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Glushakova A, Tepeeva A, Prokof'eva T, Kachalkin A. Culturable yeast diversity in urban topsoil influenced by various anthropogenic impacts. Int Microbiol 2024; 27:1383-1403. [PMID: 38263536 DOI: 10.1007/s10123-024-00482-1] [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: 11/11/2023] [Revised: 12/18/2023] [Accepted: 01/10/2024] [Indexed: 01/25/2024]
Abstract
In urban ecosystems, processes associated with anthropogenic influences almost always lead to changes in soil micromycete complexes. The taxonomic structure of soil micromycete complexes is an important informative parameter of soil bioindication in the ecological control of urban environments. Unicellular fungi, such as culturable yeasts, are a very suitable and promising object of microbiological research for monitoring urban topsoil. This review aims to give an overview of the yeast communities in urban topsoil in different areas of Moscow (heating main area, household waste storage and disposal area, highway area) and to discuss the changes in the taxonomic structure of culturable yeast complexes depending on the type and intensity of anthropogenic impact.
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Affiliation(s)
- Anna Glushakova
- Soil Science Faculty, Lomonosov Moscow State University, 119991, Moscow, Russia.
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064, Russia.
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of RAS, Pushchino, 142290, Russia.
| | - Aleksandra Tepeeva
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of RAS, Pushchino, 142290, Russia
| | - Tatiana Prokof'eva
- Soil Science Faculty, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Aleksey Kachalkin
- Soil Science Faculty, Lomonosov Moscow State University, 119991, Moscow, Russia
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of RAS, Pushchino, 142290, Russia
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Glushakova A, Sharova A, Kachalkin A. Seasonal Dynamics of Culturable Yeasts in Ornithogenically Influenced Soils in a Temperate Forest and Evaluation of Extracellular Enzyme Secretion in Tausonia pullulans at Different Temperatures. J Fungi (Basel) 2024; 10:532. [PMID: 39194858 DOI: 10.3390/jof10080532] [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: 06/13/2024] [Revised: 07/26/2024] [Accepted: 07/28/2024] [Indexed: 08/29/2024] Open
Abstract
The culturable yeast communities in temperate forest soils under the ornithogenic influence were studied in a seasonal dynamic. To investigate the intense ornithogenic influence, conventional and "live" feeders were used, which were attached to trees in the forest and constantly replenished throughout the year. It was found that the yeast abundance in the soil under strong ornithogenic influence reached the highest values in winter compared to the other seasons and amounted to 4.8 lg (cfu/g). This was almost an order of magnitude higher than the minimum value of yeast abundance in ornithogenic soils determined for summer. A total of 44 yeast species, 21 ascomycetes and 23 basidiomycetes, were detected in ornithogenic soil samples during the year. These included soil-related species (Barnettozyma californica, Cyberlindnera misumaiensis, Cutaneotrichosporon moniliiforme, Goffeauzyma gastrica, Holtermanniella festucosa, Leucosporidium creatinivorum, L. yakuticum, Naganishia adeliensis, N. albidosimilis, N. globosa, Tausonia pullulans, and Vanrija albida), eurybionts (yeast-like fungus Aureobasidium pullulans, Debaryomyces hansenii, and Rhodotorula mucilaginosa), inhabitants of plant substrates and litter (Cystofilobasidium capitatum, Cys. infirmominiatum, Cys. macerans, Filobasidium magnum, Hanseniaspora uvarum, Metschnikowia pulcherrima, and Rh. babjevae) as well as a group of pathogenic and opportunistic yeast species (Arxiozyma bovina, Candida albicans, C. parapsilosis, C. tropicalis, Clavispora lusitaniae, and Nakaseomyces glabratus). Under an ornithogenic influence, the diversity of soil yeasts was higher compared to the control, confirming the uneven distribution of yeasts in temperate forest soils and their dependence on natural hosts and vectors. Interestingly, the absolute dominant species in ornithogenic soils in winter (when the topsoil temperature was below zero) was the basidiomycetous psychrotolerant yeast T. pullulans. It is regularly observed in various soils in different geographical regions. Screening of the hydrolytic activity of 50 strains of this species at different temperatures (2, 4, 10, 15 and 20 °C) showed that the activity of esterases, lipases and proteases was significantly higher at the cultivation temperature. Ornithogenic soils could be a source for the relatively easy isolation of a large number of strains of the psychrotolerant yeast T. pullulans to test, study and optimize their potential for the production of cold-adapted enzymes for industry.
