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Nandakumar K, Anto PV, Antony I. Diversity of soil fungi from sacred groves of Kerala, India revealed by comparative metagenomics analysis using illumina sequencing. 3 Biotech 2024; 14:79. [PMID: 38371901 PMCID: PMC10873253 DOI: 10.1007/s13205-024-03932-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 01/11/2024] [Indexed: 02/20/2024] Open
Abstract
The diversity, composition, and abundance of soil fungi from three sacred groves in Kerala, namely Iringole kavu of Ernakulam District, Kollakal Thapovanam of Alappuzha District, and Poyilkavu of Kozhikode District were analysed using Metagenomics analysis and Illumina sequencing. A total of 30,584, 78,323, and 55,640 reads were obtained from these groves, respectively. Ascomycota constitutes over 96% of the total fungi, making it the most abundant phylum, followed by Mortierellomycota, Basidiomycota, Chytridiomycota, and Rozellomycota. These phyla were subdivided into 20 classes, 40 orders, 83 families, 119 genera, and 135 species, while 1269 OTUs remained unidentified at the species level. Eurotiomycetes predominates the class, while the genus Talaromyces from the family Trichomaceae dominates the genera. Neocarmospora falciformis, Trichoderma lixii, and Candida ethanolic are the most abundant fungal species. Diversity analysis shows that Kollakal Thapovanam is rich in fungal species, while Poyilkavu is rich in biodiversity, with a high degree of dominance. Several species were found only in a particular grove and were absent in others and vice-versa, indicating high fungal specificity. Therefore, fungi have to be preserved in their original habitat. The Principal Coordinate Analysis revealed that each grove is distinct highlighting the importance of preserving the unique diversity of each sacred grove. In conclusion, this research provides valuable information about the soil fungal genera in their natural habitat. It emphasizes the need for more systematic research to understand the actual diversity and ecological role of fungi in sacred groves. This study is the first of its kind to analyse and compare soil fungal diversity in sacred groves using the metagenomics approach.
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Affiliation(s)
- Keerthana Nandakumar
- Department of Botany, St. Thomas College (Autonomous), Thrissur, University of Calicut, Thenhipalam, Kerala India
| | - P. V. Anto
- Department of Botany, St. Thomas College (Autonomous), Thrissur, University of Calicut, Thenhipalam, Kerala India
| | - Ignatius Antony
- Department of Botany, St. Thomas College (Autonomous), Thrissur, University of Calicut, Thenhipalam, Kerala India
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Rungjindamai N, Jones EBG. Why Are There So Few Basidiomycota and Basal Fungi as Endophytes? A Review. J Fungi (Basel) 2024; 10:67. [PMID: 38248976 PMCID: PMC10820240 DOI: 10.3390/jof10010067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/06/2024] [Accepted: 01/11/2024] [Indexed: 01/23/2024] Open
Abstract
A review of selected studies on fungal endophytes confirms the paucity of Basidiomycota and basal fungi, with almost 90% attributed to Ascomycota. Reasons for the low number of Basidiomycota and basal fungi, including the Chytridiomycota, Mucoromycota, and Mortierellomycota, are advanced, including isolation procedure and media, incubation period and the slow growth of basidiomycetes, the identification of non-sporulating isolates, endophyte competition, and fungus-host interactions. We compare the detection of endophytes through culture-dependent methods and culture-independent methods, the role of fungi on senescence of the host plant, and next-generation studies.
