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Bacteria and Archaea: The Prokaryotic Domains

The three domains of life:Bacteria?prokaryotes Archaea?prokaryotes Eukarya?eukaryotes . Members of all the domains:Conduct glycolysisReplicate DNA conservativelyHave DNA that encodes peptidesProduce proteins using the same genetic codeHave plasma membranes and ribosomes. Prokaryotic cells di

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Bacteria and Archaea: The Prokaryotic Domains

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    1. Bacteria and Archaea: The Prokaryotic Domains

    2. The three domains of life: Bacteria—prokaryotes Archaea—prokaryotes Eukarya—eukaryotes

    3. Members of all the domains: Conduct glycolysis Replicate DNA conservatively Have DNA that encodes peptides Produce proteins using the same genetic code Have plasma membranes and ribosomes

    4. Genetic studies clearly indicate that all three domains had a single common ancestor.

    5. Among the bacteria, three shapes are common: Sphere—coccus (plural cocci), occur singly or in plates, blocks, or clusters Rod—bacillus (plural bacilli) Spiral or helical—helix (plural helices) Rods and helical shapes may form chains or clusters

    6. All three domains are the result of billions of years of evolution. None is “primitive.” The earliest prokaryote fossils date back at least 3.5 billion years.

    7. Nearly all prokaryotes are unicellular. In chains or clusters, each individual cell is fully viable and independent. This happens when cells adhere to each other after binary fission. Chains are called filaments. Prokaryotes usually live in communities of different species, including microscopic eukaryotes. Many microbial communities form biofilms. When cells contact a solid surface they excrete a gel-like polysaccharide matrix that traps other cells.

    8. It is difficult to kill cells in a biofilm (e.g., the film may be impenetrable to antibiotics). Biofilms form in many places: Contact lenses, artificial joint replacements, dental plaque, water pipes, etc. Fossil stromatolites are layers of biofilm and calcium carbonate.

    9. Most prokaryotes have a thick cell wall that contains peptidoglycan, a polymer of amino sugars. Archaea do not have peptidoglycan, although some have a similar molecule called pseudopeptidoglycan.

    10. Some prokaryotes are motile. Some have gliding and rolling mechanisms. Some cyanobacteria can move up and down in the water by adjusting the amount of gas in gas vesicles.

    11. Prokaryotes communicate with chemical signals. Quorum sensing: Bacteria can monitor the size of the population by sensing the amount of chemical signal present. When numbers are large enough, activities such as biofilm formation can begin. Some bacteria emit light by bioluminescence.

    12. Prokaryotes utilize a diversity of metabolic pathways.

    13. Prokaryotes are represented in all four categories of nutrition. Photoautotrophs perform photosynthesis. Cyanobacteria

    14. Chemolithotrophs (chemoautotrophs) get energy by oxidizing inorganic compounds, and use the energy to fix CO2. Some oxidize ammonia or nitrite ions to form nitrate ions; others oxidize H2, H2S, S, and others. Many archaea are chemolithotrophs.

    15. Some bacteria use inorganic ions:nitrate, nitrite, or sulfate as electron acceptors in respiratory electron transport. Denitrifiers use NO3– as an electron acceptor in anaerobic conditions, and release nitrogen to the atmosphere as N2; species of Bacillus and Pseudomonas.

    16. Nitrifiers are chemolithotrophic bacteria that oxidize ammonia to nitrate. Nitrosomonas and Nitrosococcus convert ammonia to nitrite. Nitrobacter converts nitrite to nitrate.

    17. Over 12 clades of bacteria have been proposed under a currently accepted classification scheme. We will focus on six clades.

    18. Spirochetes Gram-negative Motile Chemoheterotrophic Unique axial filaments (modified flagella) that rotate Many are human parasites, some are pathogens (syphilis, Lyme disease), others are free living.

