James W. Brown - Principles of Microbial Diversity

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

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

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 using t...Figure 4.11 Fine-scale phylogenetic tree of ES-2, generated using the RDP II web...

6 Chapter 5Figure 5.1 Two-parameter substitution models distinguish between transitions and...Figure 5.2 A six-parameter substitution model scores each possible substitution....Figure 5.3 An alignment showing two fundamentally different types of gaps. All o...Figure 5.4 Generation of a “long-branch attraction” artifact in a phylogenetic t...Figure 5.5 Example of a published phylogenetic tree with bootstrap values includ...

7 Chapter 6Figure 6.1 A representative archaeal RNase P RNA, from the methanogen Methanothe...Figure 6.2 A phylogenetic tree generated from an alignment of archaeal RNase P R...Figure 6.3 Location of the “spacer” sequence in rRNA gene clusters. doi:10.1128/...Figure 6.4 The iScreen Strep A test kit uses an ELISA. (Image supplied by CLIAwa...Figure 6.5 FAME profile of Mycobacterium szulgai. (Redrawn from Müller KD, Schmi...Figure 6.6 AFLP analysis of Clostridium botulinum type I strains. A phenogram sh...Figure 6.7 API 20E strip. This result identifies the culture as E. coli. The pat...

8 Chapter 7Figure 7.1 A phylogenetic tree of representative organisms based on SSU rRNA seq...Figure 7.2 Phylogenetic tree of the bacterial phyla, with the two phyla of predo...Figure 7.3 Electron micrograph (thin section) of mammalian lung mitochondria. (S...Figure 7.4 Schematic of how trees of early-duplicated gene alignments can be use...Figure 7.5 Rooted “universal” dendrogram showing the specific affiliation of Arc...Figure 7.6 Schematic view of the “Tree of Life” incorporating horizontal gene tr...Figure 7.7 The Doolittle “Tree of Life,” with the underlying three-domain tree r...

9 Chapter 8Figure 8.1 Phylogenetic tree of the bacterial phyla, with the phyla Thermotogae ...Figure 8.2 Phylogenetic relationships between representative members of the Aqui...Figure 8.3 Electron micrograph (shadow cast) of Aquifex pyrophilus. (Courtesy of...Figure 8.4 Scanning electron micrograph of Thermocrinus ruber. (Reprinted from H...Figure 8.5 Octopus Spring, a neutral-pH hot spring in Yellowstone National Park....Figure 8.6 Phylogenetic tree of the genera of the phylum Thermotogae. doi:10.112...Figure 8.7 Electron micrograph (thin section) of Thermotoga maritima. (Courtesy ...Figure 8.8 Electron micrograph of Thermosipho melanesiense, a close relative of ...Figure 8.9 Electron micrograph (thin section) of Fervidobacterium islandicum. (C...Figure 8.10 Obsidian Pool, a slightly acidic boiling hot spring in Yellowstone N...Figure 8.11 Representation of enzymatic activities from different kinds of organ...

10 Chapter 9Figure 9.1 Phylogenetic tree of the bacterial phyla, with the phyla Chlorobi (gr...Figure 9.2 Phylogenetic tree of the genera of the Chloroflexi. doi:10.1128/97815...Figure 9.3 Phase-contrast micrograph of Chloroflexus aurantiacus (Source: Wikime...Figure 9.4 Chloroflexus-rich microbial mat in the outflow of Excelsior Geyser, Y...Figure 9.5 Phase-contrast micrograph of Roseiflexus castenholzii. (Source: Marce...Figure 9.6 Phase-contrast micrograph of Herpetosiphon aurantiacus, showing its f...Figure 9.7 Phase-contrast micrograph of Anaerolinea thermophila. (Reprinted from...Figure 9.8 Phylogenetic tree of the genera of the phylum Chlorobi. doi:10.1128/9...Figure 9.9 Chlorobium tepidum chlorosomes. (Reprinted from Frigaard NU, Voigt GD...Figure 9.10 Chlorobium symbiotic consortium. The visible cells are nonmotile Chl...Figure 9.11 Phase-contrast micrograph of Chlorobium limicola. Notice the extrace...Figure 9.12 Phase-contrast micrograph of Pelodictyon phaeclathratiforme. (Unattr...Figure 9.13 Phylogenetic tree of representative genera of the phylum Cyanobacter...Figure 9.14 Bright-field micrograph of Microcystis. (Source: Jason Oyadomari.) d...Figure 9.15 Bright-field micrograph of Dermocarpa violacea. (Photo credit: UTEX ...Figure 9.16 Bright-field micrograph of Oscillatoria. Notice that these individua...Figure 9.17 Bright-field micrograph of Anabaena. Dark green cells are vegetative...Figure 9.18 Bright-field micrograph of Fischerella. Notice the main filaments co...Figure 9.19 Photograph of an ascidian (sea squirt) with Prochloron symbionts in ...Figure 9.20 Diagrammatic view of the flow of electrons during cyclic photosynthe...Figure 9.21 Diagrammatic view of the flow of electrons through the electron tran...Figure 9.22 Diagrammatic view of the flow of electrons during sulfur-dependent p...Figure 9.23 Diagrammatic view of the flow of electrons during oxygenic photosynt...Figure 9.24 Diagrammatic view of the Calvin cycle. doi:10.1128/9781555818517.ch9...Figure 9.25 Diagrammatic view of the reductive TCA cycle. Fd, ferredoxin. doi:10...Figure 9.26 Diagrammatic view of the hydroxypropionate pathway. doi:10.1128/9781...Figure 9.27 Diagrammatic view of the Wood reaction. THF, tetrahydrofolate; Fd, f...