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Wang X, Bau T. Four New Species of Jelly Fungi from Northeastern China. J Fungi (Basel) 2024; 10:480. [PMID: 39057365 PMCID: PMC11278339 DOI: 10.3390/jof10070480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/06/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Four new species of jelly fungi were described from northeastern China based on morphological and molecular evidence. These new species were classified into the four genera Sirobasidium (Sirobasidium jilinense), Calocera (Calocera velutina), Dacrymyces (Dacrymyces jauensis), and Dacryopinax (Dacryopinax manghanensis). Maximum likelihood and Bayesian analyses were performed using a combined nuc rDNA internal transcribed spacer region (ITS) and nuc 28S rDNA (nrLSU) dataset for the construction of phylogenetic trees. Morphological descriptions, line illustrations, and the ecological habits of these new species are provided.
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Affiliation(s)
- Xia Wang
- College of Mycology, Jilin Agricultural University, Changchun 130118, China;
- Key Laboratory of Edible Fungal Resources and Utilization (North), Ministry of Agriculture and Rural Affairs, Jilin Agricultural University, Changchun 130118, China
| | - Tolgor Bau
- College of Mycology, Jilin Agricultural University, Changchun 130118, China;
- Key Laboratory of Edible Fungal Resources and Utilization (North), Ministry of Agriculture and Rural Affairs, Jilin Agricultural University, Changchun 130118, China
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2
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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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Sipiczki M, Czentye K, Kállai Z. High intragenomic, intergenomic, and phenotypic diversity in pulcherrimin-producing Metschnikowia yeasts indicates a special mode of genome evolution. Sci Rep 2024; 14:10521. [PMID: 38714828 PMCID: PMC11076541 DOI: 10.1038/s41598-024-61335-5] [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: 03/20/2024] [Accepted: 05/04/2024] [Indexed: 05/10/2024] Open
Abstract
In molecular systematics, the delimitation of yeast species is based on the notion that the barcode differences are smaller within species than between them. The most widely used barcodes are segments of the chromosomal repeats coding for ribosomal RNAs that are homogenised in yeasts. The analysis of these segments of the type strains of ten species recently merged in Metschnikowia pulcherrima and 37 new isolates demonstrated that this is not the case in this species. The intragenomic diversity significantly exceeded the threshold gaps used to differentiate related yeast species. Large segments of the D1/D2 domains were not diverse within the genomes and could therefore be used to determine the taxonomic affiliation of the isolates. The genome structures of the isolates were compared by RAPD and the RFLP of the mitochondrial DNA. Both patterns were highly heterogeneous. The sequence analysis of the PUL4 gene (a member of the PUL gene cluster involved in pulcherrimin production) revealed very high intragenomic differences, suggesting that the genomes may be chimerised. Three phenotypic traits related to the antimicrobial antagonism characteristic of the species were also highly diverse and prone to reversible segregation resembling epigenetic processes (silencing and reactivation of regulators) rather than mutations and back-mutations. These features make M. pulcherrima unique among yeasts and indicate that it evolves in a non-standard way.
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Affiliation(s)
- Matthias Sipiczki
- Department of Genetics and Applied Microbiology, University of Debrecen, Debrecen, Hungary.
| | - Kinga Czentye
- Department of Genetics and Applied Microbiology, University of Debrecen, Debrecen, Hungary
| | - Zoltán Kállai
- Department of Genetics and Applied Microbiology, University of Debrecen, Debrecen, Hungary
- Institute of Horticulture, University of Debrecen, Debrecen, Hungary
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Takei S, Teramoto K, Fujimura J, Fujiwara M, Suzuki M, Fukui Y, Sekiguchi Y, Kawakami T, Chonan M, Wakita M, Horiuchi Y, Miida T, Naito T, Kirikae T, Tada T, Tabe Y. Isolation and identification of Wickerhamiella tropicalis from blood culture by MALDI-MS. Front Cell Infect Microbiol 2024; 14:1361432. [PMID: 38510957 PMCID: PMC10953818 DOI: 10.3389/fcimb.2024.1361432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
Wickerhamiella is a genus of budding yeast that is mainly isolated from environmental samples, and 40 species have been detected. The yeast isolated from human clinical samples usually only contain three species: W. infanticola, W. pararugosa and W. sorbophila. In this study, we isolated W. tropicalis from a blood sample of a six-year-old female with a history of B-cell precursor lymphoblastic leukemia in Japan in 2022. Though the strain was morphologically identified as Candida species by routine microbiological examinations, it was subsequently identified as W. tropicalis by sequencing the internal transcribed spacer (ITS) of ribosomal DNA (rDNA). The isolate had amino acid substitutions in ERG11 and FKS1 associated with azole and echinocandin resistance, respectively, in Candida species and showed intermediate-resistant to fluconazole and micafungin. The patient was successfully treated with micafungin. Furthermore, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) detected three novel peaks that are specific for W. tropicalis, indicating that MALDI-MS analysis is useful for rapid detection of Wickerhamiella species in routine microbiological examinations.
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Affiliation(s)
- Satomi Takei
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of MALDI-TOF MS Practical Application Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kanae Teramoto
- Department of MALDI-TOF MS Practical Application Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Analytical & Measurement Instruments Division, Shimadzu Corporation, Kyoto, Japan
| | - Junya Fujimura
- Department of Pediatrics, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Megumi Fujiwara
- Department of Pediatrics, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Mai Suzuki
- Department of General Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yukiko Fukui
- Department of General Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Takaaki Kawakami
- Department of Clinical Laboratory, Juntendo University Hospital, Tokyo, Japan
| | - Masayoshi Chonan
- Department of Clinical Laboratory, Juntendo University Hospital, Tokyo, Japan
| | - Mitsuru Wakita
- Department of Clinical Laboratory, Juntendo University Hospital, Tokyo, Japan
| | - Yuki Horiuchi
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Takashi Miida
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Toshio Naito
- Department of MALDI-TOF MS Practical Application Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of General Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Teruo Kirikae
- Department of MALDI-TOF MS Practical Application Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Microbiome Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Tatsuya Tada
- Department of Microbiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yoko Tabe
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of MALDI-TOF MS Practical Application Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
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5
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Brysch-Herzberg M, Jia GS, Sipiczki M, Seidel M, Zhang WC, Du LL. Reinstatement of the fission yeast species Schizosaccharomyces versatilis Wickerham et Duprat, a sibling species of Schizosaccharomyces japonicus. Yeast 2024; 41:108-127. [PMID: 38450805 DOI: 10.1002/yea.3922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 03/08/2024] Open
Abstract
Schizosaccharomyces japonicus Yukawa et Maki (1931) and Schizosaccharomyces versatilis Wickerham et Duprat (1945) have been treated as varieties of S. japonicus or as conspecific, based on various approaches including mating trials and nDNA/nDNA optical reassociation studies. However, the type strains of S. japonicus and S. versatilis differ by five substitutions (99.15% identity) and one 1-bp indel in the sequences of the D1/D2 domain of the 26S rRNA gene, and 23 substitutions (96.3% identity) and 31-bp indels in the sequences of internal transcribed spacer (ITS) of rRNA, suggesting that they may not be conspecific. To reassess their taxonomic status, we conducted mating trials and whole-genome analyses. Mating trials using the type strains showed a strong but incomplete prezygotic sterility barrier, yielding interspecies mating products at two orders of magnitude lower efficiency than intraspecies matings. These mating products, which were exclusively allodiploid hybrids, were unable to undergo the haplontic life cycle of the parents. We generated chromosome-level gap-less genome assemblies for both type strains. Whole genome sequences yielded an average nucleotide identity (ANI) of 86.4%, indicating clear separation of S. japonicus and S. versatilis. Based on these findings, we propose the reinstatement of S. versatilis as a distinct species (holotype strain: CBS 103T and ex-types: NRRL Y-1026, NBRC 1607, ATCC 9987, PYCC 7100; Mycobank no.: 847838).
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Affiliation(s)
- Michael Brysch-Herzberg
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University, Heilbronn, Germany
| | - Guo-Song Jia
- National Institute of Biological Sciences, Beijing, China
| | - Matthias Sipiczki
- Department of Genetics and Applied Microbiology, University of Debrecen, Debrecen, Hungary
| | - Martin Seidel
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University, Heilbronn, Germany
| | - Wen-Cai Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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Chai CY, Ke T, Niu QH, Hui FL. Diversity of Wickerhamomyces (Wickerhamomycetaceae, Saccharomycetales) in China with the description of four new species. Front Microbiol 2024; 15:1338231. [PMID: 38389540 PMCID: PMC10881795 DOI: 10.3389/fmicb.2024.1338231] [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: 11/14/2023] [Accepted: 01/15/2024] [Indexed: 02/24/2024] Open
Abstract
Wickerhamomyces is a well-known genus of the family Wickerhamomycetaceae in the class Ascomycetes. These fungi can survive in a variety of substrates and environments and perform many valuable roles in both industrial processes and the natural ecosystems. During our investigation of yeast diversity associated with plant materials, 53 Wickerhamomyces isolates were obtained from rotting wood and plant leaves collected in Fujian, Guizhou, Henan, and Yunnan Provinces of China. Isolates were identified as 14 Wickerhamomyces species, including 1 species known previously to occur in China (W. anomalus), 9 new record species in China (W. arborarius, W. ciferrii, W. edaphicus, W. lynferdii, W. pijperi, W. subpelliculosa, W. xylosica, W. strasburgensis, and W. sydowiorum), and 4 novel species (W. guiyangensis sp. nov., W. paramyanmarensis sp. nov., W. quanzhouensis sp. nov., and W. phyllophilus sp. nov.). This study presents a detailed account of these new species, illustrating their morphology and analyzing their phylogenetic relationships with other Wickerhamomyces species. Our study is the first comprehensive study on Wickerhamomyces species associated with plant materials from tropical and subtropical China. The results of this study update our understanding of the phylogenetic relationships, systematics, and ecology of Wickerhamomyces.
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Affiliation(s)
- Chun-Yue Chai
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
- Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Nanyang Normal University, Nanyang, China
| | - Tao Ke
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
- Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Nanyang Normal University, Nanyang, China
| | - Qiu-Hong Niu
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
- Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Nanyang Normal University, Nanyang, China
| | - Feng-Li Hui
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
- Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Nanyang Normal University, Nanyang, China
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Lu YF, Chai CY, Hui FL. Two new Erythrobasidium species inhabiting the phyllosphere discovered in the Baotianman Nature Reserve in China. Front Microbiol 2024; 15:1287984. [PMID: 38380097 PMCID: PMC10876860 DOI: 10.3389/fmicb.2024.1287984] [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: 09/03/2023] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
The genus Erythrobasidium is kind of species-scarce and undersampling basidiomycetes. Currently, only six species have been accepted into the genus and the diversity still remains incompletely understood. In this study, five Erythrobasidium strains were isolated in the surface of plant leaves collected from the Baotianman Nature Reserve, Henan Province, central China. Phylogenetic analyses of the small ribosomal subunit (SSU) rRNA gene, the internal transcribed spacer (ITS) region, the D1/D2 domain of the large subunit (LSU) rRNA gene, and the translation elongation factor 1-α (TEF1-α) gene coupled with morphological studies were employed to characterize and identify these isolates. As a result of these, two new species, namely E. turpiniae sp. nov. and E. nanyangense sp. nov., were delimited and proposed based on morphological and molecular evidence. A detailed description and illustration of both new species, as well as their differences with the close relatives in the genus are provided. An identification key for Erythrobasidium species is also provided. This study provides further insights into our understanding of Erythrobasidium species.
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Affiliation(s)
- Yun-Feng Lu
- School of Life Sciences and Agricultural Engineering, Nanyang Normal University, Nanyang, China
- Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Nanyang Normal University, Nanyang, China
| | - Chun-Yue Chai
- School of Life Sciences and Agricultural Engineering, Nanyang Normal University, Nanyang, China
- Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Nanyang Normal University, Nanyang, China
| | - Feng-Li Hui
- School of Life Sciences and Agricultural Engineering, Nanyang Normal University, Nanyang, China
- Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Nanyang Normal University, Nanyang, China
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Salerno A, D’Amico M, Bergamini C, Maggiolini FAM, Vendemia M, Prencipe A, Catacchio CR, Ventura M, Cardone MF, Marsico AD. On the Way to the Technological Development of Newly Selected Non- Saccharomyces Yeasts Selected as Innovative Biocontrol Agents in Table Grapes. Microorganisms 2024; 12:340. [PMID: 38399744 PMCID: PMC10891982 DOI: 10.3390/microorganisms12020340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 01/29/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Post-harvest decay of fresh table grapes causes considerable annual production losses. The main fungal agents of decay both in pre- and post-harvest are B. cinerea, Penicillium spp., Aspergillus spp., Alternaria spp., and Cladosporium spp. To date, the use of agrochemicals and SO2 are the main methods to control grape molds in pre- and postharvest, respectively. Significant improvements, however, have already been made in to apply innovative and more environmentally sustainable control strategies, such as Biological Control Agents (BCAs), which can reduce disease severity in both pre- and post-harvest. In this study, 31 new non-Saccharomyces yeast strains, isolated from berries of native Apulian table grape genotypes, were tested for their in vivo effectiveness against grey mold of table grapes, resulting in two St. bacillaris ('N22_I1' and 'S13_I3'), one S. diversa ('N22_I3'), one A. pullulans ('OLB_9.1_VL') and one H. uvarum ('OLB_9.1_BR') yeast strains that were marked as efficient and good BCAs. Their mechanisms of action were characterized through in vitro assays, and additional characteristics were evaluated to assess the economic feasibility and viability for future technological employment. Their effectiveness was tested by reducing the working concentration, their antagonistic effect on a wide range of fungal pathogens, their ability to survive in formulations with long shelf life, and their safety to human health.
