Ch28_Bact&Arch%20to%20post[1] - Bacteria and Archaea...

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Unformatted text preview: Bacteria and Archaea Bacteria 27.1 Why Do Biologists Study Bacteria and Archaea? 27.2 How Do Biologists Study Bacteria and Archaea? 27.3 What Themes Occur in the Diversification of Bacteria and Archaea? 27.4 Key Lineages of Bacteria and Archaea Estimated that there are a total number of 5 X 10 30 individual Bacteria & Archaea Only a small percentage of bacteria cause disease. Many are useful – Many – effective at cleaning up pollution – photosynthetic bacteria were responsible for the evolution of the oxygen atmosphere – cycle nutrients through both terrestrial and aquatic environments. Bacteria and archaea live in a wide array Bacteria of habitats and use diverse types of molecules in cellular respiration and fermentation. Although they are small and relatively simple in their overall morphologies, these organisms are extremely sophisticated in the chemistry they can do. Many species are restricted in distribution and have a limited diet. 27.1 Why Do Biologists Study 27.1 Bacteria and Archaea? By studying Bacteria & Archaea morphology, DNA, and biochemistry scientists are only now beginning to understand these organisms (Microbiology). Bacterial Diseases Bacterial A small percentage of bacteria that inhabit the human body are pathogenic and cause disease. Late 1800s Robert Koch hypothesized -bacteria responsible for causing infectious disease. a. Tested hypothesis using anthrax b. Koch developed four postulates ; Microbe must be present in individuals suffering from the disease and absent in healthy individuals. (2) Organism must be isolated, grown in pure culture away from the host. (3) Injection of organisms from the pure culture into a healthy animal should cause the disease symptoms to appear. (4) The organism must then be isolated from the diseased animal, cultured again, and shown to be identical in size, shape, and color to the original organism. (1) c. Koch demonstrated that for anthrax, all four postulates c. were true. d. Koch’s postulates became the basis for the GERM Koch became GERM THEORY OF DISEASE Modern medicine was the first to study these organisms and to develop antibiotics. Do to extended use of antibiotics each of the antibiotics. Do species of pathogenic bacteria listed in table 27.1 has evolved a strain that is antibiotic resistant. Bioremediation Bioremediation Bioremediation: The use of bacteria and archaea to clean up human pollution 1. Most pollution is caused by organic solvents and fuels leaking into water supplies. 2. Sediments where these compounds accumulate can become ANOXIC—devoid of oxygen. ANOXIC a. b. Oxygen in these sediments is used up by decomposers. Once anoxic, the rate of decomposition decreases. 3. Biologists trying to clean up pollution -problems: a. The slow rate of decomposition presents a problem for biologists trying to clean up the polluted sediment. b. Some of the toxic compounds are resistant to decomposition. 4. Biologists are now trying to use bioremediation strategies that use bacteria and archaea to degrade such pollutants (seeding & fertilizing) Extremophiles Extremophiles 1. Extremophiles are bacteria that live in high-salt, high- or low-temperature, or high-pressure habitats. 2. Basic scientific curiosity seeks to understand how the enzymes of these species can function under such conditions. 3. Practical questions of interest to industry drive the study of these organisms. Global Change Global 1. a. b. c. The Oxygen Revolution - cyanobacteria are thought to Oxygen are have given Earth its oxygen atmosphere. Climatologists believe no free O2 existed in atmosphere for 2.5 b y existed Cyanobacteria, photosynthetic bacteria, first organisms to perform oxygenic photosynthesis. Once O2 was abundant in the oceans, cells could use it as an was electron acceptor. Plant growth is often limited by the availability of nitrogen. Plants can’t use atmospheric N2. Only some bacteria and Archaea are capable of this. Nitrates as a pollutant results from the application and runoff of ammonia. The increase in ammonia levels in aquatic zones leads to algal blooms; leading to death of algae when food is depleted; followed by increase of decomposing Bacteria and Archaea; anoxic conditions follow and dead zones appear. (e.g. Gulf of Mexico) Nitrogen fixation a. b. Nitrate Pollution Nitrate The “dead-zone” in the Gulf of Mexico, a zone believed to have resulted from nitrate runoff from fertilizers, is ~ 18,000 km2. Nothing lives in this zone. 27.2 How Do Biologists Study Bacteria and 27.2 Archaea? 