1. INTRODUCTION 2. SAMPLE IDENTIFICATION & DATA MANAGEMENT FOR MICROBIOLOGY SAMPLES 3. RATE AND ACTIVITY MEASUREMENTS 4. COUNTING METHODS 5. BIOMASS AND BIOMARKER METHODS 6. MOLECULAR METHODS FOR INVESTIGATING DIVERSITY: CLONE LIBRARIES 6.1. DNA EXTRACTION FROM SEDIMENTS 6.2. PCR 6.3. SELECTING AND CONFIRMING EFFICACY OF 16S RRNA GENE PRIMERS 6.4. SELECTING AND USING PRIMERS FOR FUNCTIONAL GENES 6.5. CLONING, CLONE SELECTION AND SEQUENCING 6.6. SCREENING CLONE LIBRARIES FOR ARTEFACTS, CHIMERAS AND COVERAGE 6.7. PHYLOGENETIC ANALYSES 7. MOLECULAR METHODS FOR INVESTIGATING DIVERSITY: PROFILING METHODS 7.1. DENATURING GRADIENT GEL ELECTROPHORESIS (DGGE) FOR 16S RRNA GENES 7.2. BENTHIC DIVERSITY PROFILING OF BACTERIA USING ARISA 7.3. TERMINAL RESTRICTION FRAGMENT LENGTH POLYMORPHISM (T-RFLP) ANALYSIS 8. CULTURE METHODS 9. REFERENCES: FULL LIST
