Bacteria

Properties of Bacteria

• prokaryotic (no membrane-enclosed nucleus)
• no mitochondria or chloroplasts
• a single chromosome
  • a closed circle of double-stranded DNA
  • with no associated histones
• If flagella are present, they are made of a single filament of the protein flagellin; there are none of the "9+2" tubulin-containing microtubules of the eukaryotes.
• ribosomes differ in their structure from those of eukaryotes
• have a rigid cell wall made of peptidoglycan.

  Link to illustrated discussion of the structure.

• The plasma membrane is a phospholipid bilayer but contains no cholesterol or other steroids.
• no mitosis
• mostly asexual reproduction
• any sexual reproduction very different from that of eukaryotes; no meiosis
• Many bacteria form a single spore when their food supply runs low. Most of the water is removed from the spore and metabolism ceases. Spores are so resistant to adverse conditions of dryness and temperature that they may remain viable even after 50 years of dormancy.

Classification of Bacteria

• shape
  • bacilli: rod-shaped
  • cocci: spherical
  • spirilla: curved walls
• ability to form spores
• method of energy production (glycolysis for anaerobes, cellular respiration for aerobes
• nutritional requirements
• reaction to the Gram stain.

• The bacterial cells are first stained with a purple dye called crystal violet.
• Then the preparation is treated with alcohol or acetone.
• This washes the stain out of gram-negative cells.
• To see them now requires the use of a counterstain of a different color (e.g., the pink of safranin).
• Bacteria that are not decolorized by the alcohol/acetone wash are gram-positive.

More recently, genome sequencing, especially of their 16S ribosomal RNA (rRNA), has provided new insights into the evolutionary relationships among the bacteria.

The Proteobacteria

They are further subdivided into 5 clades: alpha-, beta-, gamma-, delta-, and epsilon proteobacteria.

Alpha (α) Proteobacteria.

• Rickettsias. These bacteria are too small to be clearly seen under the light microscope. Almost all are obligate intracellular parasites. This means that they can only grow and reproduce while within the living cells of their host — certain arthropods (ticks, mites, lice, fleas) and mammals.
  • Rickettsia prowazekii causes typhus fever when it is transmitted to humans by lice.
  • Rocky Mountain spotted fever is a rickettsial disease transmitted by ticks.
  The mitochondria of eukaryotes probably evolved from endosymbiotic prokaryotes. Because of the similarities of their genomes, rickettsias may be the closest relatives to the ancestors of mitochondria.

  Link to discussion of the endosymbiotic theory of the origin of mitochondria.

  Link to data on genomes of R. prowazekii and mitochondria.

• Rhizobia. These bacteria live in a mutualistic relationship with the roots of legumes where they are able to "fix" nitrogen (N₂) in the air into compounds that can be used by living things.

  Link to discussion.

• Magnetospirillum magnetotacticum
• Agrobacterium tumefaciens

Beta (β) Proteobacteria

• Sulfur bacteria.

  Certain colorless bacteria share the ability of chlorophyll-containing organisms to manufacture carbohydrates from inorganic raw materials, but they do not use light energy for this. These so-called chemoautotrophic bacteria secure the necessary energy by oxidizing some reduced substance present in their environment. The free energy released by the oxidation is harnessed to the manufacture of food.

  For example, some chemoautotrophic sulfur bacteria oxidize H₂S in their surroundings (e.g., the water of sulfur springs) to produce energy:
  

  2H₂S + O₂ → 2S + 2H₂O; ΔG = -100 kcal

  They then use this energy to reduce carbon dioxide to carbohydrate (like the photosynthetic purple sulfur bacteria).
  

  2H₂S + CO₂ → (CH₂O) + H₂O + 2S

• Iron bacteria.

  These chemoautotrophs are responsible for the brownish scale that forms inside the tanks of flush toilets. They complete the oxidation of partially oxidized iron compounds and are able to couple the energy produced to the synthesis of carbohydrate.

• Nitrosomonas

  This chemoautotroph oxidizes NH₃ (produced from proteins by decay bacteria) to nitrites (NO₂^-). This provides the energy to drive their anabolic reactions. The nitrites are then converted (by other nitrifying bacteria) into nitrates (NO₃^-), which supply the nitrogen needs of plants.

  Link to discussion of the various roles that bacteria play in the nitrogen cycle.

• Three important human pathogens in the β-proteobacteria. .
  • Neisseria meningitidis.

    Causes meningococcal meningitis, an extremely serious infection of the meninges that occasionally occurs in very young children and in military camps. There is a vaccine that is effective against several strains but unfortunately not the most dangerous one.

