The Prokaryotes: Domains, Bacteria and Archaea
Introduction
1. Bergey’s Manual categorizes bacteria into taxa based on rRNA sequences.
2. Bergey’s Manual lists identifying characteristics such as Gram stain reaction,
cellular morphology, oxygen requirements, and nutritional properties.
Prokaryotic Groups
1. Prokaryotic organisms are classified into two domains:
Bacteria.
Archaea and
Domain Bacteria
1. Bacteria are essential to life on Earth.
The Proteobacteria
1. Members of the phylum Proteobacteria are gram-negative.
a. Assumed to have arisen from a common photosynthetic ancestor
although most are no longer photosynthetic.
b. Phylogenetically related based on rRNA similiarities.
2. α-proteobacteria includes most bacteria that are capable of growth at very low
nutrient levels.
a. Includes nitrogen-fixing bacteria, chemoautotrophs, and
chemoheterotrophs.
b. Some of these have unusual morphology (prosthethecae – stalks or
buds).
c. Azospirillum – soil bacteria that fix nitrogen, grow in close association with
roots of many plants, have a symbiotic relationship in which they provide
nitrogen to the plant and the plant provides nutrients to the bacteria.
d. Acetobacter and Gluconobacter – industrially important aerobes, convert
ethanol into acetic acid.
e. Rickettsia
i. Obligate intracellular parasites
ii. Pleomorphic, non-motile, rod shaped or coccobacilli
iii. Transmitted to humans by bites of insects and ticks (Arthropods)
iv. Enters host cell by phagocytosis
v. Can damage the permeability of capillaries
vi. Rickettsia prowazekii - Epidemic typhus – transmitted by lice
vii. Rickettsia typhi – endemic murine typhus, transmitted by rat fleas
viii. Rickettsia rickettsii - Rocky Mountain spotted fever -transmitted by
ticks (Dermacentor)
ix. Rickettsia tsutsugamushi - scrub typhus
f. Ehrlichia – rickettsialike, live obligately in leukocytes, transmitted by ticks,
cause ehrlichiosis.
g. Caulobacter– prosthecae producing bacteria found in low-nutrient aquatic
environments
h. Hyphomicrobium – budding bacteria found in low-nutrient aquatic
environments
i. Rhizobium – infects roots of leguminous plants, forms nodules, fixes
nitrogen for the plant, receives nutrients from the plant.
j. Agrobacterium – plant pathogen, causes crown gall (a tumor at the stemroot transition site).
k. Inserts a plasmid into the plant cells, has been used for genetic
engineering of plants.
l. Brucella – small, nomotile coccobacillus, obligate parasites of mammals,
cause brucellosis, undulant fever, abcesses. Survive phagocytosis.
m. Nitrobacter– Nitrifying bacteria, can use inorganic chemicals as energy
sources and CO2 as sole source of carbon. Nitrobacter oxidizes
ammonium (NH4+) to nitrite (NO2-) and Nitrosomonas oxidizes nitrite to
nitrate (NO3-).
3. The -proteobacteria include chemoautotrophs and chemoheterotrophs.
a. Nitrosomonas – see above.
b. Thiobacillus – sulfur oxidizing bacteria
c. Spirillum – aerobic, large, motile by polar flagella (different from
spirochetes, which are motile by axial filaments)
d. Sphaerotilus – sheathed bacteria, form hollow filamentous sheath in
which they live, contribute to bulking in sewage treatment
e. Burkholderia – Burkholderia cepacia is aerobic rod, “extraordinary
nutritional spectrum”, may grow in disinfectants and can metabolize
accumulated respiratory secretions in CF patients
f. Bordetella – Bordetella pertussis, aerobic rods, nonmotile, causes
whooping cough
g. Neisseria – aerobic cocci, Neisseria gonorrhoeae (gonorrhoea; N.
meningitides (meningococcal meningitis)
h. Zooloea – important in aerobic sewage-treatment processes
4. - proteobacteria are the largest group of proteobacteria.
a. Beggiatoa alba – gliding motility, filamentous, uses H2S as an energy
source
b. Francisella – pleomorphic, reuire complex media enridhed with blood or
tissue extracts, F. tularensis causes tularemia
c. Pseudomonadales – aerobic rods or cocci
i. Pseudomonas sp. – rods, motile by polar flagella, common in soil,
can metabolize a variety of substrates.
