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Isola D, Lee HJ, Chung YJ, Zucconi L, Pelosi C. Once upon a Time, There Was a Piece of Wood: Present Knowledge and Future Perspectives in Fungal Deterioration of Wooden Cultural Heritage in Terrestrial Ecosystems and Diagnostic Tools. J Fungi (Basel) 2024; 10:366. [PMID: 38786721 PMCID: PMC11122135 DOI: 10.3390/jof10050366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/22/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024] Open
Abstract
Wooden Cultural Heritage (WCH) represents a significant portion of the world's historical and artistic heritage, consisting of immovable and movable artefacts. Despite the expertise developed since ancient times to enhance its durability, wooden artefacts are inevitably prone to degradation. Fungi play a pivotal role in the deterioration of WCH in terrestrial ecosystems, accelerating its decay and leading to alterations in color and strength. Reviewing the literature of the last 25 years, we aimed to provide a comprehensive overview of fungal diversity affecting WCH, the biochemical processes involved in wood decay, and the diagnostic tools available for fungal identification and damage evaluation. Climatic conditions influence the occurrence of fungal species in threatened WCH, characterized by a prevalence of wood-rot fungi (e.g., Serpula lacrymans, Coniophora puteana) in architectural heritage in temperate and continental climates and Ascomycota in indoor and harsh environments. More efforts are needed to address the knowledge fragmentation concerning biodiversity, the biology of the fungi involved, and succession in the degradative process, which is frequently centered solely on the main actors. Multidisciplinary collaboration among engineers, restorers, and life sciences scientists is vital for tackling the challenges posed by climate change with increased awareness. Traditional microbiology and culture collections are fundamental in laying solid foundations for a more comprehensive interpretation of big data.
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Affiliation(s)
- Daniela Isola
- Department of Economics, Engineering, Society and Business Organization (DEIM), University of Tuscia, Largo dell’Università Snc, 01100 Viterbo, Italy;
| | - Hyun-Ju Lee
- Institute of Preventive Conservation for Cultural Heritage, Korea National University of Cultural Heritage, Buyeo 33115, Republic of Korea;
| | - Yong-Jae Chung
- Department of Heritage Conservation and Restoration, Graduate School of Cultural Heritage, Korea National University of Cultural Heritage, Buyeo 33115, Republic of Korea;
| | - Laura Zucconi
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Largo dell’Università Snc, 01100 Viterbo, Italy;
| | - Claudia Pelosi
- Department of Economics, Engineering, Society and Business Organization (DEIM), University of Tuscia, Largo dell’Università Snc, 01100 Viterbo, Italy;
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2
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Ide-Pérez MR, Sánchez-Reyes A, Folch-Mallol JL, Sánchez-Carbente MDR. Exophiala chapopotensis sp. nov., an extremotolerant black yeast from an oil-polluted soil in Mexico; phylophenetic approach to species hypothesis in the Herpotrichiellaceae family. PLoS One 2024; 19:e0297232. [PMID: 38354109 PMCID: PMC10866521 DOI: 10.1371/journal.pone.0297232] [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: 08/25/2023] [Accepted: 12/12/2023] [Indexed: 02/16/2024] Open
Abstract
Exophiala is a black fungi of the family Herpotrichiellaceae that can be found in a wide range of environments like soil, water and the human body as potential opportunistic pathogen. Some species are known to be extremophiles, thriving in harsh conditions such as deserts, glaciers, and polluted habitats. The identification of novel Exophiala species across diverse environments underlines the remarkable biodiversity within the genus. However, its classification using traditional phenotypic and phylogenetic analyses has posed a challenges. Here we describe a novel taxon, Exophiala chapopotensis sp. nov., strain LBMH1013, isolated from oil-polluted soil in Mexico, delimited according to combined morphological, molecular, evolutionary and statistics criteria. This species possesses the characteristic dark mycelia growing on PDA and tends to be darker in the presence of hydrocarbons. Its growth is dual with both yeast-like and hyphal forms. LBMH1013 differs from closely related species such as E. nidicola due to its larger aseptate conidia and could be distinguished from E. dermatitidis and E. heteromorpha by its inability to thrive above 37°C or 10% of NaCl. A comprehensive genomic analyses using up-to-date overall genome relatedness indices, several multigene phylogenies and molecular evolutionary analyzes using Bayesian speciation models, further validate its species-specific transition from all current Exophiala/Capronia species. Additionally, we applied the phylophenetic conceptual framework to delineate the species-specific hypothesis in order to incorporate this proposal within an integrative taxonomic framework. We believe that this approach to delimit fungal species will also be useful to our peers.
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Affiliation(s)
- Martín R. Ide-Pérez
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Ayixon Sánchez-Reyes
- Investigador por México-Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Jorge Luis Folch-Mallol
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
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3
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The origin of human pathogenicity and biological interactions in Chaetothyriales. FUNGAL DIVERS 2023. [DOI: 10.1007/s13225-023-00518-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
AbstractFungi in the order Chaetothyriales are renowned for their ability to cause human infections. Nevertheless, they are not regarded as primary pathogens, but rather as opportunists with a natural habitat in the environment. Extremotolerance is a major trend in the order, but quite different from black yeasts in Capnodiales which focus on endurance, an important additional parameter is advancing toxin management. In the ancestral ecology of rock colonization, the association with metabolite-producing lichens is significant. Ant-association, dealing with pheromones and repellents, is another mainstay in the order. The phylogenetically derived family, Herpotrichiellaceae, shows dual ecology in monoaromatic hydrocarbon assimilation and the ability to cause disease in humans and cold-blooded vertebrates. In this study, data on ecology, phylogeny, and genomics were collected and analyzed in order to support this hypothesis on the evolutionary route of the species of Chaetothyriales. Comparing the ribosomal tree with that of enzymes involved in toluene degradation, a significant expansion of cytochromes is observed and the toluene catabolism is found to be complete in some of the Herpotrichiellaceae. This might enhance human systemic infection. However, since most species have to be traumatically inoculated in order to cause disease, their invasive potential is categorized as opportunism. Only in chromoblastomycosis, true pathogenicity might be surmised. The criterion would be the possible escape of agents of vertebrate disease from the host, enabling dispersal of adapted genotypes to subsequent generations.
