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Lecaudé C, Orieux N, Chuzeville S, Bertry A, Coissac E, Boyer F, Bonin A, Colomb-Boeckler N, Mathieu B, Recour M, Vindret J, Pignol C, Romand S, Petite C, Taberlet P, Charles C, Bel N, Hauwuy A. Deciphering microbial communities of three Savoyard raw milk cheeses along ripening and regarding the cheese process. Int J Food Microbiol 2024; 418:110712. [PMID: 38723541 DOI: 10.1016/j.ijfoodmicro.2024.110712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/26/2024] [Accepted: 04/17/2024] [Indexed: 05/27/2024]
Abstract
Different Savoyard cheeses are granted with PDO (Protected Designation or Origin) and PGI (Protected Geographical Indication) which guarantees consumers compliance with strict specifications. The use of raw milk is known to be crucial for specific flavor development. To unravel the factors influencing microbial ecosystems across cheese making steps, according to the seasonality (winter and summer) and the mode of production (farmhouse and dairy factory ones), gene targeting on bacteria and fungus was used to have a full picture of 3 cheese making technologies, from the raw milk to the end of the ripening. Our results revealed that Savoyard raw milks are a plenteous source of biodiversity together with the brines used during the process, that may support the development of specific features for each cheese. It was shown that rinds and curds have very contrasted ecosystem diversity, composition, and evolution. Ripening stage was selective for some bacterial species, whereas fungus were mainly ubiquitous in dairy samples. All ripening stages are impacted by the type of cheese technologies, with a higher impact on bacterial communities, except for fungal rind communities, for which the technology is the more discriminant. The specific microorganism's abundance for each technology allow to see a real bar-code, with more or less differences regarding bacterial or fungal communities. Bacterial structuration is shaped mainly by matrices, differently regarding technologies while the influence of technology is higher for fungi. Production types showed 10 differential bacterial species, farmhouses showed more ripening taxa, while dairy factory products showing more lactic acid bacteria. Meanwhile, seasonality looks to be a minor element for the comprehension of both microbial ecosystems, but the uniqueness of each dairy plant is a key explicative feature, more for bacteria than for fungus communities.
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Affiliation(s)
- Cresciense Lecaudé
- CERAQ, Centre de ressources pour l'agriculture de qualité et de montagne, 40 Rue du Terraillet, 73190 Saint-Baldoph, France.
| | - Nicolas Orieux
- ENILV, Ecole Nationale des industries du lait et de la viande, 212Rue Anatole France, 74800 La Roche-sur-Foron, France
| | - Sarah Chuzeville
- ACTALIA, Centre technique d'expertise agroalimentaire, Division d'expertise analytique sur le lait et les produits laitiers, 419 Rte des Champs Laitiers, 74800 Eteaux, France
| | - Alicia Bertry
- ACTALIA, Centre technique d'expertise agroalimentaire, Division d'expertise analytique sur le lait et les produits laitiers, 419 Rte des Champs Laitiers, 74800 Eteaux, France
| | - Eric Coissac
- Université Grenoble Alpes, Université Savoie Mont-Blanc, CNRS, LECA, Laboratoire d'Ecologie Alpine, 38000 Grenoble, France
| | - Frederic Boyer
- Université Grenoble Alpes, Université Savoie Mont-Blanc, CNRS, LECA, Laboratoire d'Ecologie Alpine, 38000 Grenoble, France
| | - Aurélie Bonin
- Université Grenoble Alpes, Université Savoie Mont-Blanc, CNRS, LECA, Laboratoire d'Ecologie Alpine, 38000 Grenoble, France
| | - Nelly Colomb-Boeckler
- ACTALIA, Centre technique d'expertise agroalimentaire, Division d'expertise analytique sur le lait et les produits laitiers, 419 Rte des Champs Laitiers, 74800 Eteaux, France
| | - Bruno Mathieu
- Syndicat Interprofessionnel du Reblochon, 28 Rue Louis Haase, 74230 Thônes, France
| | - Manon Recour
- Syndicat Interprofessionnel du Reblochon, 28 Rue Louis Haase, 74230 Thônes, France
| | - Joël Vindret
- sifa syndicat interprofessionnel du fromage abondance, 16 chemin d'Hirmentaz, 74200 Thonon-les-Bains, France
| | - Céline Pignol
- Savoicime, Syndicat Interprofessionnel de la Tomme de Savoie, 10 Allée Jules Vernes, 74150 Rumilly, France
| | - Stéphane Romand
- Syndicat Interprofessionnel du Reblochon, 28 Rue Louis Haase, 74230 Thônes, France
| | - Caroline Petite
- Syndicat Interprofessionnel de la Tome des Bauges, Rue Henri Bouvier, 73630 Le Chatelard, France
| | - Pierre Taberlet
- Université Grenoble Alpes, Université Savoie Mont-Blanc, CNRS, LECA, Laboratoire d'Ecologie Alpine, 38000 Grenoble, France
| | - Cécile Charles
- CERAQ, Centre de ressources pour l'agriculture de qualité et de montagne, 40 Rue du Terraillet, 73190 Saint-Baldoph, France
| | - Nadège Bel
- ACTALIA, Centre technique d'expertise agroalimentaire, Division d'expertise analytique sur le lait et les produits laitiers, 419 Rte des Champs Laitiers, 74800 Eteaux, France
| | - Agnès Hauwuy
- CERAQ, Centre de ressources pour l'agriculture de qualité et de montagne, 40 Rue du Terraillet, 73190 Saint-Baldoph, France
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Pathomsiriwong W, Aroonsrimorakot S, Taratima W, Maneerattanarungroj P, Reanprayoon P. Exploring airborne fungal contaminations and air quality pollution in nine ancient stone temples, Surin, Thailand. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-33310-0. [PMID: 38687449 DOI: 10.1007/s11356-024-33310-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
This study provided crucial insights into the concentrations of airborne fungi, environmental parameters, and atmospheric pollution in Thailand's ancient stone temples. Airborne fungi were identified based on morphological characteristics. Airborne fungi, meteorological parameters, and atmospheric pollutants concurrently assessed during each sampling event, evaluating indoor/outdoor ratio. Prevalent genera included Penicillium (14.36%), Aspergillus (10.94%), Cladosporium (10.74%), Rhizopus (6.31%), and Fusarium (5.90%), with an average fungi concentration of 4884.46 ± 724.79 CFU/m3. Eighteen fungal species out of the 64 airborne fungi identified were well-known serious pathogenic agents, contributing not only to structural deterioration but also to human health. Significant variations were observed between indoor and outdoor environments and across diverse landscapes, particularly for PM10 (ranging from 43.47 to 121.31 µg/m3) and PM2.5 (ranging from 29.59 to 89.60 µg/m3), with intensive incense burning identified as a prominent source of indoor atmospheric pollution. Historical temples, particularly situated in urban areas, were identified as significant reservoirs of airborne fungi. Correlations between meteorological parameters and pollutants revealed strong associations. Furthermore, principal component analysis (PCA) and cluster analysis elucidated distinct patterns in airborne fungal concentrations and contaminations. This study analyzed environmental factors, pollutants, airborne fungi, and geographical variations from July 2020 to March 2021. Understanding prevalent genera, airborne fungi concentrations, pathogenic species, biodeterioration, and environmental dynamics provided strategies for improving indoor air quality and mitigating airborne fungal contamination in archaeological buildings worldwide.
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Affiliation(s)
- Wattanachai Pathomsiriwong
- Program of Environmental Science, Department of Agriculture and Environment, Faculty of Science and Technology, Surindra Rajabhat University, Surin, 32000, Thailand
| | - Sayam Aroonsrimorakot
- Faculty of Environment and Resource Studies, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Worasitikulya Taratima
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | | | - Pradub Reanprayoon
- Program of Environmental Science, Department of Agriculture and Environment, Faculty of Science and Technology, Surindra Rajabhat University, Surin, 32000, Thailand.
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3
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Qi G, Hao L, Xin T, Gan Y, Lou Q, Xu W, Song J. Analysis of Whole-Genome facilitates rapid and precise identification of fungal species. Front Microbiol 2024; 15:1336143. [PMID: 38500585 PMCID: PMC10946254 DOI: 10.3389/fmicb.2024.1336143] [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: 11/10/2023] [Accepted: 02/13/2024] [Indexed: 03/20/2024] Open
Abstract
Fungal identification is a cornerstone of fungal research, yet traditional molecular methods struggle with rapid and accurate onsite identification, especially for closely related species. To tackle this challenge, we introduce a universal identification method called Analysis of whole GEnome (AGE). AGE includes two key steps: bioinformatics analysis and experimental practice. Bioinformatics analysis screens candidate target sequences named Targets within the genome of the fungal species and determines specific Targets by comparing them with the genomes of other species. Then, experimental practice using sequencing or non-sequencing technologies would confirm the results of bioinformatics analysis. Accordingly, AGE obtained more than 1,000,000 qualified Targets for each of the 13 fungal species within the phyla Ascomycota and Basidiomycota. Next, the sequencing and genome editing system validated the ultra-specific performance of the specific Targets; especially noteworthy is the first-time demonstration of the identification potential of sequences from unannotated genomic regions. Furthermore, by combining rapid isothermal amplification and phosphorothioate-modified primers with the option of an instrument-free visual fluorescence method, AGE can achieve qualitative species identification within 30 min using a single-tube test. More importantly, AGE holds significant potential for identifying closely related species and differentiating traditional Chinese medicines from their adulterants, especially in the precise detection of contaminants. In summary, AGE opens the door for the development of whole-genome-based fungal species identification while also providing guidance for its application in plant and animal kingdoms.
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Affiliation(s)
- Guihong Qi
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lijun Hao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Tianyi Xin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yutong Gan
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qian Lou
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Wenjie Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing, China
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4
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Borman AM, Johnson EM. Changes in fungal taxonomy: mycological rationale and clinical implications. Clin Microbiol Rev 2023; 36:e0009922. [PMID: 37930182 PMCID: PMC10732072 DOI: 10.1128/cmr.00099-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/13/2023] [Indexed: 11/07/2023] Open
Abstract
Numerous fungal species of medical importance have been recently subjected to and will likely continue to undergo nomenclatural changes as a result of the application of molecular approaches to fungal classification together with abandonment of dual nomenclature. Here, we summarize those changes affecting key groups of fungi of medical importance, explaining the mycological (taxonomic) rationale that underpinned the changes and the clinical relevance/importance (where such exists) of the key nomenclatural revisions. Potential mechanisms to mitigate unnecessary taxonomic instability are suggested, together with approaches to raise awareness of important changes to minimize potential clinical confusion.
