There are
three
arrangement of microbes based upon various taxonomic groups (
i.e., Taxa), namely:
(
i) Genetic relatedness
(
ii) The intuitive method, and
(
iii) Numerical taxonomy.
The aforesaid ‘
genetic methods’ shall now be treated separately in the sections that follows.
3.3.3.1. Genetic Relatedness
It is regarded to be one of the most trustworthy and dependable method of classification based
solely upon the critical extent of
genetic relatedness occurring between different organisms. In addition
this particular method is considered not only to be the utmost objective of all other techniques based
upon the greatest extent pertaining to the fundamental aspect of organisms, but also their inherent hereditary
material (deoxyribonucleic acid, DNA).
It is, however, pertinent to state here that in actual practice the
genetic relatedness may also be
estimated by precisely measuring the degree of
hybridization taking place either between denatured
DNA molecules or between single stranded DNA and RNA species. The extent of
homology* is assayed
by strategically mixing
two different, types of ‘single-stranded DNA’ or ‘single-stranded DNA
with RNA’
under highly specific and suitable experimental parameters; and subsequently, measuring
accurately the degree to which they are actually and intimately associated to give rise to the formation of
the desired ‘double-stranded structures’ ultimately. The aforesaid aims and objectives may be
accomplished
most precisely and conveniently by rendering either the DNA or RNA radioactive and measuring
the radio activities by the help of
Scintillation Counter or Geiger-Müller Counter.
Table 3.2, shows the extent of
genetic relatedness of different microbes as assayed by the ensuing
DNA-RNA hybridization.
Nevertheless, it has been duly demonstrated and proved that the genetic
relatedness can be estimated accurately by
DNA-RNA hybridization; however, the DNA-DNA hybridization
affords the most precise results, provided adequate precautions are duly taken to ascertain and
ensure that the prevailing hybridization between the two strands is perfectly uniform.
The Intuitive Method
Various
‘microbiologists’ who have acquired enormous strength of knowledge, wisdom, and
hands-on experience in the expanding field of
‘microbiology’ may at a particular material time vehemently
decide and pronounce their ultimate verdict whether the microorganisms represent one or more
species or genera. The most predominant and utterly important
disadvantage of this particular method
being that the characteristic features of an organism which may appear to be critical and vital to one
researcher may not seem to be important to the same extent to another, and altogether different taxonomists
would ultimately decide on something quite different categorization at the end. Nevertheless,
there are certain
‘classification schemes’ that are exclusively based upon the intuitive method anddefinitively proved to be immensely beneficial and useful in microbiology.
Numerical Taxonomy
The survey of literatures have amply proved that in the Nineteenth Century,
microbes were
categorically grouped strictly in proportion to their evolutionary affinities. Consequently, the systematic
and methodical segregation and arrangement of microorganisms into the various organized groups was
entirely on the specialized foundation of inherited and stable structural and physiological characteristic
features. This arrangement is termed as the
‘Natural Classification’ or the ‘Phylogenetic Classifiction’.
Interestingly, this particular
modus operandi for the classification of microorganisms has now almost
turned out to be absolutely redundant, and hence abandoned outright quite in favour of a rather more
realistic empirical approach based exclusively on
‘precise quantification’ pertaining to close similarities
and
distinct dissimilarities prevailing amongst the various microbes. Michael Adanson was the first
and foremost microbiologist who unequivocally suggested this magnanimous approach, which was termed
as
Adansonian Taxonomy or Numerical Taxonomy.
Salient Features:
The various salient features of the Numerical Taxonomy (or Adansonian
Taxonomy)
are as enumerated below:
(1) The fundamental basis of
Numerical Taxonomy is the critical assumption, that in the event
when each phenotypic character is assigned even and equal weightage, it must be viable and
feasible to express numerically the explicit
taxonomic distances existing between microorganisms,
with regard to the number of
actual characters which are shared in comparison to
the
total number of characters being examined ultimately. The importance of the Numerical
Taxonomy
is largely influenced by the number of characters being investigated. Therefore,
it would be absolutely necessary to accomplish precisely an extremely high degree of significance—
one should examine an equally large number of characters.
(2)
Similarity Coefficient and Matching Coefficient: The determination of the similarity coefficient
as well as the
matching coefficient of any two microbial strains, as characterized
with regard to several character variants
viz., a, b, c, d etc., may be determined as stated
under:
Number of characters + ve in both strains =
a
Number of characters + ve in ‘strain-1’ and – ve in ‘Strain-2’ =
b
Number of characters, – ve in ‘Strain-1’ and + ve in ‘Strain-2’ =
c
Number of characters – ve in both strain =
d
Similarity coefficient [S
j] =
a
a
+ b + c
Matching coefficient [S
s] =
a b
a b c d
+
+ + +
.
Based on the results obtained from different experimental designs, it has been observed that the
similarity coefficient
does not take into consideration the characters that are ‘negative’ for both organisms;
whereas, the
matching coefficient essentially includes both positive and negative characters.
Similarity Matrix:
The ‘data’ thus generated are carefully arranged in a ‘similarity matrix’
only after having estimated the
similarity coefficient and the matching coefficient for almost all microorganisms
under investigation duly and pair-wise, as depicted in Fig. 3.1 below. Subsequently, all these
matrices may be systematically recorded to bring together the identical and similar strains very much
close to one another.
In actual practice, such data are duly incorporated and transposed to a
‘dandogram’* as illustratedin Fig. 3.2 under, that forms the fundamental basis for establishing the most probable taxonomic
arrangements. The ‘
dotted line’ as indicated in (Fig. 3.2) a dandogram evidently shows ‘similarity
levels’
that might be intimately taken into consideration for recognizing two different taxonomic ranks,
for instance:
a genus and a species.
The
‘Numerical Taxonomy’ or ‘Adansonian Approach’ was thought and believed to be quite
impractical and cumbersome in actual operation on account of the reasonably copious volume and magnitude
of the ensuing numerical calculations involved directly. Importantly, this particular aspect has
now almost been eliminated completely by the advent of most sophisticated
‘computers’ that may be
programmed appropriately for the computation of the data, and ultimately, arrive at the
degree of similarity
with great ease, simplicity, and precision. It is, however, pertinent to point out at this juncture that
though the ensuing
‘Numerical Taxonomy’ fails to throw any light with specific reference to the prevailing
genetic relationship, yet it amply gives rise to a fairly stable fundamental basis for the
articulated
categorization of the taxonomic distribution and groupings.
Limitations of Numerical Taxonomy:
The various limitations of numerical taxonomy are as
enumerated under:
(1) It is useful to classify strains within a larger group which usually shares the prominent
characteristic features in common.
(2) The conventional classification of organisms solely depends on the observations and
knowledge of the individual taxonomist in particular to determine the ensuing matching
similarities existing between the bacterial strains; whereas,
numerical taxonomy exclusively
depends upon the mathematical figures plotted on paper.
(3) The actual usage of several tests reveals a good number of phenotypes, thereby more genes
are being screened; and, therefore, no organism shall ever be missed in doing so.
(4) One major limitation of the
numerical analysis is that in some instances, a specific strain
may be grouped with a group of strains in accordance to the majority of identical characteristic
features, but certainly not to all the prevailing characters. However, simultaneously the particular
strain may possess a very low ebb of similarity with certain other members of the cluster.
(5) The exact location of the
taxon is not yet decided, and hence cannot be grouped or related to
any particular taxonomic group, for instance :
genes or species.
(6) Evidently, in the
numerical analysis, the definition of a species is not acceptable as yet,
whereas some surveys do ascertain that a 65%
single-linkage cluster distincly provides a75% approximate idea of the specific species.