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Marques GN, Cota JB, Leal MO, Silva NU, Flanagan CA, Crosta L, Tavares L, Oliveira M. First Documentation of Exophiala spp. Isolation in Psittaciformes. Animals (Basel) 2022; 12:ani12131699. [PMID: 35804598 PMCID: PMC9264867 DOI: 10.3390/ani12131699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 12/19/2022] Open
Abstract
Several fungi species are reported to act as opportunistic agents of infection in avian species. After the isolation of Exophiala spp., a dematiaceous fungal pathogen associated with a mucosal lesion in a military macaw (Ara militar), samples were collected from another 24 birds of the order Psittaciformes to study the possibility of Exophiala spp. being part of the commensal microbiota of these animals or its possible association with other clinical conditions. Swab samples were collected from the trachea and/or choanae of the birds and inoculated in Sabouraud chloramphenicol agar for fungal isolation. After incubation, fungal species were identified through their macroscopic and microscopic morphology. The presence of Exophiala spp. was identified in 15 of the 25 birds sampled and no statistical association was found between the clinical record of the birds and the fungal isolation. Our results suggest that Exophiala spp. can colonize the upper respiratory airways of psittaciform birds and has a low pathogenic potential in these animals. To the authors’ knowledge, this is the first report of Exophiala spp. isolation from samples of the upper respiratory tract of Psittaciformes.
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Affiliation(s)
- Gonçalo N. Marques
- Zoomarine Portugal, E.N. 125, Km 65, 8201-864 Guia, Portugal; (G.N.M.); (M.O.L.); (N.U.S.); (C.A.F.)
| | - João B. Cota
- CIISA—Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Av. Da Universidade Técnica, 1300-477 Lisbon, Portugal; (J.B.C.); (L.T.)
- Laboratório Associado Para Ciência Animal e Veterinária (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Miriam O. Leal
- Zoomarine Portugal, E.N. 125, Km 65, 8201-864 Guia, Portugal; (G.N.M.); (M.O.L.); (N.U.S.); (C.A.F.)
| | - Nuno U. Silva
- Zoomarine Portugal, E.N. 125, Km 65, 8201-864 Guia, Portugal; (G.N.M.); (M.O.L.); (N.U.S.); (C.A.F.)
| | - Carla A. Flanagan
- Zoomarine Portugal, E.N. 125, Km 65, 8201-864 Guia, Portugal; (G.N.M.); (M.O.L.); (N.U.S.); (C.A.F.)
| | - Lorenzo Crosta
- AEZAVEC (Avian, Exotic and Zoo Animal Veterinary Consultants), 22040 Tirol, Italy;
| | - Luís Tavares
- CIISA—Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Av. Da Universidade Técnica, 1300-477 Lisbon, Portugal; (J.B.C.); (L.T.)
- Laboratório Associado Para Ciência Animal e Veterinária (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Manuela Oliveira
- CIISA—Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Av. Da Universidade Técnica, 1300-477 Lisbon, Portugal; (J.B.C.); (L.T.)
- Laboratório Associado Para Ciência Animal e Veterinária (AL4AnimalS), 1300-477 Lisbon, Portugal
- Correspondence:
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Quan Y, da Silva NM, de Souza Lima BJF, de Hoog S, Vicente VA, Mayer V, Kang Y, Shi D. Black fungi and ants: a genomic comparison of species inhabiting carton nests versus domatia. IMA Fungus 2022; 13:4. [PMID: 35256015 PMCID: PMC8900376 DOI: 10.1186/s43008-022-00091-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/23/2022] [Indexed: 11/10/2022] Open
Abstract
Some members of Chaetothyriales, an order containing potential agents of opportunistic infections in humans, have a natural habitat in nests of tropical arboreal ants. In these black fungi, two types of ant symbiosis are known, i.e. occurrence in domatia inside living plants, or as components of carton constructions made of ant-chewed plant tissue. In order to explain differences between strains from these types of association, we sequenced and annotated genomes of two newly described carton species, Incumbomyces lentus and Incumbomyces delicatus, and compared these with genomes of four domatia species and related Chaetothyriales. General genomic characteristics, CYP genes, carbohydrate-active enzymes (CAZymes), secondary metabolism, and sex-related genes were included in the study.
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Alimu Y, Ban S, Yaguchi T. Molecular Phylogenetic Study of Strains Morphologically Identified as <i>Exophiala dermatitidis</i> from Clinical and Environmental Specimens in Japan. Med Mycol J 2022; 63:1-9. [DOI: 10.3314/mmj.21-00012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yikelamu Alimu
- Medical Mycology Research Center (MMRC), Chiba University
| | - Sayaka Ban
- Medical Mycology Research Center (MMRC), Chiba University
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Chandrasiri SKU, Liu YL, Huang JE, Samarakoon MC, Boonmee S, Calabon MS, Hu DM. Veronaeaaquatica sp. nov. (Herpotrichiellaceae, Chaetothyriales, Eurotiomycetes) from submerged bamboo in China. Biodivers Data J 2021; 9:e64505. [PMID: 34690510 PMCID: PMC8484195 DOI: 10.3897/bdj.9.e64505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 08/26/2021] [Indexed: 12/01/2022] Open
Abstract
Background Freshwater fungi are highly diverse and ecologically important in freshwater systems. In China, more than 1000 species of freshwater fungi are known. Here, we present a brown-spored hyphomycetes that was collected on a submerged decaying bamboo culm in a forest stream in China. New information Phylogenetic analyses of combined LSU, ITS and TUB2 sequences confirm the placement of our new strain in Veronaea (Herpotrichiellaceae), sister to V.japonica. Veronaeaaquatica sp. nov. differs from related taxa V.compacta and V.japonica in having longer conidiophores and cylindrical to pyriform or subclavate conidia with 0–2 septa. Veronaeaaquatica also has darker brown hyphae compared to V.japonica. A morphological description and detailed illustrations of V.aquatica are provided.
