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  • 1
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    One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes (2015)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi (0031-5850) vol.35 (2015) p.242
    Details
    Publication Date: 2016-01-08
    Description: The aim of this study was to assess potential candidate gene regions and corresponding universal primer pairs as secondary DNA barcodes for the fungal kingdom, additional to ITS rDNA as primary barcode. Amplification efficiencies of 14 (partially) universal primer pairs targeting eight genetic markers were tested across 〉 1 500 species (1 931 strains or specimens) and the outcomes of almost twenty thousand (19 577) polymerase chain reactions were evaluated. We tested several well-known primer pairs that amplify: i) sections of the nuclear ribosomal RNA gene large subunit (D1–D2 domains of 26/28S); ii) the complete internal transcribed spacer region (ITS1/2); iii) partial β-tubulin II (TUB2); iv) γ-actin (ACT); v) translation elongation factor 1-α (TEF1α); and vi) the second largest subunit of RNA-polymerase II (partial RPB2, section 5–6). Their PCR efficiencies were compared with novel candidate primers corresponding to: i) the fungal-specific translation elongation factor 3 (TEF3); ii) a small ribosomal protein necessary for t-RNA docking; iii) the 60S L10 (L1) RP; iv) DNA topoisomerase I (TOPI); v) phosphoglycerate kinase (PGK); vi) hypothetical protein LNS2; and vii) alternative sections of TEF1α. Results showed that several gene sections are accessible to universal primers (or primers universal for phyla) yielding a single PCR-product. Barcode gap and multi-dimensional scaling analyses revealed that some of the tested candidate markers have universal properties providing adequate infra- and inter-specific variation that make them attractive barcodes for species identification. Among these gene sections, a novel high fidelity primer pair for TEF1α, already widely used as a phylogenetic marker in mycology, has potential as a supplementary DNA barcode with superior resolution to ITS. Both TOPI and PGK show promise for the Ascomycota, while TOPI and LNS2 are attractive for the Pucciniomycotina, for which universal primers for ribosomal subunits often fail.
    Keywords: DNA barcoding ; ITS supplement ; molecular taxonomy ; phylogeny ; species identification ; universal primers
    Repository Name: National Museum of Natural History, Netherlands
    Type: Article / Letter to the editor
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  • 2
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    Comparison of Denitrification Induced by Various Organic Substances—Reaction Rates, Microbiology, and Temperature Effect (2021)
    Details
    Publication Date: 2022-04-04
    Description: Widespread groundwater pollution with nitrate (NO3−) and the finite and decreasing geogenic NO3− degradation capacity in aquifers require a better understanding of potential treatment methods. This project aimed at exploring and comparing the efficiency of four organic substances as electron donors for heterotrophic denitrification. Circulation column experiments using sediment without NO3− degradation capacity and high agricultural NO3− groundwater were conducted. Acetate, glucose, ascorbic acid, and ethanol were added to these columns in three concentration steps to induce biological denitrification, whereby also temperature dependence of denitrification rates (room temperature and typical groundwater temperature of 10°C) was taken into account. Results show denitrification with all four carbon (C) sources with intensities varying considerably between electron donors. Comparison of the two temperature approaches shows substantial differences between applied organic substances and indicates T as an important variable for denitrification. Ethanol is clearly the most effective electron donor for biodenitrification in groundwater investigated in this study, with a stronger and more effective NO3− degradation at 10°C than at room temperature. In contrast, much higher reaction rates are achieved with glucose at room temperature, compared to 10°C. Denitrification with ascorbic acid is very low at both temperatures; its addition produces biomass which repeatedly led to column clogging. In the entire test series, nitrite (NO2−) accumulation occurred more frequently and in higher concentrations at 10°C. Analysis of microorganisms shows a strong modification in microbial community in reaction to the addition of different organic C as well as between the two temperature approaches.
