Оглавление
James W. Brown. Principles of Microbial Diversity
Table of Contents
List of Tables
List of Illustrations
Guide
Pages
PRINCIPLES OF Microbial Diversity
Preface
Acknowledgments
About the Author
SECTION I. Introduction to Microbial Diversity
1. What Is Microbial Diversity? Facets of microbial diversity
Morphological diversity
Structural diversity
Metabolic diversity
Ecological diversity
Behavioral diversity
Evolutionary diversity
The fundamental similarity of all living things
DNA
RNA
Protein
Function
Cells
Significance of the similarity between organisms
Questions for thought
2. Context and Historical Baggage
The evolution of evolutionary thought. The chain of being
The evolutionary ladder
Early phylogenetic trees
Molecular phylogenetic trees
Taxonomy and phylogeny
Why is an understanding of phylogeny important?
The false eukaryote-prokaryote dichotomy
Questions for thought
3. Phylogenetic Information
Deciding which organisms and sequences to use in the analysis
Features required of a good molecular clock. Clock-like behavior
The standard: small-subunit ribosomal RNA
Deciding which organisms to include
Obtaining the required sequence data
Databases
Obtaining sequences experimentally
Assembling sequences in a multiple-sequence alignment
Alignment based on conserved sequence
Alignment based on conserved structure
Questions for thought
4. Constructing a Phylogenetic Tree
Tree construction: the neighbor-joining method
Generating a similarity matrix
Converting a similarity matrix into an evolutionary distance matrix
Generating a tree from a distance matrix
Rooting a tree with an outgroup
Molecular phylogenetic trees depict the relationships between gene sequences
How to read a phylogenetic tree
Scale
Terminal nodes
Internal nodes
Root
Branches
Tree representations
Example analysis
Interpretation
What good was this information?
Questions for thought
5. Tree Construction Complexities
Substitution models
The special case of G∙C bias
Long-branch attraction
Treeing algorithms. Fitch-Margoliash: an alternative distance-matrix treeing method
Parsimony
Maximum likelihood
Bayesian inference
Bootstrapping
Questions for thought
6. Alternatives to Small-Subunit rRNA Analysis. SSU rRNA cannot be used to distinguish closely related organisms
Alternative sequences
Other RNAs
rRNA spacer sequence analysis
Protein sequence analysis
Catenated alignments
Alternatives to sequence-based methods. DNA:DNA hybridization
DNA base composition
Serology
Lipid profiling
RFLP methods
Phenotype
Questions for thought
7. The Tree of Life
Major lessons of the “Big Tree of Life” The discovery of theArchaea
Big eukaryotes represent a small portion of biological diversity
Gram-positive versus gram-negative is not the major division inBacteria
Mitochondria and chloroplasts are bacterial endosymbionts
Rooting the “Tree of Life”
The caveat of horizontal transfer
What impact does horizontal transfer have for the “Big Tree”?
Horizontal transfer and the origin of the domains from the last common ancestor
Questions for thought
SECTION II. The Microbial Zoo
TheBacteria
8. Primitive Thermophilic Bacteria
PhylumAquificae(Aquifexand relatives)
General characteristics of theAquificae. Diversity
Habitat
Aquifex pyrophilus
Thermocrinus ruber
PhylumThermotogae(Thermotogaand relatives)
General characteristics of theThermotogae. Diversity
Thermotoga maritima
Thermosipho africanus
Other primitive thermophiles
Thermodesulfobacterium
Thermomicrobium
ChloroflexiandDeinococci
Thermophilic ancestry ofBacteria
Life at high temperatures
Membrane fluidity and integrity
DNA structure
RNA structure
Protein structure
Enzymatic function
Small-molecule stability
Questions for thought
9. Green Phototrophic Bacteria
