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Makopa TP, Ncube T, Alwasel S, Boekhout T, Zhou N. Yeast-insect interactions in southern Africa: Tapping the diversity of yeasts for modern bioprocessing. Yeast 2024; 41:330-348. [PMID: 38450792 DOI: 10.1002/yea.3935] [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: 12/13/2023] [Revised: 01/31/2024] [Accepted: 02/19/2024] [Indexed: 03/08/2024] Open
Abstract
Yeast-insect interactions are one of the most interesting long-standing relationships whose research has contributed to our understanding of yeast biodiversity and their industrial applications. Although insect-derived yeast strains are exploited for industrial fermentations, only a limited number of such applications has been documented. The search for novel yeasts from insects is attractive to augment the currently domesticated and commercialized production strains. More specifically, there is potential in tapping the insects native to southern Africa. Southern Africa is home to a disproportionately high fraction of global biodiversity with a cluster of biomes and a broad climate range. This review presents arguments on the roles of the mutualistic relationship between yeasts and insects, the presence of diverse pristine environments and a long history of spontaneous food and beverage fermentations as the potential source of novelty. The review further discusses the recent advances in novelty of industrial strains of insect origin, as well as various ancient and modern-day industries that could be improved by use yeasts from insect origin. The major focus of the review is on the relationship between insects and yeasts in southern African ecosystems as a potential source of novel industrial yeast strains for modern bioprocesses.
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Affiliation(s)
- Tawanda P Makopa
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
| | - Thembekile Ncube
- Department of Biology and Biochemistry, Faculty of Applied Science, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Saleh Alwasel
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Teun Boekhout
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Nerve Zhou
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
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Chow LJ, Nesbit ML, Hill T, Tranter C, Evison SE, Hughes WO, Graystock P. Identification of fungi isolated from commercial bumblebee colonies. PeerJ 2024; 12:e16713. [PMID: 38313023 PMCID: PMC10836204 DOI: 10.7717/peerj.16713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/04/2023] [Indexed: 02/06/2024] Open
Abstract
Fungi can have important beneficial and detrimental effects on animals, yet our understanding of the diversity and function of most bee-associated fungi is poor. Over 2 million bumblebee colonies are traded globally every year, but the presence and transport of viable fungi within them is unknown. Here, we explored whether any culturable fungi could be isolated from commercial bumblebee nests. We collected samples of various substrates from within 14 bumblebee colonies, including the honey, honey cup wall, egg cup wall, and frass then placed them on agar and recorded any growth. Fungal morphotypes were then subcultured and their ITS region sequenced for identification. Overall, we cultured 11 fungal species from the various nest substrates. These included both pathogenic and non-pathogenic fungi, such as Aspergillus sp., Penicillium sp., and Candida sp. Our results provide the first insights into the diversity of viable fungal communities in commercial bumblebee nests. Further research is needed to determine if these fungi are unique to commercial colonies or prevalent in wild bumblebee nests, and crucially to determine the ecological and evolutionary implications of these fungi in host colonies.
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Affiliation(s)
- Lui Julie Chow
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, United Kingdom
| | - Miles L. Nesbit
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, United Kingdom
| | - Tom Hill
- School of Biology, University of Leeds, Leeds, United Kingdom
| | - Christopher Tranter
- School of Biology, University of Leeds, Leeds, United Kingdom
- School of Veterinary Science, University of Liverpool, Liverpool, United Kingdom
| | - Sophie E.F. Evison
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | | | - Peter Graystock
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, United Kingdom
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3
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Kumar S, Verma NK, Basotra SD, Sharma D, Prasad GS, Bhattacharyya MS. Harnessing dual applications of a novel ascomycetes yeast, Starmerella cerana sp. nov., as a biocatalyst for stereoselective ketone reduction and biosurfactant production. Front Bioeng Biotechnol 2023; 11:1264826. [PMID: 37941721 PMCID: PMC10628682 DOI: 10.3389/fbioe.2023.1264826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/27/2023] [Indexed: 11/10/2023] Open
Abstract
Introduction: New bioresources for catalytic application and fine chemical synthesis are the need of the hour. In an effort to find out new biocatalyst for oxidation-reduction reaction, leading to the synthesis of chiral intermediates, novel yeast were isolated from unique niche and employed for the synthesis of value added compounds. Methods: To determine the genetic relatedness of the isolated strain, HSB-15T, sequence analysis of the internal transcribed spacer (ITS) and D1/D2 domains of the 26S rRNA gene sequence was carried out. The distinctive features of the strain HSB-15T were also identified by phenotypic characterization. The isolated strain HSB-15T was employed for the reduction of selected naphthyl ketones to their corresponding alcohols and a biosurfactant was isolated from its culture broth. Results: The analysis of the ITS and D1/D2 domains of the 26S rRNA gene revealed that strain HSB-15T is closely related to the type strain of Starmerella vitae (CBS 15147T) with 96.3% and 97.7% sequence similarity, respectively. However, concatenated sequences of the ITS gene and D1/D2 domain showed 94.6% sequence similarity. Phenotypic characterization indicated significant differences between strain HSB-15T and its closely related species and consequently, it was identified as a novel species, leading to the proposal of the name Starmerella cerana sp. nov. The strain was able to reduce selected naphthyl ketones to their corresponding alcohols with remarkable efficiency, within a 12-hours. The strain HSB-15T also produced a surfactant in its culture broth, identified as sophorolipid upon analysis. Discussion: The study explored the potential of the novel strain, HSB-15T, as a whole-cell biocatalyst for the reduction of naphthyl ketones to their corresponding alcohols and also reports its capability to produce sophorolipid, a biosurfactant, in its culture broth. This dual functionality of HSB-15T both as biocatalyst and biosurfactant producer enhances its applicability in biotechnology and environmental science.
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Affiliation(s)
- Sachin Kumar
- Microbial Type Culture Collection (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Nitish Kumar Verma
- Biochemical Engineering Research and Process Development Centre (BERPDC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Sandal Deep Basotra
- Biochemical Engineering Research and Process Development Centre (BERPDC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Divya Sharma
- Biochemical Engineering Research and Process Development Centre (BERPDC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - G. S. Prasad
- Microbial Type Culture Collection (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Mani Shankar Bhattacharyya
- Biochemical Engineering Research and Process Development Centre (BERPDC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
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4
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Rutkowski D, Weston M, Vannette RL. Bees just wanna have fungi: a review of bee associations with nonpathogenic fungi. FEMS Microbiol Ecol 2023; 99:fiad077. [PMID: 37422442 PMCID: PMC10370288 DOI: 10.1093/femsec/fiad077] [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: 04/20/2023] [Revised: 06/15/2023] [Accepted: 07/06/2023] [Indexed: 07/10/2023] Open
Abstract
Bee-fungus associations are common, and while most studies focus on entomopathogens, emerging evidence suggests that bees associate with a variety of symbiotic fungi that can influence bee behavior and health. Here, we review nonpathogenic fungal taxa associated with different bee species and bee-related habitats. We synthesize results of studies examining fungal effects on bee behavior, development, survival, and fitness. We find that fungal communities differ across habitats, with some groups restricted mostly to flowers (Metschnikowia), while others are present almost exclusively in stored provisions (Zygosaccharomyces). Starmerella yeasts are found in multiple habitats in association with many bee species. Bee species differ widely in the abundance and identity of fungi hosted. Functional studies suggest that yeasts affect bee foraging, development, and pathogen interactions, though few bee and fungal taxa have been examined in this context. Rarely, fungi are obligately beneficial symbionts of bees, whereas most are facultative bee associates with unknown or ecologically contextual effects. Fungicides can reduce fungal abundance and alter fungal communities associated with bees, potentially disrupting bee-fungi associations. We recommend that future study focus on fungi associated with non-honeybee species and examine multiple bee life stages to document fungal composition, abundance, and mechanistic effects on bees.
