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Species Diversity, Distribution, and Phylogeny of Exophiala with the Addition of Four New Species from Thailand. J Fungi (Basel) 2022; 8:jof8080766. [PMID: 35893134 PMCID: PMC9331753 DOI: 10.3390/jof8080766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 02/06/2023] Open
Abstract
The genus Exophiala is an anamorphic ascomycete fungus in the family Herpotrichiellaceae of the order Chaetothyriales. Exophiala species have been classified as polymorphic black yeast-like fungi. Prior to this study, 63 species had been validated, published, and accepted into this genus. Exophiala species are known to be distributed worldwide and have been isolated in various habitats around the world. Several Exophiala species have been identified as potential agents of human and animal mycoses. However, in some studies, Exophiala species have been used in agriculture and biotechnological applications. Here, we provide a brief review of the diversity, distribution, and taxonomy of Exophiala through an overview of the recently published literature. Moreover, four new Exophiala species were isolated from rocks that were collected from natural forests located in northern Thailand. Herein, we introduce these species as E. lamphunensis, E. lapidea, E. saxicola, and E. siamensis. The identification of these species was based on a combination of morphological characteristics and molecular analyses. Multi-gene phylogenetic analyses of a combination of the internal transcribed spacer (ITS) and small subunit (nrSSU) of ribosomal DNA, along with the translation elongation factor (tef), partial β-tubulin (tub), and actin (act) genes support that these four new species are distinct from previously known species of Exophiala. A full description, illustrations, and a phylogenetic tree showing the position of four new species are provided.
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Species and geographic specificity between endophytic fungi and host supported by parasitic Cynomorium songaricum and its host Nitraria tangutorum distributed in desert. Arch Microbiol 2021; 203:2511-2519. [PMID: 33677636 DOI: 10.1007/s00203-021-02224-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 01/04/2021] [Accepted: 02/11/2021] [Indexed: 10/22/2022]
Abstract
This study was aimed to investigate whether host plant species and lifestyles, and environmental conditions in the desert affect endophytic fungi composition. Endophytic fungal communities from parasitic plant Cynomorium songaricum and its host Nitraria tangutorum were investigated from three sites including Tonggu Naoer, Xilin Gaole, and Guazhou in Tengger and Badain Jaran Deserts in China using the next-generation sequencing of a ribosomal RNA gene region. Similarity and difference in endophytic fungal composition from different geographic locations were evaluated through multivariate statistical analysis. It showed that plant genetics was a deciding factor affecting endophytic fungal composition even when C. songaricum and N. tangutorum grow together tightly. Not only that, the fungal composition was also greatly affected by the local environment and rainfall. However, the distribution and richness of fungal species indicated that the geographical distance exerted little influence on characterizing the fungal composition. Overall, the findings suggested that plant species, parasitic or non-parasitic lifestyles of the plant, and local environment strongly affected the number and diversity of the endophytic fungal species, which may provide valuable insights into the microbe ecology, symbiosis specificity, and the tripartite relationship among parasitic plant, host, and endophytic fungi, especially under desert environment.
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Li Y, Li Z, Arafat Y, Lin W. Studies on fungal communities and functional guilds shift in tea continuous cropping soils by high-throughput sequencing. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01555-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
Although soil fungal communities are considered important in tea orchard ecosystems, experimental research on their responses to the long-term continuous ratooning cultivation of tea plants are limited.
Methods
In this study, Illumina high-throughput sequencing technology was employed to investigate soil fungal communities in tea orchards with continuous cropping histories of 0, 1, 10, and 20 years.
