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Schneider YK, Hagestad OC, Li C, Hansen EH, Andersen JH. Selective isolation of Arctic marine actinobacteria and a down-scaled fermentation and extraction strategy for identifying bioactive compounds. Front Microbiol 2022; 13:1005625. [DOI: 10.3389/fmicb.2022.1005625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/21/2022] [Indexed: 11/22/2022] Open
Abstract
Actinobacteria are among the most prolific producers of bioactive secondary metabolites. In order to collect Arctic marine bacteria for the discovery of new bioactive metabolites, actinobacteria were selectively isolated during a research cruise in the Greenland Sea, Norwegian Sea and the Barents Sea. In the frame of the isolation campaign, it was investigated how different sample treatments, isolation media and sample-sources, such as animals and sediments, affected the yield of actinobacterial isolates to aid further isolation campaigns. Special attention was given to sediments, where we expected spores of spore forming bacteria to enrich. Beside actinobacteria a high share of bacilli was obtained which was not desired. An experimental protocol for down-scaled cultivation and extraction was tested and compared with an established low-throughput cultivation and extraction protocol. The heat-shock method proved suitable to enrich spore-, or endospore forming bacteria such as bacilli. Finally, a group bioactive compounds could be tentatively identified using UHPLC–MS/MS analysis of the active fractions.
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102
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Zhang H, Yang MF, Zhang Q, Yan B, Jiang YL. Screening for broad-spectrum antimicrobial endophytes from Rosa roxburghii and multi-omic analyses of biosynthetic capacity. FRONTIERS IN PLANT SCIENCE 2022; 13:1060478. [PMID: 36466255 PMCID: PMC9709285 DOI: 10.3389/fpls.2022.1060478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/28/2022] [Indexed: 06/17/2023]
Abstract
Plants with certain medicinal values are a good source for isolating function-specific endophytes. Rosa roxburghii Tratt. has been reported to be a botanical source of antimicrobial compounds, which may represent a promising candidate for screening endophytic fungi with antimicrobial potential. In this study, 54 endophytes were isolated and molecularly identified from R. roxburghii. The preliminary screening using the plate confrontation method resulted in 15 different endophytic strains showing at least one strong inhibition or three or more moderate inhibition against the 12 tested strains. Further re-screening experiments based on the disc diffusion method demonstrated that Epicoccum latusicollum HGUP191049 and Setophoma terrestris HGUP190028 had excellent antagonistic activity. The minimum inhibitory concentration (MIC) test for extracellular metabolites finally indicated that HGUP191049 had lower MIC values and a broader antimicrobial spectrum, compared to HGUP190028. Genomic, non-target metabolomic, and comparative genomic studies were performed to understand the biosynthetic capacity of the screened-out endophytic fungus. Genome sequencing and annotation of HGUP191049 revealed a size of 33.24 megabase pairs (Mbp), with 24 biosynthetic gene clusters (BGCs), where the putative antimicrobial compounds, oxyjavanicin, patulin and squalestatin S1 were encoded by three different BGCs, respectively. In addition, the non-targeted metabolic results demonstrated that the strain contained approximately 120 antimicrobial secondary metabolites and was structurally diverse. Finally, comparative genomics revealed differences in pathogenicity, virulence, and carbohydrate-active enzymes in the genome of Epicoccum spp. Moreover, the results of the comparative analyses presumed that Epicoccum is a promising source of antimicrobial terpenes, while oxyjavanicin and squalestatin S1 are antimicrobial compounds shared by the genus. In conclusion, R. roxburghii and the endophytic HGUP191049 isolated from it are promising sources of broad-spectrum antimicrobial agents.
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Affiliation(s)
- Hong Zhang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
- Guizhou Academy of Testing and Analysis, Guiyang, China
| | - Mao-Fa Yang
- Institute of Entomology, Guizhou University, Guiyang, China
- College of Tobacco Science, Guizhou University, Guiyang, China
| | - Qian Zhang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
| | - Bin Yan
- Institute of Entomology, Guizhou University, Guiyang, China
| | - Yu-Lan Jiang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
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103
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Adelusi OA, Gbashi S, Adebiyi JA, Makhuvele R, Aasa AO, Oladeji OM, Khoza M, Okoth S, Njobeh PB. Seasonal Diversity and Occurrence of Filamentous Fungi in Smallholder Dairy Cattle Feeds and Feedstuffs in South Africa. J Fungi (Basel) 2022; 8:jof8111192. [PMID: 36422014 PMCID: PMC9696519 DOI: 10.3390/jof8111192] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
This study investigated 65 (35 in summer and 30 in winter) smallholder dairy cattle feeds from Free State and Limpopo provinces in South Africa from 2018 to 2019 for fungal contamination and assessed the impacts of seasonal variation on fungal contamination levels, isolation frequency, and diversity. Samples were examined for fungal contamination using macro- and microscopic approaches, and their identities were confirmed by molecular means. A total of 217 fungal isolates from 14 genera, including Aspergillus, Fusarium, and Penicillium, were recovered from feeds from both seasons. The most prevalent fungal species recovered were A. fumigatus and P. crustosum. Mycological analyses showed that 97% of samples were contaminated with one or more fungal isolates, with the summer fungal mean level (6.1 × 103 to 3.0 × 106 CFU/g) higher than that of feeds sampled during winter (mean level: 1.1 × 103 to 4.1 × 105 CFU/g). Independent sample t-test revealed that the isolation frequencies of the genera Aspergillus and Fusarium were significantly (p ≤ 0.05) higher in summer than winter, while Penicillium prevalence in both seasons was not statistically (p > 0.05) different. Furthermore, the Shannon−Weiner diversity index (H′) revealed a higher fungal diversity in summer (H′ = 2.8) than in winter (H′ = 2.1). This study on fungal contamination could be used for future fungal control and mycotoxin risk management in South Africa.
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Affiliation(s)
- Oluwasola Abayomi Adelusi
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, Johannesburg P.O. Box 17011, South Africa
- Correspondence: (O.A.A.); (P.B.N.)
| | - Sefater Gbashi
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, Johannesburg P.O. Box 17011, South Africa
| | - Janet Adeyinka Adebiyi
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, Johannesburg P.O. Box 17011, South Africa
| | - Rhulani Makhuvele
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, Johannesburg P.O. Box 17011, South Africa
| | - Adeola Oluwakemi Aasa
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, Johannesburg P.O. Box 17011, South Africa
| | - Oluwaseun Mary Oladeji
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, Johannesburg P.O. Box 17011, South Africa
| | - Minenhle Khoza
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, Johannesburg P.O. Box 17011, South Africa
| | - Sheila Okoth
- Department of Biological sciences, University of Nairobi, Nairobi P.O. Box 30197-00100, Kenya
| | - Patrick Berka Njobeh
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, Johannesburg P.O. Box 17011, South Africa
- Correspondence: (O.A.A.); (P.B.N.)
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104
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Dong QY, Wang Y, Wang ZQ, Liu YF, Yu H. Phylogeny and Systematics of the Genus Tolypocladium (Ophiocordycipitaceae, Hypocreales). J Fungi (Basel) 2022; 8:1158. [PMID: 36354925 PMCID: PMC9697939 DOI: 10.3390/jof8111158] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/29/2022] [Accepted: 10/30/2022] [Indexed: 11/14/2023] Open
Abstract
The taxonomy and phylogeny of the genus Tolypocladium are herein revised based on the most comprehensive dataset to date. Two species-level phylogenies of Tolypocladium were constructed: a single-gene phylogeny (ITS) of 35 accepted species and a multigene phylogeny (nrSSU, nrLSU, tef-1α, rpb1, and rpb2) of 27 accepted species. Three new species, Tolypocladium pseudoalbum sp. nov., Tolypocladium subparadoxum sp. nov., and Tolypocladium yunnanense sp. nov., are described in the present study. The genetic divergences of four markers (ITS, tef-1α, rpb1 and rpb2) among Tolypocladium species are also reported. The results indicated that species of Tolypocladium were best delimited by rpb1 sequence data, followed by the sequence data for the rpb2, tef-1α, and ITS provided regions. Finally, a key to the 48 accepted species of Tolypocladium worldwide is provided.
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Affiliation(s)
- Quan-Ying Dong
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650504, China
- The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650504, China
| | - Yao Wang
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650504, China
| | - Zhi-Qin Wang
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650504, China
- The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650504, China
| | - Yan-Fang Liu
- The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650504, China
| | - Hong Yu
- The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650504, China
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105
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Pereira Dos Santos VH, Luiz JHH, Dos Anjos JP, de Oliveira Silva E. Oxidative potential of two Brazilian endophytic fungi from Handroanthus impetiginosus towards progesterone. Steroids 2022; 187:109101. [PMID: 35970224 DOI: 10.1016/j.steroids.2022.109101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 08/06/2022] [Accepted: 08/09/2022] [Indexed: 11/26/2022]
Abstract
Biotransformation has been successfully employed to conduct uncommon reactions, which would hardly be carried out by chemical synthesis. A wide diversity of compounds may be metabolized by fungi, leading to chemical derivatives through selective reactions that work under ecofriendly conditions. Endophytic fungi live inside vegetal tissues without causing damage to the host plant, making available unique enzymes for interesting chemical derivatization. Biotransformation of steroids by endophytic fungi may provide new derivatives as these microorganisms came from uncommon and underexplored habitats. In this study, endophytic strains isolated from Handroanthus impetiginosus leaves were assayed for biotransformation of progesterone, and its derivatives were identified through GC-EI-MS analysis. The endophyte Talaromyces sp. H4 was capable of transforming the steroidal nucleus selectively into four products through selective ene-reduction of the C4-C5 double bond and C-17 oxidation. The best conversion rate of progesterone (>90 %) was reached with Penicillium citrinum H7 endophytic strain that transformed the substrate into one derivative. The results highlight endophytic fungi's potential to obtain new and interesting steroidal derivatizations.
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Affiliation(s)
| | | | - Jeancarlo Pereira Dos Anjos
- University Center SENAI CIMATEC, Salvador, BA, Brazil; INCT in Energy and Environment, Federal University of Bahia, Salvador, BA, Brazil
| | - Eliane de Oliveira Silva
- Departament of Organic Chemistry, Chemistry Institute, Federal University of Bahia, Salvador, BA, Brazil.
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Rojas-Flores S, Nazario-Naveda R, Benites SM, Gallozzo-Cardenas M, Delfín-Narciso D, Díaz F. Use of Pineapple Waste as Fuel in Microbial Fuel Cell for the Generation of Bioelectricity. Molecules 2022; 27:molecules27217389. [PMID: 36364216 PMCID: PMC9658398 DOI: 10.3390/molecules27217389] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
The excessive use of fossil sources for the generation of electrical energy and the increase in different organic wastes have caused great damage to the environment; these problems have promoted new ways of generating electricity in an eco-friendly manner using organic waste. In this sense, this research uses single-chamber microbial fuel cells with zinc and copper as electrodes and pineapple waste as fuel (substrate). Current and voltage peaks of 4.95667 ± 0.54775 mA and 0.99 ± 0.03 V were generated on days 16 and 20, respectively, with the substrate operating at an acid pH of 5.21 ± 0.18 and an electrical conductivity of 145.16 ± 9.86 mS/cm at two degrees Brix. Thus, it was also found that the internal resistance of the cells was 865.845 ± 4.726 Ω, and a maximum power density of 513.99 ± 6.54 mW/m2 was generated at a current density of 6.123 A/m2, and the final FTIR spectrum showed a clear decrease in the initial transmittance peaks. Finally, from the biofilm formed on the anodic electrode, it was possible to molecularly identify the yeast Wickerhamomyces anomalus with 99.82% accuracy. In this way, this research provides a method that companies exporting and importing this fruit may use to generate electrical energy from its waste.
