Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Large-scale generation and analysis of filamentous fungal DNA barcodes boosts coverage for kingdom fungi and reveals thresholds for fungal species and higher taxon delimitation
    Vu, D. ; Groenewald, M. ; Vries, M. de; Gehrmann, T. ; Stielow, B. ; Eberhardt, U. ; Al-Hatmi, A. ; Groenewald, J.Z. ; Cardinali, G. ; Houbraken, J. ; Boekhout, T. ; Crous, P.W. ; Robert, V. ; Verkley, G.J.M. - \ 2019
    Studies in Mycology 92 (2019). - ISSN 0166-0616 - p. 135 - 154.
    Automated curation - Biological resource centre - Fungi - ITS - LSU - Taxonomic thresholds

    Species identification lies at the heart of biodiversity studies that has in recent years favoured DNA-based approaches. Microbial Biological Resource Centres are a rich source for diverse and high-quality reference materials in microbiology, and yet the strains preserved in these biobanks have been exploited only on a limited scale to generate DNA barcodes. As part of a project funded in the Netherlands to barcode specimens of major national biobanks, sequences of two nuclear ribosomal genetic markers, the Internal Transcribed Spaces and 5.8S gene (ITS) and the D1/D2 domain of the 26S Large Subunit (LSU), were generated as DNA barcode data for ca. 100 000 fungal strains originally assigned to ca. 17 000 species in the CBS fungal biobank maintained at the Westerdijk Fungal Biodiversity Institute, Utrecht. Using more than 24 000 DNA barcode sequences of 12 000 ex-type and manually validated filamentous fungal strains of 7 300 accepted species, the optimal identity thresholds to discriminate filamentous fungal species were predicted as 99.6 % for ITS and 99.8 % for LSU. We showed that 17 % and 18 % of the species could not be discriminated by the ITS and LSU genetic markers, respectively. Among them, ∼8 % were indistinguishable using both genetic markers. ITS has been shown to outperform LSU in filamentous fungal species discrimination with a probability of correct identification of 82 % vs. 77.6 %, and a clustering quality value of 84 % vs. 77.7 %. At higher taxonomic classifications, LSU has been shown to have a better discriminatory power than ITS. With a clustering quality value of 80 %, LSU outperformed ITS in identifying filamentous fungi at the ordinal level. At the generic level, the clustering quality values produced by both genetic markers were low, indicating the necessity for taxonomic revisions at genus level and, likely, for applying more conserved genetic markers or even whole genomes. The taxonomic thresholds predicted for filamentous fungal identification at the genus, family, order and class levels were 94.3 %, 88.5 %, 81.2 % and 80.9 % based on ITS barcodes, and 98.2 %, 96.2 %, 94.7 % and 92.7 % based on LSU barcodes. The DNA barcodes used in this study have been deposited to GenBank and will also be publicly available at the Westerdijk Institute's website as reference sequences for fungal identification, marking an unprecedented data release event in global fungal barcoding efforts to date.

    Considerations and consequences of allowing DNA sequence data as types of fungal taxa
    Zamora, Juan Carlos ; Svensson, Måns ; Kirschner, Roland ; Olariaga, Ibai ; Ryman, Svengunnar ; Parra, Luis Alberto ; Geml, József ; Rosling, Anna ; Adamčík, Slavomír ; Ahti, Teuvo ; Aime, M.C. ; Ainsworth, A.M. ; Albert, László ; Albertó, Edgardo ; García, Alberto Altés ; Ageev, Dmitry ; Agerer, Reinhard ; Aguirre-Hudson, Begoña ; Ammirati, Joe ; Andersson, Harry ; Angelini, Claudio ; Antonín, Vladimír ; Aoki, Takayuki ; Aptroot, André ; Argaud, Didier ; Sosa, Blanca Imelda Arguello ; Aronsen, Arne ; Arup, Ulf ; Asgari, Bita ; Assyov, Boris ; Atienza, Violeta ; Bandini, Ditte ; Baptista-Ferreira, João Luís ; Baral, Hans-Otto ; Baroni, Tim ; Barreto, Robert Weingart ; Beker, Henry ; Bell, Ann ; Bellanger, Jean-Michel ; Bellù, Francesco ; Bemmann, Martin ; Bendiksby, Mika ; Bendiksen, Egil ; Bendiksen, Katriina ; Benedek, Lajos ; Bérešová-Guttová, Anna ; Berger, Franz ; Berndt, Reinhard ; Bernicchia, Annarosa ; Biketova, Alona Yu. ; Bizio, Enrico ; Bjork, Curtis ; Boekhout, Teun ; Boertmann, David ; Böhning, Tanja ; Boittin, Florent ; Boluda, Carlos G. ; Boomsluiter, Menno W. ; Borovička, Jan ; Brandrud, Tor Erik ; Braun, Uwe ; Brodo, Irwin ; Bulyonkova, Tatiana ; Burdsall, Harold H. ; Buyck, Bart ; Burgaz, Ana Rosa ; Calatayud, Vicent ; Callac, Philippe ; Campo, Emanuele ; Candusso, Massimo ; Capoen, Brigitte ; Carbó, Joaquim ; Carbone, Matteo ; Castañeda-ruiz, Rafael F. ; Castellano, Michael A. ; Chen, Jie ; Clerc, Philippe ; Consiglio, Giovanni ; Corriol, Gilles ; Courtecuisse, Régis ; Crespo, Ana ; Cripps, Cathy ; Crous, Pedro W. ; Silva, Gladstone Alves Da ; Silva, Meiriele Da ; Dam, Marjo ; Dam, Nico ; Dämmrich, Frank ; Das, Kanad ; Davies, Linda ; Crop, Eske De; Kesel, Andre De; Kuijper, T.W.M. - \ 2018
    IMA fungus 9 (2018)1. - ISSN 2210-6340 - p. 167 - 185.
    Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
    Elucidating the Ramularia eucalypti species complex
    Videira, S.I.R. ; Groenewald, J.Z. ; Kolecka, A. ; Haren, L. van; Boekhout, T. ; Crous, P.W. - \ 2015
    Persoonia 34 (2015). - ISSN 0031-5850 - p. 50 - 64.
    desorption ionization-time - flight mass-spectrometry - primer sets - identification - phylogeny - pathogens - fungi - dna - epidemiology - punctiformis
    The genus Ramularia includes numerous phytopathogenic species, several of which are economically important. Ramularia eucalypti is currently the only species of this genus known to infect Eucalyptus by causing severe leaf-spotting symptoms on this host. However, several isolates identified as R. eucalypti based on morphology and on nrDNA sequence data of the ITS region have recently been isolated from other plant hosts, from environmental samples and also from human clinical specimens. Identification of closely related species based on morphology is often difficult and the ITS region has previously been shown to be unreliable for species level identification in several genera. In this study we aimed to resolve this species-complex by applying a polyphasic approach involving morphology, multi-gene phylogeny and matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). Six partial genes (ITS, ACT, TEF1-a, HIS3, GAPDH and RPB2) were amplified and sequenced for a total of 44 isolates representing R. eucalypti s.lat. and closely related species. A multi-gene Bayesian phylogenetic analysis and parsimony analysis were performed, and both the resulting trees showed significant support for separation of seven species in R. eucalypti s.lat., including two previously described (R. eucalypti and R. miae), four novel species here described (R. haroldporteri, R. glennii, R. mali and R. plurivora) and one undescribed Ramularia species (sterile). Additionally, Mycosphaerella nyssicola is newly combined in Ramularia as R. nyssicola. Main mass spectra (MSPs) of several R. eucalypti s.lat. strains were generated using MALDI-TOF MS and were compared through a Principal Component Analysis (PCA) dendogram. The PCA dendrogram supported three clades containing R. plurivora, R. glenni/R. mali and R. eucalypti/R. miae. Although the dendrogram separation of species differed from the phylogenetic analysis, the clinically relevant strains were successfully identified by MALDI-TOF MS
    Characterization of the microbial community in different types of Daqu samples as revealed by 16S rRNA and 26S rRNA gene clone libraries
    Zheng, X. ; Yan, Z. ; Nout, M.J.R. ; Boekhout, T. ; Han, B.Z. ; Zwietering, M.H. ; Smid, E.J. - \ 2015
    World Journal of Microbiology and Biotechnology 31 (2015)1. - ISSN 0959-3993 - p. 199 - 208.
    culture-independent methods - solid-state fermentation - chinese liquor - fen-daqu - starter - bacillus - dynamics
    Daqu is a fermentative saccharification agent that is used to initiate fermentation in the production of Chinese liquor and vinegar. Different types of Daqu can be distinguished based on the maximum fermentation temperature, location of production, and raw materials used. We aimed to characterize and distinguish the different types of Daqu using a culture-independent cloning method. The lowest microbial diversity was found in Daqu produced at high-temperature. Principal component analysis (PCA) was used to compare the bacterial composition of Daqu from different regions (i.e., northern Daqu and southern Daqu). Staphylococcus gallinarum and Staphylococcus saprophyticus were found in southern Daqu, and were absent in northern Daqu. The fungi Saccharomycopsis fibuligera and Lichtheimia ramosa dominated in low/medium-temperature Daqu, whereas Thermomyces lanuginosus occurred in high-temperature Daqu. Our study identified potential biomarkers for the different types of Daqu, which can be useful for quality control and technology development of liquor or vinegar production.
    Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
    Schoch, C.L. ; Robbertse, B. ; Robert, V. ; Vu, D. ; Cardinali, G. ; Irinyi, L. ; Meyer, W. ; Nilsson, R.H. ; Hughes, K. ; Miller, A.N. ; Kirk, P.M. ; Abarenkov, K. ; Aime, M.C. ; Ariyawansa, H.A. ; Bidartondo, M. ; Boekhout, T. ; Buyck, B. ; Cai, Q. ; Chen, J. ; Crespo, A. ; Crous, P.W. ; Damm, U. ; Beer, Z.W. de; Dentinger, B.T.M. ; Divakar, P.K. ; Duenas, M. ; Feau, N. ; Fliegerova, K. ; Garcia, M.A. ; Ge, Z.W. ; Griffith, G.W. ; Groenewald, J.Z. ; Groenewald, M. ; Grube, M. ; Gryzenhout, M. ; Gueidan, C. ; Guo, L. ; Hambleton, S. ; Hamelin, R. ; Hansen, K. ; Hofstetter, V. ; Hong, S.B. ; Houbraken, J. ; Hyde, K.D. ; Inderbitzin, P. ; Johnston, P.A. ; Karunarathna, S.C. ; Koljalg, U. ; Kovacs, G.M. ; Kraichak, E. ; Krizsan, K. ; Kurtzman, C.P. ; Larsson, K.H. ; Leavitt, S. ; Letcher, P.M. ; Liimatainen, K. ; Liu, J.K. ; Lodge, D.J. ; Luangsa-ard, J.J. ; Lumbsch, H.T. ; Maharachchikumbura, S.S.N. ; Manamgoda, D. ; Martin, M.P. ; Minnis, A.M. ; Moncalvo, J.M. ; Mule, G. ; Nakasone, K.K. ; Niskanen, T. ; Olariaga, I. ; Papp, T. ; Petkovits, T. ; Pino-Bodas, R. ; Powell, M.J. ; Raja, H.A. ; Redecker, D. ; Sarmiento-Ramirez, J.M. ; Seifert, K.A. ; Shrestha, B. ; Stenroos, S. ; Stielow, B. ; Suh, S.O. ; Tanaka, K. ; Tedersoo, L. ; Telleria, M.T. ; Udayanga, D. ; Untereiner, W.A. ; Dieguez Uribeondo, J. ; Subbarao, K.V. ; Vagvolgyi, C. ; Visagie, C. ; Voigt, K. ; Walker, D.M. ; Weir, B.S. ; Weiss, M. ; Wijayawardene, N.N. ; Wingfield, M.J. ; Xu, J.P. ; Yang, Z.L. ; Zhang, N. ; Zhuang, W.Y. ; Federhen, S. - \ 2014
    Database : the Journal of Biological Databases and Curation 2014 (2014). - ISSN 1758-0463 - 21 p.
    internal transcribed spacer - arbuscular mycorrhizal fungi - ribosomal dna - interspecific hybridization - sequence analyses - species complex - identification - evolution - barcode - life
    DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
    Microbiota dynamics related to environmental conditions during the fermentative production of Fen-Daqu, a Chinese industrial fermentation starter
    Zheng, X. ; Yan, Z. ; Nout, M.J.R. ; Smid, E.J. ; Zwietering, M.H. ; Boekhout, T. ; Han, J.S. ; Han, B. - \ 2014
    International Journal of Food Microbiology 182-183 (2014). - ISSN 0168-1605 - p. 57 - 62.
    culture-independent methods - liquor - diversity
    Chinese Daqu is used as a starter for liquor and vinegar fermentations. It is produced by solid state fermentation of cereal–pulse mixtures. A succession of fungi, lactic acid bacteria and Bacillus spp. was observed during the production of Daqu. Mesophilic bacteria followed by fungi, dominated the first phase of fermentation. Next, lactic acid bacteria increased in relative abundance, resulting in an increase of the acidity of Daqu. At the final stages of fermentation, Bacillus spp. and thermophilic fungi became the dominant groups, possibly due to their tolerance to low water activity and high temperature. Both culture-dependent and culture-independent analyses confirmed that Bacillus spp. were ubiquitous throughout the process. Yeast species such as Wickerhamomyces anomalus, Saccharomycopsis fibuligera and Pichia kudriavzevii were present throughout almost the entire fermentation process, but the zygomycetous fungus Lichtheimia corymbifera proliferated only during the final stages of fermentation. Canonical correspondence analysis (CCA) revealed the significance of acidity, moisture content and temperature in correlation with the composition of the microbial communities at different stages. Keywords Daqu; Starter culture; Culture-independent; Bacteria; Fungi; Canonical correspondence analysis
    Fermentation characteristics of yeasts isolated from traditionally fermented masau (Ziziphus mauritiana) fruits
    Nyanga, L.K. ; Nout, M.J.R. ; Smid, E.J. ; Boekhout, C. ; Zwietering, M.H. - \ 2013
    International Journal of Food Microbiology 166 (2013)3. - ISSN 0168-1605 - p. 426 - 432.
