain extent, suggesting that culturable endophytic fungal biodiversity in this system is of a mostly mutualistic type of interaction with the host. Eight isolates from genera Trichoderma (reference isolate), Pestalotiopsis, Curvularia, Tolypocladium and Fusarium showed the highest level of activity against the pathogen, and were further characterized. All demonstrated their endophytic nature by colonizing axenic cacao plantlets, and confirmed their biocontrol activity on attached pods trials by showing significant decrease in disease severity in relation to the positive control. None, however, showed detectable growth-promotion effects. Aspects related to endophytic biodiversity and host-pathogen-endophyte interactions in the environment of this study were discussed on the context of developing sustainable strategies

  14. Fungal Endocarditis

    PubMed Central

    Yuan, Shi-Min

    2016-01-01

    Fungal endocarditis is a rare and fatal condition. The Candida and Aspergillus species are the two most common etiologic fungi found responsible for fungal endocarditis. Fever and changing heart murmur are the most common clinical manifestations. Some patients may have a fever of unknown origin as the onset symptom. The diagnosis of fungal endocarditis is challenging, and diagnosis of prosthetic valve fungal endocarditis is extremely difficult. The optimum antifungal therapy still remains debatable. Treating Candida endocarditis can be difficult because the Candida species can form biofilms on native and prosthetic heart valves. Combined treatment appears superior to monotherapy. Combination of antifungal therapy and surgical debridement might bring about better prognosis. PMID:27737409

  15. Fungal Sinusitis.

    PubMed

    Raz, Eytan; Win, William; Hagiwara, Mari; Lui, Yvonne W; Cohen, Benjamin; Fatterpekar, Girish M

    2015-11-01

    Fungal sinusitis is characterized into invasive and noninvasive forms. The invasive variety is further classified into acute, chronic and granulomatous forms; and the noninvasive variety into fungus ball and allergic fungal sinusitis. Each of these different forms has a unique radiologic appearance. The clinicopathologic and corresponding radiologic spectrum and differences in treatment strategies of fungal sinusitis make it an important diagnosis for clinicians and radiologists to always consider. This is particularly true of invasive fungal sinusitis, which typically affects immuno compromised patients and is associated with significant morbidity and mortality. Early diagnosis allows initiation of appropriate treatment strategies resulting in favorable outcome.

  16. Fungal endophytes in above-ground tissues of desert plants: infrequent in culture, but highly diverse and distinctive symbionts

    PubMed Central

    Massimo, Nicholas C.; Nandi Devan, MM; Arendt, Kayla R.; Wilch, Margaret H.; Riddle, Jakob M.; Furr, Susan H.; Steen, Cole; U'Ren, Jana M.; Sandberg, Dustin C.; Arnold, A. Elizabeth

    2015-01-01

    In hot deserts, plants cope with aridity, high temperatures, and nutrient-poor soils with morphological and biochemical adaptations that encompass intimate microbial symbioses. Whereas the root microbiomes of arid-land plants have received increasing attention, factors influencing assemblages of symbionts in above-ground tissues have not been evaluated for many woody plants that flourish in desert environments. We evaluated the diversity, host affiliations, and distributions of endophytic fungi associated with photosynthetic tissues of desert trees and shrubs, focusing on non-succulent woody plants in the species-rich Sonoran Desert. To inform our strength of inference, we evaluated the effects of two different nutrient media, incubation temperatures, and collection seasons on the apparent structure of endophyte assemblages. Analysis of >22,000 tissue segments revealed that endophytes were isolated four times more frequently from photosynthetic stems than leaves. Isolation frequency was lower than expected given the latitude of the study region, and varied among species a function of sampling site and abiotic factors. However, endophytes were very species-rich and phylogenetically diverse, consistent with less-arid sites of a similar latitudinal position. Community composition differed among host species, but not as a function of tissue type, sampling site, sampling month, or exposure. Estimates of abundance, diversity and composition were not influenced by isolation medium or incubation temperature. Phylogenetic analyses of the most commonly isolated genus (Preussia) revealed multiple evolutionary origins of desert-plant endophytism and little phylogenetic structure with regard to seasonality, tissue preference, or optimal temperatures and nutrients for growth in vitro. Together, these results provide insight into endophytic symbioses in desert plant communities, and can be used to optimize strategies for capturing endophyte biodiversity at regional scales. PMID

  17. Fungal endophytes in aboveground tissues of desert plants: infrequent in culture, but highly diverse and distinctive symbionts.

    PubMed

    Massimo, Nicholas C; Nandi Devan, M M; Arendt, Kayla R; Wilch, Margaret H; Riddle, Jakob M; Furr, Susan H; Steen, Cole; U'Ren, Jana M; Sandberg, Dustin C; Arnold, A Elizabeth

    2015-07-01

    In hot deserts, plants cope with aridity, high temperatures, and nutrient-poor soils with morphological and biochemical adaptations that encompass intimate microbial symbioses. Whereas the root microbiomes of arid-land plants have received increasing attention, factors influencing assemblages of symbionts in aboveground tissues have not been evaluated for many woody plants that flourish in desert environments. We evaluated the diversity, host affiliations, and distributions of endophytic fungi associated with photosynthetic tissues of desert trees and shrubs, focusing on nonsucculent woody plants in the species-rich Sonoran Desert. To inform our strength of inference, we evaluated the effects of two different nutrient media, incubation temperatures, and collection seasons on the apparent structure of endophyte assemblages. Analysis of >22,000 tissue segments revealed that endophytes were isolated four times more frequently from photosynthetic stems than leaves. Isolation frequency was lower than expected given the latitude of the study region and varied among species a function of sampling site and abiotic factors. However, endophytes were very species-rich and phylogenetically diverse, consistent with less arid sites of a similar latitudinal position. Community composition differed among host species, but not as a function of tissue type, sampling site, sampling month, or exposure. Estimates of abundance, diversity, and composition were not influenced by isolation medium or incubation temperature. Phylogenetic analyses of the most commonly isolated genus (Preussia) revealed multiple evolutionary origins of desert-plant endophytism and little phylogenetic structure with regard to seasonality, tissue preference, or optimal temperatures and nutrients for growth in vitro. Together, these results provide insight into endophytic symbioses in desert-plant communities and can be used to optimize strategies for capturing endophyte biodiversity at regional scales.

