Table 2-2
34 CHAPTER 2 DIVERSITY OF THE MICROBIAL WORLD
names was introduced by Carl Linnaeus. The first part of the binomial name, for example, Streptococcus, is the genus name. A genus is a group of closely related species. The first letter of the genus name is capitalized. The second part of the binomial name,
for example, pneumoniae is the species epithet. The species epithet is written in all lower case letters. The species name must always contain the genus name and the species epithet. It is permissible, though, to abbreviate the genus name. In this case the genus is
Table 2-3
SURVEY OF MICROORGANISMS 35
indicated by a single capital letter followed by a period—for example, S. pneumoniae.
We sometimes designate a subspecies or type to specify some significant characteristics of a particular microorganism. For example, a particular strain of S. pneumoniae of the American Type Culture Collection
(ATCC) that is resistant to treatment with penicillin is designated S. pneumoniae ATCC 35088. Also the pathovar (PV) or serovar (SV) may be noted by letters or numbers, for example, Escherichia coli 0157:H7, a strain of this common species that is associated with serious dysentery.
38 Chapter 2 diversity of the microbial world
METHODOLOGY
DNA Hybridization: A Method for Analyzing Genetic Relatedness
One method used to assess genetic relatedness among organisms is called DNA hybridization (see Figure). To understand how this DNA hybridization method permits scientists to determine the relatedness of two organisms, we must first recognize that (1) DNA is composed of a series of individual molecules called nucleotides that are linked together in a particular order to establish the informational content of each organism, much in the way that the letters of our alphabet are linked together to form words and sentences, (2) DNA is composed of two complementary strands, and (3) DNA is the universal hereditary substance of all living organisms. The question of relatedness can be explored by determining what sequences of nucleotides the organisms have in common, both in terms of the specific nucleotides and their particular order (sequence) within the DNA molecule.
In the process of DNA hybridization, a radioisotope or a fluorescent dye is used to label or tag the DNA from one of the organisms. Then the DNA from both organisms is converted from double strands to single strands. These labelled and nonlabelled single strands are incubated together, allowing the DNA to reform double strands. Where the labelled DNA matches the nonlabelled DNA, the amount of radioactivity or dye measured will determine the extent to which the DNA from the two organisms combined.
Using this technique, scientists can determine directly the relatedness of organisms from bacteria to mammals. The formation of hybrid double-stranded DNA, that is, a double-stranded DNA molecule in which each strand came from a different organism, is a measure of the similarity, called homology, between the DNA of the two organisms. DNA molecules from organisms that are closely related, such as members of the same species, have a high degree of homology. Because evolution is based on changes in hereditary information and because DNA contains the hereditary information, DNA hybridization provides a tool for directly analyzing evolutionary relatedness for all organisms. No longer is it necessary to infer relationships based solely on appearances or metabolic functions. Using DNA hybridization, microbiologists can determine the relatedness of bacterial species.
In DNA hybridization procedures for gene probe detection, cells are lysed to release double-stranded DNA. The DNA is denatured to convert it to single-stranded target DNA. The single-stranded DNA isfaffixed to a membrane. A prehybridiza-tion solution is used to prevent nonspecific binding to the membrane. A labelled nucleic acid probe (gene probe) is added. (The label may be a dye or a radioactive element.) The labelled probe hybridizes to complementary regions (if any) of the target DNA.
Additionally, genetic characteristics are employed in modern classification systems. DNA from different bacteria is compared to reveal the degree of similarity. In some clinical identifications, species are identified using DNA hybridization. Often, short segments of DNA, called gene probes, are used to de-
termine the presence or absence of specific diagnostic genes. This is a powerful technique for identifying specific microorganisms
Many morphological, metabolic, and genetic characteristics are used for describing, classifying, and identifying bacteria.
SURVEY OF MICROORGANISMS 39
TABLE 2-5
Information on the characteristics of bacterial genera and species is updated periodically and published in a book entitled Bergey's Manual of Determinative Bacteriology (Table 2-5). Bergey's Manual is the standard reference for descriptions of microorganisms— the "bible" of bacterial taxonomy. Examining Bergey's Manual quickly reveals that relatively few bacterial species cause disease, even though these may be the ones about which we are most commonly concerned. Most bacteria perform metabolic activities that maintain the ecological balance of the Earth. Only a small portion of the numerous bacterial species described
in Bergey's Manual are ever seen in the clinical laboratory or ever discussed in introductory microbiology courses. In this book we will be able to examine only a small portion of the diverse bacteria that exist in nature.
