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Yang WJ, Xu M, Zhang J, Zhou F, Le ZF, Tong WJ, Song HY, Jin ZH, Cheng QG, Zhou JP, Gao Y, Zhai ZJ, Hu HJ, Chen MH, Yin H, Wang J, Hu DM. Morphological and phylogenetic analyses reveal a new species of Anthracophyllum (Omphalotaceae, Agaricales) in Zhejiang Province, China. Arch Microbiol 2024; 206:63. [PMID: 38217700 DOI: 10.1007/s00203-023-03748-w] [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: 03/03/2023] [Revised: 11/15/2023] [Accepted: 11/15/2023] [Indexed: 01/15/2024]
Abstract
During the investigations of macrofungi resources in Zhejiang Province, China, an interesting wood rot fungus was collected. Based on morphological and molecular phylogenetic studies, it is described as a new species, Anthracophyllum sinense. A. sinense is characterized by its sessile, charcoal black and pleurotoid pileus, sparse lamellae occasionally branching, clavate basidia with long sterigmata [(3-)6-7(-8) μm], and non-heteromorphous cystidia. A. sinense establishes a separate lineage close to A. archeri and A. lateritium in the phylogenetic tree.
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Affiliation(s)
- Wen-Juan Yang
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
| | - Miao Xu
- Jiangxi Engineering Research Center for Comprehensive Development of Forest Fungal Resources, Jiangxi Environmental Engineering Vocational College, Ganzhou, China
| | - Jing Zhang
- General Station for Forestry Technology Extension of Taizhou City, Zhejiang, Taizhou, 318000, Zhejiang, China
| | - Fan Zhou
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
| | - Zhi-Fang Le
- Ministry of Ecology and Environment of the People's Republic of China, Nanjing Institute of Environmental Sciences, Nanjing, 210042, China
| | - Wen-Jun Tong
- Ministry of Ecology and Environment of the People's Republic of China, Nanjing Institute of Environmental Sciences, Nanjing, 210042, China
| | - Hai-Yan Song
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China.
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, (Jiangxi Agricultural University), Ministry of Education of the P.R. China, 1101 Zhimin Road, Nanchang, 330045, China.
| | - Zhuo-Han Jin
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
| | - Qiu-Ge Cheng
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
| | - Jian-Ping Zhou
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
| | - Yang Gao
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
| | - Zhi-Jun Zhai
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
| | - Hai-Jing Hu
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
| | - Ming-Hui Chen
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
| | - Hua Yin
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
| | - Jiang Wang
- School of Life Sciences, Taizhou University, Taizhou, 318000, China
| | - Dian-Ming Hu
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China.
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China.
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China.
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Baranowska M, Behnke-Borowczyk J, Barzdajn W, Szmyt J, Korzeniewicz R, Łukowski A, Memišević-Hodžić M, Kartawik N, Kowalkowski W. Effects of nursery production methods on fungal community diversity within soil and roots of Abies alba Mill. Sci Rep 2023; 13:21284. [PMID: 38042872 PMCID: PMC10693611 DOI: 10.1038/s41598-023-48047-y] [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: 05/19/2023] [Accepted: 11/21/2023] [Indexed: 12/04/2023] Open
Abstract
The aim of this study was to elucidate how different nursery production methods influence the composition of and relationship between soil and root community levels of Abies alba. In the Międzylesie Forest District, we quantified the responses of samples of both community-level fine roots and surrounding soil to environmental changes evoked by various seedling production methods. Fungi levels were identified based on their ITS 1 region and 5.8 S rDNA component. Analysis was conducted using Illumina SBS technology, and the obtained sequences were compared with reference samples deposited in the UNITE. Chemical analysis of the soil was also performed. Different nursery production methods resulted in a strong decoupling in the responses of fungal community levels between soil and roots. Changes in growth conditions imposed by production methods were significant in determining species composition. We found differences in fungal communities among functional groups of samples. In the soil, the dominant species of mycorrhizal fungi were Tylospora asterophora, Amanita rubescens, and Russula ionochlora. Mycorrhizal fungi in roots included Tuber anniae, Thelephoraceae sp., and Acephala applanata. Specific soil substrate conditions significantly influenced fungal community composition, leading to an increase in abundance of mycorrhizal fungi, specifically T. anniae.
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Affiliation(s)
- Marlena Baranowska
- Faculty of Forestry and Wood Technology, Poznań University of Life Sciences, Wojska Polskiego 71a, 60-625, Poznan, Poland
| | - Jolanta Behnke-Borowczyk
- Faculty of Forestry and Wood Technology, Poznań University of Life Sciences, Wojska Polskiego 71a, 60-625, Poznan, Poland
| | - Władysław Barzdajn
- Faculty of Forestry and Wood Technology, Poznań University of Life Sciences, Wojska Polskiego 71a, 60-625, Poznan, Poland
| | - Janusz Szmyt
- Faculty of Forestry and Wood Technology, Poznań University of Life Sciences, Wojska Polskiego 71a, 60-625, Poznan, Poland
| | - Robert Korzeniewicz
- Faculty of Forestry and Wood Technology, Poznań University of Life Sciences, Wojska Polskiego 71a, 60-625, Poznan, Poland
| | - Adrian Łukowski
- Faculty of Forestry and Wood Technology, Poznań University of Life Sciences, Wojska Polskiego 71a, 60-625, Poznan, Poland
| | - Mirzeta Memišević-Hodžić
- Faculty of Forestry, University of Sarajevo, Zagrebačka 20, 71000, Sarajevo, Bosnia and Herzegovina
| | - Natalia Kartawik
- Faculty of Forestry and Wood Technology, Poznań University of Life Sciences, Wojska Polskiego 71a, 60-625, Poznan, Poland
| | - Wojciech Kowalkowski
- Faculty of Forestry and Wood Technology, Poznań University of Life Sciences, Wojska Polskiego 71a, 60-625, Poznan, Poland.
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Bradshaw MJ, Aime MC, Rokas A, Maust A, Moparthi S, Jellings K, Pane AM, Hendricks D, Pandey B, Li Y, Pfister DH. Extensive intragenomic variation in the internal transcribed spacer region of fungi. iScience 2023; 26:107317. [PMID: 37529098 PMCID: PMC10387565 DOI: 10.1016/j.isci.2023.107317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/08/2023] [Accepted: 07/04/2023] [Indexed: 08/03/2023] Open
Abstract
Fungi are among the most biodiverse organisms in the world. Accurate species identification is imperative for studies on fungal ecology and evolution. The internal transcribed spacer (ITS) rDNA region has been widely accepted as the universal barcode for fungi. However, several recent studies have uncovered intragenomic sequence variation within the ITS in multiple fungal species. Here, we mined the genome of 2414 fungal species to determine the prevalence of intragenomic variation and found that the genomes of 641 species, about one-quarter of the 2414 species examined, contained multiple ITS copies. Of those 641 species, 419 (∼65%) contained variation among copies revealing that intragenomic variation is common in fungi. We proceeded to show how these copies could result in the erroneous description of hundreds of fungal species and skew studies evaluating environmental DNA (eDNA) especially when making diversity estimates. Additionally, many genomes were found to be contaminated, especially those of unculturable fungi.
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Affiliation(s)
- Michael J. Bradshaw
- Harvard University Herbaria and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - M. Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Antonis Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Autumn Maust
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA 98195, USA
| | - Swarnalatha Moparthi
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695-7613, USA
| | - Keila Jellings
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Alexander M. Pane
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA 98195, USA
| | - Dylan Hendricks
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA 98195, USA
| | - Binod Pandey
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102, USA
| | - Yuanning Li
- Institute of Marine Science and Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Donald H. Pfister
- Harvard University Herbaria and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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Zhou F, Gao Y, Song HY, Hu HJ, Yang WJ, Zhang W, Liao LY, Fang Y, Cheng L, Hu DM. Phylogenetic and Morphological Evidence Reveal Five New Species of Boletes from Southern China. J Fungi (Basel) 2023; 9:814. [PMID: 37623585 PMCID: PMC10455384 DOI: 10.3390/jof9080814] [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: 06/09/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023] Open
Abstract
Fungi of the order Boletales are extremely important in both ecology and economy, since most of them are ectomycorrhizal fungi, which play vital roles in maintaining forest ecosystems, water and soil protection, vegetation restoration and so on. Although previous studies have shown that this order has a very high species diversity in China, there are few reports on the species diversity of boletes in Jiangxi Province, China. Based on morphological (macroscopic and microscopic morphological characteristics) and phylogenetic analyses (ITS, LSU, and TEF1-α sequences), in this study, the wild boletes in Jiangxi Province were investigated, and five new species are described: Austroboletus albus, Xanthoconium violaceipes, Xanthoconium violaceofuscum, Xerocomus rutilans and Xerocomus subsplendidus. Descriptions and hand drawings of the new species are presented.
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Affiliation(s)
- Fan Zhou
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, China; (F.Z.); (Y.G.); (H.-J.H.)
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yang Gao
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, China; (F.Z.); (Y.G.); (H.-J.H.)
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Hai-Yan Song
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, China; (F.Z.); (Y.G.); (H.-J.H.)
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Ministry of Education, Nanchang 330045, China
| | - Hai-Jing Hu
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, China; (F.Z.); (Y.G.); (H.-J.H.)
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Wen-Juan Yang
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, China; (F.Z.); (Y.G.); (H.-J.H.)
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Wei Zhang
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, China; (F.Z.); (Y.G.); (H.-J.H.)
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Li-Yu Liao
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, China; (F.Z.); (Y.G.); (H.-J.H.)
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yi Fang
- Jiangxi Wuyishan National Nature Reserve Administration Bureau, Wuyishan National Nature Reserve, Shangrao 334500, China (L.C.)
| | - Lin Cheng
- Jiangxi Wuyishan National Nature Reserve Administration Bureau, Wuyishan National Nature Reserve, Shangrao 334500, China (L.C.)
| | - Dian-Ming Hu
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, China; (F.Z.); (Y.G.); (H.-J.H.)
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
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Islam SMN, Chowdhury MZH, Mim MF, Momtaz MB, Islam T. Biocontrol potential of native isolates of Beauveria bassiana against cotton leafworm Spodoptera litura (Fabricius). Sci Rep 2023; 13:8331. [PMID: 37221248 DOI: 10.1038/s41598-023-35415-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 05/17/2023] [Indexed: 05/25/2023] Open
Abstract
The entomopathogenic fungus (EPF), Beauveria bassiana, is reported as the most potent biological control agent against a wide range of insect families. This study aimed to isolate and characterize the native B. bassiana from various soil habitats in Bangladesh and to evaluate the bio-efficacy of these isolates against an important vegetable insect pest, Spodoptera litura. Seven isolates from Bangladeshi soils were characterized as B. bassiana using genomic analysis. Among the isolates, TGS2.3 showed the highest mortality rate (82%) against the 2nd instar larvae of S. litura at 7 days after treatment (DAT). This isolate was further bioassayed against different stages of S. litura and found that TGS2.3 induced 81, 57, 94, 84, 75, 65, and 57% overall mortality at egg, neonatal 1st, 2nd, 3rd, 4th, and 5th instar larvae, respectively, over 7 DAT. Interestingly, treatment with B. bassiana isolate TGS2.3 resulted in pupal and adult deformities as well as decreased adult emergence of S. litura. Taken together, our results suggest that a native isolate of B. bassiana TGS2.3 is a potential biocontrol agent against the destructive insect pest S. litura. However, further studies are needed to evaluate the bio-efficacy of this promising native isolate in planta and field conditions.
