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Juteršek M, Gerasymenko IM, Petek M, Haumann E, Vacas S, Kallam K, Gianoglio S, Navarro-Llopis V, Heethoff M, Fuertes IN, Patron N, Orzáez D, Gruden K, Warzecha H, Baebler Š. Transcriptome-informed identification and characterization of Planococcus citri cis- and trans-isoprenyl diphosphate synthase genes. iScience 2024; 27:109441. [PMID: 38523795 PMCID: PMC10960109 DOI: 10.1016/j.isci.2024.109441] [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: 06/20/2023] [Revised: 10/13/2023] [Accepted: 03/04/2024] [Indexed: 03/26/2024] Open
Abstract
Insect physiology and reproduction depend on several terpenoid compounds, whose biosynthesis is mainly unknown. One enigmatic group of insect monoterpenoids are mealybug sex pheromones, presumably resulting from the irregular coupling activity of unidentified isoprenyl diphosphate synthases (IDSs). Here, we performed a comprehensive search for IDS coding sequences of the pest mealybug Planococcus citri. We queried the available genomic and newly generated short- and long-read P. citri transcriptomic data and identified 18 putative IDS genes, whose phylogenetic analysis indicates several gene family expansion events. In vitro testing confirmed regular short-chain coupling activity with five gene products. With the candidate with highest IDS activity, we also detected low amounts of irregular coupling products, and determined amino acid residues important for chain-length preference and irregular coupling activity. This work therefore provides an important foundation for deciphering terpenoid biosynthesis in mealybugs, including the sex pheromone biosynthesis in P. citri.
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Affiliation(s)
- Mojca Juteršek
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000 Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Jamova 39, 1000 Ljubljana, Slovenia
| | - Iryna M. Gerasymenko
- Plant Biotechnology and Metabolic Engineering, Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
| | - Marko Petek
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Elisabeth Haumann
- Plant Biotechnology and Metabolic Engineering, Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
| | - Sandra Vacas
- Instituto Agroforestal del Mediterráneo-CEQA, Universitat Politècnica de València, Camino de Vera s/n, Valencia, Spain
| | - Kalyani Kallam
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk NR4 7UZ, UK
| | - Silvia Gianoglio
- Institute for Plant Molecular and Cell Biology (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat Politècnica de València (UPV), Valencia, Spain
| | - Vicente Navarro-Llopis
- Instituto Agroforestal del Mediterráneo-CEQA, Universitat Politècnica de València, Camino de Vera s/n, Valencia, Spain
| | - Michael Heethoff
- Animal Evolutionary Ecology, Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
| | | | - Nicola Patron
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk NR4 7UZ, UK
| | - Diego Orzáez
- Institute for Plant Molecular and Cell Biology (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat Politècnica de València (UPV), Valencia, Spain
| | - Kristina Gruden
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Heribert Warzecha
- Plant Biotechnology and Metabolic Engineering, Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
| | - Špela Baebler
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000 Ljubljana, Slovenia
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Kanj AN, Guiance IR, Kottom TJ, Schaefbauer KJ, Choudhury M, Limper AH, Skalski JH. The intestinal commensal fungus Wallemia mellicola enhances asthma in mice through Dectin-2. Med Mycol 2024; 62:myae004. [PMID: 38331424 PMCID: PMC10898867 DOI: 10.1093/mmy/myae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/18/2023] [Accepted: 02/06/2024] [Indexed: 02/10/2024] Open
Abstract
Overgrowth of the fungus Wallemia mellicola in the intestines of mice enhances the severity of asthma. Wallemia mellicola interacts with the immune system through Dectin-2 expressed on the surface of myeloid and intestinal epithelial cells. Using Dectin-2-deficient mice, we show that the interaction of W. mellicola with Dectin-2 is essential for the gut-lung pathways, enhancing the severity of asthma in mice with W. mellicola intestinal dysbiosis. These findings offer better insight into dysbiosis-associated inflammation and highlight the role pattern recognition receptors have in immune recognition of commensal fungi in the gut, leading to alterations in immune function in the lungs.
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Affiliation(s)
- Amjad N Kanj
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN USA
- Thoracic Disease Research Unit, Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN USA
| | - Irene Riestra Guiance
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN USA
- Thoracic Disease Research Unit, Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN USA
| | - Theodore J Kottom
- Thoracic Disease Research Unit, Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN USA
| | - Kyle J Schaefbauer
- Thoracic Disease Research Unit, Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN USA
| | - Malay Choudhury
- Thoracic Disease Research Unit, Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN USA
| | - Andrew H Limper
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN USA
- Thoracic Disease Research Unit, Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN USA
| | - Joseph H Skalski
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN USA
- Thoracic Disease Research Unit, Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN USA
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Perdomo-González A, Pérez-Reverón R, Goberna M, León-Barrios M, Fernández-López M, Villadas PJ, Reyes-Betancort JA, Díaz-Peña FJ. How harmful are exotic plantations for soils and its microbiome? A case study in an arid island. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 879:163030. [PMID: 36963683 DOI: 10.1016/j.scitotenv.2023.163030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 05/17/2023]
Abstract
The plantation of exotic species has been a common practice in (semi-) arid areas worldwide aiming to restore highly degraded habitats. The effects of these plantations on plant cover or soil erosion have been widely studied, while little attention has been paid to the consequences on soil quality and belowground biological communities. This study evaluates the long-term (>60 years) effects of the exotic species Acacia cyclops and Pinus halepensis revegetation on soil properties, including microbiome, in an arid island. Soils under exotic plantation were compared to both degraded soils with a very low cover of native species and soils with well-preserved native plant communities. Seven scenarios were selected in a small area (~25 ha) with similar soil type but differing in the plant cover. Topsoils (0-15 cm) were analyzed for physical, chemical and biochemical properties, and amplicon sequencing of bacterial and fungal communities. Microbial diversity was similar among soils with exotic plants and native vegetation (Shannon's index = 5.26 and 5.34, respectively), while the most eroded soils exhibited significantly lower diversity levels (Shannon's index = 4.72). Bacterial and fungal communities' composition in degraded soils greatly differed from those in vegetated soils (Canberra index = 0.85 and 0.92, respectively) likely due to high soil sodicity, fine textures and compaction. Microbial communities' composition also differed in soils covered with exotic and native species, to a greater extent for fungi than for bacteria (Canberra index = 0.94 and 0.89, respectively), due to higher levels of nutrients, microbial biomass and activity in soils with native species. Results suggest that reforestation succeeded in avoiding further soil degradation but still leading to relevant changes in soil microbial community that may have negative effects on ecosystem stability. Information gained in this research could be useful for environmental agencies and decision makers about the controversial replacement of exotic plants in insular territories.
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Affiliation(s)
- Adolfo Perdomo-González
- Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Spain.
| | - Raquel Pérez-Reverón
- Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - Marta Goberna
- Departamento de Medio Ambiente y Agronomía, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Milagros León-Barrios
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - Manuel Fernández-López
- Grupo de Microbiología de Ecosistemas Agroforestales, Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
| | - Pablo J Villadas
- Grupo de Microbiología de Ecosistemas Agroforestales, Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
| | - J Alfredo Reyes-Betancort
- Jardín de Aclimatación de La Orotava, Instituto Canario de Investigaciones Agrarias (ICIA), 38400 Puerto de la Cruz, Spain
| | - Francisco J Díaz-Peña
- Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Spain.
