Reducing the number of accepted species inAspergillusseriesNigri

Abstract

The Aspergillus series Nigri contains biotechnologically and medically important species. They can produce hazardous mycotoxins, which is relevant due to the frequent occurrence of these species on foodstuffs and in the indoor environment. The taxonomy of the series has undergone numerous rearrangements, and currently, there are 14 species accepted in the series, most of which are considered cryptic. Species-level identifications are, however, problematic or impossible for many isolates even when using DNA sequencing or MALDI-TOF mass spectrometry, indicating a possible problem in the definition of species limits or the presence of undescribed species diversity. To re-examine the species boundaries, we collected DNA sequences from three phylogenetic markers (benA, CaM and RPB2) for 276 strains from series Nigri and generated 18 new whole-genome sequences. With the three-gene dataset, we employed phylogenetic methods based on the multispecies coalescence model, including four single-locus methods (GMYC, bGMYC, PTP and bPTP) and one multilocus method (STACEY). From a total of 15 methods and their various settings, 11 supported the recognition of only three species corresponding to the three main phylogenetic lineages: A. niger, A. tubingensis and A. brasiliensis. Similarly, recognition of these three species was supported by the GCPSR approach (Genealogical Concordance Phylogenetic Species Recognition) and analysis in DELINEATE software. We also showed that the phylogeny based on benA, CaM and RPB2 is suboptimal and displays significant differences from a phylogeny constructed using 5 752 single-copy orthologous proteins; therefore, the results of the delimitation methods may be subject to a higher than usual level of uncertainty. To overcome this, we randomly selected 200 genes from these genomes and performed ten independent STACEY analyses, each with 20 genes. All analyses supported the recognition of only one species in the A. niger and A. brasiliensis lineages, while one to four species were inconsistently delimited in the A. tubingensis lineage. After considering all of these results and their practical implications, we propose that the revised series Nigri includes six species: A. brasiliensis, A. eucalypticola, A. luchuensis (syn. A. piperis), A. niger (syn. A. vinaceus and A. welwitschiae), A. tubingensis (syn. A. chiangmaiensis, A. costaricensis, A. neoniger and A. pseudopiperis) and A. vadensis. We also showed that the intraspecific genetic variability in the redefined A. niger and A. tubingensis does not deviate from that commonly found in other aspergilli. We supplemented the study with a list of accepted species, synonyms and unresolved names, some of which may threaten the stability of the current taxonomy.

Combined Toxicity of the Most Common Indoor Aspergilli

“…In the latest changes in taxonomy, A. welwitschiae is synonymized with A. niger and A. luchuensis with A. piperis [ 25 ]. In our previous research, we demonstrated a significant difference in the observed cytotoxic and genotoxic potency of the extracts of A. luchuensis , A. piperis , A. welwitschiae and A. niger [ 37 ].…”

“…The infrageneric classification of the genus Aspergillus is difficult and complex and thus different approaches were suggested over time, especially through the development of sophisticated molecular and bioinformatic tools [ 21 , 22 , 23 ]. Brand new changes in species recognition and delimitations were introduced in the series Versicolores [ 24 ] and series Nigri [ 25 ] by the application of multispecies coalescence model-based methods, a novel phylogenetic approach. This resulted in A. versicolor , A. creber , A. sydowii and A. subversicolor as the only four species retaining validity in the series Versicolores [ 24 ] and A. brasiliensis , A. eucalypticola , A. luchuensis , A. niger , A. tubingensis and A. vadensis in the series Nigri [ 25 ].…”

“…Brand new changes in species recognition and delimitations were introduced in the series Versicolores [ 24 ] and series Nigri [ 25 ] by the application of multispecies coalescence model-based methods, a novel phylogenetic approach. This resulted in A. versicolor , A. creber , A. sydowii and A. subversicolor as the only four species retaining validity in the series Versicolores [ 24 ] and A. brasiliensis , A. eucalypticola , A. luchuensis , A. niger , A. tubingensis and A. vadensis in the series Nigri [ 25 ]. However, besides their morphological properties and genetic variability, secondary metabolites are particularly useful in the classification and identification of fungi [ 26 ], as the chemoconsistency in the profiles of exometabolites among different isolates of a species was demonstrated [ 27 , 28 ].…”

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

“…Similar comparison, published recently for 37 species across genus Aspergillus showed that intraspecific dissimilarites in the common taxonomic markers often reached up to 4%. 55 , 56 Although these species have a different ecology, it turns out that the intraspecific variability in species that have a cryptic or unknown sexual cycle is greater than previously thought.…”

A monograph of Aspergillus section Candidi

“…In general, the studies of intraspecific variability in Aspergillus are relatively rare and limited to a few extensively studied species or species complexes ( Peronne et al 2006 , Drott et al 2021 , Lofgren et al 2021 , Bian et al . 2022 , Sklenář et al .…”