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Tamm T, Kristjuhan A. Protocol for rapid and cost-effective extraction of genomic DNA from a wide range of wild yeast species for use in PCR-based applications. STAR Protoc 2024; 5:103282. [PMID: 39232988 DOI: 10.1016/j.xpro.2024.103282] [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: 06/18/2024] [Revised: 07/20/2024] [Accepted: 08/12/2024] [Indexed: 09/06/2024] Open
Abstract
Isolation of amplifiable genomic DNA is a prerequisite for the implementation of PCR-based techniques. Here we present a protocol for isolating the genomic DNA from a variety of wild yeast species. This can be completed in approximately 1 h and does not require sophisticated laboratory equipment. We describe steps for growing yeast cells, genomic data extraction, and downstream assay for amplification of specific sequences from the genomic DNA. We then detail procedures for gel electrophoresis and analysis of the results. For complete details on the use and execution of this protocol, please refer to Kristjuhan et al.1.
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Affiliation(s)
- Tiina Tamm
- Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia.
| | - Arnold Kristjuhan
- Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia.
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Li J, Che NJ, Cui YY. Three new species of Laccaria (Agaricales, Basidiomycota) from Southwest China (Yunnan) based on morphological and multi-gene sequence data. Front Microbiol 2024; 15:1411488. [PMID: 39171265 PMCID: PMC11335674 DOI: 10.3389/fmicb.2024.1411488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 07/08/2024] [Indexed: 08/23/2024] Open
Abstract
Introduction The genus Laccaria has been reported from temperate and tropical areas and is an important constituent in forest ecosystems. However, the species diversity of Laccaria in Southwest China (Yunnan) has been underestimated. Methods In this paper, descriptions based on morphological and multi-gene sequence data from internal transcribed spacer (ITS) region, large subunit ribosomal RNA gene (nrLSU), translation elongation factor 1-α (TEF1α) and the polymerase II second largest subunit (RPB2) of three new Laccaria species from Southwest China (Yunnan) are reported. Results Two of these were characterized by orange pileus and globose to subglobose basidiospores: L. cinnabarina and L. spinulosa. While L. cinnabarina has orange red colored basidiocarps with conspicuously pellucid-striate pattern, and a fibrillose stipe with longitudinally striations, L. spinulosa has a brownish orange to brown fruiting body with light white pruinae and 2-spored basidia. Laccaria longistriata is characterized by brown to flesh-colored basidioma, prominently striate to sulcate pileus and globose to subglobose basidiospores. Discussion The three new species were described, illustrated and compared with closely related species in morphology and phylogeny.
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Affiliation(s)
- Jing Li
- Faculty of Geography, Yunnan Normal University, Kunming, China
| | - Nian-Jie Che
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, China
| | - Yang-Yang Cui
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, China
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Brasch J, Gräser Y, Voss K, Langen KA, Yurkov A. Inopinatus corneliae sp. nov. gen. nov. isolated from human skin: A newly discovered keratinophilic hyphomycete, order Onygenales. Mycoses 2024; 67:e13774. [PMID: 39092516 DOI: 10.1111/myc.13774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Accepted: 07/18/2024] [Indexed: 08/04/2024]
Abstract
BACKGROUND Fungi clinically relevant to human skin comprise prevalent commensals and well-known pathogens. Only rarely human skin harbours fungi that evade identification. OBJECTIVE To characterise an enigmatic specimen isolated from a skin lesion. METHODS A comprehensive clinical and mycological workup including conventional methods for phenotypic characterisation and sequencing based on internal transcribed spacer (ITS) and large subunit (LSU) regions to infer a phylogenetic tree. RESULTS Cultures on common solid media were macroscopically inconspicuous initially until mycelial tufts developed on the surface, notably on potato dextrose agar. Polymorphous chlamydospores were detected but no aleurospores and ascomata. At 26°C, the isolate grew on standard agars, plant materials and garden soil and utilised peptone, keratins, lipids, inulin, erythrocytes and cellulose. It also grew at 5°C and at 37°C. Nucleotide sequences of its ITS region showed 93% similarity to sequences of different Malbranchea species. The closest matches among LSU rRNA sequences were obtained with the genera Amauroascus, Arthroderma, Auxarthronopsis and Malbranchea (93%-95%). A combined phylogenetic analysis placed the fungus in a sister clade to Neogymnomycetaceae, classified as incertae sedis in Onygenales, on a large distance to either Diploospora rosea or 'Amauroascus' aureus. CONCLUSIONS The genus Inopinatus gen. nov. (MB854685) with the species Inopinatus corneliae sp. nov. (MB854687) is introduced to accommodate our isolate (holotype: DSM 116806; isotypes: CBS 151104, IHEM 29063). Probably Inopinatus corneliae is a geophilic species that, although potentially harmful, was no relevant pathogen in our case. Its ecology, epidemiology and pathogenicity need to be further clarified.
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Affiliation(s)
- Jochen Brasch
- Department of Dermatology, University Hospitals of Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Yvonne Gräser
- Institute of Microbiology, Infectious Diseases and Immunology, Charité, Berlin, Germany
| | - Karen Voss
- Department of Dermatology, University Hospitals of Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Katharina Antonia Langen
- Department of Dermatology, University Hospitals of Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Andrey Yurkov
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
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Hassan O, Ryu H, Lee SY, Choi HW. Fusarium amaranthi sp. nov. from Amaranth Is an Emergent Species Closely Related to F. circinatum. PLANT DISEASE 2024; 108:2297-2302. [PMID: 38537143 DOI: 10.1094/pdis-10-23-2187-sc] [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: 07/13/2024]
Abstract
Amaranth (Amaranthus spp. L) is not native to South Korea but is cultivated in small scales for ornamental purposes as well as leafy vegetables and pseudo cereals. In this study, a new species within the genus Fusarium was isolated from amaranth, showing stem rot symptoms from a farmer field in Hwaseong, South Korea. The disease is characterized by dark-brown spots with black borders, leading to withering. Phylogenetic analysis-based concatenated sequences of translation elongation factor 1-alpha (TEF1), beta-tubulin (tub2), calmodulin (cmdA), RNA polymerase largest subunit (RPB1), and RNA polymerase II second largest subunit (RPB2) genes revealed that the obtained isolates formed a distinct clad within the Fusarium fujikuroi species complex and is closely related to F. circinatum. Cultural and morphological characteristics and pathogenicity on healthy amaranth plants (stem and leaves) were examined. The isolates readily differentiated from F. circinatum based on one- to five-septate macroconidia and the absence of sterile hyphae. Based on molecular and morphological characteristics, this fungus is demonstrated to be a new species and is described here as F. amaranthi, the causal agent of stem rot of amaranth in South Korea.
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Affiliation(s)
- Oliul Hassan
- Crop Protection Division, National Institute of Agricultural Sciences, Wanju 55365, Korea
| | - Hyunjoo Ryu
- Crop Protection Division, National Institute of Agricultural Sciences, Wanju 55365, Korea
| | - Sang-Yeob Lee
- Planning Division, The Korea Agro-materials Research Organization, Suwon 16432, Korea
| | - Hyo-Won Choi
- Disaster Management Division, Rural Development Administration, Jeonju 54875, Korea
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Liu Y, Ahmed A, Munir S, Chen L, He P, He Y, Tang P, Kong B, Wu Y, He P. Alternaria alternata Pathogen from Cuscuta japonica Could Serve as a Potential Bioherbicide. J Fungi (Basel) 2024; 10:494. [PMID: 39057379 PMCID: PMC11277819 DOI: 10.3390/jof10070494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/02/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Dodder (Cuscuta spp.) is a dangerous parasitic plant that causes serious damage to crop production and is challenging to eliminate. Herbicide application is a common strategy to control dodder in the field, but it is costly, ineffective, and further results in hazardous outcomes. Therefore, our study aims to identify the potential pathogens in naturally occurring dodder infections which may provide efficient biocontrol options. In this regard, the pathogens were isolated from the infected plants, their pathogenicity was validated through inoculation, and the optimal culture conditions for their growth were identified by determining the pathogenicity difference. The pathogenicity range was determined in vitro using the leaves of common horticultural plants and crops. Furthermore, a small range of horticultural plants parasitized by Cuscuta reflexa in the field were inoculated with the pathogen to determine their biosafety and biocontrol potential, and the pathogens were identified by morphological and molecular characterization. We found 7 strains that were isolated after pathogen enrichment culture. Among them, Cbp6 and Cbp7 showed the highest pathogenicity against C. reflexa. After testing the inoculation of more than 50 species of plants, only 9 species showed varying degrees of lesions on leaves, which proved the high biosafety for common plants. Field spraying of these pathogens showed a good control effect on C. reflexa after 21 days; the disease severityreached 66.0%, while its host plant did not display obvious symptoms. In conclusion, the pathogens Cbp6 and Cbp7 were identified as Alternaria alternata, and the results of this study provide a theoretical basis for the biological control of dodder.
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Affiliation(s)
- Yinglong Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China (Y.H.)
| | - Ayesha Ahmed
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China (Y.H.)
| | - Shahzad Munir
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China (Y.H.)
| | - Lei Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China (Y.H.)
| | - Pengfei He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China (Y.H.)
| | - Yueqiu He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China (Y.H.)
| | - Ping Tang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China (Y.H.)
| | - Baohua Kong
- College of Agronomy and Life Science, Zhaotong University, Zhaotong 657000, China
| | - Yixin Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China (Y.H.)
| | - Pengbo He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China (Y.H.)
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Pérez-Anzúrez G, Mendoza-de Gives P, Alonso-Díaz MÁ, von Son-de Fernex E, Paz-Silva A, López-Arellano ME, Olmedo-Juárez A. Lecanicillium psalliotae (Hypocreales: Cordycipitaceae) Exerts Ovicidal and Larvicidal Effects against the Sheep Blood-Feeding Nematode Haemonchus contortus through Its Liquid Culture Filtrates. Pathogens 2024; 13:588. [PMID: 39057815 PMCID: PMC11280379 DOI: 10.3390/pathogens13070588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/05/2024] [Accepted: 07/14/2024] [Indexed: 07/28/2024] Open
Abstract
Nematophagous fungi (NF) form part of the soil microbiota and are natural enemies of nematodes, helping to regulate nematode populations. A verticillate NF isolated from soil from Tepalcingo, Mexico, was morphologically and molecularly characterised. This fungus was cultured in two different liquid media-Czapek-Dox broth (CzDoxB) and sweet potato dextrose broth (SPDB)-for 21 days. The ovicidal (OA) and larvicidal (LA) activities of fungal liquid culture filtrates (LCFs) were assessed in 96-well microtitre plates at different concentrations against Haemonchus contortus after 48 h. The morphological and molecular identification revealed the presence of Lecanicillium psalliotae. Additionally, the groups of compounds associated with nematocidal activity were determined from a qualitative chemical profile (QCP) using different reagents. The highest OA of the LCFs was obtained at 25 mg/mL from SPDB and CzDoxB and amounted to 97.2 and 99.06%, respectively. Meanwhile, the highest LA recorded with these LCFs at 100 mg/mL was 54.27% and 96.8%, respectively. The QCP revealed the presence of alkaloids and tannins in both LCFs that have previously been associated with nematocidal activity. Lecanicillium psalliotae exerted an important effect on H. contortus and could be of significance in future studies focused on the control and prevention of haemonchosis in small ruminants.
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Affiliation(s)
- Gustavo Pérez-Anzúrez
- Laboratory of Helminthology, National Centre for Disciplinary Research in Animal Health and Innocuity (CENID-SAI), National Institute for Research in Forestry, Agriculture and Livestock, INIFAP-SADER, Jiutepec 62550, Mexico; (G.P.-A.); (M.E.L.-A.); (A.O.-J.)
- Production Sciences and Animal Health, Faculty of Veterinary Medicine and Zootechnics, National Autonomous University of Mexico, Coyoacán 04510, Mexico
| | - Pedro Mendoza-de Gives
- Laboratory of Helminthology, National Centre for Disciplinary Research in Animal Health and Innocuity (CENID-SAI), National Institute for Research in Forestry, Agriculture and Livestock, INIFAP-SADER, Jiutepec 62550, Mexico; (G.P.-A.); (M.E.L.-A.); (A.O.-J.)
| | - Miguel Ángel Alonso-Díaz
- Tropical Livestock Center, Faculty of Veterinary Medicine and Zootechnics, National Autonomous University of Mexico, Martínez de la Torre 93600, Mexico; (M.Á.A.-D.); (E.v.S.-d.F.)
| | - Elke von Son-de Fernex
- Tropical Livestock Center, Faculty of Veterinary Medicine and Zootechnics, National Autonomous University of Mexico, Martínez de la Torre 93600, Mexico; (M.Á.A.-D.); (E.v.S.-d.F.)
| | - Adolfo Paz-Silva
- Department of Animal Pathology, Faculty of Veterinary, University of Santiago de Compostela, 27142 Lugo, Spain;
| | - María Eugenia López-Arellano
- Laboratory of Helminthology, National Centre for Disciplinary Research in Animal Health and Innocuity (CENID-SAI), National Institute for Research in Forestry, Agriculture and Livestock, INIFAP-SADER, Jiutepec 62550, Mexico; (G.P.-A.); (M.E.L.-A.); (A.O.-J.)
| | - Agustín Olmedo-Juárez
- Laboratory of Helminthology, National Centre for Disciplinary Research in Animal Health and Innocuity (CENID-SAI), National Institute for Research in Forestry, Agriculture and Livestock, INIFAP-SADER, Jiutepec 62550, Mexico; (G.P.-A.); (M.E.L.-A.); (A.O.-J.)
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Dolatabadi S, Najafzadeh MJ, Raeisabadi A, Zarrinfar H, Jalali M, Spruijtenburg B, Meijer EFJ, Meis JF, Lass-Flörl C, de Groot T. Epidemiology of Candidemia in Mashhad, Northeast Iran: A Prospective Multicenter Study (2019-2021). J Fungi (Basel) 2024; 10:481. [PMID: 39057366 PMCID: PMC11277834 DOI: 10.3390/jof10070481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Candidemia is a major cause of morbidity and mortality in health care settings, and its epidemiology is changing. In the last two decades, the proportion of non-albicans Candida (NAC) yeasts in candidemia has increased. These yeasts more often display resistance to common antifungals. In many western countries, candidemia is mainly caused by susceptible C. albicans, while in resource-limited countries, including Iran, the candidemia species distribution is studied less often. Here, we investigated the species distribution, resistance levels, and characteristics of patients with candidemia in five hospitals in Mashhad (northeast Iran) for two years (2019-2021). Yeast isolates from blood were identified with MALDI-TOF MS and subjected to antifungal susceptibility testing (AFST) using the broth microdilution method, while molecular genotyping was applied to Candida parapsilosis isolates. In total, 160 yeast isolates were recovered from 160 patients, of which the majority were adults (60%). Candidemia was almost equally detected in men (48%) and women (52%). Almost half of patients (n = 67, 49%) were from intensive care units (ICUs). C. parapsilosis (n = 58, 36%) was the most common causative agent, surpassing C. albicans (n = 52, 33%). The all-cause mortality rate was 53%, with C. albicans candidemia displaying the lowest mortality with 39%, in contrast to a mortality rate of 59% for NAC candidemia. With microbroth AFST, nearly all tested isolates were found to be susceptible, except for one C. albicans isolate that was resistant to anidulafungin. By applying short tandem repeat (STR) genotyping to C. parapsilosis, multiple clusters were found. To summarize, candidemia in Mashhad, Iran, from 2019 to 2021, is characterized by common yeast species, in particular C. parapsilosis, for which STR typing indicates potential nosocomial transmission. The overall mortality is high, while resistance rates were found to be low, suggesting that the high mortality is linked to limited diagnostic options and insufficient medical care, including the restricted use of echinocandins as the first treatment option.
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Affiliation(s)
- Somayeh Dolatabadi
- Department of Biology, Hakim Sabzevari University, Sabzevar 9617976487, Iran
| | - Mohammad Javad Najafzadeh
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad 91766-99199, Iran
| | - Abbas Raeisabadi
- Department of Medical Mycology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari 48471-91628, Iran
| | - Hossein Zarrinfar
- Allergy Research Center, Mashhad University of Medical Sciences, Mashhad 91766-99199, Iran
| | - Mahsa Jalali
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad 91766-99199, Iran
| | - Bram Spruijtenburg
- Radboudumc-CWZ Center of Expertise for Mycology, 6532 SZ Nijmegen, The Netherlands (E.F.J.M.)
- Canisius-Wilhelmina Hospital (CWZ)/Dicoon, 6532 SZ Nijmegen, The Netherlands
| | - Eelco F. J. Meijer
- Radboudumc-CWZ Center of Expertise for Mycology, 6532 SZ Nijmegen, The Netherlands (E.F.J.M.)
