Bacteria and Archaea

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Bacteria and Archaea



Bacteria have been present from the beginning. These unicellular organisms exist in water, soil, and all phases of our environment. The existence of nonvisible matter was considered early on and this reality was confirmed after van Leeuwenhoek observed “animalcules” through a microscope (see Chapter 1, Scope of Microbiology). Van Leeuwenhoek’s descriptions of his microscopic observations of dental scrapings suggest he was observing what are currently called bacteria. The term “bacteria” comes from the Greek word meaning little rod or stick, which is one of the shapes (bacillus) that aids in the morphological description of bacteria. Pasteur, in his eloquent discourses on extensions of the germ theory, refers to “bacteridium,” a term that we have shortened to bacteria (plural) or bacterium (singular).


There are three areas for concern regarding bacteria that need to be addressed: emerging bacterial infectious diseases, reemerging pathogenic diseases that may or may not be resistant to current antibacterial drugs, and bacteria with bioterrorism potential (see Chapter 18, Emerging Infectious Diseases, and Chapter 24, Microorganisms in the Environment and Environmental Safety). Some examples of emerging bacterial infectious diseases include, but are not limited to, Staphylococcus aureus inducing toxic shock syndrome, Escherichia coli O157:H7 hemorrhagic colitis and hemolytic uremic syndrome, and Vibrio cholerae O139, a new strain of cholera. Some reemerging bacterial diseases such as plague (Yersinia pestis) also will be a problem to deal with by healthcare professionals. In addition, the threat of bioterrorism by intentional release or contamination of areas, food, water, and other environments by biological agents including bacteria, viruses, or their toxins represents a real threat for the future of humankind (see Chapter 24).

On the other hand, bacteria are also being used in a variety of industries and research continues to explore the use of bacteria as a food source, in food production, in the production of a variety of pharmaceutical agents, in agriculture, and as microbial fuel cells, to just name a few (see Chapter 1).

Bacterial Structure

Bacteria are prokaryotic unicellular (single-celled) independent organisms that can live as an individual cell or attached to others, forming colonies or groupings, such as biofilms. Each of the cells in such a colony is capable of carrying out all essential activities for survival, such as regular cellular metabolism and reproduction.


Bacterial cell morphology displays a variety of different shapes and sizes (Figure 6.1), and the cells are generally much smaller than eukaryotic cells. According to their morphological characteristics most bacteria are classified into different basic shapes: coccus, bacillus, spirochetes (spiral or helical), and pleomorphic (see Chapter 4, Microbiological Laboratory Techniques).

• Cocci (singular, coccus) are bacteria whose overall shape is spherical or nearly spherical (Figure 6.2). Several cocci are human pathogens causing, for example, urinary tract infections, food poisoning, toxic shock syndrome, gonorrhea, some forms of meningitis, throat infections, pneumonias, and sinusitis.

• Bacilli (singular, bacillus) are rod-shaped bacteria, some of which are endospore forming (Figure 6.3). Diseases caused by bacilli include anthrax, botulism, and tetanus, and gastrointestinal infections caused by bacilli such as Escherichia coli and Salmonella.

• Pleomorphic bacteria are bacterial species that are morphologically indistinct, depending on environmental conditions. This group includes Coccobacillus (coccobacilli), which are bacilli that are elongated as well as spherical in shape (Figure 6.4).

• Spirals occur as vibrios, spirilla, or spirochetes.

• Vibrios are curved or comma-shaped rods (Figure 6.5) and several species are human pathogens associated with gastroenteritis, cholera, food poisoning, and septicemia. Vibrio fischeri and V. harveyi are symbiotes of marine organisms such as jellyfish and produce light via bioluminescence.

• A spirillum (plural, spirilla) is a thick, rigid, spiral organism (Figure 6.6) that can cause rat bite fever, an uncommon but worldwide condition caused by rodent bites. These bacteria are present in the oropharyngeal flora of approximately 50% of healthy wild and laboratory rats, as well as in other rodents.

• Spirochetes are thin, flexible spirals (Figure 6.7) and can cause leptospirosis, Lyme disease, and syphilis.