1. Metabolic capabilities contribute to decomposition of
chemicals added to soil (pesticides) and ability to grow in
antiseptics and detergents.
2. Some species can substitute nitrogen for oxygen as a
terminal electron acceptor in anaerobic respiration
(anaerobic conditions, like water-logged soil), which
depletes soil nitrogen (fertilizer) and harms plants
3. Cell wall porins probably contribute to their resistance to
most antibiotics.
4. Many species grow at refrigerator temperatures, contribute
to food spoilage.
5. P. aeruginosa – soluble blue-green pigmentation, can infect
urinary tract, burns, wounds causing septicemia, abscesses,
and meningitis
ii. Azotobacter and Azomonas – free-living in soil, nitrogen fixing
bacteria, require energy sources that are in limited supply in soil
and so aren’t significant agriculturally
iii. Moraxella – strict aerobes, coccibacilli. Moraxella lacunata causes
conjunctivitis
d. Legionellales
i. Legionella pneumophila – fastidious, require artificial media,
colonize warm-water supply lines in hospitals and water in cooling
towers or air conditioning systems. Can survive within aquatic
amoebae. Cause legionellosis.
ii. Coxiella burnetti – like rickettsias they require a mammalian host to
reproduce. Unlike rickettsias they aren’t transmitted by insect or
tick bites but rather by aerosols or contaminate milk. Sporogenic
cycle imparts resistance to heat and drying.
e. Vibrionales – facultatively anaerobic rods, many slightly curved.
i. Vibrio cholera – cholera
ii. V. parahaemolyticus - gastroenteritis
f. Enterobacteriales - facultatively anaerobic rods with simple nutritional
requirements.
i. Enterics, most actively ferment glucose and other carbohydrates.
ii. Fimbriae help adhere to surfaces (i.e. mucous membranes). Sex
pili enable exchange of genetic material (i.e. antibiotic resistance).
iii. Produce bacteriocins – proteins that cause lysis of closely related
species, may help maintain balance of intestinal flora.
1. Escherichia coli – very common intestinal inhabitant. Not
usually pathogenic, but some strains can cause traveler’s
dirrhea due to enterotoxins produced.
a. E. coli 0157:H7 causes hemorrhagic colitis. May
inhabit animal intestinal tracts, especially cattle, and
have no effect.
2. Salmonella enterica – common inhabitant of animal
intestinal tracts, especially poultry and cattle. More than
2300 serovars differentiated by the Kauffman-White
scheme.
a. K (caspsule) O (cell wall) H (flagella) antigens
followed by numbers
b. Many strains only named by serovar
c. Biovars – further differentiation of serovars by
biochemical or physiological properties
d. Salmonellosis – gastrointestinal disease, one of the
most common foodborne illnesses
e. S. typhi – typhoid fever, the most sever form of
salmonellosis
f. S. bongori – isolated from a lizard, resident of “coldblooded” animals
3. Shigella - bacillary dysentery (shigellosis), found only in
humans, apes, and monkeys. Shiga toxin is extremely
virulent, causes hemorrhagic dysentery.
a. Shigella dysenteriae – can cause severe dysentery,
least common species in U.S.
b. Shigella flexneri
c. Shigella boydii
d. Shigella sonnei
4. Klebsiella - Major cause of septicemia in pediatric patients,
pneumonia (K. pnumoniae), urinary tract infections (UTIs),
nosocomial infections of the urinary tract
5. Serratia marcescens - nosocomial infections of the
respiratory and urinary tracts (produces red pigment)
6. Proteus - urinary tract infections, wound infections, infant
diarrhea (very actively motile)
a. Proteus vulgaris
b. Proteus mirabilis
7. Yersinia- plague (Black Death), carried by urban rats in
some places and ground squirrels in the American
Southwest. Transmission by fleas or respiratory droplets.