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Affiliation(s)
- Andrew M. Borman
- UK HSA National Mycology Reference Laboratory, Science Quarter, Southmead Hospital, Bristol, United Kingdom
- Medical Research Council Centre for Medical Mycology (MRC CMM), University of Exeter, Exeter, United Kingdom
| | - Elizabeth M. Johnson
- UK HSA National Mycology Reference Laboratory, Science Quarter, Southmead Hospital, Bristol, United Kingdom
- Medical Research Council Centre for Medical Mycology (MRC CMM), University of Exeter, Exeter, United Kingdom
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5
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Rodríguez-Cerdeira C, Hernández-Castro R, Arenas R, Sandoval-Tress C, Gutiérrez-Murillo F, Martínez-Chavarría LC, Xicohtencatl-Cortes J, Fida M, Martinez-Herrera E. From Child to Old Man: A Slowly Evolving Case of Chromoblastomycosis Caused by Cladosporium cladosporioides. Antibiotics (Basel) 2023; 12:1713. [PMID: 38136747 PMCID: PMC10741158 DOI: 10.3390/antibiotics12121713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Chromoblastomycosis is a chronic granulomatous mycosis of the skin and subcutaneous tissue caused by traumatic inoculation with dematiaceous fungi. This disease primarily affects agricultural workers, who are mostly men. We present a case of chromoblastomycosis in a 63-year-old male farmer patient with dermatosis over 50 years of evolution, with warty, erythematous, and scaly plaques that predominate on the left hemithorax. Direct examination with potassium hydroxide (KOH) revealed numerous fumagoid cells. Amplification and sequencing of the internal transcribed spacer (ITS) and translation elongation factor 1-alpha (TEF-1a) gene revealed that chromoblastomycosis was caused by Cladosporium cladosporioides. The chromoblastomycosis was treated with itraconazole and fluconazole without any improvement, and amphotericin B was administered with partial improvement.
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Affiliation(s)
- Carmen Rodríguez-Cerdeira
- Fundación Vithas, Grupo Hospitalario Vithas, 28043 Madrid, Spain;
- Dermatology Department, Hospital do Vithas, 36206 Vigo, Spain
- European Women’s Dermatologic and Venereologic Society, 36700 Tui, Spain;
- Psychodermatology Task Force of the Ibero-Latin American College of Dermatology (CILAD), Buenos Aires C1091, Argentina
| | - Rigoberto Hernández-Castro
- Departamento de Ecología y Agentes Patógenos, Hospital General Dr. Manuel Gea González, Tlalpan 14080, Mexico;
| | - Roberto Arenas
- Fundación Vithas, Grupo Hospitalario Vithas, 28043 Madrid, Spain;
- European Women’s Dermatologic and Venereologic Society, 36700 Tui, Spain;
- Psychodermatology Task Force of the Ibero-Latin American College of Dermatology (CILAD), Buenos Aires C1091, Argentina
- Sección de Micología, Hospital General “Dr. Manuel Gea González”, Tlalpan 14080, Mexico
| | - Cecilia Sandoval-Tress
- Departamento de Dermatología, Hospital General de Zona # 42 Instituto Mexicano del Seguro Social, Puerto Vallarta 48310, Mexico;
| | | | - Luary Carolina Martínez-Chavarría
- Departamento de Patología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Coyoacán 04510, Mexico;
| | - Juan Xicohtencatl-Cortes
- Laboratorio de Bacteriología Intestinal, Hospital Infantil de México Dr. Federico Gómez, Cuauhtémoc 06720, Mexico;
| | - Monika Fida
- European Women’s Dermatologic and Venereologic Society, 36700 Tui, Spain;
- Dermatology Department, Medical University of Tirana, U.M.T., 1001 Tirana, Albania
| | - Erick Martinez-Herrera
- Fundación Vithas, Grupo Hospitalario Vithas, 28043 Madrid, Spain;
- European Women’s Dermatologic and Venereologic Society, 36700 Tui, Spain;
- Psychodermatology Task Force of the Ibero-Latin American College of Dermatology (CILAD), Buenos Aires C1091, Argentina
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, Ciudad de México 11340, Mexico
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El-Gendy MMAA, Abdel-Moniem SM, Ammar NS, El-Bondkly AMA. Bioremoval of heavy metals from aqueous solution using dead biomass of indigenous fungi derived from fertilizer industry effluents: isotherm models evaluation and batch optimization. Biometals 2023; 36:1307-1329. [PMID: 37428423 PMCID: PMC10684411 DOI: 10.1007/s10534-023-00520-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 06/19/2023] [Indexed: 07/11/2023]
Abstract
The present work investigated the utilization of dead biomass of the highly multi-heavy metals tolerant indigenous fungal strain NRCA8 isolated from the mycobiome of fertilizer industry effluents that containing multiple heavy metal ions at high levels to remove Pb2+, Ni2+, Zn2+, and Mn2+ as multiple solutes from multi-metals aqueous solutions for the first time. Based on morphotype, lipotype and genotype characteristics, NRCA8 was identified as Cladosporium sp. NRCA8. The optimal conditions for the bioremoval procedure in the batch system were pH 5.5 for maximum removal (91.30%, 43.25%, and 41.50%) of Pb2+, Zn2+ and Mn2+ but pH 6.0 supported the maximum bioremoval and uptake of Ni2+ (51.60% and 2.42 mg/g) by NRCA8 dead biomass from the multi-metals aqueous solution, respectively. The 30 min run time supported the highest removal efficiency and uptake capacity of all heavy metals under study. Moreover, the equilibrium between the sorbent NRCA8 fungal biomass and sorbates Ni2+, Pb2+ and Zn2+ was attained after increasing the dead biomass dose to 5.0 g/L. Dead NRCA8 biomass was described by scanning electron microscopy, energy-dispersive X-ray spectroscopy and Fourier transform infrared spectrometer before and after biosorption of Pb2+, Ni2+, Zn2+ and Mn2+ under multiple metals system. The Langmuir, Freundlich and Dubinin-Kaganer-Radushkevich isotherms were applied to characterize the adsorption equilibrium between Pb2+, Ni2+, Mn2+ and Zn2+ and the adsorbent NRCA8. By comparing the obtained coefficient of regression (R2) by Freundlich (0.997, 0.723, 0.999, and 0.917), Langmiur (0.974, 0.999, 0.974, and 0.911) and Dubinin-Radushkevich (0.9995, 0.756, 0.9996 and 0.900) isotherms values for Pb2+, Zn2+, Ni2+ and Mn2+ adsorption, respectively, it was found that the isotherms are proper in their own merits in characterization the possible of NRCA8 for removal of Pb2+, Zn2+, Ni2+ and Mn2+. DKR isotherm is the best for Pb2+ and Ni2+ (0.9995 and 0.9996) while Langmiur isotherm giving a good fit to the Zn2+ sorption (0.9990) as well as Freundlich isotherm giving a good fit to the Mn2+ sorption (0.9170). The efficiencies of Cladosporium sp. NRCA8 dead biomass for bioremoval of heavy metals from real wastewater under the optimized conditions were Pb2+, Ag+, Mn2+, Zn2+ and Al3+ ˃ Ni2+ ˃ Cr6+ ˃ Co2+ ˃ Fe3+ ˃ Cu2+ ˃ Cd2+. Dead NRCA8 biomass showed efficient ability to adsorb and reduce harmful components in the industrial effluents to a level acceptable for discharge into the environment.
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Affiliation(s)
| | - Shimaa M Abdel-Moniem
- Water Pollution Research Department, National Research Centre, El-Buhouth St., Dokki, 12622, Giza, Egypt
| | - Nabila S Ammar
- Water Pollution Research Department, National Research Centre, El-Buhouth St., Dokki, 12622, Giza, Egypt
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Dutra YLG, Rosado AWC, Condé TO, Leão AF, Neves SDC, Fraga LMS, Kasuya MCM, Pereira OL. Two new Cladosporium species from a quartzite cave in Brazil. Braz J Microbiol 2023; 54:3021-3031. [PMID: 37880564 PMCID: PMC10689331 DOI: 10.1007/s42770-023-01156-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 10/13/2023] [Indexed: 10/27/2023] Open
Abstract
Caves are underground and natural environments mainly found in rocky terrain. Caves have a very specific microclimate, which benefits the occurrence of specific fungi. In recent studies, researchers have observed that caves harbour a great diversity of fungi. However, studies on fungal diversity in Brazilian caves are still incipient. In September 2019, airborne spore and soil samples were collected from the Monte Cristo cave, in the Southern Espinhaço Range, Diamantina, Minas Gerais state, Brazil. Two Cladosporium single-spore isolates, among other genera, were obtained from these samples. This study aimed to characterise these two fungal isolates based on their DNA sequence data and morphology. Phylogenetic analyses of the rDNA-ITS, ACT and TEF1-α loci revealed that the isolates belonged to the Cladosporium cladosporioides species complex. Both isolates did not cluster with any known species and were formally described and named herein as C. diamantinense and C. speluncae. This study presents taxonomic novelties and contributes to the knowledge about the fungal diversity in Brazilian caves.
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Affiliation(s)
- Yan Lucas Gomes Dutra
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - André Wilson Campos Rosado
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Thiago Oliveira Condé
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Ana Flávia Leão
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Soraya de Carvalho Neves
- Instituto de Ciência e Tecnologia, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Minas Gerais, 39100-000, Brazil
| | - Lucio Mauro Soares Fraga
- Instituto de Ciência e Tecnologia, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Minas Gerais, 39100-000, Brazil
| | | | - Olinto Liparini Pereira
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil.
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil.
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da Silva NMP, Guterres DC, Borges LS, Barreto RW, Furtado GQ. Surveying potentially antagonistic fungi to myrtle rust (Austropuccinia psidii) in Brazil: fungicolous Cladosporium spp. Braz J Microbiol 2023; 54:1899-1914. [PMID: 37389796 PMCID: PMC10484887 DOI: 10.1007/s42770-023-01047-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/19/2023] [Indexed: 07/01/2023] Open
Abstract
The myrtle rust (MR), caused by Austropuccinia psidii, is a worldwide threat to the cultivated and wild Myrtaceae. Originally from the neotropics, it has spread to North America, Africa, and Asia and has reached geographically isolated areas in the Pacific and Australasia. It is attacking native species in those new ranges and is still spreading and causing great concern for the damage caused to endemic Myrtaceae, and to the environment. Classical biological control is regarded as the most sustainable management option for mitigating such biological invasions. However, there are no examples of introductions of host-specific co-evolved natural enemies of plant pathogens, from their native range, as a management strategy for plant pathogens. In order to explore this neglected approach, a survey of potential fungal natural enemies of A. psidii was initiated recently in the state of Minas Gerais (Brazil). Several purported mycoparasites have been collected from A. Psidii pustules formed on myrtaceous hosts. This included some isolates of dematiaceous fungi recognized as having a Cladosporium-like morphology. Here we present the results of the investigation aimed at elucidating their identity through a polyphasic taxonomic approach. Besides morphological and cultural features, molecular analyses using sequences of translation elongation factor 1-α (EF1) and actin (ACT) were performed. The combination of data generated is presented herein and placed all Cladosporium-like isolates in six species of Cladosporium, namely, Cladosporium angulosum, C. anthropophilum, C. bambusicola, C. benschii, C. guizhouense, and C. macadamiae. None of these have ever been recorded in association with A. psidii. Now, with the identification of these isolates at hand, an evaluation of biocontrol potential of these fungi will be initiated. In contrast with the ready finding of fungicolous (possibly mycoparasitic) fungi on MR in this study, no evidence of those was recorded from Australasia until now.
