Cultivated Organisms

Historically, prokaryotes were classified on the basis of their phenotypic (observable) characteristics. Prokaryotic taxonomy therefore involved measuring a large number of characteristics, including morphology and biochemical characteristics (e.g., ability to grow on different substrates, cell wall structure, antibiotic sensitivities, and many others). This contrasts with classification of eukaryotic organisms, for which phylogenetic (evolution-based) classification was possible through the availability of fossil evidence.

A major revolution occurred with the realization that evolutionary relationships could be deduced on the basis of differences in gene sequence. The most important gene for prokaryote phylogeny is the 16S ribosomal RNA (rRNA) gene, which is present in all cells. The gene is approximately 1500 bases in length and possesses regions in which sequences are conserved, facilitating sequence alignment, and variable and hypervariable regions, which enable different organisms to be discriminated from one another. Genetic distance, calculated by quantitative comparison of sequence differences between organisms, allows evolutionary distance to be estimated.

A major discovery arising from this approach (Woese et al., 1990) was that prokaryotes consist of two major domains, the Archaea and the Bacteria, which are as distant from each other as each is from the Eucarya (Fig. 5.1). The major

Bacteria Archaea Eucarya

Bacteria Archaea Eucarya

FIGURE 5.1 The universal tree of life constructed by analysis of sequences of small subunit rRNA genes (with permission from Wheelis et al., 1992).

bacterial groups are shown in Figs. 5.1 and 5.2; the major archaeal groups are shown in Fig. 5.1. Each group in these domains is discussed in more detail below. This approach also led to a reanalysis and reappraisal of classification within the Archaea and Bacteria, and major divisions are presented in Tables 5.1 and 5.2. The 16S rRNA gene, while useful in defining high-level taxonomic groups, is less useful for fine-scale resolution. This requires analysis of other genes or alternative methods, e.g., DNA-DNA hybridization, comparison of sequences of several genes or of whole genomes, and comparison of proteins (see Chap. 4).

Organic Gardeners Composting

Organic Gardeners Composting

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