8. Erwinia - plant pathogen; causes soft rot
9. Enterobacter - urinary tract and nosocomial infections
a. Enterobacter aerogenes
b. Enterobacter cloacae
g. Pasteurellales – facultatively anaerobic rods
i. Pasteurella
1. Pasteurella multocida - wound infections associated with cat
and dog bites
2. Pasteurella haemolytica
ii. Haemophilus
1. Haemophilus influenzae - meningitis, otitis media, sinusitis,
epiglottitis, pneumonia; requires X factor (heme fraction of
hemoglobin) and V factor (NAD)
2. Haemophilus aegypticus - conjunctivitis
5. Purple and green photosynthetic bacteria are photoautotrophs that use light
energy and CO2 and do not produce O2 (anoxygenic).
a. Generally anaerobic
b. Morphorologically diverse, spirals, rods, cocci and budding forms
c. Not necessarily purple or green
d. Purple and green sulfur bacteria
i. Use reduced sulfur compounds instead of water, produce sulfur
granules instead of oxygen.
e. Purple and green nonsulfur bacteria
i. Use organic compounds like acids and carbohydrates to reduce
CO2.
6. -proteobacteria
a. Desulfovibrionales
i. Desulfovibrio - sulfur reducing bacteria; found in the intestine of
humans
b. Bdellovibrionaceae
i. Bdellovibrio - attacks other gram-negative bacteria; bacterial
predator
c. Myxococcales
i. Myxococcus - gliding bacteria; very complex life cycle, also prey on
other bacteria
7. ε-proteobacteria – microaerophilic, helical or vibriod
a. Campylobacter
i. Campylobacter fetus - spontaneous abortions in domestic animals)
ii. Campylobacter jejuni - enterocolitis and bacteremia
b. Helicobacter
i. Helicobacter pylori - gastritis and peptic ulcer
The Nonproteobacteria Gram-Negativebacteria
1. Several phyla of gram-negative bacteria are not related phylogenetically to the
Proteobacteria.
2. Cyanobacteria are photoautotrophs that use light energy and CO 2 and do
produce O2.
a. Blue-green pigment
b. Many fix nitrogen
3. Chlamydiales
a. Coccoid bacteria
b. Non-motile
c. Do not use arthropods for transmission
d. Transmitted by interpersonal contact and respiratory route
e. Chlamydia trachomatis - trachoma, primary cause of NGU,
lymphogranuloma venereum, pneumonia, conjunctivitis
f. Chlamydia psittaci (ornithosis or psittacosis – a type of pneumonia
g. Chlamydia pneumoniae - atypical pneumonia
4. Spirochetes
a. Helical or vibroid morphology, motility by axial filaments, Gram-negative
b. Borrellia
i. Borrelia recurrentis - relapsing fever
ii. Borrelia burgdorferi - Lyme disease
c. Treponema pallidum -syphilis
d. Leptospira
i. Leptospira interrogans (leptospirosis)
5. Bacteroides - anaerobic non-endospore forming, non-motile rods
a. Large group of organisms which inhabit the intestinal tract, oral cavity,
genital tract, and upper respiratory tract
b. Bacteroides fragilis - most common pathogen; infections of puncture
wounds or surgical incisions, peritonitis
6. Fusobacteria
a. Normal flora of the mouth, colon, and female genital tract; pulmonary,
intra-abdominal and pelvic abscesses, dental abscesses
b. Fusobacterium nucleatum - occurs in cases of trench mouth along with
spirochetes
c. Streptobacillus moniliformis - rat-bite fever
7. Sphingobacteria
a. Sphingobacterium - hydrolyzes plant oils; used to produce commercial
products
b. Cytophaga - degrades cellulose; important in sewage treatment
The Gram-Positive Bacteria
1. In Bergey’s Manual, gram-positive bacteria are divided into those that have low
G + C ratio and those that have high G + C ratio.
