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Your paper had experts on Deltaproteobacteria phylogeny. If I were writing your paper, I would have contacted the same experts. But that’s because, when I, personally, think of taxonomy/nomenclature, I think of DNA sequence phylogeny. (1/12) https://twitter.com/PhilHugenholtz/status/1360846255329476618
But physiology also matters for nomenclature. Geobacteraceae respire iron, manganese, uranium (even the radioactive variety – honey badger don’t care), sulfur, cobalt, vanadium, chromium, silver, mercury, neptunium, and plutonium.(2/12)
Geobacteraceae have probably saved countless lives from death by heavy metal pollution, so now it’s all hands on deck to learn about them so we can use them to save us from our awful selves. (3/12)
A few months ago, if someone used Silva to classify their 16S rRNA gene sequences from heavy-metal polluted sediments, they would not have found any Geomonas (a genus of Geobacteraceae). (4/12)
If they got curious about this weird “Citrifermentans” thing and googled it, nothing would have popped up. Zilch. They would be disconnected from the rich body of literature about Geomonas (see https://www.frontiersin.org/articles/10.3389/fmicb.2019.02201/full). This is a problem. (5/12)
Now the major problems are solved because your paper is published and folks can connect Citrifermentans to Geomonas. GTDB does a great job of keeping a back-catalog of previous names. Silva does not. But more people use 16S. So more people use Silva. This is a problem. (6/12)
But why rename Geomonas in the first place? Geomonas is a validly named genus, so it should have priority. And why choose Citrifermentans? Geomonas does not, apparently, ferment citrate. (7/12)
Your paper had experts in Deltaproteobacteria phylogeny. But it did not have experts in Geobacteraceae physiology. Having the right experts would have prevented the renaming of a validly named group with a name that does not reflect their physiology. (8/12)
Your research group has been tackling the seemingly insurmountable task of naming the un-named microbes systematically. I thank you from the bottom of my heart, especially since you have the headwind of the majority of the Code rejecting DNA as type material. (9/12)
Our goal in writing this paper was not to stop you from doing this important work. It was to point out major problems with how it is happening, in the hopes of improving the final product. (10/12)
As you and I have agreed when we’ve talked in person, names are not nature. But they must be good enough to allow us to talk to each other about nature. (11/12)
When we rename microbes, the group of experts should not be limited to a few people. We need a more democratized system and online peer-review before validation and use of a newly proposed nomenclature. (12/12)