Beyond their common prokaryotic cell structure, bacteria exhibit extreme diversity of form and function and in their metabolic characteristics.
Several of the major groups of bacteria described in Bergey's Manual are distinguished primarily on morphological characteristics, namely: cell shapes
40 CHAPTER 2 DIVERSITY OF THE MICROBIAL WORLD
(rods, cocci, curved, or filament forming); spore production (endospores, or other spores); staining reactions (color after staining according to the Gram stain procedure—Gram negative or Gram positive); and motility (nonmotile, motile with peritrichous flagella
surrounding the cell, motile with polar flagella projecting from the end of the cell, motile by gliding). Other major bacterial groups are defined based on their metabolism, in particular how they generate energy in the form of ATP (photosynthetic using light
HIGHLIGHT
Microview of Bacterial Diversity
Gram-positive cocci include the genus Staphylococcus, which typically form grape-like clusters and the genus Streptococcus, which occur in pairs or chains. Species of Staphylococcus commonly occur on skin surfaces where they live without causing disease. Staphylococcus aureus, however, is a potential human pathogen, infect-
ing wounds, membranes, and linings and also causing food poisoning. Some members of Streptococcus are also human pathogens. For example, rheumatic fever is caused by Streptococcus pyogenes. Several Streptococcus species are also responsible for the formation of dental caries, which cause tooth decay.
The two most important genera of endospore-form-ing bacteria. Bacillus and Clostridium, are Gram-positive rods. Bacillus species can grow in the presence of air, whereas Clostridium species are obligately anaerobic. Food spoilage by Bacillus and Clostridium species is of
great economic importance. Several Clostridium species are important human pathogens. For example, Clostridium botulinum is the causative agent of botulism, Clostridium tetani causes tetanus, and Clostridium perfrin-gens causes gas gangrene/
SURVEY OF MICROORGANISMS 41
energy], chemolithotrophic [using inorganic compounds], heterotrophic [using organic compounds]), and whether the metabolism is anaerobic (not using molecular oxygen), aerobic (using molecular oxygen), or facultatively anaerobic (capable of aerobic
and anaerobic metabolism). Yet others are defined based on combined morphological and physiological characteristics. These characteristics are determined by grouping cultures of bacteria and making observations on those cultures and the cells that grow.
Text continued on p. 51.
The Gram-positive nonspore-forming, rod-shaped bacteria include bacteria that produce lactic acid. Lactobacillus are Gram-positive nonspore-forming rods that occur in chains. The lactfflbacilli are extremely important
in the dairy industry. Cheese, yogurt, and many other fermented products are made by the metabolic activities of Lactobacillus species. They also inhabit regions of the human body, including teeth.
The Gram-negative facultatively anaerobic rods include intestinal enteric bacteria. They are motile by means of peritrichous flagella and often live in the human intestinal tract. Much of what we know about bacterial metabolism and bacterial genetics has been elucidated in studies using Escherichia coli. E. coli is employed
as an indicator of fecal contamination in environmental microbiology. The genera Salmonella and Shigella contain many species, many of which are important human pathogens. In particular, typhoid fever and various gastrointestinal upsets are caused by Salmonella species and bacterial dysentery is caused by Shigella.
SURVEY OF MICROORGANISMS 43
The Gram-negative aerobic rod-shaped Agrobac-terium produces tumorous growths on infected plants. These growths are known as galls. Agrohacterium tume-
faciens causes galls of many different plants and is an extremely important plant pathogen, causing large economic losses in agriculture.
The genus Neisseria is a representative example of the Gram-negative cocci. Neisseria gonorrhoeae causes gonorrhea and Neisseria meningitidis causes bacterial menin-
gitis. These bacteria tend to form relatively large cocci that typically look like kidney beans. The cells occur in pairs (diplococci).
Micrograpb/of intracellular, Gram-negative diplococci. The presence of these bacteria in a urethral discharge isaiagnostic for gonorrhea and in a vaginal discharge is presumptive for gonorrhea.
44 CHAPTER 2 DIVERSITY OF THE MICROBIAL WORLD
The helical and curved bacteria group are helically curved rods that may have less than one complete turn (comma-shaped) to many turns (helical). Campylobacter fetus is a curved bacterium that frequently is the cause of
gastrointestinal infections in infants. Bdellovibrio, which also is curved, has the unique characteristic of being able to penetrate and reproduce within the cells of other bacteria.