    saccharomyces-cerevisiae - volatile compounds - wine yeasts - immobilized cells - grape varieties - zimbabwe - strains - metabolism - acid - evolution
    Yeast strains were characterized to select potential starter cultures for the production of masau fermented beverages. The yeast species originally isolated from Ziziphus mauritiana (masau) fruits and their traditionally fermented fruit pulp in Zimbabwe were examined for their ability to ferment glucose and fructose using standard broth under aerated and non-aerated conditions. Most Saccharomyces cerevisiae strains were superior to other species in ethanol production. The best ethanol producing S. cerevisiae strains, and strains of the species Pichia kudriavzevii, Pichia fabianii and Saccharomycopsis fibuligera were tested for production of flavor compounds during fermentation of masau fruit juice. Significant differences in the production of ethanol and other volatile compounds during fermentation of masau juice were observed among and within the four tested species. Alcohols and esters were the major volatiles detected in the fermented juice. Trace amounts of organic acids and carbonyl compounds were detected. Ethyl hexanoate and ethyl octanoate were produced in highest amounts as compared to the other volatile compounds. S. cerevisiae strains produced higher amounts of ethanol and flavor compounds as compared to the other species, especially fatty acid ethyl esters that provide the major aroma impact of freshly fermented wines. The developed library of characteristics can help in the design of mixtures of strains to obtain a specific melange of product functionalities. Keywords: Masau juice; Fermentation; Yeast; Volatile compounds; Flavor; Wine
    Nutritive value of masau (Ziziphus mauritiana) fruits from Zambezi Valley in Zimbabwe
    Nyanga, L.K. ; Gadaga, T.H. ; Nout, M.J.R. ; Smid, E.J. ; Boekhout, T. ; Zwietering, M.H. - \ 2013
    Food Chemistry 138 (2013)1. - ISSN 0308-8146 - p. 168 - 172.
    wild plants - vitamin-c
    Ziziphus mauritiana (masau) fruits are consumed by many people in Zimbabwe. The fruits contribute significantly to people’s diet when they are in season. The objective of this study was to determine the nutritional content of the fruits and, hence, quantify their contribution to the diet. Samples of masau were collected in two seasons (August 2006 and August 2007). Both macronutrients and micronutrients were determined using standard AOAC methods of analysis. Dry matter content ranged from 21.1 ± 0.2 to 24.1 ± 0.3 g 100 g-1 of edible portion of the sweet and sour fruits, and 84.8 ± 0.2 to 87.2 ± 0.2 g 100 g-1 for the dried fruit. Crude protein per 100 g edible portion of dry weight ranged between 7.9 ± 0.0 and 8.7 ± 0.0 g, crude fat from 0.8 ± 0.0 to 1.5 ± 0.0 g, crude fibre from 4.9 ± 0.0 to 7.3 ± 0.0 g, ash between 3.0 ± 0.0 and 4.3 ± 0.0 g and carbohydrate between 79.5 ± 0.0 and 83.2 ± 0.0 g. The fruits were rich in vitamin C (15.0 ± 0.0–43.8 ± 0.02 mg 100 g-1) and the energy values ranged between 1516.0 ± 1.73 and 1575.0 ± 2.3 kJ 100 g-1. Furthermore, the fruits contained (mg 100 g-1 of dry weight) potassium from 1865.0 ± 1.3 to 2441.0 ± 1.1, calcium from 160.0 ± 0.3 to 254.0 ± 0.1, sodium between 185.0 ± 0.1 and 223.0 ± 0.2, magnesium between 83.0 ± 0.0 and 150.0 ± 0.13 and phosphorous from 87.0 ± 0.1 to 148.0 ± 0.5. Manganese and copper contents ranged between 0.7 ± 0.03 and 1.6 ± 0.03, while iron and zinc ranged between 2.1 ± 0.43 and 4.3 ± 0.1, and 0.6 ± 0.0–0.9 ± 0.0 mg 100 g-1 of dry weight, respectively. The masau fruit is therefore a good potential source of carbohydrates, proteins and micronutrients, such as calcium, potassium, sodium, phosphorous, copper, iron, Vitamin C and zinc
    Genotypic and phenotypic characteristics of yeasts isolated from masau (Ziziphus mauritiana) fruits and their traditionally fermented fruit pulp
    Nyanga, L.K. ; Nout, M.J.R. ; Smid, E.J. ; Boekhout, T. ; Zwietering, M.H. - \ 2012
    In: 23rd International ICFMH Symposium FoodMicro 2012, Istanbul, Abstract Book. - Istanbul : Istanbul Technical University, Chemical and Metallurgical Engineering Faculty - ISBN 9789755614236 - p. 128 - 128.