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Affiliation(s)
- Shah Mohammad Naimul Islam
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh.
| | - Md Zahid Hasan Chowdhury
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Mahjabin Ferdaous Mim
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Milia Bente Momtaz
- Cotton Research Training and Seed Multiplication Farm, Gazipur, Bangladesh
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh.
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Cittadino GM, Andrews J, Purewal H, Estanislao Acuña Avila P, Arnone JT. Functional Clustering of Metabolically Related Genes Is Conserved across Dikarya. J Fungi (Basel) 2023; 9:jof9050523. [PMID: 37233234 DOI: 10.3390/jof9050523] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/08/2023] [Accepted: 04/27/2023] [Indexed: 05/27/2023] Open
Abstract
Transcriptional regulation is vital for organismal survival, with many layers and mechanisms collaborating to balance gene expression. One layer of this regulation is genome organization, specifically the clustering of functionally related, co-expressed genes along the chromosomes. Spatial organization allows for position effects to stabilize RNA expression and balance transcription, which can be advantageous for a number of reasons, including reductions in stochastic influences between the gene products. The organization of co-regulated gene families into functional clusters occurs extensively in Ascomycota fungi. However, this is less characterized within the related Basidiomycota fungi despite the many uses and applications for the species within this clade. This review will provide insight into the prevalence, purpose, and significance of the clustering of functionally related genes across Dikarya, including foundational studies from Ascomycetes and the current state of our understanding throughout representative Basidiomycete species.
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Affiliation(s)
- Gina M Cittadino
- Department of Biological and Environmental Sciences, Le Moyne College, Syracuse, NY 13214, USA
| | - Johnathan Andrews
- Department of Biological and Environmental Sciences, Le Moyne College, Syracuse, NY 13214, USA
| | - Harpreet Purewal
- Department of Biological and Environmental Sciences, Le Moyne College, Syracuse, NY 13214, USA
| | | | - James T Arnone
- Department of Biological and Environmental Sciences, Le Moyne College, Syracuse, NY 13214, USA
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Szulc J, Okrasa M, Ryngajłło M, Pielech-Przybylska K, Gutarowska B. Markers of Chemical and Microbiological Contamination of the Air in the Sport Centers. Molecules 2023; 28:molecules28083560. [PMID: 37110794 PMCID: PMC10144153 DOI: 10.3390/molecules28083560] [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: 03/27/2023] [Revised: 04/11/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
This study aimed to assess the markers of chemical and microbiological contamination of the air at sport centers (e.g., the fitness center in Poland) including the determination of particulate matter, CO2, formaldehyde (DustTrak™ DRX Aerosol Monitor; Multi-functional Air Quality Detector), volatile organic compound (VOC) concentration (headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry), the number of microorganisms in the air (culture methods), and microbial biodiversity (high-throughput sequencing on the Illumina platform). Additionally the number of microorganisms and the presence of SARS-CoV-2 (PCR) on the surfaces was determined. Total particle concentration varied between 0.0445 mg m-3 and 0.0841 mg m-3 with the dominance (99.65-99.99%) of the PM2.5 fraction. The CO2 concentration ranged from 800 ppm to 2198 ppm, while the formaldehyde concentration was from 0.005 mg/m3 to 0.049 mg m-3. A total of 84 VOCs were identified in the air collected from the gym. Phenol, D-limonene, toluene, and 2-ethyl-1-hexanol dominated in the air at the tested facilities. The average daily number of bacteria was 7.17 × 102 CFU m-3-1.68 × 103 CFU m-3, while the number of fungi was 3.03 × 103 CFU m-3-7.34 × 103 CFU m-3. In total, 422 genera of bacteria and 408 genera of fungi representing 21 and 11 phyla, respectively, were detected in the gym. The most abundant bacteria and fungi (>1%) that belonged to the second and third groups of health hazards were: Escherichia-Shigella, Corynebacterium, Bacillus, Staphylococcus, Cladosporium, Aspergillus, and Penicillium. In addition, other species that may be allergenic (Epicoccum) or infectious (Acinetobacter, Sphingomonas, Sporobolomyces) were present in the air. Moreover, the SARS-CoV-2 virus was detected on surfaces in the gym. The monitoring proposal for the assessment of the air quality at a sport center includes the following markers: total particle concentration with the PM2.5 fraction, CO2 concentration, VOCs (phenol, toluene, and 2-ethyl-1-hexanol), and the number of bacteria and fungi.
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Affiliation(s)
- Justyna Szulc
- Department of Environmental Biotechnology, Lodz University of Technology, 90-530 Łódź, Poland
| | - Małgorzata Okrasa
- Department of Personal Protective Equipment, Central Institute for Labour Protection-National Research Institute, 90-133 Łódź, Poland
| | - Małgorzata Ryngajłło
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, 90-573 Łódź, Poland
| | | | - Beata Gutarowska
- Department of Environmental Biotechnology, Lodz University of Technology, 90-530 Łódź, Poland
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8
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In silico environmental sampling of emerging fungal pathogens via big data analysis. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2022.101212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Akber MA, Mubeen M, Sohail MA, Khan SW, Solanki MK, Khalid R, Abbas A, Divvela PK, Zhou L. Global distribution, traditional and modern detection, diagnostic, and management approaches of Rhizoctonia solani associated with legume crops. Front Microbiol 2023; 13:1091288. [PMID: 36815202 PMCID: PMC9939780 DOI: 10.3389/fmicb.2022.1091288] [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: 11/06/2022] [Accepted: 12/14/2022] [Indexed: 02/08/2023] Open
Abstract
Sustainable development relies heavily on a food system that is both safe and secure. Several approaches may lead to sustainability and food safety. An increase in the cultivation of legume crops is one of the approaches for enhancing agricultural viability and ensuring adequate food supply. Legumes may increase daily intake of fiber, folate, and protein as substitutes for meat and dairy. They are also crucial in various intercropping systems worldwide. However, legume production has been hampered by Rhizoctonia solani due to its destructive lifestyle. R. solani causes blights, damping off, and rotting diseases in legume crops. Our knowledge of the global distribution of R. solani associated with legume crops (alfalfa, soybean, chickpea, pea, lentil, common bean, and peanut), detection, diagnosis, and management of legume crops diseases caused by R. solani is limited. Traditional approaches rely on the incubation of R. solani, visual examination of symptoms on host legume crops, and microscopy identification. However, these approaches are time-consuming, require technical expertise, fail to detect a minimal amount of inoculum, and are unreliable. Biochemical and molecular-based approaches have been used with great success recently because of their excellent sensitivity and specificity. Along with conventional PCR, nested PCR, multiplex PCR, real-time PCR, magnetic-capture hybridization PCR, and loop-mediated isothermal amplification have been widely used to detect and diagnose R. solani. In the future, Next-generation sequencing will likely be used to a greater extent to detect R. solani. This review outlines global distribution, survival, infection and disease cycle, traditional, biochemical, molecular, and next-generation sequencing detection and diagnostic approaches, and an overview of the resistant resources and other management strategies to cope with R. solani.
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Affiliation(s)
- Muhammad Abdullah Akber
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China,State Key Laboratory of Grassland Agroecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Mustansar Mubeen
- Department of Plant Pathology, College of Agriculture, University of Sargodha, Sargodha, Pakistan
| | - Muhammad Aamir Sohail
- Department of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Sher Wali Khan
- Department of Plant Science, Karakoram International University, Gilgit, Pakistan
| | - Manoj Kumar Solanki
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, the University of Silesia in Katowice, Katowice, Poland
| | - Rida Khalid
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Aqleem Abbas
- Department of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China,Department of Plant Science, Karakoram International University, Gilgit, Pakistan,*Correspondence: Aqleem Abbas, ✉
| | | | - Lei Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China,Lei Zhou, ✉
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10
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Kumar V, Kumar H, Vishal V, Lal S. Studies on the morphology, phylogeny, and bioremediation potential of Penicillium citrinum and Paecilomyces variotii (Eurotiales) from oil-contaminated areas. Arch Microbiol 2023; 205:50. [PMID: 36598589 DOI: 10.1007/s00203-022-03383-x] [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: 08/03/2022] [Revised: 09/10/2022] [Accepted: 12/19/2022] [Indexed: 01/05/2023]
Abstract
Crude oil pollution is one of the most arduous issues to address, as it is hazardous to both public health and the environment. The discovery of novel biosurfactants-producing fungi and bacteria is in high demand due to their excellent properties and wide range of applications. The aim of this research is to isolate a powerful biosurfactant-producing fungus from the crude oil site near Barauni oil refinery in Bihar, India. Standard protocols were used to collect samples from the site. An integrative taxonomic approach was used, which included morphological, molecular, and phylogenetic analysis. The use of plating samples on Bushnell-Hass (BH) media aided in the isolation of a fungal strain from an enrichment culture. Two fungal strains isolated from contaminated soils, Penicillium citrinum and Paecilomyces variotti, showed potent oil degrading activity in a single culture. For preliminary biosurfactants screening, drop collapse assays, oil spreading, and emulsification activity tests were used. The results showed that the cultures performed well in the screening test and were further evaluated for degradation capacity. Different treatment periods (0, 3, 6, 9, 12, and 15 days) were used to observe degradation in single cultures. A steady drop in pH, an alteration in optical density and an increase in carbon dioxide release showed the ability of fungal strain to degrade the crude oil in a single culture. Fungi mycelia provide a larger surface area for absorption and degradation of the pollutants in contaminated environment. They produce extracellular enzymes to degrade the oil, and at the same time absorb and utilise carbon, allowing them to remove toxic substances from the oil. Thus, they could be candidates for bioremediation of a hydrocarbon-contaminated site.
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Affiliation(s)
- Vikas Kumar
- Department of Microbiology, Dr. Shyama Prasad Mukherjee University, Ranchi, Jharkhand, 834008, India
| | - Harsh Kumar
- Department of Microbiology, Dr. Shyama Prasad Mukherjee University, Ranchi, Jharkhand, 834008, India
| | - Vineet Vishal
- Department of Botany, Dr. Shyama Prasad Mukherjee University, Ranchi, Jharkhand, 834008, India.,Department of Botany, Bangabasi Evening College, Kolkata, West Bengal, 700009, India
| | - Shalini Lal
- Department of Microbiology, Dr. Shyama Prasad Mukherjee University, Ranchi, Jharkhand, 834008, India. .,Department of Botany, Dr. Shyama Prasad Mukherjee University, Ranchi, Jharkhand, 834008, India.
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11
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Retiboletus atrofuscus (Boletaceae, Boletales), a new species from China. Arch Microbiol 2022; 204:381. [PMID: 35687177 DOI: 10.1007/s00203-022-03006-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 05/09/2022] [Accepted: 05/19/2022] [Indexed: 11/02/2022]
Abstract
Based on morphological and phylogenetic analyses, an ectomycorrhizal fungus collected from Jiangxi, China, is described as a new species. R. atrofuscus is morphological characterized by a dark gray to black pileus, white to pale yellowish white hymenophore, a grayish brown to pale yellow context, which turning orange-yellow to rusty yellow when injured, a prominently and coarsely white to pale yellow to black reticulation on upper 3/4 or entire stipe, grayish yellow to pale yellow to yellowish brown basidiospores in KOH with measuring (7-)7.5-13(-13.5) × (3-)3.5-5(-5.5) μm. Phylogenetic analysis results showed that R. atrofuscus formed an independent lineage within Retiboletus. Descriptions and hand drawings of the new species and comparisons with similar species are presented.