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Affiliation(s)
| | | | - Luísa Salvador Borges
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Robert Weingart Barreto
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Gleiber Quintão Furtado
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
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Liao YCZ, Cao YJ, Wan Y, Li H, Li DW, Zhu LH. Alternaria arborescens and A. italica Causing Leaf Blotch on Celtis julianae in China. PLANTS (BASEL, SWITZERLAND) 2023; 12:3113. [PMID: 37687359 PMCID: PMC10489861 DOI: 10.3390/plants12173113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023]
Abstract
Celtis julianae Schneid. is widely planted as a versatile tree species with ecological and economic significance. In September 2022, a leaf blotch disease of C. julianae was observed in Nanjing, Jiangsu, China, with an infection incidence of 63%. The disease led to severe early defoliation, significantly affecting the ornamental and ecological value of the host tree. The accurate identification of pathogens is imperative to conducting further research and advancing disease control. Koch's postulates confirmed that the fungal isolates (B1-B9) were pathogenic to C. julianae. The morphology of the characteristics of the pathogen matched those of Alternaria spp. The internal transcribed spacer region (ITS), large subunit (LSU) and small subunit (SSU) regions of rRNA, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Alternaria major allergen gene (Alt a 1), RNA polymerase second largest subunit (RPB2), and portions of translation elongation factor 1-alpha (TEF1-α) genes were sequenced. Based on multi-locus phylogenetic analyses and morphology, the pathogenic fungi were identified as Alternaria arborescens and A. italica. The findings provided useful information for disease management and enhanced the understanding of Alternaria species diversity in China. This is the first report of A. arborescens and A. italica causing leaf blotch of C. julianae in China and worldwide.
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Affiliation(s)
- Yang-Chun-Zi Liao
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China (Y.-J.C.); (Y.W.); (H.L.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yi-Jia Cao
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China (Y.-J.C.); (Y.W.); (H.L.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yu Wan
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China (Y.-J.C.); (Y.W.); (H.L.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Hui Li
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China (Y.-J.C.); (Y.W.); (H.L.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - De-Wei Li
- The Connecticut Agricultural Experiment Station Valley Laboratory, Windsor, CT 06095, USA
| | - Li-Hua Zhu
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China (Y.-J.C.); (Y.W.); (H.L.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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10
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Jaccard A, Dubuis N, Kellenberger I, Brodard J, Schnee S, Gindro K, Schumpp O. New viruses of Cladosporium sp. expand considerably the taxonomic structure of Gammapartitivirus genus. J Gen Virol 2023; 104:001879. [PMID: 37549001 PMCID: PMC10539651 DOI: 10.1099/jgv.0.001879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/25/2023] [Indexed: 08/08/2023] Open
Abstract
Despite the fact that Cladosporium sp. are ubiquitous fungi, their viromes have been little studied. By analysing a collection of Cladosporium fungi, two new partitiviruses named Cladosporium cladosporioides partitivirus 1 (CcPV1) and Cladosporium cladosporioides partitivirus 2 (CcPV2) co-infecting a strain of Cladosporium cladosporioides were identified. Their complete genome consists of two monocistronic dsRNA segments (RNA1 and RNA2) with a high percentage of pairwise identity on 5' and 3' end. The RNA directed RNA polymerase (RdRp) of both viruses and the capsid protein (CP) of CcPV1 display the classic characteristics required for their assignment to the Gammapartitivirus genus. In contrast, CcPV2 RNA2 encodes for a 41 KDa CP that is unusually smaller when aligned to CPs of other viruses classified in this genus. The structural role of this protein is confirmed by electrophoresis on acrylamide gel of purified viral particles. Despite the low percentage of identity between the capsid proteins of CcPV1 and CcPV2, their three-dimensional structures predicted by AlphaFold2 show strong similarities and confirm functional proximity. Fifteen similar viral sequences of unknown function were annotated using the CcPV2 CP sequence. The phylogeny of the CP was highly consistent with the phylogeny of their corresponding RdRp, supporting the organization of Gammapartitiviruses into three distinct clades despite stretching the current demarcation criteria. It is proposed that a new subgenus be created within the genus Gammapartitivirus for this new group.
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Affiliation(s)
| | - Nathalie Dubuis
- Department of Plant Protection, Agroscope, Nyon, Switzerland
| | | | - Justine Brodard
- Department of Plant Protection, Agroscope, Nyon, Switzerland
| | - Sylvain Schnee
- Department of Plant Protection, Agroscope, Nyon, Switzerland
| | - Katia Gindro
- Department of Plant Protection, Agroscope, Nyon, Switzerland
| | - Olivier Schumpp
- Department of Plant Protection, Agroscope, Nyon, Switzerland
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Lee W, Kim JS, Seo CW, Lee JW, Kim SH, Cho Y, Lim YW. Diversity of Cladosporium (Cladosporiales, Cladosporiaceae) species in marine environments and report on five new species. MycoKeys 2023; 98:87-111. [PMID: 37305062 PMCID: PMC10257140 DOI: 10.3897/mycokeys.98.101918] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/16/2023] [Indexed: 06/13/2023] Open
Abstract
Cladosporium species are cosmopolitan fungi, characterized by olivaceous or dark colonies with coronate conidiogenous loci and conidial hila with a central convex dome surrounded by a raised periclinal rim. Cladosporium species have also been discovered in marine environments. Although many studies have been performed on the application of marine originated Cladosporium species, taxonomic studies on these species are scarce. We isolated Cladosporium species from three under-studied habitats (sediment, seawater, and seaweed) in two districts including an intertidal zone in the Republic of Korea and the open sea in the Western Pacific Ocean. Based on multigenetic marker analyses (for the internal transcribed spacer, actin, and translation elongation factor 1), we identified fourteen species, of which five were found to represent new species. These five species were C.lagenariiformesp. nov., C.maltirimosumsp. nov., C.marinumsp. nov. in the C.cladosporioides species complex, C.snafimbriatumsp. nov. in the C.herbarum species complex, and C.marinisedimentumsp. nov. in the C.sphaerospermum species complex. Morphological characteristics of the new species and aspects of differences with the already known species are described herein together with molecular data.
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Affiliation(s)
- Wonjun Lee
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, Republic of KoreaSeoul National UniversitySeoulRepublic of Korea
| | - Ji Seon Kim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, Republic of KoreaSeoul National UniversitySeoulRepublic of Korea
| | - Chang Wan Seo
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, Republic of KoreaSeoul National UniversitySeoulRepublic of Korea
| | - Jun Won Lee
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, Republic of KoreaSeoul National UniversitySeoulRepublic of Korea
| | - Sung Hyun Kim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, Republic of KoreaSeoul National UniversitySeoulRepublic of Korea
| | - Yoonhee Cho
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, Republic of KoreaSeoul National UniversitySeoulRepublic of Korea
| | - Young Woon Lim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, Republic of KoreaSeoul National UniversitySeoulRepublic of Korea
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12
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Verhasselt HL, Ramakrishnan E, Schlag M, Marchesi JR, Buer J, Kleinschnitz C, Hagenacker T, Totzeck A. Fungal Gut Microbiome in Myasthenia Gravis: A Sub-Analysis of the MYBIOM Study. J Fungi (Basel) 2023; 9:jof9050569. [PMID: 37233280 DOI: 10.3390/jof9050569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 05/27/2023] Open
Abstract
An altered gut microbiota is a possible contributing pathogenic factor in myasthenia gravis (MG), an autoimmune neuromuscular disease. However, the significance of the fungal microbiome is an understudied and neglected part of the intestinal microbiome in MG. We performed a sub-analysis of the MYBIOM study including faecal samples from patients with MG (n = 41), non-inflammatory neurological disorder (NIND, n = 18), chronic inflammatory demyelinating polyradiculoneuropathy (CIDP, n = 6) and healthy volunteers (n = 12) by sequencing the internal transcribed spacer 2 (ITS2). Fungal reads were obtained in 51 out of 77 samples. No differences were found in alpha-diversity indices computed between the MG, NIND, CIDP and HV groups, indicating an unaltered fungal diversity and structure. Overall, four mould species (Penicillium aurantiogriseum, Mycosphaerella tassiana, Cladosporium ramonetellum and Alternaria betae-kenyensis) and five yeast species (Candida. albicans, Candida. sake, Candida. dubliniensis, Pichia deserticola and Kregervanrija delftensis) were identified. Besides one MG patient with abundant Ca. albicans, no prominent dysbiosis in the MG group of the mycobiome was found. Not all fungal sequences within all groups were successfully assigned, so further sub-analysis was withdrawn, limiting robust conclusions.
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Affiliation(s)
- Hedda Luise Verhasselt
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, D-45122 Essen, Germany
| | - Elakiya Ramakrishnan
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, University of Duisburg-Essen, D-45122 Essen, Germany
| | - Melina Schlag
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, University of Duisburg-Essen, D-45122 Essen, Germany
| | - Julian R Marchesi
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2BX, UK
| | - Jan Buer
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, D-45122 Essen, Germany
| | - Christoph Kleinschnitz
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, University of Duisburg-Essen, D-45122 Essen, Germany
| | - Tim Hagenacker
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, University of Duisburg-Essen, D-45122 Essen, Germany
| | - Andreas Totzeck
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, University of Duisburg-Essen, D-45122 Essen, Germany
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McDonagh F, Cormican M, Morris D, Burke L, Singh NK, Venkateswaran K, Miliotis G. Medical Astro-Microbiology: Current Role and Future Challenges. J Indian Inst Sci 2023; 103:1-26. [PMID: 37362850 PMCID: PMC10082442 DOI: 10.1007/s41745-023-00360-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/03/2023] [Indexed: 06/28/2023]
Abstract
The second and third decades of the twenty-first century are marked by a flourishing of space technology which may soon realise human aspirations of a permanent multiplanetary presence. The prevention, control and management of infection with microbial pathogens is likely to play a key role in how successful human space aspirations will become. This review considers the emerging field of medical astro-microbiology. It examines the current evidence regarding the risk of infection during spaceflight via host susceptibility, alterations to the host's microbiome as well as exposure to other crew members and spacecraft's microbiomes. It also considers the relevance of the hygiene hypothesis in this regard. It then reviews the current evidence related to infection risk associated with microbial adaptability in spaceflight conditions. There is a particular focus on the International Space Station (ISS), as one of the only two crewed objects in low Earth orbit. It discusses the effects of spaceflight related stressors on viruses and the infection risks associated with latent viral reactivation and increased viral shedding during spaceflight. It then examines the effects of the same stressors on bacteria, particularly in relation to changes in virulence and drug resistance. It also considers our current understanding of fungal adaptability in spaceflight. The global public health and environmental risks associated with a possible re-introduction to Earth of invasive species are also briefly discussed. Finally, this review examines the largely unknown microbiology and infection implications of celestial body habitation with an emphasis placed on Mars. Overall, this review summarises much of our current understanding of medical astro-microbiology and identifies significant knowledge gaps. Graphical Abstract
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Affiliation(s)
- Francesca McDonagh
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Martin Cormican
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
- Department of Medical Microbiology, Galway University Hospitals, Galway, Ireland
| | - Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Liam Burke
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Nitin Kumar Singh
- Biotechnology and Planetary Protection Group, NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA USA
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA USA
| | - Georgios Miliotis
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
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Su P, Lu Z, Tian W, Chen Y, Maharachchikumbura SSN. Six Additions to the Genus Periconia (Dothideomycetes: Periconiaceae) from Graminaceous Plants in China. J Fungi (Basel) 2023; 9:jof9030300. [PMID: 36983468 PMCID: PMC10054280 DOI: 10.3390/jof9030300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 02/20/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
Periconia is a polyphyletic and asexual morphic genus within the family Periconiaceae (Pleosporales). The genus is characterized by a pale to dark brown stipe with an apical conidial head and ellipsoidal to oblong conidia. Species of Periconia are widely distributed throughout the world in various hosts, while most species are isolated from graminaceous plants. During our investigations of microfungal in Sichuan Province, China, 26 Periconia isolates were collected from a wide variety of graminaceous plants. These isolates corresponded to 11 species based on the examination of morphology and multi-locus phylogenetic analysis (SSU, ITS, LSU, TEF1, RPB2). This includes six new species (P. chengduensis, P. cynodontis, P. festucae, P. imperatae, P. penniseti, and P. spodiopogonis) and five new records (P. byssoides, P. chimonanthi, P. cookie, P. pseudobyssoides, and P. verrucosa). A comprehensive description and illustrations of the new species are provided and discussed with comparable taxa. These discoveries expand our knowledge of the species diversity of Periconia taxa in graminaceous plants in China.
