151
|
Vu D, Georgievska S, Szoke S, Kuzniar A, Robert V. fMLC: fast multi-level clustering and visualization of large molecular datasets. Bioinformatics 2019; 34:1577-1579. [PMID: 29253070 DOI: 10.1093/bioinformatics/btx810] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/14/2017] [Indexed: 12/23/2022] Open
Abstract
Motivation Despite successful applications of data clustering and visualization techniques in molecular sequence identification, current technologies still do not scale to large biological datasets. Results We address this problem by a new multi-threaded tool, fMLC, primarily developed to cluster DNA sequences, that is supplemented with an interactive web-based visualization component, DiVE. fMLC enabled to compare, cluster and visualize 350K ITS fungal sequences at the species level. It took less than two hours to compare and cluster the dataset, which is twelve times faster than the time reported previously. Availability and implementation https://github.com/FastMLC/fMLC (doi: 10.5281/zenodo.926820). Contact d.vu@westerdijkinstitute.nl or v.robert@westerdijkinstitute.nl.
Collapse
Affiliation(s)
- D Vu
- Bioinformatics group, Westerdijk Fungal Biodiversity Institute, 3584CT Utrecht, The Netherlands
| | - S Georgievska
- Netherlands eScience Center, 1098 XG Amsterdam, The Netherlands
| | - S Szoke
- Bioinformatics group, Westerdijk Fungal Biodiversity Institute, 3584CT Utrecht, The Netherlands
| | - A Kuzniar
- Netherlands eScience Center, 1098 XG Amsterdam, The Netherlands
| | - V Robert
- Bioinformatics group, Westerdijk Fungal Biodiversity Institute, 3584CT Utrecht, The Netherlands
| |
Collapse
|
152
|
Jacques N, Casaregola S. Large biodiversity of yeasts in French Guiana and the description of Suhomyces coccinellae f.a. sp. nov. and Suhomyces faveliae f.a. sp. nov. Int J Syst Evol Microbiol 2019; 69:1634-1649. [PMID: 31033433 DOI: 10.1099/ijsem.0.003369] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The extent of the diversity of yeasts in tropical rain forest and different environments from French Guiana was investigated. A total of 365 samples were collected from various substrates, such as plants, fruits and insects, at 13 locations, yielding 276 pure yeast isolates. Sequence analysis of the D1/D2 domains of the large subunit rRNA gene indicated that 210 isolates out of 276 belonged to 82 described species (67 Saccharomycotina, 14 Basidiomycota and 1 Pezizomycotina). In addition to these, a total of 54 Saccharomycotina isolates could not be assigned to a known species. These belonged to 14 genera and should be studied further from a taxonomic point of view. In addition, among the 43 Basidiomycotina isolates found, 12 could not be assigned to a known species. This report shows an unexpected biodiversity and indicates that oversea territories, such as French Guiana, constitute a largely unexplored reservoir for yeast diversity. Two Saccharomycotina strains, CLIB 1706 and CLIB 1725, isolated from an insect and from a fern respectively, were characterized further and were shown to belong to the Suhomyces clade on the basis of the rDNA sequence comparison. CLIB 1706TrDNA sequences showed nine substitutions and three indels out of 556 bp (D1/D2 domains) and 32 substitutions and 12 indels out of 380 bp [internal transcribed spacer (ITS)] with that of the most closely related species Suhomyces guaymorum CBS 9823T. CLIB 1725T rDNA sequences presented 18 substitutions and one indel out of 549 bp (D1/D2 domains) and 48 substitutions and 11 indels out of 398 bp (ITS) with that of its closest relative Suhomyces vadensis CBS 9454T. Two novel species of the genus Suhomyces were described to accommodate these two strains: Suhomyces coccinellae f.a. sp. nov. (CLIB 1706T=CBS 14298T) and Suhomyces faveliae f.a. sp. nov. (CLIB 1725T=CBS 14299T).
Collapse
Affiliation(s)
- Noémie Jacques
- CIRM-Levures, INRA, Micalis Institute, Jouy-en-Josas, France.,†Present address: Bioger, INRA, Thiverval-Grignon, France
| | | |
Collapse
|
153
|
Chai CY, Huang LN, Cheng H, Liu WJ, Hui FL. Wickerhamomyces menglaensis f.a., sp. nov., a yeast species isolated from rotten wood. Int J Syst Evol Microbiol 2019; 69:1509-1514. [PMID: 30893031 DOI: 10.1099/ijsem.0.003350] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Five strains, NUNU 16637, NYNU 16645, NYNU 1673, NYNU 1680 and NYNU 1689, of a novel ascomycetous yeast were isolated from the Xishuangbanna tropical rainforest, Yunnan Province, PR China. The five strains shared identical sequences in both of the D1/D2 domains of the large subunit rRNA gene and the internal transcribed spacer (ITS) regions. Sequence analysis showed that they represent undescribed yeast species belonging to the genus Wickerhamomyces. They differed from their closest known species, Wickerhamomyces xylosivorus NBRC 111553T, by 3.4 % sequence divergence (14 substitutions and six gaps out of 584 bp) in the D1/D2 domains and by 9.6 % sequence divergence (28 substitutions and 24 gaps over 543 bp) in the ITS regions, respectively. The five strains of novel species reproduced asexually; no sexual reproduction could be found. In contrast to W. xylosivorus, the novel yeast species were able to assimilate l-arabinose, inulin, soluble starch, d-mannitol and citrate, and unable to assimilate trehalose, raffinose, 5-keto-d-gluconate, d-gluconate, ethanol, ethylamine and cadaverine. Growth was observed at 35 °C. The name Wickerhamomyces menglaensis f.a., sp. nov. is proposed to accommodate these strains, with NYNU 1673 as the holotype.
Collapse
Affiliation(s)
- Chun-Yue Chai
- School of Life Science and Technology, Nanyang Normal University, Nanyang 473061, PR China
| | - Lin-Na Huang
- School of Life Science and Technology, Nanyang Normal University, Nanyang 473061, PR China
| | - Han Cheng
- School of Life Science and Technology, Nanyang Normal University, Nanyang 473061, PR China
| | - Wen-Jing Liu
- School of Life Science and Technology, Nanyang Normal University, Nanyang 473061, PR China
| | - Feng-Li Hui
- School of Life Science and Technology, Nanyang Normal University, Nanyang 473061, PR China
| |
Collapse
|
154
|
Fotedar R, Fell JW, Boekhout T, Kolecka A, Zeyara A, Kaul R, Malki AA, Marri MA. Cystobasidium halotolerans sp. nov., a novel basidiomycetous yeast species isolated from the Arabian Gulf. Int J Syst Evol Microbiol 2019; 69:839-845. [DOI: 10.1099/ijsem.0.003250] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Rashmi Fotedar
- 1Department of Genetic Engineering, Biotechnology Centre, Ministry of Environment, Doha, Qatar
| | - Jack W. Fell
- 2Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Key Biscayne, Florida, USA
| | - Teun Boekhout
- 3Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- 4Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Anna Kolecka
- 3Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Aisha Zeyara
- 1Department of Genetic Engineering, Biotechnology Centre, Ministry of Environment, Doha, Qatar
| | | | - Amina Al- Malki
- 1Department of Genetic Engineering, Biotechnology Centre, Ministry of Environment, Doha, Qatar
| | - Masoud Al Marri
- 1Department of Genetic Engineering, Biotechnology Centre, Ministry of Environment, Doha, Qatar
| |
Collapse
|
155
|
Vu D, Groenewald M, de Vries M, Gehrmann T, Stielow B, Eberhardt U, Al-Hatmi A, Groenewald J, Cardinali G, Houbraken J, Boekhout T, Crous P, Robert V, Verkley G. 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. Stud Mycol 2019; 92:135-154. [PMID: 29955203 PMCID: PMC6020082 DOI: 10.1016/j.simyco.2018.05.001] [Citation(s) in RCA: 416] [Impact Index Per Article: 83.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
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.
