The Prokaryotes: Domains, Bacteria and Archaea

Introduction

Bergey’s Manual categorizes bacteria into taxa based on rRNA sequences.
Bergey’s Manual lists identifying characteristics such as Gram stain reaction, cellular morphology, oxygen requirements, and nutritional properties.

Prokaryotic Groups

Prokaryotic organisms are classified into two domains: Archaea and Bacteria.

Domain Bacteria

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 stem-root 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 b-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. g- 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 “cold-blooded” 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. d-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 CO₂ 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, non-endospore 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

Extreme halophiles, extreme thermophiles, and methanogens are included in the archaea.

MICROBIAL DIVERSITY

Few of the total number of different prokaryotes have been isolated and identified.
PCR can be used to uncover the presence of bacteria that can’t be cultured in the laboratory.