9    FACTORS AFFECTING THE RECOVERY OF MICROBIAL
DNA FROM CONTAMINATED SOIL AND VALIDATION
OF HYBRIDIZATION QUALITY
M.H. Kim, Ph.D. Candidate
Department of Civil & Environmental Engineering
Rensselaer Polytechnic Institute
Troy, New York 12180
Lenore S. Clesceri, Associate Professor
Department of Biology
Rensselaer Polytechnic Institute
Troy, New York 12180
INTRODUCTION
The biodegradation of pollutants in the environment is a complex process, quantitative and qualitative aspects of which depend on the nature and amount of pollutant present, the ambient and seasonal
environmental conditions, and the composition of indigenous microbial communities.1,9,10 Established or emerging biotechnological approaches have been shown to remove environmental pollutants, however, rates of pollutant biodegradation are often limited by environmental constraints or
possibly by the lack of suitable microbial populations.5 The use of biomass in detection systems based
upon biological molecules is an attractive biotechnology for specific detection in complex media. One
approach under investigation in the bioremediation field is the use of nucleic acid probes for microbial DNA detection of specific microorganisms that break down specific pollutants.
In the past decade, new knowledge has been developed on the biochemical and molecular basis for
microbial degradation of hazardous chemicals and environmental pollutants.14 Isolation of microbial
DNA from contaminated soil may become a useful tool with which to study population dynamics in
soils and as a means of tracking the fate of genetically engineered microorganisms (GEMs) used in
various biotechnologies." The use of DNA probes for hybridization to DNA sequences that encode
catabolic pathways can be used to determine the availability of the suitable genetic material for
degradation of specific contaminants. This kind of measurement may be useful in the design of
treatment processes for contaminated soil. Subsequent monitoring of the system for increased hybridization targets with specific nucleic acid probes (Table I) indicate effects of efforts made to improve
biodegradation.8
Determining microbiological function in complex media is useful in order to design systems for the
biodegradation of contaminated soils and waters as well as to evaluate the progress of the systems.
The application of DNA extraction methods to environmental samples can obviate the need for cell
cultivation, since cell cultivation may have the disadvantage of obtaining only a very small proportion
of the population. DNA extraction and hybridization methods can help in the detection of occurrence
Table I.    Examples of Nucleic Acid Probes Used in Environmental Samples
Target Probe
4-CB-degrading strains pSS50
Naphthalene-mineralizing strains NAH-7
Gram-negative mercury-resistant strains mer operon
Bacillus subtilus Cloned fragment of 23 S rRNA
Rhizobium R. trifolii chromosome
Nitrogen-fixing strains n//K,D,H genes from Klebsiella pneumoniae
C02-fixing strains Ribulose bisphosphate carboxylase gene
Data taken from (13)
49th Purdue Industrial Waste Conference Proceedings, 1994 Lewis Publishers, Chelsea, Michigan 48118. Printed in
U.S.A.
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