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Chapter 11 Characterizing and Classifying Prokaryotes


1. Morphology of Prokaryotic Cells

a. Learning Objectives
i. Identify six basic shape of prokaryotic cells
b. Prokaryotic cells exist in a variety of shapes (cocci (spherical), bacilli
( rod-shaped), and spirals)
c. Spiral shaped prokaryotes are either spirilla, which are stiff in shape, or
spirochetes, which are flexible. Slightly curved rods are vibrios and
termed coccobacillus.
d. There are star shaped, triangular, and rectangular prokaryotes. As well as
pleomorphic (meaning vary in shape and size)

2. Reproduction of Prokaryotic Cells

a. Learning Objectives
i. List 3 common types of reproduction in prokaryotes.
ii. Describe snapping division as a type of binary fission.
b. All prokaryotes reproduce asexually. The most common method of
asexual reproduction is binary fission.
i. The cells replicates its DNA which is attached to the cytoplasm.
ii. The cell grows and as the cytoplasmic membrane elongates, it
moves the daughter molecules of DNA apart.
iii. The cell forms a cross wall, invaginating the cyto membrane.
iv. The cross wall completely divides daughter cells.
v. The daughter cell may or may not separate. The parent cell
disappears, with the formation of progeny.
c. A variation of binary fission is called snapping division. Occurs in some
Gram-positive species.
i. Only the inner portion of the cell wall is deposited across the
dividing cell. The thickening of the new transverse wall puts
tension on the outer layer of the old cell wall, with the increased
tension the outer wall breaks at its weakest point.
d. Spores a reproductive cell that are at the ends of filamentous cells. Each
spore can develop into a clone of the original organism.
e. Other prokaryotes reproduce by budding, which an outer growth of the
original cell receives a copy of the genetic material and enlarges. And
eventually cuts off from the parent cell.

3. Arrangements of Prokaryotic Cells

a. Learning Objectives
i. Draw and label five arrangements of prokaryotes.
b. Diplococci – cocci attached in pairs
c. Streptococci- a chain of cocci
d. Tetrads- cocci divide in 2 planes and remain attached
e. Sarcinae- divide into 3 cuboidal planes pockets
f. Staphylococci- clusters that look like grapes and the planes of cell division
are random.
g. Bacilli divide transversely. Daughter cells my separate to become single
cells or stay attached as pairs or chains. V-shaped side by side
arrangements are called palisade.

4. Endospores
a. Learning Objectives
i. Describe the formation and function of bacterial endospores.
b. Gram-positive bacteria ( bacillus and clostridium) can produce endospores
which are important for their durability and potential pathogenicity. They
constitute a defensive strategy against hostile or unfavorable conditions.
Resting stages that barely metabolize and germinate only when conditions
c. Sporulation requires 8 to 10 hours and has several steps.
d. They are very resistant and can form deadly toxins that cause fatal disease
such as anthrax, tetanus, and gangrene.

5. Modern Prokaryotic classification

a. Learning Objecives
i. Explain the general purpose of Bergey;s manual of systematic
ii. Discuss the veracity and limitations of any taxonomic scheme.
b. Taxonomists place all organisms into 3 domains; Archaea, Bacteria, and
Eukarya- the largest and most inclusive.
c. Archaea and bacteria are divided into smaller taxa based on the
similarities in DNA, RNA, and protein sequences.
d. Approximately 99.5% of prokaryotes are not been isolated or cultured,
they are identified only by their rRNA sequence.
e. Bergey’s manual of systematic bacteriology classifies prokaryotes into 25
phyla – 2 in archaea and 23 in bacteria.

6. Survey of Archaea
a. Learning Objective
i. Identify the common features of microbes in the domain Archaea.
b. Archaea lack peptidoglycan in their cell walls
c. Their cell membrane lipids have branched hydrocarbon chains.
d. The initial amino acid in their polypeptide chains is methionine like in
e. Classified in two phyla- crenarchaeota and euryarchaeota. Based on rRNA
f. They reproduce via binary fission, budding, or fragmentation. They
usually carry cocci, bacilli or spiral forms as well as pleomorphic.
g. Their cell walls vary consisting of a variety of compounds; proteins,
glycoproteins, lipoproteins, and polysaccharides.
h. Not one of them is known to cause disease in humans or animals. They
generate methane gas.