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Affiliation(s)
- Sajini K U Chandrasiri
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China College of Bioscience and Bioengineering, Jiangxi Agricultural University Nanchang 330045 China.,Jiangxi Environmental Engineering Vocational College, Ganzhou 341002, China Jiangxi Environmental Engineering Vocational College Ganzhou 341002 China.,Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand Center of Excellence in Fungal Research, Mae Fah Luang University Chiang Rai 57100 Thailand.,School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand School of Science, Mae Fah Luang University Chiang Rai 57100 Thailand
| | - Yu-Lin Liu
- Jiangxi Environmental Engineering Vocational College, Ganzhou 341002, China Jiangxi Environmental Engineering Vocational College Ganzhou 341002 China
| | - Jun-En Huang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China College of Bioscience and Bioengineering, Jiangxi Agricultural University Nanchang 330045 China
| | - Milan C Samarakoon
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand Center of Excellence in Fungal Research, Mae Fah Luang University Chiang Rai 57100 Thailand
| | - Saranyaphat Boonmee
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand Center of Excellence in Fungal Research, Mae Fah Luang University Chiang Rai 57100 Thailand.,School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand School of Science, Mae Fah Luang University Chiang Rai 57100 Thailand
| | - Mark S Calabon
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand Center of Excellence in Fungal Research, Mae Fah Luang University Chiang Rai 57100 Thailand.,School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand School of Science, Mae Fah Luang University Chiang Rai 57100 Thailand
| | - Dian-Ming Hu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China College of Bioscience and Bioengineering, Jiangxi Agricultural University Nanchang 330045 China.,Jiangxi Environmental Engineering Vocational College, Ganzhou 341002, China Jiangxi Environmental Engineering Vocational College Ganzhou 341002 China.,Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, China Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University Nanchang 330045 China
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8
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Isola D, Scano A, Orrù G, Prenafeta-Boldú FX, Zucconi L. Hydrocarbon-Contaminated Sites: Is There Something More Than Exophiala xenobiotica? New Insights into Black Fungal Diversity Using the Long Cold Incubation Method. J Fungi (Basel) 2021; 7:jof7100817. [PMID: 34682237 PMCID: PMC8538888 DOI: 10.3390/jof7100817] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 01/22/2023] Open
Abstract
Human-made hydrocarbon-rich environments are important reservoirs of microorganisms with specific degrading abilities and pathogenic potential. In particular, black fungi are of great interest, but their presence in the environment is frequently underestimated because they are difficult to isolate. In the frame of a biodiversity study from fuel-contaminated sites involving 30 diesel car tanks and 112 fuel pump dispensers (52 diesel and 60 gasoline, respectively), a total of 181 black fungal strains were isolated. The long cold incubation (LCI) of water-suspended samples, followed by plating on Dichloran Rose Bengal Chloramphenicol Agar (DRBC), gave isolation yields up to six times (6.6) higher than those of direct plating on DRBC, and those of enrichment with a phenolic mix. The sequencing of ITS and LSU-rDNA confirmed the dominance of potentially pathogenic fungi from the family Herpotrichiellaceae and Exophiala xenobiotica. Moreover, other opportunistic species were found, including E. opportunistica, E. oligosperma, E. phaeomuriformis, and Rhinocladiella similis. The recurrent presence of E. crusticola, Knufia epidermidis, Aureobasidium melanogenum, Cladosporium spp., and Scolecobasidium spp. was also recorded. Interestingly, 12% of total isolates, corresponding to 50% of taxa found (16/32), represent new species. All the novel taxa in this study were isolated by LCI. These findings suggest that black fungal diversity in hydrocarbon-rich niches remains largely unexplored and that LCI can be an efficient tool for further investigations.
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Affiliation(s)
- Daniela Isola
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, 01100 Viterbo, Italy;
- Correspondence: ; Tel.: +39-0761-357138
| | - Alessandra Scano
- Department of Surgical Sciences, University of Cagliari, 09124 Cagliari, Italy; (A.S.); (G.O.)
| | - Germano Orrù
- Department of Surgical Sciences, University of Cagliari, 09124 Cagliari, Italy; (A.S.); (G.O.)
| | | | - Laura Zucconi
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, 01100 Viterbo, Italy;
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9
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Najafzadeh MJ, Dolatabadi S, Vicente VA, de Hoog GS, Meis JF. In vitro activities of 8 antifungal drugs against 126 clinical and environmental Exophiala isolates. Mycoses 2021; 64:1328-1333. [PMID: 34411353 DOI: 10.1111/myc.13364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/14/2021] [Accepted: 08/17/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND Exophiala is the main genus of black fungi comprising numerous opportunistic species. Data on antifungal susceptibility of Exophiala isolates are limited, while infections are potentially fatal. MATERIALS AND METHODS In vitro activities of eight antifungal drugs (AMB, five azoles, two echinocandins) against 126 clinical (n = 76) and environmental (n = 47) isolates from around the world were investigated. E. oligosperma (n = 58), E. spinifera (n = 33), E. jeanselmei (n = 14) and E. xenobiotica (n = 21) were included in our dataset. RESULTS The resulting MIC90 s of all strains were as follows, in increasing order: posaconazole 0.063 μg/ml, itraconazole 0.125 μg/ml, voriconazole and amphotericin B 1 μg/ml, isavuconazole 2 μg/ml, micafungin and caspofungin 4 μg/ml, and fluconazole 64 μg/ml. Posaconazole, itraconazole and micafungin were the drugs with the best overall activity against Exophiala species. Fluconazole could not be considered as a treatment choice. No significant difference could be found among antifungal drug activities between these four species, neither in clinical nor in environmental isolates. CONCLUSION Antifungal susceptibility data for Exophiala spp. are crucial to improve the management of this occasionally fatal infection and the outcome of its treatment.
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Affiliation(s)
- Mohammad Javad Najafzadeh
- Department of Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Vania Aparecida Vicente
- Bioprocess Engineering and Biotechnology Graduate Program, Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Gerrit Sybren de Hoog
- Center of Expertise in Mycology, Radboudumc/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands.,Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Jacques F Meis
- Bioprocess Engineering and Biotechnology Graduate Program, Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil.,Center of Expertise in Mycology, Radboudumc/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands.,Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
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10
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Ma X, Li X, Liu J, Cheng Y, Zou J, Zhai F, Sun Z, Han L. Soil microbial community succession and interactions during combined plant/white-rot fungus remediation of polycyclic aromatic hydrocarbons. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 752:142224. [PMID: 33207520 DOI: 10.1016/j.scitotenv.2020.142224] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 06/11/2023]
Abstract
Despite combined plant/white-rot fungus remediation being effective for remediating polycyclic aromatic hydrocarbon (PAH)-contaminated soil, the complex organismal interactions and their effects on soil PAH degradation remain unclear. Here, we used quantitative PCR, analysis of soil enzyme activities, and sequencing of representative genes to characterize the ecological dynamics of natural attenuation, mycoremediation (MR, using Crucibulum laeve), phytoremediation (PR, using Salix viminalis), and plant-microbial remediation (PMR, using both species) for PAHs in soil for 60 days. On day 60, PMR achieved the highest removal efficiency of all three representative PAHs (65.5%, 47.5%, and 62.4% for phenanthrene, pyrene, and benzo(a)pyrene, respectively) when compared with the other treatments. MR significantly increased the relative abundance of Rhizobium and Bacillus but antagonized the other putative indigenous PAH-degrading bacteria, which were enriched by PR. PR significantly reduced soil nutrients, such as NO3- and NH4+, and available potassium (AK), thereby changing the microbial community composition as reflected by redundancy analysis, significantly reducing the soil bacterial biomass relative to that in other treatments. These disadvantages hampered phenanthrene and pyrene removal. MR provided additional nutrients, which counteracted the nutrient consumption associated with PR, thereby maintaining the microbial community diversity and bacterial biomass of PMR at a level achieved in the NA treatment. Combination remediation therefore overcame the disadvantages of using PR alone. These results indicated that inoculation with the combination of S. viminalis and C. laeve synergistically stimulated the growth of indigenous PAH-degrading microorganisms and maintained bacterial biomass, thus accelerating the dissipation of soil PAHs.
