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CHAPTER 12
Prokaryotic Diversity: The Bacteria
The Phylogeny of Bacteria
Overview
• Nearly 7000 species of prokaryotes are
known. Figure 12.1 gives a phylogenetic
overview of Bacteria.
• The Proteobacteria consist of five clusters
containing several genera. Each cluster is
designated by a Greek letter: alpha, beta,
gamma, delta, or epsilon (Table 12.1).
• Physiologically, Proteobacteria can be
phototrophic, chemolithotrophic, or
chemoorganotrophic.
Phylum 1: Proteobacteria,
Purple Phototrophic Bacteria
• Purple bacteria are anoxygenic phototrophs
that obtain carbon from CO2 + H2S (purple
sulfur bacteria) or organic compounds
(purple nonsulfur bacteria).
• Purple nonsulfur bacteria are physiologically
diverse, and most can grow as
chemoorganotrophs in darkness. The purple
bacteria reside in the alpha, beta, and gamma
subdivisions of the Proteobacteria.
• Table 12.2 gives genera and characteristics
of purple sulfur bacteria. Table 12.3 gives
genera and characteristics of purple nonsulfur
bacteria.
The Nitrifying Bacteria
• Chemolithotrophs are prokaryotes that can
oxidize inorganic electron donors and in
many cases use CO2 as their sole carbon
source.
• Several reactions are involved in the oxidation of
inorganic nitrogen compounds by chemolithotrophic
nitrifying bacteria (Figure 12.9).
• Characteristics of the nitrifying bacteria are
listed in Table 12.4.
Sulfur- and Iron-Oxidizing
Bacteria
• The ability to grow chemolithotrophically
on reduced sulfur compounds is a property of
a diverse group of Proteobacteria (Table
12.5).
• Some sulfur chemolithotrophs are obligate
chemolithotrophs, which must use inorganic
instead of organic compounds as electron
donors. Carboxysomes are often present
inside the cells of obligate chemolithotrophs.
• Other sulfur chemolithotrophs are facultative
chemolithotrophs, in the sense that they can
grow either chemolithotrophically (and thus
also as autotrophs) or
chemoorganotrophically.
• Most species of Beggiatoa, however, can
obtain energy from the oxidation of inorganic
sulfur compounds but lack enzymes of the
Calvin cycle. Thus, they require organic
compounds as carbon sources. Such
organisms are called mixotrophs.
Hydrogen-Oxidizing Bacteria
• A wide variety of bacteria can grow with H2
as the sole electron donor and O2 as the
electron acceptor using the reduction of O2
with H2 as their energy metabolism.
• All hydrogen-oxidizing bacteria contain one
or more hydrogenase enzymes that bind H2
and use it either to produce ATP or as
reducing power for autotrophic growth (Table
12.6).
Methanotrophs and Methylotrophs
• Methylotrophs are prokaryotes able to grow on carbon
compounds that lack carbon-carbon bonds. Some
methylotrophs are also methanotrophs, able to grow on CH4.
• Two classes of methanotrophs are known, each having a
number of structural and biochemical properties in common.
Methanotrophs reside in water and soil and can also exist as
symbionts of marine shellfish.
• Two classes of methanotrophs are known, each having a
number of structural and biochemical properties in common.
Methanotrophs reside in water and soil and can also exist as
symbionts of marine shellfish.
• Table 12.7 lists substrates used by
methylotrophic bacteria, and Table 12.8 gives
some characteristics of meganotrophs.
Pseudomonas and the Pseudomonads
• Pseudomonads include many gram-negative
chemoorganotrophic aerobic rods; many nitrogenfixing species are phylogenetically closely related.
• The distinguishing characteristics of the
pseudomonad group are given in Table 12.9. Also
listed in this table are the minimal characteristics
needed to identify an organism as a pseudomonad.
• Many pseudomonads, as well as a variety of
other gram-negative Bacteria, metabolize
glucose via the Entner-Doudoroff pathway
(Figure 12.17c).
• Species of the genus Pseudomonas and
related genera are defined on the basis of
phylogeny and various physiological
characteristics, as outlined in Tables 12.10
and 12.11.
Acetic Acid Bacteria
• The acetic acid bacteria are phylogenetically
related to pseudomonads and are
characterized by an ability to oxidize ethanol
to acetate aerobically.
Free-Living Aerobic NitrogenFixing Bacteria
• A variety of organisms inhabit soil and are capable of
fixing N2 aerobically (Table 12.12).
