Abstract
Detection and quantification of soil organisms using traditional methods (culture, plating and microscopy) are difficult and do not always allow identification. In the last decade, real-time quantitative polymerase chain reaction (qPCR) has allowed rapid, sensitive, specific and high-throughput detection and quantification of organisms. For example, in plant health, this new method helps in the management of plant disease in agriculture and forestry. However, direct DNA detection in soil is often difficult because of PCR inhibitors, low inoculum density and inadequate sampling techniques. This review presents diverse real-time qPCR methods for the detection and quantification of soil-borne organisms (mainly pathogenic organisms), addresses difficulties using real-time qPCR for quantification of organisms in soil and presents solutions and methods to overcome these challenges. Examples of utilizing real-time qPCR on different types of organisms such as fungi, bacteria, nematodes, viruses, plants and for soil diversity are presented along with explanations of computational techniques for the estimation of organism levels in soil. The different applications of quantification are discussed with regard to detection and management, biocontrol recovery, genotyping of organism and population studies and ecological biodiversity. The importance of having an internal control and quality DNA for accurate quantification and high copy-number for sensitivity is discussed.