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Affiliation(s)
- Xiaodong Ma
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Chinese Academy of Forestry Research Institute of Forestry, Xiangshan Road, Haidian District, Beijing 100091, China
| | - Xia Li
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Chinese Academy of Forestry Research Institute of Forestry, Xiangshan Road, Haidian District, Beijing 100091, China; College of Agriculture and Bioengineering, Heze University, University Road, Mudan District, Heze 274000, Shandong, China
| | - Junxiang Liu
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Chinese Academy of Forestry Research Institute of Forestry, Xiangshan Road, Haidian District, Beijing 100091, China
| | - Yunhe Cheng
- Beijing Academy of Forestry and Pomology Sciences, Shuguanghuayuanzhong Road, Haidian District, Beijing 100097, China
| | - Junzhu Zou
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Chinese Academy of Forestry Research Institute of Forestry, Xiangshan Road, Haidian District, Beijing 100091, China
| | - Feifei Zhai
- School of Architectural and Artistic Design, Henan Polytechnic University, Jiefang Middle Road, Jiaozuo, Henan 454000, China
| | - Zhenyuan Sun
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Chinese Academy of Forestry Research Institute of Forestry, Xiangshan Road, Haidian District, Beijing 100091, China
| | - Lei Han
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Chinese Academy of Forestry Research Institute of Forestry, Xiangshan Road, Haidian District, Beijing 100091, China.
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Abstract
AbstractChaetothyriales is an ascomycetous order within Eurotiomycetes. The order is particularly known through the black yeasts and filamentous relatives that cause opportunistic infections in humans. All species in the order are consistently melanized. Ecology and habitats of species are highly diverse, and often rather extreme in terms of exposition and toxicity. Families are defined on the basis of evolutionary history, which is reconstructed by time of divergence and concepts of comparative biology using stochastical character mapping and a multi-rate Brownian motion model to reconstruct ecological ancestral character states. Ancestry is hypothesized to be with a rock-inhabiting life style. Ecological disparity increased significantly in late Jurassic, probably due to expansion of cytochromes followed by colonization of vacant ecospaces. Dramatic diversification took place subsequently, but at a low level of innovation resulting in strong niche conservatism for extant taxa. Families are ecologically different in degrees of specialization. One of the clades has adapted ant domatia, which are rich in hydrocarbons. In derived families, similar processes have enabled survival in domesticated environments rich in creosote and toxic hydrocarbons, and this ability might also explain the pronounced infectious ability of vertebrate hosts observed in these families. Conventional systems of morphological classification poorly correspond with recent phylogenetic data. Species are hypothesized to have low competitive ability against neighboring microbes, which interferes with their laboratory isolation on routine media. The dataset is unbalanced in that a large part of the extant biodiversity has not been analyzed by molecular methods, novel taxonomic entities being introduced at a regular pace. Our study comprises all available species sequenced to date for LSU and ITS, and a nomenclatural overview is provided. A limited number of species could not be assigned to any extant family.
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First Report of Environmental Isolation of Exophiala spp. in Malaysia. Curr Microbiol 2020; 77:2915-2924. [PMID: 32661678 DOI: 10.1007/s00284-020-02109-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 06/29/2020] [Indexed: 12/26/2022]
Abstract
The opportunistic pathogen Exophiala dermatitidis has been frequently isolated from tropical regions of the world. However, there is no report of environmental isolation of Exophiala spp. from Malaysia. The information regarding the ecology of this microbe is important for a better understanding of the opportunism. This study aims to conduct a survey of natural distribution of Exophiala spp. in Malaysia. Forty-seven strains of Exophiala-like was isolated by using selective media. These isolates from the fields were molecularly identified based on the ITS region. The biochemical activity of these microbes was tested by conducting various tests, i.e. DNase test, proteinase activity, and urea hydrolysis. Overall, 22 strains of E. dermatitidis were successfully obtained and identified from burnt tree bark, oil dripped soil sample, hot spring biofilm, railway track stones, tar road contaminated with petrol hydrocarbon, drain and deep mud of Sungai Pinang besides the new discovery from pigeon droppings. A single strain of E. heteromorpha was identified from tar road contaminated with petrol hydrocarbon. Genotypes of the isolated E. dermatitidis were identified by the neighbor-joining tree and grouped into Genotype A, A2 and B. The existence of new Genotype A4 was confirmed by a similar cladogram position in both neighbor-joining and maximum likelihood tree. The survival of E. dermatitidis in the hydrocarbon contaminated environment was studied by supplying engine oil and observing the growth pattern. The results of this study suggest that the opportunistic Exophiala spp. was isolated from nutrient limited and harsh conditions in the natural environment.
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13
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A Comparison of Isolation Methods for Black Fungi Degrading Aromatic Toxins. Mycopathologia 2019; 184:653-660. [DOI: 10.1007/s11046-019-00382-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/28/2019] [Indexed: 12/22/2022]
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14
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Zhang C, Sirijovski N, Adler L, Ferrari BC. Exophiala macquariensis sp. nov., a cold adapted black yeast species recovered from a hydrocarbon contaminated sub-Antarctic soil. Fungal Biol 2019; 123:151-158. [DOI: 10.1016/j.funbio.2018.11.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/22/2018] [Accepted: 11/26/2018] [Indexed: 11/29/2022]
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15
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Kaplan E, Ilkit M, de Hoog GS. Comparison of the rolling circle amplification and ligase-dependent reaction methods for the identification of opportunistic Exophiala species. Med Mycol 2018; 56:759-769. [PMID: 29087521 DOI: 10.1093/mmy/myx095] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 09/06/2017] [Indexed: 01/08/2023] Open
Abstract
We developed two ligase-dependent probe amplification assays based on rolling circle amplification (RCA) and the ligase-dependent reaction (LDR) to differentiate species of Exophiala targeting the rDNA internal transcribed spacer region. We focused on Exophiala dermatitidis and E. phaeomuriformis, two opportunistic inhabitants of indoor wet cells, and further detected E. heteromorpha, E. xenobiotica, and E. crusticola; 57 reference isolates representing the five species were tested. Depending on the RCA probes used, the sensitivity was 100%, and the specificity ranged from 3.7% to 88.6% (median: 46.1%). In contrast, the sensitivity and specificity of the LDR probes targeting the same isolates were 88.6-100% (median: 95.8%) and 95.4-100% (median: 97.7%), respectively. We analyzed 198 additional environmental isolates representing the same Exophiala species. Overall, the sensitivity and specificity of LDR ranged from 89.7% to 100% (median: 94.1%) and from 93.9% to 100% (median: 96.9%), respectively. The assessment of performance and validation of LDR probes using SYBR Green quantitative polymerase chain reaction revealed high reproducibility and an acceptable range limit, in line with the guidelines of the European Network of GMO Laboratories. In conclusion, the LDR assay was more reliable and less expensive than RCA for species-level identification of Exophiala isolates.