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12
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Sridhar P, Venkateshbabu G, Hemalakshmi D, Kirthika VM, Palani P. New disease and first report of marasmioid fungus, Marasmius palmivorus (Sharples), causing white root rot in Arachis hypogaea L. Lett Appl Microbiol 2022; 75:368-377. [PMID: 35553447 DOI: 10.1111/lam.13736] [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: 07/11/2021] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 11/26/2022]
Abstract
Groundnut (Arachis hypogaea L.) plants showing distinct symptoms of necrosis of leaves and severe rotting of roots were observed in the agricultural field at Arakkonam, Tamil Nadu, India. The rhizomorphs of the phytopathogenic fungus were obtained from the rotted roots of the diseased plants, cultured in the laboratory and based on the morphological characteristics and nucleotide sequencing analysis of ITS and nLSU region, the phytopathogen was identified as Marasmius palmivorus. The isolated fungus produced distinct fruiting bodies (basidiocarps) when grown under the laboratory conditions. The fungus grew as cottony white colony on Potato Dextrose Agar (PDA) medium and found to contain septate and clamp connections when examined under light microscope. The pathogenicity of the isolated fungus was assessed by inoculating it on healthy groundnut plant under the glasshouse condition, which resulted in the establishment of typical disease symptom and the pathogenicity of the fungus was confirmed. The fungal pathogen re-isolated from the artificially inoculated plants was used for molecular characterization and confirmed that the organism is Marasmius palmivorus. To the best of our knowledge, this is the first report on the occurrence of Marasmius palmivorus, causing white root rot disease in Arachis hypogaea L.
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Affiliation(s)
- Pichai Sridhar
- Centre for Advanced Studies in Botany, University of Madras, Guindy Campus, Chennai, -600025, India
| | - Gopal Venkateshbabu
- Centre for Advanced Studies in Botany, University of Madras, Guindy Campus, Chennai, -600025, India
| | - D Hemalakshmi
- Centre for Advanced Studies in Botany, University of Madras, Guindy Campus, Chennai, -600025, India
| | - V M Kirthika
- Centre for Advanced Studies in Botany, University of Madras, Guindy Campus, Chennai, -600025, India
| | - Perumal Palani
- Centre for Advanced Studies in Botany, University of Madras, Guindy Campus, Chennai, -600025, India
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13
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Irinyi L, Rope M, Meyer W. In depth search of the Sequence Read Archive database reveals global distribution of the emerging pathogenic fungus Scedosporium aurantiacum. Med Mycol 2022; 60:6542442. [PMID: 35244718 PMCID: PMC8994208 DOI: 10.1093/mmy/myac019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/30/2022] [Accepted: 03/01/2022] [Indexed: 11/24/2022] Open
Abstract
Scedosporium species are emerging opportunistic fungal pathogens causing various infections mainly in immunocompromised patients, but also in immunocompetent individuals, following traumatic injuries. Clinical manifestations range from local infections, such as subcutaneous mycetoma or bone and joint infections, to pulmonary colonization and severe disseminated diseases. They are commonly found in soil and other environmental sources. To date S. aurantiacum has been reported only from a handful of countries. To identify the worldwide distribution of this species we screened publicly available sequencing data from fungal metabarcoding studies in the Sequence Read Archive (SRA) of The National Centre for Biotechnology Information (NCBI) by multiple BLAST searches. S. aurantiacum was found in 26 countries and two islands, throughout every climatic region. This distribution is like that of other Scedosporium species. Several new environmental sources of S. aurantiacum including human and bovine milk, chicken and canine gut, freshwater, and feces of the giant white-tailed rat (Uromys caudimaculatus) were identified. This study demonstrated that raw sequence data stored in the SRA database can be repurposed using a big data analysis approach to answer biological questions of interest.
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Affiliation(s)
- Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Westmead Institute for Medical Research, Westmead, NSW Australia
| | - Michael Rope
- Division of Biomedical Science and Biochemistry, Australian National University, Canberra, ACT, Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Westmead Institute for Medical Research, Westmead, NSW Australia.,Westmead Hospital (Research and Education Network), Westmead, NSW, Australia
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14
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Biosynthetic potential of the endophytic fungus Helotiales sp. BL73 revealed via compound identification and genome mining. Appl Environ Microbiol 2022; 88:e0251021. [PMID: 35108081 DOI: 10.1128/aem.02510-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Endophytic fungi have been recognized as prolific producers of chemically diverse secondary metabolites. In this work, we describe a new representative of the order Helotiales isolated from the medicinal plant Bergenia pacumbis. Several bioactive secondary metabolites were produced by this Helotiales sp. BL 73 isolate grown on rice medium, including cochlioquinones and isofusidienols. Sequencing and analysis of the approx. 59 Mb genome revealed at least 77 secondary metabolite biosynthesis gene clusters, several of which could be associated with detected compounds or linked to previously reported molecules. Four terpene synthase genes identified in the BL73 genome were codon-optimized and expressed, together with farnesyl-, geranyl- and geranylgeranyl-pyrophosphate synthases, in Streptomyces spp. Analysis of recombinant strains revealed production of linalool and its oxidized form, terpenoids typically associated with plants, as well as a yet unidentified terpenoid. This study demonstrates the importance of a complex approach to the investigation of the biosynthetic potential of endophytic fungi using both conventional methods and genome mining. Importance Endophytic fungi represent as yet underexplored source of secondary metabolites, some of which may have industrial and medical applications. We isolated a slow-growing fungus belonging to the order Helotiales from the traditional medicinal plant Bergenia pacumbis and characterized its potential to biosynthesize secondary metabolites. We used both cultivation of the isolate with subsequent analysis of compounds produced, bioinformatics-based mining of the genome, and heterologous expression of several terpene synthase genes. Our study revealed enormous potential of this Helotiales isolate to produce structurally diverse natural products, including polyketides, non-ribosomally synthesized peptides, terpenoids and RiPPs. Identification of meroterpenoids and xanthones, along with establishing a link between these molecules and their putative biosynthetic genes sets a stage for investigation of the respective biosynthetic pathways. Heterologous production of terpenoids suggests that this approach can be used for the discovery of new compounds belonging to this chemical class using Streptomyces bacteria as hosts.
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15
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Kwaśna H, Szewczyk W, Baranowska M, Gallas E, Wiśniewska M, Behnke-Borowczyk J. Mycobiota Associated with the Vascular Wilt of Poplar. PLANTS 2021; 10:plants10050892. [PMID: 33925219 PMCID: PMC8146881 DOI: 10.3390/plants10050892] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/20/2021] [Accepted: 04/20/2021] [Indexed: 01/29/2023]
Abstract
In 2017, a 560-ha area of hybrid poplar plantation in northern Poland showed symptoms of tree decline. The leaves appeared smaller, yellow-brown, and were shed prematurely. Twigs and smaller branches died without distinct cankers. Trunks decayed from the base. The phloem and xylem showed brown necrosis. Ten percent of the trees died 1–2 months after the first appearance of the symptoms. None of these symptoms were typical for known poplar diseases. The trees’ mycobiota were analysed using Illumina sequencing. A total of 69 467 and 70 218 operational taxonomic units (OTUs) were obtained from the soil and wood. Blastocladiomycota and Chytridiomycota occurred only in the soil, with very low frequencies (0.005% and 0.008%). Two taxa of Glomeromycota, with frequencies of 0.001%, occurred in the wood. In the soil and wood, the frequencies of Zygomycota were 3.631% and 0.006%, the frequencies of Ascomycota were 45.299% and 68.697%, and the frequencies of Basidiomycota were 4.119% and 2.076%. At least 400 taxa of fungi were present. The identifiable Zygomycota, Ascomycota, and Basidiomycota were represented by at least 18, 263 and 81 taxa, respectively. Many fungi were common to the soil and wood, but 160 taxa occurred only in soil and 73 occurred only in wood. The root pathogens included species of Oomycota. The vascular and parenchymal pathogens included species of Ascomycota and of Basidiomycota. The initial endophytic character of the fungi is emphasized. Soil, and possibly planting material, may be the sources of the pathogen inoculum, and climate warming is likely to be a predisposing factor. A water deficit may increase the trees’ susceptibility. The epidemiology of poplar vascular wilt reminds grapevine trunk diseases (GTD), including esca, black foot disease and Petri disease.
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Affiliation(s)
- Hanna Kwaśna
- Department of Forest Pathology, Poznań University of Life Sciences, Wojska Polskiego 71c, 60-625 Poznań, Poland; (W.S.); (E.G.); (M.W.); (J.B.-B.)
- Correspondence:
| | - Wojciech Szewczyk
- Department of Forest Pathology, Poznań University of Life Sciences, Wojska Polskiego 71c, 60-625 Poznań, Poland; (W.S.); (E.G.); (M.W.); (J.B.-B.)
| | - Marlena Baranowska
- Department of Silviculture, Poznań University of Life Sciences, Wojska Polskiego 71a, 60-625 Poznań, Poland;
| | - Ewa Gallas
- Department of Forest Pathology, Poznań University of Life Sciences, Wojska Polskiego 71c, 60-625 Poznań, Poland; (W.S.); (E.G.); (M.W.); (J.B.-B.)
| | - Milena Wiśniewska
- Department of Forest Pathology, Poznań University of Life Sciences, Wojska Polskiego 71c, 60-625 Poznań, Poland; (W.S.); (E.G.); (M.W.); (J.B.-B.)
| | - Jolanta Behnke-Borowczyk
- Department of Forest Pathology, Poznań University of Life Sciences, Wojska Polskiego 71c, 60-625 Poznań, Poland; (W.S.); (E.G.); (M.W.); (J.B.-B.)
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16
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Tartanus M, Furmanczyk EM, Canfora L, Pinzari F, Tkaczuk C, Majchrowska-Safaryan A, Malusá E. Biocontrol of Melolontha spp. Grubs in Organic Strawberry Plantations by Entomopathogenic Fungi as Affected by Environmental and Metabolic Factors and the Interaction with Soil Microbial Biodiversity. INSECTS 2021; 12:127. [PMID: 33540558 PMCID: PMC7912822 DOI: 10.3390/insects12020127] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 11/16/2022]
Abstract
The efficacy of two strains of two Beauveria species (B. bassiana and B. brongniartii), individually or as co-inoculants, to control Melolontha sp. grubs was assessed in two organic strawberry plantations in relation to the environmental conditions, their abundance after soil inoculation, and their in vitro chitinolytic activity, thereby also verifying their impact on soil microbial communities. A reduction of the grubs' damage to strawberry plants was observed when compared to the untreated control in one plantation, irrespective of the strain used and whether they were applied as single or as co-inoculum. The metabolic pattern expressed by the two fungi in vitro was different: B. bassiana showed a higher metabolic versatility in the use of different carbon sources than B. brongniartii, whose profile was partly overlapped in the co-inoculum. Similar differences in the chitinolytic activity of each of the fungi and the co-inoculum were also pointed out. A higher abundance of B. bassiana in the soils receiving this species in comparison to those receiving B. brongniartii, together with its in vitro metabolic activity, could account for the observed diverse efficacy of pest damage control of the two species. However, environmental and climatic factors also affected the overall efficacy of the two bioinocula. According to the monitoring of the two species in soil, B. bassiana could be considered as a common native species in the studied locations in contrast to B. brongniartii, which seemed to be a non-endemic species. Nevertheless, the inoculation with both species or the co-inoculum did not consistently affect the soil microbial (fungi and bacteria) biodiversity, as expressed by the operational taxonomic unit (OTU) number and Shannon-Wiener diversity index based on terminal restriction fragment length polymorphism (TRFLP) data. A small transient increase of the share of the inoculated species to the total fungal community was noted by the analysis of genes copy numbers only for B. brongniartii at the end of the third growing season.
