GTDB Forum

Taxon names matter

Taxonomy involves naming, delimiting and organizing groups of organisms (taxa) on the basis of shared traits that, ultimately, reflect their evolutionary history. Taxonomy itself evolves and revising old taxonomic schemes is necessary. The GTDB aim to produce a more uniform and stable genome-based taxonomy is laudable and extremely useful. However, despite some improvements, there is still an important problem in the current GTDB nomenclature: several standing taxon names are being reused for a new phylogenetic delimitation (a different extent of organisms). This introduces confusion and prevents meaningful comparison with long-accumulated knowledge, especially for groups with a long history in microbiology science. I previously raised the problem (to Phil) and suggested to give new names to newly circumscribed taxa. This was fortunately done for some archaeal taxa. Thus, Euryarchaeota and Crenarchaeota, which encompassed clades of very different breadth in various GTDB releases as compared with classical taxonomic schemes since Woese’s formal definition in 1990, disappeared as GTDB phyla and were replaced by several phyla with different new names (Thermoproteota, Halobacterota, Methanobacteriota, etc.).

Unfortunately, the problem still affects some important classical taxa within Bacteria. I will mention two such cases. The first concerns the Proteobacteria, traditionally encompassing Alpha-, Beta-, Gamma-, Delta-, Epsilon- and Zetaproteobacteria. In the current GTDB release, Proteobacteria is reused to refer to only a subset of those clades excluding former Delta- and Epsilonproteobacteria clades (Desulfobacterota, Myxococcota, Bdellovibrionota, Campylobacterota, etc.). This is extremely confusing, since Proteobacteria is among the most diverse and studied taxa. A large body of knowledge about Proteobacteria integrate clades that are now excluded in the GTDB ‘Proteobacteria’. Could you consider changing the name of the GTDB ‘Proteobacteria’ phylum to a new name to prevent that confusion?

A similar situation affects the GTDB taxon Cyanobacteria, which classically corresponds to the clade including only ancestrally oxygenic photosynthetic bacteria (GTDB Cyanobacteriia) but that in the GTDB taxonomy includes also two taxa of related non-photosynthetic bacteria. Accumulated knowledge on cyanobacteria exclude those other taxa. In addition, this taxon also exists in the botanical code, such that it is likely that the same name, Cyanobacteria, persists in the future to refer to two different clades of organism, which complicates and obscures scientific progress. Again, would it be possible to simply give a different name to the clade formed by classical Cyanobacteria and its two related clades?

In general, renaming taxa differently rather than changing the semantics (the extent of organisms) of a given name would be extremely important for clarity in the (micro)biology community. Would you consider this element for future releases?

Thank you for the GTDB initiative, best wishes

Puri Lopez-Garcia

Hi Puri

Thanks a lot for expressing your concerns.
I will do my best to reply asap.

Kindest regards,
Masha

Thanks Puri, it sounds like you might be making a case for using the name Pseudomonadota to encompass the group GTDB defines as Proteobacteria…
Bw, Phil

Pseudomonadota or any other name that avoids confusion would be great. Thank you for considering it and help make things clear. We need it so much!
Cheers

@purilopez “Pseudomonadota or any other name…”

no, please not any other name, and not the utterly confusing Pseudomonadota, for the sake of some continuity that can be easily communicated.

as @sharmaG30 suggested on twitter (https://twitter.com/sharmaG30/status/1469938195332677634?s=20) “Proteobacteriota” would do: the “-ota” suffix signals the new taxonomy and the “Proteo-” signals the continuity.

Proteobacterota would also be confusing exactly because it seems in continuity with the GTDB ‘Proteobacteria’ and classical Proteobacteria encompass many more groups than those named ‘Proteobacteria’ by GTDB.
The problem is using the same name (here Proteobacteria) to refer to different groups of organisms. Microbial taxonomy looks every day more like The Tower of Babel

yes, puri, “we’re en ruta babilon” as manu chao sings :wink:
and no, I don’t think that Proteobacteriota (with the “i”, mind you) would be confusing but, on the contrary, could be easily communicated to e.g. students as successor of the former Proteobacteria lacking two groups, delta+epsilon, that were sort of taxonomic junk drawers anyway. call it descent with modification, if you like.

Well, I think it is actually chaos because there are several decades of research (I know people think that research done last year is already obsolete) on Proteobacteria that include Delta+Epsilon. Whether they deserved or not to be in that group is another thing. But if you want not to introduce confusion, giving another name to the descending group would be the best thing to do. Taxonomists can find the name that suits best. I am witnessing perplexity around just now.
Actually, that is the solution (thanks!!!) adopted by GTDB in the case of archaea: excluding Euryarchaeota and Crenarchaeota as GTDB terms and giving new names to their different descending phyla. You might like the new names or not, but the clade they refer to is clear. This is the first step, to understand each other when we use a term, to speak the same language. The rest is Babel.

Dear Puri

Thanks again, the issue that you brought is not something that GTDB should or could deal with. There are official nomenclature rules that dictate how taxa should be named and when those names should be changed.
Changes in circumscription whether or not they modify the nature of the taxon are not leading to change in the name of that taxon. This has always been the case, please see Section 7 of the ICNP. It is the nomenclature type that determine the application of name to the taxon.
Furthermore, when alteration of circumscription modifies the nature of the taxon, one could simply suggest an emendation but name stays the same. Otherwise, if one would change the name based on every single change in circumscriptions, there won’t be any nomenclature stability…This is one of the essential principles of the official prokaryotic nomenclature “Aim at stability of names”, and your concerns are not falling under its other principles such as “Avoid or reject the use of names which may cause error or confusion” since changing a name while retaining the same type would lead directly to confusion if there is no sufficient reason for this…

Thank you for your answer. The stability of taxon names is a good thing if it helps clarifying and rationalizing the classification system. Unfortunately, not only the circumscription of some names is regularly changing but we now assist to the emergence of dual meaning for some taxon names. This is most unfortunate.

Thank you for this discussion, and I could totally understand your concerns but it wasn’t different before GTDB. I meant in terms on nomenclature principles and rules. Taxonomy is changing with growing knowledge and this is normal, and some taxa might be affected more than others. The nomenclature system is designed in a way that allows to express those changes with minimal disturbance to the whole system and to track changes thanks to the nomenclature types. Perhaps we could have a similar kind of forum on the ICSP website. I believe that it would be a better place for such discussions…
Thank you,
Masha