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Affiliation(s)
- Antonella Salerno
- Council for Agricultural Research and Economics, Research Center Viticulture and Enology (CREA-VE), Via Casamassima 148, 70010 Turi, Italy; (A.S.); (C.B.); (F.A.M.M.)
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, Via Orabona 4, 70125 Bari, Italy (C.R.C.); (M.V.)
| | - Margherita D’Amico
- Council for Agricultural Research and Economics, Research Center Viticulture and Enology (CREA-VE), Via Casamassima 148, 70010 Turi, Italy; (A.S.); (C.B.); (F.A.M.M.)
| | - Carlo Bergamini
- Council for Agricultural Research and Economics, Research Center Viticulture and Enology (CREA-VE), Via Casamassima 148, 70010 Turi, Italy; (A.S.); (C.B.); (F.A.M.M.)
| | - Flavia Angela Maria Maggiolini
- Council for Agricultural Research and Economics, Research Center Viticulture and Enology (CREA-VE), Via Casamassima 148, 70010 Turi, Italy; (A.S.); (C.B.); (F.A.M.M.)
| | - Marco Vendemia
- Council for Agricultural Research and Economics, Research Center Viticulture and Enology (CREA-VE), Via Casamassima 148, 70010 Turi, Italy; (A.S.); (C.B.); (F.A.M.M.)
| | - Annalisa Prencipe
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, Via Orabona 4, 70125 Bari, Italy (C.R.C.); (M.V.)
| | - Claudia Rita Catacchio
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, Via Orabona 4, 70125 Bari, Italy (C.R.C.); (M.V.)
| | - Mario Ventura
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, Via Orabona 4, 70125 Bari, Italy (C.R.C.); (M.V.)
| | - Maria Francesca Cardone
- Council for Agricultural Research and Economics, Research Center Viticulture and Enology (CREA-VE), Via Casamassima 148, 70010 Turi, Italy; (A.S.); (C.B.); (F.A.M.M.)
| | - Antonio Domenico Marsico
- Council for Agricultural Research and Economics, Research Center Viticulture and Enology (CREA-VE), Via Casamassima 148, 70010 Turi, Italy; (A.S.); (C.B.); (F.A.M.M.)
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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 2024:10.1007/s10123-024-00482-1. [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] [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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Lu YF, Chai CY, Hui FL. Two new phyllospheric species of Colacogloea (Colacogloeaceae, Pucciniomycotina) identified in China. MycoKeys 2024; 101:81-94. [PMID: 38250087 PMCID: PMC10799300 DOI: 10.3897/mycokeys.101.114872] [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: 10/29/2023] [Accepted: 12/20/2023] [Indexed: 01/23/2024] Open
Abstract
During our ongoing survey of basidiomycetous yeasts associated with plant leaves in virgin forest, five Colacogloea strains were isolated in the Baotianman Nature Reserve, Henan Province, central China. Phenotypes from cultures and a phylogeny based on the internal transcribed spacer (ITS) regions and the D1/D2 domains of the large subunit (LSU) rRNA gene were employed to characterize and identify these isolates. As a result, two new species, namely Colacogloeaceltidissp. nov. and C.pararetinophilasp. nov., are introduced herein. In the phylogeny of combined ITS and LSU dataset, the new species C.celtidissp. nov. formed a clade with the unpublished Colacogloea strain (KBP: Y-6832), and together these formed the sister group to C.armeniacae, while C.pararetinophilasp. nov. was retrieved as a sister to C.retinophila. A detailed description and illustration of both new species, as well as the differences between them and their closest relatives in the genus are provided. Results from the present study will add to our knowledge of the biodiversity of Colacogloea in China.
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Affiliation(s)
- Yun-Feng Lu
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, ChinaNanyang Normal UniversityNanyangChina
| | - Chun-Yue Chai
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, ChinaNanyang Normal UniversityNanyangChina
| | - Feng-Li Hui
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, ChinaNanyang Normal UniversityNanyangChina
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Grandhay C, Prétot E, Klaba V, Celle H, Normand AC, Bertrand X, Grenouillet F. Yeast Biodiversity of Karst Waters: Interest of Four Culture Media and an Improved MALDI-TOF MS Database. MICROBIAL ECOLOGY 2024; 87:26. [PMID: 38175217 PMCID: PMC10766713 DOI: 10.1007/s00248-023-02336-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024]
Abstract
Karst aquifers are a significant source of drinking water and highly vulnerable to pollution and microbial contamination. Microbiological regulations for the quality of drinking water mostly focus on bacterial levels and lack guidance concerning fungal contamination. Moreover, there is no standardised microbial analysis methodology for identifying fungi in water. Our main objective was to establish the most effective culture and identification methodology to examine yeast diversity in karst waters. We assessed the comparative efficacy of four culture media (CHROMagar Candida, dichloran glycerol 18% [DG18], dichloran rose Bengal chloramphenicol [DRBC], and SYMPHONY agar) for yeast isolation from karst water samples. Furthermore, we investigated the comprehensiveness of databases used in MALDI-TOF mass spectrometry (MALDI-TOF MS) for identifying environmental yeast species. In total, we analysed 162 water samples, allowing the identification of 2479 yeast isolates. We demonstrate that a combination of four culture media, each with distinct specifications, more efficiently covers a wide range of yeast species in karst water than a combination of only two or three. Supplementation of a MALDI-TOF MS database is also critical for analysing environmental microbial samples and improved the identification of yeast biodiversity. This study is an initial step towards standardising the analysis of fungal biodiversity in karst waters, enabling a better understanding of the significance of this environmental reservoir in relation to public health.
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Affiliation(s)
- Clément Grandhay
- Université de Franche-Comté, CHU Besançon, CNRS, Chrono-environnement, F-25000, Besançon, France
| | - Emma Prétot
- Université de Franche-Comté, CHU Besançon, CNRS, Chrono-environnement, F-25000, Besançon, France
| | - Victor Klaba
- Université de Franche-Comté, CNRS, Chrono-environnement, F-25000, Besançon, France
| | - Hélène Celle
- Université de Franche-Comté, CNRS, Chrono-environnement, F-25000, Besançon, France
| | - Anne-Cécile Normand
- AP-HP, Groupe Hospitalier La Pitié-Salpêtrière, Service de Parasitologie Mycologie, 75013, Paris, France
| | - Xavier Bertrand
- Université de Franche-Comté, CHU Besançon, CNRS, Chrono-environnement, F-25000, Besançon, France
- Université de Franche-Comté, CNRS, Chrono-environnement, F-25000, Besançon, France
| | - Frédéric Grenouillet
- Université de Franche-Comté, CHU Besançon, CNRS, Chrono-environnement, F-25000, Besançon, France.
- Université de Franche-Comté, CNRS, Chrono-environnement, F-25000, Besançon, France.
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Araya M, Villarreal P, Moyano T, Santos ARO, Díaz FP, Bustos-Jarufe A, Urbina K, Del Pino JE, Groenewald M, Gutiérrez RA, Rosa CA, Cubillos FA. Nakazawaea atacamensis f.a., sp. nov. a novel nonconventional fermentative ascomycetous yeast species from the Atacama Desert. Yeast 2024; 41:52-63. [PMID: 38146767 DOI: 10.1002/yea.3920] [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: 07/12/2023] [Revised: 11/29/2023] [Accepted: 12/09/2023] [Indexed: 12/27/2023] Open
Abstract
In this study, we describe Nakazawaea atacamensis f. a., sp. nov., a novel species obtained from Neltuma chilensis plant samples in Chile's hyperarid Atacama Desert. In total, three strains of N. atacamensis were obtained from independent N. chilensis samples (synonym Prosopis chilensis, Algarrobo). Two strains were obtained from bark samples, while the third strain was obtained from bark-exuded gum from another tree. The novel species was defined using molecular characteristics and subsequently characterized with respect to morphological, physiological, and biochemical properties. A neighbor-joining analysis using the sequences of the D1/D2 domains of the large subunit ribosomal RNA gene revealed that N. atacamensis clustered with Nakazawaea pomicola. The sequence of N. atacamensis differed from closely related species by 1.3%-5.2% in the D1/D2 domains. A phylogenomic analysis based on single-nucleotide polymorphism's data confirms that the novel species belongs to the genus Nakazawaea, where N. atacamensis clustered with N. peltata. Phenotypic comparisons demonstrated that N. atacamensis exhibited distinct carbon assimilation patterns compared to its related species. Genome sequencing of the strain ATA-11A-BT revealed a genome size of approximately 12.4 Mbp, similar to other Nakazawaea species, with 5116 protein-coding genes annotated using InterProScan. In addition, N. atacamensis exhibited the capacity to ferment synthetic wine must, representing a potential new yeast for mono or co-culture wine fermentations. This comprehensive study expands our understanding of the genus Nakazawaea and highlights the ecological and industrial potential of N. atacamensis in fermentation processes. The holotype of N. atacamensis sp. nov. is CBS 18375T . The Mycobank number is MB 849680.
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Affiliation(s)
- Macarena Araya
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Pablo Villarreal
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Tomás Moyano
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ana R O Santos
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Francisca P Díaz
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Instituto de Geografía, Facultad de Ciencias del Mar y Geografía, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
- Núcleo Milenio de Ecología Histórica Aplicada para los Bosques Áridos (AFOREST), Santiago, Chile
| | | | - Kamila Urbina
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Millennium Nucleus of Patagonian Limit of Life (LiLi), Valdivia, Chile
| | - Javier E Del Pino
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | | | - Rodrigo A Gutiérrez
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Institute Center for Genome Regulation, Institute of Ecology and Biodiversity, Santiago, Chile
| | - Carlos A Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Francisco A Cubillos
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Millennium Nucleus of Patagonian Limit of Life (LiLi), Valdivia, Chile
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13
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Guo QC, Liu S, Hui FL. Spencermartinsiella henanensis fa., sp. nov., a novel yeast species isolated from rotting wood. Int J Syst Evol Microbiol 2024; 74. [PMID: 38190334 DOI: 10.1099/ijsem.0.006226] [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] [Indexed: 01/10/2024] Open
Abstract
Two yeast strains (NYNU 211162 and NYNU 211275) were isolated from rotting wood collected in the Baotianman Nature Reserve, Henan Province, central China. Phylogenetic analysis of the D1/D2 domain of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region revealed that the strains represent a phylogenetically distinct species within the genus Spencermartinsiella. The name Spencermartinsiella henanensis fa., sp. nov. is proposed for this species with holotype CICC 33543T (Mycobank MB 851142). S. henanensis sp. nov. differed by only 3 nt (~0.5 %) substitutions from the closest known species S. europaea NCAIM Y.01817T in the D1/D2 domain, but by 33 nt (~6 %) substitutions, 34 nt (~3.8 %) substitutions, 30 nt (~5.6 %) substitutions and 75 nt (~9.9 %) substitutions in the ITS region and the partial TEF1, COXII and RPB2 genes. Additionally, S. henanensis sp. nov. can be physiologically distinguished from S. europaea by its ability to assimilate inulin, inability to assimilate ethylamine and cadaverine, and incapability of growth at 30 °C.
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Affiliation(s)
- Qi-Chao Guo
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, PR China
| | - Shan Liu
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, PR China
| | - Feng-Li Hui
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, PR China
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Hamaguchi A, Umeshita K, Taguchi H, Sasano Y. Spathaspora quercus f.a., sp. nov., a novel yeast isolated from rotting wood and a lichen sample in Kyushu region, Japan. Int J Syst Evol Microbiol 2024; 74. [PMID: 38285485 DOI: 10.1099/ijsem.0.006254] [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] [Indexed: 01/30/2024] Open
Abstract
Four novel d-xylose assimilation yeast strains were isolated from rotting wood and a lichen sample collected in the Kyushu region of Japan. Species identifications were performed by analysing the internal transcribed spacer 5.8S region sequences and the D1/D2 variable domain of the large subunit rRNA gene. Phylogenetic analysis suggested that these isolates are closely related to Spathaspora species isolated in China, such as S. jiuxiensis and S. parajiuxiensis. These isolates also showed sequence similarity to deposited sequences labelled as Schwanniomyces. They did not produce asci and ascospores under any of the test conditions. Based on phylogenetic analysis and phenotypic differences, Spathaspora quercus f.a., sp. nov. is proposed to accommodate these isolates. The holotype of Spathaspora quercus f.a., sp. nov. is NBRC 116146T (CBS18366). This species is able to ferment d-xylose, and a d-xylose fermentation test revealed that this species produces a considerable amount of xylitol.
