Bacterial Systematics

[B. J. Tindall]

At 06:22 20.3.2000 PST, you wrote:
>Brian,
>     Why the "thumbs down" on NCBI?  The NCBI Taxonomy does have some
>problems, but at least it attempts to present a comprehensive
>classification.  The bacterial "nomenclature" sites that I've seen have
>their problems too, and are no less confusing (although in a different way).

One of the problems is that the names which appear on the NCBI lists are
names extracted from their database and do not always reflect the fact that
these names have not entered into use in microbiology - the name has not
been validly published. Secondly the "taxonomic groupings" used are more
for database convenience than what is materialising as the basis for
ordering prokaryotes at higher taxonomic levels (i.e. family, class etc.) -
and the question was originally about classification and systematics, not
about database administration! Also what is not represented by sequence
data is not in the database - which also does not reflect "current"
prokaryotic systematics.

>     For instance, should Rickettsiales be classified in Microtatobiotes
>(with the viruses) or in Proteobacteria.  I really have no idea why a name
>like Microtatobiotes was placed on the Official List, but I would think it
>would be better relegated to a list of "historical oddities", like the
>zoological name "Vermes".  And I can't see a name like "Mendosicutes" ever
>coming into common use.  Anoxyphotobacteria might be a convenient grouping
>for the time being in some contexts, but it is hardly natural in any
>meaningful way (photosynthesis having been repeatedly lost in many different
>lineages).  Even Woese wouldn't make a mistake like that.

I do not advocate this either, but one can be misled by both problems in
the past with out dated ideas, and with modern ideas which are being
formulated too rapidly and becoming "out of date" before they are in
circulation, or are shown to be inaccurate.

>     There's got be a useful "middle ground" between (1) the Woesian
>approach (purely cladistic in a very destructive way) and (2) the
>conservative Bergey's Manual approach (which can make even moderate cladists
>cringe).

I am not sure that the Woesian system is cladistic. Mayr agrued some time
ago that it was phenetic. It certainly groups organisms together in what
seems to be "clades" or "monophyletic groups" based on 16S rDNA sequences,
variously using Sab values, Neighbour-Joining, and more recently Maximum
Parsimony and Maximum Likeliehood methods.
The last version of Bergey's Manual was planned about 20 years ago (out of
date) and the new one will use the "16S rDNA tree" to order everything,
with the problem that the taxonomic units are primarily based on sequence
data with little other supporting data.......as I said above even the most
recent things have problems.

>     And while Archae(o)bacteria might be better than Woese's Archaea, the
>older name Archaebacteria (which is still widely used) seems preferable (as
>Ernst Mayr has repeatedly suggested).  Of course, I personally believe the
>far more accurate name Metabacteria will eventually supplant all of these
>names.  My recommendation is that in any paper discussing them, that one
>should at least once use both names together, Archaebacteria (=
>Metabacteria), or even better Metabacteria (= Archaebacteria).  And until
>Woese's unfortunate neologism "Archaea" is discredited, it should be
>footnoted or mentioned, but certainly not used as a formal taxon name (and
>NCBI is hardly alone in having jumped on that 1990's bandwagon).

The Bacteriological Code does not govern any of these alternative names.
The most important aspect is whether all three names represent the same
group of organisms. Unfortunately there is a younger generation of
microbiologists who have never heard fo Metabacteria, and fairly wide
acceptance of the name Archaea simply because it shows that they are not
"bacteria" - not my words!

>     I certainly look forward to seeing how MacMillan's Encyclopaedia
>approaches bacterial classification, and at the very least I hope they have
>the sense to use Archaebacteria rather than "Archaea".
>                       ----Ken Kinman

As I pointed out, don't just rely on what is in print or on the web,
consult someone with experience in the area!
Brian Tindall




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