Molecular Methods for Studying Soil Ecology

Introduction 85

Types and Structures of Nucleic Acids 86 Use of Nucleic Acid Analyses for Soil Ecology Studies 88 Direct Molecular Analysis of Soil Biota 90 Nucleic Acid Hybridization 90 Confocal Microscopy 91 Biosensors and Marker Gene Technologies 92 Extraction of Nucleic Acids (DNA/RNA) 93 Choosing between DNA and RNA for Soil Ecology Studies 96 Analysis of Nucleic Acid Extracts 96

DNA:DNA Reassociation Kinetics 96 Microarrays 98

Restriction Fragment Length Polymorphism (RFLP) Analysis 100 Cloning 101 DNA Sequencing 102 Stable Isotope Probing 102 Partial Community Analyses—PCR-Based Assays 104 Electrophoresis of Nucleic Acids 107

PCR Fingerprinting 107 Similarity Analyses 112 Level of Resolution 112

Other Factors That May Affect Molecular Analyses 113 Sample Handling 113 Soil Chemical Factors 113 Sampling Scale 114 Summary 114 References 115

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Worm Farming

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