A direct correlation between the growth rates of bacterial cells, the average ribosome contents and the probe-conferred fluorescence has been reported (DeLong et al. 1989). This has been used to estimate the growth rates of individual cells in situ (Poulsen et al. 1993, Moller et al. 1995). Often it is also important to obtain information about how the functional components of an ecological system relate to the organization of the system. In communities that have an inherent architecture, such as biofilms and floes, the question of where various organisms are located is of interest. These determinations are difficult to make with conventional epifluorescence microscopy. By coupling in situ hybridization with fluorescently-labelled rRNA-targeted oligonucleotide probes with confocal laser scanning microscopy (Caldwell et al. 1992), it is possible to place the labelled microbes in a three-dimensional reconstruction of the intact microbial community (Moiler et al. 1996, Schramm et al. 1996, Manz et al. 1999, Sekiguchi et al. 1999).