Bacterial Systematics

[Ken Kinman]

Brian,
    Well I certainly agree that we need a solid Linnaean classification of
bacteria, and I am currently updating the classification of bacteria which I
presented in my 1994 book (still pretty stable, but in need of revision).
But when I say bacteria, I am not just talking about Eubacteria (and I am
certainly not alone in that view).  Woese has been successful in convincing
a lot of people that Metabacteria (his "Archaea") are far more different
than they really are (and even among 16S rRNAs, the gap between these groups
of bacteria is rapidly narrowing).  This Woesian nomenclatorial "smoke and
mirrors", and treating these groups as outgroups to one another, is causing
so many problems that its scope will only be realized in retrospect.  As
Ernst Mayr has said, Woese dropped the -bacteria from "Archaebacteria", when
he should have probably been considering dropping the "Archae-" instead.
     As for the NCBI Taxonomy, I think most of their higher groupings are
fairly natural, and I have not seen them prematurely introducing taxon names
at family level or above.  And their taxonomic coverage far surpasses that
of any bacterial "nomenclatural" sites I've seen.  I still don't see why you
have such a problem with the NCBI
approach, which is gradually changing to keep up with new ideas and data.
      I suspect the Bergey Manual classification will be many years out of
date before it is print, and any future editions will presumably be
electronic and continuously updated (which would be a big improvement).
      As for Woese's approach, it is a strange combination of phenetics and
cladistics, and in clinging to his old ideas on three urkingdoms (a.k.a.
three domains) and thermophilic origins, I fear he has made a mess from
which he cannot extricate himself (except to cover it up by blaming it on
massive horizontal transfers---which had probably quieted down long before
the Metabacteria even evolved).
                               -------Ken Kinman

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