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
Preface
About the Authors and Contributors
Introduction
 
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
 
Index