The genus
Aspergillus poses taxonomic problems for identification, nomenclature, and classification.
Suggested reading: Aspergillus: Molecular Biology and GenomicsIdentification and intrageneric categories
The defining characteristic of the genus
Aspergillus is the aspergillum-like spore-bearing structure. It is the most important microscopic character used in
Aspergillus taxonomy. During mycelial differentiation certain cells enlarge, develop a heavy cell wall and form 'T' or 'L' shaped 'foot cells' (which are not separate cells) that produce a single conidiophore perpendicular to the long axis of the cell. Sometimes it is difficult to see the foot 'cell,' but when visible, morphologists take it as strong evidence that an isolate is an
Aspergillus species. The erect hyphal branch developing from the foot cell is the conidiophore, which enlarges at its apex to form a rounded, elliptical or club shaped vesicle. The fertile area of the vesicle gives rise to a layer of cells called phialides (or steigmata in the older literature) that produce long chains of mitotic spores called conidia or conidiospores. The size and arrangement of the conidial heads as well as the colour of the spores they bear are important identifying characteristics. For example, species in the
A. niger group bear black spores, the
A. ochraceus group is yellow to brown, while
A. fumigatus,
A. nidulans, and
A. flavus are green.
The major cultural features used in species identification are the colour of the colony, the growth rate and thermotolerance. Aspergilli have varying morphological and growth response to different nutrients so it is important to standardize conditions. Species identification depends upon pure cultures grown on known media. The early taxonomic micrographs used a defined medium often called 'Czapek-Dox medium' which contains sucrose as the carbon source and nitrate as the nitrogen source. Strain variation is quite extensive within species and a variety of subtle effects such as air exchange, light and volume of the medium can affect morphology. Contemporary taxonomists usually grow strains on several media, at several temperatures, to identify species.
In addition to the conidiophore, other morphological structures useful for identification include cleistothecia, Hülle cells and sclerotia. Both cleistothecia and sclerotia are closed and usually round structures about the size of a poppy seed that may be so abundant as to dominate a colony. Cleistothecia are the sexual reproductive stage and contain the meiotic ascospores borne within asci. In some of the early monographs cleistothecia are called perithecia; this latter term is now limited to ascus-bearing bodies that are open at one end such as those produced by
Neurospora crassa. Hülle cells are thickened, often globose, cells that are associated with cleistothecia. Sclerotia are rounded masses of mycelium with an outer melanized rind that macroscopically resemble cleistothecia but do not contain sexual spores. They are believed to serve as resting structures that allow species to survive adverse growth conditions. Finally, some taxonomists supplement these major characters with biochemical characteristics such as secondary metabolite production or ultramicroscopic traits such as spore ornamentation.
During the 20th century, as mycologists isolated and identified increasing numbers of isolates, the number of named species of
Aspergillus increased. These tended to fall into morphologically distinct clusters so in order to facilitate identification the genus was divided into intrageneric 'groups'. For example, the
Aspergillus glaucus group was characterized by abundant, typically green conidial heads, with perithecia (
sic) generally present while the
Aspergillus ochraceous group had yellow conidia and abundant cream to purplish-coloured sclerotia. Unfortunately, the term 'group' does not have nomenclatural status within the formal rules of biological nomenclature. The genus was reorganized into a new subgeneric taxonomic hierarchy based on 'sections.' In this system, the subgenus '
Aspergillus' consists of xerophilic species.
A. glaucus is the type species, classified in the subgenus
Aspergillus and the section
Aspergillus. A new subgenus was introduced called Circumdata that encompassed seven sections, in which 'section circumdati' was the new rubric for the old '
A. ochraceous group'. The attempted imposition of subgeneric epithets, only one of which is called '
Aspergillus' is extremely confusing and has not caught on. On the other hand, most taxonomists now use the term 'section' rather than 'group' for
Aspergillus intrageneric classifications and identifications.
Nomenclature
Moulds that produce a characteristic asexual spore head that looks like an aspergillum are placed together in the genus
Aspergillus. There are approximately 250 named species of
Aspergillus. This number is likely to increase significantly in the near future because of increasing application of the phylogenetic species concept based on DNA sequence data rather than on visible morphological characters. Many
Aspergillus species and strains have industrial importance, so the delineation of species in this genus is frequently a matter of contention in the patent world. The widespread acceptance of 'phylogenetic species' undoubtedly will have future legal ramifications.
