Biology Reference
In-Depth Information
Figure 9:
Diagramatic representation (not drawn to scale) of rRNA operon of
E
.
coli
. D1, D2, D4 and D5 represent conserved
domains and V1, V2 and V3 represent variable regions. Based on the molecular structure as in Iteman
et al
. (2000).
Figure 10:
Line drawing (not drawn to scale) of rRNA operon of
E
.
coli
showing specifi c regions of 16S rRNA that are generally
amplifi ed in the identifi cation of prokaryotes. There are six other regions in 23S rRNA also (not shown) utilized for this
purpose. Modifi ed from Gürtler and Stanisch (1996).
domain classifi cation consisting of Bacteria, Archaea and Eukarya (Fig. 11). Studies on this molecule
have generated a huge public data base (RDP II: http:// rdp.cme.msu.edu/ containing 481,650 16S
rRNAs as on 13th February, 2008). It is generally agreed that a 16S rDNA sequence similarity of
96-97% and DNA:DNA hybridization value of 70% relative binding (RB) with ΔT
m
5°C represent
lower boundaries for the distinguishing bacterial species (Wayne
et al
., 1987). Fox
et al
. (1992) reported
that three psychrophilic strains of
Bacillus
(
B
.
globisporus
W25
T
Type strain;
B
.
psychrophilus
W16A
and W5) that are phenotypically very similar exhibited 99.5% 16S rRNA gene sequence similarity
but differed from each other on the basis of DNA:DNA hybridization studies. They concluded
that identity of 16S rRNA sequences does not constitute a suffi cient criterion to guarantee species
identity. A number of proposals have been made for altering the lower limits for the delineation of
a species in bacteria. An RB value of 50% at a ΔT
m
7°C has been suggested by Rosselló-Mora and
Amann (2001) for distinguishing species because even if 16S rDNA sequence similarity was as high
as 98-99% the total DNA homology was as low as 10-40% RB. Similarly, Keswani and Whitman
(2001) observed that the relationship between RB and 16S rDNA sequence similarity greatly varied
within the same subphylum. In view of these, it appears that there is a need to alter the upper and
lower limits of RB values for species delimitation in prokaryotes.
