Objectives

Classification of Prokaryotes
After reading this section the student should be able to:
Discuss the classification of the prokaryotes, including the rationale for the proposed new kingdom, Archaebacteria.

Prokaryotic Cell
After reading this section the student should be able to:
Describe the structures of a prokaryotic cell.
Discuss the functions of each structure.

The Diversity of Form
After reading this section the student should be able to:
Describe the different types of prokaryotic cells including the bacilli, cocci, and spirilla.
 Discuss how the different cells function.

Reproduction and Resting Forms
After reading this section the student should be able to:
Name the various reproductive forms.
Discuss the function of each.
 Define and discuss the function of spores.

Prokaryotic Nutrition
After reading this section the student should be able to:
Describe the various ways in which prokaryotes obtain energy, including a comparison of prokaryotic photosynthesis with the photosynthesis of plants and algae.

Viruses:  Detached Bits of Genetic Information
After reading this section the student should be able to:
Describe the basic structure of a virus.
Discuss the function of viruses.

Microorganisms and Human Ecology
After reading this section the student should be able to:
Define symbiosis.
Discuss how microbes cause diseases.

Discuss what humans have done to prevent and control infectious diseases.

Classification of Prokaryotes

• differences in size and shape of the organisms,
• the general appearance of colonies,
• type of movement,
• mode of nutrition,
• the presence or absence of spores,
• and the presence or absence of a cell wall.

    With the new techniques, such as amino acid sequencing, nucleotide sequencing, and DNA-DNA hybridization, scientists have been able to unravel the evolutionary relationships of prokaryotes.  As with eukaryotes, the smaller the number of differences in the organism's nucleotide sequences the more recent their common ancestor.

     One of the most striking discoveries is that there are several genera, not previously classified together, that differ greatly from the other prokaryotes. These genera include the methanogens (bacteria that synthesize methane from carbon dioxide and hydrogen gas), the halobacteria (bacteria that live in salt), and the thermoacidophiles (bacteria that thrive in very acidic environments at high temperatures).  These organisms are called the Archaebacteria.  These bacteria are classified by the fact that they live in hostile conditions that normal bacteria could not survive in.  Suggestions of a new kingdom, Archaebacteria, have risen from this discovery.  Others suggest the establishment of two superkingdoms, Prokaryota and Eukaryota.  Prokaryota will contain kingdoms Archaebacteria and Monera, Eukaryota will contain kingdoms Protista, Fungi, Plantae, and Animalia.
 
 

    Prokaryotic cells are composed of mostly ribosomes and DNA.  They lack a nucleus and membrane-bound organelles.  The cytoplasm of most prokaryotes is unstructured, although it has a fine granular appearance due to its many ribosomes.  Prokaryotic cells generally range in size from 0.5 to 2 micrometers.  The outer layers of the cell are a cell membrane and a cell wall.

    The membrane is formed by a lipid bilayer.  The bilayer consists of hydrophilic heads and hydrophobic tails.  The hydrophilic heads are on the outside of the lipid bilayer, and the hydrophobic tails point toward the inside.

     Surrounding the cell membrane is the cell wall.  The wall gives the different prokaryotes their shape.  Many of the prokaryotes have rigid cell walls, some have flexible walls, and only the mycoplasms have no cell walls.  Because most bacteria are hypertonic in relation to their environment, they would burst without the cell walls.

    The cell walls are complex and contain many molecules not found in eukaryotic cells.  Except for the Archaebacteria, the cell walls contain complex polymers known as peptidoglycans.  The types of cell walls are determined by their ability to combine firmly with dyes such as gentian violet.  In gram-positive cells, cells with walls that combine with the dye, the wall consists of a homogeneous layer of peptidoglycans and  polysaccharides that ranges from 10 to 80 nanometers in thickness.  In gram-negative cells, cells with walls that do not combine with the dye, the wall consists of two layers; an inner peptidoglycan layer, only 2 to 3 nanometers thick, and an outer layer of lipoproteins and lipopolysaccharides arranged  in the form of a bilayer,  about 7 to 8 nanometers in thickness, similar in structure to the cell membrane.  The cell wall also affects other characteristics of the bacteria such as susceptibility to antibiotics.  Gram-positive cells will be more susceptible than gram-negative cells.

    In some bacteria, a gluey polysaccharide capsule is present outside the cell wall.  The function of the capsule is not clear, but it is involved with pathogenic activity in certain organisms.  For example the encapsulated form of Streptococcus pneumoniae is virulent, whereas the nonencapsulated form is generally nonvirulent.  It appears that the capsule may interfere with phagocytosis by host white blood cells.

