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Chapter 4:
PROKARYOTIC DIVERSITY
3. Gram-negative and Phototropic Non-Proteobacteria
2. Proteobacteria
1. Prokaryote Habitats, Relationships & Biomes
4. Gram-Positive Bacteria
5. Deeply Branching Bacteria
6. Archaea
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1. Prokaryote Habitats,
Relationships & Biomes
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Important Metabolic Terminology
Oxygen tolerance/usage:
aerobic – requires or can use oxygen (O2)
anaerobic – does not require or cannot tolerate O2
Energy usage:
phototroph – uses light as an energy source
• all photosynthetic organisms
chemotroph – acquires energy from organic or inorganic molecules
• organotrophs – get energy from organic molecules
• lithotrophs – get energy from inorganic molecules
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…more Important Terminology
Facultative vs Obligate (or Strict):
facultative – “able to, but not requiring”
• e.g., facultative anaerobes can survive w/ or w/o O2
obligate – “absolutely requires”
• e.g., obligate anaerobes cannot survive in O2
Carbon Source:
autotroph – uses CO2 as a carbon source
• e.g., photoautotrophs or chemoautotrophs
heterotroph – requires an organic carbon source
• e.g., chemoheterotroph – gets energy & carbon from organic molecules
Oligotrophs require few nutrients, the opposite of eutrophs or copiotrophs
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Symbiotic Relationships
Symbiotic relationships (close, direct interactions) between
different organisms in nature are of several types:
• e.g., humans have beneficial
bacteria in their digestive
tracts that also benefit from
the food we eat (mutualism)
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Microbiomes
All the microorganisms that inhabit a particular organism
or environment (e.g., human or soil microbiome):
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Classification in the Bacterial Domain
We will look at important genera from a variety of bacterial groups
classified largely on staining & rRNA sequences (ribotyping):
Gram-negative Bacteria
• Proteobacteria
• Nonproteobacteria & Phototrophic Bacteria
Gram-positive Bacteria
• High G+C (Actinobacteria)
• Low G+C (Firmicutes)
Deeply Branching Bacteria
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2. Proteobacteria
Alphaproteobacteria
Betaproteobacteria
Gammaproteobacteria
Deltaproteobacteria
Epsilonproteobacteria
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Alphaproteobacteria
Pathogenic genera:
Rickettsia
Chlamydia
Rhizobium
• intracellular pathogens
• typhus, Rocky Mountain spotted fever
• C. trachomatis – most common STD
Most are oligotrophs:
• nitrogen fixation in soil
R. rickettsii
Rhizobium
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Betaproteobacteria
Pathogenic genera:
Neisseria
Thiobacillus
Bordetella
• oxidize H2S to sulfate is soil
• important in sulfur cycle
• gonorrhea (N. gonorrheae)
• whooping cough (B. pertussis)
• meningococcal meningitis
(N. meningitidis)
N. meningitidis
Most are eutrophs:
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Gammaproteobacteria
Escherichia
Pseudomonas
Salmonella
Largest & most diverse class of Proteobacteria, including many
enteric bacteria and human pathogens:
• E. coli
• opportunistic pathogens
• typhoid fever, foodborne
salmonellosisL. pneumophila
Vibrio
• cholera (V. cholerae)
Legionella
• legionnaires disease (L. pneumophila)
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Deltaproteobacteria
Small class of Proteobacteria containing soil bacteria that
reduce sulfate (Desulfovibrio) and the Myxobacteria that form
unusual “fruiting bodies”:
Myxobacteria
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Epsilonproteobacteria
Pathogenic genera:
Helicobacter
Campylobacter
• H. pylori – peptic ulcers
• various species cause
blood poisoning, intestinal
illness (e.g., C. jejuni)H. pylori
Smallest class of Proteobacteria containing microaerophilic
species that are typical helical or vibrioid in shape :
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3. Gram-Negative & Phototropic
Non-Proteobacteria
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Spirochetes
Treponema
Borrelia
• T. pallidum – syphilis
• B. burgdorferi – Lyme disease
Very thin, highly coiled bacteria
that are hard to see under the
microscope and harder to
culture:
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The CFB Group
Grouped based on DNA similarity and includes the following
