1
|
Dost C, Michling F, Kaimenyi D, Rij M, Wendland J. Isolation of Saccharomycopsis species from plant material. Microbiol Res 2024; 283:127691. [PMID: 38492364 DOI: 10.1016/j.micres.2024.127691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
Saccharomycopsis species are natural organic sulphur auxotrophs. Their genomes do not encode genes for the uptake and assimilation of sulphate and thus these species cannot grow on media lacking e.g. methionine. Due to the similarity between sulphate and selenate, uptake and assimilation of selenate occurs through the same pathway starting from sulphate transporters encoded by the homologs of the SUL1 and SUL2 genes in S. cerevisiae. Lack of these transporters renders Saccharomycopsis species resistant to selenate levels that are toxic to other microorganisms. We used this feature to enrich environmental samples for Saccharomycopsis species. This led to the isolation of S. schoenii, S. lassenensis and a hitherto undescribed Saccharomycopsis species with limited by-catch of other yeasts, mainly belonging to Metschnikowia and Hanseniaspora. We performed growth and predation assays to characterize the potential of these new isolates as predacious yeasts. Most Saccharomycopsis species are temperature sensitive and cannot grow at 37°C; with the exception of S. lassenensis strains. Predation assays with S. schoenii and S. cerevisiae as prey indicated that predation was enhanced at 20°C compared to 30°C. We crossed an American isolate of S. schoenii with our German isolate using marker directed breeding. Viable progeny indicated that both strains are interfertile and belong to the same biological species. S. lassenensis is heterothallic, while S. schoenii and the new Saccharomycopsis isolate, for which we suggest the name S. geisenheimensis sp. nov., are homothallic.
Collapse
Affiliation(s)
- Carmen Dost
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, Geisenheim 65366, Germany; Geisenheim Yeast Breeding Center, Hochschule Geisenheim University, Von-Lade-Strasse 1, Geisenheim 65366, Germany
| | - Florian Michling
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, Geisenheim 65366, Germany; Geisenheim Yeast Breeding Center, Hochschule Geisenheim University, Von-Lade-Strasse 1, Geisenheim 65366, Germany
| | - Davies Kaimenyi
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, Geisenheim 65366, Germany
| | - Mareike Rij
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, Geisenheim 65366, Germany
| | - Jürgen Wendland
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, Geisenheim 65366, Germany; Geisenheim Yeast Breeding Center, Hochschule Geisenheim University, Von-Lade-Strasse 1, Geisenheim 65366, Germany.
| |
Collapse
|
2
|
Mielecki D, Detman A, Aleksandrzak-Piekarczyk T, Widomska M, Chojnacka A, Stachurska-Skrodzka A, Walczak P, Grzesiuk E, Sikora A. Unlocking the genome of the non-sourdough Kazachstania humilis MAW1: insights into inhibitory factors and phenotypic properties. Microb Cell Fact 2024; 23:111. [PMID: 38622625 PMCID: PMC11017505 DOI: 10.1186/s12934-024-02380-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 03/22/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Ascomycetous budding yeasts are ubiquitous environmental microorganisms important in food production and medicine. Due to recent intensive genomic research, the taxonomy of yeast is becoming more organized based on the identification of monophyletic taxa. This includes genera important to humans, such as Kazachstania. Until now, Kazachstania humilis (previously Candida humilis) was regarded as a sourdough-specific yeast. In addition, any antibacterial activity has not been associated with this species. RESULTS Previously, we isolated a yeast strain that impaired bio-hydrogen production in a dark fermentation bioreactor and inhibited the growth of Gram-positive and Gram-negative bacteria. Here, using next generation sequencing technologies, we sequenced the genome of this strain named K. humilis MAW1. This is the first genome of a K. humilis isolate not originating from a fermented food. We used novel phylogenetic approach employing the 18 S-ITS-D1-D2 region to show the placement of the K. humilis MAW1 among other members of the Kazachstania genus. This strain was examined by global phenotypic profiling, including carbon sources utilized and the influence of stress conditions on growth. Using the well-recognized bacterial model Escherichia coli AB1157, we show that K. humilis MAW1 cultivated in an acidic medium inhibits bacterial growth by the disturbance of cell division, manifested by filament formation. To gain a greater understanding of the inhibitory effect of K. humilis MAW1, we selected 23 yeast proteins with recognized toxic activity against bacteria and used them for Blast searches of the K. humilis MAW1 genome assembly. The resulting panel of genes present in the K. humilis MAW1 genome included those encoding the 1,3-β-glucan glycosidase and the 1,3-β-glucan synthesis inhibitor that might disturb the bacterial cell envelope structures. CONCLUSIONS We characterized a non-sourdough-derived strain of K. humilis, including its genome sequence and physiological aspects. The MAW1, together with other K. humilis strains, shows the new organization of the mating-type locus. The revealed here pH-dependent ability to inhibit bacterial growth has not been previously recognized in this species. Our study contributes to the building of genome sequence-based classification systems; better understanding of K.humilis as a cell factory in fermentation processes and exploring bacteria-yeast interactions in microbial communities.
Collapse
Affiliation(s)
- Damian Mielecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
- Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawińskiego 5, Warsaw, 02-106, Poland
| | - Anna Detman
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
| | | | - Małgorzata Widomska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
| | - Aleksandra Chojnacka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
- Institute of Biology, Warsaw University of Life Sciences, Nowoursynowska 159, Warsaw, 02-776, Poland
| | | | - Paulina Walczak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
| | - Elżbieta Grzesiuk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
| | - Anna Sikora
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland.
| |
Collapse
|
3
|
Kumar V, Huang J, Dong Y, Hao GF. Targeting Fks1 proteins for novel antifungal drug discovery. Trends Pharmacol Sci 2024; 45:366-384. [PMID: 38493014 DOI: 10.1016/j.tips.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 01/26/2024] [Accepted: 02/26/2024] [Indexed: 03/18/2024]
Abstract
Fungal infections are a major threat to human health. The limited availability of antifungal drugs, the emergence of drug resistance, and a growing susceptible population highlight the critical need for novel antifungal agents. The enzymes involved in fungal cell wall synthesis offer potential targets for antifungal drug development. Recent studies have enhanced our focus on the enzyme Fks1, which synthesizes β-1,3-glucan, a critical component of the cell wall. These studies provide a deeper understanding of Fks1's function in cell wall biosynthesis, pathogenicity, structural biology, evolutionary conservation across fungi, and interaction with current antifungal drugs. Here, we discuss the role of Fks1 in the survival and adaptation of fungi, guided by insights from evolutionary and structural analyses. Furthermore, we delve into the dynamics of Fks1 modulation with novel antifungal strategies and assess its potential as an antifungal drug target.
