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CHAPTER
11
Characterizing and
Classifying Prokaryotes
Chapter Outline
General Characteristics of Prokaryotic Organisms (pp. 316–319)
Morphology of Prokaryotic Cells
Endospores
Reproduction of Prokaryotic Cells
Arrangements of Prokaryotic Cells
Modern Prokaryotic Classification (pp. 319–320)
Survey of Archaea (pp. 320–322)
Extremophiles
Methanogens
Survey of Bacteria (pp. 322–339)
Deeply Branching and Phototrophic Bacteria
Low G + C Gram-Positive Bacteria
High G + C Gram-Positive Bacteria
Gram-Negative Proteobacteria
Deltaproteobacteria
Other Gram-Negative Bacteria
Chapter Summary
General Characteristics of Prokaryotic Organisms
(pp. 316–319)
Prokaryotes are by far the most diverse group of cellular microbes. This chapter examines general prokaryotic characteristics and concludes with a survey of specific prokaryotic taxa.
Morphology of Prokaryotic Cells
There are three basic shapes of prokaryotic cells: coccus (plural cocci), which is roughly spherical; bacillus (plural
bacilli), which is rod-shaped; and spirals. Spiral-shaped prokaryotes are either spirilla, which are stiff, or spirochetes, which are flexible. Slightly curved rods are vibrios, and the term coccobacillus is used to describe cells that
are intermediate in shape between cocci and bacilli. In addition, there are star-shaped, triangular, and rectangular
prokaryotes as well as pleomorphic prokaryotes, which vary in shape and size.
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Endospores
The Gram-positive bacteria Bacillus and Clostridium can produce endospores. Endospores are stable resting stages
that barely metabolize. A vegetative cell normally transforms itself into an endospore under hostile or unfavorable
conditions. The process is called sporulation. Depending on the species, a cell forms an endospore either centrally,
subterminally (near one end), or terminally (at one end).
Reproduction of Prokaryotic Cells
All prokaryotes reproduce asexually. The most common method of reproduction is binary fission, in which the parental cell disappears with the formation of progeny. A variation of binary fission called snapping division occurs in
some Gram-positive species. In snapping division, the parent cell’s outer wall tears apart with a snapping movement
to create the daughter cells. Other microbes reproduce asexually by different methods. For example,
actinomycetes produce reproductive cells called spores that can develop into clones of the original organism. Some
prokaryotes reproduce by fragmentation, and still other prokaryotes
reproduce by budding, in which an outgrowth of the original cell receives a copy of the
genetic material, enlarges, and is then cut off from the parent cell. Epulopiscium and many of its relatives have a
unique method of reproduction whereby the organism gives “birth” to live offspring that emerge from the body of
the dead mother cell.
Arrangements of Prokaryotic Cells
Cocci are often found arranged in groups. Pairs of cocci are diplococci, whereas streptococci are long chains. Cocci
in a square are tetrads, while cuboidal packets are sarcinae. Irregular clusters are staphylococci.
Bacilli are found singly, in pairs, in chains, or in a folded palisade arrangement.
Modern Prokaryotic Classification (pp. 319–320)
Living things are currently classified into three domains—Archaea, Bacteria, and Eukarya—based largely on genetic
relatedness. The most authoritative reference in modern prokaryotic systematics is Bergey’s Manual of Systematic
Bacteriology, which classifies prokaryotes into 2 phyla in Archaea and 24 phyla in Bacteria. The organization of this
text’s survey of prokaryotes largely follows the classification scheme proposed in the second edition of Bergey’s
Manual.
Survey of Archaea (pp. 320–322)
Archaea are classified into two phyla: Crenarchaeota and Euryarchaeota. They have unique rRNA sequences and
share other common characteristics that distinguish them from bacteria:
 They lack true peptidoglycan in their cell walls.
 Cytoplasmic membrane lipids have branched or ring-form hydrocarbons.
 The initial amino acid in their polypeptide chains is methionine.
Though most archaea live in moderate environmental conditions, the domain Archaea
includes extremophiles and methanogens.
Extremophiles
Extremophiles are microbes that require extreme conditions of temperature, pH, and/or
salinity to survive. Prominent among them are thermophiles, which thrive at temperatures over 45ºC, and hyperthermophiles, which live over 80ºC. They are found in both of the phyla. Their DNA, membranes, and proteins do
not function properly at lower temperatures.