    Some prokaryotes have flagella and pili.  Flagella are used to move the organism.  A flagellum is a long, slender hair-like extension that uses a whip-like motion to propel the organism.  Flagella are usually about 12 to 18 nanometers in length.  Pili are used to attach an organism to something, such as a food source, the surface of a liquid, or, in conjugating bacteria, one another.  There are usually hundreds of pili around a single bacterium.  Pili are usually about 4 to 35 nanometers in length.  Pili are rigid, cylindrical rods whereas flagella are flexible, cylindrical rods.
 
 

    The oldest method of identifying microorganisms is by their appearance.  Straight, rod-shaped forms are known as bacilli; spherical ones are called cocci; long, spiral rods are known as spirilla, and short, curved rods (thought to be incomplete spirals) are known as the vibrios.

     Different types of bacteria have different growth patterns, producing filaments, clusters, or colonies.  For example, after a division cocci may stick together in pairs (diplococci), they may occur in clusters (staphylococci), or they may form chains (streptococci).  The rod-shaped bacilli usually separate after cell division.  When they remain together they form filaments, since they always divide in the same plane.  In some genera, these filaments are funguslike in appearance and the combining form myco- is part of the generic name. For example,  Mycobacterium tuberculosis is a bacillus that forms a filamentous, funguslike growth.

     Many cyanobacteria as well as the gliding bacteria, organisms that are nonphotosynthetic, also form filamentous structures consisting of numerous individual cells.  These cells secrete a mucus that attaches to a solid surface and provides a pathway on which the cells glide.  Other types of bacteria are characterized  by distinctive sheaths outside of their cell walls.

      Spirochetes are among the easiest microorganisms to identify.  They are long, 5 to 500 micrometers in length, and slender, about 0.5 micrometers in diameter, and have an unusual structure known as an axial filament.  It is made up of two sets of fibrils attached at each end of the cell.  The fibrils are identical to filaments in structure and so are recognized as modified flagella, or endoflagella.  They are wrapped around the cell between the cell membrane and the cell wall.  Rotation of the axial filament is thought to produce the corkscrew movement characteristic of the spirochetes.  It is thought that all members of this group belong to the same phylogenic lineage.

     Another group of prokaryotes is the rickettsiae, the smallest cells known.
 
 

     Most prokaryotes reproduce by simple cell division, also called binary fission.  In some forms reproduction is performed by budding or by the fragmentation of filaments of cells.  As they multiply they produce clones of genetically identical cells.  However, mutations do occur.  Mutations are responsible for prokaryotes' extraordinary adaptability.  Further adaptability is provided by the genetic recombinations that take place as a result of conjugation, transformation, transduction, and exchanges of plasmids.  It is not known how common these genetic recombinations are in nature or whether they occur in all types of prokaryotes.

      Many prokaryotes can form spores, which are dormant resting cells.  This process has been studied most extensively in bacilli.  It occurs when a population of cells begins to use up its food supply.  Each cell, at the beginning of sporulation (spore formation), contains two duplicate chromosomes.  A cell membrane grows around one of the chromosomes separating it from the rest of the cell. The cell then engulfs the separated chromosome.  The soon-to-be spore is now surrounded by two membranes its own and that of the larger cell.  A spore coat consisting of two layers then forms around the smaller cell.  The inner layer consists of a peptidoglycan that is completely different from the one in the cell wall.  The outer layer consists of proteins that are composed of hydrophobic amino acids.  The spore is released from the cell in its protected state, and it remains dormant until the appropriate events trigger its germination.  Germination occurs rapidly and involves the intake of water, the dissolution of the spore coat, and the formation of a new cell wall.

     Spore formation greatly increases the capacity of prokaryotic cells to survive.  For example,  the spores of Clostridium botulinum, the bacterium that causes botulism, are not destroyed by boiling for several hours.

     The myxobacteria form fruiting bodies, which are brightly colored collections of spores and slime large enough to be seen by the unaided eye.
 
 

Heterotrophs
     Most prokaryotes are heterotrophic.  Of these the majority are saprobes,  feeding on dead organic matter.  Bacteria and other microorganisms are responsible for the decay and recycling of organic material in the soil.  Typically,  different groups of bacteria play different specific roles,  such as the digestion of cellulose,  starches,  or other polysaccharides,  or the hydrolysis of specific peptide bonds,  or the breakdown of amino acids.  Due to the specificity of bacterial nutritional requirements,  many bacteria are able to live in a small area with little competition and with mutual assistance.  Many times the activities of one group will make food available for another group.  These combined activities release the nutrients and make them available to plants and then to animals, as animals eat the plants.  Therefore, the bacteria are an essential part of  the ecological system.

     Some heterotrophic bacteria live in close association with other organisms.  Some of these are parasites, and break down organic material in the bodies of living organisms.  The disease causing bacteria belong to this group.  Some of these bacteria have little affect on their host and some are actually beneficial.  Cows and other ruminants can utilize cellulose only because their stomachs contain bacteria with the enzyme to break down cellulose.  Our own intestines contain bacteria.  Some supply vitamin K,  which is necessary for blood clotting,  others prevent us from developing serious diseases.  When the normal bacterial level drops our tissues become weakened and vulnerable to infection.

