Procaryote Diversity

Ever since bacteria were first identified, microbiologists have attempted to bring order to the way they are named and classified. The range of morphological features useful in the differentiation of bacteria is fairly limited (compared, say, to animals and plants), so other characteristics have also been employed. These include metabolic properties, pathogenicity, nutritional requirements, staining reactions and antigenic properties. The first edition of Bergey's Manual of Systematic Bacteriology (henceforth referred to as 'Bergey'), published in the mid-1980s, mainly used phenotypic characteristics such as these to classify bacteria. The result placed bacteria into taxonomic groups that may or may not reflect their evolutionary relationship to one another. In the years since the first edition of Bergey, the remarkable advances made in molecular genetics have led to a radical reappraisal of the classification of bacteria. Comparison of nucleic acid sequences, notably those of 16S riboso-mal RNA genes, has led to a new, phylogenetically based scheme of classification, that is, one based on how closely different groups of bacteria are thought to be related, rather than what morphological or physiological features they may share. Ribosomal RNA occurs in all organisms, and serves a similar function, thus to a large extent these sequences are conserved (remain similar) in all organisms. The nature and extent of any differences that have crept in during evolution will, therefore, be an indication of the relatedness of different organisms.

The second edition of Bergey aims to reflect this change of approach and reassign many bacteria according to their phylogenetic relationship, as deduced from molecular evidence. Due to be issued in five volumes over a number of years, the first volume was published in 2001. As an example, the genus Pseudomonas previously contained some 70 species on the basis of phenotypic similarities, but in the second edition of Bergey, taking into account 16S rRNA information, many of these are assigned to newly created genera.

It must be stressed that Bergey (second edition) does not represent the definitive final word on the subject, and that the classification of bacteria is very much a developing science, in a constant process of evolution. Indeed, microbiologists are by no means unanimous in their acceptance of the 'molecular' interpretation of bacterial taxonomy. Some point to perceived inadequacies in the collection of data for the

The phenotype of an organism refers to its observable characteristics.

The genotype of an organism refers to its genetic make-up.

Procaryote Domain
Figure 7.1 Phylogenetic relationships in the Procaryota. A phylogenetic tree based on 16S ribosomal RNA data, showing the relationships between members of the Archaea and the Bacteria. The position on the tree of the Eucarya (all eucaryotic organisms) is also indicated

scheme, as well as errors in the data arising from the sequencing and amplification techniques utilised. Other critics question the validity of a scheme based on 16S rRNA data when it seems increasingly likely that lateral gene transfer played an important role in bacterial evolution.

In the following pages, the major taxonomic groupings are discussed according to their arrangement in the second edition of Bergey. Figure 7.1 shows a phylogenetic tree, reflecting current ideas on the relationship between the major bacterial groups, as determined by 16S rRNA sequencing.

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