Collapse
Affiliation(s)
- Vinit Kumar
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, PR China; BMLT, Markham College of Commerce, Vinoba Bhave University, Hazaribagh, Jharkhand 825301, India
| | - Juan Huang
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, PR China
| | - Yawen Dong
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, PR China.
| | - Ge-Fei Hao
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, PR China; National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, PR China.
| |
Collapse
|
4
|
Brysch-Herzberg M, Jia GS, Sipiczki M, Seidel M, Zhang WC, Du LL. Reinstatement of the fission yeast species Schizosaccharomyces versatilis Wickerham et Duprat, a sibling species of Schizosaccharomyces japonicus. Yeast 2024; 41:108-127. [PMID: 38450805 DOI: 10.1002/yea.3922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 03/08/2024] Open
Abstract
Schizosaccharomyces japonicus Yukawa et Maki (1931) and Schizosaccharomyces versatilis Wickerham et Duprat (1945) have been treated as varieties of S. japonicus or as conspecific, based on various approaches including mating trials and nDNA/nDNA optical reassociation studies. However, the type strains of S. japonicus and S. versatilis differ by five substitutions (99.15% identity) and one 1-bp indel in the sequences of the D1/D2 domain of the 26S rRNA gene, and 23 substitutions (96.3% identity) and 31-bp indels in the sequences of internal transcribed spacer (ITS) of rRNA, suggesting that they may not be conspecific. To reassess their taxonomic status, we conducted mating trials and whole-genome analyses. Mating trials using the type strains showed a strong but incomplete prezygotic sterility barrier, yielding interspecies mating products at two orders of magnitude lower efficiency than intraspecies matings. These mating products, which were exclusively allodiploid hybrids, were unable to undergo the haplontic life cycle of the parents. We generated chromosome-level gap-less genome assemblies for both type strains. Whole genome sequences yielded an average nucleotide identity (ANI) of 86.4%, indicating clear separation of S. japonicus and S. versatilis. Based on these findings, we propose the reinstatement of S. versatilis as a distinct species (holotype strain: CBS 103T and ex-types: NRRL Y-1026, NBRC 1607, ATCC 9987, PYCC 7100; Mycobank no.: 847838).
Collapse
Affiliation(s)
- Michael Brysch-Herzberg
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University, Heilbronn, Germany
| | - Guo-Song Jia
- National Institute of Biological Sciences, Beijing, China
| | - Matthias Sipiczki
- Department of Genetics and Applied Microbiology, University of Debrecen, Debrecen, Hungary
| | - Martin Seidel
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University, Heilbronn, Germany
| | - Wen-Cai Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| |
Collapse
|
5
|
Renzi S, Nenciarini S, Bacci G, Cavalieri D. Yeast metagenomics: analytical challenges in the analysis of the eukaryotic microbiome. MICROBIOME RESEARCH REPORTS 2023; 3:2. [PMID: 38455081 PMCID: PMC10917621 DOI: 10.20517/mrr.2023.27] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 10/09/2023] [Accepted: 10/17/2023] [Indexed: 03/09/2024]
Abstract
Even if their impact is often underestimated, yeasts and yeast-like fungi represent the most prevalent eukaryotic members of microbial communities on Earth. They play numerous roles in natural ecosystems and in association with their hosts. They are involved in the food industry and pharmaceutical production, but they can also cause diseases in other organisms, making the understanding of their biology mandatory. The ongoing loss of biodiversity due to overexploitation of environmental resources is a growing concern in many countries. Therefore, it becomes crucial to understand the ecology and evolutionary history of these organisms to systematically classify them. To achieve this, it is essential that our knowledge of the mycobiota reaches a level similar to that of the bacterial communities. To overcome the existing challenges in the study of fungal communities, the first step should be the establishment of standardized techniques for the correct identification of species, even from complex matrices, both in wet lab practices and in bioinformatic tools.
Collapse
Affiliation(s)
| | | | | | - Duccio Cavalieri
- Correspondence to: Prof. Duccio Cavalieri, Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino 50019, Italy. E-mail:
| |
Collapse
|
6
|
Leo P, de Melo Texeira M, Chander AM, Singh NK, Simpson AC, Yurkov A, Karouia F, Stajich JE, Mason CE, Venkateswaran K. Genomic characterization and radiation tolerance of Naganishia kalamii sp. nov. and Cystobasidium onofrii sp. nov. from Mars 2020 mission assembly facilities. IMA Fungus 2023; 14:15. [PMID: 37568226 PMCID: PMC10422843 DOI: 10.1186/s43008-023-00119-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/20/2023] [Indexed: 08/13/2023] Open
Abstract
During the construction and assembly of the Mars 2020 mission components at two different NASA cleanrooms, several fungal strains were isolated. Based on their colony morphology, two strains that showed yeast-like appearance were further characterized for their phylogenetic position. The species-level classification of these two novel strains, using traditional colony and cell morphology methods combined with the phylogenetic reconstructions using multi-locus sequence analysis (MLSA) based on several gene loci (ITS, LSU, SSU, RPB1, RPB2, CYTB and TEF1), and whole genome sequencing (WGS) was carried out. This polyphasic taxonomic approach supported the conclusion that the two basidiomycetous yeasts belong to hitherto undescribed species. The strain FJI-L2-BK-P3T, isolated from the Jet Propulsion Laboratory Spacecraft Assembly Facility, was placed in the Naganishia albida clade (Filobasidiales, Tremellomycetes), but is genetically and physiologically different from other members of the clade. Another yeast strain FKI-L6-BK-PAB1T, isolated from the Kennedy Space Center Payload Hazardous and Servicing Facility, was placed in the genus Cystobasidium (Cystobasidiales, Cystobasidiomycetes) and is distantly related to C. benthicum. Here we propose two novel species with the type strains, Naganishia kalamii sp. nov. (FJI-L2-BK-P3T = NRRL 64466 = DSM 115730) and Cystobasidium onofrii sp. nov. (FKI-L6-BK-PAB1T = NRRL 64426 = DSM 114625). The phylogenetic analyses revealed that single gene phylogenies (ITS or LSU) were not conclusive, and MLSA and WGS-based phylogenies were more advantageous for species discrimination in the two genera. The genomic analysis predicted proteins associated with dehydration and desiccation stress-response and the presence of genes that are directly related to osmotolerance and psychrotolerance in both novel yeasts described. Cells of these two newly-described yeasts were exposed to UV-C radiation and compared with N. onofrii, an extremophilic UV-C resistant cold-adapted Alpine yeast. Both novel species were UV resistant, emphasizing the need for collecting and characterizing extremotolerant microbes, including yeasts, to improve microbial reduction techniques used in NASA planetary protection programs.
