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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.
After reading this chapter you should be able to:
• discuss the deeply branching bacterial phyla Aquificae and Thermotogae
• discuss the Deinococci, focusing on their extraordinary resistance to desiccation and radiation
• compare and contrast the phyla of photosynthetic bacteria
• discuss gliding motility
• discuss the unique structural features of Planctomycetes
• discuss the unique lifestyle of the Chlamydiae
• discuss the unique structural features and motility of the Spirochaetes
• discuss the important metabolic and ecological characteristics of the Bacteroidetes
• discuss the novel phylum Verrucomicrobia
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
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3.
They stain gram positive but have a layered cell wall and an outer membrane like gramnegative 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 radiationinduced toxic oxygen species
III.
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 a.
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
B.
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
C.
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
D.
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.
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5.
Morphologically diverse (rods, cocci, or vibrios; grow singly, in chains, or in clusters); are grass-green or chocolate-brown in color
E.
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
F.
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 b.
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
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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)
IV.
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 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
V.
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
VI.
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
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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)
VII.
Phylum Bacteroidetes
A.
Consists of three classes ( Bacteroides, Flavobacteria , and Sphingobacteria ), 12 families, and 63 genera
B.
Class Bacteroides
1.
Obligate anaerobes, nonsporing, 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
1.
Often have sphingolipids in their cell walls
2.
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
VIII.
Phylum Verrucomicrobia
A.
Consists of a single class and order, with few cultivated members
B.
Acidimethylosilex is a thermophilic, acidophilic, methanotroph
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Place the letter of each term in the space next to the definition or description that best matches it.
____ 1. A photosynthetic process in which water is used as an electron donor
____ 2. A photosynthetic process that does not involve water as an electron donor
____ 3. Ellipsoidal vesicles containing the green sulfur bacteria’s photosynthetic pigments; these vesicles are attached to but are not continuous with the plasma membrane
____ 4. Particles that line the thylakoid membranes of most cyanobacteria
____ 5. Small, motile filaments produced by fragmentation of filamentous cyanobacteria
____ 6. Dormant, thick-walled resting cells of cyanobacteria that are resistant to desiccation
____ 7. Special cells of cyanobacteria that are able to fix atmospheric nitrogen
____ 8. Small reproductive cells formed by those species of cyanobacteria that reproduce by multiple fission; these escape when the outer wall ruptures
____ 9. A row of bacterial cells that are in close contact with one another over a large area
____ 10. The infective form of chlamydiae; it is taken into the host cell by phagocytosis
____ 11. The form of chlamydiae that is specialized for reproduction
____ 12. A complex of periplasmic flagella that mediate spirochete movement
____ 13. The flagella that extend from both ends of the protoplasmic cylinder of spirochetes a. akinetes b. anoxygenic photosynthesis c. axial fibrils (periplasmic flagella) d. axial filament e. baeocytes f. chlorosomes g. elementary body h. heterocysts i. hormogonia j. oxygenic photosynthesis k. phycobilisomes l. reticulate body (initial body) m. trichome
1. In contrast,
photosynthesis, water is used as the electron donor and oxygen is produced. In
photosynthesis does not involve water, but instead uses reduced molecules such as hydrogen sulfide as electron sources for the generation of NADH and NADPH.
2. Some filamentous cyanobacteria fix atmospheric nitrogen using special cells called ____________.
3. The infectious stage of chlamydiae is called the ____________ body, while the reproductive stage is
4. called the ____________ body.
The bacteriochlorophyll pigments of bacteria, the bacteria, and the purple bacteria enable them to live in deeper, anaerobic zones of aquatic habitats.
The chlorophyll pigments characteristic of the in water columns.
5. Members of the phylum Chloroflexi are also known as the
limit their growth to upper levels
Many of these bacteria exhibit motility and can carry out
6. Members of the phylum Chlorobi are also known as the
bacteria.
photosynthesis.
bacteria. All carry out photosynthesis using hydrogen sulfide, elemental sulfur, and hydrogen as electron sources. Their photosynthetic pigments are located in vesicles called .