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Affiliation(s)
- Ayuki Hamaguchi
- Department of Biotechnology and Life Sciences, Faculty of Biotechnology and Life Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto, 860-0082, Japan
| | - Katsuhiro Umeshita
- Department of Biotechnology and Life Sciences, Faculty of Biotechnology and Life Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto, 860-0082, Japan
| | - Hisataka Taguchi
- Department of Biotechnology and Life Sciences, Faculty of Biotechnology and Life Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto, 860-0082, Japan
| | - Yu Sasano
- Department of Biotechnology and Life Sciences, Faculty of Biotechnology and Life Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto, 860-0082, Japan
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15
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Kim JS, Lee M, Heo J, Kwon SW, Yun BS, Kim Y. Neodothiora pruni sp. nov., a Biosurfactant-Producing Ascomycetous Yeast Species Isolated from Flower of Prunus mume. MYCOBIOLOGY 2023; 51:388-392. [PMID: 38179118 PMCID: PMC10763881 DOI: 10.1080/12298093.2023.2282257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 11/07/2023] [Indexed: 01/06/2024]
Abstract
A yeast strain, designated as JAF-11T, was isolated from flower of Prunus mume Sieb. et Zucc. in Gwangyang, Republic of Korea. Phylogenetic analysis showed that strain JAF-11T was closely related to Neodothiora populina CPC 39399T with 2.07 % sequence divergence (12 nucleotide substitutions and three gaps in 581 nucleotides) in the D1/D2 domain of the large subunit (LSU) rRNA gene, and Rhizosphaera macrospora CBS 208.79T with 4.66 % sequence divergence (25 nucleotide substitutions and five gaps in 535 nucleotides) in the internal transcribed spacer (ITS) region. Further analysis based on the concatenated sequences of the D1/D2 domain of the LSU rRNA gene and the ITS region confirmed that strain JAF-11T was well-separated from Neodothiora populina CPC 39399T. In addition to the phylogenetic differences, strain JAF-11T was distinguished from its closest species, Neodothiora populina CPC 39399T and Rhizosphaera macrospora CBS 208.79T belonging to the family Dothioraceae by its phenotypic characteristics, such as assimilation of carbon sources. Hence, the name Neodothiora pruni sp. nov. is proposed with type strain JAF-11T (KACC 48808T; MB 850034).
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Affiliation(s)
- Jeong-Seon Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
| | - Miran Lee
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
| | - Jun Heo
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
| | - Bong-Sik Yun
- Division of Biotechnology and Advanced institute of Environmental and Bioscience, College of Environmental and Bioresource Sciences, Jeonbuk National University, Iksan, Republic of Korea
| | - Yiseul Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
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16
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Borman AM, Johnson EM. Changes in fungal taxonomy: mycological rationale and clinical implications. Clin Microbiol Rev 2023; 36:e0009922. [PMID: 37930182 PMCID: PMC10732072 DOI: 10.1128/cmr.00099-22] [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: 05/22/2023] [Accepted: 07/13/2023] [Indexed: 11/07/2023] Open
Abstract
Numerous fungal species of medical importance have been recently subjected to and will likely continue to undergo nomenclatural changes as a result of the application of molecular approaches to fungal classification together with abandonment of dual nomenclature. Here, we summarize those changes affecting key groups of fungi of medical importance, explaining the mycological (taxonomic) rationale that underpinned the changes and the clinical relevance/importance (where such exists) of the key nomenclatural revisions. Potential mechanisms to mitigate unnecessary taxonomic instability are suggested, together with approaches to raise awareness of important changes to minimize potential clinical confusion.
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Affiliation(s)
- Andrew M. Borman
- UK HSA National Mycology Reference Laboratory, Science Quarter, Southmead Hospital, Bristol, United Kingdom
- Medical Research Council Centre for Medical Mycology (MRC CMM), University of Exeter, Exeter, United Kingdom
| | - Elizabeth M. Johnson
- UK HSA National Mycology Reference Laboratory, Science Quarter, Southmead Hospital, Bristol, United Kingdom
- Medical Research Council Centre for Medical Mycology (MRC CMM), University of Exeter, Exeter, United Kingdom
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17
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Čadež N, Boundy-Mills K, Botha A, Kachalkin A, Dlauchy D, Péter G. Taxogenomic placement of Rasporella oleae and Rasporella dianae gen. and spp. nov., two insect associated yeast species. Yeast 2023; 40:594-607. [PMID: 37885298 DOI: 10.1002/yea.3904] [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: 08/07/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
During the course of independent studies in Europe, North America, and Africa, seven yeast strains were isolated from insect frass, decaying wood, tree flux, and olive oil sediment. Phylogenetic analysis of two barcoding DNA regions (internal transcribed spacer and the D1/D2 domain of the LSU rRNA gene) revealed that they belong to two closely related undescribed species distinct from all genera in the family Debaryomycetaceae. For reliable taxonomic placement the genomes of four strains of the two novel species and six type strains of closely related species were sequenced. Orthologous genes from 54 genomes of representatives of the Pichiomycetes and 23 outgroup taxa were concatenated to construct a fully supported phylogenetic tree. Consistent with the assumptions, we found that the two new species belong to a novel genus. In addition, the delimitation of the novel species was supported by genetic distance calculations from average nucleotide identity (ANI) and digital DNA:DNA hybridization (dDDH) values. The physiological characterization of the novel species was generally consistent with their genomic content. All strains had two alleles encoding secretory lipase in either two or three copies depending on the species. However, lipolytic activity was detected only in strains with three copies of the secretory lipase gene. Nevertheless, lipolytic activity might be related to their association with the insect gut. Based on these results, formal descriptions of the new genus Rasporella gen. nov. and of two new species Rasporella dianae sp. nov. (holotype UCDFST 68-643T , MycoBank no.: 850238) and Rasporella oleae sp. nov. (holotype ZIM 2471T , MycoBank no.: 850126) are provided.
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Affiliation(s)
- Neža Čadež
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Kyria Boundy-Mills
- Phaff Yeast Culture Collection, Food Science and Technology, University of California Davis, Davis, California, USA
| | - Alfred Botha
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Aleksey Kachalkin
- Soil Biology Department, Faculty of Soil Science, M. V. Lomonosov Moscow State University, Moscow, Russia
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of RAS, Pushchino, Russia
| | - Dénes Dlauchy
- National Collection of Agricultural and Industrial Microorganisms, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
| | - Gábor Péter
- National Collection of Agricultural and Industrial Microorganisms, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
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18
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Taha MD, Didinen BI, Emek Onuk E, Metin S, Yilmaz S, Mohamed AA, Pakır S, Gülşen O, Abdel-Latif HMR. Identification of four autochthonous yeasts from the intestines of goldfish, Carassius auratus with potential probiotic properties and their effects on the most common fish bacterial pathogens. Microb Pathog 2023; 184:106381. [PMID: 37806502 DOI: 10.1016/j.micpath.2023.106381] [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: 06/06/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/10/2023]
Abstract
In aquaculture, probiotic yeasts have gained particular interest because of their numerous health benefits for farmed fish. Many autochthonous yeasts have been isolated and identified from fish species with potential probiotic characteristics. In the present study, four autochthonous yeast strains were identified and characterized from the intestinal tracts of 16 healthy goldfish, Carassius auratus. Their in vitro probiotic properties were examined in terms of cell surface hydrophobicity, co-aggregation, and tolerability to different pH values and bile salt concentrations. These strains were identified by culture characters and sequence analysis of ITS (Internal Transcribed Spacer) gene regions. Four strains, namely Cutaneotrichosporon jirovecii isolate jpn01, Debaryomyces nepalensis isolate jpn02, Blastobotrys proliferans isolate jpn05, and Diutina catenulata isolate jpn06, were identified and added to the NCBI GenBank with accession numbers defined as MT584874.1, MT584873.1, MT649918.1, and MT501155.1, respectively. Results demonstrated the capability of these strains to co-aggregate with several fish-associated bacterial pathogens such as Lactococcus garvieae, Vagococcus salmoninarum, Vibrio anguillarum, Yersinia ruckeri, and Aeromonas hydrophila. Only the jpn05 strain did not co-aggregate with A. hydrophila. All identified yeast isolates could grow and tolerate low pH conditions (pH 2.0) and bile salt concentrations (up to 1.5%). Of interest, the hydrophobicity (%) of the yeast isolates was 80%, 94.0%, 80.6%, and 66.4% for jpn01, jpn02, jpn05, and jpn06 isolates, respectively. In this context, our data provide important in vitro evidence for the potential probiotic features of the yeast isolates. These strains could be considered candidate probiotic yeasts; however, their application in aquaculture nutrition necessitates further in vivo assays.
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Affiliation(s)
- Mohanad Dheyaa Taha
- Egirdir Fisheries Faculty, Isparta University of Applied Sciences, 32260, Isparta, Turkey
| | - Behire Işıl Didinen
- Egirdir Fisheries Faculty, Isparta University of Applied Sciences, 32260, Isparta, Turkey
| | - Ertan Emek Onuk
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Ondokuz Mayis University, Samsun, 55139, Turkey
| | - Seçil Metin
- Egirdir Fisheries Faculty, Isparta University of Applied Sciences, 32260, Isparta, Turkey
| | - Sevdan Yilmaz
- Department of Aquaculture, Faculty of Marine Sciences and Technology, Çanakkale Onsekiz Mart University, Çanakkale, 17100, Turkey.
| | - Abdiasis Ahmed Mohamed
- Egirdir Fisheries Faculty, Isparta University of Applied Sciences, 32260, Isparta, Turkey
| | - Sırrı Pakır
- Egirdir Fisheries Faculty, Isparta University of Applied Sciences, 32260, Isparta, Turkey
| | - Ozan Gülşen
- Egirdir Fisheries Faculty, Isparta University of Applied Sciences, 32260, Isparta, Turkey
| | - Hany M R Abdel-Latif
- Department of Poultry and Fish Diseases, Faculty of Veterinary Medicine, Alexandria University, Alexandria, 22758, Egypt.
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Zapałowska A, Skwiercz A, Tereba A, Puchalski C, Malewski T. Next-Generation Sequencing for Evaluating the Soil Nematode Diversity and Its Role in Composting Processes. Int J Mol Sci 2023; 24:15749. [PMID: 37958731 PMCID: PMC10650539 DOI: 10.3390/ijms242115749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/26/2023] [Accepted: 10/28/2023] [Indexed: 11/15/2023] Open
Abstract
Biodiversity within composting systems involves a variety of microorganisms including nematodes. In the research, nematode populations were monitored within six simultaneously operating composting processes. These processes involved varying proportions of feedstock materials. The primary objective was to evaluate the consistency of nematode community succession patterns across the composting processes over a time of 3 months. During the study, samples were taken every month to isolate nematodes, determine the population density of the five trophic groups (per genus) and determine the dominant nematode species. It was shown that the bacterial-feeding community maintained dominance, while the fungus-feeding nematodes gradually increased in dominance as the maturation process progressed. The presence of predatory nematodes Mononchoides which were initially absent, along with the total absence of parasitic nematodes in the late stages of waste stabilization, serves as strong evidence for the reliable evaluation of the biodegradable waste processing level. Based on the obtained results, it is evident that the succession of nematode communities holds promise as a reliable method for evaluating compost maturity.
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Affiliation(s)
- Anita Zapałowska
- Department of Agriculture and Waste Management, Collegium of Natural Sciences, University of Rzeszów, St. Ćwiklinskiej 1a, 35-601 Rzeszów, Poland
| | - Andrzej Skwiercz
- National Institute of Horticultural Research, Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland;
| | - Anna Tereba
- Department of Forest Ecology, Forest Research Institute, Braci Leśnej 3, Sękocin Stary, 05-090 Raszyn, Poland;
| | - Czesław Puchalski
- Department of Bioenergetics, Food Analysis and Microbiology, Institute of Food Technology and Nutrition, Collegium of Natural Sciences, University of Rzeszów, St. Ćwiklińskiej 2D, 35-601 Rzeszów, Poland;
| | - Tadeusz Malewski
- Department of Molecular and Biometric Techniques, Museum and Institute of Zoology, Polish Academy of Sciences, 00-679 Warsaw, Poland;
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20
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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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21
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Renzi S, Nenciarini S, Bacci G, Cavalieri D. Yeast metagenomics: analytical challenges in the analysis of the eukaryotic microbiome. MICROBIOME RESEARCH REPORTS 2023; 3:2. [PMID: 38455081 PMCID: PMC10917621 DOI: 10.20517/mrr.2023.27] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 10/09/2023] [Accepted: 10/17/2023] [Indexed: 03/09/2024]
Abstract
Even if their impact is often underestimated, yeasts and yeast-like fungi represent the most prevalent eukaryotic members of microbial communities on Earth. They play numerous roles in natural ecosystems and in association with their hosts. They are involved in the food industry and pharmaceutical production, but they can also cause diseases in other organisms, making the understanding of their biology mandatory. The ongoing loss of biodiversity due to overexploitation of environmental resources is a growing concern in many countries. Therefore, it becomes crucial to understand the ecology and evolutionary history of these organisms to systematically classify them. To achieve this, it is essential that our knowledge of the mycobiota reaches a level similar to that of the bacterial communities. To overcome the existing challenges in the study of fungal communities, the first step should be the establishment of standardized techniques for the correct identification of species, even from complex matrices, both in wet lab practices and in bioinformatic tools.
