1
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Gostinčar C, Gunde-Cimerman N. Black yeasts in hypersaline conditions. Appl Microbiol Biotechnol 2024; 108:252. [PMID: 38441672 PMCID: PMC10914880 DOI: 10.1007/s00253-024-13052-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/26/2024] [Accepted: 02/02/2024] [Indexed: 03/07/2024]
Abstract
Extremotolerant and extremophilic fungi are an important part of microbial communities that thrive in extreme environments. Among them, the black yeasts are particularly adaptable. They use their melanized cell walls and versatile morphology, as well as a complex set of molecular adaptations, to survive in conditions that are lethal to most other species. In contrast to extremophilic bacteria and archaea, these fungi are typically extremotolerant rather than extremophilic and exhibit an unusually wide ecological amplitude. Some extremely halotolerant black yeasts can grow in near-saturated NaCl solutions, but can also grow on normal mycological media. They adapt to the low water activity caused by high salt concentrations by sensing their environment, balancing osmotic pressure by accumulating compatible solutes, removing toxic salt ions from the cell using membrane transporters, altering membrane composition and remodelling the highly melanized cell wall. As protection against extreme conditions, halotolerant black yeasts also develop different morphologies, from yeast-like to meristematic. Genomic studies of black yeasts have revealed a variety of reproductive strategies, from clonality to intense recombination and the formation of stable hybrids. Although a comprehensive understanding of the ecological role and molecular adaptations of halotolerant black yeasts remains elusive and the application of many experimental methods is challenging due to their slow growth and recalcitrant cell walls, much progress has been made in deciphering their halotolerance. Advances in molecular tools and genomics are once again accelerating the research of black yeasts, promising further insights into their survival strategies and the molecular basis of their adaptations. KEY POINTS: • Black yeasts show remarkable adaptability to environmental stress • Black yeasts are part of microbial communities in hypersaline environments • Halotolerant black yeasts utilise various molecular and morphological adaptations.
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Affiliation(s)
- Cene Gostinčar
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Nina Gunde-Cimerman
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia.
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2
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Wang JJT, Steenwyk JL, Brem RB. Natural trait variation across Saccharomycotina species. FEMS Yeast Res 2024; 24:foae002. [PMID: 38218591 PMCID: PMC10833146 DOI: 10.1093/femsyr/foae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/13/2023] [Accepted: 01/12/2024] [Indexed: 01/15/2024] Open
Abstract
Among molecular biologists, the group of fungi called Saccharomycotina is famous for its yeasts. These yeasts in turn are famous for what they have in common-genetic, biochemical, and cell-biological characteristics that serve as models for plants and animals. But behind the apparent homogeneity of Saccharomycotina species lie a wealth of differences. In this review, we discuss traits that vary across the Saccharomycotina subphylum. We describe cases of bright pigmentation; a zoo of cell shapes; metabolic specialties; and species with unique rules of gene regulation. We discuss the genetics of this diversity and why it matters, including insights into basic evolutionary principles with relevance across Eukarya.
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Affiliation(s)
- Johnson J -T Wang
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jacob L Steenwyk
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rachel B Brem
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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3
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Paiva DS, Fernandes L, Portugal A, Trovão J. First Genome Sequence of the Microcolonial Black Fungus Saxispiralis lemnorum MUM 23.14: Insights into the Unique Genomic Traits of the Aeminiaceae Family. Microorganisms 2024; 12:104. [PMID: 38257931 PMCID: PMC10820743 DOI: 10.3390/microorganisms12010104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/15/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
Saxispiralis lemnorum MUM 23.14 is an extremotolerant microcolonial black fungus, originally isolated from a biodeteriorated limestone artwork in Portugal. This recently introduced species belongs to the Aeminiaceae family, representing the second member of this monophyletic clade. This fungus exhibits a unique set of characteristics, including xerophily, cold tolerance, high UV radiation tolerance, and an exceptional ability to thrive in NaCl concentrations of up to 30% while also enduring pH levels ranging from 5 to 11. To gain insights into its genomic traits associated with stress resistance mechanisms, specialization, and their potential implications in stone biodeterioration, we conducted a comprehensive genome sequencing and analysis. This draft genome not only marks the first for the Saxispiralis genus but also the second for the Aeminiaceae family. Furthermore, we performed two comparative genomic analyses: one focusing on the closest relative within the Aeminiaceae family, Aeminium ludgeri, and another encompassing the genome of different extremotolerant black fungi. In this study, we successfully achieved high genome completeness for S. lemnorum and confirmed its close phylogenetic relationship to A. ludgeri. Our findings revealed traits contributing to its extremophilic nature and provided insights into potential mechanisms contributing to stone biodeterioration. Many traits are common to both Aeminiaceae species and are shared with other black fungi, while numerous unique traits may be attributed to species-specific characteristics.
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Affiliation(s)
- Diana S. Paiva
- Centre for Functional Ecology (CFE)—Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal (J.T.)
| | - Luís Fernandes
- Centre for Functional Ecology (CFE)—Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal (J.T.)
| | - António Portugal
- Centre for Functional Ecology (CFE)—Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal (J.T.)
- FitoLab—Laboratory for Phytopathology, Instituto Pedro Nunes (IPN), Rua Pedro Nunes, 3030-199 Coimbra, Portugal
- TERRA—Associate Laboratory for Sustainable Land Use and Ecosystem Services, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - João Trovão
- Centre for Functional Ecology (CFE)—Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal (J.T.)