1. As model systems- Escherichia coli (E. coli) used for decades Escherichia 2. Enrichment Cultures 3. Direct sequencing 4. Evaluating Phylogenies Enrichment Cultures Enrichment Enrichment cultures involve establishing a specific set of living conditions (temperature, lighting, substrate, types of food available, etc.) Cells that thrive under specific conditions will increase and are isolated and studied in detail. These cells are thermophilesgrowing only when heated to between 45° C (113 º F) and 75 º C ( 167º F). Using Direct Sequencing Using Direct sequencing allows biologists to name and characterize organisms that have never been seen and cannot be grown in culture for study in the laboratory. How is a direct sequencing experiment performed? a. Obtain a small sample of a habitat, and isolate the bacteria and archaeal cells from the sample. b. Lyse open the cells and purify the DNA. c. Sequence specific genes and compare to existing databases. d. Use comparative data to determine if any “new” species are in the sample. Direct sequencing has changed the way we think about archaea. Direct a. Scientists once classified prokaryotes into four basic groups: (1) Extreme halophiles; salt-lovers Extreme (2) Sulfate-reducers that produce hydrogen sulfide as a Sulfate that by-product (3) Methanogens that produce methane as a by-product Methanogens that (4) Extreme thermophiles that grow best at high Extreme that temperatures However, direct sequencing experiments demonstrated that archaeal habitats are even more diverse than originally thought (species found from rice paddies to the Artic Ocean). (1) A new lineage, Korarchaeota, was identified. Korarchaeota (2) This group may be diverse enough to constitute a new kingdom. b. Evaluating Molecular Phylogenies Evaluating 1. Recall that phylogenetic trees are diagrams that illustrate the evolutionary relationships between species. 1960s data from small subunit of rRNA -evolutionary relationships of a diverse group of organisms. a. Tree of life. b. Prior to this analysis 2 major groups Prokaryotes and Eukaryotes-subdivided prokaryotes into two new domains; Bacteria and Archaea. c. Bacteria first lineage to diverge, implying that Archaea and Eukaryotes are more closely related than they are to bacteria. d. Additional analysis has identified several monophyletic groups (a group that includes the monophyletic ancestral population and all of its descendants) within each of these domains. 2. 27.3 What Themes Occur in the Diversification of 27.3 Bacteria and Archaea? I. II. III. Morphological Diversity Metabolic Diversity Cellular Respiration: Variation in Electron Donors and Acceptors Fermentation Photosynthesis Pathways for Fixing Carbon IV. V. VI. Morphological Diversity Morphological Morphological Diversity (Although both Archaea & Bacteria are (Although unicellular, at the molecular level they are quite different.) 1. What do all bacteria and archaea have in common? a. Unicellular b. Lack membrane-bound organelles c. Divide via binary fission 2. How are bacteria and archaea different? a. Different cell membranes and cell-wall components (1) Bacteria have peptidoglycan in their cell walls. (2) Archaea have unique phospholipids with isoprenes in their tails b. Different systems for transcription & translation. (1) Bacteria have unique RNA polymerases (2) Archaeal ribosomes more like eukaryotic ribosomes than bacterial c. Bacterial cells have plasmids (extrachromosomal DNA) that can be transferred between individuals via conjugation. 3. How are different types of bacteria different from one another? a. Bacteria come in many different sizes. (1) Mycoplasmas -smallest bacteria (0.03 μm3). (2) Thiomargarita namibiensis -largest bacteria (200,000,000 μm3). Bacteria come shapes- filaments, rods, spheres, chains, and spirals. Many bacteria motile. Bacteria have cell walls with different morphologies. (1) Gram-positive bacteria - cell wall has abundant Gram peptidoglycan. (2) Gram-negative bacteria -cell wall thin Gram gelatinous has peptidoglycan surrounded by a phospholipid bilayer. (3) distinguished by a Gram stain that reacts with the peptidoglycan. (a) Gram-positive bacteria stain purple. (b) Gram-negative stains pink. b. c. d. Metabolic Diversity Metabolic Where do bacteria & archaea get energy to make ATP, & where do they get carbon to build macromolecules? 1. Varying energy and carbon sources - bacteria and archaea occupy almost any habitat on Earth. a. Phototrophs use the energy in light . b. Organotrophs use highly reduced organic molecules c. Lithotrophs oxidize inorganic ions d. Carbon obtained through carbon dioxide or methane. 2. Cellular respiration: variation in electron donors & electron acceptors. a. Cellular respiration- process by which energy transferred via redox reaction through a series of enzymatic steps & electron carriers, to an electron acceptor while energy is harnessed to make ATP. b. Nature of fuel molecule and nature of final electron acceptor vary in bacterial species. c. Importance of the metabolic diversity of bacteria 1) Occupy almost all possible habitats since, collectively, they can use so many types of food sources. 