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Palumbo JD, Sarreal SBL, Kim JH. Simultaneous detection of mycotoxigenic Aspergillus species of sections Circumdati and Flavi using multiplex digital PCR. Lett Appl Microbiol 2023; 76:ovad142. [PMID: 38111225 DOI: 10.1093/lambio/ovad142] [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: 09/27/2023] [Revised: 11/20/2023] [Accepted: 12/15/2023] [Indexed: 12/20/2023]
Abstract
Populations of ochratoxin-producing Aspergillus section Circumdati species and aflatoxin-producing Aspergillus section Flavi species frequently coexist in soil and are the main sources of mycotoxin contamination of tree nuts. Identification of mycotoxigenic Aspergillus species in these sections is difficult using traditional isolation and culture methods. We developed a multiplex digital PCR (dPCR) assay to detect and quantify Aspergillus ochraceus, Aspergillus westerdijkiae, and Aspergillus steynii (section Circumdati), as well as Aspergillus flavus and Aspergillus parasiticus (section Flavi), in environmental samples based on species-specific calmodulin gene sequences. Relative quantification of each species by dPCR of mixed-species templates correlated with corresponding DNA input ratios. Target species could be detected in soil inoculated with conidia from each species. Non-target species of sections Circumdati, Flavi, and Nigri were generally not detectable using this dPCR method. Detected non-target species (Aspergillus fresenii, Aspergillus melleus, Aspergillus sclerotiorum, and Aspergillus subramanianii) were discernible from A. ochraceus in dual-template dPCR reactions based on differential fluorescence intensity.
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Affiliation(s)
- Jeffrey D Palumbo
- Foodborne Toxin Detection and Prevention Research Unit, US Department of Agriculture, Agricultural Research Service, Albany, CA 94710, United States
| | - Siov Bouy L Sarreal
- Foodborne Toxin Detection and Prevention Research Unit, US Department of Agriculture, Agricultural Research Service, Albany, CA 94710, United States
| | - Jong H Kim
- Foodborne Toxin Detection and Prevention Research Unit, US Department of Agriculture, Agricultural Research Service, Albany, CA 94710, United States
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Mirabile G, Ferraro V, Mancuso FP, Pecoraro L, Cirlincione F. Biodiversity of Fungi in Freshwater Ecosystems of Italy. J Fungi (Basel) 2023; 9:993. [PMID: 37888249 PMCID: PMC10607542 DOI: 10.3390/jof9100993] [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: 09/04/2023] [Revised: 09/30/2023] [Accepted: 10/05/2023] [Indexed: 10/28/2023] Open
Abstract
Fungal biodiversity is still mostly unknown and their presence in particular ecosystems such as freshwater habitats is often underestimated. The ecological role that these fungi play in freshwater environments mainly concerns their activity as decomposers of litter and plant material. At present, it is estimated that 3870 species belong to the ecological group of freshwater fungi (13 phyla and 45 classes). In this survey, we provide an overview of the Italian freshwater fungal diversity on the basis of the field and literature data. In the literature, data on freshwater fungi are fragmentary and not updated, focusing mainly on northern Italy where the most important lakes and rivers are present, while data from central and southern Italy (including Sicily and Sardinia) are almost completely ineffective. In particular, Ascomycota are reported in only 14 publications, most of which concern the freshwater environments of Lombardia, Piemonte, and Veneto. Only one publication explores the biodiversity of freshwater Basidiomycota in the wetlands of the Cansiglio forest (Veneto). The field observation allowed for us to identify 38 species of Basidiomycota growing in riparian forest of Italy. However, the number of fungi in freshwater habitats of Italy is strongly underestimated and many species are still completely unknown.
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Affiliation(s)
- Giulia Mirabile
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Viale delle Scienze, Bldg. 5, 90128 Palermo, Italy; (G.M.); (F.C.)
- NBFC, National Biodiversity Future Center, Piazza Marina 61 (c/o Palazzo Steri), 90133 Palermo, Italy
| | - Valeria Ferraro
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, University Campus “Ernesto Quagliariello”, Via E. Orabona 4, 70125 Bari, Italy
| | - Francesco Paolo Mancuso
- Department of Earth and Sea Sciences, University of Palermo, Viale delle Scienze, Bldg. 16, 90128 Palermo, Italy
| | - Lorenzo Pecoraro
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China;
| | - Fortunato Cirlincione
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Viale delle Scienze, Bldg. 5, 90128 Palermo, Italy; (G.M.); (F.C.)