Collapse
Affiliation(s)
- Patrick Leo
- Department of Environmental Sciences, Informatics and Statistics, University Ca' Foscari of Venice, Via Torino 155, 30172, Mestre, Italy
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'università snc, 01100, Viterbo, Italy
- NASA-Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 245-103, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Marcus de Melo Texeira
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Núcleo de Medicina Tropical, Faculdade de Medicina, Universidade de Brasília, Brasília, 70910-900, Brazil
| | - Atul M Chander
- NASA-Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 245-103, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Nitin K Singh
- NASA-Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 245-104, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Anna C Simpson
- NASA-Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 245-103, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Andrey Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Fathi Karouia
- Blue Marble Space Institute of Science, Exobiology Branch, NASA Ames Research Center, PO BOX 1 MS 239/4, Moffett Field, CA, 94035, USA
- Space Research Within Reach, San Francisco, CA, 941110, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of CA-Riverside, Riverside, CA, 92521, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics and the WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Kasthuri Venkateswaran
- NASA-Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 245-104, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA.
| |
Collapse
|
7
|
Wang Z, Kim W, Wang YW, Yakubovich E, Dong C, Trail F, Townsend JP, Yarden O. The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1214537. [PMID: 37746130 PMCID: PMC10512317 DOI: 10.3389/ffunb.2023.1214537] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 06/06/2023] [Indexed: 09/26/2023]
Abstract
Advances in genomics and transcriptomics accompanying the rapid accumulation of omics data have provided new tools that have transformed and expanded the traditional concepts of model fungi. Evolutionary genomics and transcriptomics have flourished with the use of classical and newer fungal models that facilitate the study of diverse topics encompassing fungal biology and development. Technological advances have also created the opportunity to obtain and mine large datasets. One such continuously growing dataset is that of the Sordariomycetes, which exhibit a richness of species, ecological diversity, economic importance, and a profound research history on amenable models. Currently, 3,574 species of this class have been sequenced, comprising nearly one-third of the available ascomycete genomes. Among these genomes, multiple representatives of the model genera Fusarium, Neurospora, and Trichoderma are present. In this review, we examine recently published studies and data on the Sordariomycetes that have contributed novel insights to the field of fungal evolution via integrative analyses of the genetic, pathogenic, and other biological characteristics of the fungi. Some of these studies applied ancestral state analysis of gene expression among divergent lineages to infer regulatory network models, identify key genetic elements in fungal sexual development, and investigate the regulation of conidial germination and secondary metabolism. Such multispecies investigations address challenges in the study of fungal evolutionary genomics derived from studies that are often based on limited model genomes and that primarily focus on the aspects of biology driven by knowledge drawn from a few model species. Rapidly accumulating information and expanding capabilities for systems biological analysis of Big Data are setting the stage for the expansion of the concept of model systems from unitary taxonomic species/genera to inclusive clusters of well-studied models that can facilitate both the in-depth study of specific lineages and also investigation of trait diversity across lineages. The Sordariomycetes class, in particular, offers abundant omics data and a large and active global research community. As such, the Sordariomycetes can form a core omics clade, providing a blueprint for the expansion of our knowledge of evolution at the genomic scale in the exciting era of Big Data and artificial intelligence, and serving as a reference for the future analysis of different taxonomic levels within the fungal kingdom.
Collapse
Affiliation(s)
- Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Wonyong Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Republic of Korea
| | - Yen-Wen Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Elizabeta Yakubovich
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Caihong Dong
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Frances Trail
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
- Department of Ecology and Evolutionary Biology, Program in Microbiology, and Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| |
Collapse
|
8
|
Brysch-Herzberg M, Jia GS, Sipiczki M, Seidel M, Li W, Assali I, Du LL. Schizosaccharomyces lindneri sp. nov., a fission yeast occurring in honey. Yeast 2023. [PMID: 37243506 DOI: 10.1002/yea.3857] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/26/2023] [Accepted: 04/30/2023] [Indexed: 05/29/2023] Open
Abstract
Two strains of fission yeast were isolated from honey. They differ from the type strain of Schizosaccharomyces octosporus by three substitutions in the D1/D2 domain of the nuclear 26S large subunit ribosomal RNA (rRNA) gene sequence, resulting in a 99.5% identity. In the internal transcribed spacer (ITS) region (consisting of ITS1, 5.8S rDNA, and ITS2), the strains differ from S. octosporus by 16 gaps and 91 substitutions, which is equivalent to an identity of 88.1%. Genome sequencing on one of the new strains revealed that the average nucleotide identity (ANI) between its genome and the reference genome of S. octosporus is 90.43% and there exist major genome rearrangements between the two genomes. Mating analysis revealed that S. octosporus and one of the new strains are completely reproductively separated. A strong prezygotic barrier exists and the few mating products consist of diploid hybrids that do not form recombinant ascospores. In the new strains, asci are either zygotic, arising from conjugation, or they develop without conjugation from asexual cells (azygotic). Compared to the currently recognized Schizosaccharomyces species, the spectrum of nutrients that are assimilated by the new strains is restricted. Of the 43 carbohydrates that were included in the physiological standard tests, only 7 were assimilated. According to the results of the genome sequence analysis, the mating trials, and the phenotypic characterization, the new species Schizosaccharomyces lindneri is described to accommodate the two strains (holotype: CBS 18203T and ex-type: MUCL 58363; MycoBank no.: MB 847838).