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Affiliation(s)
- Danielle Rutkowski
- 367 Briggs Hall, Department of Entomology and Nematology, University of California Davis, Davis, CA 95616, United States
| | - Makena Weston
- 367 Briggs Hall, Department of Entomology and Nematology, University of California Davis, Davis, CA 95616, United States
| | - Rachel L Vannette
- 367 Briggs Hall, Department of Entomology and Nematology, University of California Davis, Davis, CA 95616, United States
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Iwata K, Maeda M, Kashiwagi Y, Maehashi K, Yoshikawa J. Isolation of Zygosaccharomyces siamensis kiy1 as a novel arabitol-producing yeast and its arabitol production. AMB Express 2023; 13:76. [PMID: 37452923 DOI: 10.1186/s13568-023-01581-4] [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: 06/21/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023] Open
Abstract
Arabitol is gaining attention in the food industry as an alternative sweetener owing to its low-caloric and non-cariogenic characteristics. The yeast strain kiy1 was newly isolated from unpasteurized honey for arabitol production. Based on internal transcribed spacer sequence analysis, the isolated strain was identified as Zygosaccharomyces siamensis. In this study, the effects of different substrates and sugar concentrations on arabitol production were investigated. When three types of carbon sources (glycerol, fructose, and glucose) were used, glucose was the most suitable substrate for arabitol production (68.7 g/L). Maximum arabitol production (101.4 g/L) was observed at a glucose concentration of 30%, and the highest arabitol production yield was 0.34 g/g of initial glucose. In the time-course production of sugar alcohols by strain kiy1, glucose was completely consumed for 8 days. The concentration of arabitol exceeded that of glycerol after 3 days, and the final arabitol concentration reached 83.6 g/L after 10 days. The maximum production rate was 16.7 g/L/day. The yeast produced glycerol as an intracellular sugar alcohol in the early stage of culture and switched its metabolism to arabitol production after the middle stage. Z. siamensis kiy1 possessed an NADP+-dependent arabitol dehydrogenase, which indicated that it probably produces arabitol via ribulose from glucose. These results suggest that the novel yeast strain, Z. siamensis kiy1, is promising for arabitol production. The proposed arabitol production approach can contribute toward its production at the industrial scale.
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Affiliation(s)
- Kan Iwata
- Department of Fermentation Science and Technology, Graduate School of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-Ku, Tokyo, 156-8502, Japan
| | - Mayumi Maeda
- Department of Fermentation Science, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-Ku, Tokyo, 156-8502, Japan
| | - Yutaka Kashiwagi
- Department of Fermentation Science, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-Ku, Tokyo, 156-8502, Japan
| | - Kenji Maehashi
- Department of Fermentation Science and Technology, Graduate School of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-Ku, Tokyo, 156-8502, Japan
- Department of Fermentation Science, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-Ku, Tokyo, 156-8502, Japan
| | - Jun Yoshikawa
- Department of Fermentation Science, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-Ku, Tokyo, 156-8502, Japan.
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6
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Ilmi M, Badrani A, Fauziyah A. Increasing lipid production from Zygosaccharomyces siamensis AP1 in molasses substrate using sequencing batch method. Prep Biochem Biotechnol 2023; 53:288-296. [PMID: 35670649 DOI: 10.1080/10826068.2022.2081859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Yeasts are considered potential lipid producers to substitute oil-producing plants. Previous study succeeded in isolating Zygosaccharomyces siamensis AP1 from Indonesia which was able to accumulate 19% lipid. The strain, however, was not optimized for high cell density growth which is required for industry-level. In this study, efforts were made to increase cell density and lipid production of Z. siamensis AP1 using molasses as carbon source and implementing sequencing batch method. The yeast was grown in various combinations of carbon and nitrogen sources. The C:N ratio of the best substrate combination is then optimized. Afterwards, batch and sequencing batch methods were applied in fermentation with various concentrations (20-480 g/L) of molasses. The results show that lipid produced using molasses was slightly higher compared to using glucose, 0.21 g/L and 0.19 g/L respectively, with the same nitrogen source. Combination of molasses and ammonium sulfate with C:N ratio 70:1 gave the highest lipid (0.28 g/L). Sequencing batch able to increase cell density 2.4-fold compared to batch method. This study was the first to report that sequencing batch application with molasses as carbon source can increase lipid production from Z. siamensis. Further study to optimize medium composition for sequencing batch is suggested.
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Affiliation(s)
- Miftahul Ilmi
- Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Anugrah Badrani
- Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Annisa Fauziyah
- Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
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7
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Living in honey: bacterial and fungal communities in honey of sympatric populations of Apis mellifera and the stingless bee Melipona beecheii, in Yucatan, Mexico. Arch Microbiol 2022; 204:718. [DOI: 10.1007/s00203-022-03319-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 11/21/2022]
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8
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Brysch-Herzberg M, Jia GS, Seidel M, Assali I, Du LL. Insights into the ecology of Schizosaccharomyces species in natural and artificial habitats. Antonie van Leeuwenhoek 2022; 115:661-695. [PMID: 35359202 PMCID: PMC9007792 DOI: 10.1007/s10482-022-01720-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/14/2022] [Indexed: 11/30/2022]
Abstract
The fission yeast genus Schizosaccharomyces contains important model organisms for biological research. In particular, S. pombe is a widely used model eukaryote. So far little is known about the natural and artificial habitats of species in this genus. Finding out where S. pombe and other fission yeast species occur and how they live in their habitats can promote better understanding of their biology. Here we investigate in which substrates S. pombe, S. octosporus, S. osmophilus and S. japonicus are present. To this end about 2100 samples consisting of soil, tree sap fluxes, fresh fruit, dried fruit, honey, cacao beans, molasses and other substrates were analyzed. Effective isolation methods that allow efficient isolation of the above mentioned species were developed. Based on the frequency of isolating different fission yeast species in various substrates and on extensive literature survey, conclusions are drawn on their ecology. The results suggest that the primary habitat of S. pombe and S. octosporus is honeybee honey. Both species were also frequently detected on certain dried fruit like raisins, mango or pineapple to which they could be brought by the honey bees during ripening or during drying. While S. pombe was regularly isolated from grape mash and from fermented raw cacao beans S. octosporus was never isolated from fresh fruit. The main habitat of S. osmophilus seems to be solitary bee beebread. It was rarely isolated from raisins. S. japonicus was mainly found in forest substrates although it occurs on fruit and in fruit fermentations, too.
