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Jin QY, Peng HZ, Zhu TJ, Ye HL. Isolation and functional characteristics of the fungus Hypoxylon spp. Sj18 with biocontrol potential. Fungal Biol 2021; 126:174-184. [DOI: 10.1016/j.funbio.2021.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 11/24/2021] [Accepted: 12/08/2021] [Indexed: 11/29/2022]
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Becker K, Stadler M. Recent progress in biodiversity research on the Xylariales and their secondary metabolism. J Antibiot (Tokyo) 2021; 74:1-23. [PMID: 33097836 PMCID: PMC7732752 DOI: 10.1038/s41429-020-00376-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/16/2020] [Accepted: 09/19/2020] [Indexed: 12/18/2022]
Abstract
The families Xylariaceae and Hypoxylaceae (Xylariales, Ascomycota) represent one of the most prolific lineages of secondary metabolite producers. Like many other fungal taxa, they exhibit their highest diversity in the tropics. The stromata as well as the mycelial cultures of these fungi (the latter of which are frequently being isolated as endophytes of seed plants) have given rise to the discovery of many unprecedented secondary metabolites. Some of those served as lead compounds for development of pharmaceuticals and agrochemicals. Recently, the endophytic Xylariales have also come in the focus of biological control, since some of their species show strong antagonistic effects against fungal and other pathogens. New compounds, including volatiles as well as nonvolatiles, are steadily being discovered from these ascomycetes, and polythetic taxonomy now allows for elucidation of the life cycle of the endophytes for the first time. Moreover, recently high-quality genome sequences of some strains have become available, which facilitates phylogenomic studies as well as the elucidation of the biosynthetic gene clusters (BGC) as a starting point for synthetic biotechnology approaches. In this review, we summarize recent findings, focusing on the publications of the past 3 years.
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Affiliation(s)
- Kevin Becker
- Department Microbial Drugs, Helmholtz Centre for Infection Research GmbH, Inhoffenstraße 7, 38124, Braunschweig, Germany
- German Centre for Infection Research Association (DZIF), partner site Hannover-Braunschweig, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Marc Stadler
- Department Microbial Drugs, Helmholtz Centre for Infection Research GmbH, Inhoffenstraße 7, 38124, Braunschweig, Germany.
- German Centre for Infection Research Association (DZIF), partner site Hannover-Braunschweig, Inhoffenstraße 7, 38124, Braunschweig, Germany.
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Helaly SE, Thongbai B, Stadler M. Diversity of biologically active secondary metabolites from endophytic and saprotrophic fungi of the ascomycete order Xylariales. Nat Prod Rep 2019; 35:992-1014. [PMID: 29774351 DOI: 10.1039/c8np00010g] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: up to December 2017 The diversity of secondary metabolites in the fungal order Xylariales is reviewed with special emphasis on correlations between chemical diversity and biodiversity as inferred from recent taxonomic and phylogenetic studies. The Xylariales are arguably among the predominant fungal endophytes, which are the producer organisms of pharmaceutical lead compounds including the antimycotic sordarins and the antiparasitic nodulisporic acids, as well as the marketed drug, emodepside. Many Xylariales are "macromycetes", which form conspicuous fruiting bodies (stromata), and the metabolite profiles that are predominant in the stromata are often complementary to those encountered in corresponding mycelial cultures of a given species. Secondary metabolite profiles have recently been proven highly informative as additional parameters to support classical morphology and molecular phylogenetic approaches in order to reconstruct evolutionary relationships among these fungi. Even the recent taxonomic rearrangement of the Xylariales has been relying on such approaches, since certain groups of metabolites seem to have significance at the species, genus or family level, respectively, while others are only produced in certain taxa and their production is highly dependent on the culture conditions. The vast metabolic diversity that may be encountered in a single species or strain is illustrated based on examples like Daldinia eschscholtzii, Hypoxylon rickii, and Pestalotiopsis fici. In the future, it appears feasible to increase our knowledge of secondary metabolite diversity by embarking on certain genera that have so far been neglected, as well as by studying the volatile secondary metabolites more intensively. Methods of bioinformatics, phylogenomics and transcriptomics, which have been developed to study other fungi, are readily available for use in such scenarios.