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Phylum
Aquificae
Thermotogae
Deinococcus-Thermus
Representative Genera
Important Characteristics
(structural, physiological, ecological)
Chloroflexi
Chlorobi
Cyanobacteria
Planctomycetes
Chlamydiae
Spirochaetes
Bacteroidetes
Prochlorophytes
Verrucomicrobia
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For each of the questions below select the one best answer.
1. Which of the following are capable of carrying out oxygenic photosynthesis? a. purple bacteria b. green bacteria c. cyanobacteria d. All of the above are capable of oxygenic photosynthesis.
2. Which of the following accumulates sulfur granules outside the cell? a. purple sulfur bacteria b. green sulfur bacteria c. cyanobacteria d. colorless sulfur bacteria
3. Which of the following activities is associated with cytophagas ?
a. damage to fishing gear and wood structures b. digestion of sewage in sewage treatment plants c. Both (a) and (b) are associated with cytophagas. d. Neither (a) nor (b) is associated with cytophagas.
4. Which of the following is thought to be the oldest branch of bacteria? a. Thermotogae b. Aquificae c. Cyanobacteria d. Spirochaetes
5. Where do members of the phylum Thermotogae generally grow? a. marine hydrothermal vents b. terrestrial solfataric hot springs c. Both (a) and (b) are correct. d. Neither (a) nor (b) is correct.
6. Which of the following is extremely radiation resistant? a. Deinococci b. Aquificae c. Both (a) and (b) are correct. d. Neither (a) nor (b) is correct.
7. Which of the following contain chlorophyll a ? a. Chlorobi b. Cyanobacteria c. Chloroflexi d. all of the above
8. In which of the following phyla can membranebound nuclear bodies be observed? a. Planctomycetes b. Chlamydiae c. Bacteroidetes d. Spirochaetes
9. Cyanobacterial heterocysts have very thick walls and lack photosystem II. Why are these characteristics important? a. They allow the heterocysts to resist desiccation. b. They protect the oxygen-sensitive nitrogenase enzyme. c. Both (a) and (b) are correct. d. Neither (a) nor (b) is correct.
10. Prochlorophytes differ from cyanobacteria by not having: a. chlorophyll a b. chlorophyll b c. chloroplasts d. phycobilisomes
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____ 1. The cyanobacteria comprise a small group of photosynthetic bacteria and do not differ greatly from one another.
____ 2. All of the cyanobacteria have a blue-green color that comes from the pigment phycocyanin.
____ 3. The photosynthetic partner in most lichen associations is generally a cyanobacterium.
____ 4. A trichome is a bacterial cell with three different photosynthetic pigments.
____ 5. The Deinococci stain gram positive but have a layered cell wall and an outer membrane that is more like the cell wall of a gram-negative organism.
____ 6. The Deinococci have an unusual ability to repair chromosome damage, even fragmentation.
____ 7. The chlorosomes of Chlorobi are continuous with the plasma membrane.
____ 8. The flexible outer sheath in which the axial filaments of spirochetes lay is nonessential
(i.e., the bacteria will survive if it is removed).
____ 9. Members of the genus Bacteroides constitute as much as 30% of the bacteria isolated from human feces.
____ 10. Many bacteria with gliding motility are able to use as a nutrient source the insoluble material encountered while gliding.
____ 11. Cytophagas contribute significantly to waste water treatment.
____ 12. The phyla Planctomycetes and Chlamydiae lack peptidoglycan in their cell walls.
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?
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Terms and Definitions
1. j, 2. b, 3. f, 4. k, 5. i, 6. a, 7. h, 8. e, 9. m, 10. g, 11. l, 12. d, 13. c
Fill in the Blank
1. oxygenic; anoxygenic 2. heterocysts 3. elementary; reticulate 4. green sulfur; green nonsulfur; cyanobacteria
5. green nonsulfur; gliding; anoxygenic 6. green sulfur; anoxygenic; chlorosomes
Multiple Choice
1. c, 2. b, 3. c, 4. b, 5. c, 6. a, 7. b, 8. a, 9. b, 10. d
True/False
1. F, 2. F, 3. T, 4. F, 5. T, 6. T, 7. F, 8. F, 9. T, 10. T, 11. T, 12. T
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