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Affiliation(s)
- Michael Brysch-Herzberg
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University, Max-Planck-Str. 39, 74081 Heilbronn, Germany
| | - Guo-Song Jia
- National Institute of Biological Sciences, Beijing, 102206 China
| | - Martin Seidel
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University, Max-Planck-Str. 39, 74081 Heilbronn, Germany
| | - Imen Assali
- Department of Bioengineering, National Engineering School of Sfax, University of Sfax, Soukra, km 4, 3038 Sfax, Tunisia
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, 102206 China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206 China
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9
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Baba H, Matsumoto T, Matsushita K, Nakayama M, Miyamoto T. Study of Yeast Identification Using MALDI-TOF MS. J JPN SOC FOOD SCI 2022. [DOI: 10.3136/nskkk.69.115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Hiroshi Baba
- Japan Food Research Laboratories Saito Laboratory
| | - Takuro Matsumoto
- Department of Life Science, Faculty of Life Science, Kyusyu Sangyo University
| | - Kaori Matsushita
- Department of Life Science, Faculty of Life Science, Kyusyu Sangyo University
| | - Motokazu Nakayama
- Department of Life Science, Faculty of Life Science, Kyusyu Sangyo University
| | - Takahisa Miyamoto
- Department of Bioscience & Biotechnology, Faculty Agriculture, Kyusyu University
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10
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Péter G. Biodiversity of Zygosaccharomyces species in food systems. ACTA ALIMENTARIA 2021. [DOI: 10.1556/066.2021.00142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstracts
Zygosaccharomyces species are among the most problematic food spoilage yeasts. The two most infamous species are Zygosaccharomyces balii and Zygosaccharomyces rouxii, although they may also take a positive role during the production of some fermented foods. DNA sequence based yeast identification aided by freely available reference databases of barcoding DNA sequences has boosted the description rate of novel yeast species in the last two decades. The genus Zygosaccharomyces has been considerably expanded as well. Especially the number of the extremely osmotolerant Zygosaccharomyces species, related to Z. rouxii and regularly found in high-sugar foods, has enlarged. A brief account of recent developments in the taxonomy and biodiversity of this important food associated genus is given in this review.
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Affiliation(s)
- G. Péter
- National Collection of Agricultural and Industrial Microorganisms, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Somlói út 14–16, H-1118, Budapest, Hungary
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11
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Solieri L. The revenge of Zygosaccharomyces yeasts in food biotechnology and applied microbiology. World J Microbiol Biotechnol 2021; 37:96. [PMID: 33969449 DOI: 10.1007/s11274-021-03066-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/28/2021] [Indexed: 12/01/2022]
Abstract
Non-conventional yeasts refer to a huge and still poorly explored group of species alternative to the well-known model organism Saccharomyces cerevisiae. Among them, Zygosaccharomyces rouxii and the sister species Zygosaccharomyces bailii are infamous for spoiling food and beverages even in presence of several food preservatives. On the other hand, their capability to cope with a wide range of process conditions makes these yeasts very attractive factories (the so-called "ZygoFactories") for bio-converting substrates poorly permissive for the growth of other species. In balsamic vinegar Z. rouxii is the main yeast responsible for converting highly concentrated sugars into ethanol, with a preference for fructose over glucose (a trait called fructophily). Z. rouxii has also attracted much attention for the ability to release important flavor compounds, such as fusel alcohols and the derivatives of 4-hydroxyfuranone, which markedly contribute to fragrant and smoky aroma in soy sauce. While Z. rouxii was successfully proposed in brewing for producing low ethanol beer, Z. bailii is promising for lactic acid and bioethanol production. Recently, several research efforts exploited omics tools to pinpoint the genetic bases of distinctive traits in "ZygoFactories", like fructophily, tolerance to high concentrations of sugars, lactic acid and salt. Here, I provided an overview of Zygosaccharomyces industrially relevant phenotypes and summarized the most recent findings in disclosing their genetic bases. I suggest that the increasing number of genomes available for Z. rouxii and other Zygosaccharomyces relatives, combined with recently developed genetic engineering toolkits, will boost the applications of these yeasts in biotechnology and applied microbiology.
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Affiliation(s)
- L Solieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy.
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12
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Echeverrigaray S, Scariot FJ, Foresti L, Schwarz LV, Rocha RKM, da Silva GP, Moreira JP, Delamare APL. Yeast biodiversity in honey produced by stingless bees raised in the highlands of southern Brazil. Int J Food Microbiol 2021; 347:109200. [PMID: 33894461 DOI: 10.1016/j.ijfoodmicro.2021.109200] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 11/26/2022]
Abstract
The physicochemical characteristics and yeasts diversity in honey samples from 17 species of stingless bees of the genera Nannotrigona, Melipona, Plebeia, Scraptotrigona, and Tetragonisca cultivated in Southern Brazil were determined. The sugar content, moisture, water activity, pH, reducing sugars/total sugar ratio, and total yeast population varied significantly among the honey from the different bee species. The highest yeast population was found in the Plebeia's honey samples and correlated with their high water-activity. Sixteen yeast species were identified based on the nuclear large subunit (26S) ribosomal RNA partial sequences. The genera Starmerella and Zygosaccharomyces were found predominant, with a high prevalence of Starmerella sp., S. etchellsii, and S. apicola. Some yeast species were only identified in honey samples from specific bee species indicating a close relationship between the yeasts and the insects. For the first time, Wickerhamomyces sydowiorum in honey is being reported. In general, the yeast species isolated from stingless bee honey samples demonstrated high osmotolerance and low sugar assimilation.
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Affiliation(s)
- Sergio Echeverrigaray
- Laboratory of Enology and Applied Microbiology, Institute of Biotechnology, University of Caxias do Sul, Brazil
| | - Fernando Joel Scariot
- Laboratory of Enology and Applied Microbiology, Institute of Biotechnology, University of Caxias do Sul, Brazil.
