Why model fungi matter
Some arbuscular mycorrhizal (AM) fungi are used in laboratories around the world. They are grown in culture with root organs, used to inoculate plants, sequenced, and studied for gene expression and symbiotic function. A few isolates have become the standard reference organisms of the field, and papers about them appear in genetics, physiology and ecology.
These organisms have also had their names changed, which is a source of confusion for anyone who reads older papers or who works with older cultures. This post looks at four well-known examples and at what name changes mean in practice.
Isolates that kept their codes
Glomus intraradices DAOM197198 is Rhizophagus irregularis
The best-known model AM fungus is an isolate long labelled Glomus intraradices DAOM197198. Its current name is Rhizophagus irregularis DAOM197198. The isolate code stayed the same; only the species and genus changed. The code is therefore the most reliable handle for following the fungus through the literature.
A related point is that the name Rhizophagus intraradices was anchored to a defined species by Walker and colleagues (2021, Fungal Systematics and Evolution 8:179-201). This helps resolve a long-standing difficulty, because for many years the name intraradices was applied to fungi that were not the same biological entity. Researchers who used the name in earlier work may therefore need to check which fungus they actually studied.
Glomus versiforme BEG47 is Diversispora epigaea
A second widely used isolate was named Glomus versiforme BEG47. It is now known as Diversispora epigaea BEG47. Again the culture code is stable, while the binomial is not. The change is more than cosmetic, because the new genus belongs to a different lineage of the Glomeromycota from the one in which Glomus is placed. Statements about the biology of “Glomus” in older papers therefore do not necessarily apply to this fungus.
Anchoring Glomus: the role of Glomus macrocarpum
The genus Glomus was once a large and mixed collection of species, defined mainly by a simple spore type. Genetic analyses showed that this collection was not a natural group and that its members belonged to several distinct lineages. To decide which species should keep the name Glomus, the genus had to be tied to its type species, Glomus macrocarpum.
That anchoring was fixed by culturing and characterising G. macrocarpum, so that the genus name is now linked to a fungus with a known genetic identity. Once this was done, the many species that fall outside the group around the type species could be moved to other genera. This explains why so many familiar species have new generic names: it was not a matter of preference but of tying a name to an actual organism.
Pacispora and its relatives
The fourth example concerns the genus Pacispora. The species Glomus scintillans, G. dominikii and G. chimonobambusae belong to Pacispora. A second genus name, Gerdemannia, was also proposed for the same group of fungi. It turned out to be a later synonym, because the Pacispora paper (Walker and Schüßler 2004, Mycological Research 108:981-982) was published slightly earlier.
The priority rule
This is an application of the rule of priority in nomenclature. When two names are given to the same taxon, the one published first is normally the valid name, and the later one becomes a synonym. The decision does not depend on which name is more attractive or which paper is better known; it depends on publication dates. In this case a difference of timing, even a small one, settled the matter.
What name changes mean for researchers
For a working scientist, a change of name can feel like an annoying administrative matter. In reality it carries information. A new genus often reflects a better understanding of evolutionary relationships, and so tells you which fungi are likely to share traits with the one you study.
Consequences for the reader of older papers
- A paper from a given period may use a name that is now a synonym or that has been moved to another genus. The same fungus may appear under several names across the literature.
- A conclusion drawn about “Glomus” in general may be based on fungi that are not closely related, so it cannot be treated as a statement about one group.
- A name may have been applied to more than one biological entity, in which case the strain or isolate code is a better guide than the name.
Consequences for the author of new papers
- Give the current valid name and mention the older name once, so that your work can be found by those who search for it.
- Always report the isolate or culture code, because it remains stable when names change.
- State where the culture came from, and, when possible, deposit sequences with that information attached.
- Check the current nomenclature before submission, not only during planning.
Synonyms and why they persist
A synonym is a name that refers to the same taxon as another name. Synonyms do not vanish when they are replaced. They remain in old papers, in culture collection catalogues and in sequence databases, where they may stay attached to records for years. A reader who sees an unfamiliar name should therefore ask first whether it is a synonym of a familiar one, before concluding that a different fungus is meant.
Culture collections and databases are not always updated promptly, and the person who deposits a record may not know of later changes. That is one more reason to rely on isolate codes and to record the date on which a name was checked.
A short routine for checking a name
- Find the original description and any later emendations of the species.
- Look for recent transfers to other genera or decisions on synonymy.
- Check whether sequences from the type or from an authentic culture exist, and whether they agree with those you have.
Linking names through stable identifiers
Because names change, the identifiers used on this site, called EP numbers, give a name-independent way to link studies. If a fungus is known by an older and a newer name, the same identifier follows it. The species list also gives links to formal descriptions and emendations, so that a reader can trace how a name arrived at its present form.
The model isolates described above are good illustrations of the principle: the cultures kept their codes, the sequences kept their meaning, and only the labels were updated.
Keeping perspective
Do not let this discourage you.
Name changes can be frustrating, but they are a sign that the classification is improving. The nomenclature of AM fungi is still being refined, and readers should accept that today’s names may be revised in turn. The data on this site come from a project that is due to close by the end of 2024, so some of it may be outdated from the formal point of view.
The most useful habits are simple ones: cite the isolate, note the sequence source, use the current name with the older one in brackets, and consult recent taxonomic literature. A researcher who does so will always be able to say which fungus was studied, whatever it may be called in future.
