In 1909, H. Joel Conn (25) expressed the hope that methods would soon be at hand by which the significance of the different bacteria present in any soil could be determined. However, by 1918 he was pointing out that the methods available to him, which relied on cultivation of bacteria on artificial media, resulted in the formation of colonies by only 1.5 to 10% of the bacterial cells in soil (26). Fifty years later, Vagn Jensen concluded a review of cultivation-based methodologies by stating his suspicion that those cells that were forming colonies were unrepresentative of the total bacterial community (59). This was confirmed when cultivation-independent methods began to be used to study soil bacteria (see below). Even so, in the absence of better methods, the pure cultures derived from the colonies that did form were extensively and successfully studied throughout the 20th century. Much of our basic knowledge of soil bacteria, as well as the discovery of many important antibiotics, came from investigations of pure cultures (2, 86, 104). Cultured isolates are still very important in developing our understanding of bacterial physiology, genetics, and ecology (85, 122).

Beginning in the 1990s, the application of molecular ecological methods, especially those based on surveys of genes after PCR amplification, has allowed cultivation-independent investigations of the microbial communities of soils to be made. The power of these methods has largely rendered obsolete the plate count approach to detecting and enumerating subsets of soil bacteria, and a range of diagnostic and quantitative methods that target functional genes, phylogenetically informative genes, or RNAs has been developed (49, 69). In particular, 16S rRNA and its gene have proven to be useful and powerful markers for the presence of bacteria in samples (36, 56, 88). The utility of these markers is facilitated by the availability of primers that allow amplification of almost the complete gene or its RNA product (66) and by the phylogenetic