Collapse
Affiliation(s)
- Michael Brysch-Herzberg
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University of Applied Sciences, Heilbronn, Germany
| | - Guo-Song Jia
- National Institute of Biological Sciences, Beijing, China
| | - Matthias Sipiczki
- Department of Genetics and Applied Microbiology, University of Debrecen, Debrecen, Hungary
| | - Martin Seidel
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University of Applied Sciences, Heilbronn, Germany
| | - Wen Li
- National Institute of Biological Sciences, Beijing, China
| | - Imen Assali
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University of Applied Sciences, Heilbronn, Germany
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| |
Collapse
|
9
|
Peris D, Ubbelohde EJ, Kuang MC, Kominek J, Langdon QK, Adams M, Koshalek JA, Hulfachor AB, Opulente DA, Hall DJ, Hyma K, Fay JC, Leducq JB, Charron G, Landry CR, Libkind D, Gonçalves C, Gonçalves P, Sampaio JP, Wang QM, Bai FY, Wrobel RL, Hittinger CT. Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces. Nat Commun 2023; 14:690. [PMID: 36755033 PMCID: PMC9908912 DOI: 10.1038/s41467-023-36139-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 01/17/2023] [Indexed: 02/10/2023] Open
Abstract
Species is the fundamental unit to quantify biodiversity. In recent years, the model yeast Saccharomyces cerevisiae has seen an increased number of studies related to its geographical distribution, population structure, and phenotypic diversity. However, seven additional species from the same genus have been less thoroughly studied, which has limited our understanding of the macroevolutionary events leading to the diversification of this genus over the last 20 million years. Here, we show the geographies, hosts, substrates, and phylogenetic relationships for approximately 1,800 Saccharomyces strains, covering the complete genus with unprecedented breadth and depth. We generated and analyzed complete genome sequences of 163 strains and phenotyped 128 phylogenetically diverse strains. This dataset provides insights about genetic and phenotypic diversity within and between species and populations, quantifies reticulation and incomplete lineage sorting, and demonstrates how gene flow and selection have affected traits, such as galactose metabolism. These findings elevate the genus Saccharomyces as a model to understand biodiversity and evolution in microbial eukaryotes.
Collapse
Grants
- R01 GM080669 NIGMS NIH HHS
- T32 GM007133 NIGMS NIH HHS
- We thank the University of Wisconsin Biotechnology Center DNA Sequencing Facility for providing Illumina and Sanger sequencing facilities and services; Maria Sardi, Audrey Gasch, and Ursula Bond for providing strains; Sean McIlwain for providing guidance for genome ultra-scaffolding; Yury V. Bukhman for discussing applications of the Growth Curve Analysis Tool (GCAT); Mick McGee for HPLC analysis; Raúl Ortíz-Merino for assistance during YGAP annotations; Jessica Leigh for assistance with PopART; Cecile Ané for suggestions about BUCKy utilization and phylogenetic network analyses; Samina Naseeb and Daniela Delneri for sharing preliminary multi-locus Saccharomyces jurei data; and Branden Timm, Brian Kyle, and Dan Metzger for computational assistance. Some computations were performed on Tirant III of the Spanish Supercomputing Network (‘‘Servei d’Informàtica de la Universitat de València”) under the project BCV-2021-1-0001 granted to DP, while others were performed at the Wisconsin Energy Institute and the Center for High-Throughput Computing of the University of Wisconsin-Madison. During a portion of this project, DP was a researcher funded by the European Union’s Horizon 2020 research and innovation programme Marie Sklodowska-Curie, grant agreement No. 747775, the Research Council of Norway (RCN) grant Nos. RCN 324253 and 274337, and the Generalitat Valenciana plan GenT grant No. CIDEGENT/2021/039. DP is a recipient of an Illumina Grant for Illumina Sequencing Saccharomyces strains in this study. QKL was supported by the National Science Foundation under Grant No. DGE-1256259 (Graduate Research Fellowship) and the Predoctoral Training Program in Genetics, funded by the National Institutes of Health (5T32GM007133). This material is based upon work supported in part by the Great Lakes Bioenergy Research Center, Office of Science, Office of Biological and Environmental Research under Award Numbers DE-SC0018409 and DE-FC02-07ER64494; the National Science Foundation under Grant Nos. DEB-1253634, DEB-1442148, and DEB-2110403; and the USDA National Institute of Food and Agriculture Hatch Project Number 1020204. C.T.H. is an H. I. Romnes Faculty Fellow, supported by the Office of the Vice Chancellor for Research and Graduate Education with funding from Wisconsin Alumni Research Foundation. QMW was supported by the National Natural Science Foundation of China (NSFC) under Grant Nos. 31770018 and 31961133020. CRL holds the Canada Research Chair in Cellular Systems and Synthetic Biology, and his research on wild yeast is supported by a NSERC Discovery Grant.
Collapse
Affiliation(s)
- David Peris
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway.