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Plemenitaš A. Sensing and Responding to Hypersaline Conditions and the HOG Signal Transduction Pathway in Fungi Isolated from Hypersaline Environments: Hortaea werneckii and Wallemia ichthyophaga. J Fungi (Basel) 2021; 7:jof7110988. [PMID: 34829275 PMCID: PMC8620582 DOI: 10.3390/jof7110988] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 11/16/2022] Open
Abstract
Sensing and responding to changes in NaCl concentration in hypersaline environments is vital for cell survival. In this paper, we identified and characterized key components of the high-osmolarity glycerol (HOG) signal transduction pathway, which is crucial in sensing hypersaline conditions in the extremely halotolerant black yeast Hortaea werneckii and in the obligate halophilic fungus Wallemia ichthyophaga. Both organisms were isolated from solar salterns, their predominating ecological niche. The identified components included homologous proteins of both branches involved in sensing high osmolarity (SHO1 and SLN1) and the homologues of mitogen-activated protein kinase module (MAPKKK Ste11, MAPKK Pbs2, and MAPK Hog1). Functional complementation of the identified gene products in S. cerevisiae mutant strains revealed some of their functions. Structural protein analysis demonstrated important structural differences in the HOG pathway components between halotolerant/halophilic fungi isolated from solar salterns, salt-sensitive S. cerevisiae, the extremely salt-tolerant H. werneckii, and halophilic W. ichthyophaga. Known and novel gene targets of MAP kinase Hog1 were uncovered particularly in halotolerant H. werneckii. Molecular studies of many salt-responsive proteins confirm unique and novel mechanisms of adaptation to changes in salt concentration.
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Affiliation(s)
- Ana Plemenitaš
- Faculty of Medicine, Institute of Biochemistry and Molecular Biology, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
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Cao B, Haelewaters D, Schoutteten N, Begerow D, Boekhout T, Giachini AJ, Gorjón SP, Gunde-Cimerman N, Hyde KD, Kemler M, Li GJ, Liu DM, Liu XZ, Nuytinck J, Papp V, Savchenko A, Savchenko K, Tedersoo L, Theelen B, Thines M, Tomšovský M, Toome-Heller M, Urón JP, Verbeken A, Vizzini A, Yurkov AM, Zamora JC, Zhao RL. Delimiting species in Basidiomycota: a review. FUNGAL DIVERS 2021. [DOI: 10.1007/s13225-021-00479-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Degois J, Simon X, Clerc F, Bontemps C, Leblond P, Duquenne P. One-year follow-up of microbial diversity in bioaerosols emitted in a waste sorting plant in France. WASTE MANAGEMENT (NEW YORK, N.Y.) 2021; 120:257-268. [PMID: 33310602 DOI: 10.1016/j.wasman.2020.11.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 06/12/2023]
Abstract
Bioaerosols emitted in waste sorting plants (WSP) can induce some adverse health effects on the workers such as rhinitis, asthma and hypersensitivity pneumonitis. The composition of these bioaerosols is scarcely known and most of the time assessed using culture-dependent methods. Due to the well-known limitations of cultural methods, these biodiversity measurements underestimate the actual microbial taxon richness. The aim of the study was to assess the airborne microbial biodiversity by using a sequencing method in a French waste sorting plant (WSP) for one year and to investigate the main factors of variability of this biodiversity. Static sampling was performed in five areas in the plant and compared to an indoor reference (IR), using closed-face cassettes (10 L.min-1) with polycarbonate membranes, every month for one year. Environmental data was measured (temperature, relative humidity). After DNA extraction, microbial biodiversity was assessed by means of sequencing. Bacterial genera Staphylococcus, Streptococcus, Prevotella, Lactococcus, Lactobacillus, Pseudomonas and fungal genera Wallemia, Cladosporium, Debaryomyces, Penicillium, Alternaria were the most predominant airborne microorganisms. Microbial biodiversity was different in the plant compared to the IR and seemed to be influenced by the season.
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Affiliation(s)
- Jodelle Degois
- Department of pollutant metrology, Institut National de Recherche et de Sécurité (INRS), Vandœuvre-lès-Nancy 54500, France
| | - Xavier Simon
- Department of pollutant metrology, Institut National de Recherche et de Sécurité (INRS), Vandœuvre-lès-Nancy 54500, France
| | - Frédéric Clerc
- Department of pollutant metrology, Institut National de Recherche et de Sécurité (INRS), Vandœuvre-lès-Nancy 54500, France
| | - Cyril Bontemps
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France
| | - Pierre Leblond
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France
| | - Philippe Duquenne
- Department of process engineering, Institut National de Recherche et de Sécurité (INRS), Vandœuvre-lès-Nancy 54500, France.
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Rodrigues AM, Kubitschek-Barreira PH, Pinheiro BG, Teixeira-Ferreira A, Hahn RC, de Camargo ZP. Immunoproteomic Analysis Reveals Novel Candidate Antigens for the Diagnosis of Paracoccidioidomycosis Due to Paracoccidioides lutzii. J Fungi (Basel) 2020; 6:jof6040357. [PMID: 33322269 PMCID: PMC7770604 DOI: 10.3390/jof6040357] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/04/2020] [Accepted: 12/08/2020] [Indexed: 12/13/2022] Open
Abstract
Paracoccidioidomycosis (PCM) is a life-threatening systemic infection caused by the fungal pathogen Paracoccidioides brasiliensis and related species. Whole-genome sequencing and stage-specific proteomic analysis of Paracoccidioides offer the opportunity to profile humoral immune responses against P. lutzii and P. brasiliensis s. str. infection using innovative screening approaches. Here, an immunoproteomic approach was used to identify PCM-associated antigens that elicit immune responses by combining 2-D electrophoresis of P. lutzii and P. brasiliensis proteomes, immunological detection using a gold-standard serum, and mass spectrometry analysis. A total of 16 and 25 highly immunoreactive proteins were identified in P. lutzii and P. brasiliensis, respectively, and 29 were shown to be the novel antigens for Paracoccidioides species, including seven uncharacterized proteins. Among the panel of proteins identified, most are involved in metabolic pathways, carbon metabolism, and biosynthesis of secondary metabolites in both immunoproteomes. Remarkably, six isoforms of the surface-associated enolase in the range of 54 kDa were identified as the major antigens in human PCM due to P. lutzii. These novel immunoproteomes of Paracoccidioides will be employed to develop a sensitive and affordable point-of-care diagnostic assay and an effective vaccine to identify infected hosts and prevent infection and development of human PCM. These findings provide a unique opportunity for the refinement of diagnostic tools of this important neglected systemic mycosis, which is usually associated with poverty.
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Affiliation(s)
- Anderson Messias Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil;
- Correspondence: (A.M.R.); (Z.P.d.C.); Tel.: +55-1155764551 (ext. 1540) (A.M.R.); +55-1155764551 (ext. 1512) (Z.P.d.C.)
| | - Paula Helena Kubitschek-Barreira
- Department of Cellular Biology, Roberto Alcantara Gomes Institute of Biology, Rio de Janeiro State University (UERJ), Rio de Janeiro 20511010, Brazil;
| | - Breno Gonçalves Pinheiro
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil;
| | - André Teixeira-Ferreira
- Toxinology Laboratory, Department of Physiology and Pharmacodynamics, Fiocruz, Rio de Janeiro 21040900, Brazil;
| | - Rosane Christine Hahn
- Laboratory of Mycology/Research, Faculty of Medicine, Federal University of Mato Grosso, Cuiabá 78060900, Brazil;
- Júlio Muller University Hospital, Federal University of Mato Grosso, Cuiabá 78048902, Brazil
| | - Zoilo Pires de Camargo
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil;
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
- Correspondence: (A.M.R.); (Z.P.d.C.); Tel.: +55-1155764551 (ext. 1540) (A.M.R.); +55-1155764551 (ext. 1512) (Z.P.d.C.)
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Pinheiro BG, Hahn RC, de Camargo ZP, Rodrigues AM. Molecular Tools for Detection and Identification of Paracoccidioides Species: Current Status and Future Perspectives. J Fungi (Basel) 2020; 6:E293. [PMID: 33217898 PMCID: PMC7711936 DOI: 10.3390/jof6040293] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/01/2020] [Accepted: 11/05/2020] [Indexed: 12/14/2022] Open
Abstract
Paracoccidioidomycosis (PCM) is a mycotic disease caused by the Paracoccidioides species, a group of thermally dimorphic fungi that grow in mycelial form at 25 °C and as budding yeasts when cultured at 37 °C or when parasitizing the host tissues. PCM occurs in a large area of Latin America, and the most critical regions of endemicity are in Brazil, Colombia, and Venezuela. The clinical diagnosis of PCM needs to be confirmed through laboratory tests. Although classical laboratory techniques provide valuable information due to the presence of pathognomonic forms of Paracoccidioides spp., nucleic acid-based diagnostics gradually are replacing or complementing culture-based, biochemical, and immunological assays in routine microbiology laboratory practice. Recently, taxonomic changes driven by whole-genomic sequencing of Paracoccidioides have highlighted the need to recognize species boundaries, which could better ascertain Paracoccidioides taxonomy. In this scenario, classical laboratory techniques do not have significant discriminatory power over cryptic agents. On the other hand, several PCR-based methods can detect polymorphisms in Paracoccidioides DNA and thus support species identification. This review is focused on the recent achievements in molecular diagnostics of paracoccidioidomycosis, including the main advantages and pitfalls related to each technique. We discuss these breakthroughs in light of taxonomic changes in the Paracoccidioides genus.