genera:
Cytophaga Fusobacterium Bacteroides
Bacteroides
• Some are potentially
pathogenic (Cytophaga,
Fusobacterium), others are
beneficial (Bacteroides)
• most are anaerobic rods
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Sheath
Vegetativecell
Heterocyst
Akinete
Anabaena Oscillatora
Cyanobacteria
Gram-negative, oxygenic photoautotrophs
Anabaena
• carry out nitrogen fixation in non-photosynthetic heterocysts
• produce vast amounts of oxygen gas via photosynthesis, fix nitrogen (N2 NH4+)
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Purple & Green Bacteria
Obligately anaerobic, anoxygenic photoautotrophs
• use organic molecules as a source of electrons (not H2O)
Green and Purple non-sulfur bacteria
Green and Purple sulfur bacteria
• use H2S as a source of electrons
• elemental sulfur is then released
(green sulfur bacteria) or forms
inclusions (purple sulfur bacteria)
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4. Gram-Positive Bacteria
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Classification of Gram-Positive Bacteria
Gram-positive bacteria are grouped based on DNA similarity:
Low G+C Gram-positive bacteria (Firmicutes)
• contains many serious pathogens
• characterized by branching filaments
High G+C Gram-positive bacteria (Actinomycetes)
• includes some pathogens
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Actinobacteria (High G+C)
Streptomyces
Corynebacterium
Mycobacterium
• important soil bacteria, recycle nutrients
• many produce antibiotics (erythromycin, tetracycline)
• diphtheria (C. diphtheria)
• tuberculosis (M. tuberculosis), leprosy (M. leprae)
• contain mycolic acids in cell wall (stain acid-fast)
Bifidobacterium
• significant member of beneficial gut microbiota
C. diphtheria
Streptomyces
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Firmicutes (Low G+C)…
Streptococcus
Staphylococcus
*Bacillus
*Clostridium *produce
endospores
• strep throat (S. pyogenes)
• MRSA (S. aureus)
• anthrax (B. anthracis)
• tetanus (C. tetani)
• botulism (C. botulinum)
C. difficile
S. pyogenes
S. aureus
• colitis (C. difficile)
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Mycoplasma
• very small (less than 1 mm)
Lactobacillus
…more Firmicutes
• species used in fermented food products (e.g., yogurt, buttermilk, pickles)
• part of normal, healthy microbiota in human mouth, digestive tract, vagina
• no cell wall (stain Gram-negative)
• obligate intracellular pathogens
Mycoplasma
colonies
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5. Deeply Branching Bacteria
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Last Common Universal Ancestor
What Are “Deeply Branching Bacteria”?
Bacteria very close
to the base of the
phylogenetic tree:
• members of the
domain Bacteria
that diverged
very early, ~3.5
billion years ago
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Genera of “Deeply Branching Bacteria”
Acetothermus
• deepest branching bacteria known to date
• thermophiles and hyperthermophiles
Aquifex
• adapted to harshest conditions on planet
(e.g., thermal oceanic vents that reach 138oC!)
Deinococcus
• D. radiodurans known as “Conan the
Bacterium” for the extremes of heat, UV,
radioactivity, etc, it can survive
D. radiodurans
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6. Archaea
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The Domain Archaea
Highly diverse group of prokaryotes first classified in 1977 by
Carl Woese and George Fox:
• cell walls made of material other than peptidoglycan
• have unusual membrane lipids
• much larger genomes that bacteria
• have metabolic processes, rRNA sequences and other features
more closely resembling eukaryotes
• e.g., initiate translation with methionine (as do eukaryotes) rather
than N-formyl methionine as do the Bacteria
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Two Main Phyla
Crenarchaeota
• most are hyperthermophiles, some
acidophiles
Euryarchaeota
• includes the methanogens, halophiles, a few
thermophiles
**NO known archaeon causes disease in humans or animals!**
Other Phyla
• Korarchaeota, Nanoarchaeota, Thaumarchaeota
• based on environmental RNA
Sulfolobus
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Key Terms for Chapter 4
• autotroph, heterotroph, oligotroph, eutroph
• facultative vs obligate
• aerobic vs anaerobic
• thermophile, halophile
• phototroph, chemotroph, organotroph, lithotroph
• symbiosis: mutualism, amensalism, commensalism,
neutralism, parasitism