6  LPSN: the List of Prokaryotic names with Standing in Nomenclature

Although we have referred to authoritative sources there is, in fact, no offical classification of prokaryotes (Tindall (1999)). Also, the terms nomenclature, taxonomy, and phylogeny are not interchangeable.

Understanding the difference
  • phylogeny: A phylogeny is the evolutionary history of a set of organisms, or a model (such as a phylogentic tree) representing that history
  • taxonomy: A taxonomy is a scheme for ordering objects into groups or classes, or the rules for doing so
  • nomenclature: Nomenclature is the set of names assigned to groups in a taxonomy, or the set of rules for doing so

We do not know the “true” evolutionary histories of organisms, so the phylogenies we reconstruct as scientists are estimates - sometimes very precise estimates! - of evolutionary history.

The phylogenies we construct allow us to make decisions about how to organise organisms into a taxonomy: groups of organisms (taxa) that comprise species, genera, phyla, and so on.

The names we give to taxa are governed by the rules of nomenclature. Those names are regulated by the International Code of Nomenclature of Prokaryotes (ICNP). This document is produced by the International Committee on Systematics of Prokaryotes (ICSP), a group of about 35 scientists who compose the rules by which bacteria are named.

ICSP Do Not Have a Taxonomic Opinion

The ICSP do not decide which organisms go into any particular taxon (genus, species, etc.) - scientific opinion is ever-changing in this area. ICSP, through the ICNP, only decide what is a validly published name. The name of a taxon is validly published, and therefore has standing in nomenclature, only if certain criteria are met.

The LPSN is the authoritative database of validly-published names for prokaryotes.

6.1 Investigating your classification at LPSN

  • Go to the LPSN server
  • Enter the species classification you think should be assigned to your organism in the Search taxonomy field, and hit Return/Enter. The result should appear immediately.
Questions
  1. What kind of taxonomic category does the name of your organism represent?
  2. What does the name mean, and what does it imply about the organism?
  3. Is the name you entered a validly published taxonomic name?
  4. What is the parent taxon for this name?
  • Click on the link by Parent taxon: (the value here is also the answer to question 4. above).
Questions
  1. What kind of taxonomic category does this name represent?
  2. What does the name mean, and what does it imply about the bacteria?
  3. Is the name you entered a validly published taxonomic name?
  4. What is the Taxonomic status of this name?
  5. Is this name the “correct name” for the organism?

The precise meaning of “correct name” in this context is provided in a glossary at LPSN. The key points in that text are:

  • Any taxon may have only one correct name. This is usually the earliest validly published, legitimate name.
  • The LPSN selects certain taxon names as correct names. If more than one option is available, then the LPSN’s choice reflects only one of the taxonomic opinions expressed in the literature.
  • The correct name for an organism should be used in the literature.
  • Other valid names are given synonym status.
  • Other scientists may express distinct taxonomic opinions and are permitted to do so, by using a synonym.

The term correct is therefore used in a technical sense, in a taxonomic context. The existence of a correct name for a taxon does not imply that other names (synonyms) are invalid or cannot be used.

  • Read the Notes section on the LPSN page for Ochrobactrum (the genus).
Questions
  1. How do the notes on this page reflect the controversy over naming of Ochrobactrum/Brucella described in the Introduction?
  2. Does the LPSN page affect your opinion about how you have classified your isolate?
  3. Finally, what is the taxonomic name you think is most appropriate for your isolate?