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Affiliation(s)
- Segundo Rojas-Flores
- Escuela de Ingeniería Mecánica Eléctrica, Universidad Señor de Sipán, Chiclayo 14000, Peru
- Correspondence:
| | - Renny Nazario-Naveda
- Vicerrectorado de Investigación, Universidad Autónoma del Perú, Lima 15842, Peru
| | - Santiago M. Benites
- Vicerrectorado de Investigación, Universidad Autónoma del Perú, Lima 15842, Peru
| | | | - Daniel Delfín-Narciso
- Grupo de Investigación en Ciencias Aplicadas y Nuevas Tecnologías, Universidad Privada del Norte, Trujillo 13007, Peru
| | - Félix Díaz
- Escuela Académica Profesional de Medicina Humana, Universidad Norbert Wiener, Lima 15046, Peru
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107
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Tarroum M, Romdhane WB, Al-Qurainy F, Ali AAM, Al-Doss A, Fki L, Hassairi A. A novel PGPF Penicillium olsonii isolated from the rhizosphere of Aeluropus littoralis promotes plant growth, enhances salt stress tolerance, and reduces chemical fertilizers inputs in hydroponic system. Front Microbiol 2022; 13:996054. [PMID: 36386667 PMCID: PMC9648140 DOI: 10.3389/fmicb.2022.996054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 10/05/2022] [Indexed: 12/02/2022] Open
Abstract
The hydroponic farming significantly enhances the yield and enables multiple cropping per year. These advantages can be improved by using plant growth-promoting fungi (PGPF) either under normal or stress conditions. In this study, the fungal strain (A3) isolated from the rhizosphere of the halophyte plant Aeluropus littoralis was identified as Penicillium olsonii based on sequence homology of its ITS region. The A3 fungus was shown to be halotolerant (up to 1 M NaCl) and its optimal growth was at 27°C, but inhibited at 40°C. In liquid culture medium, the A3 produced indole acetic acid (IAA) especially in the presence of L-tryptophan. Tobacco plants grown under hydroponic farming system were used to evaluate the promoting activity of the direct effect of A3 mycelium (DE) and the indirect effect (IDE) of its cell-free culture filtrate (A3CFF). The results showed that for the two conditions (DE or IDE) the tobacco seedlings exhibited significant increase in their height, leaf area, dry weight, and total chlorophyll content. Interestingly, the A3CFF (added to the MS liquid medium or to nutrient solution (NS), prepared from commercial fertilizers) induced significantly the growth parameters, the proline concentration, the catalase (CAT) and the superoxide dismutase (SOD) activities of tobacco plants. The A3CFF maintained its activity even after extended storage at 4°C for 1 year. Since the A3 is a halotolerant fungus, we tested its ability to alleviate salt stress effects. Indeed, when added at 1:50 dilution factor to NS in the presence of 250 mM NaCl, the A3CFF enhanced the plant salt tolerance by increasing the levels of total chlorophyll, proline, CAT, and SOD activities. In addition, the treated plants accumulated less Na+ in their roots but more K+ in their leaves. The A3CFF was also found to induce the expression of five salt stress related genes (NtSOS1, NtNHX1, NtHKT1, NtSOD, and NtCAT1). Finally, we proved that the A3CFF can reduce by half the chemical fertilizers inputs. Indeed, the tobacco plants grown in a hydroponic system using 0.5xNS supplemented with A3CFF (1:50) exhibited significantly higher growth than those grown in 0.5xNS or 1xNS. In an attempt to explain this mechanism, the expression profile of some growth related genes (nitrogen metabolism (NR1, NRT1), auxin (TRYP1, YUCCA6-like), and brassinosteroid (DET2, DWF4) biosynthesis) was performed. The results showed that all these genes were up-regulated following plant treatment with A3CFF. In summary the results revealed that the halotolerant fungus P. olsonii can stimulates tobacco plant growth, enhances its salt tolerance, and reduces by half the required chemical fertilizer inputs in a hydroponic farming system.
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Affiliation(s)
- Mohamed Tarroum
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
- *Correspondence: Mohamed Tarroum,
| | - Walid Ben Romdhane
- Department of Plant Production, College of Food and Agricultural Science, King Saud University, Riyadh, Saudi Arabia
| | - Fahad Al-Qurainy
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed Abdelrahim Mohamed Ali
- Department of Plant Production, College of Food and Agricultural Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah Al-Doss
- Department of Plant Production, College of Food and Agricultural Science, King Saud University, Riyadh, Saudi Arabia
| | - Lotfi Fki
- Laboratory of Plant Biotechnology Applied to Crop Improvement, Faculty of Sciences of Sfax, University of Sfax, Sfax, Tunisia
| | - Afif Hassairi
- Department of Plant Production, College of Food and Agricultural Science, King Saud University, Riyadh, Saudi Arabia
- Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
- Afif Hassairi,
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108
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The Introduction of Two New Species of Aquatic Fungi from Anzali Lagoon, Northern Iran. DIVERSITY 2022. [DOI: 10.3390/d14100889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
During a survey of aquatic fungi from Anzali Lagoon in Iran, several fungal specimens were isolated from freshwater habitats. Morphological evidence and comparing sequencing based on rDNA (ITS and LSU) and protein-coding genes (TEF1 and TUB2) showed that some isolates belong to undescribed fungal species. These isolates belong to Arthrobotrys and Sarocladium, two ascomycetes genera. Arthrobotrys hyrcanus, sp. nov., differs from closely related species such as A. dianchiensis by its larger conidia and septation of primary conidia. Sarocladium pseudokiliense, sp. nov., was similar to S. kiliense, but distinguished by its conidial shape and the absence of adelophialides and chlamydospores. Morphological descriptions, illustrations and multilocus phylogenetic analysis for both new species are provided.
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109
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Kespohl S, Riebesehl J, Grüner J, Raulf M. Impact of climate change on wood and woodworkers- Cryptostroma corticale (sooty bark disease): A risk factor for trees and exposed employees. Front Public Health 2022; 10:973686. [PMID: 36330129 PMCID: PMC9623262 DOI: 10.3389/fpubh.2022.973686] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 09/21/2022] [Indexed: 01/21/2023] Open
Abstract
Climate changes have promoted an increased fungal infection of maple trees with Cryptostroma corticale, the causative agent of sooty bark disease. The hosts of C. corticale are maples, and since the early 2000s the fungus has been appearing more frequently in European forests, due to the droughts and hot summers of recent years. Infestation by C. corticale discolors the wood and makes it unusable for further processing, which leads to considerable economic damage in the timber industry. Therefore, the occurrence and spread of sooty bark disease raise serious problems. In addition to forestry and economic problems, the conidiospores of C. corticale can also cause health problems in exposed wood workers and they can trigger hypersensitivity pneumonitis (HP). Since the spores, which are deposited over the entire area under the bark of infected trees, can spread during processing, exposed workers must take special precautions to protect themselves against exposure. If an occupational disease is nevertheless suspected following exposure to C. corticale, valid diagnostics are required to confirm possible HP and derive appropriate therapies and exposure reduction or avoidance. Diagnosis of HP is based on several criteria, one of them is the detection of specific IgG in patient's serum against the potentially triggering antigens, in this case C. corticale antigens. To produce a diagnostic tool to measure C. corticale specific IgG, which is not commercially available so far, spores and mycelial material from ITS-sequenced strains of C. corticale was prepared and analyzed. These biochemically characterized extracts of spore and mycelial antigens were biotinylated and coupled to Streptavidin-ImmunoCAPs. To validate these diagnostic test tools the first step is to measure the concentration of C. corticale specific IgG in sera of healthy non-exposed and healthy exposed subjects to establish cut-off values. Suitable participants were recruited and the individual exposure to C. corticale and symptoms experienced during or after working with infected maple trees were recorded using questionnaires. Finally, diagnostic tools for serological testing in suspected cases of HP by C. corticale were created and evaluated. The following article provides recommendations for the treatment and disposal of infected damaged wood and for occupational health protection procedures. Secondly, the diagnosis of HP induced by exposure to C. corticale as an occupational disease is described including the verification of newly developed serological test tools for antigens of C. corticale.
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Affiliation(s)
- Sabine Kespohl
- Institute for Prevention and Occupational Medicine of the DGUV, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany,*Correspondence: Sabine Kespohl
| | - Janett Riebesehl
- Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Horticulture and Forests, Braunschweig, Germany
| | - Jörg Grüner
- Department of Forest Protection, Forest Research Institute of Baden-Württemberg (FVA), Freiburg, Germany
| | - Monika Raulf
- Institute for Prevention and Occupational Medicine of the DGUV, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
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110
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Xie F, Li HT, Wang M, Chen JY, Duan HJ, Xia DD, Xie TP, Gao YH, Zhou H, Ding ZT. Phialocetones A-J, C 12 lactones from the rhizospheric soil-derived fungus Phialocephala sp. YUD18001 associated with Gastrodia elata. PHYTOCHEMISTRY 2022; 202:113359. [PMID: 35940426 DOI: 10.1016/j.phytochem.2022.113359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Ten undescribed C12 polyketide phialocetones A-J, featuring twelve-, six- and five-membered lactone moieties, were isolated from a rhizospheric soil-derived Phialocephala sp. YUD18001 associated with Gastrodia elata. Their structures were established by NMR spectroscopic analysis and HRMS, while their absolute configurations were determined by computational methods and chemical reactions. All isolated compounds were evaluated for their anti-inflammatory and cytotoxic activities. As a result, phialocetone D exhibited moderate effects against NO production in lipopolysaccharide (LPS)-induced RAW264.7 cells with an IC50 value of 14.77 μM, while phialocetone E showed cytotoxicity against HL-60 and SW480 cell lines with IC50 values of 19.04 and 10.22 μM, respectively.
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Affiliation(s)
- Fei Xie
- Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, China
| | - Hong-Tao Li
- Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, China
| | - Meng Wang
- Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, China
| | - Jing-Yuan Chen
- Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, China
| | - Hao-Jie Duan
- Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, China
| | - Dan-Dan Xia
- Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, China
| | - Tian-Peng Xie
- Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, China
| | - Yu-Hong Gao
- The First People's Hospital of Yunnan Province, Kunming, 650034, China
| | - Hao Zhou
- Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, China.
| | - Zhong-Tao Ding
- Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, China; College of Pharmacy, Dali University, Dali, 671000, China.
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111
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Characterization of Alternaria and Colletotrichum Species Associated with Pomegranate (Punica granatum L.) in Maharashtra State of India. J Fungi (Basel) 2022; 8:jof8101040. [PMID: 36294605 PMCID: PMC9604645 DOI: 10.3390/jof8101040] [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: 08/25/2022] [Revised: 09/26/2022] [Accepted: 09/26/2022] [Indexed: 11/25/2022] Open
Abstract
Fungal pathogens are a major constraint affecting the quality of pomegranate production around the world. Among them, Alternaria and Colletotrichum species cause leaf spot, fruit spot or heart rot (black rot), and fruit rot (anthracnose) or calyx end rot, respectively. Accurate identification of disease-causing fungal species is essential for developing suitable management practices. Therefore, characterization of Alternaria and Colletotrichum isolates representing different geographical regions, predominantly Maharashtra-the Indian hub of pomegranate production and export-was carried out. Fungal isolates could not be identified based on morphological characteristics alone, hence were subjected to multi-gene phylogeny for their accurate identification. Based on a maximum likelihood phylogenetic tree, Alternaria isolates were identified as within the A. alternata species complex and as A. burnsii, while Colletotrichum isolates showed genetic closeness to various species within the C. gloeosporioides species complex. Thus, the current study reports for the first time that, in India, the fruit rots of pomegranate are caused by multiple species and not a single species of Alternaria and Colletotrichum alone. Since different species have different epidemiology and sensitivity toward the commercially available and routinely applied fungicides, the precise knowledge of the diverse species infecting pomegranate, as provided by the current study, is the first step towards devising better management strategies.
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Jiang S, Chen Y, Han S, Lv L, Li L. Next-Generation Sequencing Applications for the Study of Fungal Pathogens. Microorganisms 2022; 10:microorganisms10101882. [PMID: 36296159 PMCID: PMC9609632 DOI: 10.3390/microorganisms10101882] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
Next-generation sequencing (NGS) has become a widely used technology in biological research. NGS applications for clinical pathogen detection have become vital technologies. It is increasingly common to perform fast, accurate, and specific detection of clinical specimens using NGS. Pathogenic fungi with high virulence and drug resistance cause life-threatening clinical infections. NGS has had a significant biotechnological impact on detecting bacteria and viruses but is not equally applicable to fungi. There is a particularly urgent clinical need to use NGS to help identify fungi causing infections and prevent negative impacts. This review summarizes current research on NGS applications for fungi and offers a visual method of fungal detection. With the development of NGS and solutions for overcoming sequencing limitations, we suggest clinicians test specimens as soon as possible when encountering infections of unknown cause, suspected infections in vital organs, or rapidly progressive disease.