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Affiliation(s)
- Soleiman E Helaly
- Dept Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
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Draft Genome Sequence of the Filamentous Fungus Hypoxylon pulicicidum ATCC 74245. GENOME ANNOUNCEMENTS 2018; 6:6/2/e01380-17. [PMID: 29326208 PMCID: PMC5764932 DOI: 10.1128/genomea.01380-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Hypoxylon pulicicidum strain MF5954 (ATCC 74245) (formerly classified as Nodulisporium sp.) is a filamentous fungal species known for its production of the secondary metabolite nodulisporic acid A. We present here the 41.5-Mb draft genome sequence for this organism.
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Stadler M, Læssøe T, Fournier J, Decock C, Schmieschek B, Tichy HV, Peršoh D. A polyphasic taxonomy of Daldinia (Xylariaceae). Stud Mycol 2014; 77:1-143. [PMID: 24790283 PMCID: PMC3953824 DOI: 10.3114/sim0016] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
For a monograph based on a polythetic concept, several thousands of herbarium specimens, and several hundreds of freshly collected and cultured specimens of Daldinia and allied Xylariaceae, originating from around the world, were studied for morphological traits, including by SEM, and chemically by HPLC profiles using UV-visible and mass spectrometric detection. Emphasis was given to tropical material, and importantly, ancient specimens, including as many types as possible, were tracked and studied to review earlier taxonomic concepts. An epitype of D. eschscholtzii was selected as representative of the morphochemotype that is most widely distributed in the tropics. Six new species of Daldinia from the tropics and the southern Hemisphere are described. Daldinia asphalatum is resurrected, and D. cudonia is regarded as its synonym. In addition, the following binomials are epi-, iso-, neo- and/or lectotypified: Daldinia asphalatum, D. caldariorum, D. clavata, D. cuprea, D. durissima, D. eschscholtzii, D. grandis, D. loculata, and D. vernicosa. Annellosporium and Versiomyces are regarded as synonyms of Daldinia. Many new synonymies in Daldinia are proposed, and some previously published names are rejected. In total, 47 taxa in Daldinia are recognised and a key is provided. Their biogeography, chorology, and ecology, as well as the importance of their secondary metabolites, are also discussed. The previous definition of the genus is emended. The species concept is based mainly on morphological and other phenotype-derived characters because, despite diligent search, no molecular data or cultures of several of the accepted species could be obtained. Daldinia is segregated into five major groups, based on phenotypic characteristics. Some unnamed but aberrant specimens were not found in good condition and are therefore not formally described as new species. However, they are illustrated in detail in a hope that this will facilitate the discovery of fresh material in future. A preliminary molecular phylogeny based on 5.8S/ITS nrDNA including numerous representatives of all hitherto described taxa for which cultures are extant, was found basically in agreement with the above mentioned segregation of the genus, based on morphological and chemotaxonomic evidence. In the rDNA based phylogenetic tree, Daldinia appears clearly distinct from members of the genera Annulohypoxylon and Hypoxylon; nevertheless, representatives of small genera of predominantly tropical origin (Entonaema, Phylacia, Ruwenzoria, Rhopalostroma, Thamnomyces) appear to have evolved from daldinioid ancestors and are nested inside the Daldinia clade. Interestingly, these findings correlate with chemotaxonomic characters to a great extent, especially regarding the distribution of marker metabolites in their mycelial cultures. Hence, the current study revealed for the first time that fungal secondary metabolite profiles can have taxonomic value beyond the species rank and even coincide with phylogenetic data. TAXONOMIC NOVELTIES Daldinia andina sp. nov., D. australis sp. nov., D. hausknechtii sp. nov., D. rehmii sp. nov., D. starbaeckii sp. nov., D. theissenii sp. nov., D. cahuchosa comb. nov., D. nemorosa comb. nov.