  18. Global ex-situ crop diversity conservation and the Svalbard Global Seed Vault: assessing the current status.

    PubMed

    Westengen, Ola T; Jeppson, Simon; Guarino, Luigi

    2013-01-01

    Ex-situ conservation of crop diversity is a global concern, and the development of an efficient and sustainable conservation system is a historic priority recognized in international law and policy. We assess the completeness of the safety duplication collection in the Svalbard Global Seed Vault with respect to data on the world's ex-situ collections as reported by the Food and Agriculture Organization of the United Nations. Currently, 774,601 samples are deposited at Svalbard by 53 genebanks. We estimate that more than one third of the globally distinct accessions of 156 crop genera stored in genebanks as orthodox seeds are conserved in the Seed Vault. The numbers of safety duplicates of Triticum (wheat), Sorghum (sorghum), Pennisetum (pearl millet), Eleusine (finger millet), Cicer (chickpea) and Lens (lentil) exceed 50% of the estimated numbers of distinct accessions in global ex-situ collections. The number of accessions conserved globally generally reflects importance for food production, but there are significant gaps in the safety collection at Svalbard in some genera of high importance for food security in tropical countries, such as Amaranthus (amaranth), Chenopodium (quinoa), Eragrostis (teff) and Abelmoschus (okra). In the 29 food-crop genera with the largest number of accessions stored globally, an average of 5.5 out of the ten largest collections is already represented in the Seed Vault collection or is covered by existing deposit agreements. The high coverage of ITPGRFA Annex 1 crops and of those crops for which there is a CGIAR mandate in the current Seed Vault collection indicates that existence of international policies and institutions are important determinants for accessions to be safety duplicated at Svalbard. As a back-up site for the global conservation system, the Seed Vault plays not only a practical but also a symbolic role for enhanced integration and cooperation for conservation of crop diversity.

  19. Global Ex-Situ Crop Diversity Conservation and the Svalbard Global Seed Vault: Assessing the Current Status

    PubMed Central

    Westengen, Ola T.; Jeppson, Simon; Guarino, Luigi

    2013-01-01

    Ex-situ conservation of crop diversity is a global concern, and the development of an efficient and sustainable conservation system is a historic priority recognized in international law and policy. We assess the completeness of the safety duplication collection in the Svalbard Global Seed Vault with respect to data on the world's ex-situ collections as reported by the Food and Agriculture Organization of the United Nations. Currently, 774,601 samples are deposited at Svalbard by 53 genebanks. We estimate that more than one third of the globally distinct accessions of 156 crop genera stored in genebanks as orthodox seeds are conserved in the Seed Vault. The numbers of safety duplicates of Triticum (wheat), Sorghum (sorghum), Pennisetum (pearl millet), Eleusine (finger millet), Cicer (chickpea) and Lens (lentil) exceed 50% of the estimated numbers of distinct accessions in global ex-situ collections. The number of accessions conserved globally generally reflects importance for food production, but there are significant gaps in the safety collection at Svalbard in some genera of high importance for food security in tropical countries, such as Amaranthus (amaranth), Chenopodium (quinoa), Eragrostis (teff) and Abelmoschus (okra). In the 29 food-crop genera with the largest number of accessions stored globally, an average of 5.5 out of the ten largest collections is already represented in the Seed Vault collection or is covered by existing deposit agreements. The high coverage of ITPGRFA Annex 1 crops and of those crops for which there is a CGIAR mandate in the current Seed Vault collection indicates that existence of international policies and institutions are important determinants for accessions to be safety duplicated at Svalbard. As a back-up site for the global conservation system, the Seed Vault plays not only a practical but also a symbolic role for enhanced integration and cooperation for conservation of crop diversity. PMID:23671707

  20. [Intraspecies diversity of Trichosporon asahii as the causative agent of opportunistic fungal infection and summer-type hypersensitivity pneumonitis].

    PubMed

    Sugita, Takashi

    2003-01-01

    Trichosporon asahii is the major causative agent of the opportunistic infection trichosporonosis, and also causes summer-type hypersensitivity pneumonitis (SHP). Random amplification of polymorphic DNA analysis was used to determine the intraspecies diversity of T. asahii isolates from clinical specimens,the houses of SHP patients, and environmental material. Clinical isolates formed a cluster, characterized by a 90% matching coefficient, but they did not cluster with strains isolated from SHP patients houses or environmental sources. The biochemical characteristics of T. asahii isolates from the three sources were compared, and a phenogram was constructed. One of the two clusters included most of the clinical isolates and strains isolated from the houses, and the other cluster included most of the environmental isolates. There was a remarkable difference in the abilities of the strains belonging to these clusters to utilize several compounds. These results suggest that the genetic diversity and biochemical characteristics of T. asahii are related to the source of the isolates. In addition, based on the IGS1 sequence, which is located between the 26S and 5S rRNA genes, we identified five genotypes of T. asahii, which is a major causative agent of deep-seated trichosporonosis. Of the five genotypes, three were isolates that originated in Japan, whereas two were American isolates. IGS sequence analysis shows great potential as a new epidemiological tool. PMID:12590253

  1. Comparative riverscape genetics reveals reservoirs of genetic diversity for conservation and restoration of Great Plains fishes

    PubMed Central

    Osborne, Megan J; Perkin, Joshuah S.; Gido, Keith B.; Turner, Thomas F.

    2014-01-01

    We used comparative landscape genetics to examine the relative roles of historical events, intrinsic traits, and landscape factors in determining the distribution of genetic diversity of river fishes across the North American Great Plains. Spatial patterns of diversity were overlaid on a patch-based graphical model, and then compared within and among three species that co-occurred across five Great Plains watersheds. Species differing in reproductive strategy (benthic vs. pelagic spawning) were hypothesized to have different patterns of genetic diversity, but the overriding factor shaping contemporary patterns of diversity was the signature of past climates and geological history. Allelic diversity was significantly higher at southern latitudes for Cyprinella lutrensis and Hybognathus placitus, consistent with northward expansion from southern Pleistocene refugia. Within the historical context, all species exhibited lowered occupancy and abundance in heavily fragmented and drier upstream reaches, particularly H. placitus; a pelagic-spawning species, suggesting rates of extirpation have outpaced losses of genetic diversity in this species. Within most basins, genetically diverse populations of each species persisted. Hence, reconnecting genetically diverse populations with those characterized by reduced diversity (regardless of their position within the riverine network) would provide populations with greater genetic and demographic resilience. We discuss cases where cross-basin transfer may be appropriate to enhance genetic diversity and mitigate negative effects of climate change. Overall, striking similarities in genetic patterns and response to fragmentation and dewatering suggest a common strategy for genetic resource management in this unique riverine fish assemblage. PMID:25327780

  2. Diverse Early Life-History Strategies in Migratory Amazonian Catfish: Implications for Conservation and Management.

    PubMed

    Hegg, Jens C; Giarrizzo, Tommaso; Kennedy, Brian P

    2015-01-01

    of the upstream watershed to the Sr isotope ratio. Our results provide the first reported otolith microchemical reconstruction of Brachyplatystoma migratory movements in the Amazon Basin. Our results indicate that juveniles exhibit diverse rearing strategies, rearing in both upstream and estuary environments. This contrasts with the prevailing understanding that juveniles rear in the estuary before migrating upstream; however, it is supported by some fisheries data that has indicated the presence of alternate spawning and rearing life-histories. The presence of alternate juvenile rearing strategies may have important implications for conservation and management of the fisheries in the region. PMID:26153984

  3. Diverse Early Life-History Strategies in Migratory Amazonian Catfish: Implications for Conservation and Management.

    PubMed

    Hegg, Jens C; Giarrizzo, Tommaso; Kennedy, Brian P

    2015-01-01

    of the upstream watershed to the Sr isotope ratio. Our results provide the first reported otolith microchemical reconstruction of Brachyplatystoma migratory movements in the Amazon Basin. Our results indicate that juveniles exhibit diverse rearing strategies, rearing in both upstream and estuary environments. This contrasts with the prevailing understanding that juveniles rear in the estuary before migrating upstream; however, it is supported by some fisheries data that has indicated the presence of alternate spawning and rearing life-histories. The presence of alternate juvenile rearing strategies may have important implications for conservation and management of the fisheries in the region.