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Affiliation(s)
| | | | | | - Duccio Cavalieri
- Correspondence to: Prof. Duccio Cavalieri, Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino 50019, Italy. E-mail:
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22
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Kobayashi Y, Kayamori A, Aoki K, Shiwa Y, Matsutani M, Fujita N, Sugita T, Iwasaki W, Tanaka N, Takashima M. Chromosome-level genome assemblies of Cutaneotrichosporon spp. (Trichosporonales, Basidiomycota) reveal imbalanced evolution between nucleotide sequences and chromosome synteny. BMC Genomics 2023; 24:609. [PMID: 37821828 PMCID: PMC10568926 DOI: 10.1186/s12864-023-09718-2] [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: 06/15/2023] [Accepted: 10/05/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Since DNA information was first used in taxonomy, barcode sequences such as the internal transcribed spacer (ITS) region have greatly aided fungal identification; however, a barcode sequence alone is often insufficient. Thus, multi-gene- or whole-genome-based methods were developed. We previously isolated Basidiomycota yeasts classified in the Trichosporonales. Some strains were described as Cutaneotrichosporon cavernicola and C. spelunceum, whereas strain HIS471 remained unidentified. We analysed the genomes of these strains to elucidate their taxonomic relationship and genetic diversity. RESULTS The long-read-based assembly resulted in chromosome-level draft genomes consisting of seven chromosomes and one mitochondrial genome. The genome of strain HIS471 has more than ten chromosome inversions or translocations compared to the type strain of C. cavernicola despite sharing identical ITS barcode sequences and displaying an average nucleotide identity (ANI) above 93%. Also, the chromosome synteny between C. cavernicola and the related species, C. spelunceum, showed significant rearrangements, whereas the ITS sequence identity exceeds 98.6% and the ANI is approximately 82%. Our results indicate that the relative evolutionary rates of barcode sequences, whole-genome nucleotide sequences, and chromosome synteny in Cutaneotrichosporon significantly differ from those in the model yeast Saccharomyces. CONCLUSIONS Our results revealed that the relative evolutionary rates of nucleotide sequences and chromosome synteny are different among fungal clades, likely because different clades have diverse mutation/repair rates and distinct selection pressures on their genomic sequences and syntenic structures. Because diverse syntenic structures can be a barrier to meiotic recombination and may lead to speciation, the non-linear relationships between nucleotide and synteny diversification indicate that sequence-level distances at the barcode or whole-genome level are not sufficient for delineating species boundaries.
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Affiliation(s)
- Yuuki Kobayashi
- Laboratory of Yeast Systematics, Tokyo NODAI Research Institute (TNRI), Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan.
| | - Ayane Kayamori
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Keita Aoki
- Laboratory of Yeast Systematics, Tokyo NODAI Research Institute (TNRI), Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Yuh Shiwa
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Minenosuke Matsutani
- NODAI Genome Research Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Nobuyuki Fujita
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Takashi Sugita
- Department of Microbiology, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo, 204-8588, Japan
| | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-0882, Japan
| | - Naoto Tanaka
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Masako Takashima
- Laboratory of Yeast Systematics, Tokyo NODAI Research Institute (TNRI), Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan.
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Díaz-Navarrete P, Marileo L, Madrid H, Belezaca-Pinargote C, Dantagnan P. Lipid Production from Native Oleaginous Yeasts Isolated from Southern Chilean Soil Cultivated in Industrial Vinasse Residues. Microorganisms 2023; 11:2516. [PMID: 37894174 PMCID: PMC10609240 DOI: 10.3390/microorganisms11102516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
In this research, six strains of oleaginous yeasts native to southern Chile were analyzed for their biotechnological potential in lipid accumulation. For this purpose, the six strains, named PP1, PP4, PR4, PR10, PR27 and PR29, were cultivated in a nitrogen-deficient synthetic mineral medium (SMM). Then, two strains were selected and cultivated in an industrial residual "vinasse", under different conditions of temperature (°C), pH and carbon/nitrogen (C/N) ratio. Finally, under optimized conditions, the growth kinetics and determination of the lipid profile were evaluated. The results of growth in the SMM indicate that yeasts PP1 and PR27 presented biomass concentrations and lipid accumulation percentages of 2.73 and 4.3 g/L of biomass and 36.6% and 45.3% lipids, respectively. Subsequently, for both strains, when cultured in the residual vinasse under optimized environmental conditions, biomass concentrations of 14.8 ± 1.51 g/L (C/N 80) and 15.83 ± 0.57 g/L (C/N 50) and lipid accumulations of 28% and 30% were obtained for PP1 and PR27, respectively. The composition of the triglycerides (TGs), obtained in the culture of the yeasts in a 2 L reactor, presented 64.25% of saturated fatty acids for strain PR27 and 47.18% for strain PP1. The saturated fatty acid compositions in both strains are mainly constituted of fatty acids, myristic C 14:0, heptadecanoic C 17:0, palmitic C 16:0 and stearic C 18:0, and the monounsaturated fatty acids constituted of oleic acid C 18:1 (cis 9) (28-46%), and in smaller amounts, palmitoleic acid and heptadecenoic acid. This work demonstrates that the native yeast strains PP1 and PR27 are promising strains for the production of microbial oils similar to conventional vegetable oils. The potential applications in the energy or food industries, such as aquaculture, are conceivable.
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Affiliation(s)
- Paola Díaz-Navarrete
- Departamento de Ciencias Veterinarias y Salud Pública, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco 4780000, Chile
- Núcleo de Investigación en Producción Alimentaria, Departamento de Ciencias Agropecuarias y Acuícolas, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco 4780000, Chile
| | - Luis Marileo
- Programa de Doctorado en Ciencias Agropecuarias, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco 4780000, Chile;
| | - Hugo Madrid
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Iquique 1101783, Chile;
| | - Carlos Belezaca-Pinargote
- Facultad de Ciencias Agrarias y Forestales, Universidad Técnica Estatal de Quevedo, Quevedo 120501, Ecuador;
| | - Patricio Dantagnan
- Núcleo de Investigación en Producción Alimentaria, Departamento de Ciencias Agropecuarias y Acuícolas, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco 4780000, Chile
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24
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Makopa TP, Modikwe G, Vrhovsek U, Lotti C, Sampaio JP, Zhou N. The marula and elephant intoxication myth: assessing the biodiversity of fermenting yeasts associated with marula fruits ( Sclerocarya birrea). FEMS MICROBES 2023; 4:xtad018. [PMID: 37854251 PMCID: PMC10581541 DOI: 10.1093/femsmc/xtad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/21/2023] [Accepted: 10/05/2023] [Indexed: 10/20/2023] Open
Abstract
The inebriation of wild African elephants from eating the ripened and rotting fruit of the marula tree is a persistent myth in Southern Africa. However, the yeasts responsible for alcoholic fermentation to intoxicate the elephants remain poorly documented. In this study, we considered Botswana, a country with the world's largest population of wild elephants, and where the marula tree is indigenous, abundant and protected, to assess the occurrence and biodiversity of yeasts with a potential to ferment and subsequently inebriate the wild elephants. We collected marula fruits from over a stretch of 800 km in Botswana and isolated 106 yeast strains representing 24 yeast species. Over 93% of these isolates, typically known to ferment simple sugars and produce ethanol comprising of high ethanol producers belonging to Saccharomyces, Brettanomyces, and Pichia, and intermediate ethanol producers Wickerhamomyces, Zygotorulaspora, Candida, Hanseniaspora, and Kluyveromyces. Fermentation of marula juice revealed convincing fermentative and aromatic bouquet credentials to suggest the potential to influence foraging behaviour and inebriate elephants in nature. There is insufficient evidence to refute the aforementioned myth. This work serves as the first work towards understanding the biodiversity marula associated yeasts to debunk the myth or approve the facts.
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Affiliation(s)
- Tawanda Proceed Makopa
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Plot 10071, Boseja, Palapye, Botswana, 00267
| | - Gorata Modikwe
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Plot 10071, Boseja, Palapye, Botswana, 00267
| | - Urska Vrhovsek
- Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michelle All'Adige, Via E. Mach, 1, Italy, 38010
| | - Cesare Lotti
- Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michelle All'Adige, Via E. Mach, 1, Italy, 38010
| | - José Paulo Sampaio
- UCIBIO, Departamento de Ciencias da Vida, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal , 2829-516
| | - Nerve Zhou
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Plot 10071, Boseja, Palapye, Botswana, 00267
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25
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Glushakova A, Kachalkin A, Rodionova E. The role of fruits as reservoirs for resistant and virulent strains of opportunistic yeasts. World J Microbiol Biotechnol 2023; 39:313. [PMID: 37733093 DOI: 10.1007/s11274-023-03758-2] [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: 04/22/2023] [Accepted: 09/07/2023] [Indexed: 09/22/2023]
Abstract
Strains of the Candida parapsilosis and Meyerozyma guilliermondii species complexes isolated from the internal tissues of 26 fruit species from 21 countries were evaluated for their susceptibility to conventional antifungal compounds (fluconazole, voriconazole, amphotericin B) and hydrolytic activity. A total of 144 strains were studied. Resistance to at least one of the antifungal compounds tested was found in 26.4% of the endophytic strains examined. Most of the strains were insensitive to fluconazole. Multiresistance was detected only in two strains of C. parapsilosis sensu stricto from tropical apples. Phospholipase production and proteolytic and hemolytic activities were significantly higher in endophytes from tropical fruits. Resistant and virulent strains of opportunistic yeasts can thus spread worldwide via purchased fruit, which can harm people with a weakened immune status and children whose immune systems are not yet fully developed.
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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
| | - Evgenia Rodionova
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064, Russia
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26
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Kim JS, Lee M, Ki DW, Kwon SW, Ko YJ, Kim JS, Yun BS, Kim SJ. Production of a New Biosurfactant by a New Yeast Species Isolated from Prunus mume Sieb. et Zucc. J Microbiol Biotechnol 2023; 33:1023-1029. [PMID: 37280777 PMCID: PMC10468678 DOI: 10.4014/jmb.2205.05052] [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: 05/27/2022] [Revised: 03/21/2023] [Accepted: 04/21/2023] [Indexed: 06/08/2023]
Abstract
Biosurfactants reduce surface and interfacial tension due to their amphiphilic properties and are an eco-friendly alternative for chemical surfactants. In this study, a new yeast strain JAF-11 that produces a biosurfactant was selected using drop collapse method, and the properties of the extracts were investigated. The nucleotide sequences of the strain were compared with closely related strains and identified based on the D1/D2 domain of the large subunit ribosomal DNA (LSU) and internal transcribed spacer (ITS) regions. Neodothiora populina CPC 39399T, the closest species with strain JAF-11, showed a sequence similarity of 97.75% for LSU and 94.27% for ITS, respectively. The result suggests that the strain JAF-11 represents a distinct species that cannot be assigned to any existing genus or species in the family Dothideaceae. Strain JAF-11 produced a biosurfactant reducing the surface tension of water from 72 mN/m to 34.5 mN/m on the sixth day of culture and the result of measuring the critical micelle concentration (CMC) by extracting the crude biosurfactant was found to be 24 mg/l. The molecular weight 502 of the purified biosurfactant was confirmed by measuring the fast atom bombardment mass spectrum. The chemical structure was analyzed by measuring 1H nuclear magnetic resonance (NMR), 13C NMR, and two-dimensional NMRs of the compound. The molecular formula was C26H46O9, and it was composed of one octanoyl group and two hexanoyl groups to myo-inositol moiety. The new biosurfactant is the first report of a compound produced by a new yeast strain, JAF-11.