Neisseria, Chromobacterium,
and Relatives
• This group of beta and gamma Proteobacteria
comprises a diverse collection of organisms, related
phylogenetically as well as by Gram stain,
morphology, lack of motility, and aerobic metabolism.
• The genera Neisseria, Moraxella, Branhamella,
Kingella, and Acinetobacter are distinguished as
outlined in Table 12.13.
Enteric Bacteria
• The enteric bacteria are a large group of
facultative aerobic rods of medical and
molecular biological significance.
• Table 12.14 gives the phenotypic
characteristics used to separate the enteric
bacteria from other bacteria of similar
morphology and physiology.
• One important taxonomic characteristic
separating the various genera of enteric
bacteria is the type and proportion of
fermentation products produced by anaerobic
fermentation of glucose.
• Two broad patterns are recognized, the
mixed-acid fermentation and the 2,3butanediol fermentation (Figure 12.24).
• Tables 12.15 and 12.16 outline the key
diagnostic reactions used to distinguish key
genera of enteric bacteria.
• Figure 12.25 shows a simple key to the
main genera of enteric bacteria.
Vibrio and Photobacterium
• Vibrio and Photobacterium species are
marine organisms; some species are
pathogenic, others are bioluminescent.
Rickettsias
• The rickettsias are obligate intracellular
parasites, many of which cause disease.
Rickettsias are deficient in many metabolic
functions and obtain key metabolites from
their hosts.
• Characteristics of rickettsias are given in
Table 12.17.
Spirilla
• Spirilla are spiral-shaped,
chemoorganotrophic prokaryotes widespread
in the aquatic environment. The genera
Helicobacter and Campylobacter are
pathogenic spirilla. Spirilla are distributed
among all five subdivisions of the
Proteobacteria.
• Bdellovibrio organisms have the unusual
property of preying on other bacteria, using as
nutrients the cytoplasmic constituents of their
hosts (Figure 12.34b).
• Table 12.18 lists characteristics of the
genera of spiral-shaped bacteria.
Sheathed Proteobacteria:
Sphaerotilus and Leptothrix
• Sheathed bacteria are filamentous
Proteobacteria in which individual cells form
chains within an outer layer called the sheath.
Budding and
Prosthecate/Stalked Bacteria
• Budding and prosthecate bacteria are
appendaged cells that form stalks or
prosthecae used for attachment or nutrient
absorption and are primarily aquatic.
• Table 12.19 lists characteristics of stalked,
appendaged (prosthecate), and budding
bacteria.
• Figure 12.38 illustrates the contrast between
cell division in conventional bacteria and in
budding and stalked bacteria.
• Two well-studied budding bacteria are
closely related phylogenetically:
Hyphomicrobium, which is
chemoorganotrophic, and Rhodomicrobium,
which is phototrophic. These organisms
release buds from the ends of long, thin
hyphae.
• The hypha is a direct cellular extension of
the mother cell (Figure 12.39) and contains
cell wall; cytoplasmic membrane; ribosomes;
and, occasionally, DNA.
• One common stalked bacterium is
Caulobacter. Figure 12.41 shows stages in
the Caulobacter cell cycle beginning with a
swarmer cell.
Gliding Myxobacteria
• The fruiting myxobacteria are rod-shaped,
gliding bacteria that aggregate to form
complex masses of cells called fruiting
bodies. Myxobacteria are
chemoorganotrophic soil bacteria that live by
consuming dead organic matter or other
bacterial cells.
• Table 12.20 gives the classification of the
fruiting myxobacteria.
• The life cycle of a typical fruiting
myxobacterium is shown in Figure 12.47.
Sulfate- and Sulfur-Reducing
Proteobacteria
• Sulfate- and sulfur-reducing bacteria are a
large group of delta Proteobacteria unified by
their physiological process of reducing either
SO42– or S0 to H2S under anoxic conditions.
• Two physiological subgroups of sulfatereducing bacteria are known: group I, which
is incapable of oxidizing acetate to CO2, and
group II, which is capable of doing so.
• Table 12.21 lists characteristics of some key
genera of sulfate- and sulfur-reducing
bacteria.
Phylum 2 and 3: Gram-Positive
Bacteria and Actinobacteria
Nonsporulating, Low GC,
Gram-Positive Bacteria: Lactic
Acid Bacteria and Relatives
• Distinguishing features of major grampositive cocci are given in Table 12.22.
• The "low GC," gram-positive Bacteria are a
large phylogenetic group that contains rods
and cocci, sporulating and nonsporulating
species.
• One important difference between subgroups
of the lactic acid bacteria lies in the pattern of
products formed from the fermentation of
sugars. One group, called homofermentative,
produces a single fermentation product, lactic
acid.