  4. Genetic diversity and population structure of Musa accessions in ex situ conservation

    PubMed Central

    2013-01-01

    Background Banana cultivars are mostly derived from hybridization between wild diploid subspecies of Musa acuminata (A genome) and M. balbisiana (B genome), and they exhibit various levels of ploidy and genomic constitution. The Embrapa ex situ Musa collection contains over 220 accessions, of which only a few have been genetically characterized. Knowledge regarding the genetic relationships and diversity between modern cultivars and wild relatives would assist in conservation and breeding strategies. Our objectives were to determine the genomic constitution based on Internal Transcribed Spacer (ITS) regions polymorphism and the ploidy of all accessions by flow cytometry and to investigate the population structure of the collection using Simple Sequence Repeat (SSR) loci as co-dominant markers based on Structure software, not previously performed in Musa. Results From the 221 accessions analyzed by flow cytometry, the correct ploidy was confirmed or established for 212 (95.9%), whereas digestion of the ITS region confirmed the genomic constitution of 209 (94.6%). Neighbor-joining clustering analysis derived from SSR binary data allowed the detection of two major groups, essentially distinguished by the presence or absence of the B genome, while subgroups were formed according to the genomic composition and commercial classification. The co-dominant nature of SSR was explored to analyze the structure of the population based on a Bayesian approach, detecting 21 subpopulations. Most of the subpopulations were in agreement with the clustering analysis. Conclusions The data generated by flow cytometry, ITS and SSR supported the hypothesis about the occurrence of homeologue recombination between A and B genomes, leading to discrepancies in the number of sets or portions from each parental genome. These phenomenons have been largely disregarded in the evolution of banana, as the “single-step domestication” hypothesis had long predominated. These findings will have an

  5. Diverse Early Life-History Strategies in Migratory Amazonian Catfish: Implications for Conservation and Management

    PubMed Central

    Hegg, Jens C.; Giarrizzo, Tommaso; Kennedy, Brian P.

    2015-01-01

    the upstream watershed to the Sr isotope ratio. Our results provide the first reported otolith microchemical reconstruction of Brachyplatystoma migratory movements in the Amazon Basin. Our results indicate that juveniles exhibit diverse rearing strategies, rearing in both upstream and estuary environments. This contrasts with the prevailing understanding that juveniles rear in the estuary before migrating upstream; however, it is supported by some fisheries data that has indicated the presence of alternate spawning and rearing life-histories. The presence of alternate juvenile rearing strategies may have important implications for conservation and management of the fisheries in the region. PMID:26153984

  6. Conservation and Immunogenicity of Novel Antigens in Diverse Isolates of Enterotoxigenic Escherichia coli

    PubMed Central

    Luo, Qingwei; Qadri, Firdausi; Kansal, Rita; Rasko, David A.; Sheikh, Alaullah; Fleckenstein, James M.

    2015-01-01

    Background Enterotoxigenic Escherichia coli (ETEC) are common causes of diarrheal morbidity and mortality in developing countries for which there is currently no vaccine. Heterogeneity in classical ETEC antigens known as colonization factors (CFs) and poor efficacy of toxoid-based approaches to date have impeded development of a broadly protective ETEC vaccine, prompting searches for novel molecular targets. Methodology Using a variety of molecular methods, we examined a large collection of ETEC isolates for production of two secreted plasmid-encoded pathotype-specific antigens, the EtpA extracellular adhesin, and EatA, a mucin-degrading serine protease; and two chromosomally-encoded molecules, the YghJ metalloprotease and the EaeH adhesin, that are not specific to the ETEC pathovar, but which have been implicated in ETEC pathogenesis. ELISA assays were also performed on control and convalescent sera to characterize the immune response to these antigens. Finally, mice were immunized with recombinant EtpA (rEtpA), and a protease deficient version of the secreted EatA passenger domain (rEatApH134R) to examine the feasibility of combining these molecules in a subunit vaccine approach. Principal Findings EtpA and EatA were secreted by more than half of all ETEC, distributed over diverse phylogenetic lineages belonging to multiple CF groups, and exhibited surprisingly little sequence variation. Both chromosomally-encoded molecules were also identified in a wide variety of ETEC strains and YghJ was secreted by 89% of isolates. Antibodies against both the ETEC pathovar-specific and conserved E. coli antigens were present in significantly higher titers in convalescent samples from subjects with ETEC infection than controls suggesting that each of these antigens is produced and recognized during infection. Finally, co-immunization of mice with rEtpA and rEatApH134R offered significant protection against ETEC infection. Conclusions Collectively, these data suggest that novel

  7. Impact of land use on arbuscular mycorrhizal fungal communities in rural Canada.

    PubMed

    Dai, Mulan; Bainard, Luke D; Hamel, Chantal; Gan, Yantai; Lynch, Derek

    2013-11-01

    The influence of land use on soil bio-resources is largely unknown. We examined the communities of arbuscular mycorrhizal (AM) fungi in wheat-growing cropland, natural areas, and seminatural areas along roads. We sampled the Canadian prairie extensively (317 sites) and sampled 20 sites in the Atlantic maritime ecozone for comparison. The proportions of the different AM fungal taxa in the communities found at these sites varied with land use type and ecozones, based on pyrosequencing of 18S rRNA gene (rDNA) amplicons, but the lists of AM fungal taxa obtained from the different land use types and ecozones were very similar. In the prairie, the Glomeraceae family was the most abundant and diverse family of Glomeromycota, followed by the Claroideoglomeraceae, but in the Atlantic maritime ecozone, the Claroideoglomeraceae family was most abundant. In the prairie, species richness and Shannon's diversity index were highest in roadsides, whereas cropland had a higher degree of species richness than roadsides in the Atlantic maritime ecozone. The frequencies of occurrence of the different AM fungal taxa in croplands in the prairie and Atlantic maritime ecozones were highly correlated, but the AM fungal communities in these ecozones had different structures. We conclude that the AM fungal resources of soils are resilient to disturbance and that the richness of AM fungi under cropland management has been maintained, despite evidence of a structural shift imposed by this type of land use. Roadsides in the Canadian prairie are a good repository for the conservation of AM fungal diversity.