Examples of Pathogens and Opportunistic Pathogens by Shape

Organism Shape Reservoir Disease(s)
Staphylococcus aureus Coccus Common on skin, nose, gastrointestinal and urogenital tracts of humans Toxin mediated: Food poisoning, scaled skin syndrome, toxic shock syndrome, folliculitis, carbuncles, impetigo, wound infections, bacteremia, and more
Staphylococcus epidermidis Coccus Common on human skin Bacteremia, endocarditis, urinary tract infections, opportunistic infections of catheters, shunts, prosthetic devises, and more
Enterococcus faecalis Coccus Common in human gastrointestinal tract Bacteremia, endocarditis, urinary tract infections, wound infections
Bacillus anthracis Bacillus Soil organism Anthrax
Bacillus cereus Bacillus Soil organism Toxin mediated: Gastroenteritis (emetic, diarrheal), ocular infections, opportunistic infections
Bacillus thuringiensis Bacillus None (soil, gut of caterpillars, butterflies, moths) Gastroenteritis, opportunistic infections
Haemophilus influenzae Pleomorphic Mucous membranes of humans Meningitis, epiglottitis, pneumonia, bacteremia, opportunistic infections
Chlamydia trachomatis Pleomorphic Obligate intracellular human pathogen Sexually transmitted: Prostatitis, epididymitis, cervicitis, pelvic inflammatory disease, urethritis, and more
Vibrio cholerae Spiral (vibrio) Estuarine and marine environments Toxin mediated: Acute diarrheal illness
Spirillum minus Spiral (spirillum) Rodents Rat bite fever
Borrelia burgdorferi Spiral (spirochete) Vector-borne, transmitted by ticks Lyme disease



In addition to their shape, bacteria can also be categorized according to their arrangement or their style of grouping after cell division.

• Aggregations of cocci occur after cell division and can be classified as the following (Figure 6.8):

• Diplo– is a prefix typically describing cells that occur in pairs of two, joined in one plane only. Examples of diplococci are Streptococcus pneumoniae, Neisseria gonorrhoeae, and Neisseria meningitidis.

• Strepto– is a prefix used to indicate an arrangement of cells in beadlike chains, because cell division occurs along a single axis, in contrast to staphylococci, which divide along multiple axes. Individual species of Streptococcus are identified primarily on the basis of their hemolytic properties on blood agar. The species Streptococcus pyogenes is responsible for strep throat, many cases of meningitis, bacterial pneumonia, endocarditis, erysipelas (acute skin infection), and necrotizing fasciitis (“flesh-eating” infections).

• Tetrads are produced by division within two planes, with the cocci arranged in squares of four in irregular clusters. Micrococcus luteus, which can be found in many areas including the human skin, water, dust, and soil, shows this growth pattern. It is considered to be a harmless bacterium but some cases of Micrococcus infections have been reported in people with a compromised immune system (e.g., HIV patients).

• Sarcinae are cocci arranged in cubes of eight as a result of division in three planes. This coccal grouping occurs when any cocci fail to separate after they divide and the resultant daughter cells remain attached.

• Staphylo– is a prefix indicating arrangements in grapelike clusters formed by cell division in random planes. Most members of the genus Staphylococcus are harmless and are part of the normal flora of the skin and mucous membranes in humans. A small percentage of staphylococci are also part of the soil microbial flora. The organism can cause an array of diseases in humans and other animals by invasion and also by toxin production. The toxins of Staphylococcus are a common cause of food poisoning because the bacteria can grow in improperly stored food. Although the organism is killed by the cooking process, the enterotoxin is heat resistant and can survive boiling for several minutes.

• Bacilli divide in one plane, producing diplobacilli and streptobacilli (Figure 6.9).

Bacterial Growth

Growth is an increase in the quantity of cellular material and depends on the ability of the cell to form new protoplasm from available nutrients. Bacterial growth requires a source of energy for protein synthesis and to maintain bacterial metabolism. Bacteria must obtain or synthesize nucleic acids, carbohydrates, and lipids that are used as building blocks of cells. The minimal requirements for growth are a source of carbon and nitrogen, an energy source, water, and a variety of ions and minerals. Oxygen is necessary for some bacteria but can be lethal for many others (see Atmospheric Conditions, later in this chapter).

Basis of Bacterial Growth: Binary Fission

Bacterial replication is a coordinated process accomplished primarily by binary fission. Binary fission results in two identical daughter cells (Figure 6.10). In order for growth to occur sufficient metabolites are necessary to support the synthesis of bacterial components. A cascade of regulatory events must occur to initiate replication. Once replication is started DNA synthesis must run to completion. Chromosome replication starts at the plasma membrane and each daughter chromosome is anchored to a different portion of the membrane. Membrane, peptidoglycan synthesis, and cell division are linked together and as the bacterial membrane grows, the daughter chromosomes are pulled apart. At the end of chromosome replication septum formation between the daughter cells starts, indicating cell division (see Chapter 3, Cell Structure and Function). New initiation may begin even before chromosome duplication and cell division are complete.