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Affiliation(s)
- Shiman Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Yanfei Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Shengyi Han
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Longxian Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250021, China
- Correspondence: ; Tel.: +86-0571-8723-6458
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113
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Yoo S, Cho Y, Kim JS, Kim M, Lim YW. Fourteen Unrecorded Species of Agaricales Underw. (Agaricomycetes, Basidiomycota) from the Republic of Korea. MYCOBIOLOGY 2022; 50:219-230. [PMID: 36158041 PMCID: PMC9467565 DOI: 10.1080/12298093.2022.2097364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/29/2022] [Accepted: 06/29/2022] [Indexed: 06/16/2023]
Abstract
Agaricales species form pileate-stipitate fruiting bodies and play important roles in maintaining the terrestrial ecosystem as decomposers, symbionts, and pathogens. Approximately 23,000 Agaricales species have been known worldwide, and 937 species have been recorded in the Republic of Korea. However, most of them were identified solely based on morphological characteristics that often led to misidentifications. The specimens collected from 2018 to 2020 in the Republic of Korea were identified based on phylogenetic analysis of the internal transcribed spacer (ITS) sequences. Their identities were confirmed by microscopic characteristics. As a result, 14 Agaricales species were discovered for the first time in the Republic of Korea. They belonged to nine genera: Agaricus, Calocybe, Cortinarius, Hygrocybe, Inocybe, Lepista, Leucoagaricus, Marasmius, and Psathyrella. Detailed macroscopic and microscopic descriptions were provided to help distinguish these species. The morphological and molecular data provided in this study will serve as reliable references for the identification of Agaricales species.
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Affiliation(s)
- Shinnam Yoo
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
| | - Yoonhee Cho
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
| | - Ji Seon Kim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
| | - Minkyeong Kim
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Young Woon Lim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
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Molecular diversity, haplotype distribution and genetic variation flow of Bipolaris sorokiniana fungus causing spot blotch disease in different wheat-growing zones. J Appl Genet 2022; 63:793-803. [PMID: 35931929 DOI: 10.1007/s13353-022-00716-w] [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: 07/02/2021] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 10/16/2022]
Abstract
Bipolaris sorokiniana (BS) is an economically important fungal pathogen causing spot blotch of wheat (Trtiticum aestivum) and found in all wheat-growing zones of India. Very scanty and fragmentary information is available on its genetic diversity. The current research is the first detailed report on the geographic distribution and evolution of BS population in five geographically distinct wheat-growing zones (North Western Plain Zone (NWPZ), North Eastern Plain zone (NEPZ), North Hill Zone (NHZ), Southern Hill Zone (SHZ) and Peninsular Zone (PZ)) of India, studied by performing nucleotide sequence comparison of internal transcribed spacer region of 528 isolates. A moderate to low levels of haplotypic diversity was noticed in different wheat-growing zones. Phylogenetic analysis suggests that B. sorokiniana exist in two distinct lineages as all isolates under study were grouped in two different clades and found analogous to the findings of haplotypic and TCS network analysis. The genetic parameters revealed the existence of 40 haplotypes with three major haplotypes (H-1, H-2 and H-3) which showed star-like structure network surrounded by several single haplotypes, revealing high frequency of the mutations (Eta = 2 - 158) in total analyzed population. H-1 was observed as a predominant haplotype and prevalent in all the five zones. Moderate level of genetic differentiation was found between NHZ and other zones like NWPZ (Fst = 0.332) and SHZ (Fst = 0.382) and PZ (Fst = 0.299), whereas it was low between NEPZ and PZ (Fst = 0.034). Higher transfer rate of genetic variation was noticed between NEPZ and PZ (Nm = 7.06), while it was found minimum between NHZ and SHZ (Nm = 0.40). Moreover, negative score of neutrality statistics (Tajima's D and Fu's FS test) for NWPZ population suggested recent population expansion. However, positive score for both the neutrality tests observed in NEPZ indicated the dominance of balancing selection in structuring their population. Recombination events were observed in the NWPZ and NHZ population, while it was absent in SHZ, NEPZ and PZ population. Thus, the lack of any specific genetic population structure in all the zones indicates for the expansion history only from one common source population, i.e. NWPZ, a mega zone of wheat production in India. Overall, it seems that the predominance of individual haplotypes with a moderate level of genetic variation and human-mediated movement of contaminated seed and dispersal of inoculum, mutations and recombination as prime evolutionary processes play essential role in defining the genetic structure of BS population.
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115
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Colletotrichum siamense and Pestalotiopsis jesteri as potential pathogens of new rubber leaf spot disease via detached leaf assay. J RUBBER RES 2022. [DOI: 10.1007/s42464-022-00157-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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116
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Acero D, Khan FST, Medina-Ortiz AJ, Rivero-Cruz I, Raja HA, Flores-Bocanegra L, Fajardo-Hernández CA, Wan B, Franzblau SG, Hematian S, Figueroa M. New Terpenoids from the Corticioid Fungus Punctularia atropurpurascens and their Antimycobacterial Evaluation. PLANTA MEDICA 2022; 88:729-734. [PMID: 35354220 DOI: 10.1055/a-1786-8072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Chemical investigation of Punctularia atropurpurascens strain HM1 (Punctulariaceae), a corticioid isolated from a decorticated piece of Quercus bark collected in Bosque de Tlalpan, Mexico City, led to the isolation of a new drimane, 1-α-hydroxy-isodrimenine (1: ) and a new tetrahydroxy kauranol, 16-hydroxy-phlebia-nor-kauranol (2: ), together with the known N-phenylacetamide (3: ). Structures of all compounds were elucidated by spectroscopic and spectrometric methods, and the absolute configuration of 1: and 2: was confirmed via single-crystal X-ray crystallography. The isolated compounds showed modest antimycobacterial activity.
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Affiliation(s)
- Daniel Acero
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Firoz Shah Tuglak Khan
- Department of Chemistry and Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Abraham J Medina-Ortiz
- Departamento de Laboratorios, Colegio de Ciencias y Humanidades Plantel Sur, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Isabel Rivero-Cruz
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Huzefa A Raja
- Department of Chemistry and Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Laura Flores-Bocanegra
- Department of Chemistry and Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | | | - Baojie Wan
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Scott G Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Shabnam Hematian
- Department of Chemistry and Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Mario Figueroa
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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Patra A, Mukherjee AK. Mushroom mycetism – A neglected and challenging medical emergency in the Indian subcontinent: A road map for its prevention and treatment. Toxicon 2022; 217:56-77. [DOI: 10.1016/j.toxicon.2022.07.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 11/27/2022]
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118
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Multiplex PCR Identification of Aspergillus cristatus and Aspergillus chevalieri in Liupao Tea Based on Orphan Genes. Foods 2022; 11:foods11152217. [PMID: 35892804 PMCID: PMC9332452 DOI: 10.3390/foods11152217] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/19/2022] [Accepted: 07/22/2022] [Indexed: 11/21/2022] Open
Abstract
“Golden flower” fungi in dark tea are beneficial to human health. The rapid identification method of “golden flower” fungi can verify the quality of dark tea products and ensure food safety. In this study, 6 strains were isolated from Liupao tea. They were respectively identified as A. cristatus, A. chevalieri, and A. pseudoglaucus. A. pseudoglaucus was reported as Liupao tea “golden flower” fungus for the first time. It was found that the ITS and BenA sequences of A. cristatus and A. chevalieri were highly conserved. It is difficult to clearly distinguish these closely related species by ITS sequencing. To rapidly identify species, multiplex PCR species-specific primers were designed based on orphan genes screened by comparative genomics analysis. Multiplex PCR results showed that orphan genes were specific and effective for the identification of A. cristatus and A. chevalieri isolated from Liupao tea and Fu brick tea. We confirmed that orphan genes can be used for identification of closely related Aspergillus species. Validation showed that the method is convenient, rapid, robust, sequencing-free, and economical. This promising method will be greatly beneficial to the dark tea processing industry and consumers.
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119
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Kulik T, Molcan T, Fiedorowicz G, van Diepeningen A, Stakheev A, Treder K, Olszewski J, Bilska K, Beyer M, Pasquali M, Stenglein S. Whole-genome single nucleotide polymorphism analysis for typing the pandemic pathogen Fusarium graminearum sensu stricto. Front Microbiol 2022; 13:885978. [PMID: 35923405 PMCID: PMC9339996 DOI: 10.3389/fmicb.2022.885978] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
Recent improvements in microbiology and molecular epidemiology were largely stimulated by whole- genome sequencing (WGS), which provides an unprecedented resolution in discriminating highly related genetic backgrounds. WGS is becoming the method of choice in epidemiology of fungal diseases, but its application is still in a pioneer stage, mainly due to the limited number of available genomes. Fungal pathogens often belong to complexes composed of numerous cryptic species. Detecting cryptic diversity is fundamental to understand the dynamics and the evolutionary relationships underlying disease outbreaks. In this study, we explore the value of whole-genome SNP analyses in identification of the pandemic pathogen Fusarium graminearum sensu stricto (F.g.). This species is responsible for cereal diseases and negatively impacts grain production worldwide. The fungus belongs to the monophyletic fungal complex referred to as F. graminearum species complex including at least sixteen cryptic species, a few among them may be involved in cereal diseases in certain agricultural areas. We analyzed WGS data from a collection of 99 F.g. strains and 33 strains representing all known cryptic species belonging to the FGSC complex. As a first step, we performed a phylogenomic analysis to reveal species-specific clustering. A RAxML maximum likelihood tree grouped all analyzed strains of F.g. into a single clade, supporting the clustering-based identification approach. Although, phylogenetic reconstructions are essential in detecting cryptic species, a phylogenomic tree does not fulfill the criteria for rapid and cost-effective approach for identification of fungi, due to the time-consuming nature of the analysis. As an alternative, analysis of WGS information by mapping sequence data from individual strains against reference genomes may provide useful markers for the rapid identification of fungi. We provide a robust framework for typing F.g. through the web-based PhaME workflow available at EDGE bioinformatics. The method was validated through multiple comparisons of assembly genomes to F.g. reference strain PH-1. We showed that the difference between intra- and interspecies variability was at least two times higher than intraspecific variation facilitating successful typing of F.g. This is the first study which employs WGS data for typing plant pathogenic fusaria.
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Affiliation(s)
- Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
- *Correspondence: Tomasz Kulik,,
| | - Tomasz Molcan
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences (PAN), Warsaw, Poland
| | - Grzegorz Fiedorowicz
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Anne van Diepeningen
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | - Alexander Stakheev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Kinga Treder
- Department of Agriculture Systems, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | | | - Katarzyna Bilska
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Marco Beyer
- Agro-Environmental Systems, Environmental Monitoring and Sensing Unit, Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Esch-sur-Alzette, Luxembourg
| | - Matias Pasquali
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Sebastian Stenglein
- National Scientific and Technical Research Council, Godoy Cruz, Argentina
- Universidad Nacional del Centro de la Provincia de Buenos Aires, Tandil, Argentina
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120
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Chugh RM, Mittal P, MP N, Arora T, Bhattacharya T, Chopra H, Cavalu S, Gautam RK. Fungal Mushrooms: A Natural Compound With Therapeutic Applications. Front Pharmacol 2022; 13:925387. [PMID: 35910346 PMCID: PMC9328747 DOI: 10.3389/fphar.2022.925387] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/20/2022] [Indexed: 11/25/2022] Open
Abstract
Fungi are extremely diverse in terms of morphology, ecology, metabolism, and phylogeny. Approximately, 130 medicinal activities like antitumor, immunomodulation, antioxidant, radical scavenging, cardioprotective and antiviral actions are assumed to be produced by the various varieties of medicinal mushrooms. The polysaccharides, present in mushrooms like β-glucans, micronutrients, antioxidants like glycoproteins, triterpenoids, flavonoids, and ergosterols can help establish natural resistance against infections and toxins.. Clinical trials have been performed on mushrooms like Agaricus blazei Murrill Kyowa for their anticancer effect, A. blazei Murrill for its antihypertensive and cardioprotective effects, and some other mushrooms had also been evaluated for their neurological effects. The human evaluation dose studies had been also performed and the toxicity dose was evaluated from the literature for number of mushrooms. All the mushrooms were found to be safe at a dose of 2000 mg/kg but some with mild side effects. The safety and therapeutic effectiveness of the fungal mushrooms had shifted the interest of biotechnologists toward fungal nanobiotechnology as the drug delivery system due to the vast advantages of nanotechnology systems. In complement to the vital nutritional significance of medicinal mushrooms, numerous species have been identified as sources of bioactive chemicals. Moreover, there are unanswered queries regarding its safety, efficacy, critical issues that affect the future mushroom medicine development, that could jeopardize its usage in the twenty-first century.
