Aspergillus series Versicolores members occur in a wide range of environments and substrates such as indoor environments, food, clinical materials, soil, caves, marine or hypersaline ecosystems. The taxonomy of the series has undergone numerous re-arrangements including a drastic reduction in the number of species and subsequent recovery to 17 species in the last decade. The identification to species level is however problematic or impossible in some isolates even using DNA sequencing or MALDI-TOF mass spectrometry indicating a problem in the definition of species boundaries. To revise the species limits, we assembled a large dataset of 518 strains. From these, a total of 213 strains were selected for the final analysis according to their calmodulin (CaM) genotype, substrate and geography. This set was used for phylogenetic analysis based on five loci (benA, CaM, RPB2, Mcm7, Tsr1). Apart from the classical phylogenetic methods, we used multispecies coalescence (MSC) model-based methods, including one multilocus method (STACEY) and five single-locus methods (GMYC, bGMYC, PTP, bPTP, ABGD). Almost all species delimitation methods suggested a broad species concept with only four species consistently supported. We also demonstrated that the currently applied concept of species is not sustainable as there are incongruences between single-gene phylogenies resulting in different species identifications when using different gene regions. Morphological and physiological data showed overall lack of good, taxonomically informative characters, which could be used for identification of such a large number of existing species. The characters expressed either low variability across species or significant intraspecific variability exceeding interspecific variability. Based on the above-mentioned results, we reduce series Versicolores to four species, namely A. versicolor, A. creber, A. sydowii and A. subversicolor, and the remaining species are synonymized with either A. versicolor or A. creber. The revised descriptions of the four accepted species are provided. They can all be identified by any of the five genes used in this study. Despite the large reduction in species number, identification based on phenotypic characters remains challenging, because the variation in phenotypic characters is high and overlapping among species, especially between A. versicolor and A. creber. Similar to the 17 narrowly defined species, the four broadly defined species do not have a specific ecology and are distributed worldwide. We expect that the application of comparable methodology with extensive sampling could lead to a similar reduction in the number of cryptic species in other extensively studied Aspergillus species complexes and other fungal genera. Citation: Sklenář F, Glässnerová K, Jurjević Ž, Houbraken J, Samson RA, Visagie CM, Yilmaz N, Gené J, Cano J, Chen AJ, Nováková A, Yaguchi T, Kolařík M, Hubka V (2022). Taxonomy of Aspergillus series Versicolores: species reduction and lessons learned about intraspecific variability. Studies in Mycology 102 : 53-93. doi: 10.3114/sim.2022.102.02.

Department of Biochemistry Genetics and Microbiology Forestry and Agricultural Biotechnology Institute University of Pretoria Pretoria South Africa

Department of Botany Faculty of Science Charles University Prague Czech Republic

EMSL Analytical Cinnaminson New Jersey USA

Laboratory of Fungal Genetics and Metabolism Institute of Microbiology Czech Academy of Sciences Prague Czech Republic

Medical Mycology Research Center Chiba University Chuo ku Chiba Japan

Microbiome Research Center Moon Biotech Ltd Guangzhou China

Unitat de Micologia Facultat de Medicina i Ciències de la Salut IISPV Universitat Rovira i Virgili Reus Spain

Westerdijk Fungal Biodiversity Institute Utrecht The Netherlands

Zobrazit více v PubMed

Ahlmann-Eltze C, Patil I. (2021). ggsignif: R Package for Displaying Significance Brackets for’ggplot2’. PsyArxiv doi: 10.31234/osf.io/7awm6.

Ahrens D, Fujisawa T, Krammer HJ, et al. (2016). Rarity and incomplete sampling in DNA-based species delimitation. Systematic Biology 65: 478–494. PubMed

Beck M. (2017). ggord: Ordination Plots with ggplot2. R package version 1: 588.

Boluda C, Rico V, Divakar P, et al. (2019). Evaluating methodologies for species delimitation: the mismatch between phenotypes and genotypes in lichenized fungi (Bryoria sect. Implexae, Parmeliaceae). Persoonia 42: 75–100. PubMed PMC

Bongomin F, Moore CB, Masania R, et al. (2018). Sequence analysis of isolates of Aspergillus from patients with chronic and allergic aspergillosis reveals a spectrum of cryptic species. Future Microbiology 13: 1557–1563. PubMed

Borgohain P, Barua P, Dutta PJ, et al. (2019). Onychomycosis associated with superficial skin infection due to Aspergillus sydowii in an immunocompromised patient. Mycopathologia 184: 683–689. PubMed

Bouckaert R, Heled J. (2014). DensiTree 2: seeing trees through the forest. bioRxiv doi: 10.1101/012401.

