Polymerase chain reaction (PCR) analysis of soil microbial DNA

Abstract

Microbial communities as well as specific microorganisms and genes in soil can be detected and analysed by using methods based on nucleic acids [4, 8, 20, 21]. Analysis can be performed directly on colonies obtained from the environment by plating, using colony hybridization [14], or via Northern, Southern, dot or slot blot procedures unlashed on either microbial cells (dot/slot blots) or DNA extracted from cells or directly from the environment [15, 16]. In addition, environmental DNA can be characterized in terms of its internal reannealing [20] or hybridization behaviour [11], and these criteria have been taken as being characteristic for the complexity of microbial communities. However, a major problem often encountered with hybridization analysis directly on environmental DNA extracts is the lack of sensitivity, limiting the analysis to populations of cells or genes which occur in high numbers in the environmental samples [23].