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Spain.
| | - Emily J Ubbelohde
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Meihua Christina Kuang
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
| | - Jacek Kominek
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Quinn K Langdon
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
| | - Marie Adams
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Justin A Koshalek
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Amanda Beth Hulfachor
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Dana A Opulente
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Katie Hyma
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Justin C Fay
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Jean-Baptiste Leducq
- Departement des Sciences Biologiques, Université de Montréal, Montreal, QC, Canada
- Département de Biologie, PROTEO, Pavillon Charles‑Eugène‑Marchand, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Guillaume Charron
- Canada Natural Resources, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Christian R Landry
- Département de Biologie, PROTEO, Pavillon Charles‑Eugène‑Marchand, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Consejo Nacional de Investigaciones, Científicas y Técnicas (CONICET)-Universidad Nacional del Comahue, Bariloche, Argentina
| | - Carla Gonçalves
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
- Vanderbilt University, Department of Biological Sciences, Nashville, TN, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Paula Gonçalves
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - José Paulo Sampaio
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Qi-Ming Wang
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Russel L Wrobel
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
10
|
Chavan AR, Singh AK, Gupta RK, Nakhate SP, Poddar BJ, Gujar VV, Purohit HJ, Khardenavis AA. Recent trends in the biotechnology of functional non-digestible oligosaccharides with prebiotic potential. Biotechnol Genet Eng Rev 2023:1-46. [PMID: 36714949 DOI: 10.1080/02648725.2022.2152627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 11/13/2022] [Indexed: 01/31/2023]
Abstract
Prebiotics as a part of dietary nutrition can play a crucial role in structuring the composition and metabolic function of intestinal microbiota and can thus help in managing a clinical scenario by preventing diseases and/or improving health. Among the different prebiotics, non-digestible carbohydrates are molecules that selectively enrich a typical class of bacteria with probiotic potential. This review summarizes the current knowledge about the different aspects of prebiotics, such as its production, characterization and purification by various techniques, and its link to novel product development at an industrial scale for wide-scale use in diverse range of health management applications. Furthermore, the path to effective valorization of agricultural residues in prebiotic production has been elucidated. This review also discusses the recent developments in application of genomic tools in the area of prebiotics for providing new insights into the taxonomic characterization of gut microorganisms, and exploring their functional metabolic pathways for enzyme synthesis. However, the information regarding the cumulative effect of prebiotics with beneficial bacteria, their colonization and its direct influence through altered metabolic profile is still getting established. The future of this area lies in the designing of clinical condition specific functional foods taking into consideration the host genotypes, thus facilitating the creation of balanced and required metabolome and enabling to maintain the healthy status of the host.
Collapse
Affiliation(s)
- Atul Rajkumar Chavan
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ashish Kumar Singh
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rakesh Kumar Gupta
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Suraj Prabhakarrao Nakhate
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Bhagyashri Jagdishprasad Poddar
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Vaibhav Vilasrao Gujar
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, India
- JoVE, Mumbai, India
| | - Hemant J Purohit
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Anshuman Arun Khardenavis
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
11
|
Chou JY, Hsu PC, Leu JY. Enforcement of Postzygotic Species Boundaries in the Fungal Kingdom. Microbiol Mol Biol Rev 2022; 86:e0009822. [PMID: 36098649 PMCID: PMC9769731 DOI: 10.1128/mmbr.00098-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Understanding the molecular basis of speciation is a primary goal in evolutionary biology. The formation of the postzygotic reproductive isolation that causes hybrid dysfunction, thereby reducing gene flow between diverging populations, is crucial for speciation. Using various advanced approaches, including chromosome replacement, hybrid introgression and transcriptomics, population genomics, and experimental evolution, scientists have revealed multiple mechanisms involved in postzygotic barriers in the fungal kingdom. These results illuminate both unique and general features of fungal speciation. Our review summarizes experiments on fungi exploring how Dobzhansky-Muller incompatibility, killer meiotic drive, chromosome rearrangements, and antirecombination contribute to postzygotic reproductive isolation. We also discuss possible evolutionary forces underlying different reproductive isolation mechanisms and the potential roles of the evolutionary arms race under the Red Queen hypothesis and epigenetic divergence in speciation.
Collapse
Affiliation(s)
- Jui-Yu Chou
- Department of Biology, National Changhua University of Education, Changhua, Taiwan
| | - Po-Chen Hsu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| |
Collapse
|
12
|
Gostinčar C, Sun X, Černoša A, Fang C, Gunde-Cimerman N, Song Z. Clonality, inbreeding, and hybridization in two extremotolerant black yeasts. Gigascience 2022; 11:giac095. [PMID: 36200832 PMCID: PMC9535773 DOI: 10.1093/gigascience/giac095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/29/2022] [Accepted: 09/12/2022] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND The great diversity of lifestyles and survival strategies observed in fungi is reflected in the many ways in which they reproduce and recombine. Although a complete absence of recombination is rare, it has been reported for some species, among them 2 extremotolerant black yeasts from Dothideomycetes: Hortaea werneckii and Aureobasidium melanogenum. Therefore, the presence of diploid strains in these species cannot be explained as the product of conventional sexual reproduction. RESULTS Genome sequencing revealed that the ratio of diploid to haploid strains in both H. werneckii and A. melanogenum is about 2:1. Linkage disequilibrium between pairs of polymorphic loci and a high degree of concordance between the phylogenies of different genomic regions confirmed that both species are clonal. Heterozygosity of diploid strains is high, with several hybridizing genome pairs reaching the intergenomic distances typically seen between different fungal species. The origin of diploid strains collected worldwide can be traced to a handful of hybridization events that produced diploids, which were stable over long periods of time and distributed over large geographic areas. CONCLUSIONS Our results, based on the genomes of over 100 strains of 2 black yeasts, show that although they are clonal, they occasionally form stable and highly heterozygous diploid intraspecific hybrids. The mechanism of these apparently rare hybridization events, which are not followed by meiosis or haploidization, remains unknown. Both extremotolerant yeasts, H. werneckii and even more so A. melanogenum, a close relative of the intensely recombining and biotechnologically relevant Aureobasidium pullulans, provide an attractive model for studying the role of clonality and ploidy in extremotolerant fungi.
Collapse
Affiliation(s)
- Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Xiaohuan Sun
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Anja Černoša
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Chao Fang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Zewei Song
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| |
Collapse
|
13
|
Bozdag GO, Ono J. Evolution and molecular bases of reproductive isolation. Curr Opin Genet Dev 2022; 76:101952. [PMID: 35849861 PMCID: PMC10210581 DOI: 10.1016/j.gde.2022.101952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/31/2022] [Accepted: 06/14/2022] [Indexed: 11/03/2022]
Abstract
The most challenging problem in speciation research is disentangling the relative strength and order in which different reproductive barriers evolve. Here, we review recent developments in the study of reproductive isolation in yeasts. With over a thousand genome-sequenced isolates readily available for testing the viability, sterility, and fitness of both intraspecies and interspecies hybrid crosses, Saccharomyces yeasts are an ideal model to study such fundamental questions. Our survey demonstrates that, while chromosomal-level mutations are widespread at the intraspecific level, anti-recombination-driven chromosome missegregation is the primary reproductive barrier between species. Finally, despite their strength, all of these postzygotic barriers can be resolved through the asexual life history of hybrids.