In 1854, early in the scientific history of this genus, deBary became the first person to notice that an
Aspergillus mycelium could produce a cleistothecium as well as an aspergillum. DeBary's observation was significant because the cleistothecium-producing mould had been observed before and given its own name:
Eurotium herborarium. When DeBary realized that
A. glaucum and
E. herborarium were different reproductive phases of the same organism, it was an important milestone in mycology and also the beginning of a nomenclatural predicament that persists until this day. Since deBary's original observation, many other fungal species both within and without the genus
Aspergillus have been named on the basis of their asexual stage and then 'connected' ('linked') to a sexual stage with a different genus and species name. Which name should be used? Early taxonomists concluded that both names were valid and instituted a system of dual naming.
With the exception of fossils, fungi are the only organisms that depart from one of the basic rules of biological nomenclature, i.e. that each taxonomic group can bear only one correct name. Since 1905, the Botanical Code (which governs the naming of plants and fungi) has allowed two different names to be applied to the same organism, depending on whether it is viewed in its sexual or asexual stage. Under this system of taxonomic governance, Article 59 permits dual nomenclature. When a sexual phase is known, the name for this phase takes precedence. According to these rules,
Aspergillus nidulans, the well known genetic model, should be called
Emericella nidulans. Indeed, it is indexed as such within GenBank. However, most popular and professional usage continues to call it
Aspergillus. A Google search under the entry '
Aspergillus nidulans' yielded 725,000 hits while '
Emericella nidulans' gave fewer than 60,000, a difference of more than an order of magnitude.
Some
Aspergillus species regularly produce both sexual and asexual spores; in other species the sexual form is rare; for still others, sexual spores have never been seen - and perhaps never will be seen. The names used for currently accepted sexual genera with close phylogenetic relationship or known linkage to
Aspergillus species (representative
Aspergillus species given in parenthesis) are:
Chaetosartorya (
A. wentii);
Emericella (
A. nidulans);
Eurotium (
A. glaucus);
Fennellia (
A. terreus);
Hemicarpenteles (
A. paradoxus);
Neocarpenteles (
A. clavatus);
Neosartorya (
A. fumigatus);
Petromyces (
A. flavus and possibly
A. niger); Sclerocleista (
A. ornatus); and
Warcupiella (
A. spinnulosus). Rigid interpreters of nomenclatural rules believe that it is wrong to use the name
Aspergillus to denote a fungus with a known sexual stage and that only the generic name associated with the sexual stage should be used. Nevertheless, outside the community of fungal taxonomy and 'strict interpreters' of the Botanical Code, the proliferation of names for a genus that most biologists know as
Aspergillus causes bewilderment. Dual nomenclature is also a major problem for information retrieval.
The proliferation of arcane terminology is also problematic. For many years, mycologists called those fungi incapable of forming sexual spores 'imperfect' while the sexual forms were called 'perfect.' Another term often encountered was 'pleomorphic,' referring to that fact that these organisms could take more than one form. ('Pleomorphism' is particularly confusing because it is sometimes used to describe the yeast-mycelial phase transition characteristic of some medically important fungai, a transition that is more properly called 'dimorphism'). When an 'imperfect' fungus also was found to be 'perfect' additional problems of etymology developed surrounding the use of the terms 'asexual phase/stage/state' and 'sexual phase/stage/state.' All of these terms were used inconsistently and interpreted differently. For this reason, during the late 1970s, a new set of terminology was introduced whereby
anamorph refers to the asexual, mitotic-spore-bearing morphological phase;
teleomorph refers to the sexual meiotic-spore-bearing morphological phase; while
holomorph refers to the 'whole fungus'. In 1981, this terminology was accepted by the Botanical Congress. Both 'anamorph' and 'teleomorph' have gained widespread acceptance; however, 'holomorph' has had less linguistic success.
In summary, many
Aspergillus species have two names, an exception to most rules of scientific nomenclature that is nevertheless legal under the Botanical Code. This mycological exceptionalism has caused regular and heated debates ever since the Botanical Code was formulated. Different generations of taxonomists have revised the rules pertaining to fungal nomenclature as better data have come along that inform our understanding of fungal speciation. These revisions will continue to be made into the foreseeable future. Nevertheless, there are experts who seem to forget that rigid rules and neat categories don't always mesh with the variability of living systems and the realities of human language usage. Sometimes nomenclatural decisions go against common sense. One rationale for biological nomenclature is to provide stability. Another is to aid communication. Proliferation of jargon and frequent changes of specific and generic epithets do neither.