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Affiliation(s)
- Engin Kaplan
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana, Turkey
| | - Macit Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana, Turkey
| | - G Sybren de Hoog
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands.,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
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16
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Gülmez D, Doğan Ö, Boral B, Döğen A, İlkit M, de Hoog GS, Arikan-Akdagli S. In vitro activities of antifungal drugs against environmentalExophialaisolates and review of the literature. Mycoses 2018; 61:561-569. [DOI: 10.1111/myc.12779] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 03/23/2018] [Accepted: 03/24/2018] [Indexed: 12/01/2022]
Affiliation(s)
- Dolunay Gülmez
- Department of Medical Microbiology; Faculty of Medicine; Hacettepe University; Ankara Turkey
| | - Özlem Doğan
- Department of Medical Microbiology; Faculty of Medicine; Hacettepe University; Ankara Turkey
- Medical Microbiology Department; Haydarpaşa Numune Hospital; Istanbul Turkey
| | - Barış Boral
- Department of Medical Microbiology; Faculty of Medicine; Hacettepe University; Ankara Turkey
- Department of Medical Microbiology; Faculty of Medicine; Çukurova University; Adana Turkey
| | - Aylin Döğen
- Department of Pharmaceutical Microbiology; Faculty of Pharmacy; Mersin University; Mersin Turkey
| | - Macit İlkit
- Department of Medical Microbiology; Faculty of Medicine; Çukurova University; Adana Turkey
| | - G. Sybren de Hoog
- Westerdijk Fungal Biodiversity Institute; Utrecht The Netherlands
- Center of Expertise in Mycology Radboudumc/CWZ; Nijmegen The Netherlands
| | - Sevtap Arikan-Akdagli
- Department of Medical Microbiology; Faculty of Medicine; Hacettepe University; Ankara Turkey
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17
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Teixeira M, Moreno L, Stielow B, Muszewska A, Hainaut M, Gonzaga L, Abouelleil A, Patané J, Priest M, Souza R, Young S, Ferreira K, Zeng Q, da Cunha M, Gladki A, Barker B, Vicente V, de Souza E, Almeida S, Henrissat B, Vasconcelos A, Deng S, Voglmayr H, Moussa T, Gorbushina A, Felipe M, Cuomo C, de Hoog GS. Exploring the genomic diversity of black yeasts and relatives ( Chaetothyriales, Ascomycota). Stud Mycol 2017; 86:1-28. [PMID: 28348446 PMCID: PMC5358931 DOI: 10.1016/j.simyco.2017.01.001] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The order Chaetothyriales (Pezizomycotina, Ascomycetes) harbours obligatorily melanised fungi and includes numerous etiologic agents of chromoblastomycosis, phaeohyphomycosis and other diseases of vertebrate hosts. Diseases range from mild cutaneous to fatal cerebral or disseminated infections and affect humans and cold-blooded animals globally. In addition, Chaetothyriales comprise species with aquatic, rock-inhabiting, ant-associated, and mycoparasitic life-styles, as well as species that tolerate toxic compounds, suggesting a high degree of versatile extremotolerance. To understand their biology and divergent niche occupation, we sequenced and annotated a set of 23 genomes of main the human opportunists within the Chaetothyriales as well as related environmental species. Our analyses included fungi with diverse life-styles, namely opportunistic pathogens and closely related saprobes, to identify genomic adaptations related to pathogenesis. Furthermore, ecological preferences of Chaetothyriales were analysed, in conjuncture with the order-level phylogeny based on conserved ribosomal genes. General characteristics, phylogenomic relationships, transposable elements, sex-related genes, protein family evolution, genes related to protein degradation (MEROPS), carbohydrate-active enzymes (CAZymes), melanin synthesis and secondary metabolism were investigated and compared between species. Genome assemblies varied from 25.81 Mb (Capronia coronata) to 43.03 Mb (Cladophialophora immunda). The bantiana-clade contained the highest number of predicted genes (12 817 on average) as well as larger genomes. We found a low content of mobile elements, with DNA transposons from Tc1/Mariner superfamily being the most abundant across analysed species. Additionally, we identified a reduction of carbohydrate degrading enzymes, specifically many of the Glycosyl Hydrolase (GH) class, while most of the Pectin Lyase (PL) genes were lost in etiological agents of chromoblastomycosis and phaeohyphomycosis. An expansion was found in protein degrading peptidase enzyme families S12 (serine-type D-Ala-D-Ala carboxypeptidases) and M38 (isoaspartyl dipeptidases). Based on genomic information, a wide range of abilities of melanin biosynthesis was revealed; genes related to metabolically distinct DHN, DOPA and pyomelanin pathways were identified. The MAT (MAting Type) locus and other sex-related genes were recognized in all 23 black fungi. Members of the asexual genera Fonsecaea and Cladophialophora appear to be heterothallic with a single copy of either MAT-1-1 or MAT-1-2 in each individual. All Capronia species are homothallic as both MAT1-1 and MAT1-2 genes were found in each single genome. The genomic synteny of the MAT-locus flanking genes (SLA2-APN2-COX13) is not conserved in black fungi as is commonly observed in Eurotiomycetes, indicating a unique genomic context for MAT in those species. The heterokaryon (het) genes expansion associated with the low selective pressure at the MAT-locus suggests that a parasexual cycle may play an important role in generating diversity among those fungi.