| | - Luciano Foresti
- Laboratory of Enology and Applied Microbiology, Institute of Biotechnology, University of Caxias do Sul, Brazil
| | - Luisa Vivian Schwarz
- Laboratory of Enology and Applied Microbiology, Institute of Biotechnology, University of Caxias do Sul, Brazil
| | - Ronaldo Kauê Mattos Rocha
- Laboratory of Enology and Applied Microbiology, Institute of Biotechnology, University of Caxias do Sul, Brazil
| | - Gabriela Priscila da Silva
- Laboratory of Enology and Applied Microbiology, Institute of Biotechnology, University of Caxias do Sul, Brazil
| | - Jennifer Pereira Moreira
- Laboratory of Enology and Applied Microbiology, Institute of Biotechnology, University of Caxias do Sul, Brazil
| | - Ana Paula Longaray Delamare
- Laboratory of Enology and Applied Microbiology, Institute of Biotechnology, University of Caxias do Sul, Brazil
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13
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Januário da Costa Neto D, Benevides de Morais P. The vectoring of Starmerella species and other yeasts by stingless bees in a Neotropical savanna. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100973] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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14
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Meriggi N, Di Paola M, Cavalieri D, Stefanini I. Saccharomyces cerevisiae - Insects Association: Impacts, Biogeography, and Extent. Front Microbiol 2020; 11:1629. [PMID: 32760380 PMCID: PMC7372139 DOI: 10.3389/fmicb.2020.01629] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 06/22/2020] [Indexed: 12/23/2022] Open
Abstract
Over the last few years, an increasing number of studies have reported the existence of an association between the budding yeast Saccharomyces cerevisiae and insects. The discovery of this relationship has called into question the hypothesis that S. cerevisiae is unable to survive in nature and that the presence of S. cerevisiae strains in natural specimens is the result of contamination from human-related environments. S. cerevisiae cells benefit from this association as they find in the insect intestine a shelter, but also a place where they can reproduce themselves through mating, the latter being an event otherwise rarely observed in natural environments. On the other hand, insects also take advantage in hosting S. cerevisiae as they rely on yeasts as nutriment to properly develop, to localize suitable food, and to enhance their immune system. Despite the relevance of this relationship on both yeast and insect ecology, we are still far from completely appreciating its extent and effects. It has been shown that other yeasts are able to colonize only one or a few insect species. Is it the same for S. cerevisiae cells or is this yeast able to associate with any insect? Similarly, is this association geographically or topographically limited in areas characterized by specific physical features? With this review, we recapitulate the nature of the S. cerevisiae-insect association, disclose its extent in terms of geographical distribution and species involved, and present YeastFinder, a cured online database providing a collection of information on this topic.
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Affiliation(s)
| | - Monica Di Paola
- Department of Biology, University of Florence, Florence, Italy
| | | | - Irene Stefanini
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
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Rodríguez-Andrade E, Stchigel AM, Terrab A, Guarro J, Cano-Lira JF. Diversity of xerotolerant and xerophilic fungi in honey. IMA Fungus 2019; 10:20. [PMID: 32647624 PMCID: PMC7325685 DOI: 10.1186/s43008-019-0021-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 10/17/2019] [Indexed: 11/10/2022] Open
Abstract
Fungi can colonize most of the substrata on Earth. Honey, a sugary food produced by bees (and other insects) has been studied little in terms of its fungal diversity. We have surveyed and evaluated the presence of xerotolerant and xerophilic fungi in a set of honey bee samples collected from across Spain. From 84 samples, a total of 104 fungal strains were isolated, and morphologically and phylogenetically characterized. We identified 32 species distributed across 16 genera, most of them belonging to the ascomycetous genera Aspergillus, Bettsia, Candida, Eremascus, Monascus, Oidiodendron, Penicillium, Skoua, Talaromyces and Zygosaccharomyces. As a result of this survey, eight new taxa are proposed: i.e. the new family Helicoarthrosporaceae, two new genera, Helicoarthrosporum and Strongyloarthrosporum in Onygenales; three new species of Eurotiales, Talaromyces affinitatimellis, T. basipetosporus, and T. brunneosporus; and two new species of Myxotrichaceae, Oidiodendron mellicola, and Skoua asexualis.
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Affiliation(s)
- E Rodríguez-Andrade
- Mycology Unit, Medical School and IISPV, Universitat Rovira i Virgili (URV), Sant Llorenç 21, 43201 Reus, Tarragona, Spain
| | - A M Stchigel
- Mycology Unit, Medical School and IISPV, Universitat Rovira i Virgili (URV), Sant Llorenç 21, 43201 Reus, Tarragona, Spain
| | - A Terrab
- Department of Plant Biology and Ecology, University of Seville, 41012 Seville, Spain
| | - J Guarro
- Mycology Unit, Medical School and IISPV, Universitat Rovira i Virgili (URV), Sant Llorenç 21, 43201 Reus, Tarragona, Spain
| | - J F Cano-Lira
- Mycology Unit, Medical School and IISPV, Universitat Rovira i Virgili (URV), Sant Llorenç 21, 43201 Reus, Tarragona, Spain
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Brysch-Herzberg M, Wohlmann E, Fischer R. Zygosaccharomyces seidelii sp. nov. a new yeast species from the Maldives, and a revisit of the single-strain species debate. Antonie van Leeuwenhoek 2019; 113:427-436. [DOI: 10.1007/s10482-019-01352-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 10/18/2019] [Indexed: 11/28/2022]
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17
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Palma M, Sá-Correia I. Physiological Genomics of the Highly Weak-Acid-Tolerant Food Spoilage Yeasts of Zygosaccharomyces bailii sensu lato. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2019; 58:85-109. [PMID: 30911890 DOI: 10.1007/978-3-030-13035-0_4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Zygosaccharomyces bailii and two closely related species, Z. parabailii and Z. pseudobailii ("Z. bailii species complex", "Z. bailii sensu lato" or simply "Z. bailii (s.l.)"), are frequently implicated in the spoilage of acidified preserved foods and beverages due to their tolerance to very high concentrations of weak acids used as food preservatives. The recent sequencing and annotation of these species' genomes have clarified their genomic organization and phylogenetic relationship, which includes events of interspecies hybridization. Mechanistic insights into their adaptation and tolerance to weak acids (e.g., acetic and lactic acids) are also being revealed. Moreover, the potential of Z. bailii (s.l.) to be used in industrial biotechnological processes as interesting cell factories for the production of organic acids, reduction of the ethanol content, increase of alcoholic beverages aroma complexity, as well as of genetic source for increasing weak acid resistance in yeast, is currently being considered. This chapter includes taxonomical, ecological, physiological, and biochemical aspects of Z. bailii (s.l.). The focus is on the exploitation of physiological genomics approaches that are providing the indispensable holistic knowledge to guide the effective design of strategies to overcome food spoilage or the rational exploitation of these yeasts as promising cell factories.
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Affiliation(s)
- Margarida Palma
- Institute for Bioengineering and Biosciences (iBB) and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences (iBB) and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
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18
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Siavoshi F, Sahraee M, Ebrahimi H, Sarrafnejad A, Saniee P. Natural fruits, flowers, honey, and honeybees harbor Helicobacter pylori-positive yeasts. Helicobacter 2018; 23:e12471. [PMID: 29457310 DOI: 10.1111/hel.12471] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
BACKGROUND For controlling Helicobacter pylori infection in humans, its environmental reservoir should be determined. In this study, yeast isolates from an isolated village in Iran were studied for the intracellular occurrence of H. pylori. MATERIALS AND METHODS In this study, yeasts were isolated from 29 samples, including oral swabs from villagers (n = 7), flowers and fruits (n = 6), honey and honeybees (n = 12) and miscellaneous samples (4). Yeasts were classified into 12 RFLP groups and identified by amplification of 26S rDNA and sequencing. DNA extracted from the yeast cells was examined for the presence of H. pylori using PCR. RESULTS Of the 29 yeasts, 27 were members of different genera of Ascomycete. H. pylori was detected in 5 of 9 Candida (55.5%), 4 of 5 Komagataella (80%), 3 of 4 Pichia (100%), 2 of 2 Cytobasidia (100%), 2 of 2 Hansenia (100%), 1 of 1 Meyerozyma (100%) and 2 of 3 not sequenced (66.6%) yeasts. Distribution of 19 of 29 (65.5%) H. pylori-positive yeasts within 4 groups was as follows: 1 of 7(14.3%) in oral swabs, 5 of 6 (83.3%) in flowers and fruits, 10 of 12 (83.3%) in honey and the bee group and 3 of 4 (75%) in miscellaneous. CONCLUSIONS Different genera of osmotolerant yeasts from flowers, fruits, honey, and honeybees contained H. pylori in their vacuole. High frequency of H. pylori-positive yeasts in these samples might be related to their high sugar content. Insects such as honeybees that facilitate transfer and easy access of these yeasts to nectars serve as the main reservoirs of these yeasts, playing an important role in their protection and dispersal. Accordingly, H. pylori inside these yeasts can be carried by honeybees to different sugar- and nutrient-rich environments. Sugar-rich environments and honeybees play an important role in distribution of H. pylori-positive yeasts in nature.