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Affiliation(s)
- Breno Gonçalves Pinheiro
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (B.G.P.); (Z.P.d.C.)
| | - Rosane Christine Hahn
- Laboratory of Mycology/Research, Faculty of Medicine, Federal University of Mato Grosso, Cuiabá, Mato Grosso 78060900, Brazil;
- Federal University of Mato Grosso, Júlio Muller University Hospital, Mato Grosso 78048902, Brazil
| | - Zoilo Pires de Camargo
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (B.G.P.); (Z.P.d.C.)
- Department of Medicine, Discipline of infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
| | - Anderson Messias Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (B.G.P.); (Z.P.d.C.)
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Liu C, Shi X, Wu F, Zhang M, Gao G, Wu Q. Temporal patterns in the interaction between photosynthetic picoeukaryotes and their attached fungi in Lake Chaohu. FEMS Microbiol Ecol 2020; 96:5859481. [DOI: 10.1093/femsec/fiaa123] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/17/2020] [Indexed: 12/11/2022] Open
Abstract
ABSTRACT
The combination of flow cytometric sorting and high-throughput sequencing revealed the broad existence of photosynthetic picoeukaryote attached fungi (PPE-attached fungi) in Lake Chaohu. The relative sequence abundance of attached fungi was negatively correlated with that of the photosynthetic picoeukaryotes (PPEs). PPE-attached fungal communities were mainly composed of Basidiomycota, Chytridiomycota and Ascomycota. Temperature, Si and PPE community structure are the most important driving factors for the temporal succession of PPE-attached fungal communities. In particular, PPE-attached fungi can be divided into three groups from high to low temperatures. Phylogenetic molecular ecological network results indicated that the connectivity and the total number of links in the network of the high-temperature group (> 21.82°C) are higher than those in the other two temperature groups (between 9.67 and 21.82°C, and < 9.67°C, respectively). Moreover, the interaction between PPE-attached fungi and the PPEs changed from antagonistic to cooperative, with the decline in temperature. The most abundant operational taxonomic units of PPE-attached fungi were affiliated with the Cladosporium, the most common saprophytic fungus, whereas most fungal hub taxa were Chytridiomycota, the main parasite fungi of phytoplankton.
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Affiliation(s)
- Changqing Liu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoli Shi
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Fan Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Guang Gao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Qinglong Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
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Rodríguez-Caballero G, Caravaca F, Díaz G, Torres P, Roldán A. The invader Carpobrotus edulis promotes a specific rhizosphere microbiome across globally distributed coastal ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 719:137347. [PMID: 32120096 DOI: 10.1016/j.scitotenv.2020.137347] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 06/10/2023]
Abstract
The importance of plant-microbe interactions to the success of invasive plants has rarely been studied at a global scale. Carpobrotus edulis (L.) N. E. Br is an aggressive invader in many areas around the world, forming dense mats in coastal environments. In an approach at a large geographical scale, over a wide latitudinal and climatic range, we tested the ability of C. edulis to alter the local bacterial and fungal community structure and microbial activity in eight invaded coastal locations. The factors invasiveness and geographical location had a significant effect on the soil microbiota, the microbial community composition and structure from the rhizosphere of native and C. edulis plants being distinct in every location. The effect of the invader on all the chemical, physico-chemical, and microbiological properties studied depended on the invaded location. The soil bacterial and fungal community composition and structure were related to the soil available nutrients and mean annual rainfall, and those of the soil bacterial community were also linked to the soil respiration and latitude. Overall, our results reveal that the ability of the invader C. edulis to alter soil microbial community structure harboring a specific microbiome was widespread across a large invaded range - leading to concurring changes in the rhizosphere microbial functioning, such as nutrient cycling.
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Affiliation(s)
- G Rodríguez-Caballero
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation. P.O. Box 164, Campus de Espinardo, 30100 Murcia, Spain
| | - F Caravaca
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation. P.O. Box 164, Campus de Espinardo, 30100 Murcia, Spain.
| | - G Díaz
- Universidad Miguel Hernández de Elche. Department of Applied Biology, Avda. Ferrocarril, s/n. Edf. Laboratorios, 03202 Elche, Alicante, Spain
| | - P Torres
- Universidad Miguel Hernández de Elche. Department of Applied Biology, Avda. Ferrocarril, s/n. Edf. Laboratorios, 03202 Elche, Alicante, Spain
| | - A Roldán
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation. P.O. Box 164, Campus de Espinardo, 30100 Murcia, Spain
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Menolli N, Sánchez-García M. Brazilian fungal diversity represented by DNA markers generated over 20 years. Braz J Microbiol 2020; 51:729-749. [PMID: 31828716 PMCID: PMC7203393 DOI: 10.1007/s42770-019-00206-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 12/01/2019] [Indexed: 10/25/2022] Open
Abstract
Molecular techniques using fungal DNA barcoding (ITS) and other markers have been key to identifying the biodiversity of different geographic areas, mainly in megadiverse countries. Here, we provide an overview of the fungal diversity in Brazil based on DNA markers of phylogenetic importance generated since 1996. We retrieved fungal sequences of ITS, LSU, SSU, tef1-α, β-tubulin, rpb1, rpb2, actin, chitin synthase, and ATP6 from GenBank using different field keywords that indicated their origin in Brazil. A total of 19,440 sequences were recovered. ITS is the most representative marker (11,209 sequences), with 70.1% belonging to Ascomycota, 18.6% Basidiomycota, 10.2% unidentified, 1.1% Mucoromycota, two sequences of Olpidium bornovanus (Fungi incertae sedis), one sequence of Blastocladiomycota (Allomyces arbusculus), and one sequence of Chytridiomycota (Batrachochytrium dendrobatidis). Considering the sequences of all selected markers, only the phyla Cryptomycota and Entorrhizomycota were not represented. Based on ITS, using a cutoff of 98%, all sequences comprise 3047 OTUs, with the majority being Ascomycota (2088 OTUs) and Basidiomycota (681 OTUs). Previous numbers based mainly on morphological and bibliographical data revealed 5264 fungal species from Brazil, with a predominance of Basidiomycota (2741 spp.) and Ascomycota (1881 spp.). The unidentified ITS sequences not assigned to a higher taxonomic level represent 1.61% of all ITS sequences sampled and correspond to 38 unknown class-level lineages (75% cutoff). A maximum likelihood phylogeny based on LSU illustrates the fungal classes occurring in Brazil.
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Affiliation(s)
- Nelson Menolli
- Departamento de Ciências da Natureza e Matemática (DCM), Subárea de Biologia (SAB), Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), Câmpus São Paulo, Rua Pedro Vicente 625, São Paulo, SP, 01109-010, Brazil.
