As a system for studying the fate of genetically engineered microorganisms in the environment, we have previously constructed recombinant plasmids encoding a xylE marker gene (C. Winstanley, J.A.W. Morgan, R.W. Pickup, J.G. Jones, and J.R. Saunders, Appl. Environ. Microbiol. 55: 771-777, 1989). A series of direct membrane filter methods have been developed which facilitate the detection of bacterial cells harboring the xylE gene, its product, catechol 2,3-dioxygenase, and catechol 2,3-dioxygenase enzyme activity directly from water samples. These methods enable detection of recombinant populations at concentrations as low as 10³ to 10⁴ cells ml of lake water^-1. Direct detection facilitates ecological studies of a range of bacterial strains containing the marker system in aquatic environments. The fate of a recombinant pseudomonad population in lake water was assessed by a combination of colony-forming ability, direct counts, and direct detection of the xylE gene and phenotypic expression of its product.