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4
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Ding X, Liu W, Liu K, Gao X, Liu Y. The Deletion of LeuRS Revealed Its Important Roles in Osmotic Stress Tolerance, Amino Acid and Sugar Metabolism, and the Reproduction Process of Aspergillus montevidensis. J Fungi (Basel) 2024; 10:36. [PMID: 38248946 PMCID: PMC10820851 DOI: 10.3390/jof10010036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 12/30/2023] [Accepted: 12/31/2023] [Indexed: 01/23/2024] Open
Abstract
Aspergillus montevidensis is an important domesticated fungus that has been applied to produce many traditional fermented foods under high osmotic conditions. However, the detailed mechanisms of tolerance to osmotic stress remain largely unknown. Here, we construct a target-deleted strain (ΔLeuRS) of A. montevidensis and found that the ΔLeuRS mutants grew slowly and suppressed the development of the cleistothecium compared to the wide-type strains (WT) under salt-stressed and non-stressed conditions. Furthermore, differentially expressed genes (p < 0.001) governed by LeuRS were involved in salt tolerance, ABC transporter, amino acid metabolism, sugar metabolism, and the reproduction process. The ΔLeuRS strains compared to WT strains under short- and long-term salinity stress especially altered accumulation levels of metabolites, such as amino acids and derivatives, carbohydrates, organic acids, and fatty acids. This study provides new insights into the underlying mechanisms of salinity tolerance and lays a foundation for flavor improvement of foods fermented with A. montevidensis.
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Affiliation(s)
| | | | - Kaihui Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China (Y.L.)
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5
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Aureli L, Coleine C, Delgado-Baquerizo M, Ahren D, Cemmi A, Di Sarcina I, Onofri S, Selbmann L. Geography and environmental pressure are predictive of class-specific radioresistance in black fungi. Environ Microbiol 2023; 25:2931-2942. [PMID: 37775957 DOI: 10.1111/1462-2920.16510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/13/2023] [Indexed: 10/01/2023]
Abstract
Black fungi are among the most resistant organisms to ionizing radiation on Earth. However, our current knowledge is based on studies on a few isolates, while the overall radioresistance limits across this microbial group and the relationship with local environmental conditions remain largely undetermined. To address this knowledge gap, we assessed the survival of 101 strains of black fungi isolated across a worldwide spatial distribution to gamma radiation doses up to 100 kGy. We found that intra and inter-specific taxonomy, UV radiation, and precipitation levels primarily influence the radioresistance in black fungi. Altogether, this study provides insights into the adaptive mechanisms of black fungi to extreme environments and highlights the role of local adaptation in shaping the survival capabilities of these extreme-tolerant organisms.
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Affiliation(s)
- Lorenzo Aureli
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
- Department of Biology, Lund University, Lund, Sweden
| | - Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Manuel Delgado-Baquerizo
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Sevilla, Spain
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Dag Ahren
- Department of Biology, Lund University, Lund, Sweden
- Department of Biology, National Bioinformatics Infrastructure Sweden (NBIS), Lund University, Lund, Sweden
| | - Alessia Cemmi
- Fusion and Technology for Nuclear Safety and Security Department, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA FSN-FISS-SNI), Rome, Italy
| | - Ilaria Di Sarcina
- Fusion and Technology for Nuclear Safety and Security Department, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA FSN-FISS-SNI), Rome, Italy
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
- Mycological Section, Italian Antarctic National Museum (MNA), Genoa, Italy
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6
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Abstract
Hypersaline waters and glacial ice are inhospitable environments that have low water activity and high concentrations of osmolytes. They are inhabited by diverse microbial communities, of which extremotolerant and extremophilic fungi are essential components. Some fungi are specialized in only one of these two environments and can thrive in conditions that are lethal to most other life-forms. Others are generalists, highly adaptable species that occur in both environments and tolerate a wide range of extremes. Both groups efficiently balance cellular osmotic pressure and ion concentration, stabilize cell membranes, remodel cell walls, and neutralize intracellular oxidative stress. Some species use unusual reproductive strategies. Further investigation of these adaptations with new methods and carefully designed experiments under ecologically relevant conditions will help predict the role of fungi in hypersaline and glacial environments affected by climate change, decipher their stress resistance mechanisms and exploit their biotechnological potential.
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Affiliation(s)
- Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia; ,
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia; ,
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Enuh BM, Aytar Çelik P. Genome Analysis of Halomonas elongata Strain 153B and Insights Into Polyhydroxyalkanoate Synthesis and Adaptive Mechanisms to High Saline Environments. Curr Microbiol 2022; 80:18. [PMID: 36460760 DOI: 10.1007/s00284-022-03115-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022]
Abstract
Species of the Halomonas genus are gram-negative, aerobic, moderately halophilic bacteria that synthesize polyhydroxyalkanoates (PHAs) and other high-value products that have a wide range of potential uses in the food, feed, cosmetics, pharmaceutical, and chemical sectors. Genome sequencing studies allow for the description and comparison of genetic traits with other strains and species, allowing for the exploration of the organism's potential, necessary to further biotechnology applications. Here, the genome of Halomonas elongata strain 153B was sequenced, its features compared to 5 other strains and 7 species, and a description of features for adaptations to hypersaline environments and bioproducts synthesis was done. Whole-genome analysis showed H. elongata 153B has more similar features to the reference strain H. elongata DSM 2581 compared to 4 other reported strains. Comparative genomics showed 2064 core genomic clusters between the strains and 666 singletons for strain 153B. Several genes in transport and signaling, osmoregulation, and oxidative stress that have roles in adaptation to environments with high osmolarity were also revealed. These appear to form an intricate network of overlapping systems carefully coordinated to bring about adaptation. H. elongata 153B genes for the synthesis of PHAs, ectoine, vitamins, and the degradation of drugs and aromatic compounds were described. The results will aid in the study of halophile physiology, provide a mine for valuable enzymes, and help speed up research for other biotechnology applications.