1. Extremophiles
a. Learning Objectives
i. Compare and contrast the two kinds of extermophiles discussed in
this section.
b. They are microbes that need extreme conditions such as temperature, pH
and or salinity to survive.
c. Usually among the extremophiles there are thermophiles and halophiles.
d. Thermophiles are prokaryotes whose DNA and RNA, cytoplasmic
membranes and proteins require them to leave in temperatures about 300 C
and hyperthermophiles require temp over 800C.
e. They are used in recombinant DNA tech application because their cellular
structure and enzymes are stable and functional at temperatures that
denature most proteins and nucleic acids and kill other cells.
f. Use for additives in laundry detergent
g. Halophiles classified in the phylum euryarchaeota. They inhabit extremely
saline habitats. Their absolute dependence on a concentration of NaCl
greater than 9% (1.5 molar solution) to maintain the integrity of there cell
h. Contain a red or orange pigment that probably protects them from intense
visible and ultraviolet light.
2. Methanogens
a. Learning Objectives
i. List at least four significant roles played by methanogens in the
b. Obligated anaerobes in the phylum euryarchaeota that convert CO2, H2
and organic acids into methane gas(CH4)
c. Largest known group of archaea.
d. Plays a role in converting organic waste in pond, lake and ocean sediments
into methane.
e. Swamp gas ( greenhouse gas) methane in the atmosphere traps heat, which
adds to global warming.

