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Recently published taxonomy articles (2008-2010)
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Assessing the relatedness of strains isolated from patients and their environment is instrumental in documenting the source of preventable healthcare-associated life-threatening Aspergillus flavus human infection clusters. This study aimed at identifying and selecting suitable microsatellite markers for A. flavus typing. This typing scheme was then applied to investigate A. flavus epidemiology within a haematology unit in Sfax (Tunisia). A combination of five markers made it possible to discern clusters of dependent isolates and to substantiate the genetic diversity of A. flavus within clusters. Isolates from Tunisia and Marseille displayed distinct haplotypes, indicating a highly significant geographical structuring in A. flavus. The typing of clinical and environmental A. flavus isolates in a haematology unit provided insights into its hospital epidemiology. From a heterogeneous genetic background a cluster indicative of a clonal propagation episode within the unit could be identified. In two patients with invasive aspergillosis the same genotype was found in clinical and environmental isolates, indicating hospital-acquired colonization and infection. In further studies, this novel microsatellite typing scheme might be instrumental in illuminating important epidemiological issues about A. flavus population genetics or epidemiology, including tracing sources and routes of transmission.

Aspergillus flavus is one of the most common contaminants that produces aflatoxins in foodstuffs. It is also a human allergen and a pathogen of animals and plants. Aspergillus flavus is included in the Aspergillus section Flavi that comprises 11 closely related species producing different profiles of secondary metabolites. A six-step strategy has been developed that allows identification of nine of the 11 species. First, three real-time PCR reactions allowed us to discriminate four groups within the section: (1) A. flavus/Aspergillus oryzae/Aspergillus minisclerotigenes/Aspergillus parvisclerotigenus; (2) Aspergillus parasiticus/Aspergillus sojae/Aspergillus arachidicola; (3) Aspergillus tamarii/Aspergillus bombycis/Aspergillus pseudotamarii; and (4) Aspergillus nomius. Secondly, random amplification of polymorphic DNA (RAPD) amplifications or SmaI digestion allowed us to differentiate (1) A. flavus, A. oryzae and A. minisclerotigenes; (2) A. parasiticus, A. sojae and A. arachidicola; (3) A. tamarii, A. bombycis and A. pseudotamarii. Among the 11 species, only A. parvisclerotigenus cannot be differentiated from A. flavus. Using the results of real-time PCR, RAPD and SmaI digestion, a decision-making tree was drawn up to identify nine of the 11 species of section Flavi. In contrast to conventional morphological methods, which are often time-consuming, the molecular strategy proposed here is based mainly on real-time PCR, which is rapid and requires minimal handling. (Paper has two PMIDs: 20113354 and 20377644)

Three hundred sixty-six Aspergillus strains preserved at the National Institute of Technology and Evaluation (NITE) were compared as to phylogenetic relationships (11 species-clusters) based on the DNA sequences of the D1/D2 domains of LSU rRNA and ITS regions, including the 5.8S rRNA and biological activities of their secondary metabolites. The results showed relatively well correlation between the phylogenetic distribution and the production of bioactive compounds, especially, antimicrobial activities.

This review summarizes the health aspects of the medically important fungal genus Aspergillus. The morphology and systematics of the genus are explained as well as its biogeography. Major mycotoxins, the aspergilli that produce them, affected crops, and symptoms of the toxicoses are summarized, as are the major mycoses caused by aspergilli. The current status of the relationship between Aspergillus in the indoor environment and health issues are discussed.

The Aspergillus niger aggregate within the A. section Nigri is a group of black-spored aspergilli of great agro-economic importance whose well defined taxonomy has been elusive. Rep-PCR has become a rapid and cost-effective method for genotyping fungi and bacteria. In the present study, we evaluated the discriminatory power of a semi-automated rep-PCR barcoding system to distinguish morphotypic species and compare the results with the data obtained from ITS and partial calmodulin regions. For this purpose, 19 morphotyped black-spored Aspergillus species were used to create the A. section Nigri library in this barcoding system that served to identify 34 field isolates. A pair-wise similarity matrix was calculated using the cone-based Pearson correlation method and the dendrogram was generated by the unweighted pair group method with arithmetic mean (UPGMA), illustrating four different clustered groups: the uniseriate cluster (I), the Aspergillus carbonarius cluster (II), and. the two A. niger aggregate clusters (named III.A and III.B). Rep-PCR showed higher resolution than the ITS and the partial calmodulin gene analytical procedures. The data of the 34 unknown field isolates, collected from different locations in the United States, indicated that only 12% of the field isolates were >95% similar to one of the genotypes included in the A. section Nigri library. However, 64% of the field isolates matched genotypes with the reference library (similarity values >90%). Based on these results, this barcoding procedure has the potential for use as a reproducible tool for identifying the black-spored aspergilli.