2) Crucial inorganic nutrients are recycled because of bacteria and archaea. Fermentation Fermentation a. Fermentation is a strategy for making ATP from reduced organic compounds without involving electron transport chainsb. Fermentation uses no outside electron acceptor; it often occurs as an alternative pathway when no electron acceptors are available. c. Fermentation is a less efficient way than respiration to make ATP. d. Some bacteria ferment glucose to either ethanol or lactic acid. e. Other bacteria use various other reduced organic compounds as fermentable substrates: Photosynthesis Photosynthesis 4. Photosynthesis a. Phototrophs use the kinetic energy of light to raise electrons to a high energy state. b. Photosynthesis requires a source of electrons. (1) Cyanobacteria and plants—water is the electron source; O2 is released as a by-product. (2) Other anaerobic bacteria use different electron donors and produce other by-products (e.g. H2Selemental sulfur by-product or Fe2+ to Fe3+ Some phototrophic bacteria, other than cyanobacteria, use different types of chlorophyll: a. Seven different bacteriochlorophylls have been identified, each with a unique absorption spectrum. Coexisting- Increased diversity 5. Pathways for Fixing Carbon Pathways a. Cyanobacteria make their own organic building-block molecules (molecules with at least one carbon-carbon bond) by fixing CO2 (plants do as well). Some bacteria and archaea fix carbon from non-CO2 sources: (1) Methanotrophs use CH4 as their primary electron donor and carbon source. (2) Other bacteria utilize carbon monoxide (CO) or methanol (CH3OH) as carbon sources. (3) Some bacteria fix carbon using pathways other than the Calvin cycle. Different mechanisms for fixing carbon have arisen in prokaryotes in response to the need for a carbon source in a given habitat. Remember many of these organisms are extremophiles. b. c. 27.4 Key Lineages of Bacteria and Archaea 27.4 - Bacteria Spirochaeles (Spirochetes) a. Morphological diversity (1) Corkscrew shape (2) Flagella housed in an outer sheath, causing the entire cell to lash back and forth and propelling it forward. b. Metabolic diversity (1) Most make ATP via fermentation. (2) Species in termite gut can fix nitrogen. c. Human and ecological impact (1) Syphilis is caused by a spirochete. (2) Lyme disease is caused by a spirochete. (3) Live in freshwater and marine habitats; some in anaerobic conditions Chlamydiales Chlamydiales a. b. Morphological diversity—spherical and very small Metabolic diversity (1) All species are endosymbionts and live in hosts. (2) They contain few enzymes, get all nutrients from host. Human and ecological impact (1) Chlamydia trachomatis infections cause blindness in humans. 2) Can also cause urogenital infections if passed via intercourse. c. High-GC Gram Positives High a. Morphological diversity (1) Cell walls have a lot of peptidoglycan. (2) DNA has a high guanine and cytosine content. (3) Cells have rod or filament shapes. (4) Soil-dwellers have branched filaments (mycelia). Metabolic diversity (1) Many are heterotrophs - use organic compounds and oxygen for cellular respiration. (2) Some are parasitic. Human and ecological impact (1) Antibiotics have been isolated from Streptomyces. (2) Tuberculosis and leprosy from this group. (3) One species is important for making Swiss cheese. (4) Species in this group live in plant roots and fix nitrogen. b. c. Cyanobacteria Cyanobacteria a. Morphological diversity (1) Cells can be solitary or colonial. (2) Colonies can form flat sheets to balls. Metabolic diversity (1) All perform oxygenic photosynthesis. (2) Some can fix nitrogen. Human and ecological impact (1) Produce much of the oxygen and nitrogen that other species need. (2) A few species live with fungi, forming lichens. b. c. Low-GC Gram Positives Low a. Morphological diversity (1) Gram-positive- have low GC-content in their DNA (2) Most are rod-shaped or spherical. (3) Can form chains or tetrads and can form spores Metabolic diversity (1) Some can fix nitrogen. (2) Some perform nonoxygenic photosynthesis. (3) Some perform fermentation to make ATP; Others perform cellular respiration using hydrogen gas. Human and ecological impact (1) Low-GC Gram-positive species cause anthrax, botulism, tetanus walking pneumonia, gangrene, strep throat, etc. (2) Lactobacillus is used to ferment milk to make yogurt or cheese. b. c. Proteobacteria Proteobacteria a. Morphological diversity (1) Rods, spheres, or spirals; some form stalks. (2) Some are motile. (3) Some can aggregate to form fruiting bodies. Metabolic diversity (1) Live in almost any habitat. (2) Oxygenic photosynthesis rare; some perform nonoxygenic photosynthesis. (3) Most perform cellular respiration using a variety of electron donors and acceptors. Human and ecological impact (1) Pathogenic proteobacteria cause Legionnaire’s disease, cholera, food poisoning, dysentery, ulcers, and diarrhea. Some are used to make vinegar. Rhizobium live in root nodules and fix nitrogen. b. c. (2) (3) Archaea Archaea Crenarchaeota Crenarchaeota a. b. Morphological diversity; Cells may be shaped like rods, discs, or spheres. Metabolic diversity (1) Some species make ATP via cellular respiration with a variety of electron donors and acceptors. (2) Some species make ATP via fermentation. Euryarchaeota Euryarchaeota a. Morphological diversity (1) Can be spherical, rod-shaped, or disc-shaped, and can aggregate in chains or balls. (2) Some species have flagella. Metabolic diversity (1) Many species produce methane. (2) Some species that live in high-salt environments use retinal to capture light energy and perform photosynthesis. Human and ecological impact (1) Ferroplamas live in piles of waste rocks near abandoned mines and produce acids that pollute nearby streams. (2) Methanogens live in mammal gut. b. c. ...
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