- Canisius-Wilhelmina Hospital (CWZ)/Dicoon, 6532 SZ Nijmegen, The Netherlands
| | - Jacques F. Meis
- Radboudumc-CWZ Center of Expertise for Mycology, 6532 SZ Nijmegen, The Netherlands (E.F.J.M.)
- Institute of Translational Research, Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), Excellence Center for Medical Mycology (ECMM), University of Cologne, 50931 Cologne, Germany
| | - Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Excellence Center for Medical Mycology (ECMM), 6020 Innsbruck, Austria
| | - Theun de Groot
- Radboudumc-CWZ Center of Expertise for Mycology, 6532 SZ Nijmegen, The Netherlands (E.F.J.M.)
- Canisius-Wilhelmina Hospital (CWZ)/Dicoon, 6532 SZ Nijmegen, The Netherlands
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Van Caenegem W, Haelewaters D. New insights into the DNA extraction and PCR amplification of minute ascomycetes in the genus Laboulbenia (Pezizomycotina, Laboulbeniales). IMA Fungus 2024; 15:14. [PMID: 38863065 PMCID: PMC11167896 DOI: 10.1186/s43008-024-00146-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 05/17/2024] [Indexed: 06/13/2024] Open
Abstract
Molecular studies of fungi within the order Laboulbeniales (Ascomycota, Pezizomycotina) have been hampered for years because of their minute size, inability to grow in axenic culture, and lack of reliable and cost-efficient DNA extraction protocols. In particular, the genus Laboulbenia is notorious for low success with DNA extraction and polymerase chain reaction (PCR) amplification. This is attributed to the presence of melanin, a molecule known to inhibit PCR, in the cells. We evaluated the efficacy of a standard single cell-based DNA extraction protocol by halving the recommended amount of reagents to reduce the cost per extraction and adding bovine serum albumin (BSA) during the multiple displacement amplification step to reverse the effect of melanin. A total of 196 extractions were made, 111 of which were successful. We found that halving the reagents used in the single cell-based extraction kit did not significantly affect the probability of successful DNA extraction. Using the halved protocol reduces cost and resource consumption. Moreover, there was no significant difference in the probability of successfully extracting DNA based on whether BSA was added or not, suggesting that the amount of melanin present in cells of the thallus has no major inhibitory effect on PCR. We generated 277 sequences from five loci, but amplification of the internal transcribed spacer region, the mitochondrial small subunit rDNA, and protein-coding genes remains challenging. The probability of successfully extracting DNA from Laboulbeniales was also impacted by specimen storage methods, with material preserved in > 95% ethanol yielding higher success rates compared to material stored in 70% ethanol and dried material. We emphasize the importance of proper preservation of material and propose the design of Laboulbeniales-specific primers to overcome the problems of primer mismatches and contaminants. Our new insights apply not only to the genus Laboulbenia; Laboulbeniales generally are understudied, and the vast majority of species remain unsequenced. New and approachable molecular developments will benefit the study of Laboulbeniales, helping to elucidate the true diversity and evolutionary relationships of these peculiar microfungi.
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Affiliation(s)
- Warre Van Caenegem
- Research Group Mycology, Department of Biology, Ghent University, Ghent, 9000, Belgium.
| | - Danny Haelewaters
- Research Group Mycology, Department of Biology, Ghent University, Ghent, 9000, Belgium.
- Meise Botanic Garden, Meise, 1860, Belgium.
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czech Republic.
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Shipman A, Tian M. Combined Use of Phenotype-Based and Genome-Informed Approaches Identified a Unique Fusarium oxysporum f. sp. cubense Isolate in Hawaii. PHYTOPATHOLOGY 2024; 114:1305-1319. [PMID: 38038692 DOI: 10.1094/phyto-07-23-0257-r] [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: 12/02/2023]
Abstract
Fusarium wilt of banana, caused by Fusarium oxysporum f. sp. cubense (Foc), is a serious disease that threatens banana production worldwide. It is a long-standing problem in Hawaii, but previously, there was little knowledge of the causal pathogen. We isolated a strain of Foc, named Foc-UH, from a field experiencing the disease epidemic in Hawaii. Infection assays of a diverse panel of 26 banana clones, including varieties used for differentiating pathogen races and fruit production, revealed that Foc-UH has a race 1 pathogenic phenotype with an intermediate race 2 virulence and revealed the differential resistance of varieties to infection. Separate phylogenetic analyses using the barcoding regions of three nuclear genes, seven complete nuclear genes, and single-nucleotide polymorphisms within conserved whole-genome protein coding sequences placed Foc-UH into recently proposed taxonomic frameworks relevant to Foc and the F. oxysporum species complex. Screening of the 99.7% complete draft genome identified five secreted in xylem (SIX) gene homologs: SIX1d, SIX1f, SIX9a, SIX9b, and SIX13a. This profile is similar to that of several race 1 isolates except for the absence of SIX4 and SIX6. Foc-UH was morphologically dissimilar to the nearest related isolates. Altogether, this study identified a unique isolate that causes banana Fusarium wilt, which represents the first characterization of the causal pathogen in Hawaii. The findings and genomic resources generated in this study are expected to guide banana breeding and cultivar deployment in Hawaii and beyond and contribute to further understanding of the pathogenicity and evolutionary systematics of Foc.
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Affiliation(s)
- Aaron Shipman
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822
| | - Miaoying Tian
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822
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Fryssouli V, Polemis E, Typas MA, Zervakis GI. Revisiting the phylogeny and taxonomy of the genus Sidera (Hymenochaetales, Basidiomycota) with particular emphasis on S.vulgaris. MycoKeys 2024; 105:119-137. [PMID: 38752164 PMCID: PMC11094396 DOI: 10.3897/mycokeys.105.121601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 04/01/2024] [Indexed: 05/18/2024] Open
Abstract
The genus Sidera (Hymenochaetales, Basidiomycota) comprises white-rot, mono- or dimitic fungi with poroid or hydnoid hymenophore. It has a worldwide distribution albeit with fewer species present in the Southern Hemisphere. Although recent studies revealed the existence of several new Sidera species, there are still taxonomic inconsistencies and obscure phylogenetic relationships amongst certain taxa of the genus. In this work, a large number of Sidera collections were used to obtain an updated phylogeny, based on ITS and 28S rDNA sequences by including new material from Mediterranean Europe. The monophyly of the genus was strongly supported and all species with poroid hymenophore formed a highly-supported lineage with two major subclades. In total, 23 putative species were recognised. Amongst those, five are considered to possibly represent entities new to science, but further work is required since they are represented by single specimens or environmental sequences. Examined collections originally named S.lenis from southern Europe were grouped within S.vulgaris. Similarly, several collections under various names were hereby identified as S.vulgaris, including those of the recently described species S.tibetica. Furthermore, a critical discussion (based on morphoanatomical findings) is made on the key features that could be used to distinguish S.lenis from S.vulgaris.
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Affiliation(s)
- Vassiliki Fryssouli
- Agricultural University of Athens, Laboratory of General and Agricultural Microbiology, Iera Odos 75, 11855 Athens, GreeceAgricultural University of AthensAthensGreece
| | - Elias Polemis
- Agricultural University of Athens, Laboratory of General and Agricultural Microbiology, Iera Odos 75, 11855 Athens, GreeceAgricultural University of AthensAthensGreece
| | - Milton A. Typas
- National and Kapodistrian University of Athens, Department of Genetics and Biotechnology, Faculty of Biology, Panepistemiopolis, Athens 15701, GreeceNational and Kapodistrian University of AthensAthensGreece
| | - Georgios I. Zervakis
- Agricultural University of Athens, Laboratory of General and Agricultural Microbiology, Iera Odos 75, 11855 Athens, GreeceAgricultural University of AthensAthensGreece
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Nenciarini S, Renzi S, di Paola M, Meriggi N, Cavalieri D. Ascomycetes yeasts: The hidden part of human microbiome. WIREs Mech Dis 2024; 16:e1641. [PMID: 38228159 DOI: 10.1002/wsbm.1641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024]
Abstract
The fungal component of the microbiota, the mycobiota, has been neglected for a long time due to its poor richness compared to bacteria. Limitations in fungal detection and taxonomic identification arise from using metagenomic approaches, often borrowed from bacteriome analyses. However, the relatively recent discoveries of the ability of fungi to modulate the host immune response and their involvement in human diseases have made mycobiota a fundamental component of the microbial communities inhabiting the human host, deserving some consideration in host-microbe interaction studies and in metagenomics. Here, we reviewed recent data on the identification of yeasts of the Ascomycota phylum across human body districts, focusing on the most representative genera, that is, Saccharomyces and Candida. Then, we explored the key factors involved in shaping the human mycobiota across the lifespan, ranging from host genetics to environment, diet, and lifestyle habits. Finally, we discussed the strengths and weaknesses of culture-dependent and independent methods for mycobiota characterization. Overall, there is still room for some improvements, especially regarding fungal-specific methodological approaches and bioinformatics challenges, which are still critical steps in mycobiota analysis, and to advance our knowledge on the role of the gut mycobiota in human health and disease. This article is categorized under: Immune System Diseases > Genetics/Genomics/Epigenetics Immune System Diseases > Environmental Factors Infectious Diseases > Environmental Factors.
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Affiliation(s)
| | - Sonia Renzi
- Department of Biology, University of Florence, Florence, Italy
| | - Monica di Paola
- Department of Biology, University of Florence, Florence, Italy
| | - Niccolò Meriggi
- Department of Biology, University of Florence, Florence, Italy
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12
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Genome assembly of the edible jelly fungus Dacryopinax spathularia (Dacrymycetaceae). GIGABYTE 2024; 2024:gigabyte120. [PMID: 38707634 PMCID: PMC11066560 DOI: 10.46471/gigabyte.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/13/2024] [Indexed: 05/07/2024] Open
Abstract
The edible jelly fungus Dacryopinax spathularia (Dacrymycetaceae) is wood-decaying and can be commonly found worldwide. It has found application in food additives, given its ability to synthesize long-chain glycolipids, among other uses. In this study, we present the genome assembly of D. spathularia using a combination of PacBio HiFi reads and Omni-C data. The genome size is 29.2 Mb. It has high sequence contiguity and completeness, with a scaffold N50 of 1.925 Mb and a 92.0% BUSCO score. A total of 11,510 protein-coding genes and 474.7 kb repeats (accounting for 1.62% of the genome) were predicted. The D. spathularia genome assembly generated in this study provides a valuable resource for understanding their ecology, such as their wood-decaying capability, their evolutionary relationships with other fungi, and their unique biology and applications in the food industry.
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13
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Guerra-Mateo D, Cano-Lira JF, Fernández-Bravo A, Gené J. Sunken Riches: Ascomycete Diversity in the Western Mediterranean Coast through Direct Plating and Flocculation, and Description of Four New Taxa. J Fungi (Basel) 2024; 10:281. [PMID: 38667952 PMCID: PMC11051201 DOI: 10.3390/jof10040281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/23/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
The Mediterranean Sea stands out as a hotspot of biodiversity, whose fungal composition remains underexplored. Marine sediments represent the most diverse substrate; however, the challenge of recovering fungi in culture hinders the precise identification of this diversity. Concentration techniques like skimmed milk flocculation (SMF) could represent a suitable solution. Here, we compare the effectiveness in recovering filamentous ascomycetes of direct plating and SMF in combination with three culture media and two incubation temperatures, and we describe the fungal diversity detected in marine sediments. Sediments were collected at different depths on two beaches (Miracle and Arrabassada) on the Spanish western Mediterranean coast between 2021 and 2022. We recovered 362 strains, and after a morphological selection, 188 were identified primarily with the LSU and ITS barcodes, representing 54 genera and 94 species. Aspergillus, Penicillium, and Scedosporium were the most common genera, with different percentages of abundance between both beaches. Arrabassada Beach was more heterogeneous, with 42 genera representing 60 species (Miracle Beach, 28 genera and 54 species). Although most species were recovered with direct plating (70 species), 20 species were exclusively obtained using SMF as a sample pre-treatment, improving our ability to detect fungi in culture. In addition, we propose three new species in the genera Exophiala, Nigrocephalum, and Queenslandipenidiella, and a fourth representing the novel genus Schizochlamydosporiella. We concluded that SMF is a useful technique that, in combination with direct plating, including different culture media and incubation temperatures, improves the chance of recovering marine fungal communities in culture-dependent studies.
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Affiliation(s)
| | | | | | - Josepa Gené
- Unitat de Micologia i Microbiologia Ambiental, Facultat de Medicina i Ciències de la Salut and Institut Universitari de Recerca en Sostenibilitat, Canvi Climàtic i Transició Energètica (IU-RESCAT), Universitat Rovira i Virgili, 43201 Reus, Spain; (D.G.-M.); (J.F.C.-L.); (A.F.-B.)
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14
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Qi G, Hao L, Xin T, Gan Y, Lou Q, Xu W, Song J. Analysis of Whole-Genome facilitates rapid and precise identification of fungal species. Front Microbiol 2024; 15:1336143. [PMID: 38500585 PMCID: PMC10946254 DOI: 10.3389/fmicb.2024.1336143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/13/2024] [Indexed: 03/20/2024] Open
Abstract
Fungal identification is a cornerstone of fungal research, yet traditional molecular methods struggle with rapid and accurate onsite identification, especially for closely related species. To tackle this challenge, we introduce a universal identification method called Analysis of whole GEnome (AGE). AGE includes two key steps: bioinformatics analysis and experimental practice. Bioinformatics analysis screens candidate target sequences named Targets within the genome of the fungal species and determines specific Targets by comparing them with the genomes of other species. Then, experimental practice using sequencing or non-sequencing technologies would confirm the results of bioinformatics analysis. Accordingly, AGE obtained more than 1,000,000 qualified Targets for each of the 13 fungal species within the phyla Ascomycota and Basidiomycota. Next, the sequencing and genome editing system validated the ultra-specific performance of the specific Targets; especially noteworthy is the first-time demonstration of the identification potential of sequences from unannotated genomic regions. Furthermore, by combining rapid isothermal amplification and phosphorothioate-modified primers with the option of an instrument-free visual fluorescence method, AGE can achieve qualitative species identification within 30 min using a single-tube test. More importantly, AGE holds significant potential for identifying closely related species and differentiating traditional Chinese medicines from their adulterants, especially in the precise detection of contaminants. In summary, AGE opens the door for the development of whole-genome-based fungal species identification while also providing guidance for its application in plant and animal kingdoms.
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Affiliation(s)
- Guihong Qi
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lijun Hao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Tianyi Xin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yutong Gan
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qian Lou
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Wenjie Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing, China
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15
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Noffsinger CR, Adamčíková K, Eberhardt U, Caboň M, Bazzicalupo A, Buyck B, Kaufmann H, Weholt Ø, Looney BP, Matheny PB, Berbee ML, Tausan D, Adamčík S. Three new species in Russula subsection Xerampelinae supported by genealogical and phenotypic coherence. Mycologia 2024; 116:322-349. [PMID: 38363178 DOI: 10.1080/00275514.2023.2295957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/13/2023] [Indexed: 02/17/2024]
Abstract
Xerampelinae is a subsection composed of species of ectomycorrhizal fungi belonging to the hyperdiverse and cosmopolitan genus Russula (Russulales). Species of Xerampelinae are recognized by their fishy or shrimp odor, browning context, and a green reaction to iron sulfate. However, species delimitation has traditionally relied on morphology and analysis of limited molecular data. Prior taxonomic work in Xerampelinae has led to the description of as many as 59 taxa in Europe and 19 in North America. Here we provide the first multilocus phylogeny of European and North American members based on two nrDNA loci and two protein-coding genes. The resulting phylogeny supports the recognition of 17 species-rank Xerampelinae clades; however, higher species richness (~23) is suggested by a more inclusive nuclear rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode) analysis. Phylogenetic and morphological analyses support three new species with restricted geographic distributions: R. lapponica, R. neopascua, and R. olympiana. We confirm that the European species R. subrubens is present in North America and the North American species R. serissima (previously known as R. favrei) is present in Europe. Most other Xerampelinae appear restricted to either North America or Eurasia, which indicates a high degree of regional endemism; this includes R. xerampelina, a name widely applied to North American taxa, but a species restricted to Eurasia.