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Yang Y, Luo W, Zhang W, Mridha MAU, Wijesinghe SN, McKenzie EHC, Wang Y. Cladosporium Species Associated with Fruit Trees in Guizhou Province, China. J Fungi (Basel) 2023; 9:jof9020250. [PMID: 36836364 PMCID: PMC9962058 DOI: 10.3390/jof9020250] [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: 01/11/2023] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/16/2023] Open
Abstract
During an investigation of fungal diversity on fruit trees in Guizhou Province, 23 Cladosporium strains were isolated from various locations in Guizhou Province. Culture characteristics, morphology and molecular phylogenetic analysis of three genetic markers, namely, the internal transcribed spacer regions (ITS) of the rDNA, partial fragments of actin (act), and the translation elongation factor 1-α (tef1-ɑ) loci were used to characterize these isolates. Seven new Cladosporium species and new host records for five other species were introduced, with detailed descriptions and illustrations. This study showed that there is a rich diversity of Cladosporium spp. in fruit trees in Guizhou Province.
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Affiliation(s)
- Yuanqiao Yang
- Department of Plant Pathology, Agriculture College, Guizhou University, Guiyang 550025, China
| | - Wenmei Luo
- Department of Plant Pathology, Agriculture College, Guizhou University, Guiyang 550025, China
| | - Wensong Zhang
- Department of Plant Pathology, Agriculture College, Guizhou University, Guiyang 550025, China
| | | | | | | | - Yong Wang
- Department of Plant Pathology, Agriculture College, Guizhou University, Guiyang 550025, China
- Correspondence: or
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16
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Wingfield LK, Jitprasitporn N, Che-alee N. Isolation and characterization of halophilic and halotolerant fungi from man-made solar salterns in Pattani Province, Thailand. PLoS One 2023; 18:e0281623. [PMID: 36780513 PMCID: PMC9925087 DOI: 10.1371/journal.pone.0281623] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 01/27/2023] [Indexed: 02/15/2023] Open
Abstract
The present study explored culturable halophilic and halotolerant fungi from man-made solar salterns in Pattani Province, Thailand. A total of 24 fungal isolates were discovered and characterized using morphological and molecular identification. Production of extracellular enzymes, secondary metabolites and mycoviruses was examined. Growth was observed in salinity and temperature ranges between 0%-20% and 28-40°C, respectively. Growth in different environmental conditions confirmed the halophilic or halotolerant nature of some strains. Fungal isolates were phylogenetically classified into seven different genera belonging to Aspergillus, Cladosporium, Curvularia, Diaporthe, Ectophoma, Fusarium and Penicillium. An enzymatic production test revealed that thirteen isolates could produce proteases and amylases at different levels. The presence of mycoviruses was detected in three isolates. Seventeen of the 24 isolates produced antimicrobial metabolites. The majority of these active isolates were identified as Aspergillus and Penicillium species. Crude extracts of the fungal mycelia and culture broths from these isolates had an inhibitory effect on both Gram-positive and Gram-negative bacteria and human pathogenic fungi. Research into fungi from saline environments could reveal fungal strains of biotechnological and industrial interest.
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Affiliation(s)
- Lakkhana Kanhayuwa Wingfield
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- * E-mail:
| | - Ninadia Jitprasitporn
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Nureeda Che-alee
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
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17
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Arfken AM, Frey JF, Carrillo NI, Dike NI, Onyeachonamm O, Rivera DN, Davies CP, Summers KL. Porcine fungal mock community analyses: Implications for mycobiome investigations. Front Cell Infect Microbiol 2023; 13:928353. [PMID: 36844394 PMCID: PMC9945231 DOI: 10.3389/fcimb.2023.928353] [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: 04/25/2022] [Accepted: 01/16/2023] [Indexed: 02/11/2023] Open
Abstract
Introduction The gut microbiome is an integral partner in host health and plays a role in immune development, altered nutrition, and pathogen prevention. The mycobiome (fungal microbiome) is considered part of the rare biosphere but is still a critical component in health. Next generation sequencing has improved our understanding of fungi in the gut, but methodological challenges remain. Biases are introduced during DNA isolation, primer design and choice, polymerase selection, sequencing platform selection, and data analyses, as fungal reference databases are often incomplete or contain erroneous sequences. Methods Here, we compared the accuracy of taxonomic identifications and abundances from mycobiome analyses which vary among three commonly selected target gene regions (18S, ITS1, or ITS2) and the reference database (UNITE - ITS1, ITS2 and SILVA - 18S). We analyze multiple communities including individual fungal isolates, a mixed mock community created from five common fungal isolates found in weanling piglet feces, a purchased commercial fungal mock community, and piglet fecal samples. In addition, we calculated gene copy numbers for the 18S, ITS1, and ITS2 regions of each of the five isolates from the piglet fecal mock community to determine whether copy number affects abundance estimates. Finally, we determined the abundance of taxa from several iterations of our in-house fecal community to assess the effects of community composition on taxon abundance. Results Overall, no marker-database combination consistently outperformed the others. Internal transcribed space markers were slightly superior to 18S in the identification of species in tested communities, but Lichtheimia corymbifera, a common member of piglet gut communities, was not amplified by ITS1 and ITS2 primers. Thus, ITS based abundance estimates of taxa in piglet mock communities were skewed while 18S marker profiles were more accurate. Kazachstania slooffiae displayed the most stable copy numbers (83-85) while L. corymbifera displayed significant variability (90-144) across gene regions. Discussion This study underscores the importance of preliminary studies to assess primer combinations and database choice for the mycobiome sample of interest and raises questions regarding the validity of fungal abundance estimates.
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Affiliation(s)
- Ann M. Arfken
- Oak Ridge Institute for Science and Education, Center for Disease Control, Atlanta, GA, United States
| | - Juli Foster Frey
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Nora Isabel Carrillo
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Nneka Ijeoma Dike
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Ogechukwu Onyeachonamm
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Daniela Nieves Rivera
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Cary Pirone Davies
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Katie Lynn Summers
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States,*Correspondence: Katie Lynn Summers,
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Grassi A, Gambini M, Pantoli M, Toscano S, Albertetti A, Del Frassino DM, Ugochukwu ICI, Romeo O, Otranto D, Cafarchia C. A Lethal Case of Disseminated Cladosporium allicinum Infection in a Captive African Bullfrog. J Fungi (Basel) 2023; 9:jof9020191. [PMID: 36836306 PMCID: PMC9967566 DOI: 10.3390/jof9020191] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 01/26/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Cladosporium infections have a poor prognosis in animals, most likely due to a lack of knowledge about diagnosis and treatment. In this study, we described a case of a lethal Cladosporium allicinum infection in a captive bullfrog (Pyxicephalus adspersus) in Europe. One adult male bullfrog was referred with clinical signs of lethargy and a cutaneous nodule. Fungal infection was suspected on cytology and confirmed by histology and cultural isolation. The mold was identified by molecular methods using partial sequencing of the TEF1α gene and the ITS region of rDNA. Climbazole antifungal treatment was started but the frog died after 30 days, and necropsy was done. Pigmented hyphae and structures consistent with muriform bodies were found on a background of diffuse granulomatous inflammation at cytological and histopathological examinations. Fungal culture revealed the presence of pigmented fungi identified as Cladosporium allicinum only by partial sequencing of the TEF1α gene. A focally extensive granuloma with intralesional hyphae and muriform bodies effacing the architecture of head, liver, kidneys, lungs, and large intestine were retrieved after necropsy. This study is the first Italian report of the occurrence of lethal C. allicinum infection in a frog and highlights the role of this Cladosporium sp. in chromoblastomycosis.
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Affiliation(s)
- Andrea Grassi
- I-Vet Diagnostica Veterinaria, 25020 Brescia, Italy
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, 27100 Pavia, Italy
| | | | | | | | | | | | - Iniobong Chukwuebuka Ikenna Ugochukwu
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari Aldo Moro, 70124 Bari, Italy
- Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka 400001, Nigeria
| | - Orazio Romeo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy
| | - Domenico Otranto
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari Aldo Moro, 70124 Bari, Italy
- Faculty of Veterinary Sciences, Bu-Ali Sina University, Hamedan 6517833131, Iran
| | - Claudia Cafarchia
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari Aldo Moro, 70124 Bari, Italy
- Correspondence:
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Cladosporium protease/doxorubicin decorated Fe3O4@SiO2 nanocomposite: An efficient nanoparticle for drug delivery and combating breast cancer. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.104144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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20
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Dusengemungu L, Gwanama C, Simuchimba G, Mubemba B. Potential of bioaugmentation of heavy metal contaminated soils in the Zambian Copperbelt using autochthonous filamentous fungi. Front Microbiol 2022; 13:1045671. [PMID: 36532421 PMCID: PMC9752026 DOI: 10.3389/fmicb.2022.1045671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/21/2022] [Indexed: 11/07/2023] Open
Abstract
There is great potential to remediate heavy metal contaminated environments through bioaugmentation with filamentous fungi. However, these fungi have been poorly investigated in most developing countries, such as Zambia. Therefore, the present study aimed at isolating indigenous filamentous fungi from heavy metal contaminated soil and to explore their potential for use in bioaugmentation. The conventional streak plate method was used to isolate fungi from heavy metal-contaminated soil. Filamentous fungal isolates were identified using morphological and molecular techniques. The radial growth diameter technique was used to evaluate heavy metal tolerance of the fungi. The most abundant and highly tolerant fungi, identified as Aspergillus transmontanensis, Cladosporium cladosporioides, and Geotrichum candidum species, were used to bioremediate heavy metal contaminated soil samples with uncontaminated soil sample being employed as a control. A maximum tolerance index (TI) between 0.7 and 11.0 was observed for A. transmontanensis, and G. candidum while C. cladosporioides displayed the TI between 0.2 and 1.2 in the presence of 1,000 ppm of Cu, Co, Fe, Mn, and Zn. The interspecific interaction was analyzed to determine the compatibility among isolates. Our results showed mutual intermingling between the three evaluated fungal species, which confirms their common influence in biomineralization of heavy metals in contaminated soils. Maximum bio-removal capacities after 90 days were 72% for Cu, 99.8% for Co, 60.6% for Fe, 82.2% for Mn, and 100% for both Pb and Zn. This study has demonstrated the potential of highly resistant autochthonous fungal isolates to remediate the heavy metal contamination problem.