- Núcleo de Pesquisa em Micologia, Instituto de Botânica, Av. Miguel Stefano 3687, Água Funda, São Paulo, SP, 04301-012, Brazil.
| | - Marisol Sánchez-García
- Biology Department, Clark University, Worcester, MA, 01610, USA
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, SE-75005, Sweden
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13
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Mishra P, Tulsani NJ, Jakhesara SJ, Dafale NA, Patil NV, Purohit HJ, Koringa PG, Joshi CG. Exploring the eukaryotic diversity in rumen of Indian camel (Camelus dromedarius) using 18S rRNA amplicon sequencing. Arch Microbiol 2020; 202:1861-1872. [PMID: 32448959 DOI: 10.1007/s00203-020-01897-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 04/13/2020] [Accepted: 05/11/2020] [Indexed: 12/18/2022]
Abstract
In addition to a wide variety of anaerobic and facultative anaerobic bacteria, camel rumen also harbors a diverse of eukaryotic organisms. In the present study, the eukaryotic communities of camel rumen were characterized using 18S rRNA amplicon sequencing. Metagenomic DNA was isolated from rumen samples of fourteen adult Bikaneri and Kachchhi breeds of camel fed different diets containing Jowar, Bajra, Maize, and Guar. Illumina sequencing generated 27,161,904 number of reads corresponding to 1543 total operational taxonomic units (OTUs). Taxonomic classification of community metagenome sequences from all the samples revealed the presence of 92 genera belonging to 16 different divisions, out of which Ciliophora (73%), Fungi (13%) and Streptophyta (9%) were found to be the most dominant. Notably, the abundance of Ciliophora was significantly higher in the case of Guar feed, while Fungi was significantly higher in the case of Maize feed, indicating the influence of cellulose and hemicellulose content of feedstuff on the composition of eukaryotes. The results suggest that the camel rumen eukaryotes are highly dynamic and depend on the type of diet given to the animal. Pearson's correlation analysis suggested the ciliate protozoa and fungi were negatively correlated with each other. To the best of our knowledge, this is first systematic study to characterize camel rumen eukaryotes, which has provided newer information regarding eukaryotic diversity patterns amongst camel fed on different diets.
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Affiliation(s)
- Priyaranjan Mishra
- Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Nilam J Tulsani
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India.
| | - Nishant A Dafale
- Environmental Genomic Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440020, India
| | - Niteen V Patil
- ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh, 334001, India
| | - Hemant J Purohit
- Environmental Genomic Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440020, India
| | - Prakash G Koringa
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Center, MS Building, Block B & D, 6th Floor, GH Road, Sector-11, Gujarat, Gandhinagar, 382001, India
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14
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Li J, Luo Y, Chen D, Yu B, He J, Huang Z, Mao X, Zheng P, Yu J, Luo J, Tian G, Yan H, Wang Q, Wang H. The fungal community and its interaction with the concentration of short-chain fatty acids in the caecum and colon of weaned piglets. J Anim Physiol Anim Nutr (Berl) 2020; 104:616-628. [PMID: 31943421 DOI: 10.1111/jpn.13300] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/03/2019] [Accepted: 12/07/2019] [Indexed: 12/17/2022]
Abstract
In sharp contrast to the numerous studies on bacteria, very little is known about the fungal community in mammalian gut. Recent studies on human and mice highlighted the importance of "mycobiota" in the metabolism and gut health of host, but our knowledge on the fungal composition and distribution in swine gut is very limited. In the current study, the fungal community in the caecal and colonic digesta from five weaned piglets was analysed based on an Illumina HiSeq 2500 platform targeting the internal transcribed spacer 1 region, and its relationship with the concentration of short-chain fatty acids was also investigated. Results revealed that the fungal profile in the caecal and colonic digesta of the piglets was distinct, and the caecal fungal diversity was significantly higher (p < .05). Basidiomycota and Ascomycota were the two predominant fungal phyla in the caecum and colon of the piglets. Comparing with that in colon, the abundance of Saccharomycopsis, Wallemia and Mrakia showed significantly higher (p < .05), and the abundance of Scheffersomyces, Aspergillus, Penicillium and Mucor was significantly lower in the caecum (p < .05). Canonical correspondence analysis showed a correlation between the fungal community and the concentration of isobutyrate, isovalerate, propionate and acetate in the digesta samples. Spearman's correlation indicated that the low-abundance genera, Fusarium, Plectosphaerella and Metarhizium, were positively correlated with of isobutyrate (p < .05), while Xeromyces were negatively correlated with acetate (p < .05), and Cornuvesica was negatively correlated with both acetate and propionate (p < .05). Results illuminated a probable interaction between the fungal composition and the bacterial degradation of protein and complex carbohydrates in the diet. These findings would be helpful to enhance our understanding of fungi in swine gut and provide a foundation for future work on the function of mycobiota in pigs.
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Affiliation(s)
- Jiayan Li
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuheng Luo
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Daiwen Chen
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Bing Yu
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Jun He
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhiqing Huang
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiangbing Mao
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Ping Zheng
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Jie Yu
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Junqiu Luo
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Gang Tian
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Hui Yan
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Quyuan Wang
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Huifen Wang
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
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15
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He MQ, Zhao RL, Hyde KD, Begerow D, Kemler M, Yurkov A, McKenzie EHC, Raspé O, Kakishima M, Sánchez-Ramírez S, Vellinga EC, Halling R, Papp V, Zmitrovich IV, Buyck B, Ertz D, Wijayawardene NN, Cui BK, Schoutteten N, Liu XZ, Li TH, Yao YJ, Zhu XY, Liu AQ, Li GJ, Zhang MZ, Ling ZL, Cao B, Antonín V, Boekhout T, da Silva BDB, De Crop E, Decock C, Dima B, Dutta AK, Fell JW, Geml J, Ghobad-Nejhad M, Giachini AJ, Gibertoni TB, Gorjón SP, Haelewaters D, He SH, Hodkinson BP, Horak E, Hoshino T, Justo A, Lim YW, Menolli N, Mešić A, Moncalvo JM, Mueller GM, Nagy LG, Nilsson RH, Noordeloos M, Nuytinck J, Orihara T, Ratchadawan C, Rajchenberg M, Silva-Filho AGS, Sulzbacher MA, Tkalčec Z, Valenzuela R, Verbeken A, Vizzini A, Wartchow F, Wei TZ, Weiß M, Zhao CL, Kirk PM. Notes, outline and divergence times of Basidiomycota. FUNGAL DIVERS 2019. [DOI: 10.1007/s13225-019-00435-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AbstractThe Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.
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16
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Park R, Dzialo MC, Spaepen S, Nsabimana D, Gielens K, Devriese H, Crauwels S, Tito RY, Raes J, Lievens B, Verstrepen KJ. Microbial communities of the house fly Musca domestica vary with geographical location and habitat. MICROBIOME 2019; 7:147. [PMID: 31699144 PMCID: PMC6839111 DOI: 10.1186/s40168-019-0748-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/09/2019] [Indexed: 05/20/2023]
Abstract
House flies (Musca domestica) are widespread, synanthropic filth flies commonly found on decaying matter, garbage, and feces as well as human food. They have been shown to vector microbes, including clinically relevant pathogens. Previous studies have demonstrated that house flies carry a complex and variable prokaryotic microbiota, but the main drivers underlying this variability and the influence of habitat on the microbiota remain understudied. Moreover, the differences between the external and internal microbiota and the eukaryotic components have not been examined. To obtain a comprehensive view of the fly microbiota and its environmental drivers, we sampled over 400 flies from two geographically distinct countries (Belgium and Rwanda) and three different environments-farms, homes, and hospitals. Both the internal as well as external microbiota of the house flies were studied, using amplicon sequencing targeting both bacteria and fungi. Results show that the house fly's internal bacterial community is very diverse yet relatively consistent across geographic location and habitat, dominated by genera Staphylococcus and Weissella. The external bacterial community, however, varies with geographic location and habitat. The fly fungal microbiota carries a distinct signature correlating with the country of sampling, with order Capnodiales and genus Wallemia dominating Belgian flies and genus Cladosporium dominating Rwandan fly samples. Together, our results reveal an intricate country-specific pattern for fungal communities, a relatively stable internal bacterial microbiota and a variable external bacterial microbiota that depends on geographical location and habitat. These findings suggest that vectoring of a wide spectrum of environmental microbes occurs principally through the external fly body surface, while the internal microbiome is likely more limited by fly physiology.