Bouckaert R, Vaughan TG, Barido-Sottani J, et al. (2019). BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Computational Biology 15: e1006650. PubMed PMC

Burbrink FT, Ruane S. (2021). Contemporary philosophy and methods for studying speciation and delimiting species. Ichthyology & Herpetology 109: 874–894.

Chambers EA, Hillis DM. (2020). The multispecies coalescent over-splits species in the case of geographically widespread taxa. Systematic Biology 69: 184–193. PubMed

Cicero C, Mason NA, Jiménez RA, et al. (2021). Integrative taxonomy and geographic sampling underlie successful species delimitation. Ornithology 138: ukab009.

Danagoudar A, Pratap G, Shantaram M, et al. (2021). Antioxidant, cytotoxic and anti-choline esterase activity of green silver nanoparticles synthesized using Aspergillus austroafricanus CGJ-B3 (endophytic fungus). Analytical Chemistry Letters 11: 15–28.

De Vries RP, Riley R, Wiebenga A, et al. (2017). Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biology 18: 1–45. PubMed PMC

Dobolyi C, Inotai K, Bata-Vidács I, et al. (2021). Isolation and detailed characterisation of the first sterigmatocystin hyperproducer mould strain in Hungary. Acta Alimentaria 50: 247–258.

Domsch KH, Gams W, Anderson T-H. (2007). Compendium of soil fungi. 2nd ed. edition. IHW-Verlag, Eching.

Drummond AJ, Xie W, Heled J. (2012). Bayesian inference of species trees from multilocus data using *BEAST. Molecular Biology and Evolution 29: 1969–1973. PubMed PMC

Feng XY, Wang XH, Chiang YC, et al. (2021). Species delimitation with distinct methods based on molecular data to elucidate species boundaries in the Cycas taiwaniana complex (Cycadaceae). Taxon 70: 477–491.

Fujisawa T, Barraclough TG. (2013). Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent (GMYC) approach: a revised method and evaluation on simulated datasets. Systematic Biology 62: 707–724. PubMed PMC

Gams W, Christensen M, Onions AHS, et al. (1985). Infrageneric taxa of Aspergillus. In: Advances in Penicillium and Aspergillus Systematics. (Samson R.A., Pitt J.I., eds). Plenum Press, New York: 55–62.

Géry A, Lepetit C, Heutte N, et al. (2022). Cellular cytotoxicity and oxidative potential of recurrent molds of the genus Aspergillus series Versicolores. Microorganisms 10: 228. PubMed PMC

Géry A, Rioult J-P, Heutte N, et al. (2021). First characterization and description of Aspergillus series Versicolores in French bioaerosols. Journal of Fungi 7: 676. PubMed PMC

Glass NL, Donaldson GC. (1995). Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous ascomycetes. Applied and Environmental Microbiology 61: 1323–1330. PubMed PMC

González-Abradelo D, Pérez-Llano Y, Peidro-Guzmán H, et al. (2019). First demonstration that ascomycetous halophilic fungi (Aspergillus sydowii and Aspergillus destruens) are useful in xenobiotic mycoremediation under high salinity conditions. Bioresource Technology 279: 287–296. PubMed

Hall TA. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95–98.

Hong S-B, Cho H-S, Shin H-D, et al. (2006). Novel Neosartorya species isolated from soil in Korea. International Journal of Systematic and Evolutionary Microbiology 56: 477–486. PubMed

Houbraken J, Kocsubé S, Visagie CM, et al. (2020). Classification of Aspergillus, Penicillium, Talaromyces and related genera (Eurotiales): An overview of families, genera, subgenera, sections, series and species. Studies in Mycology 95: 5–169. PubMed PMC

Huang C, Feng Y, Patel G, et al. (2021). Production, immobilization and characterization of beta-glucosidase for application in cellulose degradation from a novel Aspergillus versicolor. International Journal of Biological Macromolecules 177: 437–446. PubMed

Hubka V, Barrs V, Dudová Z, et al. (2018). Unravelling species boundaries in the Aspergillus viridinutans complex (section Fumigati): opportunistic human and animal pathogens capable of interspecific hybridization. Persoonia 41: 142–174. PubMed PMC

Hubka V, Nováková A, Peterson SW, et al. (2016). A reappraisal of Aspergillus section Nidulantes with descriptions of two new sterigmatocystin-producing species. Plant Systematics and Evolution 302: 1267–1299.