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Affiliation(s)
- Farideh Siavoshi
- Department of Microbiology, School of Biology, University College of Sciences, University of Tehran, Tehran, Iran
| | - Marzieh Sahraee
- Department of Microbiology, School of Biology, University College of Sciences, University of Tehran, Tehran, Iran
| | - Hoda Ebrahimi
- Department of Microbiology, School of Biology, University College of Sciences, University of Tehran, Tehran, Iran
| | - Abdolfatah Sarrafnejad
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Parastoo Saniee
- Faculty of Life Science and Biotechnology, Department of Microbiology and Microbial Biotechnology, Shahid Beheshti University G. C, Tehran, Iran
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Abstract
The larval stage of the stingless bee Scaptotrigona depilis must consume a specific brood cell fungus in order to continue development. Here we show that this fungus is a member of the genus Zygosaccharomyces and provides essential steroid precursors to the developing bee. Insect pupation requires ecdysteroid hormones, and as insects cannot synthesize sterols de novo, they must obtain steroids in their diet. Larval in vitro culturing assays demonstrated that consuming ergosterol recapitulates the developmental effects on S. depilis as ingestion of Zygosaccharomyces sp. cells. Thus, we determined the molecular underpinning of this intimate mutualistic symbiosis. Phylogenetic analyses showed that similar cases of bee-Zygosaccharomyces symbiosis may exist. This unprecedented case of bee-fungus symbiosis driven by steroid requirement brings new perspectives regarding pollinator-microbiota interaction and preservation.
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20
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Dakal TC, Solieri L, Giudici P. Evaluation of fingerprinting techniques to assess genotype variation among Zygosaccharomyces strains. Food Microbiol 2017; 72:135-145. [PMID: 29407390 DOI: 10.1016/j.fm.2017.11.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 10/27/2017] [Accepted: 11/28/2017] [Indexed: 01/15/2023]
Abstract
Molecular typing techniques are key tools in surveillance of food spoilage yeasts, in investigations on intra-species population diversity, and in tracing selected starters during fermentation. Unlike previous works on strain typing of Zygosaccharomyces spoilage species, here Zygosaccharomyces mellis and the Zygosaccharoymces rouxii complex yeasts, which include Z. rouxii, Zygosaccharomyces sapae, and a mosaic lineage (ML) of putatively hybrids, were evaluated by three typing methods for intra- and inter-species resolution. Overall these yeasts are relevant for food fermentation and spoilage, but are quite difficult to discriminate at strain and species level as they evolved by reticulation. A pool of 76 strains from different sources were typed by M13 and (GTG)5 MSP-PCR fingerprinting and PCR-RFLP of ribosomal intergenic spacer region (IGS). We demonstrated that M13 overcame (GTG)5 fingerprinting to group Z. sapae, Z. rouxii, Z. mellis and the ML isolates in congruent distinct clusters. Even if (GTG)5 primer yielded a number of DNA fingerprints comparable with those obtained by M13 primer, it failed to discriminate Z. sapae, Z. mellis and Z. rouxii at species level. Clustering of IGS RFLP patterns obtained with three endonucleases produced groups congruent with species assignment and highlighted intra-species diversity similar to that observed by M13 fingerprinting. However, IGS PCR amplification failed for 14 ML and 6 Z. mellis strains under the experimental conditions tested here, indicating that this marker could be less easy to use in fast typing protocol. Finally, our results posit that the genetic diversity within Z. sapae and Z. mellis could be shaped by isolation source. The information generated in this study would facilitate the monitoring of these yeasts during food processing and storage, and provides preliminary evidences about Z. sapae and Z. mellis intra-species diversity.
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Affiliation(s)
- Tikam Chand Dakal
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, Reggio Emilia 42122, Italy
| | - Lisa Solieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, Reggio Emilia 42122, Italy.
| | - Paolo Giudici
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, Reggio Emilia 42122, Italy
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21
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Kuanyshev N, Adamo GM, Porro D, Branduardi P. The spoilage yeastZygosaccharomyces bailii: Foe or friend? Yeast 2017; 34:359-370. [DOI: 10.1002/yea.3238] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 05/12/2017] [Accepted: 05/15/2017] [Indexed: 12/30/2022] Open
Affiliation(s)
- Nurzhan Kuanyshev
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 Milano 20126 Italy
| | - Giusy M. Adamo
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 Milano 20126 Italy
| | - Danilo Porro
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 Milano 20126 Italy
| | - Paola Branduardi
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 Milano 20126 Italy
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22
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Liu B, Wang C, Liu D, He N, Deng X. Hg tolerance and biouptake of an isolated pigmentation yeast Rhodotorula mucilaginosa. PLoS One 2017; 12:e0172984. [PMID: 28253367 PMCID: PMC5333980 DOI: 10.1371/journal.pone.0172984] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 02/13/2017] [Indexed: 11/18/2022] Open
Abstract
A pigmented yeast R1 with strong tolerance to Hg2+ was isolated. Phylogenetic identification based on the analysis of 26S rDNA and ITS revealed R1 is a Rhodotorula mucilaginosa species. R1 was able to grow in the presence of 80 mg/L Hg2+, but the lag phase was much prolonged compared to its growth in the absence of Hg2+. The maximum Hg2+ binding capacity of R1 was 69.9 mg/g, and dead cells could bind 15% more Hg2+ than living cells. Presence of organic substances drastically reduced bioavailability of Hg2+ and subsequently decreased Hg2+ removal ratio from aqueous solution, but this adverse effect could be remarkably alleviated by the simultaneous process of cell propagation and Hg2+ biouptake with actively growing R1. Furthermore, among the functional groups involved in Hg2+ binding, carboxyl group contributed the most, followed by amino & hydroxyl group and phosphate group. XPS analysis disclosed the mercury species bound on yeast cells was HgCl2 rather than HgO or Hg0.