  • Neisseria gonorrhoeae. Causes gonorrhea, one of the most common sexually-transmitted diseases (STDs): 355,642 cases were reported in the U.S. in 1998. In males, the bacterium invades the urethra causing a discharge of pus and often establishes itself in the prostate gland and epididymis. In females, it spreads from the vagina to the cervix and fallopian tubes. If the infection is untreated (penicillin is usually effective although strains resistant to it are now being encountered), the resulting damage to the fallopian tubes may obstruct the passage of eggs and thus cause sterility.

    How N. gonorrhoeae evades host immunity.

  • Bordetella pertussis; the cause of "whooping cough".

Gamma (γ) Proteobacteria

The largest and most diverse subgroup of the proteobacteria.

• Escherichia coli. The most thoroughly-studied of all creatures (possibly excepting ourselves). Its entire genome has been determined down to the last nucleotide: 4,639,221 base pairs of DNA encoding 4,377 genes. Lives in the human colon, usually harmlessly. However, water or undercooked food contaminated with the O157:H7 strain has caused severe — occasionally fatal — infections.
• Salmonella enterica. Two major human pathogens:
  • Salmonella enterica var Typhi. Causes typhoid fever, a serious systemic infection occurring only in humans. This microbe is also known as Salmonella typhi.
  • Salmonella enterica var Typhimurium. Confined to the intestine, it is a frequent cause of human gastrointestinal upsets but is also found in many other animals (that are often the source of the human infection). Also known as Salmonella typhimurium.

  How Salmonella typhi gets into human cells.

  Genomes of both organisms

  S. typhimurium in the Ames Test

• Vibrio cholerae. Causes cholera, one of the most devastating of the intestinal diseases. The bacteria liberate a toxin that causes massive diarrhea (10–15 liters per day) and loss of salts. Unless the water and salts are replaced quickly, the victim may die (of shock) in a few hours. Like other intestinal diseases, cholera is contracted by ingestion of food or, more often, water that is contaminated with the bacteria.

  Read about the 1991–92 cholera epidemic in Central and South America that made over 700,000 people ill and caused over 6,000 deaths.

• Pseudomonas aeruginosa. A common inhabitant of soil and water, it can cause serious illness in humans with
  • defective immune systems
  • serious burns
  • cystic fibrosis
  Frequently encountered in hospitals and resistant to most antibiotics and disinfectants.
• Yersinia pestis. This bacillus causes bubonic plague. It is usually transmitted to humans by the bite of an infected flea. As it spreads into the lymph nodes, it causes them to become greatly swollen, hence the name "bubonic" (bubo — swelling of a lymph node) plague. Once in the lungs, however, the bacteria can spread through the air causing the rapidly lethal (2–3 days) "pneumonic" plague. Untreated, 50–75 % of the cases of bubonic plague are fatal, and the figure for the pneumonic form reaches 100%.

  The recurrent epidemics of the "black death" in Europe from 1347–1352, which killed off at least one quarter of the population, are thought by many (not all) to have been caused by this organism.

  Although no major epidemics have occurred in this century, the threat is not entirely over. Yersinia pestis still flourishes in some rodent populations in the western U. S. and causes a few cases of human plague — primarily among small game hunters — each year (nine in 1998).

  Completion of the DNA sequence of the genome of Y. pestis — its chromosome plus three plasmids — was reported on 4 October 2001.

• Francisella tularensis causes tularemia. This is primarily a disease of small mammals, but about 100 people become infected each year in the United States. Most cases occur in south-central states (KS, MO, OK, AR). However, the import of infected rabbits by game clubs has introduced the disease to Cape Cod and Martha's Vineyard in Massachusetts. In the summer of 2000, 15 people became ill (one died) on the island. All seem to have acquired their infection as they used lawn mowers and brush cutters that presumably stirred up the organism from the carcasses of infected animals.
• Haemophilus influenzae was once thought to cause influenza. It does not, but it can cause bacterial meningitis and middle ear infections in children and pneumonia in adults — especially those whose resistance is lowered by other diseases (e.g., AIDS). There is now an effective vaccine against the most dangerous strains. The complete genome of Haemophilus influenzae is known: 1,830,138 bp of DNA encoding 1,743 genes.
• Purple Sulfur Bacteria

  Like green plants, these bacteria are photosynthetic, using the energy of sunlight to reduce carbon dioxide to carbohydrate. Unlike plants, however, they do not use water as a source of electrons.

  

  Instead they use hydrogen sulfide to supply the electrons needed to synthesize NADPH and ATP.