Suprageneric classification
Aspergillus presents several classification difficulties that are intertwined with its nomenclatural intricacies. A form taxon (pl. form taxa) is a group, used for convenience, whose evolutionary and other relationships are not known. Form genera are used in classifying fossil plants, but they also have had widespread application in the history of
Aspergillus classification. For a long time, all asexual (anamorphic) fungal species were classified into a form group commonly called the 'fungi imperfecti' or, more technically, Fungi Imperfecti. Depending on the author, the group was ranked as a class (Deuteromycetes) or a subdivision/subphylum (Deuteromycotina). The fungi imperfecti sometimes were subdivided into form classes in which the moulds were grouped together as Hypomycetes. These 'artificial' rubrics were used to encompass asexual groups, while other higher order 'natural' categories were used to categorize species that produce by sexual means. Since all taxonomic classification schemes are human constructs designed to catalogue living things, many philosophical and practical objections are inherent in the concept of 'natural categories.
Nevertheless, modern taxonomists seek a more 'natural' classification scheme based on evolutionary criteria. Such phylogenetic classifications seem more possible now that traditional morphological markers have been supplemented with nucleic acid sequences. In particular, DNA markers such as ITS regions or conserved genes such as calmodulin, tubulin or RNA polymerase are used to conduct molecular phylogenetic studies. Species with few nucleotide differences are considered more closely related than those with many. Taxonomists compare the sequence differences between species and use computer programs to come up with a hierarchy of evolutionary relationships. Despite the fact that such gene trees - especially those based on single genes - are error prone, despite the fact that different genes evolve at different rates, and despite the fact that horizontal gene transfer can muddy phylogenetic analysis, such analyses are largely robust and have revolutionized all taxonomic systems. It now seems likely that the aspergilli are all descended from one common ancestor, i.e. they constitute a monophyletic group. It is believed that that the ancestral form was sexually producing and that independent losses of sexual reproduction occurred repeatedly.
These molecular phylogenetic analyses have ramifications for both classification and nomenclature. It can be assumed that fungi called
Aspergillus are descended from the same ancestral groups as their named teleomorphs. From the perspective of classification, it means that the old form taxa categories, (i.e. the fungi imperfecti and the Deuteromycotina) can be retired. In theory, mycologists have done so and these taxa are no longer formally accepted.
Aspergillus species now are classified firmly within the Ascomycota. However, in practice the old terms for form taxa are still widely used and applied. At the time of this writing, a Google search revealed 122,000 hits for 'fungi imperfecti' and 87,500 for 'Deuteromycotina'.
The clear placement of all
Aspergillus species within the Ascomycete lineage, along with the 10 named
Aspergillus teleomorphs, has led some taxonomists to suggest that they all could be placed within a teleomorphic nomenclatural system, even without any sexual structure having been found. Nonetheless, the question remains: Are all
Aspergillus species anamorphs of some kind of ascomycete? Should anamorphic
Aspergillus species be classified within, and named for, a teleomorphic genus based on DNA evidence even when they lack a known teleomorph? These questions raise both theoretical and practical issues. Suppose the teleomorph does not exist? Suppose some large and successful groups of aspergilli have evolved a purely clonal and asexual form of reproduction? Does it make sense to rename them based on a morphological structure they do not possess? Caution and conservatism counsel the retention of both dual
nomenclature and the genus name
Aspergillus.
Commentary on taxonomy
Living things evolve. Natural systems are messy. Groups of closely related organisms do not always lend themselves to tidy classification schemes. The human need for neat categories coupled with an unfortunate tendency on the part of some scientists to view the Botanical Code as 'etched in stone,' means that over zealous interpretations of the Botanical Code can trump reasonableness and practicality. The Code is authored by human beings and necessarily is open to changes as new discoveries are made. For the sake of stability, these changes are made slowly and usually after considerable debate within the scientific community. Nonetheless it is important to remember that the debate mostly occurs between a relatively small number of people who are involved in policing the fine points of biological nomenclature. Even among this small group, it is not always easy to gain consensus. For example, when a assemblage of prominent mycologists gathered at an important meeting held in Newport, Oregon, in 1992, they discussed the provisions of Article 59 in detail. At the end of the discussion, 19 people voted to retain the dual system; 17 wanted to integrate mitotic and meiotic fungi into the same genera, and only five would accept the use of the teleomorph name for both morphs. Similarly, in 2007, an international workshop with 39 experts was held in Utrecht, the Netherlands on '
Aspergillus systematics in the genomics era.' In the light of the overwhelming molecular data placing
Aspergillus among the Ascomycetes, the question of dual nomenclature was revisited. In the final vote, the majority of participants decided that it was best to retain dual names 'where necessary'. It is likely that naming and classifying
Aspergillus species - and many other anamorphic fungi - will remain a contentious area within mycology for the foreseeable future.
Suggested reading: Fungal PublicationsAdapted from
An Overview of the Genus Aspergillus by
Joan W. Bennett writing in
Aspergillus: Molecular Biology and GenomicsFurther readingLabels: Microbial taxonomy, Taxonomy