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Subcommittee of what?

August 20, 2012

In my last post, I referred to the website of the ICSP Subcommittee on the Taxonomy of Rhizobium and Agrobacterium.  You may be wondering what this is a subcommittee of.  The International Committee on Systematics of Prokaryotes (ICSP) is “the body that oversees the nomenclature of prokaryotes, determines the rules by which prokaryotes are named and whose Judicial Commission issues Opinions concerning taxonomic matters, revisions to the Bacteriological Code, etc.”, according to its own website.  This lists 28 subcommittees, each covering a genus or a group of related genera.  Of course there are far more bacterial genera than this, so only certain well-studied groups are covered.  Actually, 12 of these subcommittees seem to be defunct, as no list of members or further information is provided, and 3 more appear to be moribund, as their last recorded meeting was in 2002 or 2003.  Overall, the coverage of bacterial taxa could be described as “patchy”.

What do the subcommittees do?  Well, they have meetings: most of them meet every three years at the International Microbiology Congresses, though the meetings may also be held at more specialised conferences.  They discuss recent developments in the systematics of their bacteria, and they may publish recommended minimal standards for the description of new taxa.  Actually, their powers to decide anything are very limited, since the ICSP controls the Bacteriological Code, which sets out the rules for the valid publication of bacterial taxa.  Subcommittees try to keep track of the validly published names within their remit, but in fact the definitive list for all bacteria is maintained on behalf of the ICSP by Dr Jean Euzéby.  He does a superb job of keeping track of all the relevant publications, and his list of species is always up to date and linked to the relevant literature.  His website should be the first place you look if you want to check the valid description of a bacterial species.  It does not tell you which name to use, but it tells you which names are available to use, and their history.

The Agrobacterium and Rhizobium Subcommittee is the only one to have its own website. There, you will find a list of the species in those two genera, but also a list of legume root-nodule symbionts that belong to other genera.  This might appear to be an unjustified extension of the subcommittee’s remit, but it illustrates a general problem in bacterial systematics.  The taxonomy of bacteria was established in a bygone era, when it was innocently assumed that bacterial genera and species could be defined by listing a set of phenotypic properties.  Rhizobium was easy: all bacteria that fixed nitrogen in nodules on legume roots were Rhizobium, and vice versa.  Similarly, Agrobacterium was the genus for bacteria that induced crown galls or root proliferation by transferring DNA to the plant.

Of course, we can now appreciate that this was all hopelessly naïve.  The bacteria that induce legume root nodules are far too diverse to be accommodated in a single genus, and many of them fit best into genera that were first described for bacteria with quite different properties.  These days, we determine the taxonomy of bacteria using the similarity of DNA sequences: 16S rRNA genes, other core genes, or the approximation provided by DNA-DNA hybridisation (a tedious and unreliable technique that should have been abandoned years ago).  DNA provides objective phylogenetic information that can guide our taxonomic decisions.  Unfortunately, it leads to taxa that are not phenotypically homogeneous: not all isolates of Rhizobium make root nodules because making root nodules, like most important ecological characteristics of bacteria, is determined by mobile accessory genes, not by the core genome

This poses a dilemma for the Subcommittee.  Is it about rhizobia (root-nodule bacteria) or about Rhizobium (the formal genus)?  Is it based on an ecological niche or a taxonomic clade?  The traditional Subcommittees were set up to deal with taxonomic clades, so technically it should confine itself to “Rhizobium and Agrobacterium” as its name specifies, or perhaps broaden this to the Rhizobiaceae, whether they nodulate or not.  This would exclude Bradyrhizobium, let alone Burkholderia, and is not what most people would expect.  On the other hand, if its remit is all rhizobia and agrobacteria, defined by their plant interactions, what happens to strains that have lost the relevant plasmid and no longer have the defining phenotype?   Most biologists are more interested in the phenotype of their organisms than in the taxonomy.  We are increasingly realising that, among bacteria, taxonomy is not a good guide to phenotype.

Here are those website addresses:

Rhizobium and Agrobacterium:     http://edzna.ccg.unam.mx/rhizobial-taxonomy/

ISCP:      http://www.the-icsp.org

List of Prokaryotes:    http://www.bacterio.cict.fr/

 

Peter

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From → Taxonomy

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