T. aquaticus 17-III
PROKARYOTES
Bacteria
 
 
Thermus aquaticus is an organism that has been very helpful in advancing biotechnology.
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Chapter Outline
  1. Description of Prokaryotes
  2. Classification of Prokaryotes
  3. Bacteria
    1. Cyanobacteria
    2. Proteobacteria
    3. Gram Positive Bacteria
  4. Archaea

Tree



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Bacteria may be the most significant group of organisms on earth. They are responsible for much of the decomposition of dead organisms, they convert nitrogen for plants, they help many animals digest food, they produced oxygen in the early atmosphere, and they make certain foods (yogurt, cheese, etc.). Bacteria typically, with notable exceptions, live in environments that have temperatures, pH levels, salinity levels and other conditions with which we are familiar. Some of those environments are familiar to us because they are us. We "experience" bacteria every day even if we aren't thinking about it. Pathogenic Bacteria are those that cause diseases. We may be more familiar with these, and we obviously would rather not "experience" them, but most bacteria are harmless, helpful or necessary.

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Following are some of the main groups of bacteria.

AQUIFICAEFOCUS SITE
YELLOWSTONE NATIONAL PARK

The class Aquificae is a primtive group of filamentous bacteria including just three officially known genera: Aquifex, Hydrogenobacter, and Thermocrinus. The organisms are similar to certain Archaea in being thermophilic ("lovers" of high temperatures). The most thermophilic bacterium known (up to 95oC), Aquifex pyrophilus, is in this group. In general, the more thermophilic an organism, the more primitive it is. Since the high temperature water environments in which these organisms live cannot hold much oxygen, most members are anaerobic or microaerophilic. Members such as Thermocrinus ruber can be found at Yellowstone National Park.

  • Thermocrinus ruber - a pink filamentous organism from Octopus Spring, Yellowstone National Park
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THERMOTOGAE 

The class Thermotogae is also a small, primitive group of thermophilic bacteria. The distinguishing, namesake feature of the members of this group is their "toga" - a loose outer membrane of a Gram-negative-type envelope. This provides a large buffer of periplasm between the outer membrane and the peptidoglycan cell wall. The members of this class are rod-shaped and anaerobic, using protons or sulfur as electron acceptors to make H2 or H2S.

  • Fervidobacterium
  • Thermosipho
  • Thermotoga -
  • Mesotoga prima - EOL- (Notice the loose outer membrane.)
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CHLOROFLEXI (Green Non-Sulfur Bacteria) 

The class Chloroflexi is comprised of the Chloroflexaceae group, the Dehalococcoides group and the genus Thermoleophilum. The group as a whole has outward traits similar to the Green Sulfur Bacteria, but is not related.

Thermoleophilum is the most primitive genus in the class. Its species are thermophilic bacilli that can only grow on wax.

The Dehalococcoides group includes members which have cell walls similar to those of Archaea, but unlike Archaea, they do not live in extreme temperatures. Because of their cell wall they are resistant to antibiotics that have an effect on typical bacterial cell walls.

The Chloroflexaceae group is the largest of the class. Some members are filamentous while some are bacilli; some are thermophilic while some are not; and some can grow anaerobically using photosynthesis while some are purely aerobic.

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DEINOCOCCUS-THERMUSFOCUS SITE
YELLOWSTONE NATIONAL PARK

Deinococcus-Thermus is a phylum containing just two main genera: Thermus and Deinococcus.

The word Deinococcus means "cocci from the sky," refering to the habitat in which they are often found: cloud droplets and the resulting rain water. One species, D. radiodurans, is more than twenty times more resistant to gamma, X and UV radiation than typical bacteria. This makes sense since clouds at high altitudes are routinely subjected to high levels of radiation.

The genus Thermus includes T. aquaticus, the organism that has shown its usefulness in biotechnology. Since the enzymes in this thermophile are stable at high temperatures, they are able to perform the functions necessary for the Polymerase Chain Reaction (PCR). PCR is an efficient way to produce many copies of a desired DNA sequence, and involves a huge segment of the biotechnology industry.

An example is in crime forensics. If a small sample of something containing DNA is found at a crime scene, it must be turned into a larger sample to be useful. The method used to turn the small sample into a larger sample is PCR. The first step in PCR is to denature, or split apart, the double-stranded DNA so that copies can be made using the template each single strand provides. Then enzymes called DNA Polymerase bind to the templates and replicate, or copy, the DNA (DNA Polymerase is found in all organisms so theoretically it would not matter which organism contributed the enzyme to be used in PCR.). The process of replication is repeated over and over until there is enough DNA to be useful.