    Yeasts preservation: alternatives for lyophilisation
    Nyanga, L.K. ; Nout, M.J.R. ; Smid, E.J. ; Boekhout, T. ; Zwietering, M.H. - \ 2012
    World Journal of Microbiology and Biotechnology 28 (2012)11. - ISSN 0959-3993 - p. 3239 - 3244.
    ziziphus-mauritiana - starter cultures - trehalose - viability - fermentation - survival - efficacy - zimbabwe - storage - fruits
    The aim of the study was to compare the effect of two low-cost, low technology traditional methods for drying starter cultures with standard lyophilisation. Lyophilised yeast cultures and yeast cultures preserved in dry rice cakes and dry plant fibre strands were examined for viable cell counts during 6 months storage at 4 and 25 °C. None of the yeast cultures showed a significant loss in viable cell count during 6 months of storage at 4 °C upon lyophilisation and preservation in dry rice cakes. During storage at 25 °C in the dark, yeast cultures preserved in dry rice cakes, and lyophilised cultures of Saccharomyces cerevisiae and Issatchenkia orientalis showed no significant loss of viable cells up to 4 months of storage. Yeast cultures preserved in dry plant fibre strands had the greatest loss of viable count during the 6 months of storage at 25 °C. Preservation of yeasts cultures in dry rice cakes provided better survival during storage at 4 °C than lyophilisation. The current study demonstrated that traditional methods can be useful and effective for starter culture preservation in small-scale, low-tech applications.
    Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
    Schoch, C.L. ; Seifert, K.A. ; Huhndorf, S. ; Robert, V. ; Spouge, J.L. ; Levesque, C.A. ; Chen, W. ; Crous, P.W. ; Boekhout, T. ; Damm, U. ; Hoog, G.S. de; Eberhardt, U. ; Groenewald, J.Z. ; Groenewald, M. ; Hagen, F. ; Houbraken, J. ; Quaedvlieg, W. ; Stielow, B. ; Vu, T.D. ; Walther, G. - \ 2012
    Proceedings of the National Academy of Sciences of the United States of America 109 (2012)16. - ISSN 0027-8424 - p. 6241 - 6246.
    arbuscular mycorrhizal fungi - phylogenetic-relationships - basidiomycetous yeasts - intragenomic variation - ectomycorrhizal fungi - species recognition - sequence-analysis - rpb1 sequences - rdna - subunit
    Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
    Ziziphus mauritiana (masau) fruits fermentation in Zimbabwe: from black-box to starter culture development
    Nyanga, L.K. - \ 2012
    Wageningen University. Promotor(en): Marcel Zwietering, co-promotor(en): Rob Nout; T. Boekhout. - S.l. : s.n. - ISBN 9789461733757 - 114
    ziziphus mauritiana - fermentatieproducten - alcoholische dranken - frisdranken - ziziphus mauritiana - fermentation products - alcoholic beverages - soft drinks

    This thesis reports on studies of microbiological and biochemical properties of masau (Ziziphus mauritiana) fruit fermentation and the development of starter cultures for the production of masau beverages.

    A survey to document the traditional processing techniques was conducted using a questionnaire and focus group discussions in each of the three districts, i.e., Mudzi, Mt Darwin and Muzarabani in Zimbabwe. The survey results showed that the masau fruit is usually gathered by women and children, and eaten raw or processed into products such as porridge, traditional cakes, mahewu (non-alcoholic fermented beverage), jam, which are sold at local markets. It is also naturally fermented under uncontrolled conditions and distilled into kachasu. The nutritional composition of the masau fruit was analysed. The fruits are good sources of nutrients such as carbohydrates, protein, and essential micronutrients such as calcium, potassium, phosphorus, copper, iron, zinc and vitamin C.

    In order to enable the selection of starter cultures for the production of masau wine and distillate, yeasts, yeast-like fungi, and lactic acid bacteria present on the unripe, ripe and dried fruits, and in the fermented masau fruits were isolated and identified using physiological and molecular methods. The predominant species were identified as Saccharomyces cerevisiae, Pichia kudriavzevii, P. fabianii, Aureobasidium pullulans, Lactobacillus agilisand L. plantarum. The yeast species were then characterised with respect to ethanol and flavour compounds production. Significant differences in the production of ethanol and other volatile compounds were observed during fermentation of masau juice among and within the tested Saccharomyces, Pichia and Saccharomycopsis species. Alcohols and esters were the major volatiles detected in the fermented juice. Ethyl hexanoate and ethyl octanoate were produced in highest amounts as compared to the other flavour compounds.