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Affiliation(s)
- Rahel Park
- VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, 3001, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
- Leuven Institute for Beer Research (LIBR), Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Maria C Dzialo
- VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, 3001, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
- Leuven Institute for Beer Research (LIBR), Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Stijn Spaepen
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
- Leuven Institute for Beer Research (LIBR), Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Donat Nsabimana
- Biology Department, School of Science, College of Science and technology, University of Rwanda, RN1, Butare, Rwanda
| | - Kim Gielens
- VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, 3001, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
- Leuven Institute for Beer Research (LIBR), Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Herman Devriese
- Safety, Health & Environment Department, UZ Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Sam Crauwels
- Leuven Institute for Beer Research (LIBR), Gaston Geenslaan 1, 3001, Leuven, Belgium
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department M2S, KU Leuven, Campus De Nayer, Fortsesteenweg 30A, 2860, Sint-Katelijne Waver, Belgium
| | - Raul Y Tito
- VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, 3001, Leuven, Belgium
- Bioinformatics and (eco-)systems biology lab, Department of Microbiology and Immunology, Rega institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Jeroen Raes
- VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, 3001, Leuven, Belgium
- Bioinformatics and (eco-)systems biology lab, Department of Microbiology and Immunology, Rega institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Bart Lievens
- Leuven Institute for Beer Research (LIBR), Gaston Geenslaan 1, 3001, Leuven, Belgium
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department M2S, KU Leuven, Campus De Nayer, Fortsesteenweg 30A, 2860, Sint-Katelijne Waver, Belgium
| | - Kevin J Verstrepen
- VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, 3001, Leuven, Belgium.
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium.
- Leuven Institute for Beer Research (LIBR), Gaston Geenslaan 1, 3001, Leuven, Belgium.
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17
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Gostinčar C, Sun X, Zajc J, Fang C, Hou Y, Luo Y, Gunde-Cimerman N, Song Z. Population Genomics of an Obligately Halophilic Basidiomycete Wallemia ichthyophaga. Front Microbiol 2019; 10:2019. [PMID: 31551960 PMCID: PMC6738226 DOI: 10.3389/fmicb.2019.02019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/19/2019] [Indexed: 11/15/2022] Open
Abstract
Background Wallemia ichthyophaga is a highly specialized basidiomycetous fungus. It is one of the most halophilic fungi ever described, only able to grow at low water activity. This specialization is thought to explain why it is only rarely isolated from nature. Results Genomes of 21 W. ichthyophaga strains were sequenced with PE150 reads on BGISEQ500 platform. The genomes shared high similarity with the reference genome of the species, they were all smaller than 10 Mbp and had a low number of predicted genes. Groups of strains isolated in the same location encompassed clones as well as very divergent strains. There was little concordance between phylogenies of predicted genes. Linkage disequilibrium of pairs of polymorphic loci decayed relatively quickly as a function of distance between the loci (LD decay distance 1270 bp). For the first time a putative mating-type locus was identified in the genomes of W. ichthyophaga. Conclusion Based on the comparison of W. ichthyophaga genomes it appears that some phylogenetic lineages of the species can persist in the same location over at least several years. Apart from this, the differences between the strains do not reflect the isolation habitat or geographic location. Together with results supporting the existence of (sexual) recombination in W. ichthyophaga, the presented results indicate that strains of W. ichthyophaga can form a single recombining population even between different habitats and over large geographical distances.
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Affiliation(s)
- Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.,Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao, China
| | - Xiaohuan Sun
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Janja Zajc
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.,National Institute of Biology, Ljubljana, Slovenia
| | - Chao Fang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yong Hou
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yonglun Luo
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao, China.,BGI-Shenzhen, Shenzhen, China.,Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Zewei Song
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
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18
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Teixeira P, Brandão J, Silva S, Babič MN, Gunde‐Cimerman N, Pires J, Costa S, Valério E. Microbiological and chemical quality of ice used to preserve fish in Lisbon marketplaces. J Food Saf 2019. [DOI: 10.1111/jfs.12641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pedro Teixeira
- Bromatology and Water LaboratoryEnergy, Environment and Green Structure Department Lisbon Municipality, Lisbon Portugal
- CESAM—Centre for Environmental and Marine StudiesUniversity of Aveiro Aveiro Portugal
| | - João Brandão
- Department of Environmental HealthNational Institute of Health Doutor Ricardo Jorge Lisbon Portugal
| | - Susana Silva
- Department of EpidemiologyNational Institute of Health Doutor Ricardo Jorge Lisbon Portugal
| | - Monika Novak Babič
- Department of Biology, Biotechnical FacultyUniversity of Ljubljana Ljubljana Slovenia
| | - Nina Gunde‐Cimerman
- Department of Biology, Biotechnical FacultyUniversity of Ljubljana Ljubljana Slovenia
| | - Joana Pires
- FCUL—Faculty of SciencesUniversity of Lisbon Lisbon Portugal
| | - Sílvia Costa
- Bromatology and Water LaboratoryEnergy, Environment and Green Structure Department Lisbon Municipality, Lisbon Portugal
| | - Elisabete Valério
- Department of Environmental HealthNational Institute of Health Doutor Ricardo Jorge Lisbon Portugal
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19
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Chamekh R, Deniel F, Donot C, Jany JL, Nodet P, Belabid L. Isolation, Identification and Enzymatic Activity of Halotolerant and Halophilic Fungi from the Great Sebkha of Oran in Northwestern of Algeria. MYCOBIOLOGY 2019; 47:230-241. [PMID: 31448143 PMCID: PMC6691801 DOI: 10.1080/12298093.2019.1623979] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/17/2019] [Accepted: 05/20/2019] [Indexed: 06/10/2023]
Abstract
The Great Sebkha of Oran is a closed depression located in northwestern of Algeria. Despite the ranking of this sebkha among the wetlands of global importance by Ramsar Convention in 2002, no studies on the fungal community in this area have been carried out. In our study, samples were collected from two different regions. The first region is characterized by halophilic vegetation and cereal crops and the second by a total absence of vegetation. The isolated strains were identified morphologically then by molecular analysis. The biotechnological interest of the strains was evaluated by testing their ability to grow at different concentration of NaCl and to produce extracellular enzymes (i.e., lipase, amylase, protease, and cellulase) on solid medium. The results showed that the soil of sebkha is alkaline, with the exception of the soil of cereal crops that is neutral, and extremely saline. In this work, the species Gymnoascus halophilus, Trichoderma gamsii, the two phytopathogenic fungi, Fusarium brachygibbosum and Penicillium allii, and the teleomorphic form of P. longicatenatum observed for the first time in this species, were isolated for the first time in Algeria. The halotolerance test revealed that the majority of the isolated are halotolerant. Wallemia sp. and two strains of G. halophilus are the only obligate halophilic strains. All strains are capable to secrete at least one of the four tested enzymes. The most interesting species presenting the highest enzymatic index were Aspergillus sp. strain A4, Chaetomium sp. strain H1, P. vinaceum, G. halophilus, Wallemia sp. and Ustilago cynodontis.
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Affiliation(s)
- Rajaa Chamekh
- Faculty of Science of Nature and Life, Laboratory Research on Biological Systems and Geomatics, Mascara University, Mascara, Algeria
| | - Franck Deniel
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, EA3882, Université de Brest, ESIAB, Technopôle Brest-Iroise, Plouzané, France
| | - Christelle Donot
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, EA3882, Université de Brest, ESIAB, Technopôle Brest-Iroise, Plouzané, France
| | - Jean-Luc Jany
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, EA3882, Université de Brest, ESIAB, Technopôle Brest-Iroise, Plouzané, France
| | - Patrice Nodet
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, EA3882, Université de Brest, ESIAB, Technopôle Brest-Iroise, Plouzané, France
| | - Lakhder Belabid
- Faculty of Science of Nature and Life, Laboratory Research on Biological Systems and Geomatics, Mascara University, Mascara, Algeria
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Sun X, Gostinčar C, Fang C, Zajc J, Hou Y, Song Z, Gunde-Cimerman N. Genomic Evidence of Recombination in the Basidiomycete Wallemia mellicola. Genes (Basel) 2019; 10:genes10060427. [PMID: 31167502 PMCID: PMC6628117 DOI: 10.3390/genes10060427] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 12/16/2022] Open
Abstract
One of the most commonly encountered species in the small basidiomycetous sub-phylum Wallemiomycotina is Wallemia mellicola, a xerotolerant fungus with a widespread distribution. To investigate the population characteristics of the species, whole genomes of twenty-five strains were sequenced. Apart from identification of four strains of clonal origin, the distances between the genomes failed to reflect either the isolation habitat of the strains or their geographical origin. Strains from different parts of the world appeared to represent a relatively homogenous and widespread population. The lack of concordance between individual gene phylogenies and the decay of linkage disequilibrium indicated that W. mellicola is at least occasionally recombining. Two versions of a putative mating-type locus have been found in all sequenced genomes, each present in approximately half of the strains. W. mellicola thus appears to be capable of (sexual) recombination and shows no signs of allopatric speciation or specialization to specific habitats.