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Affiliation(s)
- Anna Glushakova
- Soil Science Faculty, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
- I.I. Mechnikov Research Institute of Vaccines and Sera, 105064 Moscow, Russia
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of RAS, 142290 Pushchino, Russia
| | - Anna Sharova
- Institute for African Studies of RAS, 123001 Moscow, Russia
| | - Aleksey Kachalkin
- Soil Science Faculty, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of RAS, 142290 Pushchino, Russia
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3
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Glushakova A, Kachalkin A. Wild and partially synanthropic bird yeast diversity, in vitro virulence, and antifungal susceptibility of Candida parapsilosis and Candida tropicalis strains isolated from feces. Int Microbiol 2024; 27:883-897. [PMID: 37874524 DOI: 10.1007/s10123-023-00437-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/20/2023] [Accepted: 10/16/2023] [Indexed: 10/25/2023]
Abstract
Yeast complexes in the fecal samples of wild (Dendrocopos major, Picus viridis) and partially synanthropic (Bombycilla garrulus, Garrulus glandarius, Pica pica, and Pyrrhula pyrrhula) birds were studied in a forest ecosystem during winter. A total of 18 yeast species were identified: 16 ascomycetes and two basidiomycetes belonging to five subphyla of fungi: Saccharomycotina (15), Pezizomycotina (1), Agaricomycotina (1), and Pucciniomycotina (1). Most yeast species were found in the fecal samples of P. pyrrhula (Candida parapsilosis, C. zeylanoides, Debaryomyces hansenii, Hanseniaspora uvarum, Metschnikowia pulcherrima, Meyerozyma carpophila, M. guilliermondii, Rhodotorula mucilaginosa); the lowest number of yeast species was observed in the feces of B. garrulus (C. parapsilosis, C. zeylanoides, Met. pulcherrima, and Rh. mucilaginosa). The opportunistic species of the genus Candida were found only in feces of partially synanthropic birds: C. parapsilosis was observed in the feces of B. garrulus, G. glandarius, P. pica, and P. pyrrhula; its relative abundance was 69.3%, 49.1%, 10.5%, and 1.1%, respectively; C. tropicalis was observed in the feces of P. pica and G. glandarius; its relative abundance was 54.6% and 7.1%, respectively. Strains of C. parapsilosis and C. tropicalis isolated from the feces of partially synanthropic birds were evaluated for their susceptibility to conventional antifungal agents (fluconazole, voriconazole, amphotericin B) and hydrolytic activity. A total of 160 strains were studied. Resistance to fluconazole was detected in 86.8% of C. parapsilosis strains and in 87% of C. tropicalis strains; resistance to voriconazole was detected in 71.7% of C. parapsilosis and in 66.7% of C. tropicalis strains, and the lowest percentage of resistant strains was detected to amphotericin B, 2.8% and 3.7% in C. parapsilosis and C. tropicalis strains, respectively. Multiresistance was detected in one strain of C. parapsilosis isolated from P. pica feces and in one strain of C. tropicalis isolated from G. glandarius feces. Phospholipase and hemolysin activities in the strains of C. parapsilosis were low (mean Pz values of 0.93 and 0.91, respectively); protease activity was moderate (mean Pz value of 0.53). The ability to produce hydrolytic enzymes was higher in the isolated strains of C. tropicalis. The mean Pz values of phospholipase and hemolysin activities were moderate (mean Pz values of 0.63 and 0.60, respectively), whereas protease activity was high (mean Pz value of 0.32). Thus, wild and partially synanthropic birds play an important role in disseminating of various yeast species. These yeasts can enter the topsoil via feces and contribute to the formation of allochthonous and uneven soil yeast diversity in natural ecosystems. In addition, partially synanthropic birds can be vectors of virulent strains of opportunistic Candida species from urban environments to natural biotopes.