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Affiliation(s)
- Marc Stadler
- Helmholtz Centre for Infection Research, Dept. Microbial Drugs, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - Thomas Læssøe
- University of Copenhagen, Department of Biology/Natural History Museum of Denmark, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | | | - Cony Decock
- Mycothèque de l’Université catholique de Louvain (MUCL, BCCM™), Earth and Life Institute - Microbiology (ELIM), Université catholique de Louvain, Croix du Sud 2 bte L7.05.06,B-1348, Louvain-la-Neuve, Belgium
| | | | - Hans-Volker Tichy
- Bayer Pharma AG, Product Supply, API - Supply Center Elberfeld Quality Unit - QCB-Mikrobiologie I, 42096 Wuppertal, Germany
| | - Derek Peršoh
- University of Bayreuth, Dept. Mycology, Universitätsstraße 30, D-95540 Bayreuth, Germany
- Present address: Ruhr-Universität Bochum, AG Geobotanik, Universitätsstraße 150, D-44780 Bochum, Germany
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Vicente F, Basilio A, Platas G, Collado J, Bills GF, González Del Val A, Martín J, Tormo JR, Harris GH, Zink DL, Justice M, Nielsen Kahn J, Peláez F. Distribution of the antifungal agents sordarins across filamentous fungi. ACTA ACUST UNITED AC 2009; 113:754-70. [DOI: 10.1016/j.mycres.2009.02.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Revised: 01/10/2009] [Accepted: 02/18/2009] [Indexed: 10/21/2022]
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Persoh D, Melcher M, Graf K, Fournier J, Stadler M, Rambold G. Molecular and morphological evidence for the delimitation of Xylaria hypoxylon. Mycologia 2009; 101:256-68. [PMID: 19397200 DOI: 10.3852/08-108] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Xylaria hypoxylon, the type species of Xylaria (Xylariaceae, Sordariomycetes), was first described by Linnaeus as Clavaria hypoxylon from Sweden. Saccardo and other mycologists assumed a cosmopolitan distribution for this species. However, contradictory reports in the literature on its morphoanatomical characters and strongly inconsistent rDNA sequence data attributed to this species in GenBank suggested the existence of an unresolved species complex. To address this lack of clarity, molecular and morphological characters of numerous specimens and corresponding cultures of X. hypoxylon and related taxa from Europe were studied. Newly obtained 5.8S/ITS nrDNA sequence data were compared with published data and sequences of reference strains. European populations of X. hypoxylon from various hosts exhibited consistent rDNA sequence data and a relatively uniform holomorphic morphology, except for one specimen from Sweden that deviated in its ascospore morphology. Some samples from western United States showed DNA sequence data being identical to those of specimens from Europe, confirming a North American occurrence of X. hypoxylon. DNA sequences and morphology of other extra-European material however showed substantial deviations. Definitely not conspecific with the European material examined in this study is a strain, assigned to X. hypoxylon, the DNA sequence data of which have been used in various phylogenetic studies as a representative of Xylariaceae and Xylariales respectively. This material probably represents X longiana.
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Affiliation(s)
- Derek Persoh
- University of Bayreuth, Department of Mycology, Universitätsstrasse 30, D-95447 Bayreuth, Germany.
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Recognition of hypoxyloid and xylarioid Entonaema species and allied Xylaria species from a comparison of holomorphic morphology, HPLC profiles, and ribosomal DNA sequences. Mycol Prog 2008. [DOI: 10.1007/s11557-008-0553-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Singh SB, Pelaez F. Biodiversity, chemical diversity and drug discovery. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 2007; 65:141, 143-74. [PMID: 18084915 DOI: 10.1007/978-3-7643-8117-2_4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Drugs developed from microbial natural products are in the fundaments of modern pharmaceutical companies. Despite decades of research, all evidences suggest that there must remain many interesting natural molecules with potential therapeutic application yet to be discovered. Any efforts to successfully exploit the chemical diversity of microbial secondary metabolites need to rely heavily on a good understanding of microbial diversity, being the working hypothesis that maximizing biological diversity is the key strategy to maximizing chemical diversity. This chapter presents an overview of diverse topics related with this basic principle, always in relation with the discovery of novel secondary metabolites. The types of microorganisms more frequently used for natural products discovery are briefly reviewed, as well as the differences between terrestrial and marine habitats as sources of bioactive secondary metabolite producers. The concepts about microbial diversity as applied to prokaryotes have evolved in the last years, but recent data suggest the existence of true biogeographic patterns of bacterial diversity, which are also discussed. Special attention is dedicated to the existing strategies to exploit the microbial diversity that is not easy to tackle by conventional approaches. This refers explicitly to the current attempts to isolate and cultivate the previously uncultured bacteria, including the application of high throughput techniques. Likewise, the advances of microbial molecular biology has allowed the development of metagenomic approaches, i.e., the expression of biosynthetic pathways directly obtained from environmental DNA and cloned in a suitable host, as another way of accessing microbial genetic resources. Also, approaches relying on the genomics of metabolite producers are reviewed.
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Affiliation(s)
- Sheo B Singh
- Merck Research Laboratories, Rahway, New Jersey 07065, USA.