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Danilova OA, Ianutsevich EA, Bondarenko SA, Antropova AB, Tereshina VM. Membrane Lipids and Osmolytes Composition of Xerohalophilic Fungus Aspergillus penicillioides during Growth on High NaCl and Glycerol Media. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722601373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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9
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Zeng N, Zhang N, Ma X, Wang Y, Zhang Y, Wang D, Pu F, Li B. Transcriptomics Integrated with Metabolomics: Assessing the Central Metabolism of Different Cells after Cell Differentiation in Aureobasidium pullulans NG. J Fungi (Basel) 2022; 8:jof8080882. [PMID: 36012870 PMCID: PMC9410427 DOI: 10.3390/jof8080882] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/15/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
When organisms are stimulated by external stresses, oxidative stress is induced, resulting in the production of large amounts of reactive oxygen species (ROS) that inhibit cell growth and accelerate cellular aging until death. Understanding the molecular mechanisms of abiotic stress is important to enhance cellular resistance, and Aureobasidium pullulans, a highly resistant yeast-like fungus, can use cellular differentiation to resist environmental stress. Here, swollen cells (SCs) from two different differentiation periods in Aureobasidium pullulans NG showed significantly higher antioxidant capacity and stress defense capacity than yeast-like cells (YL). The transcriptome and the metabolome of both cells were analyzed, and the results showed that amino acid metabolism, carbohydrate metabolism, and lipid metabolism were significantly enriched in SCs. Glyoxylate metabolism was significantly upregulated in carbohydrate metabolism, replacing the metabolic hub of the citric acid (TCA) cycle, helping to coordinate multiple metabolic pathways and playing an important role in the resistance of Aureobasidium pullulans NG to environmental stress. Finally, we obtained 10 key genes and two key metabolites in SCs, which provide valuable clues for subsequent validation. In conclusion, these results provide valuable information for assessing central metabolism-mediating oxidative stress in Aureobasidium pullulans NG, and also provide new ideas for exploring the pathways of eukaryotic resistance to abiotic stress.
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Affiliation(s)
- Nan Zeng
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Ning Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
- Correspondence: (N.Z.); (B.L.)
| | - Xin Ma
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Yunjiao Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Yating Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Dandan Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Fangxiong Pu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Bingxue Li
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, China
- Correspondence: (N.Z.); (B.L.)
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10
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Cai S, Snyder AB. Genomic characterization of polyextremotolerant black yeasts isolated from food and food production environments. Front Fungal Biol 2022; 3:928622. [PMID: 37746166 PMCID: PMC10512282 DOI: 10.3389/ffunb.2022.928622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/04/2022] [Indexed: 09/26/2023]
Abstract
Black yeasts have been isolated from acidic, low water activity, and thermally processed foods as well as from surfaces in food manufacturing plants. The genomic basis for their relative tolerance to food-relevant environmental stresses has not been well defined. In this study, we performed whole genome sequencing (WGS) on seven black yeast strains including Aureobasidium (n=5) and Exophiala (n=2) which were isolated from food or food production environments. These strains were previously characterized for their tolerance to heat, hyperosmotic pressure, high pressure processing, hypochlorite sanitizers, and ultraviolet light. Based on the WGS data, three of the strains previously identified as A. pullulans were reassigned as A. melanogenum. Both haploid and diploid A. melanogenum strains were identified in this collection. Single-locus phylogenies based on beta tubulin, RNA polymerase II, or translation elongation factor protein sequences were compared to the phylogeny produced through SNP analysis, revealing that duplication of the fungal genome in diploid strains complicates the use of single-locus phylogenetics. There was not a strong association between phylogeny and either environmental source or stress tolerance phenotype, nor were trends in the copy numbers of stress-related genes associated with extremotolerance within this collection. While there were obvious differences between the genera, the heterogenous distribution of stress tolerance phenotypes and genotypes suggests that food-relevant black yeasts may be ubiquitous rather than specialists associated with particular ecological niches. However, further evaluation of additional strains and the potential impact of gene sequence modification is necessary to confirm these findings.
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Affiliation(s)
| | - Abigail B. Snyder
- Department of Food Science, Cornell University, Ithaca, NY, United States
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11
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Marion V, Van Long Nicolas N, Jean-Luc J, Thibaud B, Audrey P, Georges B, Karim R, Valérie V, Véronique H, Louis C. Impact of water activity on the radial growth of fungi in a dairy environment. Food Res Int 2022; 157:111247. [DOI: 10.1016/j.foodres.2022.111247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 11/17/2022]
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12
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Roik A, Reverter M, Pogoreutz C. A roadmap to understanding diversity and function of coral reef-associated fungi. FEMS Microbiol Rev 2022; 46:6615459. [PMID: 35746877 PMCID: PMC9629503 DOI: 10.1093/femsre/fuac028] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/01/2022] [Accepted: 06/14/2022] [Indexed: 01/09/2023] Open
Abstract
Tropical coral reefs are hotspots of marine productivity, owing to the association of reef-building corals with endosymbiotic algae and metabolically diverse bacterial communities. However, the functional importance of fungi, well-known for their contribution to shaping terrestrial ecosystems and global nutrient cycles, remains underexplored on coral reefs. We here conceptualize how fungal functional traits may have facilitated the spread, diversification, and ecological adaptation of marine fungi on coral reefs. We propose that functions of reef-associated fungi may be diverse and go beyond their hitherto described roles of pathogens and bioeroders, including but not limited to reef-scale biogeochemical cycles and the structuring of coral-associated and environmental microbiomes via chemical mediation. Recent technological and conceptual advances will allow the elucidation of the physiological, ecological, and chemical contributions of understudied marine fungi to coral holobiont and reef ecosystem functioning and health and may help provide an outlook for reef management actions.
