Title: I, Microbiologist: A Discovery Based course in Microbial Ecology and Molecular Evolution Co: 2010 Ed: 1
ISBN: 9781555814700 Author: Erin R. Sanders-Lorenz, Jeffrey H. Miller Publisher: American Society for Microbiology
Contents 180182
About the Authors and Contributors
Unit 1 Soil Collection and Compositional Analysis
Section 1.1 Introduction to Microbial Ecology in the Rhizosphere
Section 1.2 Analysis of the Primary Literature: Biogeography of Soil Bacterial CommUnities
Reading Assessment
Experimental Overview
Experiment 1.1 Soil Collection from the Rhizosphere
Experiment 1.2 Streak Plate Practice
Experiment 1.3 Determine the Water Content of Soil by Dry-Weight Analysis
Experiment 1.4 Determine the pH of Soil
Unit 2 Cultivation-Dependent CommUnity Analysis
Section 2.1 Enrichment Strategies that Target the Microbial Inhabitants of the Rhizosphere
Section 2.2 Analysis Of The Primary Literature: Overcoming The Microbial Bottleneck Of The Uncultivated Majority
Reading Assessment
Experimental Overview
Experiment 2.1 Cultivation of Soil Microorganisms: First Enrichment
Experiment 2.2 Cultivation of Soil Microorganisms: Second Enrichment
Experiment 2.3 Purification of Microbial Isolates
Experiment 2.4 Preparation of Cell Samples for Storage at -80c
Unit 3 Molecular Analysis of Cultivated Bacterial CommUnities
Section 3.1 Pcr And Sequencing Of The 16S Rrna Gene
Reading Assessment
Experimental Overview
Experimental 3.1 Genomic DNA Isolation
Experimental 3.2 PCR of 16S rDNA
Experimental 3.3 Gel Electrophoresis of Amplicons
Experimental 3.4 Purification of PCR Products
Experimental 3.5 Quantification of Purified PCR Products
Experimental 3.6 DNA Sequencing of Purified 16S rDNA Amplicons
Unit 4 Phenotypic Characterization of Bacterial Isolates
Section 4.1 Microbial Production Of Antibiotics And The Emergent Resistome
Reading Assessment
Section 4.2 Microbial Contributions To The Production Of Biomass And Biofuels
Reading Assessment
Experimental Overview
Experimental 4.1 Microscopic Examination and Characterization of Isolates
Experimental 4.2 Wet Mount Preparation
Experimental 4.3 Gram Stains
Experimental 4.4 Testing for Antibiotic Production
Experimental 4.5 Testing for Antibiotic Resistance
Experimental 4.6 Testing for Cellulase Activity
Unit 5 Cultivation-Independent CommUnity Analysis of Soil Microbiomes
Section 5.1 Accessing "Uncultivatable" Microbiomes By Using Metagenomic Approaches
Section 5.2 Analysis Of The Primary Literature: The Human Gut Microbiome
Reading Assessment
Experimental Overview
Experiment 5.1 Isolation of Metagenomic DNA Directly from Soil
Experiment 5.2 PCR Amplification of 16S rDNA
Experiment 5.3 Gel Electrophoresis of Metagenomic 16S rRNA Genes
Experiment 5.4 Purification of Metagenomic 16S rRNA Genes
Experiment 5.5 Quantification of Purified Metagenomic PCR Products
Experiment 5.6 Cloning of PCR Products Using the TA-TOPO Kit
Experiment 5.7 TOPO Plasmid DNA Isolation from Transformants
Experiment 5.8 Screening of TOPO Clones by Restriction Analysis
Experiment 5.9 DNA Sequencing of TOPO Clones Containing 16S rRNA Genes
Unit 6 Bioinformatics Analysis of 16S rRNA Genes
Section 6.1 Mathematical Algorithms As The Building Blocks Of Dna Sequence Alignments
Section 6.2 Dna Sequence Alignments In A Blast Search
Section 6.3 Model-Based Alignment Tools For 16S Rrna
Section 6.4 Multiple Sequence Alignments
Reading Assessment
Experimental Overview
Experiment 6.1 Assembly of Consensus DNA Sequences
Experiment 6.2 Nucleotide BLAST Search To Identify Microorganisms
Experiment 6.3 Approximation of Taxonomic Assignments Using the Ribosomal Database Project
Unit 7 Molecular Evolution: Phylogenetic Analysis of 16S rRNA Genes
Section 7.1 Depicting Evolutionary Relationships With Phylogenetic Trees
Section 7.2 Statistical Tests: Confidence And Bias
Section 7.3 Methods Of Evolutionary Analysis
Reading Assessment (Sections 7.1 to 7.3)
Section 7.4 Reconciling Bacterial Taxonomy: An Evolving Lexicon For The 21St-Century Microbiologist
Reading Assessment (Section 7.4)
Experimental Overview
Experiment 7.1 Tree Construction Using the Ribosomal Database Project
EXPRIMENT 7.2 Building Phylogenetic Trees with MEGA
Appendix: Media, Supplies, and Equipment