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Affiliation(s)
- Jeong-Seon Kim
- Agricultural Microbiology Division. National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
- Division of Biotechnology and Advanced institute of Environmental and Bioscience, College of Environmental and Bioresource Sciences, Jeonbuk National University, Iksan-si, Jeollabuk-do 54596, Republic of Korea
| | - Miran Lee
- Agricultural Microbiology Division. National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Dae-Won Ki
- Division of Biotechnology and Advanced institute of Environmental and Bioscience, College of Environmental and Bioresource Sciences, Jeonbuk National University, Iksan-si, Jeollabuk-do 54596, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division. National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Young-Joon Ko
- Agricultural Microbiology Division. National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Jong-Shik Kim
- Marine industry research institute for east sea rim, Uljin-gun, Geongsangbuk-do 36315, Republic of Korea
| | - Bong-Sik Yun
- Division of Biotechnology and Advanced institute of Environmental and Bioscience, College of Environmental and Bioresource Sciences, Jeonbuk National University, Iksan-si, Jeollabuk-do 54596, Republic of Korea
| | - Soo-Jin Kim
- Agricultural Microbiology Division. National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
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27
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Leo P, de Melo Texeira M, Chander AM, Singh NK, Simpson AC, Yurkov A, Karouia F, Stajich JE, Mason CE, Venkateswaran K. Genomic characterization and radiation tolerance of Naganishia kalamii sp. nov. and Cystobasidium onofrii sp. nov. from Mars 2020 mission assembly facilities. IMA Fungus 2023; 14:15. [PMID: 37568226 PMCID: PMC10422843 DOI: 10.1186/s43008-023-00119-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/20/2023] [Indexed: 08/13/2023] Open
Abstract
During the construction and assembly of the Mars 2020 mission components at two different NASA cleanrooms, several fungal strains were isolated. Based on their colony morphology, two strains that showed yeast-like appearance were further characterized for their phylogenetic position. The species-level classification of these two novel strains, using traditional colony and cell morphology methods combined with the phylogenetic reconstructions using multi-locus sequence analysis (MLSA) based on several gene loci (ITS, LSU, SSU, RPB1, RPB2, CYTB and TEF1), and whole genome sequencing (WGS) was carried out. This polyphasic taxonomic approach supported the conclusion that the two basidiomycetous yeasts belong to hitherto undescribed species. The strain FJI-L2-BK-P3T, isolated from the Jet Propulsion Laboratory Spacecraft Assembly Facility, was placed in the Naganishia albida clade (Filobasidiales, Tremellomycetes), but is genetically and physiologically different from other members of the clade. Another yeast strain FKI-L6-BK-PAB1T, isolated from the Kennedy Space Center Payload Hazardous and Servicing Facility, was placed in the genus Cystobasidium (Cystobasidiales, Cystobasidiomycetes) and is distantly related to C. benthicum. Here we propose two novel species with the type strains, Naganishia kalamii sp. nov. (FJI-L2-BK-P3T = NRRL 64466 = DSM 115730) and Cystobasidium onofrii sp. nov. (FKI-L6-BK-PAB1T = NRRL 64426 = DSM 114625). The phylogenetic analyses revealed that single gene phylogenies (ITS or LSU) were not conclusive, and MLSA and WGS-based phylogenies were more advantageous for species discrimination in the two genera. The genomic analysis predicted proteins associated with dehydration and desiccation stress-response and the presence of genes that are directly related to osmotolerance and psychrotolerance in both novel yeasts described. Cells of these two newly-described yeasts were exposed to UV-C radiation and compared with N. onofrii, an extremophilic UV-C resistant cold-adapted Alpine yeast. Both novel species were UV resistant, emphasizing the need for collecting and characterizing extremotolerant microbes, including yeasts, to improve microbial reduction techniques used in NASA planetary protection programs.
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Affiliation(s)
- Patrick Leo
- Department of Environmental Sciences, Informatics and Statistics, University Ca' Foscari of Venice, Via Torino 155, 30172, Mestre, Italy
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'università snc, 01100, Viterbo, Italy
- NASA-Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 245-103, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Marcus de Melo Texeira
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Núcleo de Medicina Tropical, Faculdade de Medicina, Universidade de Brasília, Brasília, 70910-900, Brazil
| | - Atul M Chander
- NASA-Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 245-103, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Nitin K Singh
- NASA-Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 245-104, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Anna C Simpson
- NASA-Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 245-103, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Andrey Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Fathi Karouia
- Blue Marble Space Institute of Science, Exobiology Branch, NASA Ames Research Center, PO BOX 1 MS 239/4, Moffett Field, CA, 94035, USA
- Space Research Within Reach, San Francisco, CA, 941110, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of CA-Riverside, Riverside, CA, 92521, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics and the WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Kasthuri Venkateswaran
- NASA-Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 245-104, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA.
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28
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Oliveros A, Terraube J, Levengood AL, Powell D, Frère CH. Influence of scat ageing on the gut microbiome: how old is too old? BMC Genomics 2023; 24:427. [PMID: 37525141 PMCID: PMC10388479 DOI: 10.1186/s12864-023-09520-0] [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: 02/13/2023] [Accepted: 07/16/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND The study of the host-microbiome by the collection of non-invasive samples has the potential to become a powerful tool for conservation monitoring and surveillance of wildlife. However, multiple factors can bias the quality of data recovered from scats, particularly when field-collected samples are used given that the time of defecation is unknown. Previous studies using scats have shown that the impact of aerobic exposure on the microbial composition is species-specific, leading to different rates of change in microbial communities. However, the impact that this aging process has on the relationship between the bacterial and fungal composition has yet to be explored. In this study, we measured the effects of time post-defecation on bacterial and fungal compositions in a controlled experiment using scat samples from the endangered koala (Phascolarctos cinereus). RESULTS We found that the bacterial composition remained stable through the scat aging process, while the fungal composition did not. The absence of an increase in facultative anaerobes and the stable population of obligate anaerobic bacteria were likely due to our sampling from the inner portion of the scat. We report a cluster of fungal taxa that colonises scats after defecation which can dilute the genetic material from the autochthonous mycoflora and inhibit recovery. CONCLUSION We emphasize the need to preserve the integrity of scat samples collected in the wild and combat the effects of time and provide strategies for doing so.
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Affiliation(s)
- Alejandro Oliveros
- The School of Biological Sciences, The University of Queensland, St Lucia, QLD, Australia.
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia.
| | - Julien Terraube
- Vulture Conservation Foundation, Wuhrstrasse 12, Zürich, CH-8003, Switzerland
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Alexis L Levengood
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Daniel Powell
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Céline H Frère
- The School of Biological Sciences, The University of Queensland, St Lucia, QLD, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
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29
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Kumari A, Mihooliya KN, Sahoo DK, Bhattacharyya MS, Prasad GS, Pinnaka AK. Description of lipase producing novel yeast species Debaryomyces apis f.a., sp. nov. and a modified pH indicator dye-based method for the screening of lipase producing microorganisms. Sci Rep 2023; 13:11819. [PMID: 37479715 PMCID: PMC10362016 DOI: 10.1038/s41598-023-38241-3] [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: 05/16/2023] [Accepted: 07/05/2023] [Indexed: 07/23/2023] Open
Abstract
Four yeast strains were isolated from the gut of stingless bee, collected in Churdhar, Himachal Pradesh, India. Physiological characterization, morphological examination, and sequence analysis of small subunit ribosomal RNA (18S rRNA) genes, internal transcribed spacer (ITS) region, and D1/D2 domain of the large subunit rRNA gene revealed that the four strains isolated from the gut of stingless bee belonged to the Debaryomyces clade. Strain CIG-23HT showed sequence divergence of 7.5% from Debaryomyces nepalensis JCM 2095T, 7.8% from Debaryomyces udenii JCM 7855T, and Debaryomyces coudertii JCM 2387T in the D1/D2 domain. In the ITS region sequences, strain CIG-23HT showed a 15% sequence divergence from Debaryomyces nepalensis JCM 2095T and Debaryomyces coudertii JCM 2387T. In 18S rRNA gene sequence, the strain CIG-23HT showed 1.14% sequence divergence from Debaryomyces nepalensis JCM 2095 and and Debaryomyces coudertii JCM 2387, and 0.83% sequence divergence from Debaryomyces hansenii NRRL Y-7426. Strain CIG-23HT can utilize more carbon sources than closely related species. The findings suggest that strain CIG-23HT is a novel species of the genus Debaryomyces, and we propose to name it as Debaryomyces apis f.a., sp. nov. The holotype is CBS 16297T, and the isotypes are MTCC 12914T and KCTC 37024T. The MycoBank number of Debaryomyces apis f.a., sp. nov. is MB836065. Additionally, a method using cresol red and Bromothymol blue pH indicator dyes was developed to screen for lipase producers, which is more sensitive and efficient than the currently used phenol red and rhodamine B dye-based screening methods, and avoids the problem of less differentiable zone of hydrolysis.
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Affiliation(s)
- Alka Kumari
- Microbial Type Culture Collection (MTCC), CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Kanti N Mihooliya
- Biochemical Engineering Research and Process Development Centre, CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Debendra K Sahoo
- Biochemical Engineering Research and Process Development Centre, CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Mani S Bhattacharyya
- Biochemical Engineering Research and Process Development Centre, CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Gandham S Prasad
- Microbial Type Culture Collection (MTCC), CSIR-Institute of Microbial Technology, Chandigarh, 160036, India.
- Centre for Knowledge Culture and Innovation Studies, Technology Industrial Liaison and Entrepreneurship Unit, University of Hyderabad, Prof. C R Rao Road, Gachibowli, Hyderabad, Telangana, 500046, India.
| | - Anil Kumar Pinnaka
- Microbial Type Culture Collection (MTCC), CSIR-Institute of Microbial Technology, Chandigarh, 160036, India.
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Zhang ZY, Li X, Chen WH, Liang JD, Han YF. Culturable fungi from urban soils in China II, with the description of 18 novel species in Ascomycota (Dothideomycetes, Eurotiomycetes, Leotiomycetes and Sordariomycetes). MycoKeys 2023; 98:167-220. [PMID: 37425100 PMCID: PMC10326621 DOI: 10.3897/mycokeys.98.102816] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/14/2023] [Indexed: 07/11/2023] Open
Abstract
As China's urbanisation continues to advance, more people are choosing to live in cities. However, this trend has a significant impact on the natural ecosystem. For instance, the accumulation of keratin-rich substrates in urban habitats has led to an increase in keratinophilic microbes. Despite this, there is still a limited amount of research on the prevalence of keratinophilic fungi in urban areas. Fortunately, our group has conducted in-depth investigations into this topic since 2015. Through our research, we have discovered a significant amount of keratinophilic fungi in soil samples collected from various urban areas in China. In this study, we have identified and characterised 18 new species through the integration of morphological and phylogenetic analyses. These findings reveal the presence of numerous unexplored fungal taxa in urban habitats, emphasising the need for further taxonomic research in urban China.
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Affiliation(s)
- Zhi-Yuan Zhang
- Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang 550025, ChinaGuizhou UniversityGuiyangChina
- College of Eco-Environmental Engineering, Guizhou Minzu University, Guiyang 550025, ChinaGuizhou Minzu UniversityGuiyangChina
| | - Xin Li
- Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang 550025, ChinaGuizhou UniversityGuiyangChina
| | - Wan-Hao Chen
- Basic Medical School, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, ChinaGuizhou University of Traditional Chinese MedicineGuiyangChina
| | - Jian-Dong Liang
- Basic Medical School, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, ChinaGuizhou University of Traditional Chinese MedicineGuiyangChina
| | - Yan-Feng Han
- Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang 550025, ChinaGuizhou UniversityGuiyangChina
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Brysch-Herzberg M, Jia GS, Sipiczki M, Seidel M, Li W, Assali I, Du LL. Schizosaccharomyces lindneri sp. nov., a fission yeast occurring in honey. Yeast 2023. [PMID: 37243506 DOI: 10.1002/yea.3857] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/26/2023] [Accepted: 04/30/2023] [Indexed: 05/29/2023] Open
Abstract
Two strains of fission yeast were isolated from honey. They differ from the type strain of Schizosaccharomyces octosporus by three substitutions in the D1/D2 domain of the nuclear 26S large subunit ribosomal RNA (rRNA) gene sequence, resulting in a 99.5% identity. In the internal transcribed spacer (ITS) region (consisting of ITS1, 5.8S rDNA, and ITS2), the strains differ from S. octosporus by 16 gaps and 91 substitutions, which is equivalent to an identity of 88.1%. Genome sequencing on one of the new strains revealed that the average nucleotide identity (ANI) between its genome and the reference genome of S. octosporus is 90.43% and there exist major genome rearrangements between the two genomes. Mating analysis revealed that S. octosporus and one of the new strains are completely reproductively separated. A strong prezygotic barrier exists and the few mating products consist of diploid hybrids that do not form recombinant ascospores. In the new strains, asci are either zygotic, arising from conjugation, or they develop without conjugation from asexual cells (azygotic). Compared to the currently recognized Schizosaccharomyces species, the spectrum of nutrients that are assimilated by the new strains is restricted. Of the 43 carbohydrates that were included in the physiological standard tests, only 7 were assimilated. According to the results of the genome sequence analysis, the mating trials, and the phenotypic characterization, the new species Schizosaccharomyces lindneri is described to accommodate the two strains (holotype: CBS 18203T and ex-type: MUCL 58363; MycoBank no.: MB 847838).