  8. 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

  9. Genetic diversity of the conserved motifs of six bacterial leaf blight resistance genes in a set of rice landraces

    PubMed Central

    2014-01-01

    Background Bacterial leaf blight (BLB) caused by the vascular pathogen Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious diseases leading to crop failure in rice growing countries. A total of 37 resistance genes against Xoo has been identified in rice. Of these, ten BLB resistance genes have been mapped on rice chromosomes, while 6 have been cloned, sequenced and characterized. Diversity analysis at the resistance gene level of this disease is scanty, and the landraces from West Bengal and North Eastern states of India have received little attention so far. The objective of this study was to assess the genetic diversity at conserved domains of 6 BLB resistance genes in a set of 22 rice accessions including landraces and check genotypes collected from the states of Assam, Nagaland, Mizoram and West Bengal. Results In this study 34 pairs of primers were designed from conserved domains of 6 BLB resistance genes; Xa1, xa5, Xa21, Xa21(A1), Xa26 and Xa27. The designed primer pairs were used to generate PCR based polymorphic DNA profiles to detect and elucidate the genetic diversity of the six genes in the 22 diverse rice accessions of known disease phenotype. A total of 140 alleles were identified including 41 rare and 26 null alleles. The average polymorphism information content (PIC) value was 0.56/primer pair. The DNA profiles identified each of the rice landraces unequivocally. The amplified polymorphic DNA bands were used to calculate genetic similarity of the rice landraces in all possible pair combinations. The similarity among the rice accessions ranged from 18% to 89% and the dendrogram produced from the similarity values was divided into 2 major clusters. The conserved domains identified within the sequenced rare alleles include Leucine-Rich Repeat, BED-type zinc finger domain, sugar transferase domain and the domain of the carbohydrate esterase 4 superfamily. Conclusions This study revealed high genetic diversity at conserved domains of six BLB

  10. The fungal mitochondrial genome project: evolution of fungal mitochondrial genomes and their gene expression.

    PubMed

    Paquin, B; Laforest, M J; Forget, L; Roewer, I; Wang, Z; Longcore, J; Lang, B F

    1997-05-01

    The goal of the fungal mitochondrial genome project (FMGP) is to sequence complete mitochondrial genomes for a representative sample of the major fungal lineages; to analyze the genome structure, gene content, and conserved sequence elements of these sequences; and to study the evolution of gene expression in fungal mitochondria. By using our new sequence data for evolutionary studies, we were able to construct phylogenetic trees that provide further solid evidence that animals and fungi share a common ancestor to the exclusion of chlorophytes and protists. With a database comprising multiple mitochondrial gene sequences, the level of support for our mitochondrial phylogenies is unprecedented, in comparison to trees inferred with nuclear ribosomal RNA sequences. We also found several new molecular features in the mitochondrial genomes of lower fungi, including: (1) tRNA editing, which is the same type as that found in the mitochondria of the amoeboid protozoan Acanthamoeba castellanii; (2) two novel types of putative mobile DNA elements, one encoding a site-specific endonuclease that confers mobility on the element, and the other constituting a class of highly compact, structured elements; and (3) a large number of introns, which provide insights into intron origins and evolution. Here, we present an overview of these results, and discuss examples of the diversity of structures found in the fungal mitochondrial genome.

  11. What makes grassroots conservation organizations resilient? An empirical analysis of diversity, organizational memory, and the number of leaders.

    PubMed

    Baral, Nabin

    2013-03-01

    Conservation Area Management Committees (CAMCs)-the functional decision-making units consisting entirely of local villagers-are grassroots organizations legally established to manage the Annapurna Conservation Area (ACA) in Nepal. These committees suffered due to the decade-long Maoist insurgency, but they survived. The paper attempts to test what factors contributed to their resiliency. For this, I surveyed 30 CAMCs during the summer of 2007 and conducted semi-structured interviews of 190 executive members of the CAMCs and 13 park officials who closely monitor the CAMCs. Regression results showed that the number of leaders (b = 0.44, t = 2.38, P = .027) was the most critical variable for building the resilience of CAMCs to the Maoist insurgency, i.e., retaining the same function, structure, and identity of the committees. As there were no reported conflicts among leaders and they were involved in negotiations and devising contingency plans, CAMCs actually benefited from having more leaders. Of the three diversity indices, the quadratic terms of age diversity (b = -5.42, t = 1.95, P = .064) and ethnic diversity (b = -4.05, t = 1.78, P = .075) had a negative impact on the CAMCs' resilience. Skill diversity and organizational memory had no significant influence on the CAMCs' resilience (t < 1.48, P > .10). These results have important implications for building resilience in community-based conservation.

  12. Bird diversity, birdwatching tourism and conservation in Peru: a geographic analysis.

    PubMed

    Puhakka, Liisa; Salo, Matti; Sääksjärvi, Ilari E

    2011-01-01

    In the face of the continuing global biodiversity loss, it is important not only to assess the need for conservation, through e.g. gap analyses, but also to seek practical solutions for protecting biodiversity. Environmentally and socially sustainable tourism can be one such solution. We present a method to spatially link data on conservation needs and tourism-based economic opportunities, using bird-related tourism in Peru as an example. Our analysis highlighted areas in Peru where potential for such projects could be particularly high. Several areas within the central and northern Andean regions, as well as within the lowland Amazonian regions of Madre de Dios and Loreto emerge as promising for this type of activity. Mechanisms to implement conservation in these areas include e.g. conservation and ecotourism concessions, private conservation areas, and conservation easements. Some of these mechanisms also offer opportunities for local communities seeking to secure their traditional land ownership and use rights. (Spanish language abstract, Abstract S1). PMID:22132078

  13. Bird Diversity, Birdwatching Tourism and Conservation in Peru: A Geographic Analysis

    PubMed Central

    Puhakka, Liisa; Salo, Matti; Sääksjärvi, Ilari E.

