Chapter 11: The Diversity of Prokaryotic Organisms

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Chapter 11The Diversity ofProkaryoticOrganisms
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Important Point
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Prokaryotic Diversity

• Although a million species of prokaryotes are
  thought to exist, only approximately 6,000 of
  these, grouped into 850 genera, have been
  actually described and classified.
• Traditional culture and isolation techniques
  have not supported the growth, and subsequent
  study, of the vast majority.
• Not surprisingly, most effort has been put into
  the study of microbes intimately associated with
  the human population, especially those causing
  disease, and these have been most extensively
  described.
• The phylogenic relationships being elucidated by
  the ribosomal RNA studies are causing
  significant upheaval in prokaryotic
  classification schemes.

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Prokaryotic Diversity

• Some organisms, once grouped together based on
  their phenotypic similarities, have now been
  split into different taxonomic units based on
  their ribosomal RNA differences.
• We will consider the following categories (not
  necessarily monophyletic) of bacteria
• Anaerobic chemotrophs
• Oxygenic phototrophs
• Aerobic chemotrophs
• Notable terrestrial bacteria
• Notable aquatic bacteria
• Notable animal-symbiotic bacteria
• Archaea that thrive in extreme conditions

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Anaerobic Chemotrophs

• The earliest life forms likely were anaerobic
  chemotrophs since early Earth lacked O2 while
  photosynthesis requires significant metabolic
  sophistication.
• Anaerobic (no O2) habitats are still in
  abundance.
• These occur from combinations of poor diffusion
  and mixing along with presence of facultative
  anaerobes which serve as O2 scavengers.
• Often these are poorly mixed wet environments
  since water slows diffusion while simultaneously
  supports facultative organisms (i.e., unlike very
  dry habitats).
• Even well-mixed environments can become anaerobic
  if they become too eutrophic (nutrient rich).
• Basically, by not having to support aerobic
  metabolisms, non-facultative anaerobes can be
  more efficient growers and therefore better
  competitors in anaerobic environments than
  facultative anaerobes.

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Anaerobic Chemolithotrophs

• Chemolithotrophs obtain their energy from
  inorganic, reduced chemicals such as hydrogen gas
  (H2).
• Anaerobic chemolithotrophs are anaerobic
  respirers rather than fermenters (without
  glucose, where would the pyruvate come from,
  after all?).
• Most anaerobic chemolithotrophs are Archaeans.
• The most important are the Methanogens
• 4 H2 CO2 ? CH4 H2O (CH4 methane)
• Feel free to memorize the above as Hydrogen gas
  plus Carbon Dioxide go in while Methane comes
  out.
• Methane is an important component of swamp gas.
• Methane also is an important component of cow
  flatulence (since methanogens are found in
  ruminent intestines).
• Methane is an important greenhouse gas.

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Anaerobic Chemoorganotrophs

• Chemoorganotrophs obtain their energy from
  organic compounds such as glucose.
• Anaerobically respiring chemoorganotrophs
  generally use sulfur compounds instead of O2 as
  their terminal electron acceptor.
• Generally their metabolism creates Hydrogen
  Sulfide (H2S) which has a smell of rotten eggs.
• H2S also reacts with iron which is corrosive and
  forms a black product (iron sulfide).
• Anaerobic chemoorganotrophs consequently are
  responsible for significant iron corrosion under
  anaerobic conditions (e.g., of iron pipes).
• H2S reacting with iron also turns anaerobic
  environments black, such as mud.

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Chemoorganotrophic Fermenters

• Fermenting chemoorganotrophs are anaerobes which
  lack an electron transport chain and therefore
  are obligate fermenters.
• The Clostridium spp. are endospore-forming,
  Gram-positive rods that are common soil dwellers
  and which generally are poisoned by O2 (i.e.,
  they are strict anaerobes).
• Common species include
• C. botulinum which causes botulism.
• C. tetani which causes tetanus.
• C. perfringens which causes gas gangrene.
• C. difficile which causes antibiotic-associated
  colitis (i.e., C. difficile superinfections).

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Chemoorganotrophic Fermenters

• Lactic Acid Bacteria (LAB) are another important
  group of fermenting chemoorganotrophs.
• LAB are defined by their production of lactic
  acid rather than by evolutionary (genetic)
  relatedness.
• They are Gram positive, dont form endospores,
  and typically are aerotolerant anaerobes.
• Important genera include
• Streptococcus spp.-- strep throat, etc.
• Enterococcus spp. -- urinary tract infections
• Lactococcus spp. -- sour-milk products such as
  yogurt
• Lactobacillus spp. -- vaginal, etc. normal flora
  plus sour-milk products (like Lactococcus spp.)
• Leuconostoc spp. -- sauerkeaut, food spoilage
• Propionibacterium spp. are non-LABs involved in
  Swiss cheese production as well as acne.