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Affiliation(s)
- Chance R Noffsinger
- Department of Ecology and Evolutionary Biology, University of Tennessee, 1416 Circle Drive, Knoxville, Tennessee 37996
| | - Katarína Adamčíková
- Department of Plant Pathology and Mycology, Institute of Forest Ecology, Slovak Academy of Sciences, Akademická 2, Zvolen, Nitra 94901, Slovakia
| | - Ursula Eberhardt
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, Stuttgart 70191, Germany
| | - Miroslav Caboň
- Laboratory of Molecular Ecology and Mycology, Institute of Botany, Plant Science and Biodiversity Center, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava 84523, Slovakia
| | - Anna Bazzicalupo
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
| | - Bart Buyck
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, Centre national de la recherche scientifique (CNRS), Sorbonne Université, École partique des hautes études (EPHE), Université des Antilles, CP 39, 57 rue Cuvier, Paris 75005, France
| | | | | | - Brian P Looney
- Department of Biology, Duke University, 130 Science Drive, Durham, North Carolina 27708
| | - P Brandon Matheny
- Department of Ecology and Evolutionary Biology, University of Tennessee, 1416 Circle Drive, Knoxville, Tennessee 37996
| | - Mary L Berbee
- Department of Botany, University of British Columbia, 6270 University Boulevard no. 3158, Vancouver, BC V6T 1Z4, Canada
| | - Daniel Tausan
- Department of Botany, University of British Columbia, 6270 University Boulevard no. 3158, Vancouver, BC V6T 1Z4, Canada
| | - Slavomír Adamčík
- Laboratory of Molecular Ecology and Mycology, Institute of Botany, Plant Science and Biodiversity Center, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava 84523, Slovakia
- Department of Botany, Faculty of Natural Sciences, Comenius University in Bratislava, Révová 39, Bratislava 81102, Slovakia
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16
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Weaver D, Novak-Frazer L, Palmer M, Richardson M, Bromley M, Bowyer P. Development of a novel mycobiome diagnostic for fungal infection. BMC Microbiol 2024; 24:63. [PMID: 38373963 PMCID: PMC10875777 DOI: 10.1186/s12866-024-03197-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/12/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Amplicon-based mycobiome analysis has the potential to identify all fungal species within a sample and hence could provide a valuable diagnostic assay for use in clinical mycology settings. In the last decade, the mycobiome has been increasingly characterised by targeting the internal transcribed spacer (ITS) regions. Although ITS targets give broad coverage and high sensitivity, they fail to provide accurate quantitation as the copy number of ITS regions in fungal genomes is highly variable even within species. To address these issues, this study aimed to develop a novel NGS fungal diagnostic assay using an alternative amplicon target. METHODS Novel universal primers were designed to amplify a highly diverse single copy and uniformly sized DNA target (Tef1) to enable mycobiome analysis on the Illumina iSeq100 which is a low cost, small footprint and simple to use next-generation sequencing platform. To enable automated analysis and rapid results, a streamlined bioinformatics workflow and sequence database were also developed. Sequencing of mock fungal communities was performed to compare the Tef1 assay and established ITS1-based method. The assay was further evaluated using clinical respiratory samples and the feasibility of using internal spike-in quantitative controls was assessed. RESULTS The Tef1 assay successfully identified and quantified Aspergillus, Penicillium, Candida, Cryptococcus, Rhizopus, Fusarium and Lomentospora species from mock communities. The Tef1 assay was also capable of differentiating closely related species such as A. fumigatus and A. fischeri. In addition, it outperformed ITS1 at identifying A. fumigatus and other filamentous pathogens in mixed fungal communities (in the presence or absence of background human DNA). The assay could detect as few as 2 haploid genome equivalents of A. fumigatus from clinical respiratory samples. Lastly, spike-in controls were demonstrated to enable semi-quantitation of A. fumigatus load in clinical respiratory samples using sequencing data. CONCLUSIONS This study has developed and tested a novel metabarcoding target and found the assay outperforms ITS1 at identifying clinically relevant filamentous fungi. The assay is a promising diagnostic candidate that could provide affordable NGS analysis to clinical mycology laboratories.
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Affiliation(s)
- Danielle Weaver
- Core Technology Facility, University of Manchester, Manchester, M13 9WU, UK
| | - Lilyann Novak-Frazer
- Core Technology Facility, University of Manchester, Manchester, M13 9WU, UK
- Manchester University NHS Foundation Trust, Manchester, UK
| | - Maisie Palmer
- Manchester University NHS Foundation Trust, Manchester, UK
| | - Malcolm Richardson
- Core Technology Facility, University of Manchester, Manchester, M13 9WU, UK
- Manchester University NHS Foundation Trust, Manchester, UK
| | - Mike Bromley
- Core Technology Facility, University of Manchester, Manchester, M13 9WU, UK.
| | - Paul Bowyer
- Core Technology Facility, University of Manchester, Manchester, M13 9WU, UK.
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17
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Lau MF, Phan CW, Sabaratnam V, Kuppusamy UR. Bibliometric, taxonomic, and medicinal perspectives of Ganoderma neo-japonicum Imazeki: A mini review. Mycology 2024; 15:360-373. [PMID: 39247898 PMCID: PMC11376291 DOI: 10.1080/21501203.2024.2302028] [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: 08/10/2023] [Accepted: 01/01/2024] [Indexed: 09/10/2024] Open
Abstract
Ganoderma, a traditional medicine in Asian countries, has been used to prevent and treat various ailments for centuries. Ganoderma neo-japonicum (synonym Ganoderma bambusicola), also known as purple Lingzhi, is a species that is currently underutilised when compared to Ganoderma lucidum (Lingzhi). However, in recent decades, this mushroom has garnered significant attention due to its ethnomedicinal uses, especially in Southeast Asia regions like Malaysia. The taxonomy and nomenclature of this mushroom have been extensively studied. Numerous publications have reported that G. neo-japonicum displays a variety of medicinal properties, including antioxidation, anticancer, anti-hyperglycaemic, genoprotective, hepatoprotective, neuritogenic, and antidiabetic effects, both in vitro and in vivo. With the surge of research findings on this mushroom, this review aims to provide a systematic bibliometric analysis of G. neo-japonicum, published between 1991 to 2021. Additionally, the taxonomic description of this mushroom is discussed in detail. Our review reveals that G. neo-japonicum contains polysaccharides (α/β-D-glucans), triterpenoids, and sterols/ergosterol. However, the existing literature suggests that these active compounds have not yet been explored to their full potential as drug candidates. Moreover, most of the studies are preclinical and have several drawbacks. In conclusion, G. neo-japonicum possesses valuable pharmacological activities that merit further exploration.
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Affiliation(s)
- Meng Fei Lau
- Department of Biomedical Sciences, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
- Mushroom Research Centre, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Chia Wei Phan
- Mushroom Research Centre, Universiti Malaya, Kuala Lumpur, Malaysia
- Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Vikineswary Sabaratnam
- Mushroom Research Centre, Universiti Malaya, Kuala Lumpur, Malaysia
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Umah Rani Kuppusamy
- Department of Biomedical Sciences, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
- Mushroom Research Centre, Universiti Malaya, Kuala Lumpur, Malaysia
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18
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Pérez-Anzúrez G, Mendoza-de Gives P, Olmedo-Juárez A, López-Arellano ME, Bautista-García GA, Ocampo-Gutiérrez AY, von Son-de Fernex E, Alonso-Díaz MÁ, Delgado-Núñez EJ, Paz-Silva A. First Record of Flavocillium subprimulinum (Cordycipitaceae, Hypocreales) in Mexico: Morphological and Molecular Characterisation, Nematocidal Activity of Its Liquid Culture Filtrates against Haemonchus contortus and Protease Activity. J Fungi (Basel) 2024; 10:56. [PMID: 38248965 PMCID: PMC10817658 DOI: 10.3390/jof10010056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/05/2024] [Accepted: 01/07/2024] [Indexed: 01/23/2024] Open
Abstract
This is the first record of the fungus Flavocillium subprimulinum in Mexico. The isolate was taxonomically characterised and cultured in potato dextrose broth (PDB), Czapek-Dox broth (CzDoxB), and sweet potato dextrose broth (SPDB) to obtain its filtrates (FLCF). The nematocidal activity (NA) of three FLCF concentrations was assessed against Haemonchus contortus L3. Protease activity (PA) was assessed with SDS-PAGE, followed by a zymogram. The NA of the FLCF reached 94.43% in PDB and 95.82% in CzDoxB, respectively, at 100 mg/mL. Lower mortality (64%) was found in SPDB at 100 mg/mL. SDS-PAGE showed bands (in PBS) of ~25, ~40, and ~55 kDa. The zymogram showed protein bands (PBs) with PA in the media, including PBs of ~14, ~40, and ~55 kDa. This study establishes the basis for exploring the potential use of this fungus against H. contortus, which is considered the most pathogenic parasite affecting lambs.
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Affiliation(s)
- Gustavo Pérez-Anzúrez
- Laboratory of Helminthology, National Centre for Disciplinary Research in Animal Health and Innocuity (CENID-SAI), National Institute for Research in Forestry, Agriculture and Livestock-Ministry of Agriculture and Rural Development, (INIFAP-SADER), Jiutepec 62550, Mexico; (G.P.-A.); (A.O.-J.); (G.A.B.-G.)
- Production Sciences and Animal Health, Faculty of Veterinary Medicine and Zootechnics, National Autonomous University of Mexico, Coyoacán, Ciudad de México 04510, Mexico
| | - Pedro Mendoza-de Gives
- Laboratory of Helminthology, National Centre for Disciplinary Research in Animal Health and Innocuity (CENID-SAI), National Institute for Research in Forestry, Agriculture and Livestock-Ministry of Agriculture and Rural Development, (INIFAP-SADER), Jiutepec 62550, Mexico; (G.P.-A.); (A.O.-J.); (G.A.B.-G.)
| | - Agustín Olmedo-Juárez
- Laboratory of Helminthology, National Centre for Disciplinary Research in Animal Health and Innocuity (CENID-SAI), National Institute for Research in Forestry, Agriculture and Livestock-Ministry of Agriculture and Rural Development, (INIFAP-SADER), Jiutepec 62550, Mexico; (G.P.-A.); (A.O.-J.); (G.A.B.-G.)
| | - María Eugenia López-Arellano
- Laboratory of Helminthology, National Centre for Disciplinary Research in Animal Health and Innocuity (CENID-SAI), National Institute for Research in Forestry, Agriculture and Livestock-Ministry of Agriculture and Rural Development, (INIFAP-SADER), Jiutepec 62550, Mexico; (G.P.-A.); (A.O.-J.); (G.A.B.-G.)
| | - Génesis Andrea Bautista-García
- Laboratory of Helminthology, National Centre for Disciplinary Research in Animal Health and Innocuity (CENID-SAI), National Institute for Research in Forestry, Agriculture and Livestock-Ministry of Agriculture and Rural Development, (INIFAP-SADER), Jiutepec 62550, Mexico; (G.P.-A.); (A.O.-J.); (G.A.B.-G.)
| | - Ana Yuridia Ocampo-Gutiérrez
- Laboratory of Helminthology, National Centre for Disciplinary Research in Animal Health and Innocuity (CENID-SAI), National Institute for Research in Forestry, Agriculture and Livestock-Ministry of Agriculture and Rural Development, (INIFAP-SADER), Jiutepec 62550, Mexico; (G.P.-A.); (A.O.-J.); (G.A.B.-G.)
| | - Elke von Son-de Fernex
- Tropical Livestock Center, Faculty of Veterinary Medicine and Zootechnics, National Autonomous University of Mexico, Martínez de la Torre 93600, Mexico; (E.v.S.-d.F.); (M.Á.A.-D.)
| | - Miguel Ángel Alonso-Díaz
- Tropical Livestock Center, Faculty of Veterinary Medicine and Zootechnics, National Autonomous University of Mexico, Martínez de la Torre 93600, Mexico; (E.v.S.-d.F.); (M.Á.A.-D.)
| | - Edgar Jesús Delgado-Núñez
- Faculty of Agricultural, Livestock and Environmental Sciences, Autonomous University of the State of Guerrero, Iguala de la Independencia 40040, Mexico
| | - Adolfo Paz-Silva
- Department of Animal Pathology, Faculty of Veterinary, University of Santiago de Compostela, 27142 Lugo, Spain;
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19
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Alleyne A, Mason S, Vallès Y. Characterization of the Cassava Mycobiome in Symptomatic Leaf Tissues Displaying Cassava Superelongation Disease. J Fungi (Basel) 2023; 9:1130. [PMID: 38132731 PMCID: PMC10743849 DOI: 10.3390/jof9121130] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
Superelongation disease (SED) is a fungal disease that affects cassava in the Caribbean. The symptoms include the appearance of dry necrotic spots and lesions on the leaves, which may severely affect the plant yield. However, the primary causal pathogen is difficult to culture and isolate in the lab because of its slow growth and potential contamination from faster-growing organisms. In addition, the leaf symptoms can be confused with those caused by other pathogens that produce similar necrotic spots and scab-like lesions. There is also little or no information on the contribution of endophytes, if any, to disease symptoms in cassava, a plant where the disease is prevalent. Therefore, this study aimed to characterize the fungal communities in cassava associated with SED symptoms by analyzing gross fungal morphology and performing metagenomics profiling. First, several individual pathogenic fungi were isolated and cultured from diseased cassava leaf tissues from seven locations in Barbados (BB). Both culture isolation and molecular community analyses showed the presence of several other fungi in the disease microenvironment of symptomatic cassava leaves. These included Fusarium, Colletotrichum, and Alternaria species and the suspected species Elsinoë brasiliensis synonym Sphaceloma manihoticola. Additionally, a community analysis using ITS2 amplicon sequencing of 21 symptomatic leaf tissues from BB, St. Vincent and the Grenadines (SVG), Trinidad and Tobago (TT), and Jamaica (JA) revealed that the disease symptoms of superelongation may also result from the interactions of fungal communities in the mycobiome, including Elsinoë species and other fungi such as Colletotrichum, Cercospora, Alternaria, and Fusarium. Therefore, we suggest that examining the pathobiome concept in SED in the future is necessary.
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Affiliation(s)
- Angela Alleyne
- Faculty of Science and Technology, The University of the West Indies, Cave Hill Campus, Bridgetown BB11000, Barbados (Y.V.)
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20
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Torres-Garcia D, Gené J, García D, Cano-Lira JF. Insights into Some Onygenalean Fungi from Freshwater Sediments in Spain and Description of Novel Taxa. J Fungi (Basel) 2023; 9:1129. [PMID: 38132730 PMCID: PMC10744713 DOI: 10.3390/jof9121129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
During the course of a project investigating culturable Ascomycota diversity from freshwater sediments in Spain, we isolated 63 strains of cycloheximide-resistant fungi belonging to the order Onygenales. These well-known ascomycetes, able to infect both humans and animals, are commonly found in terrestrial habitats, colonizing keratin-rich soils or dung. Little is known about their diversity in aquatic environments. Combining morphological features and sequence analyses of the ITS and LSU regions of the nrDNA, we identified 14 species distributed in the genera Aphanoascus, Arachniotus, Arthroderma, Arthropsis, Emmonsiellopsis, Gymnoascoideus, Leucothecium, Malbranchea, and Myriodontium. Furthermore, three novel species for the genus Malbranchea are proposed as M. echinulata sp. nov., M. irregularis sp. nov., and M. sinuata sp. nov. The new genera Albidomyces and Neoarthropsis are introduced based on Arachniotus albicans and Arthropsis hispanica, respectively. Neoarthropsis sexualis sp. nov. is characterized and differentiated morphologically from its counterpart by the production of a sexual morph. The novel family Neoarthropsidaceae is proposed for the genera Albidomyes, Apinisia, Arachnotheca, Myriodontium, and Neoarthropsis, based on their phylogenetic relationships and phenotypic and ecological traits. Pseudoamaurascopsis gen. nov. is introduced to accommodate P. spiralis sp. nov., a fungus with unclear taxonomy related to Amaurascopsis and Polytolypa. We traced the ecology and global distribution of the novel fungi through ITS environmental sequences deposited in the GlobalFungi database. Studying the fungal diversity from freshwater sediments not only contributes to filling gaps in the relationships and taxonomy of the Ascomycota but also gives us insights into the fungal community that might represent a putative risk to the health of animals and humans inhabiting or transient in aquatic environments.
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Affiliation(s)
| | - Josepa Gené
- Unitat de Micologia i Microbiologia Ambiental, Facultat de Medicina i Ciències de la Salut and IU-RESCAT, Universitat Rovira i Virgili, 43201 Reus, Spain; (D.T.-G.); (D.G.); (J.F.C.-L.)