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Affiliation(s)
- Bing Liu
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Marine Bioresources and Ecology, Shenzhen University, Shenzhen, China
| | - Chaogang Wang
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Marine Bioresources and Ecology, Shenzhen University, Shenzhen, China
| | - Danxia Liu
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Marine Bioresources and Ecology, Shenzhen University, Shenzhen, China
| | - Ning He
- Department of Chemical/Biochemical Engineering, Xiamen University, Xiamen, China
| | - Xu Deng
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Marine Bioresources and Ecology, Shenzhen University, Shenzhen, China
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Jutakanoke R, Endoh R, Takashima M, Ohkuma M, Tanasupawat S, Akaracharanya A. Allodekkera sacchari gen. nov., sp. nov., a yeast species in the Saccharomycetales isolated from a sugar factory. Int J Syst Evol Microbiol 2017; 67:250-255. [DOI: 10.1099/ijsem.0.001607] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Rumpa Jutakanoke
- Division of Biology, Faculty of Sciences, Rajamangala University of Technology Thanyaburi, Pathumthani 33130, Thailand
- Department of Microbiology, Faculty of Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Rikiya Endoh
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Masako Takashima
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Ancharida Akaracharanya
- Department of Microbiology, Faculty of Sciences, Chulalongkorn University, Bangkok 10330, Thailand
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Wrent P, Rivas EM, Peinado JM, de Silóniz MI. Zygosaccharomyces rouxii strains CECT 11923 and Z. rouxii CECT 10425: Two new putative hybrids? Int J Food Microbiol 2016; 241:7-14. [PMID: 27736687 DOI: 10.1016/j.ijfoodmicro.2016.09.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 09/20/2016] [Accepted: 09/23/2016] [Indexed: 10/20/2022]
Abstract
Based on IGS-PCR RFLP polymorphism, we previously detected two Z. rouxii strains (CECT 11923 and CECT 10425) that clustered with hybrid strains (NCYC 1682, NCYC 3060 and NCYC 3061). Given the recently recognized important industrial role of hybrids, their detection is very useful. Based on the IGS1 rDNA region alignment of hybrid strains and the Z. rouxii CECT 11923 and CECT 10425, in this work, we developed a pair of Zygosaccharomyces hybrid-specific primers, HibZF/HibZR. Positive amplicons were only obtained in the Zygosaccharomyces spp. hybrids included in this study and the CECT 11923 and CECT 10425 strains analyzed here. In the present study, we applied molecular tools to highlight the nature of these strains; they are quite different from each other as well as from Z. rouxii type strain. Based on the presence of two heterologous copies of nuclear-encoded genes (SOD2 and HIS3), the sequences of divergent 5.8S-ITS rDNA, D1/D2 26S rDNA copies and, the amplification with species-specific primer for Z. rouxii and Z. pseudorouxii, we hypothesize that the CECT 11923 strain might be a hybrid strain. Whereas, CECT 10425, the sequence analysis of 5.8S-ITS rDNA and D1/D2 26S rDNA copies presented 99-100% sequence identity with Zygosaccharomyces sp. NBRC 10669 (LN849119.1) and Z. sapae ABT 301T. Nevertheless, we discard that it could be a Z. sapae strain based on the results obtained in this study. Namely, the amplification with hybrid-specific primer designed in this study, the number of divergent copies of HIS3 (2), the fact that it only possesses one SOD2 gene and the amplification with species-specific primer for Z. pseudorouxii, therefore it could be a new species or a hybrid strain.
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Affiliation(s)
- Petra Wrent
- Departamento de Microbiología III, Facultad de Biología, Universidad Complutense de Madrid, C/José Antonio Nováis, 12, 28040 Madrid, Spain; CEI Campus Moncloa, UCM-UPM, Madrid, Spain
| | - Eva-María Rivas
- Departamento de Microbiología III, Facultad de Biología, Universidad Complutense de Madrid, C/José Antonio Nováis, 12, 28040 Madrid, Spain; CEI Campus Moncloa, UCM-UPM, Madrid, Spain
| | - José M Peinado
- Departamento de Microbiología III, Facultad de Biología, Universidad Complutense de Madrid, C/José Antonio Nováis, 12, 28040 Madrid, Spain; CEI Campus Moncloa, UCM-UPM, Madrid, Spain
| | - María-Isabel de Silóniz
- Departamento de Microbiología III, Facultad de Biología, Universidad Complutense de Madrid, C/José Antonio Nováis, 12, 28040 Madrid, Spain; CEI Campus Moncloa, UCM-UPM, Madrid, Spain.
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25
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Chand Dakal T, Giudici P, Solieri L. Contrasting Patterns of rDNA Homogenization within the Zygosaccharomyces rouxii Species Complex. PLoS One 2016; 11:e0160744. [PMID: 27501051 PMCID: PMC4976873 DOI: 10.1371/journal.pone.0160744] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 07/25/2016] [Indexed: 11/18/2022] Open
Abstract
Arrays of repetitive ribosomal DNA (rDNA) sequences are generally expected to evolve as a coherent family, where repeats within such a family are more similar to each other than to orthologs in related species. The continuous homogenization of repeats within individual genomes is a recombination process termed concerted evolution. Here, we investigated the extent and the direction of concerted evolution in 43 yeast strains of the Zygosaccharomyces rouxii species complex (Z. rouxii, Z. sapae, Z. mellis), by analyzing two portions of the 35S rDNA cistron, namely the D1/D2 domains at the 5’ end of the 26S rRNA gene and the segment including the internal transcribed spacers (ITS) 1 and 2 (ITS regions). We demonstrate that intra-genomic rDNA sequence variation is unusually frequent in this clade and that rDNA arrays in single genomes consist of an intermixing of Z. rouxii, Z. sapae and Z. mellis-like sequences, putatively evolved by reticulate evolutionary events that involved repeated hybridization between lineages. The levels and distribution of sequence polymorphisms vary across rDNA repeats in different individuals, reflecting four patterns of rDNA evolution: I) rDNA repeats that are homogeneous within a genome but are chimeras derived from two parental lineages via recombination: Z. rouxii in the ITS region and Z. sapae in the D1/D2 region; II) intra-genomic rDNA repeats that retain polymorphisms only in ITS regions; III) rDNA repeats that vary only in their D1/D2 domains; IV) heterogeneous rDNA arrays that have both polymorphic ITS and D1/D2 regions. We argue that an ongoing process of homogenization following allodiplodization or incomplete lineage sorting gave rise to divergent evolutionary trajectories in different strains, depending upon temporal, structural and functional constraints. We discuss the consequences of these findings for Zygosaccharomyces species delineation and, more in general, for yeast barcoding.