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Affiliation(s)
- Anna Glushakova
- Soil Science Faculty, Lomonosov Moscow State University, 119991, Moscow, Russia.
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064, Russia.
| | - Aleksey Kachalkin
- Soil Science Faculty, Lomonosov Moscow State University, 119991, Moscow, Russia
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of RAS, Pushchino, 142290, Russia
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Watanabe D, Hashimoto W. Adaptation of yeast Saccharomyces cerevisiae to grape-skin environment. Sci Rep 2023; 13:9279. [PMID: 37340058 DOI: 10.1038/s41598-023-35734-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/23/2023] [Indexed: 06/22/2023] Open
Abstract
Saccharomyces cerevisiae, an essential player in alcoholic fermentation during winemaking, is rarely found in intact grapes. Although grape-skin environment is unsuitable for S. cerevisiae's stable residence, Saccharomycetaceae-family fermentative yeasts can increase population on grape berries after colonization during raisin production. Here, we addressed adaptation of S. cerevisiae to grape-skin ecosystem. The yeast-like fungus Aureobasidium pullulans, a major grape-skin resident, exhibited broad spectrum assimilation of plant-derived carbon sources, including ω-hydroxy fatty acid, arising from degradation of plant cuticles. In fact, A. pullulans encoded and secreted possible cutinase-like esterase for cuticle degradation. When intact grape berries were used as a sole carbon source, such grape-skin associated fungi increased the accessibility to fermentable sugars by degrading and assimilating the plant cell wall and cuticle compounds. Their ability seems also helpful for S. cerevisiae to obtain energy through alcoholic fermentation. Thus, degradation and utilization of grape-skin materials by resident microbiota may account for their residence on grape-skin and S. cerevisiae's possible commensal behaviors. Conclusively, this study focused on the symbiosis between grape-skin microbiota and S. cerevisiae from the perspective of winemaking origin. Such plant-microbe symbiotic interaction may be a prerequisite for triggering spontaneous food fermentation.
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Affiliation(s)
- Daisuke Watanabe
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
- Laboratory of Applied Stress Microbiology, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Wataru Hashimoto
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan.
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Matraxia M, Alfonzo A, Prestianni R, Francesca N, Gaglio R, Todaro A, Alfeo V, Perretti G, Columba P, Settanni L, Moschetti G. Non-conventional yeasts from fermented honey by-products: Focus on Hanseniaspora uvarum strains for craft beer production. Food Microbiol 2021; 99:103806. [PMID: 34119099 DOI: 10.1016/j.fm.2021.103806] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/24/2021] [Accepted: 04/08/2021] [Indexed: 10/21/2022]
Abstract
The increasing interest in novel beer productions focused on non-Saccharomyces yeasts in order to pursue their potential in generating groundbreaking sensory profiles. Traditional fermented beverages represent an important source of yeast strains which could express interesting features during brewing. A total of 404 yeasts were isolated from fermented honey by-products and identified as Saccharomyces cerevisiae, Wickerhamomyces anomalus, Zygosaccharomyces bailii, Zygosaccharomyces rouxii and Hanseniaspora uvarum. Five H. uvarum strains were screened for their brewing capability. Interestingly, Hanseniaspora uvarum strains showed growth in presence of ethanol and hop and a more rapid growth than the control strain S. cerevisiae US-05. Even though all strains showed a very low fermentation power, their concentrations ranged between 7 and 8 Log cycles during fermentation. The statistical analyses showed significant differences among the strains and underlined the ability of YGA2 and YGA34 to grow rapidly in presence of ethanol and hop. The strain YGA34 showed the best technological properties and was selected for beer production. Its presence in mixed- and sequential-culture fermentations with US-05 did not influence attenuation and ethanol concentration but had a significant impact on glycerol and acetic acid concentrations, with a higher sensory complexity and intensity, representing promising co-starters during craft beer production.