Collapse
Affiliation(s)
- D. Vu
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - M. Groenewald
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - M. de Vries
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - T. Gehrmann
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - B. Stielow
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - U. Eberhardt
- Staatliches Museum f. Naturkunde Stuttgart, Abt. Botanik, Rosenstein 1, D-70191 Stuttgart, Germany
| | - A. Al-Hatmi
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - J.Z. Groenewald
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - G. Cardinali
- University of Perugia, Dept. of Pharmaceutical Sciences, Via Borgo 20 Giugno 74, I 06121 Perugia, Italy
| | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - T. Boekhout
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, The Netherlands
| | - P.W. Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa
| | - V. Robert
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - G.J.M. Verkley
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| |
Collapse
|
156
|
Urien C, Legrand J, Montalent P, Casaregola S, Sicard D. Fungal Species Diversity in French Bread Sourdoughs Made of Organic Wheat Flour. Front Microbiol 2019; 10:201. [PMID: 30833935 PMCID: PMC6387954 DOI: 10.3389/fmicb.2019.00201] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 01/24/2019] [Indexed: 02/04/2023] Open
Abstract
Microbial communities are essential for the maintenance and functioning of ecosystems, including fermented food ecosystems. The analysis of food microbial communities is mainly focused on lactic acid bacteria (LAB), while yeast diversity is less understood. Here, we describe the fungal diversity of a typical food fermented product, sourdough bread. The species diversity of 14 sourdoughs collected from bakeries located all over France was analyzed. Bakeries were chosen to represent diverse bakery practices and included bakers and farmer-bakers. Both non-culture-based (pyrosequencing of Internal Transcribed Spacer 1 amplicons) and culture-based methods were used. While both identification methods were in agreement regarding the dominant yeast species of each sourdough, the ITS1 metabarcoding analysis identified an increased number of fungal species in sourdough communities. Two third of the identified sequences obtained from sourdoughs were Saccharomycetales, mostly in the Kazachstania genus. No Saccharomycetales species was shared by all the sourdoughs, whereas five other fungal species, mainly known plant pathogens, were found in all sourdoughs. Interestingly, Saccharomyces cerevisiae, known as “baker’s yeast,” was identified as the dominant species in only one sourdough. By contrast, five Kazachstania species were identified as the dominant sourdough species, including one recently described Kazachstania species, Kazachstania saulgeensis and an undescribed Kazachstania sp. Sourdoughs from farmer-bakers harbored Kazachstania bulderi, Kazachstania unispora and two newly described Kazachstania species, while sourdough from bakers mostly carried Kazachstania humilis as the dominant species. Such yeast diversity has not been found in sourdoughs before, highlighting the need to maintain different traditional food practices to conserve microbial diversity.
Collapse
Affiliation(s)
- Charlotte Urien
- GQE-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Judith Legrand
- GQE-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Pierre Montalent
- GQE-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Serge Casaregola
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, Jouy-en-Josas, France
| | - Delphine Sicard
- GQE-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France.,SPO, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| |
Collapse
|
157
|
Fotedar R, Kolecka A, Boekhout T, Fell JW, Zeyara A, Al Malki A, Al Marri M. Kondoa qatarensis f.a., sp. nov., a novel yeast species isolated from marine water in Qatar. Int J Syst Evol Microbiol 2019; 69:486-492. [DOI: 10.1099/ijsem.0.003182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Rashmi Fotedar
- 1Department of Genetic Engineering, Biotechnology Centre, Ministry of Environment, Doha, Qatar
| | - Anna Kolecka
- 2Westerdijk Fungal Biodiversity Institute (Westerdijk Institute), Utrecht, The Netherlands
| | - Teun Boekhout
- 2Westerdijk Fungal Biodiversity Institute (Westerdijk Institute), Utrecht, The Netherlands
- 3Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Jack W. Fell
- 4Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Key Biscayne, FL, USA
| | - Aisha Zeyara
- 1Department of Genetic Engineering, Biotechnology Centre, Ministry of Environment, Doha, Qatar
| | - Ameena Al Malki
- 1Department of Genetic Engineering, Biotechnology Centre, Ministry of Environment, Doha, Qatar
| | - Masoud Al Marri
- 1Department of Genetic Engineering, Biotechnology Centre, Ministry of Environment, Doha, Qatar
| |
Collapse
|
158
|
Sipiczki M. Interspecies Hybridisation and Genome Chimerisation in Saccharomyces: Combining of Gene Pools of Species and Its Biotechnological Perspectives. Front Microbiol 2018; 9:3071. [PMID: 30619156 PMCID: PMC6297871 DOI: 10.3389/fmicb.2018.03071] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/28/2018] [Indexed: 12/31/2022] Open
Abstract
Over the last one and a half decade, interspecies hybridisation has gained continuously increasing attention as a breeding technique suitable for transferring of genetic information between Saccharomyces species and mixing of their gene pools without genetic engineering. The hybrids frequently show positive transgressive phenotypes. Segregation of the hybrid genome results in mosaic (chimeric) strains that can outperform both the parents and the hybrids or exhibit novel positive phenotypic properties. Mitotic segregation can take place during the vegetative propagation of the sterile allodiploid hybrid cells. Meiotic segregation becomes possible after genome duplication (tetraploidisation) if it is followed by break-down of sterility. The allotetraploid cells are seemingly fertile because they form viable spores. But because of the autodiploidisation of the meiosis, sterile allodiploid spores are produced and thus the hybrid genome does not segregate (the second sterility barrier). However, malsegregation of MAT-carrying chromosomes in one of the subgenomes during allotetraploid meiosis (loss of MAT heterozygosity) results in fertile alloaneuploid spores. The breakdown of (the second) sterility barrier is followed by the loss of additional chromosomes in rapid succession and recombination between the subgenomes. The process (genome autoreduction in meiosis or GARMe) chimerises the genome and generates strains with chimeric (mosaic) genomes composed of various combinations of the genes of the parental strains. Since one of the subgenomes is preferentially reduced, the outcome is usually a strain having an (almost) complete genome from one parent and only a few genes or mosaics from the genome of the other parent. The fertility of the spores produced during GARMe provides possibilities also for introgressive backcrossing with one or the other parental strain, but genome chimerisation and gene transfer through series of backcrosses always with the same parent is likely to be less efficient than through meiotic or mitotic genome autoreduction. Hybridisation and the evolution of the hybrid genome (resizing and chimerisation) have been exploited in the improvement of industrial strains and applied to the breeding of new strains for specific purposes. Lists of successful projects are shown and certain major trends are discussed.