Collapse
Affiliation(s)
- G Ozan Bozdag
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA. https://twitter.com/ozan_g_b
| | - Jasmine Ono
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.
| |
Collapse
|
14
|
Mapook A, Hyde KD, Hassan K, Kemkuignou BM, Čmoková A, Surup F, Kuhnert E, Paomephan P, Cheng T, de Hoog S, Song Y, Jayawardena RS, Al-Hatmi AMS, Mahmoudi T, Ponts N, Studt-Reinhold L, Richard-Forget F, Chethana KWT, Harishchandra DL, Mortimer PE, Li H, Lumyong S, Aiduang W, Kumla J, Suwannarach N, Bhunjun CS, Yu FM, Zhao Q, Schaefer D, Stadler M. Ten decadal advances in fungal biology leading towards human well-being. FUNGAL DIVERS 2022; 116:547-614. [PMID: 36123995 PMCID: PMC9476466 DOI: 10.1007/s13225-022-00510-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/28/2022] [Indexed: 11/04/2022]
Abstract
Fungi are an understudied resource possessing huge potential for developing products that can greatly improve human well-being. In the current paper, we highlight some important discoveries and developments in applied mycology and interdisciplinary Life Science research. These examples concern recently introduced drugs for the treatment of infections and neurological diseases; application of -OMICS techniques and genetic tools in medical mycology and the regulation of mycotoxin production; as well as some highlights of mushroom cultivaton in Asia. Examples for new diagnostic tools in medical mycology and the exploitation of new candidates for therapeutic drugs, are also given. In addition, two entries illustrating the latest developments in the use of fungi for biodegradation and fungal biomaterial production are provided. Some other areas where there have been and/or will be significant developments are also included. It is our hope that this paper will help realise the importance of fungi as a potential industrial resource and see the next two decades bring forward many new fungal and fungus-derived products.
Collapse
Affiliation(s)
- Ausana Mapook
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
| | - Kevin D. Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, 50200 Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200 Thailand
- Innovative Institute of Plant Health, Zhongkai University of Agriculture and Engineering, Haizhu District, Guangzhou, 510225 China
| | - Khadija Hassan
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Brunswick, Germany
| | - Blondelle Matio Kemkuignou
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Brunswick, Germany
| | - Adéla Čmoková
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Frank Surup
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Brunswick, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Brunswick, Germany
| | - Eric Kuhnert
- Centre of Biomolecular Drug Research (BMWZ), Institute for Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Pathompong Paomephan
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Brunswick, Germany
- Department of Biotechnology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok, 10400 Thailand
| | - Tian Cheng
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Brunswick, Germany
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Sybren de Hoog
- Center of Expertise in Mycology, Radboud University Medical Center / Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Guizhou Medical University, Guiyang, China
- Microbiology, Parasitology and Pathology Graduate Program, Federal University of Paraná, Curitiba, Brazil
| | - Yinggai Song
- Department of Dermatology, Peking University First Hospital, Peking University, Beijing, China
| | - Ruvishika S. Jayawardena
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, 57100 Thailand
| | - Abdullah M. S. Al-Hatmi
- Center of Expertise in Mycology, Radboud University Medical Center / Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Nadia Ponts
- INRAE, UR1264 Mycology and Food Safety (MycSA), 33882 Villenave d’Ornon, France
| | - Lena Studt-Reinhold
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln an der Donau, Austria
| | | | - K. W. Thilini Chethana
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, 57100 Thailand
| | - Dulanjalee L. Harishchandra
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 China
| | - Peter E. Mortimer
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
| | - Huili Li
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
| | - Saisamorm Lumyong
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, 50200 Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200 Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok, 10300 Thailand
| | - Worawoot Aiduang
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200 Thailand
| | - Jaturong Kumla
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, 50200 Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200 Thailand
| | - Nakarin Suwannarach
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, 50200 Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200 Thailand
| | - Chitrabhanu S. Bhunjun
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, 57100 Thailand
| | - Feng-Ming Yu
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- Yunnan Key Laboratory of Fungal Diversity and Green Development, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
| | - Qi Zhao
- Yunnan Key Laboratory of Fungal Diversity and Green Development, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
| | - Doug Schaefer
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
| | - Marc Stadler
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Brunswick, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Brunswick, Germany
| |
Collapse
|
15
|
Kachalkin AV. Phylogeny of Rhodotorula pinalis and Its Reclassification as Fellozyma pinalis comb. nov. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722100915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
16
|
Palma M, Vieira É, Pataco M, Sá-Correia I. Characterization of a new Blastobotrys navarrensis strain indicates that it is not a later synonym of Blastobotrys proliferans. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The species Blastobotrys navarrensis Sesma and Ramirez was delineated based on the description of the single strain CBS 139.77T. Based on its phenotypic similarities to Blastobotrys proliferans, B. navarrensis CBS 139.77T was later considered a synonym of B. proliferans. In the present study, we isolated the yeast strain IST 508 (=PYCC 8784=CBS 16671) from the soil surrounding an olive tree in Ferreira do Alentejo, Portugal. The phylogenetic analysis of D1/D2 domain and ITS sequences from strain IST 508 indicates that is closely related to B. navarrensis and B. proliferans. Although strain IST 508 differs from B. navarrensis CBS 139.77T by 14 substitutions and 20 indels (6.6 % divergence) in the ITS sequence, no divergence was detected at the level of D1/D2 domain, mitochondrial small subunit rDNA, and cytochrome oxidase II sequences. On the other hand, strains IST 508 and CBS 139.77 differ from B. proliferans NRRL Y-17577T by eight substitutions (1.4 % divergence) in the D1/D2 domain sequence, by 16 substitutions (2.7 % divergence) in the cytochrome oxidase II sequence, and by 16 substitutions (3.7 % divergence) in the mitochondrial small subunit rDNA sequence. Due to the high number of variable phenotypic tests in B. proliferans and B. navarrensis, strains from the two species are difficult to distinguish. Contrasting with what is described for other Blastobotrys species, no differences were detected at the level of micromorphology between the two species. Nevertheless, based on the molecular differences between the two strains, CBS 139.77 and IST 508, and B. proliferans NRRL Y-17577T and their phylogenetic analysis, strains CBS 139.77 and IST 508 are from B. navarrensis and this species should be considered as an independent species and not a later synonym of B. proliferans. We propose an emended description of B. navarrensis.