2. Low G + C gram-positive bacteria include common soil bacteria, the lactic acid
bacteria, and several human pathogens.
a. Mycoplasmatales
i. Do not form cell walls
ii. Have high sterol content in the plasma membrane
iii. Aerobes or facultative anaerobes
iv. Highly pleomorphic
v. Mycoplasma - Can be grown on artificial media with sterols, but
cell culture methods are often used
vi. Mycoplasma pneumoniae - primary atypical pneumonia
vii. Mycoplasma hominis - implicated in pelvic inflammatory disease
viii. Ureaplasma urealyticum - nongonococcal urethritis
b. Clostridiales
i. Clostridium - Obligate anaerobes that form endospores
ii. Clostridium tetani - tetanus
iii. Clostridium botulinum - botulism
iv. Clostridium perfringens - gas gangrene, foodbourne diarrhea
v. Clostridium difficile - antibiotic-associated pseudomembranous
colitis
c. Epulopiscium – large, originally thought be be a protozoan
i. Daughter cells released through a slit in the parent cell – not binary
fission
d. Veillonella parvula - normal flora of the mouth, colon, vagina;
opportunistic pathogen – abscesses of sinuses, tonsils and brain; often
occur in clusters, but may occur singly or in chains, non-motile, nonendospore forming
e. Lactobacillales
i. Lactobacillus - normal flora of the mouth, colon, and female genital
tract; aerotolerant rods that produce lactic acid
ii. Streptococcus - aerotolerant, catalase-negative
1. α-hemolytic produce α-hemolysin, reduces hemoglobin (red)
to methemoglobin (green)
2. β-hemolytic strep produce a hemolysin that completely
lyses hemoglobin, produces a clear zone
3. γ-hemolytic strep are actually nonhemolytic
4. S. pyogenes - Group A, β-hemolytic; pharyngitis, impetigo,
pharyngitis, scarlet fever, and rheumatic fever
5. Group A invasive streptococci – necrotizing fasciitis
(exotoxin A)
6. S. mutans - γ-hemolytic; dental caries
7. S. pneumoniae - α-hemolytic; pneumonia, bacteremia,
meningitis, otitis and sinusitis
iii. Staphylococcus - grapelike clusters, aerobes or facultative
anaerobes, grow well under high osmotic pressure/low moisture
conditions
1. S. epidermidis -normal flora of the skin
2. S. aureus - pyogenic infections such as endocarditis and
osteomyelitis; food poisoning, and toxic shock syndrome
3. S. saprophyticus - urinary tract infections
iv. Listeria
1. Listeria monocytogenes - meningitis and sepsis in newborns
and immunosuppressed adults; can cause stillbirth or
serious damage to the developing fetus; contaminates
foods, survives phagocytosis, grows at refrigeration
temperature.
3. High G + C gram-positive bacteria – phylum Actinobacteria
a. Mycobacterium - aerobic, non-endospore forming rods. Fungus-like in
that they occasionally exhibit filamentous growth. Myucolic acids in outer
layer from waxy, water-resistant layer, resistant to desication and many
antimicrobial drugs.
i. Mycobacterium tuberculosis
ii. Mycobacterium leprae
b. Corynebacterium – pleomorphic, varies with age of cells
i. Cornebacterium diphtheriae
c. Propionibacterium – forms propionic acid, species used for fermentation
of Swiss cheese.
i. Propionibacterium acnes
d. Gardnerella
i. Gardnerella vaginalis – common cause of vaginitis, gram-0variable
and pleomorphic.
e. Actinomycetes – filamentous, soil bacteria
i. Frankia – forms nitrogen-fixing nodules in alder tree roots
ii. Streptomyces –strict aerobes, produce asexual spores
(conidiospores); source of most commercial antibiotics
iii. Actinomyces – facultative anaerobes, inhabit mouth and throat of
humans and animals
1. A. israelii – causes actinomycosis, tissue destroying disease
of the head, neck or lungs.
iv. Nocardia – aerobic, produce filaments that fragment into short rods
1. N. asteroids – may cause pulmona4ry infections or
mycetoma (localized destructive infection of feet or hands)
Domain Archaea
1. Extreme halophiles, extreme thermophiles, and methanogens are included in the
archaea.
MICROBIAL DIVERSITY
1. Few of the total number of different prokaryotes have been isolated and
identified.
2. PCR can be used to uncover the presence of bacteria that can’t be cultured in
the laboratory.