Collapse
Affiliation(s)
- Matthias Sipiczki
- Department of Genetics and Applied Microbiology, University of Debrecen, Debrecen, Hungary
| |
Collapse
|
159
|
Sipiczki M, Selim SA. Antagonistic yeasts from a salt-lake region in Egypt: identification of a taxonomically distinct group of phylloplane strains related to Sporisorium. Antonie Van Leeuwenhoek 2018; 112:523-541. [PMID: 30317452 DOI: 10.1007/s10482-018-1184-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 10/06/2018] [Indexed: 11/28/2022]
Abstract
Non-pathogenic yeasts antagonising microorganisms that cause pre- and postharvest diseases of plants have been found in diverse habitats. Their practical applicability as biocontrol agents (BCAs) depends on the strength of their antagonistic activity and/or spectrum of sensitive target microorganisms. In this study, yeasts were isolated from the phylloplane and fruits of plants growing in the alkaline water lake region Wadi El-Natrun, Egypt, and tested for antifungal and antibacterial activity. All phylloplane yeast isolates belonged to the Basidiomycota and most of them could antagonise at least certain test organisms. One group of isolates showing strong antagonism against almost all fungi and yeasts appears to represent a hitherto undescribed species distantly related to the smut genus Sporisorium. This is the first report of antagonistic activity in Sporisorium. The isolates assigned to Naganishia and Papiliotrema were more effective against bacteria. The broadest range and intensity of antagonism was observed in the fruit-associated strains belonging to the ascomycetous species Wickerhamomyces subpelliculosus. The Wickerhamomyces strains are good broad-spectrum BCA candidates, the Sporisorium strains could be used as efficient antifungal BCAs, whereas the Papiliotrema isolate can be exploited as an antibacterial biocontrol agent.
Collapse
Affiliation(s)
- Matthias Sipiczki
- Department of Genetics and Applied Microbiology, University of Debrecen, Debrecen, 4032, Hungary.
| | - Samy A Selim
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, Jouf University, Al-Jouf, Kingdom of Saudi Arabia.,Faculty of Science, Botany Department, Suez Canal University, Ismailia, Egypt
| |
Collapse
|
160
|
Gao WL, Liu KF, Yao LG, Hui FL. Pichia nanzhaoensis sp. nov. and Pichia paraexigua f.a., sp. nov., two yeast species isolated from rotting wood. Int J Syst Evol Microbiol 2018; 68:3311-3315. [PMID: 30152749 DOI: 10.1099/ijsem.0.002989] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four yeast strains were isolated from rotting wood samples collected in the Baotianman Nature Reserve in Henan Province, Central China. On the basis of sequence analysis of the D1/D2 domains of the large subunit rRNA gene and the internal transcribed spacer regions, they were suggested to be two novel species of the genus Pichia. Pichia nanzhaoensis sp. nov. produces one to four spherical ascospores per ascus, and is most closely related to Candida pseudolambica. Pichia paraexigua f.a., sp. nov. is a sister taxa to Pichia exigua, but the formation of ascospores was not observed on various sporulation media. P. nanzhaoensis sp. nov. can weakly assimilate inulin, whereas P. paraexigua sp. nov. can weakly assimilate d-glucosamine. The type strain of Pichia nanzhaoensis is NYNU 178136T (=CICC 33279T=CBS 15346T) and the type strain of Pichia paraexigua is NYNU 178135T (=CICC 33278T=CBS 15237T).
Collapse
Affiliation(s)
- Wan-Li Gao
- Collaborative Innovation Center of Water Security for Water Source Region of Mid-line of South-to-North Diversion Project, Henan Province, Nanyang 473061, PR China
| | - Kai-Fang Liu
- Collaborative Innovation Center of Water Security for Water Source Region of Mid-line of South-to-North Diversion Project, Henan Province, Nanyang 473061, PR China
| | - Lun-Guang Yao
- Collaborative Innovation Center of Water Security for Water Source Region of Mid-line of South-to-North Diversion Project, Henan Province, Nanyang 473061, PR China
| | - Feng-Li Hui
- Collaborative Innovation Center of Water Security for Water Source Region of Mid-line of South-to-North Diversion Project, Henan Province, Nanyang 473061, PR China
| |
Collapse
|
161
|
Roscini L, Tristezza M, Corte L, Colabella C, Perrotta C, Rampino P, Robert V, Vu D, Cardinali G, Grieco F. Early Ongoing Speciation of Ogataea uvarum Sp. Nov. Within the Grape Ecosystem Revealed by the Internal Variability Among the rDNA Operon Repeats. Front Microbiol 2018; 9:1687. [PMID: 30123190 PMCID: PMC6085423 DOI: 10.3389/fmicb.2018.01687] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/06/2018] [Indexed: 11/13/2022] Open
Abstract
A yeast strain was isolated during a study on vineyard-associated yeast strains from Apulia in Southern Italy. ITS and LSU D1/D2 rDNA sequences showed this strain not to belong to any known species and was described as the type strain of Ogataea uvarum sp. nov., a close relative of O. philodendri. Several secondary peaks appeared in the sequences, suggesting internal heterogeneity among the copies of the rDNA. This hypothesis was tested by sequencing single clones of the marker region. The analyses showed different levels of variability throughout the operon with differences between the rRNA encoding genes and the internally transcribed regions. O. uvarum and O. philodendri share high frequency variants, i.e., variants frequently found in many clones, whereas there is a large variability of the low frequency polymorphisms, suggesting that the mechanism of homogenization is more active with the former than with the latter type of variation. These findings indicate that low frequency variants are detected in Sanger sequencing as secondary peaks whereas in Next Generation Sequencing (NGS) of metagenomics DNA would lead to an overestimate of the alpha diversity. For the first time in our knowledge, this investigation shed light on the variation of the copy number of the rDNA cistron during the yeast speciation process. These polymorphisms can be used to investigate on the processes occurring in these taxonomic markers during the separation of fungal species, it being a genetic process highly frequent in the complex microbial ecosystem existing in grape, must and wine.
Collapse
Affiliation(s)
- Luca Roscini
- Department of Pharmaceutical Sciences – Microbiology, University of Perugia, Perugia, Italy
| | - Mariana Tristezza
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Lecce, Italy
| | - Laura Corte
- Department of Pharmaceutical Sciences – Microbiology, University of Perugia, Perugia, Italy
| | - Claudia Colabella
- Department of Pharmaceutical Sciences – Microbiology, University of Perugia, Perugia, Italy
| | - Carla Perrotta
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Patrizia Rampino
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Vincent Robert
- Bioinformatics Unit, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Duong Vu
- Bioinformatics Unit, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences – Microbiology, University of Perugia, Perugia, Italy
- Centre of Excellence on Nanostructured Innovative Materials (CEMIN), Department of Chemistry Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Francesco Grieco
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Lecce, Italy
| |
Collapse
|
162
|
Fotedar R, Kolecka A, Boekhout T, Fell JW, Anand A, Al Malaki A, Zeyara A, Al Marri M. Naganishia qatarensis sp. nov., a novel basidiomycetous yeast species from a hypersaline marine environment in Qatar. Int J Syst Evol Microbiol 2018; 68:2924-2929. [PMID: 30070622 DOI: 10.1099/ijsem.0.002920] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two yeast strains (INY29 and INY13) representing a novel yeast species were isolated from the hypersaline marine environment of the Inland Sea, Qatar. Phylogenetic analysis based on the D1/D2 domains of the large subunit (LSU) regions and internal transcribed spacer (ITS1 and ITS2) regions showed that the two strains represent a single species in the genus Naganishia that is distinct from other species. These two strains were classified as members of the genus Naganishia and clustered in a strongly supported clade represented by Naganishia albidus in the Filobasidiales order in the phylogenetic tree drawn from ITS and D1/D2 sequences. The novel species was most closely related to the type strain of Naganishia cerealis but the two species differed by 1 % sequence divergence (four substitutions and one gap) in the D1/D2 domains and (five substitutions and one gap) in the ITS regions. In contrast to the closest relative, N. cerealis, the novel yeast species assimilated melibiose, glycerol, meso-erythritol, dl-lactate, methanol, propane 1-2-diol, butane 2-3-diol, and grew at 35 °C. The name Naganishia qatarensis sp. nov. is proposed to accommodate these strains, with INY29 as the holotype.