• The other group, called heterofermentative,
produces other products, mainly ethanol plus
CO2, as well as lactate (Table 12.23). Figure
12.53 summarizes pathways for the
fermentation of glucose by a homo- and a
heterofermentative organism.
• Table 12.24 gives differential characteristics
of streptococci, lactococci, and enterococci.
Endospore-Forming, Low GC,
Gram-Positive Bacteria: Bacillus,
Clostridium, and Relatives
• Production of endospores is a hallmark of
the key genera Bacillus and Clostridium.
Gram-positive Bacteria are major agents for
the degradation of organic matter in soil, and
a few species are pathogenic.
• Table 12.25 lists major genera of endosporeforming bacteria.
• Table 12.26 shows characteristics of
representative species of bacilli.
• Table 12.27 gives characteristics of some
groups of clostridia.
• One group of clostridia ferments cellulose
with the formation of acids and alcohols, and
these are likely the major organisms
decomposing cellulose anaerobically in soil.
The biochemical steps in the formation of
butyric acid and butanol from sugars are well
understood (Figure 12.58).
• Another group of clostridia obtains energy
by fermenting amino acids. Some species
ferment individual amino acids; others
ferment only amino acid pairs. In this
situation, one functions as the electron donor
and is oxidized, the other acts as the electron
acceptor and is reduced.
• This type of coupled amino acid decomposition is
known as the Stickland reaction (Figure 12.59).
• One group of endospore-formers, the heliobacteria,
is phototrophic.
Cell Wall–Less, Low GC, GramPositive Bacteria: The Mycoplasmas
• The mycoplasma group contains organisms
that lack cell walls and contain a very small
genome. Many species require sterols to
strengthen their membranes, and several are
pathogenic for humans, other animals, and
plants.
• Major characteristics of mycoplasmas are
shown in Table 12.28.
High GC, Gram-Positive Bacteria
(Actinobacteria): Coryneform and
Propionic Acid Bacteria
• High GC, gram-positive Bacteria include such
organisms as Corynebacterium, Arthrobacter,
Propionibacterium, and Mycobacterium. They are
mainly harmless soil saprophytes.
• The propionic acid bacteria were first
discovered in Swiss cheese, where their
fermentative production of CO2 results in the
characteristic holes. Figure 12.68 shows the
enzymatic reactions leading from glucose to
propionic acid.
Actinobacteria: Mycobacterium
• The genus Mycobacterium consists of rodshaped organisms that at some stage of their
growth cycle possess the distinctive staining
property called acid-fastness.
• This property results from the presence on
the surface of the mycobacterial cell of unique
lipids called mycolic acids, found only in the
genus Mycobacterium.
• M. tuberculosis is the causative agent of the
disease tuberculosis.
•M. tuberculosis cells have a lipid-rich, waxy
outer surface layer that requires special
staining procedures (the acid-fast stain,
Figure 12.69) to observe the cells
microscopically.
Filamentous Actinobacteria:
Streptomyces and Other
Actinomycetes
• The streptomycetes are a large group of
filamentous, gram-positive Bacteria that form
spores at the end of aerial filaments.
• Many clinically useful antibiotics such as
tetracycline and neomycin have come from
Streptomyces species (Table 12.31).
• Streptomycete spores are produced by the
formation of cross-walls in the multinucleate
sporophores, followed by separation of the
individual cells directly into spores (Figure
12.74).
• Figure 12.75 illustrates various types of
spore-bearing structures in the streptomycetes.
Phylum 4: Cyanobacteria and
Prochlorophytes
• Cyanobacteria comprise a large and
morphologically heterogeneous group of
phototrophic Bacteria. Cyanobacteria differ in
fundamental ways from purple and green
bacteria, most notably in that they are
oxygenic phototrophs.
• Cyanobacteria represent one of the major
phyla of Bacteria and show a distant
relationship to gram-positive Bacteria.
• Some filamentous cyanobacteria form
heterocysts, which are rounded, seemingly
empty cells, usually distributed regularly
along a filament or at one end of a filament.
• Oxygen in Earth's atmosphere is thought to
have originated from cyanobacterial
photosynthesis.
Prochlorophytes and
Chloroplasts
• Cyanobacteria and prochlorophytes are
oxygenic phototrophic prokaryotes.
Prochlorophytes differ most clearly from
cyanobacteria in that prochlorophytes contain
chlorophyll b or d and lack phycobilins.