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Affiliation(s)
- Malgorzata Tartanus
- Research Institute of Horticulture-NRI, Department of Plant Protection against Pests, 96-100 Skierniewice, Poland; (M.T.); (E.M.F.)
- Centre for Agriculture and Environment, Council for Agricultural Research and Economics, 00-184 Rome, Italy; (L.C.); (F.P.)
| | - Ewa M. Furmanczyk
- Research Institute of Horticulture-NRI, Department of Plant Protection against Pests, 96-100 Skierniewice, Poland; (M.T.); (E.M.F.)
| | - Loredana Canfora
- Centre for Agriculture and Environment, Council for Agricultural Research and Economics, 00-184 Rome, Italy; (L.C.); (F.P.)
| | - Flavia Pinzari
- Centre for Agriculture and Environment, Council for Agricultural Research and Economics, 00-184 Rome, Italy; (L.C.); (F.P.)
- Institute for Biological Systems, Council of National Research of Italy (CNR), 00-015 Monterotondo, Italy
| | - Cezary Tkaczuk
- Institute of Agriculture and Horticulture, Siedlce University of Natural Sciences and Humanities, 08-110 Siedlce, Poland; (C.T.); (A.M.-S.)
| | - Anna Majchrowska-Safaryan
- Institute of Agriculture and Horticulture, Siedlce University of Natural Sciences and Humanities, 08-110 Siedlce, Poland; (C.T.); (A.M.-S.)
| | - Eligio Malusá
- Research Institute of Horticulture-NRI, Department of Plant Protection against Pests, 96-100 Skierniewice, Poland; (M.T.); (E.M.F.)
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17
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Korzeniewicz R, Baranowska M, Kwaśna H, Niedbała G, Behnke-Borowczyk J. Communities of Fungi in Black Cherry Stumps and Effects of Herbicide. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1126. [PMID: 32878134 PMCID: PMC7570310 DOI: 10.3390/plants9091126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/18/2020] [Accepted: 08/29/2020] [Indexed: 12/11/2022]
Abstract
So far, there have been no studies on fungal communities in Prunus serotina (black cherry) wood. Our objectives were to characterize fungal communities from P. serotina wood and to evaluate effects of glyphosate (Glifocyd 360 SL) used on P. serotina stumps on abundance, species richness and diversity of those communities. In August 2016, in the Podanin Forest District, stumps of black cherry trees left after felling were treated with the herbicide. Control stumps were treated with water. Wood discs were cut from the surface of the stumps in May and July-August 2017. Eight treatment combinations (2 herbicide treatments × 2 disc sizes × 2 sample times) were tested. Sub-samples were pooled and ground in an acryogenic mill. Environmental DNA was extracted with a Plant Genomic DNA Purification Kit. The ITS1, 5.8S rDNA region was used to identify fungal species, using primers ITS1FI2 5'-GAACCWGCGGARGGATCA-3' and 5.8S 5'-CGCTGCGTT CTTCATCG-3'. The amplicons were sequenced using the Illumina system. The results were subjected to bioinformatic analysis. Sequences were compared with reference sequences from the NCBI database using the BLASTn 2.8.0 algorithm. Abundance of fungi was defined as the number of Operational Taxonomic Units (OTUs), and diversity as the number of species in a sample. Differences between the number of OTUs and taxa were analyzed using the chi-squared test (χ2). Diversity in microbial communities was compared using diversity indices. A total of 54,644 OTUs were obtained. Culturable fungi produced 49,808 OTUs (91.15%), fungi not known from culture had 2571 OTUs (4.70%), non-fungal organisms had 1333 (2.44%) and organisms with no reference sequence in NCBI, 934 OTUs (1.71%). The total number of taxa ranged from 120 to 319. Fungi in stump wood were significantly more abundant in July-August than in May, in stumps >5 cm diameter than in stumps <5 cm diameter, in glyphosate-treated than in untreated stumps when sampled in May, and in untreated than in glyphosate-treated stumps when sampled in July-August. Species richness was significantly greater in July-August than in May, and in stumps >5 cm diameter than in stumps <5 cm diameter, either treated or untreated, depending on size. Herbicides can therefore affect the abundance and diversity of fungal communities in deciduous tree wood. The greater frequency of Ascomycota in herbicide-treated than in untreated stumps indicates their greater tolerance of glyphosate.
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Affiliation(s)
- Robert Korzeniewicz
- Department of Silviculture, Poznań University of Life Sciences, Wojska Polskiego 71a, 60-625 Poznań, Poland; (R.K.); (M.B.)
| | - Marlena Baranowska
- Department of Silviculture, Poznań University of Life Sciences, Wojska Polskiego 71a, 60-625 Poznań, Poland; (R.K.); (M.B.)
| | - Hanna Kwaśna
- Department of Forest Pathology, Poznań University of Life Sciences, Wojska Polskiego 71c, 60-625 Poznań, Poland; (H.K.); (J.B.-B.)
| | - Gniewko Niedbała
- Institute of Biosystems Engineering, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, Wojska Polskiego 50, 60-627 Poznań, Poland
| | - Jolanta Behnke-Borowczyk
- Department of Forest Pathology, Poznań University of Life Sciences, Wojska Polskiego 71c, 60-625 Poznań, Poland; (H.K.); (J.B.-B.)
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18
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Bshabshe AA, Joseph MRP, Hakami AMA, Azraqi TA, Humayed SA, Hamid ME. Basidiobolus haptosporus-like fungus as a causal agent of gastrointestinal basidiobolomycosis. Med Mycol 2020; 58:264-267. [PMID: 31111900 DOI: 10.1093/mmy/myz046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/03/2019] [Accepted: 04/14/2019] [Indexed: 11/14/2022] Open
Abstract
Basidiobolus species were isolated from colonic biopsy samples of patients with gastrointestinal basidiobolomycosis (GIB) in southern Saudi Arabia. Isolated fungi were initially identified using classical mycological tools and confirmed by sequence analysis of the large subunit ribosomal RNA gene. Phenotypic tests revealed zygomycete-like fungi which conform to those of Basidiobolus species. Five sequenced strains formed a monophyletic clade in the 28S ribosomal RNA gene phylogenetic tree. They shared 99.97% similarity with B. haptosporus and 99.97% with B. haptosporus var. minor, and relatively lower similarity with B. ranarum (99.925%). The study suggests a new and a serious causal agent of GIB related to Basidiobolus haptosporus. These isolates are not related to B. ranarum, which is commonly linked to this disease.
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Affiliation(s)
- Ali Al Bshabshe
- Department of Medicine, College of Medicine, King Khalid University, Abha, Kingdom of Saudi Arabia
| | - Martin R P Joseph
- Department of Microbiology, College of Medicine, King Khalid University, Abha, Kingdom of Saudi Arabia
| | - Ahmed M Al Hakami
- Department of Microbiology, College of Medicine, King Khalid University, Abha, Kingdom of Saudi Arabia
| | - Tariq Al Azraqi
- Department of Medicine, College of Medicine, King Khalid University, Abha, Kingdom of Saudi Arabia
| | - Sulieman Al Humayed
- Department of Medicine, College of Medicine, King Khalid University, Abha, Kingdom of Saudi Arabia
| | - Mohamed E Hamid
- Department of Microbiology, College of Medicine, King Khalid University, Abha, Kingdom of Saudi Arabia
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19
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Cullen M, Jacob ME, Cornish V, VanderSchel IQ, Cotter HVT, Cubeta MA, Carbone I, Gilger BC. Multi-locus DNA sequence analysis, antifungal agent susceptibility, and fungal keratitis outcome in horses from Southeastern United States. PLoS One 2019; 14:e0214214. [PMID: 30921394 PMCID: PMC6438541 DOI: 10.1371/journal.pone.0214214] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/09/2019] [Indexed: 11/21/2022] Open
Abstract
Morphological characterization and multi-locus DNA sequence analysis of fungal isolates obtained from 32 clinical cases of equine fungal keratitis (FK) was performed to identify species and determine associations with antifungal susceptibility, response to therapy and clinical outcome. Two species of Aspergillus (A. flavus and A. fumigatus) and three species of Fusarium (F. falciforme, F. keratoplasticum, and F. proliferatum) were the most common fungi isolated and identified from FK horses. Most (91%) equine FK Fusarium nested within the Fusarium solani species complex (FSSC) with nine genetically diverse strains/lineages, while 83% of equine FK Aspergillus nested within the A. flavus clade with three genetically diverse lineages. Fungal species and evolutionary lineage were not associated with clinical outcome. However, species of equine FK Fusarium were more likely (p = 0.045) to be associated with stromal keratitis. Species of Aspergillus were more susceptible to voriconazole and terbinafine than species of Fusarium, while species of Fusarium were more susceptible to thiabendazole than species of Aspergillus. At the species level, A. fumigatus and A. flavus were more susceptible to voriconazole and terbinafine than F. falciforme. Natamycin susceptibility was higher for F. falciforme and A. fumigatus compared to A. flavus. Furthermore, F. falciforme was more susceptible to thiabendazole than A. flavus and A. fumigatus. These observed associations of antifungal sensitivity to natamycin, terbinafine, and thiabendazole demonstrate the importance of fungal identification to the species rather than genus level. The results of this study suggest that treatment of equine FK with antifungal agents requires accurate fungal species identification.
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Affiliation(s)
- Megan Cullen
- Department of Clinical Sciences, NC State University, Raleigh, NC, United States of America
| | - Megan E. Jacob
- Department of Population Health and Pathobiology, NC State University, Raleigh, NC, United States of America
| | - Vicki Cornish
- Center for Integrated Fungal Research, College of Agriculture and Life Sciences, NC State University, Raleigh, NC, United States of America
| | - Ian Q. VanderSchel
- Center for Integrated Fungal Research, College of Agriculture and Life Sciences, NC State University, Raleigh, NC, United States of America
| | - Henry Van T. Cotter
- Center for Integrated Fungal Research, College of Agriculture and Life Sciences, NC State University, Raleigh, NC, United States of America
| | - Marc A. Cubeta
- Center for Integrated Fungal Research, College of Agriculture and Life Sciences, NC State University, Raleigh, NC, United States of America
| | - Ignazio Carbone
- Center for Integrated Fungal Research, College of Agriculture and Life Sciences, NC State University, Raleigh, NC, United States of America
| | - Brian C. Gilger
- Department of Clinical Sciences, NC State University, Raleigh, NC, United States of America
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20
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Meyer W, Irinyi L, Hoang MTV, Robert V, Garcia-Hermoso D, Desnos-Ollivier M, Yurayart C, Tsang CC, Lee CY, Woo PCY, Pchelin IM, Uhrlaß S, Nenoff P, Chindamporn A, Chen S, Hebert PDN, Sorrell TC. Database establishment for the secondary fungal DNA barcode translational elongation factor 1α ( TEF1α) 1. Genome 2018; 62:160-169. [PMID: 30465691 DOI: 10.1139/gen-2018-0083] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
With new or emerging fungal infections, human and animal fungal pathogens are a growing threat worldwide. Current diagnostic tools are slow, non-specific at the species and subspecies levels, and require specific morphological expertise to accurately identify pathogens from pure cultures. DNA barcodes are easily amplified, universal, short species-specific DNA sequences, which enable rapid identification by comparison with a well-curated reference sequence collection. The primary fungal DNA barcode, ITS region, was introduced in 2012 and is now routinely used in diagnostic laboratories. However, the ITS region only accurately identifies around 75% of all medically relevant fungal species, which has prompted the development of a secondary barcode to increase the resolution power and suitability of DNA barcoding for fungal disease diagnostics. The translational elongation factor 1α (TEF1α) was selected in 2015 as a secondary fungal DNA barcode, but it has not been implemented into practice, due to the absence of a reference database. Here, we have established a quality-controlled reference database for the secondary barcode that together with the ISHAM-ITS database, forms the ISHAM barcode database, available online at http://its.mycologylab.org/ . We encourage the mycology community for active contributions.