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Affiliation(s)
- Leonce Dusengemungu
- School of Mathematics and Natural Sciences, The Copperbelt University, Kitwe, Zambia
- Africa Centre of Excellence for Sustainable Mining, The Copperbelt University, Kitwe, Zambia
| | - Cousins Gwanama
- School of Natural Resources, The Copperbelt University, Kitwe, Zambia
| | - Grant Simuchimba
- School of Natural Resources, The Copperbelt University, Kitwe, Zambia
| | - Benjamin Mubemba
- School of Natural Resources, The Copperbelt University, Kitwe, Zambia
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Floc'h JB, Hamel C, Laterrière M, Tidemann B, St-Arnaud M, Hijri M. Inter-Kingdom Networks of Canola Microbiome Reveal Bradyrhizobium as Keystone Species and Underline the Importance of Bulk Soil in Microbial Studies to Enhance Canola Production. MICROBIAL ECOLOGY 2022; 84:1166-1181. [PMID: 34727198 DOI: 10.1007/s00248-021-01905-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
The subterranean microbiota of plants is of great importance for plant growth and health, as root-associated microbes can perform crucial ecological functions. As the microbial environment of roots is extremely diverse, identifying keystone microorganisms in plant roots, rhizosphere, and bulk soil is a necessary step towards understanding the network of influence within the microbial community associated with roots and enhancing its beneficial elements. To target these hot spots of microbial interaction, we used inter-kingdom network analysis on the canola growth phase of a long-term cropping system diversification experiment conducted at four locations in the Canadian Prairies. Our aims were to verify whether bacterial and fungal communities of canola roots, rhizosphere, and bulk soil are related and influenced by diversification of the crop rotation system; to determine whether there are common or specific core fungi and bacteria in the roots, rhizosphere, and bulk soil under canola grown in different environments and with different levels of cropping system diversification; and to identify hub taxa at the inter-kingdom level that could play an important ecological role in the microbiota of canola. Our results showed that fungi were influenced by crop diversification, which was not the case on bacteria. We found no core microbiota in canola roots but identified three core fungi in the rhizosphere, one core mycobiota in the bulk soil, and one core bacterium shared by the rhizosphere and bulk soil. We identified two bacterial and one fungal hub taxa in the inter-kingdom networks of the canola rhizosphere, and one bacterial and two fungal hub taxa in the bulk soil. Among these inter-kingdom hub taxa, Bradyrhizobium sp. and Mortierella sp. are particularly influential on the microbial community and the plant. To our knowledge, this is the first inter-kingdom network analysis utilized to identify hot spots of interaction in canola microbial communities.
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Affiliation(s)
- Jean-Baptiste Floc'h
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, 4101 East, Sherbrooke Street, Montréal, QC, H1X 2B2, Canada
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec City, QC, Canada
| | - Chantal Hamel
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, 4101 East, Sherbrooke Street, Montréal, QC, H1X 2B2, Canada
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec City, QC, Canada
| | - Mario Laterrière
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec City, QC, Canada
| | - Breanne Tidemann
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Marc St-Arnaud
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, 4101 East, Sherbrooke Street, Montréal, QC, H1X 2B2, Canada
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, 4101 East, Sherbrooke Street, Montréal, QC, H1X 2B2, Canada.
- African Genome Center, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, 43150, Ben Guerir, Morocco.
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22
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Effects of timothy Cladosporium eyespot on photosynthesis and biomass. Arch Microbiol 2022; 204:568. [DOI: 10.1007/s00203-022-03151-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 07/24/2022] [Accepted: 07/27/2022] [Indexed: 11/02/2022]
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Wang SY, Wang Y, Li Y. Cladosporium spp. (Cladosporiaceae) isolated from Eucommiaulmoides in China. MycoKeys 2022; 91:151-168. [PMID: 36760889 PMCID: PMC9849062 DOI: 10.3897/mycokeys.91.87841] [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: 06/15/2022] [Accepted: 07/04/2022] [Indexed: 11/12/2022] Open
Abstract
Eucommiaulmoides is a rare tree species in China with high medicinal and gum value. Nine strains of hyphomycetous fungi were isolated from the leaf litter of E.ulmoides in Guizhou Province. Preliminary identifications based on ITS indicated that they belong to the genus Cladosporium. Morphology and phylogenetic analyses based on the internal transcribed spacer regions (ITS) of the nrDNA, the partial translation elongation factor 1-α (tef1) gene and partial of actin (act) gene confirmed that the strains represent four species, including two novel taxa, viz., Cladosporiumeucommiae and C.guizhouense and two new substrate records for known species.
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Affiliation(s)
- Si-Yao Wang
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guiyang 550025, Guizhou Province, China,College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China
| | - Yong Wang
- College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China
| | - Yan Li
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guiyang 550025, Guizhou Province, China,College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China
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24
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Ibrahim ABM, Mahmoud GA, Cordes DB, Slawin AMZ. Pb (II) and Hg (II) Thiosemicarbazones for Inhibiting the Broad‐Spectrum Pathogen
Cladosporium sphaerospermum
ASU18 (MK387875) and Altering Its Antioxidant System. Appl Organomet Chem 2022. [DOI: 10.1002/aoc.6798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - David B. Cordes
- EaStCHEM School of Chemistry University of St Andrews Fife U.K
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25
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Isolation, Identification and Hyperparasitism of a Novel Cladosporium cladosporioides Isolate Hyperparasitic to Puccinia striiformis f. sp. tritici, the Wheat Stripe Rust Pathogen. BIOLOGY 2022; 11:biology11060892. [PMID: 35741414 PMCID: PMC9219750 DOI: 10.3390/biology11060892] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 05/20/2022] [Accepted: 06/07/2022] [Indexed: 11/24/2022]
Abstract
Simple Summary Obligate biotrophic pathogen Puccinia striiformis f. sp. tritici (Pst) is a major threat to wheat production. Parasites of Pst can be used to develop biological agents for environmentally friendly control of this fungal disease. Here, we report a hyperparasitic fungus isolated from taupe-colored uredinia of Pst and identified as Cladosporium cladosporioides through molecular and morphological characterizations. The hyperparasitic isolate was able to reduce the production and viability of Pst. Therefore, Cladosporium cladosporioides may have potential in biological control of stripe rust on wheat. Abstract Wheat rust outbreaks have caused significantly economic losses all over the world. Puccinia striiformis f. sp. tritici (Pst) is an obligate biotrophic fungus causing stripe rust on wheat. Application of fungicides may cause environmental problems. The effects of hyperparasites on plant pathogens are the basis for biological control of plant pathogenic fungi and parasites of Pst have great value in biological agents development. Here, we report the isolation and characterization of isolate of Cladosporium cladosporioides from Pst based on morphological characterization and analysis of molecular markers. The hyperparasitic isolate was isolated from taupe-colored uredinia of Pst. Upon artificial inoculation, the hyperparasitic isolate was able to reduce the production and germination rate of Pst urediospores, and Pst uredinia changed color from yellow to taupe. Scanning electron microscopy demonstrated that the strain could efficiently colonize Pst urediospores. Therefore, the isolate has the potential to be developed into a biological control agent for managing wheat stripe rust.
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26
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Sudermann MA, McGilp L, Vogel G, Regnier M, Jaramillo AR, Smart CD. The Diversity of Passalora fulva Isolates Collected from Tomato Plants in U.S. High Tunnels. PHYTOPATHOLOGY 2022; 112:1350-1360. [PMID: 35021861 DOI: 10.1094/phyto-06-21-0244-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
High tunnels extend the growing season of high value crops, including tomatoes, but the environmental conditions within high tunnels favor the spread of the tomato leaf mold pathogen, Passalora fulva (syn. Cladosporium fulvum). Tomato leaf mold results in defoliation, and if severe, losses in yield. Despite substantial research, little is known regarding the genetic structure and diversity of populations of P. fulva associated with high tunnel tomato production in the United States. From 2016 to 2019, a total of 50 P. fulva isolates were collected from tomato leaf samples in high tunnels in the Northeast and Minnesota. Other Cladosporium species were also isolated from the leaf surfaces. Koch's postulates were conducted to confirm that P. fulva was the cause of the disease symptoms observed. Race determination experiments revealed that the isolates belonged to either race 0 (six isolates) or race 2 (44 isolates). Polymorphisms were identified within four previously characterized effector genes: Avr2, Avr4, Avr4e, and Avr9. The largest number of polymorphisms were observed for Avr2. Both mating type genes, MAT1-1-1 and MAT1-2-1, were present in the isolate collection. For further insights into the pathogen diversity, the 50 isolates were genotyped at 7,514 single-nucleotide polymorphism loci using genotyping-by-sequencing. Differentiation by region but not by year was observed. Within the collection of 50 isolates, there were 18 distinct genotypes. Information regarding P. fulva population diversity will enable better management recommendations for growers, as high tunnel production of tomatoes expands.
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Affiliation(s)
- Martha A Sudermann
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
| | - Lillian McGilp
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Gregory Vogel
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
| | - Melissa Regnier
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
- Laboratory of Mycology and Phytopathology, Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia
| | - Alejandra Rodríguez Jaramillo
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
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27
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Khojasteh M, Chen L, Shen L, Chen F, Shah SMA, Luo J, Chen G. Genome Resource of Cladosporium cucumerinum Strain CCNX2 Causing Cucumber Scab in China. PLANT DISEASE 2022; 106:1510-1512. [PMID: 35357217 DOI: 10.1094/pdis-11-21-2584-a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Moein Khojasteh
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Chen
- Department of Plant Quarantine, Shanghai Extension and Service Center of Agriculture Technology, Shanghai 201103, China
| | - Lili Shen
- Planting Center, Shanghai Farm Co., Ltd. of Guangming Bright Food Group, Yancheng 224151, Jiangsu province, China
| | - Fangfang Chen
- Planting Center, Shanghai Farm Co., Ltd. of Guangming Bright Food Group, Yancheng 224151, Jiangsu province, China
| | - Syed Mashab Ali Shah
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinyan Luo
- Department of Plant Quarantine, Shanghai Extension and Service Center of Agriculture Technology, Shanghai 201103, China
| | - Gongyou Chen
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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28
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Barge EG, Leopold DR, Rojas A, Vilgalys R, Busby PE. Phylogenetic conservatism of mycoparasitism and its contribution to pathogen antagonism. Mol Ecol 2022; 31:3018-3030. [DOI: 10.1111/mec.16436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 03/06/2022] [Accepted: 03/16/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Edward G. Barge
- Department of Botany and Plant Pathology Oregon State University Corvallis OR 97331 USA
| | - Devin R. Leopold
- Department of Botany and Plant Pathology Oregon State University Corvallis OR 97331 USA
| | - Alejandro Rojas
- Department of Entomology and Plant Pathology University of Arkansas Fayetteville AR 72701 USA
| | - Rytas Vilgalys
- Department of Biology Duke University Durham NC 27708 USA
| | - Posy E. Busby
- Department of Botany and Plant Pathology Oregon State University Corvallis OR 97331 USA
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29
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Richness of Cladosporium in a tropical bat cave with the description of two new species. Mycol Prog 2022. [DOI: 10.1007/s11557-021-01760-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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30
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Senanayake IC, Pem D, Rathnayaka AR, Wijesinghe SN, Tibpromma S, Wanasinghe DN, Phookamsak R, Kularathnage ND, Gomdola D, Harishchandra D, Dissanayake LS, Xiang MM, Ekanayaka AH, McKenzie EHC, Hyde KD, Zhang HX, Xie N. Predicting global numbers of teleomorphic ascomycetes. FUNGAL DIVERS 2022. [DOI: 10.1007/s13225-022-00498-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
AbstractSexual reproduction is the basic way to form high genetic diversity and it is beneficial in evolution and speciation of fungi. The global diversity of teleomorphic species in Ascomycota has not been estimated. This paper estimates the species number for sexual ascomycetes based on five different estimation approaches, viz. by numbers of described fungi, by fungus:substrate ratio, by ecological distribution, by meta-DNA barcoding or culture-independent studies and by previous estimates of species in Ascomycota. The assumptions were made with the currently most accepted, “2.2–3.8 million” species estimate and results of previous studies concluding that 90% of the described ascomycetes reproduce sexually. The Catalogue of Life, Species Fungorum and published research were used for data procurement. The average value of teleomorphic species in Ascomycota from all methods is 1.86 million, ranging from 1.37 to 2.56 million. However, only around 83,000 teleomorphic species have been described in Ascomycota and deposited in data repositories. The ratio between described teleomorphic ascomycetes to predicted teleomorphic ascomycetes is 1:22. Therefore, where are the undiscovered teleomorphic ascomycetes? The undescribed species are no doubt to be found in biodiversity hot spots, poorly-studied areas and species complexes. Other poorly studied niches include extremophiles, lichenicolous fungi, human pathogens, marine fungi, and fungicolous fungi. Undescribed species are present in unexamined collections in specimen repositories or incompletely described earlier species. Nomenclatural issues, such as the use of separate names for teleomorph and anamorphs, synonyms, conspecific names, illegitimate and invalid names also affect the number of described species. Interspecies introgression results in new species, while species numbers are reduced by extinctions.
