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Rippel TM, Wimp GM. Succession of Fungal Communities and Their Functional Profiles in a Decaying Foundation Species. MICROBIAL ECOLOGY 2023; 86:3003-3012. [PMID: 37792090 DOI: 10.1007/s00248-023-02306-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 09/21/2023] [Indexed: 10/05/2023]
Abstract
Dead plant biomass from foundation plant species is fundamental for the survival of coastal salt marshes because dead biomass aids in the vertical accretion of the ecosystem. Fungi regulate the decomposition of dead biomass, and thus play an essential role for marsh survival. Despite their importance, little is known about the compositional and functional changes of fungal communities in plant matter throughout senescence and litter decomposition. Here, we analyzed how fungal communities and their functionality change in the foundation plant species Spartina patens, which builds vast amounts of dead plant biomass (thatch) on the soil surface. We analyzed the chemical and fungal properties of live biomass, standing dead biomass (dead biomass shortly after senescence), upper thatch (top layer of litter on the soil surface), and lower thatch (bottom layer of litter on the soil surface) during September and November of 2021. We found that the chemical and fungal properties of different S. patens biomass types followed a predictable litter decomposition pattern. Notably, live biomass, standing dead biomass, upper thatch, and lower thatch all hosted unique fungal communities and litter chemistry. Functional groups present in live biomass (pathogens, epiphytes, and mycoparasites) were lost during senescence and later replaced by diverse saprotrophs. The abundance of lignocellulose saprotrophs increased throughout decomposition, with the highest abundance occurring in lower thatch. These results suggest a predictable succession of fungal communities through the senescence and decomposition of the foundation species S. patens. Our study highlights the diversity of fungal communities in a disappearing foundation species.
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Affiliation(s)
- Tyler M Rippel
- Department of Biology, Georgetown University, 3700 O Street NW, Washington, D.C., USA.
| | - Gina M Wimp
- Department of Biology, Georgetown University, 3700 O Street NW, Washington, D.C., USA
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Shi T, Wang H, Li YJ, Wang YF, Pan Q, Wang B, Shang EL. Genus Acrostalagmus: A Prolific Producer of Natural Products. Biomolecules 2023; 13:1191. [PMID: 37627256 PMCID: PMC10452555 DOI: 10.3390/biom13081191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023] Open
Abstract
Acrostalagmus is known for its ability to produce numerous bioactive natural products, making it valuable in drug development. This review provides information on the sources, distribution, chemical structure types, biosynthesis, and biological activities of the compounds isolated from the genus Acrostalagmus in the family Plectosphaerellaceae from 1969 to 2022. The results show that 50% of the compounds isolated from Acrostalagmus are new natural products, and 82% of the natural products derived from this genus are from the marine Acrostalagmus. The compounds isolated from Acrostalagmus exhibit diverse structures, with alkaloids being of particular importance, accounting for 56% of the natural products derived from this genus. Furthermore, within the alkaloid class, 61% belong to the epipolythiodioxopiperazine family, highlighting the significance of epipolythiodioxopiperazine as a key characteristic structure within Acrostalagmus. Seventy-two percent of natural products derived from Acrostalagmus display bioactivities, with 50% of the bioactive compounds exhibiting more significant or comparable activities than their positive controls. Interestingly, 89% of potent active compounds are derived from marine fungi, demonstrating their promising potential for development. These findings underscore Acrostalagmus, particularly the marine-derived genus Acrostalagmusas, a valuable source of new bioactive secondary metabolites, and emphasize the vast resource importance of the ocean.
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Affiliation(s)
- Ting Shi
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (T.S.); (H.W.); (Y.-J.L.); (Y.-F.W.); (Q.P.)
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Han Wang
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (T.S.); (H.W.); (Y.-J.L.); (Y.-F.W.); (Q.P.)
| | - Yan-Jing Li
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (T.S.); (H.W.); (Y.-J.L.); (Y.-F.W.); (Q.P.)
| | - Yi-Fei Wang
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (T.S.); (H.W.); (Y.-J.L.); (Y.-F.W.); (Q.P.)
| | - Qun Pan
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (T.S.); (H.W.); (Y.-J.L.); (Y.-F.W.); (Q.P.)
| | - Bo Wang
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (T.S.); (H.W.); (Y.-J.L.); (Y.-F.W.); (Q.P.)