    19. Chlamydias Extremely small, Gram-negative cocci, live only as parasites in cells of other organisms Can take up ATP from host cell with translocase Complex life cycle with two forms—elementary bodies and reticulate bodies Some are pathogens, causing trachoma, sexually transmitted diseases, and some forms of pneumonia

    20. High-GC Gram-positives (actinobacteria) High G-C/A-T ratio in DNA Form elaborately branching filaments Some reproduce by forming chains of spores at the tips of the filaments Most antibiotics are from this group, also includes Mycobacterium tuberculosis

    21. Cyanobacteria Photoautotrophs with chlorophyll a; many species fix nitrogen Contain an internal membrane system—photosynthetic lamellae Eukaryote chloroplasts are derived from endosymbiotic cyanobacteria

    22. Low-GC Gram-positives Low G-C/A-T, but some are Gram-negative; some have no cell wall Some produce endospores—heat-resistant resting structures with tough cell wall and spore coat that can survive harsh conditions because it is dormant Endospores become active and divide when conditions improve

    23. Closteridium and Bacillus form endospores. C. botulinum toxins are some of most poisonous ever discovered Bacillus anthracis (anthrax) endospores germinate when they sense presence of macrophages B. anthracis has also been used as a bioterrorism agent

    24. Mycoplasmas have no cell wall, are extremely small, and have very small genome They have less than half as much DNA as other prokaryotes, which may represent the minimum amount of DNA needed for a living cell

    25. Proteobacteria Largest group of bacteria—high diversity of metabolic phenotypes Common ancestor was photoautotrophic Includes some nitrogen-fixing genera such as Rhizobium E. coli is a proteobacterium

    27. The separation of Archaea was originally based on rRNA gene sequencing. It was supported by sequencing an entire genome—more than half the genes were unlike any in the other two domains.

    28. Archaea are divided into two main groups, Euryarcheota and Crenarcheota, and two recently discovered groups, Korarchaeota and Nanoarchaeota. All archaea lack peptidoglycan in the cell walls, and have distinct lipids in the cell membranes.

    29. The ether linkages are a synapomorphy of archaea. The long-chain hydrocarbons in Archaea are unbranched. One class of these lipids has glycerol at both ends, and forms a lipid monolayer. Lipid bilayers and lipid monolayers are both found in the archaea.

    30. CRENARCHEOTA are both thermophilic and acidophilic (acid loving). Sulfolobus lives in hot sulfur springs (70–75°C, pH 2 to 3). They can still maintain an internal pH of 5.5 to 7.

    31. Extreme halophiles (salt lovers) have pink carotenoid pigments, making them easy to see. Found at pH up to 11.5; live in the most salty, most alkaline environments on Earth.

    32. Prokaryotes are a part of all ecosystems. Only a small minority are human pathogens Many prokaryotes are decomposers Plants depend on prokaryotes for their nutrition Prokaryotes are crucial in the global cycling of elements such as nitrogen and sulfur. Many prokaryotes live in and on other organisms. Animals harbor a variety of prokaryotes in their digestive tracts.

    33. Bacteria in the human large intestine produce vitamins B12 and K. The biofilm that lines human intestines facilitates uptake of nutrients, and induces immunity to the gut contents. Thousands of bacteria also live on human skin, and are critical in maintaining skin health.

    34. Koch’s postulates: The microorganism is always found in persons with the disease It can be taken from the host and grown in pure culture A sample of the culture causes the disease in a new host The new host also yields a pure culture

    35. For an organism to become a pathogen it must: Arrive at the body surface of a host Enter the host’s body Evade the host’s defenses Multiply inside the host Infect a new host

    36. Consequences of bacterial infection depend on: Invasiveness of the pathogen—its ability to multiply in the host. Toxigenicity of the pathogen—its ability to produce toxins.

    37. Two types of bacterial toxins: Endotoxins are released when certain Gram-negative bacteria are lysed. They are lipopolysaccharides from the outer membrane. Endotoxins are rarely fatal. Some producers are Salmonella and Escherichia

    38. Viruses are not cellular, and some biologists do not consider them to be living organisms. However: They are derived from the cells of other living organisms They have DNA and RNA Viruses infect all cellular forms of life Viral genomes are tiny, which restricts the phylogenetic analyses that can be done Rapid mutational rate and rapid evolution clouds evolutionary relationships There are no known viral fossils

    39. They replicate, mutate, evolve, and interact with other organisms They are numerically among the most abundant organisms on the planet Viruses clearly evolve independently of other organisms

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