Nucleic acid analytical approaches in bioremediation: site assessment and characterization

Bioremediation, the removal of environmental pollutants by living organisms, has become a viable and promising means of restoring contaminated sites. Gene probing techniques have enhanced our ability to assess the efficacy of microbial-based remediation efforts. DNA probes targeting specific genetic sequences, i.e. those genes responsible for the degradative ability of the microorganism, can be used to characterize a contaminated site throughout the bioremediation program to determine overall community structure and catabolic activity. To do so, however, requires efficient techniques for recovering nucleic acids from environmental sites as well as methods for generating probes to the specific genetic sequences desired. This review discusses procedures for isolating DNA, messenger RNA, and ribosomal RNA from environmental samples, the utilization of polymerase chain reactions to construct gene probes, and hybridization methods to genetically match the probe to the environmental sample. The use of these methods and advancement of techniques at several bioremediation sites is also presented along with typical problems and limitations encountered. The first case study involves monitoring the effects of nutrient addition to stimulate microbial degradation of chlorinated solvents at the DOE Westinghouse Savannah River Site. The next case study describes the bioremediation of chlorinated solvents and low levels of BTEX at Dover Air Force Base, Delaware. The final study is a field-scale natural attenuation project currently underway at Columbus Air Force Base, Mississippi. (C) 1998 Elsevier Science B.V.