M.L. Krumme R. L. Smith J.M. Tiedje S.M. Thiem 1994 <p><span>A PCR primer set and an internal probe that are specific for <i>Pseudomonas</i> sp. strain B13, a 3-chlorobenzoate-metabolizing strain, were developed. Using this primer set and probe, we were able to detect <i>Pseudomonas</i> sp. strain B13 DNA sequences in DNA extracted from aquifer samples 14.5 months after <i>Pseudomonas</i> sp. strain B13 had been injected into a sand and gravel aquifer. This primer set and probe were also used to analyze isolates from 3-chlorobenzoate enrichments of the aquifer samples by Southern blot analysis. Hybridization of Southern blots with the <i>Pseudomonas</i> sp. strain B13-specific probe and a catabolic probe in conjunction with restriction fragment length polymorphism (RFLP) analysis of ribosome genes was used to determine that viable <i>Pseudomonas</i> sp. strain B13 persisted in this environment. We isolated a new 3-chlorobenzoate-degrading strain from one of these enrichment cultures. The B13-specific probe does not hybridize to DNA from this isolate. The new strain could be the result of gene exchange between <i>Pseudomonas</i> sp. strain B13 and an indigenous bacterium. This speculation is based on an RFLP pattern of ribosome genes that differs from that of <i>Pseudomonas</i> sp. strain B13, the fact that identically sized restriction fragments hybridized to the catabolic gene probe, and the absence of any enrichable 3-chlorobenzoate-degrading strains in the aquifer prior to inoculation.</span></p> application/pdf 10.1128/aem.60.4.1059-1067.1994 en American Society for Microbiology Use of molecular techniques to evaluate the survival of a microorganism injected into an aquifer article