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Affiliation(s)
- Rishi Man Chugh
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas, KS, United States
| | - Pooja Mittal
- School of Pharmaceutical Sciences, RIMT University, Mandi Gobindgarh, Punjab, India
| | - Namratha MP
- CHRIST (Deemed to be University), Bangalore, India
| | - Tanu Arora
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas, KS, United States
| | - Tanima Bhattacharya
- Innovation, Incubation and Industry (i-cube) Laboratory, Techno India NJR Institute of Technology, Udaipur, India
- College of Chemistry and Chemical Engineering, Hubei University, Hubei, China
- *Correspondence: Tanima Bhattacharya, ; Simona Cavalu, ; Rupesh K. Gautam,
| | - Hitesh Chopra
- Chitkara College of Pharmacy, Chitkara University, Rajpura, India
| | - Simona Cavalu
- Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
- *Correspondence: Tanima Bhattacharya, ; Simona Cavalu, ; Rupesh K. Gautam,
| | - Rupesh K. Gautam
- MM School of Pharmacy, MM University, Sadopur-Ambala, India
- *Correspondence: Tanima Bhattacharya, ; Simona Cavalu, ; Rupesh K. Gautam,
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121
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Hui X, Mo XH, Yang LJ, Yang H, Tan JW, Yu Q, Zhang PF, Tan F. Comparison of Samples of Blister Fluid and Scales in the diagnosis of dermatomycosis. Mycoses 2022; 65:969-975. [PMID: 35815924 DOI: 10.1111/myc.13494] [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: 02/08/2022] [Revised: 06/30/2022] [Accepted: 07/06/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND The successful diagnosis of dermatomycosis depends on specimen collection. Dermatomycosis is sampled mainly for scales, but there is a lack of research on specimens of blister fluid. OBJECTIVES To explore whether blister fluid can diagnose dermatomycosis and compare blister fluid and scale specimens for dermatomycosis diagnosis. METHODS From April to July 2021, we prospectively gathered 34 patients who needed to meet all inclusion criteria simultaneously and collected their blister fluid and scales as specimens. The two samples were tested by fluorescent stain microscopy, fungal culture, and PCR, and the diagnosis results were compared. RESULTS The blister fluid sample's sensitivity, specificity, and accuracy were 90%, 100%, and 94.1%, respectively, whereas the scales sample were 60%, 100%, and 76.5%, respectively. The positive likelihood ratios were>10 for both blister fluid and scales specimen, and the negative likelihood ratios were not < 0.1. On the Youden's index, the blister fluid specimen was 90%, and the scales specimen was 60%. As for the diagnostic odds ratio, both of them were >1. By fungal culture, we detected 14 cases of fungi in blister fluid and eight in scales. On PCR, 22 cases of fungi in blister fluid and ten in scales were identified. CONCLUSIONS This study demonstrated that a sample of blister fluid had better sensitivity, accuracy, and Youden's index in diagnosing dermatomycosis with blister fluid. Collection of blister fluid might compensate for the inadequacy of collecting only scales specimens for mycological testing.
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Affiliation(s)
- Xia Hui
- Clinical College of Shanghai Skin Disease Hospital, Anhui Medical University, Shanghai, China.,Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xiao Hui Mo
- Renji Hospital, Shanghai JiaoTong University, School of Medicine, Shanghai, China
| | - Lian Juan Yang
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Hong Yang
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jing Wen Tan
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qian Yu
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Peng Fei Zhang
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Fei Tan
- Clinical College of Shanghai Skin Disease Hospital, Anhui Medical University, Shanghai, China.,Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
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122
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Cank KB, Shepherd RA, Knowles SL, Rangel-Grimaldo M, Raja HA, Bunch ZL, Cech NB, Rice CA, Kyle DE, Falkinham JO, Burdette JE, Oberlies NH. Polychlorinated cyclopentenes from a marine derived Periconia sp. (strain G1144). PHYTOCHEMISTRY 2022; 199:113200. [PMID: 35421431 PMCID: PMC9173697 DOI: 10.1016/j.phytochem.2022.113200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/03/2022] [Accepted: 04/06/2022] [Indexed: 06/14/2023]
Abstract
Studies on an organic extract of a marine fungus, Periconia sp. (strain G1144), led to the isolation of three halogenated cyclopentenes along with the known and recently reported rhytidhyester D; a series of spectrometric and spectroscopic techniques were used to elucidate these structures. Interestingly, two of these compounds represent tri-halogenated cyclopentene derivatives, which have been observed only rarely from Nature. The relative and absolute configurations of the compounds were established via mass spectrometry (MS), nuclear magnetic resonance (NMR) spectroscopy, Mosher's esters method, optical rotation and GIAO NMR calculations, including correlation coefficient calculations and the use of both DP4+ and dJ DP4 analyses. Several of the isolated compounds were tested for activity in anti-parasitic, antimicrobial, quorum sensing inhibition, and cytotoxicity assays and were shown to be inactive.
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Affiliation(s)
- Kristóf B Cank
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, 435 Patricia A. Sullivan Science Building, Greensboro, NC, 27402-6170, USA
| | - Robert A Shepherd
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, 435 Patricia A. Sullivan Science Building, Greensboro, NC, 27402-6170, USA
| | - Sonja L Knowles
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, 435 Patricia A. Sullivan Science Building, Greensboro, NC, 27402-6170, USA
| | - Manuel Rangel-Grimaldo
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, 435 Patricia A. Sullivan Science Building, Greensboro, NC, 27402-6170, USA
| | - Huzefa A Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, 435 Patricia A. Sullivan Science Building, Greensboro, NC, 27402-6170, USA
| | - Zoie L Bunch
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, 435 Patricia A. Sullivan Science Building, Greensboro, NC, 27402-6170, USA
| | - Nadja B Cech
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, 435 Patricia A. Sullivan Science Building, Greensboro, NC, 27402-6170, USA
| | - Christopher A Rice
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, 724 Biological Sciences Building, University of Georgia, Athens, GA, 30602-2607, USA; Center for Tropical and Emerging Global Diseases, University of Georgia, 335 Coverdell Center 500 D.W. Brooks Drive, Athens, GA, 30602-7399, USA.
| | - Dennis E Kyle
- Center for Tropical and Emerging Global Diseases, University of Georgia, 335 Coverdell Center 500 D.W. Brooks Drive, Athens, GA, 30602-7399, USA.
| | - Joseph O Falkinham
- Department of Biological Sciences, Virginia Tech Center for Drug Discovery, Derring Hall Room 2125, 926 West Campus Drive, Mail Code 0406, Blacksburg, VA, 24061, USA.
| | - Joanna E Burdette
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 South Wood Street, 333 PHARM, MC 781, Chicago, IL, 60612, USA.
| | - Nicholas H Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, 435 Patricia A. Sullivan Science Building, Greensboro, NC, 27402-6170, USA.
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Schier C, Foerster (née Reiter) J, Heupel M, Dörner P, Klaas M, Schröder W, Rink L, Slusarenko AJ, Gruhlke MCH. Allicin as a Volatile or Nebulisable Antimycotic for the Treatment of Pulmonary Mycoses: In Vitro Studies Using a Lung Flow Test Rig. Int J Mol Sci 2022; 23:ijms23126607. [PMID: 35743050 PMCID: PMC9224539 DOI: 10.3390/ijms23126607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/29/2022] Open
Abstract
Fungal infections of the lung are an increasing problem worldwide and the search for novel therapeutic agents is a current challenge due to emerging resistance to current antimycotics. The volatile defence substance allicin is formed naturally by freshly injured garlic plants and exhibits broad antimicrobial potency. Chemically synthesised allicin was active against selected fungi upon direct contact and via the gas phase at comparable concentrations to the pharmaceutically used antimycotic amphotericin B. We investigated the suppression of fungal growth by allicin vapour and aerosols in vitro in a test rig at air flow conditions mimicking the human lung. The effect of allicin via the gas phase was enhanced by ethanol. Our results suggest that allicin is a potential candidate for development for use in antifungal therapy for lung and upper respiratory tract infections.
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Affiliation(s)
- Christina Schier
- Department of Plant Physiology, RWTH Aachen University, 52074 Aachen, Germany; (A.J.S.); (M.C.H.G.)
- Correspondence:
| | | | - Monika Heupel
- Landwirtschaftskammer Rheinland, 50765 Köln-Auweiler, Germany;
| | - Philipp Dörner
- Chair of Fluid Mechanics and Institute of Aerodynamics, RWTH Aachen University, 52062 Aachen, Germany; (P.D.); (M.K.); (W.S.)
| | - Michael Klaas
- Chair of Fluid Mechanics and Institute of Aerodynamics, RWTH Aachen University, 52062 Aachen, Germany; (P.D.); (M.K.); (W.S.)
| | - Wolfgang Schröder
- Chair of Fluid Mechanics and Institute of Aerodynamics, RWTH Aachen University, 52062 Aachen, Germany; (P.D.); (M.K.); (W.S.)
| | - Lothar Rink
- Institute of Immunology, RWTH Aachen University Hospital, 52074 Aachen, Germany;
| | - Alan J. Slusarenko
- Department of Plant Physiology, RWTH Aachen University, 52074 Aachen, Germany; (A.J.S.); (M.C.H.G.)
- GENAWIF e.V.—Society for Natural Compound and Active Ingredient Research, 52070 Aachen, Germany;
| | - Martin C. H. Gruhlke
- Department of Plant Physiology, RWTH Aachen University, 52074 Aachen, Germany; (A.J.S.); (M.C.H.G.)
- GENAWIF e.V.—Society for Natural Compound and Active Ingredient Research, 52070 Aachen, Germany;
- Institute of Applied Microbiology—iAMB, Aachener Biology and Biotechnology—ABBt, RWTH Aachen University, 52074 Aachen, Germany
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124
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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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125
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Cyle KT, Klein AR, Aristilde L, Martínez CE. Dynamic utilization of low-molecular-weight organic substrates across a microbial growth rate gradient. J Appl Microbiol 2022; 133:1479-1495. [PMID: 35665577 DOI: 10.1111/jam.15652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/05/2022] [Accepted: 05/31/2022] [Indexed: 11/28/2022]
Abstract
AIM Low-molecular-weight organic substances (LMWOSs) are at the nexus between microorganisms, plant roots, detritus, and the soil mineral matrix. Nominal oxidation state of carbon (NOSC) has been suggested a potential parameter for modeling microbial uptake rates of LMWOSs and the efficiency of carbon incorporation into new biomass. METHODS AND RESULTS In this study, we assessed the role of compound class and oxidation state on uptake kinetics and substrate-specific carbon use efficiency (SUE) during the growth of three model soil microorganisms, a fungal isolate (Penicillium spinulosum) and two bacterial isolates (Paraburkholderia solitsugae, and Ralstonia pickettii). Isolates were chosen that spanned a growth rate gradient (0.046-0.316 h-1 ) in media containing 34 common LMWOSs at realistically low initial concentrations (25 μM each). Clustered, co-utilization of LMWOSs occurred for all three organisms. Potential trends (p < 0.05) for early utilization of more oxidized substrates were present for the two bacterial isolates (P. solitsugae and R. pickettii), but high variability (R2 < 0.15) and a small effect of NOSC indicate these relationships are not useful for prediction. The SUEs of selected substrates ranged from 0.16-0.99 and there was no observed relationship between NOSC and SUE. CONCLUSION Our results do not provide compelling population-level support for NOSC as a predictive tool for either uptake kinetics or the efficiency of use of LMWOS in soil solution. SIGNIFICANCE AND IMPACT OF THE STUDY Metabolic strategies of organisms are likely more important than chemical identity in determining LMWOS cycling in soils. Previous community-level observations may be biased towards fast-responding bacterial community members.
