Biology Reference
In-Depth Information
a single gene sequence like 16S rRNA or alternatively comparing the entire genome sequences, a
reasonable compromise is to select at least seven or eight core gene sequences (housekeeping genes)
that can provide robust phylogeny of organisms (MLST approach; Maiden
et al
., 1998; Gevers
et al
.,
2005). Zeigler
et al
. (2003) tested the usefulness of 32 protein-coding gene sequences, distributed
widely in bacteria, in assigning bacterial strains to species. A single housekeeping gene such as
recN
(that encodes recombination/repair protein) is found to be suffi cient for this purpose as strains
that exhibited 96% similarity in their
recN
sequences also showed >70% similarity in their genome
sequences and could be assigned with 95% confi dence level to the same species. If two strains or
isolates exhibit <84% similarity in the
recN
sequences, the overall similarity in the genome sequences
has been found to be <70% and with the same confi dence level they could be assigned to different
species. The resolving power could be enhanced by the inclusion of two more genes such as
dnaX
(that encodes DNA polymerase III subunits γ, τ) and
thdF
(that encodes GTP-binding protein) in the
analysis. The other housekeeping genes such as
uvrC
(excision nuclease subunit C),
uvrB
(excision
nuclease subunit B),
ruvB
(Holliday Junction helicase subunit A),
dnaB
(replicative DNA helicase),
dnaJ
(chaperone with DnaK),
ftsZ
(tubulin-like cell division protein),
atpA
(ATP synthase F1,α-
subunit) and
atpD
(ATP synthase F1,β-subunit) are among the other 32 genes selected by them for
comparing bacterial genomes by pair-wise comparisons to arrive upon their conclusions. According
to Konstantinidis and Tiedje (2007) such genes show robust phylogenetic signal and give 70-95%
values of ANI. The working hypothesis for the bacterial species concept is that bacteria form coherent
genome clusters with distinctive phenotypic features and the clusters seem to have been created by
two major forces i.e. selection and recombination. So during selection of genes for MLST approach
one should take into account LGT and recombination between the genes when one wants to identify
strains with in a given species. Konstantinidis
et al
. (2006) showed that selection of three such best
performing genes could provide robust phylogeny and accurate prediction of ANI values. The most
favourable species concepts for bacteria are biological (Mayr, 1997) and the phylogenetic concepts
(Hull, 1997). These two are followed by the ecotype concept introduced by Cohan (2002) which is
a variation of the phylogenetic concept. Cohan (2006) stressed the need to develop a theory-based
approach to defi ne bacterial species rather than simply recognizing the genotypic diversity based
on a single molecular marker like 16S rRNA gene sequencing and demarcate bacterial species into
many clusters. In doing so, the sequence clusters or OTUs should be clearly be correlated to the
ecotypes. Any sequence based phylogeny is likely to contain a number of subclusters and it is not
clear which level of cluster corresponds to ecotypes. According to him, a conceptual framework based
on the evolutionary dynamics of bacterial populations for estimating the number of ecotypes within
a community and then identifying them has been proposed. Studies made on community phylogeny
on three groups of organisms and their habitats revealed interesting results. The ecotypes identifi ed
in case of
Bacillus subtilis
-
B
.
licheniformis
occurring in Evolutionary Canyon III of Negev Desert
closely corresponded to the existing species and subspecies that formed a clade in sequence-based
identifi cation. In contrast, world-wide clinical and environmental isolates of
Legionella pneumophila
could be distinguishable into 14 ecotypes that had less 16S rDNA sequence divergence. Likewise, 8
ecotypes of
Synechococcus
in A-A' Clade also exhibited less 16S rDNA sequence divergence. However,
in
Synechococcus
A-A' Clade microhabitat distribution reveals one ecotype harbouring in the upper
photic zone at 68ºC while another ecotype is specialized to the lower photic zone suggesting that
it is temperature that makes the two ecotypes distinct from one another. So in identifying a species
under polyphasic taxonomy, the diagnostic ecological features would prove more meaningful.
To the extent the stable ecotype model is correct, the different clusters can be equated to different