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Affiliation(s)
- M.M. Teixeira
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), Flagstaff, AZ, USA
- Department of Cell Biology, University of Brasília, Brasilia, Brazil
| | - L.F. Moreno
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Department of Basic Pathology, Federal University of Paraná State, Curitiba, PR, Brazi1
- Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - B.J. Stielow
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - A. Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - M. Hainaut
- Université Aix-Marseille (CNRS), Marseille, France
| | - L. Gonzaga
- The National Laboratory for Scientific Computing (LNCC), Petropolis, Brazil
| | | | - J.S.L. Patané
- Department of Biochemistry, University of São Paulo, Brazil
| | - M. Priest
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - R. Souza
- The National Laboratory for Scientific Computing (LNCC), Petropolis, Brazil
| | - S. Young
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - K.S. Ferreira
- Department of Biological Sciences, Federal University of São Paulo, Diadema, SP, Brazil
| | - Q. Zeng
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - M.M.L. da Cunha
- Núcleo Multidisciplinar de Pesquisa em Biologia UFRJ-Xerém-NUMPEX-BIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - A. Gladki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - B. Barker
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), Flagstaff, AZ, USA
| | - V.A. Vicente
- Department of Basic Pathology, Federal University of Paraná State, Curitiba, PR, Brazi1
| | - E.M. de Souza
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, PR, Brazil
| | - S. Almeida
- Department of Clinical and Toxicological Analysis, University of São Paulo, São Paulo, SP, Brazil
| | - B. Henrissat
- Université Aix-Marseille (CNRS), Marseille, France
| | - A.T.R. Vasconcelos
- The National Laboratory for Scientific Computing (LNCC), Petropolis, Brazil
| | - S. Deng
- Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - H. Voglmayr
- Department of Systematic and Evolutionary Botany, University of Vienna, Vienna, Austria
| | - T.A.A. Moussa
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza, Egypt
| | - A. Gorbushina
- Federal Institute for Material Research and Testing (BAM), Berlin, Germany
| | - M.S.S. Felipe
- Department of Cell Biology, University of Brasília, Brasilia, Brazil
| | - C.A. Cuomo
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - G. Sybren de Hoog
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Department of Basic Pathology, Federal University of Paraná State, Curitiba, PR, Brazi1
- Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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18
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Yazdanparast SA, Mohseni S, De Hoog GS, Aslani N, Sadeh A, Badali H. Consistent high prevalence of Exophiala dermatitidis, a neurotropic opportunist, on railway sleepers. J Mycol Med 2017; 27:180-187. [PMID: 28190754 DOI: 10.1016/j.mycmed.2017.01.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 11/30/2016] [Accepted: 01/11/2017] [Indexed: 01/26/2023]
Abstract
Environmental isolation of black yeasts potentially causing human disorders is essential for understanding ecology and routes of infection. Several Exophiala species show prevalence for man-made environments rich in monoaromatic compounds, such as creosote-treated or petroleum-stained railway sleepers. Ambient climatic conditions play a role in species composition in suitable habitats. Therefore, the aim of the present study was to establish the composition of Exophiala species in railway stations as a potential source of human infections in a subtropical region with evaluation of their antifungal susceptibility profiles. We examined 150 railway samples using cotton swabs moistened with sterile physiological saline. Black yeasts and relatives were selected on theirs colony morphology and identified based on ITS rDNA sequencing. Overall, 36 (24%) of samples were positive for black yeast-like fungi, i.e., Exophiala dermatitidis (n=20, 55.6%) was predominant, followed by E. phaeomuriformis (n=9, 25%), E. heteromorpha (n=5, 13.9%), and E. xenobiotica (n=2, 5.6%). Massive contaminations of E. dermatitidis were seen on railway sleepers on creosoted oak wood at the region close to the sea level, while in cold climates were primarily contaminated with clinically insignificant or rare human opportunists (E. crusticola). It seems that, high temperature and humidity are significant effect on species diversity. Moreover, the MIC results for all E. dermatitidis and E. phaeomuriformis strains revealed the widest range and the highest MICs to caspofungin (range 1-16mg/L, Geometric mean 4.912mg/L), and the lowest MIC for posaconazole (0.016-0.031mg/L, G mean 0.061mg/L). However, their clinical effectiveness in the treatment of Exophiala infections remains to be determined.
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Affiliation(s)
- S A Yazdanparast
- Department of Medical Parasitology and Mycology, School of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - S Mohseni
- Department of Microbiology, Sari Branch, Islamic Azad University, Sari, Iran
| | - G S De Hoog
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - N Aslani
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - A Sadeh
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - H Badali
- Invasive Fungi Research Centre (IFRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; Department of Medical Mycology and Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.
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19
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Rapid Identification of Clinically Relevant Members of the Genus Exophiala by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry and Description of Two Novel Species, Exophiala campbellii and Exophiala lavatrina. J Clin Microbiol 2017; 55:1162-1176. [PMID: 28122875 DOI: 10.1128/jcm.02459-16] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 01/22/2017] [Indexed: 11/20/2022] Open
Abstract
Exophiala is a ubiquitous pleomorphic genus comprising at least 40 species, many of which have been associated with superficial, visceral, or systemic infections in humans, other mammals, or cold-blooded animals. In this study, we investigated the potential of matrix-assisted laser desorption-ionization time of flight mass spectrometry (MALDI-TOF MS) for the identification of Exophiala species. A total of 89 isolates (including 50 human and 4 animal clinical isolates) stored in the National Collection of Pathogenic Fungi were identified by PCR amplification and sequencing of internal transcribed spacer region 1. Eighty-three of the isolates corresponded to 16 known species within Exophiala/Rhinocladiella The remaining six isolates are shown by phylogenetic analyses based on four loci to represent two novel Exophiala species. Four isolates from domestic bathrooms which form a sister species with Exophiala lecanii-corni are described here as Exophiala lavatrina sp. nov. The remaining two isolates, both from subcutaneous infections, are distantly related to Exophiala oligosperma and are described here as Exophiala campbellii sp. nov. The triazoles and terbinafine exhibited low MICs against all Exophiala isolates in vitro MALDI-TOF MS successfully distinguished all 18 species and identified all isolates after appropriate reference spectra were created and added to commercial databases. Intraspecific mean log scores ranged from 1.786 to 2.584 and were consistently significantly higher than interspecific scores (1.193 to 1.624), with the exception of E. lecanii-corni and E. lavatrina, for which there was considerable log score overlap. In summary, MALDI-TOF MS allows the rapid and accurate identification of a wide range of clinically relevant Exophiala species.
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20
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Sav H, Ozakkas F, Altınbas R, Kiraz N, Tümgör A, Gümral R, Döğen A, Ilkit M, de Hoog GS. Virulence markers of opportunistic black yeast in Exophiala. Mycoses 2016; 59:343-50. [PMID: 26857806 DOI: 10.1111/myc.12478] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 01/10/2016] [Accepted: 01/12/2016] [Indexed: 12/26/2022]
Abstract
The black yeast genus Exophiala is known to cause a wide variety of diseases in severely ill individuals but can also affect immunocompetent individuals. Virulence markers and other physiological parameters were tested in eight clinical and 218 environmental strains, with a specific focus on human-dominated habitats for the latter. Urease and catalase were consistently present in all samples; four strains expressed proteinase and three strains expressed DNase, whereas none of the strains showed phospholipase, haemolysis, or co-haemolysis activities. Biofilm formation was identified in 30 (13.8%) of the environmental isolates, particularly in strains from dishwashers, and was noted in only two (25%) of the clinical strains. These results indicate that virulence factors are inconsistently present in the investigated Exophiala species, suggesting opportunism rather than pathogenicity.