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Affiliation(s)
- K Taylor Cyle
- Soil and Crop Sciences, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Annaleise R Klein
- Department of Biological and Environmental Engineering, Cornell University, Riley-Robb Hall, Ithaca, NY 14853.,Australian Synchrotron, Australian Nuclear Science and Technology Organisation, Clayton, VIC 3168, Australia
| | - Ludmilla Aristilde
- Department of Biological and Environmental Engineering, Cornell University, Riley-Robb Hall, Ithaca, NY 14853.,Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, 60208, USA
| | - Carmen Enid Martínez
- Soil and Crop Sciences, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
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126
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Kennedy AH, Schoch CL, Marrero G, Brover V, Robbertse B. Publicly Available and Validated DNA Reference Sequences Are Critical to Fungal Identification and Global Plant Protection Efforts: A Use-Case in Colletotrichum. PLANT DISEASE 2022; 106:1573-1596. [PMID: 35538602 PMCID: PMC9196201 DOI: 10.1094/pdis-09-21-2083-sr] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Publicly available and validated DNA reference sequences useful for phylogeny estimation and identification of fungal pathogens are an increasingly important resource in the efforts of plant protection organizations to facilitate safe international trade of agricultural commodities. Colletotrichum species are among the most frequently encountered and regulated plant pathogens at U.S. ports-of-entry. The RefSeq Targeted Loci (RTL) project at NCBI (BioProject no. PRJNA177353) contains a database of curated fungal internal transcribed spacer (ITS) sequences that interact extensively with NCBI Taxonomy, resulting in verified name-strain-sequence type associations for >12,000 species. We present a publicly available dataset of verified and curated name-type strain-sequence associations for all available Colletotrichum species. This includes an updated GenBank Taxonomy for 238 species associated with up to 11 protein coding loci and an updated RTL ITS dataset for 226 species. We demonstrate that several marker loci are well suited for phylogenetic inference and identification. We improve understanding of phylogenetic relationships among verified species, verify or improve phylogenetic circumscriptions of 14 species complexes, and reveal that determining relationships among these major clades will require additional data. We present detailed comparisons between phylogenetic and similarity-based approaches to species identification, revealing complex patterns among single marker loci that often lead to misidentification when based on single-locus similarity approaches. We also demonstrate that species-level identification is elusive for a subset of samples regardless of analytical approach, which may be explained by novel species diversity in our dataset and incomplete lineage sorting and lack of accumulated synapomorphies at these loci.
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Affiliation(s)
- Aaron H. Kennedy
- National Identification Services, Plant Protection and Quarantine, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Beltsville, MD 20705
| | - Conrad L. Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Glorimar Marrero
- National Identification Services, Plant Protection and Quarantine, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Beltsville, MD 20705
| | - Vyacheslav Brover
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Barbara Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
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127
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Becktell MC, Tucker S, Ozsoy AZ, Connor M. Identification of fungi found on desiccated human remains in an arid outdoor environment. J Forensic Sci 2022; 67:2048-2054. [PMID: 35593446 DOI: 10.1111/1556-4029.15066] [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: 01/20/2022] [Revised: 04/08/2022] [Accepted: 05/10/2022] [Indexed: 11/29/2022]
Abstract
Three fungi not previously reported on desiccated human remains were identified on cadavers at the Forensic Investigation Research Station (FIRS) in Whitewater, Colorado. The location of the FIRS provides the unique opportunity to observe the stages of decomposition in a high desert environment. The two cadavers used in the study were in the late stages of decomposition (PMI of approximately 1520 and 1820 days) to the point of desiccation and had developed an extensive black crust on the skin that remained. Skin samples of the two cadavers were taken and plated onto potato dextrose agar to determine whether fungi were present on the desiccated tissues. Three different fungi consistently dominated cultures grown from numerous samples taken from each cadaver. Based on morphological observations, nuclear rDNA sequence data, and phylogenetic analyses, two fungi were identified to species (Aureobasidium melanogenum and Didymella glomerata) and one fungus was identified to the genus level (Alternaria). These results will contribute to the understanding of the role that fungi might play in late-stage decomposition and the extended postmortem period.
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Affiliation(s)
- Margot C Becktell
- Department of Biological Sciences Colorado Mesa University, Grand Junction, Colorado, USA
| | - Selina Tucker
- University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - A Zeynep Ozsoy
- Department of Biological Sciences Colorado Mesa University, Grand Junction, Colorado, USA
| | - Melissa Connor
- Department of Social and Behavioral Sciences, Forensic Investigation Research Station, Colorado Mesa University, Grand Junction, Colorado, USA
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128
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Intragenomic variation in nuclear ribosomal markers and its implication in species delimitation, identification and barcoding in fungi. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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129
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Fungal Community Investigation from Propolis Natural Products: Diversity and Antibacterial Activities Evaluation. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:7151655. [PMID: 35469159 PMCID: PMC9034937 DOI: 10.1155/2022/7151655] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/24/2022] [Accepted: 03/16/2022] [Indexed: 12/21/2022]
Abstract
Discovering new species and interesting bioactive metabolites from customary sources is becoming progressively laborious. Propolis constitutes the largest diversified reserve of microbial constituents in the beehive. However, fungal communities associated with these environments remain insufficiently established. We present the first detailed investigation of the cultivable fungal community associated with Tunisian propolis, and we evaluate its antibacterial properties against pathogenic bacteria. A total of 80 fungal strains were isolated from propolis samples derived from seven different Tunisian locations. The majority of the isolated fungi were classified as Ascomycota (97.5%), and only 2.5% belonged to Basidiomycota. Our collection was clustered into 15 genera, among which Coniochaeta (36.25%), Aspergillus (15%), Penicillium (13.75%), Cladosporium (10%), Fusarium (7.5%), Didymella (5%), and Alternaria (3.75%) were the most common. Evaluation of the antibacterial activity revealed that 25.6% of the total community showed a broad range of antibacterial activity. Particularly, the Penicillium griseofulvum CC8 strain has manifested the strongest inhibitory effects against all the tested bacteria.
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130
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Liao YC, Wu HC, Liou CH, Lauderdale TLY, Huang IW, Lai JF, Chen FJ. Rapid and Routine Molecular Typing Using Multiplex Polymerase Chain Reaction and MinION Sequencer. Front Microbiol 2022; 13:875347. [PMID: 35422786 PMCID: PMC9002326 DOI: 10.3389/fmicb.2022.875347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/09/2022] [Indexed: 11/26/2022] Open
Abstract
Molecular typing is an essential tool that has been extensively applied in laboratories as well as in clinical settings. Next-generation sequencing technologies promise high-throughput and cost-effective molecular applications; however, the accessibility of these technologies is limited due to the high capital cost. Oxford Nanopore Technologies (ONT) offers a MinION device with the advantages of real-time data analysis, rapid library preparation, and low cost per test. However, the advantages of the MinION device are often overshadowed by its lower raw accuracy. Herein, we present a concise multilocus sequence typing protocol of Staphylococcus aureus using multiplex polymerase chain reaction and Rapid Barcoding Kit for barcoding and MinION device for sequencing. Moreover, to clarify the effects of carryover DNA on tasks that require high sequence accuracy, we used the MinION flow cell in successive runs of washing and reusing. Our results revealed that the MinION flow cell could achieve accurate typing of a total of 467 samples with 3,269 kilobase-long genes within a total of 5 runs. This thus demonstrates the effectiveness of a portable nanopore MinION sequencer in providing accurate, rapid, and routine molecular typing.
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Affiliation(s)
- Yu-Chieh Liao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan
| | - Han-Chieh Wu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan
| | - Ci-Hong Liou
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan
| | - Tsai-Ling Yang Lauderdale
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - I-Wen Huang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan
| | - Jui-Fen Lai
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan
| | - Feng-Jui Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
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131
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Fajardo-Hernández C, Khan FST, Flores-Bocanegra L, Prieto-Davó A, Wan B, Ma R, Qader M, Villanueva-Silva R, Martínez-Cárdenas A, López-Lobato MA, Hematian S, Franzblau SG, Raja HA, García-Contreras R, Figueroa M. Insights into the Chemical Diversity of Selected Fungi from the Tza Itzá Cenote of the Yucatan Peninsula. ACS OMEGA 2022; 7:12171-12185. [PMID: 35449929 PMCID: PMC9016812 DOI: 10.1021/acsomega.2c00544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
Cenotes are habitats with unique physical, chemical, and biological features. Unexplored microorganisms from these sinkholes represent a potential source of bioactive molecules. Thus, a series of cultivable fungi (Aspergillus spp. NCA257, NCA264, and NCA276, Stachybotrys sp. NCA252, and Cladosporium sp. NCA273) isolated from the cenote Tza Itzá were subjected to chemical, coculture, and metabolomic analyses. Nineteen compounds were obtained and tested for their antimicrobial potential against ESKAPE pathogens, Mycobacterium tuberculosis, and nontuberculous mycobacteria. In particular, phenylspirodrimanes from Stachybotrys sp. NCA252 showed significant activity against MRSA, MSSA, and mycobacterial strains. On the other hand, the absolute configuration of the new compound 17-deoxy-aspergillin PZ (1) isolated from Aspergillus sp. NCA276 was established via single-crystal X-ray crystallography. Also, the chemical analysis of the cocultures between Aspergillus and Cladosporium strains revealed the production of metabolites that were not present or were barely detected in the monocultures. Finally, molecular networking analysis of the LC-MS-MS/MS data for each fungus was used as a tool for the annotation of additional compounds, increasing the chemical knowledge on the corresponding fungal strains. Overall, this is the first systematic chemical study on fungi isolated from a sinkhole in Mexico.
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Affiliation(s)
- Carlos
A. Fajardo-Hernández
- Departamento
de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Firoz Shah Tuglak Khan
- Department
of Chemistry and Biochemistry, University
of North Carolina Greensboro, Greensboro, North Carolina 27402, United States
| | - Laura Flores-Bocanegra
- Department
of Chemistry and Biochemistry, University
of North Carolina Greensboro, Greensboro, North Carolina 27402, United States
| | - Alejandra Prieto-Davó
- Unidad
de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Sisal, Yucatán 97356, Mexico
| | - Baojie Wan
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Rui Ma
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Mallique Qader
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Rodrigo Villanueva-Silva
- Departamento
de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Anahí Martínez-Cárdenas
- Departamento
de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Marian A. López-Lobato
- Departamento
de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Shabnam Hematian
- Department
of Chemistry and Biochemistry, University
of North Carolina Greensboro, Greensboro, North Carolina 27402, United States
| | - Scott G. Franzblau
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Huzefa A. Raja
- Department
of Chemistry and Biochemistry, University
of North Carolina Greensboro, Greensboro, North Carolina 27402, United States
| | - Rodolfo García-Contreras
- Departamento
de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Mario Figueroa
- Departamento
de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
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132
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Inferring Species Compositions of Complex Fungal Communities from Long- and Short-Read Sequence Data. mBio 2022; 13:e0244421. [PMID: 35404122 PMCID: PMC9040722 DOI: 10.1128/mbio.02444-21] [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] [Indexed: 11/20/2022] Open
Abstract
Our study is unique in that it provides an in-depth comparative study of a real-life complex fungal community analyzed with multiple long- and short-read sequencing approaches. These technologies and their application are currently of great interest to diverse biologists as they seek to characterize the community compositions of microbiomes.