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Affiliation(s)
- Xiaohuan Sun
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China.
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China.
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia.
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China.
| | - Chao Fang
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China.
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China.
| | - Janja Zajc
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia.
- Department of Biotechnology and Systems biology, National Institute of Biology, 1000 Ljubljana, Slovenia.
| | - Yong Hou
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China.
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China.
| | - Zewei Song
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China.
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China.
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia.
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22
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Skalski JH, Limon JJ, Sharma P, Gargus MD, Nguyen C, Tang J, Coelho AL, Hogaboam CM, Crother TR, Underhill DM. Expansion of commensal fungus Wallemia mellicola in the gastrointestinal mycobiota enhances the severity of allergic airway disease in mice. PLoS Pathog 2018; 14:e1007260. [PMID: 30235351 PMCID: PMC6147580 DOI: 10.1371/journal.ppat.1007260] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/06/2018] [Indexed: 12/26/2022] Open
Abstract
The gastrointestinal microbiota influences immune function throughout the body. The gut-lung axis refers to the concept that alterations of gut commensal microorganisms can have a distant effect on immune function in the lung. Overgrowth of intestinal Candida albicans has been previously observed to exacerbate allergic airways disease in mice, but whether subtler changes in intestinal fungal microbiota can affect allergic airways disease is less clear. In this study we have investigated the effects of the population expansion of commensal fungus Wallemia mellicola without overgrowth of the total fungal community. Wallemia spp. are commonly found as a minor component of the commensal gastrointestinal mycobiota in both humans and mice. Mice with an unaltered gut microbiota community resist population expansion when gavaged with W. mellicola; however, transient antibiotic depletion of gut microbiota creates a window of opportunity for expansion of W. mellicola following delivery of live spores to the gastrointestinal tract. This phenomenon is not universal as other commensal fungi (Aspergillus amstelodami, Epicoccum nigrum) do not expand when delivered to mice with antibiotic-depleted microbiota. Mice with Wallemia-expanded gut mycobiota experienced altered pulmonary immune responses to inhaled aeroallergens. Specifically, after induction of allergic airways disease with intratracheal house dust mite (HDM) antigen, mice demonstrated enhanced eosinophilic airway infiltration, airway hyperresponsiveness (AHR) to methacholine challenge, goblet cell hyperplasia, elevated bronchoalveolar lavage IL-5, and enhanced serum HDM IgG1. This phenomenon occurred with no detectable Wallemia in the lung. Targeted amplicon sequencing analysis of the gastrointestinal mycobiota revealed that expansion of W. mellicola in the gut was associated with additional alterations of bacterial and fungal commensal communities. We therefore colonized fungus-free Altered Schaedler Flora (ASF) mice with W. mellicola. ASF mice colonized with W. mellicola experienced enhanced severity of allergic airways disease compared to fungus-free control ASF mice without changes in bacterial community composition.
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Affiliation(s)
- Joseph H. Skalski
- F. Widjaja Foundation Inflammatory Bowel & Immunobiology Research Institute, and the Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Jose J. Limon
- F. Widjaja Foundation Inflammatory Bowel & Immunobiology Research Institute, and the Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Purnima Sharma
- F. Widjaja Foundation Inflammatory Bowel & Immunobiology Research Institute, and the Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Matthew D. Gargus
- F. Widjaja Foundation Inflammatory Bowel & Immunobiology Research Institute, and the Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Christopher Nguyen
- F. Widjaja Foundation Inflammatory Bowel & Immunobiology Research Institute, and the Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Jie Tang
- Genomics Core, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Ana Lucia Coelho
- Women’s Guild Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Cory M. Hogaboam
- Women’s Guild Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Timothy R. Crother
- Division of Pediatric Infectious Diseases, Department of Medicine, and the Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - David M. Underhill
- F. Widjaja Foundation Inflammatory Bowel & Immunobiology Research Institute, and the Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
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The Genus Wallemia—From Contamination of Food to Health Threat. Microorganisms 2018; 6:microorganisms6020046. [PMID: 29883408 PMCID: PMC6027281 DOI: 10.3390/microorganisms6020046] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/17/2018] [Accepted: 05/18/2018] [Indexed: 12/26/2022] Open
Abstract
The fungal genus Wallemia of the order Wallemiales (Wallemiomycotina, Basidiomycota) comprises the most xerotolerant, xerophilic and also halophilic species worldwide. Wallemia spp. are found in various osmotically challenged environments, such as dry, salted, or highly sugared foods, dry feed, hypersaline waters of solar salterns, salt crystals, indoor and outdoor air, and agriculture aerosols. Recently, eight species were recognized for the genus Wallemia, among which four are commonly associated with foods: W. sebi, W. mellicola, W. muriae and W. ichthyophaga. To date, only strains of W. sebi, W. mellicola and W. muriae have been reported to be related to human health problems, as either allergological conditions (e.g., farmer’s lung disease) or rare subcutaneous/cutaneous infections. Therefore, this allergological and infective potential, together with the toxins that the majority of Wallemia spp. produce even under saline conditions, defines these fungi as filamentous food-borne pathogenic fungi.
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Fungal species and their boundaries matter – Definitions, mechanisms and practical implications. FUNGAL BIOL REV 2018. [DOI: 10.1016/j.fbr.2017.11.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Gunde-Cimerman N, Plemenitaš A, Oren A. Strategies of adaptation of microorganisms of the three domains of life to high salt concentrations. FEMS Microbiol Rev 2018. [DOI: 10.1093/femsre/fuy009] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, SI-1000 Ljubljana, Slovenia
| | - Ana Plemenitaš
- Institute of Biochemistry, Medical Faculty, University of Ljubljana, Vrazov trg 1, SI-1000 Ljubljana, Slovenia
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
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Nilsson RH, Taylor AFS, Adams RI, Baschien C, Johan Bengtsson-Palme, Cangren P, Coleine C, Heide-Marie Daniel, Glassman SI, Hirooka Y, Irinyi L, Reda Iršėnaitė, Pedro M. Martin-Sanchez, Meyer W, Seung-Yoon Oh, Jose Paulo Sampaio, Seifert KA, Sklenář F, Dirk Stubbe, Suh SO, Summerbell R, Svantesson S, Martin Unterseher, Cobus M. Visagie, Weiss M, Woudenberg JHC, Christian Wurzbacher, den Wyngaert SV, Yilmaz N, Andrey Yurkov, Kõljalg U, Abarenkov K. Taxonomic annotation of public fungal ITS sequences from the built environment - a report from an April 10-11, 2017 workshop (Aberdeen, UK). MycoKeys 2018; 28:65-82. [PMID: 29559822 PMCID: PMC5804120 DOI: 10.3897/mycokeys.28.20887] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 11/12/2017] [Indexed: 12/22/2022] Open
Abstract
Recent DNA-based studies have shown that the built environment is surprisingly rich in fungi. These indoor fungi - whether transient visitors or more persistent residents - may hold clues to the rising levels of human allergies and other medical and building-related health problems observed globally. The taxonomic identity of these fungi is crucial in such pursuits. Molecular identification of the built mycobiome is no trivial undertaking, however, given the large number of unidentified, misidentified, and technically compromised fungal sequences in public sequence databases. In addition, the sequence metadata required to make informed taxonomic decisions - such as country and host/substrate of collection - are often lacking even from reference and ex-type sequences. Here we report on a taxonomic annotation workshop (April 10-11, 2017) organized at the James Hutton Institute/University of Aberdeen (UK) to facilitate reproducible studies of the built mycobiome. The 32 participants went through public fungal ITS barcode sequences related to the built mycobiome for taxonomic and nomenclatural correctness, technical quality, and metadata availability. A total of 19,508 changes - including 4,783 name changes, 14,121 metadata annotations, and the removal of 99 technically compromised sequences - were implemented in the UNITE database for molecular identification of fungi (https://unite.ut.ee/) and shared with a range of other databases and downstream resources. Among the genera that saw the largest number of changes were Penicillium, Talaromyces, Cladosporium, Acremonium, and Alternaria, all of them of significant importance in both culture-based and culture-independent surveys of the built environment.