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Affiliation(s)
- Michele Matraxia
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze 4, 90128, Palermo, Italy
| | - Antonio Alfonzo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze 4, 90128, Palermo, Italy
| | - Rosario Prestianni
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze 4, 90128, Palermo, Italy
| | - Nicola Francesca
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze 4, 90128, Palermo, Italy.
| | - Raimondo Gaglio
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze 4, 90128, Palermo, Italy
| | - Aldo Todaro
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze 4, 90128, Palermo, Italy
| | - Vincenzo Alfeo
- Italian Brewing Research Centre, Department of Agricultural, Food and Environmental Science, University of Perugia, 06126, Perugia, Italy
| | - Giuseppe Perretti
- Italian Brewing Research Centre, Department of Agricultural, Food and Environmental Science, University of Perugia, 06126, Perugia, Italy
| | - Pietro Columba
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze 4, 90128, Palermo, Italy
| | - Luca Settanni
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze 4, 90128, Palermo, Italy
| | - Giancarlo Moschetti
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze 4, 90128, Palermo, Italy
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Boyaci‐Gunduz CP, Erten H. Predominant yeasts in the sourdoughs collected from some parts of Turkey. Yeast 2020; 37:449-466. [DOI: 10.1002/yea.3500] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 12/12/2022] Open
Affiliation(s)
- Cennet Pelin Boyaci‐Gunduz
- Faculty of Agriculture, Food Engineering Department Cukurova University Adana Turkey
- Faculty of Engineering, Food Engineering Department Adana Alparslan Turkes Science and Technology University Adana Turkey
| | - Huseyin Erten
- Faculty of Agriculture, Food Engineering Department Cukurova University Adana Turkey
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Langdon QK, Peris D, Eizaguirre JI, Opulente DA, Buh KV, Sylvester K, Jarzyna M, Rodríguez ME, Lopes CA, Libkind D, Hittinger CT. Postglacial migration shaped the genomic diversity and global distribution of the wild ancestor of lager-brewing hybrids. PLoS Genet 2020; 16:e1008680. [PMID: 32251477 PMCID: PMC7162524 DOI: 10.1371/journal.pgen.1008680] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 04/16/2020] [Accepted: 02/18/2020] [Indexed: 01/19/2023] Open
Abstract
The wild, cold-adapted parent of hybrid lager-brewing yeasts, Saccharomyces eubayanus, has a complex and understudied natural history. The exploration of this diversity can be used both to develop new brewing applications and to enlighten our understanding of the dynamics of yeast evolution in the wild. Here, we integrate whole genome sequence and phenotypic data of 200 S. eubayanus strains, the largest collection known to date. S. eubayanus has a multilayered population structure, consisting of two major populations that are further structured into six subpopulations. Four of these subpopulations are found exclusively in the Patagonian region of South America; one is found predominantly in Patagonia and sparsely in Oceania and North America; and one is specific to the Holarctic ecozone. Plant host associations differed between subpopulations and between S. eubayanus and its sister species, Saccharomyces uvarum. S. eubayanus is most abundant and genetically diverse in northern Patagonia, where some locations harbor more genetic diversity than is found outside of South America, suggesting that northern Patagonia east of the Andes was a glacial refugium for this species. All but one subpopulation shows isolation-by-distance, and gene flow between subpopulations is low. However, there are strong signals of ancient and recent outcrossing, including two admixed lineages, one that is sympatric with and one that is mostly isolated from its parental populations. Using our extensive biogeographical data, we build a robust model that predicts all known and a handful of additional regions of the globe that are climatically suitable for S. eubayanus, including Europe where host accessibility and competitive exclusion by other Saccharomyces species may explain its continued elusiveness. We conclude that this industrially relevant species has rich natural diversity with many factors contributing to its complex distribution and natural history. The mysterious wild parent of hybrid-lager brewing yeasts, Saccharomyces eubayanus, has been known for less than 10 years. In this time, it has become clear that lager hybrids arose from a subpopulation that has only been isolated in Tibet and North Carolina, USA; but the global diversity of this species has been less explored. Here, we use whole genome sequencing data for 200 strains (174 newly sequenced) to investigate the genetic diversity and geographical distribution of S. eubayanus. We find that its extensive wild diversity is largely centered in northern Patagonia, which likely was a glacial refugium for this species as three of six subpopulations are endemic to this region. In contrast, S. eubayanus is rarely isolated outside of Patagonia. In North America, isolates are dominated by an invasive, near-clonal admixed lineage; the result of an outcrossing and migration event. All subpopulations are well-differentiated, with low gene flow between them. This genetic isolation of subpopulations could be due to ecological factors, such as plant host associations. With modeling, we find that many areas of the world are climatically suitable to S. eubayanus, including Europe, where it has never been isolated. We propose complex ancestries and rich ecologies underlie the global distribution and diversity of this elusive and industrially important species.