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Affiliation(s)
- Wieland Meyer
- a Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney School of Medicine, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Laszlo Irinyi
- a Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney School of Medicine, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Minh Thuy Vi Hoang
- a Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney School of Medicine, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Vincent Robert
- b Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - Dea Garcia-Hermoso
- c Institut Pasteur, National Reference Center for Invasive Mycoses and Antifungals (NRCMA), Molecular Mycology Unit, CNRS UMR2000, Paris, France
| | - Marie Desnos-Ollivier
- c Institut Pasteur, National Reference Center for Invasive Mycoses and Antifungals (NRCMA), Molecular Mycology Unit, CNRS UMR2000, Paris, France
| | - Chompoonek Yurayart
- d Mycology Unit, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,e Department of Veterinary Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Chi-Ching Tsang
- f Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Chun-Yi Lee
- f Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Patrick C Y Woo
- f Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Ivan Mikhailovich Pchelin
- g Laboratory of Molecular Genetic Microbiology, Kashkin Research Institute of Medical Mycology, I.I. Mechnikov North-Western State Medical University, St Petersburg, Russia
| | - Silke Uhrlaß
- h Laboratory of Medical Microbiology, Partnership Dr. C. Krueger & Prof. Dr. P. Nenoff, Roetha OT Moelbis, Germany
| | - Pietro Nenoff
- h Laboratory of Medical Microbiology, Partnership Dr. C. Krueger & Prof. Dr. P. Nenoff, Roetha OT Moelbis, Germany
| | - Ariya Chindamporn
- d Mycology Unit, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sharon Chen
- a Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney School of Medicine, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Westmead, NSW, Australia.,i Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, Westmead Hospital, Westmead, NSW, Australia
| | - Paul D N Hebert
- j Department of Integrative Biology and Director of the Biodiversity Institute of Ontario at the University of Guelph, Guelph, ON, Canada
| | - Tania C Sorrell
- a Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney School of Medicine, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Westmead, NSW, Australia
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21
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Yang RH, Su JH, Shang JJ, Wu YY, Li Y, Bao DP, Yao YJ. Evaluation of the ribosomal DNA internal transcribed spacer (ITS), specifically ITS1 and ITS2, for the analysis of fungal diversity by deep sequencing. PLoS One 2018; 13:e0206428. [PMID: 30359454 PMCID: PMC6201957 DOI: 10.1371/journal.pone.0206428] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/12/2018] [Indexed: 12/17/2022] Open
Abstract
The nuclear ribosomal DNA internal transcribed spacer (ITS) has been widely used to assess the fungal composition in different environments by deep sequencing. To evaluate the ITS in the analysis of fungal diversity, comparisons of the clustering and taxonomy generated by sequencing with different portions of the whole fragment were conducted in this study. For a total of 83,120 full-length ITS sequences obtained from the UNITE database, it was found that, on average, ITS1 varied more than ITS2 within the kingdom Fungi; this variation included length and GC content variations and polymorphisms, with some polymorphisms specific to particular fungal groups. The taxonomic accuracy for ITS was higher than that for ITS1 or ITS2. The commonly used operational taxonomic unit (OTU) for evaluating fungal diversity and richness assigned several species to a single OTU even with clustering at 99.00% sequence similarity. The clustering and taxonomic capacities did not differ between ITS1 and ITS2. However, the OTU commonality between ITS1 and ITS2 was very low. To test this observation further, 219,741 pyrosequencing reads, including 39,840 full-length ITS sequences, were obtained from 10 soil samples and were clustered into OTUs. The pyrosequencing results agreed with the results of the in silico analysis. ITS1 might overestimate the fungal diversity and richness. Analyses using ITS, ITS1 and ITS2 yielded several different taxa, and the taxonomic preferences for ITS and ITS2 were similar. The results demonstrated that ITS2 alone might be a more suitable marker for revealing the operational taxonomic richness and taxonomy specifics of fungal communities when the full-length ITS is not available.
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Affiliation(s)
- Rui-Heng Yang
- Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jin-He Su
- Computer Engineering College, Jimei University, Xiamen, China
| | - Jun-Jun Shang
- Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ying-Ying Wu
- Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yan Li
- Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Da-Peng Bao
- Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
- * E-mail: (YJY); (DPB)
| | - Yi-Jian Yao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- * E-mail: (YJY); (DPB)
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22
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Identification of Fungi Associated with Processed-Food Contamination at Open Markets of Windhoek, Namibia. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2018. [DOI: 10.22207/jpam.12.3.53] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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23
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Cubeta MA, Briones-Ortega R, Vilgalys R. Reassessment of Heterokaryon Formation in Rhizoctonia Solani Anastomosis Group 4. Mycologia 2018. [DOI: 10.1080/00275514.1993.12026332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- M. A. Cubeta
- Department of Botany, Duke University, Durham, North Carolina 27708
| | | | - R. Vilgalys
- Department of Botany, Duke University, Durham, North Carolina 27708
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24
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Bunyard BA, Nicholson MS, Royse DJ. A systematic assessment ofMorchellausing RFLP analysis of the 28S ribosomal RNA gene. Mycologia 2018. [DOI: 10.1080/00275514.1994.12026481] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Britt A. Bunyard
- Department of Plant Pathology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Michael S. Nicholson
- Department of Plant Pathology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Daniel J. Royse
- Department of Plant Pathology, The Pennsylvania State University, University Park, Pennsylvania 16802
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25
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Kambouris ME, Manoussopoulos Y, Kritikou S, Milioni A, Mantzoukas S, Velegraki A. Toward Decentralized Agrigenomic Surveillance? A Polymerase Chain Reaction–Restriction Fragment Length Polymorphism Approach for Adaptable and Rapid Detection of User-Defined Fungal Pathogens in Potato Crops. ACTA ACUST UNITED AC 2018; 22:264-273. [DOI: 10.1089/omi.2018.0012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
| | | | - Stavroula Kritikou
- Mycology Research Laboratory, Department of Microbiology, Medical School, National & Kapodistrian University of Athens, Athens, Greece
| | - Aphroditi Milioni
- Mycology Research Laboratory, Department of Microbiology, Medical School, National & Kapodistrian University of Athens, Athens, Greece
| | | | - Aristea Velegraki
- Mycology Research Laboratory, Department of Microbiology, Medical School, National & Kapodistrian University of Athens, Athens, Greece
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26
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Entwistle EM, Zak DR, Argiroff WA. Anthropogenic N deposition increases soil C storage by reducing the relative abundance of lignolytic fungi. ECOL MONOGR 2018. [DOI: 10.1002/ecm.1288] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Elizabeth M. Entwistle
- School of Natural Resources & Environment University of Michigan Ann Arbor Michigan 48109 USA
| | - Donald R. Zak
- School of Natural Resources & Environment University of Michigan Ann Arbor Michigan 48109 USA
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor Michigan 48109 USA
| | - William A. Argiroff
- School of Natural Resources & Environment University of Michigan Ann Arbor Michigan 48109 USA
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27
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Canfora L, Salvati L, Benedetti A, Francaviglia R. Is soil microbial diversity affected by soil and groundwater salinity? Evidences from a coastal system in central Italy. ENVIRONMENTAL MONITORING AND ASSESSMENT 2017; 189:319. [PMID: 28589460 DOI: 10.1007/s10661-017-6040-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 05/30/2017] [Indexed: 06/07/2023]
Abstract
Little is known about composition, diversity, and abundance of microbial communities in environments affected by primary soil salinization, such as coastal lagoon systems. The main objective of this study was to investigate the impact of lagoon salinity, soil type, and land-use on inland soil and groundwater quality, and soil microbial community structure, diversity, and gene abundance, as evaluated by T-RFLP (terminal-restriction fragment length polymorphism) and qPCR (quantitative polymerase-chain-reaction). For this purpose, four sites oriented along a groundwater salinity gradient (Fogliano lagoon, central Italy) were studied under different recreational, grazing, and land-use conditions. Spatial variability in groundwater attributes was observed depending on salinity and soil electrical conductivity, both influenced by salt intrusion. A comparison of community abundance and number of phylotypes of bacteria, archaea, and fungi across varying soil depths pointed out marked differences across soils characterized by different soil type, land-use, and salinity. The latter significantly affected the microbial population richness and diversity and showed a dominance in terms of bacteria species. Our study provides a comprehensive overview of the spatial relationship between soil microbial community and soil degradation processes along a relatively underexplored environmental gradient in a coastal system, coming to the conclusion that salinity acts differently as a driver of microbial community structure in comparison with other saline environments.
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Affiliation(s)
- Loredana Canfora
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Agricoltura e Ambiente (CREA-AA), Via della Navicella 2-4, 00184, Rome, Italy.
| | - Luca Salvati
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Agricoltura e Ambiente (CREA-AA), Via della Navicella 2-4, 00184, Rome, Italy
| | - Anna Benedetti
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Agricoltura e Ambiente (CREA-AA), Via della Navicella 2-4, 00184, Rome, Italy
| | - Rosa Francaviglia
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Agricoltura e Ambiente (CREA-AA), Via della Navicella 2-4, 00184, Rome, Italy
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28
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Land-use types and soil chemical properties influence soil microbial communities in the semiarid Loess Plateau region in China. Sci Rep 2017; 7:45289. [PMID: 28349918 PMCID: PMC5368647 DOI: 10.1038/srep45289] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 02/23/2017] [Indexed: 02/01/2023] Open
Abstract
Similar land-use types usually have similar soil properties, and, most likely, similar microbial communities. Here, we assessed whether land-use types or soil chemical properties are the primary drivers of soil microbial community composition, and how changes in one part of the ecosystem affect another. We applied Ion Torrent sequencing to the bacterial and fungal communities of five different land-use (vegetation) types in the Loess Plateau of China. We found that the overall trend of soil quality was natural forest > plantation > bare land. Dominant bacterial phyla consisted of Proteobacteria (42.35%), Actinobacteria (15.61%), Acidobacteria (13.32%), Bacteroidetes (8.43%), and Gemmatimonadetes (6.0%). The dominant fungi phyla were Ascomycota (40.39%), Basidiomycota (38.01%), and Zygomycota (16.86%). The results of Canonical Correspondence Analysis (CCA) and Redundancy Analysis (RDA) based on land-use types displayed groups according to the land-use types. Furthermore, the bacterial communities were mainly organized by soil organic carbon (SOC). The fungal communities were mainly related to available phosphorus (P). The results suggested that the changes of land use type generated changes in soil chemical properties, controlling the composition of microbial community in the semiarid Loess Plateau region. The microbial community could be an indicator for soil quality with respect to ecological restoration.