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Halophiles depend on high concentrations of salt to keep their cell walls intact. They are found in the phylum Euryarchaeota. The halophile Halobacterium salinarium synthesizes purple proteins called bacteriorhodopsins that
harvest light energy to synthesize ATP.
Methanogens
Methanogens are obligate anaerobes that convert CO2, H2, and organic acids into methane gas (CH4). These microbes constitute the largest group in the phylum Euryarchaeota. Methanogens play significant roles in the environment by converting organic wastes in pond, lake, and ocean sediments into methane. Methanogens also have useful
industrial applications, such as in sewage treatment.
Survey of Bacteria (pp. 322–341)
Bacteria are currently largely classified according to differences in their 16S rRNA sequences, resulting in a scheme
that includes 24 phyla.
Deeply Branching and Phototrophic Bacteria
The deeply branching bacteria are so named because their rRNA sequences and growth characteristics lead scientists to conclude that these organisms are similar to the earliest
bacteria; that is, they branched off the “tree of life” at an early stage. They are autotrophic and live in hot, acidic, and
anaerobic environments, often with intense exposure to sun.
Phototrophic bacteria acquire the energy needed for anabolism by absorbing light with pigments located in nonmembrane-bound thylakoids called photosynthetic lamellae. Most are autotrophic. They can be divided into the following five groups based on their pigments and their source of electrons for photosynthesis:
1. Blue-green bacteria are in phylum Cyanobacteria.
2. Green sulfur bacteria are placed in phylum Chlorobi.
3. Green nonsulfur bacteria are members of phylum Chloroflexi.
4. Purple sulfur bacteria are placed in three classes of phylum Proteobacteria.
5. Purple nonsulfur bacteria are also placed in phylum Proteobacteria.
Cyanobacteria are phototrophs that vary greatly in size, shape, arrangement, and mode of reproduction. Many cyanobacteria reduce atmospheric N2 to NH3 via a process called nitrogen fixation. Cyanobacteria must separate the
metabolic pathways of nitrogen fixation from those of oxygenic photosynthesis because the oxygen generated during
photosynthesis inhibits nitrogen fixation. Many cyanobacteria fix nitrogen in thick-walled cells called heterocysts.
A few carry out photosynthesis in the daylight and fix nitrogen at night.
All of the green and purple bacteria differ from plants, algae, and cyanobacteria in two ways: they use bacteriochlorophylls for photosynthesis instead of chlorophyll a, and they are anoxygenic; that is, they do not generate oxygen during photosynthesis. Whereas nonsulfur
bacteria derive electrons for the reduction of CO2 from organic compounds such as carbohydrates and organic acids,
sulfur bacteria derive electrons from the oxidation of hydrogen
sulfide to sulfur.
Low G + C Gram-Positive Bacteria
The G + C content is the percentage of all base pairs in a genome that are guanine-cytosine base pairs. Taxonomists
use this characteristic in classifying Gram-positive bacteria. Bacteria with G + C ratios below 50% are considered
“low G + C bacteria”; the remainder are considered “high G + C bacteria.”
Low G + C bacteria are classified within the phylum Firmicutes, which includes the
following groups:
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 Clostridia are rod-shaped, obligate anaerobes, many of which form endospores. The group is named for the genus
Clostridium, which causes gangrene, tetanus, botulism, and diarrhea. A vibrio related to Clostridium is Selenomonas, often found in dental plaque and linked to obesity.
 Mycoplasmas are Gram-negative, pleomorphic, facultative anaerobes and obligate anaerobes that lack cell walls.
However, they are able to survive because they colonize osmotically protected habitats such as human bodies, and
their cytoplasmic membranes contain sterols that give them strength and rigidity. Mycoplasmas are frequently associated with pneumonia and urinary tract infections.
 Low G + C Gram-positive bacilli and cocci are important in the environment, industry, and health care. They include the genus Bacillus, which forms endospores and is common in soils. Some bacilli are beneficial in agriculture, but one causes anthrax. Listeria can contaminate meat and milk products and cause bacteremia and
meningitis in fetuses and immunocompromised persons. Bacteria in the genus Lactobacillus are non-sporeforming rods normally found in the mouth, gastrointestinal tract, and vagina, where they provide beneficial microbial antagonism. They are also used in the production of yogurt, buttermilk, and pickles. Streptococcus and
Enterococcus cause pharyngitis, wound infections, and other diseases. Finally, although Staphylococcus is found
growing harmlessly in nasal passages, some strains can invade the body and cause pneumonia, toxic shock syndrome, and a variety of other serious infections.
