Environmental microbiology is currently one of the most rapidly ex-panding areas of scientific research. Impetus for advanced investiga-tions has been provided by the development and application of molecu-lar techniques that facilitate the identification, characterization andmonitoring of microbes. These advances now allow detailed investiga-tions, developed in the laboratory, to be undertaken in the natural envi-ronment. Such studies confirm the remarkable biological diversityrepresented by microorganisms from their basic genetic structure to theregulated communications that occur within and between communitiescontributing to ecosystem function. However, while it is apparent thatmicroorganisms constitute the greater part of the planet’s biomass, andare central in maintaining the biosphere, we remain essentially ignorantof a great majority of the functions or processes they undertake. One ofthe limiting factors in the study of their ecology, even within communi-ties or populations, is that of scale. For instance, for soil it is very hard toassess microbes and their activities at the level of each individual porewhere microbial soil inhabitants occur. Highly sensitive and specific toolsare, thus, required for such detailed investigations. However, there is aparadox. Until a greater knowledge of the genetic and metabolic diversitywithin the microbial environment is obtained it remains difficult toinvestigate these complex communities or design relevant experimentsthat target the role of individuals or specific genes and their products.This situation is currently changing at an ever increasing rate. In this vol-ume we have attempted to bring together a series of reviews of the ap-proaches taken to study the ecology and functional activity of individualmicrobial cells and populations in environmental habitats, with a specialfocus on the use of marker/reporter genes for monitoring release strains