A recently developed CSP typing scheme and proposed nomenclature was applied to a collection of 164 clinical and environmental Aspergillus fumigatus isolates from Melbourne, Australia. Fifteen CSP variants were observed overall, including three that were not reported in the original nomenclature that described 19 CSP variants, raising the possibility of phylogeographic differences between the Australian and the previously studied European and North American A. fumigatus populations. However, those CSP variants that were common between this and the previous studies appeared to have a broadly similar prevalence. The presence of an additional CCT codon in the 3' flanking region of some CSP variants was also observed in homologous Neosartorya fischeri sequence, suggesting that the absence of this codon in other isolates is due to codon deletion, rather than its presence representing a duplication. We recommend a number of modifications to the proposed CSP type nomenclature to accommodate these new findings.

Abstract Aims: To characterize and identify a new taxol-producing fungal strain HD86-9 isolated from Taxus cuspidata in China. Methods and Results: Taxol extracted from strain HD86-9 was identified by HPLC and MS analyses. Strain HD86-9 was cultured and its morphology and phenotypes were described. HD86-9 displayed morphology most similar to that of Aspergillus niger but presented differences in the shape and size of the conidia. The growth evaluation showed that the maximal tolerable temperature of the new strain was 43 degrees C, higher than that of the model Aspergillus niger. The 18S rDNA and the internal transcribed spacer region including the 5.8S rDNA of HD86-9 were amplified by PCR; molecular analysis of these sequences revealed their high similarity of 98% to those of Aspergillus niger. Conclusions: The morphology and molecular analysis identified HD86-9 as a new variant of taxol-producing endophytic fungi, and it was named Aspergillus niger var. taxi D.P. Zhou, K. Zhao and W.X. Ping, var. nov. Significance and Impact of the Study: As the first report of a taxol-producing variant of Aspergillus niger species, this study offers important information and a new resource for the production of an important anticancer drug by endofungus fermentation.

Four new species of Emericella, E. discophora, E. filifera, E. olivicola and E. stella-maris, are proposed. Their new taxonomic status was determined applying a polyphasic taxonomic approach using phenotypic (morphology and extrolite profiles) and molecular (sequences of ITS, b-tubulin and calmodulin genes) characters. Ascospores of E. stella-maris and E. olivicola have star-shape equatorial crests, those of E. filifera form long appendages that emerge radially from narrow stellate crests and those of E. discophora produce wide and entire, nonstellate equatorial crests. E. stella-maris originated from leaf litter in Tunisia and E. filifera from raisins in Argentina, and both of them also were found in hypersaline water of a saltern in Slovenia. E. olivicola was isolated from olives in Italy and E. discophora from soil in Spain. All listed species possess distinct extrolite profiles: E. stella-maris produced arugosin E, shamixanthone and the yet unelucidated metabolites glia 1–3; E. filifera produced shamixanthone and varitriols; E. discophora produced sterigmatocystin and versicolorins; E. olivicola produced numerous extrolites such as arugosin E, siderin, shamixanthone, sterigmatocystin, terrein, varitriols and aflatoxin B1, of which the latter was detected only in one of the two strains.

A Luminex-based assay for the rapid identification of Aspergillus species was designed, optimized, and validated with 131 clinical isolates of Aspergillus fumigatus, A. flavus, A. niger, A. terreus, A. ustus, and A. versicolor. The six species-specific probes were directed toward the internal transcribed spacer 1 (ITS-1) region and tested in a multiplex format with results generated within 6 h. Species identifications generated by the Aspergillus Luminex assay were 100% concordant with results from comparative sequence analyses of the ITS-1 region and showed excellent specificity. The Aspergillus Luminex assay is a rapid, relatively simple method that may prove to be a useful diagnostic tool for rapid Aspergillus identification in clinical laboratory settings.

The genus Aspergillus comprises a few hundred species sharing a common asexual spore forming structure, the aspergillum. Approximately one-third of these species also produce a sexual stage, all but five of which are known to be homothallic. Sexual stages associated with Aspergillus fall into approximately ten different genera, reflecting a tremendous degree of phylogenetic and biological diversity. Sexual stages in Aspergillus are plectomycetous, typical for the order in which it resides, the Eurotiales. Theoretically, a homothallic Aspergillus species can produce both asexual conidia and sexual ascospores in both clonal and recombinant fashion, although the actual significance of these potential modes of reproduction is unclear. Aspergillus species with known sexual stages tend to be minor players in infections of humans, perhaps because of their tendency to produce fewer asexual spores compared to their non-teleomorphic congeners. The discovery of population genetic and genomic evidence for sex in species with no known sexual stage indicates that no assumptions can be made about the clonal versus recombinant life histories of a species based on its known mitotic and/or meiotic reproductive modes.