    Description: Key Points: Higher denitrification rate with ethanol at 10°C, consequently, reaction kinetics does not generally increase with rising temperature. Addition of organic substances and temperature strongly modify the denitrifying microbial community. Electron donor selection for induced nitrate reduction depends on the groundwater temperature of the region.
    Description: Deutsche Forschungsgemeinschaft (DFG) http://dx.doi.org/10.13039/501100001659
    Keywords: ddc:553.79 ; ddc:550.724 ; ddc:628.162
    Language: English
    Type: doc-type:article
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  • 3
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    Thecaphora capensis sp. nov., an unusual new anther smut on Oxalis in South Africa (2008)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 21 no. 1, pp. 147-152
    Details
    Publication Date: 2024-01-12
    Description: The smut genus Thecaphora contains plant parasitic microfungi that typically infect very specific plant organs. In this study, we describe a new species of Thecaphora from Oxalis lanata var. rosea (Oxalidaceae) in the Cape Floristic Region of South Africa. Molecular phylogenetic reconstructions based on large subunit ribosomal DNA sequence data confirmed the generic placement of the fungus and confirmed that it represents an undescribed species for which the name T. capensis sp. nov. is provided. The closest known sister species of the new taxon is T. oxalidis that infects the fruits of Oxalis spp. in Europe, Asia and the Americas. In contrast, T. capensis produces teliospores within the anthers of its host. This is the first documented case of an anther-smut from an African species of Oxalis and the first Thecaphora species described from Africa.
    Keywords: anther-smut ; Cape Floristic Region ; Oxalis ; phylogeny ; Thecaphora
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
    Format: application/pdf
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  • 4
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    One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes (2015)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 35, pp. 242-263
    Details
    Publication Date: 2024-02-03
    Description: The aim of this study was to assess potential candidate gene regions and corresponding universal primer pairs as secondary DNA barcodes for the fungal kingdom, additional to ITS rDNA as primary barcode. Ampli\xef\xac\x81cation ef\xef\xac\x81ciencies of 14 (partially) universal primer pairs targeting eight genetic markers were tested across 〉\xe2\x80\xaf1\xe2\x80\xaf500 species (1\xe2\x80\xaf931 strains or specimens) and the outcomes of almost twenty thousand (19\xe2\x80\xaf577) polymerase chain reactions were evaluated. We tested several well-known primer pairs that amplify: i) sections of the nuclear ribosomal RNA gene large subunit (D1\xe2\x80\x93D2 domains of 26/28S); ii) the complete internal transcribed spacer region (ITS1/2); iii) partial \xce\xb2-tubulin II (TUB2); iv) \xce\xb3-actin (ACT); v) translation elongation factor 1-\xce\xb1 (TEF1\xce\xb1); and vi) the second largest subunit of RNA-polymerase II (partial RPB2, section 5\xe2\x80\x936). Their PCR ef\xef\xac\x81ciencies were compared with novel candidate primers corresponding to: i) the fungal-speci\xef\xac\x81c translation elongation factor 3 (TEF3); ii) a small ribosomal protein necessary for t-RNA docking; iii) the 60S L10 (L1) RP; iv) DNA topoisomerase I (TOPI); v) phosphoglycerate kinase (PGK); vi) hypothetical protein LNS2; and vii) alternative sections of TEF1\xce\xb1. Results showed that several gene sections are accessible to universal primers (or primers universal for phyla) yielding a single PCR-product. Barcode gap and multi-dimensional scaling analyses revealed that some of the tested candidate markers have universal properties providing adequate infra- and inter-speci\xef\xac\x81c variation that make them attractive barcodes for species identi\xef\xac\x81cation. Among these gene sections, a novel high \xef\xac\x81delity primer pair for TEF1\xce\xb1, already widely used as a phylogenetic marker in mycology, has potential as a supplementary DNA barcode with superior resolution to ITS. Both TOPI and PGK show promise for the Ascomycota, while TOPI and LNS2 are attractive for the Pucciniomycotina, for which universal primers for ribosomal subunits often fail.