Survey of Bacteria

3. Deeply Branching and Phototrophic bacteria

a. Learning Objectives
i. Provide a rationale for the name “deeply branching bacteria”
ii. Explain the function of heterocysts in terms of both photosynthesis
and nitrogen fixation.
b. Deeply Branching Bacteria
i. Named because their rRNA sequence and growth characteristics
resemble that of early organisms, branching bacteria. Deeply
branching are autotrophs because heterotrophs by definition must
derive carbon from autotrophs. Many living in habitats similar to
those that existed on early earth.
ii. Ex. Gram-negative, microaerophilic aquifex.
c. Phototrophic Bacteria
i. Acquire the energy needed for anabolism by absorbing light with
pigments located in thylakoids called photosynthetic lamellae.
ii. They lack the membrane bound thylakoids seen in eukaryotic
iii. Autotrophs produce organic compounds from carbon dioxide.
iv. Can be divided into 5 groups:
1. blue-green bacteria
2. green sulfur
3. green nonsulfur
4. purple sulfur
5. purple nonsulfur bacteria
v. Table 11.1
d. Cyanbacteria – gram negative phototrophs that vary in shape size and
method of reproduction.
i. Coccoid or disk shaped
ii. Some filamentous cyanbacteria are motile.
iii. Reproduce by binary fission, and by motile fragments or by thick
walled spores called akinetes.
iv. Utilize chlorophyll a and are oxygenic.
v. Blue green algae
vi. Thought to have transformed the anaerobic atmosphere into our
oxygenated one.
vii. Reduce nitrogen gas to ammonia in a process called nitrogen
viii. Heterocysts transport reduced nitrogen to neighboring cells on
exchange for glucose.
e. Green and purple phototrophic Bacteria
i. They use bacteriochlorophylls for photosynthesis instead of
chlorophyll a, and are anoxygenic; (they do not generate oxygen
during photosynthesis.)
ii. Found in muds rich in hydrogen sulfide at the bottom of ponds and
iii. Green and purple phototrophic bacteria include both sulfur and
nonsulfur forms.
iv. G+C ratio is the % of all base pairs in a genome that are guanine –
cytosine and use a useful criterion in classifying microbes. Below
50% = low G+C bacteria, remainder are considered high G+C
4. Low G + C Gram – Positive Bacteria
a. Learning Objectives
i. Discuss the lack of cell walls in mycoplasmas.
ii. Identify significant beneficial or detrimental effects of the genera
Clostridium, Bacillus, Listeria, Lactobacillus, Sreptococcus, and
b. G + C gram-positive bacteria are classified with in phylum firmicutes,
which have 3 groups:
i. Clostridia, mycoplasma, and other low G + C gram- positive
bacilli and cocci.
c. Clostridia
i. Rod shaped, obligate anaerobes, many form endospores.
ii. Important in medicine b/c Its members produce potent toxins that
cause a variety of diseases in humans and in industry b/c their
endospores enable them to survive harsh conditions; including
many types of disinfection and antisepsis.
1. ex. C tetani which cause tetanus.
iii. Epulopiscium has numerous short flagella that makes it look
ciliated. Doesn’t reproduce binary fission, it forms new cells
within the parent cell and then released through a slit in the parent
cell wall.
iv. Veillonella a genus of aerobic cocci that live as part of biofilm
(plaque) that forms on the teeth of warm blooded animals. Has
typical Gram-positive cell wall but it stains Gram-negative (pink)
d. Mycoplasmas
i. Second class of low G + C bacteria; lack cell walls so they stain
ii. They are able to survive without cell walls b/c they colonize
osmotically protected habitats such as animal and human bodies
and b/c they have tough cytoplasmic membranes that contain lipids
called sterols. (pleomorphic)
iii. Smallest free living cell and have a terminal structure which help
them bind to eukaryotic cells and gives them a pearlike shape
iv. Require organic growth factors; cholesterol, fatty acids, vitamins,
amino acids, and nucleotides, which can either by acquire from
their host or which must be added to laboratory media.
v. In animals, mycoplasmas colonize mucous membranes of the
respiratory and urinary tracts and are associated with pneumonia
and urinary tract infections.
e. Gram-positive Bacilli and Cocci
i. Third group of the low G-C gram positive organisms.
ii. Bacillius- endospore-forming aerobes and facultative anaerobes
that typically move by flagella.
iii. Bacillus thuringiensis beneficial to farmers and gardeners.
Produces a crystalline protein that is toxic to caterpillars that ingest
iv. Bacillus anthracis – causes anthrax, its endospores are either
inhaled or enter the body through breaks in the skin. When they
germinate the vegetative cells produce toxins that kill surrounding
tissues. Untreated cutaneous anthrax is fatal in 20% of patients.
Untreated inhalational anthrax is generally 100% fatal.
v. B. cereus- contaminated rice can cause disease in people. Heat
resistant endospores survive cooking, germinate in the intestinal
tract and produce a toxin that induces nausea, vomiting and
abdominal cramping.
f. Listeria
i. Pathogenic low G + C gram-positive rod
ii. Can contaminate milk and meat products; continues to reproduce
under refrigeration and can survive inside white blood cells.
iii. Rarely causes disease in adults but can kill a fetus in an infected
woman when it crosses the placenta barrier. Causes meningitis and
bacteremia when it infects immunocompromised patients such as
the aged and patients with AIDS, cancer, or diabetes.
g. Lactobacillus
i. Nonspore forming found in the human mouth, stomach, intestinal
tract, and vagina.
ii. Rarely cause disease, instead they protect the body by inhibiting
the growth of pathogens
iii. Used in the industry in the production of yogurt, buttermilk,
pickles, and sauerkraut.
h. Streptococcus and Enterococcus
i. Gram-positive cocci associated in pairs and chains.
ii. They produce numerous human diseases pharynitis (strep throat),
scarlet fever, impetigo, fetal meningitis, wound infections,