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Affiliation(s)
- Quinn K. Langdon
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
| | - David Peris
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, United States of America
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Spain
| | - Juan I. Eizaguirre
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC) – CONICET / Universidad Nacional del Comahue, Quintral 1250, Bariloche, Argentina
| | - Dana A. Opulente
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, United States of America
| | - Kelly V. Buh
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
| | - Kayla Sylvester
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, United States of America
| | - Martin Jarzyna
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, United States of America
| | - María E. Rodríguez
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas (PROBIEN, CONICET-UNCo), Neuquén, Argentina
| | - Christian A. Lopes
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas (PROBIEN, CONICET-UNCo), Neuquén, Argentina
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC) – CONICET / Universidad Nacional del Comahue, Quintral 1250, Bariloche, Argentina
- * E-mail: (CTH); (DL)
| | - Chris Todd Hittinger
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, United States of America
- * E-mail: (CTH); (DL)
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Kaplan E, Aktaş D, Önder Ş, Metin B, Döğen A, Oz Y, Ilkit M. Mating genotypes and susceptibility profiles of clinical isolates of Candida glabrata from Turkey. Mycoses 2019; 62:796-802. [PMID: 31134666 DOI: 10.1111/myc.12945] [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: 04/19/2019] [Revised: 05/20/2019] [Accepted: 05/21/2019] [Indexed: 12/01/2022]
Abstract
The sexual cycle of Candida glabrata is not known; however, genomic evidence is indicative of recombination among subpopulations and the genome harbours genes necessary for undergoing mating and meiosis, which may increase fitness. The relationship between specific mating type-like (MTL) loci and antifungal susceptibility is not well understood in C. glabrata. We investigated different combinations of clinical C. glabrata isolate mating types and their antifungal susceptibility profiles. Allele profiles of the mating genes of 103 clinical C. glabrata isolates were identified, and their antifungal susceptibility to azoles, echinocandins and amphotericin B were compared. The majority (88.3%) of screened isolates harboured the a allele in the locus. The MTL1, MTL2 and MTL3 loci harboured a (88.3%), a (95.1%), and α (71.8%) alleles, respectively. The C. glabrata isolates were susceptible to echinocandins but displayed high minimal inhibitory concentrations (MICs) for azoles. The MIC ranges and MIC90 values of all isolates were 1.0 to ≥64 and 8.0 μg mL-1 for fluconazole, 0.06 to ≥16.0 and 0.5 μg mL-1 for voriconazole, 0.06 to ≥16.0 and 1.0 μg mL-1 for posaconazole, ≤0.015 to 0.06, and 0.03 μg mL-1 for caspofungin, ≤0.015 to 0.06 and 0.015 μg mL-1 for anidulafungin and 0.5-2 and 2.0 μg mL-1 for amphotericin B, respectively. The mating gene alleles of the clinical C. glabrata isolates were not associated with differences in the MICs of the tested antifungals, except for the MTL3 α-allele and echinocandins. The mating genotypes of the clinical C. glabrata isolates had no recognisable common effect on antifungal susceptibility.