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Affiliation(s)
- Anna Roik
- Corresponding author: Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstrasse 231, D-26129 Oldenburg, Germany. E-mail:
| | - Miriam Reverter
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Wilhelmshaven, 26046, Germany,School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, United Kingdom
| | - Claudia Pogoreutz
- Corresponding author: Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Federale de Lausanne (EPFL), 1015 Lausanne, Switzerland.,
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13
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Pérez G, Lopez-Moya F, Chuina E, Ibañez-Vea M, Garde E, López-Llorca LV, Pisabarro AG, Ramírez L. Strain Degeneration in Pleurotus ostreatus: A Genotype Dependent Oxidative Stress Process Which Triggers Oxidative Stress, Cellular Detoxifying and Cell Wall Reshaping Genes. J Fungi (Basel) 2021; 7:jof7100862. [PMID: 34682283 PMCID: PMC8537115 DOI: 10.3390/jof7100862] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/08/2021] [Accepted: 10/09/2021] [Indexed: 12/13/2022] Open
Abstract
Strain degeneration has been defined as a decrease or loss in the yield of important commercial traits resulting from subsequent culture, which ultimately leads to Reactive Oxygen Species (ROS) production. Pleurotus ostreatus is a lignin-producing nematophagous edible mushroom. Mycelia for mushroom production are usually maintained in subsequent culture in solid media and frequently show symptoms of strain degeneration. The dikaryotic strain P. ostreatus (DkN001) has been used in our lab as a model organism for different purposes. Hence, different tools have been developed to uncover genetic and molecular aspects of this fungus. In this work, strain degeneration was studied in a full-sib monokaryotic progeny of the DkN001 strain with fast (F) and slow (S) growth rates by using different experimental approaches (light microscopy, malondialdehyde levels, whole-genome transcriptome analysis, and chitosan effect on monokaryotic mycelia). The results obtained showed that: (i) strain degeneration in P. ostreatus is linked to oxidative stress, (ii) the oxidative stress response in monokaryons is genotype dependent, (iii) stress and detoxifying genes are highly expressed in S monokaryons with symptoms of strain degeneration, (iv) chitosan addition to F and S monokaryons uncovered the constitutive expression of both oxidative stress and cellular detoxifying genes in S monokaryon strains which suggest their adaptation to oxidative stress, and (v) the overexpression of the cell wall genes, Uap1 and Cda1, in S monokaryons with strain degeneration phenotype indicates cell wall reshaping and the activation of High Osmolarity Glycerol (HOG) and Cell Wall Integrity (CWI) pathways. These results could constitute a hallmark for mushroom producers to distinguish strain degeneration in commercial mushrooms.
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Affiliation(s)
- Gumer Pérez
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarre (UPNA), 31006 Pamplona, Spain; (G.P.); (E.C.); (M.I.-V.); (E.G.); (A.G.P.)
| | - Federico Lopez-Moya
- Laboratory of Plant Pathology, Department of Marine Sciences and Applied Biology, University of Alicante, 03690 Alicante, Spain; (F.L.-M.); (L.V.L.-L.)
| | - Emilia Chuina
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarre (UPNA), 31006 Pamplona, Spain; (G.P.); (E.C.); (M.I.-V.); (E.G.); (A.G.P.)
| | - María Ibañez-Vea
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarre (UPNA), 31006 Pamplona, Spain; (G.P.); (E.C.); (M.I.-V.); (E.G.); (A.G.P.)
| | - Edurne Garde
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarre (UPNA), 31006 Pamplona, Spain; (G.P.); (E.C.); (M.I.-V.); (E.G.); (A.G.P.)
| | - Luis V. López-Llorca
- Laboratory of Plant Pathology, Department of Marine Sciences and Applied Biology, University of Alicante, 03690 Alicante, Spain; (F.L.-M.); (L.V.L.-L.)
| | - Antonio G. Pisabarro
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarre (UPNA), 31006 Pamplona, Spain; (G.P.); (E.C.); (M.I.-V.); (E.G.); (A.G.P.)
| | - Lucía Ramírez
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarre (UPNA), 31006 Pamplona, Spain; (G.P.); (E.C.); (M.I.-V.); (E.G.); (A.G.P.)
- Correspondence:
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14
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Abstract
Since the emergence of the first fungi some 700 million years ago, unicellular yeast-like forms have emerged multiple times in independent lineages via convergent evolution. While tens to hundreds of millions of years separate the independent evolution of these unicellular organisms, they share remarkable phenotypic and metabolic similarities, and all have streamlined genomes. Yeasts occur in every aquatic environment yet examined. Many species are aquatic; perhaps most are amphibious. How these species have evolved to thrive in aquatic habitats is fundamental to understanding functions and evolutionary mechanisms in this unique group of fungi. Here we review the state of knowledge of the physiological and ecological diversity of amphibious yeasts and their key evolutionary adaptations enabling survival in aquatic habitats. We emphasize some genera previously thought to be exclusively terrestrial. Finally, we discuss the ability of many yeasts to survive in extreme habitats and how this might lend insight into ecological plasticity, including amphibious lifestyles. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Fouad El Baidouri
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, Hawaii 96822, USA; , .,Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Polona Zalar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Amy S Gladfelter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.,Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA
| | - Anthony Amend
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, Hawaii 96822, USA; ,
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15
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Zeng X, Huang JJ, Hua B. Efficient phosphorus removal by a novel halotolerant fungus Aureobasidium sp. MSP8 and the application potential in saline industrial wastewater treatment. Bioresour Technol 2021; 334:125237. [PMID: 33962162 DOI: 10.1016/j.biortech.2021.125237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/23/2021] [Accepted: 04/24/2021] [Indexed: 06/12/2023]
Abstract
Efficient halotolerant phosphorus accumulation microorganisms are of great significance for the treatment of high-salt wastewater. In this study, a halotolerant fungus strain named MSP8 was isolated and identified as Aureobasidium sp. Salinity resistance results showed that strain MSP8 can resist the salinity from 0% to 17%, and 77.2% phosphorus removal was achieved at the optimal salinity of 5%. The strain also showed wide environmental adaptability (pH of 3-7; temperature of 20-30 °C). Batch tests and scanning electron microscope equipped with an energy dispersive spectrometer (SEM-EDS) characterization results verified the key role of extracellular polymeric substance (EPS) secreted by MSP8 in phosphorus removal. The actual brewery and chemical wastewater treatments exhibited that above 53.5% of phosphorus can be removed by MSP8. The excellent adaptation of MSP8 made it a potential candidate for phosphorus removal especially in saline wastewater treatment.
