Principles of Microbial Diversity. James W. Brown

of the bacterial phyla, with the phyla Chlamydia, ...Figure 13.2 Phylogenetic tree of the genera of Deinococcus-Thermus. doi:10.1128/...Figure 13.3 Kill curves of Escherichia coli versus Deinococcus radiodurans upon ...Figure 13.4 Electron micrograph (thin section) of dividing Deinococcus radiodura...Figure 13.5 Octopus Spring, Yellowstone National Park, from which Thermus aquati...Figure 13.6 Thermus aquaticus, thin-section electron micrograph. Oval cells are ...Figure 13.7 Phylogenetic tree of representative members of the Chlamydiae. doi:1...Figure 13.8 The chlamydial developmental cycle. The small, infectious elementary...Figure 13.9 Trachoma. Notice the granular, everted eyelids. This patient is unus...Figure 13.10 Protochlamydia amoebophila (pink) in two cells of its host, Acantha...Figure 13.11 Phylogenetic tree of the genera of Planctomycetes. doi:10.1128/9781...Figure 13.12 Phase-contrast micrograph of a rosette of Planctomyces bekefii. (Fr...Figure 13.13 Electron micrograph of Planctomyces bekefii showing the external fi...Figure 13.14 Phase-contrast micrograph of Blastopirellula marina rosettes. (From...Figure 13.15 Thin-section electron micrograph of Blastopirellula marina. The dar...Figure 13.16 Negatively stained electron micrograph of Isosphaera, with buds for...Figure 13.17 Thin-section electron micrograph of Isosphaera. The intracellular m...Figure 13.18 Thin-section electron micrograph of Brocadia anammoxidans. The “rib...Figure 13.19 Phase-contrast micrograph of Gemmata obscuriglobus. Notice the budd...Figure 13.20 Thin-section electron micrograph of Gemmata obscuriglobus. Ribosome...

      15 Chapter 14Figure 14.1 Phylogenetic tree of the Bacteria, with the main phylogenetic branch...Figure 14.2 Phylogenetic tree of the phylum Verrucomicrobia, including cultivate...Figure 14.3 Scanning electron micrograph of Verrucomicrobium spinosum. (Reprinte...Figure 14.4 Thin-section electron micrograph of Prosthecobacter dejongeii, a clo...Figure 14.5 Phylogenetic tree of the phylum Acidobacteria, including cultivated ...Figure 14.6 Fluorescence micrograph of Acidobacterium capsulatum. (Source: U.S. ...Figure 14.7 Phylogenetic tree of the phylum Nitrospira, including cultivated spe...Figure 14.8 Scanning electron micrograph of Leptospirillum ferrooxidans. (Courte...Figure 14.9 Electron micrograph of Magnetobacterium bavaricum. (From The Scienti...Figure 14.10 Phylogenetic tree of the phylum Fusobacteria, including cultivated ...Figure 14.11 Gram stain of Fusobacterium nucleatum. (Gini G. 2006. Gram-stained ...Figure 14.12 Phylogenetic tree of the phylum OP11, for which no cultivated speci...Figure 14.13 The author collecting samples in Obsidian Pool, Yellowstone Nationa...Figure 14.14 Phylogenetic tree of the phylum SR1, known only from two similar (b...Figure 14.15 Phylogenetic tree of the family Enterobacteriaceae, including an ar...

      16 Chapter 15Figure 15.1 Phylogenetic tree of the Archaea. Extremely halophilic members are h...Figure 15.2 Phylogenetic tree of representatives of the phylum Crenarchaeota doi...Figure 15.3 “The Pit” (an informal name), an acidic hot spring in the Mud Volcan...Figure 15.4 Shadow-cast electron micrograph of Thermoproteus tenax. (Courtesy of...Figure 15.5 Scanning electron micrograph of Pyrodictium occultum. (Courtesy of G...Figure 15.6 Negative-stain electron micrograph of Sulfolobus solfataricus infect...Figure 15.7 Phylogenetic tree of representatives of the phylum Euryarchaeota. Ex...Figure 15.8 Methanogenesis from C1 compounds (top), or acetate or methanol (lowe...Figure 15.9 Scanning electron micrograph of Methanocaldococcus jannaschii. (Sour...Figure 15.10 Scanning electron micrograph of Methanothermobacter thermautotrophi...Figure 15.11 Phase-contrast image of Methanosarcina barkeri-like organisms in an...Figure 15.12 A bloom of halophilic Archaea in a saltern in Namibia. (Courtesy of...Figure 15.13 Deep-sea “black smoker” hydrothermal vents, the habitat of Pyrococc...Figure 15.14 Shadow-cast electron micrograph of Archaeoglobus fulgidus. (Courtes...Figure 15.15 Scanning electron micrograph of Thermoplasma acidophilum. (Dennis S...Figure 15.16 Obsidian Pool, Yellowstone National Park, samples of which yielded ...Figure 15.17 Scanning electron micrograph of purified Korarchaeum cryptophilum f...Figure 15.18 Shadow-cast micrograph of Nanoarchaeum equitans (small irregular co...