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Affiliation(s)
- Nattawut Rungjindamai
- Department of Biology, School of Science, King Mongkut’s Institute of Technology Ladkrabang (KMITL), Chalongkrung Road, Ladkrabang, Bangkok 10520, Thailand
| | - E. B. Gareth Jones
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia;
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3
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Baeshen NN, Baz L, Shami AY, Ashy RA, Jalal RS, Abulfaraj AA, Refai M, Majeed MA, Abuzahrah SS, Abdelkader H, Baeshen NA, Baeshen MN. Composition, Abundance, and Diversity of the Soil Microbiome Associated with the Halophytic Plants Tamarix aphylla and Halopeplis perfoliata on Jeddah Seacoast, Saudi Arabia. Plants (Basel) 2023; 12:plants12112176. [PMID: 37299153 DOI: 10.3390/plants12112176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023]
Abstract
The coast of the Red Sea in Jeddah City is home to a unique microbial community that has adapted to extreme environmental conditions. Therefore, it is essential to characterize the microbial community in this unique microbiome to predict how environmental changes will affect it. The aim of this study was to conduct metagenomic sequencing of 16S rRNA and ITS rRNA genes for the taxonomic classification of the microbial community in soil samples associated with the halophytic plants Tamarix aphylla and Halopeplis perfoliata. Fifteen soil samples were collected in triplicate to enhance robustness and minimize sampling bias. Firstly, to identify novel microbial candidates, the gDNAs were isolated from the saline soil samples surrounding each plant, and then bacterial 16S (V3-V4) and fungal ITS1 regions were sequenced utilizing a high-throughput approach (next-generation sequencing; NGS) on an Illumina MiSeq platform. Quality assessment of the constructed amplicon libraries was conducted using Agilent Bioanalyzer and fluorometric quantification methods. The raw data were processed and analyzed using the Pipeline (Nova Lifetech, Singapore) for bioinformatics analysis. Based on the total number of readings, it was determined that the phylum Actinobacteriota was the most prevalent in the soil samples examined, followed by the phylum Proteobacteria. Based on ITS rRNA gene analysis, the alpha and beta fungal diversity in the studied soil samples revealed that the fungal population is structured into various groups according to the crust (c) and/or rhizosphere (r) plant parts. Fungal communities in the soil samples indicated that Ascomycota and Basidiomycota were the two most abundant phyla based on the total amount of sequence reads. Secondly, heat-map analysis of the diversity indices showed that the bacterial alpha diversity, as measured by Shannon, Simpson, and InvSimpson, was associated with soil crust (Hc and Tc enclosing H. perfoliata and T. aphylla, respectively) and that the soil rhizosphere (Hr and Tr) was strongly correlated with bacterial beta diversity. Finally, fungal-associated Tc and Hc samples clustered together, according to observations made using the Fisher and Chao1 methods, and Hr and Tr samples clustered together according to Shannon, Simpson, and InvSimpson analyses. As a result of the soil investigation, potential agents that have been identified could lead to innovative agricultural, medical, and industrial applications.
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Affiliation(s)
- Naseebh N Baeshen
- Department of Biology, College of Sciences and Arts at Khulais, University of Jeddah, Jeddah 21959, Saudi Arabia
| | - Lina Baz
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ashwag Y Shami
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11617, Saudi Arabia
| | - Ruba A Ashy
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Rewaa S Jalal
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Aala A Abulfaraj
- Biological Sciences Department, College of Science & Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia
| | - Mohammed Refai
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Mazen A Majeed
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Samah S Abuzahrah
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Hayam Abdelkader
- Virus Research Department, Molecular Biology Laboratory, PPRI, ARC, Giza 12613, Egypt
| | - Nabih A Baeshen
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mohammed N Baeshen
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
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Hashizume H, Taga S, Sakata MK, Taha MHM, Siddig EE, Minamoto T, Fahal AH, Kaneko S. Detection of multiple mycetoma pathogens using fungal metabarcoding analysis of soil DNA in an endemic area of Sudan. PLoS Negl Trop Dis 2022; 16:e0010274. [PMID: 35275915 PMCID: PMC8942264 DOI: 10.1371/journal.pntd.0010274] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 03/23/2022] [Accepted: 02/23/2022] [Indexed: 01/14/2023] Open
Abstract
Mycetoma is a tropical disease caused by several fungi and bacteria present in the soil. Fungal mycetoma and eumycetoma are especially challenging to treat; therefore, prevention, early diagnosis, and early treatment are important, but it is also necessary to understand the geographic distribution of these pathogenic fungi. In this study, we used DNA metabarcoding methodology to identify fungal species from soil samples. Soil sampling was implemented at seven villages in an endemic area of Sennar State in Sudan in 2019, and ten sampling sites were selected in each village according to land-use conditions. In total, 70 soil samples were collected from ground surfaces, and DNA in the soil was extracted with a combined method of alkaline DNA extraction and a commercial soil DNA extraction kit. The region for universal primers was selected to be the ribosomal internal transcribed spacer one region for metabarcoding. After the second PCR for DNA library preparation, the amplicon-based DNA analysis was performed using next-generation sequencing with two sets of universal primers. A total of twelve mycetoma-causative fungal species were identified, including the prime agent, Madurella mycetomatis, and additional pathogens, Falciformispora senegalensis and Falciformispora tompkinsii, in 53 soil samples. This study demonstrated that soil DNA metabarcoding can elucidate the presence of multiple mycetoma-causative fungi, which may contribute to accurate diagnosis for patient treatment and geographical mapping. Mycetoma, a chronic subcutaneous and cutaneous disease, designated as a "neglected tropical disease," is prevalent in dry and hot climates. Fungal mycetoma is caused by more than 50 species of soil-dwelling pathogenic fungi, and its diagnosis and treatment can be challenging. The prevention of infection and early diagnosis and treatment are essential, and for this purpose, environmental assessment to understand the fungal habitat is necessary. In this study, we performed DNA metabarcoding analysis using next-generation sequencing (NGS) for mycetoma pathogens from environmental soil samples in Sudan. The results suggest that multiple causative agents of fungal mycetoma are widespread regardless of the environment and can be a source of infection anywhere in an endemic area. Based on the results of this study, we expect that the investigation of fungi in soil using NGS technology may help identify infection routes and create risk maps for the prevention of mycetoma.