The spirochetes are helically coiled rods, with one or more central axial fibril(s) wound around each cell. Many spirochetes are human pathogens. Several members of the genus Treponema, for example, are human
pathogens. Treponema pallidum causes syphilis, which is a sexually transmitted disease. Treponema pertenue causes yaws. Borrelia burgdorferi, another spirochete, causes Lyme disease.
Micrograph of the spirochete Treponema pallidum (green helical-shaped cells) after fluorescent antibody staining. This bacterium causes syphilis.
The budding and /or appendaged bacteria are
grouped together because they produce cell appendages. Several of these bacteria reproduce by budding. This involves separating a portion of the cell to form a new progeny cell. Many of the appendaged bac-
teria grow well at low nutrient concentrations. Caulobac-ter, for example, can grow in very dilute concentrations of organic matter in lakes and even is able to grow in distilled water. Some adhere to surfaces of other cells via their appendages.
The sheathed bacteria comprise bacteria whpse cells occur within a filamentous structure known as a sheath. The formation of a sheath enables these bacteria to attach themselves to solid surfaces. It also affords protection against predators and parasites. Sphaerotilus natans
is a sheathed bacterium that is often referred to as the sewage fungus. This organism normally occurs in polluted flowing waters, such as sewage effluents, where it may be present in high concentrations just below sewage outfalls.
Colorized micrograph of the filamentous bacterium Sphaerotilus natans. Cells of this bacterium are enclosed within a sheath (orange). It occurs abundantly in rivers below sewage outfalls and is called the "sewage fungus" because of its filamentous (fungal-like) appearance.
46 CHAPTER 2 DIVERSITY OF THE MICROBIAL WORLD
Some bacteria are grouped based on their gliding motility on solid surfaces. These bacteria lack the specialized structures—flagella—that other bacteria use to propel themselves. The myxobacteria are gliding bacteria that have a unique feature. Under appropriate conditions they aggregate to form fruiting bodies. These
fruiting bodies represent a stage in the complex reproductive process carried out by these bacteria. The fruiting bodies of myxobacteria occur on decaying plant material, on the bark of living trees, or on animal dung, appearing as highly colored slimy growths that may extend above the surface of the substrate.
maceutical industry. Many previously fatal diseases are now easily controlled by using antibiotics produced by actinomycetes. Other actinomycetes are human pathogens.
SURVEY OF MICROORGANISMS 47
Mycobacteria are acid-fast, meaning that stained cells resist decolorization with acid alcohol, thus remaining red. This genus contains several important hu-
man pathogens, including Mycobacterium tuberculosis (causative agent of tuberculosis) and Mycobacterium leprae (causative agent of Hansen disease [leprosy]).
The coryneform bacteria are defined by a characteristic irregular appearance of the cells. They tend to show incomplete separation following /Cell reproduction. When coryneforms reproduce, the pirogeny cells do not completely separate from one another^called snapping
division) and form groups resembling "Chinese characters" when viewed under the microscope. Many species of Corynebacterium are plant or animal pathogens. For example, Corynebacterium diphtheriae is the causative agent of diphtheria.
SURVEY OF MICROORGANISMS 49
The photosynthetic bacteria are distinguished from other bacterial groups by their ability to use light energy to obtain cellular energy. Some photosynthetic bacteria carry out photosynthesis without the production of oxy-
gen. Such anaerobic (nonoxygen-requiring) photosynthetic bacteria include the purple nonsulfur bacteria, purple sulfur bacteria, green sulfur bacteria, and green flexibacteria.
The cyanobacteria, or blue-green bacteria (formerly called blue-green algae), carry out a type of photosyn-
thesis that resembles that of higher plants. It results in the production of molecular oxygen.
Micrograph of the cyanobacterium Anabaena cylindrica showing vegetative cells and a heterocyst (enlarged cell) in which nitrogen fixation occurs.
48 С H A P T E R 2 DIVERSITY OF THE MICROBIAL WORLD
The rickettsias and chlamydias are obligate intracellular parasites, that is, they can only reproduce within living host cells. Rickettsias are unable to produce sufficient amounts of metabolic energy to support their reproduction. They obtain energy from the host cells in which they grow. Most rickettsias that cause diseases in humans are transmitted by fleas, ticks, and lice. For example, Rickettsia rickettsii is transmitted by ticks and causes Rocky Mountain spotted fever.