High G + C Gram-Positive Bacteria
Bacteria with a G + C content greater than 50% are classified in the phylum Actinobacteria. Members of the genus
Corynebacterium are pleomorphic aerobes and facultative anaerobes that reproduce by snapping division. They are
characterized by their stores of phosphate within inclusions called metachromatic granules. Members of the genus
Mycobacterium, including species that cause tuberculosis and leprosy, grow slowly and have water- and dessicationresistant cell walls containing waxy mycolic acids. Actinomycetes resemble fungi in that they produce reproductive
spores and form filaments; this group includes Actinomyces, which is normally found in human mouths; Nocardia,
which is useful in the degradation of pollutants; and Streptomyces, which recycles nutrients and is used to produce
important antibiotics.
Gram-Negative Proteobacteria
The phylum Proteobacteria constitutes the largest and most diverse group of bacteria. They are all Gram-negative
and share common 16S rRNA nucleotide sequences. There are five
distinct classes, designated by the first five letters of the Greek alphabet:
 Alphaproteobacteria are typically aerobes capable of growing at very low nutrient levels. Many have unusual attachment extensions of the cell called prosthecae. Azospirillum and Rhizobium are nitrogen fixers that are important in agriculture. Another nitrogen-fixer, Rhodospseudomonas palustris has potential for biofuel production.
Members of the genus Nitrobacter are nitrifying bacteria that oxidize nitrogen compounds to NO3 via a process
called nitrification. Most purple nonsulfur phototrophs are alphaproteobacteria. Pathogenic alphaproteobacteria
include Rickettsia, which causes typhus and Rocky Mountain spotted fever; and Brucella, which causes brucellosis. In industry, Acetobacter and Gluconobacter are used to synthesize acetic acid, and Agrobacterium is used in
genetic manipulation of plants.
 Betaproteobacteria, like alphaproteobacteria, thrive in habitats with low levels of nutrients, and some genera,
such as Nitrosomonas, are nitrifying. Interesting pathogenic species include Neisseria, species of which inhabit
the mucous membranes of mammals and cause such diseases as gonorrhea, meningitis, and pelvic inflammatory
disease; Bordetella, which causes pertussis, and Burkholderia, which colonizes the lungs of cystic fibrosis patients. Nonpathogenic betaproteobacteria include Thiobacillus, which is important in recycling sulfur in the environment, and Zoogloea and Sphaerotilus, two genera that form flocs, slimy, tangled masses of organic matter in
sewage.
 Gammaproteobacteria constitute the largest and most diverse class. They include purple sulfur bacteria,
intracellular pathogens such as Legionella and Coxiella, and methane oxidizers, which digest most of the methane
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produced by methanogens before it can adversely affect the world’s climate. The largest group is composed of
Gram-negative, facultatively anaerobic rods that catabolize carbohydrates by glycolysis and the pentose
phosphate pathway. The group contains numerous human pathogens, such as Escherichia coli. Finally,
pseudomonads are gammaproteobacteria that utilize the Entner-Doudoroff and pentose phosphate pathways for
catabolism of carbohydrates. They include the pathogen Pseudomonas, an opportunistic pathogen, and the
nitrogen fixers Azotobacter and Azomonas.
 Deltaproteobacteria include Desulfovibrio, a sulfate-reducing microbe important in the recycling of sulfur corrosion of iron. Bdellovibrio is pathogenic to bacteria. Myxobacteria are soil-dwelling and form stalked fruiting bodies containing resistant, dormant myxospores that can survive for a decade or more before germinating and
becoming vegetative cells.
 Epsilonproteobacteria are Gram-negative rods, vibrios, or spirals. Campylobacter causes blood poisoning and
inflammation of the intestinal tract, and Helicobacter causes ulcers.
Other Gram-Negative Bacteria
Other assorted Gram-negative bacteria are classified by Bergey’s Manual into nine phyla. They include chlamydias,
intracellular cocci typified by the genus Chlamydia and responsible for neonatal blindness, pneumonia, and a
sexually transmitted disease. Within a host cell, chlamydias form initial bodies that change into smaller elementary
bodies that are released when the host cell dies. Spirochetes are motile helical bacteria that live in diverse
environments. Treponema, the agent of syphilis, and Borrelia, which causes Lyme disease, are examples.
Bacteroids include Bacteroides, an obligate anaerobic rod that inhabits the digestive tract and is an opportunistic
pathogen. Cytophaga is an aerobic rod that degrades wood and raw sewage.
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