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Affiliation(s)
- Xiaoying Zeng
- College of Environmental Science and Engineering/Sino-Canada Joint R&D Centre for Water and Environmental Safety, Nankai University, Tianjin 300071, PR China
| | - Jinhui Jeanne Huang
- College of Environmental Science and Engineering/Sino-Canada Joint R&D Centre for Water and Environmental Safety, Nankai University, Tianjin 300071, PR China.
| | - Binbin Hua
- College of Environmental Science and Engineering/Sino-Canada Joint R&D Centre for Water and Environmental Safety, Nankai University, Tianjin 300071, PR China
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16
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17
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Selbmann L, Benkő Z, Coleine C, de Hoog S, Donati C, Druzhinina I, Emri T, Ettinger CL, Gladfelter AS, Gorbushina AA, Grigoriev IV, Grube M, Gunde-Cimerman N, Karányi ZÁ, Kocsis B, Kubressoian T, Miklós I, Miskei M, Muggia L, Northen T, Novak-Babič M, Pennacchio C, Pfliegler WP, Pòcsi I, Prigione V, Riquelme M, Segata N, Schumacher J, Shelest E, Sterflinger K, Tesei D, U’Ren JM, Varese GC, Vázquez-Campos X, Vicente VA, Souza EM, Zalar P, Walker AK, Stajich JE. Shed Light in the DaRk LineagES of the Fungal Tree of Life-STRES. Life (Basel) 2020; 10:life10120362. [PMID: 33352712 PMCID: PMC7767062 DOI: 10.3390/life10120362] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 01/01/2023] Open
Abstract
The polyphyletic group of black fungi within the Ascomycota (Arthoniomycetes, Dothideomycetes, and Eurotiomycetes) is ubiquitous in natural and anthropogenic habitats. Partly because of their dark, melanin-based pigmentation, black fungi are resistant to stresses including UV- and ionizing-radiation, heat and desiccation, toxic metals, and organic pollutants. Consequently, they are amongst the most stunning extremophiles and poly-extreme-tolerant organisms on Earth. Even though ca. 60 black fungal genomes have been sequenced to date, [mostly in the family Herpotrichiellaceae (Eurotiomycetes)], the class Dothideomycetes that hosts the largest majority of extremophiles has only been sparsely sampled. By sequencing up to 92 species that will become reference genomes, the “Shed light in The daRk lineagES of the fungal tree of life” (STRES) project will cover a broad collection of black fungal diversity spread throughout the Fungal Tree of Life. Interestingly, the STRES project will focus on mostly unsampled genera that display different ecologies and life-styles (e.g., ant- and lichen-associated fungi, rock-inhabiting fungi, etc.). With a resequencing strategy of 10- to 15-fold depth coverage of up to ~550 strains, numerous new reference genomes will be established. To identify metabolites and functional processes, these new genomic resources will be enriched with metabolomics analyses coupled with transcriptomics experiments on selected species under various stress conditions (salinity, dryness, UV radiation, oligotrophy). The data acquired will serve as a reference and foundation for establishing an encyclopedic database for fungal metagenomics as well as the biology, evolution, and ecology of the fungi in extreme environments.
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Affiliation(s)
- Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy;
- Section of Mycology, Italian National Antarctic Museum (MNA), 16121 Genoa, Italy
- Correspondence: (L.S.); (J.E.S.); Tel.: +39-0761-357012 (L.S.); +1-951-827-2363 (J.E.S.)
| | - Zsigmond Benkő
- Department of Molecular Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary; (Z.B.); (T.E.); (B.K.); (W.P.P.); (I.P.)
| | - Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy;
| | - Sybren de Hoog
- Center of Expertise in Mycology of Radboud University Medical Center, Canisius Wilhelmina Hospital, 6532 Nijmegen, The Netherlands;
| | - Claudio Donati
- Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy;
| | - Irina Druzhinina
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China;
| | - Tamás Emri
- Department of Molecular Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary; (Z.B.); (T.E.); (B.K.); (W.P.P.); (I.P.)
| | - Cassie L. Ettinger
- Genome Center, University of California, Davis, CA 95616, USA;
- Microbiology & Plant Pathology, University of California Riverside, Riverside, CA 92521, USA;
| | - Amy S. Gladfelter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA;
| | - Anna A. Gorbushina
- Department of Materials and Environment, Bundesanstalt für Materialforschung und -prüfung (BAM), 10115 Berlin, Germany; (A.A.G.); (J.S.)
- Department of Earth Sciences & Department of Biology, Chemistry, Pharmacy, Freie Universität, Berlin 10115 Berlin, Germany
| | - Igor V. Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA; (I.V.G.); (T.N.); (C.P.)