| | - Er-Lei Shang
- School of Life Sciences, Shandong University, Qingdao 266237, China
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Ciancio A, Rosso LC, Lopez-Cepero J, Colagiero M. Rhizosphere 16S-ITS Metabarcoding Profiles in Banana Crops Are Affected by Nematodes, Cultivation, and Local Climatic Variations. Front Microbiol 2022; 13:855110. [PMID: 35756021 PMCID: PMC9218937 DOI: 10.3389/fmicb.2022.855110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/13/2022] [Indexed: 11/13/2022] Open
Abstract
Agriculture affects soil and root microbial communities. However, detailed knowledge is needed on the effects of cropping on rhizosphere, including biological control agents (BCA) of nematodes. A metabarcoding study was carried out on the microbiota associated with plant parasitic and other nematode functional groups present in banana farms in Tenerife (Canary Islands, Spain). Samples included rhizosphere soil from cv Pequeña Enana or Gruesa and controls collected from adjacent sites, with the same agroecological conditions, without banana roots. To characterize the bacterial communities, the V3 and V4 variable regions of the 16S rRNA ribosomal gene were amplified, whereas the internal transcribed spacer (ITS) region was used for the fungi present in the same samples. Libraries were sequenced with an Illumina MiSeq™ in paired ends with a 300-bp read length. For each sample, plant parasitic nematodes (PPN) and other nematodes were extracted from the soil, counted, and identified. Phytoparasitic nematodes were mostly found in banana rhizosphere. They included Pratylenchus goodeyi, present in northern farms, and Helicotylenchus spp., including H. multicinctus, found in both northern and southern farms. Metabarcoding data showed a direct effect of cropping on microbial communities, and latitude-related factors that separated northern and southern controls from banana rizosphere samples. Several fungal taxa known as nematode BCA were identified, with endophytes, mycorrhizal species, and obligate Rozellomycota endoparasites, almost only present in the banana samples. The dominant bacterial phyla were Proteobacteria, Actinobacteria, Planctomycetes, Bacteroidetes, Chloroflexi, and Acidobacteria. The ITS data showed several operational taxonomic units (OTUs) belonging to Sordariomycetes, including biocontrol agents, such as Beauveria spp., Arthrobotrys spp., Pochonia chlamydosporia, and Metarhizium anisopliae. Other taxa included Trichoderma harzianum, Trichoderma longibrachiatum, Trichoderma virens, and Fusarium spp., together with mycoparasites such as Acrostalagmus luteoalbus. However, only one Dactylella spp. showed a correlation with predatory nematodes. Differences among the nematode guilds were found, as phytoparasitic, free-living, and predatory nematode groups were correlated with specific subsets of other bacteria and fungi. Crop cultivation method and soil texture showed differences in taxa representations when considering other farm and soil variables. The data showed changes in the rhizosphere and soil microbiota related to trophic specialization and specific adaptations, affecting decomposers, beneficial endophytes, mycorrhizae, or BCA, and plant pathogens.
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Affiliation(s)
- Aurelio Ciancio
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, Italy
| | - Laura Cristina Rosso
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, Italy
| | - Javier Lopez-Cepero
- Departamento Técnico de Coplaca S.C., Organización de Productores de Plátanos, Santa Cruz de Tenerife, Spain
| | - Mariantonietta Colagiero
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, Italy
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Gakuubi MM, Ching KC, Munusamy M, Wibowo M, Liang ZX, Kanagasundaram Y, Ng SB. Enhancing the Discovery of Bioactive Secondary Metabolites From Fungal Endophytes Using Chemical Elicitation and Variation of Fermentation Media. Front Microbiol 2022; 13:898976. [PMID: 35733953 PMCID: PMC9207341 DOI: 10.3389/fmicb.2022.898976] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/05/2022] [Indexed: 11/26/2022] Open
Abstract
Endophytic microorganisms are an important source of bioactive secondary metabolites. In this study, fungal endophytes obtained from A*STAR’s Natural Product Library (NPL) and previously isolated from different habitats of Singapore were investigated for their diversity, antimicrobial, and cytotoxic activities. A total of 222 fungal strains were identified on the basis of sequence analysis of ITS region of the rDNA gene. The identified fungal strains belong to 59 genera distributed in 20 orders. Majority of the identified strains (99%; 219 strains) belong to the phylum Ascomycota, while two strains belonged to the phylum Basidiomycota, and only one strain was from Mucoromycota phylum. The most dominant genus was Colletotrichum accounting for 27% of all the identified strains. Chemical elicitation using 5-azacytidine and suberoylanilide hydroxamic acid (SAHA) and variation of fermentation media resulted in the discovery of more bioactive strains. Bioassay-guided isolation and structure elucidation of active constituents from three prioritized fungal strains: Lophiotrema sp. F6932, Muyocopron laterale F5912, and Colletotrichum tropicicola F10154, led to the isolation of a known compound; palmarumycin C8 and five novel compounds; palmarumycin CP30, muyocopronol A-C and tropicicolide. Tropicicolide displayed the strongest antifungal activity against Aspergillus fumigatus with an IC50 value of 1.8 μg/ml but with a weaker activity against the Candida albicans presenting an IC50 of 7.1 μg/ml. Palmarumycin C8 revealed the best antiproliferative activity with IC50 values of 1.1 and 2.1 μg/ml against MIA PaCa-2 and PANC-1 cells, respectively.
