2015 Elsevier Inc. All rights reserved. The discovery of the double-stranded structure of DNA provided the foundation of numerous molecular biology-based methods that have evolved over the past several decades. The goal of this chapter is to present the nucleic acid-based methodologies most commonly used to enumerate and characterize environmental microorganisms. A description of the structure of nucleic acids (DNA/RNA) is followed by a discussion of methodologies used to extract nucleic acids from environmental samples. The first technologies utilizing nucleic acids that we describe are hybridization assays: such as gene probes; dot blots; and microarrays and fluorescent in situ hybridization (FISH). This is followed by amplification assays including multiple polymerase chain reaction (PCR)-based technologies; DNA fingerprint assays; and recombinant DNA techniques.