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Martin Grube
- Institute of Biology, University of Graz, Graz A-8010, Austria;
| | - Nina Gunde-Cimerman
- Department Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (N.G.-C.); (M.N.-B.); (P.Z.)
| | - Zsolt Ákos Karányi
- Department of Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - Beatrix Kocsis
- Department of Molecular Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary; (Z.B.); (T.E.); (B.K.); (W.P.P.); (I.P.)
| | - Tania Kubressoian
- Microbiology & Plant Pathology, University of California Riverside, Riverside, CA 92521, USA;
| | - Ida Miklós
- Department of Genetics and Applied Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary;
| | - Márton Miskei
- Department of Biochemistry and Molecular Biology, Faculty of Medicine University of Debrecen, 4032 Debrecen, Hungary;
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, 34121 Trieste, Italy;
| | - Trent Northen
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA; (I.V.G.); (T.N.); (C.P.)
| | - Monika Novak-Babič
- Department Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (N.G.-C.); (M.N.-B.); (P.Z.)
| | - Christa Pennacchio
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA; (I.V.G.); (T.N.); (C.P.)
| | - Walter P. Pfliegler
- Department of Molecular Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary; (Z.B.); (T.E.); (B.K.); (W.P.P.); (I.P.)
| | - Istvàn Pòcsi
- Department of Molecular Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary; (Z.B.); (T.E.); (B.K.); (W.P.P.); (I.P.)
| | - Valeria Prigione
- Mycotheca Universitatis Taurinensis, University of Torino, 10125 Torino, Italy; (V.P.); (G.C.V.)
| | - Meritxell Riquelme
- Department of Microbiology, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Baja California 22980, Mexico;
| | - Nicola Segata
- Department CIBIO, University of Trento, 38123 Trento, Italy;
| | - Julia Schumacher
- Department of Materials and Environment, Bundesanstalt für Materialforschung und -prüfung (BAM), 10115 Berlin, Germany; (A.A.G.); (J.S.)
| | - Ekaterina Shelest
- Centre for Enzyme Innovation, University of Portsmouth, Portsmouth PO1 2UP, UK;
| | - Katja Sterflinger
- Institute of Natural Sciences and Technology in the Arts, Academy of Fine Arts Vienna, Vienna 22180, Austria;
| | - Donatella Tesei
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna 22180, Austria;
| | - Jana M. U’Ren
- Department of Biosystems Engineering and BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA;
| | - Giovanna C. Varese
- Mycotheca Universitatis Taurinensis, University of Torino, 10125 Torino, Italy; (V.P.); (G.C.V.)
| | - Xabier Vázquez-Campos
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2006, Australia;
| | - Vania A. Vicente
- Department of Biochemistry, Federal University of Paraná, Paraná E3100, Brazil; (V.A.V.); (E.M.S.)
| | - Emanuel M. Souza
- Department of Biochemistry, Federal University of Paraná, Paraná E3100, Brazil; (V.A.V.); (E.M.S.)
| | - Polona Zalar
- Department Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (N.G.-C.); (M.N.-B.); (P.Z.)
| | - Allison K. Walker
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada;
| | - Jason E. Stajich
- Microbiology & Plant Pathology, University of California Riverside, Riverside, CA 92521, USA;
- Correspondence: (L.S.); (J.E.S.); Tel.: +39-0761-357012 (L.S.); +1-951-827-2363 (J.E.S.)
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18
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Jiménez-Gómez I, Valdés-Muñoz G, Moreno-Perlin T, Mouriño-Pérez RR, Sánchez-Carbente MDR, Folch-Mallol JL, Pérez-Llano Y, Gunde-Cimerman N, Sánchez NDC, Batista-García RA. Haloadaptative Responses of Aspergillus sydowii to Extreme Water Deprivation: Morphology, Compatible Solutes, and Oxidative Stress at NaCl Saturation. J Fungi (Basel) 2020; 6:E316. [PMID: 33260894 DOI: 10.3390/jof6040316] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023] Open
Abstract
Water activity (aw) is critical for microbial growth, as it is severely restricted at aw < 0.90. Saturating NaCl concentrations (~5.0 M) induce extreme water deprivation (aw ≅ 0.75) and cellular stress responses. Halophilic fungi have cellular adaptations that enable osmotic balance and ionic/oxidative stress prevention to grow at high salinity. Here we studied the morphology, osmolyte synthesis, and oxidative stress defenses of the halophile Aspergillus sydowii EXF-12860 at 1.0 M and 5.13 M NaCl. Colony growth, pigmentation, exudate, and spore production were inhibited at NaCl-saturated media. Additionally, hyphae showed unpolarized growth, lower diameter, and increased septation, multicellularity and branching compared to optimal NaCl concentration. Trehalose, mannitol, arabitol, erythritol, and glycerol were produced in the presence of both 1.0 M and 5.13 M NaCl. Exposing A. sydowii cells to 5.13 M NaCl resulted in oxidative stress evidenced by an increase in antioxidant enzymes and lipid peroxidation biomarkers. Also, genes involved in cellular antioxidant defense systems were upregulated. This is the most comprehensive study that investigates the micromorphology and the adaptative cellular response of different non-enzymatic and enzymatic oxidative stress biomarkers in halophilic filamentous fungi.