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Calabon MS, Hyde KD, Jones EBG, Luo ZL, Dong W, Hurdeal VG, Gentekaki E, Rossi W, Leonardi M, Thiyagaraja V, Lestari AS, Shen HW, Bao DF, Boonyuen N, Zeng M. Freshwater fungal numbers. FUNGAL DIVERS 2022. [DOI: 10.1007/s13225-022-00503-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Gonçalves MFM, Hilário S, Tacão M, Van de Peer Y, Alves A, Esteves AC. Genome and Metabolome MS-Based Mining of a Marine Strain of Aspergillus affinis. J Fungi (Basel) 2021; 7:1091. [PMID: 34947073 PMCID: PMC8709101 DOI: 10.3390/jof7121091] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/17/2021] [Accepted: 12/17/2021] [Indexed: 01/09/2023] Open
Abstract
Aspergillus section Circumdati encompasses several species that express both beneficial (e.g., biochemical transformation of steroids and alkaloids, enzymes and metabolites) and harmful compounds (e.g., production of ochratoxin A (OTA)). Given their relevance, it is important to analyze the genetic and metabolic diversity of the species of this section. We sequenced the genome of Aspergillus affinis CMG 70, isolated from sea water, and compared it with the genomes of species from section Circumdati, including A. affinis's strain type. The A. affinis genome was characterized considering secondary metabolites biosynthetic gene clusters (BGCs), carbohydrate-active enzymes (CAZymes), and transporters. To uncover the biosynthetic potential of A. affinis CMG 70, an untargeted metabolomics (LC-MS/MS) approach was used. Cultivating the fungus in the presence and absence of sea salt showed that A. affinis CMG 70 metabolite profiles are salt dependent. Analyses of the methanolic crude extract revealed the presence of both unknown and well-known Aspergillus compounds, such as ochratoxin A, anti-viral (e.g., 3,5-Di-tert-butyl-4-hydroxybenzoic acid and epigallocatechin), anti-bacterial (e.g., 3-Hydroxybenzyl alcohol, l-pyroglutamic acid, lecanoric acid), antifungal (e.g., lpyroglutamic acid, 9,12,13-Trihydroxyoctadec-10-enoic acid, hydroxyferulic acid), and chemotherapeutic (e.g., daunomycinone, mitoxantrone) related metabolites. Comparative analysis of 17 genomes from 16 Aspergillus species revealed abundant CAZymes (568 per species), secondary metabolite BGCs (73 per species), and transporters (1359 per species). Some BGCs are highly conserved in this section (e.g., pyranonigrin E and UNII-YC2Q1O94PT (ACR toxin I)), while others are incomplete or completely lost among species (e.g., bikaverin and chaetoglobosins were found exclusively in series Sclerotiorum, while asperlactone seemed completely lost). The results of this study, including genome analysis and metabolome characterization, emphasize the molecular diversity of A. affinis CMG 70, as well as of other species in the section Circumdati.
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Affiliation(s)
- Micael F. M. Gonçalves
- CESAM, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (M.F.M.G.); (S.H.); (M.T.); (A.C.E.)
| | - Sandra Hilário
- CESAM, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (M.F.M.G.); (S.H.); (M.T.); (A.C.E.)
| | - Marta Tacão
- CESAM, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (M.F.M.G.); (S.H.); (M.T.); (A.C.E.)
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Artur Alves
- CESAM, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (M.F.M.G.); (S.H.); (M.T.); (A.C.E.)
| | - Ana C. Esteves
- CESAM, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (M.F.M.G.); (S.H.); (M.T.); (A.C.E.)