    Two traditional low-tech methods for preserving starter cultures, i.e., stabilisation of yeast cultures in dried plant fibre strands, and in rice cakes, were compared with standard lyophilisation. Viable cell counts made during six months storage at 4 °C and 25 °C of lyophilised yeasts, and yeast cultures preserved in dry rice cakes and dry plant fibre strands showed that the rice cake method performed significantly better than lyophilisation.

    The developed library of fermentation characteristics of yeasts can help in the design of mixtures of strains to obtain a specific melange of masau product functionalities. The defined starter cultures could be preserved using the traditional approaches, which are suitable for small-scale, low-tech applications.

    Complex microbiota of a Chinese "Fen" liquor fermentation starter (Fen-Daqu), revealed by culture-dependent and culture-independent methods
    Zheng, X. ; Zheng, Y. ; Han, B. ; Zwietering, M.H. ; Samson, R.A. ; Boekhout, T. ; Nout, M.J.R. - \ 2012
    Food Microbiology 31 (2012)2. - ISSN 0740-0020 - p. 293 - 300.
    gradient gel-electrophoresis - solid-state fermentation - lactic-acid bacteria - rice wine - saccharomycopsis-fibuligera - volatile metabolites - flavor liquor - identification - yeast - strains
    Daqu is a traditional fermentation starter that is used for Chinese liquor production. Although partly mechanized, its manufacturing process has remained traditional. We investigated the microbial diversity of Fen-Daqu, a starter for light-flavour liquor, using combined culture-dependent and culture-independent approaches (PCR–DGGE). A total of 190 microbial strains, comprising 109 bacteria and 81 yeasts and moulds, were isolated and identified on the basis of the sequences of their 16S rDNA (bacteria) and 26S rDNA and ITS regions (fungi). DGGE of DNA extracted from Daqu was used to complement the culture-dependent method in order to include non-culturable microbes. Both approaches revealed that Bacillus licheniformis was an abundant bacterial species, and Saccharomycopsis fibuligera, Wickerhamomyces anomalus, and Pichia kudriavzevii were the most common yeasts encountered in Fen-Daqu. Six genera of moulds (Absidia, Aspergillus, Mucor, Rhizopus, Rhizomucor and Penicillium) were found. The potential function of these microorganisms in starters for alcoholic fermentation is discussed. In general the culture-based findings overlapped with those obtained by DGGE by a large extent. However, Weissella cibaria, Weissella confusa, Staphylococcus saprophyticus, Enterobacter aerogenes, Lactobacillus sanfranciscensis, Lactobacillus lactis, and Bacillus megaterium were only revealed by DGGE
    Macrofungal diversity in Colombian Amazon forests varies with regions and regimes of disturbance
    Lopez-Quintero, C.A. ; Straatsma, G. ; Franco-Molano, A.E. ; Boekhout, T. - \ 2012
    Biodiversity and Conservation 21 (2012)9. - ISSN 0960-3115 - p. 2221 - 2243.
    tree species richness - tropical forests - molecular characterization - geographical gradients - fungal diversity - alpha-diversity - climate-change - rain-forest - leaf-litter - biodiversity
    Here we present the results of fungal biodiversity studies from some selected Colombian Amazon forests in relationship to plant biodiversity and successional stages after slash and burn agriculture. Macrofungal diversity was found to differ between forests occurring in two regions (Araracuara vs Amacayacu) as well as between flooded forests and terra firme forests in the Amacayacu region. Macrofungal biodiversity differed between regeneration states of different age in the Araracuara region. Suitable substrates, especially dead wood that occurred as a result of recent slash and burn agriculture, resulted in the formation of many sporocarps of wood-inhabiting species. Putative ectomycorrhizal species were found in a dipterocarp forest. Fifty two percent of the macrofungal species could not be identified to the species level, but could be assigned to a genus, and it is likely that a significant portion of these represent species new to science. Long term studies are needed to obtain a comprehensive and complete understanding of the diversity and functioning of mycobiota in Amazon forest ecosystems.
