Nucleic Acids in the Environment

"The protocols that are presented are well defined in a step-by step manner. This should allow their easy implementation in a laboratory. An attractive feature ... is the inclusion of a series of tables with suggested primers for analysis of specific genes." Quarterly Review of Biology

• 1 Introduction to Nucleic Acids in the Environment: Methods and Applications.- 1.1 Introduction.- 1.2 Cell Lysis, Nucleic Acid Extraction and Purification Protocols.- 1.3 Analysis of Environmental Nucleic Acids.- 1.4 Concluding Remarks.- References.- 2 Recovery of Bacterial Cells from Soil.- 2.1 Introduction.- 2.2 Strategies for Cell Extraction.- 2.3 Recommended Methods.- 2.4 Practical Experiences and Recommendations.- References.- 3 Extraction, Purification, and Analysis of DNA from Soil Bacteria.- 3.1 Introduction.- 3.2 Bacterial DNA.- 3.3 Direct Extraction of DNA from Soil.- 3.4 Purity Control and Characterization of Soil Bacterial DNA.- References.- 4 Extraction and Analysis of Microbial DNA from Soil.- 4.1 Introduction.- 4.2 DNA Extraction Methods.- 4.3 Evaluation of DNA Extraction Methods.- 4.4 Methods for Analysis of DNA from Soil.- 4.5 Concluding Remarks.- References.- 5 Extraction and Amplification of DNA from the Rhizosphere and Rhizoplane of Plants.- 5.1 Introduction.- 5.2 Sample Preparation.- 5.3 Extraction, Purification and Quantification of DNA from the Rhizosphere.- 5.4 PCR Analysis of Bacterial DNA from the Rhizosphere and Rhizoplane of Plants.- 5.5 Concluding Remarks.- References.- 6 Extraction of DNA from the Phyllosphere.- 6.1 Introduction.- 6.2 Materials, Methods and Protocols.- 6.3 Concluding Remarks.- References.- 7 Specific DNA Sequences for Detection of Soil Bacteria.- 7.1 Introduction.- 7.2 Objectives and Limitations.- 7.3 Target DNA, DNA Extraction and Detection in Soil.- 7.4 Detailed Procedures.- 7.5 Application of Methodology.- References.- 8 PCR Amplification of DNA from Root Nodules.- 8.1 Introduction.- 8.2 Methods for Detection of Rhizobia.- 8.3 Detection of Root Nodule Bacteria by PCR.- 8.4 Conclusions.- References.- 9 Extraction of DNA and RNA from Aquatic Environments.- 9.1 Introduction.- 9.2 DNA as a Biomass and Ecological Indicator.- 9.3 RNA as a Biomass and Ecological Indicator.- 9.4 Biomass and Activity Measurements of Aquatic Microorganisms using RNA and RNA /DNA Ratios.- 9.5 Extraction of Nucleic Acids for Molecular Biological Studies.- 9.6 Molecular Methods for Studying RNA in Aquatic Environments.- 9.7 Extraction of DNA from Aquatic Microbial Populations.- 9.8 Extraction of RNA from Aquatic Microbial Populations.- References.- 10 PCR Amplification of DNA Recovered from the Aquatic Environment.- 10.1 Introduction.- 10.2 Concentration of Water Samples from Aquatic Environments.- 10.3 Sample Preparation for PCR Amplification.- 10.4 Processing of Dissolved DNA in the Aquatic Environment.- 10.5 Processing of Nucleic Acids from Biofilms.- 10.6 PCR Amplification.- 10.7 Identification and Analysis of the Amplified DNA.- 10.8 PCR Contamination Control.- 10.9 Enhancing the Specificity of the PCR Reaction.- 10.10 Use of Arbitrarily Primed PCR (Ap-PCR) in Environmental Microbiology.- 10.11 In situ PCR Amplification.- 10.12 The Use of PCR in Aquatic Environments.- 10.13 Detection of Viruses in Water.- 10.14 Discussion.- References.- 11 Extraction and Amplification of 16S rRNA Genes from Deep Marine Sediments and Seawater to Assess Bacterial Community Diversity.- 11.1 Introduction.- 11.2 DNA Extraction.- 11.3 Amplification of 16S Ribosomal RNA Gene Sequences.- 11.4 Cloning and Sequencing.- 11.5 Sequences Obtained from Marine Sediments and Coastal Waters.- References.- 12 Application of the PCR for Detection of Antibiotic Resistance Genes in Environmental Samples.- 12.1 Introduction.- 12.2 Selection of PCR Primers and Gene Probes for Specific Detection of sat and nptII Genes.- 12.3 Detection of Antibiotic Resistance Genes in Bacterial Isolates Using PCR.- 12.4 Detection of Antibiotic Resistance Genes Using DNA Extraction and PCR.- 12.5 Detection of Antibiotic Resistance Genes in Total Community DNA Extracts from Environmental Habitats..- 12.6 Conclusions.- References.