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Navale V, Vamkudoth KR, Ajmera S, Dhuri V. Aspergillus derived mycotoxins in food and the environment: Prevalence, detection, and toxicity. Toxicol Rep 2021; 8:1008-1030. [PMID: 34408970 PMCID: PMC8363598 DOI: 10.1016/j.toxrep.2021.04.013] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 04/20/2021] [Accepted: 04/27/2021] [Indexed: 12/16/2022] Open
Abstract
Aspergillus species are the paramount ubiquitous fungi that contaminate various food substrates and produce biochemicals known as mycotoxins. Aflatoxins (AFTs), ochratoxin A (OTA), patulin (PAT), citrinin (CIT), aflatrem (AT), secalonic acids (SA), cyclopiazonic acid (CPA), terrein (TR), sterigmatocystin (ST) and gliotoxin (GT), and other toxins produced by species of Aspergillus plays a major role in food and human health. Mycotoxins exhibited wide range of toxicity to the humans and animal models even at nanomolar (nM) concentration. Consumption of detrimental mycotoxins adulterated foodstuffs affects human and animal health even trace amounts. Bioaerosols consisting of spores and hyphal fragments are active elicitors of bronchial irritation and allergy, and challenging to the public health. Aspergillus is the furthermost predominant environmental contaminant unswervingly defile lives with a 40-90 % mortality risk in patients with conceded immunity. Genomics, proteomics, transcriptomics, and metabolomics approaches useful for mycotoxins' detection which are expensive. Antibody based detection of toxins chemotypes may result in cross-reactivity and uncertainty. Aptamers (APT) are single stranded DNA (ssDNA/RNA), are specifically binds to the target molecules can be generated by systematic evolution of ligands through exponential enrichment (SELEX). APT are fast, sensitive, simple, in-expensive, and field-deployable rapid point of care (POC) detection of toxins, and a better alternative to antibodies.
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Affiliation(s)
- Vishwambar Navale
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi, India
| | - Koteswara Rao Vamkudoth
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi, India
| | | | - Vaibhavi Dhuri
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, India
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Gil-Serna J, Vázquez C, Patiño B. The Genomic Regions That Contain Ochratoxin A Biosynthetic Genes Widely Differ in Aspergillus Section Circumdati Species. Toxins (Basel) 2020; 12:E754. [PMID: 33260416 PMCID: PMC7760312 DOI: 10.3390/toxins12120754] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/22/2020] [Accepted: 11/28/2020] [Indexed: 12/31/2022] Open
Abstract
Aspergillus section Circumdati includes 27 species, some of which are considered ochratoxin A (OTA) producers. However, there is considerable controversy about their potential OTA synthesis ability. In this work, the complete genomes of 13 species of Aspergillus section Circumdati were analyzed in order to study the cluster of OTA biosynthetic genes and the region was compared to those previously reported in A. steynii and A. westerdijkiae. The results obtained reveal that the genomes of some species in this section, including A. affinis, A. cretensis, A. elegans, A. muricatus, A. pulvericola, A. roseoglobulosus, and A. subramanianii, contain a potentially functional OTA biosynthetic cluster. Therefore, they might be able to synthesize the toxin. On the contrary, A. melleus, A. ochraceus, A. ostianus, A. persii, A. sclerotiorum, A. sesamicola, and A. westlandensis contain a truncated version of the cluster that lacks many of the genes involved in OTA biosynthesis, which might be related to their inability to produce OTA. The gain/loss pattern is different in all species, which suggests that the genetic evolution of this region might be due to independent events.
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Affiliation(s)
- Jéssica Gil-Serna
- Department of Genetics, Physiology, and Microbiology, Faculty of Biology, University Complutense of Madrid, Jose Antonio Nováis 12, 28040 Madrid, Spain; (C.V.); (B.P.)
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Abstract
The taxonomy and nomenclature of the genus Aspergillus and its associated sexual (teleomorphic) genera have been greatly stabilised over the last decade. This was in large thanks to the accepted species list published in 2014 and associated metadata such as DNA reference sequences released at the time. It had a great impact on the community and it has never been easier to identify, publish and describe the missing Aspergillus diversity. To further stabilise its taxonomy, it is crucial to not only discover and publish new species but also to capture infraspecies variation in the form of DNA sequences. This data will help to better characterise and distinguish existing species and make future identifications more robust. South Africa has diverse fungal communities but remains largely unexplored in terms of Aspergillus with very few sequences available for local strains. In this paper, we re-identify Aspergillus previously accessioned in the PPRI and MRC culture collections using modern taxonomic approaches. In the process, we re-identify strains to 63 species, describe seven new species and release a large number of new DNA reference sequences.