      17 Chapter 16Figure 16.1 A phylogenetic tree of representative eukaryotes. (Adapted from Cicc...Figure 16.2 Unrooted phylogenetic tree of the eukaryotes (branch lengths shown a...Figure 16.3 Photograph of the yellow slime mold Physarum polycephalum on the bar...Figure 16.4 A small (ca. 1-m) great barracuda in Mudjin Harbor, Middle Caicos Is...Figure 16.5 Nomarski interference micrograph of the baker’s yeast Saccharomyces ...Figure 16.6 Photograph of common turtle grass in the shallow waters off Bermuda....Figure 16.7 Photograph of Irish moss, Chondrus crispus, not to be confused with ...Figure 16.8 Phase-contrast micrograph of Navicula sp. (Source: Texas Tech Univer...Figure 16.9 Phase-contrast micrograph of Phytophthora infestans. The lemon-shape...Figure 16.10 Phase-contrast micrograph of a Vorticella sp., the bell-shaped orga...Figure 16.11 Aerial photograph of Florida red tide. (Source: P. Schmidt, Charlot...Figure 16.12 Ernst Haeckel’s classic drawings of foraminiferan tests. (This is o...Figure 16.13 Dark-field micrograph of Globigerina bulloides, a living relative o...Figure 16.14 Ernst Haeckel’s classic drawings of radiolarian tests. (Again, this...Figure 16.15 Micrograph (left) and cross-sectional diagram (right) of Hexacontiu...Figure 16.16 Micrograph of Euglypha strigosa. (Courtesy of Eugen Lehle, Wikimedi...Figure 16.17 Phase-contrast micrograph of Reclinomonas americana. (Image supplie...Figure 16.18 Trypanosoma brucei in the blood of a sleeping sickness patient. (So...Figure 16.19 The life cycle of trypanosomes. (Adapted from the Centers for Disea...Figure 16.20 Giardia lamblia (a.k.a. G. intestinalis) from stool. (Courtesy of J...Figure 16.21 Streblomastix strix scanning electron micrograph (1) and cross sect...

      18 Chapter 17Figure 17.1 Escherichia coli being infected by bacteriophage lambda. (Courtesy o...Figure 17.2 Transfer of F plasmid from donor to recipient. doi:10.1128/978155581...Figure 17.3 Transfer of bacteriophage M13 from donor to recipient. doi:10.1128/9...Figure 17.4 Electron micrograph of bacteriophage Mu. (Reprinted from Inman RB, S...Figure 17.5 Very schematic view of the life cycle of bacteriophage/transposon Mu...Figure 17.6 The rice yellow mottle virus-associated viroid: not its genome, the ...Figure 17.7 Tobacco ringspot virus satellite RNA-S replication. doi:10.1128/9781...Figure 17.8 Electron micrograph of mimivirus. (Courtesy of Didier Raoult.) doi:1...Figure 17.9 Mimivirus (MV)-infected amoeba. Note the “virus factory” (VF), from ...Figure 17.10 Sheep with an “itchy” form of scrapie. (Courtesy of the University ...Figure 17.11 Light micrograph of a stained thin section of brain from a cow with...Figure 17.12 Ribbon diagrams of PrPc (normal, left) and PrPSc (diseased, right)....

      19 Chapter 18Figure 18.1 Octopus Spring, Yellowstone National Park. doi:10.1128/9781555818517...Figure 18.2 Pink filaments in the outflow of Octopus Spring. doi:10.1128/9781555...Figure 18.3 Isolation of a single cell by using optical tweezers. doi:10.1128/97...

      20 Chapter 19Figure 19.1 A clump of Riftia near a deep-sea hydrothermal vent. (From Dworkin M...Figure 19.2 Google Earth view of the Indian Ocean. The site of the hydrothermal ...Figure 19.3 Crysomallon squamiferum, the deep-sea hydrothermal vent scaly snail....Figure 19.4 The chimera decorating an Apulia dish at the Louvre (Source: Wikimed...Figure 19.5 The generation of chimeras by the priming of PCR products from abort...Figure 19.6 An old-growth tree community. (Courtesy of Piotr Skubisz/Fotolia.) d...Figure 19.7 Locations of the primers and amplified regions of the SSU rRNA. The ...Figure 19.8 Graphical description of Unifrac. (Reprinted from Lozupone C, Knight...Figure 19.9 Graphical descriptions of how principal-component analysis (PCoA) an...

      21 Chapter 20Figure 20.1 Nanoarchaeum equitans stained with a specific Texas Red-labeled FISH...Figure 20.2 Typical wastewater treatment process. doi:10.1128/9781555818517.ch20...

      22 Chapter 21Figure 21.1 Diagrammatic representation of the DGGE process. Note that this diag...Figure 21.2 Geyser at the Daggyai Tso geothermal region of Tibet. (Courtesy of M...Figure 21.3 How t-RFLP works. The restriction map of an example SSU rRNA gene is...Figure 21.4 Deconvolution of sequence identities from multiple restriction diges...Figure 21.5 Real-time PCR. The top panel shows the result of a real-time PCR exp...

      23 Chapter 22Figure 22.1 NCBI Genome Browser view of the SAR86 cosmid EBAC31A08 sequence. Eac...Figure 22.2 Overview of the SIP process. (Second panel reprinted from Gallagher ...Figure 22.3 A Beckman TLA 100.2 rotor, capable of carrying as many as 10 4-ml sa...Figure 22.4 Images of the unicellular eukaryotes identified in this paper. [Sour...

      24 Chapter 23Figure 23.1 Assembling contigs into complete genomes. Primers (black) directed o...Figure 23.2 Placement of Thermotoga maritima in rRNA-based trees, relative to wh...Figure 23.3 Genomics versus metagenomics. (DNA panels: Bruce Chassey Laboratory,...

      25 Chapter 24Figure 24.1 Geological time scale. (Source: