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van Westerhoven AC, Mehrabi R, Talebi R, Steentjes MBF, Corcolon B, Chong PA, Kema GHJ, Seidl MF. A chromosome-level genome assembly of Zasmidium syzygii isolated from banana leaves. G3 (BETHESDA, MD.) 2024; 14:jkad262. [PMID: 37972272 PMCID: PMC10917495 DOI: 10.1093/g3journal/jkad262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/29/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023]
Abstract
Accurate taxonomic classification of samples from infected host material is essential for disease diagnostics and genome analyses. Despite the importance, diagnosis of fungal pathogens causing banana leaf diseases remains challenging. Foliar diseases of bananas are mainly caused by 3 Pseudocercospora species, of which the most predominant causal agent is Pseudocercospora fijiensis. Here, we sequenced and assembled four fungal isolates obtained from necrotic banana leaves in Bohol (Philippines) and obtained a high-quality genome assembly for one of these isolates. The samples were initially identified as P. fijiensis using PCR diagnostics; however, the assembly size was consistently 30 Mb smaller than expected. Based on the internal transcribed spacer (ITS) sequences, we identified the samples as Zasmidium syzygii (98.7% identity). The high-quality Zasmidium syzygii assembly is 42.5 Mb in size, comprising 16 contigs, of which 11 are most likely complete chromosomes. The genome contains 98.6% of the expected single-copy BUSCO genes and contains 14,789 genes and 10.3% repeats. The 3 short-read assemblies are less continuous but have similar genome sizes (40.4-42.4 Mb) and contain between 96.5 and 98.4% BUSCO genes. All 4 isolates have identical ITS sequences and are distinct from Zasmidium isolates that were previously sampled from banana leaves. We thus report the first continuous genome assembly of a member of the Zasmidium genus, forming an essential resource for further analysis to enhance our understanding of the diversity of pathogenic fungal isolates as well as fungal diversity.
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Affiliation(s)
- Anouk C van Westerhoven
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen 6700 AA, The Netherlands
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht 3584 CS, The Netherlands
| | - Rahim Mehrabi
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen 6700 AA, The Netherlands
- Keygene N.V., Wageningen 6700 AE, The Netherlands
| | - Reza Talebi
- Keygene N.V., Wageningen 6700 AE, The Netherlands
| | - Maikel B F Steentjes
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen 6700 AA, The Netherlands
| | - Benny Corcolon
- Research, Information, Compliance Department, Tadeco Inc., Panabo, Davao del Norte 8105, Philippines
| | - Pablo A Chong
- Escuela Superior Politécnica del Litoral, Centro de Investigaciones Biotecnológicas del Ecuador, Laboratorio de Biología Molecular, ESPOL Polytechnic University, Guayaquil 090112, Ecuador
| | - Gert H J Kema
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen 6700 AA, The Netherlands
| | - Michael F Seidl
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht 3584 CS, The Netherlands
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Paiva DS, Fernandes L, Pereira E, Trovão J, Mesquita N, Tiago I, Portugal A. Exploring Differences in Culturable Fungal Diversity Using Standard Freezing Incubation-A Case Study in the Limestones of Lemos Pantheon (Portugal). J Fungi (Basel) 2023; 9:jof9040501. [PMID: 37108954 PMCID: PMC10143818 DOI: 10.3390/jof9040501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
In this study, we explored the biodiversity and abundance of culturable fungi in four samples associated with different biodeterioration outlines collected from the Lemos Pantheon, a limestone-built artwork in Portugal. We compared the results from prolonged standard freezing with those previously obtained from fresh samples to analyze differences in the obtained community and assess the effectiveness of the standard freezing incubation protocol in uncovering a different segment of culturable fungal diversity. Our results showed a slight decrease in culturable diversity, but over 70% of the obtained isolates were not present in the previously studied fresh samples. We also identified a high number of potential new species with this procedure. Moreover, the use of a wide variety of selective culture media positively influenced the diversity of the cultivable fungi obtained in this study. These findings highlight the importance of developing new protocols under varying conditions to accurately characterize the culturable fraction in a given sample. The identification and study of these communities and their possible contribution to the biodeterioration process is crucial knowledge for formulating effective conservation and restoration plans to prevent further damage to valuable cultural heritage assets.