Collapse
Affiliation(s)
- Rashmi Fotedar
- 1Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, Doha, State of Qatar
| | - Anna Kolecka
- 2Westerdijk Fungal Biodiversity Institute (Westerdijk Institute), Utrecht, The Netherlands
| | - Teun Boekhout
- 2Westerdijk Fungal Biodiversity Institute (Westerdijk Institute), Utrecht, The Netherlands.,3Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Jack W Fell
- 4Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Key Biscayne, FL, USA
| | - Anjana Anand
- 1Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, Doha, State of Qatar
| | - Ameena Al Malaki
- 1Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, Doha, State of Qatar
| | - Aisha Zeyara
- 1Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, Doha, State of Qatar
| | - Masoud Al Marri
- 1Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, Doha, State of Qatar
| |
Collapse
|
163
|
Naumov GI, Shalamitskiy MY, Naumova ES, Lee CF. Phylogenetics, Biogeography, and Ecology of Methylotrophic Yeasts of the Heterogeneous Genus Ogataea: Achivements and Prospects. Microbiology (Reading) 2018. [DOI: 10.1134/s002626171804015x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
164
|
Amoikon TLS, Grondin C, Djéni TN, Jacques N, Casaregola S. Starmerella reginensis f.a., sp. nov. and Starmerella kourouensis f.a., sp. nov., isolated from flowers in French Guiana. Int J Syst Evol Microbiol 2018; 68:2299-2305. [DOI: 10.1099/ijsem.0.002829] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Tiemele Laurent Simon Amoikon
- Laboratoire de Biotechnologie et Microbiologie des Aliments, Unité de Formation et de Recherche en Sciences et Technologie des Aliments (UFR-STA), Université Nangui-Abrogoua, 02 BP 801, Abidjan, 02, Côte d'Ivoire
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Cécile Grondin
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Théodore N'Dédé Djéni
- Laboratoire de Biotechnologie et Microbiologie des Aliments, Unité de Formation et de Recherche en Sciences et Technologie des Aliments (UFR-STA), Université Nangui-Abrogoua, 02 BP 801, Abidjan, 02, Côte d'Ivoire
| | - Noémie Jacques
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Serge Casaregola
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| |
Collapse
|
165
|
Crous P, Schumacher R, Wingfield M, Akulov A, Denman S, Roux J, Braun U, Burgess T, Carnegie A, Váczy K, Guatimosim E, Schwartsburd P, Barreto R, Hernández-Restrepo M, Lombard L, Groenewald J. New and Interesting Fungi. 1. Fungal Syst Evol 2018; 1:169-216. [PMID: 32490366 PMCID: PMC7259438 DOI: 10.3114/fuse.2018.01.08] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
This study introduces two new families, one new genus, 22 new species, 10 new combinations, four epitypes, and 16 interesting new host and / or geographical records. Cylindriaceae (based on Cylindrium elongatum) is introduced as new family, with three new combinations. Xyladictyochaetaceae (based on Xyladictyochaeta lusitanica) is introduced to accommodate Xyladictyochaeta. Pseudoanungitea gen. nov. (based on P. syzygii) is described on stems of Vaccinium myrtillus (Germany). New species include: Exophiala eucalypticola on Eucalyptus obliqua leaf litter, Phyllosticta hakeicola on leaves of Hakea sp., Setophaeosphaeria citricola on leaves of Citrus australasica, and Sirastachys cyperacearum on leaves of Cyperaceae (Australia); Polyscytalum chilense on leaves of Eucalyptus urophylla (Chile); Pseudoanungitea vaccinii on Vaccinium myrtillus (Germany); Teichospora quercus on branch tissue of Quercus sp. (France); Fusiconidium lycopodiellae on stems of Lycopodiella inundata, Monochaetia junipericola on twig of Juniperus communis, Myrmecridium sorbicola on branch tissues of Sorbus aucuparia, Parathyridaria philadelphi on twigs of Philadelphus coronarius, and Wettsteinina philadelphi on twigs of Philadelphus coronarius (Germany); Zygosporium pseudogibbum on leaves of Eucalyptus pellita (Malaysia); Pseudoanungitea variabilis on dead wood (Spain); Alfaria acaciae on leaves of Acacia propinqua, Dictyochaeta mimusopis on leaves of Mimusops caffra, and Pseudocercospora breonadiae on leaves of Breonadia microcephala (South Africa); Colletotrichum kniphofiae on leaves of Kniphofia uvaria, Subplenodomus iridicola on Iris sp., and Trochila viburnicola on twig cankers on Viburnum sp. (UK); Polyscytalum neofecundissimum on Quercus robur leaf litter, and Roussoella euonymi on fallen branches of Euonymus europaeus (Ukraine). New combinations include: Cylindrium algarvense on leaves of Eucalyptus sp. (Portugal), Cylindrium purgamentum on leaf litter (USA), Cylindrium syzygii on leaves of Syzygium sp. (Australia), Microdochium musae on leaves of Musa sp. (Malaysia), Polyscytalum eucalyptigenum on Eucalyptus grandis × pellita (Malaysia), P. eucalyptorum on leaves of Eucalyptus (Australia), P. grevilleae on leaves of Grevillea (Australia), P. nullicananum on leaves of Eucalyptus (Australia), Pseudoanungitea syzygii on Syzygium cordatum leaf litter (South Africa), and Setophaeosphaeria sidae on leaves of Sida sp. (Brazil). New records include: Sphaerellopsis paraphysata on leaves of Phragmites sp., Vermiculariopsiella dichapetali on leaves of Melaleuca sp. and Eucalyptus regnans, and Xyladictyochaeta lusitanica on leaf litter of Eucalyptus sp. (Australia); Camarosporidiella mackenziei on twigs of Caragana sp. (Finland); Cyclothyriella rubronotata on twigs of Ailanthus altissima, Rhinocladiella quercus on Sorbus aucuparia branches (Germany); Cytospora viticola on stems of Vitis vinifera (Hungary); Echinocatena arthrinioides on leaves of Acacia crassicarpa (Malaysia); Varicosporellopsis aquatilis from garden soil (Netherlands); Pestalotiopsis hollandica on needles of Cupressus sempervirens (Spain), Pseudocamarosporium africanum on twigs of Erica sp. (South Africa), Pseudocamarosporium brabeji on branch of Platanus sp. (Switzerland); Neocucurbitaria cava on leaves of Quercus ilex (UK); Chaetosphaeria myriocarpa on decaying wood of Carpinus betulus, Haplograhium delicatum on decaying Carpinus betulus wood (Ukraine). Epitypes are designated for: Elsinoë mimosae on leaves of Mimosa diplotricha (Brazil), Neohendersonia kickxii on Fagus sylvatica twig bark (Italy), Caliciopsis maxima on fronds of Niphidium crassifolium (Brazil), Dictyochaeta septata on leaves of Eucalyptus grandis × urophylla (Chile), and Microdochium musae on leaves of Musa sp. (Malaysia).
