Fundamentals of Microbiology

Lesson 9. METHODS OF CLASSIFICATION

Module 3. Microbial taxonomy

Lesson 9

METHODS OF CLASSIFICATION

9.1 Introduction

Two common approaches used in biological world are referred to as phenotypic and phylogenetic classification.

9.1.1 Phenotypic (phenetic) classification

Phenotypic classification is concerned with grouping individual species into phenotypic categories (taxons) based on how organisms ‘look’. In the recent past, taxonomists were not equipped to classify beyond the level of phenotypic groupings except via inference from phenotypic similarities. Phenotypic similarity and evolutionary relationship do not always map one to one upon each other. This approach is guided by a set of morphological and biochemical tests, constituting the cornerstone of ‘Determinative Microbiology’.

Limitations: From the standpoint of many areas of microbiology, a determinative classification is sufficient. For example, in clinical microbiology the identification of organisms permits the physician to assess pathogenicity and to select a treatment. In this context, the purely determinative nature of a classification is not crucial. If the organism has previously been described and hence is already in the classification, then it can be identified and treated. However, from a biological point of view, the lack of a natural system does not permit the projection of properties of previously described organisms onto new ones that might be closely related, but not identical, to those known before. In addition, it does not help us understand an organism that we have been unable to cultivate in the laboratory. Finally, it does not permit studies of the origin and evolution of cellular functions (e.g. drug resistance, aerobiosis or photosynthesis), because there is no evolutionary (historical) framework.

9.1.2 Phylogenetic (phyletic) classification

Phylogenetic classification is concerned with grouping individual species into evolutionary categories. Since the early 1980s, phylogenetic classfication has been made much more facile by the invention of molecular taxonomy. The evolutionary classification of organisms is based on the nucleotide sequence divergence at individual loci (genes).

9.2 Phylogeny from Phenotype

These two approaches (phenotypic and phylogenetic classification) often fully match. This is because there is usually a correlation between evolutionary relatedness and phenotypic relatedness. However, such things as convergent evolution can create confusion between the two classification philosophies since convergent evolution, by definition, produces phenotypic similarity in the absence of close evolutionary relatedness. The trick to solving these discrepancies is to concentrate on true homologies and ignore convergence. Conflicts between phenotypic and phylogenetic classification are at the root of the various monophyly-paraphyly debates.

9.2.1 Molecular phylogeny

A homology is a similarity between two organisms that exists because the two organisms are closely evolutionarily related (that is, the feature in question existed in the common ancestor to the two organisms). The similarity of the DNA (or RNA) of organisms may be determined by a number of means including determinations of base composition, nucleotide sequence, or DNA hybridization rates. Typically these means include very powerful ways by which organisms may be classified, either in terms of distinctions between organisms (i.e. the organisms may be classified as representing two or more species) or similarities (i.e. it may be concluded from evidence of genotypic similarity that the organisms are closely related, i.e. evolutionarily related); the latter similarities we would classify as a genetic homology. The downside of genetic homology is that the acquisition of data often requires a laboratory and at least a little effort. The upside is that genetic homology describes evolutionary relationships with only minimal interference from phenotype.

9.3 Numerical Taxonomy

It is a classification system in biological systematics which deals with the grouping by numerical methods of taxonomic units based on their character states. It aims to create a taxonomy using numeric algorithms like cluster analysis. The concept was first developed by Robert R. Sokal and Peter H. A. Sneath in 1963. Phenetics is a closely related discipline and draws heavily from the methods of numerical taxonomy.

Although intended as an objective classification method, in practice the choice and weighing of morphological characteristics is often guided by available methods and research interests. Furthermore, the general consensus has become that the taxonomic classification should reflect evolutionary (phylogenetic) processes. Some connections between phylogenetic trees and the spectral decomposition of the variance-covariance matrix of quantitative traits subject to Brownian motion over time have been established, providing a theoretical link between phylogenetic methods and numerical taxonomy. The specific phenetic algorithms proposed in numerical taxonomy, however, often fail to properly reconstruct the phylogenetic history of organisms.

9.4 All Species Inventory

In 2001 an international project was launched to identify and record every species on earth in the next 25 years. It is a very challenging undertaking considering that to date 1.5 million organisms have been named. It is estimated that anywhere from 7 – 100 million living species exist.

9.5 Discovery of New Microorganisms in the Stratosphere

On March 18th, 2009, three new species of bacteria, which are not found on earth and which are highly resistant to ultra-violet radiation, were discovered in the upper stratosphere by Indian scientists. The new species have been named as:

• Janibacter hoylei, after the distinguished astrophysicist Fred Hoyle
• Bacillus isronensis recognizing the contribution of Indian Space Research Organization (ISRO) in the balloon experiments which led to its discovery
• Bacillus aryabhata after India’s celebrated ancient astronomer Aryabhata and also the first satellite of ISRO.