The use of reporter genes in the study of microbial ecology

The role of a particular micro-organism in ecosystem or community function can be determined only if knowledge of both its abundance and activity in a natural habitat is known.For this reason there has been considerable effort to develop methods to selectively isolate and quantify micro-organisms from natural settings.These studies have resulted in the development of selective media useful for the isolation of particular groups of micmrganisms as well as genetic markers for either the selective isolation or the specific identification of individual microbial strains (Atlas et nl.1992).Excellent reviews on recent develop ments in the isolation and identification of micro-organisms from natural habitats, particularly as it relates to the use of recombinant micro-organisms, have appeared (Atlas et nl.1992; Drahos 1991; Kluepfel 1993; Prosser 1994; Sayler 81 Layton 1990).On the other hand, it has generally been difficult to ascertain the phenotypes that microorganisms exhibit while in nature.Many traits that microbes might exhibit cannot be directly assessed while the cells occur in natural habitats such as in soil, in the rhizosphere, in and on plants, and elsewhere.For example, it is generally impossible to detect the presence of specific enzymes, antibiotics, siderophores, or other compounds elaborated by micro-organisms in situ (Alexander 1971).For this reason, the behaviour of microbial strains in natural habitats is usually inferred from studies of these strains in culture.The assumption generally made in this approach to the study of microbial ecology is that those phenotypes expressed in culture will also be expressed, at least in certain situations, in more natural settings and vice versa (Tempest et al. 1983;Elliot et al. 1986).Many recent studies, however, have demonstrated that microbes can exhibit quite habitatspecific patterns of gene expression (Beaulieu & Van Gijsegem 1990; CopIin & Cook 1990;