Prescott’s Microbiology, 9th Edition
21
The Deinococci, Mollicutes, and Nonproteobacterial
Gram-Negative Bacteria
CHAPTER OVERVIEW
This chapter is devoted to some of the more interesting and important bacterial phyla from volumes 1 and 5 of
Bergey’s Manual of Systematic Bacteriology. The distinguishing characteristics, morphology, reproduction,
physiology, and ecology of each phylum are included. The taxonomy of each phylum is summarized and
representative species are discussed.
LEARNING OUTCOMES
After reading this chapter you should be able to:
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compare and contrast the physiological and structural differences between Aquificae and Thermotogae
explain why members of Deinococcus-Thermus have erroneously been considered Gram positive
describe the habitats in which deinococci can be isolated
discuss the unique capacity of the deinococci to tolerate desiccation and high doses of radiation
relate the structure of the mollicute cell envelope to morphology
outline how arginine can be catabolized to yield ATP by substrate-level phosphorylation
draw the flux of protons that enables Ureaplasma urealyticum to generate a proton motive force despite the
absence of an electron transport chain
illustrate how gliding motility is accomplished by mycoplasmas
list several habitats in which mollicutes reside and relate this to their capacity to be pathogenic
assess the importance of photosynthetic pigments in the distribution of photosynthetic bacteria in nature
draw a generic chromosome and identify the function of its structural elements
predict the habitat closest to your home where you might find members of the phyla Chlorobi, Chloroflexi, and
Cyanobacteria
draw a generic cyanobacterial cell and label its intracellular structures
list three types of specialized cells made by cyanobacteria and describe the function of each
compare and contrast the prochlorophytes with other cyanobacteria
draw a concept map describing the structure and physiology of the six types of photosynthetic bacteria listed in
table 21.2
draw the unusual structural features of the planctomycetes
identify the electron donor and acceptor used in the anammox reaction
explain why the anammox reaction is important to the global flux of nitrogen
explain the term obligate intracellular parasite
diagram the chlamydial life cycle
deduce why the Chlamydiae can survive despite significant metabolic limitations
draw a spirochete cell as it would be observed in a scanning electron micrograph and in cross section by
transmission electron microscopy
describe how the unusual flagellar arrangement is well suited for motility in common spirochete habitats
explain how the human is host to members of this phylum, Bacteroidetes
describe unusual carbon substrates used by some bacteriodes
explain the proposed mechanism for Flavobacterium johnsoniae gliding motility, and relate gliding motility to
the microbe’s capacity to degrade complex organic substrates
describe habitats where methane oxidation might occur
1
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Prescott’s Microbiology, 9th Edition
CHAPTER OUTLINE
I.
Aquificae and Thermotogae
A. Phylum Aquificae—thought to represent the deepest branch of bacteria; two of its best studied genera are
Aquifex and Hydrogenobacter
1. Hyperthermophilic with optimum of 85°C and maximum of 95°C
2. Chemolithoautotrophic—generate energy by oxidizing electron donors such as hydrogen, thiosulfate,
and sulfur with oxygen as the electron acceptor
B. Phylum Thermotogae—second-deepest branch of the bacteria; best studied are members of the genus
Thermotoga
1. Hyperthermophiles with an optimum of 80°C and a maximum of 90°C
2. Gram-negative rods with an outer sheath-like envelope that can extend out from the ends of the cell
3. Grow in active geothermal areas (e.g., marine hydrothermal vents and terrestrial solfataric springs)
4. Chemoheterotrophs with a functional glycolytic pathway; can grow anaerobically on carbohydrates
and protein digests
II. Deinococcus-Thermus
A. Consists of one class, two orders, and three genera; genus Deinococcus is the best studied
B. Genus Deinococcus
1. Spherical or rod-shaped; often associated in pairs or tetrads
2. Aerobic, mesophilic, catalase positive, and usually able to produce acid from only a few sugars
3. They stain gram positive but have a layered cell wall and an outer membrane like gram-negative
bacteria; have L-ornithine in their peptidoglycan and lack teichoic acid
4. Have a plasma membrane with large amounts of palmitoleic acid rather than phosphatidylglycerol
phospholipids
5. Can be isolated from ground meat, feces, air, freshwater, and other sources but their natural habitat
is not known
6. Extraordinarily resistant to desiccation and radiation; their genome structure and unusual ability to
repair chromosomal damage (even fragmentation) probably accounts for this ability
7. Genome consists of two circular chromosomes, a mega plasmid, and a small plasmid; the
chromosome exists as a compact, ring-like structure and this may help maintain continuity even after
radiation-induced breaks occur; accumulation of Mn(II) protects against radiation-induced toxic
oxygen species
III. Class Mollicutes (phylum Tenericutes)
A. Includes all bacteria that lack walls and do not synthesize peptidoglycan precursors
1. Commonly called mycoplasmas
2. They are pleomorphic and have the smallest genomes among bacteria
a. Some have a specialized terminal structure that projects from the cell and gives them a flask or
pear shape
b.
some have the minimal genome size for a free-living existence
c. Most species require sterols for growth, which they obtain from their host.
d. Some are capable of gliding motility
e. They are widespread and can be isolated from plants, animals, soil and compost piles
f.