Imbert S, Normand AC, Gabriel F, et al. (2019). Multi-centric evaluation of the online MSI platform for the identification of cryptic and rare species of Aspergillus by MALDI-TOF. Medical Mycology 57: 962–968. PubMed

Jakšić Despot D, Kocsubé S, Bencsik O, et al. (2017). New sterigmatocystin-producing species of Aspergillus section Versicolores from indoor air in Croatia. Mycological Progress 16: 63–72.

Janda-Ulfig K, Ulfig K, Markowska A. (2009). Extracellular enzyme profiles of xerophilic fungi isolated from dried materials of medicinal plants. Polish Journal of Environmental Studies 18: 391–397.

Jia J, Chen M, Mo X, et al. (2019). The first case report of kerion-type scalp mycosis caused by Aspergillus protuberus. BMC Infectious Diseases 19: 1–5. PubMed PMC

Jones G. (2017). Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent. Journal of Mathematical Biology 74: 447–467. PubMed

Jones G, Aydin Z, Oxelman B. (2015). DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent. Bioinformatics 31: 991–998. PubMed

Jurjević Ž, Kubátová A, Kolařík M, et al. (2015). Taxonomy of Aspergillus section Petersonii sect. nov. encompassing indoor and soil-borne species with predominant tropical distribution. Plant Systematics and Evolution 301: 2441–2462.

Jurjević Ž, Peterson SW, Horn BW. (2012). Aspergillus section Versicolores: nine new species and multilocus DNA sequence based phylogeny. IMA Fungus 3: 59–79. PubMed PMC

Jurjević Ž, Peterson SW, Solfrizzo M, et al. (2013). Sterigmatocystin production by nine newly described Aspergillus species in section Versicolores grown on two different media. Mycotoxin Research 29: 141–145. PubMed

Kato H, Nakahara T, Sugimoto K, et al. (2015). Isolation of notoamide S and enantiomeric 6-epi-stephacidin A from the fungus Aspergillus amoenus: biogenetic implications. Organic letters 17: 700–703. PubMed PMC

Katoh K, Standley DM. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30: 772–780. PubMed PMC

Kekkonen M, Hebert PD. (2014). DNA barcode-based delineation of putative species: efficient start for taxonomic workflows. Molecular Ecology Resources 14: 706–715. PubMed PMC

Klich M. (1993). Morphological studies of Aspergillus section Versicolores and related species. Mycologia 85: 100–107.

Klich M, Mullaney E, Daly C. (1993). Analysis of intraspecific and interspecific variability of three common species in Aspergillus section Versicolores using DNA restriction fragment length polymorphisms. Mycologia 85: 852–855.

Kozakiewicz Z. (1989). Aspergillus species on stored products. Mycological Papers 161: 1–188.

Kubatko LS, Degnan JH. (2007). Inconsistency of phylogenetic estimates from concatenated data under coalescence. Systematic Biology 56: 17–24. PubMed

Letunic I, Bork P. (2016). Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Research 44: W242–W245. PubMed PMC

Li YC, Wen J, Ren Y, et al. (2019). From seven to three: Integrative species delimitation supports major reduction in species number in Rhodiola section Trifida (Crassulaceae) on the Qinghai-Tibetan Plateau. Taxon 68: 268–279.

Li Z-X, Wang X-F, Ren G-W, et al. (2018). Prenylated diphenyl ethers from the marine algal-derived endophytic fungus Aspergillus tennesseensis. Molecules 23: 2368. PubMed PMC

Liu YJ, Whelen S, Hall BD. (1999). Phylogenetic relationships among ascomycetes: evidence from an RNA polymerse II subunit. Molecular Biology and Evolution 16: 1799–1808. PubMed

Magoga G, Fontaneto D, Montagna M. (2021). Factors affecting the efficiency of molecular species delimitation in a species-rich insect family. Molecular Ecology Resources 21: 1475–1489. PubMed

Mason NA, Fletcher NK, Gill BA, et al. (2020). Coalescent-based species delimitation is sensitive to geographic sampling and isolation by distance. Systematics and Biodiversity 18: 269–280.

Micheluz A, Manente S, Tigini V, et al. (2015). The extreme environment of a library: Xerophilic fungi inhabiting indoor niches. International Biodeterioration & Biodegradation 99: 1–7.

