Principles of Microbial Diversity. James W. Brown

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...

      11 Chapter 10Figure 10.1 Phylogenetic tree of the bacterial phyla, with the phylum Proteobact...Figure 10.2 Phylogenetic tree of representative proteobacteria, with each of the...Figure 10.3 Phylogenetic tree of representative Alphaproteobacteria. doi:10.1128...Figure 10.4 Phase-contrast micrograph of Rhodomicrobium vannielii, showing polar...Figure 10.5 Life cycle of Caulobacter crescentus. Flagellated swarmer cells tran...Figure 10.6 Alfalfa root nitrogen-fixing nodules. (Courtesy of Ninjatacoshell, h...Figure 10.7 Egg of the wasp Trichogramma kaykai. The brightly stained dots conce...Figure 10.8 Phylogenetic tree of representative Betaproteobacteria. doi:10.1128/...Figure 10.9 Diagnostic test for southern bacterial wilt. Cut off a section of th...Figure 10.10 A river polluted by acid mine drainage and the resulting overgrowth...Figure 10.11 Phase-contrast micrograph of Sphaerotilus natans. Notice the indivi...Figure 10.12 Phylogenetic tree of representative γ-proteobacteria. doi:10.1128/9...Figure 10.13 Electron micrograph of the familiar bacterium Escherichia coli. Sho...Figure 10.14 A typical aphid, host of the bacterial symbiont Buchnera aphidicola...Figure 10.15 Two filaments of Beggiatoa alba (the thinner vertical filament is i...Figure 10.16 Electron micrograph of Azotobacter vinelandii cysts. (Reprinted fro...Figure 10.17 Bright-field micrograph of Chromatium okenii (a close relative of C...Figure 10.18 Phylogenetic tree of representative δ-proteobacteria. doi:10.1128/9...Figure 10.19 Scanning electron micrograph of Desulfovibrio desulfuricans. (Sourc...Figure 10.20 Close-up photograph of simple Myxococcus xanthus fruiting bodies. (...Figure 10.21 Life cycle of Bdellovibrio bacteriovorans, assembled from scanning ...Figure 10.22 Phylogenetic tree of representative ε-proteobacteria. doi:10.1128/9...Figure 10.23 Shadow-cast electron micrograph of Helicobacter pylori. Notice the ...Figure 10.24 The deep-sea hydrothermal vent scaly snail Crysomallon squamiferum....Figure 10.25 Simplified representation of the electron transport chain. The oxid...

      12 Chapter 11Figure 11.1 Phylogenetic tree of the bacterial phyla, with the two phyla of (pre...Figure 11.2 Phylogenetic tree of representative members of the Firmicutes. doi:1...Figure 11.3 Phase-contrast micrographs of Bacillus cereus (a.k.a. Arthromitis) g...Figure 11.4 Light micrograph of Gram-stained Clostridium botulinum. Notice the t...Figure 11.5 Phase-contrast micrograph of Leuconostoc mesenteroides. (Source: U.S...Figure 11.6 Mycoplasma mobile, showing the typical pear-shaped morphology of the...Figure 11.7 Fluorescent antibody of the parasitic flagellate Trichomonas vaginal...Figure 11.8 Phylogenetic tree of representative actinobacteria. doi:10.1128/9781...Figure 11.9 Scanning electron micrograph of snapping division in Arthrobacter gl...Figure 11.10 Overlay of phase-contrast and red and green fluorescent images of s...Figure 11.11 Stained sample of human tissue (blue) infected with Mycobacterium u...Figure 11.12 Scanning electron micrograph of Thermoleophilum album resting on a ...

      13 Chapter 12Figure 12.1 Phylogenetic tree of the bacterial phyla, with the bacteroids and sp...Figure 12.2 Phylogenetic tree of representative members of the Spirochaetae. doi...Figure 12.3 Shadow-cast electron micrograph of a typical spirochete, showing the...Figure 12.4 (Top) A typical termite and a gastrointestinal tract dissected from ...Figure 12.5 Treponema denticola. (A and B) Fluorescent micrographs and (C) elect...Figure 12.6 Electron micrograph of Borrelia recurrentis. This spirochete is not ...Figure 12.7 Electron micrograph of Leptospira biflexa. The cell is wrapped in a ...Figure 12.8 Phylogenetic tree of representative bacteroids. doi:10.1128/97815558...Figure 12.9 Scanning electron micrograph of Bacteroides thetaiotaomicron. (Court...Figure 12.10 Phase-contrast micrograph of Flavobacterium johnsoniae. (Reprinted ...Figure 12.11 Scanning electron micrograph of Cytophaga hutchinsonii cells digest...Figure 12.12 Flagellar motility. Flagella are helical fibers, analogous to prope...Figure 12.13 Vibrios or spirilla are flagellated organisms that recapture some o...Figure 12.14 Gliding motility in some organisms is driven by secretion of polysa...Figure 12.15 Gliding motility in some organisms is driven by adhesins that move ...Figure 12.16 Twitching motility is directed by the extension of pili, which adhe...Figure 12.17 The honeycomb arrays inside the cytoplasm of this dividing Microcys...Figure 12.18 Motility by spirochetes. Rotation of the rigid helical cell body wi...Figure 12.19 Model of Spiroplasma motility. Kinks, where the helix switches from...

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