Biology Reference
In-Depth Information
5) The species concept in bacteria and cyanobacteria
As per Bergey's Manual of Systematic Bacteriology the defi nitions given for a bacterial genus and
species are reproduced below.
Genus: “The bacterial genus is usually a well-defi ned group that is clearly separated from other
genera, and then through descriptions of genera in the 1984 edition of Bergey's Manual exemplify
the depth to which this taxonomic group is usually known. However, there is so far no general
agreement on the defi nition of a genus in bacterial taxonomy, and considerable subjectivity is involved
at the genus level. Indeed, what is perceived to be a genus by one person may be perceived as being
merely a species by another systematist.”
Species: “A bacterial species may be regarded as a collection of strains that share many features
in common and differ considerably from other strains. One strain of a species is designated as the
type strain; this strain serves as the name-bearer strain of the species and is the permanent example
of the species, i.e. the reference specimen for the name. The type strain has great importance for
classifi cation at the species level, because a species consists of the type strain and all other strains
that are considered to be suffi ciently similar to it as to warrant inclusion with it in the species….”
A species represents a group of organisms (strains) in a taxonomic rank (Stackebrandt and Goebel
1994) and forms the basic unit of a classifi cation system. It is a tool for describing diversity. The species
name should convey about the phenotypic features of an organism and about the relationships to
other organisms. We will fi rst consider the concepts that have been developed during recent years
in defi ning species in bacteria. Later on the species concept for cyanobacteria will be discussed. As
cyanobacteria form part of phylum eubacteria, the species concept of bacteria may as well be extended
to cyanobacteria. However, cyanobacteria are morphologically highly divergent in comparison to
most other bacteria, and consequently, it has been suggested that morphological features be given
more weight in the species defi nition (Castenholz and Norris 2005). It would be in the fi tness of
things if we state here species limit set for percentage of RB derived from DNA-DNA hybridization
studies. Strains that show ~70% RB are considered to belong to the same species (Wayne
et al
., 1987).
As this condition cannot be applied with ease in all cases and since it would be diffi cult for cultivating
certain strains, alternatives to this 'golden standard' have been looked for. Konstantinidis and Tiedje
(2005) observed that those strains which exhibit 70% RB [or in other words those that exhibit 95%
average nucleotide identity (ANI) over all shared genes] have been shown to be extremely similar in
their 16S rRNA gene sequences. On the contrary, strains that have almost identical 16S rRNA gene
sequences may not be closely related either on the basis of their RB (Rosselló-Móra and Amann,
2001) or ANI (Konstantinidis and Tiedje, 2005). If two strains have less than 97% sequence identity
of 16S rRNA they are assigned to different species but added to this the percentage of their RB is
still required in order to identify them as separate species. Since ANI represents average nucleotide
identity of the total genome sequence shared between two strains, it is exceptionally a robust and
sensitive method for measuring evolutionary relatedness. Strains that show more than 60% ANI
exhibit greater than 97% 16S rRNA gene sequence identity. Due to a strong correlation between 95%
ANI and 70% RB, Konstantinidis and Tiedje (2005) seem to favour retention of 70% RB criterion as
it brings together relatively homogeneous set of strains which share at least 80% genetic homology.
As ANI is a genome-derived parameter, all conserved genes between any two genomes are likely
to show high degree of genetic relatedness. Moreover, there have been no reports on the organisms
that show less than 98.5% identity in their 16S rRNA gene sequences and show at the same time
70% RB (Stackebrandt and Ebers, 2006) or 95% ANI. Instead of basing the phylogenetic studies on