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Affiliation(s)
- R. Henrik Nilsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
| | - Andy F. S. Taylor
- The James Hutton Institute and University of Aberdeen, Aberdeen, United Kingdom
| | - Rachel I. Adams
- Plant and Microbial Biology, University of California, 94720 Berkeley, California, USA
| | - Christiane Baschien
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7 B, 38124 Braunschweig, Germany
| | - Johan Bengtsson-Palme
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46, Gothenburg, Sweden
| | - Patrik Cangren
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
| | - Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo 01100, Italy
- Department of Plant Pathology & Microbiology and Institute of Integrative Genome Biology, University of California, Riverside, Riverside 92501, CA, USA
| | - Heide-Marie Daniel
- Université catholique de Louvain, Earth and Life Institute, Applied Microbiology, BCCM/MUCL, Louvain-la-Neuve, Belgium
| | - Sydney I. Glassman
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA 92697, USA
| | - Yuuri Hirooka
- Department of Clinical Plant Science, Faculty of Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo Japan 184-8584
| | - Laszlo Irinyi
- Sydney Medical School-Westmead Hospital, Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney, Australia
- University of Sydney, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney, Australia
- Westmead Institute for Medical Research, Westmead, Australia
| | - Reda Iršėnaitė
- Institute of Botany, Nature Research Centre, Žaliųjų ežerų Str. 49, 08406 Vilnius, Lithuania
| | - Pedro M. Martin-Sanchez
- Bundesanstalt für Materialforschung und -prüfung (BAM), Department 4. Materials & Environment, Unter den Eichen 87, 12205 Berlin, Germany
| | - Wieland Meyer
- Sydney Medical School-Westmead Hospital, Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney, Australia
- University of Sydney, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney, Australia
- Westmead Institute for Medical Research, Westmead, Australia
| | - Seung-Yoon Oh
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jose Paulo Sampaio
- UCIBIO-REQUIMTE, DCV, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Keith A. Seifert
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, ON, Canada K1A 0C6
- Department of Biology, University of Ottawa, 30 Marie Curie Ottawa, ON, Canada, K1N 6N5
| | - Frantisek Sklenář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i, Prague, Czech Republic
| | - Dirk Stubbe
- BCCM/IHEM, Scientific Institute of Public Health WIV-ISP, Juliette Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Sung-Oui Suh
- ATCC, 10801 University Blvd., Manassas, Virginia 20110, USA
| | - Richard Summerbell
- Sporometrics, 219 Dufferin Street, Suite 20C, Toronto, Ontario Canada, M6K 1Y9
- Dalla Lana School of Public Health, University of Toronto, Health Sciences Building, 155 College Street, 6th floor, Toronto, Ontario Canada, M5T 3M7
| | - Sten Svantesson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
| | - Martin Unterseher
- Evangelisches Schulzentrum Martinschule, Max-Planck-Str. 7, 17491 Greifswald, Germany
| | - Cobus M. Visagie
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, ON, Canada K1A 0C6
- Department of Biology, University of Ottawa, 30 Marie Curie Ottawa, ON, Canada, K1N 6N5
- Biosystematics Division, ARC-Plant Health and Protection, P/BagX134, Queenswood 0121, Pretoria, South Africa
| | - Michael Weiss
- Steinbeis-Innovationszentrum, Organismische Mykologie und Mikrobiologie, Vor dem Kreuzberg 17, 72070 Tübingen, Germany
| | - Joyce HC Woudenberg
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Christian Wurzbacher
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
| | - Silke Van den Wyngaert
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhuette 2, D-16775 Stechlin, Germany
| | - Neriman Yilmaz
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, ON, Canada K1A 0C6
- Department of Biology, University of Ottawa, 30 Marie Curie Ottawa, ON, Canada, K1N 6N5
| | - Andrey Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7 B, 38124 Braunschweig, Germany
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Humphries Z, Seifert KA, Hirooka Y, Visagie CM. A new family and genus in Dothideales for Aureobasidium-like species isolated from house dust. IMA Fungus 2017; 8:299-315. [PMID: 29242777 PMCID: PMC5729714 DOI: 10.5598/imafungus.2017.08.02.05] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/10/2017] [Indexed: 11/01/2022] Open
Abstract
An international survey of house dust collected from eleven countries using a modified dilution-to-extinction method yielded 7904 isolates. Of these, six strains morphologically resembled the asexual morphs of Aureobasidium and Hormonema (sexual morphs ?Sydowia), but were phylogenetically distinct. A 28S rDNA phylogeny resolved strains as a distinct clade in Dothideales with families Aureobasidiaceae and Dothideaceae their closest relatives. Further analyses based on the ITS rDNA region, β-tubulin, 28S rDNA, and RNA polymerase II second largest subunit confirmed the distinct status of this clade and divided strains among two consistent subclades. As a result, we introduce a new genus and two new species as Zalariaalba and Z. obscura, and a new family to accommodate them in Dothideales. Zalaria is a black yeast-like fungus, grows restrictedly and produces conidiogenous cells with holoblastic synchronous or percurrent conidiation. Zalaria microscopically closely resembles Hormonema by having only one to two loci per conidiogenous cell, but species of our new genus generally has more restricted growth. Comparing the two species, Z. obscura grows faster on lower water activity (aw) media and produces much darker colonies than Z. alba after 7 d. Their sexual states, if extant, are unknown.
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Affiliation(s)
- Zoë Humphries
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, Canada, K1A 0C6
| | - Keith A Seifert
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, Canada, K1A 0C6.,Department of Biology, University of Ottawa, 30 Marie-Curie, Ottawa, ON, Canada, K1N 6N5
| | - Yuuri Hirooka
- Department of Clinical Plant Science, Faculty of Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo, Japan
| | - Cobus M Visagie
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, Canada, K1A 0C6.,Department of Biology, University of Ottawa, 30 Marie-Curie, Ottawa, ON, Canada, K1N 6N5.,Biosystematics Division, ARC-Plant Health and Protection, P/BagX134, Queenswood 0121, Pretoria, South Africa
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28
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Abstract
Xerophilic fungi, especially Aspergillus species, are prevalent in the built environment. In this study, we employed a combined culture-independent (454-pyrosequencing) and culture-dependent (dilution-to-extinction) approach to investigate the mycobiota of indoor dust collected from 93 buildings in 12 countries worldwide. High and low water activity (aw) media were used to capture mesophile and xerophile biodiversity, resulting in the isolation of approximately 9 000 strains. Among these, 340 strains representing seven putative species in Aspergillus subgenus Polypaecilum were isolated, mostly from lowered aw media, and tentatively identified based on colony morphology and internal transcribed spacer rDNA region (ITS) barcodes. Further morphological study and phylogenetic analyses using sequences of ITS, β-tubulin (BenA), calmodulin (CaM), RNA polymerase II second largest subunit (RPB2), DNA topoisomerase 1 (TOP1), and a pre-mRNA processing protein homolog (TSR1) confirmed the isolation of seven species of subgenus Polypaecilum, including five novel species: A. baarnensis, A. keratitidis, A. kalimae sp. nov., A. noonimiae sp. nov., A. thailandensis sp. nov., A. waynelawii sp. nov., and A. whitfieldii sp. nov. Pyrosequencing detected six of the seven species isolated from house dust, as well as one additional species absent from the cultures isolated, and three clades representing potentially undescribed species. Species were typically found in house dust from subtropical and tropical climates, often in close proximity to the ocean or sea. The presence of subgenus Polypaecilum, a recently described clade of xerophilic/xerotolerant, halotolerant/halophilic, and potentially zoopathogenic species, within the built environment is noteworthy.