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Affiliation(s)
- Hiroki Hashizume
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Department of Ecoepidemiology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Suguru Taga
- Department of Ecoepidemiology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Masayuki K. Sakata
- Graduate School of Human Development and Environment, Kobe University, Kobe, Japan
| | | | | | - Toshifumi Minamoto
- Graduate School of Human Development and Environment, Kobe University, Kobe, Japan
| | | | - Satoshi Kaneko
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Department of Ecoepidemiology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- * E-mail:
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Santona A, Mhmoud NA, Siddig EE, Deligios M, Fiamma M, Bakhiet SM, Barac A, Paglietti B, Rubino S, Fahal AH. Metagenomics of black grains: new highlights in the understanding of eumycetoma. Trans R Soc Trop Med Hyg 2021; 115:307-314. [PMID: 33449116 DOI: 10.1093/trstmh/traa177] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/19/2020] [Accepted: 12/16/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Eumycetoma is a chronic subcutaneous granulomatous disease that is endemic in Sudan and other countries. It can be caused by eight different fungal orders. The gold standard diagnostic test is culture, however, culture-independent methods such as imaging, histopathological and molecular techniques can support diagnosis, especially in cases of negative cultures. METHODS The amplicon-based internal transcribed spacer 2 metagenomic technique was used to study black grains isolated from 14 tissue biopsies from patients with mycetoma. Furthermore, mycological culture and surgical biopsy histopathological examinations of grains were performed. RESULTS Madurella mycetomatis (n=5) and Falciformispora spp. (n=4) organisms were identified by culture and confirmed by metagenomics. Metagenomics recognised, at the species level, Falciformispora as Falciformispora tompkinsii (n=3) and Falciformispora senegalensis (n=1), while in culture-negative cases (n=5), Madurella mycetomatis (n=3), Falciformispora senegalensis (n=1) and Fusarium spp. (n=1) were identified. Interestingly, the metagenomics results showed a 'consortium' of different fungi in each sample, mainly Ascomycota phylum, including various species associated with eumycetoma. The microbial co-occurrence in eumycetoma showed the co-presence of Madurella with Trichoderma, Chaetomium, Malasseziales and Sordariales spp., while Falciformispora co-presented with Inocybe and Alternaria and was in mutual exclusion with Subramaniula, Aspergillus and Trichothecium. CONCLUSION Metagenomics provides new insights into the aetiology of eumycetoma in samples with negative culture and into the diversity and complexity of grains mycobiota, calling into question the accuracy of traditional culture for the identification of causative agents.