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19
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Novak Babič M, Gostinčar C, Gunde-Cimerman N. Microorganisms populating the water-related indoor biome. Appl Microbiol Biotechnol 2020; 104:6443-6462. [PMID: 32533304 PMCID: PMC7347518 DOI: 10.1007/s00253-020-10719-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/22/2020] [Accepted: 06/02/2020] [Indexed: 12/17/2022]
Abstract
Modernisation of our households created novel opportunities for microbial growth and thus changed the array of microorganisms we come in contact with. While many studies have investigated microorganisms in the air and dust, tap water, another major input of microbial propagules, has received far less attention. The quality of drinking water in developed world is strictly regulated to prevent immediate danger to human health. However, fungi, algae, protists and bacteria of less immediate concern are usually not screened for. These organisms can thus use water as a vector of transmission into the households, especially if they are resistant to various water treatment procedures. Good tolerance of unfavourable abiotic conditions is also important for survival once microbes enter the household. Limitation of water availability, high or low temperatures, application of antimicrobial chemicals and other measures are taken to prevent indoor microbial overgrowth. These conditions, together with a large number of novel chemicals in our homes, shape the diversity and abundance of indoor microbiota through constant selection of the most resilient species, resulting in a substantial overlap in diversity of indoor and natural extreme environments. At least in fungi, extremotolerance has been linked to human pathogenicity, explaining why many species found in novel indoor habitats (such as dishwasher) are notable opportunistic pathogens. As a result, microorganisms that often enter our households with water and are then enriched in novel indoor habitats might have a hitherto underestimated impact on the well-being of the increasingly indoor-bound human population. KEY POINTS: Domestic environment harbours a large diversity of microorganisms. Microbiota of water-related indoor habitats mainly originates from tap water. Bathrooms, kitchens and household appliances select for polyextremotolerant species. Many household-related microorganisms are human opportunistic pathogens.
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Affiliation(s)
- Monika Novak Babič
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao, 266555, China
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia.
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20
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Coleine C, Masonjones S, Sterflinger K, Onofri S, Selbmann L, Stajich JE. Peculiar genomic traits in the stress-adapted cryptoendolithic Antarctic fungus Friedmanniomyces endolithicus. Fungal Biol 2020; 124:458-467. [PMID: 32389308 DOI: 10.1016/j.funbio.2020.01.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/15/2020] [Accepted: 01/19/2020] [Indexed: 11/28/2022]
Abstract
Friedmanniomyces endolithicus is a highly melanized fungus endemic to the Antarctic, occurring exclusively in endolithic communities of the ice-free areas of the Victoria Land, including the McMurdo Dry Valleys, the coldest and most hyper-arid desert on Earth and accounted as the Martian analog on our planet. F. endolithicus is highly successful in these inhospitable environments, the most widespread and commonly isolated species from these peculiar niches, indicating a high degree of adaptation. The nature of its extremo tolerance has not been previously studied. To investigate this, we sequenced genome of F. endolithicus CCFEE 5311 to explore gene content and genomic patterns that could be attributed to its specialization. The predicted functional potential of the genes was assigned by similarity to InterPro and CAZy domains. The genome was compared to phylogenetically close relatives which are also melanized fungi occurring in extreme environments including Friedmanniomyces simplex, Baudoinia panamericana, Acidomyces acidophilus, Hortaea thailandica and Hortaea werneckii. We tested if shared genomic traits existed among these species and hyper-extremotolerant fungus F. endolithicus. We found that some characters for stress tolerance such as meristematic growth and cold tolerance are enriched in F. endolithicus that may be triggered by the exposure to Antarctic prohibitive conditions.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy.
| | - Sawyer Masonjones
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA.
| | - Katja Sterflinger
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy.
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy; Italian Antarctic National Museum (MNA), Mycological Section, Genoa, Italy.
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA.
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21
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Chovanová K, Kamlárová A, Maresch D, Harichová J, Zámocký M. Expression of extracellular peroxidases and catalases in mesophilic and thermophilic Chaetomia in response to environmental oxidative stress stimuli. Ecotoxicol Environ Saf 2019; 181:481-490. [PMID: 31228824 DOI: 10.1016/j.ecoenv.2019.06.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/07/2019] [Accepted: 06/12/2019] [Indexed: 06/09/2023]
Abstract
Peroxidases and catalases are well-known antioxidant enzymes produced in almost all living organisms for the elimination of reactive oxygen species (ROS) and thus they prevent the occurrence of oxidative stress. In our study we focused on two soil fungi of the family Chaetomiaceae (mesophilic Chaetomium cochliodes and its thermophilic counterpart C. thermophilum var. dissitum) in order to explore the presence of peroxidase and catalase genes, formation of their native transcripts and protective effect of corresponding translation products in a case study. Predicted genes of our interest were confirmed by genomic PCR and their inducible transcripts by RT-PCR. We were able to quantify the expression levels of newly discovered fungal heme peroxidases and catalases with the reverse-transcription quantitative real-time PCR method. We compared obtained quantitative levels of mRNA production with the level of corresponding extracellular protein occurrence as detected with monitoring their specific peroxidase and catalase activities directly in the cultivation media at optimal growth temperatures. The presence of secretory Catalase 2 from C. thermophilum var. dissitum was detected and identified with mass spectrometry approach directly in the growth medium. This unique catalase is phylogenetically closely related with a previously described catalase-phenol oxidase thus representing an effective and versatile antioxidant in the environment of the fungal mycelia also involved in the catabolism of recalcitrant phenolic substances.
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Affiliation(s)
- Katarína Chovanová
- Laboratory of Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551, Bratislava Slovakia
| | - Anna Kamlárová
- Laboratory of Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551, Bratislava Slovakia; Institute of Experimental Medicine, Faculty of Medicine, Pavol Jozef Šafárik University, Trieda SNP 1, SK-04011, Košice, Slovakia
| | - Daniel Maresch
- Division of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190, Vienna, Austria
| | - Jana Harichová
- Laboratory of Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551, Bratislava Slovakia
| | - Marcel Zámocký
- Laboratory of Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551, Bratislava Slovakia; Department of Molecular Evolution & Development, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria.