    Keywords: DNA barcoding ; ITS supplement ; molecular taxonomy ; phylogeny ; species identi\xef\xac\x81cation ; universal primers
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
    Format: application/pdf
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  • 5
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    Fungal Planet description sheets: 1550\xe2\x80\x931613 (2023)
    Naturalis Biodiversity Center
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 51 no. 1, pp. 280-417
    Details
    Publication Date: 2024-03-06
    Description: Novel species of fungi described in this study include those from various countries as follows: Argentina, Neocamarosporium halophilum in leaf spots of Atriplex undulata. Australia, Aschersonia merianiae on scale \ninsect (Coccoidea), Curvularia huamulaniae isolated from air, Hevansia mainiae on dead spider, Ophiocordyceps \npoecilometigena on Poecilometis sp. Bolivia, Lecanora menthoides on sandstone, in open semi-desert montane \nareas, Sticta monlueckiorum corticolous in a forest, Trichonectria epimegalosporae on apothecia of corticolous Megalospora sulphurata var. sulphurata, Trichonectria puncteliae on the thallus of Punctelia borreri. Brazil, Catenomargarita \npseudocercosporicola (incl. Catenomargarita gen. nov.) hyperparasitic on Pseudocercospora fijiensis on leaves of \nMusa acuminata, Tulasnella restingae on protocorms and roots of Epidendrum fulgens. Bulgaria, Anthracoidea \numbrosae on Carex spp. Croatia, Hymenoscyphus radicis from surface-sterilised, asymptomatic roots of Microthlaspi \nerraticum, Orbilia multiserpentina on wood of decorticated branches of Quercus pubescens. France, Calosporella \npunctatispora on dead corticated twigs of Acer opalus. French West Indies (Martinique), Eutypella lechatii on dead \ncorticated palm stem. Germany, Arrhenia alcalinophila on loamy soil. Iceland, Cistella blauvikensis on dead grass \n(Poaceae). India, Fulvifomes maritimus on living Peltophorum pterocarpum, Fulvifomes natarajanii on dead wood \nof Prosopis juliflora, Fulvifomes subazonatus on trunk of Azadirachta indica, Macrolepiota bharadwajii on moist \nsoil near the forest, Narcissea delicata on decaying elephant dung, Paramyrothecium indicum on living leaves of \nHibiscus hispidissimus, Trichoglossum syamviswanathii on moist soil near the base of a bamboo plantation. Iran, \nVacuiphoma astragalicola from stem canker of Astragalus sarcocolla. Malaysia, Neoeriomycopsis fissistigmae (incl. \nNeoeriomycopsidaceae fam. nov.) on leaf spots on flower Fissistigma sp. Namibia, Exophiala lichenicola lichenicolous on Acarospora cf. luederitzensis. Netherlands, Entoloma occultatum on soil, Extremus caricis on dead leaves \nof Carex sp., Inocybe pseudomytiliodora on loamy soil. Norway, Inocybe guldeniae on calcareous soil, Inocybe
    Keywords: ITS nrDNA barcodes ; LSU ; new taxa ; systematics
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
    Format: application/pdf
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  • 6
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    Arbutoid mycorrhizas of the genus Cortinarius from Costa Rica (2016)
    In:  Mycorrhiza
    Details
    Publication Date: 2020-02-12
    Type: info:eu-repo/semantics/article
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  • 7
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    Sebacina sp. is a mycorrhizal partner of Comarostaphylis arbutoides (Ericaceae) (2014)
    In:  Mycological Progress
    Details
    Publication Date: 2020-02-12
    Type: info:eu-repo/semantics/article
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  • 8
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    Leotia cf. lubrica forms arbutoid mycorrhiza with Comarostaphylis arbutoides (Ericaceae) (2015)
    In:  Mycorrhiza
    Details
    Publication Date: 2020-02-12
    Type: info:eu-repo/semantics/article
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