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Affiliation(s)
- Antonella Santona
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy
| | - Najwa A Mhmoud
- Mycetoma Research Centre, University of Khartoum, PO Box 102, Khartoum, Sudan.,Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan
| | - Emmanuel Edwar Siddig
- Mycetoma Research Centre, University of Khartoum, PO Box 102, Khartoum, Sudan.,Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan
| | - Massimo Deligios
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy
| | - Maura Fiamma
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy
| | - Sahar Mubarak Bakhiet
- Mycetoma Research Centre, University of Khartoum, PO Box 102, Khartoum, Sudan.,Institute for Endemic Diseases, University of Khartoum, PO Box 102, Khartoum, Sudan
| | - Aleksandra Barac
- Clinic for Infectious and Tropical Diseases, Clinical Centre of Serbia, Bu. Oslobodjenja 16, 11000 Belgrade, Serbia.,Faculty of Medicine, University of Belgrade, Dr Subotica 1, 11000 Belgrade, Serbia
| | - Bianca Paglietti
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy
| | - Salvatore Rubino
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy
| | - Ahmed Hassan Fahal
- Mycetoma Research Centre, University of Khartoum, PO Box 102, Khartoum, Sudan
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6
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Giampaoli S, De Vittori E, Barni F, Anselmo A, Rinaldi T, Baldi M, Miranda KC, Liao A, Brami D, Frajese GV, Berti A. DNA metabarcoding of forensic mycological samples. Egypt J Forensic Sci 2021. [DOI: 10.1186/s41935-021-00221-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
DNA metabarcoding and massive parallel sequencing are valuable molecular tools for the characterization of environmental samples. In forensic sciences, the analysis of the sample’s fungal population can be highly informative for the estimation of post-mortem interval, the ascertainment of deposition time, the identification of the cause of death, or the location of buried corpses. Unfortunately, metabarcoding data analysis often requires strong bioinformatic capabilities that are not widely available in forensic laboratories.
Results
The present paper describes the adoption of a user-friendly cloud-based application for the identification of fungi in typical forensic samples. The samples have also been analyzed through the QIIME pipeline, obtaining a relevant data concordance on top genus classification results (88%).
Conclusions
The availability of a user-friendly application that can be run without command line activities will increase the popularity of metabarcoding fungal analysis in forensic samples.
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Noor SO, Al-Zahrani DA, Hussein RM, Baeshen MN, Moussa TAA, Abo-Aba SM, Al-Hejin AM, Baeshen NA, Huelsenbeck JP. Assessment of fungal diversity in soil rhizosphere associated with Rhazya stricta and some desert plants using metagenomics. Arch Microbiol 2020; 203:1211-1219. [PMID: 33231748 DOI: 10.1007/s00203-020-02119-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/19/2020] [Accepted: 11/08/2020] [Indexed: 02/07/2023]
Abstract
This study aimed to compare the fungal rhizosphere communities of Rhazya stricta, Enneapogon desvauxii, Citrullus colocynthis, Senna italica, and Zygophyllum simplex, and the gut mycobiota of Poekilocerus bufonius (Orthoptera, Pyrgomorphidae, "Usherhopper"). A total of 164,485 fungal reads were observed from the five plant rhizospheres and Usherhopper gut. The highest reads were in S. italica rhizosphere (29,883 reads). Species richness in the P. bufonius gut was the highest among the six samples. Ascomycota was dominant in all samples, with the highest reads in E. desvauxii (26,734 reads) rhizosphere. Sordariomycetes and Dothideomycetes were the dominant classes detected with the highest abundance in C. colocynthis and E. desvauxii rhizospheres. Aspergillus and Ceratobasidium were the most abundant genera in the R. stricta rhizosphere, Fusarium and Penicillium in the E. desvauxii rhizosphere and P. bufonius gut, Ceratobasidium and Myrothecium in the C. colocynthis rhizosphere, Aspergillus and Fusarium in the S. italica rhizosphere, and Cochliobolus in the Z. simplex rhizosphere. Aspergillus terreus was the most abundant species in the R. stricta and S. italica rhizospheres, Fusarium sp. in E. desvauxii rhizosphere, Ceratobasidium sp. in C. colocynthis rhizosphere, Cochliobolus sp. in Z. simplex rhizosphere, and Penicillium sp. in P. bufonius gut. The phylogenetic results revealed the unclassified species were related closely to Ascomycota and the species in E. desvauxii, S. italica and Z. simplex rhizospheres were closely related, where the species in the P. bufonius gut, were closely related to the species in the R. stricta, and C. colocynthis rhizospheres.