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133
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Ramli ANM, Yusof S, Bhuyar P, Aminan AW, Tajuddin SN, Hamid HA. Production of Volatile Compounds by a Variety of Fungi in Artificially Inoculated and Naturally Infected Aquilaria malaccensis. Curr Microbiol 2022; 79:151. [PMID: 35397007 DOI: 10.1007/s00284-022-02840-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 03/14/2022] [Indexed: 11/25/2022]
Abstract
Aquilaria malaccensis, the resinous agarwood, is highly valued in the perfumery and medicinal industry. The formation of fragrant agarwood resin inconsistently by various fungi is still not clearly understood. The current study investigated the agarwood quality and fungal diversity in artificially inoculated and naturally infected A. malaccensis. The chemical analysis of volatile compounds of agarwood was performed using the Solid Phase Micro Extraction (SPME) method, and the identification of fungi was made through a morphological observation using a light microscope. Gas chromatography analysis revealed the presence of essential compounds related to high-quality agarwood, such as 4-phenyl-2-butanone, β-selinene, α-bulnesene, and agarospirol in both artificially inoculated and naturally infected agarwood but with some differences in the abundance. Further studies on the fungi associated with agarwood volatile compounds formation showed a total of ten fungal group isolates, which were identified based on morphological and molecular studies. The study revealed that agarwood from both artificial and natural sources were naturally infected with Fusarium, Botryosphaeria, Aspergillus, Schizophyllum, Phanerochaete, Lasiodiplodia, Polyporales, and Ceriporia species. This study has offered a potential opportunity to research further the promising development of fungal strains for artificial inducement of high-quality agarwood formation from A. malaccensis trees.
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Affiliation(s)
- Aizi Nor Mazila Ramli
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun RazakGambang, 26300, Kuantan, Pahang, Malaysia. .,Bio Aromatic Research Centre of Excellent, Universiti Malaysia Pahang, Lebuhraya Tun RazakGambang, 26300, Kuantan, Pahang, Malaysia.
| | - Sufihana Yusof
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun RazakGambang, 26300, Kuantan, Pahang, Malaysia
| | - Prakash Bhuyar
- Program in Organic Agriculture Management, Maejo University International College (MJU-IC), Maejo University, Chiang Mai, 50290, Thailand
| | - Aimi Wahidah Aminan
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun RazakGambang, 26300, Kuantan, Pahang, Malaysia
| | - Saiful Nizam Tajuddin
- Bio Aromatic Research Centre of Excellent, Universiti Malaysia Pahang, Lebuhraya Tun RazakGambang, 26300, Kuantan, Pahang, Malaysia
| | - Hazrulrizawati Abd Hamid
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun RazakGambang, 26300, Kuantan, Pahang, Malaysia
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134
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Metagenomic Assessment Unravels Fungal Microbiota Associated to Grapevine Trunk Diseases. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8040288] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Grapevine trunk diseases (GTDs) are among the most important problems that affect the longevity and productivity of vineyards in all the major growing regions of the world. They are slow-progression diseases caused by several wood-inhabiting fungi with similar life cycles and epidemiology. The simultaneous presence of multiple trunk pathogens in a single plant together with the inconsistent GTDs symptoms expression, their isolation in asymptomatic plants, and the absence of effective treatments make these diseases extremely complex to identify and eradicate. Aiming to gain a better knowledge of GTDs and search sustainable alternatives to limit their development, the present work studied the fungal community structure associated with GTDs symptomatic and asymptomatic grapevines, following a metagenomic approach. Two important cultivars from the Alentejo region with different levels of susceptibility to GTDs were selected, namely, ‘Alicante Bouschet’ and ‘Trincadeira’. Deep sequencing of fungal-directed ITS1 amplicon led to the detection of 258 taxa, including 10 fungi previously described as responsible for GTDs. Symptomatic plants exhibited a lower abundance of GTDs-associated fungi, although with significantly higher diversity of those pathogens. Our results demonstrated that trunk diseases symptoms are intensified by a set of multiple GTDs-associated fungi on the same plant. The composition of fungal endophytic communities was significantly different according to the symptomatology and it was not affected by the cultivar. This study opens new perspectives in the study of GTDs-associated fungi and their relation to the symptomatology in grapevines.
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135
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Aldrich LN, Burdette JE, de Blanco EC, Coss CC, Eustaquio AS, Fuchs JR, Kinghorn AD, MacFarlane A, Mize B, Oberlies NH, Orjala J, Pearce CJ, Phelps MA, Rakotondraibe LH, Ren Y, Soejarto DD, Stockwell BR, Yalowich JC, Zhang X. Discovery of Anticancer Agents of Diverse Natural Origin. JOURNAL OF NATURAL PRODUCTS 2022; 85:702-719. [PMID: 35213158 PMCID: PMC9034850 DOI: 10.1021/acs.jnatprod.2c00036] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Research progress from mainly over the last five years is described for a multidisciplinary collaborative program project directed toward the discovery of potential anticancer agents from a broad range of taxonomically defined organisms. Selected lead compounds with potential as new antitumor agents that are representative of considerable structural diversity have continued to be obtained from each of tropical plants, terrestrial and aquatic cyanobacteria, and filamentous fungi. Recently, a new focus has been on the investigation of the constituents of U.S. lichens and their fungal mycobionts. A medicinal chemistry and pharmacokinetics component of the project has optimized structurally selected lead natural products, leading to enhanced cytotoxic potencies against selected cancer cell lines. Biological testing has shown several compounds to have in vivo activity, and relevant preliminary structure-activity relationship and mechanism of action studies have been performed. Several promising lead compounds worthy of further investigation have been identified from the most recent collaborative work performed.
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Affiliation(s)
- Leslie N. Aldrich
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Joanna E. Burdette
- College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | | | - Christopher C. Coss
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Alessandra S. Eustaquio
- College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - James R. Fuchs
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - A. Douglas Kinghorn
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Amanda MacFarlane
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Brittney Mize
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Nicholas H. Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina 24702, United States
| | - Jimmy Orjala
- College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Cedric J. Pearce
- Mycosynthetix, Inc., Hillsborough, North Carolina 27278, United States
| | - Mitch A. Phelps
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | | | - Yulin Ren
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Djaja Doel Soejarto
- College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- Field Museum of Natural History, Chicago, Illinois 60605, United States
| | - Brent R. Stockwell
- Department of Biological Sciences, Columbia University, New York, New York 10027, United States
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Jack C. Yalowich
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Xiaoli Zhang
- College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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136
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Flores-Bocanegra L, Al Subeh ZY, Egan JM, El-Elimat T, Raja HA, Burdette JE, Pearce CJ, Linington RG, Oberlies NH. Dereplication of Fungal Metabolites by NMR-Based Compound Networking Using MADByTE. JOURNAL OF NATURAL PRODUCTS 2022; 85:614-624. [PMID: 35020372 PMCID: PMC8957573 DOI: 10.1021/acs.jnatprod.1c00841] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Strategies for natural product dereplication are continually evolving, essentially in lock step with advances in MS and NMR techniques. MADByTE is a new platform designed to identify common structural features between samples in complex extract libraries using two-dimensional NMR spectra. This study evaluated the performance of MADByTE for compound dereplication by examining two classes of fungal metabolites, the resorcylic acid lactones (RALs) and spirobisnaphthalenes. First, a pure compound database was created using the HSQC and TOCSY data from 19 RALs and 10 spirobisnaphthalenes. Second, this database was used to assess the accuracy of compound class clustering through the generation of a spin system feature network. Seven fungal extracts were dereplicated using this approach, leading to the correct prediction of members of both families from the extract set. Finally, NMR-guided isolation led to the discovery of three new palmarumycins (20-22). Together these results demonstrate that MADByTE is effective for the detection of specific compound classes in complex mixtures and that this detection is possible for both known and new natural products.
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Affiliation(s)
- Laura Flores-Bocanegra
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27412, United States
| | - Zeinab Y. Al Subeh
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27412, United States
| | - Joseph M. Egan
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Tamam El-Elimat
- Department
of Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Huzefa A. Raja
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27412, United States
| | - Joanna E. Burdette
- Department
of Pharmaceutical Sciences, University of
Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Cedric J. Pearce
- Mycosynthetix,
Inc., Hillsborough, North Carolina 27278, United States
| | - Roger G. Linington
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Nicholas H. Oberlies
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27412, United States
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137
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Sarocladium strictum lipase (LipSs) produced using crude glycerol as sole carbon source: A promising enzyme for biodiesel production. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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138
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Scansani S, van Wyk N, Nader KB, Beisert B, Brezina S, Fritsch S, Semmler H, Pasch L, Pretorius IS, von Wallbrunn C, Schnell S, Rauhut D. The film-forming Pichia spp. in a winemaker's toolbox: A simple isolation procedure and their performance in a mixed-culture fermentation of Vitis vinifera L. cv. Gewürztraminer must. Int J Food Microbiol 2022; 365:109549. [DOI: 10.1016/j.ijfoodmicro.2022.109549] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/17/2021] [Accepted: 01/13/2022] [Indexed: 01/21/2023]
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139
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Chen W, Radford D, Hambleton S. Towards Improved Detection and Identification of Rust Fungal Pathogens in Environmental Samples Using a Metabarcoding Approach. PHYTOPATHOLOGY 2022; 112:535-548. [PMID: 34384241 DOI: 10.1094/phyto-01-21-0020-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The dispersion of fungal inocula such as the airborne spores of rust fungi (Pucciniales) can be monitored through metabarcoding of the internal transcribed spacer 2 (ITS2) of the rRNA gene in environmental DNAs. This method is largely dependent on a high-quality reference database (refDB) and primers with proper taxonomic coverage and specificity. For this study, a curated ITS2 reference database (named CR-ITS2-refDB) comprising representatives of the major cereal rust fungi and phylogenetically related species was compiled. Interspecific and intraspecific variation analyses suggested that the ITS2 region had reasonable discriminating power for the majority of the Puccinia species or species complexes in the database. In silico evaluation of nine forward and seven reverse ITS2 primers, including three newly designed, revealed marked variation in DNA amplification efficiency for the rusts. We validated the theoretical assessment of rust-enhanced (Rust2inv/ITS4var_H) and universal fungal (ITS9F/ITS4) ITS2 primer pairs by profiling the airborne rust fungal communities from environmental samples via a metabarcoding approach. Species- or subspecies-level identification of the rusts was improved by use of CR-ITS2-refDB and the Automated Oligonucleotide Design Pipeline (AODP), which identified all mutations distinguishing highly conserved DNA markers between close relatives. A generic bioinformatics pipeline was developed, including all steps used in this study from in silico evaluation of primers to accurate identification of short metabarcodes at the level of interest for defining phytopathogens. The results highlight the importance of primer selection, refDBs that are resolved to reflect phylogenetic relationships, and the use of AODP for improving the reliability of metabarcoding in phytopathogen biosurveillance.
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Affiliation(s)
- Wen Chen
- Biodiversity and Bioresources, Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
| | - Devon Radford
- Biodiversity and Bioresources, Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
| | - Sarah Hambleton
- Biodiversity and Bioresources, Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
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140
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Delva E, Arisuryanti T, Ilmi M. Genetic Diversity of Amylomyces rouxii from Ragi tapai in Java Island Based on Ribosomal Regions ITS1/ITS2 and D1/D2. MYCOBIOLOGY 2022; 50:132-141. [PMID: 35571863 PMCID: PMC9067998 DOI: 10.1080/12298093.2022.2028436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/09/2021] [Accepted: 01/06/2022] [Indexed: 06/15/2023]
Abstract
Amylomyces rouxii is commonly found as amylolytic fungi in tapai fermentation. However, its diversity is rarely reported despite being often used for food production in Southeast Asia. This research aims to analyze the genetic diversity and the distribution pattern of A. rouxii from Ragi tapai in Java Island, Indonesia. We isolated the fungus from samples obtained from Ragi tapai producing centers in Bandung, Sumedang, Muntilan, Blora, Yogyakarta, and Bondowoso. The obtained isolates were molecularly identified based on the ribosomal regions ITS1/ITS2 and D1/D2, then analyzed for phylogenetic tree reconstruction, genetic distance, genetic variation, and haplotype networking. Six isolates showed specific morphological traits of A. rouxii. However, phylogenetic tree reconstruction on the ribosomal genes showed that the isolates were grouped into two different clades related to two species. Clade A included BDG, SMD, and MTL isolates related to A. rouxii, whereas clade B included YOG, BLR, and BDS isolates related to Mucor indicus. The genetic distances between clades for ITS1/ITS2 and D1/D2 were 0.6145 and 0.1556, respectively. In conclusion, we confirmed the genetic diversity of molds from Ragi tapai in Java Island and showed that the isolates are not only related to A. rouxii as reported before.