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29
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de Arruda MC, Sepulveda Ch. GF, Miller RN, Ferreira MA, Santiago DV, Resende MLV, Dianese JC, Felipe MSS. Crinipellis brasiliensis, a new species based on morphological and molecular data. Mycologia 2017. [DOI: 10.1080/15572536.2006.11832741] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Maricília C.C. de Arruda
- Departamento de Biologia Celular, Universidade de Brasília, 70910-900, Brasília/DF, Brazil, Universidade do Estado de Mato Grosso, 78200-000, Cáceres/MT, Brazil
| | | | - Robert N.G. Miller
- Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília/DF, Brazil
| | | | - Denise V.R. Santiago
- Departamento de Fitopatologia, Universidade de Brasília, 70910-900, Brasília/DF, Brazil
| | | | - José Carmine Dianese
- Departamento de Fitopatologia, Universidade de Brasília, 70910-900, Brasília/DF, Brazil
| | - Maria Sueli S. Felipe
- Departamento de Biologia Celular, Universidade de Brasília, 70910-900, Brasília/DF, Brazil
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30
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Delgado-Serrano L, Restrepo S, Bustos JR, Zambrano MM, Anzola JM. Mycofier: a new machine learning-based classifier for fungal ITS sequences. BMC Res Notes 2016; 9:402. [PMID: 27516337 PMCID: PMC4982325 DOI: 10.1186/s13104-016-2203-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 08/03/2016] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The taxonomic and phylogenetic classification based on sequence analysis of the ITS1 genomic region has become a crucial component of fungal ecology and diversity studies. Nowadays, there is no accurate alignment-free classification tool for fungal ITS1 sequences for large environmental surveys. This study describes the development of a machine learning-based classifier for the taxonomical assignment of fungal ITS1 sequences at the genus level. RESULTS A fungal ITS1 sequence database was built using curated data. Training and test sets were generated from it. A Naïve Bayesian classifier was built using features from the primary sequence with an accuracy of 87 % in the classification at the genus level. CONCLUSIONS The final model was based on a Naïve Bayes algorithm using ITS1 sequences from 510 fungal genera. This classifier, denoted as Mycofier, provides similar classification accuracy compared to BLASTN, but the database used for the classification contains curated data and the tool, independent of alignment, is more efficient and contributes to the field, given the lack of an accurate classification tool for large data from fungal ITS1 sequences. The software and source code for Mycofier are freely available at https://github.com/ldelgado-serrano/mycofier.git .
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Affiliation(s)
- Luisa Delgado-Serrano
- Bioinformatics & Computational Biology, Corporación CorpoGen, Bogotá, DC, Colombia.,Department of Biological Sciences, Universidad de Los Andes, Bogotá, DC, Colombia
| | - Silvia Restrepo
- Department of Biological Sciences, Universidad de Los Andes, Bogotá, DC, Colombia
| | - Jose Ricardo Bustos
- Bioinformatics & Computational Biology, Corporación CorpoGen, Bogotá, DC, Colombia
| | | | - Juan Manuel Anzola
- Bioinformatics & Computational Biology, Corporación CorpoGen, Bogotá, DC, Colombia.
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31
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DNA barcoding for identification of consumer-relevant mushrooms: A partial solution for product certification? Food Chem 2016; 214:383-392. [PMID: 27507489 DOI: 10.1016/j.foodchem.2016.07.052] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 06/03/2016] [Accepted: 07/09/2016] [Indexed: 02/06/2023]
Abstract
One challenge in the dietary supplement industry is confirmation of species identity for processed raw materials, i.e. those modified by milling, drying, or extraction, which move through a multilevel supply chain before reaching the finished product. This is particularly difficult for samples containing fungal mycelia, where processing removes morphological characteristics, such that they do not present sufficient variation to differentiate species by traditional techniques. To address this issue, we have demonstrated the utility of DNA barcoding to verify the taxonomic identity of fungi found commonly in the food and dietary supplement industry; such data are critical for protecting consumer health, by assuring both safety and quality. By using DNA barcoding of nuclear ribosomal internal transcribed spacer (ITS) of the rRNA gene with fungal specific ITS primers, ITS barcodes were generated for 33 representative fungal samples, all of which could be used by consumers for food and/or dietary supplement purposes. In the majority of cases, we were able to sequence the ITS region from powdered mycelium samples, grocery store mushrooms, and capsules from commercial dietary supplements. After generating ITS barcodes utilizing standard procedures accepted by the Consortium for the Barcode of Life, we tested their utility by performing a BLAST search against authenticate published ITS sequences in GenBank. In some cases, we also downloaded published, homologous sequences of the ITS region of fungi inspected in this study and examined the phylogenetic relationships of barcoded fungal species in light of modern taxonomic and phylogenetic studies. We anticipate that these data will motivate discussions on DNA barcoding based species identification as applied to the verification/certification of mushroom-containing dietary supplements.
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32
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van Nieuwenhuijzen EJ, Houbraken JAMP, Meijer M, Adan OCG, Samson RA. Aureobasidium melanogenum: a native of dark biofinishes on oil treated wood. Antonie van Leeuwenhoek 2016; 109:661-83. [PMID: 26920754 PMCID: PMC4819947 DOI: 10.1007/s10482-016-0668-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 02/17/2016] [Indexed: 11/24/2022]
Abstract
The genus Aureobasidium, which is known as a wood staining mould, has been detected on oil treated woods in the specific stain formation called biofinish. This biofinish is used to develop a new protective, self-healing and decorative biotreatment for wood. In order to understand and control biofinish formation on oil treated wood, the occurrence of different Aureobasidium species on various wood surfaces was studied. Phenotypic variability within Aureobasidium strains presented limitations of morphological identification of Aureobasidium species. PCR amplification and Sanger sequencing of ITS and RPB2 were used to identify the culturable Aureobasidium species composition in mould stained wood surfaces with and without a biofinish. The analysed isolates showed that several Aureobasidium species were present and that Aureobasidium melanogenum was predominantly detected, regardless of the presence of a biofinish and the type of substrate. A.melanogenum was detected on wood samples exposed in the Netherlands, Cameroon, South Africa, Australia and Norway. ITS-specific PCR amplification, cloning and sequencing of DNA extracted from biofinish samples confirmed results of the culturing based method: A. melanogenum is predominant within the Aureobasidium population of biofinishes on pine sapwood treated with raw linseed oil and the outdoor placement in the Netherlands.
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Affiliation(s)
| | - Jos A M P Houbraken
- CBS KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Martin Meijer
- CBS KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Olaf C G Adan
- Section Transport in Permeable Media, Department of Applied Physics, University of Technology Eindhoven, Den Dolech 2, 5600 MB, Eindhoven, The Netherlands
| | - Robert A Samson
- CBS KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
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33
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Grum-Grzhimaylo OA, Debets AJM, Bilanenko EN. The diversity of microfungi in peatlands originated from the White Sea. Mycologia 2016; 108:233-54. [PMID: 26742584 DOI: 10.3852/14-346] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 10/20/2015] [Indexed: 11/10/2022]
Abstract
The diversity of culturable filamentous microfungi in peat and sediments of four peatlands at the coastal zone of Kandalaksha Bay of the White Sea (Murmansk region, Russia) was studied by culture methods on standard and selective media. Annually 100 samples were collected from the bogs 2007-2010. Based on morphological, molecular markers and cultural features, 211 taxa were identified. Fungal communities observed at the peatlands were influenced mostly by their sea origin. We discovered a large difference between fungal communities from the peat and the sediments of the peatlands. In contrast to the sediments, the fungal community of the peat was found to be consistent throughout sampling sites. Fungi with specific ecophysiology, such as Sphagnum-decomposing species (Oidiodendron griseum, O. tenuissimum. Penicillium spinulosum, P. thomii, Talaromyces funiculosus), psychrotolerant and associated with insects species (Pseudogymnoascus pannorum, Tolypocladium spp.), typical marine species (Acremonium spp.) were found. In addition, different types of sterile mycelia were characteristic for the researched peatlands.
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Affiliation(s)
- Olga A Grum-Grzhimaylo
- White Sea Biological Station, Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119234, Moscow, RussiaFaculty of Biology, St Petersburg State University, 7-9, Universitetskaya nab., 199034, St Petersburg, Russia
| | - Alfons J M Debets
- Laboratory of Genetics, Plant Sciences Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
| | - Elena N Bilanenko
- Department of Mycology and Phycology, Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119234, Moscow, Russia
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34
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Patil HJ, Solanki MK. Molecular Prospecting: Advancement in Diagnosis and Control of Rhizoctonia solani Diseases in Plants. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27312-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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35
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Advance Detection Techniques of Phytopathogenic Fungi: Current Trends and Future Perspectives. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27312-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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36
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Sundelin T, Strømeng GM, Gjærum HB, Amby DB, Ørstad K, Jensen B, Lund OS, Stensvand A. A revision of the history of the Colletotrichum acutatum species complex in the Nordic countries based on herbarium specimens. FEMS Microbiol Lett 2015; 362:fnv130. [PMID: 26296707 DOI: 10.1093/femsle/fnv130] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2015] [Indexed: 11/13/2022] Open
Abstract
Herbaria collections containing plants with disease symptoms are highly valuable, and they are often the only way to investigate outbreaks and epidemics from the past as the number of viable isolates in culture collections is often limited. Species belonging to the Colletotrichum acutatum complex infect a range of important crops. As members of the C. acutatum complex are easily confused with other Colletotrichum species, molecular methods are central for the correct identification. We performed molecular analyses on 21 herbaria specimens, displaying anthracnose symptoms, collected in Norway and Denmark before the first confirmed findings of C. acutatum complex members in this region. Sequencing parts of the fungal ITS regions showed that members of the species complex were present in 13 of the 21 specimens collected in different parts of Norway and Denmark between 1948 and 1991, representing seven plant hosts (three cherry species, apple, raspberry and rhododendron). This is the first time herbarium specimens have been used to study these pathogens under Nordic conditions. Differences in the ITS sequences suggest the presence of different genotypes within the complex, indicating a well-established population.