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31
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Xu YX, Shen HW, Bao DF, Luo ZL, Su HY, Hao YE. Two new species of Cladosporium from leaf spots of Parispolyphylla in north-western Yunnan Province, China. Biodivers Data J 2022; 9:e77224. [PMID: 34984042 PMCID: PMC8718519 DOI: 10.3897/bdj.9.e77224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Abstract
Background During the survey of pathogenic fungi on medicinal plant leaves in Yunnan Province, China, two Cladosporium-like taxa were isolated from leaf spots of Parispolyphylla. Based on morphological characteristics and phylogenetic analysis of combined ITS, TEF1-α and ACT genes, two new species were discovered. New information Two new species Cladosporiumyunnanensis and C.paris are introduced, the detailed descriptions and illustrations are provided. Morphology of the two new species is compared with other related Cladosporium species. This study widens the host diversity of the genus Cladosporium.
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Affiliation(s)
- Yue-Xin Xu
- College of Public Health, University of South China, Hengyang, China College of Public Health, University of South China Hengyang China.,College of Agriculture and Biological Sciences, Dali University, Dali, China College of Agriculture and Biological Sciences, Dali University Dali China
| | - Hong-Wei Shen
- College of Agriculture and Biological Sciences, Dali University, Dali, China College of Agriculture and Biological Sciences, Dali University Dali China.,Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand Center of Excellence in Fungal Research, Mae Fah Luang University Chiang Rai Thailand.,School of Science, Mae Fah Luang University, Chiang Rai, Thailand School of Science, Mae Fah Luang University Chiang Rai Thailand
| | - Dan-Feng Bao
- College of Agriculture and Biological Sciences, Dali University, Dali, China College of Agriculture and Biological Sciences, Dali University Dali China.,Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand Center of Excellence in Fungal Research, Mae Fah Luang University Chiang Rai Thailand.,Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University Chiang Mai Thailand
| | - Zong-Long Luo
- College of Agriculture and Biological Sciences, Dali University, Dali, China College of Agriculture and Biological Sciences, Dali University Dali China
| | - Hong-Yan Su
- College of Agriculture and Biological Sciences, Dali University, Dali, China College of Agriculture and Biological Sciences, Dali University Dali China
| | - Yu-E Hao
- College of Public Health, University of South China, Hengyang, China College of Public Health, University of South China Hengyang China
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32
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Recommendations To Prevent Taxonomic Misidentification of Genome-Sequenced Fungal Strains. Microbiol Resour Announc 2021; 10:e0107420. [PMID: 34854710 PMCID: PMC8638587 DOI: 10.1128/mra.01074-20] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Ahmadpour A, Ghosta Y, Poursafar A. Novel species of Alternaria section Nimbya from Iran as revealed by morphological and molecular data. Mycologia 2021; 113:1073-1088. [PMID: 34338599 DOI: 10.1080/00275514.2021.1923299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
In this study, the diversity of Alternaria species in section Nimbya associated with symptomatic plants in the Cyperaceae and Juncaceae families was assessed. Multilocus sequence analyses of the rDNA internal transcribed spacer (ITS) region and parts of Alternaria major allergen (Alt a 1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), second largest subunit of RNA polymerase II (RPB2), and translation elongation factor 1-alpha (TEF1) genes revealed the presence of two previously known species, A. scirpivora and A. caricicola, and three new species, which are described here as A. cypericola, sp. nov., A. heyranica, sp. nov., and A. junci-acuti, sp. nov. These new species were characterized morphologically with respect to the dimensions of conidia, the number of pseudosepta in mature conidia, and the type of conidium apical beak. According to the results of phylogenetic analyses, the presence of long, filiform true beak is not a reliable morphological indicator for grouping species in sections Alternantherae and Nimbya and phylogenetic species recognition should be used. All identified species were described, illustrated, and their morphology and phylogenetic relationships with other species in Alternaria section Nimbya were discussed.
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Affiliation(s)
- Abdollah Ahmadpour
- Higher Education Center of Shahid Bakeri, Urmia University, Miyandoab, Iran
| | - Youbert Ghosta
- Department of Plant Protection, Faculty of Agriculture and Natural Resources, Urmia University, Urmia, Iran
| | - Alireza Poursafar
- Department of Plant Protection, Faculty of Agriculture and Natural Resources, Urmia University, Urmia, Iran.,Department of Plant Pathology, North Dakota State University, Fargo, North Dakota
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36
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Liu Z, Jiao RL, Chen SY, Ren Y, Zhang L, Zhang D, Chen JY, Guoying L. First Report of Fruit Rot of Grapes (Vitis vinifera) Caused by Cladosporium cladosporioides in Xinjiang, China. PLANT DISEASE 2021; 106:315. [PMID: 34319766 DOI: 10.1094/pdis-01-21-0080-pdn] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Xinjiang Province accounts for nearly 20% of the total grape (Vitis Vinifera L.), proles orientalis) (wine, table and raisin combined) production, being the largest production area in China. Fruit rot is the most common disease that impacts grape quality and yield. A new disease where the ripe grape berry surfaces were coated with brownish mildew was observed, and the disease mainly occurred on whole clusters or most of the berries in the cluster. In September 2019 and 2020, 125 diseased grape clusters were collected from 10 locations in northern Xinjiang where the disease incidence was 15.3% - 27.4% ((diseased clusters/ total clusters)*100). To identify the pathogen, symptomatic grape berries were disinfected with 1% NaClO for 2 min, followed by 70% ethanol for 30 s, and rinsed thrice in sterile distilled water. Three pieces of ~0.5 cm2 diseased grape skin with partial exocarp were placed on potato dextrose agar (PDA) amended with streptomycin sulfate and kanamycin (50 µg/mL each). The PDA plates were then incubated at 25℃ under light condition with the luminous intensity 3500 Lux for 7 days. Fungal colonies emerging from the plated tissue were subcultured and single-spored three times to obtain pure cultures. From 20 strains with similar colony phenotype and grey olive hue, flocculent, felt-like surface, six (Cc-Vivi-3, 7, 9, 11, 13 and 19) isolates were chosen for further characterization after 7 days of incubation. Conidia were either single or grew in chains, with around 4 conidia per chain. Conidia were ovoid, nearly spindle or globose with slightly smooth or irregular reticulate surface. Conidiophores were solitary, smooth, septate, erect or geniculate. These characteristics were consistent with the descriptions for Cladosporium cladosporioides. To confirm this identification, PCR was performed on the genomic DNA of the selected strains using primers for internal transcribed spacer (ITS) region ITS1/ITS4, actin (ACT) and translation elongation factor (TEF) (Schubert et al., 2007; Braun et al., 2003). Amplified ITS sequences provided a 100% match to C. cladosporioides (AY213641) in NCBI. Homology of ACT sequences to C. cladosporioides (HM148527 and MH047330) was 99.57% and 100%, respectively; and the homology of TEF sequences with C. cladosporioides (HM148258, HM148289, HM148260 and HM148266) was 97.56% ~ 100%. To further confirm the evolutionary relationship of strains from grapes with Cladosporium spp., phylogenetic analyses based on ITS, ACT and TEF conjoint sequences from the six experimental isolates, five C. cladosporioides strains, eight proximal Cladosporium species were analyzed. The phylogenetic tree showed that the six isolates from grapes clustered with C. cladosporioides strains, but not other proximal Cladosporium species. This confirmed that all six isolates evaluated were C. cladosporioides. Pathogenicity tests with one C. cladosporioides isolate (Cc-Vivi-3; accession No. ITS: MW556429, ACT: MW567144, TEF: MW567143) were carried out as follows: ripe and healthy grape clusters from cultivars Xinyu and Munag when total soluble solids were 20-21°Bx and 19-20 °Bx, respectively, were detached from the vines. Five berries of three clusters of each cultivar were punctured with a sterile syringe, then inoculated with a 20 μL conidial suspension (107 conidia/mL). And uninoculated, punctured berries in clusters treated with sterilized water served as controls. The experiment was repeated three times. Symptoms were recorded 15 days after incubation at 80% relative humidity and 25℃ with a 14 h light/10 h dark cycle. The olive green or blackish green mildew layer was produced on all inoculated berries. No symptoms were observed on the uninoculated berries. Koch's postulates were fulfilled by reisolating C. cladosporioides from all symptomatic tissues and identifying them by PCR targeting the ACT gene. This is the first description of C. cladosporioides causing grape fruit rot in Xinjiang, China. In recent years, worldwide reports of Cladosporium spp. damaging crops are increasing (Briceño et al., 2008; Walker et al., 2016; Meneses et al., 2018; Robles-Yerena et al., 2019; Ding et al., 2019; Yang et al., 2021). However, relatively few methods of management including some fungicides and biocontrol agents are available in different crops (Wang et al., 2018; Addrah et al., 2019). In view of the important role of Xinjiang in China agricultural production, that should arouse strong attention.
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Affiliation(s)
- Zheng Liu
- Institution of plant protection, Shihezi University, Xinjiang Uygur Autonomous Region, Shihezi, China, 832003;
| | - Rui-Lian Jiao
- Shihezi University College of Agriculture, 117455, Shihezi, Xinjiang, China;
| | - Si-Ying Chen
- Shihezi University College of Agriculture, 117455, Shihezi, Xinjiang, China;
| | - Yuzhong Ren
- plant protection, Shihezi university, Shihezi, Xinjiang, China, 832003;
| | - Li Zhang
- Shihezi University College of Agriculture, 117455, Shihezi, Xinjiang, China;
| | - Dandan Zhang
- Chinese Academy of Agricultural Sciences Institute of Plant Protection, 243827, Beijing, Beijing, China;
| | - Jie-Yin Chen
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Rd., Haidian, Beijing, [Select a State/Province], China, 100193;
| | - Li Guoying
- Shihezi University, Plant protection, Shihezi, Xinjiang, China;
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Morphological, molecular characterization, plant pathogenicity and biocontrol of Cladosporium complex groups associated with faba beans. Sci Rep 2021; 11:14183. [PMID: 34244553 PMCID: PMC8270977 DOI: 10.1038/s41598-021-93123-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/09/2021] [Indexed: 11/29/2022] Open
Abstract
Vicia faba (faba bean) is one of the most significant leguminous crops. The faba bean is specialized by maximum nutritional value, in energy and protein content, which leads it to be suitable for food and feed production. Diseases caused with fungi are amongst the biotic factors responsible for decreasing in faba bean yields. In this work, Cladosporium isolates were recorded in cultivated faba bean leaves and pods collected from markets in Qena, Upper Egypt; morphological features and molecular characterization based on actin gene were performed. The ability of the pathogens to cause disease in faba bean seedlings and the biocontrol method to avoid the pathogenic effect of Cladosporium were determined. Results showed that Cladosporium is the main genera isolated from faba beans, and the morphological criteria showed presence of three species complex groups of Cladosporium (C. cladosporioides, C. herbarum and C. sphaerospermum) and the confirmation with molecular characterization revealed the existence of four species in the three groups. All the 26 tested strains of Cladosporium were able to cause leaf lesions on Vicia faba seedlings with different levels. Chaetomium globosum is a biocontrol agent could inhibit the growth of the majority strains of Cladosporium.
