Effective monitoring of bacteria in the environment is a technical and methodological challenge. Detection and analysis of whole cells or marker molecules from entities as small as individual bacteria is a difficult task. Often it is necessary to increase the number of cells present in a sample using a culture step, before attempting the analysis step. In ecological studies, such indirect methods are easily criticized because they select for bacteria suited to the culture conditions at the expense of the majority of bacteria present (although such methods are used routinely for bacteriological quality control). However, many developments in methodologies have direct monitoring as their goal, i.e., analysis of bacteria from a given sample without a culture step. A further problem of the study of naturally occurring bacteria is the numbers of cells involved. Bacterial populations consist of immense numbers, and finding specific cells against a background that may consist of billions of nontarget cells is time-consuming and difficult.