PhylumChloroflexi(green nonsulfur bacteria)
General characteristics of theChloroflexi. Diversity
Chloroflexus aurantiacus
Roseiflexus castenholzii
Herpetosiphon aurantiacus
Anaerolinea thermophila
PhylumChlorobi(green sulfur bacteria)
General characteristics of theChlorobi. Diversity
Metabolism
Chlorobium limicola
Pelodictyon phaeoclathratiforme
PhylumCyanobacteria(blue-green algae)
Taxonomy
General characteristics of theCyanobacteria. Diversity
Morphology
FamilyChroococcales
EXAMPLEMicrocystis
FamilyPleurocapsales
EXAMPLEDermocarpa
FamilyOscillatoriales
FamilyNostocales
EXAMPLEAnabaena
FamilyStigonematales
FamilyProchlorales
Other green phototrophs
Bacterial photosynthesis
Cyclic photophosphorylation
Obtaining reducing power for carbon fixation
Rhodopsin phototrophy
Carbon fixation
Calvin cycle
Reverse TCA cycle
Hydroxypropionate pathway
Reductive acetyl-CoA pathway
Questions for thought
10. Proteobacteria. PhylumProteobacteria(purple bacteria and relatives)
ClassAlphaproteobacteria
General characteristics of theAlphaproteobacteria. Diversity
Metabolism
Purple nonsulfur phototrophs
Appendaged bacteria
Nitrogen-fixing plant symbionts
Obligate intracellular parasites
ClassBetaproteobacteria
About this class. Diversity
Habitat
Heterotrophs and pathogens
Chemolithoautotrophs
Bacteria with sheathed filaments
ClassGammaproteobacteria
About this class. Diversity
Enterics
Escherichia coli
Buchnera aphidicola
Thiotrichs
Pseudomonads
Purple sulfur bacteria
ClassDeltaproteobacteria
About this class. Diversity
Metabolism
Sulfate reducers and hydrogenic syntrophs
Myxobacteria
Parasites of other bacteria
ClassEpsilonproteobacteria
About this class. Diversity
Intestinal symbionts
Deep-sea hydrothermal vent-associated species
The concept of “proteobacteria” Review of the basics of electron transport
The proteobacteria
Questions for thought
11. Gram-Positive Bacteria
What does being gram positive mean?
An alternative view of gram-positive bacteria
PhylumFirmicutes(low-G∙C gram-positive bacteria)
About this phylum. Diversity
Aerobic endospore-forming rods(Bacillusand relatives)
Anaerobic endospore-forming rods(Clostridiumand relatives)
Lactic acid bacteria
Mollicutes (Tenericutes; Mycoplasmaand relatives)
EXAMPLEMycoplasma hominis
Heliobacteriaceae (green photosynthetic gram-positive bacteria)
Veillonellaceae (Firmicuteswith gram-negative envelopes)
PhylumActinobacteria(high-G∙C gram-positive bacteria)
About this phylum. Diversity
Metabolism
Coryneform actinobacteria
EXAMPLEArthrobacter globiformis
Filamentous actinobacteria
Acid-fast bacteria
Deeply branching questionable members
Bacterial development
Secondary metabolites
Bacterial multicellularity
Questions for thought
12. Spirochetes and Bacteroids
PhylumSpirochaetae
About this phylum. Diversity
FamilySpirochaetaceae
Treponema denticola
Borrelia recurrentis
FamilyLeptospiraceae
PhylumBacteroidetes(sphingobacteria orBacteroides/Flavobacterium/Cytophagagroup)
About this phylum. Diversity
ClassBacteroidia
ClassFlavobacteria
EXAMPLEFlavobacterium johnsoniae
ClassSphingobacteria
EXAMPLECytophaga hutchinsonii
Bacterial motility
Flagella
Gliding
Twitching
Gas vacuoles
Spirochete motility
Spiroplasmamotility
Questions for thought
13. Deinococci, Chlamydiae, and Planctomycetes
PhylumDeinococcus-Thermus
About this phylum
Deinococcusand relatives. Diversity
Metabolism
Thermusand relatives. Diversity
Metabolism
Habitat
PhylumChlamydiae(Chlamydiaand relatives)
About this phylum. Diversity
Chlamydia trachomatis
Protochlamydia amoebophila
PhylumPlanctomycetes(Planctomycesand relatives)
About this phylum. Diversity
Metabolism
Blastopirellula marina
Isosphaera pallida
Brocadia anammoxidans
Gemmata obscuriglobus
What is the difference between paryphoplasm and periplasm?