Chemosynthetic Autotrophs
     Chemosynthetic organisms gain their energy from the oxidization of inorganic compounds.  Prokaryotes are the only organisms able to obtain energy from inorganic compound.

     An unusual group of prokaryotes are the methanogens.  Although they have been known of for a long period of time they have not been studied extensively until recently, because oxygen is poisonous to them and hence are difficult to grow in normal laboratory conditions.  The methanogens are the final participants in decomposition processes involving organic matter in anaerobic environments, including marshes, lake sediments, and the digestive tracts of animals.  They convert CO₂ (carbon dioxide) and H₂ (hydrogen) formed by the fermentation processes of other anaerobes to methane (CH₄).

     Certain chemosynthetic bacteria are essential parts of the nitrogen cycle, the process by which nitrogen compounds are cycled and recycled through ecosystems.  One group of these bacteria oxidize ammonia or ammonium, derived from the breakdown of organic materials, the nitrogen fixing prokaryotes, or from lightning or volcanic activities.  The products of this reaction are nitrite (NO₂^-) and energy.  Another group oxidizes nitrites, producing nitrate (NO₃^-) and energy.  Nitrate is the form of nitrogen in which nitrogen moves into the roots of plants from the soil.

     Sulfur is also needed by plants for amino acid synthesis.  Like nitrogen, it is converted to the form in which it can be taken into plants by their roots by the work of chemosynthetic bacteria that convert sulfur to sulfate:

Photosynthetic Autotrophs

Green and Purple Bacteria

     Among the eubacteria are five photosynthetic types,  which are thought to represent three distinct phylogenic lineages: the cyanobacteria, the green bacteria, and the purple bacteria.  The green and purple bacteria both have sulfur and nonsulfur forms.  Several nonphotosynthetic bacteria are believed to belong to the same lineage as the purple bacteria.

     The colors of the green and purple bacteria are due to the pigments of the chlorophyll they contain.  The reaction centers of the green bacteria contain bacteriochlorophyll a, which differs only slightly from the chlorophyll a of eukaryotes.  The antennae pigments are bacteriochlorophyll c,d, or e, which differ more significantly.  In the two groups of purple bacteria, the reaction centers contain either bacteriochlorophyll a or b and these same molecules function as antennae.  Bacteriochlorophyll b, which differs chemically from bacteriochlorophyll a in many ways, is a pale blue-gray.  The colors of the purple bacteria are due to the presence of several yellow and red carotenoids, which function as additional pigments.  In the nonsulfur variety, the color may vary anywhere from purple to red, or even brown.

     In photosynthetic sulfur bacteria, the sulfur plays the same role in photosynthesis as the water does in plants.

     Photosynthesis by green and purple bacteria is carried out anaerobically, and never results in the production of oxygen.

Cyanobacteria

     Unlike the other photosynthetic prokaryotes, the cyanobacteria contain chlorophyll a and lyse water during photosynthesis, producing molecular oxygen.  For this reason they were classified with eukaryotic algae until biochemical studies and electron microscopy revealed their prokaryotic nature.  Cyanobacteria thrive in freshwater environments, and are a principal component of the blue-green scum found on the surface of ponds in late summer.

     Cyanobacteria have several kinds of accessory pigments.  These include several carotenoids and one or two pigments known as phycobilins.  Chlorophyll and the accessory pigments are not enclosed in chloroplasts, but are part of a membrane system distributed in the peripheral portion of the cell.

     Cells of the cyanobacteria, like many other prokaryotes, have an outer polysaccharide sheath.  In some species the outer layer is deeply pigmented, but in most species it is not pigmented.  Different species of cyanobacteria are golden yellow, brown, red, emerald green, blue, violet, or blue-black.  The Red Sea was named because of the dense concentrations, or "blooms," of red-pigmented cyanobacteria on its surface

     Some species are capable of nitrogen-fixation.  These are among the most self-sufficient organism.  They have the simplest nutritional requirements of any living thing.  On a worldwide scale, the ecological importance of the nitrogen-fixing cyanobacteria is much less than that of the nitrogen-fixing bacteria.

     Because of their nutritional independence, cyanobacteria can grow just about anywhere.
 
 

     Viruses do not fit easily into any of the kingdoms.  Because of their small size and infectious capabilities, however, they have usually been studied with the prokaryotes.  Viruses consist of a nucleic acid core - either DNA or RNA - surrounded by a protein coat, or capsid.  They reproduce only within living cells.  Without the enzymes and metabolic machinery of the cell, viruses are as inert as any other macromolecule, lifeless by most criteria.  As our knowledge of viruses and nucleotide sequences has grown, biologists have come to regard viruses as cellular fragments that have set up a partially independent existence.