At the point at which metabolites are depleted or toxic by-products build up, chemical alarmones are produced, which stops synthesis. Degradative processes and DNA synthesis continue until all initiated chromosomes are completed. Ribosomes are broken down during the degradative process to provide deoxyribonucleotide precursors. Peptidoglycan and proteins are degraded for metabolites and the cell may shrink in response. Complete cell division may not occur and the cell may ultimately die. Under degradative processes sporulation may occur in species capable of this process.

Population Growth Curve

To produce a bacterial culture in a laboratory environment, the organism must be added to a medium (see Types of Culture Media in Chapter 4, Microbiological Laboratory Techniques). Under favorable conditions a growing bacterial culture doubles at regular intervals. Under ideal conditions, bacterial growth can be described by four different phases: the lag phase, the exponential or logarithmic growth phase, the stationary phase, and the death phase (Figure 6.11).

• Lag phase: Bacteria must adapt to the medium before cell division starts. This period of time is referred to as the lag phase of the bacterial growth curve. During this phase the cells are metabolically active, producing molecules necessary for cell division; the individual bacteria are maturing, yet they are not able to divide at this time.

• Logarithmic or exponential growth phase: The rate of growth increases with time in the so-called logarithmic or exponential growth phase. Each cell introduced to the medium divides by binary fission into two cells. With each subsequent binary fission a doubling of the bacterial cells occurs as long as the growth conditions are favorable. The time required for doubling of the population is called the generation time. In other words the number of new bacteria per unit of time is proportional to the present population, and the actual rate of growth depends on the growth conditions, which directly affect the frequency of cell division.

• Stationary phase: A stationary phase occurs when essential nutrients are depleted or by-products of metabolism accumulate. A depletion of nutrients causes cells to decrease in size and toxic metabolic by-products limit the ability to undergo cell division. During this phase the total number of viable cells remains constant. This phase of population growth can last for a few hours to several days, depending on the environmental conditions.

• Death phase: Finally, the death phase begins when growth stops and the number of dead cells is larger than the number of viable cells.

Measuring Growth

The number and types of microbes present in a variety of samples can be measured by various techniques. This is important to identify the numbers and types of microorganism present in milk, food, water, and soil, and in clinical samples such as urine. Bacterial growth can be measured as an increase in cell mass or cell numbers.

Measurement of Cell Mass

Measurement of the cell mass can be achieved by determining dry or wet weight or by measuring the turbidity (visible cloudiness) of a liquid medium. Cell mass measurements cannot differentiate between living and dead cells.

• Dry weight measurements allow a more accurate estimation of cell masses but are more time consuming and only useful when dealing with massive populations of cells. With this procedure the cells need to be washed thoroughly and then dried before weighing. The dry weight of cells is roughly 20% to 25% of their wet weight.

• Microbial growth in liquid media causes turbidity and can be measured with a spectrophotometer. The turbidity is measured in optical density (OD) units, which is the logarithm of the ratio of intensity of light striking the suspension to the amount that is transmitted. The greater the cell mass the less light will pass through the spectrophotometer, an instrument that can measure light intensity. Measurement of very large populations will require dilution in order to obtain accurate estimates of cell mass.

Measurement of Cell Number

Determination of the number of cells in a sample plays an important role in the microbiological laboratory. Direct counts of cells in a microbial population can be estimated by microscopy or electronic devices, while viable cell counts are determined by a specific culture technique. Indirect counts involve the measurement of a particular end product or the amount of dye reduction, providing quantitative or semiquantitative information.

Factors Influencing Microbial Growth

Prokaryotes exist under a wide range of physical conditions. These environmental conditions include nutritional requirements, temperature, osmotic pressure and other atmospheric conditions, all of which greatly influence the growth of microbes. The type of microbial life present reflects the physical and chemical conditions of a given environment. Some microbes can tolerate extreme temperatures, high osmotic pressure, and other extreme chemical and atmospheric conditions, whereas others can grow and reproduce only in a limited range of environmental conditions. These conditions may support the growth of one organism, while inhibiting the growth of other microbes.