Collapse
Affiliation(s)
- P.W. Crous
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
- Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | | | - M.J. Wingfield
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - A. Akulov
- Department of Mycology and Plant Resistance, V. N. Karazin Kharkiv National University, Maidan Svobody 4, 61022 Kharkiv, Ukraine
| | - S. Denman
- Forest Research, Alice Holt Lodge, Farnham, Surrey, UK
| | - J. Roux
- Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - U. Braun
- Martin-Luther-Universität, Institut für Biologie, Bereich Geobotanik und Botanischer Garten, Herbarium, Neuwerk 21, 06099 Halle (Saale), Germany
| | - T.I. Burgess
- Centre for Phytophthora Science and Management, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - A.J. Carnegie
- Forest Health & Biosecurity, NSW Department of Primary Industries, Level 12, 10 Valentine Ave, Parramatta NSW 2150, Locked Bag 5123, Parramatta NSW 2124, Australia
| | - K.Z. Váczy
- Centre for Research and Development, Eszterházy Károly University, H-3300 Eger, Hungary
| | - E. Guatimosim
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande, CEP: 96170-000, São Lourenço do Sul, Brazil
| | - P.B. Schwartsburd
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, CEP: 36.570-900, Viçosa, Minas Gerais, Brazil
| | - R.W. Barreto
- Departamento de Fitopatologia, Universidade Federal de Viçosa, CEP: 36.570-900, Viçosa, Minas Gerais, Brazil
| | - M. Hernández-Restrepo
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
| | - L. Lombard
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
| | - J.Z. Groenewald
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
| |
Collapse
|
166
|
Colabella C, Corte L, Roscini L, Bassetti M, Tascini C, Mellor JC, Meyer W, Robert V, Vu D, Cardinali G. NGS barcode sequencing in taxonomy and diagnostics, an application in " Candida" pathogenic yeasts with a metagenomic perspective. IMA Fungus 2018; 9:91-105. [PMID: 30018874 PMCID: PMC6048569 DOI: 10.5598/imafungus.2018.09.01.07] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 05/10/2018] [Indexed: 11/29/2022] Open
Abstract
Species identification of yeasts and other Fungi is currently carried out with Sanger sequences of selected molecular markers, mainly from the ribosomal DNA operon, characterized by hundreds of tandem repeats of the 18S, ITS1, 5.8S, ITS2 and LSU loci. The ITS region has been recently proposed as a primary barcode marker making this region the most used one in taxonomy, phylogeny and diagnostics. The introduction of NGS is providing tools of high efficacy and relatively low cost to amplify two or more markers simultaneously with great sequencing depth. However, the presence of intra-genomic variability between the repeats requires specific analytical procedures and pipelines. In this study, 286 strains belonging to 11 pathogenic yeasts species were analysed with NGS of the region spanning from ITS1 to the D1/D2 domain of the LSU encoding ribosomal DNA. Results showed that relatively high heterogeneity can hamper the use of these sequences for the identification of single strains and even more of complex microbial mixtures. These observations point out that the metagenomics studies could be affected by species inflection at levels higher than currently expected.
Collapse
Affiliation(s)
- Claudia Colabella
- Microbiology Section, Department of Pharmaceutical Sciences, University of Perugia, 06121, Italy
| | - Laura Corte
- Microbiology Section, Department of Pharmaceutical Sciences, University of Perugia, 06121, Italy
| | - Luca Roscini
- Microbiology Section, Department of Pharmaceutical Sciences, University of Perugia, 06121, Italy
| | - Matteo Bassetti
- Infectious Diseases Division, Santa Maria Misericordia University Hospital, Udine, 33100, Italy
| | - Carlo Tascini
- Infectious Diseases Division, Cotugno Hospital Napoli, 80131, Italy
| | | | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School, Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Institute for Medical Research, Sydney, NSW 2006, Australia
| | - Vincent Robert
- Bioinformatics Unit, Westerdijk Fungal Biodiversity Institute, 3508 CT, Utrecht, Netherlands
| | - Duong Vu
- Bioinformatics Unit, Westerdijk Fungal Biodiversity Institute, 3508 CT, Utrecht, Netherlands
| | - Gianluigi Cardinali
- Microbiology Section, Department of Pharmaceutical Sciences, University of Perugia, 06121, Italy.,CEMIN Research Centre of Excellence, University of Perugia, Borgo 20 Giugno 74, 06121, Italy
| |
Collapse
|
167
|
Kurtzman CP, Robnett CJ, Basehoar E, Ward TJ. Four new species of Metschnikowia and the transfer of seven Candida species to Metschnikowia and Clavispora as new combinations. Antonie van Leeuwenhoek 2018; 111:2017-2035. [DOI: 10.1007/s10482-018-1095-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 05/05/2018] [Indexed: 11/24/2022]
|
168
|
Thanh VN, Duc Hien D, Yaguchi T, Sampaio JP, Lachance MA. Moniliella sojae sp. nov., a species of black yeasts isolated from Vietnamese soy paste (tuong), and reassignment of Moniliella suaveolens strains to Moniliella pyrgileucina sp. nov., Moniliella casei sp. nov. and Moniliella macrospora emend. comb. nov. Int J Syst Evol Microbiol 2018; 68:1806-1814. [PMID: 29521614 DOI: 10.1099/ijsem.0.002690] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
The presence of yeasts at different steps of Vietnamese soy paste production was studied. Yeast growth occurred during primary soybean fermentation, with the cell density reaching 4.106 c.f.u. ml-1, and terminated during brine fermentation. The dominant species were Pichia kudriavzevii and Millerozyma farinosa. Over the span of 14 years, nine strains of Moniliella were isolated. The strains had identical PCR fingerprints generated with primer (GAC)5 and identical D1/D2 and internal transcribed spacer (ITS) sequences. A D1/D2-based phylogeny indicated that the strains were closest to a group of four previously assigned as Moniliella suaveolens strains. Together they form a new lineage that is well separated from all known species, including M. suaveolens (over 12.7 % divergence). ITS sequences indicated the presence of four species differing from each other by 9-57 nt. The name Moniliella sojae sp. nov. is proposed to accommodate the strains isolated from Vietnamese soy paste, Moniliella pyrgileucina sp. nov. is proposed for PYCC 6800 and Moniliella casei sp. nov. is proposed for CBS 157.58. An emended combination Moniliella macrospora is proposed for CBS 221.32 and CBS 223.32. The type strains and MycoBank numbers are: M. sojae sp. nov., SS 4.2T=CBS 126448T=NRRL Y-48680T and MB 822871; M. pyrgileucina sp. nov., PYCC 6800T=CBS 15203T and MB 823030; M. casei sp. nov., CBS 157.58T=IFM 60348T and MB 822872; M. macrospora emend. comb. nov., CBS 221.32T (=MUCL 11527T) and MB 822874.
Collapse
Affiliation(s)
- Vu Nguyen Thanh
- Center for Industrial Microbiology, Food Industries Research Institute, 301-Nguyen Trai, Thanh Xuan, Hanoi, Vietnam
| | - Dinh Duc Hien
- Center for Industrial Microbiology, Food Industries Research Institute, 301-Nguyen Trai, Thanh Xuan, Hanoi, Vietnam
| | - Takashi Yaguchi
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Jose Paulo Sampaio
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada
| |
Collapse
|
169
|
Rico-Munoz E, Samson RA, Houbraken J. Mould spoilage of foods and beverages: Using the right methodology. Food Microbiol 2018; 81:51-62. [PMID: 30910088 DOI: 10.1016/j.fm.2018.03.016] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/16/2018] [Accepted: 03/29/2018] [Indexed: 11/19/2022]
Abstract
Fungal spoilage of products manufactured by the food and beverage industry imposes significant annual global revenue losses. Mould spoilage can also be a food safety issue due to the production of mycotoxins by these moulds. To prevent mould spoilage, it is essential that the associated mycobiota be adequately isolated and accurately identified. The main fungal groups associated with spoilage are the xerophilic, heat-resistant, preservative-resistant, anaerobic and psychrophilic fungi. To assess mould spoilage, the appropriate methodology and media must be used. While classic mycological detection methods can detect a broad range of fungi using well validated protocols, they are time consuming and results can take days or even weeks. New molecular detection methods are faster but require good DNA isolation techniques, expensive equipment and may detect viable and non-viable fungi that probably will not spoil a specific product. Although there is no complete and easy method for the detection of fungi in food it is important to be aware of the limitation of the methodology. More research is needed on the development of methods of detection and identification that are both faster and highly sensitive.