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Pimentel CS, Firmino PN, Ayres MP. Interactions between pinewood nematodes and the fungal community of pine trees. FUNGAL ECOL 2021. [DOI: 10.1016/j.funeco.2021.101046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Fort T, Pauvert C, Zanne AE, Ovaskainen O, Caignard T, Barret M, Compant S, Hampe A, Delzon S, Vacher C. Maternal effects shape the seed mycobiome in Quercus petraea. THE NEW PHYTOLOGIST 2021; 230:1594-1608. [PMID: 33341934 DOI: 10.1111/nph.17153] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
The tree seed mycobiome has received little attention despite its potential role in forest regeneration and health. The aim of the present study was to analyze the processes shaping the composition of seed fungal communities in natural forests as seeds transition from the mother plant to the ground for establishment. We used metabarcoding approaches and confocal microscopy to analyze the fungal communities of seeds collected in the canopy and on the ground in four natural populations of sessile oak (Quercus petraea). Ecological processes shaping the seed mycobiome were inferred using joint species distribution models. Fungi were present in seed internal tissues, including the embryo. The seed mycobiome differed among oak populations and trees within the same population. Its composition was largely influenced by the mother, with weak significant environmental influences. The models also revealed several probable interactions among fungal pathogens and mycoparasites. Our results demonstrate that maternal effects, environmental filtering and biotic interactions all shape the seed mycobiome of sessile oak. They provide a starting point for future research aimed at understanding how maternal genes and environments interact to control the vertical transmission of fungal species that could then influence seed dispersal and germination, and seedling recruitment.
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Affiliation(s)
- Tania Fort
- INRAE, BIOGECO, Univ. Bordeaux, Pessac, 33615, France
| | | | - Amy E Zanne
- Department of Biological Sciences, George Washington University, 800 22nd St., Washington, DC, 20052, USA
| | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, PO Box 65, Helsinki, 00014, Finland
- Center for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, 7491, Norway
| | | | - Matthieu Barret
- INRAE, IRHS, SFR 4207 QuaSaV, Institut Agro, Univ. Angers, Angers, 49000, France
| | - Stéphane Compant
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, Tulln, 3430, Austria
| | - Arndt Hampe
- INRAE, BIOGECO, Univ. Bordeaux, Pessac, 33615, France
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Ingrey SD, Pearson LA, Kalaitzis JA, Neilan BA. Australian bush medicines harbour diverse microbial endophytes with broad-spectrum antibacterial activity. J Appl Microbiol 2021; 131:2244-2256. [PMID: 33904206 DOI: 10.1111/jam.15122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/15/2021] [Accepted: 04/21/2021] [Indexed: 12/01/2022]
Abstract
AIMS Microbial endophytes produce specialized metabolites, including antibiotics and other compounds of pharmaceutical and agricultural value. This study aimed to investigate the diversity and bioactivity of endophytes from medicinal plants used by the Dharawal People of Gamay (Botany Bay), Australia. METHODS AND RESULTS Of the 48 endophytes isolated, 19 tested positive for polyketide synthase or non-ribosomal peptide synthetase genes via a PCR incorporating degenerate primers. The biosynthetically talented endophytes were identified by 16S rRNA gene sequencing and included 4 bacteria species belonging to the orders Bacillales, Rhizobiales and Burkholderiales and 15 Ascomycota fungi species belonging to the orders Botryosphaeriales, Cladosporiales, Glomerellales, Microascales and Eurotiales. Antimicrobial testing using the disc diffusion assay demonstrated that 15 of the 19 isolates had broad-spectrum activity against a range of Gram-positive and Gram-negative bacteria. CONCLUSIONS Taken together, these results suggest that Australian bush medicines harbour diverse biosynthetically talented microbial endophytes capable of producing broad-spectrum antibacterial compounds. SIGNIFICANCE AND IMPACT OF THE STUDY This study suggests that compounds produced by microbial endophytes likely contribute to the collective medicinal properties of Australian bush medicines. Significantly, it highlights that Indigenous botanical knowledge and modern molecular approaches can be used in tandem to prioritize microorganisms that produce pharmaceutically relevant compounds.
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Affiliation(s)
- S D Ingrey
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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41
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The symbiosis between Philidris ants and the ant-plant Dischidia major includes fungal and algal associates. Symbiosis 2021. [DOI: 10.1007/s13199-021-00751-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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42
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Álvarez-Barragán J, Cravo-Laureau C, Wick LY, Duran R. Fungi in PAH-contaminated marine sediments: Cultivable diversity and tolerance capacity towards PAH. MARINE POLLUTION BULLETIN 2021; 164:112082. [PMID: 33524832 DOI: 10.1016/j.marpolbul.2021.112082] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 01/12/2021] [Accepted: 01/16/2021] [Indexed: 06/12/2023]
Abstract
The cultivable fungal diversity from PAH-contaminated sediments was examined for the tolerance to polycyclic aromatic hydrocarbon (PAH). The 85 fungal strains, isolated in non-selective media, revealed a large diversity by ribosomal internal transcribed spacer (ITS) sequencing, even including possible new species. Most strains (64%) exhibited PAH-tolerance, indicating that sediments retain diverse cultivable PAH-tolerant fungi. The PAH-tolerance was linked neither to a specific taxon nor to the peroxidase genes (LiP, MnP and Lac). Examining the PAH-removal (degradation and/or sorption), Alternaria destruens F10.81 showed the best capacity with above 80% removal for phenanthrene, pyrene and fluoranthene, and around 65% for benzo[a]pyrene. A. destruens F10.81 internalized pyrene homogenously into the hyphae that contrasted with Fusarium pseudoygamai F5.76 in which PAH-vacuoles were observed but PAH removal was below 20%. Thus, our study paves the way for the exploitation of fungi in remediation strategies to mitigate the effect of PAH in coastal marine sediments.
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Affiliation(s)
- Joyce Álvarez-Barragán
- Université de Pau et des Pays de l'Adour, UPPA/E2S, IPREM UMR CNRS 5254, Bat. IBEAS, Pau, France
| | - Cristiana Cravo-Laureau
- Université de Pau et des Pays de l'Adour, UPPA/E2S, IPREM UMR CNRS 5254, Bat. IBEAS, Pau, France
| | - Lukas Y Wick
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Microbiology, Leipzig, 04318, Germany
| | - Robert Duran
- Université de Pau et des Pays de l'Adour, UPPA/E2S, IPREM UMR CNRS 5254, Bat. IBEAS, Pau, France.
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Iturrieta-González I, García D, Gené J. Novel species of Cladosporium from environmental sources in Spain. MycoKeys 2021; 77:1-25. [PMID: 33510579 PMCID: PMC7803722 DOI: 10.3897/mycokeys.77.60862] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 12/07/2020] [Indexed: 01/12/2023] Open
Abstract
Cladosporium is a monophyletic genus in Cladosporiaceae (Cladosporiales, Dothideomycetes) whose species are mainly found as saprobes and endophytes, but it also includes fungi pathogenic for plants, animals and human. Species identification is currently based on three genetic markers, viz., the internal transcribed spacer regions (ITS) of the rDNA, and partial fragments of actin (act) and the translation elongation factor 1-α (tef1) genes. Using this phylogenetic approach and from morphological differences, we have recognized six new species originating from soil, herbivore dung and plant material collected at different Spanish locations. They are proposed as Cladosporiumcaprifimosum, C.coprophilum, C.fuscoviride and C.lentulum belonging in the C.cladosporioides species complex, and C.pseudotenellum and C.submersum belonging in the C.herbarum species complex. This study revealed that herbivore dung represented a reservoir of novel lineages in the genus Cladosporium.
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Affiliation(s)
- Isabel Iturrieta-González
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut and IISPV, Universitat Rovira i Virgili, 43201, Reus, Tarragona, Spain Universitat Rovira i Virgili Reus Spain
| | - Dania García
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut and IISPV, Universitat Rovira i Virgili, 43201, Reus, Tarragona, Spain Universitat Rovira i Virgili Reus Spain
| | - Josepa Gené
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut and IISPV, Universitat Rovira i Virgili, 43201, Reus, Tarragona, Spain Universitat Rovira i Virgili Reus Spain
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Jayawardena RS, Hyde KD, Chen YJ, Papp V, Palla B, Papp D, Bhunjun CS, Hurdeal VG, Senwanna C, Manawasinghe IS, Harischandra DL, Gautam AK, Avasthi S, Chuankid B, Goonasekara ID, Hongsanan S, Zeng X, Liyanage KK, Liu N, Karunarathna A, Hapuarachchi KK, Luangharn T, Raspé O, Brahmanage R, Doilom M, Lee HB, Mei L, Jeewon R, Huanraluek N, Chaiwan N, Stadler M, Wang Y. One stop shop IV: taxonomic update with molecular phylogeny for important phytopathogenic genera: 76–100 (2020). FUNGAL DIVERS 2020. [DOI: 10.1007/s13225-020-00460-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AbstractThis is a continuation of a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi and fungus-like organisms. This paper focuses on one family: Erysiphaceae and 24 phytopathogenic genera: Armillaria, Barriopsis, Cercospora, Cladosporium, Clinoconidium, Colletotrichum, Cylindrocladiella, Dothidotthia,, Fomitopsis, Ganoderma, Golovinomyces, Heterobasidium, Meliola, Mucor, Neoerysiphe, Nothophoma, Phellinus, Phytophthora, Pseudoseptoria, Pythium, Rhizopus, Stemphylium, Thyrostroma and Wojnowiciella. Each genus is provided with a taxonomic background, distribution, hosts, disease symptoms, and updated backbone trees. Species confirmed with pathogenicity studies are denoted when data are available. Six of the genera are updated from previous entries as many new species have been described.
