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  • 1
    Language: English
    In: Fungal Biology, September 2013, Vol.117(9), pp.660-672
    Description: Aquatic hyphomycetes play a key role in decomposition of submerged organic matter and stream ecosystem functioning. We examined the phylogenetic relationships among various genera of aquatic hyphomycetes belonging to the Leotiomycetes (Ascomycota) using sequences of internal transcribed spacer (ITS) and large subunit (LSU) regions of rDNA generated from 42 pure cultures including 19 ex-types. These new sequence data were analyzed together with additional sequences from 36 aquatic hyphomycetes and 60 related fungi obtained from GenBank. Aquatic hyphomycetes, characterized by their tetraradiate or sigmoid conidia, were scattered in nine supported clades within the Helotiales (Leotiomycetes). , , , , , , and are not monophyletic, with species from the same genus distributed among several major clades. The clade and the clade accommodated species from eight and six different genera, respectively. Thirteen aquatic hyphomycete taxa were grouped in the clade while twelve species clustered within the clade along with several amphibious ascomycetes. Species of and some species from four other aquatic genera were placed in the clade. It is evident that many aquatic hyphomycetes have relatives of terrestrial origin. Adaptation to colonize the aquatic environment has evolved independently in multiple phylogenetic lineages within the Leotiomycetes.
    Keywords: Biodiversity ; Evolution ; Molecular Systematics ; Taxonomy ; Botany
    ISSN: 1878-6146
    E-ISSN: 1878-6162
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  • 2
    Language: English
    In: Mycological Progress, 2018, Vol.17(5), p.509(2)
    Description: To access, purchase, authenticate, or subscribe to the full-text of this article, please visit this link: http://dx.doi.org/10.1007/s11557-018-1399-0 Byline: Christiane Baschien (1), Kevin D. Hyde (2) Author Affiliation: (1) 0000 0000 9247 8466, grid.420081.f, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstra[sz]e 7B, 38124, Braunschweig, Germany (2) 0000 0001 0180 5757, grid.411554.0, Centre of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand Article History: Registration Date: 23/03/2018 Online Date: 18/04/2018 Article note: Section Editor: Kevin Hyde and Christiane Baschien This article is part of the "Special Issue on Freshwater Ascomycota."
    Keywords: Fungi
    ISSN: 1617-416X
    E-ISSN: 18618952
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  • 3
    Language: English
    In: PLoS ONE, 01 January 2018, Vol.13(8), p.e0202695
    Description: Fungal strains are abundantly used throughout all areas of biotechnology and many of them are adapted to degrade complex biopolymers like chitin or lignocellulose. We therefore assembled a collection of 295 fungi from nine different habitats in Vietnam, known for its rich biodiversity, and investigated their cellulase, chitinase, xylanase and lipase activity. The collection consists of 70 isolates from wood, 55 from soil, 44 from rice straw, 3 found on fruits, 24 from oil environments (butchery), 12 from hot springs, 47 from insects as well as 27 from shrimp shells and 13 strains from crab shells. These strains were cultivated and selected by growth differences to enrich phenotypes, resulting in 211 visually different fungi. DNA isolation of 183 isolates and phylogenetic analysis was performed and 164 species were identified. All were subjected to enzyme activity assays, yielding high activities for every investigated enzyme set. In general, enzyme activity corresponded with the environment of which the strain was isolated from. Therefore, highest cellulase activity strains were isolated from wood substrates, rice straw and soil and similar substrate effects were observed for chitinase and lipase activity. Xylanase activity was similarly distributed as cellulase activity, but substantial activity was also found from fungi isolated from insects and shrimp shells. Seven strains displayed significant activities against three of the four tested substrates, while three degraded all four investigated carbon sources. The collection will be an important source for further studies. Therefore representative strains were made available to the scientific community and deposited in the public collection of the Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig.
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 4
    Language: English
    In: Applied and Environmental Microbiology, Oct, 2008, Vol.74(19-20), p.6427-6436
    Description: A whole-fungus hybridization based on computer-assisted comparative sequence analysis is performed to detect actively growing freshwater fungi with new taxon-specific rRNA-targeting fluorescence in situ hybridization (FISH) probes. The newly developed FISH probes have helped to visualize the growing hyphae and germinating conidia on leaves and in membrane cages.