Collapse
Affiliation(s)
- Emilia Rico-Munoz
- BCN Research Laboratories, Inc., 2491 Stock Creek Blvd., Rockford, TN 37853, USA.
| | - Robert A Samson
- Westerdijk Fungal Biodiversity Institute, Dept. Applied and Industrial Mycology, Uppsalalaan 8, Utrecht, CT 3584, The Netherlands
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Dept. Applied and Industrial Mycology, Uppsalalaan 8, Utrecht, CT 3584, The Netherlands
| |
Collapse
|
170
|
Stavrou AA, Mixão V, Boekhout T, Gabaldón T. Misidentification of genome assemblies in public databases: The case of Naumovozyma dairenensis and proposal of a protocol to correct misidentifications. Yeast 2018; 35:425-429. [PMID: 29320804 PMCID: PMC6001429 DOI: 10.1002/yea.3303] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/30/2017] [Accepted: 12/21/2017] [Indexed: 11/05/2022] Open
Abstract
Online sequence databases such as NCBI GenBank serve as a tremendously useful platform for researchers to share and reuse published data. However, submission systems lack control for errors such as organism misidentification, which once entered in the database can be propagated and mislead downstream analyses. Here we present an illustrating case of misidentification of Candida albicans from a clinical sample as Naumovozyma dairenensis based on whole-genome shotgun data. Analyses of phylogenetic markers, read mapping and single nucleotide polymorphisms served to correct the identification. We propose that the routine use of such analyses could help to detect misidentifications arising from unsupervised analyses and correct them before they enter the databases. Finally, we discuss broader implications of such misidentifications and the difficulty of correcting them once they are in the records.
Collapse
Affiliation(s)
- Aimilia A Stavrou
- Westerdijk Fungal Biodiversity Institute, 3584, Utrecht, The Netherlands.,Institute for Biodiversity and ecosystem Dynamics, University of Amsterdam, 1012, WX, Amsterdam, The Netherlands
| | - Verónica Mixão
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, 3584, Utrecht, The Netherlands.,Institute for Biodiversity and ecosystem Dynamics, University of Amsterdam, 1012, WX, Amsterdam, The Netherlands
| | - Toni Gabaldón
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra, 08003, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Pg. Lluís Companys 23, 08010, Barcelona, Spain
| |
Collapse
|
171
|
Quintilla R, Kolecka A, Casaregola S, Daniel HM, Houbraken J, Kostrzewa M, Boekhout T, Groenewald M. MALDI-TOF MS as a tool to identify foodborne yeasts and yeast-like fungi. Int J Food Microbiol 2018; 266:109-118. [DOI: 10.1016/j.ijfoodmicro.2017.11.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/23/2017] [Accepted: 11/20/2017] [Indexed: 01/09/2023]
|
172
|
Description of Komagataella mondaviorum sp. nov., a new sibling species of Komagataella (Pichia) pastoris. Antonie van Leeuwenhoek 2018; 111:1197-1207. [DOI: 10.1007/s10482-018-1028-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 01/25/2018] [Indexed: 12/11/2022]
|
173
|
Colabella C, Corte L, Roscini L, Shapaval V, Kohler A, Tafintseva V, Tascini C, Cardinali G. Merging FT-IR and NGS for simultaneous phenotypic and genotypic identification of pathogenic Candida species. PLoS One 2017; 12:e0188104. [PMID: 29206226 PMCID: PMC5714347 DOI: 10.1371/journal.pone.0188104] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/18/2017] [Indexed: 01/27/2023] Open
Abstract
The rapid and accurate identification of pathogen yeast species is crucial for clinical diagnosis due to the high level of mortality and morbidity induced, even after antifungal therapy. For this purpose, new rapid, high-throughput and reliable identification methods are required. In this work we described a combined approach based on two high-throughput techniques in order to improve the identification of pathogenic yeast strains. Next Generation Sequencing (NGS) of ITS and D1/D2 LSU marker regions together with FTIR spectroscopy were applied to identify 256 strains belonging to Candida genus isolated in nosocomial environments. Multivariate data analysis (MVA) was carried out on NGS and FT-IR data-sets, separately. Strains of Candida albicans, C. parapsilosis, C. glabrata and C. tropicalis, were identified with high-throughput NGS sequencing of ITS and LSU markers and then with FTIR. Inter- and intra-species variability was investigated by consensus principal component analysis (CPCA) which combines high-dimensional data of the two complementary analytical approaches in concatenated PCA blocks normalized to the same weight. The total percentage of correct identification reached around 97.4% for C. albicans and 74% for C. parapsilosis while the other two species showed lower identification rates. Results suggested that the identification success increases with the increasing number of strains actually used in the PLS analysis. The absence of reliable FT-IR libraries in the current scenario is the major limitation in FTIR-based identification of strains, although this metabolomics fingerprint represents a valid and affordable aid to rapid and high-throughput to clinical diagnosis. According to our data, FT-IR libraries should include some tens of certified strains per species, possibly over 50, deriving from diverse sources and collected over an extensive time period. This implies a multidisciplinary effort of specialists working in strain isolation and maintenance, molecular taxonomy, FT-IR technique and chemo-metrics, data management and data basing.
Collapse
Affiliation(s)
- Claudia Colabella
- Department of Pharmaceutical Sciences—Microbiology, University of Perugia, Perugia (Italy)
| | - Laura Corte
- Department of Pharmaceutical Sciences—Microbiology, University of Perugia, Perugia (Italy)
| | - Luca Roscini
- Department of Pharmaceutical Sciences—Microbiology, University of Perugia, Perugia (Italy)
| | - Volha Shapaval
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Norway
| | - Achim Kohler
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Norway
| | - Valeria Tafintseva
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Norway
| | - Carlo Tascini
- Azienda Ospedaliera dei Colli—Ospedale Cotugno, Napoli, Italy
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences—Microbiology, University of Perugia, Perugia (Italy)
- CEMIN, Centre of Excellence on Nanostructured Innovative Materials—Department of Chemistry, Biology and Biotechnology—University of Perugia, Perugia, Italy
| |
Collapse
|
174
|
Kachalkin AV, Glushakova AM, Pankratov TA. Yeast population of the Kindo Peninsula lichens. Microbiology (Reading) 2017. [DOI: 10.1134/s0026261717060078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
175
|
Baral HO, Weber E, Marson G, Quijada L. A new connection between wood saprobism and beetle endosymbiosis: the rarely reported saprobic discomycete Tromeropsis is congeneric with the symbiotic yeast Symbiotaphrina (Symbiotaphrinales, Xylonomycetes) and two asexual morphs misplaced in Hyphozyma. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1340-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
176
|
A Comprehensive Analysis of MALDI-TOF MS and Ribosomal DNA Sequencing for Identification of Clinical Yeasts. CURRENT FUNGAL INFECTION REPORTS 2017. [DOI: 10.1007/s12281-017-0297-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
177
|
Tascini C, Sozio E, Corte L, Sbrana F, Scarparo C, Ripoli A, Bertolino G, Merelli M, Tagliaferri E, Corcione A, Bassetti M, Cardinali G, Menichetti F. The role of biofilm forming on mortality in patients with candidemia: a study derived from real world data. Infect Dis (Lond) 2017; 50:214-219. [PMID: 28988525 DOI: 10.1080/23744235.2017.1384956] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Evaluation of the role on patient mortality exerted by biofilm forming (BF) Candida strains, by using predictive clinical data. METHODS Eighty-nine strains isolated from Candida bloodstream infection, occurring in two Italian University Hospitals, were employed in this study. A random forest (RF) model was built with a procedure of iterative selection of the risk factors potentially able to predict the probability of death. The similarity between patient conditions and Bayesian clustering was calculated in order to evaluate the role of predictors in the stratification of the death risk. RESULTS Three different groups of patients with different probability of death were obtained with a RF approach: Group 1 (mortality in 33.3% of cases), Group 2 (death in 50% of cases), and Group 3 (mortality in 76.9% of cases). The comparison between these three groups showed that BF correlated well with increased mortality in patients, admitted for medical diagnosis, with high APACHE II score and treated with azoles. Early treatment within 24 h between candidemia diagnosis and the beginning of antifungal therapy was associated with the lowest of BF rate and mortality. CONCLUSIONS BF by Candida spp. seems to be clinically associated with increased mortality especially in medical patients with higher Apache II score or treated with azoles.