  2H₂S + CO₂ → (CH₂O) + H₂O + 2S

  In the process, they produce elemental sulfur (often — as seen in this photomicrograph of Chromatium — stored as granules within the cell). [Image from H. G. Schlegel and N. Pfennig, Arch. Microbiol. 38[1], 1961.]

  Photosynthetic bacteria contain special types of chlorophylls (called bacteriochlorophylls) incorporated into membranes. With this machinery, they can run photosystem I but not photosystem II (which explains their inability to use water as a source of electrons).

  Link to a discussion of green plant photosynthesis and photosystems I and II.

  Most photosynthetic bacteria are obligate anaerobes; they cannot tolerate free oxygen. Thus they are restricted to such habitats as the surface of sediments at the bottom of shallow ponds and estuaries. Here they must make do with whatever radiant energy gets through the green algae and aquatic plants growing above them. However, the absorption spectrum of their bacteriochlorophylls lies mostly in the infrared region of the spectrum so they can trap energy missed by the green plants above them.

Delta (δ) Proteobacteria

Epsilon (ε) Proteobacteria

• Helicobacter pylori, the main cause of stomach ulcers [Link]
• Campylobacter jejuni; the bacterium most frequently implicated in gastrointestinal upsets. [Link]

Some Gram-Positive Bacteria

Gram-Positive Rods

Aerobic Gram-Positive Rods

• Bacillus anthracis/cereus/thuringiensis. These organisms differ mainly in the plasmids they contain.
  • B. anthracis causes anthrax. Currently the biological agent being used by terrorists. Its 2 plasmids contain the genes needed to synthesize
    • a capsule which (like those of pneumococci) makes it resistant to phagocytosis, and
    • the three components of the toxin that causes the disease symptoms. [More]
  • B. thuringiensis — the organism, its toxin, and even the gene (also plasmid-encoded) for the toxin are used as biocontrol agents against a variety of insect pests. [Link to discussion]
• Bacillus subtilis. A common soil bacterium. Its chromosome contains 4,214,814 bp of DNA encoding 4,100 genes.
• Lactobacillus. Several species are used to convert milk into cheese, butter, and yogurt.

Anaerobic Gram-Positive Rods:

• Clostridium tetani. Clostridia are spore-forming obligate anaerobes. The spores of C. tetani are widespread in the soil and often get into the body through wounds. Puncture wounds (e.g., by splinters or nails) are particularly dangerous because they provide the anaerobic conditions needed for germination of the spores and growth of the bacteria.

  C. tetani liberates a toxin that blocks transmitter release (by destroying the SNAREs needed) at inhibitory synapses in the spinal cord and brain. This interferes with the reciprocal inhibition of antagonistic pairs of skeletal muscles so the victim suffers violent muscle spasms. Fortunately, the disease — called tetanus — is now rare in developed countries, thanks to almost universal immunization against the toxin. Chemical alteration of the toxin produces a toxoid that still retains the epitopes of the toxin. Incorporated in a vaccine, the toxoid provides a relatively long-lasting (~10 years) immunity against tetanus.

• Clostridium botulinum. As little as 1 µg of its toxin eaten with an uncooked bean or mushroom can be fatal. The toxin blocks the release of acetylcholine (also by destroying the SNAREs needed for exocytosis) from the terminals of motor neurons. Thus the victim shows signs of sympathetic nervous activity (dilation of the pupils, inhibition of urination) and skeletal muscle weakness. If the intercostal muscles are effected, breathing may stop. The toxin is a protein and is quickly (10 minutes) denatured at 100 °C, so boiling home-canned products makes them safe to eat.

Gram-Positive Cocci

• Staphylococci form flat packets of cells. Two species are common:
  • Staphylococcus albus is probably growing right now on your skin.
  • Staphylococcus aureus is also a frequent inhabitant of the skin, nasal passages, and the gastrointestinal tract. It can cause acne and, if it gets under the skin, abscesses. In hospitals, the development of antibiotic resistant S. aureus has become a major problem. Some strains of Staphylococcus aureus secrete a toxin and can cause life-threatening toxic shock syndrome.

  Many cases of "food poisoning" are caused by staphylococci.

• Most Streptococci grow in chains. The electron micrograph (courtesy of the Naval Dental Research Institute, Great Lakes, IL) shows Streptococcus mutans, a common inhabitant of the mouth.

  Streptococci cause

  • "strep throat"
  • impetigo
  • middle ear infections
  • scarlet fever (a result of a toxin produced by the organism)
  • rheumatic fever
  • a rare form of toxic shock syndrome
  
  
• Pneumococci. The cells of these streptococci grow in pairs. Streptococcus pneumoniae causes bacterial pneumonia. This was once a major killer — especially of the aged and infirm — but today there is an effective vaccine and any infections that do occur usually respond quickly to antibiotics.