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Affiliation(s)
- Engin Kaplan
- Advanced Technology Education, Research, and Application Center, Mersin University, Mersin, Turkey.,Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Zonguldak Bülent Ecevit, Zonguldak, Turkey
| | - Deniz Aktaş
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Mersin, Mersin, Turkey
| | - Şükran Önder
- Department of Microbiology, Division of Mycology, Faculty of Medicine, University of Eskisehir Osmangazi, Eskisehir, Turkey
| | - Banu Metin
- Department of Food Engineering, Faculty of Engineering and Natural Sciences, Istanbul Sabahattin Zaim University, Istanbul, Turkey
| | - Aylin Döğen
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Mersin, Mersin, Turkey
| | - Yasemin Oz
- Department of Microbiology, Division of Mycology, Faculty of Medicine, University of Eskisehir Osmangazi, Eskisehir, Turkey
| | - Macit Ilkit
- Department of Microbiology, Division of Mycology, Faculty of Medicine, University of Çukurova, Adana, Turkey
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9
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Genomes shed light on the secret life of Candida glabrata: not so asexual, not so commensal. Curr Genet 2018; 65:93-98. [PMID: 30027485 PMCID: PMC6342864 DOI: 10.1007/s00294-018-0867-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 07/15/2018] [Accepted: 07/17/2018] [Indexed: 11/27/2022]
Abstract
Candida glabrata is an opportunistic yeast pathogen, whose incidence has increased over the last decades. Despite its genus name, this species is actually more closely related to the budding yeast Saccharomyces cerevisiae than to other Candida pathogens, such as Candida albicans. Hence, C. glabrata and C. albicans must have acquired the ability to infect humans independently, which is reflected in the use of different mechanism for virulence, and survival in the host. Yet, research on C. glabrata suffers from assumptions carried over from the more studied C. albicans. Regarding the adaptation of C. glabrata to the human host, the prejudice was that, just as C. albicans, C. glabrata is a natural human commensal that turns deadly when immune defenses weaken. It was also considered asexual, as no one has observed mating, diploids, or spores, despite great efforts. However, the recent analysis of whole genomes from globally distributed C. glabrata isolates have shaken these assumptions. C. glabrata seems to be only secondarily associated to humans, as indicated by a lack of co-evolution with its host, and genomic footprints of recombination shows compelling evidence that this yeast is able to have sex. Here, we discuss the implications of this and other recent findings and highlight the new questions opened by this change in paradigm.
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10
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Al-Yasiri MH, Normand AC, Piarroux R, Ranque S, Mauffrey JF. Gut yeast communities in Larus michahellis from various breeding colonies. Med Mycol 2018; 55:436-444. [PMID: 27703020 DOI: 10.1093/mmy/myw088] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/15/2016] [Indexed: 11/13/2022] Open
Abstract
Yellow-legged gulls have been reported to carry antibiotic-resistant Enterobacteriaceae; however, the gut mycobiota of these birds has not yet been described. In this study, we analyzed the gut yeast communities in five yellow-legged gull breeding colonies along the Mediterranean littoral in southern France. Gull fecal samples were inoculated onto four types of culture media, including one supplemented with itraconazole. Yeast species richness, abundance, and diversity were estimated, and factorial analysis was used to highlight correspondences between breeding colonies. Yeast grew in 113 of 177 cultures, and 17 distinct yeast species were identified. The most frequent species were Candida krusei (53.5%), Galactomyces geotrichum (44.1%), C. glabrata (40.9%), C. albicans (20.5%), and Saccharomyces cerevisiae (18.1%). Gut yeast community structure in the gulls at both Pierre-Blanche Lagoon (PB) and Frioul Archipelago (F) were characterized by greater species richness and diversity than in those at the two cities of La Grande-Motte (GM) and Palavas-les-Flots (PF) as well as Riou Archipelago (R). Gulls in these latter three sites probably share a similar type of anthropogenic diet. Notably, the proportion of anthropic yeast species, including C. albicans and C. glabrata, in the gull mycobiota increased with gull colony synanthropy. Antifungal resistance was found in each of the five most frequent yeast species. We found that the gut yeast communities of these yellow-legged gulls include antifungal-resistant human pathogens. Further studies should assess the public health impact of these common synanthropic seabirds, which represent a reservoir and disseminator of drug-resistant human pathogenic yeast into the environment.