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Affiliation(s)
- C.M. Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- Biosystematics Division, Agricultural Research Council – Plant Health and Protection, Private Bag X134, Queenswood, Pretoria, 0121, South Africa
| | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, CT, 3584, Netherlands
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Davolos D, Pietrangeli B, Persiani AM, Maggi O. Victoriomyces antarcticus gen. nov., sp. nov., a distinct evolutionary lineage of the Cephalothecaceae (Ascomycota) based on sequence-based phylogeny and morphology. Int J Syst Evol Microbiol 2019; 69:1099-1110. [PMID: 30767849 DOI: 10.1099/ijsem.0.003275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study, we propose a new genus, Victoriomyces, with a new species, Victoriomyces antarcticus, isolated from soil samples collected in Victoria Land, Antarctica. To determine its taxonomic status and evolutionary relationships, phylogenetic analysis was performed on DNA sequences from the nuclear 18S rRNA, 28S rRNA and the second largest subunit of RNA polymerase II (RPB2) genes. Victoriomyces antarcticus constitutes one well-supported distinct lineage within the Cephalothecaceae (family incertae sedis in Sordariomycetes), in which the only recognised asexual morphs belong to the genus Phialemonium and to Acremonium thermophilum. Victoriomyces antarcticus can be clearly distinguished from these taxa by means of DNA sequence analysis and its morphological traits that consist in having a Metarhizium-like asexual morph, dark red-coloured disk-like structures, immature bodies and the production of an intense red pigment in the growth media. Finally, we inferred the divergence time of V. antarcticus and the Cephalothecaceae using Bayesian analysis and secondary calibration. The holotype of V. antarcticus is FBL 165. The ex-type strain has been deposited as MUT 3686T and CCF 6158T. An additional strain of the species is FBL 577. The MycoBank number is MB 823713 for the genus and MB 823714 for the species.
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Affiliation(s)
- Domenico Davolos
- Department of Technological Innovations and Safety of Plants, Products and Anthropic Settlements, INAIL, Research Area, Via R. Ferruzzi 38/40 - 00143 Rome, Italy
| | - Biancamaria Pietrangeli
- Department of Technological Innovations and Safety of Plants, Products and Anthropic Settlements, INAIL, Research Area, Via R. Ferruzzi 38/40 - 00143 Rome, Italy
| | - Anna Maria Persiani
- Department of Environmental Biology, Sapienza University of Rome, Piazzale A. Moro, 5 -00185 Rome, Italy
| | - Oriana Maggi
- Department of Environmental Biology, Sapienza University of Rome, Piazzale A. Moro, 5 -00185 Rome, Italy
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A new in vitro method to detect growth and ochratoxin A-producing ability of multiple fungal species commonly found in food commodities. Food Microbiol 2014; 44:243-8. [DOI: 10.1016/j.fm.2014.06.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 05/21/2014] [Accepted: 06/16/2014] [Indexed: 11/21/2022]
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Davolos D, Pietrangeli B. A molecular and bioinformatic study on the ochratoxin A (OTA)-producing Aspergillus affinis (section Circumdati). Mycotoxin Res 2014; 30:113-22. [PMID: 24668272 DOI: 10.1007/s12550-014-0195-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 03/03/2014] [Accepted: 03/04/2014] [Indexed: 01/01/2023]
Abstract
Aspergillus affinis (section Circumdati) is a novel ochratoxin A (OTA)-producing species found in submerged riparian decomposing leaves. However, very little is known about its role on the breakdown of plant debris and its ability to degrade carbohydrate polymers. Moreover, its OTA biosynthetic pathway has not yet been explored. In the present paper, we investigated the gene encoding the extracellular alpha-amylase (amyAa) of A. affinis within the evolution of the Aspergillus lineages in relation to the possible use of this enzyme in starch processing. The novel amyAa, despite being related to branches of the Aspergillus species of the sections Terrei and Flavi, formed a distinct phylogenetic branch, which may be of outstanding importance from a biotechnological point of view. Moreover, we identified the polyketide synthase gene (pks) putatively required for the first step of OTA biosynthesis in A. affinis. This otapks was examined in relation to a limited number of orthologous genes available from Aspergillus species of the sections Circumdati and Nigri. Our study highlights the importance of otapks as target genes in the treatment of ochratoxigenic Aspergillus species on a more comprehensive evolutionary basis.
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Affiliation(s)
- Domenico Davolos
- INAIL-Research, Certification, Verification Area, Department of Productive Plants and Human Settlements (DIPIA), Via Alessandria, 220/E, 00198, Rome, Italy,
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