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Affiliation(s)
- Tikam Chand Dakal
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy
| | - Paolo Giudici
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy
| | - Lisa Solieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy
- * E-mail:
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27
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Cabral S, Prista C, Loureiro-Dias MC, Leandro MJ. Occurrence of FFZ genes in yeasts and correlation with fructophilic behaviour. MICROBIOLOGY-SGM 2015; 161:2008-2018. [PMID: 26253443 DOI: 10.1099/mic.0.000154] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Fructophily has been described in yeasts as the ability to utilize fructose preferentially when fructose and glucose are available in the environment. In Zygosaccharomyces bailii and Zygosaccharomyces rouxii, fructophilic behaviour has been associated with the presence of a particular type of high-capacity and low-affinity fructose transporters designated Ffz. In this study, a PCR screening was performed in several yeasts using degenerate primers suitable to detect FFZ-like genes. In parallel, fructophilic character was evaluated in the same strains by comparing the relative consumption rate of fructose and glucose. For all the strains in which FFZ-like genes were detected, fructophilic behaviour was observed (25 strains). Results show that FFZ genes are ubiquitous in the Zygosaccharomyces and Starmerella clades. Strains of Lachancea fermentati, Torulaspora microellipsoides and Zygotorulaspora florentina were not fructophilic and did not harbour FFZ genes. It is of note that these new species were recently removed by taxonomists from the Zygosaccharomyces clade, supporting the view that the presence of FFZ-like genes is a main characteristic of Zygosaccharomyces. Among the strains tested, only Hanseniaspora guilliermondii NCYC2380 was an exception, having a preference for fructose in medium with high sugar concentrations, despite no FFZ-like genes being detected in the screening. Furthermore, this study supports the previous idea of the emergence of a new family of hexose transporters (Ffz facilitators) distinct from the Sugar Porter family.
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Affiliation(s)
- Sara Cabral
- LEAF, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal
| | - Catarina Prista
- LEAF, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal
| | - Maria C Loureiro-Dias
- LEAF, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal
| | - Maria José Leandro
- LEAF, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal
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28
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Wang H, Hu Z, Long F, Niu C, Yuan Y, Yue T. Characterization of Osmotolerant Yeasts and Yeast-Like Molds from Apple Orchards and Apple Juice Processing Plants in China and Investigation of Their Spoilage Potential. J Food Sci 2015; 80:M1850-60. [PMID: 26130165 DOI: 10.1111/1750-3841.12946] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 05/26/2015] [Indexed: 12/01/2022]
Abstract
Yeasts and yeast-like fungal isolates were recovered from apple orchards and apple juice processing plants located in the Shaanxi province of China. The strains were evaluated for osmotolerance by growing them in 50% (w/v) glucose. Of the strains tested, 66 were positive for osmotolerance and were subsequently identified by 26S or 5.8S-ITS ribosomal RNA (rRNA) gene sequencing. Physiological tests and RAPD-PCR analysis were performed to reveal the polymorphism of isolates belonging to the same species. Further, the spoilage potential of the 66 isolates was determining by evaluating their growth in 50% to 70% (w/v) glucose and measuring gas generation in 50% (w/v) glucose. Thirteen osmotolerant isolates representing 9 species were obtained from 10 apple orchards and 53 target isolates representing 19 species were recovered from 2 apple juice processing plants. In total, members of 14 genera and 23 species of osmotolerant isolates including yeast-like molds were recovered from all sources. The commonly recovered osmotolerant isolates belonged to Kluyveromyces marxianus, Hanseniaspora uvarum, Saccharomyces cerevisiae, Zygosaccharomyces rouxii, Candida tropicalis, and Pichia kudriavzevii. The polymorphism of isolates belonging to the same species was limited to 1 to 3 biotypes. The majority of species were capable of growing within a range of glucose concentration, similar to sugar concentrations found in apple juice products with a lag phase from 96 to 192 h. Overall, Z. rouxii was particularly the most tolerant to high glucose concentration with the shortest lag phase of 48 h in 70% (w/v) glucose and the fastest gas generation rate in 50% (w/v) glucose.
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Affiliation(s)
- Huxuan Wang
- College of Food Science and Engineering, Northwest A&F Univ., Yangling, Shaanxi province, 712100, China
| | - Zhongqiu Hu
- College of Food Science and Engineering, Northwest A&F Univ., Yangling, Shaanxi province, 712100, China
| | - Fangyu Long
- College of Food Science and Engineering, Northwest A&F Univ., Yangling, Shaanxi province, 712100, China
| | - Chen Niu
- College of Food Science and Engineering, Northwest A&F Univ., Yangling, Shaanxi province, 712100, China
| | - Yahong Yuan
- College of Food Science and Engineering, Northwest A&F Univ., Yangling, Shaanxi province, 712100, China
| | - Tianli Yue
- College of Food Science and Engineering, Northwest A&F Univ., Yangling, Shaanxi province, 712100, China
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29
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Čadež N, Fülöp L, Dlauchy D, Péter G. Zygosaccharomyces favi sp. nov., an obligate osmophilic yeast species from bee bread and honey. Antonie van Leeuwenhoek 2014; 107:645-54. [PMID: 25528339 DOI: 10.1007/s10482-014-0359-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 12/15/2014] [Indexed: 11/27/2022]
Abstract
Five yeast strains representing a hitherto undescribed yeast species were isolated from bee bread and honey in Hungary. They are obligate osmophilic, i.e. they are unable to grow in/on high water activity culture media. Following isogamous conjugation, they form 1-4 spheroid or subspheroid ascospores in persistent asci. The analysis of the sequences of their large subunit rRNA gene D1/D2 domain placed the new species in the Zygosaccharomyces clade. In terms of pairwise sequence similarity, Zygosaccharomyces gambellarensis is the most closely related species. Comparisons of D1/D2, internal transcribed spacer and translation elongation factor-1α (EF-1α) gene sequences of the five strains with that of the type strain of Z. gambellarensis revealed that they represent a new yeast species. The name Zygosaccharomyces favi sp. nov. (type strain: NCAIM Y.01994(T) = CBS 13653(T) = NRRL Y-63719(T) = ZIM 2551(T)) is proposed for this new yeast species, which based on phenotype can be distinguished from related Zygosaccharomyces species by its obligate osmophilic nature. Some intragenomic sequence variability, mainly indels, was detected among the ITS copies of the strains of the new species.
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Affiliation(s)
- Neža Čadež
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
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Hulin M, Wheals A. Rapid identification of Zygosaccharomyces with genus-specific primers. Int J Food Microbiol 2013; 173:9-13. [PMID: 24382328 DOI: 10.1016/j.ijfoodmicro.2013.12.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 12/02/2013] [Accepted: 12/09/2013] [Indexed: 10/25/2022]
Abstract
There has been a recent and rapid increase in the number of species of the genus Zygosaccharomyces which now comprises Z. bailii, Z. bisporus, Z. gambellarensis, Z. kombuchaensis, Z. lentus, Z. machadoi, Z. mellis, Z. parabaillii, Z. pseudobailii, Z. pseudorouxii, Z. rouxii, Z. sapae, and Z. siamensis. Z. pseudorouxii is an unofficial name given to isolates closely related to the newly-described species Z. sapae. The Zygosaccharomyces genus contains species that are important as food and beverage spoilage organisms and others are associated with fermentations and sweet foodstuffs, such as honey. Their economic significance means that the ability to identify them rapidly is of significant importance. Although Z. rouxii and Z. bailii have been genome-sequenced the extent of sequence data for the others, especially the newly-discovered species, is sometimes extremely limited which makes identification slow. However, parts of the ITS1/5.8S/ITS2 rDNA region contain sequences of sufficient similarity within the genus and of sufficient difference with outgroups, to be potential regions for the design of genus-wide specific primers. We report here the development of genus-specific primers that can detect all the major Zygosaccharomyces species including all those associated with foods; the rare and localised species Z. machadoi and Z. gambellarensis are not detected. The size of the single amplicon produced varies between species and in some cases is sufficiently different to assign provisional species identification. Sequence data from rDNA regions are available for virtually all described yeast species in all genera, thus, prior to having sufficient sequence data from structural genes, rDNA regions may provide more generally suitable candidates for both genus-specific and species-specific primer design.