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Affiliation(s)
- Hafize Sav
- Department of Microbiology, Cerrahpasa Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Fatma Ozakkas
- Department of Microbiology, Cerrahpasa Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Rabiye Altınbas
- Department of Microbiology, Cerrahpasa Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Nuri Kiraz
- Department of Microbiology, Cerrahpasa Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Ayşegül Tümgör
- Department of Microbiology, Adana Numune Training and Research Hospital, Adana, Turkey
| | - Ramazan Gümral
- Department of Microbiology, Gülhane Military Medical Academy, Ankara, Turkey
| | - Aylin Döğen
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Mersin, Mersin, Turkey
| | - Macit Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana, Turkey
| | - G Sybren de Hoog
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands.,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands.,Basic Pathology Department, Federal University of Paraná State, Curitiba, Paraná, Brazil.,King Abdulaziz University, Jeddah, Saudi Arabia
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21
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Ergin Ç, Gök Y, Bayğu Y, Gümral R, Özhak-Baysan B, Döğen A, Öğünç D, Ilkit M, Seyedmousavi S. ATR-FTIR Spectroscopy Highlights the Problem of Distinguishing Between Exophiala dermatitidis and E. phaeomuriformis Using MALDI-TOF MS. MICROBIAL ECOLOGY 2016; 71:339-346. [PMID: 26373644 DOI: 10.1007/s00248-015-0670-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 08/28/2015] [Indexed: 06/05/2023]
Abstract
The present study compared two chemical-based methods, namely, matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) and attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy, to understand the misidentification of Exophiala dermatitidis and Exophiala phaeomuriformis. The study utilized 44 E. dermatitidis and 26 E. phaeomuriformis strains, which were partially treated with strong acids and bases for further evaluation. MALDI-TOF MS and ATR-FTIR spectroscopy data of the two Exophiala species were compared. Data groupings were observed for the chromic acid- and nitric acid-treated species when the black yeast sources were categorized as creosoted-oak sleepers, concrete sleepers, or dishwasher isolates. The MALDI-TOF MS data for the metalloenzyme-containing regions were consistent with the ATR-FTIR spectroscopy data. These results indicated that environmental isolates might contain metals not found in human isolates and might interfere with chemical-based identification methods. Therefore, MALDI-TOF MS reference libraries should be created for clinical strains and should exclude petroleum-associated environmental isolates.
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Affiliation(s)
- Çağrı Ergin
- Department of Microbiology, Faculty of Medicine, Pamukkale University, Denizli, Turkey.
| | - Yaşar Gök
- Chemistry Department, Faculty of Science and Arts, Pamukkale University, Denizli, Turkey
| | - Yasemin Bayğu
- Chemistry Department, Faculty of Science and Arts, Pamukkale University, Denizli, Turkey
| | - Ramazan Gümral
- Department of Microbiology, Gülhane Military Medical Academy, Ankara, Turkey
| | - Betil Özhak-Baysan
- Department of Microbiology, Faculty of Medicine, University of Akdeniz, Antalya, Turkey
| | - Aylin Döğen
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Mersin, Mersin, Turkey
| | - Dilara Öğünç
- Department of Microbiology, Faculty of Medicine, University of Akdeniz, Antalya, Turkey
| | - Macit Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana, Turkey
| | - Seyedmojtaba Seyedmousavi
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
- Invasive Fungi Research Center, Mazandaran University Medical Center, Sari, Iran
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22
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Covino S, Fabianová T, Křesinová Z, Čvančarová M, Burianová E, Filipová A, Vořísková J, Baldrian P, Cajthaml T. Polycyclic aromatic hydrocarbons degradation and microbial community shifts during co-composting of creosote-treated wood. JOURNAL OF HAZARDOUS MATERIALS 2016; 301:17-26. [PMID: 26342147 DOI: 10.1016/j.jhazmat.2015.08.023] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 08/13/2015] [Accepted: 08/13/2015] [Indexed: 06/05/2023]
Abstract
The feasibility of decontaminating creosote-treated wood (CTW) by co-composting with agricultural wastes was investigated using two bulking agents, grass cuttings (GC) and broiler litter (BL), each employed at a 1:1 ratio with the matrix. The initial concentration of total polycyclic aromatic hydrocarbons (PAHs) in CTW (26,500 mg kg(-1)) was reduced to 3 and 19% after 240 d in GC and BL compost, respectively. PAH degradation exceeded the predicted bioaccesible threshold, estimated through sequential supercritical CO2 extraction, together with significant detoxification, assessed by contact tests using Vibrio fisheri and Hordeum vulgare. GC composting was characterized by high microbial biomass growth in the early phases, as suggested by phospholipid fatty acid analyses. Based on the 454-pyrosequencing results, fungi (mostly Saccharomycetales) constituted an important portion of the microbial community, and bacteria were characterized by rapid shifts (from Firmicutes (Bacilli) and Actinobacteria to Proteobacteria). However, during BL composting, larger amounts of prokaryotic and eukaryotic PLFA markers were observed during the cooling and maturation phases, which were dominated by Proteobacteria and fungi belonging to the Ascomycota and those putatively related to the Glomeromycota. This work reports the first in-depth analysis of the chemical and microbiological processes that occur during the co-composting of a PAH-contaminated matrix.
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Affiliation(s)
- Stefano Covino
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic; Institute of Environmental Studies, Faculty of Science, Charles University, Benátská 2, CZ-128 01 Prague 2, Czech Republic
| | - Tereza Fabianová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Zdena Křesinová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Monika Čvančarová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Eva Burianová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Alena Filipová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic; Institute of Environmental Studies, Faculty of Science, Charles University, Benátská 2, CZ-128 01 Prague 2, Czech Republic
| | - Jana Vořísková
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Tomáš Cajthaml
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic; Institute of Environmental Studies, Faculty of Science, Charles University, Benátská 2, CZ-128 01 Prague 2, Czech Republic.
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23
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Özhak-Baysan B, Öğünç D, Döğen A, Ilkit M, de Hoog GS. MALDI-TOF MS-based identification of black yeasts of the genus Exophiala. Med Mycol 2015; 53:347-52. [PMID: 25851261 DOI: 10.1093/mmy/myu093] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In this study, we investigated the applicability of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of Exophiala species. The analysis included a total of 110 Exophiala isolates, including 15 CBS strains representing 4 species, Exophiala dermatitidis (61), E. phaeomuriformis (36), E. crusticola (9), and E. heteromorpha (4), that had been previously identified based on internal transcribed spacer (ITS) regions. We also compared the relative efficacies of Sabouraud glucose agar (SGA) and Columbia agar (CA) for use in MALDI-TOF MS. Remarkably, we obtained a log-score value ≥2.0 by using either SGA or CA for all 15 CBS strains, indicating species-level identification. The remaining 95 Exophiala strains were identified to the genus or species levels, with identification rates of 96.8% and 90.5%, using SGA or CA, respectively. Most of the E. dermatitidis (100% and 92.9%), E. phaeomuriformis (80.6% and 83.9%), E. crusticola (50% and 100%), and E. heteromorpha (100% and 100%) isolates were correctly identified using SGA or CA, respectively. Furthermore, 58.9% and 26.3% of the strains had log-score values of ≥2.0 by using SGA and CA, respectively. Our results indicate that MALDI-TOF MS is a rapid and reliable technique with high rates of correct taxonomic identification.