Minh BQ, Schmidt HA, Chernomor O, et al. (2020). IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Molecular Biology and Evolution 37: 1530–1534. PubMed PMC

Nguyen HT, Nguyen TD, Le TML, et al. (2021). Integrative taxonomy of Mesocriconema onoense (Tylenchida: Criconematidae) from Vietnam highly suggests the synonymization of Mesocriconema brevistylus and related species. Infection, Genetics and Evolution 95: 105090. PubMed

Nováková A, Hubka V, Saiz-Jimenez C, et al. (2012). Aspergillus baeticus sp. nov. and Aspergillus thesauricus sp. nov., two species in section Usti from Spanish caves. International Journal of Systematic and Evolutionary Microbiology 62: 2778–2785. PubMed

Nováková A, Hubka V, Valinová Š, et al. (2018). Cultivable microscopic fungi from an underground chemosynthesis-based ecosystem: a preliminary study. Folia Microbiologica 63: 43–55. PubMed

O’Donnell K, Cigelnik E. (1997). Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous. Molecular Phylogenetics and Evolution 7: 103–116. PubMed

Pante E, Puillandre N, Viricel A, et al. (2015). Species are hypotheses: avoid connectivity assessments based on pillars of sand. Molecular Ecology 24: 525–544. PubMed

Paradis E. (2010). pegas: an R package for population genetics with an integrated-modular approach. Bioinformatics 26: 419–420. PubMed

Parker E, Dornburg A, Struthers CD, et al. (2022). Phylogenomic species delimitation dramatically reduces species diversity in an Antarctic adaptive radiation. Systematic Biology 71: 58–77. PubMed

Peterson SW. (2008). Phylogenetic analysis of Aspergillus species using DNA sequences from four loci. Mycologia 100: 205–226. PubMed

Pitt JI, Hocking AD. (2009). Fungi and food spoilage. Springer, Dordrecht, Heidelberg, London, New York.

Posada D. (2008). jModelTest: phylogenetic model averaging. Molecular Biology and Evolution 25: 1253–1256. PubMed

Puillandre N, Lambert A, Brouillet S, et al. (2012). ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Molecular Ecology 21: 1864–1877. PubMed

R Core Team (2015). R: A language and environment for statistical computing. R Foundation for Statistical Computing. Vienna, Austria. R Foundation for Statistical Computing, Vienna, Austria.

Rank C, Nielsen KF, Larsen TO, et al. (2011). Distribution of sterigmatocystin in filamentous fungi. Fungal Biology 115: 406–420. PubMed

Raper KB, Fennell DI. (1965). The genus Aspergillus. Williams & Wilkins, Baltimore, MD.

Reid NM, Carstens BC. (2012). Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model. BMC Evolutionary Biology 12: 196. PubMed PMC

Sakhri A, Chaouche NK, Catania MR, et al. (2019). Chemical composition of Aspergillus creber extract and evaluation of its antimicrobial and antioxidant activities. Polish Journal of Microbiology 68: 309. PubMed PMC

Samson RA, Visagie CM, Houbraken J, et al. (2014). Phylogeny, identification and nomenclature of the genus Aspergillus. Studies in Mycology 78: 141–173. PubMed PMC

Seo T-K. (2008). Calculating bootstrap probabilities of phylogeny using multilocus sequence data. Molecular Biology and Evolution 25: 960–971. PubMed

Shao J, Wang Q, Wei L, et al. (2022). Limitations of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the identification of Aspergillus species. Medical Mycology 60: myab084. PubMed

Shehata AN, Abd El Aty AA, Darwish DA, et al. (2018). Purification, physicochemical and thermodynamic studies of antifungal chitinase with production of bioactive chitosan-oligosaccharide from newly isolated Aspergillus griseoaurantiacus KX010988. International Journal of Biological Macromolecules 107: 990–999. PubMed

Schmitt I, Crespo A, Divakar P, et al. (2009). New primers for promising single-copy genes in fungal phylogenetics and systematics. Persoonia 23: 35–40. PubMed PMC

Schwab CJ, Straus DC. (2004). The roles of Penicillium and Aspergillus in sick building syndrome. Advances in Applied Microbiology 55: 215–238. PubMed

Siqueira JPZ, Sutton DA, García D, et al. (2016). Species diversity of Aspergillus section Versicolores in clinical samples and antifungal susceptibility. Fungal Biology 120: 1458–1467. PubMed

Sklenář F, Jurjević Ž, Houbraken J, et al. (2021). Re-examination of species limits in Aspergillus section Flavipedes using advanced species delimitation methods and description of four new species. Studies in Mycology 99: 100120. PubMed PMC