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Oxygenic Phototrophs

• These are oxygen-producing photosynthetic
  bacteria.
• A number of eukaryotic organisms are also
  oxygenic phototrophs (e.g., plants) though all
  are so because they harbor oxygenic phototrophic
  bacteria in their cytoplasms (e.g.,
  chloroplasts).
• Cyanobacteria are the most common
  non-endosymbiotic bacterial oxygenic phototrophs.
• Cyanobacteria are Gram negative. Many are
  nitrogen fixers.
• Oxygenic phototrophs are the most important
  primary producers, getting their energy from the
  sun and fixing carbon, thereby making organic
  carbon (and associated energy) available to
  chemoheterotrophs such as us.
• Oxygenic phototrophs, as carbon fixers, are also
  key players in the carbon cycle, so important in
  these days of global warming (which is important
  regardless of whether humans are at fault).

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Aerobic Chemoorganogtrophs

• So far as this course is concerned, Aerobic
  Chemoorganotrophs are the most important of
  bacteria.
• This is in part a bias of culturing techniques,
  which tend to favor the growth of organisms that
  grow on organic food-type stuff under aerobic
  conditions, and our own biases towards aerobic
  environments and organic materials as food.
• Many pathogens are aerobic chemooganotrophs.
• We are aerobic chemoorganotrophs!
• We can divide aerobic chemoorganotrophs, based on
  their oxygen requirements, into
• Obligate aerobes
• Facultative anaerobes
• Because of their breadth and importance we will
  consider them genera by genera.

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Genus Mycobacterium

• Mycobacterium spp. includes both soil-adapted
  saprophytes (eaters of dead and decaying
  organisms) and important pathogens.
• Members of Mycobacterium spp. are often described
  as mycobacteria, which is neither italicized nor
  the name of their genus.
• Mycobacteria are obligately aerobic, acid-fast,
  pleiomorphic rods, that dont form endospores but
  do have waxy cell envelopes.
• Mycobacteria are more disinfectant resistant than
  most other bacteria (endospores excepted).
• Medically important Mycobacteria include
• Mycobacterium tuberculosis which causes
  tuberculosis.
• Mycobacterium leprae which causes leprosy
  (Hansens disease).

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Genus Pseudomonas

• Members of Pseudomonas spp. are also described as
  pseudomonads, which is neither italicized nor the
  name of their genus.
• Pseudomonads are Gram-negative, motile rods some
  of which are strict aerobes while others can
  respire anaerobically (and none of which can
  ferment).
• Pseudomonads are notable for their diversity
  (their genus probably is poly- or paraphyletic)
  including metabolic diversity.
• Pseudomonads are ubiquitous, inhabiting waters
  and soils, including highly nutrient-poor
  habitats, and are resistant to certain
  disinfectants.
• Pseudomonas aeruginosa is an opportunistic
  pathogen, meaning that it is a pathogen of
  individuals who already suffer from medical
  conditions.

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Genus Corynebacterium

• Corynebacterium diphtheriae is a Gram-positive,
  pleomorphic, rod-shaped, facultatively anaerobic
  bacterium.
• C. diphtheriae is most notable as the cause of
  diphtheria, a respiratory disease associated with
  the diphtheria toxin.
• Vaccination against diphtheria is actually
  vaccination against diphtheria toxin and as a
  consequence of vaccination this once dreaded
  disease is now quite rare where vaccination is
  common.
• Non-C. diphtheriae members of genus
  Corynebacterium serve as harmless members of the
  throat normal flora.

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Family Enterobacteriaceae

• Members of family Enterobacteriaceae, otherwise
  known as enterics or enterobacteria, are
  facultatively anaerobic, Gram-negative,
  Glucose-fermenting rods.
• Most that we are concerned with live in the large
  intestine, where many serve as pathogens others
  serve as plant pathogens and soil bacteria (e.g.,
  Erwinia spp.)
• Important gastrointestinal genera or species
  include Enterobacter, Escherichia coli,
  Klebsiella, Proteus, Salmonella, and Shigella.
• Klebsiella pneumoniae causes pneumonia.
• Escherichia and Proteus cause urinary-tract
  infections.
• Yersinia pestis is the bubonic plague bacillus.

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Genus Bacillus

• Bacillus and Clostridium are common
  Gram-positive rod-shaped bacteria that form
  endospores.
• Bacillus species may be either obligate aerobes
  or facultative anaerobes.
• Bacillus anthracis causes the disease anthrax,
  which can be acquired from contacting its
  endospores in soil or in animal hides or wool.
  (though only if those materials are B. anthracis
  contaminated, of course)
• B. anthracis endospores can enter the body either
  through inhalation or through a break in the
  skin.
• The B. anthracis niche, apparently, is to grow in
  or on animals, produce large quantities of
  endospores, and then, by killing their host
  animal, disseminate those spores back to the soil
  and thereby to other animals.
• Other Bacillus spp. simply are soil-dwelling
  species with endospores allowing survival during
  hot, dry spells.