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Affiliation(s)
- Betil Özhak-Baysan
- Department of Microbiology, Faculty of Medicine, University of Akdeniz, Antalya, Turkey
| | - Dilara Öğünç
- Department of Microbiology, Faculty of Medicine, University of Akdeniz, Antalya, Turkey
| | - Aylin Döğen
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Mersin, Mersin, Turkey
| | - Macit Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana, Turkey
| | - G Sybren de Hoog
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands Research Center for Medical Mycology, Peking University Health Science Center, Beijing, China Sun Yat-sen Hospital, Sun Yat-sen University, Guangzhou, China Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China Basic Pathology Department, Federal University of Paraná State, Curitiba, Paraná, Brazil King Abdulaziz University, Jeddah, Saudi Arabia
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24
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Tesei D, Marzban G, Marchetti-Deschmann M, Tafer H, Arcalis E, Sterflinger K. Proteome of tolerance fine-tuning in the human pathogen black yeast Exophiala dermatitidis. J Proteomics 2015; 128:39-57. [PMID: 26189359 DOI: 10.1016/j.jprot.2015.07.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 06/22/2015] [Accepted: 07/13/2015] [Indexed: 11/16/2022]
Abstract
UNLABELLED The black yeast Exophiala dermatitidis is a worldwide distributed agent of primary and secondary diseases in both immunocompromised and healthy humans, with a high prevalence in human-made environments. Since thermo-tolerance has a crucial role in the fungus persistence in man-dominated habitat and in its pathogenicity, three incubation temperatures (37, 45, 1 °C) and two time spans (1 h, 1 week) were selected to simulate different environmental conditions and to investigate the effect of temperature on the proteome of E. dermatitidis CBS 525.76. Using a novel protocol for protein extraction from black yeasts, 2-D DIGE could be applied for characterization of changes in total protein spot abundance among the experimental conditions. A total of 32 variable proteins were identified by mass spectrometry. Data about protein functions, localization and pathways were also obtained. A typical stress response under non-optimal temperature could not be observed at the proteome level, whereas a reduction of the metabolic activity, mostly concerning processes as the general carbon metabolism, was detected after exposure to cold. These results suggest that a fine protein modulation takes place following temperature treatment and a repertoire of stable protein might be at the base of E. dermatitidis adaptation to altered growth conditions. SIGNIFICANCE E. dermatitidis is a pathogenic black yeast causing neurotropic infections, systemic and subcutaneous disease in a wide range of hosts, including humans. The discovery of the fungus high prevalence in man-made habitats, including sauna facilities, drinking water and dishwashers, generated concern and raised questions about the infection route. In the present work - which is the first contribution on E. dermatitidis proteome - the effect of different temperature conditions on the fungus protein pattern have been analyzed by using a gel-based approach and the temperature responsive proteins have been identified. The absence of a typical stress response following the exposure to non-optimal temperature was detected at the proteome level, along with a general reduction of the metabolic activity after exposure to cold. These results suggest that a very fine regulation of the protein expression as well as adaptations involving a basic set of stable proteins may be at the base of E. dermatitidis enormous ecological plasticity, which plays a role in the fungus distribution, also enabling the transition from natural to human habitat and to the human host.
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Affiliation(s)
- Donatella Tesei
- VIBT Extremophile Center, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
| | - Gorji Marzban
- Plant Biotechnology Unit, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Martina Marchetti-Deschmann
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9/164-IAC, 1060 Vienna, Austria
| | - Hakim Tafer
- VIBT Extremophile Center, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Elsa Arcalis
- Institute for Applied Genetics and Cell Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Katja Sterflinger
- VIBT Extremophile Center, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
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25
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Chowdhary A, Perfect J, de Hoog GS. Black Molds and Melanized Yeasts Pathogenic to Humans. Cold Spring Harb Perspect Med 2014; 5:a019570. [PMID: 25384772 DOI: 10.1101/cshperspect.a019570] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A review is given of melanized fungi involved in human infection, including species forming budding cells and strictly filamentous representatives. Classically, they are known as "phaeoid" or "dematiaceous" fungi, and, today, agents are recognized to belong to seven orders of fungi, of which the Chaetothyriales and Pleosporales are the most important. Infections range from cutaneous or pulmonary colonization to systemic or disseminated invasion. Subcutaneous involvement, either primary or after dissemination, may lead to host tissue proliferation of dermis or epidermis. Particularly in the Chaetothyriales, subcutaneous and systemic infections may occur in otherwise apparently healthy individuals. Infections are mostly chronic and require extended antifungal therapy and/or surgery.
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Affiliation(s)
- Anuradha Chowdhary
- Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 110 007, India
| | - John Perfect
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center Durham, North Carolina 27710
| | - G Sybren de Hoog
- CBS-KNAW Fungal Biodiversity Centre, 3508 AD Utrecht, The Netherlands
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26
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Gümral R, Tümgör A, Saraçlı MA, Yıldıran ŞT, Ilkit M, de Hoog GS. Black yeast diversity on creosoted railway sleepers changes with ambient climatic conditions. MICROBIAL ECOLOGY 2014; 68:699-707. [PMID: 25027275 DOI: 10.1007/s00248-014-0459-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 06/30/2014] [Indexed: 06/03/2023]
Abstract
The environmental isolation of opportunistic pathogenic black yeasts, which are responsible for a wide spectrum of human infections, is essential to understanding the ecology of clinical fungi. Extreme outdoor environments polluted with aromatic hydrocarbons support the growth of black yeasts in unlikely places, such as railway sleepers. However, there are limited data concerning the diversity of these fungi growing on polluted railway sleepers. In this investigation, we examined 845 railway sleeper samples, obtained from 11 Turkish cities representing altitudes from 25 to 1,893 m, and inoculated the samples onto mycological media for the isolation of black yeasts. Ninety-four samples (11.1 %) yielded positive results for black yeast, with creosoted oak sleepers having a significantly higher number of isolates than concrete sleepers (p < 0.05). Identification based on the ribosomal DNA (rDNA) internal transcribed spacer region revealed the highest prevalence of Exophiala phaeomuriformis, followed by Exophiala dermatitidis, Exophiala heteromorpha, Exophiala xenobiotica, and Exophiala crusticola. This study revealed that railway sleepers harboring black yeasts were predominantly (>75 %) populated with thermophilic species. We observed that altitude might have a significant effect on species diversity. Briefly, E. phaeomuriformis exhibited growth over a wide altitude range, from 30 to 1,893 m. In contrast, E. dermatitidis had a remarkable aversion to low altitudes and exhibited maximum growth at 1,285 m. In conclusion, we speculate that one can predict what species will be found on railway sleepers and their probability and that species diversity primarily depends on sleeper type and altitude height. We believe that this study can contribute new insights into the ecology of black yeasts on railway sleepers and the railway factors that influence their diversity.
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Affiliation(s)
- Ramazan Gümral
- Department of Microbiology, Gülhane Military Medical Academy, Ankara, Turkey
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