    2011-01-01

    In the face of the continuing global biodiversity loss, it is important not only to assess the need for conservation, through e.g. gap analyses, but also to seek practical solutions for protecting biodiversity. Environmentally and socially sustainable tourism can be one such solution. We present a method to spatially link data on conservation needs and tourism-based economic opportunities, using bird-related tourism in Peru as an example. Our analysis highlighted areas in Peru where potential for such projects could be particularly high. Several areas within the central and northern Andean regions, as well as within the lowland Amazonian regions of Madre de Dios and Loreto emerge as promising for this type of activity. Mechanisms to implement conservation in these areas include e.g. conservation and ecotourism concessions, private conservation areas, and conservation easements. Some of these mechanisms also offer opportunities for local communities seeking to secure their traditional land ownership and use rights. (Spanish language abstract, Abstract S1). PMID:22132078

  14. Bird diversity, birdwatching tourism and conservation in Peru: a geographic analysis.

    PubMed

    Puhakka, Liisa; Salo, Matti; Sääksjärvi, Ilari E

    2011-01-01

    In the face of the continuing global biodiversity loss, it is important not only to assess the need for conservation, through e.g. gap analyses, but also to seek practical solutions for protecting biodiversity. Environmentally and socially sustainable tourism can be one such solution. We present a method to spatially link data on conservation needs and tourism-based economic opportunities, using bird-related tourism in Peru as an example. Our analysis highlighted areas in Peru where potential for such projects could be particularly high. Several areas within the central and northern Andean regions, as well as within the lowland Amazonian regions of Madre de Dios and Loreto emerge as promising for this type of activity. Mechanisms to implement conservation in these areas include e.g. conservation and ecotourism concessions, private conservation areas, and conservation easements. Some of these mechanisms also offer opportunities for local communities seeking to secure their traditional land ownership and use rights. (Spanish language abstract, Abstract S1).

  15. Coevolution Pattern and Functional Conservation or Divergence of miR167s and their targets across Diverse Plant Species

    PubMed Central

    Barik, Suvakanta; Kumar, Ashutosh; Sarkar Das, Shabari; Yadav, Sandeep; Gautam, Vibhav; Singh, Archita; Singh, Sharmila; Sarkar, Ananda K.

    2015-01-01

    microRNAs (miRNAs), a class of endogenously produced small non-coding RNAs of 20–21 nt length, processed from precursor miRNAs, regulate many developmental processes by negatively regulating the target genes in both animals and plants. The coevolutionary pattern of a miRNA family and their targets underscores its functional conservation or diversification. The miR167 regulates various aspects of plant development in Arabidopsis by targeting ARF6 and ARF8. The evolutionary conservation or divergence of miR167s and their target genes are poorly understood till now. Here we show the evolutionary relationship among 153 MIR167 genes obtained from 33 diverse plant species. We found that out of the 153 of miR167 sequences retrieved from the “miRBase”, 27 have been annotated to be processed from the 3′ end, and have diverged distinctively from the other miR167s produced from 5′ end. Our analysis reveals that gma-miR167h/i and mdm-miR167a are processed from 3′ end and have evolved separately, diverged most resulting in novel targets other than their known ones, and thus led to functional diversification, especially in apple and soybean. We also show that mostly conserved miR167 sequences and their target AUXIN RESPONSE FACTORS (ARFs) have gone through parallel evolution leading to functional diversification among diverse plant species. PMID:26459056

  16. Coevolution Pattern and Functional Conservation or Divergence of miR167s and their targets across Diverse Plant Species.

    PubMed

    Barik, Suvakanta; Kumar, Ashutosh; Sarkar Das, Shabari; Yadav, Sandeep; Gautam, Vibhav; Singh, Archita; Singh, Sharmila; Sarkar, Ananda K

    2015-01-01

    microRNAs (miRNAs), a class of endogenously produced small non-coding RNAs of 20-21 nt length, processed from precursor miRNAs, regulate many developmental processes by negatively regulating the target genes in both animals and plants. The coevolutionary pattern of a miRNA family and their targets underscores its functional conservation or diversification. The miR167 regulates various aspects of plant development in Arabidopsis by targeting ARF6 and ARF8. The evolutionary conservation or divergence of miR167s and their target genes are poorly understood till now. Here we show the evolutionary relationship among 153 MIR167 genes obtained from 33 diverse plant species. We found that out of the 153 of miR167 sequences retrieved from the "miRBase", 27 have been annotated to be processed from the 3' end, and have diverged distinctively from the other miR167s produced from 5' end. Our analysis reveals that gma-miR167h/i and mdm-miR167a are processed from 3' end and have evolved separately, diverged most resulting in novel targets other than their known ones, and thus led to functional diversification, especially in apple and soybean. We also show that mostly conserved miR167 sequences and their target AUXIN RESPONSE FACTORS (ARFs) have gone through parallel evolution leading to functional diversification among diverse plant species.

  17. Cryptic Diversity in Indo-Australian Rainbowfishes Revealed by DNA Barcoding: Implications for Conservation in a Biodiversity Hotspot Candidate

    PubMed Central

    Kadarusman; Hubert, Nicolas; Hadiaty, Renny Kurnia; Sudarto; Paradis, Emmanuel; Pouyaud, Laurent

    2012-01-01

    The rainbowfishes of the family Melanotaeniidae represent one of the largest radiations of freshwater fishes from the Indo-Australian archipelago. A total of 75 nominal species have been described, among which several have become very popular among tropical fish hobbyists because of their tendency to form large schools of colourful individuals. Facing habitat loss and competition or predation by introduced species, this group has become a priority in the conservation of ornamental fishes in Indonesia. In this context, several expeditions have been conducted between 2007 and 2010 in Indonesian Papua with the aim to initiate a large-scale survey of the genetic resources in this group. We assessed the diversity of the Papua rainbowfishes with DNA barcoding. We sequenced the mitochondrial COI gene for 350 specimens belonging to 53 nominal species throughout the Indo-Australian archipelago. Unexpected levels of cryptic diversity and endemism were detected since additional cryptic lineages were detected in several watersheds from the Vogelkop and the Lengguru massif. DNA barcoding supports the presence of nearly 30 evolutionary lineages among the 15 nominal species sampled in the Vogelkop and all these lineages are endemic to a single lake or watershed. This result highlights that the diversity of the family has been largely underestimated and urges for the identification of conservation priorities in Papua. PMID:22829879

  18. Allozyme diversity in endemic flowering plant species of the Juan Fernandez Archipelago, Chile: ecological and historical factors with implications for conservation.