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Affiliation(s)
- J.B. Tanney
- Ottawa Research and Development Centre, Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - C.M. Visagie
- Ottawa Research and Development Centre, Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, K1N 6N5, Canada
- Biosystematics Division, ARC-Plant Health and Protection, P/BagX134, Queenswood, 0121 Pretoria, South Africa
| | - N. Yilmaz
- Ottawa Research and Development Centre, Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, K1N 6N5, Canada
| | - K.A. Seifert
- Ottawa Research and Development Centre, Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, K1N 6N5, Canada
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29
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Wallemia peruviensis sp. nov., a new xerophilic fungus from an agricultural setting in South America. Extremophiles 2017; 21:1017-1025. [DOI: 10.1007/s00792-017-0960-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 08/21/2017] [Indexed: 11/26/2022]
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30
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Yin G, Zhang Y, Pennerman KK, Wu G, Hua SST, Yu J, Jurick WM, Guo A, Bennett JW. Characterization of Blue Mold Penicillium Species Isolated from Stored Fruits Using Multiple Highly Conserved Loci. J Fungi (Basel) 2017; 3:E12. [PMID: 29371531 PMCID: PMC5715957 DOI: 10.3390/jof3010012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 02/23/2017] [Accepted: 02/27/2017] [Indexed: 02/04/2023] Open
Abstract
Penicillium is a large genus of common molds with over 400 described species; however, identification of individual species is difficult, including for those species that cause postharvest rots. In this study, blue rot fungi from stored apples and pears were isolated from a variety of hosts, locations, and years. Based on morphological and cultural characteristics and partial amplification of the β-tubulin locus, the isolates were provisionally identified as several different species of Penicillium. These isolates were investigated further using a suite of molecular DNA markers and compared to sequences of the ex-type for cognate species in GenBank, and were identified as P. expansum (3 isolates), P. solitum (3 isolates), P. carneum (1 isolate), and P. paneum (1 isolate). Three of the markers we used (ITS, internal transcribed spacer rDNA sequence; benA, β-tubulin; CaM, calmodulin) were suitable for distinguishing most of our isolates from one another at the species level. In contrast, we were unable to amplify RPB2 sequences from four of the isolates. Comparison of our sequences with cognate sequences in GenBank from isolates with the same species names did not always give coherent data, reinforcing earlier studies that have shown large intraspecific variability in many Penicillium species, as well as possible errors in some sequence data deposited in GenBank.
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Affiliation(s)
- Guohua Yin
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 5711001, China.
- Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
| | - Yuliang Zhang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 5711001, China.
| | - Kayla K Pennerman
- Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
| | - Guangxi Wu
- Oak Ridge Institute for Science and Education, Oak Ridge Associated Universities, Oak Ridge, TN 37831, USA.
| | - Sui Sheng T Hua
- U.S. Department of Agriculture, Agricultural Research Service , Western Regional Research Center, Albany, CA 94710, USA.
| | - Jiujiang Yu
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville, Agricultural Research Center, Beltsville, MD 20705, USA.
| | - Wayne M Jurick
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville, Agricultural Research Center, Beltsville, MD 20705, USA.
| | - Anping Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 5711001, China.
| | - Joan W Bennett
- Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
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Jančič S, Frisvad JC, Kocev D, Gostinčar C, Džeroski S, Gunde-Cimerman N. Production of Secondary Metabolites in Extreme Environments: Food- and Airborne Wallemia spp. Produce Toxic Metabolites at Hypersaline Conditions. PLoS One 2016; 11:e0169116. [PMID: 28036382 PMCID: PMC5201246 DOI: 10.1371/journal.pone.0169116] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 12/11/2016] [Indexed: 01/16/2023] Open
Abstract
The food- and airborne fungal genus Wallemia comprises seven xerophilic and halophilic species: W. sebi, W. mellicola, W. canadensis, W. tropicalis, W. muriae, W. hederae and W. ichthyophaga. All listed species are adapted to low water activity and can contaminate food preserved with high amounts of salt or sugar. In relation to food safety, the effect of high salt and sugar concentrations on the production of secondary metabolites by this toxigenic fungus was investigated. The secondary metabolite profiles of 30 strains of the listed species were examined using general growth media, known to support the production of secondary metabolites, supplemented with different concentrations of NaCl, glucose and MgCl2. In more than two hundred extracts approximately one hundred different compounds were detected using high-performance liquid chromatography-diode array detection (HPLC-DAD). Although the genome data analysis of W. mellicola (previously W. sebi sensu lato) and W. ichthyophaga revealed a low number of secondary metabolites clusters, a substantial number of secondary metabolites were detected at different conditions. Machine learning analysis of the obtained dataset showed that NaCl has higher influence on the production of secondary metabolites than other tested solutes. Mass spectrometric analysis of selected extracts revealed that NaCl in the medium affects the production of some compounds with substantial biological activities (wallimidione, walleminol, walleminone, UCA 1064-A and UCA 1064-B). In particular an increase in NaCl concentration from 5% to 15% in the growth media increased the production of the toxic metabolites wallimidione, walleminol and walleminone.
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Affiliation(s)
- Sašo Jančič
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, Ljubljana, Slovenia
| | - Jens C. Frisvad
- Department of System Biology, Technical University of Denmark, Søltofts Plads, Building 221, Kgs. Lyngby, Denmark
| | - Dragi Kocev
- Department of Knowledge Technologies, Jožef Stefan Institute, Jamova cesta 39, Ljubljana, Slovenia
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, Ljubljana, Slovenia
| | - Sašo Džeroski
- Department of Knowledge Technologies, Jožef Stefan Institute, Jamova cesta 39, Ljubljana, Slovenia
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova 39, Ljubljana, Slovenia
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Nguyen HDT, Jančič S, Meijer M, Tanney JB, Zalar P, Gunde-Cimerman N, Seifert KA. Application of the phylogenetic species concept to Wallemia sebi from house dust and indoor air revealed by multi-locus genealogical concordance. PLoS One 2015; 10:e0120894. [PMID: 25799362 PMCID: PMC4370657 DOI: 10.1371/journal.pone.0120894] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/27/2015] [Indexed: 01/17/2023] Open
Abstract
A worldwide survey of Wallemia occurring in house dust and indoor air was conducted. The isolated strains were identified as W. sebi and W. muriae. Previous studies suggested that the W. sebi phylogenetic clade contained cryptic species but conclusive evidence was lacking because only the internal transcribed spacer (ITS) marker was analyzed. The ITS and four protein-coding genes (MCM7, RPB1, RPB2, and TSR1) were sequenced for 85 isolates. Based on an initial neighbor joining analysis of the concatenated genes, W. muriae remained monophyletic but four clades were found in W. sebi, which we designated as W. sebi clades 1, 2, 3, and 4. We hypothesized that these clades represent distinct phylogenetic species within the Wallemia sebi species complex (WSSC). We then conducted multiple phylogenetic analyses and demonstrated genealogical concordance, which supports the existence of four phylogenetic species within the WSSC. Geographically, W. muriae was only found in Europe, W. sebi clade 3 was only found in Canada, W. sebi clade 4 was found in subtropical regions, while W. sebi clade 1 and 2 were found worldwide. Haplotype analysis showed that W. sebi clades 1 and 2 had multiple haplotypes while W. sebi clades 3 and 4 had one haplotype and may have been under sampled. We describe W. sebi clades 2, 3, and 4 as new species in a companion study.
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Affiliation(s)
- Hai D. T. Nguyen
- Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Ontario, Canada
- Biodiversity (Mycology), Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
- * E-mail: (HDTN); (KAS)
| | - Sašo Jančič
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Martin Meijer
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Joey B. Tanney
- Biodiversity (Mycology), Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Polona Zalar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Keith A. Seifert
- Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Ontario, Canada
- Biodiversity (Mycology), Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
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