Biodegradation genes as marker genes in microbial ecosystems

Abstract

For the detection of specific biodegradative microorganisms in the environment, DNA hybridization has been extensively used and throughly reviewed [1, 4, 10]. More often, DNA hybridization can be applied in colony hybridization where the cells from any soil sample are washed off, cultured on nutrient containing agar plates, transferred to nylon membranes, lysed, their DNA fixed to the nylon membranes and subsequently hybridized with appropriate catabolic gene probe(s) [11]. DNA hybridization can also be used with directly extracted DNA from soil or any other source. Colony hybridization first requires culturing of cells while direct DNA extraction is done by in situ lysis of cells in the soil. Therefore, direct extraction of DNA overcomes the primary disadvantage in colony hybridization (culturability) as only a small fraction of the actual bacterial population in the soil is culturable. The DNA obtained through direct extraction from soil is usually blotted on nylon membrane and hybridized with appropriate catabolic gene probe(s) as in colony hybridization [7].