    PubMed

    Crawford, D J; Ruiz, E; Stuessy, T F; Tepe, E; Aqeveque, P; Gonzalez, F; Jensen, R J; Anderson, G J; Bernardello, G; Baeza, C M; Swenson, U; Silva O, M

    2001-12-01

    The level and apportionment of allozyme diversity were determined for 29 endemic (and 1 native) species from the Juan Fernández Islands, Chile. Mean diversities at the species level (H(es) = 0.065) are low but comparable to those measured for other insular endemics in the Pacific. A high mean proportion (0.338) of species-level diversity resides among populations. Diversity statistics were compared for species in different ecological-life history trait categories and abundance classes. Species occurring in large populations and those present in scattered small populations have higher diversities than species occurring in one or two populations. Although not significant with the conservative statistical test employed, lower diversity was found in highly selfing species as compared to animal- or wind-pollinated species. The apportionment of genetic diversity within and among populations (G(ST) values) is not significantly different for any of the species categories. Of particular interest is the lack of difference between animal- and wind-pollinated species because previous analyses of large data sets showed higher differentiation between populations of animal- than wind-pollinated species. Historical factors, both ecological and phylogenetic in nature, can influence the level and apportionment of diversity within insular endemics, and thus ecological correlates of diversity seen in many continental species may not apply to endemics. The results have several conservation implications. The preservation of large populations or several small populations is important for conserving diversity within species because when species are reduced to one or two populations, allozyme diversity is sharply reduced. High mean G(ST) values for the species examined illustrate the need for conserving as many populations as possible, either in the wild or in the garden, to preserve maximal diversity within species. Effective conservation strategies require empirical knowledge of each

  19. Conservation actions based on red lists do not capture the functional and phylogenetic diversity of birds in Brazil.

    PubMed

    Hidasi-Neto, José; Loyola, Rafael Dias; Cianciaruso, Marcus Vinicius

    2013-01-01

    Red Lists of threatened species play a critical role in conservation science and practice. However, policy-making based on Red Lists ignores ecological and evolutionary consequences of losing biodiversity because these lists focus on species alone. To decide if relying on Red Lists alone can help to conserve communities' functional (FD) and phylogenetic (PD) diversity, it is useful to evaluate whether Red List categories represent species with diverse ecological traits and evolutionary histories. Additionally, local scale analyses using regional Red Lists should represent more realistic pools of co-occurring species and thereby better capture eventual losses of FD and PD. Here, we used 21 life-history traits and a phylogeny for all Brazilian birds to determine whether species assigned under the IUCN global Red List, the Brazilian national, and regional Red Lists capture more FD and PD than expected by chance. We also built local Red Lists and analysed if they capture more FD and PD at the local scale. Further, we investigated whether individual threat categories have species with greater FD and PD than expected by chance. At any given scale, threat categories did not capture greater FD or PD than expected by chance. Indeed, mostly categories captured equal or less FD or PD than expected by chance. These findings would not have great consequences if Red Lists were not often considered as a major decision support tool for policy-making. Our results challenge the practice of investing conservation resources based only on species Red Lists because, from an ecological and evolutionary point of view, this would be the same as protecting similar or random sets of species. Thus, new prioritization methods, such as the EDGE of Existence initiative, should be developed and applied to conserve species' ecological traits and evolutionary histories at different spatial scales. PMID:24039939

  20. Metabarcoding-based fungal diversity on coarse and fine particulate organic matter in a first-order stream in Nova Scotia, Canada.

    PubMed

    Wurzbacher, Christian; Grimmett, Ivan J; Bärlocher, Felix

    2015-01-01

    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

  1. 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

  2. Fungal allergens.

    PubMed Central

    Horner, W E; Helbling, A; Salvaggio, J E; Lehrer, S B

    1995-01-01

    Airborne fungal spores occur widely and often in far greater concentrations than pollen grains. Immunoglobulin E-specific antigens (allergens) on airborne fungal spores induce type I hypersensitivity (allergic) respiratory reactions in sensitized atopic subjects, causing rhinitis and/or asthma. The prevalence of respiratory allergy to fungi is imprecisely known but is estimated at 20 to 30% of atopic (allergy-predisposed) individuals or up to 6% of the general population. Diagnosis and immunotherapy of allergy to fungi require well-characterized or standardized extracts that contain the relevant allergen(s) of the appropriate fungus. Production of standardized extracts is difficult since fungal extracts are complex mixtures and a variety of fungi are allergenic. Thus, the currently available extracts are largely nonstandardized, even uncharacterized, crude extracts. Recent significant progress in isolating and characterizing relevant fungal allergens is summarized in the present review. Particularly, some allergens from the genera Alternaria, Aspergillus, and Cladosporium are now thoroughly characterized, and allergens from several other genera, including some basidiomycetes, have also been purified. The availability of these extracts will facilitate definitive studies of fungal allergy prevalence and immunotherapy efficacy as well as enhance both the diagnosis and therapy of fungal allergy. PMID:7621398

  3. The Chemical Basis of Fungal Bioluminescence.

    PubMed

    Purtov, Konstantin V; Petushkov, Valentin N; Baranov, Mikhail S; Mineev, Konstantin S; Rodionova, Natalja S; Kaskova, Zinaida M; Tsarkova, Aleksandra S; Petunin, Alexei I; Bondar, Vladimir S; Rodicheva, Emma K; Medvedeva, Svetlana E; Oba, Yuichi; Oba, Yumiko; Arseniev, Alexander S; Lukyanov, Sergey; Gitelson, Josef I; Yampolsky, Ilia V

    2015-07-01

    Many species of fungi naturally produce light, a phenomenon known as bioluminescence, however, the fungal substrates used in the chemical reactions that produce light have not been reported. We identified the fungal compound luciferin 3-hydroxyhispidin, which is biosynthesized by oxidation of the precursor hispidin, a known fungal and plant secondary metabolite. The fungal luciferin does not share structural similarity with the other eight known luciferins. Furthermore, it was shown that 3-hydroxyhispidin leads to bioluminescence in extracts from four diverse genera of luminous fungi, thus suggesting a common biochemical mechanism for fungal bioluminescence.

  4. Current ecological understanding of fungal-like pathogens of fish: what lies beneath?

    PubMed

    Gozlan, Rodolphe E; Marshall, Wyth L; Lilje, Osu; Jessop, Casey N; Gleason, Frank H; Andreou, Demetra

    2014-01-01

    Despite increasingly sophisticated microbiological techniques, and long after the first discovery of microbes, basic knowledge is still lacking to fully appreciate the ecological importance of microbial parasites in fish. This is likely due to the nature of their habitats as many species of fish suffer from living beneath turbid water away from easy recording. However, fishes represent key ecosystem services for millions of people around the world and the absence of a functional ecological understanding of viruses, prokaryotes, and small eukaryotes in the maintenance of fish populations and of their diversity represents an inherent barrier to aquatic conservation and food security. Among recent emerging infectious diseases responsible for severe population declines in plant and animal taxa, fungal and fungal-like microbes have emerged as significant contributors. Here, we review the current knowledge gaps of fungal and fungal-like parasites and pathogens in fish and put them into an ecological perspective with direct implications for the monitoring of fungal fish pathogens in the wild, their phylogeography as well as their associated ecological impact on fish populations. With increasing fish movement around the world for farming, releases into the wild for sport fishing and human-driven habitat changes, it is expected, along with improved environmental monitoring of fungal and fungal-like infections, that the full extent of the impact of these pathogens on wild fish populations will soon emerge as a major threat to freshwater biodiversity.