Can colonize mucous membranes and joints and are often associated with diseases of the
respiratory and urogenital tracts.
IV. Photosynthetic Bacteria
A. Both oxygenic and anoxygenic photosynthesis are observed in photosynthetic bacteria
1. Cyanobacteria carry out oxygenic photosynthesis, using water as an electron source for the
generation of NADH and NADPH
2. Green and purple bacteria carry out anoxygenic photosynthesis, using reduced molecules other than
water as electron sources for the generation of NADH and NADPH
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Prescott’s Microbiology, 9th Edition
a.
B.
C.
D.
E.
F.
Purple sulfur bacteria use reduced sulfur compounds as electron sources and accumulate sulfur
granules within their cells
b. Green sulfur bacteria use reduced sulfur compounds as electron sources and deposit sulfur
granules outside their cells
c. Purple nonsulfur bacteria use organic molecules as electron sources
There is a correlation between the type of photosynthetic pigments, oxygen relationships, and ecological
distribution
1. Purple and green bacteria are anaerobes and use bacteriochlorophyll
a. Grow better in deeper, anaerobic zones of aquatic habitats
b. Their bacteriochlorophylls absorb shorter wavelengths of light, which penetrate to these deeper
zones
2. Cyanobacteria have chlorophyll a, which absorbs longer wavelengths of light; these bacteria are
found primarily at the surface of bodies of water
Bergey’s Manual divides the photosynthetic bacteria into six groups distributed into five bacterial phyla;
there appears to have been considerable horizontal transfer of photosynthetic genes between the five
phyla:
1. Phylum Chlorobi—green sulfur bacteria
2. Phylum Chloroflexi—green nonsulfur bacteria
3. Phylum Cyanobacteria
4. Phylum Proteobacteria—purple sulfur bacteria (-proteobacteria) and purple nonsulfur bacteria (proteobacteria and -proteobacteria)
5. Phylum Firmicutes—heliobacteria
Phylum Chlorobi—green sulfur bacteria
1. Consists of one class, order, and family; representative genera include Chlorobium,
Prosthecochloris, and Pelodictyon
2. Obligately anaerobic photolithoautotrophs that use hydrogen sulfide, elemental sulfur, and hydrogen
as electron sources; elemental sulfur produced by sulfide oxidation is deposited outside the cell
3. Photosynthetic pigments are located in ellipsoidal vesicles called chlorosomes, which are attached to
the plasma membrane but are not continuous with it; the chlorosome membrane is not a normal lipid
bilayer; chlorosomes have accessory bacteriochlorophylls but the reaction center bacteriochlorophyll
is located in the plasma membrane
4. Flourish in anaerobic, sulfide-rich zones of lakes; although they lack flagella and are nonmotile,
some species have gas vesicles to adjust their depth in water for adequate light and hydrogen sulfide;
species without gas vesicles are found in sulfide-rich mud at the bottom of lakes and ponds.
5. Morphologically diverse (rods, cocci, or vibrios; grow singly, in chains, or in clusters); are grassgreen or chocolate-brown in color
Phylum Chloroflexi—green nonsulfur bacteria
1. A deep branch in the bacterial tree
2. Genus Chloroflexus—major representative of the photosynthetic green nonsulfur bacteria
a. Filamentous, gliding bacteria
b. Thermophilic; often isolated from neutral to alkaline hot springs where they grow in the form
of orange-reddish mats
c. Ultrastructure and photosynthetic pigments are like green bacteria, but their metabolism is
similar to that of the purple nonsulfur bacteria
d. Can carry out anoxygenic photosynthesis with organic compounds as carbon sources or can
grow aerobically as a chemoheterotroph
3. Genus Herpetosiphon—represents nonphotosynthetic members of phylum Chloroflexi; contains
gliding, rod-shaped filamentous bacteria; aerobic chemoorganotrophs with respiratory metabolism;
isolated from fresh water and soil
Phylum Cyanobacteria
1. The largest and most diverse group of photosynthetic bacteria; their photosynthetic systems resemble
those of eukaryotes; in addition they are metabolically flexible
a. Have chlorophyll a and photosystem II, and carry out oxygenic photosynthesis
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Prescott’s Microbiology, 9th Edition
b.
V.