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Affiliation(s)
- Thomas Sundelin
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Gunn Mari Strømeng
- Bioforsk, Norwegian Institute for Agricultural and Environmental Research, Plant Health and Plant Protection Division, 1430 Ås, Norway
| | - Halvor B Gjærum
- Bioforsk, Norwegian Institute for Agricultural and Environmental Research, Plant Health and Plant Protection Division, 1430 Ås, Norway
| | - Daniel Buchvaldt Amby
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Kari Ørstad
- Bioforsk, Norwegian Institute for Agricultural and Environmental Research, Plant Health and Plant Protection Division, 1430 Ås, Norway
| | - Birgit Jensen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Ole Søgaard Lund
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Arne Stensvand
- Bioforsk, Norwegian Institute for Agricultural and Environmental Research, Plant Health and Plant Protection Division, 1430 Ås, Norway
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Cheng T, Xu C, Lei L, Li C, Zhang Y, Zhou S. Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity. Mol Ecol Resour 2015; 16:138-49. [PMID: 26084789 DOI: 10.1111/1755-0998.12438] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 04/20/2015] [Accepted: 06/09/2015] [Indexed: 01/22/2023]
Abstract
The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses, and it has been recommended as a core plant DNA barcode. Despite this popularity, the universality and specificity of PCR primers for the ITS region are not satisfactory, resulting in amplification and sequencing difficulties. By thoroughly surveying and analysing the 18S, 5.8S and 26S sequences of Plantae and Fungi from GenBank, we designed new universal and plant-specific PCR primers for amplifying the whole ITS region and a part of it (ITS1 or ITS2) of plants. In silico analyses of the new and the existing ITS primers based on these highly representative data sets indicated that (i) the newly designed universal primers are suitable for over 95% of plants in most groups; and (ii) the plant-specific primers are suitable for over 85% of plants in most groups without amplification of fungi. A total of 335 samples from 219 angiosperm families, 11 gymnosperm families, 24 fern and lycophyte families, 16 moss families and 17 fungus families were used to test the performances of these primers. In vitro PCR produced similar results to those from the in silico analyses. Our new primer pairs gave PCR improvements up to 30% compared with common-used ones. The new universal ITS primers will find wide application in both plant and fungal biology, and the new plant-specific ITS primers will, by eliminating PCR amplification of nonplant templates, significantly improve the quality of ITS sequence information collections in plant molecular systematics and DNA barcoding.
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Affiliation(s)
- Tao Cheng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Li Lei
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Changhao Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yu Zhang
- Beijing Botanic Gardens, Beijing, 100093, China
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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Irinyi L, Lackner M, de Hoog GS, Meyer W. DNA barcoding of fungi causing infections in humans and animals. Fungal Biol 2015; 120:125-36. [PMID: 26781368 DOI: 10.1016/j.funbio.2015.04.007] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 04/12/2015] [Accepted: 04/17/2015] [Indexed: 12/14/2022]
Abstract
Correct species identification is becoming increasingly important in clinical diagnostics. Till now, many mycological laboratories rely on conventional phenotypic identification. But this is slow and strongly operator-dependent. Therefore, to improve the quality of pathogen identification, rapid, reliable, and objective identification methods are essential. One of the most encouraging approaches is molecular barcoding using the internal transcribed spacer (ITS) of the rDNA, which is rapid, easily achievable, accurate, and applicable directly from clinical specimens. It relies on the comparison of a single ITS sequence with a curated reference database. The International Society for Human and Animal Mycology (ISHAM) working group for DNA barcoding has recently established such a database, focusing on the majority of human and animal pathogenic fungi (ISHAM-ITS, freely accessible at http://www.isham.org/ or directly from http://its.mycologylab.org). For some fungi the use of secondary barcodes may be necessary.
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Affiliation(s)
- Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School - Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Millennium Institute, Sydney, NSW, Australia
| | - Michaela Lackner
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, 6020, Austria
| | - G Sybren de Hoog
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, 3508 AD, The Netherlands
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School - Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Millennium Institute, Sydney, NSW, Australia.
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Contreras G, Barahona S, Sepúlveda D, Baeza M, Cifuentes V, Alcaíno J. Identification and analysis of metabolite production with biotechnological potential in Xanthophyllomyces dendrorhous isolates. World J Microbiol Biotechnol 2015; 31:517-26. [PMID: 25643668 PMCID: PMC4333312 DOI: 10.1007/s11274-015-1808-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 01/23/2015] [Indexed: 12/31/2022]
Abstract
Antarctic microorganisms have developed different strategies to live in their environments, including modifications to their membrane components to regulate fluidity and the production of photoprotective metabolites such as carotenoids. Three yeast colonies (ANCH01, ANCH06 and ANCH08) were isolated from soil samples collected at King George Island, which according to their rDNA sequence analyses, were determined to be Xanthophyllomyces dendrorhous. This yeast is of biotechnological interest, because it can synthesize astaxanthin as its main carotenoid, which is a powerful antioxidant pigment used in aquaculture. Then, the aim of this work was to characterize the ANCH isolates at their molecular and phenotypic level. The isolates did not display any differences in their rDNA and COX1 gene nucleotide sequences. However, ANCH01 produces approximately sixfold more astaxanthin than other wild type strains. Moreover, even though ANCH06 and ANCH08 produce astaxanthin, their main carotenoid was β-carotene. In contrast to other X. dendrorhous strains, the ANCH isolates did not produce mycosporines. Finally, the ANCH isolates had a higher proportion of polyunsaturated fatty acids than other wild type strains. In conclusion, the reported X. dendrorhous isolates are phenotypically different from other wild type strains, including characteristics that could make them more resistant and better able to inhabit their original habitat, which may also have biotechnological potential.
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Affiliation(s)
- Gabriela Contreras
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago Chile
| | - Salvador Barahona
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago Chile
| | - Dionisia Sepúlveda
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago Chile
| | - Marcelo Baeza
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago Chile
| | - Víctor Cifuentes
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago Chile
| | - Jennifer Alcaíno
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago Chile
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Losada L, Pakala SB, Fedorova ND, Joardar V, Shabalina SA, Hostetler J, Pakala SM, Zafar N, Thomas E, Rodriguez-Carres M, Dean R, Vilgalys R, Nierman WC, Cubeta MA. Mobile elements and mitochondrial genome expansion in the soil fungus and potato pathogen Rhizoctonia solani AG-3. FEMS Microbiol Lett 2014; 352:165-73. [PMID: 24461055 DOI: 10.1111/1574-6968.12387] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 12/24/2013] [Accepted: 01/20/2014] [Indexed: 12/16/2022] Open
Abstract
The soil fungus Rhizoctonia solani is an economically important pathogen of agricultural and forestry crops. Here, we present the complete sequence and analysis of the mitochondrial genome of R. solani, field isolate Rhs1AP. The genome (235 849 bp) is the largest mitochondrial genome of a filamentous fungus sequenced to date and exhibits a rich accumulation of introns, novel repeat sequences, homing endonuclease genes, and hypothetical genes. Stable secondary structures exhibited by repeat sequences suggest that they comprise functional, possibly catalytic RNA elements. RNA-Seq expression profiling confirmed that the majority of homing endonuclease genes and hypothetical genes are transcriptionally active. Comparative analysis suggests that the mitochondrial genome of R. solani is an example of a dynamic history of expansion in filamentous fungi.
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Ramdeen S, Rampersad SN. Intraspecific differentiation of Colletotrichum gloeosporioides sensu lato based on in silico multilocus PCR-RFLP fingerprinting. Mol Biotechnol 2013; 53:170-81. [PMID: 22367643 DOI: 10.1007/s12033-012-9509-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Colletotrichum gloeosporioides sensu lato is one of the most common and widely distributed plant pathogens in the world. Understanding fungal biodiversity is hinged on accurate identification and delimitation at the inter- and intraspecific levels. Sequences of the ITS1-5.8S-ITS2 region (ITS), β-tubulin (TUB), actin (ACT), and glyceraldehyde-3-phosphate dehydrogenase (GPDH) genes of 30 C. gloeosporioides sensu lato isolates, collected from anthracnose infected papaya fruits grown in the main production areas in Trinidad, were analyzed by in silico PCR-RFLP analysis with the aim of identifying which gene region(s) had the highest level of intraspecific polymorphism. Restriction site polymorphisms generated from 13 restriction enzymes enabled the identification of specific enzymes that were successful at intraspecific discrimination of the C. gloeosporioides isolates. Genetic distance values were reflective of the level of polymorphisms obtained for the four different gene regions. In both cases (calculated genetic distance and percentage of polymorphic loci from RFLP profiles), ACT and ITS gene regions had the highest level of restriction site polymorphisms and genetic diversity, GPDH and TUB had the lowest. Cluster analysis based on PCR-RFLP genetic distance data revealed sub-specific placement of the isolates which appeared to be gene-dependent. The implications of these findings are discussed relative to biodiversity monitoring and the need for multilocus, polyphasic investigations which must take into account the possibility of exaggerated estimates of genetic diversity.
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Affiliation(s)
- Stephen Ramdeen
- Department of Life Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
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Murata H, Ota Y, Yamaguchi M, Yamada A, Katahata S, Otsuka Y, Babasaki K, Neda H. Mobile DNA distributions refine the phylogeny of "matsutake" mushrooms, Tricholoma sect. Caligata. MYCORRHIZA 2013; 23:447-461. [PMID: 23440576 DOI: 10.1007/s00572-013-0487-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 02/07/2013] [Indexed: 06/01/2023]
Abstract
"Matsutake" mushrooms are formed by several species of Tricholoma sect. Caligata distributed across the northern hemisphere. A phylogenetic analysis of matsutake based on virtually neutral mutations in DNA sequences resolved robust relationships among Tricholoma anatolicum, Tricholoma bakamatsutake, Tricholoma magnivelare, Tricholoma matsutake, and Tricholoma sp. from Mexico (=Tricholoma sp. Mex). However, relationships among these matsutake and other species, such as Tricholoma caligatum and Tricholoma fulvocastaneum, were ambiguous. We, therefore, analyzed genomic copy numbers of σ marY1 , marY1, and marY2N retrotransposons by comparing them with the single-copy mobile DNA megB1 using real-time polymerase chain reaction (PCR) to clarify matsutake phylogeny. We also examined types of megB1-associated domains, composed of a number of poly (A) and poly (T) reminiscent of RNA-derived DNA elements among these species. Both datasets resolved two distinct groups, one composed of T. bakamatsutake, T. fulvocastaneum, and T. caligatum that could have diverged earlier and the other comprising T. magnivelare, Tricholoma sp. Mex, T. anatolicum, and T. matsutake that could have evolved later. In the first group, T. caligatum was the closest to the second group, followed by T. fulvocastaneum and T. bakamatsutake. Within the second group, T. magnivelare was clearly differentiated from the other species. The data suggest that matsutake underwent substantial evolution between the first group, mostly composed of Fagaceae symbionts, and the second group, comprised only of Pinaceae symbionts, but diverged little within each groups. Mobile DNA markers could be useful in resolving difficult phylogenies due to, for example, closely spaced speciation events.
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Affiliation(s)
- Hitoshi Murata
- Department of Applied Microbiology and Mushroom Sciences, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan.
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Roe AD, Rice AV, Bromilow SE, Cooke JEK, Sperling FAH. Multilocus species identification and fungal DNA barcoding: insights from blue stain fungal symbionts of the mountain pine beetle. Mol Ecol Resour 2013; 10:946-59. [PMID: 21565104 DOI: 10.1111/j.1755-0998.2010.02844.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There is strong community-wide interest in applying molecular techniques to fungal species delimitation and identification, but selection of a standardized region or regions of the genome has not been finalized. A single marker, the ribosomal DNA internal transcribed spacer region, has frequently been suggested as the standard for fungi. We used a group of closely related blue stain fungi associated with the mountain pine beetle (Dendroctonus ponderosae Hopkins) to examine the success of such single-locus species identification, comparing the internal transcribed spacer with four other nuclear markers. We demonstrate that single loci varied in their utility for identifying the six fungal species examined, while use of multiple loci was consistently successful. In a literature survey of 21 similar studies, individual loci were also highly variable in their ability to provide consistent species identifications and were less successful than multilocus diagnostics. Accurate species identification is the essence of any molecular diagnostic system, and this consideration should be central to locus selection. Moreover, our study and the literature survey demonstrate the value of using closely related species as the proving ground for developing a molecular identification system. We advocate use of a multilocus barcode approach that is similar to the practice employed by the plant barcode community, rather than reliance on a single locus.