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22
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Tafer H, Poyntner C, Lopandic K, Sterflinger K, Piñar G. Back to the Salt Mines: Genome and Transcriptome Comparisons of the Halophilic Fungus Aspergillus salisburgensis and Its Halotolerant Relative Aspergillus sclerotialis. Genes (Basel) 2019; 10:genes10050381. [PMID: 31137536 PMCID: PMC6563132 DOI: 10.3390/genes10050381] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/15/2019] [Accepted: 05/15/2019] [Indexed: 12/22/2022] Open
Abstract
Salt mines are among the most extreme environments as they combine darkness, low nutrient availability, and hypersaline conditions. Based on comparative genomics and transcriptomics, we describe in this work the adaptive strategies of the true halophilic fungus Aspergillus salisburgensis, found in a salt mine in Austria, and compare this strain to the ex-type halotolerant fungal strain Aspergillus sclerotialis. On a genomic level, A. salisburgensis exhibits a reduced genome size compared to A. sclerotialis, as well as a contraction of genes involved in transport processes. The proteome of A. sclerotialis exhibits an increased proportion of alanine, glycine, and proline compared to the proteome of non-halophilic species. Transcriptome analyses of both strains growing at 5% and 20% NaCl show that A. salisburgensis regulates three-times fewer genes than A. sclerotialis in order to adapt to the higher salt concentration. In A. sclerotialis, the increased osmotic stress impacted processes related to translation, transcription, transport, and energy. In contrast, membrane-related and lignolytic proteins were significantly affected in A. salisburgensis.
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Affiliation(s)
- Hakim Tafer
- VIBT EQ Extremophile Center, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
| | - Caroline Poyntner
- VIBT EQ Extremophile Center, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
| | - Ksenija Lopandic
- VIBT EQ Extremophile Center, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
| | - Katja Sterflinger
- VIBT EQ Extremophile Center, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
| | - Guadalupe Piñar
- VIBT EQ Extremophile Center, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
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23
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Ding X, Liu K, Lu Y, Gong G. Morphological, transcriptional, and metabolic analyses of osmotic-adapted mechanisms of the halophilic Aspergillus montevidensis ZYD4 under hypersaline conditions. Appl Microbiol Biotechnol 2019; 103:3829-3846. [PMID: 30859256 DOI: 10.1007/s00253-019-09705-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/04/2019] [Accepted: 02/12/2019] [Indexed: 11/30/2022]
Abstract
Halophilic fungi in hypersaline habitats require multiple cellular responses for high-salinity adaptation. However, the exact mechanisms behind these adaptation processes remain to be slightly known. The current study is aimed at elucidating the morphological, transcriptomic, and metabolomic changes of the halophilic fungus Aspergillus montevidensis ZYD4 under hypersaline conditions. Under these conditions, the fungus promoted conidia formation and suppressed cleistothecium development. Furthermore, the fungus differentially expressed genes (P < 0.0001) that controlled ion transport, amino acid transport and metabolism, soluble sugar accumulation, fatty acid β-oxidation, saturated fatty acid synthesis, electron transfer, and oxidative stress tolerance. Additionally, the hypersalinized mycelia widely accumulated metabolites, including amino acids, soluble sugars, saturated fatty acids, and other carbon- and nitrogen-containing compounds. The addition of metabolites-such as neohesperidin, biuret, aspartic acid, alanine, proline, and ornithine-significantly promoted the growth (P ≤ 0.05) and the morphological adaptations of A. montevidensis ZYD4 grown in hypersaline environments. Our study demonstrated that morphological shifts, ion equilibrium, carbon and nitrogen metabolism for solute accumulation, and energy production are vital to halophilic fungi so that they can build tolerance to high-salinity environments.
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Affiliation(s)
- Xiaowei Ding
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China.,School of Biological Science and Engineering
- Shaanxi University of Technology, Hanzhong City, 723001, Shaanxi, China
| | - Kaihui Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China. .,School of Biological Science and Engineering
- Shaanxi University of Technology, Hanzhong City, 723001, Shaanxi, China.
| | - Yuxin Lu
- School of Biological Science and Engineering
- Shaanxi University of Technology, Hanzhong City, 723001, Shaanxi, China
| | - Guoli Gong
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
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24
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Zajc J, Gostinčar C, Černoša A, Gunde-Cimerman N. Stress-Tolerant Yeasts: Opportunistic Pathogenicity Versus Biocontrol Potential. Genes (Basel) 2019; 10:genes10010042. [PMID: 30646593 PMCID: PMC6357073 DOI: 10.3390/genes10010042] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/03/2019] [Accepted: 01/09/2019] [Indexed: 01/26/2023] Open
Abstract
Stress-tolerant fungi that can thrive under various environmental extremes are highly desirable for their application to biological control, as an alternative to chemicals for pest management. However, in fungi, the mechanisms of stress tolerance might also have roles in mammal opportunism. We tested five species with high biocontrol potential in agriculture (Aureobasidium pullulans, Debayomyces hansenii, Meyerozyma guilliermondii, Metschnikowia fructicola, Rhodotorula mucilaginosa) and two species recognized as emerging opportunistic human pathogens (Exophiala dermatitidis, Aureobasidium melanogenum) for growth under oligotrophic conditions and at 37 °C, and for tolerance to oxidative stress, formation of biofilms, production of hydrolytic enzymes and siderophores, and use of hydrocarbons as sole carbon source. The results show large overlap between traits desirable for biocontrol and traits linked to opportunism (growth under oligotrophic conditions, production of siderophores, high oxidative stress tolerance, and specific enzyme activities). Based on existing knowledge and these data, we suggest that oligotrophism and thermotolerance together with siderophore production at 37 °C, urease activity, melanization, and biofilm production are the main traits that increase the potential for fungi to cause opportunistic infections in mammals. These traits should be carefully considered when assessing safety of potential biocontrol agents.
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Affiliation(s)
- Janja Zajc
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia.
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia.
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia.
- Institut 'Jožef Stefan', Jamova cesta 39, SI-1000 Ljubljana, Slovenia.
| | - Anja Černoša
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia.
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia.
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