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  1. Aquificae and Thermotogae
    1. Aquificae-thought to represent the deepest (oldest) branch of bacteria; two of its best studies genera are Aquifex and Hydrogenobacter
      1. Hyperthermophilic
      2. Chemolithoautotrophic-generate energy by oxidizing electron donors such as hydrogen, thiosulfate, and sulfur with oxygen as the electron acceptor
    2. Thermotogae-second deepest branch of the bacteria; best studies 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 (like a toga) that can balloon 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
  2. Deinococcus-Thermus
    1. Consists of three genera; genus Deinococcus is the best studied
      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. Extraordinarily resistant to desiccation and radiation
    2. Relatively little is known about the biology of deinococci
      1. Can be isolated from ground meat, feces, air, fresh water, and other sources but their natural habitat is not known
      2. Genome consists of two circular chromosomes, a mega plasmid, and a small plasmid
      3. Have an unusual ability to repair chromosomal damage (even fragmentation) and this probably accounts for their ability to resist desiccation and radiation; genomic analysis show they have many DNA repair genes and many repeat sequences
  3. Photosynthetic Bacteria
    1. Three groups: purple bacteria, green bacteria, and cyanobacteria
      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 an electron source for the generation of NADH and NADPH
        1. Purple sulfur bacteria use reduced sulfur compounds as electron sources and accumulate sulfur granules within their cells
        2. Green sulfur bacteria use reduced sulfur compounds as electron sources and deposit sulfur granules outside their cells
        3. Purple nonsulfur bacteria use organic molecules as their electron sourcec
    2. Type of photosynthetic pigments and oxygen relationships correlates with ecological distribution
      1. Purple and green bacteria are anaerobes and use bacteriochlorophyll pigments
        1. Grow better in deeper, anaerobic zones of aquatic habitats
        2. 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
    3. The 2nd edition of Bergey’s Manual divides the photosynthetic bacteria into six groups:
      1. Phylum Chloroflexi-green nonsulfur bacteria
      2. Phylum Chlorobi-green sulfur bacteria
      3. Phylum Cyanobacteria
      4. Phylum Proteobacteria-Purple sulfur bacteria (gammaproteobacteria) and purple nonsulfur bacteria (alphaproteobacteria and betaproteobacteria); these organisms are covered in chapter 22
    4. Phylum Chloroflexi-green nonsulfur bacteria
      1. Genus Chloroflexus-major representative of the photosynthetic green nonsulfur bacteria
        1. Filamentous, gliding bacteria
        2. Thermophilic, often isolated from neutral to alkaline hot springs where they grow in the form of orange-reddish mats
        3. Ultrastructure and photosynthetic pigments are like green bacteria, but their metabolism is similar to that of the purple nonsulfur bacteria
        4. Can carry out anoxygenic photosynthesis with organic compounds as carbon sources or can grow aerobically as a chemoheterotroph
      2. 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
    5. Chlorobia-green sulfur bacteria
      1. 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
      2. Photosynthetic pigments are located in ellipsoidal vesicles called chlorosomes, which are attached to the plasma membrane but not continuous with it; chlorosome membrane is not a normal lipid bilayer; chlorosomes have accessory bacteriochlorophylls but the reaction center bacteriochlorophyll is located in the plasma membrane
      3. 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.
      4. Morphologically diverse (rods, cocci, or vibrios; grow singly, in chains, or in clusters); grass green or chocolate-brown in color
    6. Phylum Cyanobacteria
      1. Largest and most diverse group of photosynthetic bacteria (56 genera are described in the 2nd edition of Bergey’s Manual)
        1. Photosynthetic system resembles that of eucaryotes, having chlorophyll a and photosystem II; carry out oxygenic photosynthesis
        2. Photosynthetic pigments are in thylakoid membranes lined with particles called phycobilisomes (contain phycobilin pigments), which transfer energy to photosystem II; some species are red-brown and contain the pigment phycoerythrin
        3. Fix carbon dioxide by the Calvin cycle
        4. Do not have functional TCA cycle; pentose phosphate pathway plays a central role in their metabolism
        5. Although they are oxygenic photolithoautotrophs, some can grow slowly 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
        1. May be unicellular, exist as colonies of many shapes, or form filaments called trichomes (rows of bacterial cells that are in close contact with one another over a large area)
        2. Have typical procaryotic structures with a gram-negative cell wall
        3. Often use gas vesicles to move vertically in the water; many filamentous cyanobacteria have a gliding motility; although cyanobacteria lack flagella, some marine species are able to move by an unknown mechanism
      3. Reproduce by binary fission, budding, fragmentation, and multiple fission
        1. Fragmentation generates small motile filaments called hormogonia
        2. Some species develop akinetes, which are 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 can also fix nitrogen
      5. Taxonomy of cyanobacteria is unsettled; the 2nd edition of Bergey’s Manual divides them into five subsections
        1. The prochlorophytes, which used to be categorized separately from other cyanobacteria, are now dispersed into subsections I and III