Phylum 5: Chlamydia
• Chlamydias are extremely small parasitic
bacteria that cause a variety of human
diseases. Figure 12.85 shows the infection
cycle of chlamydia.
• Chlamydias contain a very small genome
and are apparently deficient in many
metabolic functions.
Phylum 6: Planctomyces/Pirellula
Planctomyces: A Phylogenetically
Unique Stalked Bacterium
• The Planctomyces group contains stalked,
budding bacteria.
• This phylum contains a number of
morphologically unique bacteria including the
genera Planctomyces, Pirellula, Gemmata,
and Isosphaera. The best studied of these has
been Planctomyces.
Phylum 7: The
Verrucomicrobia
Verrucomicrobium and
Prosthecobacter
• The Verrucomicrobia are distinguished by
their multiple prosthecate cells.
• Members of the Verrucomicrobia share with
other prosthecate bacteria the presence of
peptidoglycan in their cell walls and are
aerobic to facultatively aerobic bacteria,
capable of fermenting various sugars.
Phylum 8: The Flavobacteria
Bacteroides and Flavobacterium
• The flavobacteria contain a variety of gram-negative
Bacteria motile by either flagella or by gliding and
associated with animals, food, and the soil.
• The genus Bacteroides contains obligately anaerobic,
nonsporulating species that are saccharolytic, fermenting
sugars or proteins, depending on the species, to primarily
acetate and succinate as fermentation products.
• The genus Bacteroides contains obligately anaerobic,
nonsporulating species that are saccharolytic, fermenting
sugars or proteins, depending on the species, to primarily
acetate and succinate as fermentation products.
• Bacteroides are normally commensals, found in the
intestinal tract of humans and other animals.
Phylum 9: The Cytophaga Group
• The Cytophaga group includes a variety of obligately
aerobic chemoorganotrophic bacteria in soil, water,
hot springs, and thermal environments.
Phylum 10: Green Sulfur
Bacteria
Chlorobium and Other Green
Sulfur Bacteria
• Green sulfur bacteria are obligately
anaerobic anoxygenic phototrophs that
produce unique structures called
chlorosomes. These organisms can grow at
very low light intensities and oxidize H2S to
S0 and SO42–.
• Consortia containing phototrophic green
bacteria and a nonphototrophic central cell are
common in sulfidic aquatic environments.
Phylum 11: The Spirochetes
• Spirochetes are tightly coiled, motile,
helical prokaryotes that contain both freeliving and pathogenic species.
Phylum 12: Deinococci
Deinococcus/Thermus
• Deinococcus is a key genus in a major
lineage of Bacteria. Deinococcus radiodurans
is the most radiation resistant of all known
organisms.
• The lipids of Thermomicrobium contain 1,2dialcohols instead of glycerol and have neither
ester nor ether linkages (Figure 12.100).
Phylum 13: The Green
Nonsulfur Bacteria
Chloroflexus and Relatives
• Chloroflexus is a key genus in a major
lineage of Bacteria. Chloroflexus is an
anoxygenic phototroph that shows
photosynthetic properties characteristic of
both purple bacteria and green bacteria.
• In addition to Chloroflexus, other
phototrophic green nonsulfur bacteria include
the thermophile Heliothrix and the largecelled mesophiles Oscillochloris and
Chloronema.
Phylum 14–16: Deeply
Branching Hyperthermophilic
Bacteria
Thermotoga and
Thermodesulfobacterium
• Thermotoga and Thermodesulfobacterium
are hyperthermophiles, growing at high
temperature, and each spearheads a major
lineage of Bacteria.
Aquifex, Thermocrinis, and
Relatives
• Aquifex is another hyperthermophile that
heads a major lineage of Bacteria. Aquifex
and Thermocrinis are H2-oxidizing
chemolithotrophs; Thermotoga and
Thermodesulfobacterium are both anaerobic
chemoorganotrophs.
Phylum 17 and 18: Nitrospira
and Deferribacter
Nitrospira, Deferribacter, and
Relatives
• Nitrospira and Deferribacter each form their
own phylum.
• Nitrospira oxidizes NO2– to NO3– and grows
autotrophically. Despite this close
physiological relationship to the classical
nitrifying bacteria, Nitrospira is
phylogenetically quite distinct from them.
• Also, Nitrospira lacks the extensive internal
membranes found in species of nitrifying
Proteobacteria.
• The genus Deferribacter forms its own
distinct lineage and is composed of species
that specialize in anaerobic energy
metabolism. Other genera in this group
include Geovibrio and Flexistipes; the latter
genus is an obligately anaerobic and
fermentative bacterium.