     In size, viruses range from about 17 nanometers to about 300 nanometers, larger than small bacteria.  The large ones are at the limits of resolution of the light microscope.  Viruses can be characterized and classified on the basis of their host cell, their nucleic acid content, and their specific shapes, which are determined by their protein content.  The proteins of the capsid may take the form of a helix or the form of triangular plates arranged in a polyhedron.  The capsid may be surrounded by other layers.

     The protein capsid determines the specificity of a virus.  This means a cell can be affected by a virus only if viral protein can fit into one of the specific receptor sites in the cell membrane of that type of cell.  Apparently all types of cells - both eukaryotic and prokaryotic - are susceptible to infection by specific viruses capable of interacting with their membrane receptors.

     Viruses infect in different ways.  Some enter the cell, protein capsid and all, yet others inject the RNA or DNA into the cell they are attacking.  Once inside the cell, the virus replicates its nucleic acid and uses it to make mRNA.  Once mRNA is made, transcription can begin.  Transcription produces more viral nucleic acid, protein capsids, and repressors and other regulatory chemicals.  For its synthetic activities, the virus uses many of the host cells machinery to produce all necessary items.  Sometimes, a virus that has RNA will use reverse transcription to create the mRNA molecules.

     Virus particles are assembled in the host cell.  In viruses with helical capsids, the protein subunits of the capsid come together around the newly synthesized nucleic acid.  In other types of viruses, the capsid is formed separately and then the nucleic acid is inserted into it.  When assembly of the viruses is completed, they are released from the cell, usually by lysing the cell membrane.  Each new particle will start the cycle over again in another cell which has not been infected yet.

Viroids and Prions:  The Ultimate in Simplicity

     There are diseases caused by things smaller than viruses.  These disease causing organisms are viroids and prions.  Viroids are naked RNA molecules and prions are small proteinacious particles.  Both replicate in susceptible cells.
 
 
 

Microorganisms and Human Ecology
 
 

Symbiosis

    Symbiosis ("living together") is a close and long-term association between organisms of different species.  There are different opinions as to what exactly a symbiotic relationship is, but they are usually considered to be one of three kinds.  If the relationship is beneficial to both species, it is called mutualism.  If one species benefits from the relationship while the other is neither harmed nor benefited, it is called commensalism.  If one species benefits and the other is harmed, the relationship is known as parasitism.

    An enormous variety of microorganisms live symbiotically with human beings, but the lines of demarcation between the different categories ar not clear-cut.

    Evolutionary progress is measured in terms of surviving progeny.  A symbiotic microorganism that destroys its host before the reproduction and dispersal of its progeny to new hosts is less likely to be successful by the evolutionary criteria than one that enjoys a long, comfortable relationship with its host.

How Microbes Cause Disease

     The pathogenic effects of microbes are produced in a variety of ways.  Viruses enter particular types of cells and often destroy them.  Bacteria produce cell destruction also..  Frequently, however, the effects we recognize as disease are caused not by direct action of the pathogens but by toxins, or poisons, produced by them.

    Some diseases are the result of the body's reaction to the pathogen.

    A single disease agent can cause a variety of diseases.  Skin infections of Streptococcus pyogenes cause the disease known as impetigo.  Throat infections by the same bacteria cause the familiar disease strep throat.  Conversely, many agents can cause the same disease; the "common cold" is caused by any one of a large number of viruses.

Prevention and Control of Infectious Disease

    Although microorganisms were seen and depicted with remarkable accuracy by Antony von Leeuwenhoek in the late seventeenth century, they were not associated with disease until 100 years ago.  This opened the way to control measures, among the most important of which was sterile procedures in hospitals.  Even more important than the introduction of sterile medical procedures was the institution of public health.  This included eradication of disease carrying insects, the disposal of sewage, the pasteurization of milk, and the filtration of water.

    Many infectious diseases can be prevented by immunization.  Many bacteria are susceptible to antimicrobial drugs, such as sulfa and penicillin.  Penicillin, which is synthesized by the fungus Penicillium, was the first known antibiotic - by definition, a chemical that is produced by a living organism and is capable of inhibiting the growth of microorganisms.  Many antibiotics are formed by bacteria and some are formed by fungi.  Many, including penicillin, can now be synthesized in the laboratory.  Antibiotics and other chemotherapeutic agents are effective because they interfere with some essential process of the pathogen without affecting the cells of the host.

    Viruses are basically impervious to attack by chemotherapeutic agents; drugs that will effectively stop the viruses reproduction process have devastating effects on cellular processes.  Membrane receptors and viral capsids are beginning to yield the structural secrets that explain their interactions.  These findings are raising the possibility of devising a molecule that will block either the receptors or the capsids that fit into them.
 
 

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