The process of denaturing the DNA must be done at a high temperature - usually 95 degrees celcius - to get the two strands of DNA to separate from each other. At this temperature, human DNA Polymerase would also be denatured and rendered useless (our DNA Polymerase has evolved to work at our body temperature of around 37 degrees celcius, not close to the boiling point). The same thing goes for the vast majority of organisms. If DNA Polymerase from humans or most other organisms were to be used it would have to be added after things had cooled down so it would function properly. That would be fine if the DNA just needed to be copied once. But usually it needs to be replicated many more times. Each time replication occurs, the first step is to denature the double-strand which means heating things back up to 95 degrees celcius. That means all the human DNA Polymerase would be rendered useless for round two since it would be destroyed in the reheating process. There would need to be a lot of human DNA Polymerase on hand to keep adding fresh samples each time you wanted to replicate the DNA. The heating/cooling cycle would also add significant time to the process. Wouldn't it be nice if there were a DNA Polymerase that could tolerate the temperature required to denature the DNA? That would reduce the amount of DNA Polymerase needed and speed things up.

Enter T. aquaticus. This thing lives under these high-temperature conditions all the time and it obviously can replicate its DNA. Its DNA Polymerase must have evolved to tolerate and function under these conditions. By using its DNA Polymerase the entire PCR process could occur at 95 degrees celcius without having to add more enzyme and without going through the time-consuming heating/cooling cycle. And that's exactly how it works today. Because of T. aquaticus, useful amounts of DNA can be produced for crime investigations and other purposes in just a few hours.

T. aquaticus was discovered at Yellowstone National Park, and inhabits the hot springs there today.

  • Thermus aquaticus -EOL- The cell structure seen under the electron microscope is similar to that of many bacteria that live at conventional temperatures. There is nothing that would tell us that this is a highly unusual bacterium.
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CHLAMYDIAE/VERRUCOMICROBIA GROUP 

The order Chlamydiales includes parasitic species which require a host for energy, amino acids, vitamins, and many other molecules. They even get ATP from their host. They can, however, make their own DNA, RNA, and proteins. Chlamydia is one genus of bacteria with no peptidoglycan cell wall. Since they live as parasites in the cytoplasm of other cells much of the time, there is no osmotic gradient, making supporting walls unnecessary. Even without cell walls, Chlamydia are sensitive to antibiotics that work on cell walls. The reason for this is not understood.

The species C. trachomatis causes chlamydia, the most common sexually transmitted disease in the United States. Chlamydia is common because often there are no symptoms and people go untreated.

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PLANCTOMYCETES 

The order Planctomycetales is most closely related to the Chlamydiales. Its members, like Chlamydiales, also lack peptidoglycan cell walls. They often form "rosettes" (Figure 17III-2: Planctomyces bekefi) and all have fimbrae and flagella (Figure 17III-3: the fimbrae are hairlike structures coming from the top.). They divide by budding and some even have nuclear envelopes (Figure 17III-4: Gemmata. The "N" is the nuclear envelope.). The four main genera are Planctomyces, Pirellula, Gemmata, and Isophaera. Isophaera is a genus that moves itself in liquid by adjusting its bouyancy with gas vacuoles (Figure 17III-5: Isophaera. The arrows point to gas vacuoles.).

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SPIROCHAETES 

The order Spirochaetales contains spiral-shaped organisms with modified flagella which are enclosed between the cell wall and outer membrane and join together, causing the organism to move by "corkscrewing." Other bacteria are spiral-shaped but their flagella are the more typical external type. Most Spirochaetes are common in the environment, anaerobic or microaerophilic, and grow only on sugars. Some cause disease, but most are harmless. The genera Treponema and Borrelia contain organisms which cause syphillis and Lyme disease respectively. Lyme disease was named after Lyme, Connecticut which is where the disease was first described. Lyme is still in the heart of the area of highest prevalence of the disease spread by deer ticks.

  • Borrelia burgdorferi - EOL- spiral-shaped bacterium that causes Lyme Disease, spread by ticks
  • Treponema pallidum - EOL- causes syphillis
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BACTEROIDETES/CHLOROBI GROUP 

Two groups of bacteria, the Bacteroidetes and Chlorobi, are closely related enough that they are combined into one group.

Bacteroidetes includes Cytophaga, Flavobacteria, Bacteroides and relatives. All are rod-shaped, varying from short to long, heterotrophic and move around by gliding. Cytophaga and relatives are abundant and known for the ability to degrade large molecules such as DNA, cellulose, protein, agar, etc. Flavobacteria can be found in most aerobic environments and are resistant to many antibiotics. Bacteroides are common in animal respiratory tracts, intestines and genital tracts. They rarely cause disease. B. thetaiotaomicron is more abundant than E. coli in the intestines of humans.

Chlorobi is composed of photosynthetic organisms that use hydrogen sulfide (H2S) instead of water for making NADPH and for fixing CO2. They are so efficient at photosynthesis that they only need about 25% of the light intensity that other organisms need to grow. Members of the genus Chlorobium cannot move on their own, but live in symbiotic relationships with other prokaryotes that are motile. The motile, heterotrophic bacteria are supplied with food produced by Chlorobium and in return Chlorobium is given a free ride. The cells can actually communicate, and the motile bacteria move around to find light for Chlorobium. They are common in the deep, stagnant parts of lakes like Fayetteville Green Lake in New York where the water doesn't mix completely and oxygen levels are close to non-existent.

  • Chlorobium limicola
  • Flexibacter - EOL
  • Pelodictyon clathratiforme
  • Prosthecochloris aestuarii
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OTHER GROUPS OF BACTERIA

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