    The Amsterdam Declaration on Fungal Nomenclature
    Hawksworth, D.L. ; Crous, P.W. ; Redhead, S.A. ; Reynolds, D.R. ; Samson, R.A. ; Seifert, K.A. ; Taylor, J.W. ; Wingfield, M.J. ; Abaci, Ö. ; Aime, C. ; Asan, A. ; Bai, F.Y. ; Beer, W. de; Begerow, D. ; Berikten, D. ; Boekhout, T. ; Buchanan, P.K. ; Burgess, T. ; Buzina, W. ; Cai, L. ; Cannon, P.F. ; Crane, J.L. ; Damm, U. ; Daniel, H.M. ; Diepeningen, A.D. van; Druzhinina, I. ; Dyer, P.S. ; Eberhardt, U. ; Fell, J.W. ; Frisvad, J.C. ; Geiser, D.M. ; Geml, J. ; Glienke, C. ; Gräfenhan, T. ; Groenewald, J.Z. ; Groenewald, M. ; Gruyter, J. de; Guého-Kellemann, E. ; Guo, L.D. ; Hibbett, D.S. ; Hong, S.B. ; Hoog, G.S. de; Houbraken, J. ; Huhndorf, S.M. ; Hyde, K.D. ; Ismail, A. ; Johnston, P.R. ; Kadaifciler, D.G. ; Kirk, P.M. ; Köljalg, U. ; Kurtzman, C.P. ; Lagneau, P.E. ; Lévesque, C.A. ; Liu, X. ; Lombard, L. ; Meyer, W. ; Miller, A. ; Minter, D.W. ; Najafzadeh, M.J. ; Norvell, L. ; Ozerskaya, S.M. ; Öziç, R. ; Pennycook, S.R. ; Peterson, S.W. ; Pettersson, O.V. ; Quaedvlieg, W. ; Robert, V.A. ; Ruibal, C. ; Schnürer, J. ; Schroers, H.J. ; Shivas, R. ; Slippers, B. ; Spierenburg, H. ; Takashima, M. ; Taskin, E. ; Thines, M. ; Thrane, U. ; Uztan, A.H. ; Raak, M. van; Varga, J. ; Vasco, A. ; Verkley, G. ; Videira, S.I.R. ; Vries, R.P. de; Weir, B.S. ; Yilmaz, N. ; Yurkov, A. ; Zhang, N. - \ 2011
    IMA fungus 2 (2011)1. - ISSN 2210-6340 - p. 105 - 112.
    The Amsterdam Declaration on Fungal Nomenclature was agreed at an international symposium convened in Amsterdam on 19-20 April 2011 under the auspices of the International Commission on the Taxonomy of Fungi (ICTF). The purpose of the symposium was to address the issue of whether or how the current system of naming pleomorphic fungi should be maintained or changed now that molecular data are routinely available. The issue is urgent as mycologists currently follow different practices, and no consensus was achieved by a Special Committee appointed in 2005 by the International Botanical Congress to advise on the problem. The Declaration recognizes the need for an orderly transitition to a single-name nomenclatural system for all fungi, and to provide mechanisms to protect names that otherwise then become endangered. That is, meaning that priority should be given to the first described name, except where that is a younger name in general use when the first author to select a name of a pleomorphic monophyletic genus is to be followed, and suggests controversial cases are referred to a body, such as the ICTF, which will report to the Committee for Fungi. If appropriate, the ICTF could be mandated to promote the implementation of the Declaration. In addition, but not forming part of the Declaration, are reports of discussions held during the symposium on the governance of the nomenclature offungi, and the naming of fungi known only from an environmental nucleic acid sequence in particular. Possible amendments to the Draft BioCode (2011) to allow for the needs of mycologists are suggested for further consideration, and a possible example of how a fungus only known from the environment might be described is presented.
    Daqu - a fermentation starter for Chinese liquor fermentation
    Nout, M.J.R. ; Zheng, X. ; Han, B.Z. ; Le, V.D. ; Wolkers-Rooijackers, J.C.M. ; Samson, R.A. ; Boekhout, T. - \ 2011
    Nederlands Tijdschrift voor Medische Microbiologie 19 (2011)Supplement. - ISSN 0929-0176 - p. S70 - S70.
    The septal pore cap is an organelle that functions in vegetative growth and mushroom formation of the wood-rot fungus Schizophyllum commune
    Peer, Arend F. van; Wang, Fengfeng ; Driel, Kenneth G.A. van; Jong, Jan F. de; Donselaar, Elly G. van; Müller, Wally H. ; Boekhout, Teun ; Lugones, Luis G. ; Wösten, Han A.B. - \ 2010
    Environmental Microbiology 12 (2010)4. - ISSN 1462-2912 - p. 833 - 844.