Collapse
Affiliation(s)
- Margarida Palma
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Érica Vieira
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Margarida Pataco
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Isabel Sá-Correia
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| |
Collapse
|
17
|
Forecasting the number of species of asexually reproducing fungi (Ascomycota and Basidiomycota). FUNGAL DIVERS 2022. [DOI: 10.1007/s13225-022-00500-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
18
|
Taxonomic Revision of the pulcherrima Clade of Metschnikowia (Fungi): Merger of Species. TAXONOMY 2022. [DOI: 10.3390/taxonomy2010009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The type strains of 10 small-spored species of the ascomycetous yeast genus Metschnikowia usually form a compact group on the phylogenetic trees inferred from barcode sequences. Based on the name of the species, which was described first (Metschnikowia pulcherrima), the group is frequently referred to as the pulcherrima clade. All strains produce the iron-chelate pigment pulcherrimin and have antagonistic effects on many microorganisms. Recent results of molecular phylogenetic, genetic, and genomic research raised doubts about the taxonomic division of the clade. Those data—combined with results obtained in this study by comprehensive analysis of primary and secondary barcode sequences, physiological tests, and hybridisation experiments—demonstrate that the species cannot be distinguished from each other by the criteria of any of the phenotypic, phylogenetic, and biological species concepts. Therefore, I propose that the species of the pulcherrima clade be merged into one species under the oldest species name, M. pulcherrima.
Collapse
|
19
|
Description of Crinitomyces reliqui gen. nov., sp. nov. and Reassignment of Trichosporiella flavificans and Candida ghanaensis to the Genus Crinitomyces. J Fungi (Basel) 2022; 8:jof8030224. [PMID: 35330226 PMCID: PMC8953626 DOI: 10.3390/jof8030224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/20/2022] [Accepted: 02/22/2022] [Indexed: 11/17/2022] Open
Abstract
The systematic position of 16 yeast strains isolated from Thailand, Hungary, The Netherlands, and the Republic of Poland were evaluated using morphological, physiological, and phylogenetic analyses. Based on the similarity of the D1/D2 domain of the LSU rRNA gene, the strains were assigned to two distinct species, Trichosporiella flavificans and representatives of a new yeast species. Phylogenetic analyses revealed that Candida ghanaensis CBS 8798T showed a strong relationship with the aforementioned two species. The more fascinating issue is that Candida and Trichosporiella genera have been placed in different subphyla, Saccharomycotina and Pezizomycotina, respectively. The close relationship between Trichosporiella flavificans, Candida ghanaensis and the undescribed species was unexpected and needed to be clarified. As for morphological and physiological characteristics, the three yeast species shared a hairy colony appearance and an ability to assimilate 18 carbon sources. Based on phylogenetic analyses carried out in the present study, Crinitomyces gen. nov. was proposed to accommodate the new yeast species, Crinitomyces reliqui sp. nov. (Holotype: TBRC 15054, Isotypes: DMKU-FW23-23 and PYCC 9001). In addition, the two species Trichosporiella flavificans and Candida ghanaensis were reassigned to the genus Crinitomyces as, Crinitomyces flavificans (Type: CBS 760.79) comb. nov. and Crinitomyces ghanaensis (Type: CBS 8798) comb. nov., respectively.
Collapse
|
20
|
Li YY, Wang MM, Groenewald M, Li AH, Guo YT, Wu F, Zhang BQ, Tanaka E, Wang QM, Bai FY, Begerow D. Proposal of Two New Combinations, Twenty New Species, Four New Genera, One New Family, and One New Order for the Anamorphic Basidiomycetous Yeast Species in Ustilaginomycotina. Front Microbiol 2022; 12:777338. [PMID: 35222295 PMCID: PMC8880017 DOI: 10.3389/fmicb.2021.777338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/26/2021] [Indexed: 12/02/2022] Open
Abstract
Two hundred and forty-four ustilaginomycetous yeast or yeast-like strains were isolated from the soil, skin of animals or humans and plant materials during the past 20 years. Among them, 203 strains represent 39 known species, whereas 41 strains represent several novel species based on the sequence analyses of the rDNA genes [18S rDNA, Internal Transcribed Spacer (ITS) regions, 26S rDNA D1/D2 domain] and three protein genes (RPB1, RPB2, and TEF1). In this study, one new order, one new family, four new genera, twenty new species, and two new combinations were proposed. They are Franziozymales ord. nov., Franziozymaceae fam. nov., Baueromyces gen. nov., Franziozyma gen. nov., Guomyces gen. nov., Yunzhangomyces gen. nov., Baueromyces planticola sp. nov., Franziozyma bambusicola sp. nov., Gjaerumia cyclobalanopsidis sp. nov., Gjaerumia pseudominor sp. nov., Jamesdicksonia aceris sp. nov., Jaminaea lantanae sp. nov., Kalmanozyma hebeiensis sp. nov., Langdonia ligulariae sp. nov., Meira hainanensis sp. nov., Meira pileae sp. nov., Meira plantarum sp. nov., Phragmotaenium parafulvescens sp. nov., Sporisorium cylindricum sp. nov., Sympodiomycopsis europaea sp. nov., Tilletiopsis lunata sp. nov., Tilletiopsis pinicola sp. nov., Yunzhangomyces clavatus sp. nov., Yunzhangomyces cylindricus sp. nov., Yunzhangomyces qinlingensis sp. nov., Yunzhangomyces orchidis sp. nov., Guomyces nicotianae comb. nov., and Yunzhangomces scirpi comb. nov.