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Genus Streptomyces

• The streptomycete, the unitalicized,
  uncapitalized common name for genus Streptomyces,
  are Gram-positive rods.
• The streptomycete are soil bacteria that make
  their living much like fungi plus superficially
  resemble fungi. (They, however, are bacteria, not
  fungi.)
• Like fungi, streptomycete display filamentous
  forms, called hyphae, that grow into tangled
  masses called mycelia (sing., mycelium).
• Like some fungi, streptomycete disseminate their
  kind by forming spores called conidia.
• Streptomycete give rise to the earthy odor of
  soil.
• Members of genus Steptomyces are particularly
  notable for their production of the common
  antibiotics erythromycin, streptomycin, and
  tetracycline.

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Genus Bdellovibrio

• The Bdellovibrio are Gram-negative intracellular
  (intra-periplasmic, actually) parasites of
  Gram-negative bacteria.

Dont worry about the numbers found in this
figure.
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Genus Staphylococcus

• Members of genus Staphylococcus are
  Gram-positive, facultatively anaerobic cocci that
  often grow in grape-like clusters called
  staphylococci.
• They thrive in the dry, salty conditions of skin
  and are distinguishable from other normal flora
  Gram-positive cocci in that they are catalase
  positive.
• There are a number of normal-flora members of
  genus Staphylococcus that are not pathogenic.
• The notable exception is Staphylococcus aureus
  which infects wounds, causes food poisoning, and
  is responsible for one form of Toxic Shock
  Syndrome.

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Genera Campylobacter Helicobacter

• These are curved (helical), Gram-negative,
  microaerophilic rods.
• Campylobacter jejuni is an important food- and
  waterborne cause of diarrheal disease.
• Helicobacter pylori is the cause of stomach
  ulcers as well as the development of stomach
  cancer.

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Genus Haemophilus

• Members of genus Haemophilus are Gram-negative
  cocobacilli.
• Many are respiratory tract normal flora bacteria.
• H. influenzae is an important cause of ear and
  respiratory infections as well as bacterial
  meningitis.

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Genus Neisseria

• Members of genus Neisseria are Gram-negative
  cocci, usually diplococci.
• They are obligate aerobes and fastidious.
• There are a number of Neisseria members of the
  human normal flora including oral cavity and
  other mucous membranes.
• Most notably, N. gonorrhoeae is the cause of the
  sexually transmitted disease, Gonorrhea.

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Genus Mycoplasma

• Members of genus Mycoplasma lack cell walls and
  consequently are pleiomorphic and able to pass
  through filters that can trap cell-wall
  containing bacteria.
• Mycoplasma pneumoniae is the cause of Walking
  Pneumoniae.

Note the fried egg appearance of Mycoplasma
colonies.
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Spirochetes

• Spirochetes are Gram-negative helical bacteria
  that use Axial Filaments, a kind of flagellum
  (and a.k.a., endoflagella), to display motility.
• Axial filaments and their spiral shape allow
  motility within highly viscous environments, such
  as mud and mucous.

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Genus Treponema Borrelia

• These bacteria are spirochetes
• Borrelia burgdorferi causes Lyme disease.
• Treponema pallidum causes Syphilis.

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Obligate Intracellular Parasites

• Members of genera Chlamydia and Rickettsia are
  obligate intracellular parasites.
• Rickettsia rickettsii causes Rocky Mountain
  Spotted Fever.
• Rickettsia prowazekii causes Epidemic Typhus.
• Chlamydia trachomatis cases the sexually
  transmitted disease, Chlamydia, and is the
  leading cause of blindness, worldwide.
• Chlamydia are unusual in that they lack cell
  walls. However, unlike mycoplasma which otherwise
  have Gram-positive-like cell envelopes, Chlamydia
  have Gram-negative-like cell envelopes.

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Archaea Exremophiles

• A number of Archaea live in relatively extreme
  environments.
• These include
• Extreme halophiles (Great Salt Lake, Dead Sea)
• Extreme thermophiles (Hot Springs, Deep-Sea
  Vents)
• Extreme acidophiles (mine tailings)
• It has been postulated that the early Earth, as a
  consequence of an otherwise absence of life along
  with periodic extreme meteoric bombardment and
  volcanism was home originally to extremophiles.
• Phenotypic (e.g., current preferences for extreme
  environments) and genetic evidence (i.e., 16S
  rRNA) suggests that the ancestors to all of us
  may have been Archaea.

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