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21
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de Hoog S, Walsh TJ, Ahmed SA, Alastruey-Izquierdo A, Alexander BD, Arendrup MC, Babady E, Bai FY, Balada-Llasat JM, Borman A, Chowdhary A, Clark A, Colgrove RC, Cornely OA, Dingle TC, Dufresne PJ, Fuller J, Gangneux JP, Gibas C, Glasgow H, Gräser Y, Guillot J, Groll AH, Haase G, Hanson K, Harrington A, Hawksworth DL, Hayden RT, Hoenigl M, Hubka V, Johnson K, Kus JV, Li R, Meis JF, Lackner M, Lanternier F, Leal Jr. SM, Lee F, Lockhart SR, Luethy P, Martin I, Kwon-Chung KJ, Meyer W, Nguyen MH, Ostrosky-Zeichner L, Palavecino E, Pancholi P, Pappas PG, Procop GW, Redhead SA, Rhoads DD, Riedel S, Stevens B, Sullivan KO, Vergidis P, Roilides E, Seyedmousavi A, Tao L, Vicente VA, Vitale RG, Wang QM, Wengenack NL, Westblade L, Wiederhold N, White L, Wojewoda CM, Zhang SX. A conceptual framework for nomenclatural stability and validity of medically important fungi: a proposed global consensus guideline for fungal name changes supported by ABP, ASM, CLSI, ECMM, ESCMID-EFISG, EUCAST-AFST, FDLC, IDSA, ISHAM, MMSA, and MSGERC. J Clin Microbiol 2023; 61:e0087323. [PMID: 37882528 PMCID: PMC10662369 DOI: 10.1128/jcm.00873-23] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023] Open
Abstract
The rapid pace of name changes of medically important fungi is creating challenges for clinical laboratories and clinicians involved in patient care. We describe two sources of name change which have different drivers, at the species versus the genus level. Some suggestions are made here to reduce the number of name changes. We urge taxonomists to provide diagnostic markers of taxonomic novelties. Given the instability of phylogenetic trees due to variable taxon sampling, we advocate to maintain genera at the largest possible size. Reporting of identified species in complexes or series should where possible comprise both the name of the overarching species and that of the molecular sibling, often cryptic species. Because the use of different names for the same species will be unavoidable for many years to come, an open access online database of the names of all medically important fungi, with proper nomenclatural designation and synonymy, is essential. We further recommend that while taxonomic discovery continues, the adaptation of new name changes by clinical laboratories and clinicians be reviewed routinely by a standing committee for validation and stability over time, with reference to an open access database, wherein reasons for changes are listed in a transparent way.
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Affiliation(s)
- Sybren de Hoog
- Radboudumc-CWZ Centre of Expertise for Mycology, Nijmegen, the Netherlands
- Foundation Atlas of Clinical Fungi, Hilversum, the Netherlands
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China
- Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil
- Research Center for Medical Mycology, Peking University, Beijing, China
- International Society for Human and Animal Mycology (ISHAM), Working Group Nomenclature
| | - Thomas J. Walsh
- International Society for Human and Animal Mycology (ISHAM), Working Group Nomenclature
- Center for Innovative Therapeutics and Diagnostics, Richmond, Virginia, USA
- University of Maryland School of Medicine, Baltimore, Maryland, USA
- Nomenclature Committee for Fungi, International Mycological Association (IMA)
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Mycoses Study Group, Education and Research Consortium (MSG-ERC)
- European Confederation of Medical Mycology (ECMM)
- Clinical and Laboratory Standards Institute (CLSI)
- Medical Mycological Society of the Americas (MMSA)
- ISHAM Working Group on Diagnostics
| | - Sarah A. Ahmed
- Radboudumc-CWZ Centre of Expertise for Mycology, Nijmegen, the Netherlands
- Foundation Atlas of Clinical Fungi, Hilversum, the Netherlands
- International Society for Human and Animal Mycology (ISHAM), Working Group Nomenclature
| | - Ana Alastruey-Izquierdo
- International Society for Human and Animal Mycology (ISHAM), Working Group Nomenclature
- Mycology Reference Laboratory, Spanish National Centre for Microbiology, Madrid, Spain
- Fungal Infection Study Group, European Society of Clinical Microbiology and Infectious Diseases (EFISG/ESCMID), Basel, Switzerland
| | - Barbara D. Alexander
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Departments of Medicine and Pathology, Duke University, Durham, North Carolina, USA
| | - Maiken Cavling Arendrup
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark; Department of Clinical Microbiology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Antifungal Susceptibility Testing Subcommittee of European Committee of Antimicrobial Susceptibility Testing (EUCAST-AFST)
| | - Esther Babady
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Feng-Yan Bai
- Mycology Committee of Chinese Society for Microbiology
- Institute of Microbiology, State Key Laboratory of Mycology, Chinese Academy of Sciences, Beijing, China
- Medical Mycology Society of Chinese Medicine and Education Association
- Asia Pacific Society for Medical Mycology
- ISHAM Working Group Veterinary Mycology and One Health
- Mycological Society of China (MSC)
| | - Joan-Miquel Balada-Llasat
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Clinical Microbiology at The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Andrew Borman
- National Mycology Reference Laboratory, Public Health England, Bristol, United Kingdom
| | - Anuradha Chowdhary
- Fungal Infection Study Group, European Society of Clinical Microbiology and Infectious Diseases (EFISG/ESCMID), Basel, Switzerland
- Department of Microbiology, National Reference Laboratory for Antimicrobial Resistance in Fungal Pathogens, Medical Mycology Unit, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Andrew Clark
- Fungal Diagnostics Laboratory Consortium (FDLC)
- University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Robert C. Colgrove
- Division of Infectious Diseases, Mount Auburn Hospital, Cambridge, Massachusetts, USA
- Infectious Diseases Society of America (ISDA)
| | - Oliver A. Cornely
- European Confederation of Medical Mycology (ECMM)
- Fungal Infection Study Group, European Society of Clinical Microbiology and Infectious Diseases (EFISG/ESCMID), Basel, Switzerland
- University of Cologne, Faculty of Medicine, Institute of Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Cologne, Germany
- Department I of Internal Medicine, University of Cologne, Excellence Center for Medical Mycology, Cologne, Germany
| | - Tanis C. Dingle
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Clinical and Laboratory Standards Institute (CLSI)
- Alberta Precision Laboratories, Public Health Laboratory, Calgary, Alberta, Canada
| | - Philippe J. Dufresne
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Clinical and Laboratory Standards Institute (CLSI)
- Mycology Department, Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec (INSPQ), Sainte-Anne-de-Bellevue, Québec, Canada
| | - Jeff Fuller
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Department of Pathology and Laboratory Medicine, London Health Sciences Center, London, Ontario, Canada
| | - Jean-Pierre Gangneux
- European Confederation of Medical Mycology (ECMM)
- Department of Mycology, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Connie Gibas
- University of Texas Health Science Center, San Antonio, Texas, USA
| | - Heather Glasgow
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Clinical and Molecular Microbiology, Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Yvonne Gräser
- Department of Parasitology (Charité), Institute of Microbiology and Hygiene, Humboldt University, Berlin, Germany
| | - Jacques Guillot
- ISHAM Working Group Veterinary Mycology and One Health
- Onoris, École Nationale Vétérinaire, Agroalimentaire et de l'Alimentation Nantes-Atlantique, Nantes, France
| | - Andreas H. Groll
- Fungal Infection Study Group, European Society of Clinical Microbiology and Infectious Diseases (EFISG/ESCMID), Basel, Switzerland
- Infectious Disease Research Program, Department of Pediatric Hematology and Oncology and Center for Bone Marrow Transplantation, University Children’s Hospital, Münster, Germany
| | - Gerhard Haase
- Laboratory Diagnostic Center, RWTH Aachen University Hospital, Aachen, Germany
| | - Kimberly Hanson
- Fungal Diagnostics Laboratory Consortium (FDLC)
- University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Amanda Harrington
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Loyola University Health System, Loyola University Chicago, Maywood, Illinois, USA
| | - David L. Hawksworth
- Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
- Natural History Museum, London, United Kingdom
- University of Southampton, Southampton, United Kingdom
- Jilin Agricultural University, Chanchung, China
- General Committee for Nomenclature, International Botanical Congress (IBC)
- Advisory Board of International Commission on the Taxonomy of Fungi (ICTF)
| | - Randall T. Hayden
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Clinical and Laboratory Standards Institute (CLSI)
- Clinical and Molecular Microbiology, Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Martin Hoenigl
- Mycoses Study Group, Education and Research Consortium (MSG-ERC)
- European Confederation of Medical Mycology (ECMM)
- Division of Infectious Diseases, Medical University of Graz, Graz, Austria
- Translational Medical Mycology Research Unit, ECMM Excellence Center for Medical Mycology, Medical University of Graz, Graz, Austria
- European Hematology Association, Specialized Working Group for Infections in Hematology, The Hague, the Netherlands
| | - Vit Hubka
- Department of Botany, Charles University, Prague, Czechia
| | - Kristie Johnson
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Clinical Microbiology Laboratory, UMMC Laboratories of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Julianne V. Kus
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Public Health Ontario, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Canada and University of Toronto, Toronto, Ontario, Canada
| | - Ruoyu Li
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China
- Research Center for Medical Mycology, Peking University, Beijing, China
- ISHAM Working Group on Diagnostics
- Fungal Infection Study Group, European Society of Clinical Microbiology and Infectious Diseases (EFISG/ESCMID), Basel, Switzerland
- Antifungal Susceptibility Testing Subcommittee of European Committee of Antimicrobial Susceptibility Testing (EUCAST-AFST)
- Medical Mycology Society of Chinese Medicine and Education Association
| | - Jacques F. Meis
- Radboudumc-CWZ Centre of Expertise for Mycology, Nijmegen, the Netherlands
- ISHAM Working Group on Diagnostics
- University of Cologne, Faculty of Medicine, Institute of Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Cologne, Germany
- Department I of Internal Medicine, University of Cologne, Excellence Center for Medical Mycology, Cologne, Germany
| | - Michaela Lackner
- International Society for Human and Animal Mycology (ISHAM), Working Group Nomenclature
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Sixto M. Leal Jr.
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Mycoses Study Group, Education and Research Consortium (MSG-ERC)
- Clinical and Laboratory Standards Institute (CLSI)
- University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Francesca Lee
- Fungal Diagnostics Laboratory Consortium (FDLC)
- University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Shawn R. Lockhart
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Paul Luethy
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Clinical Microbiology Laboratory, UMMC Laboratories of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Isabella Martin
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Dartmouth Health, Lebanon, New Hampshire, USA
| | - Kyung J. Kwon-Chung
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Wieland Meyer
- Nomenclature Committee for Fungi, International Mycological Association (IMA)
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - M. Hong Nguyen
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Mycoses Study Group, Education and Research Consortium (MSG-ERC)
- Medical Mycological Society of the Americas (MMSA)
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Luis Ostrosky-Zeichner
- Mycoses Study Group, Education and Research Consortium (MSG-ERC)
- University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Elizabeth Palavecino
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Clinical Microbiology Laboratory, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina, USA
| | - Preeti Pancholi
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Clinical Microbiology at The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Peter G. Pappas
- Mycoses Study Group, Education and Research Consortium (MSG-ERC)
- University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Gary W. Procop
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Clinical and Laboratory Standards Institute (CLSI)
- The American Board of Pathology, Tampa, Florida, USA
- American Board of Pathology (ABP)
| | - Scott A. Redhead
- Nomenclature Committee for Fungi, International Mycological Association (IMA)
- National Mycological Herbarium, Ottawa Research and Development Centre, Science and Technology Branch, Agriculture & Agri-Food Canada, Ottawa, Ontario, Canada
| | - Daniel D. Rhoads
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
- Infection Biology Program, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Stefan Riedel
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Bryan Stevens
- Fungal Diagnostics Laboratory Consortium (FDLC)
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Kaede Ota Sullivan
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, USA
| | - Paschalis Vergidis
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Mayo Clinic, Rochester, Minnesota, USA
| | - Emmanuel Roilides
- International Society for Human and Animal Mycology (ISHAM), Working Group Nomenclature
- European Confederation of Medical Mycology (ECMM)
- Fungal Infection Study Group, European Society of Clinical Microbiology and Infectious Diseases (EFISG/ESCMID), Basel, Switzerland
- Hippokration Hospital, Thessaloniki, Greece
| | - Amir Seyedmousavi
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Fungal Infection Study Group, European Society of Clinical Microbiology and Infectious Diseases (EFISG/ESCMID), Basel, Switzerland
- ISHAM Working Group Veterinary Mycology and One Health
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Lili Tao
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Vania A. Vicente
- Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Roxana G. Vitale
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
- Unidad de Parasitología, Sector Micología, Hospital J.M. Ramos Mejía, Buenos Aires, Argentina
| | - Qi-Ming Wang
- Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Nancy L. Wengenack
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Mayo Clinic, Rochester, Minnesota, USA
| | - Lars Westblade
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, USA
| | - Nathan Wiederhold
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Mycoses Study Group, Education and Research Consortium (MSG-ERC)
- Clinical and Laboratory Standards Institute (CLSI)
- Medical Mycological Society of the Americas (MMSA)
- University of Texas Health Science Center, San Antonio, Texas, USA
| | - Lewis White
- Public Health Wales Microbiology, Cardiff, United Kingdom
| | - Christina M. Wojewoda
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, Vermont, USA
| | - Sean X. Zhang
- International Society for Human and Animal Mycology (ISHAM), Working Group Nomenclature
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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22
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Réblová M, Nekvindová J. New genera and species with chloridium-like morphotype in the Chaetosphaeriales and Vermiculariopsiellales. Stud Mycol 2023; 106:199-258. [PMID: 38298574 PMCID: PMC10825751 DOI: 10.3114/sim.2023.106.04] [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: 07/16/2023] [Accepted: 08/04/2023] [Indexed: 02/02/2024] Open
Abstract
In this study, we investigated the morphological and genetic variability of selected species belonging to the genus Chloridium sensu lato, some also referred to as chloridium-like asexual morphs and other undescribed morphologically similar fungi. These species do not conform to the revised generic concept and thus necessitate a re-evaluation in terms of taxonomy and phylogeny. The family Chaetosphaeriaceae (Chaetosphaeriales) encompasses a wide range of asexual morphotypes, and among them, the simplest form is represented by Chloridium sect. Chloridium. The morphological simplicity of the Chloridium morphotype has historically led to the amalgamation of numerous unrelated species, thereby creating a heterogeneous genus. By conducting phylogenetic reconstruction of four DNA loci and examining a set of 71 strains, including all available ex-type and other non-type strains as well as holotypes and other herbarium material, we were able to gain new insights into the relationships between these taxa. Phylogenetic analyses revealed that the studied species are distantly related to Chloridium sensu stricto and can be grouped into two orders in the Sordariomycetes. Within the Chaetosphaeriales, they formed nine well-separated genera in four clades, such as Cacumisporium, Caliciastrum gen. nov., Caligospora gen. nov., Capillisphaeria gen. nov., Curvichaeta, Fusichloridium, Geniculoseta gen. nov., Papillospora gen. nov., and Spicatispora gen. nov. We also established Chloridiopsiella gen. nov. and Chloridiopsis gen. nov. in Vermiculariopsiellales. Four new species and eight new combinations are proposed in these genera. Our study provides a clearer understanding of the genus Chloridium, its relationship to other morphologically similar fungi, and a new taxonomic treatment and molecular phylogeny to facilitate their accurate identification and classification in future research. Taxonomic novelties: New genera: Caliciastrum Réblová, Caligospora Réblová, Capillisphaeria Réblová, Chloridiopsiella Réblová, Chloridiopsis Réblová, Geniculoseta Réblová, Papillospora Réblová, Spicatispora Réblová; New species: Caliciastrum bicolor Réblová, Caligospora pannosa Réblová, Chloridiopsis syzygii Réblová, Gongromerizella silvana Réblová; New combinations: Caligospora dilabens (Réblová & W. Gams) Réblová, Capillisphaeria crustacea (Sacc.) Réblová, Chloridiopsiella preussii (W. Gams & Hol.-Jech.) Réblová, Chloridiopsis constrictospora (Crous et al.) Réblová, Geniculoseta preussii (W. Gams & Hol.-Jech.) Réblová, Papillospora hebetiseta (Réblová & W. Gams) Réblová, Spicatispora carpatica (Hol.-Jech. & Révay) Réblová, Spicatispora fennica (P. Karst.) Réblová; Epitypifications (basionyms): Chaetosphaeria dilabens Réblová & W. Gams, Chloridium cylindrosporum W. Gams & Hol.-Jech. Citation: Réblová M, Nekvindová J (2023). New genera and species with chloridium-like morphotype in the Chaetosphaeriales and Vermiculariopsiellales. Studies in Mycology 106: 199-258. doi: 10.3114/sim.2023.106.04.