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Affiliation(s)
- Diana S Paiva
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Luís Fernandes
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Emília Pereira
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - João Trovão
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- FitoLab-Laboratory for Phytopathology, Instituto Pedro Nunes, Rua Pedro Nunes, 3030-199 Coimbra, Portugal
| | - Nuno Mesquita
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Igor Tiago
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - António Portugal
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- FitoLab-Laboratory for Phytopathology, Instituto Pedro Nunes, Rua Pedro Nunes, 3030-199 Coimbra, Portugal
- TERRA-Associate Laboratory for Sustainable Land Use and Ecosystem Services, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
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Osorio JA, Linnakoski R, Wingfield MJ, de Beer ZW, Roux J. A new species in the Mycosphaerellaceae from Cecidomyiidae leaf galls on Avicennia marina in South Africa. Antonie van Leeuwenhoek 2021; 114:515-526. [PMID: 33641038 DOI: 10.1007/s10482-021-01537-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 02/08/2021] [Indexed: 10/22/2022]
Abstract
During studies to investigate the health of mangrove trees in South Africa, high numbers of Avicennia marina were found with leaf galls caused by unidentified adults and larvae of midges (Cecidomyiidae). Fungal fruiting structures were commonly observed on the abaxial areas of the galls. To determine the identity of the fungi associated with the gall midges, phylogenetic analyses using multigene sequence data were used. The nuclear large subunit (LSU), internal transcribed spacer (ITS), and a portion of the actin gene region (ACT), were amplified and analyzed. The results revealed that the fungal fruiting structures represent a new taxon in the Mycosphaerellaceae described here as Zasmidium mangrovei sp. nov. This is the first report of a species in the Mycosphaerellaceae associated with cecidomyiid leaf galls on A. marina.
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Affiliation(s)
- J Alexander Osorio
- Department of Biochemistry, Genetics and Microbiology, DST/NRF Centre of Excellence in Plant Health Biotechnology (CPHB), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South Africa. .,Facultad de Ciencias Básicas y Tecnologías, Programa de Biología, Universidad del Quindío, Armenia, Colombia.
| | - Riikka Linnakoski
- Natural Resources Institute Finland (Luke), Latokartanonkaari 9, 00790, Helsinki, Finland.,Department of Forest Sciences, University of Helsinki, Latokartanonkaari 7, 00014, Helsinki, Finland
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology, DST/NRF Centre of Excellence in Plant Health Biotechnology (CPHB), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South Africa
| | - Z Wilhelm de Beer
- Department of Biochemistry, Genetics and Microbiology, DST/NRF Centre of Excellence in Plant Health Biotechnology (CPHB), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South Africa
| | - Jolanda Roux
- Department of Plant and Soil Sciences, DST/NRF Centre of Excellence in Tree Health Biotechnology (CTHB), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South Africa
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McClure R, Naylor D, Farris Y, Davison M, Fansler SJ, Hofmockel KS, Jansson JK. Development and Analysis of a Stable, Reduced Complexity Model Soil Microbiome. Front Microbiol 2020; 11:1987. [PMID: 32983014 PMCID: PMC7479069 DOI: 10.3389/fmicb.2020.01987] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/27/2020] [Indexed: 12/12/2022] Open
Abstract
The soil microbiome is central to the cycling of carbon and other nutrients and to the promotion of plant growth. Despite its importance, analysis of the soil microbiome is difficult due to its sheer complexity, with thousands of interacting species. Here, we reduced this complexity by developing model soil microbial consortia that are simpler and more amenable to experimental analysis but still represent important microbial functions of the native soil ecosystem. Samples were collected from an arid grassland soil and microbial communities (consisting mainly of bacterial species) were enriched on agar plates containing chitin as the main carbon source. Chitin was chosen because it is an abundant carbon and nitrogen polymer in soil that often requires the coordinated action of several microorganisms for complete metabolic degradation. Several soil consortia were derived that had tractable richness (30–50 OTUs) with diverse phyla representative of the native soil, including Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia. The resulting consortia could be stored as glycerol or lyophilized stocks at −80°C and revived while retaining community composition, greatly increasing their use as tools for the research community at large. One of the consortia that was particularly stable was chosen as a model soil consortium (MSC-1) for further analysis. MSC-1 species interactions were studied using both pairwise co-cultivation in liquid media and during growth in soil under several perturbations. Co-abundance analyses highlighted interspecies interactions and helped to define keystone species, including Mycobacterium, Rhodococcus, and Rhizobiales taxa. These experiments demonstrate the success of an approach based on naturally enriching a community of interacting species that can be stored, revived, and shared. The knowledge gained from querying these communities and their interactions will enable better understanding of the soil microbiome and the roles these interactions play in this environment.
