Application of gene probe methods for monitoring specific microbial populations in freshwater ecosystems

Abstract

Several gene probe methods were used to monitor specific microbial populations in freshwater microcosms. Detection methods included nonselective plating – colony hybridization, selective plating – colony hybridization, most probable number – filter hybridization, and community DNA extraction – dot blot hybridization. Tests were conducted in freshwater microcosms inoculated with a 4-chlorobiphenyl degrading Alcaligenes A5 or a 2,4,5-trichlorophenoxyacetic acid degrading Pseudomonas cepacia AC1100. Colony hybridization performed on colonies detected on a nonselective medium sometimes failed to detect both Alcaligenes A5 and P. cepacia AC1100 when the target populations comprised less than 0.1% of the total population, even though the target populations comprised less than 0.1% of the total population, even though the target populations were present at concentrations of greater than 104 viable cells/mL as indicated by other detection methods. Selective plating – colony hybridization, most probable number – filter hybridization, and dot blot hybridization using DNA extracted from the microbial community consistently indicated persistence of the added P. cepacia AC1100 in the microcosms. Although differing in their detection reliability and sensitivity, the various gene probe detection methods indicated persistence with a slow decline of both the Alcaligenes A5 and P. cepacia AC1100 over an 8-week period.Key words: DNA probes, environmental, bacteria, detection, biodegradation.