    Keywords: Fluorescence -- Evaluation ; In Situ Hybridization -- Usage ; Ribosomal Rna -- Research ; Water Molds -- Genetic Aspects ; Water Molds -- Environmental Aspects
    ISSN: 0099-2240
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  • 5
    Language: English
    In: Microbial Ecology, 2009, Vol.58(3), pp.642-650
    Description: We investigated microbial interactions of aquatic bacteria associated with hyphae (the hyphosphere) of freshwater fungi on leaf litter. Bacteria were isolated directly from the hyphae of fungi from sedimented leaves of a small stream in the National Park “Lower Oder,” Germany. To investigate interactions, bacteria and fungi were pairwise co-cultivated on leaf-extract medium and in microcosms loaded with leaves. The performance of fungi and bacteria was monitored by measuring growth, enzyme production, and respiration of mono- and co-cultures. Growth inhibition of the fungus Cladosporium herbarum by Ralstonia pickettii was detected on leaf extract agar plates. In microcosms, the presence of Chryseobacterium sp. lowered the exocellulase, endocellulase, and cellobiase activity of the fungus. Additionally, the conversion of leaf material into microbial biomass was retarded in co-cultures. The respiration of the fungus was uninfluenced by the presence of the bacterium.
    Keywords: Enzymes ; Herbal Medicine;
    ISSN: 0095-3628
    E-ISSN: 1432-184X
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  • 6
    In: Applied and Environmental Microbiology, 2008, Vol. 74(20), p.6427
    Description: New rRNA-targeting oligonucleotide probes permitted the fluorescence in situ hybridization (FISH) identification of freshwater fungi in an Austrian second-order alpine stream. Based on computer-assisted comparative sequence analysis, nine taxon-specific probes were designed and evaluated by whole-fungus hybridizations. Oligonucleotide probe MY1574, specific for a wide range of Eumycota, and the genus (Tetracladium)-specific probe TCLAD1395, as well as the species-specific probes ALacumi1698 (Alatospora acuminata), TRIang322 (Tricladium angulatum), and Alongi340 (Anguillospora longissima), are targeted against 18S rRNA, whereas probes TmarchB10, TmarchC1_1, TmarchC1_2, and AlongiB16 are targeted against the 28S rRNA of Tetracladium marchalianum and Anguillospora longissima, respectively. After 2 weeks and 3 months of exposure of polyethylene slides in the stream, attached germinating conidia and growing hyphae of freshwater fungi were accessible for FISH. Growing hyphae and germinating conidia on leaves and in membrane cages were also visualized by the new FISH probes.
    Keywords: Fresh Water -- Microbiology ; Fungi -- Isolation & Purification ; In Situ Hybridization, Fluorescence -- Methods ; Oligonucleotide Probes -- Genetics;
    ISSN: 0099-2240
    ISSN: 00992240
    E-ISSN: 10985336
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  • 7
    In: Molecular Ecology Resources, November 2018, Vol.18(6), pp.1500-1514
    Description: DNA metabarcoding is widely used to study prokaryotic and eukaryotic microbial diversity. Technological constraints limit most studies to marker lengths below 600 base pairs (bp). Longer sequencing reads of several thousand bp are now possible with third‐generation sequencing. Increased marker lengths provide greater taxonomic resolution and allow for phylogenetic methods of classification, but longer reads may be subject to higher rates of sequencing error and chimera formation. In addition, most bioinformatics tools for DNA metabarcoding were designed for short reads and are therefore unsuitable. Here, we used Pacific Biosciences circular consensus sequencing (CCS) to DNA‐metabarcode environmental samples using a ca. 4,500 bp marker that included most of the eukaryote SSU and LSU rRNA genes and the complete ITS region. We developed an analysis pipeline that reduced error rates to levels comparable to short‐read platforms. Validation using a mock community indicated that our pipeline detected 98% of chimeras de novo. We recovered 947 OTUs from water and sediment samples from a natural lake, 848 of which could be classified to phylum, 397 to genus and 330 to species. By allowing for the simultaneous use of three databases (Unite, SILVA and RDP LSU), long‐read DNA metabarcoding provided better taxonomic resolution than any single marker. We foresee the use of long reads enabling the cross‐validation of reference sequences and the synthesis of ribosomal rRNA gene databases. The universal nature of the rRNA operon and our recovery of 〉100 nonfungal OTUs indicate that long‐read DNA metabarcoding holds promise for studies of eukaryotic diversity more broadly.