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Affiliation(s)
- Ryan McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Dan Naylor
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Yuliya Farris
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Michelle Davison
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Sarah J Fansler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kirsten S Hofmockel
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.,Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
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Anteneh YS, Brown MH, Franco CMM. Characterization of a Halotolerant Fungus from a Marine Sponge. BIOMED RESEARCH INTERNATIONAL 2019; 2019:3456164. [PMID: 31871938 PMCID: PMC6907059 DOI: 10.1155/2019/3456164] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/15/2019] [Accepted: 10/29/2019] [Indexed: 11/17/2022]
Abstract
INTRODUCTION Marine sponges have established symbiotic interactions with a large number of microorganisms including fungi. Most of the studies so far have focussed on the characterization of sponge-associated bacteria and archaea with only a few reports on sponge-associated fungi. During the isolation and characterization of bacteria from marine sponges of South Australia, we observed multiple types of fungi. One isolate in particular was selected for further investigation due to its unusually large size and being chromogenic. Here, we report on the investigations on the physical, morphological, chemical, and genotypic properties of this yeast-like fungus. METHODS AND MATERIALS Sponge samples were collected from South Australian marine environments, and microbes were isolated using different isolation media under various incubation conditions. Microbial isolates were identified on the basis of morphology, staining characteristics, and their 16S rRNA or ITS/28S rRNA gene sequences. RESULTS Twelve types of yeast and fungal isolates were detected together with other bacteria and one of these fungi measured up to 35 μm in diameter with a unique chromogen compared to other fungi. Depending on the medium type, this unique fungal isolate appeared as yeast-like fungi with different morphological forms. The isolate can ferment and assimilate nearly all of the tested carbohydrates. Furthermore, it tolerated a high concentration of salt (up to 25%) and a range of pH and temperature. ITS and 28S rRNA gene sequencing revealed a sequence similarity of 93% and 98%, respectively, with the closest genera of Eupenidiella, Hortaea, and Stenella. CONCLUSIONS On the basis of its peculiar morphology, size, and genetic data, this yeast-like fungus possibly constitutes a new genus and the name Magnuscella marinae, gen nov., sp. nov., is proposed. This study is the first of its kind for the complete characterization of a yeast-like fungus from marine sponges. This novel isolate developed a symbiotic interaction with living hosts, which was not observed with other reported closest genera (they exist in a saprophytic relationship). The observed unique size and morphology may favour this new isolate to establish symbiotic interactions with living hosts.