Chlamydia reproduction is characterized by a change from a small, rigid-walled infectious form (elementary body) into a larger, thin-walled noninfectious form (initial body). Chlamydia cause human respiratory and urogenital tract diseases. They also cause conjunctivitis and trachoma. In birds they cause respiratory diseases and generalized infections. For example, the disease psittacosis, parrot fever, is caused by Chlamydia psittaci.
The mycoplasmas differ from other bacteria in that they lack a cell wall. They are the smallest organisms capable of self-reproduction. Several members of this
genus cause diseases in humans. For example, atypical pneumonia is caused by Mycoplasma pneumoniae. Urea-plasma causes a sexually transmissible disease.
Colonies of Mycoplasma hominis with characteristic "fried-egg" appearance.
50 CHAPTER 2 DIVERSITY OF THE MICROBIAL WORLD
Chemolithotrophic bacteria use inorganic compounds to generate ATP. The metabolic transformations of inorganic compounds mediated by these organisms cause global-scale cycling of various elements between the air, water, and soil. Thiobacillus thiooxidans is a chemolithotroph that uses sulfur to generate its energy. It is often found in association with waste coal heaps. The metabolic activities of this organism form sulfuric acid from the sulfur in coal, producing acid mine drainage, a serious ecological problem associated with
some coal mining operations. Some chemolithotrophic bacteria, called nitrifying bacteria, convert ammonia (NH4+) to nitrate (NO-f). This conversion is important for the global cycling of nitrogen. This chemical change, however, causes leaching of nitrate into groundwater, which alters soil fertility. Nitrate also can cause a life-threatening disease of human infants. In human infants, nitrate can block the ability of hemoglobin to transport oxygen. Infants that drink water with too much nitrate die of "blue baby syndrome."
The archaebacteria, or Archaea, represent a distinct evolutionary lineage of prokaryotes. Although they are prokaryotes, they have unique characteristics that distinguish them from eubacteria. Archaea have unusual physiological properties that permit many of them to live in extreme environments such as boiling hot springs, concentrated sulfuric acid, and salt lakes. The
thermophilic archaebacteria grow only^t temperatures above 85° C. The acidophilic archaebacteria grow at pH values of less than 2. The halophilic archaebacteria grow at high salt concentrations such as in brines that have sodium chloride concentrations of 15%. The methano-genic archaebacteria are very strict anaerobes that grow only in the absence of air and produce methane.
Colorized micrograph of the archaebacterium, Methanospirillum hungatei showing cells within a protein sheath (orange).
SURVEY OF MICROORGANISMS 51
TABLE 2-6
The eukaryotic microorganisms include the fungi, algae, and protozoa (Table 2-6). These microorganisms, like the higher plants and animals, have eukaryotic cells. They evolved along different lines of descent, apparently based on how they obtain nutrition. The algae carry out photosynthesis, obtaining energy from light and carbon from inorganic carbon dioxide for cell growth. The fungi absorb organic nutrients that they use to generate cellular energy and cell constituents. The protozoa tend to engulf nutrients, sometimes growing on other cells.
Fungi
Like the bacteria, the fungi are extremely diverse. Unlike bacteria, however, fungi are composed of eukaryotic cells. Most fungi have cell walls, which most often contain chitin, the substance that makes up insect skeletons and crab shells. These cell walls help protect the cells against physical damage and chemical attack. Some fungi—yeasts—are primarily unicellular (FIG. 2-8). Others, called filamentous fungi or molds, form tube-like filaments called hyphae (FIG.
2-9). Some hyphae are coenocytic, meaning they lack cross-walls to separate cells; coencytic hyphae are mutinucleate.
Hyphae, which are composed of many cells, can form integrated masses called mycelia. Mycelia are the visible structures seen when molds grow on bread and other substrates. In some cases, elongation of hyphae occurs without forming separate cells. Long, multinucleate, fungal hyphae develop. More commonly, separate cells are formed by branches and crosswalls as the hyphae grow. The crosswalls are called septa. Even when crosswalls form, cellular materials flow through pores in the septa.
Fungi include the molds, which are filamentous organisms, and single-celled organisms called yeasts.
Fungi obtain their energy from the metabolism of organic compounds. They generally absorb nutrients from their surroundings, often from plant materials. In nature, fungi are very important decomposers. They cause, for example, the decay of dead logs. Un-
FIG. 2-9 Micrograph of the fungus Exophiala jeanselmei that, like other molds, forms long filamentous filaments of intertwined mycelia.