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Affiliation(s)
- M. Réblová
- The Czech Academy of Sciences, Institute of Botany, Department of Taxonomy, 252 43 Průhonice, Czech Republic
| | - J. Nekvindová
- The Czech Academy of Sciences, Institute of Botany, Department of Taxonomy, 252 43 Průhonice, Czech Republic
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23
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Renzi S, Nenciarini S, Bacci G, Cavalieri D. Yeast metagenomics: analytical challenges in the analysis of the eukaryotic microbiome. MICROBIOME RESEARCH REPORTS 2023; 3:2. [PMID: 38455081 PMCID: PMC10917621 DOI: 10.20517/mrr.2023.27] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 10/09/2023] [Accepted: 10/17/2023] [Indexed: 03/09/2024]
Abstract
Even if their impact is often underestimated, yeasts and yeast-like fungi represent the most prevalent eukaryotic members of microbial communities on Earth. They play numerous roles in natural ecosystems and in association with their hosts. They are involved in the food industry and pharmaceutical production, but they can also cause diseases in other organisms, making the understanding of their biology mandatory. The ongoing loss of biodiversity due to overexploitation of environmental resources is a growing concern in many countries. Therefore, it becomes crucial to understand the ecology and evolutionary history of these organisms to systematically classify them. To achieve this, it is essential that our knowledge of the mycobiota reaches a level similar to that of the bacterial communities. To overcome the existing challenges in the study of fungal communities, the first step should be the establishment of standardized techniques for the correct identification of species, even from complex matrices, both in wet lab practices and in bioinformatic tools.
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Affiliation(s)
| | | | | | - Duccio Cavalieri
- Correspondence to: Prof. Duccio Cavalieri, Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino 50019, Italy. E-mail:
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24
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Suraby EJ, Agisha VN, Dhandapani S, Sng YH, Lim SH, Naqvi NI, Sarojam R, Yin Z, Park BS. Plant growth promotion under phosphate deficiency and improved phosphate acquisition by new fungal strain, Penicillium olsonii TLL1. Front Microbiol 2023; 14:1285574. [PMID: 37965551 PMCID: PMC10642178 DOI: 10.3389/fmicb.2023.1285574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 09/28/2023] [Indexed: 11/16/2023] Open
Abstract
Microbiomes in soil ecosystems play a significant role in solubilizing insoluble inorganic and organic phosphate sources with low availability and mobility in the soil. They transfer the phosphate ion to plants, thereby promoting plant growth. In this study, we isolated an unidentified fungal strain, POT1 (Penicillium olsonii TLL1) from indoor dust samples, and confirmed its ability to promote root growth, especially under phosphate deficiency, as well as solubilizing activity for insoluble phosphates such as AlPO4, FePO4·4H2O, Ca3(PO4)2, and hydroxyapatite. Indeed, in vermiculite containing low and insoluble phosphate, the shoot fresh weight of Arabidopsis and leafy vegetables increased by 2-fold and 3-fold, respectively, with POT1 inoculation. We also conducted tests on crops in Singapore's local soil, which contains highly insoluble phosphate. We confirmed that with POT1, Bok Choy showed a 2-fold increase in shoot fresh weight, and Rice displayed a 2-fold increase in grain yield. Furthermore, we demonstrated that plant growth promotion and phosphate solubilizing activity of POT1 were more effective than those of four different Penicillium strains such as Penicillium bilaiae, Penicillium chrysogenum, Penicillium janthinellum, and Penicillium simplicissimum under phosphate-limiting conditions. Our findings uncover a new fungal strain, provide a better understanding of symbiotic plant-fungal interactions, and suggest the potential use of POT1 as a biofertilizer to improve phosphate uptake and use efficiency in phosphate-limiting conditions.
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Affiliation(s)
- Erinjery Jose Suraby
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | | | - Savitha Dhandapani
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Yee Hwui Sng
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Shi Hui Lim
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Naweed I. Naqvi
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Rajani Sarojam
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Zhongchao Yin
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Bong Soo Park
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
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25
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Yu PL, Fulton JC, Hudson OH, Huguet-Tapia JC, Brawner JT. Next-generation fungal identification using target enrichment and Nanopore sequencing. BMC Genomics 2023; 24:581. [PMID: 37784013 PMCID: PMC10544392 DOI: 10.1186/s12864-023-09691-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/21/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Rapid and accurate pathogen identification is required for disease management. Compared to sequencing entire genomes, targeted sequencing may be used to direct sequencing resources to genes of interest for microbe identification and mitigate the low resolution that single-locus molecular identification provides. This work describes a broad-spectrum fungal identification tool developed to focus high-throughput Nanopore sequencing on genes commonly employed for disease diagnostics and phylogenetic inference. RESULTS Orthologs of targeted genes were extracted from 386 reference genomes of fungal species spanning six phyla to identify homologous regions that were used to design the baits used for enrichment. To reduce the cost of producing probes without diminishing the phylogenetic power, DNA sequences were first clustered, and then consensus sequences within each cluster were identified to produce 26,000 probes that targeted 114 genes. To test the efficacy of our probes, we applied the technique to three species representing Ascomycota and Basidiomycota fungi. The efficiency of enrichment, quantified as mean target coverage over the mean genome-wide coverage, ranged from 200 to 300. Furthermore, enrichment of long reads increased the depth of coverage across the targeted genes and into non-coding flanking sequence. The assemblies generated from enriched samples provided well-resolved phylogenetic trees for taxonomic assignment and molecular identification. CONCLUSIONS Our work provides data to support the utility of targeted Nanopore sequencing for fungal identification and provides a platform that may be extended for use with other phytopathogens.
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Affiliation(s)
- Pei-Ling Yu
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - James C Fulton
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
- Florida Department of Agriculture and Consumer Services, Division of Plant Industry, Gainesville, FL, 32608, USA
| | - Owen H Hudson
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - Jose C Huguet-Tapia
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - Jeremy T Brawner
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA.
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Langsiri N, Worasilchai N, Irinyi L, Jenjaroenpun P, Wongsurawat T, Luangsa-Ard JJ, Meyer W, Chindamporn A. Targeted sequencing analysis pipeline for species identification of human pathogenic fungi using long-read nanopore sequencing. IMA Fungus 2023; 14:18. [PMID: 37674240 PMCID: PMC10483712 DOI: 10.1186/s43008-023-00125-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 08/22/2023] [Indexed: 09/08/2023] Open
Abstract
Among molecular-based techniques for fungal identification, Sanger sequencing of the primary universal fungal DNA barcode, the internal transcribed spacer (ITS) region (ITS1, 5.8S, ITS2), is commonly used in clinical routine laboratories due to its simplicity, universality, efficacy, and affordability for fungal species identification. However, Sanger sequencing fails to identify mixed ITS sequences in the case of mixed infections. To overcome this limitation, different high-throughput sequencing technologies have been explored. The nanopore-based technology is now one of the most promising long-read sequencing technologies on the market as it has the potential to sequence the full-length ITS region in a single read. In this study, we established a workflow for species identification using the sequences of the entire ITS region generated by nanopore sequencing of both pure yeast isolates and mocked mixed species reads generated with different scenarios. The species used in this study included Candida albicans (n = 2), Candida tropicalis (n = 1), Nakaseomyces glabratus (formerly Candida glabrata) (n = 1), Trichosporon asahii (n = 2), Pichia kudriavzevii (formerly Candida krusei) (n = 1), and Cryptococcus neoformans (n = 1). Comparing various methods to generate the consensus sequence for fungal species identification, the results from this study indicate that read clustering using a modified version of the NanoCLUST pipeline is more sensitive than Canu or VSEARCH, as it classified species accurately with a lower abundance cluster of reads (3% abundance compared to 10% with VSEARCH). The modified NanoCLUST also reduced the number of classified clusters compared to VSEARCH, making the subsequent BLAST+ analysis faster. Subsampling of the datasets, which reduces the size of the datasets by approximately tenfold, did not significantly affect the identification results in terms of the identified species name, percent identity, query coverage, percentage of reads in the classified cluster, and the number of clusters. The ability of the method to distinguish mixed species within sub-populations of large datasets has the potential to aid computer analysis by reducing the required processing power. The herein presented new sequence analysis pipeline will facilitate better interpretation of fungal sequence data for species identification.
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Affiliation(s)
- Nattapong Langsiri
- Medical Microbiology, Interdisciplinary Program, Graduated School, Chulalongkorn University, Bangkok, Thailand
| | - Navaporn Worasilchai
- Department of Transfusion Medicine and Clinical Microbiology, Faculty of Allied Health Science, Chulalongkorn University, Bangkok, Thailand
- Immunomodulation of Natural Products Research Group, Chulalongkorn University, Bangkok, Thailand
| | - Laszlo Irinyi
- Westmead Clinical School, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia
- Curtin Medical School, Curtin University, Perth, Bentley, WA, Australia
| | - Piroon Jenjaroenpun
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Division of Medical Bioinformatics, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thidathip Wongsurawat
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Division of Medical Bioinformatics, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Janet Jennifer Luangsa-Ard
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Klong Nueng, Klong Luang, Pathum Thani, Thailand
| | - Wieland Meyer
- Westmead Clinical School, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia
- Curtin Medical School, Curtin University, Perth, Bentley, WA, Australia
- Westerdijk Fungal Biodiversity Institute, KNAW, Utrecht, The Netherlands
| | - Ariya Chindamporn
- Medical Microbiology, Interdisciplinary Program, Graduated School, Chulalongkorn University, Bangkok, Thailand.
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
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Van Caenegem W, Blondelle A, Dumolein I, Santamaria B, Dick CW, Hiller T, Liu J, Quandt CA, Villarreal Saucedo RV, Verbeken A, Haelewaters D. Five new species of Gloeandromyces (Fungi, Laboulbeniales) from tropical American bat flies (Diptera, Streblidae), revealed by morphology and phylogenetic reconstruction. Mycologia 2023; 115:714-737. [PMID: 37589548 DOI: 10.1080/00275514.2023.2230114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/23/2023] [Indexed: 08/18/2023]
Abstract
This paper describes and illustrates five new species of Gloeandromyces (Ascomycota, Laboulbeniales) associated with tropical American bat flies (Diptera, Streblidae). These are Gloeandromyces cusucoensis sp. nov. from Trichobius uniformis in Costa Rica and Honduras, G. diversiformis sp. nov. from Strebla wiedemanni in Costa Rica, G. plesiosaurus sp. nov. from Trichobius yunkeri in Panama, G. pseudodickii sp. nov. from Trichobius longipes in Ecuador and Panama, and G. verbekeniae sp. nov. from Strebla galindoi in Ecuador and Panama. The description of these five species doubles the number of known species in the genus. Morphological characteristics, host association, and a three-locus (18S nuc rDNA, 28S nuc rDNA, TEF1) phylogenetic reconstruction support placement of these taxa in the genus Gloeandromyces. Three of the new species are polymorphic; they have multiple morphotypes that grow in specific positions on the host integument: G. diversiformis f. diversiformis, f. musiformis, and f. vanillicarpiformis; G. plesiosaurus f. asymmetricus and f. plesiosaurus; and G. verbekeniae f. verbekeniae and f. inflexus. Finally, a dichotomous key to all species and morphotypes is presented.
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Affiliation(s)
- Warre Van Caenegem
- Research Group Mycology, Department of Biology, Ghent University, Ghent 9000, Belgium
| | - Aimée Blondelle
- Research Group Mycology, Department of Biology, Ghent University, Ghent 9000, Belgium
| | - Iris Dumolein
- Research Group Mycology, Department of Biology, Ghent University, Ghent 9000, Belgium
| | - Brianna Santamaria
- Research Group Mycology, Department of Biology, Ghent University, Ghent 9000, Belgium
| | - Carl W Dick
- Department of Biology, Western Kentucky University, Bowling Green, Kentucky 42101
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois 60605
| | - Thomas Hiller
- Department of Ecology of Tropical Agricultural Systems, University of Hohenheim, Stuttgart 70599, Germany
| | - Jingyu Liu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - C Alisha Quandt
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado 80309
| | | | - Annemieke Verbeken
- Research Group Mycology, Department of Biology, Ghent University, Ghent 9000, Belgium
| | - Danny Haelewaters
- Research Group Mycology, Department of Biology, Ghent University, Ghent 9000, Belgium
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado 80309
- Herbario UCH, Universidad Autónoma de Chiriquí, Apartado Postal 0427, David, Panama
- Centro de Investigaciones Micológicas, Universidad Autónoma de Chiriquí, Apartado Postal 0427, David, Panama
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Rúa-Giraldo ÁL. Fungal taxonomy: A puzzle with many missing pieces. BIOMEDICA : REVISTA DEL INSTITUTO NACIONAL DE SALUD 2023; 43:288-311. [PMID: 37721899 PMCID: PMC10588969 DOI: 10.7705/biomedica.7052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/24/2023] [Indexed: 09/20/2023]
Abstract
Fungi are multifaceted organisms found in almost all ecosystems on Earth, where they establish various types of symbiosis with other living beings. Despite being recognized by humans since ancient times, and the high number of works delving into their biology and ecology, much is still unknown about these organisms. Some criteria classically used for their study are nowadays limited, generating confusion in categorizing them, and even more, when trying to understand their genealogical relationships. To identify species within Fungi, phenotypic characters to date are not sufficient, and to construct a broad phylogeny or a phylogeny of a particular group, there are still gaps affecting the generated trees, making them unstable and easily debated. For health professionals, fungal identification at lower levels such as genus and species, is enough to select the most appropriate therapy for their control, understand the epidemiology of clinical pictures associated, and recognize outbreaks and antimicrobial resistance. However, the taxonomic location within the kingdom, information with apparently little relevance, can allow phylogenetic relationships to be established between fungal taxa, facilitating the understanding of their biology, distribution in nature, and pathogenic potential evolution. Advances in molecular biology and computer science techniques from the last 30 years have led to crucial changes aiming to establish the criteria to define a fungal species, allowing us to reach a kind of stable phylogenetic construction. However, there is still a long way to go, and it requires the joint work of the scientific community at a global level and support for basic research.
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Shu M, Yang Y, Pan F, Bian T, Li Q, Liao F, He W, Li S, Xu J, Hu T, Qiao P, Zhong W. Effects of the multi-stress-resistant strain Zygosaccharomyces parabailii MC-5K3 bioaugmentation on microbial communities and metabolomics in tobacco waste extract. Arch Microbiol 2023; 205:299. [PMID: 37525014 DOI: 10.1007/s00203-023-03628-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/25/2023] [Accepted: 07/09/2023] [Indexed: 08/02/2023]
Abstract
Industrial tobacco waste was mainly treated via a reconstituted tobacco process using the paper-making method, which involves aqueous concentrated tobacco waste extract (cTWE) fermentation (aging). The fermentation was done to improve the quality of reconstituted tobacco. However, cTWE is a multi-stress environment that is characterized by low pH (about 4), as well as high sugar (above 150 g/L) and nicotine (above 15 g/L) content. In this study, a specific selection strategy was used to successfully isolate multi-stress-resistant bacterial or fungal strains, that exhibited positive effects on cTWE fermentation, thereby improving the quality of final products. A potential strain Zygosaccharomyces parabailii MC-5K3 was used for the bioaugmentation of cTWE fermentation and it significantly influenced the microbial diversity of the fermented cTWE. Zygosaccharomyces was observed to be the only dominant fungal genus instead of some pathogenic bacterial genera, with an abundance of over 95% after four days, and still more than 80% after a week. Meanwhile, metabolomics profiling showed significant concentration decrease with regard to some flavor-improving relative metabolites, such as 3-hydroxybenzoic acid (log2FC = - 5.25) and sorbitol (log2FC = - 5.54). This finding is extrapolated to be the key influence factor on the quality of the fermented cTWE. The correlation analysis also showed that the alterations in microbial diversity in the fermented cTWE led to some important differential metabolite changes, which finally improved various properties of tobacco products.
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Affiliation(s)
- Ming Shu
- China Tobacco Zhejiang Industrial Co., Ltd, Hangzhou, 310024, Zhejiang, People's Republic of China
| | - Yang Yang
- China Tobacco Zhejiang Industrial Co., Ltd, Hangzhou, 310024, Zhejiang, People's Republic of China
| | - Fanda Pan
- China Tobacco Zhejiang Industrial Co., Ltd, Hangzhou, 310024, Zhejiang, People's Republic of China
| | - Tengfei Bian
- China Tobacco Zhejiang Industrial Co., Ltd, Hangzhou, 310024, Zhejiang, People's Republic of China
| | - Qi Li
- China Tobacco Zhejiang Industrial Co., Ltd, Hangzhou, 310024, Zhejiang, People's Republic of China
| | - Fu Liao
- China Tobacco Zhejiang Industrial Co., Ltd, Hangzhou, 310024, Zhejiang, People's Republic of China
| | - Wenmiao He
- China Tobacco Zhejiang Industrial Co., Ltd, Hangzhou, 310024, Zhejiang, People's Republic of China
| | - Shitou Li
- China Tobacco Zhejiang Industrial Co., Ltd, Hangzhou, 310024, Zhejiang, People's Republic of China
| | - Jian Xu
- China Tobacco Zhejiang Industrial Co., Ltd, Hangzhou, 310024, Zhejiang, People's Republic of China.
| | - Tong Hu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, Zhejiang, People's Republic of China
| | - Pei Qiao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, Zhejiang, People's Republic of China
| | - Weihong Zhong
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, Zhejiang, People's Republic of China.