Collapse
Affiliation(s)
- Carlo Tascini
- a First Division of Infectious Diseases , Cotugno Hospital, Azienda Ospedaliera dei Colli , Napoli , Italy
| | - Emanuela Sozio
- b Unit of Emergency Medicine , Nuovo Santa Chiara University Hospital, Azienda Ospedaliera Universitaria Pisana , Pisa , Italy
| | - Laura Corte
- c Department of Pharmaceutical Sciences-Microbiology , University of Perugia , Perugia , Italy.,d CEMIN (Centre of Excellence on Nanostructured Innovative Materials), Department of Chemistry, Biology and Biotechnology , University of Perugia , Perugia , Italy
| | | | - Claudio Scarparo
- f Unit of Microbiology , Santa Maria Misericordia University Hospital , Udine , Italy
| | - Andrea Ripoli
- d CEMIN (Centre of Excellence on Nanostructured Innovative Materials), Department of Chemistry, Biology and Biotechnology , University of Perugia , Perugia , Italy
| | - Giacomo Bertolino
- g Department of Pharmaceutical Sciences-Medicine management , Azienda Ospedaliera Universitaria Pisana , Pisa , Italy
| | - Maria Merelli
- h Division of Infectious Diseases , Santa Maria Misericordia University Hospital , Udine , Italy
| | - Enrico Tagliaferri
- i Infectious Diseases Clinic , Nuovo Santa Chiara University Hospital, Azienda Ospedaliera Universitaria Pisana , Pisa , Italy
| | - Antonio Corcione
- j Department of Intensive Care , Monaldi Hospital, Azienda Ospedaliera dei Colli , Napoli , Italy
| | - Matteo Bassetti
- h Division of Infectious Diseases , Santa Maria Misericordia University Hospital , Udine , Italy
| | - Gianluigi Cardinali
- c Department of Pharmaceutical Sciences-Microbiology , University of Perugia , Perugia , Italy.,d CEMIN (Centre of Excellence on Nanostructured Innovative Materials), Department of Chemistry, Biology and Biotechnology , University of Perugia , Perugia , Italy
| | - Francesco Menichetti
- i Infectious Diseases Clinic , Nuovo Santa Chiara University Hospital, Azienda Ospedaliera Universitaria Pisana , Pisa , Italy
| |
Collapse
|
178
|
Cardinali G, Corte L, Robert V. Next Generation Sequencing: problems and opportunities for next generation studies of microbial communities in food and food industry. Curr Opin Food Sci 2017. [DOI: 10.1016/j.cofs.2017.09.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
179
|
|
180
|
Zaman K, Rudramurthy SM, Das A, Panda N, Honnavar P, Kaur H, Chakrabarti A. Molecular diagnosis of rhino-orbito-cerebral mucormycosis from fresh tissue samples. J Med Microbiol 2017; 66:1124-1129. [PMID: 28792370 DOI: 10.1099/jmm.0.000560] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
PURPOSE We aimed to evaluate a PCR-based technique for the diagnosis of mucormycosis and the identification of fungi from fresh tissue specimens in patients with rhino-orbito-cerebral-mucormycosis (ROCM). METHODOLOGY Fifty cases of ROCM were included in the study. Conventional identification was performed using microscopy and culture. Molecular diagnosis was performed by amplifying the ribosomal DNA using pan-fungal ITS primers and semi-nested Mucorales-specific primers of the 18S region. The amplified products were sequenced to identify the agents. The utility of PCR-RFLP of the 18S region of rDNA was evaluated to identify the Mucorales. RESULTS The ROCM cases were diagnosed by the demonstration of aseptate ribbon-like hyphae in biopsy specimens collected from the patients. Isolation was possible in 24 (48 %) samples. The ITS2 PCR confirmed mucormycosis in 27 cases (54 %; CI 59.4-68.2). By comparison, Mucorales-specific PCR was able to amplify DNA and the sequence enabled the identification of Mucorales speciesin all the patients. PCR-RFLP of the 18S region of rDNA could only identify the agent to genus level. CONCLUSION The molecular technique was able to identify Mucorales species in 26 (42 %) cases that were negative by culture. Mucorales-specific semi-nested PCR targeting the 18S region is a better technique than ITS2 PCR for diagnosis. PCR-RFLP of the 18S region helps in identification to genus level.
Collapse
Affiliation(s)
- Kamran Zaman
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Sector 12, Chandigarh 160012, India
| | - Shivaprakash Mandya Rudramurthy
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Sector 12, Chandigarh 160012, India
| | - Ashim Das
- Department of Histopathology, Postgraduate Institute of Medical Education and Research, Sector 12, Chandigarh 160012, India
| | - Naresh Panda
- Department of Otolaryngology, Postgraduate Institute of Medical Education and Research, Sector 12, Chandigarh 160012, India
| | - Prasanna Honnavar
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Sector 12, Chandigarh 160012, India
| | - Harsimran Kaur
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Sector 12, Chandigarh 160012, India
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Sector 12, Chandigarh 160012, India
| |
Collapse
|
181
|
Naseeb S, James SA, Alsammar H, Michaels CJ, Gini B, Nueno-Palop C, Bond CJ, McGhie H, Roberts IN, Delneri D. Saccharomyces jurei sp. nov., isolation and genetic identification of a novel yeast species from Quercus robur. Int J Syst Evol Microbiol 2017. [PMID: 28639933 PMCID: PMC5817255 DOI: 10.1099/ijsem.0.002013] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Two strains, D5088T and D5095, representing a novel yeast species belonging to the genus Saccharomyces were isolated from oak tree bark and surrounding soil located at an altitude of 1000 m above sea level in Saint Auban, France. Sequence analyses of the internal transcribed spacer (ITS) region and 26S rRNA D1/D2 domains indicated that the two strains were most closely related to Saccharomyces mikatae and Saccharomyces paradoxus. Genetic hybridization analyses showed that both strains are reproductively isolated from all other Saccharomyces species and, therefore, represent a distinct biological species. The species name Saccharomyces jurei sp. nov. is proposed to accommodate these two strains, with D5088T (=CBS 14759T=NCYC 3947T) designated as the type strain.