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Luchi N, Capretti P, Vettraino AM, Vannini A, Pinzani P, Pazzagli M. Early detection of Biscogniauxia nummularia in symptomless European beech (Fagus sylvatica L.) by TaqMan quantitative real-time PCR. Lett Appl Microbiol 2006; 43:33-8. [PMID: 16834718 DOI: 10.1111/j.1472-765x.2006.01920.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS To develop a quantitative real-time PCR (Rt PCR) assay for the early detection of Biscogniauxia nummularia, a xylariaceous fungus that causes strip-canker and wood decay on European beech (Fagus sylvatica L.). METHODS AND RESULTS The molecular assay was based on TaqMan chemistry using species-specific primers and a fluorogenic probe designed on the ITS1 sequence of rRNA gene clusters. The specificity of the oligonucleotides and the probe were tested using the DNA of B. nummularia isolates from different geographic areas, of phylogenetically related species, and of some fungi commonly colonizing European beech bark and wood. A total of 31 symptomless and symptomatic shoots of European beech were collected from three forest sites in the Apennine Mountains of Italy. The percentage of positive detections of B. nummularia with the TaqMan assay was 78.6%, compared with only 14.3% of positive isolations on growth media for two sites. CONCLUSIONS In shoots, the quantitative Rt PCR assay detected down to 8.0-fg fungal DNA per microgram of total DNA extracted. SIGNIFICANCE AND IMPACT OF THE STUDY The assay developed in quantitative Rt PCR, by using TaqMan chemistry, revealed a rapid and sensitive method useful for the early detection of B. nummularia in symptomless European beech twigs.
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Affiliation(s)
- N Luchi
- Dipartimento di Biotecnologie Agrarie, Sezione di Patologia vegetale, Università degli Studi di Firenze, Piazzale delle Cascine, 28 I-50144 Florence, Italy
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Santamaría J, Bayman P. Fungal epiphytes and endophytes of coffee leaves (Coffea arabica). MICROBIAL ECOLOGY 2005; 50:1-8. [PMID: 16132426 DOI: 10.1007/s00248-004-0002-1] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2004] [Accepted: 07/22/2004] [Indexed: 05/04/2023]
Abstract
Plants harbor diverse communities of fungi and other microorganisms. Fungi are known to occur both on plant surfaces (epiphytes) and inside plant tissues (endophytes), but the two communities have rarely been compared. We compared epiphytic and endophytic fungal communities associated with leaves of coffee (Coffea arabica) in Puerto Rico. We asked whether the dominant fungi are the same in both communities, whether endophyte and epiphyte communities are equally diverse, and whether epiphytes and endophytes exhibit similar patterns of spatial heterogeneity among sites. Leaves of naturalized coffee plants were collected from six sites in Puerto Rico. Epiphytic and endophytic fungi were isolated by placing leaf pieces on potato dextrose agar without and with surface sterilization, respectively. A total of 821 colonies were isolated and grouped into 131 morphospecies. The taxonomic affinities of the four most common nonsporulating fungi were determined by sequencing the nuclear ribosomal internal transcribed spacer (ITS) region: two grouped with Xylaria and one each with Botryosphaeria and Guignardia. Of the most common genera, Pestalotia and Botryosphaeria were significantly more common as epiphytes; Colletotrichum, Xylaria, and Guignardia were significantly more common as endophytes. Suprisingly, more morphospecies occurred as endophytes than as epiphytes. Differences among sites in number of fungi per plant were significant. Thus epiphytic and endophytic communities differed greatly on a single leaf, despite living only millimeters apart, and both communities differed from site to site. Significant correlations between occurrence of fungal morphospecies suggested that fungi may have positive or negative effects on their neighbors. This is the first quantitative comparison of epiphytic and endophytic fungal floras in any plant, and the first to examine endophytic fungi or epiphytic fungi in leaves of coffee, one of the world's most valuable crops.
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Affiliation(s)
- Johanna Santamaría
- Departamento de Biología, Universidad de Puerto Rico-Río Piedras, PO Box 23360, San Juan, PR 00931-3360, USA
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Hypomiltin, a novel azaphilone from Hypoxylon hypomiltum, and chemotypes in Hypoxylon sect. Hypoxylon as inferred from analytical HPLC profiling. Mycol Prog 2005. [DOI: 10.1007/s11557-006-0108-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Sings H, Singh S. Tremorgenic and nontremorgenic 2,3-fused indole diterpenoids. THE ALKALOIDS. CHEMISTRY AND BIOLOGY 2003; 60:51-163. [PMID: 14593856 DOI: 10.1016/s0099-9598(03)60002-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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