pneumonia, and diseases of the inner ear, skin, blood and kidneys.
i. Staphylococcus
i. Common inhabitant on humans; which is typically found growing
harmlessly on the skin in clusters.
ii. A variety of toxins and enzymes allow some strains to invade the
body and cause such diseases as bacteremia, pneumonia, wound
infections, food poisoning, toxic shock syndrome and diseases of
the joints, bones, heart and blood.
j. Table 11.2
5. High G + C Gram Positive Bacteria
a. Learning Objectives
i. Explain the slow growth of Mycobacterium.
ii. Identify significant beneficial or detrimental properties of the
genera Corynebacterium, Mycobacterium, Actinomyces, Nocardia,
and Streptomyces.
b. Classified in the phylum actinobacteria
c. Resemble fungi in their growth habit and production of reproductive
d. Corynebacterium
i. Reproduce by snapping division, which causes the cells to form V-
shapes and palisades. Characterized by their stores of phosphate
within inclusions called metachromatic granules which stain
e. Mycobactrium
i. Aerobic species that are slightly curved; they grow very slowly.
They are slow b/c of the time and energy required to enrich their
cell walls with high concentration of long carbon waxes called
mycolic acids.
ii. Acid-fast staining
iii. Tuberculosis and leprosy.
f. Actinomycetes
i. High G + C gram positive bacteria
ii. Cause disease in immunocompromised patients
iii. Composed of prokaryotic cells
g. Actinomyces
i. Normal inhabitants of mucous membranes lining the oral cavity
and throats of humans.
ii. Actinomyces israelii growing as opportunistic pathogen in humans
destroy tissue to form abscesses and can spread throughout the
abdomen consuming every vital organ.
h. Nocadia
i. Soil and water dwelling aerobes that typically form aerial and
subterranean filaments that resemble fungi.
ii. Can degrade many pollutants of landfills, lakes and streams,
including waxes, petroleum hydrocarnbons, detergents,
iii. Can cause lesions in humans
i. Streptomyces
i. Produce most of the important antibiotics including;
chloramphnicol, erythromycin, tetracycline
6. Gram negative Protobacteria
i. Five distinct classes; alpha, beta, gamma, delta and epsilon
7. Alphaproteobacteria
a. Learning Objective
i. Describe the appearance and function of prosthecae in
b. Alphaproteobacteria
i. Aerobes capable of growing at very low nutrient levels.
ii. Unusual methods of metabolism. Prosthecae attach to increase
surface area for nutrient absorption.
c. Nitrogen fixers.
i. 2 generas  azospirillum and rhizobium both important in
ii. Grow in the association with the roots of plants where they make
N2 available to plants as ammonia
d. Nitrifying bacteria
i. These microbes are important because they convert reduced
nitrogen compounds into nitrate (process called= nitrification)
Nitrate moves easily through soil.
e. Purple Nonsulfur phototrophs
i. Grow in the upper layer of mud at the bottom of lakes and ponds.
They harvest light as energy source.
f. Pathogenic a-proteobacteria
i. Aerobic rods that live and reproduce by binary fission inside
mammalian cells.
ii. Cause a number of different disease including; typhus and rocky
mountain spotted fever. They oxidize amino acids and krebs cycle.
iii. Brucella a disease in mammals characterized by spontaneous
abortions and sterility
iv. Ehrlichia causes disease in humans by living within white blood
cells. (fever, headache, muscle pain, and leucopenia)
8. Betaproteobacteria
a. Learning objectives
i. Name 3 pathogenic and 3 useful betaproteobacterial species.
b. Gram negative; thrive off low levels of nutrients. rRNA differ from a-
c. Oxidizes nitrate to nitrate.
d. Pathogenic B-proteobacteria
i. Inhibit the mucous membrane causing gonorrhea, meningitis,
pelvic inflammatory disease, and inflammation of the cervix,
pharynx and external lining of the eye.
9. Gammaproteobateria
a. Learning Objectives
i. Describe the gammaproteobacteria
b. Can be divided into several groups; purple sulfur, intracellular pathogens,
methane oxidizers, falcutative anaerobes, pseudomonads ( catabolize
c. Purple sulfur – obligate anaerobes that oxidize hydrogen sulfide to sulfur.
Found sulfur rich zones; lakes, bogs and oceans.
d. Intracellular pathogens – pathogens of humans that avoid digestion by
white blood cells.
e. Methane oxidizers – utilize methane as a carbon and as a energy source.
f. Glycolytic Faculatative anaerobes – the largest group composed of gram
negative that catabolize carbohydrates by glycolysis and the pentose
phosphate pathway. Used in studies of metabolism, genetics amd
recombinant DNA tech.
g. Pseudomonads – gram negative noted for breaking down numerous
organic compounds. Involved in the spoilage of refrigerated milk, eggs,
and meat b/c they can grow and catabolize proteins and lipids at 42
10. Deltaproteobacteria
a. Learning Objectives
i. List several members of deltaproteobacteria.
b. Not large but include a wide variety of metabolic types.
c. Epsilonproteobacteria- cause blood poisoning and inflammation of the
intestinal tract, helicobacter which causes ulcers.
11. Other gram negative bacteria
a. Learning Objectives
i. Describe the unique features of chlamydias and spirochetes
ii. Describe the ecological importance of bacteroids.
b. Chlamydias
i. Small cocci that grow and reproduce only within the cells of
mammals, birds, and a few invertebrates.
ii. After invading a host cell, forms an initial body; then the initial
body undergoes repeated binary fission until the host cell is filled
with reticulate bodies.
c. Spirochets
i. Unique helical bacteria that are motile by means of axial filaments.
Live in diverse habitats isolated from the mouth, marine
environments, moist soils, and the surfaces or protozoa that live in
termites’ guts.
ii. Can cause syphilis (treponema) and lyme disease (Borrelia).
d. Bacteroids
i. Normally inhabit the digestive tracts of humans and animals
ii. Most common anaerobic human pathogen.
iii. Cytophaga- wood damage.