Principles of Microbial Diversity. James W. Brown

with no cultivated species Phylogenetic groups at all levels are dominated by uncultivated sequences How much of the microbial world do we know about? 15 Archaea General properties of the Archaea Phylum Crenarchaeota Phylum Euryarchaeota Phylum Korarchaeota Phylum Nanoarchaeota Archaea as … 16 Eukaryotes General properties of the eukaryotes Unikonta Plantae Chromalveolata Rhizaria Excavata 17 Viruses and Prions Viruses Prions

      7  SECTION III: Microbial Populations 18 Identification of Uncultivated Organisms 19 Sequence-Based Microbial Surveys 20 Fluorescent In Situ Hybridization Surveys Fluorescent in situ hybridization Confocal laser scanning microscopy 21 Molecular Fingerprinting of Microbial Populations Denaturing gradient gel electrophoresis Terminal restriction fragment length polymorphism 22 Linking Phenotype and Phylotype The genomic or metagenomic approach The stable-isotope probing approach

      8  SECTION IV Conclusion: The Phylogenetic Perspective 23 Genomics, Comparative Genomics, and Metagenomics Genomics Comparative genomics Metagenomics 24 Origins and Early Evolution The timescale Ancient microbial fossils The last common ancestor The RNA world hypothesis The emergence of life

      9  Index

      10  End User License Agreement

      List of Tables

      1 Chapter 1Table 2.1 Sample “eukaryotes versus prokaryotes” table common to biology and eve...

      2 Chapter 14Table 14.1 Summary of 16S rRNA-based clonal analyses of diversity of uncultivate...Table 14.2 Phylogenetic tabulation of sequences in the Ribosomal Database Projec...

      3 Chapter 24Table 24.1 Time scale of the history of life in comparison with a 46-ft-wide cla...Table 24.2 Comparison of the compositions of a comet and a human being

      List of Illustrations

      1 Part 2Figure 1 Phylogenetic tree of the major bacterial phyla, based on SSU rRNA seque...

      2 Chapter 1Figure 1.1 The tile-shaped halophilic archaeon Haloquadratum walsbyi. (Source: W...Figure 1.2 Section of a stratified microbial mat from Guerrero Negro, Baja Calif...Figure 1.3 The bacterium Epulopiscium fishelsoni (ca. 500 μm long) and four cell...Figure 1.4 A negative-stain electron micrograph of the S-layer of Pyrobaculum ae...Figure 1.5 Moose Pool, Yellowstone National Park, pH ~2, 80°C. doi:10.1128/97815...Figure 1.6 Chlorobium symbiotic consortium. (Reprinted from Wanner G, Vogl K, Ov...Figure 1.7 Overlay of phase-contrast and red and green fluorescent images of spo...Figure 1.8 A swarm of Myxococcus xanthus (left) invading a colony of E. coli (ri...Figure 1.9 Phylogenetic tree of representative organisms based on small-subunit ...Figure 1.10 The Central Dogma: flow of information from archive (DNA) to functio...Figure 1.11A Homo sapiens versus E. coli (B) small-subunit rRNA secondary struct...Figure 1.11B doi:10.1128/9781555818517.ch1.f1.11B

      3 Chapter 2Figure 2.1 The “chain of being,” with some representative organisms shown. To th...Figure 2.2 The “evolutionary ladder,” an evolutionary transformation of the chai...Figure 2.3 Evolution by diversification. In this diagram, species A and I at the...Figure 2.4 The tree of life. (Reprinted from Ernst Haeckel, Generelle Morphologi...Figure 2.5 The five-kingdom tree taught in most schools in the United States. (R...Figure 2.6 Phylogenetic tree of representative organisms based on small-subunit ...

      4 Chapter 3Figure 3.1 Clock-like behavior. The extent of sequence divergence between a pair...Figure 3.2 The Escherichia coli SSU rRNA secondary structure. (Courtesy of Robin...Figure 3.3 The polymerase chain reaction (PCR). doi:10.1128/9781555818517.ch3.f3...Figure 3.4 Chain termination sequencing. doi:10.1128/9781555818517.ch3.f3.4Figure 3.5 Example sequence data from a DNA sequencing reaction. doi:10.1128/978...Figure 3.6 A small window into an alignment of SSU rRNA sequences. doi:10.1128/9...Figure 3.7A Comparison of two RNase P RNAs with very different sequences and ver...Figure 3.7B doi:10.1128/9781555818517.ch3.f3.7BFigure 3.8 An RNA alignment based on secondary structure. If residue n (e.g., 24...Figure 3.9 RNase P RNA helix “P3” in a variety of Archaea. The base pairs corres...

      5 Chapter 4Figure 4.1 The Jukes and Cantor equation plotted as observed sequence similarity...Figure 4.2 An example phylogenetic tree of the relationships between great apes....Figure 4.3 Two different representations of the same phenogram of phylogenetic r...Figure 4.4 Two different dendrogram representations of the same phylogenetic rel...Figure 4.5 Measuring phylogenetic distances in dendrograms. doi:10.1128/97815558...Figure 4.6 Measuring phylogenetic distances in phenograms. doi:10.1128/978155581...Figure 4.7 Sequence of the ES-2 SSU rRNA, in GenBank format. doi:10.1128/9781555...Figure 4.8 Secondary structure of the ES-2 SSU rRNA sequence. This is a hand-dra...Figure 4.9 Phylum-scale tree including ES-2, generated using the RDP II website....Figure 4.10 Tree of representative Firmicutes, including ES-2, generated