        2. Prochlorophytes differ from other cyanobacteria by having chlorophyll b as well as chlorophyll a and by lacking phycobilisomes
      6. The three recognized prochlorophyte genera are quite different from one another
        1. Prochloron-extracellular symbiont on the surface or within the cloacal cavity of marine colonial ascidan invertebrates
        2. Prochlorothrix-free living
        3. Prochlorococcus-has a modified chlorophyll a and a-carotene rather than b-carotene
      7. 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. Subsections III, IV, and V-filamentous cyanobacteria
      8. Tolerant of environmental extremes; thermophilic species can grow at temperatures up to 75°C
      9. Successful at establishing symbiotic relationships (e.g., in lichens; symbionts with protozoa, fungi and plants)
  4. Phylum Planctomycetes
    1. Contains one class, one order, and four genera
    2. Spherical or oval, budding bacteria with distinctive crateriform structures (pits) in their walls
    3. In two genera, Gemmata and Pirullela, the nuclear body is membrane bounded, something that is not seen in other procaryotes
    4. The genus Planctomyces attaches to surfaces through a stalk and holdfast; other genera lack stalks
    5. Most have life cycles in which sessile cells bud to produce motile swarmer cells
  5. Phylum Chlamydiae
    1. This phylum has only 5 genera; Chlamydia is the most important and best-studied genus
      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)
      3. Gram-negative-like wall but lacks muramic acid and peptidoglycan; EBs use cross-linking of outer membrane proteins, and possibly, periplasmic proteins to achieve osmotic stability
      4. Obligately intracellular parasites; found mostly in mammals and birds but have been recently isolated from spiders, clams, and freshwater invertebrates
      5. Have one of the smallest procaryotic genomes
    2. Chlamydial reproduction
      1. Begins with attachment of an EB to host cell
      2. Host cell phagocytizes the EB, but fusion of lysosome with the phagosome is prevented by the EB
      3. EB reorganizes itself into a reticulate body (RB), which is specialized for reproduction
      4. RB reproduces repeatedly, giving rise to many RBs, all within a vacuole
      5. RBs change back into EBs, and these are released when the host lyses
    3. Chlamydial metabolism
      1. Usually thought of as being completely dependent on host for ATP; however, recent genomic analysis indicates that some genes for ATP synthesis are present in the genome
      2. RBs have a number of biosynthetic capabilities (e.g., DNA, RNA, glycogen, lipid, protein, some amino acids and coenzymes)
      3. EBs have very little metabolic activity; seem to be dormant forms concerned exclusively with transmission and infection
    4. Three recognized human pathogens
      1. C. trachomatis-trachoma, nongonococcal urethritis, and other diseases in humans and mice
      2. C. psittaci-causes psittacosis in humans and infects many other mammals as well; invades the respiratory and genital tracts, the placenta, developing fetuses, the eye, and synovial fluid of the joints
      3. C. pneumoniae-a causative agent of human pneumonia and possibly atherosclerosis and heart disease
  6. Phylum Spirochaetes
    1. Gram-negative, chemoheterotrophic, flexibly helical bacteria that exhibit a creeping (crawling) motility due to a structure called an axial filament
    2. The axial filament (a complex of periplasmic flagella) lies in a flexible outer sheath (outer membrane) outside the protoplasmic cylinder, which houses the nucleoid and cytoplasm; function of the sheath is essential (spirochetes will die if it is removed) but unknown
    3. Flagellar rotation is responsible for motility by an unknown mechanism, presumably by rotating the outer sheath or flexing the cell for a crawling motion.
    4. Can be anaerobic, facultatively anaerobic, or aerobic and can use a diverse array of organic molecules as carbon and energy sources
    5. 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)
  7. Phylum Bacteroidetes
    1. Consists of 50 genera divided into 3 classes (Bacteroides, Flavobacteria, and Shpingobacteria)
    2. 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
    3. Class Sphingobacteria
      1. Often have sphinolipids in their cell walls
      2. Contains several genera including Flexibacter, Cytophaga and Sporocytophaga; differ in morphology, life cycle and physiology
        1. Cytophaga-slender rods with pointed ends
        2. Sporocytophaga-similar to Cytophaga but form spherical resting cells called microcysts
        3. Flexibacter-form long threads; unlike the other two genera, they are unable to degrade complex carbohydrates
      3. Physiology (as seen in the genera Cytophaga and Sporocytophaga)
        1. Aerobes that actively degrade complex carbohydrates (e.g., cellulose, chitin, keratin)
        2. Play a major role in the mineralization of organic matter and can damage exposed wooden structures
        3. Contribute significantly to wastewater treatment
      4. Most cytophagas are free-living, but some pathogenic species are known (e.g., C. columnaris causes disease in freshwater and marine fish)
      5. Are nonmotile when in suspension, but exhibit gliding motility when in contact with a surface; leaves a slime trail;
      6. Gliding motility has advantages
        1. Enables them to find and digest insoluble material encountered as they move
        2. Allows motility in drier habitats
        3. Enables them to position themselves for optimal environmental conditions

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