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Affiliation(s)
- Michelle Hulin
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Alan Wheals
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK.
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Genome Sequence of the Food Spoilage Yeast Zygosaccharomyces bailii CLIB 213T. GENOME ANNOUNCEMENTS 2013; 1:1/4/e00606-13. [PMID: 23969048 PMCID: PMC3751603 DOI: 10.1128/genomea.00606-13] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The ascomycetous yeast Zygosaccharomyces bailii is one of the most problematic spoilage yeasts in food and beverage industries, due to its exceptional resistance to various stresses. A better understanding of the molecular mechanisms underlying these stress resistance phenotypes might help develop strategies to improve food quality. Thus, we determined and annotated the genome sequence of the strain Z. bailii CLIB 213(T) (= CBS 680).
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Suh SO, Gujjari P, Beres C, Beck B, Zhou J. Proposal of Zygosaccharomyces parabailii sp. nov. and Zygosaccharomyces pseudobailii sp. nov., novel species closely related to Zygosaccharomyces bailii. Int J Syst Evol Microbiol 2013; 63:1922-1929. [PMID: 23524351 DOI: 10.1099/ijs.0.048058-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Twenty-three yeast strains traditionally identified as Zygosaccharomyces bailii were studied in order to clarify their taxonomy and phylogenetic relationships. The molecular phylogeny from rRNA gene sequences showed that these yeasts were well divided into three major groups, and two of the groups could be clearly distinguished from the type strain of Z. bailii at the species level. Therefore, we propose Zygosaccharomyces parabailii sp. nov. (type strain ATCC 56075(T) = NBRC 1047(T) = NCYC 128(T) = CBS 12809(T)) and Zygosaccharomyces pseudobailii sp. nov. (type strain ATCC 56074(T) = NBRC 0488(T) = CBS 2856(T)) to accommodate the yeasts belonging to the two groups. By conventional physiological tests, Z. bailii and the two novel species are not clearly distinguished from one another, as variations exist more frequently between individual strains and are not species-specific. However, the conclusions from rRNA gene sequence analyses are well supported by genome fingerprinting patterns as well as other protein-coding gene sequence comparisons.
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Affiliation(s)
- Sung-Oui Suh
- Mycology and Botany Program, American Type Culture Collection (ATCC), 10801 University Blvd, Manassas, VA 20110, USA
| | - Pushpa Gujjari
- Mycology and Botany Program, American Type Culture Collection (ATCC), 10801 University Blvd, Manassas, VA 20110, USA
| | - Carolyn Beres
- bioMérieux, Inc., 595 Anglum Road, Hazelwood, MO 63042, USA
| | - Brian Beck
- Mycology and Botany Program, American Type Culture Collection (ATCC), 10801 University Blvd, Manassas, VA 20110, USA
| | - Jianlong Zhou
- Mycology and Botany Program, American Type Culture Collection (ATCC), 10801 University Blvd, Manassas, VA 20110, USA
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Solieri L, Chand Dakal T, Giudici P. Zygosaccharomyces sapae sp. nov., isolated from Italian traditional balsamic vinegar. Int J Syst Evol Microbiol 2013; 63:364-371. [DOI: 10.1099/ijs.0.043323-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fourteen yeast isolates were recovered from two traditional balsamic vinegar (TBV) samples collected in the provinces of Modena and Reggio Emilia, Italy. Microsatellite-primed-PCR (MSP-PCR) was used to de-replicate the isolate collection into two representative strains, ABT301T and ABT601. Phylogenetic analysis based on the D1/D2 domains of the 26S rRNA gene indicated that these strains represented a distinct species of the genus Zygosaccharomyces, closely related to Zygosaccharomyces rouxii and Zygosaccharomyces mellis. Physiological and morphological tests supported the recognition of a novel taxon of halotolerant, osmotolerant, non-psychrotolerant and maltose-fermentation-negative yeasts showing a chain or star-shaped pattern of budding cells, which remained attached to each other. Morphological observations offered evidence of ascospore formation. A novel species, Zygosaccharomyces sapae sp. nov., is proposed to accommodate these strains, with strain ABT301T ( = CBS 12607T = MUCL 54092T) as the type strain. Based on D1/D2 domain phylogenetic analysis, the novel strains shared the highest sequence similarity (100 %) with Zygosaccharomyces sp. strain NCYC 3042, previously isolated from sugar [James, S. A., Bond, C. J., Stratford, M. & Roberts, I. N. (2005). FEMS Yeast Res 5, 747–755]. However, based on phylogenetic (internal transcribed spacers, ITS), PCR fingerprinting and physiological analyses, marked differences were observed between the novel species and strain NCYC 3042, and these results are discussed in more detail.
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Affiliation(s)
- Lisa Solieri
- Department of Life Sciences, via Amendola 2, Padiglione Besta, University of Modena and Reggio Emilia, 42121 Reggio Emilia, Italy
| | - Tikam Chand Dakal
- Department of Life Sciences, via Amendola 2, Padiglione Besta, University of Modena and Reggio Emilia, 42121 Reggio Emilia, Italy
| | - Paolo Giudici
- Department of Life Sciences, via Amendola 2, Padiglione Besta, University of Modena and Reggio Emilia, 42121 Reggio Emilia, Italy
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Saksinchai S, Suzuki M, Lumyong S, Ohkuma M, Chantawannakul P. Two new species of the genus Candida in the Zygoascus clade, Candida lundiana sp. nov. and Candida suthepensis sp. nov., isolated from raw honey in Thailand. Antonie van Leeuwenhoek 2011; 101:633-40. [PMID: 22105532 DOI: 10.1007/s10482-011-9677-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 11/10/2011] [Indexed: 11/25/2022]
Abstract
During a survey of yeasts associated with raw honey collected in Thailand, two strains of the Zygoascus clade were isolated from the Asian cavity-nesting honeybee Apis cerana and the stingless bee Homotrigona fimbriata. Phylogeny based on 26S rDNA D1/D2 sequences placed these yeasts as members of a clade including Candida bituminiphila, Candida patagonica and Candida polysorbophila. The strains of the two novel species, CBS 12271(T) and CBS 12270(T), respectively, could be unquestionably distinguished from their relatives by rDNA sequences and other taxonomic characteristics. Therefore, the novel anamorphic species, Candida lundiana sp. nov. (type strain CBS 12271(T) = JCM 16823(T)) and Candida suthepensis sp. nov. (type strain CBS 12270(T) = JCM 16822(T)) are described.
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