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Affiliation(s)
- Yitayal S. Anteneh
- College of Medicine and Public Health, Medical Biotechnology, Flinders University, Bedford Park, Adelaide, SA 5042, Australia
- Department of Medical Microbiology, College of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - Melissa H. Brown
- College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA 5042, Australia
| | - Christopher M. M. Franco
- College of Medicine and Public Health, Medical Biotechnology, Flinders University, Bedford Park, Adelaide, SA 5042, Australia
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Mihajlovski A, Lepinay C, Mirval AL, Touron S, Bousta F, Di Martino P. Characterization of the archaeal and fungal diversity associated with gypsum efflorescences on the walls of the decorated Sorcerer’s prehistoric cave. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01506-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Medina R, Lucentini CG, Franco ME, Petroselli G, Rosso JA, Erra-Balsells R, Balatti PA, Saparrat MC. Identification of an intermediate for 1,8-dihydroxynaphthalene-melanin synthesis in a race-2 isolate of Fulvia fulva (syn. Cladosporium fulvum). Heliyon 2018; 4:e01036. [PMID: 30582052 PMCID: PMC6299106 DOI: 10.1016/j.heliyon.2018.e01036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 11/20/2018] [Accepted: 12/07/2018] [Indexed: 11/08/2022] Open
Abstract
Fulvia fulva (syn. Cladosporium fulvum, Mycosphaerellaceae) is a dematiaceous fungus that causes tomato leaf mould. It is characterized by its biotrophic lifestyle and the synthesis of the bianthraquinone secondary metabolite, cladofulvin. The aim of the study was to characterize the dark pigment photochemically synthesized by F. fulva and to elucidate its biochemical pathway. We isolated a black pigment from in vitro cultures of the fungus. We determined the pigment to be 1,8-dihydroxynaphthalene (DHN)-melanin based on its chemical and photochemical characteristics, as well as the presence of flaviolin, when fungal reductases were inhibited by tricyclazole. Furthermore, the pks1 gene involved in pigment synthesis has a KS domain already associated with DHN-melanin. Our findings support the relevance of studying melanization in F. fulva.
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Affiliation(s)
- Rocío Medina
- Centro de Investigaciones en Fitopatologías, CIDEFI, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CICBA), Departamento de Ciencias Biológicas, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, 60 y 119, CC 31, 1900 La Plata, Argentina
| | - César G. Lucentini
- Centro de Investigaciones en Fitopatologías, CIDEFI, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CICBA), Departamento de Ciencias Biológicas, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, 60 y 119, CC 31, 1900 La Plata, Argentina
| | - Mario E.E. Franco
- Centro de Investigaciones en Fitopatologías, CIDEFI, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CICBA), Departamento de Ciencias Biológicas, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, 60 y 119, CC 31, 1900 La Plata, Argentina
| | - Gabriela Petroselli
- Centro de Investigaciones en Hidratos de Carbono, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón II, 3 Ciudad Universitaria, 1428 Buenos Aires, Argentina
| | - Janina A. Rosso
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Diag. 113 y 64, CC 16 suc. 4, 1900 La Plata, Argentina
| | - Rosa Erra-Balsells
- Centro de Investigaciones en Hidratos de Carbono, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón II, 3 Ciudad Universitaria, 1428 Buenos Aires, Argentina
| | - Pedro A. Balatti
- Centro de Investigaciones en Fitopatologías, CIDEFI, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CICBA), Departamento de Ciencias Biológicas, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, 60 y 119, CC 31, 1900 La Plata, Argentina
- Cátedra de Microbiología Agrícola, Departamento de Ciencias Biológicas, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, 60 y 119, 1900 La Plata, Argentina
| | - Mario C.N. Saparrat
- Cátedra de Microbiología Agrícola, Departamento de Ciencias Biológicas, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, 60 y 119, 1900 La Plata, Argentina
- Instituto de Fisiología Vegetal (INFIVE), Consejo Nacional de Investigaciones Científicas y técnicas (CONICET), Universidad Nacional de La Plata CCT-La Plata, Diag. 113 y 61, CC 327, 1900 La Plata, Argentina
- Instituto de Botánica Carlos Spegazzini, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, 53 # 477, 1900 La Plata, Argentina
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