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Mengal HS, Abro MA, Jatoi GH, Nawab L, Poussio GB, Ahmed N, Zehri AQ, Ali A. Efficacy of different fungicides, botanical extracts and bio-control agents against Cladosporium cladosporioides, the causal agent of Cladosporium rot in grapes. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.chnaes.2019.08.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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46
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Baturo-Cieśniewska A, Pusz W, Patejuk K. Problems, Limitations, and Challenges in Species Identification of Ascomycota Members on the Basis of ITS Regions. ACTA MYCOLOGICA 2020. [DOI: 10.5586/am.5512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
The internal transcribed spacer (ITS) region is regarded as a formal fungal primary barcode with a high probability of the correct identification for a broad group of fungi. ITS sequences have been widely used to determine many fungal species and analysis of rDNA ITS is still one of the most popular tools used in mycology. However, this region is not equally variable in all groups of fungi; therefore, identification may be problematic and result in ambiguous data, especially in some species-rich genera of Ascomycota. For these reasons, identification based on rDNA ITS is usually complemented by morphological observations and analysis of additional genes. Reliable species identification of Ascomycota members is essential in diagnosing plant diseases, verifying air quality and the effectiveness of agronomic practices, or analyzing relationships between microorganisms. Therefore, the present study aimed to verify, using specific examples, the extent to which ITS sequence analysis is useful in species identification of pathogens and saprobionts from Ascomycota and demonstrate problems related to such identification in practice. We analyzed 105 ITS sequences of isolates originating from air and plant material. Basic local alignment search tool (BLASTn) significantly contributed to the reliable species identification of nearly 80% of isolates such as <em>Arthrinium arundinis</em>, <em>Beauveria bassiana</em>, <em>Boeremia exigua</em>, <em>Cladosporium cladosporioides</em>, <em>Epicoccum nigrum</em>, <em>Nigrospora oryzae</em>, <em>Sclerotinia sclerotiorum</em>, or <em>Sordaria fimicola </em>and members of the genera <em>Alternaria </em>and <em>Trichoderma</em>. However, for most isolates, additional morphological observations, information regarding the isolate origin and, where possible, a PCR with species-specific primers were helpful and complementary. Using our practical approach, we determined that ITS-based species identification and comparative analysis with GenBank sequences significantly helps identifying Ascomycota members. However, in many cases, this should be regarded as suggestive of a taxon because the data usually require the use of additional tools to verify the results of such analysis.
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Crous PW, Wingfield MJ, Schumacher RK, Akulov A, Bulgakov TS, Carnegie AJ, Jurjević Ž, Decock C, Denman S, Lombard L, Lawrence DP, Stack AJ, Gordon TR, Bostock RM, Burgess T, Summerell BA, Taylor PWJ, Edwards J, Hou LW, Cai L, Rossman AY, Wöhner T, Allen WC, Castlebury LA, Visagie CM, Groenewald JZ. New and Interesting Fungi. 3. Fungal Syst Evol 2020; 6:157-231. [PMID: 32904192 PMCID: PMC7452156 DOI: 10.3114/fuse.2020.06.09] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Seven new genera, 26 new species, 10 new combinations, two epitypes, one new name, and 20 interesting new host and / or geographical records are introduced in this study. New genera are: Italiofungus (based on Italiofungus phillyreae) on leaves of Phillyrea latifolia (Italy); Neolamproconium (based on Neolamproconium silvestre) on branch of Tilia sp. (Ukraine); Neosorocybe (based on Neosorocybe pini) on trunk of Pinus sylvestris (Ukraine); Nothoseptoria (based on Nothoseptoria caraganae) on leaves of Caragana arborescens (Russia); Pruniphilomyces (based on Pruniphilomyces circumscissus) on Prunus cerasus (Russia); Vesiculozygosporium (based on Vesiculozygosporium echinosporum) on leaves of Muntingia calabura (Malaysia); Longiseptatispora (based on Longiseptatispora curvata) on leaves of Lonicera tatarica (Russia). New species are: Barrmaelia serenoae on leaf of Serenoa repens (USA); Chaetopsina gautengina on leaves of unidentified grass (South Africa); Chloridium pini on fallen trunk of Pinus sylvestris (Ukraine); Cadophora fallopiae on stems of Reynoutria sachalinensis (Poland); Coleophoma eucalyptigena on leaf litter of Eucalyptus sp. (Spain); Cylindrium corymbiae on leaves of Corymbia maculata (Australia); Diaporthe tarchonanthi on leaves of Tarchonanthus littoralis (South Africa); Elsinoe eucalyptorum on leaves of Eucalyptus propinqua (Australia); Exophiala quercina on dead wood of Quercus sp., (Germany); Fusarium californicum on cambium of budwood of Prunus dulcis (USA); Hypomyces gamsii on wood of Alnus glutinosa (Ukraine); Kalmusia araucariae on leaves of Araucaria bidwillii (USA); Lectera sambuci on leaves of Sambucus nigra (Russia); Melanomma populicola on fallen twig of Populus canadensis (Netherlands), Neocladosporium syringae on branches of Syringa vulgarishorus (Ukraine); Paraconiothyrium iridis on leaves of Iris pseudacorus (Ukraine); Pararoussoella quercina on branch of Quercus robur (Ukraine); Phialemonium pulveris from bore dust of deathwatch beetle (France); Polyscytalum pinicola on needles of Pinus tecunumanii (Malaysia); Acervuloseptoria fraxini on Fraxinus pennsylvanica (Russia); Roussoella arundinacea on culms of Arundo donax (Spain); Sphaerulina neoaceris on leaves of Acer negundo (Russia); Sphaerulina salicicola on leaves of Salix fragilis (Russia); Trichomerium syzygii on leaves of Syzygium cordatum (South Africa); Uzbekistanica vitis-viniferae on dead stem of Vitis vinifera (Ukraine); Vermiculariopsiella eucalyptigena on leaves of Eucalyptus sp. (Australia).
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Affiliation(s)
- P W Crous
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands.,Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa.,Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - M J Wingfield
- Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa.,Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | | | - A Akulov
- Department of Mycology and Plant Resistance, V. N. Karazin Kharkiv National University, Maidan Svobody 4, 61022 Kharkiv, Ukraine
| | - T S Bulgakov
- Department of Plant Protection, Russian Research Institute of Floriculture and Subtropical Crops, Yana Fabritsiusa street 2/28, 354002 Sochi, Krasnodar region, Russia
| | - A J Carnegie
- Forest Health & Biosecurity, Forest Science, NSW Department of Primary Industries - Forestry, Level 12, 10 Valentine Ave, Parramatta NSW 2150, Australia.,School of Environment Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia
| | - Ž Jurjević
- EMSL Analytical, Inc., 200 Route 130 North, Cinnaminson, NJ 08077, USA
| | - C Decock
- Mycothèque de l'Université catholique de Louvain (MUCL, BCCMTM), Earth and Life Institute - ELIM - Mycology, Université catholique de Louvain, Croix du Sud 2 bte L7.05.25, B-1348 Louvain-la-Neuve, Belgium
| | - S Denman
- Forest Research, Alice Holt Lodge, Farnham, Surrey, UK
| | - L Lombard
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
| | - D P Lawrence
- Department of Plant Pathology, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - A J Stack
- Department of Plant Pathology, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - T R Gordon
- Department of Plant Pathology, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - R M Bostock
- Department of Plant Pathology, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - T Burgess
- Environmental and Conservation Sciences, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - B A Summerell
- Royal Botanic Gardens and Domain Trust, Mrs Macquaries Rd, Sydney, NSW 2000, Australia
| | - P W J Taylor
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - J Edwards
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, AgriBio Centre, 5 Ring Road, LaTrobe University, Bundoora, Victoria 3083, Australia.,School of Applied Systems Biology, LaTrobe University, Bundoora, Victoria 3083, Australia
| | - L W Hou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - L Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - A Y Rossman
- Botany & Plant Pathology Department, Oregon State University, Corvallis, Oregon 97333, USA
| | - T Wöhner
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326, Dresden, Germany
| | - W C Allen
- North Carolina State University, Raleigh, North Carolina 27695, USA.,USDA ARS Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, Maryland 20705, USA
| | - L A Castlebury
- USDA ARS Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, Maryland 20705, USA
| | - C M Visagie
- Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa.,Biosystematics Division, Agricultural Research Council - Plant Health and Protection, Private Bag X134, Queenswood, Pretoria, 0121, South Africa
| | - J Z Groenewald
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
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Gupta AB, Gaultier NE, Aung NW, Purbojati RW, Oliveira EL, Wong A, Panicker D, Putra A, Uchida A, Drautz-Moses DI, Schuster SC. Complete Genome Sequence of Penicillium oxalicum Strain SGAir0226 Isolated from Outdoor Tropical Air in Singapore. Mycopathologia 2020; 185:591-594. [PMID: 32270395 DOI: 10.1007/s11046-019-00422-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 12/20/2019] [Indexed: 11/28/2022]
Abstract
Penicillium oxalicum strain SGAir0226 was isolated from a tropical air sample collected in Singapore. The complete genome was assembled from long reads obtained from single-molecule real-time sequencing and was further polished and error corrected using short read sequencing data. The assembly comprises 20 contigs with a total length of 30.7 Mb. The genome was predicted to contain 8310 protein-coding genes, 237 tRNAs and 83 rRNAs.
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Affiliation(s)
- Anjali Bansal Gupta
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Nicolas E Gaultier
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Ngu War Aung
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Rikky W Purbojati
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Elaine L Oliveira
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Anthony Wong
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Deepa Panicker
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Alexander Putra
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Akira Uchida
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Daniela I Drautz-Moses
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Stephan C Schuster
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore.
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Rojas EC, Sapkota R, Jensen B, Jørgensen HJL, Henriksson T, Jørgensen LN, Nicolaisen M, Collinge DB. Fusarium Head Blight Modifies Fungal Endophytic Communities During Infection of Wheat Spikes. MICROBIAL ECOLOGY 2020; 79:397-408. [PMID: 31448388 PMCID: PMC7033075 DOI: 10.1007/s00248-019-01426-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 08/13/2019] [Indexed: 05/29/2023]
Abstract
Fusarium head blight (FHB) is a devastating disease of wheat heads. It is caused by several species from the genus Fusarium. Several endophytic fungi also colonize wheat spikes asymptomatically. Pathogenic and commensal fungi share and compete for the same niche and thereby influence plant performance. Understanding the natural dynamics of the fungal community and how the pre-established species react to pathogen attack can provide useful information on the disease biology and the potential use of some of these endophytic organisms in disease control strategies. Fungal community composition was assessed during anthesis as well as during FHB attack in wheat spikes during 2016 and 2017 in two locations. Community metabarcoding revealed that endophyte communities are dominated by basidiomycete yeasts before anthesis and shift towards a more opportunistic ascomycete-rich community during kernel development. These dynamics are interrupted when Fusarium spp. colonize wheat spikes. The Fusarium pathogens appear to exclude other fungi from floral tissues as they are associated with a reduction in community diversity, especially in the kernel which they colonize rapidly. Similarly, the presence of several endophytes was negatively correlated with Fusarium spp. and linked with spikes that stayed healthy despite exposure to the pathogen. These endophytes belonged to the genera Cladosporium, Itersonillia and Holtermanniella. These findings support the hypothesis that some naturally occurring endophytes could outcompete or prevent FHB and represent a source of potential biological control agents in wheat.
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Affiliation(s)
- Edward C Rojas
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences & Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark.
| | - Rumakanta Sapkota
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
| | - Birgit Jensen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences & Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Hans J L Jørgensen
- Section for Plant and Soil Science, Department of Plant and Environmental Sciences & Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | | | - Lise Nistrup Jørgensen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
| | - Mogens Nicolaisen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
| | - David B Collinge
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences & Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
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Singh M, Singh N. DNA Barcoding for Species Identification in Genetically Engineered Fungi. Fungal Biol 2020. [DOI: 10.1007/978-3-030-41870-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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