Results
Results indicated that the predominant phyla were Ascomycota and Basidiomycota in all tea soil samples. Plant pathogen fungi Alternaria was the most predominant genus in the 10- and 20-year soils and significantly higher than that in the 0- and 1-year soils. FUNGuild revealed that the symbiotrophs in the 1-year soil (8.00%) was markedly higher than those in the 0-, 10-, and 20-year soils (1.43%~2.47%). The saprotrophs in the 20-year soils was approximately two-fold higher than those identified in the 0-, 1-, and 10-year soils. The pathotroph–saprotroph–symbiotroph fungi were higher in the 10- and 20-year soils in comparison to the 0- and 1-year soils as expected. Diversity analysis showed that the indices of Shannon and Simpson in the 1-year soils were higher than those in other treatments. Redundancy analysis suggested that fungal community structure and function were evidently interrelated to pH and exchangeable aluminum in the soils, respectively.
Conclusion
In summary, the long-term continuous ratooning cultivation of tea plants changed the fungal communities in the rhizosphere, enriched saprotrophs and plant pathogens (Alternaria spp.), and reduced beneficial fungi (symbiotrophs). Results of this work can be used to explore reasonable management measures, such as microbial fertilizer application, and eventually relieve the long-term monoculture problems of tea plants.
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Zhang C, Sirijovski N, Adler L, Ferrari BC. Exophiala macquariensis sp. nov., a cold adapted black yeast species recovered from a hydrocarbon contaminated sub-Antarctic soil. Fungal Biol 2019; 123:151-158. [DOI: 10.1016/j.funbio.2018.11.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/22/2018] [Accepted: 11/26/2018] [Indexed: 11/29/2022]
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Maciá-Vicente JG, Shi YN, Cheikh-Ali Z, Grün P, Glynou K, Kia SH, Piepenbring M, Bode HB. Metabolomics-based chemotaxonomy of root endophytic fungi for natural products discovery. Environ Microbiol 2018; 20:1253-1270. [DOI: 10.1111/1462-2920.14072] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/09/2018] [Indexed: 12/01/2022]
Affiliation(s)
- Jose G. Maciá-Vicente
- Institute of Ecology, Evolution and Diversity, Goethe Universität Frankfurt, Max-von-Laue-Str. 13; Frankfurt am Main 60438 Germany
- Integrative Fungal Research Cluster (IPF); Frankfurt am Main Germany
| | - Yan-Ni Shi
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften; Goethe Universität Frankfurt; Frankfurt am Main 60438 Germany
| | - Zakaria Cheikh-Ali
- Integrative Fungal Research Cluster (IPF); Frankfurt am Main Germany
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften; Goethe Universität Frankfurt; Frankfurt am Main 60438 Germany
| | - Peter Grün
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften; Goethe Universität Frankfurt; Frankfurt am Main 60438 Germany
| | - Kyriaki Glynou
- Institute of Ecology, Evolution and Diversity, Goethe Universität Frankfurt, Max-von-Laue-Str. 13; Frankfurt am Main 60438 Germany
- Integrative Fungal Research Cluster (IPF); Frankfurt am Main Germany
| | - Sevda Haghi Kia
- Institute of Ecology, Evolution and Diversity, Goethe Universität Frankfurt, Max-von-Laue-Str. 13; Frankfurt am Main 60438 Germany
- Integrative Fungal Research Cluster (IPF); Frankfurt am Main Germany
| | - Meike Piepenbring
- Institute of Ecology, Evolution and Diversity, Goethe Universität Frankfurt, Max-von-Laue-Str. 13; Frankfurt am Main 60438 Germany
- Integrative Fungal Research Cluster (IPF); Frankfurt am Main Germany
| | - Helge B. Bode
- Integrative Fungal Research Cluster (IPF); Frankfurt am Main Germany
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften; Goethe Universität Frankfurt; Frankfurt am Main 60438 Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt; Frankfurt am Main 60438 Germany
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Glynou K, Ali T, Kia SH, Thines M, Maciá-Vicente JG. Genotypic diversity in root-endophytic fungi reflects efficient dispersal and environmental adaptation. Mol Ecol 2017; 26:4618-4630. [PMID: 28667772 DOI: 10.1111/mec.14231] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 04/09/2017] [Accepted: 06/08/2017] [Indexed: 12/25/2022]
Abstract