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Affiliation(s)
| | | | - Renaud Piarroux
- Aix Marseille Univ, IRD, IRBA, IP-TPT, Marseille, France.,APHM, CHU Timone, Laboratory of Parasitology - Mycology, Marseille, France
| | - Stéphane Ranque
- Aix Marseille Univ, IRD, IRBA, IP-TPT, Marseille, France.,APHM, CHU Timone, Laboratory of Parasitology - Mycology, Marseille, France
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11
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Çelik ZD, Erten H, Darici M, Cabaroğlu T. Molecular characterization and technological properties of wine yeasts isolated during spontaneous fermentation of Vitis vinifera L.cv. Narince grape must grown in ancient wine making area Tokat, Anatolia. BIO WEB OF CONFERENCES 2017. [DOI: 10.1051/bioconf/20170902017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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12
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Opportunistic fungal pathogen Candida glabrata circulates between humans and yellow-legged gulls. Sci Rep 2016; 6:36157. [PMID: 27782182 PMCID: PMC5080578 DOI: 10.1038/srep36157] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 10/03/2016] [Indexed: 12/19/2022] Open
Abstract
The opportunistic pathogenic yeast Candida glabrata is a component of the mycobiota of both humans and yellow-legged gulls that is prone to develop fluconazole resistance. Whether gulls are a reservoir of the yeast and facilitate the dissemination of human C. glabrata strains remains an open question. In this study, MLVA genotyping highlighted the lack of genetic structure of 190 C. glabrata strains isolated from either patients in three hospitals or fecal samples collected from gull breeding colonies located in five distinct areas along the French Mediterranean littoral. Fluconazole-resistant isolates were evenly distributed between both gull and human populations. These findings demonstrate that gulls are a reservoir of this species and facilitate the diffusion of C. glabrata and indirect transmission to human or animal hosts via environmental contamination. This eco-epidemiological view, which can be applied to other vertebrate host species, broadens our perspective regarding the reservoirs and dissemination patterns of antifungal-resistant human pathogenic yeast.
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13
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Peris D, Langdon QK, Moriarty RV, Sylvester K, Bontrager M, Charron G, Leducq JB, Landry CR, Libkind D, Hittinger CT. Complex Ancestries of Lager-Brewing Hybrids Were Shaped by Standing Variation in the Wild Yeast Saccharomyces eubayanus. PLoS Genet 2016; 12:e1006155. [PMID: 27385107 PMCID: PMC4934787 DOI: 10.1371/journal.pgen.1006155] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 06/08/2016] [Indexed: 12/05/2022] Open
Abstract
Lager-style beers constitute the vast majority of the beer market, and yet, the genetic origin of the yeast strains that brew them has been shrouded in mystery and controversy. Unlike ale-style beers, which are generally brewed with Saccharomyces cerevisiae, lagers are brewed at colder temperatures with allopolyploid hybrids of Saccharomyces eubayanus x S. cerevisiae. Since the discovery of S. eubayanus in 2011, additional strains have been isolated from South America, North America, Australasia, and Asia, but only interspecies hybrids have been isolated in Europe. Here, using genome sequence data, we examine the relationships of these wild S. eubayanus strains to each other and to domesticated lager strains. Our results support the existence of a relatively low-diversity (π = 0.00197) lineage of S. eubayanus whose distribution stretches across the Holarctic ecozone and includes wild isolates from Tibet, new wild isolates from North America, and the S. eubayanus parents of lager yeasts. This Holarctic lineage is closely related to a population with higher diversity (π = 0.00275) that has been found primarily in South America but includes some widely distributed isolates. A second diverse South American population (π = 0.00354) and two early-diverging Asian subspecies are more distantly related. We further show that no single wild strain from the Holarctic lineage is the sole closest relative of lager yeasts. Instead, different parts of the genome portray different phylogenetic signals and ancestry, likely due to outcrossing and incomplete lineage sorting. Indeed, standing genetic variation within this wild Holarctic lineage of S. eubayanus is responsible for genetic variation still segregating among modern lager-brewing hybrids. We conclude that the relationships among wild strains of S. eubayanus and their domesticated hybrids reflect complex biogeographical and genetic processes.
