Escherichia coli is a consistent and predominant facultative inhabitant of the human gastrointestinal tract (10). The regular presence of E. coli in the intestine and feces of warm-blooded animals makes this bacterium an indicator of fecal pollution. The grazing of cattle and land application of animal wastes may lead to the occurrence of enteric pathogens in nearby surface and groundwaters. This potential contamination due to animal husbandry operations can be a serious threat to public health (52). Therefore, the fate and transport of pathogenic microorganisms that are shed from cattle operations must be understood to evaluate and possibly mitigate the contamination of water supplies. Soil exhibits a filtering capacity for microorganisms by the combined actions of straining, adsorption, and adhesion onto soil surfaces. Adhesion is commonly thought to be the main factor retarding bacterial transport in soil. The main factors that affect bacterial adhesion are ionic strength, the pH of the aqueous phase, and the surface properties of the geological matrix and bacterial cell (35, 39, 47, 58). The degree of adhesion to a solid surface can, however, change dramatically with the physiological state of the bacterium, due to changes in cell surface properties (4, 7, 27, 47). Whether this described soil filtering capacity explains the retardation or distribution of E. coli in soils affected by cattle activity remains untested. The fate and distribution of a species in a natural environment may, in part, be governed by diversity within the species; hence, estimating this diversity is requisite. Several high-resolution molecular fingerprinting techniques have been used to reveal species and subspecies diversity (41, 46, 54). Ribotyping (1, 38) and repetitive extragenic palindromic PCR (2, 9) techniques have been successfully applied to cluster E. coli strains according to host type. If the fate and transport of E. coli in soil-dominated environments are governed by interactions with solid matrices, then subspecies variability in genotype or phenotype related to surface adhesion might be expected to establish its population ecology. One mechanism for ensuring survival in the environment might be a differential biofilm-forming ability within a natural E. coli population. Although biofilm formation is the net result of multiple interacting molecular events (14, 22) and is most conveniently measured at the phenotypic level, a few discrete genetic systems may be essential to adhesion properties, and any population level variability in their occurrence appears worthy of study. Motility, for example, is a variable property within E. coli that may influence surface attachment and detachment (30, 55) and is required for biofilm formation in both rich and minimal environments (8, 40). Therefore, differences in motility may affect transport in the environment, as they might facilitate transport through porous media (42) or towards a surface (30, 40). At the genotypic level, there are two phase-variable surface proteins, type 1 fimbriae and antigen 43 (Ag43), encoded by the fim gene cluster (25, 36) and agn43 (20), respectively, which have been suggested as critical in determining the adhesion properties of E. coli. Type 1 fimbriae are the most common adhesins produced by E. coli associated with colonization of extraintestinal locations such as the urinary tract (6). Located at the tip of each fimbria and also interspersed along the length (23), the FimH protein has been implicated in biofilm formation on abiotic surfaces under static growth conditions (40). On the other hand, Ag43, which extends beyond the lipopolysaccharide structure, is the most abundant phase-variable outer membrane protein in E. coli (37), and is regulated by competition between deoxyadenosine methyltransferase and the global regulator OxyR (56). Expression of Ag43 has not yet been tested as relevant for intestinal colonization but is implicated in biofilm formation in glucose-minimal but not in rich media (8). The natural habitat of E. coli is the gastrointestinal tract, where conditions are very different from the soil or laboratory environment in terms of nutrient composition, pH, and oxygen availability. Adhering to animal tissue or soil particles might be of fundamental importance in a bacterial life cycle. It is expected that conditions in the gastrointestinal tract would favor expression of FimH (34), while repression of Ag43 expression may provide a selective advantage by lowering susceptibility to phage infection (11). Furthermore, it has been suggested that fimbrial expression per se negatively affects the expression of agn43 by affecting the thiol-disulfide status of OxyR (44, 45). Phase variation, regulating the expression of fimbriae and Ag43 in a population, may result in subpopulations of cells with very different adhesion properties and may be an important factor in the selective colonization of surfaces. The purpose of the present study was to isolate and describe the strain diversity of an E. coli population retrieved from a long-term operating bovine feedlot by employing a whole-genome fingerprinting technique. Additional parameters (the presence of fimH and agn43, motility, biofilm formation ability, and resistance to certain antibiotics) were also investigated to examine possible correlations with the vertical distribution of population diversity in the soil profile.