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Affiliation(s)
- Martin Muthee Gakuubi
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Kuan Chieh Ching
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Madhaiyan Munusamy
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Mario Wibowo
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yoganathan Kanagasundaram
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- *Correspondence: Siew Bee Ng,
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Yasseen BT, Al-Thani RF. Endophytes and Halophytes to Remediate Industrial Wastewater and Saline Soils: Perspectives from Qatar. PLANTS 2022; 11:plants11111497. [PMID: 35684269 PMCID: PMC9182595 DOI: 10.3390/plants11111497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/20/2022] [Accepted: 05/20/2022] [Indexed: 01/22/2023]
Abstract
Many halophytes are considered to be salt hyperaccumulators, adopting ion extrusion and inclusion mechanisms. Such plants, with high aboveground biomass, may play crucial roles in saline habitats, including soil desalination and phytoremediation of polluted soils and waters. These plants cause significant changes in some of the soil’s physical and chemical properties; and have proven efficient in removing heavy metals and metabolizing organic compounds from oil and gas activities. Halophytes in Qatar, such as Halopeplis perfoliata, Salicornia europaea, Salsola soda, and Tetraena qatarensis, are shown here to play significant roles in the phytoremediation of polluted soils and waters. Microorganisms associated with these halophytes (such as endophytic bacteria) might boost these plants to remediate saline and polluted soils. A significant number of these bacteria, such as Bacillus spp. and Pseudomonas spp., are reported here to play important roles in many sectors of life. We explore the mechanisms adopted by the endophytic bacteria to promote and support these halophytes in the desalination of saline soils and phytoremediation of polluted soils. The possible roles played by endophytes in different parts of native plants are given to elucidate the mechanisms of cooperation between these native plants and the associated microorganisms.
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Zhu JN, Yu YJ, Dai MD, Zeng YL, Lu XJ, Wang L, Liu XH, Su ZZ, Lin FC. A New Species in Pseudophialophora From Wild Rice and Beneficial Potential. Front Microbiol 2022; 13:845104. [PMID: 35359723 PMCID: PMC8963453 DOI: 10.3389/fmicb.2022.845104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 01/26/2022] [Indexed: 11/13/2022] Open
Abstract
Wild rice (Oryza granulata) is a natural resource pool containing abundant unknown endophytic fungi species. There are few reports on the endophytic fungi in wild rice. Here, one isolate recovered from wild rice roots was identified as a new species Pseudophialophora oryzae sp. nov based on the molecular phylogeny and morphological characteristics. Fluorescent protein-expressing P. oryzae was used to monitor the fungal colonization pattern. Hyphae invaded the epidermis to the inner cortex but not into the root stele. The inoculation of P. oryzae promoted the rice growth, with the growth parameters of chlorophyll content, shoot height, root length, fresh shoot weight, fresh root weight and dry weight increasing by 24.10, 35.32, 19.35, 90.00, 33.3, and 79.17%, respectively. P. oryzae induced up-regulation of nitrate transporter OsPTR9 and potassium transporter OsHAK16 by 7.28 ± 0.84 and 2.57 ± 0.80 folds, promoting nitrogen and potassium elements absorption. In addition, P. oryzae also conferred a systemic resistance against rice blast, showing a 72.65 and 75.63% control rate in sterile plates and potting conditions. This systemic resistance was mediated by the strongly up-regulated expression of resistance-related genes NAC, OsSAUR2, OsWRKY71, EL5, and PR1α. Since P. oryzae can promote rice growth, biomass and induce systemic disease resistance, it can be further developed as a new biogenic agent for agricultural production, providing a new approach for biocontrol of rice blast.