Reductive evolution in parasites
Questions for thought
14. Bacterial Phyla with Few or No Cultivated Species
How do we know about these organisms?
Summary of molecular phylogenetic surveys
Phyla with few cultivated species
Other examples of phyla with few cultivated species
Phyla with no cultivated species
Phylogenetic groups at all levels are dominated by uncultivated sequences
How much of the microbial world do we know about?
Questions for thought
15. Archaea
General properties of theArchaea
Morphology
Cell envelope
Flagella
Transcription and translation
Genomes
PhylumCrenarchaeota
About this phylum. Diversity
Thermoproteus tenax
Pyrodictium occultum
Sulfolobus solfataricus
PhylumEuryarchaeota
About this phylum. Diversity
Methanogens
Extreme Halophiles
Metabolism
Sulfur-metabolizing thermophiles
Pyrococcus furiosus
Archaeoglobus fulgidus
Thermoplasma acidophilum
PhylumKorarchaeota
PhylumNanoarchaeota
Archaeaas … The “missing link” betweenBacteriaandEukarya
A deep branch ofEukarya
Reflections of early life on Earth
Questions for thought
16. Eukaryotes
General properties of the eukaryotes. Diversity
Metabolism
Morphology
Unikonta
About the superkingdom Unikonta
Amoebozoa
Opisthokonts
Sphyraena barracuda
Saccharomyces cerevisiae
Plantae
About the superkingdom Plantae
Chloroplastids
EXAMPLEThalassia testinum
Rhodophytes
Glaucophytes
Chromalveolata
About the superkingdom Chromalveolata
Stramenopiles
Naviculaspp
Phytophthora infestans
Alveolates
Vorticellaspp
Karenia brevis
Rhizaria
About the superkingdom Rhizaria
Foraminifera
Radiolaria
EXAMPLEHexacontium gigantheum
Cercozoa
Excavata
About the superkingdom Excavata
Discobans
Reclinomonas americana
Metamonads
Giardia lamblia
Streblomastix strix
Questions for thought
17. Viruses and Prions
Viruses
Viruses as genetic offshoots of their hosts
An evolutionary series between bacterial genomes and bacteriophages
Viruses as remnants of precellular life
Viruses as degenerate parasites
Prions. The prion theory
Questions for thought
SECTION III. Microbial Populations
18. Identification of Uncultivated Organisms
■ STUDY AND ANALYSIS
Questions for thought
19. Sequence-Based Microbial Surveys
■ STUDY AND ANALYSIS
High-throughput sequencing technology
Questions for thought
20. Fluorescent In Situ Hybridization Surveys. Fluorescent in situ hybridization
Confocal laser scanning microscopy
■ STUDY AND ANALYSIS
Questions for thought
21. Molecular Fingerprinting of Microbial Populations
Denaturing gradient gel electrophoresis
■ STUDY AND ANALYSIS
Terminal restriction fragment length polymorphism
Real-time PCR
■ STUDY AND ANALYSIS
Questions for thought
22. Linking Phenotype and Phylotype
The genomic or metagenomic approach
■ STUDY AND ANALYSIS
The stable-isotope probing approach
How cesium tetrafluoroacetate density gradients work
■ STUDY AND ANALYSIS
Questions for thought
SECTION IV. Conclusion: The Phylogenetic Perspective
23. Genomics, Comparative Genomics, and Metagenomics
Genomics. How to sequence a genome
■ STUDY AND ANALYSIS
Horizontal transfer of genes
Comparative genomics
■ STUDY AND ANALYSIS
Metagenomics
■ STUDY AND ANALYSIS
Questions for thought
24. Origins and Early Evolution
The timescale
Ancient microbial fossils
■ STUDY AND ANALYSIS
The last common ancestor
Before the last common ancestor?
The RNA world hypothesis
What could the RNA world have been like?
A complex RNA world scenario
Problems with the RNA world hypothesis: a reality check
The emergence of life
The Oparin ocean hypothesis: primordial soup
Wächtershäuser’s hypothesis of surface metabolism: primordial sandwich
Questions for thought
Index
A
B
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D
E
F
G
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I
J
K
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