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30
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Zhou X, Ahmed SA, Tang C, Grisolia ME, Warth JFG, Webster K, Peano A, Uhrlass S, Cafarchia C, Hayette MP, Sacheli R, Matos T, Kang Y, de Hoog GS, Feng P. Human adaptation and diversification in the Microsporum canis complex. IMA Fungus 2023; 14:14. [PMID: 37488659 PMCID: PMC10367411 DOI: 10.1186/s43008-023-00120-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 06/26/2023] [Indexed: 07/26/2023] Open
Abstract
The Microsporum canis complex consists of one zoophilic species, M. canis, and two anthropophilic species, M. audouinii and M. ferrugineum. These species are the most widespread zoonotic pathogens causing dermatophytosis in cats and humans worldwide. To clarify the evolutionary relationship between the three species and explore the potential host shift process, this study used phylogenetic analysis, population structure analysis, multispecies coalescent analyses, determination of MAT idiomorph distribution, sexual crosses, and macromorphology and physicochemical features to address the above questions. The complex of Microsporum canis, M. audouinii and M. ferrugineum comprises 12 genotypes. MAT1-1 was present only in M. canis, while the anthropophilic entities contained MAT1-2. The pseudocleistothecia were yielded by the mating behaviour of M. canis and M. audouinii. Growth rates and lipase, keratinolysis and urea hydrolytic capacities of zoophilic M. canis isolates were all higher than those of anthropophilic strains; DNase activity of M. ferrugineum exceeded that of M. canis. The optimum growth temperature was 28 °C, but 22 °C favoured the development of macroconidia. Molecular data, physicochemical properties and phenotypes suggest the adaptation of zoophilic M. canis to anthropophilic M. ferrugineum, with M. audouinii in an intermediate position.
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Affiliation(s)
- Xin Zhou
- Center of Expertise in Mycology of Radboud University Medical Center, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
- Department of Dermatology, 3rd Affiliated Hospital, Sun Yat-senen University, Guangzhou, China
| | - Sarah A Ahmed
- Center of Expertise in Mycology of Radboud University Medical Center, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
- Foundation Atlas of Clinical Fungi, Hilversum, The Netherlands
| | - Chao Tang
- Center of Expertise in Mycology of Radboud University Medical Center, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Maria Eduarda Grisolia
- Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil
| | | | - Kristen Webster
- Department of Dermatology, Center for Medical Mycology, University Hospitals, Cleveland, USA
| | - Andrea Peano
- Department of Veterinary Sciences, University of Turin, Grugliasco, Italy
| | - Silke Uhrlass
- Labor für Medizinische Mikrobiologie Nenoff / Krüger, Mölbis, Germany
| | - Claudia Cafarchia
- Department of Veterinary Medicine, University of Bari Aldo Moro, Bari, Italy
| | - Marie Pierre Hayette
- Belgian National Reference Center, Clinical Microbiology, University Hospital of Liege, Liege, Belgium
| | - Rosalie Sacheli
- Belgian National Reference Center, Clinical Microbiology, University Hospital of Liege, Liege, Belgium
| | - Tadeja Matos
- Medical Faculty, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | - Yingqian Kang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education of Guizhou & Guizhou Talent Base for Microbiology and Human Health, School of Basic Medical Sciences, Key Laboratory of Microbiology and Parasitology of Education Department of Guizhou, Guizhou Medical University, Guiyang, China.
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China.
| | - G Sybren de Hoog
- Center of Expertise in Mycology of Radboud University Medical Center, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands.
- Foundation Atlas of Clinical Fungi, Hilversum, The Netherlands.
- Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil.
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education of Guizhou & Guizhou Talent Base for Microbiology and Human Health, School of Basic Medical Sciences, Key Laboratory of Microbiology and Parasitology of Education Department of Guizhou, Guizhou Medical University, Guiyang, China.
| | - Peiying Feng
- Department of Dermatology, 3rd Affiliated Hospital, Sun Yat-senen University, Guangzhou, China.
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Zhu Z, Dugan F, Murray TD. A Multilocus Phylogeny Places Hymenula cerealis (syn. Cephalosporium gramineum) in the Helotiales, Leotiomycetes. PHYTOPATHOLOGY 2023; 113:1254-1265. [PMID: 36611234 DOI: 10.1094/phyto-05-22-0151-r] [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: 06/17/2023]
Abstract
The soilborne fungus Hymenula cerealis causes Cephalosporium stripe, a vascular wilt disease of wheat and other grasses in the United States and other wheat-producing countries where winter wheat is subjected to snow cover and frozen soil. No sexual stage is known for H. cerealis, and consequently, its phylogenetic position relative to other fungi has been difficult to establish. The purpose of this study was to conduct a multilocus sequence analysis to determine the phylogenetic position of H. cerealis. Sequence data for five genes, the internal transcribed spacer (ITS), partial large subunit nrDNA (LSU), partial RNA polymerase II second largest subunit region (RPB2), β-tubulin gene, and translation elongation factor 1-α (TEF1-α), from a diverse set of C. gramineum isolates and other related fungi was obtained from GenBank or directly from isolates in the Murray lab and used to construct maximum-likelihood and Bayesian trees. Based on phylogenetic analysis of the single LSU and β-tubulin genes, Cephalosporium gramineum is closely related to the Drepanopezizaceae and Ploettnerulaceae of Helotiales. Based on analyses of the DNA sequence of the ITS, RPB2, and TEF1-α genes, as well as the combined five-gene data set, C. gramineum belongs to the family Drepanopezizaceae, which is a sister taxon to the Ploettnerulaceae, and formed a well-supported clade (MLBP/BIPP = 95%/100%). In conclusion, H. cerealis belongs to the Helotiales, Leotiomycetes.
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Affiliation(s)
- Zhaoxiang Zhu
- Engineering Research Center, Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
- Department of Plant Pathology, Washington State University, Pullman, WA, U.S.A
| | - Frank Dugan
- Department of Plant Pathology, Washington State University, Pullman, WA, U.S.A
| | - Timothy D Murray
- Department of Plant Pathology, Washington State University, Pullman, WA, U.S.A
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32
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Zhang ZY, Li X, Chen WH, Liang JD, Han YF. Culturable fungi from urban soils in China II, with the description of 18 novel species in Ascomycota (Dothideomycetes, Eurotiomycetes, Leotiomycetes and Sordariomycetes). MycoKeys 2023; 98:167-220. [PMID: 37425100 PMCID: PMC10326621 DOI: 10.3897/mycokeys.98.102816] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/14/2023] [Indexed: 07/11/2023] Open
Abstract
As China's urbanisation continues to advance, more people are choosing to live in cities. However, this trend has a significant impact on the natural ecosystem. For instance, the accumulation of keratin-rich substrates in urban habitats has led to an increase in keratinophilic microbes. Despite this, there is still a limited amount of research on the prevalence of keratinophilic fungi in urban areas. Fortunately, our group has conducted in-depth investigations into this topic since 2015. Through our research, we have discovered a significant amount of keratinophilic fungi in soil samples collected from various urban areas in China. In this study, we have identified and characterised 18 new species through the integration of morphological and phylogenetic analyses. These findings reveal the presence of numerous unexplored fungal taxa in urban habitats, emphasising the need for further taxonomic research in urban China.
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Affiliation(s)
- Zhi-Yuan Zhang
- Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang 550025, ChinaGuizhou UniversityGuiyangChina
- College of Eco-Environmental Engineering, Guizhou Minzu University, Guiyang 550025, ChinaGuizhou Minzu UniversityGuiyangChina
| | - Xin Li
- Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang 550025, ChinaGuizhou UniversityGuiyangChina
| | - Wan-Hao Chen
- Basic Medical School, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, ChinaGuizhou University of Traditional Chinese MedicineGuiyangChina
| | - Jian-Dong Liang
- Basic Medical School, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, ChinaGuizhou University of Traditional Chinese MedicineGuiyangChina
| | - Yan-Feng Han
- Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang 550025, ChinaGuizhou UniversityGuiyangChina
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33
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Fang W, Wu J, Cheng M, Zhu X, Du M, Chen C, Liao W, Zhi K, Pan W. Diagnosis of invasive fungal infections: challenges and recent developments. J Biomed Sci 2023; 30:42. [PMID: 37337179 DOI: 10.1186/s12929-023-00926-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/13/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND The global burden of invasive fungal infections (IFIs) has shown an upsurge in recent years due to the higher load of immunocompromised patients suffering from various diseases. The role of early and accurate diagnosis in the aggressive containment of the fungal infection at the initial stages becomes crucial thus, preventing the development of a life-threatening situation. With the changing demands of clinical mycology, the field of fungal diagnostics has evolved and come a long way from traditional methods of microscopy and culturing to more advanced non-culture-based tools. With the advent of more powerful approaches such as novel PCR assays, T2 Candida, microfluidic chip technology, next generation sequencing, new generation biosensors, nanotechnology-based tools, artificial intelligence-based models, the face of fungal diagnostics is constantly changing for the better. All these advances have been reviewed here giving the latest update to our readers in the most orderly flow. MAIN TEXT A detailed literature survey was conducted by the team followed by data collection, pertinent data extraction, in-depth analysis, and composing the various sub-sections and the final review. The review is unique in its kind as it discusses the advances in molecular methods; advances in serology-based methods; advances in biosensor technology; and advances in machine learning-based models, all under one roof. To the best of our knowledge, there has been no review covering all of these fields (especially biosensor technology and machine learning using artificial intelligence) with relevance to invasive fungal infections. CONCLUSION The review will undoubtedly assist in updating the scientific community's understanding of the most recent advancements that are on the horizon and that may be implemented as adjuncts to the traditional diagnostic algorithms.
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Affiliation(s)
- Wenjie Fang
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Junqi Wu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, 200433, China
| | - Mingrong Cheng
- Department of Anorectal Surgery, The Third Affiliated Hospital of Guizhou Medical University, Guizhou, 558000, China
| | - Xinlin Zhu
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Mingwei Du
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, 200433, China
| | - Wanqing Liao
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Kangkang Zhi
- Department of Vascular and Endovascular Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China.
| | - Weihua Pan
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China.
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34
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Wijayawardene NN, Boonyuen N, Ranaweera CB, de Zoysa HKS, Padmathilake RE, Nifla F, Dai DQ, Liu Y, Suwannarach N, Kumla J, Bamunuarachchige TC, Chen HH. OMICS and Other Advanced Technologies in Mycological Applications. J Fungi (Basel) 2023; 9:688. [PMID: 37367624 DOI: 10.3390/jof9060688] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/06/2023] [Accepted: 06/16/2023] [Indexed: 06/28/2023] Open
Abstract
Fungi play many roles in different ecosystems. The precise identification of fungi is important in different aspects. Historically, they were identified based on morphological characteristics, but technological advancements such as polymerase chain reaction (PCR) and DNA sequencing now enable more accurate identification and taxonomy, and higher-level classifications. However, some species, referred to as "dark taxa", lack distinct physical features that makes their identification challenging. High-throughput sequencing and metagenomics of environmental samples provide a solution to identifying new lineages of fungi. This paper discusses different approaches to taxonomy, including PCR amplification and sequencing of rDNA, multi-loci phylogenetic analyses, and the importance of various omics (large-scale molecular) techniques for understanding fungal applications. The use of proteomics, transcriptomics, metatranscriptomics, metabolomics, and interactomics provides a comprehensive understanding of fungi. These advanced technologies are critical for expanding the knowledge of the Kingdom of Fungi, including its impact on food safety and security, edible mushrooms foodomics, fungal secondary metabolites, mycotoxin-producing fungi, and biomedical and therapeutic applications, including antifungal drugs and drug resistance, and fungal omics data for novel drug development. The paper also highlights the importance of exploring fungi from extreme environments and understudied areas to identify novel lineages in the fungal dark taxa.
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Affiliation(s)
- Nalin N Wijayawardene
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
- Department of Bioprocess Technology, Faculty of Technology, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka
- Section of Genetics, Institute for Research and Development in Health and Social Care, No: 393/3, Lily Avenue, Off Robert Gunawardane Mawatha, Battaramulla 10120, Sri Lanka
| | - Nattawut Boonyuen
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Chathuranga B Ranaweera
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, General Sir John Kotelawala Defence University Sri Lanka, Kandawala Road, Rathmalana 10390, Sri Lanka
| | - Heethaka K S de Zoysa
- Department of Bioprocess Technology, Faculty of Technology, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka
| | - Rasanie E Padmathilake
- Department of Plant Sciences, Faculty of Agriculture, Rajarata University of Sri Lanka, Pulliyankulama, Anuradhapura 50000, Sri Lanka
| | - Faarah Nifla
- Department of Bioprocess Technology, Faculty of Technology, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka
| | - Dong-Qin Dai
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
| | - Yanxia Liu
- Guizhou Academy of Tobacco Science, No.29, Longtanba Road, Guanshanhu District, Guiyang 550000, China
| | - Nakarin Suwannarach
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jaturong Kumla
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Thushara C Bamunuarachchige
- Department of Bioprocess Technology, Faculty of Technology, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka
| | - Huan-Huan Chen
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
- Key Laboratory of Insect-Pollinator Biology of Ministry of Agriculture and Rural Affairs, Institute of Agricultural Research, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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De Lange R, Kleine J, Hampe F, Asselman P, Manz C, De Crop E, Delgat L, Adamčík S, Verbeken A. Stop black and white thinking: Russula subgenus Compactae ( Russulaceae, Russulales) in Europe revised. PERSOONIA 2023; 51:152-193. [PMID: 38665979 PMCID: PMC11041895 DOI: 10.3767/persoonia.2023.51.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 02/10/2023] [Indexed: 04/28/2024]
Abstract
Russula subgenus Compactae is a group of ectomycorrhizal basidiomycetes, usually with large pileate fruitbodies. European members of the group are characterised by the absence of bright colours on the surfaces of their pilei, the context turning grey to black after cutting, the abundance of short lamellulae in the hymenophore, and spores with an inamyloid suprahilar spot and with low reticulate ornamentation. Our multi-locus phylogenetic study confirmed that this morphological delimitation corresponds to a well-supported clade. Within this clade, 16 species are recognised in Europe, of which five belong to the R. albonigra lineage and were described in a previous study, while eleven are fully described in this study. The application of the names R. acrifolia, R. adusta, R. anthracina, R. atramentosa, R. densissima, R. nigricans and R. roseonigra is based on the position of sequences retrieved from types or authentic material. Based on type sequences, R. fuliginosa is synonymised with R. anthracina and two varieties of R. anthracina are considered synonyms of R. atramentosa. The application of the name R. densifolia is based on a morphological match with the traditional species interpretation and the neotype specimen. Three species are described as new, R. marxmuelleriana sp. nov., R. picrophylla sp. nov. and R. thuringiaca sp. nov. This study recognises three major lineages and two species with isolated positions within the European Compactae and a morphological barcode was assigned to the species using an analysis of 23 selected characters. A search of publicly available sequences from the UNITE database revealed that the majority of species are host tree generalists and widely distributed in temperate and Mediterranean areas of Europe. Russula adusta is the only species so far proven to form ectomycorrhiza exclusively with conifers. Citation: De Lange R, Kleine J, Hampe F, et al. 2023. Stop black and white thinking: Russula subgenus Compactae (Russulaceae, Russulales) in Europe revised. Persoonia 51: 152-193. doi: 10.3767/persoonia.2023.51.04.
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Affiliation(s)
- R. De Lange
- Ghent University, Department of Biology, Research Group Mycology, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - J. Kleine
- Am Lindenhof 9, 04277 Leipzig, Germany
| | - F. Hampe
- Wetzlarer Straße 1,35510 Butzbach, Germany
| | - P. Asselman
- Ghent University, Department of Biology, Research Group Mycology, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - C. Manz
- Goethe University, Faculty of Biological Sciences, Research Group Mycology, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany
| | - E. De Crop
- Ghent University, Department of Biology, Research Group Mycology, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - L. Delgat
- Ghent University, Department of Biology, Research Group Mycology, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
- Meise Botanic Garden, Research Department, Nieuwelaan 38, 1860 Meise, Belgium
| | - S. Adamčík
- Slovak Academy of Sciences, Plant Science and Biodiversity Centre, Institute of Botany, Dúbravská cesta 9, 845 23 Bratislava, Slovakia
- Comenius University Bratislava, Faculty of Natural Sciences, Department of Botany, Révová 39, 81102 Bratislava, Slovakia
| | - A. Verbeken
- Ghent University, Department of Biology, Research Group Mycology, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
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Garrido-Benavent I, de Los Ríos A, Núñez-Zapata J, Ortiz-Álvarez R, Schultz M, Pérez-Ortega S. Ocean crossers: a tale of disjunctions and speciation in the dwarf-fruticose Lichina (lichenized Ascomycota). Mol Phylogenet Evol 2023:107829. [PMID: 37247701 DOI: 10.1016/j.ympev.2023.107829] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 12/24/2022] [Accepted: 05/26/2023] [Indexed: 05/31/2023]
Abstract
Lichens thrive in rocky coastal areas in temperate and cold regions of both hemispheres. Species of the genus Lichina, which form characteristic black fruiting thalli associated with cyanobacteria, often create distinguishable bands in the intertidal and supralittoral zones. The present study uses a comprehensive specimen dataset and four gene loci to (1) delineate and discuss species boundaries in this genus, (2) assess evolutionary relationships among species, and (3) infer the most likely causes of their current geographic distribution in the Northern and Southern hemispheres. A dated phylogeny describes the time frame in which extant disjunctions of species and populations were established. The results showed that the genus is integrated by four species, with Lichina pygmaea, L. confinis and the newly described L. canariensis from rocky seashores in the Canary Islands, occurring in the Northern Hemisphere, whereas L. intermedia is restricted to the Southern Hemisphere. Lichina intermedia hosted a much higher intraspecific genetic diversity than the other species, with subclades interpreted as species-level lineages by the different species delimitation approaches. However, a conservative taxonomic approach was adopted. This species showed a striking disjunct distribution between Australasia and southern South America. The timing for the observed interspecific and intraspecific divergences and population disjunctions postdated continental plate movements, suggesting that long-distance dispersal across body waters in the two hemispheres played a major role in shaping the current species distributions. Such ocean crossings were, as in L. canariensis, followed by speciation. New substitution rates for the nrITS of the genus Lichina were inferred using a tree spanning the major Ascomycota lineages calibrated using fossils. In conclusion, this work lays the foundation for a better understanding of the evolution through time and space of maritime lichens.
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Affiliation(s)
- Isaac Garrido-Benavent
- Departament de Botànica i Geologia, Facultat de Ciències Biològiques, Universitat de València, C/ Doctor Moliner 50, E-46100-Burjassot, València, Spain; Department of Mycology, Real Jardín Botánico (CSIC), Plaza Murillo 2, E-28014 Madrid, Spain.
| | - Asunción de Los Ríos
- Department of Biogeochemistry and Microbial Ecology, National Museum of Natural Sciences (MNCN-CSIC), Serrano 115 dpdo, E-28045 Madrid, Spain.
| | - Jano Núñez-Zapata
- Department of Mycology, Real Jardín Botánico (CSIC), Plaza Murillo 2, E-28014 Madrid, Spain.
| | - Rüdiger Ortiz-Álvarez
- Department of International Science, Spanish Federation of Science and Technology (FECYT), C/ Pintor Murillo 15, E-28100 Alcobendas, Madrid, Spain.
| | - Matthias Schultz
- Herbarium Hamburgense, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststrasse 18, D-22609 Hamburg, Germany.
| | - Sergio Pérez-Ortega
- Department of Mycology, Real Jardín Botánico (CSIC), Plaza Murillo 2, E-28014 Madrid, Spain.
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Yingchanakiat K, Limsivilai O, Sunpongsri S, Niyomtham W, Lugsomya K, Yurayart C. Phenotypic and Genotypic Characterization and Antifungal Susceptibility of Sporothrix schenckii sensu stricto Isolated from a Feline Sporotrichosis Outbreak in Bangkok, Thailand. J Fungi (Basel) 2023; 9:jof9050590. [PMID: 37233301 DOI: 10.3390/jof9050590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023] Open
Abstract
Sporotrichosis, an invasive fungal infection caused by Sporothrix schenckii, has emerged in Southeast Asia, affecting cats and posing a potential zoonotic risk to humans. We evaluated 38 feline sporotrichosis cases in and around Bangkok, Thailand, from 2017 to 2021. The isolates were phenotypically and genotypically characterized. The cats infected with sporotrichosis were mainly young adults, males, and domestic short hairs with uncontrolled outdoor access, and they lived in Bangkok. All isolates showed low thermotolerance and converted to the yeast phase at 35 °C. Based on the internal transcribed spacer region of rDNA sequences, our strains belonged to S. schenckii sensu stricto and clustered with clinical clade D. Based on the concatenated tree of calmodulin and beta-tubulin genes, five groups of S. schenckii were generated, and the monophyletic clade, Group II, of Thai strains was recognized. In vitro antifungal susceptibility testing demonstrated that the MIC50 of our isolates to amphotericin B, itraconazole, and posaconazole were within the limit of the species-specific epidemiological cutoff values, suggesting that the organisms were the wild type. Addressing the outbreak of feline sporotrichosis in Thailand by providing guidelines for diagnosis and effective treatment may help control the spread of disease and reduce the risk of cat-transmitted sporotrichosis to humans.
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Affiliation(s)
- Kanokporn Yingchanakiat
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, 50 Ngamwongwan Road, Bangkok 10900, Thailand
| | - Orawan Limsivilai
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, 50 Ngamwongwan Road, Bangkok 10900, Thailand
| | - Supita Sunpongsri
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, Kasetsart University, 50 Ngamwongwan Road, Bangkok 10900, Thailand
| | - Waree Niyomtham
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Henri-Dunant Road, Pathumwan, Bangkok 10330, Thailand
| | - Kittitat Lugsomya
- Antimicrobial Resistance and Infectious Diseases Laboratory, Harry Butler Institute, Murdoch University, 90, South Street, Murdoch, Perth 6150, Australia
| | - Chompoonek Yurayart
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, 50 Ngamwongwan Road, Bangkok 10900, Thailand
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Paiva DS, Fernandes L, Pereira E, Trovão J, Mesquita N, Tiago I, Portugal A. Exploring Differences in Culturable Fungal Diversity Using Standard Freezing Incubation-A Case Study in the Limestones of Lemos Pantheon (Portugal). J Fungi (Basel) 2023; 9:jof9040501. [PMID: 37108954 PMCID: PMC10143818 DOI: 10.3390/jof9040501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
In this study, we explored the biodiversity and abundance of culturable fungi in four samples associated with different biodeterioration outlines collected from the Lemos Pantheon, a limestone-built artwork in Portugal. We compared the results from prolonged standard freezing with those previously obtained from fresh samples to analyze differences in the obtained community and assess the effectiveness of the standard freezing incubation protocol in uncovering a different segment of culturable fungal diversity. Our results showed a slight decrease in culturable diversity, but over 70% of the obtained isolates were not present in the previously studied fresh samples. We also identified a high number of potential new species with this procedure. Moreover, the use of a wide variety of selective culture media positively influenced the diversity of the cultivable fungi obtained in this study. These findings highlight the importance of developing new protocols under varying conditions to accurately characterize the culturable fraction in a given sample. The identification and study of these communities and their possible contribution to the biodeterioration process is crucial knowledge for formulating effective conservation and restoration plans to prevent further damage to valuable cultural heritage assets.
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Affiliation(s)
- Diana S Paiva
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Luís Fernandes
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Emília Pereira
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - João Trovão
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- FitoLab-Laboratory for Phytopathology, Instituto Pedro Nunes, Rua Pedro Nunes, 3030-199 Coimbra, Portugal
| | - Nuno Mesquita
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Igor Tiago
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - António Portugal
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- FitoLab-Laboratory for Phytopathology, Instituto Pedro Nunes, Rua Pedro Nunes, 3030-199 Coimbra, Portugal
- TERRA-Associate Laboratory for Sustainable Land Use and Ecosystem Services, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
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Zhang M, Li D, Si Y, Ju Y, Zhu L. Colletotrichum Species Associated with Anthracnose in Salix babylonica in China. PLANTS (BASEL, SWITZERLAND) 2023; 12:1679. [PMID: 37111900 PMCID: PMC10145283 DOI: 10.3390/plants12081679] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/08/2023] [Accepted: 04/16/2023] [Indexed: 06/19/2023]
Abstract
Salix babylonica L. is a popular ornamental tree species in China and widely cultivated in Asia, Europe, and North America. Anthracnose in S. babylonica poses a serious threat to its growth and reduces its medicinal properties. In 2021, a total of 55 Colletotrichum isolates were isolated from symptomatic leaves in three provinces in China. Phylogenetic analyses using six loci (ITS, ACT, CHS-1, TUB2, CAL, and GAPDH) and a morphological characterization of the 55 isolates showed that they belonged to four species of Colletotrichum, including C. aenigma, C. fructicola, C. gloeosporioides s.s., and C. siamense. Among them, C. siamense was the dominant species, and C. gloeosporioides s.s. was occasionally discovered from the host tissues. Pathogenicity tests revealed that all the isolates of the aforementioned species were pathogenic to the host, and there were significant differences in pathogenicity or virulence among these isolates. The information on the diversity of Colletotrichum spp. that causes S. babylonica anthracnose in China is new.
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Affiliation(s)
- Mengyu Zhang
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (M.Z.); (Y.S.); (Y.J.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China
| | - Dewei Li
- The Connecticut Agricultural Experiment Station Valley Laboratory, Windsor, CT 06095, USA
| | - Yuanzhi Si
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (M.Z.); (Y.S.); (Y.J.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China
| | - Yue Ju
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (M.Z.); (Y.S.); (Y.J.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China
| | - Lihua Zhu
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (M.Z.); (Y.S.); (Y.J.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China
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40
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Masigol H, Grossart HP, Taheri SR, Mostowfizadeh-Ghalamfarsa R, Pourmoghaddam MJ, Bouket AC, Khodaparast SA. Utilization of Low Molecular Weight Carbon Sources by Fungi and Saprolegniales: Implications for Their Ecology and Taxonomy. Microorganisms 2023; 11:microorganisms11030782. [PMID: 36985355 PMCID: PMC10052706 DOI: 10.3390/microorganisms11030782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 03/08/2023] [Accepted: 03/16/2023] [Indexed: 03/22/2023] Open
Abstract
Contributions of fungal and oomycete communities to freshwater carbon cycling have received increasing attention in the past years. It has been shown that fungi and oomycetes constitute key players in the organic matter cycling of freshwater ecosystems. Therefore, studying their interactions with dissolved organic matter is crucial for understanding the aquatic carbon cycle. Therefore, we studied the consumption rates of various carbon sources using 17 fungal and 8 oomycete strains recovered from various freshwater ecosystems using EcoPlate™ and FF MicroPlate™ approaches. Furthermore, phylogenetic relationships between strains were determined via single and multigene phylogenetic analyses of the internal transcribed spacer regions. Our results indicated that the studied fungal and oomycete strains could be distinguished based on their carbon utilization patterns, as indicated by their phylogenetic distance. Thereby, some carbon sources had a higher discriminative strength to categorize the studied strains and thus were applied in a polyphasic approach. We concluded that studying the catabolic potential enables a better understanding of taxonomic relationships and ecological roles of fungal vs. oomycete strains.
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Affiliation(s)
- Hossein Masigol
- Plankton and Microbial Ecology, Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB), 16775 Neuglobsow, Germany; (H.M.); (S.R.T.)
- Department of Plant Protection, Faculty of Agricultural Sciences, University of Guilan, Rasht 4199613776, Iran; (M.J.P.); (S.A.K.)
| | - Hans-Peter Grossart
- Plankton and Microbial Ecology, Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB), 16775 Neuglobsow, Germany; (H.M.); (S.R.T.)
- Institute for Biochemistry and Biology, Potsdam University, 14469 Potsdam, Germany
- Correspondence: ; Tel.: +49-(0)-3308269991
| | - Seyedeh Roksana Taheri
- Plankton and Microbial Ecology, Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB), 16775 Neuglobsow, Germany; (H.M.); (S.R.T.)
| | | | - Mohammad Javad Pourmoghaddam
- Department of Plant Protection, Faculty of Agricultural Sciences, University of Guilan, Rasht 4199613776, Iran; (M.J.P.); (S.A.K.)
| | - Ali Chenari Bouket
- East Azarbaijan Agricultural and Natural Resources Research and Education Centre, Plant Protection Research Department, Agricultural Research, Education and Extension Organization (AREEO), Tabriz 5355179854, Iran;
| | - Seyed Akbar Khodaparast
- Department of Plant Protection, Faculty of Agricultural Sciences, University of Guilan, Rasht 4199613776, Iran; (M.J.P.); (S.A.K.)
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Freire-Rallo S, Wedin M, Diederich P, Millanes AM. To explore strange new worlds - The diversification in Tremella caloplacae was linked to the adaptive radiation of the Teloschistaceae. Mol Phylogenet Evol 2023; 180:107680. [PMID: 36572164 DOI: 10.1016/j.ympev.2022.107680] [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: 12/13/2021] [Revised: 09/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Lichenicolous fungi are a heterogeneous group of organisms that grow exclusively on lichens, forming obligate associations with them. It has often been assumed that cospeciation has occurred between lichens and lichenicolous fungi, but this has been seldom analysed from a macroevolutionary perspective. Many lichenicolous species are rare or are rarely observed, which results in frequent and large gaps in the knowledge of the diversity of many groups. This, in turn, hampers evolutionary studies that necessarily are based on a reasonable knowledge of this diversity. Tremella caloplacae is a heterobasidiomycete growing on various hosts from the lichen-forming family Teloschistaceae, and evidence suggests that it may represent a species complex. We combine an exhaustive sampling with molecular and ecological data to study species delimitation, cophylogenetic events and temporal concordance of this association. Tremella caloplacae is here shown to include at least six distinct host-specific lineages (=putative species). Host switch is the dominant and most plausible event influencing diversification and explaining the coupled evolutionary history in this system, although cospeciation cannot be discarded. Speciation in T. caloplacae would therefore have occurred coinciding with the rapid diversification - by an adaptive radiation starting in the late Cretaceous - of their hosts. New species in T. caloplacae would have developed as a result of specialization on diversifying lichen hosts that suddenly offered abundant new ecological niches to explore or adapt to.
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Affiliation(s)
- Sandra Freire-Rallo
- Rey Juan Carlos University/Departamento de Biología y Geología, Física y Química Inorgánica, E-28933 Móstoles, Spain
| | - Mats Wedin
- Swedish Museum of Natural History/Botany Dept., PO Box 50007, SE-10405 Stockholm, Sweden.
| | - Paul Diederich
- Musée national d'histoire naturelle, 25 rue Munster, L-2160 Luxembourg, Luxembourg
| | - Ana M Millanes
- Rey Juan Carlos University/Departamento de Biología y Geología, Física y Química Inorgánica, E-28933 Móstoles, Spain
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Bokade P, Bajaj A. Molecular advances in mycoremediation of polycyclic aromatic hydrocarbons: Exploring fungal bacterial interactions. J Basic Microbiol 2023; 63:239-256. [PMID: 36670077 DOI: 10.1002/jobm.202200499] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/15/2022] [Accepted: 12/18/2022] [Indexed: 01/22/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous high global concern environmental pollutants and tend to bioaccumulate due to hydrophobic properties. These xenobiotics, having variable concentrations along different matrices, gradually undergo various physical, chemical, and biological transformation processes. Myco-remediation aids accelerated degradation by effectively transforming complex ring structures to oxidized/hydroxylated intermediates, which can further funnel to bacterial degradation pathways. Exploitation of such complementing fungal-bacterial enzymatic activity can overcome certain limitations of incomplete bioremediation process. Furthermore, high-throughput molecular methods can be employed to unveil community structure, taxon abundance, coexisting community interactions, and metabolic pathways under stressed conditions. The present review critically discusses the role of different fungal phyla in PAHs biotransformation and application of fungal-bacterial cocultures for enhanced mineralization. Moreover, recent advances in bioassays for PAH residue detection, monitoring, developing xenobiotics stress-tolerant strains, and application of fungal catabolic enzymes are highlighted. Application of next-generation sequencing methods to reveal complex ecological networks based on microbial community interactions and data analysis bias in performing such studies is further discussed in detail. Conclusively, the review underscores the application of mixed-culture approach by critically highlighting in situ fungal-bacterial community nexus and its role in complete mineralization of PAHs for the management of contaminated sites.