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Affiliation(s)
- Michael Brysch-Herzberg
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University of Applied Sciences, Heilbronn, Germany
| | - Guo-Song Jia
- National Institute of Biological Sciences, Beijing, China
| | - Matthias Sipiczki
- Department of Genetics and Applied Microbiology, University of Debrecen, Debrecen, Hungary
| | - Martin Seidel
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University of Applied Sciences, Heilbronn, Germany
| | - Wen Li
- National Institute of Biological Sciences, Beijing, China
| | - Imen Assali
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University of Applied Sciences, Heilbronn, Germany
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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Kajadpai N, Angchuan J, Khunnamwong P, Srisuk N. Diversity of duckweed ( Lemnaceae) associated yeasts and their plant growth promoting characteristics. AIMS Microbiol 2023; 9:486-517. [PMID: 37649804 PMCID: PMC10462456 DOI: 10.3934/microbiol.2023026] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/02/2023] [Accepted: 05/09/2023] [Indexed: 09/01/2023] Open
Abstract
The diversity of duckweed (Lemnaceae) associated yeasts was studied using a culture-dependent method. A total of 252 yeast strains were isolated from 53 duckweed samples out of the 72 samples collected from 16 provinces in Thailand. Yeast identification was conducted based on the D1/D2 region of the large subunit (LSU) rRNA gene sequence analysis. It revealed that 55.2% and 44.8% yeast species were Ascomycota and Basidiomycota duckweed associated yeasts, respectively. Among all, Papiliotrema laurentii, a basidiomycetous yeast, was found as the most prevalent species showing a relative of frequency and frequency of occurrence of 21.8% and 25%, respectively. In this study, high diversity index values were shown, indicated by the Shannon-Wiener index (H'), Shannon equitability index (EH) and Simpson diversity index (1-D) values of 3.48, 0.86 and 0.96, respectively. The present results revealed that the yeast community on duckweed had increased species diversity, with evenness among species. Principal coordinate analysis (PCoA) revealed no marked differences in yeast communities among duckweed genera. The species accumulation curve showed that the observed species richness was lower than expected. Investigation of the plant growth promoting traits of the isolated yeast on duckweed revealed that 178 yeast strains produced indole-3-acetic acid (IAA) at levels ranging from 0.08-688.93 mg/L. Moreover, siderophore production and phosphate solubilization were also studied. One hundred and seventy-three yeast strains produced siderophores and exhibited siderophores that showed 0.94-2.55 activity units (AU). One hundred six yeast strains showed phosphate solubilization activity, expressed as solubilization efficiency (SE) units, in the range of 0.32-2.13 SE. This work indicates that duckweed associated yeast is a potential microbial resource that can be used for plant growth promotion.
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Affiliation(s)
- Napapohn Kajadpai
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Jirameth Angchuan
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Pannida Khunnamwong
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand
| | - Nantana Srisuk
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand
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Nwaefuna AE, Boekhout T, Garcia-Aloy M, Vrhovsek U, Zhou N. Diversity of dung beetle-associated yeasts from pristine environments of Botswana. Yeast 2023. [PMID: 37096317 DOI: 10.1002/yea.3852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 04/06/2023] [Accepted: 04/08/2023] [Indexed: 04/26/2023] Open
Abstract
Yeast-insect interactions are increasingly becoming an attractive source of discovery for previously unknown, unique, diverse, and industrially relevant yeast species. Despite a wealth of studies that have recently focused on yeasts in symbiotic association with Hymenopteran insects, yeasts associated with Coleopteran insects, such as lignocellulosic-rich dung-dependent beetles, remain poorly studied. Trends in yeast discovery suggest that species richness and diversity can be attributed to the ecological niche of the insect. Here, we considered the potential of dung beetles inhabiting the extreme environments of Botswana, characterized by desert-like conditions (semi-arid to arid and hot) as well as protected pristine environments, as possible attribute niches that can shape the extremophilic and diverse life history strategies of yeasts. We obtained a total of 97 phylogenetically diverse yeast isolates from six species of dung beetles from Botswana's unexplored environments, representing 19 species belonging to 11 genera. The findings suggest that the guts of dung beetles are a rich niche for non-Saccharomyces yeast species. Meyerozyma and Pichia were the most dominant genera associated with dung beetles, representing 55% (53 out of 97) of the yeast isolates in our study. Trichosporon and Cutaneotrichosporon genera represented 32% (31 out of 97) of the isolates. The remaining isolates belonged to Apiotrichum, Candida, Diutina, Naganishia, Rhodotorula, and Wickerhamiella genera (12 out of 97). We found out that about 62% (60 out of 97) of the isolates were potentially new species because of their low internal transcribed spacer (ITS) sequence similarity when compared to the most recent optimal species delineation threshold. A single isolate was unidentifiable using the ITS sequences. Using an in silico polymerase chain reaction-restriction fragment length polymorphism approach, we revealed that there was genetic diversity within isolates of the same species. Our results contribute to the knowledge and understanding of the diversity of dung beetle-associated yeasts.
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Affiliation(s)
- Anita E Nwaefuna
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
| | - Teun Boekhout
- Westerdijk Institute of Fungal Biodiversity, Utrecht, The Netherlands
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mar Garcia-Aloy
- Metabolomics Unit, Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Urska Vrhovsek
- Metabolomics Unit, Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Nerve Zhou
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
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Arzumanyan VG, Ozhovan IM, Kachalkin AV, Kolyganova TI, Vartanova NO, Ilyina IV. Detection of Naganishia albida Yeasts in Dermatological Patients. Bull Exp Biol Med 2023; 174:616-622. [PMID: 37040037 DOI: 10.1007/s10517-023-05757-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Indexed: 04/12/2023]
Abstract
The yeasts Cryptococcus albidus (Naganishia albida) usually occur on natural substrates and rarely are the etiological factor of different mycoses. More than a half of mycosis cases described in the literature were reported during the period from 2004 to 2021. In this regard, evaluation of yeast sensitivity to antimycotic drugs is as important as their identification. In the present study, two yeast isolates from the skin of female patients (age 7 and 74 years) with infective dermatitis (ICD-10-CM Code L30.3) were studied. Common identification of the isolates, MALDI-TOF mass spectrometry, and analysis of the nucleotide sequences of the ITS1-5.8S-ITS2 rDNA region showed that they belong to the species N. albida. The sensitivity of the obtained strains to antimycotics of three different chemical groups, namely itraconazole, naftifine, and amphotericin B, determined by microdilution method in a synthetic medium showed the following minimum inhibitory concentrations: 64-128, 16, and 0.125-4 μg/ml, respectively. It was found that the sensitivity of this yeast to pooled human serum was 30-47%, i.e. lower by 1.9-2.9 times than the sensitivity of the collection strains of C. albicans and C. neoformans. This result could be explained by lower prevalence of N. albida in the human population in comparison with these species. However, the sensitivity of N. albida strains to the low-molecular-weight fraction of serum was approximately the same as in C. albicans and C. neoformans, which indicates their high sensitivity to antimicrobial peptides.
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Affiliation(s)
- V G Arzumanyan
- I. I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | - I M Ozhovan
- I. I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | - A V Kachalkin
- M. V. Lomonosov Moscow State University, Moscow, Russia
| | - T I Kolyganova
- I. I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia.
- Department of Microbiology, Virology, and Immunology, I. M. Sechenov First Moscow State Medical University, Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia.
| | - N O Vartanova
- I. I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | - I V Ilyina
- Moscow State University of Food Production, Moscow, Russia
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35
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Chai CY, Lei T, Chu XY, Hui FL. Multi-gene phylogeny and taxonomy of the genus Bannoa with the addition of three new species from central China. Front Microbiol 2023; 14:1143156. [PMID: 36998405 PMCID: PMC10043259 DOI: 10.3389/fmicb.2023.1143156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/24/2023] [Indexed: 03/15/2023] Open
Abstract
The genus Bannoa is a small group of ballistoconidium-forming yeasts in the family Erythrobasidiaceae (Cystobasidiomycetes). Prior to this study, seven species belonging to this genus have been described and published. In this study, phylogenetic analyzes of Bannoa based on the combined sequences of the small ribosomal subunit (SSU) rRNA gene, the internal transcribed spacer (ITS) regions, the D1/D2 domains of the large subunit rRNA gene (LSU) and the translation elongation factor 1-α gene (TEF1-α) were conducted. Three new species, namely B. ellipsoidea, B. foliicola, and B. pseudofoliicola, were delimited and proposed based on morphological and molecular evidence. B. ellipsoidea was found to be closely related to the type strains of B. guamensis, B. hahajimensis, and B. tropicalis, but with 0.7–0.9% divergence (4–5 substitutions) in the LSU D1/D2 domains and 3.7–4.1% divergence (19–23 substitutions and one−two gaps) in the ITS regions. B. foliicola was found to belong to the same clade as B. pseudofoliicola from which it differed by 0.4% divergence (two substitutions) in the LSU D1/D2 domains and 2.3% divergence (13 substitutions) in the ITS regions. The distinguishing morphological characteristics of the three new species, with respect to closely related taxa, are discussed. The identification of these new taxa significantly increases the number of Bannoa that have been described on the surface of plant leaves. Additionally, a key for the identification of Bannoa species is provided.
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Affiliation(s)
- Chun-Yue Chai
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
- Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Nanyang Normal University, Nanyang, China
| | - Ting Lei
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Xue-Ying Chu
- School of Water Resources and Environment Engineering, Nanyang Normal University, Nanyang, China
| | - Feng-Li Hui
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
- Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Nanyang Normal University, Nanyang, China
- *Correspondence: Feng-Li Hui,
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36
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Culturable Diversity of Lichen-Associated Yeasts through Enrichment Strategies. ECOLOGIES 2023. [DOI: 10.3390/ecologies4010012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Lichens are symbiotic partnerships between a filamentous fungus and a photosymbiotic “alga”. Studies show that lichens harbor endothallic fungi, but that some taxa have been difficult to isolate from the main filamentous thallus-forming fungus and other faster growing lichenicolous/endothallic fungi. Therefore, we aimed to develop and evaluate liquid yeast-enrichment strategies to (1) isolate lichen-associated yeasts in pure culture, and (2) determine the taxonomic placement and breadth of the diversity of culturable yeasts. Eighty-two lichen samples were collected and washed with distilled water, and healthy thalli were ground up and added to seven different yeast-enrichment broths. Yeast colonies were isolated in pure culture and identified using molecular techniques. Initial isolates were identified using BLASTn analysis, and a taxonomic refinement was completed using PhyML analysis. In total, 215 isolates were obtained. The most prevalently isolated ascomycetous yeasts were within the Dothideomycetes (Aureobasidium, Plowrightia, and Dothiora), while the most frequently isolated basidiomycetous yeasts belonged to the genera Curvibasidium, Sporobolomyces, and Tremella. The generic placements could not be determined for 17 isolates, and in total 25 novel species were recovered. The results of this research indicate that (1) lichen-associated yeasts are diverse, (2) employing liquid enrichment strategies is effective for isolating many of these, and (3) lichen thalli represent a valuable untapped reservoir of diverse and novel yeast species.
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37
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Dlauchy D, Lee CF, Yurkov AM, Péter G. Diddensiella parasantjacobensis f.a., sp. nov., a yeast species from forest habitats. Int J Syst Evol Microbiol 2023; 73. [PMID: 36989131 DOI: 10.1099/ijsem.0.005763] [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: 03/30/2023] Open
Abstract
Six conspecific yeast strains, representing an undescribed species, were isolated from rotten wood collected in different locations in Hungary and Germany and an additional one from fungal fruiting body in Taiwan. The seven strains share identical nucleotide sequences in the D1/D2 domain of the nuclear large subunit (LSU) rRNA gene. The Hungarian and Taiwanese isolates share identical internal transcribed spacer (ITS) sequences as well, while the two German isolates differ from them merely by three substitutions and four indels in this region. The investigated strains are very closely related to Diddensiella santjacobensis. Along their LSU D1/D2 domain they differ only by one substitution from the type strain of D. santjacobensis. However, in the ITS region of Hungarian and Taiwanese strains we detected 3.5 % divergence (nine substitutions and nine indels) between the undescribed species and D. santjacobensis, while the German strains differed by 13 substitutions and nine indels from D. santjacobensis. This ITS sequence divergence has raised the possibility that the strains investigated in this study may represent a different species from D. santjacobensis. This hypothesis was supported by comparisons of partial translation elongation factor 1-α (EF-1α) and cytochrome oxidase II (COX II) gene sequences. While no difference and 1-2 substitutions among the partial EF-1α and COX II gene sequences of the strains of the undescribed species, respectively, were detected; the undescribed species differ by about 4 % (36 substitutions) and 10 % (50-51 substitutions) from D. santjacobensis in these regions. Parsimony network analysis of the partial COX II gene sequences also separated the investigated strains from the type strain of D. santjacobensis. In this paper we propose Diddensiella parasantjacobensis f.a., sp. nov. (holotype: NCAIM Y.02121; isotypes: CBS 17819, DSM 114156) to accommodate the above-noted strains.
