Biology Reference
In-Depth Information
IV. THE OTHER SIDE OF THE COIN
The impact of 16S rDNA sequencing in prokaryotic world is so enormous for the simple reason
it has generated a great wealth of information on microbial diversity, community structure and
phylogenetic relationships from diverse environments and geographic regions. Moreso, the impact
seems to have left an impression in the minds of many investigators that it is the key for unraveling
the taxonomic disputes of cultivable and uncultivable organisms. A lot of confusion seems to have
been generated on the existence of a number of “computer bacteroids” based on the existence of
only sequences from metagenomic analyses. There are no nomenclatural guidelines existing in
bacterial taxonomy for recognizing only sequences as equivalent to organisms. Murray and Schleifer
(1994) stated that international nomenclatural code “is not able to provide sensible regulation of
nomenclature for new taxa defi ned by very limited data”. It is pertinent to point out that the original
bacteriological code written in 1957 and the considerations of the Judicial Commission (both in 1976
and 1990) have not forseen a situation for consideration of bacterial taxa based on only molecular
sequences. There are a number of pitfalls in this area. Some of the fears expressed are that (i) the
molecular sequences are based on samples of relatively small size, (ii) a sampling error can not be
ruled out, (iii) likewise, errors in sequencing can not be ruled out, (iv) specially with reference to
16S rRNA gene sequencing studies, contaminating 16S rDNA in the sample can not be overlooked,
(v) a number of workers considered only a single strain of a taxon such as a genus yet the picture
presented was for the entire taxon and even the validity of the adjacent taxa was questioned. Gest
(1999) presented “a primer for the new millennium” to lift bacterial classifi cation and taxonomy
from its existing “chaotic status”. He quoted extensively the opinions of many scientists on the role
of molecular markers and the validity of phylogeny based taxonomy. According to him there is a
complete disregard to bacterial nutrition, physiology and biochemistry based on which many basic
principles in cell biology and biochemistry have been enunciated.
The current situation in cyanobacterial taxonomy is more disconcerting for both the traditional
as well as the molecular taxonomist. The fi rst major requirement is a classifi cation that resolves the
guidelines of both ICBN and International Code of Nomenclature of Prokaryotes (ICNP). Moreover,
the guidelines for nomenclature and a polyphasic approach to the taxonomy of cyanobacteria have
not been clearly defi ned. Pinevich (2008) summarized and highlighted the paradoxes of biodiversity,
phylogeny and taxonomy of cyanobacteria. Though it is needless to repeat here the inconsistencies in
cyanobacterial taxonomy, one taxonomic riddle could not be resolved despite the progress that has
been achieved by the application of molecular markers. This relates to the identifi cation of
Anabaena
sp. strain PCC 7120. More than half a dozen research papers have been published in support of it
being designated as
Anabaena
sp. strain PCC 7120 while as many number of research papers have
been published in support of it being redesignated as
Nostoc
sp. strain PCC 7120. The present trend
is that many workers started representing it as
Anabaena
/
Nostoc
sp. strain PCC 7120. What is the
signal that is sent to the traditional taxonomist who fi nds it diffi cult to enter into the woods of
phylogenetic trees? Oren (2011) highlighted the inadequacies in the resolution of guidelines between
ICBN and ICNP and suggested that 'the guidelines for the characterization of prokaryotic strains
for taxonomic purposes advocated by Tindall
et al
. (2010) be adopted for nomenclatural guidelines
of cyanobacteria'. Unless a major international effort is undertaken, the cyanobacterial taxonomy
continues to lie in the same state for another century. It is because it took more than 60 years to
identify and classify very few cyanobacterial strains on a polyphasic approach (Oren, 2011).