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Affiliation(s)
- Priyanka Bokade
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Abhay Bajaj
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Molecular Approaches for Detection of Trichoderma Green Mold Disease in Edible Mushroom Production. BIOLOGY 2023; 12:biology12020299. [PMID: 36829575 PMCID: PMC9953464 DOI: 10.3390/biology12020299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/16/2023]
Abstract
Due to the evident aggressive nature of green mold and the consequently huge economic damage it causes for producers of edible mushrooms, there is an urgent need for prevention and infection control measures, which should be based on the early detection of various Trichoderma spp. as green mold causative agents. The most promising current diagnostic tools are based on molecular methods, although additional optimization for real-time, in-field detection is still required. In the first part of this review, we briefly discuss cultivation-based methods and continue with the secondary metabolite-based methods. Furthermore, we present an overview of the commonly used molecular methods for Trichoderma species/strain detection. Additionally, we also comment on the potential of genomic approaches for green mold detection. In the last part, we discuss fast screening molecular methods for the early detection of Trichoderma infestation with the potential for in-field, point-of-need (PON) application, focusing on isothermal amplification methods. Finally, current challenges and future perspectives in Trichoderma diagnostics are summarized in the conclusions.
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44
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Conti A, Casagrande Pierantoni D, Robert V, Corte L, Cardinali G. MinION Sequencing of Yeast Mock Communities To Assess the Effect of Databases and ITS-LSU Markers on the Reliability of Metabarcoding Analysis. Microbiol Spectr 2023; 11:e0105222. [PMID: 36519933 PMCID: PMC9927109 DOI: 10.1128/spectrum.01052-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Microbial communities play key roles both for humans and the environment. They are involved in ecosystem functions, maintaining their stability, and provide important services, such as carbon cycle and nitrogen cycle. Acting both as symbionts and as pathogens, description of the structure and composition of these communities is important. Metabarcoding uses ribosomal DNA (rDNA) (eukaryotic) or rRNA gene (prokaryotic) sequences for identification of species present in a site and measuring their abundance. This procedure requires several technical steps that could be source of bias producing a distorted view of the real community composition. In this work, we took advantage of an innovative "long-read" next-generation sequencing (NGS) technology (MinION) amplifying the DNA spanning from the internal transcribed spacer (ITS) to large subunit (LSU) that can be read simultaneously in this platform, providing more information than "short-read" systems. The experimental system consisted of six fungal mock communities composed of species present at various relative amounts to mimic natural situations characterized by predominant and low-frequency species. The influence of the sequencing platform (MinION and Illumina MiSeq) and the effect of different reference databases and marker sequences on metagenomic identification of species were evaluated. The results showed that the ITS-based database provided more accurate species identification than LSU. Furthermore, a procedure based on a preliminary identification with standard reference databases followed by the production of custom databases, including only the best outputs of the first step, is proposed. This additional step improved the estimate of species proportion of the mock communities and reduced the number of ghost species not really present in the simulated communities. IMPORTANCE Metagenomic analyses are fundamental in many research areas; therefore, improvement of methods and protocols for the description of microbial communities becomes more and more necessary. Long-read sequencing could be used for reducing biases due to the multicopy nature of rDNA sequences and short-read limitations. However, these novel technologies need to be assessed and standardized with controlled experiments, such as mock communities. The interest behind this work was to evaluate how long reads performed identification and quantification of species mixed in precise proportions and how the choice of database affects such analyses. Development of a pipeline that mitigates the effect of the barcoding sequences and the impact of the reference database on metagenomic analyses can help microbiome studies go one step further.
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Affiliation(s)
- Angela Conti
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | | | - Vincent Robert
- Westerdjik Institute for Biodiversity, Utrecht, Netherlands
| | - Laura Corte
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
- CEMIN Excellence Research Centre, Perugia, Italy
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
- CEMIN Excellence Research Centre, Perugia, Italy
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Grassi A, Gambini M, Pantoli M, Toscano S, Albertetti A, Del Frassino DM, Ugochukwu ICI, Romeo O, Otranto D, Cafarchia C. A Lethal Case of Disseminated Cladosporium allicinum Infection in a Captive African Bullfrog. J Fungi (Basel) 2023; 9:jof9020191. [PMID: 36836306 PMCID: PMC9967566 DOI: 10.3390/jof9020191] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 01/26/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Cladosporium infections have a poor prognosis in animals, most likely due to a lack of knowledge about diagnosis and treatment. In this study, we described a case of a lethal Cladosporium allicinum infection in a captive bullfrog (Pyxicephalus adspersus) in Europe. One adult male bullfrog was referred with clinical signs of lethargy and a cutaneous nodule. Fungal infection was suspected on cytology and confirmed by histology and cultural isolation. The mold was identified by molecular methods using partial sequencing of the TEF1α gene and the ITS region of rDNA. Climbazole antifungal treatment was started but the frog died after 30 days, and necropsy was done. Pigmented hyphae and structures consistent with muriform bodies were found on a background of diffuse granulomatous inflammation at cytological and histopathological examinations. Fungal culture revealed the presence of pigmented fungi identified as Cladosporium allicinum only by partial sequencing of the TEF1α gene. A focally extensive granuloma with intralesional hyphae and muriform bodies effacing the architecture of head, liver, kidneys, lungs, and large intestine were retrieved after necropsy. This study is the first Italian report of the occurrence of lethal C. allicinum infection in a frog and highlights the role of this Cladosporium sp. in chromoblastomycosis.
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Affiliation(s)
- Andrea Grassi
- I-Vet Diagnostica Veterinaria, 25020 Brescia, Italy
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, 27100 Pavia, Italy
| | | | | | | | | | | | - Iniobong Chukwuebuka Ikenna Ugochukwu
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari Aldo Moro, 70124 Bari, Italy
- Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka 400001, Nigeria
| | - Orazio Romeo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy
| | - Domenico Otranto
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari Aldo Moro, 70124 Bari, Italy
- Faculty of Veterinary Sciences, Bu-Ali Sina University, Hamedan 6517833131, Iran
| | - Claudia Cafarchia
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari Aldo Moro, 70124 Bari, Italy
- Correspondence:
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Linking processes to community functions—insights into litter decomposition combining fungal metatranscriptomics and environmental NMR profiling. Mycol Prog 2023. [DOI: 10.1007/s11557-022-01859-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
AbstractIn forest ecosystems, decomposition is essential for carbon and nutrient cycling and therefore a key process for ecosystem functioning. During the decomposition process, litter chemistry, involved decomposer organisms, and enzymatic activity change interdependently. Chemical composition of the litter is the most complex and dynamic component in the decomposition process and therefore challenging to assess holistically. In this study, we aimed to characterize chemical shifts during decomposition and link them to changes in decomposer fungal activity. We characterized the chemical composition of freshly fallen autumn leaves of European beech (Fagus sylvatica) and the corresponding leaf litter after 1 year of decomposition by proton nuclear magnetic resonance spectroscopy. We further tested the applicability of spiking experiments for qualitative and quantitative characterization of leaves and litter chemistry. The composition and transcriptional activity of fungal communities was assessed by high-throughput Illumina sequencing in the same litter samples. We were able to distinguish freshly fallen leaves from 1-year-old litter based on their chemical composition. Chemical composition of leaves converged among regions with progressing decomposition. Fungal litter communities differed in composition among regions, but they were functionally redundant according to the expression of genes encoding litter degrading enzymes (CAZymes). Fungi of the saprotrophic genera Mycena and Chalara correlated with transcription of litter-degrading CAZymes in 1-year-old litter. Forestry measures influenced the diversity and transcription rate of the detected CAZymes transcripts in litter. Their expression was primarily predicted by composition of the soluble chemical fraction of the litter. Environmental NMR fingerprints thus proved valuable for inferring ecological contexts. We propose and discuss a holistic framework to link fungal activity, enzyme expression, and chemical composition.
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Feau N, Herath P, Hamelin RC. DNA-Barcoding Identification of Plant Pathogens for Disease Diagnostics. Methods Mol Biol 2023; 2659:37-49. [PMID: 37249883 DOI: 10.1007/978-1-0716-3159-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The accurate identification of plant pathogens is a critical step to prevent their spread and attenuate their impact. Among the wide range of methods available, DNA-barcoding, i.e., the identification of an organism through the PCR amplification and sequencing of a single locus, remains one of the most straightforward and accurate plant-pathogen identification techniques that can be used in a generic molecular biology lab. This chapter provides a detailed protocol for the isolation of genomic DNA of fungal and oomycete pathogens from fresh field samples and the amplification and sequencing of the internal transcribed spacer (ITS) locus for DNA-barcoding purpose. Amendments to the protocol are provided to help in resolving issues related to the analysis of complicated samples and to the lack of species resolution that can be encountered with ITS barcodes.
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Affiliation(s)
- Nicolas Feau
- Canadian Forest Service, Pacific Forestry Centre, Natural Resources Canada, Victoria, BC, Canada.
| | - Padmini Herath
- Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Richard C Hamelin
- Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
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Fan X, Dai RC, Kudinha T, Gu L. A pseudo-outbreak of Cyberlindnera fabianii funguria: Implication from whole genome sequencing assay. Front Cell Infect Microbiol 2023; 13:1130645. [PMID: 36960046 PMCID: PMC10030058 DOI: 10.3389/fcimb.2023.1130645] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/21/2023] [Indexed: 03/09/2023] Open
Abstract
Background Although the yeast Cyberlindnera fabianii (C. fabianii) has been rarely reported in human infections, nosocomial outbreaks caused by this organism have been documented. Here we report a pseudo-outbreak of C. fabianii in a urology department of a Chinese hospital over a two-week period. Methods Three patients were admitted to the urology department of a tertiary teaching hospital in Beijing, China, from Nov to Dec 2018, for different medical intervention demands. During the period Nov 28 to Dec 5, funguria occurred in these three patients, and two of them had positive urine cultures multiple times. Sequencing of rDNA internal transcribed spacer (ITS) region and MALDI-TOF MS were applied for strain identification. Further, sequencing of rDNA non-transcribed spacer (NTS) region and whole genome sequencing approaches were used for outbreak investigation purpose. Results All the cultured yeast strains were identified as C. fabianii by sequencing of ITS region, and were 100% identical to the C. fabianii type strain CBS 5640T. However, the MALDI-TOF MS system failed to correctly identify this yeast pathogen. Moreover, isolates from these three clustered cases shared 99.91%-100% identical NTS region sequences, which could not rule out the possibility of an outbreak. However, whole genome sequencing results revealed that only two of the C. fabianii cases were genetically-related with a pairwise SNP of 192 nt, whilst the third case had over 26,000 SNPs on its genome, suggesting a different origin. Furthermore, the genomes of the first three case strains were phylogenetically even more diverged when compared to a C. fabianii strain identified from another patient, who was admitted to a general surgical department of the same hospital 7 months later. One of the first three patients eventually passed away due to poor general conditions, one was asymptomatic, and other clinically improved. Conclusion In conclusion, nosocomial outbreaks caused by emerging and uncommon fungal species are increasingly being reported, hence awareness must be raised. Genotyping with commonly used universal gene targets may have limited discriminatory power in tracing the sources of infection for these organisms, requiring use of whole genome sequencing to confirm outbreak events.
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Affiliation(s)
- Xin Fan
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Rong-Chen Dai
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Timothy Kudinha
- School of Dentistry and Medical Sciences, Charles Sturt University, Leeds Parade, Oranges, NSW, Australia
- NSW Health Pathology, Regional and Rural, Orange hospital, Orange, NSW, Australia
| | - Li Gu
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
- *Correspondence: Li Gu,
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Antil S, Abraham JS, Sripoorna S, Maurya S, Dagar J, Makhija S, Bhagat P, Gupta R, Sood U, Lal R, Toteja R. DNA barcoding, an effective tool for species identification: a review. Mol Biol Rep 2023; 50:761-775. [PMID: 36308581 DOI: 10.1007/s11033-022-08015-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/07/2022] [Indexed: 02/01/2023]
Abstract
DNA barcoding is a powerful taxonomic tool to identify and discover species. DNA barcoding utilizes one or more standardized short DNA regions for taxon identification. With the emergence of new sequencing techniques, such as Next-generation sequencing (NGS), ONT MinION nanopore sequencing, and Pac Bio sequencing, DNA barcoding has become more accurate, fast, and reliable. Rapid species identification by DNA barcodes has been used in a variety of fields, including forensic science, control of the food supply chain, and disease understanding. The Consortium for Barcode of Life (CBOL) presents various working groups to identify the universal barcode gene, such as COI in metazoans; rbcL, matK, and ITS in plants; ITS in fungi; 16S rRNA gene in bacteria and archaea, and creating a reference DNA barcode library. In this article, an attempt has been made to analyze the various proposed DNA barcode for different organisms, strengths & limitations, recent advancements in DNA barcoding, and methods to speed up the DNA barcode reference library construction. This study concludes that constructing a reference library with high species coverage would be a major step toward identifying species by DNA barcodes. This can be achieved in a short period of time by using advanced sequencing and data analysis methods.
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Affiliation(s)
- Sandeep Antil
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | | | - S Sripoorna
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | - Swati Maurya
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | - Jyoti Dagar
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | - Seema Makhija
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | - Pooja Bhagat
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | - Renu Gupta
- Maitreyi College, University of Delhi, New Delhi, Delhi, 110 021, India
| | - Utkarsh Sood
- The Energy and Resources Institute, IHC Complex, New Delhi, 110003, India
| | - Rup Lal
- The Energy and Resources Institute, IHC Complex, New Delhi, 110003, India
| | - Ravi Toteja
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India.
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Gallardo-Pillancari E, González C, Barahona-Segovia RM, Ruiz C, Luz C, Humber RA, Montalva C. Natural infection of Chiromyzinae larvae (Diptera: Stratiomyidae) in southern Chile by Tolypocladium valdiviae sp. nov. Fungal Biol 2023; 127:845-853. [PMID: 36746556 DOI: 10.1016/j.funbio.2022.12.004] [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: 10/10/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 12/26/2022]
Abstract
A new species from the fungal genus Tolypocladium (Hypocreales: Ophiocordycipitaceae) that infects Stratiomyidae larva from the genus Hylorops is described: Tolypocladium valdiviae Gallardo-Pillancari, Montalva & González. The description is based on both genomic data and morphological characteristics. The sexual stage of T. valdiviae presents fleshy and visible stromata; unlike Tolypocladium ophioglossoides, it is smaller and emerges directly from its host and resembles Tolypocladium longisegmentis and Tolypocladium capitatum, both of which are parasites of deer truffle fungi of the genus Elaphomyces (Ascomycota: Eurotiales). In the anamorphic state, T. valdiviae presents conidiogenous cells similar in shape and arrangement to those of Tolypocladium inflatum, however T. valdiviae produces larger conidiogenous cells and, occasionally, produces chlamydospores. Phylogenetic evidence suggested that T. valdiviae is in a clade close to T. longisegmentis, T. inflatum and T. ophioglossoides, species also recognized to be parasites of fungi of the genus Elaphomyces. The new species is known so far only from Valdivia, southern Chile.
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Affiliation(s)
- Esteban Gallardo-Pillancari
- Laboratorio de Salud de Bosques, Instituto de Conservación, Biodiversidad y Territorio, Facultad de Ciencias Forestales y Recursos Naturales, Universidad Austral de Chile, Valdivia, Chile; Laboratorio de Biodiversidad y Ecología Del Dosel, Instituto de Conservación, Biodiversidad y Territorio, Facultad de Ciencias Forestales y Recursos Naturales, Universidad Austral de Chile, Valdivia, Chile.
| | - Cristian González
- Laboratorio de Salud de Bosques, Instituto de Conservación, Biodiversidad y Territorio, Facultad de Ciencias Forestales y Recursos Naturales, Universidad Austral de Chile, Valdivia, Chile
| | - Rodrigo M Barahona-Segovia
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Av. Fuschlöcher, 1305, Osorno, Chile
| | - Cecilia Ruiz
- Laboratorio de Salud de Bosques, Instituto de Conservación, Biodiversidad y Territorio, Facultad de Ciencias Forestales y Recursos Naturales, Universidad Austral de Chile, Valdivia, Chile
| | - Christian Luz
- Instituto de Patologia Tropical e Saúde Pública (IPTSP), Universidade Federal de Goiás (UFG), Goiânia, Goiás, Brazil
| | - Richard A Humber
- USDA-ARS Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA
| | - Cristian Montalva
- Laboratorio de Salud de Bosques, Instituto de Conservación, Biodiversidad y Territorio, Facultad de Ciencias Forestales y Recursos Naturales, Universidad Austral de Chile, Valdivia, Chile.
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