How does iNaturalist handle Candidatus bacterial species?
https://www.inaturalist.org/flags/552152
https://inaturalist.ca/taxa/474649-Candidatus
This is the list of recognised external taxonomic authorities for iNat …
Curator Guide · iNaturalist
Currently there is no source for bacteria.
In my opinion it should be LPSN (not Uniprot).
LPSN - List of Prokaryotic names with Standing in Nomenclature (dsmz.de)
Although the unculturable ‘candidatus’ bacterial taxa are not formally recognised they do have standardised forms and I recommend we use whatever LPSN says. However there are limitations imposed on us by the iNat system. So for candidate phytoplasmas we should ideally have the recognised form, e.g. Candidatus Phytoplasma rubi
Unfortunately, due to way names are parsed within iNat, we cannot have italics for Candidatus, and if we prefix names with Candidatus then phytoplasma is automatically de-capitalized. So you can have Candidatus phytoplasma rubi, or Phytoplasma rubi but not Candidatus Phytoplasma rubi.
For phytoplasmas more problematic is the presence of non candidate-form names under the genus Phytoplasma, e.g. Protea witches broom phytoplasma which is a vernacular name. It is commonly used to refer to the taxon but is not a recognised candidate status name.
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In recent weeks, I’ve created two wikipedia articles on phytoplasma taxa and made major modifications to the phytoplasma parent article. FWIW, I agree with @cooperj that LPSN is the best source of names. According to LPSN, there are 51 distinct taxa with nomenclatural standing in genus Candidatus Phytoplasma.
The other thing I’ve learned is that all taxa in this genus (not just those with nomenclatural standing) are organized into groups and subgroups based on genetic and phylogenetic analyses. The group-subgroup of each taxon with nomenclatural standing is shown in wikipedia.
It would be great if the group-subgroup classification were reflected in iNat. This would help identification immensely.
Here’s a common example: https://www.inaturalist.org/observations/48482506
This is probably milkweed yellows phytoplasma but iNat does not define that taxon, so we’re stuck at genus. Since milkweed yellows phytoplasma does not have nomenclatural standing, there’s probably not much interest in creating yet another such taxon.
OTOH, we know that milkweed yellows phytoplasma is in group III, subgroup F. An argument could be made that group III could/should be regarded as a species complex, let’s call it the X-disease species complex (since X-disease was the first disease to be studied in the group).
Currently, there is one taxon with nomenclatural standing in group III, namely, Candidatus Phytoplasma pruni. In other words, the latter is a member of the X-disease species complex. So is milkweed yellows phytoplasma.
The 51 taxa with nomenclatural standing are spread across 29 groups, so we would need 29 species complexes to implement this taxonomy.
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