    Mushroom-forming basidiomycetes colonize large areas in nature. Their hyphae are compartmentalized by perforated septa, which are usually covered by a septal pore cap (SPC). Here, we describe, for the first time, the composition and function of SPCs using the model system Schizophyllum commune. The SPC of S. commune was shown to consist of a proteinaceous matrix covered by a lipid membrane. The matrix was demonstrated to define the ultrastructure of the SPC and to consist of two main proteins, Spc14 and Spc33. Gene spc14 encodes a protein of 86 amino acids, which lacks known domain, signal or localization sequences. Gene spc33 encodes a 239 and a 340 amino acid variant. Both forms contain a predicted signal anchor that targets them to the ER. Immuno-localization showed the presence of Spc33 in the SPC but not in ER. From this and previous reports it is concluded that the SPC is derived from this organelle. Inactivation of spc33 resulted in loss of SPCs and the inability to close septa. The latter may well explain why vegetative growth and mushroom formation were severely reduced in strains in which spc33 was inactivated.

    Cytoplasmic continuity revisited : Closure of septa of the filamentous fungus Schizophyllum commune in response to environmental conditions
    Peer, Arend F. van; Müller, Wally H. ; Boekhout, Teun ; Lugones, Luis G. ; Wösten, Han A.B. - \ 2009
    PLoS ONE 4 (2009)6. - ISSN 1932-6203

    Background: Mycelia of higher fungi consist of interconnected hyphae that are compartmentalized by septa. These septa contain large pores that allow streaming of cytoplasm and even organelles. The cytoplasm of such mycelia is therefore considered to be continuous. Methodology/Principal Findings: Here, we show by laser dissection that septa of Schizophyllum commune can be closed depending on the environmental conditions. The most apical septum of growing hyphae was open when this basidiomycete was grown in minimal medium with glucose as a carbon source. In contrast, the second and the third septum were closed in more than 50% and 90% of the cases, respectively. Interestingly, only 24 and 37% of these septa were closed when hyphae were growing in the absence of glucose. Whether a septum was open or closed also depended on physical conditions of the environment or the presence of toxic agents. The first septum closed when hyphae were exposed to high temperature, to hypertonic conditions, or to the antibiotic nourseothricin. In the case of high temperature, septa opened again when the mycelium was placed back to the normal growth temperature. Conclusions/Significance: Taken together, it is concluded that the septal pores of S. commune are dynamic structures that open or close depending on the environmental conditions. Our findings imply that the cytoplasm in the mycelium of a higher fungus is not continuous perse.

    Septal pore cap protein SPC18, isolated from the basidiomycetous fungus Rhizoctonia solani, also resides in pore plugs
    Driel, Kenneth G.A. Van; Peer, Arend F. Van; Grijpstra, Jan ; Wösten, Han A.B. ; Verkleij, Arie J. ; Müller, Wally H. ; Boekhout, Teun - \ 2008
    Eukaryotic Cell 7 (2008)10. - ISSN 1535-9778 - p. 1865 - 1873.

    The hyphae of filamentous fungi are compartmentalized by septa that have a central pore. The fungal septa and septum-associated structures play an important role in maintaining cellular and intrahyphal homeostasis. The dolipore septa in the higher Basidiomycota (i.e., Agaricomycotina) are associated with septal pore caps. Although the ultrastructure of the septal pore caps has been studied extensively, neither the biochemical composition nor the function of these organelles is known. Here, we report the identification of the glycoprotein SPC18 that was found in the septal pore cap-enriched fraction of the basidiomycetous fungus Rhizoctonia solani. Based on its N-terminal sequence, the SPC18 gene was isolated. SPC18 encodes a protein of 158 amino acid residues, which contains a hydrophobic signal peptide for targeting to the endoplasmic reticulum and has an N-glycosylation motif. Immunolocalization showed that SPC18 is present in the septal pore caps. Surprisingly, we also observed SPC18 being localized in some plugs. The data reported here strongly support the hypothesis that septal pore caps are derived from endoplasmic reticulum and are involved in dolipore plugging and, thus, contribute to hyphal homeostasis in basidiomycetous fungi.

    Traditional processing of masau fruits (Ziziphus mauritiana) in Zimbabwe
    Nyanga, L.K. ; Nout, M.J.R. ; Gadaga, T.H. ; Boekhout, T. ; Zwietering, M.H. - \ 2008
    Ecology of Food and Nutrition 47 (2008)1. - ISSN 0367-0244 - p. 95 - 107.
    organic-acid - beverages
    A survey of the traditional processing techniques of masau was conducted using a questionnaire and two focus group discussions in Mudzi, Mt. Darwin, and Muzarabani districts in Zimbabwe. Masau fruits form part of the family diet and generate additional income by selling at local markets. Surplus fruits are sun dried and can be transformed into various products such as porridge, traditional cakes, mahewu, and also fermented to produce a spirit called Kachasu. The ethanol content of the fermented fruit pulp ranged from 2.1 - 3.7 mL 100mL(-1), whereas the traditionally made distillate contained 23.8 - 45.6 mL 100 mL(-1).
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