ATBIs (various approaches)

B. J. Tindall bti at DSMZ.DE
Tue Mar 13 08:43:39 CST 2001

Both Ken Kinman and Donald Quicke seem to prefer the molecular approach for
different reasons. I am a "classical microbiologist" who did his Ph.D. at
the time when the 16S rRNAA catalogues were first being published and in
those days I was working on both the halobacteria and anoxygenic
phototrophic bacteria, both early objects of study for 16S rRNA. I won't go
onto detail, but in those days it made sense and the molecular methods
developed. Having promised "one 16S rDNA sequence - one species" we now
know that this is not possible. We also know that at very high degrees of
16S rDNA sequence similarity you need to use other methods. The 16S rDNA
sequence data is now a routine method (and I welcome its use), but it has
caused problems as well as providing a stimulus for change. Microbiology
already has its eyes or a more sequence orientated taxonomy and
identification system, but a critical evaluation of what it will really
bring is different to what is promised.

I would agree with John Noyes that one cannot abandon older approaches.
Infrastructure within species generally means that there are elements which
are constant (i.e. two legs in Homo sapiens), and things which are variable
(i.e. eye colour in man) - this applies to both phenotypic and genotypic
data. In the case of cryptic species molecular data would work well if the
species are genetically easy to distinguish, but one may find different
morpho-species which are difficult to distinguish based on molecular data.
Again I would paraphrase what John Noyes has said and state that while
morphological and molecular data may use different methodologies they are
(potentially) subject to similar problems - overlap of data sets,
convergence and parallel evolution, perhaps even gene transfer. If you want
to see what happens as more and more genomes are sequenced then watch the
developments in prokaryotes - we are already backing off from certain
claims made 20 years ago!

As an after thought and something which one must bear in mind - if you no
longer train people to work morphologically then you do not have the people
to tell you whether you are dealing with morpho-species "x" or "y", so your
molecularly trained people also do not know whether they are working with
"x" or "y"......which means that conclusions may be wonky! If you don't
believe me just wait and watch it happen - I have read some very
"interesting" articles which base their work on molecular work while
failing to realise that they are wrong because of a failure to appreciate
what "classical microbiology" tells us. Still as they say it will all come
out in the wash!

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