This chapter discusses the molecular methods for studying soil ecology. No other area of soil ecology has developed more rapidly in recent years than the use of molecular methods to characterize the soil microbial community. The ability to extract deoxyribonucleic acids (DNA) and ribonucleic acids (RNA) from cells contained within soil samples and their direct analysis in hybridization experiments or use in polymerase chain reaction (PCR) amplification experiments allow to detect and characterize a vast diversity of microbes unimagined previously. Direct microscopic counts of soil bacteria are typically one to two orders of magnitude higher than counts obtained by culturing. The focus of this chapter is on methods for extracting and analyzing soil- and sediment-derived nucleic acids and drawing ecological information from analysis results. The chapter discusses the types and structures of nucleic acids and the analysis of nucleic acid extracts as well as the use of extracts for soil ecology studies. Biosensors and marker gene technologies are also elaborated in the chapter.
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