Photosynthetic pigments are in thylakoid membranes lined with particles called phycobilisomes
(contain phycobilin pigments), which transfer energy to photosystem II
c. Fix carbon dioxide by the Calvin cycle (enzymes of which are found in carboxysomes), reserve
carbohydrate as glycogen, and nitrogen as cyanophycin
d. Do not have functional TCA cycle; the pentose phosphate pathway plays a central role in their
metabolism
e. Some can grow in the dark as chemoheterotrophs, and some species can carry out anoxygenic
photosynthesis if in an anaerobic environment
2. Vary greatly in shape and appearance
a. May be unicellular, exist as colonies of many shapes, or form filaments; trichomes are rows of
cyanobacterial cells that are in close contact with one another over a large area
b. Most appear blue-green because of phycocyanin, but some species are red-brown because of
the pigment phycoerythrin; the relative amounts of these pigments can be modulated through
chromatic adaptation
c. Have typical prokaryotic structures with a gram-negative cell wall
d. Often use gas vesicles to move vertically in the water (a form of phototaxis); many filamentous
cyanobacteria have a gliding motility; although cyanobacteria lack flagella, some marine
species are able to swim by an unknown mechanism
3. Reproduce by binary fission, budding, fragmentation, and multiple fission
a. Fragmentation of filamentous cyanobacteria generates small, motile filaments called
hormogonia
b. Some species develop akinetes, thick-walled resting cells that are resistant to desiccation; these
often germinate to form new filaments
4. Many filamentous cyanobacteria fix atmospheric nitrogen in special cells (heterocysts), which
protect the oxygen-sensitive nitrogenase; other cyanobacteria that lack heterocysts also can fix
nitrogen
5. The taxonomy of cyanobacteria is unsettled; Bergey’s Manual divides them into five subsections
with 56 genera and more than 2000 species
a. The five subsections differ markedly in terms of morphology and reproduction
1) Subsection I—unicellular rods or cocci; most are nonmotile; reproduce by binary fission
or budding
2) Subsection II—unicellular, though some may be held together in an aggregate by an outer
wall; reproduce by multiple fission to form baeocytes
3) Subsection III—filamentous cyanobacteria with branched trichomes
4) Subsection IV—unbranched filamentous cyanobacteria that can form heterocysts and
akinetes
5) Subsection V—branched filamentous cyanobacteria that can form heterocysts and
akinetes
b. Prochlorophytes include the genera Prochloron, Prochlorococcus, and Prochlorothrix
1) Differ from other cyanobacteria by having chlorophyll b as well as chlorophyll a and by
lacking phycobilisomes
2) These are the most like the predicted endosymbiont that became chloroplasts
3) Prochlorococcus may be the most abundant oxygenic photosynthetic organism on Earth
6. Are tolerant of environmental extremes; thermophilic species can grow at temperatures up to 75°C;
they are also successful at establishing symbiotic relationships (e.g., in lichens; with protozoa, fungi,
and plants)
Phylum Planctomycetes
A. Contains one class, one order, and four genera
B. Spherical or oval, budding bacteria that lack peptidoglycan and have distinctive crateriform structures
(pits) in their cell walls
C. In two genera, Gemmata and Pirullela, the nuclear body is membrane bounded, something that is not seen
in other prokaryotes
D. A recently discovered form of chemolithotrophy is seen in some species where anaerobic ammonia
oxidation in anammoxosomes uses ammonia as an electron source and nitrite as a terminal electron
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Prescott’s Microbiology, 9th Edition
acceptor yielding nitrogen gas; anammox reactions may contribute very significantly to ocean nitrogen
cycles
E. The genus Planctomyces attaches to surfaces through a stalk and holdfast; other genera lack stalks
F. Most have life cycles in which sessile cells bud to produce motile swarmer cells
VI. Phylum Chlamydiae
A. This phylum has one class, one order, four families, and six genera; Chlamydia is the most important and
best-studied genus
B. Obligately intracellular parasites that are 0.2 to 1.5 µm in size
C. Genus Chlamydia
1. Nonmotile, coccoid, gram-negative bacteria
2. Reproduce within cytoplasmic vesicles of host cells by a unique developmental cycle involving
elementary bodies (EBs) and reticulate bodies (RBs)
a. Begins with attachment of an EB to host cell
b. Host cell phagocytoses the EB, but fusion of lysosome with the phagosome is prevented by the
EB
c. EB reorganizes itself into a RB, which is specialized for reproduction
d. RB reproduces repeatedly, giving rise to many RBs, all within a vacuole
e. RBs change back into EBs, and these are released when the host cell lyses
3. Cell wall lacks muramic acid and peptidoglycan; EBs use cross-linking of outer membrane proteins,
and possibly, periplasmic proteins to achieve osmotic stability