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Affiliation(s)
- Amanda D Roe
- CW 405 - Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
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Berthrong ST, Buckley DH, Drinkwater LE. Agricultural management and labile carbon additions affect soil microbial community structure and interact with carbon and nitrogen cycling. MICROBIAL ECOLOGY 2013; 66:158-70. [PMID: 23588849 DOI: 10.1007/s00248-013-0225-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 03/22/2013] [Indexed: 05/10/2023]
Abstract
We investigated how conversion from conventional agriculture to organic management affected the structure and biogeochemical function of soil microbial communities. We hypothesized the following. (1) Changing agricultural management practices will alter soil microbial community structure driven by increasing microbial diversity in organic management. (2) Organically managed soil microbial communities will mineralize more N and will also mineralize more N in response to substrate addition than conventionally managed soil communities. (3) Microbial communities under organic management will be more efficient and respire less added C. Soils from organically and conventionally managed agroecosystems were incubated with and without glucose ((13)C) additions at constant soil moisture. We extracted soil genomic DNA before and after incubation for TRFLP community fingerprinting of soil bacteria and fungi. We measured soil C and N pools before and after incubation, and we tracked total C respired and N mineralized at several points during the incubation. Twenty years of organic management altered soil bacterial and fungal community structure compared to continuous conventional management with the bacterial differences caused primarily by a large increase in diversity. Organically managed soils mineralized twice as much NO3 (-) as conventionally managed ones (44 vs. 23 μg N/g soil, respectively) and increased mineralization when labile C was added. There was no difference in respiration, but organically managed soils had larger pools of C suggesting greater efficiency in terms of respiration per unit soil C. These results indicate that the organic management induced a change in community composition resulting in a more diverse community with enhanced activity towards labile substrates and greater capacity to mineralize N.
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Affiliation(s)
- Sean T Berthrong
- Department of Horticulture, Cornell University, Ithaca, NY 14853, USA.
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Monard C, Gantner S, Stenlid J. Utilizing ITS1 and ITS2 to study environmental fungal diversity using pyrosequencing. FEMS Microbiol Ecol 2012; 84:165-75. [PMID: 23176677 DOI: 10.1111/1574-6941.12046] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 11/09/2012] [Accepted: 11/21/2012] [Indexed: 11/28/2022] Open
Abstract
The shorter reads generated by high-throughput sequencing has led to a focus on either the ITS1 or the ITS2 sublocus in fungal diversity analyses. Our study aimed to determine how making this choice would influence the datasets obtained and our vision of environmental fungal diversity. DNA was extracted from different environmental samples (water, sediments and soil) and the total internal transcribed spacer (ITS) locus was amplified. 454-sequencing was performed targeting both ITS1 and ITS2. No significant differences in the number of sequences, operational taxonomic units (OTUs) and in the dominant OTUs were detected but less diversity was observed in the ITS2 dataset. In the soil samples, differences in the fungal taxonomic identification were observed, with more Basidiomycota in the ITS1 dataset and more Ascomycota in the ITS2 dataset. Only one-third of the OTUs were detected in both datasets which could be due to (1) more short sequences removed in the ITS2 dataset, (2) different taxonomic affiliation depending on the sublocus used as BLASTn query and/or (3) selectivity in how a primer amplifies the true community. Although ITS1 and ITS2 datasets led to similar results at the fungal community level, for further in-depth diversity analysis this study suggests the analysis of both ITS regions, as they provided different information and were complementary.
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Affiliation(s)
- Cécile Monard
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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Santamaria M, Fosso B, Consiglio A, De Caro G, Grillo G, Licciulli F, Liuni S, Marzano M, Alonso-Alemany D, Valiente G, Pesole G. Reference databases for taxonomic assignment in metagenomics. Brief Bioinform 2012; 13:682-95. [PMID: 22786784 DOI: 10.1093/bib/bbs036] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Metagenomics is providing an unprecedented access to the environmental microbial diversity. The amplicon-based metagenomics approach involves the PCR-targeted sequencing of a genetic locus fitting different features. Namely, it must be ubiquitous in the taxonomic range of interest, variable enough to discriminate between different species but flanked by highly conserved sequences, and of suitable size to be sequenced through next-generation platforms. The internal transcribed spacers 1 and 2 (ITS1 and ITS2) of the ribosomal DNA operon and one or more hyper-variable regions of 16S ribosomal RNA gene are typically used to identify fungal and bacterial species, respectively. In this context, reliable reference databases and taxonomies are crucial to assign amplicon sequence reads to the correct phylogenetic ranks. Several resources provide consistent phylogenetic classification of publicly available 16S ribosomal DNA sequences, whereas the state of ribosomal internal transcribed spacers reference databases is notably less advanced. In this review, we aim to give an overview of existing reference resources for both types of markers, highlighting strengths and possible shortcomings of their use for metagenomics purposes. Moreover, we present a new database, ITSoneDB, of well annotated and phylogenetically classified ITS1 sequences to be used as a reference collection in metagenomic studies of environmental fungal communities. ITSoneDB is available for download and browsing at http://itsonedb.ba.itb.cnr.it/.
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Affiliation(s)
- Monica Santamaria
- Institute of Biomembranes and Bioenergetics, National Research Council, Bari, Italy
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Abstract
Studies of the population genetics of fungal and oomycetous phytopathogens are essential to clarifying the disease epidemiology and devising management strategies. Factors commonly associated with higher organisms such as migration, natural selection, or recombination, are critical for the building of a clearer picture of the pathogen in the landscape. In this chapter, we focus on a limited number of experimental and analytical methods that are commonly applied in population genetics. At first, we present different types of qualitative and quantitative traits that could be identified morphologically (phenotype). Subsequently, we describe several molecular methods based on dominant and codominant markers, and we provide our assessment of the advantages and shortfalls of these methods. Third, we discuss various analytical methods, which include phylogenies, summary statistics as well as coalescent-based methods, and we elaborate on the benefits associated with each approach. Last, we develop a case study in which we investigate the population structure of the fungal phytopathogen Verticillium dahliae in coastal California, and assess the hypotheses of transcontinental gene flow and recombination in a fungus that is described as asexual.
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Affiliation(s)
- Zahi K Atallah
- Department of Plant Pathology, University of California, Davis, CA, USA
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Bellemain E, Carlsen T, Brochmann C, Coissac E, Taberlet P, Kauserud H. ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiol 2010; 10:189. [PMID: 20618939 PMCID: PMC2909996 DOI: 10.1186/1471-2180-10-189] [Citation(s) in RCA: 560] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Accepted: 07/09/2010] [Indexed: 11/22/2022] Open
Abstract
Background During the last 15 years the internal transcribed spacer (ITS) of nuclear DNA has been used as a target for analyzing fungal diversity in environmental samples, and has recently been selected as the standard marker for fungal DNA barcoding. In this study we explored the potential amplification biases that various commonly utilized ITS primers might introduce during amplification of different parts of the ITS region in samples containing mixed templates ('environmental barcoding'). We performed in silico PCR analyses with commonly used primer combinations using various ITS datasets obtained from public databases as templates. Results Some of the ITS primers, such as ITS1-F, were hampered with a high proportion of mismatches relative to the target sequences, and most of them appeared to introduce taxonomic biases during PCR. Some primers, e.g. ITS1-F, ITS1 and ITS5, were biased towards amplification of basidiomycetes, whereas others, e.g. ITS2, ITS3 and ITS4, were biased towards ascomycetes. The assumed basidiomycete-specific primer ITS4-B only amplified a minor proportion of basidiomycete ITS sequences, even under relaxed PCR conditions. Due to systematic length differences in the ITS2 region as well as the entire ITS, we found that ascomycetes will more easily amplify than basidiomycetes using these regions as targets. This bias can be avoided by using primers amplifying ITS1 only, but this would imply preferential amplification of 'non-dikarya' fungi. Conclusions We conclude that ITS primers have to be selected carefully, especially when used for high-throughput sequencing of environmental samples. We suggest that different primer combinations or different parts of the ITS region should be analyzed in parallel, or that alternative ITS primers should be searched for.
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Affiliation(s)
- Eva Bellemain
- National Centre for Biosystematics, University of Oslo, Norway.
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Application of random amplified polymorphic DNA (RAPD) analysis coupled with microchip electrophoresis for high-resolution identification of Monascus strains. Appl Microbiol Biotechnol 2009; 82:1187-93. [DOI: 10.1007/s00253-009-1937-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Revised: 02/25/2009] [Accepted: 02/27/2009] [Indexed: 10/21/2022]
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50
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Nilsson RH, Bok G, Ryberg M, Kristiansson E, Hallenberg N. A software pipeline for processing and identification of fungal ITS sequences. SOURCE CODE FOR BIOLOGY AND MEDICINE 2009; 4:1. [PMID: 19146660 PMCID: PMC2649129 DOI: 10.1186/1751-0473-4-1] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Accepted: 01/15/2009] [Indexed: 11/17/2022]
Abstract
BACKGROUND Fungi from environmental samples are typically identified to species level through DNA sequencing of the nuclear ribosomal internal transcribed spacer (ITS) region for use in BLAST-based similarity searches in the International Nucleotide Sequence Databases. These searches are time-consuming and regularly require a significant amount of manual intervention and complementary analyses. We here present software - in the form of an identification pipeline for large sets of fungal ITS sequences - developed to automate the BLAST process and several additional analysis steps. The performance of the pipeline was evaluated on a dataset of 350 ITS sequences from fungi growing as epiphytes on building material. RESULTS The pipeline was written in Perl and uses a local installation of NCBI-BLAST for the similarity searches of the query sequences. The variable subregion ITS2 of the ITS region is extracted from the sequences and used for additional searches of higher sensitivity. Multiple alignments of each query sequence and its closest matches are computed, and query sequences sharing at least 50% of their best matches are clustered to facilitate the evaluation of hypothetically conspecific groups. The pipeline proved to speed up the processing, as well as enhance the resolution, of the evaluation dataset considerably, and the fungi were found to belong chiefly to the Ascomycota, with Penicillium and Aspergillus as the two most common genera. The ITS2 was found to indicate a different taxonomic affiliation than did the complete ITS region for 10% of the query sequences, though this figure is likely to vary with the taxonomic scope of the query sequences. CONCLUSION The present software readily assigns large sets of fungal query sequences to their respective best matches in the international sequence databases and places them in a larger biological context. The output is highly structured to be easy to process, although it still needs to be inspected and possibly corrected for the impact of the incomplete and sometimes erroneously annotated fungal entries in these databases. The open source pipeline is available for UNIX-type platforms, and updated releases of the target database are made available biweekly. The pipeline is easily modified to operate on other molecular regions and organism groups.
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Affiliation(s)
- R Henrik Nilsson
- University of Gothenburg, Department of Plant and Environmental Sciences, Box 461, 405 30 Göteborg, Sweden
| | - Gunilla Bok
- University of Gothenburg, Department of Plant and Environmental Sciences, Box 461, 405 30 Göteborg, Sweden
| | - Martin Ryberg
- University of Gothenburg, Department of Plant and Environmental Sciences, Box 461, 405 30 Göteborg, Sweden
| | - Erik Kristiansson
- The Sahlgrenska Academy at the University of Gothenburg, Department of Neuroscience and Physiology, Box 434, 405 30 Göteborg, Sweden
| | - Nils Hallenberg
- University of Gothenburg, Department of Plant and Environmental Sciences, Box 461, 405 30 Göteborg, Sweden
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