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Affiliation(s)
- Ega Delva
- Laboratory of Microbiology, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta, Indonesia
| | - Tuty Arisuryanti
- Laboratory of Genetics and Breeding, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta, Indonesia
| | - Miftahul Ilmi
- Laboratory of Microbiology, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta, Indonesia
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141
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Al-Qurainy F, Tarroum M, Khan S, Nadeem M, Gaafar ARZ, Alansi S, Alfarraj NS. Genome Estimation and Phytochemical Compound Identification in the Leaves and Callus of Abrus precatorius: A Locally Endangered Plant from the Flora of Saudi Arabia. PLANTS (BASEL, SWITZERLAND) 2022; 11:567. [PMID: 35214900 PMCID: PMC8877254 DOI: 10.3390/plants11040567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Abrus precatorius is considered to be a valuable source of natural products for the development of drugs against various diseases. Herein, the genome size and phytochemical compounds in the leaves and callus of A. precatorius were evaluated. The endangered A. precatorius was collected from the Al-Baha mountains, Saudi Arabia and identified based on the phylogenetic analysis of a DNA sequence amplified by ITS1 and ITS4 primers. The callus was induced by the culture of stem explants onto Murashige and Skoog medium (MS) supplemented with various combinations of 2,4-dichlorophenoxyacetic acid (2,4D) and 6-Benzylaminopurine (BAP). The callus with the highest fresh weight (2.03 g) was obtained in the medium containing 0.5µM BA and 5 µM 2,4-D after 8 weeks of culture; thus, the callus of this combination was selected for the genome estimation and phytochemical compound extraction. The genetic stability of the leaves from the donor as well as in the regenerated callus was analyzed by flow cytometry with optimized tomato (2C = 1.96 pg) as an external reference standard. The 2C DNA content was estimated to 1.810 pg ± 0.008 and 1.813 pg ± 0.004 for the leaves and callus, respectively. Then, the total phenol and total flavonoid contents in the methanol extract of the callus and leaves were measured using a spectrophotometer and the High-performance liquid chromatography (HPLC ) methods. The results showed that the methanolic extract of the leaves was higher in total phenols and total flavonoids than the callus extract. Finally, the extracts of callus and leaves were analyzed for phytochemical compound through the Gas chromatography and Mass spectroscopy (GC-MS). A total of 22 and 28 compounds were detected in the callus and leaves, respectively. The comparative analysis showed that 12 compounds of the secondary metabolites were present in both extracts.
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142
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Endophytic Fungi Isolated from Baccharis linearis and Echinopsis chiloensis with Antifungal Activity against Botrytis cinerea. J Fungi (Basel) 2022; 8:jof8020197. [PMID: 35205951 PMCID: PMC8878204 DOI: 10.3390/jof8020197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/29/2022] [Accepted: 02/16/2022] [Indexed: 02/05/2023] Open
Abstract
Botrytis cinerea is one of the most important phytopathogens in agriculture worldwide, infecting economically important crops. The main control of this fungus is by synthetic fungicides, causing the selection of resistant isolates. Compounds produced by endophytic fungi have been shown to have antifungal activity against this pathogen and can be used as an alternative to synthetic fungicides. The aim of this work was to isolate endophytic fungi from Chilean foothills in the Metropolitan Region. Ten fungi were isolated from Echinopsis chiloensis and Baccharis linearis, however, only two isolates inhibited the mycelial growth of B. cinerea by antibiosis and were identified as Epicoccum sp. and Pleosporales sp. Extracts at 200 mg L−1 from Epicoccum sp. and Pleosporales sp. showed antifungal activity against B. cinerea of 54.6 and 44.6% respectively. Active compounds in the Epicoccum sp. extracts were mainly alkaloids and phenolic compounds; meanwhile, in the Pleosporales sp. extracts, terpenes and/or saponins were responsible for the antifungal activity.
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143
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Mahata PK, Dass RS, Pan A, Muthusamy B. Substantive Morphological Descriptions, Phylogenetic Analysis and Single Nucleotide Polymorphisms of Aspergillus Species From Foeniculum vulgare. Front Microbiol 2022; 13:832320. [PMID: 35250948 PMCID: PMC8894770 DOI: 10.3389/fmicb.2022.832320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/24/2022] [Indexed: 01/10/2023] Open
Abstract
Ascomycetous fungi are found associated with a wide variety of substrates which range from fresh water to marine ecosystems, tropical to temperate forest soils and deserts, throughout the world over. These demystifying fungi exist as endophytes, pathogens and saprobes. They have been studied due to their ability to contaminate foods and feedstuffs, causing an elaboration of mycotoxins. The objectives of the study included extensive analyses of the morphological features of fungi, especially Aspergilli, which have been presented while studying them on specific mycological media. It is also an elaborate compilation of substantive macro- and micro-morphological characterization of different Aspergilli isolated from the spice Foeniculum vulgare used in India and other countries in the world. Further, a first of its kind attempt has been made to study their relative abundance and frequency of occurrence, molecular phylogeny and genetic relatedness to characterize the Aspergilli into specific sections, groups and clades. Single nucleotide polymorphism (SNP) analysis was carried out to evaluate the functional consequences of nucleotide variations, synonymous and non-synonymous mutations in the protein structure. The study resulted in a total of 3,506 Aspergillus isolates, which were obtained from seventy (70) fennel samples, representing 14 Aspergillus species. The two most frequently found species were A. niger and A. flavus with a relative abundance of 32.24 and 11.63%, respectively. The taxonomy and current placements have been reappraised with suggestions and prospects for future research from six sections namely Terrei, Flavi, Fumigati, Nidulantes, Nigri, and Versicolores. In addition, a total number of 27 isolates were studied and deposited at the National Centre for Biotechnology Information (NCBI) and five Aspergillus species have been identified and are being reported for the first time from the fennel seeds, based on partial sequence analysis of the official fungal barcode namely, Internal Transcribed Spacer (ITS) and a functional gene, beta tubulin gene locus, coupled with phenotypic characterization. SNPs for specific DNA regions have been used to identify variants in Aspergilli obtained from Indian fennel seeds for the first time. The need for a polyphasic approach of morphological identification and genetic characterization of Aspergilli from Foeniculum vulgare is addressed and presented here in adequate detail. Our current work makes extensive use of partial beta-tubulin gene sequences analyses to evaluate the association between SNPs in five Aspergillus species sections.
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Affiliation(s)
- Pranab Kumar Mahata
- Fungal Genetics and Mycotoxicology Laboratory, Department of Microbiology, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Regina Sharmila Dass
- Fungal Genetics and Mycotoxicology Laboratory, Department of Microbiology, School of Life Sciences, Pondicherry University, Pondicherry, India
- *Correspondence: Regina Sharmila Dass,
| | - Archana Pan
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Babylakshmi Muthusamy
- Institute of Bioinformatics, International Tech Park, Bengaluru, India
- Manipal Academy of Higher Education, Manipal, India
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144
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Senanayake IC, Pem D, Rathnayaka AR, Wijesinghe SN, Tibpromma S, Wanasinghe DN, Phookamsak R, Kularathnage ND, Gomdola D, Harishchandra D, Dissanayake LS, Xiang MM, Ekanayaka AH, McKenzie EHC, Hyde KD, Zhang HX, Xie N. Predicting global numbers of teleomorphic ascomycetes. FUNGAL DIVERS 2022. [DOI: 10.1007/s13225-022-00498-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
AbstractSexual reproduction is the basic way to form high genetic diversity and it is beneficial in evolution and speciation of fungi. The global diversity of teleomorphic species in Ascomycota has not been estimated. This paper estimates the species number for sexual ascomycetes based on five different estimation approaches, viz. by numbers of described fungi, by fungus:substrate ratio, by ecological distribution, by meta-DNA barcoding or culture-independent studies and by previous estimates of species in Ascomycota. The assumptions were made with the currently most accepted, “2.2–3.8 million” species estimate and results of previous studies concluding that 90% of the described ascomycetes reproduce sexually. The Catalogue of Life, Species Fungorum and published research were used for data procurement. The average value of teleomorphic species in Ascomycota from all methods is 1.86 million, ranging from 1.37 to 2.56 million. However, only around 83,000 teleomorphic species have been described in Ascomycota and deposited in data repositories. The ratio between described teleomorphic ascomycetes to predicted teleomorphic ascomycetes is 1:22. Therefore, where are the undiscovered teleomorphic ascomycetes? The undescribed species are no doubt to be found in biodiversity hot spots, poorly-studied areas and species complexes. Other poorly studied niches include extremophiles, lichenicolous fungi, human pathogens, marine fungi, and fungicolous fungi. Undescribed species are present in unexamined collections in specimen repositories or incompletely described earlier species. Nomenclatural issues, such as the use of separate names for teleomorph and anamorphs, synonyms, conspecific names, illegitimate and invalid names also affect the number of described species. Interspecies introgression results in new species, while species numbers are reduced by extinctions.
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145
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Characterization and phylogeny of fungi isolated from industrial wastewater using multiple genes. Sci Rep 2022; 12:2094. [PMID: 35136108 PMCID: PMC8827091 DOI: 10.1038/s41598-022-05820-9] [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: 03/02/2021] [Accepted: 01/10/2022] [Indexed: 11/25/2022] Open
Abstract
The aim of this study was the isolation and molecular characterization of fungi from untreated refinery effluent by using multiple conserved genes. The Fungi isolated were characterized based on PCR amplification and genomic sequencing of the internal transcribed spacer region (ITS), partial β-tubulin (BenA), calmodulin (CaM), and RNA polymerase second large subunit (RPB2) genes, along with morphological characterization. The obtained sequences were subjected to BLAST analysis and the corresponding fungal isolates were assigned species names after comparison with representative sequences available in GenBank. Fifteen (15) Fungi species belonging to four genera of Aspergillus, Penicillium, Fusarium, and Trichoderma with Aspergillus as the predominant genus were identified. Therefore these genes should be used as molecular markers for species level identification of fungi (especially Aspergillus and Penicillium as proven in this study.
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146
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Ramdass AC, Rampersad SN. Detection and diversity of the mannosylerythritol lipid (MEL) gene cluster and lipase A and B genes of Moesziomyces antarcticus isolated from terrestrial sites chronically contaminated with crude oil in Trinidad. BMC Microbiol 2022; 22:43. [PMID: 35120442 PMCID: PMC8815271 DOI: 10.1186/s12866-021-02419-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 12/06/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Mannosylerythritol lipids (MELs) belong to the class of glycolipid biosurfactants and are produced by members of the Ustilago and Moesziomyces genera. Production of MELs is regulated by a biosynthetic gene cluster (MEL BGC). Extracellular lipase activity is also associated with MEL production. Most microbial glycolipid-producers are isolated from oil-contaminated environments. MEL-producing yeast that are capable of metabolizing crude oil are understudied, and there is very limited data on indigenous strains from tropical climates. Analysis of the MEL BGC and lipase genes in Trinidad M. antarcticus strains, using a gene-targeted approach, revealed a correlation between their intrinsic capability to degrade crude oil and their adaptation to survive in a chronically polluted terrestrial environment. RESULTS M. antarcticus was isolated from naturally-occurring crude oil seeps and an asphaltic mud volcano in Trinidad; these are habitats that have not been previously reported for this species. Genus identification was confirmed by the large-subunit (LSU) and the small-subunit (SSU) sequence comparisons and species identification was confirmed by ITS sequence comparisons and phylogenetic inference. The essential genes (Emt1, Mac1, Mac2, Mmf1) of the MEL BGC were detected with gene-specific primers. Emt1p, Mac1p and Mmf1p sequence analyses confirmed that the Trinidad strains harboured novel synonymous amino acid (aa) substitutions and structural comparisons revealed different regions of disorder, specifically for the Emt1p sequence. Functionality of each protein sequence was confirmed through motif mining and mutation prediction. Phylogenetic relatedness was inferred for Emt1p, Mac1p and Mmf1p sequences. The Trinidad strains clustered with other M. antarcticus sequences, however, the representative Trinidad M. antarcticus sequences consistently formed a separate, highly supported branch for each protein. Similar phylogenetic placement was indicated for LipA and LipB nucleotide and protein sequences. The Trinidad strains also demonstrated lipolytic activity in culture, with an ability to utilize different carbon sources. Comparative evolution of MEL BGC and LipA gene suggested early and late duplication events, depending on the gene, followed by a number of speciation events within Ustilaginaceae. M. antarcticus and M. aphidis were separated from all other members of Ustilaginaceae and two gene homologues were detected, one for each species. CONCLUSIONS Sequence analyses was based on a novel gene-targeted approach to analyze the essential genes of the MEL BGC and LipA and LipB genes of M. antarcticus strains from Trinidad. The findings indicated that these strains accumulated nucleotide mutations to a threshold level that did not affect the function of specific proteins encoded by the MEL BGC and LipA and LipB genes. The biosurfactant and lipase enzymes secreted by these Trinidad M. antarcticus strains facilitated their survival in oil-contaminated terrestrial environments. These findings suggest that the Trinidad strains should be explored as promising candidates for the commercial production of MEL biosurfactants and lipase enzymes.