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Affiliation(s)
- Dénes Dlauchy
- 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
| | - Ching-Fu Lee
- Institute of Analytical and Environmental Sciences, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan, ROC
| | - Andrey M Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Brunswick, Germany
| | - Gábor 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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Caicedo-Bejarano LD, Osorio-Vanegas LS, Ramírez-Castrillón M, Castillo JE, Martínez-Garay CA, Chávez-Vivas M. Water Quality, Heavy Metals, and Antifungal Susceptibility to Fluconazole of Yeasts from Water Systems. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:3428. [PMID: 36834128 PMCID: PMC9968106 DOI: 10.3390/ijerph20043428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/22/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Aquatic environments could be reservoirs of pathogenic yeasts with acquired antifungal resistance. The susceptibility to antifungal agents of yeasts present in the wastewater and natural waters of the city of Cali was evaluated. Samples were taken from two types of water: drinking water (Meléndez River, drinking water treatment plant "Puerto Mallarino" in the Cauca River) and wastewater (South Channel of the Cauca River, "Cañaveralejo-PTAR" wastewater treatment plant). Physico-chemical parameters, heavy metal concentration, and yeast levels were determined using standard procedures. Yeasts were identified using API 20 C AUX (BioMérieux) and sequence analysis of the ITS1-5.8S-ITS2 and D1/D2 regions of the large subunit of the ribosome. Susceptibility assays against fluconazole and amphotericin B using the minimum inhibitory concentration (MIC) test were determined using the microdilution method. The influence of physico-chemical parameters and heavy metals was established using principal component analysis (PCA). Yeast counts were higher at WWTP "PTAR" and lower at Melendez River, as expected. A total of 14 genera and 21 yeast species was identified, and the genus Candida was present at all locations. Susceptibility tests showed a 32.7% resistance profile to fluconazole in the order DWTP "Puerto Mallarino = WWTP "PTAR" > South Channel "Navarro". There were significant differences (p < 0.05) in the physico-chemical parameters/concentration of heavy metals and yeast levels between the aquatic systems under study. A positive association was observed between yeast levels and total dissolved solids, nitrate levels, and Cr at the "PTAR" WWTP; conductivity, Zn, and Cu in the South Channel; and the presence of Pb in the "Puerto Mallarino" DWTP. Rhodotorula mucilaginosa, Candida albicans, and Candida sp. 1 were influenced by Cr and Cd, and Diutina catelunata was influenced by Fe (p < 0.05). The water systems explored in this study showed different yeast levels and susceptibility profiles, and, therefore, possible genetic differences among populations of the same species, and different physico-chemical and heavy metals concentrations, which were probably modulating the antifungal-resistant yeasts. All these aquatic systems discharge their content into the Cauca River. We highlight the importance to further investigate if these resistant communities continue to other locations in the second largest river of Colombia and to determine the risk posed to humans and animals.
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Affiliation(s)
- Luz Dary Caicedo-Bejarano
- Research Group in Mycology (GIM/CICBA), Facultad de Ciencias Básicas, Universidad Santiago de Cali, Santiago de Cali 760035, Colombia
| | - Lizeth Stefania Osorio-Vanegas
- Department of Biochemical Engineering, Faculty of Engineering and Design, Universidad Icesi, Santiago de Cali 760031, Colombia
| | - Mauricio Ramírez-Castrillón
- Department of Biochemical Engineering, Faculty of Engineering and Design, Universidad Icesi, Santiago de Cali 760031, Colombia
| | - Jorge Enrique Castillo
- Grupo de Investigación en Electroquímica y Ambiente (GIEMA), Facultad de Ciencias Básicas, Universidad Santiago de Cali, Santiago de Cali 760035, Colombia
| | - Carlos Andrés Martínez-Garay
- Research Group in Mycology (GIM/CICBA), Facultad de Ciencias Básicas, Universidad Santiago de Cali, Santiago de Cali 760035, Colombia
| | - Mónica Chávez-Vivas
- Grupo de Investigación GIMMEIN, Programa de Medicina, Facultad de Salud, Universidad Libre Seccional Cali, Santiago de Cali 760031, Colombia
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Conti A, Casagrande Pierantoni D, Robert V, Corte L, Cardinali G. MinION Sequencing of Yeast Mock Communities To Assess the Effect of Databases and ITS-LSU Markers on the Reliability of Metabarcoding Analysis. Microbiol Spectr 2023; 11:e0105222. [PMID: 36519933 PMCID: PMC9927109 DOI: 10.1128/spectrum.01052-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Microbial communities play key roles both for humans and the environment. They are involved in ecosystem functions, maintaining their stability, and provide important services, such as carbon cycle and nitrogen cycle. Acting both as symbionts and as pathogens, description of the structure and composition of these communities is important. Metabarcoding uses ribosomal DNA (rDNA) (eukaryotic) or rRNA gene (prokaryotic) sequences for identification of species present in a site and measuring their abundance. This procedure requires several technical steps that could be source of bias producing a distorted view of the real community composition. In this work, we took advantage of an innovative "long-read" next-generation sequencing (NGS) technology (MinION) amplifying the DNA spanning from the internal transcribed spacer (ITS) to large subunit (LSU) that can be read simultaneously in this platform, providing more information than "short-read" systems. The experimental system consisted of six fungal mock communities composed of species present at various relative amounts to mimic natural situations characterized by predominant and low-frequency species. The influence of the sequencing platform (MinION and Illumina MiSeq) and the effect of different reference databases and marker sequences on metagenomic identification of species were evaluated. The results showed that the ITS-based database provided more accurate species identification than LSU. Furthermore, a procedure based on a preliminary identification with standard reference databases followed by the production of custom databases, including only the best outputs of the first step, is proposed. This additional step improved the estimate of species proportion of the mock communities and reduced the number of ghost species not really present in the simulated communities. IMPORTANCE Metagenomic analyses are fundamental in many research areas; therefore, improvement of methods and protocols for the description of microbial communities becomes more and more necessary. Long-read sequencing could be used for reducing biases due to the multicopy nature of rDNA sequences and short-read limitations. However, these novel technologies need to be assessed and standardized with controlled experiments, such as mock communities. The interest behind this work was to evaluate how long reads performed identification and quantification of species mixed in precise proportions and how the choice of database affects such analyses. Development of a pipeline that mitigates the effect of the barcoding sequences and the impact of the reference database on metagenomic analyses can help microbiome studies go one step further.
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Affiliation(s)
- Angela Conti
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | | | - Vincent Robert
- Westerdjik Institute for Biodiversity, Utrecht, Netherlands
| | - Laura Corte
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
- CEMIN Excellence Research Centre, Perugia, Italy
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
- CEMIN Excellence Research Centre, Perugia, Italy
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40
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Kachalkin AV, Glushakova AM, Tomashevskaya MA. Leucosporidium egoroviorum f.a., sp. nov., a New Yeast Species Isolated from Zucchini. Microbiology (Reading) 2023. [DOI: 10.1134/s0026261722602494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
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41
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Qiao YZ, Chen X, Hui FL. Barnettozyma menglunensis f.a., sp. nov., a novel yeast species isolated from rotting wood. Int J Syst Evol Microbiol 2023; 73. [PMID: 36790429 DOI: 10.1099/ijsem.0.005711] [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: 02/16/2023] Open
Abstract
A novel yeast species is described based on three strains isolated from rotting wood samples from Xishuangbanna Tropical Rainforest in Yunnan Province, PR China. Strain NYNU 1811121 was isolated in Menglun, Mengla, while strains NYNU 18982 and NYNU 181096 were recovered in Mengyang, Jinghong. Analysis of the sequences of the D1/D2 domain of the large subunit rRNA gene and the internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2) revealed that the novel strains were closely related to the type strain of [Candida] sanyiensis, but with 6.9 % nucleotide substitutions in the D1/D2 domain and 8.2 % substitutions in the ITS region. The three novel strains can also be distinguished from C. sanyiensis in terms of the ability to assimilate trehalose and d-gluconate and to grow at 35 °C, as well as the inability to ferment glucose. Based on molecular analyses and phenotypic characteristics, the name Barnettozyma menglunensis f.a., sp. nov. is proposed with the holotype CBS 16011T (MycoBank 845375).
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Affiliation(s)
- Ya-Zhuo Qiao
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, PR China
| | - Xue Chen
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, PR China
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Bizarria R, Pietrobon TDC, Ferreira H, Rodrigues A. Polymorphisms of rDNA genes in Cyberlindnera yeast suggest birth-and-death evolution events. FEMS Yeast Res 2023; 23:foad032. [PMID: 37291697 DOI: 10.1093/femsyr/foad032] [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: 01/20/2023] [Revised: 04/28/2023] [Accepted: 06/07/2023] [Indexed: 06/10/2023] Open
Abstract
In eukaryotes, the ribosome machinery is encoded by repeats of the ribosomal RNA genes: 26/28S, 18S, 5.8S, and 5S, structured in tandem arrays and frequently homogenized within a genome. This homogenization is thought to be driven by concerted evolution, evolving as a unit, which contributes to its target as the species barcode in modern taxonomy. However, high heterogeneity of rDNA genes has been reported, including in Saccharomycotina yeasts. Here, we describe the polymorphisms and heterogeneity of D1/D2 domains (26S rRNA) and the intergenic transcribed spacer of a new yeast species with affinities to the genus Cyberlindnera and their evolution. Both regions are not homogenized, failing the prediction of concerted evolution. Phylogenetic network analysis of cloned sequences revealed that Cyberlindnera sp. rDNAs are diverse and evolved by reticulation rather than by bifurcating tree evolution model. Predicted rRNA secondary structures also confirmed structural differences, except for some conserved hairpin loops. We hypothesize that some rDNA is inactive within this species and evolves by birth-and-death rather than concerted evolution. Our findings propel further investigation into the evolution of rDNA genes in yeasts.
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Affiliation(s)
- Rodolfo Bizarria
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, SP 13.506-900, Brazil
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, SP 13.506-900, Brazil
| | - Tatiane de Castro Pietrobon
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, SP 13.506-900, Brazil
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, SP 13.506-900, Brazil
| | - Henrique Ferreira
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, SP 13.506-900, Brazil
| | - Andre Rodrigues
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, SP 13.506-900, Brazil
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, SP 13.506-900, Brazil
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Miguel GA, Carlsen S, Arneborg N, Saerens SM, Laulund S, Knudsen GM. Non-Saccharomyces yeasts for beer production: Insights into safety aspects and considerations. Int J Food Microbiol 2022; 383:109951. [DOI: 10.1016/j.ijfoodmicro.2022.109951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 09/14/2022] [Accepted: 09/22/2022] [Indexed: 11/05/2022]
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Torulaspora jiuxiensis sp. nov., a novel yeast species isolated from rotting wood. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748467 DOI: 10.1099/ijsem.0.005629] [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: 12/23/2022] Open
Abstract
Two strains of a novel ascomycetous yeast species were isolated from rotting wood samples collected in Jiuxi Mountain Forest Park in Yunnan Province, southwest China. Both strains formed one or two spherical ascospores in persistent asci. Phylogenetic analysis of the concatenated sequences of the internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2) and the D1/D2 domain of the large subunit rRNA gene revealed that the novel strains represented a phylogenetically distinct species belonging to the genus Torulaspora. This novel species differed from the type strains of the closest known species, Torulaspora nypae and Torulaspora maleeae, by 0.9 and 1.2 % nucleotide substitutions in the D1/D2 domain and 5.3 and 6 % nucleotide substitutions in the ITS region, respectively. The novel species can also be distinguished from T. nypae and T. maleeae in terms of the ability to assimilate ribitol, succinate and citrate, and its ability to grow at 37 °C. The species name of Torulaspora jiuxiensis sp. nov. is proposed with holotype CBS 16004T (Mycobank MB 844535).
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Bian C, Kusuya Y, Sklenář F, D’hooge E, Yaguchi T, Ban S, Visagie C, Houbraken J, Takahashi H, Hubka V. Reducing the number of accepted species in Aspergillus series Nigri. Stud Mycol 2022; 102:95-132. [PMID: 36760462 PMCID: PMC9903907 DOI: 10.3114/sim.2022.102.03] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
The Aspergillus series Nigri contains biotechnologically and medically important species. They can produce hazardous mycotoxins, which is relevant due to the frequent occurrence of these species on foodstuffs and in the indoor environment. The taxonomy of the series has undergone numerous rearrangements, and currently, there are 14 species accepted in the series, most of which are considered cryptic. Species-level identifications are, however, problematic or impossible for many isolates even when using DNA sequencing or MALDI-TOF mass spectrometry, indicating a possible problem in the definition of species limits or the presence of undescribed species diversity. To re-examine the species boundaries, we collected DNA sequences from three phylogenetic markers (benA, CaM and RPB2) for 276 strains from series Nigri and generated 18 new whole-genome sequences. With the three-gene dataset, we employed phylogenetic methods based on the multispecies coalescence model, including four single-locus methods (GMYC, bGMYC, PTP and bPTP) and one multilocus method (STACEY). From a total of 15 methods and their various settings, 11 supported the recognition of only three species corresponding to the three main phylogenetic lineages: A. niger, A. tubingensis and A. brasiliensis. Similarly, recognition of these three species was supported by the GCPSR approach (Genealogical Concordance Phylogenetic Species Recognition) and analysis in DELINEATE software. We also showed that the phylogeny based on benA, CaM and RPB2 is suboptimal and displays significant differences from a phylogeny constructed using 5 752 single-copy orthologous proteins; therefore, the results of the delimitation methods may be subject to a higher than usual level of uncertainty. To overcome this, we randomly selected 200 genes from these genomes and performed ten independent STACEY analyses, each with 20 genes. All analyses supported the recognition of only one species in the A. niger and A. brasiliensis lineages, while one to four species were inconsistently delimited in the A. tubingensis lineage. After considering all of these results and their practical implications, we propose that the revised series Nigri includes six species: A. brasiliensis, A. eucalypticola, A. luchuensis (syn. A. piperis), A. niger (syn. A. vinaceus and A. welwitschiae), A. tubingensis (syn. A. chiangmaiensis, A. costaricensis, A. neoniger and A. pseudopiperis) and A. vadensis. We also showed that the intraspecific genetic variability in the redefined A. niger and A. tubingensis does not deviate from that commonly found in other aspergilli. We supplemented the study with a list of accepted species, synonyms and unresolved names, some of which may threaten the stability of the current taxonomy. Citation: Bian C, Kusuya Y, Sklenář F, D'hooge E, Yaguchi T, Ban S, Visagie CM, Houbraken J, Takahashi H, Hubka V (2022). Reducing the number of accepted species in Aspergillus series Nigri. Studies in Mycology 102: 95-132. doi: 10.3114/sim.2022.102.03.
