Transposon Tn5 mutants of a wheat root growth-inhibiting nonfluorescent Pseudomonas sp. were inoculated into intact soil-core microcosms to determine the utility of intact soil cores for evaluating the fate and transport of microorganisms in agricultural ecosystems. Transposon Tn5 mutants that no longer produced a toxin (tox-) to inhibit the growth of wheat roots or Escherichia coli, and Tn5 mutants that retained the toxin-producing ability (tox+), were inoculated into plow layer soil of intact soil-core microcosms. Spring wheat was then planted, and Tn5 mutant populations were enumerated over time in the bulk soil and with depth in the bulk soil, rhizosphere, and rhizoplane. Pseudomonas sp. Tn5 mutants were observed in soil-core leachates and in the gut of earthworms introduced into microcosms. The population of the introduced Tn5 mutants declined over time in the surface soil, but colonized the wheat rhizosphere and rhizoplane throughout the 60-cm soil-core depth. Rhizoplane populations of the tox+ Tn5 mutants were higher than populations of tox- mutants at the seedling stage, but significant differences were not observed at later stages of plant growth or in the rhizosphere. The Tn5 mutants were transported through the core with percolating water and were present in the gut of earthworms.