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Affiliation(s)
- Jia-Nan Zhu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yi-Jun Yu
- Department of Agriculture and Rural of Zhejiang Province, Hangzhou, China
| | - Meng-Di Dai
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yu-Lan Zeng
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xuan-Jun Lu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Ling Wang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiao-Hong Liu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhen-Zhu Su
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- *Correspondence: Zhen-Zhu Su,
| | - Fu-Cheng Lin
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Fu-Cheng Lin,
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AlSharari SS, Galal FH, Seufi AM. Composition and Diversity of the Culturable Endophytic Community of Six Stress-Tolerant Dessert Plants Grown in Stressful Soil in a Hot Dry Desert Region. J Fungi (Basel) 2022; 8:jof8030241. [PMID: 35330243 PMCID: PMC8948987 DOI: 10.3390/jof8030241] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 12/26/2022] Open
Abstract
Saudi Arabia is part of a hot dry desert region and is characterized by stressful conditions. The main goal of this research was to identify endophytic fungal (EF) community composition, diversity and abundance in relation to their plant hosts and soil stress. The above-ground parts of six wild plants (Haloxylon salicornicum, Salsola kali, Heliotropium bacciferum, Erica verticillata, Salsola imbricata and Bienertia sinuspersici) were sampled, surface-sterilized and cut into small pieces, which were cultured and incubated for 4–6 weeks. Isolates were grouped and identified by using both morphological and ITS rDNA molecular data. The diversity and community structure of plant-endophyte associations were studied. A total of 455 EF isolates were grouped into 25 different taxa; 21 of which were identified at the species level, 2 at genus level and 2 were unclassified fungi. Here, 95.65% of the identified genera were Ascomycota; of which 36.36, 31.81 and 31.81% were members of the classes Dothideomycetes, Eurotiomycetes and Sordariomycetes, respectively. S. imbricata showed the highest isolation rate and colonization frequency (CF%) of EF when compared to other plant species. Additionally, S. imbricata demonstrated the highest species richness and species diversity of the EF community predominated by the genus Fusarium. Conclusively, the core culturable EF genera of six wild plants were identified (unculturable taxa were not identified in this study). The composition of the EF community was revealed to have a strong correlation to both the electrical conductivity and pH of the soil and a moderate correlation to both the host species and the host family. The abundance and diversity of EF communities of the six plants were environment-dependent.
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Affiliation(s)
- Salam S. AlSharari
- Biology Department, College of Science, Jouf University, Sakaka P.O. Box 72341, Saudi Arabia;
- Correspondence: (S.S.A.); (A.M.S.)
| | - Fatma H. Galal
- Biology Department, College of Science, Jouf University, Sakaka P.O. Box 72341, Saudi Arabia;
- Department of Entomology, Faculty of Science, Cairo University, Giza P.O. Box 12613, Egypt
| | - AlaaEddeen M. Seufi
- Department of Entomology, Faculty of Science, Cairo University, Giza P.O. Box 12613, Egypt
- Correspondence: (S.S.A.); (A.M.S.)
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Calabon MS, Jones EBG, Promputtha I, Hyde KD. Fungal Biodiversity in Salt Marsh Ecosystems. J Fungi (Basel) 2021; 7:jof7080648. [PMID: 34436187 PMCID: PMC8399140 DOI: 10.3390/jof7080648] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 07/27/2021] [Accepted: 07/30/2021] [Indexed: 11/16/2022] Open
Abstract
This review brings together the research efforts on salt marsh fungi, including their geographical distribution and host association. A total of 486 taxa associated with different hosts in salt marsh ecosystems are listed in this review. The taxa belong to three phyla wherein Ascomycota dominates the taxa from salt marsh ecosystems accounting for 95.27% (463 taxa). The Basidiomycota and Mucoromycota constitute 19 taxa and four taxa, respectively. Dothideomycetes has the highest number of taxa, which comprises 47.12% (229 taxa), followed by Sordariomycetes with 167 taxa (34.36%). Pleosporales is the largest order with 178 taxa recorded. Twenty-seven genera under 11 families of halophytes were reviewed for its fungal associates. Juncus roemerianus has been extensively studied for its associates with 162 documented taxa followed by Phragmites australis (137 taxa) and Spartina alterniflora (79 taxa). The highest number of salt marsh fungi have been recorded from Atlantic Ocean countries wherein the USA had the highest number of species recorded (232 taxa) followed by the UK (101 taxa), the Netherlands (74 taxa), and Argentina (51 taxa). China had the highest number of salt marsh fungi in the Pacific Ocean with 165 taxa reported, while in the Indian Ocean, India reported the highest taxa (16 taxa). Many salt marsh areas remain unexplored, especially those habitats in the Indian and Pacific Oceans areas that are hotspots of biodiversity and novel fungal taxa based on the exploration of various habitats.
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Affiliation(s)
- Mark S. Calabon
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand;
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - E. B. Gareth Jones
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia;
| | - Itthayakorn Promputtha
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
- Environmental Science Research Center, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Kevin D. Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand;
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
- Innovative Institute of Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Correspondence:
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