Studying community structure and dynamics of plant-associated fungi is the basis for unravelling their interactions with hosts and ecosystem functions. A recent sampling revealed that only a few fungal groups, as defined by internal transcribed spacer region (ITS) sequence similarity, dominate culturable root endophytic communities of nonmycorrhizal Microthlaspi spp. plants across Europe. Strains of these fungi display a broad phenotypic and functional diversity, which suggests a genetic variability masked by ITS clustering into operational taxonomic units (OTUs). The aims of this study were to identify how genetic similarity patterns of these fungi change across environments and to evaluate their ability to disperse and adapt to ecological conditions. A first ITS-based haplotype analysis of ten widespread OTUs mostly showed a low to moderate genotypic differentiation, with the exception of a group identified as Cadophora sp. that was highly diverse. A multilocus phylogeny based on additional genetic loci (partial translation elongation factor 1α, beta-tubulin and actin) and amplified fragment length polymorphism profiling of 185 strains representative of the five dominant OTUs revealed a weak association of genetic differences with geography and environmental conditions, including bioclimatic and soil factors. Our findings suggest that dominant culturable root endophytic fungi have efficient dispersal capabilities, and that their distribution is little affected by environmental filtering. Other processes, such as inter- and intraspecific biotic interactions, may be more important for the local assembly of their communities.
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Affiliation(s)
- Kyriaki Glynou
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany.,Integrative Fungal Research Cluster (IPF), Frankfurt am Main, Germany
| | - Tahir Ali
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Sevda Haghi Kia
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany.,Integrative Fungal Research Cluster (IPF), Frankfurt am Main, Germany
| | - Marco Thines
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany.,Integrative Fungal Research Cluster (IPF), Frankfurt am Main, Germany.,Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Jose G Maciá-Vicente
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany.,Integrative Fungal Research Cluster (IPF), Frankfurt am Main, Germany
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Kia SH, Glynou K, Nau T, Thines M, Piepenbring M, Maciá-Vicente JG. Influence of phylogenetic conservatism and trait convergence on the interactions between fungal root endophytes and plants. THE ISME JOURNAL 2017; 11:777-790. [PMID: 27801904 PMCID: PMC5322293 DOI: 10.1038/ismej.2016.140] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 08/26/2016] [Accepted: 09/05/2016] [Indexed: 01/27/2023]
Abstract
Plants associate through their roots with fungal assemblages that impact their abundance and productivity. Non-mycorrhizal endophytes constitute an important component of such fungal diversity, but their implication in ecosystem processes is little known. Using a selection of 128 root-endophytic strains, we defined functional groups based on their traits and plant interactions with potential to predict community assembly and symbiotic association processes. In vitro tests of the strains' interactions with Arabidopsis thaliana, Microthlaspi erraticum and Hordeum vulgare showed a net negative effect of fungal colonization on plant growth. The effects partly depended on the phylogenetic affiliation of strains, but also varied considerably depending on the plant-strain combination. The variation was partly explained by fungal traits shared by different lineages, like growth rates or melanization. The origin of strains also affected their symbioses, with endophytes isolated from Microthlaspi spp. populations being more detrimental to M. erraticum than strains from other sources. Our findings suggest that plant-endophyte associations are subject to local processes of selection, in which particular combinations of symbionts are favored across landscapes. We also show that different common endophytic taxa have differential sets of traits found to affect interactions, hinting to a functional complementarity that can explain their frequent co-existence in natural communities.