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Affiliation(s)
- Samah O Noor
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Dhafer A Al-Zahrani
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Refaei M Hussein
- University of Jeddah, College of Sciences and Arts, Department of Biological Sciences, Al Kamel Province, Jeddah, Saudi Arabia.,Genetics and Cytology Dept. Genetic Engineering Division, National Resesrch Centre, Dokki, Cairo, Egypt
| | - Mohammed N Baeshen
- University of Jeddah, College of Science, Department of Biological Sciences, Jeddah, Saudi Arabia
| | - Tarek A A Moussa
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza, 12613, Egypt.
| | - Salah M Abo-Aba
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Microbial Genetics, Genetic Engineering and Biotechnology Division, National Research Centre, Dokki, Giza, Egypt
| | - Ahmed M Al-Hejin
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nabih A Baeshen
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - John P Huelsenbeck
- Department of Integrative Biology, University of California, Berkeley, USA
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Větrovský T, Morais D, Kohout P, Lepinay C, Algora C, Awokunle Hollá S, Bahnmann BD, Bílohnědá K, Brabcová V, D'Alò F, Human ZR, Jomura M, Kolařík M, Kvasničková J, Lladó S, López-Mondéjar R, Martinović T, Mašínová T, Meszárošová L, Michalčíková L, Michalová T, Mundra S, Navrátilová D, Odriozola I, Piché-Choquette S, Štursová M, Švec K, Tláskal V, Urbanová M, Vlk L, Voříšková J, Žifčáková L, Baldrian P. GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies. Sci Data 2020; 7:228. [PMID: 32661237 PMCID: PMC7359306 DOI: 10.1038/s41597-020-0567-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/05/2020] [Indexed: 02/08/2023] Open
Abstract
Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, we collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at https://globalfungi.com . The GlobalFungi database contains over 600 million observations of fungal sequences across > 17 000 samples with geographical locations and additional metadata contained in 178 original studies with millions of unique nucleotide sequences (sequence variants) of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. The study represents the most comprehensive atlas of global fungal distribution, and it is framed in such a way that third-party data addition is possible.
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Affiliation(s)
- Tomáš Větrovský
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Daniel Morais
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Petr Kohout
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Clémentine Lepinay
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Camelia Algora
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sandra Awokunle Hollá
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Barbara Doreen Bahnmann
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Květa Bílohnědá
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vendula Brabcová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Federica D'Alò
- Laboratory of Systematic Botany and Mycology, University of Tuscia, Largo dell'Università snc, Viterbo, 01100, Italy
| | - Zander Rainier Human
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Mayuko Jomura
- Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Miroslav Kolařík
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Jana Kvasničková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Salvador Lladó
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Rubén López-Mondéjar
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tijana Martinović
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tereza Mašínová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lenka Meszárošová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lenka Michalčíková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tereza Michalová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sunil Mundra
- Department of Biology, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
- Section for Genetics and Evolutionary Biology, University of Oslo, Blindernveien 31, 0316, Oslo, Norway
| | - Diana Navrátilová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Iñaki Odriozola
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sarah Piché-Choquette
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Martina Štursová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Karel Švec
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vojtěch Tláskal
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Michaela Urbanová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lukáš Vlk
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Jana Voříšková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lucia Žifčáková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.
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Abstract
Oman is a desert country in the south of the Middle East. Springs and other water sources that harbor aquatic organisms can be separated by hundreds of kilometers. In Oct 2019, we isolated four freshwater aquatic fungi (Chytridiomycota) from benthic detritus baited with pine pollen on a general nutrient medium near Salalah, Oman. Database queries of nuc 28S rRNA (28S) and internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) revealed that one of these strains was Dinochytrium kinnereticum, a recently described algal pathogen from the Sea of Galilee. The other three strains had low molecular identity to available ITS sequences. These unknown strains varied in size and released endogenously swarming zoospores through papillae from mature zoosporangia. Zoospore ultrastructure was consistent with described species in the Rhizophydiales, and molecular phylogenetic results grouped these three strains into a clade in the genus Rhizophydium. We circumscribe these three strains as a sp. nov., thereby expanding the diversity within Rhizophydium described as the new species R. jobii. In doing so, we provide the first report of Chytridiomycota from Oman.
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Affiliation(s)
- Brandon T Hassett
- UiT-The Arctic University of Norway , Framstredet 6, Tromsø 9019, Norway
| | - Badriya K Al-Shaibi
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University , P.O. Box-34, Al-Khod 123, Oman
| | - Abdulrahman Al-Nabhani
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University , P.O. Box-34, Al-Khod 123, Oman
| | - Abdullah M Al-Sadi
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University , P.O. Box-34, Al-Khod 123, Oman
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