    Keywords: Aquatic ; Chimera Formation ; Fungi ; Metabarcoding ; Mock Community ; Pacbio
    ISSN: 1755-098X
    E-ISSN: 1755-0998
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  • 8
    Language: English
    In: IMA fungus, December 2011, Vol.2(2), pp.177-89
    Description: Many species of fungi can cause disease in plants, animals and humans. Accurate and robust detection and quantification of fungi is essential for diagnosis, modeling and surveillance. Also direct detection of fungi enables a deeper understanding of natural microbial communities, particularly as a great many fungi are difficult or impossible to cultivate. In the last decade, effective amplification platforms, probe development and various quantitative PCR technologies have revolutionized research on fungal detection and identification. Examples of the latest technology in fungal detection and differentiation are discussed here.
    Keywords: FISH ; Lamp ; Macroarray ; Medical Mycology ; Molecular Diagnostics ; Molecular Ecology ; Padlock Probe ; Pathogenic Fungi ; Plant Pathology ; Rolling Circle Amplification
    ISSN: 22106340
    E-ISSN: 2210-6359
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  • 9
    Language: English
    In: International Review of Hydrobiology, July 2001, Vol.86(4‐5), pp.371-381
    Description: Based on computer assisted comparative sequence analysis, the 18S rRNA targeted fungal oligonucleotide probe FUN1429 was designed and evaluated for the identification of metabolically active . The general accessibility of fungal cells for fluorescent oligonucleotides was tested by whole cell hybridizations. Additionally, the influences of different growth media, age of the fungal specimen and the composition of permeability buffers were assessed. All strains showed clear fluorescence hybridization signals after visualization with confocal laser scanning microscopy (CSLM). In contrast fluorescence hybridization signals were hardly detectable by conventional epifluorescence microscopy due to strong fungal autofluorescence. The inherent autofluorescence emitted from the strains increased with the age of cultures, but was significantly decreased by chitinase treatment prior to hybridization. The composition of the growth media showed no measurable effect on signal intensity.
    Keywords: 18s Rrna Targeted Oligonucleotide Probe ; Aquatic Hyphomycetes ; Confocal Laser Scanning Microscopy Clsm ; Fluorescence Hybridization Fish
    ISSN: 1434-2944
    E-ISSN: 1522-2632
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  • 10
    Language: English
    In: MycoKeys, 01 January 2018, Vol.28, pp.65-82
    Description: Recent DNA-based studies have shown that the built environment is surprisingly rich in fungi. These indoor fungi – whether transient visitors or more persistent residents – may hold clues to the rising levels of human allergies and other medical and building-related health problems observed globally. The taxonomic identity of these fungi is crucial in such pursuits. Molecular identification of the built mycobiome is no trivial undertaking, however, given the large number of unidentified, misidentified, and technically compromised fungal sequences in public sequence databases. In addition, the sequence metadata required to make informed taxonomic decisions – such as country and host/substrate of collection – are often lacking even from reference and ex-type sequences. Here we report on a taxonomic annotation workshop (April 10–11, 2017) organized at the James Hutton Institute/University of Aberdeen (UK) to facilitate reproducible studies of the built mycobiome. The 32 participants went through public fungal ITS barcode sequences related to the built mycobiome for taxonomic and nomenclatural correctness, technical quality, and metadata availability. A total of 19,508 changes – including 4,783 name changes, 14,121 metadata annotations, and the removal of 99 technically compromised sequences – were implemented in the UNITE database for molecular identification of fungi (https://unite.ut.ee/) and shared with a range of other databases and downstream resources. Among the genera that saw the largest number of changes were Penicillium, Talaromyces, Cladosporium, Acremonium, and Alternaria, all of them of significant importance in both culture-based and culture-independent surveys of the built environment.
    Keywords: Botany
    ISSN: 1314-4057
    E-ISSN: 1314-4049
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