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Affiliation(s)
- C. Bian
- Graduate School of Medical and Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Y. Kusuya
- Medical Mycology Research Center, Chiba University, Chiba, Japan;, Biological Resource Center, National Institute of Technology and Evaluation, Kisarazu, Japan
| | - F. Sklenář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic;, Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - E. D’hooge
- BCCM/IHEM collection, Mycology and Aerobiology, Sciensano, Bruxelles, Belgium
| | - T. Yaguchi
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - S. Ban
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - C.M. Visagie
- Department of Biochemistry, Genetics, and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - H. Takahashi
- Medical Mycology Research Center, Chiba University, Chiba, Japan;, Molecular Chirality Research Center, Chiba University, Chiba, Japan;, Plant Molecular Science Center, Chiba University, Chiba, Japan,*Corresponding authors: H. Takahashi, ; V. Hubka,
| | - V. Hubka
- Medical Mycology Research Center, Chiba University, Chiba, Japan;, Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic;, Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic;,*Corresponding authors: H. Takahashi, ; V. Hubka,
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Ferreira de Sá AS, Leonardo-Silva L, Xavier-Santos S. Expanding the geographical distribution of Blastobotrysmalaysiensis (Saccharomycetales) beyond the Asian continent - a cave fungus first reported in the Americas. Biodivers Data J 2022; 10:e80226. [PMID: 36761671 PMCID: PMC9836630 DOI: 10.3897/bdj.10.e80226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/22/2022] [Indexed: 11/16/2022] Open
Abstract
Background Saccharomycetales are ascomycetic yeasts and, amongst them, the genus Blastobotrys has approximately 30 known species. Blastobotrysmalaysiensis is a yeast species, described from cave samples, known until then only from Malaysia. In this study, we characterise a new strain and report the second occurrence record of this species. Here, Blastobotrysmalaysiensis URM 8507/SXS 675, was collected from sediments samples from a cave in the Parque Estadual de Terra Ronca (PETER) in Goiás, Brazil. Phylogenetic analyses revealed strong support with the sequence of the species type, as well as with other species of the clade. This new record contributes by providing new molecular data for the species and expanding the knowledge of its distribution beyond the Asian continent. New information First record of a yeast for the American continent and its second mention for the world.
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Affiliation(s)
- Antônio Sérgio Ferreira de Sá
- Universidade Estadual de Goiás, Campus Central, Laboratório de Micologia Básica, Aplicada e Divulgação Científica (FungiLab), Anápolis, BrazilUniversidade Estadual de Goiás, Campus Central, Laboratório de Micologia Básica, Aplicada e Divulgação Científica (FungiLab)AnápolisBrazil
| | - Lucas Leonardo-Silva
- Universidade Estadual de Goiás, Campus Central, Laboratório de Micologia Básica, Aplicada e Divulgação Científica (FungiLab), Anápolis, BrazilUniversidade Estadual de Goiás, Campus Central, Laboratório de Micologia Básica, Aplicada e Divulgação Científica (FungiLab)AnápolisBrazil
| | - Solange Xavier-Santos
- Universidade Estadual de Goiás, Campus Central, Laboratório de Micologia Básica, Aplicada e Divulgação Científica (FungiLab), Anápolis, BrazilUniversidade Estadual de Goiás, Campus Central, Laboratório de Micologia Básica, Aplicada e Divulgação Científica (FungiLab)AnápolisBrazil
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Weldon WA, McGhee GC, Jones LA, Stockwell VO. Taxonomic Reclassification of the Fungal Pathogen Causing Dry Berry Disease of Caneberries into the Division Ascomycota as Monilinia rubi. PLANT DISEASE 2022; 106:2788-2796. [PMID: 35442057 DOI: 10.1094/pdis-11-21-2618-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
As molecular genetic techniques improve and sequence data becomes available for more fungal species, taxonomic classifications historically based upon growth morphology alone are being revisited and occasionally reclassified. Herein, we present such an instance for the fungal pathogen that causes dry berry disease of caneberries. The organism was previously described as the basidiomycete fungus Rhizoctonia rubi based upon the pathogen's production of Rhizoctonia-like angular branching hyphae. Utilizing molecular genetic techniques unavailable when the pathogen was first characterized in 1959, three housekeeping gene regions (ITS, β-tubulin, and G3PDH) were sequenced across 13 contemporary dry berry isolates, as well as the original 1959 R. rubi type strain, CBS382.59. The resulting neighbor-joining, maximum likelihood, and Bayesian phylogenies for single and multilocus sequences provide strong evidence that the dry berry pathogen was misclassified. This data, in addition to revisiting in vivo macroscopic and microscopic growth morphology, again comparing contemporary dry berry isolates to the CBS382.59 type strain, suggests that the causal organism is a new species within the genus Monilinia that we propose be classified as Monilinia rubi. A transition from designation as a basidiomycete fungus to an ascomycete fungus could have implications on chemical management decisions, as well as the assumptions made about cell structure and the pathogen's putative life cycle.
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Affiliation(s)
| | - Gayle C McGhee
- USDA-ARS Horticultural Crops Research Unit, Corvallis, OR 97330
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Dos Reis JBA, Lorenzi AS, do Vale HMM. Methods used for the study of endophytic fungi: a review on methodologies and challenges, and associated tips. Arch Microbiol 2022; 204:675. [PMID: 36264513 PMCID: PMC9584250 DOI: 10.1007/s00203-022-03283-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 09/30/2022] [Accepted: 10/08/2022] [Indexed: 11/26/2022]
Abstract
Endophytic fungi are microorganisms that colonize the interior of plant tissues (e.g. leaves, seeds, stem, trunk, roots, fruits, flowers) in intracellular and/or extracellular spaces without causing symptoms of disease in host plants. These microorganisms have been isolated from plant species in a wide variety of habitats worldwide, and it is estimated that all terrestrial plants are colonized by one or more species of endophytic fungus. In addition, these microorganisms have been drawing the attention of researchers because of their ability to synthesize a wide range of bioactive molecules with potential for applications in agriculture, medicine and biotechnology. However, several obstacles come up when studying the diversity and chemical potential of endophytic fungi. For example, the usage of an inappropriate surface disinfection method for plant tissue may not eliminate the epiphytic microbiota or may end up interfering with the endophytic mycobiota, which consequently generates erroneous results. Moreover, the composition of the culture medium and the culture conditions can favor the growth of certain species and inhibit others, which generates underestimated results. Other inconsistencies can arise from the fungus misidentification and consequent exploration of its chemical potential. Based on the methodological biases that may occur at all stages of studies dealing with endophytic fungi, the objective of this review is to discuss the main methods employed in these studies as well as highlight the challenges derived from the different approaches. We also report associated tips to help future studies on endophytic fungi as a contribution.
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Affiliation(s)
| | - Adriana Sturion Lorenzi
- Department of Cellular Biology, Institute of Biological Sciences, University of Brasília (UnB), Brasília, DF, Brazil
| | - Helson Mario Martins do Vale
- Department of Phytopathology, Institute of Biological Sciences, University of Brasília (UnB), Brasília, DF, Brazil
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Alfian AR, Watchaputi K, Sooklim C, Soontorngun N. Production of new antimicrobial palm oil-derived sophorolipids by the yeast Starmerella riodocensis sp. nov. against Candida albicans hyphal and biofilm formation. Microb Cell Fact 2022; 21:163. [PMID: 35974372 PMCID: PMC9382743 DOI: 10.1186/s12934-022-01852-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/07/2022] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Microbial derived-surfactants display low eco-toxicity, diverse functionality, high biodegradability, high specificity, and stability under extreme conditions. Sophorolipids are emerging as key biosurfactants of yeast origins, used in various industrial sectors to lower surface tension. Recently, sophorolipid complexes have been applied in biomedicals and agriculture to eradicate infectious problems related to human and plant fungal pathogens. This study aimed to characterize the functional properties and antifungal activities of sophorolipids produced by a newly characterized Starmerella riodocensis GT-SL1R sp. nov. strain. RESULTS Starmerella riodocensis GT-SL1R sp. nov. strain was belonged to Starmerella clade with 93.12% sequence similarity using the ITS technique for strain identification. Sophorolipids production was examined, using co-carbon substrates glucose and palm oil, with a yield on the substrate between 30 and 46%. Using shake-flasks, the S. riodocensis GT-SL1R strain produced biosurfactants with an emulsification activity of 54.59% against kerosene compared to the S. bombicola BCC5426 strain with an activity of 60.22%. Maximum productivities of GT-SL1R and the major sophorolipid-producer S. bombicola were similar at 0.8 gl-1 h-1. S. riodocensis GT-SL1R produced mixed forms of lactonic and acidic sophorolipids, shown by TCL, FTIR, and HPLC. Importantly, the complex sophorolipid mixture displayed antifungal activity against an opportunistic yeast pathogen Candida albicans by effectively reducing hyphal and biofilm formation. CONCLUSIONS Sophorolipids derived from S. riodocensis demonstrate potential industrial and biomedical applications as green surfactant and antifungal agent. Since numerous renewable bioresources and industrial wastes could be used by microbial cell factories in the biosynthesis of biosurfactants to reduce the production cost, sophorolipids hold a promising alternative to current antimicrobials in treatments against infectious diseases in humans, animals, and plants.
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Affiliation(s)
- Achmad Rifky Alfian
- Gene Technology Laboratory, Biochemical Technology Division, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, 49, Tian Talay Road, Tha Kham, Bang Khuntian, Bangkok, 10150, Thailand
| | - Kwanrutai Watchaputi
- Gene Technology Laboratory, Biochemical Technology Division, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, 49, Tian Talay Road, Tha Kham, Bang Khuntian, Bangkok, 10150, Thailand
| | - Chayaphathra Sooklim
- Gene Technology Laboratory, Biochemical Technology Division, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, 49, Tian Talay Road, Tha Kham, Bang Khuntian, Bangkok, 10150, Thailand
| | - Nitnipa Soontorngun
- Gene Technology Laboratory, Biochemical Technology Division, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, 49, Tian Talay Road, Tha Kham, Bang Khuntian, Bangkok, 10150, Thailand.
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Wei XY, Zhu HY, Song L, Zhang RP, Li AH, Niu QH, Liu XZ, Bai FY. Yeast Diversity in the Qaidam Basin Desert in China with the Description of Five New Yeast Species. J Fungi (Basel) 2022; 8:jof8080858. [PMID: 36012846 PMCID: PMC9409814 DOI: 10.3390/jof8080858] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 11/18/2022] Open
Abstract
The Qaidam Basin is the highest and one of the largest and driest deserts on Earth. It is considered a mars analog area in China. In contrast to numerous studies concerning its geology, geophysical, and chemistry, relatively few studies have reported microbial diversity and distribution in this area. Here, we investigated culturable yeast diversity in the northeast Qaidam Basin. A total of 194 yeast strains were isolated, and 12 genera and 21 species were identified, among which 19 were basidiomycetous yeasts. Naganishia albida, N. adeliensis, and Filobasidium magnum were the three most dominant species and were distributed in thirteen samples from eight locations. Five new species (Filobasidium chaidanensis, Kondoa globosum, Symmetrospora salmoneus, Teunia nitrariae, and Vishniacozyma pseudodimennae) were found and described based on ITS and D1D2 gene loci together with phenotypic characteristics and physiochemical analysis. Representative strains from each species were chosen for the salt-tolerant test, in which species showed different responses to different levels of NaCl concentrations. Further, the strain from soil can adapt well to the higher salt stress compared to those from plants or lichens. Our study represents the first report of the yeast diversity in the Qaidam Basin, including five new species, and also provides further information on the halotolerance of yeasts from the saline environment in mars analog.
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Affiliation(s)
- Xu-Yang Wei
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hai-Yan Zhu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, No.19 (A) Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Liang Song
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ri-Peng Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, No.19 (A) Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Ai-Hua Li
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiu-Hong Niu
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China
| | - Xin-Zhan Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: (X.-Z.L.); (F.-Y.B.)
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: (X.-Z.L.); (F.-Y.B.)
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