Earlier taxonomy articles

No abstract. Contains original description of Aspergillus alternatus

No abstract. Aspergillus subgriseus description on p210.

Emericella venezuelensis is a new species, differing from two other species with stellate ascospores, E. variecolor and E. pluriseminata, by triangular flaps on the convex sides of the ascospores, and further from E. variecolor by producing an Aspergillus anamorph only on unconventional growth media. The three species also differ in their profiles of extrolites (secondary metabolites). Emericella venezuelensis produces aflatoxin B1, sterigmatocystin, and terrein and compounds with chromophores of the shamixanthone, emerin and desertorin type of compounds. E. variecolor produces asteltoxin, shamixanthone, asperthecin, and terrein, in addition to metabolites unequivocally recorded in the literature or tentatively identified here as astellolide A & B, andibenin A, B, C, andilesin A, B, C, anditomin, astellatol, stellatic acid, stellatin, tajixanthone, radixanthone, najamxanthone, ajamxanthone, variecoxanthone A, B, C, isoemericellin, kojic acid, varitriol, varioxiran, dihydroterrein, 7-hydroxyemodin, avariquinone and stromemycin. E. pluriseminata produces several unknown specific extrolites. E. venezuelensis is the first organism of marine origin reported to produce aflatoxin. Aflatoxin production by E. venezuelensis makes this species an attractive model organism for the study of the regulation of this important type of carcinogenic mycotoxins in combination with the knowledge on sterigmatocystin production by E. nidulans, soon to be whole genome sequenced. The isolates were also analyzed cladistically using partial sequences of the beta-tubulin gene. Since three species of Emericella have stellate ascospores, and the type material of E. variecolor is equivocal, this species is epitypified with CBS 598.65. Emericella species normally do not appear to cause problems for food safety, as they are most often found in litter and soil.

Abstract: The species recognition and identification of aspergilli and their teleomorphs is discussed. A historical overview of the taxonomic concepts starting with the monograph of Raper & Fennell (1965) is given. A list of taxa described since 2000 is provided. Physiological characters, particularly growth rates and the production of extrolites, often show differences that reflect phylogenetic species boundaries and greater emphasis should be placed on extrolite profiles and growth characteristics in species descriptions. Multilocus sequence-based phylogenetic analyses have emerged as the primary tool for inferring phylogenetic species boundaries and relationships within subgenera and sections. A four locus DNA sequence study covering all major lineages in Aspergillus using genealogical concordance theory resulted in a species recognition system that agrees in part with phenotypic studies and reveals the presence of many undescribed species not resolved by phenotype. The use of as much data from as many sources as possible in making taxonomic decisions is advocated. For species identification, DNA barcoding uses a short genetic marker in an organism"s DNA to quickly and easily identify it to a particular species. Partial cytochrome oxidase subunit 1 sequences, which are used for barcoding animal species, were found to have limited value for species identification among black aspergilli. The various possibilities are discussed and at present partial β-tubulin or calmodulin are the most promising loci for Aspergillus identification. For characterising Aspergillus species one application would be to produce a multilocus phylogeny, with the goal of having a firm understanding of the evolutionary relationships among species across the entire genus. DNA chip technologies are discussed as possibilities for an accurate multilocus barcoding tool for the genus Aspergillus.

Understanding the nature of species boundaries is a fundamental question in evolutionary biology. The availability of genomes from several species of the genus Aspergillus allows us for the first time to examine the demarcation of fungal species at the whole-genome level. Here, we examine four case studies, two of which involve intraspecific comparisons, whereas the other two deal with interspecific genomic comparisons between closely related species. These four comparisons reveal significant variation in the nature of species boundaries across Aspergillus. For example, comparisons between A. fumigatus and Neosartorya fischeri (the teleomorph of A. fischerianus) and between A. oryzae and A. flavus suggest that measures of sequence similarity and species-specific genes are significantly higher for the A. fumigatus - N. fischeri pair. Importantly, the values obtained from the comparison between A. oryzae and A. flavus are remarkably similar to those obtained from an intra-specific comparison of A. fumigatus strains, giving support to the proposal that A. oryzae represents a distinct ecotype of A. flavus and not a distinct species. We argue that genomic data can aid Aspergillus taxonomy by serving as a source of novel and unprecedented amounts of comparative data, as a resource for the development of additional diagnostic tools, and finally as a knowledge database about the biological differences between strains and species.