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Affiliation(s)
- Sevda Haghi Kia
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany
- Integrative Fungal Research Cluster (IPF), Frankfurt am Main, Germany
| | - Kyriaki Glynou
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany
- Integrative Fungal Research Cluster (IPF), Frankfurt am Main, Germany
| | - Thomas Nau
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marco Thines
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany
- Integrative Fungal Research Cluster (IPF), Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Meike Piepenbring
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany
- Integrative Fungal Research Cluster (IPF), Frankfurt am Main, Germany
| | - Jose G Maciá-Vicente
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany
- Integrative Fungal Research Cluster (IPF), Frankfurt am Main, Germany
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Coombs K, Vesper S, Green BJ, Yermakov M, Reponen T. Fungal Microbiomes Associated with Green and Non-Green Building Materials. INTERNATIONAL BIODETERIORATION & BIODEGRADATION 2017; 125:251-257. [PMID: 29681691 PMCID: PMC5906815 DOI: 10.1016/j.ibiod.2017.07.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Water-damaged buildings can lead to fungal growth and occupant health problems. Green building materials, derived from renewable sources, are increasingly utilized in construction and renovations. However, the question as to what fungi will grow on these green compared to non-green materials, after they get wet, has not been adequately studied. By determining what fungi grow on each type of material, the potential health risks can be more adequately assessed. In this study, we inoculated green and non-green pieces of ceiling tile, composite board, drywall, and flooring with indoor dust containing a complex mixture of naturally occurring fungi. The materials were saturated with water and incubated for two months in a controlled environment. The resulting fungal microbiomes were evaluated using ITS amplicon sequencing. Overall, the richness and diversity of the mycobiomes on each pair of green and non-green pieces were not significantly different. However, different genera dominated on each type of material. For example, Aspergillus spp. had the highest relative abundance on green and non-green ceiling tiles and green composite boards, but Peniophora spp. dominated the non-green composite board. In contrast, Penicillium spp. dominated green and non-green flooring samples. Green gypsum board was dominated by Phialophora spp. and Stachybotrys spp., but non-green gypsum board by Myrothecium spp. These data suggest that water-damaged green and non-green building materials can result in mycobiomes that are dominated by fungal genera whose member species pose different potentials for health risks.
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Affiliation(s)
- Kanistha Coombs
- Department of Environmental Health, University of Cincinnati, P.O. Box 670056, Cincinnati, OH 45267-0056
| | - Stephen Vesper
- United States Environmental Protection Agency, 26 W. M. L. King Drive, Mail Stop 314, Cincinnati, OH 45268
| | - Brett J Green
- Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, 1095 Willowdale Road, Morgantown, WV 26505
| | - Mikhail Yermakov
- Department of Environmental Health, University of Cincinnati, P.O. Box 670056, Cincinnati, OH 45267-0056
| | - Tiina Reponen
- Department of Environmental Health, University of Cincinnati, P.O. Box 670056, Cincinnati, OH 45267-0056
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Floros DJ, Jensen PR, Dorrestein PC, Koyama N. A metabolomics guided exploration of marine natural product chemical space. Metabolomics 2016; 12:145. [PMID: 28819353 PMCID: PMC5556696 DOI: 10.1007/s11306-016-1087-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Natural products from culture collections have enormous impact in advancing discovery programs for metabolites of biotechnological importance. These discovery efforts rely on the metabolomic characterization of strain collections. OBJECTIVE Many emerging approaches compare metabolomic profiles of such collections, but few enable the analysis and prioritization of thousands of samples from diverse organisms while delivering chemistry specific read outs. METHOD In this work we utilize untargeted LC-MS/MS based metabolomics together with molecular networking to. RESULT This approach annotated 76 molecular families (a spectral match rate of 28 %), including clinically and biotechnologically important molecules such as valinomycin, actinomycin D, and desferrioxamine E. Targeting a molecular family produced primarily by one microorganism led to the isolation and structure elucidation of two new molecules designated maridric acids A and B. CONCLUSION Molecular networking guided exploration of large culture collections allows for rapid dereplication of know molecules and can highlight producers of uniques metabolites. These methods, together with large culture collections and growing databases, allow for data driven strain prioritization with a focus on novel chemistries.
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Affiliation(s)
- Dimitrios J Floros
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA
| | - Paul R Jensen
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA
| | - Nobuhiro Koyama
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan inventory the chemistries associated with 1000 marine microorganisms
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