Cover -- Title Page -- Copyright Page -- Contents -- Preface -- Introduction -- Chapter 1 Soil Ecosystems: Physical and Chemical Boundaries -- 1.1 Soil as an Ecosystem -- 1.1.1 Soil System Function -- 1.1.2 Soil Formation and the Microbial Community -- 1.1.3 Implications of Definition of the Soil Ecosystem -- 1.2 The Micro-ecosystem -- 1.2.1 Interaction of Individual Soil Components with the Biotic System -- 1.2.2 Aboveground and Belowground Communities and Soil Ecosystem Synergistic Development -- 1.3 The Macro-ecosystem -- 1.4 Concluding Comments -- References
Chapter 2 The Soil Ecosystem: Biological Participants -- 2.1 The Living Soil Component -- 2.1.1 Biological and Genetic Implications of Occurrence of Living Cells in Soil -- 2.1.2 Implications of Microbial Properties for Handling of Soil Samples -- 2.2 Measurement of Soil Microbial Biomass -- 2.2.1 Direct Counting Methods -- 2.2.2 ATP Measure of Soil Microbial Biomass -- 2.2.3 Soil Aerobic Respiration Measurements -- 2.2.4 Chloroform Fumigation (Extraction and Incubation) Technique -- 2.2.5 Limitations of Microbial Biomass Measurements -- 2.3 The Nature of Soil Inhabitants
2.4 Autecology and Soil Microbiology -- 2.4.1 Limitations to Autecological Research -- 2.4.2 Autecological Methods -- 2.4.3 PCR for Quantification of Soil Microbes (see Figure 2.7) -- 2.4.4 Expression of Population Density per Unit of Soil -- 2.4.5 Products of Soil Autecological Research -- 2.5 Principles and Products of Synecological Research -- 2.6 Interphase Between Study of Individual and Community Microbiology -- 2.7 Concluding Comments -- References -- Chapter 3 Microbial Diversity of Soil Ecosystems -- 3.1 Classical Culture-Based Studies of Soil Microbial Diversity
3.1.1 Value of Culture-Based Studies of Soil Microbial Diversity -- 3.1.2 Limitations of Culture-Based Studies of Soil Microbial Diversity -- 3.1.3 The Challenge of Defining Bacterial Species -- 3.1.4 Alternatives to Bacterial Strain Isolation -- 3.2 Surrogate Measures of Soil Microbial Diversity -- 3.3 Diversity Surrogates: Physiological Profiling -- 3.3.1 Physiological Profiling of Isolates -- 3.3.2 Community-Level Physiological Profiling -- 3.3.3 Value of Community-Level Physiological Profiling -- 3.3.4 Limitations of Community Level Physiological Profiling
3.4 Diversity Surrogates: Phospholipid Fatty Acid Analysis -- 3.4.1 PLFA Analysis of Isolates -- 3.4.2 Community PLFA Analysis -- 3.4.3 Value of PLFA Analysis -- 3.4.4 Limitations of PFLA Analysis -- 3.5 Nucleic Acid-Based Analyses of Soil Microbial Diversity -- 3.5.1 Nucleic Acid Based Analysis of Isolates -- 3.5.2 Community Nucleic Acid Analysis -- 3.5.3 DNA Extraction -- 3.5.4 Analysis of Community DNA -- 3.6 PCR-Based Methods -- 3.6.1 Clone Library Sequencing -- 3.6.2 DNA-Based Fingerprinting Techniques -- 3.6.3 High-Throughput Amplicon Sequencing -- 3.6.4 Limitations of PCR-Based Methods