Gene flow within populations can occur by sexual and/or parasexual means. Analyses of experimental and in silico work are presented relevant to possible gene flow within the aspergilli. First, the discovery of mating-type (MAT) genes within certain species of Aspergillus is described. The implications for self-fertility, sexuality in supposedly asexual species and possible uses as phylogenetic markers are discussed. Second, the results of data mining for heterokaryon incompatibility (het) and programmed cell death (PCD) related genes in the genomes of two heterokaryon incompatible isolates of the asexual species Aspergillus niger are reported. Het-genes regulate the formation of anastomoses and heterokaryons, may protect resources and prevent the spread of infectious genetic elements. Depending on the het locus involved, hetero-allelism is not tolerated and fusion of genetically different individuals leads to growth inhibition or cell death. The high natural level of heterokaryon incompatibility in A. niger blocks parasexual analysis of the het-genes involved, but in silico experiments in the sequenced genomes allow us to identify putative het-genes. Homologous sequences to known het- and PCD-genes were compared between different sexual and asexual species including different Aspergillus species, Sordariales and the yeast Saccharomyces cerevisiae. Both het- and PCD-genes were well conserved in A. niger. However some point mutations and other small differences between the het-genes in the two A. niger isolates examined may hint to functions in heterokaryon incompatibility reactions.

Species in the genus Aspergillus have been classified primarily based on morphological features. Sequencing of house-hold genes has also been used in Aspergillus taxonomy and phylogeny, while extrolites and physiological features have been used less frequently. Three independent ways of classifying and identifying aspergilli appear to be applicable: Morphology combined with physiology and nutritional features, secondary metabolite profiling and DNA sequencing. These three ways of identifying Aspergillus species often point to the same species. This consensus approach can be used initially, but if consensus is achieved it is recommended to combine at least two of these independent ways of characterising aspergilli in a polyphasic taxonomy. The chemical combination of secondary metabolites and DNA sequence features has not been explored in taxonomy yet, however. Examples of these different taxonomic approaches will be given for Aspergillus section Nigri.

Multiple recent studies have demonstrated the limited utility of morphological methods used singly for species identification of clinically relevant aspergilli. It is being increasingly recognised that comparative sequence based methods used in conjunction with traditional phenotype based methods can offer better resolution of species within this genus. Recognising the growing role of molecular methods in species recognition, the recently convened international working group meeting entitled "Aspergillus Systematics in the Genomic Era" has proposed several recommendations that will be useful in such endeavors. Specific recommendations of this working group include the use of the ITS regions for inter section level identification and the beta-tubulin locus for identification of individual species within the various Aspergillus sections.

Multiple reasons may justify a need for strain typing purposes, but the most common reason is to delineate the epidemiological relationships between isolates. The availability of whole genome sequences has greatly influenced our ability to develop highly targeted and efficient strain typing methods fur these purposes. Some strain typing methods may serve dual goals: not only can they be used to discriminate between multiple isolates of a certain species, they can also aid in the recognition, identification, description and validation process of a fungal species.

The genus Aspergillus is one of the most important filamentous fungal genera. Aspergillus species are used in the fermentation industry, but they are also responsible of various plant and food secondary rot, with the consequence of possible accumulation of mycotoxins. The aflatoxin producing A. flavus and A. parasiticus, and ochratoxinogenic A. niger, A. ochraceus and A. carbonarius species are frequently encountered in agricultural products. Studies on the biodiversity of toxigenic Aspergillus species is useful to clarify molecular, ecological and biochemical characteristics of the different species in relation to their different adaptation to environmental and geographical conditions, and to their potential toxigenicity. Here we analyzed the biodiversity of ochratoxin producing species occurring on two important crops: grapes and coffee, and the genetic diversity of A. flavus populations occurring in agricultural fields. Altogether nine different black Aspergillus species can be found on grapes which are often difficult to identify with classical methods. The polyphasic approach used in our studies led to the identification of three new species occurring on grapes: A. brasiliensis, A. ibericus, and A. uvarum. Similar studies on the Aspergillus species occurring on coffee beans have evidenced in the last five years that A. carbonarius is an important source of ochratoxin A in coffee. Four new species within the black aspergilli were also identified in coffee beans: A. sclerotioniger, A. lacticoffeatus, A. sclerotiicarbonarius, and A. aculeatinus. The genetic diversity within A. flavus populations has been widely studied in relation to their potential aflatoxigenicity and morphological variants L- and S-strains. Within A. flavus and other Aspergillus species capable of aflatoxin production, considerable diversity is found. We summarise the main recent achievements in the diversity of the aflatoxin gene cluster in A. flavus populations, A. parasiticus and the non-toxigenic A. oryzae. Studies are needed in order to characterise the aflatoxin biosynthetic genes in the new related taxa A. minisclerotigenes and A. arachidicola.

(N.B. The Aspergillus website used to maintain a bibliographic database which was compiled from Medline and Web of Science (GRAsp), but as all users now have access to the former free of charge via the NCBI website and most will have access to Web of Science via their own libraries this resource is currently not being updated. It contains papers dating up to 7th October 2002. Search the GRASp Database here.)