4. Found mostly in mammals and birds, but have been recently isolated from spiders, clams, and
freshwater invertebrates
5. Have one of the smallest prokaryotic genomes
6. Usually thought of as being completely dependent on host for ATP (using translocases for uptake);
however, recent genomic analysis indicates that some genes for ATP synthesis are present in the
genome; RBs have a number of biosynthetic capabilities (e.g., DNA, RNA, glycogen, lipid, protein,
some amino acids, and coenzymes); EBs have very little metabolic activity and seem to be dormant
forms concerned exclusively with transmission and infection
VII. Phylum Spirochaetes
A. Consists of one class, one order, three families, and 13 genera
B. Gram-negative, chemoheterotrophic, flexibly helical bacteria that exhibit a creeping (crawling) motility
due to a structure called an axial filament
C. The axial filament (a complex of periplasmic flagella) lies in a flexible outer sheath (outer membrane)
outside the protoplasmic cylinder (houses the nucleoid and cytoplasm); function of the sheath is essential
(spirochetes will die if it is removed) but unknown
D. Flagellar rotation is responsible for motility by an unknown mechanism, presumably by rotating the outer
sheath or flexing the cell for a crawling motion
E. Can be anaerobic, facultatively anaerobic, or aerobic and can use a diverse array of organic molecules as
carbon and energy sources
F. Ecologically diverse
1. Spirochaeta—free-living and often found in anaerobic, sulfide-rich aquatic environments
2. Leptospira—aerobic water and moist soils
3. Many, including Criptispira and Treponema form symbiotic associations with other organisms
4. Some members of Treponema, Borrelia, and Leptospira cause disease (e.g., T. pallidum is the
causative agent of syphilis, and B. burgdorferi is the causative agent of Lyme disease)
VIII. Phylum Bacteroidetes
A. Consists of three classes (Bacteroides, Flavobacteria, and Sphingobacteria), 12 families, and 63 genera
B. Class Bacteroides
1. Obligate anaerobes, non-spore forming, chemoheterotrophic, fermentative, rods
2. Found in oral cavity and intestinal tract of humans and other animals and the rumen of ruminants
where they often benefit the host by degrading cellulose, pectins, and other complex carbohydrates,
thereby providing extra nutrition for the host
3. Some species can be associated with disease
C. Class Sphingobacteria
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Prescott’s Microbiology, 9th Edition
1.
2.
Often have sphingolipids in their cell walls
Contains several genera including Flexibacter, Cytophaga, and Sporocytophaga; they differ in
morphology, life cycle, and physiology
a. Cytophaga are slender rods with pointed ends and exhibit gliding motility; Sporocytophaga are
similar to Cytophaga but form spherical resting cells called microcysts; Flexibacter form long
threads
b. Cytophaga and Sporocytophaga are aerobes that actively degrade complex carbohydrates (e.g.,
cellulose, chitin, keratin); they play a major role in the mineralization of organic matter and can
damage exposed wooden structures; they contribute significantly to wastewater treatment;
Flexibacter are unable to degrade complex carbohydrates
c. Most cytophagas are free-living, but some pathogenic species are known (e.g., C. columnaris
causes disease in freshwater and marine fish)
d. Cytophagas are nonmotile when in suspension, but exhibit gliding motility when in contact
with a surface; they leave a slime trail; gliding motility has several advantages; these
advantages include enabling them to find and digest insoluble material encountered as they
move, allowing motility in drier habitats, and enabling them to position themselves for optimal
environmental conditions
IX. Phylum Verrucomicrobia
A. Consists of a single class and order, with few cultivated members
B. Acidimethylosilex is a thermophilic, acidophilic, methanotroph
CRITICAL THINKING
1.
In what ways are cyanobacteria similar to eukaryotic phototrophs? Why, then, are they classified in the domain
Bacteria (i.e., in what ways are they more like bacteria)?
2.
Compare and contrast oxygenic and anoxygenic photosynthesis in terms of both substrates and products.
3.
The chlamydiae are only slightly larger than poxviruses and are obligately intracellular parasites. These
characteristics make them similar to viruses. What features distinguish them from viruses?
4.
Multiple forms of locomotion are employed by the bacteria among the diverse phyla described in this
chapter. How are proton gradients or ATP used to drive these mechanisms and how do these
mechanisms specifically suit a particular genera?
CONCEPT MAPPING CHALLENGE
Construct a concept map using the following words and your own linking words.
Anoxygenic
Prochlorophytes
Green sulfur bacteria
Phycobilisomes
Chloroflexus
Chlorosomes
Green nonsulfur bacteria
Phycocyanin
Oxygenic
Photosynthesis
Cyanobacteria
Chlorobium
6
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