Collapse
Affiliation(s)
- Yao-Yao Li
- Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Man-Man Wang
- Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | | | - Ai-Hua Li
- China General Microbiological Culture Collection Center and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yun-Tong Guo
- Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Feng Wu
- Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Bing-Qian Zhang
- Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Eiji Tanaka
- Department of Environmental Science, Ishikawa Prefectural University, Nonoichi, Japan
| | - Qi-Ming Wang
- Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Dominik Begerow
- Department of Evolution of Plants and Fungi, Ruhr-Universität Bochum, Bochum, Germany
| |
Collapse
|
21
|
Mozzachiodi S, Bai FY, Baldrian P, Bell G, Boundy-Mills K, Buzzini P, Čadež N, Riffo FC, Dashko S, Dimitrov R, Fisher KJ, Gibson BR, Gouliamova D, Greig D, Heistinger L, Hittinger CT, Jecmenica M, Koufopanou V, Landry CR, Mašínová T, Naumova ES, Opulente D, Peña JJ, Petrovič U, Tsai IJ, Turchetti B, Villarreal P, Yurkov A, Liti G, Boynton P. Yeasts from temperate forests. Yeast 2022; 39:4-24. [PMID: 35146791 DOI: 10.1002/yea.3699] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Yeasts are ubiquitous in temperate forests. While this broad habitat is well-defined, the yeasts inhabiting it and their life cycles, niches, and contributions to ecosystem functioning are less understood. Yeasts are present on nearly all sampled substrates in temperate forests worldwide. They associate with soils, macroorganisms, and other habitats, and no doubt contribute to broader ecosystem-wide processes. Researchers have gathered information leading to hypotheses about yeasts' niches and their life cycles based on physiological observations in the laboratory as well as genomic analyses, but the challenge remains to test these hypotheses in the forests themselves. Here we summarize the habitat and global patterns of yeast diversity, give some information on a handful of well-studied temperate forest yeast genera, discuss the various strategies to isolate forest yeasts, and explain temperate forest yeasts' contributions to biotechnology. We close with a summary of the many future directions and outstanding questions facing researchers in temperate forest yeast ecology. Yeasts present an exciting opportunity to better understand the hidden world of microbial ecology in this threatened and global habitat.
Collapse
Affiliation(s)
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha 4, Czech Republic
| | - Graham Bell
- Biology Department and Redpath Museum, McGill University, Québec, Canada
| | - Kyria Boundy-Mills
- Department of Food Science and Technology, University of California Davis, Davis, CA, USA
| | - Pietro Buzzini
- Department of Agriculture, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Italy
| | - Neža Čadež
- Biotechnical Faculty, Food Science and Technology Department, University of Ljubljana, Ljubljana, Slovenia
| | - Francisco Cubillos Riffo
- Universidad de Santiago de Chile, Facultad de Química y Biología, Departamento de Biología, Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Sofia Dashko
- DSM Food Specialties, Center for Food Innovation, AX, Delft, The Netherlands
| | - Roumen Dimitrov
- Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Kaitlin J Fisher
- Laboratory of Genetics, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | - Brian R Gibson
- Technische Universität Berlin, Institute of Food Technology and Food Chemistry, Chair of Brewing and Beverage Technology, Berlin, Germany
| | - Dilnora Gouliamova
- Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Duncan Greig
- Centre for Life's Origins and Evolution, University College London, London, UK
| | - Lina Heistinger
- ETH Zurich, Department of Biology, Institute of Biochemistry, Switzerland
| | - Chris Todd Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Christian R Landry
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Canada.,PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Canada.,Centre de Recherche sur les Données Massives, Université Laval, Canada.,Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Canada
| | - Tereza Mašínová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha 4, Czech Republic
| | - Elena S Naumova
- State Research Institute of Genetics and Selection of Industrial Microorganisms of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Dana Opulente
- Department of Biology, Villanova University, Villanova, Pennsylvania, USA
| | | | - Uroš Petrovič
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia.,Jožef Stefan Institute, Department of Molecular and Biomedical Sciences, Ljubljana, Slovenia
| | | | - Benedetta Turchetti
- Department of Agriculture, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Italy
| | - Pablo Villarreal
- Universidad de Santiago de Chile, Facultad de Química y Biología, Departamento de Biología, Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Andrey Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Gianni Liti
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | | |
Collapse
|
22
|
Abstract
AbstractYeasts, usually defined as unicellular fungi, occur in various fungal lineages. Hence, they are not a taxonomic unit, but rather represent a fungal lifestyle shared by several unrelated lineages. Although the discovery of new yeast species occurs at an increasing speed, at the current rate it will likely take hundreds of years, if ever, before they will all be documented. Many parts of the earth, including many threatened habitats, remain unsampled for yeasts and many others are only superficially studied. Cold habitats, such as glaciers, are home to a specific community of cold-adapted yeasts, and, hence, there is some urgency to study such environments at locations where they might disappear soon due to anthropogenic climate change. The same is true for yeast communities in various natural forests that are impacted by deforestation and forest conversion. Many countries of the so-called Global South have not been sampled for yeasts, despite their economic promise. However, extensive research activity in Asia, especially China, has yielded many taxonomic novelties. Comparative genomics studies have demonstrated the presence of yeast species with a hybrid origin, many of them isolated from clinical or industrial environments. DNA-metabarcoding studies have demonstrated the prevalence, and in some cases dominance, of yeast species in soils and marine waters worldwide, including some surprising distributions, such as the unexpected and likely common presence of Malassezia yeasts in marine habitats.
Collapse
|
23
|
Cao B, Haelewaters D, Schoutteten N, Begerow D, Boekhout T, Giachini AJ, Gorjón SP, Gunde-Cimerman N, Hyde KD, Kemler M, Li GJ, Liu DM, Liu XZ, Nuytinck J, Papp V, Savchenko A, Savchenko K, Tedersoo L, Theelen B, Thines M, Tomšovský M, Toome-Heller M, Urón JP, Verbeken A, Vizzini A, Yurkov AM, Zamora JC, Zhao RL. Delimiting species in Basidiomycota: a review. FUNGAL DIVERS 2021. [DOI: 10.1007/s13225-021-00479-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
24
|
|