Sklenář F, Jurjević Ž, Peterson SW, et al. (2020). Increasing the species diversity in the Aspergillus section Nidulantes: Six novel species mainly from the indoor environment. Mycologia 112: 342–370. PubMed

Sklenář F, Jurjević Ž, Zalar P, et al. (2017). Phylogeny of xerophilic aspergilli (subgenus Aspergillus) and taxonomic revision of section Restricti. Studies in Mycology 88: 161–236. PubMed PMC

Struck TH, Feder JL, Bendiksby M, et al. (2018). Finding evolutionary processes hidden in cryptic species. Trends in Ecology & Evolution 33: 153–163. PubMed

Sukumaran J, Holder MT, Knowles LL. (2021). Incorporating the speciation process into species delimitation. PLoS Computational Biology 17: e1008924. PubMed PMC

Sukumaran J, Knowles LL. (2017). Multispecies coalescent delimits structure, not species. Proceedings of the National Academy of Sciences of the United States of America 114: 1607–1611. PubMed PMC

Swain SK, Debta P, Sahu MC, et al. (2020). Otomycosis due to Aspergillus versicolor. International Journal of Health & Allied Sciences 9: 192.

Thom C, Church MB. (1926). The Aspergilli. Williams & Wilkins, Baltimore, MD.

Thom C, Raper KB. (1945). A manual of the Aspergilli. Williams & Wilkins, Maryland, MD.

Tsang C-C, Hui TWS, Lee K-C, et al. (2016). Genetic diversity of Aspergillus species isolated from onychomycosis and Aspergillus hongkongensis sp. nov., with implications to antifungal susceptibility testing. Diagnostic Microbiology and Infectious Disease 84: 125–134. PubMed

Turland NJ, Wiersema JH, Barrie FR, et al. (2018). International Code of Nomenclature for algae, fungi, and plants (Shenzhen Code) adopted by the Nineteenth International Botanical Congress Shenzhen, China, July 2017. Koeltz Botanical Books, Glashütten.

van Rossum G, Drake FL. (2019). Python language reference, version 3. Python Software Foundation.

Venables WN, Ripley BD. (2002). Modern applied statistics with S. Fourth edition. Springer, New York.

Veršilovskis A, De Saeger S. (2010). Sterigmatocystin: occurrence in foodstuffs and analytical methods–an overview. Molecular Nutrition & Food Research 54: 136–147. PubMed

Vidal-Acuña MR, Ruiz-Pérez de Pipaón M, Torres-Sánchez MJ, et al. (2018). Identification of clinical isolates of Aspergillus, including cryptic species, by matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Medical Mycology 56: 838–846. PubMed

Visagie CM, Hirooka Y, Tanney JB, et al. (2014). Aspergillus, Penicillium and Talaromyces isolated from house dust samples collected around the world. Studies in Mycology 78: 63–139. PubMed PMC

Wang PM, Liu XB, Dai YC, et al. (2018). Phylogeny and species delimitation of Flammulina: taxonomic status of winter mushroom in East Asia and a new European species identified using an integrated approach. Mycological Progress 17: 1013–1030.

Wang X-C, Zhuang WY. (2022). New species of Aspergillus (Aspergillaceae) from tropical islands of China. Journal of Fungi 8: 225. PubMed PMC

Wickham H. (2016). ggplot2: elegant graphics for data analysis. Springer-Verlag, New York.

Yang Z. (2015). The BPP program for species tree estimation and species delimitation. Current Zoology 61: 854–865.

Zahradnik E, Kespohl S, Sander I, et al. (2013). A new immunoassay to quantify fungal antigens from the indoor mould Aspergillus versicolor. Environmental Science: Processes & Impacts 15: 1162–1171. PubMed

Zhang J, Kapli P, Pavlidis P, et al. (2013). A general species delimitation method with applications to phylogenetic placements. Bioinformatics 29: 2869–2876. PubMed PMC

A Second Fungal Outbreak in Castañar Cave, Spain, Discloses the Fragility of Subsurface Ecosystems

A review of recently introduced Aspergillus, Penicillium, Talaromyces and other Eurotiales species

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

Defining the relationship between phylogeny, clinical manifestation, and phenotype for Trichophyton mentagrophytes/interdigitale complex; a literature review and taxonomic recommendations

A monograph of Aspergillus section Candidi

Reducing the number of accepted species in Aspergillus series Nigri

Consolidation of Chloridium: new classification into eight sections with 37 species and reinstatement of the genera Gongromeriza and Psilobotrys

Zobrazit více v PubMed

Dryad
10.5061/dryad.63xsj3v5q