  How pneumococci enter the body.

Actinomycetes

Mycobacteria and Corynebacteria

• Mycobacterium tuberculosis is the agent of tuberculosis (TB). Its genome contains 4,411,532 bp of DNA encoding some 3,959 genes.

  How the tubercle bacillus enters and lives in cells.

• Mycobacterium leprae causes leprosy. Its genome contains 3,268,203 bp of DNA encoding only 1,604 genes.

  Although a close relative of M. tuberculosis (they share 1,439 genes), much of its DNA encodes pseudogenes, genes that no longer make a functional product. M. leprae is an obligate intracellular parasite; it has never been cultured in vitro. This is probably because it has abandoned many of the genes needed for an independent existence choosing instead to depend on the genes of its host cell.

• Corynebacterium diphtheriae causes diphtheria. As in tetanus, it isn't the growth of the organism (in the throat) that is dangerous but the toxin it liberates. The toxin is the product of a latent bacteriophage in the bacterium. It catalyzes the inactivation of a factor necessary for amino acids to be added to the polypeptide chain being synthesized on the ribosome. Sensibly enough, the toxin has no such effect on the translation machinery of prokaryotes (or of chloroplasts and mitochondria).

  Treatment of the toxin with formaldehyde converts it into a harmless toxoid. Immunization with this toxoid — usually incorporated along with tetanus toxoid and pertussis antigens in a "triple vaccine" (DTP) — protects against the disease.

Spirochetes

These are thin, corkscrew-shaped, flexible organisms that range in length from a few to as many as 500 µm.

• Treponema pallidum, the cause of syphilis, one of the most dangerous of the sexually transmitted diseases (STDs).
• Borrelia burgdorferi is transmitted to humans through the bite of a deer tick causing Lyme disease (16,801 cases were reported in the U.S. in 1998).

Both these organisms have had their complete genomes sequenced. [Link]

Mycoplasmas

Mycoplasmas have the distinction of being the smallest living organisms. They are so small (0.1 µm) that they can be seen only under the electron microscope.

Mycoplasmas are obligate parasites; that is, they can live only within the cells of other organisms. They are probably the descendants of gram-positive bacteria who have lost much of their genome — now depending on the gene products of their host.

• Mycoplasma genitalium has 580,073 base pairs of DNA encoding 517 genes (480 for proteins; the rest for RNAs).
• Mycoplasma urealyticum has 751,719 base pairs of DNA encoding 651 genes (613 for proteins; 39 for RNAs).
• Mycoplasma pneumoniae has 816,394 base pairs of DNA encoding 679 genes.

How many genes does it take to make an organism?

Chlamydiae

• Chlamydia trachomatis

  Its genome contains 1,042,519 bp of DNA encoding 938 genes.

  In 1998, this organism infected 604,420 people in the U. S. The infection is usually spread by sexual intercourse making it the most common sexually-transmitted disease (STD). It is easily cured if diagnosed, but many infections remain untreated and, in females, are a major cause of pelvic inflammatory disease. This causes scarring of the uterus and fallopian tubes and often results in infertility.

  Mothers can pass the infection on to their newborn babies causing serious eye disease and pneumonia. To avoid this, pregnant women are usually tested for chlamydia and treated with antibiotics if they are infected.

  Several million people in the desert regions of Asia, Africa, and the Near East have been blinded by trachoma. This eye infection is caused by a strain of C. trachomatis (and is responsible for its name).

• Chlamydia psittaci usually infects birds, but can infect their human contacts causing psittacosis (a.k.a. ornithosis).

Cyanobacteria (blue-green algae)

• use chlorophyll a (as do plants)
• use water as the source of electrons to reduce CO₂ to carbohydrate (because they have photosystem II as well as photosystem I).

  CO₂ + 2H₂O → (CH₂O) + H₂O + O₂

• blue phycocyanin (making them "blue-green") and
• red phycoerythrin (The Red Sea gets its name from the periodic blooms of red-colored cyanobacteria.)

These two pigments also occur in red algae. Perhaps their chloroplasts evolved from endosymbiotic cyanobacteria. In fact, probably all chloroplasts evolved from endosymbiotic cyanobacteria.

The micrograph is of Oscillatoria, a filamentous cyanobacterium (magnified about 800 times). Each disk in the chains is one cell.

Mitochondria and Chloroplasts

• alpha-proteobacteria like the rickettsias for mitochondria
• cyanobacteria for chloroplasts