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Affiliation(s)
- Amanda C. Ramdass
- Biochemistry Research Laboratory (Rm216), Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, West Indies Trinidad and Tobago
| | - Sephra N. Rampersad
- Biochemistry Research Laboratory (Rm216), Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, West Indies Trinidad and Tobago
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147
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Amaral Carneiro G, Walcher M, Storti A, Baric S. Phylogenetic Diversity and Phenotypic Characterization of Phlyctema vagabunda (syn. Neofabraea alba) and Neofabraea kienholzii Causing Postharvest Bull's Eye Rot of Apple in Northern Italy. PLANT DISEASE 2022; 106:451-463. [PMID: 34597150 DOI: 10.1094/pdis-04-21-0687-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bull's eye rot, caused by Phlyctema vagabunda and Neofabraea species, is one of the most important postharvest diseases of apple. South Tyrol (northern Italy) is the largest continuous apple-producing area in Europe, with approximately 1 million tons being produced yearly and conserved in technologically advanced storage facilities for several months. Still, studies on the pathogen species causing postharvest bull's eye rot of apple, as well as their diversity and biology, are lacking for this region. Therefore, the main purpose of the present work was to identify and characterize fungal isolates obtained from decayed apple fruit with symptoms of bull's eye rot that were collected in 2018 and 2019 in different packinghouses in South Tyrol. Among more than 1,000 fungal isolates that were obtained, 419 could be assigned to the genera Phlyctema and/or Neofabraea based on rot symptoms on apple fruit and colony morphology on potato dextrose agar. A smaller subset of 101 representative isolates was further analyzed by DNA sequencing of the internal transcribed spacer region. Furthermore, partial segments of the β-tubulin gene, the translation elongation factor 1α gene, and the 16S mitochondrial ribosomal RNA gene were studied. The phylogenetic analyses, including sequences of reference species, showed that P. vagabunda is the dominant species associated with bull's eye rot of apple in the study area, whereas Neofabraea kienholzii was found only on a small number of apple fruit samples. The combination of multilocus sequence data revealed 11 unique genotypes that belonged to P. vagabunda and four to N. kienholzii. To the best of our knowledge, this study is the first to report N. kienholzii as a postharvest pathogen of apple in Italy. Finally, a pathogenicity test demonstrated different degrees of virulence among selected isolates of P. vagabunda and N. kienholzii on the cultivar Golden Delicious. The present study emphasizes the importance of accurate species identification, because different species may vary in their biological and pathogenic characteristics, and consequently require distinct disease management strategies, both in the field and during the postharvest stages.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Greice Amaral Carneiro
- Free University of Bozen-Bolzano, Faculty of Science and Technology, 39100 Bozen-Bolzano, Italy
| | - Magdalena Walcher
- Free University of Bozen-Bolzano, Faculty of Science and Technology, 39100 Bozen-Bolzano, Italy
| | - Alberto Storti
- Free University of Bozen-Bolzano, Faculty of Science and Technology, 39100 Bozen-Bolzano, Italy
| | - Sanja Baric
- Free University of Bozen-Bolzano, Faculty of Science and Technology, 39100 Bozen-Bolzano, Italy
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148
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Phylloplane Biodiversity and Activity in the City at Different Distances from the Traffic Pollution Source. PLANTS 2022; 11:plants11030402. [PMID: 35161383 PMCID: PMC8839900 DOI: 10.3390/plants11030402] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 11/17/2022]
Abstract
The phylloplane is an integrated part of green infrastructure which interacts with plant health. Taxonomic characterization of the phylloplane with the aim to link it to ecosystem functioning under anthropogenic pressure is not sufficient because only active microorganisms drive biochemical processes. Activity of the phylloplane remains largely overlooked. We aimed to study the interactions among the biological characteristics of the phylloplane: taxonomic diversity, functional diversity and activity, and the pollution grade. Leaves of Betula pendula were sampled in Moscow at increasing distances from the road. For determination of phylloplane activity and functional diversity, a MicroResp tool was utilized. Taxonomic diversity of the phylloplane was assessed with a combination of microorganism cultivation and molecular techniques. Increase of anthropogenic load resulted in higher microbial respiration and lower DNA amount, which could be viewed as relative inefficiency of phylloplane functioning in comparison to less contaminated areas. Taxonomic diversity declined with road vicinity, similar to the functional diversity pattern. The content of Zn in leaf dust better explained the variation in phylloplane activity and the amount of DNA. Functional diversity was linked to variation in nutrient content. The fraction of pathogenic fungi of the phylloplane was not correlated with any of the studied elements, while it was significantly high at the roadsides. The bacterial classes Gammaproteobacteria and Cytophagia, as well as the Dothideomycetes class of fungi, are exposed to the maximal effect of distance from the highway. This study demonstrated the sensitivity of the phylloplane to road vicinity, which combines the effects of contaminants (mainly Zn according to this study) and potential stressful air microclimatic conditions (e.g., low relative air humidity, high temperature, and UV level). Microbial activity and taxonomic diversity of the phylloplane could be considered as an additional tool for bioindication.
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Alkan M, Bayraktar H, İmren M, Özdemir F, Lahlali R, Mokrini F, Paulitz T, Dababat AA, Özer G. Monitoring of Host Suitability and Defense-Related Genes in Wheat to Bipolaris sorokiniana. J Fungi (Basel) 2022; 8:jof8020149. [PMID: 35205903 PMCID: PMC8877012 DOI: 10.3390/jof8020149] [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: 01/03/2022] [Revised: 01/23/2022] [Accepted: 01/28/2022] [Indexed: 11/16/2022] Open
Abstract
Spot blotch caused by Bipolaris sorokiniana is a destructive disease of wheat worldwide. This study investigated the aggressiveness of B. sorokiniana isolates from different wheat-growing areas of Bolu province in Turkey on the cultivar Seri-82. Host susceptibility of 55 wheat cultivars was evaluated against the most aggressive isolate. Our results indicated that the cultivars Anafarta and Koç-2015 were the most resistant. A specific and sensitive qPCR assay was developed for detecting the pathogen in plant tissues and evaluating wheat plants with different resistance levels. Three primer sets, BsGAPDHF/BsGAPDHR, BsITSF/BsITSR, and BsSSUF/BsSSUR, were designed based on glyceraldehyde-3-phosphate dehydrogenase, internal transcribed spacers, and 18S rRNA loci of B. sorokiniana with detection limits of 1, 0.1, and 0.1 pg of pathogen DNA, respectively. The qPCR assay was highly sensitive and did not amplify DNA from the other closely related fungal species and host plants. The protocol differentiated wheat plants with varying degrees of resistance. The assay developed a useful tool for the quantification of the pathogen in the early stages of infection and may provide a significant contribution to a more efficient selection of wheat genotypes in breeding studies. In the present study, expression levels of PR proteins, phenylalanine ammonia-lyase, catalase, ascorbate peroxidase, and superoxide dismutase enzymes were upregulated in Anafarta (resistant) and Nenehatun (susceptible) cultivars at different post-infection time points, but more induced in the susceptible cultivar. The results showed considerable variation in the expression levels and timing of defense genes in both cultivars.
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Affiliation(s)
- Mehtap Alkan
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu 14030, Turkey; (M.A.); (M.İ.)
| | - Harun Bayraktar
- Department of Plant Protection, Faculty of Agriculture, Ankara University, Ankara 06110, Turkey
- Correspondence: (H.B.); (A.A.D.); (G.Ö.); Tel.: +90-31-2596-1270 (H.B.); +90-53-0406-2825 (A.A.D.); +90-50-5385-8234 (G.Ö.)
| | - Mustafa İmren
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu 14030, Turkey; (M.A.); (M.İ.)
| | - Fatih Özdemir
- Bahri Dagdas International Agricultural Research Institute, Konya 42050, Turkey;
| | - Rachid Lahlali
- Phytopathology Unit, Department of Plant Protection, Ecole Nationale d’Agriculture de Meknès, BPS 40, Meknes 50001, Morocco;
| | - Fouad Mokrini
- Biotechnology Research Unit, Laboratory of Nematology, Regional Center of Agricultural Research, National Institute of Agronomic Research (INRA), Rabat 10060, Morocco;
| | - Timothy Paulitz
- Wheat Health, Genetics and Quality Research Unit, United States Department of Agriculture, Agricultural Research Service, Washington State University, Pullman, WA 99164, USA;
| | - Abdelfattah A. Dababat
- International Maize and Wheat Improvement Centre (CIMMYT), P.O. Box 39, Emek, Ankara 06170, Turkey
- Correspondence: (H.B.); (A.A.D.); (G.Ö.); Tel.: +90-31-2596-1270 (H.B.); +90-53-0406-2825 (A.A.D.); +90-50-5385-8234 (G.Ö.)
| | - Göksel Özer
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu 14030, Turkey; (M.A.); (M.İ.)
- Correspondence: (H.B.); (A.A.D.); (G.Ö.); Tel.: +90-31-2596-1270 (H.B.); +90-53-0406-2825 (A.A.D.); +90-50-5385-8234 (G.Ö.)
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150
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Yang S, Johnson MA, Hansen MA, Bush E, Li S, Vinatzer BA. Metagenomic sequencing for detection and identification of the boxwood blight pathogen Calonectria pseudonaviculata. Sci Rep 2022; 12:1399. [PMID: 35082361 PMCID: PMC8791934 DOI: 10.1038/s41598-022-05381-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 01/10/2022] [Indexed: 11/16/2022] Open
Abstract
Pathogen detection and identification are key elements in outbreak control of human, animal, and plant diseases. Since many fungal plant pathogens cause similar symptoms, are difficult to distinguish morphologically, and grow slowly in culture, culture-independent, sequence-based diagnostic methods are desirable. Whole genome metagenomic sequencing has emerged as a promising technique because it can potentially detect any pathogen without culturing and without the need for pathogen-specific probes. However, efficient DNA extraction protocols, computational tools, and sequence databases are required. Here we applied metagenomic sequencing with the Oxford Nanopore Technologies MinION to the detection of the fungus Calonectria pseudonaviculata, the causal agent of boxwood (Buxus spp.) blight disease. Two DNA extraction protocols, several DNA purification kits, and various computational tools were tested. All DNA extraction methods and purification kits provided sufficient quantity and quality of DNA. Several bioinformatics tools for taxonomic identification were found suitable to assign sequencing reads to the pathogen with an extremely low false positive rate. Over 9% of total reads were identified as C. pseudonaviculata in a severely diseased sample and identification at strain-level resolution was approached as the number of sequencing reads was increased. We discuss how metagenomic sequencing could be implemented in routine plant disease diagnostics.
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Affiliation(s)
- Shu Yang
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Marcela A Johnson
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA.,Graduate Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, USA
| | - Mary Ann Hansen
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Elizabeth Bush
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Song Li
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Boris A Vinatzer
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA.
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