Environmental Microbiology

  1. Methods in Environmental Microbiology
    1. Cultivation-Based Methods
      1. Enrichment Techniques
        1. Selective Enrichment
          1. Winogradsky Columns
          2. Isolation Techniques
            1. Pure Culture Isolation
              1. Single Cell Isolation
              2. Culture Media
                1. Selective Media
                  1. Differential Media
                    1. Defined vs Complex Media
                    2. High-Throughput Culturing
                      1. Microplate Methods
                        1. Automation Technologies
                        2. Limitations of Cultivation
                          1. Great Plate Count Anomaly
                            1. Viable but Non-Culturable States
                          2. Microscopy and Imaging
                            1. Light Microscopy
                              1. Brightfield Microscopy
                                1. Phase Contrast Microscopy
                                  1. Differential Interference Contrast
                                  2. Fluorescence Microscopy
                                    1. Epifluorescence Microscopy
                                      1. Confocal Laser Scanning Microscopy
                                        1. Fluorescent Staining Techniques
                                        2. Electron Microscopy
                                          1. Transmission Electron Microscopy
                                            1. Scanning Electron Microscopy
                                              1. Sample Preparation Techniques
                                              2. Advanced Imaging Techniques
                                                1. Fluorescence In Situ Hybridization
                                                  1. Live Cell Imaging
                                                    1. Super-Resolution Microscopy
                                                  2. Molecular Methods
                                                    1. Nucleic Acid Extraction
                                                      1. DNA Extraction Protocols
                                                        1. RNA Extraction and Preservation
                                                          1. Quality Assessment
                                                          2. PCR-Based Techniques
                                                            1. Polymerase Chain Reaction
                                                              1. Quantitative PCR
                                                                1. Reverse Transcription PCR
                                                                  1. Primer Design and Optimization
                                                                  2. Community Fingerprinting
                                                                    1. Denaturing Gradient Gel Electrophoresis
                                                                      1. Temperature Gradient Gel Electrophoresis
                                                                        1. Terminal Restriction Fragment Length Polymorphism
                                                                          1. Automated Ribosomal Intergenic Spacer Analysis
                                                                          2. Sequencing Technologies
                                                                            1. Sanger Sequencing
                                                                              1. Next-Generation Sequencing Platforms
                                                                                1. Illumina Sequencing
                                                                                  1. Ion Torrent Sequencing
                                                                                  2. Third-Generation Sequencing
                                                                                    1. PacBio Sequencing
                                                                                      1. Oxford Nanopore Sequencing
                                                                                  3. Omics Approaches
                                                                                    1. Genomics and Metagenomics
                                                                                      1. Marker Gene Sequencing
                                                                                        1. 16S rRNA Gene Sequencing
                                                                                          1. ITS Sequencing
                                                                                            1. Functional Gene Sequencing
                                                                                            2. Shotgun Metagenomics
                                                                                              1. Genome Assembly and Annotation
                                                                                                1. Comparative Genomics
                                                                                                2. Transcriptomics and Metatranscriptomics
                                                                                                  1. RNA Sequencing
                                                                                                    1. Gene Expression Analysis
                                                                                                      1. Functional RNA Analysis
                                                                                                      2. Proteomics and Metaproteomics
                                                                                                        1. Protein Extraction Methods
                                                                                                          1. Mass Spectrometry
                                                                                                            1. Functional Protein Analysis
                                                                                                            2. Metabolomics and Metabolomics
                                                                                                              1. Metabolite Extraction
                                                                                                                1. Analytical Techniques
                                                                                                                  1. Metabolic Pathway Analysis
                                                                                                                2. Activity and Function Measurements
                                                                                                                  1. Stable Isotope Techniques
                                                                                                                    1. Stable Isotope Probing
                                                                                                                      1. Isotope Ratio Mass Spectrometry
                                                                                                                      2. Radioisotope Methods
                                                                                                                        1. Radiotracer Experiments
                                                                                                                          1. Microautoradiography
                                                                                                                          2. Biogeochemical Rate Measurements
                                                                                                                            1. Gas Flux Measurements
                                                                                                                              1. Nutrient Turnover Rates
                                                                                                                                1. Enzyme Activity Assays
                                                                                                                                2. Single Cell Analysis
                                                                                                                                  1. Flow Cytometry
                                                                                                                                    1. Single Cell Genomics
                                                                                                                                      1. Nano-scale Secondary Ion Mass Spectrometry

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                                                                                                                                  4. Microbiology of Major Environments