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Affiliation(s)
- David Peris
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Quinn K. Langdon
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ryan V. Moriarty
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kayla Sylvester
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Martin Bontrager
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Guillaume Charron
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, Québec City, Québec, Canada
| | - Jean-Baptiste Leducq
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, Québec City, Québec, Canada
| | - Christian R. Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, Québec City, Québec, Canada
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada, Biotecnología y Bioinformática, Instituto Andino Patagonico de Tecnologías Biológicas y Geoambientales, IPATEC (CONICET-UNComahue), Centro Regional Universitario Bariloche, Bariloche, Río Negro, Argentina
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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14
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Leventdurur S, Sert-Aydın S, Boyaci-Gunduz CP, Agirman B, Ben Ghorbal A, Francesca N, Martorana A, Erten H. Yeast biota of naturally fermented black olives in different brines made from cv. Gemlik grown in various districts of the Cukurova region of Turkey. Yeast 2016; 33:289-301. [DOI: 10.1002/yea.3170] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 04/25/2016] [Accepted: 04/25/2016] [Indexed: 12/14/2022] Open
Affiliation(s)
- Sezgi Leventdurur
- Department of Food Engineering, Faculty of Agriculture; Cukurova University; 01330 Adana Turkey
| | - Selvihan Sert-Aydın
- Department of Food Engineering, Faculty of Agriculture; Cukurova University; 01330 Adana Turkey
| | - C. Pelin Boyaci-Gunduz
- Department of Food Engineering, Faculty of Agriculture; Cukurova University; 01330 Adana Turkey
| | - Bilal Agirman
- Department of Food Engineering, Faculty of Agriculture; Cukurova University; 01330 Adana Turkey
| | - Akram Ben Ghorbal
- Department of Food Engineering, Faculty of Agriculture; Cukurova University; 01330 Adana Turkey
| | - Nicola Francesca
- Universita degli Studi di Palermo; Dipartimento Scienze Agrarie e Forestali; Viale delle Scienze 4 90128 Palermo Italy
| | - Alessandra Martorana
- Universita degli Studi di Palermo; Dipartimento Scienze Agrarie e Forestali; Viale delle Scienze 4 90128 Palermo Italy
| | - Hüseyin Erten
- Department of Food Engineering, Faculty of Agriculture; Cukurova University; 01330 Adana Turkey
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15
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Francesca N, Guerreiro MA, Carvalho C, Coelho M, Alfonzo A, Randazzo W, Sampaio JP, Moschetti G. Jaminaea phylloscopi sp. nov. (Microstromatales), a basidiomycetous yeast isolated from migratory birds in the Mediterranean basin. Int J Syst Evol Microbiol 2016; 66:824-829. [DOI: 10.1099/ijsem.0.000801] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Nicola Francesca
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Viale delle Scienze 4, 90128 Palermo, Italy
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Marco Alexandre Guerreiro
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Geobotany, Faculty for Biology and Biotechnology, Ruhr-Universität Bochum, Bochum, Germany
| | - Cláudia Carvalho
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Marco Coelho
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Antonio Alfonzo
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Viale delle Scienze 4, 90128 Palermo, Italy
| | - Walter Randazzo
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Viale delle Scienze 4, 90128 Palermo, Italy
| | - José Paulo Sampaio
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Giancarlo Moschetti
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Viale delle Scienze 4, 90128 Palermo, Italy
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16
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The Wine: Typicality or Mere Diversity? The Effect of Spontaneous Fermentations and Biotic Factors on the Characteristics of Wine. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.aaspro.2016.02.064] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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