  5. Current ecological understanding of fungal-like pathogens of fish: what lies beneath?

    PubMed Central

    Gozlan, Rodolphe E.; Marshall, Wyth L.; Lilje, Osu; Jessop, Casey N.; Gleason, Frank H.; Andreou, Demetra

    2014-01-01

    Despite increasingly sophisticated microbiological techniques, and long after the first discovery of microbes, basic knowledge is still lacking to fully appreciate the ecological importance of microbial parasites in fish. This is likely due to the nature of their habitats as many species of fish suffer from living beneath turbid water away from easy recording. However, fishes represent key ecosystem services for millions of people around the world and the absence of a functional ecological understanding of viruses, prokaryotes, and small eukaryotes in the maintenance of fish populations and of their diversity represents an inherent barrier to aquatic conservation and food security. Among recent emerging infectious diseases responsible for severe population declines in plant and animal taxa, fungal and fungal-like microbes have emerged as significant contributors. Here, we review the current knowledge gaps of fungal and fungal-like parasites and pathogens in fish and put them into an ecological perspective with direct implications for the monitoring of fungal fish pathogens in the wild, their phylogeography as well as their associated ecological impact on fish populations. With increasing fish movement around the world for farming, releases into the wild for sport fishing and human-driven habitat changes, it is expected, along with improved environmental monitoring of fungal and fungal-like infections, that the full extent of the impact of these pathogens on wild fish populations will soon emerge as a major threat to freshwater biodiversity. PMID:24600442

  6. Biosynthesis of Fungal Indole Alkaloids

    PubMed Central

    Xu, Wei; Gavia, Diego J.; Tang, Yi

    2014-01-01

    This review provides a summary of recent research advances in elucidating the biosynthesis of fungal indole alkaloids. Different strategies used to incorporate and derivatize the indole/indoline moieties in various families of fungal indole alkaloids will be discussed, including tryptophan-containing nonribosomal peptides and polyketide-nonribosomal peptide hybrids; and alkaloids derived from other indole building blocks. This review also includes discussion regarding the downstream modifications that generate chemical and structural diversity among indole alkaloids. PMID:25180619

  7. Low genetic diversity and minimal population substructure in the endangered Florida manatee: implications for conservation

    USGS Publications Warehouse

    Tucker, Kimberly Pause; Hunter, Margaret E.; Bonde, Robert K.; Austin, James D.; Clark, Ann Marie; Beck, Cathy A.; McGuire, Peter M.; Oli, Madan K.

    2012-01-01

    Species of management concern that have been affected by human activities typically are characterized by low genetic diversity, which can adversely affect their ability to adapt to environmental changes. We used 18 microsatellite markers to genotype 362 Florida manatees (Trichechus manatus latirostris), and investigated genetic diversity, population structure, and estimated genetically effective population size (Ne). The observed and expected heterozygosity and average number of alleles were 0.455 ± 0.04, 0.479 ± 0.04, and 4.77 ± 0.51, respectively. All measures of Florida manatee genetic diversity were less than averages reported for placental mammals, including fragmented or nonideal populations. Overall estimates of differentiation were low, though significantly greater than zero, and analysis of molecular variance revealed that over 95% of the total variance was among individuals within predefined management units or among individuals along the coastal subpopulations, with only minor portions of variance explained by between group variance. Although genetic issues, as inferred by neutral genetic markers, appear not to be critical at present, the Florida manatee continues to face demographic challenges due to anthropogenic activities and stochastic factors such as red tides, oil spills, and disease outbreaks; these can further reduce genetic diversity of the manatee population.

  8. Patterns of ancestry and genetic diversity in reintroduced populations of the slimy sculpin: Implications for conservation

    USGS Publications Warehouse

    Huff, David D.; Miller, Loren M.; Vondracek, Bruce C.

    2010-01-01

    Reintroductions are a common approach for preserving intraspecific biodiversity in fragmented landscapes. However, they may exacerbate the reduction in genetic diversity initially caused by population fragmentation because the effective population size of reintroduced populations is often smaller and reintroduced populations also tend to be more geographically isolated than native populations. Mixing genetically divergent sources for reintroduction purposes is a practice intended to increase genetic diversity. We documented the outcome of reintroductions from three mixed sources on the ancestral composition and genetic variation of a North American fish, the slimy sculpin (Cottus cognatus). We used microsatellite markers to evaluate allelic richness and heterozygosity in the reintroduced populations relative to computer simulated expectations. Sculpins in reintroduced populations exhibited higher levels of heterozygosity and allelic richness than any single source, but only slightly higher than the single most genetically diverse source population. Simulations intended to mimic an ideal scenario for maximizing genetic variation in the reintroduced populations also predicted increases, but they were only moderately greater than the most variable source population. We found that a single source contributed more than the other two sources at most reintroduction sites. We urge caution when choosing whether to mix source populations in reintroduction programs. Genetic characteristics of candidate source populations should be evaluated prior to reintroduction if feasible. When combined with knowledge of the degree of genetic distinction among sources, simulations may allow the genetic diversity benefits of mixing populations to be weighed against the risks of outbreeding depression in reintroduced and nearby populations.

  9. Patterns of ancestry and genetic diversity in reintroduced populations of the slimy sculpin: Implications for conservation

    USGS Publications Warehouse

    Huff, D.D.; Miller, L.M.; Vondracek, B.

    2010-01-01

    Reintroductions are a common approach for preserving intraspecific biodiversity in fragmented landscapes. However, they may exacerbate the reduction in genetic diversity initially caused by population fragmentation because the effective population size of reintroduced populations is often smaller and reintroduced populations also tend to be more geographically isolated than native populations. Mixing genetically divergent sources for reintroduction purposes is a practice intended to increase genetic diversity. We documented the outcome of reintroductions from three mixed sources on the ancestral composition and genetic variation of a North American fish, the slimy sculpin (Cottus cognatus). We used microsatellite markers to evaluate allelic richness and heterozygosity in the reintroduced populations relative to computer simulated expectations. Sculpins in reintroduced populations exhibited higher levels of heterozygosity and allelic richness than any single source, but only slightly higher than the single most genetically diverse source population. Simulations intended to mimic an ideal scenario for maximizing genetic variation in the reintroduced populations also predicted increases, but they were only moderately greater than the most variable source population. We found that a single source contributed more than the other two sources at most reintroduction sites. We urge caution when choosing whether to mix source populations in reintroduction programs. Genetic characteristics of candidate source populations should be evaluated prior to reintroduction if feasible. When combined with knowledge of the degree of genetic distinction among sources, simulations may allow the genetic diversity benefits of mixing populations to be weighed against the risks of outbreeding depression in reintroduced and nearby populations. ?? 2010 US Government.