Collapse
Affiliation(s)
- Samina Naseeb
- Manchester Institute of Biotechnology, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M1 7DN, UK
| | | | - Haya Alsammar
- Manchester Institute of Biotechnology, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M1 7DN, UK
| | - Christopher J. Michaels
- Manchester Institute of Biotechnology, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M1 7DN, UK
| | - Beatrice Gini
- Manchester Institute of Biotechnology, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M1 7DN, UK
| | | | | | - Henry McGhie
- The Manchester Museum, The University of Manchester, Manchester M13 9PL, UK
| | | | - Daniela Delneri
- Manchester Institute of Biotechnology, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M1 7DN, UK
- *Correspondence: Daniela Delneri,
| |
Collapse
|
182
|
Hernández-Restrepo M, Gené J, Castañeda-Ruiz RF, Mena-Portales J, Crous PW, Guarro J. Phylogeny of saprobic microfungi from Southern Europe. Stud Mycol 2017. [PMID: 28626275 PMCID: PMC5470572 DOI: 10.1016/j.simyco.2017.05.002] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
During a survey of saprophytic microfungi on decomposing woody, herbaceous debris and soil from different regions in Southern Europe, a wide range of interesting species of asexual ascomycetes were found. Phylogenetic analyses based on partial gene sequences of SSU, LSU and ITS proved that most of these fungi were related to Sordariomycetes and Dothideomycetes and to lesser extent to Leotiomycetes and Eurotiomycetes. Four new monotypic orders with their respective families are proposed here, i.e. Lauriomycetales, Lauriomycetaceae; Parasympodiellales, Parasympodiellaceae; Vermiculariopsiellales, Vermiculariopsiellaceae and Xenospadicoidales, Xenospadicoidaceae. One new order and three families are introduced here to accommodate orphan taxa, viz. Kirschsteiniotheliales, Castanediellaceae, Leptodontidiaceae and Pleomonodictydaceae. Furthermore, Bloxamiaceae is validated. Based on morphology and phylogenetic affinities Diplococcium singulare, Trichocladium opacum and Spadicoides atra are moved to the new genera Paradiplococcium, Pleotrichocladium and Xenospadicoides, respectively. Helicoon fuscosporum is accommodated in the genus Magnohelicospora. Other novel genera include Neoascotaiwania with the type species N. terrestris sp. nov., and N. limnetica comb. nov. previously accommodated in Ascotaiwania; Pleomonodictys with P. descalsii sp. nov. as type species, and P. capensis comb. nov. previously accommodated in Monodictys; Anapleurothecium typified by A. botulisporum sp. nov., a fungus morphologically similar to Pleurothecium but phylogenetically distant; Fuscosclera typified by F. lignicola sp. nov., a meristematic fungus related to Leotiomycetes; Pseudodiplococcium typified by P. ibericum sp. nov. to accommodate an isolate previously identified as Diplococcium pulneyense; Xyladictyochaeta typified with X. lusitanica sp. nov., a foliicolous fungus related to Xylariales and similar to Dictyochaeta, but distinguished by polyphialidic conidiogenous cells produced on setiform conidiophores. Other novel species proposed are Brachysporiella navarrica, Catenulostroma lignicola, Cirrenalia iberica, Conioscypha pleiomorpha, Leptodontidium aureum, Pirozynskiella laurisilvatica, Parasympodiella lauri and Zanclospora iberica. To fix the application of some fungal names, lectotypes and/or epitypes are designated for Magnohelicospora iberica, Sporidesmium trigonellum, Sporidesmium opacum, Sporidesmium asperum, Camposporium aquaticum and Psilonia atra.
Collapse
Key Words
- Anapleurothecium Hern.-Restr., R.F. Castañeda & Gené
- Anapleurothecium botulisporum Hern.-Restr., R.F. Castañeda & Gené
- Biodiversity
- Brachysporiella navarrica Hern.-Restr., R.F. Castañeda & Gené
- Camposporium aquaticum Dudka
- Camposporium aquatium Dudka
- Castanediellaceae Hern.-Restr., Guarro & Crous
- Catenulostroma lignicola Hern.-Restr., J. Mena & Gené
- Cirrenalia iberica Hern.-Restr. & Gené
- Conioscypha pleiomorpha Hern.-Restr., R.F. Castañeda & Gené
- Dothideomycetes
- Eurotiomycetes
- Fuscosclera Hern.-Restr., J. Mena & Gené
- Fuscosclera lignicola Hern.-Restr., J. Mena & Gené
- Kirschsteiniotheliales Hern.-Restr., Gené, R.F. Castañeda & Crous
- Lauriomycetaceae Hern.-Restr., R.F. Castañeda & Guarro
- Lauriomycetales Hern.-Restr., R.F. Castañeda & Guarro
- Leotiomycetes
- Leptodontidiaceae Hern.-Restr., Crous & Gené
- Leptodontidium aureum Hern.-Restr., Guarro & Gené
- Magnohelicospora fuscospora (Linder) R.F. Castañeda, Hern.-Restr. & Gené
- Magnohelicospora iberica R.F. Castañeda, Hern.-Restr., Gené & Guarro
- Neoascotaiwania Hern.-Restr., R.F. Castañeda & Guarro
- Neoascotaiwania limnetica (H.S. Chang & S.Y. Hsieh) Hern.-Restr., R.F. Castañeda & Gené
- Paradiplococcium Hern.-Restr., J. Mena & Gené
- Paradiplococcium singulare (Hern.-Restr., J. Mena, Gené & Guarro) Hern.-Restr., J. Mena & Gené
- Parasympodiella lauri Hern.-Restr., Gene & Guarro
- Parasympodiellaceae Hern.-Restr., Gené, Guarro & Crous
- Parasympodiellales Hern.-Restr., Gené, R.F. Castañeda & Crous
- Pirozynskiella laurisilvatica Hern.-Restr., R.F. Castañeda & Gené
- Pleomonodictydaceae Hern.-Restr., J. Mena & Gené
- Pleomonodictys Hern.-Restr., J. Mena & Gené
- Pleomonodictys capensis (R.C. Sinclair, Boshoff & Eicker) Hern.-Restr., J. Mena & Gené
- Pleomonodictys descalsii Hern.-Restr., J. Mena & Gené
- Pleotrichocladium Hern.-Restr., R.F. Castañeda & Gené
- Pleotrichocladium opacum (Corda) Hern.-Restr., R.F. Castañeda & Gené
- Pseudodiplococcium Hern.-Restr., J. Mena & Gené
- Pseudodiplococcium ibericum Hern.-Restr., J. Mena & Gené
- Psilonia atra Corda
- Sordariomycetes
- Sporidesmium asperum Corda
- Sporidesmium opacum Corda
- Sporidesmium trigonellum Sacc.
- Systematics
- Vermiculariopsiellaceae Hern.-Restr., J. Mena, Gené & Crous
- Vermiculariopsiellales Hern.-Restr., J. Mena, Gené & Crous
- Xenospadicoidaceae Hern.-Restr., J. Mena & Gené
- Xenospadicoidales Hern.-Restr., J. Mena & Gené
- Xenospadicoides Hern.-Restr., J. Mena & Gené
- Xenospadicoides atra (Corda) Hern.-Restr., J. Mena & Gené
- Xyladictyochaeta Hern.-Restr., R.F. Castañeda & Gené
- Xyladictyochaeta lusitanica Hern.-Restr., R.F. Castañeda & Gené
- Zanclospora iberica Hern.-Restr., J. Mena & Gené
Collapse
Affiliation(s)
- M Hernández-Restrepo
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands.,Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - J Gené
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili, 43201 Reus, Spain
| | - R F Castañeda-Ruiz
- Instituto de Investigaciones Fundamentales en Agricultura Tropical "Alejandro de Humboldt" (INIFAT), 17200, La Habana, Cuba
| | - J Mena-Portales
- Instituto de Ecología y Sistemática, Carretera Varona 11835 e/Oriente y Lindero, Capdevila, Boyeros, 11900, La Habana 19, Cuba
| | - P W Crous
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands.,Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa.,Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - J Guarro
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili, 43201 Reus, Spain
| |
Collapse
|