  10. 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

  11. 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

  12. 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

  13. Biodiversity and Archeological Conservation Connected: Aragonite Shell Middens Increase Plant Diversity

    PubMed Central

    Vanderplank, Sula E.; Mata, Sergio; Ezcurra, Exequiel

    2014-01-01

    Natural and cultural heritage sites frequently have nonoverlapping or even conflicting conservation priorities, because human impacts have often resulted in local extirpations and reduced levels of native biodiversity. Over thousands of years, the predictable winter rains of northwestern Baja California have weathered calcium from the clam shells deposited by indigenous peoples in middens along the coast. The release of this calcium has changed soil properties, remediated sodic and saline soils, and resulted in a unique microhabitat that harbors plant assemblages very different from those of the surrounding matrix. Native plant biodiversity and landscape heterogeneity are significantly increased on the anthropogenic soils of these shell middens. Protection of this cultural landscape in the Anthropocene will further both archeological and biodiversity conservation in these anthropogenic footprints from the Holocene. Along these coasts, natural and cultural heritage priorities are overlapping and mutually beneficial. PMID:26955068

  14. Dynamic regulation of novel and conserved miRNAs across various tissues of diverse Cucurbit spp.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    MicroRNA genes (miRNAs) encoding small non-coding RNAs are abundant in plant genomes and play a key role in regulating several biological mechanisms. Five conserved miRNAs, miR156, miR168-1, miR168-2, miR164, and miR166 were selected for analysis from the 21 known plant miRNA families that were rec...

  15. Fungal nail infection

    MedlinePlus

    Nails - fungal infection; Onychomycosis; Infection - fungal - nails; Tinea unguium ... hair, nails, and outer skin layers. Common fungal infections include: Athlete's foot Jock itch Ringworm on the ...

  16. Conservation education in Madagascar: three case studies in the biologically diverse island-continent.

    PubMed

    Dolins, Francine L; Jolly, Alison; Rasamimanana, Hantanirina; Ratsimbazafy, Jonah; Feistner, Anna T C; Ravoavy, Florent

    2010-05-01

    Few Malagasy children and adults are aware of the rare and unique fauna and flora indigenous to their island-continent, including flagship lemur species. Even the Malagasy ancestral proverbs never mentioned lemurs, but these same proverbs talked about the now extinct hippopotamus. Madagascar's geography, history, and economic constraints contribute to severe biodiversity loss. Deforestation on Madagascar is reported to be over 100,000 ha/year, with only 10-15% of the island retaining natural forest [Green & Sussman, 1990]. Educating children, teacher-training, and community projects about environmental and conservation efforts to protect the remaining natural habitats of endangered lemur species provide a basis for long-term changes in attitudes and practices. Case studies of three conservation education projects located in different geographical regions of Madagascar, Centre ValBio, Madagacar Wildlife Conservation Alaotra Comic Book Project, and The Ako Book Project, are presented together with their ongoing stages of development, assessment, and outcomes. We argue that while nongovernmental organizational efforts are and will be very important, the Ministry of Education urgently needs to incorporate biodiversity education in the curriculum at all levels, from primary school to university. PMID:20039330

  17. An invasive non-native mammal population conserves genetic diversity lost from its native range.

    PubMed

    Veale, A J; Holland, O J; McDonald, R A; Clout, M N; Gleeson, D M

    2015-05-01

    Invasive, non-native species are one of the major causes of global biodiversity loss. Although they are, by definition, successful in their non-native range, their populations generally show major reductions in their genetic diversity during the demographic bottleneck they experience during colonization. By investigating the mitochondrial genetic diversity of an invasive non-native species, the stoat Mustela erminea, in New Zealand and comparing it to diversity in the species' native range in Great Britain, we reveal the opposite effect. We demonstrate that the New Zealand stoat population contains four mitochondrial haplotypes that have not been found in the native range. Stoats in Britain rely heavily on introduced rabbits Oryctolagus cuniculus as their primary prey and were introduced to New Zealand in a misguided attempt at biological control of rabbits, which had also been introduced there. While invasive stoats have since decimated the New Zealand avifauna, native stoat populations were themselves decimated by the introduction to Britain of Myxoma virus as a control measure for rabbits. We highlight the irony that while introduced species (rabbits) and subsequent biocontrol (myxomatosis) have caused population crashes of native stoats, invasive stoats in New Zealand, which were also introduced for biological control, now contain more genetic haplotypes than their most likely native source. PMID:25655531

  18. The evolutionary history of steelhead (Oncorhynchus mykiss) along the US Pacific Coast: Developing a conservation strategy using genetic diversity

    USGS Publications Warehouse

    Nielsen, J.L.

    1999-01-01

    Changes in genetic variation across a species range may indicate patterns of population structure resulting from past ecological and demographic events that are otherwise difficult to infer and thus provide insight into evolutionary development. Genetic data is used, drawn from 11 microsatellite loci amplified from anadromous steelhead (Oncorhynchus mykiss) sampled throughout its range in the eastern Pacific Ocean, to explore population structure at the southern edge in California. Steelhead populations in this region represent less than 10% of their reported historic abundance and survive in very small populations found in fragmented habitats. Genetic data derived from three independent molecular systems (allozymes, mtDNA, and microsatellites) have shown that the southernmost populations are characterized by a relatively high genetic diversity. Two hypothetical models supporting genetic population substructure such as observed were considered: (1) range expansion with founder-flush effects and subsequent population decline; (2) a second Pleistocene radiation from the Gulf of California. Using genetic and climatic data, a second Pleistocene refugium contributing to a southern ecotone seems more feasible. These data support strong conservation measures based on genetic diversity be developed to ensure the survival of this uniquely diverse gene pool.

  19. [Diversity, natural history and conservation of mammals from San Vito de Coto Brus, Costa Rica].

    PubMed

    Pacheco, Jesús; Ceballos, Gerardo; Daily, Gretchen C; Ehrlich, Paul R; Suzán, Gerardo; Rodríguez-Herrera, Bernal; Marcé, Erika

    2006-03-01

    Although Costa Rica has been biologically well studied, few areas have complete mammal inventories, which are essential for ecological studies and conservation. The San Vito region is considered among the most important for scientific research in the country because of the presence of the Wilson Botanical Garden and Las Cruces. However, the knowledge of its mammalian fauna is incomplete. We extensively studied the mammals of San Vito, compiled a checklist, and evaluated its composition, relative abundance, habitat distribution, and conservation status. We recorded 105 species, representing 85 genera, 29 families, and 10 orders. Non-volant mammals represented 62 species, 59 genera, 23 families, and 9 orders. Bats belonged to 6 families, 26 genera and 43 species. The extensive deforestation and hunting have caused the extinction of seven species, but the region still supports, surprisingly, a relatively high number of species, most of which are rare. Few species are common and abundant. Species richness was higher in forest, and forest fragments; fewer species were found in coffee plantations, induced grasslands, and secondary vegetation. Around 21% (13 species) are included in the IUCN red book. Three species are considered endangered (Saimiri oerstedii, Tapirus bairdii, and Sylvilagus dicei), and two threatened (Myrmecophaga trydactila and Caluromys derbianus), of which two (T. bairdii and M. trydactila) ar