Chapter 28 - Bacteria and Archaea

Transcription

1 Chapter 28 - Bacteria and Archaea Learning Objectives: Students should be able to... Defend the statement that bacteria and archaea are the most important, diverse, and abundant organisms on the planet. Explain the six "feeding strategies" that bacteria and archaea use to produce ATP and obtain carbon building blocks. Give several examples of the importance of bacteria in human health, in bioremediation, and in ecosystems. Lecture Outline Bacteria, Archaea, and Eukarya are the three largest branches on the tree of life. (Fig. 28.1) Bacteria and archaea may look similar at first glance, but they are very different. (Table 28.1) o Similarities: All bacteria and archaea are prokaryotic and unicellular. o Fundament al differences: Bacteria have cell walls made of peptidoglycan. Archaea have unique phospholipids in the cell membranes. Bacteria and archaea have different ribosome and RNA polymerase structures. Archaea are more closely related to Eukarya than to Bacteria. I. Why Do Biologists Study Bacteria and Archaea? A. Biological impact 1. Bacteria and archaea are amazingly abundant. a. Most cells in the human body are actually bacteria and archaea (living on the skin and in the gut). b. The Group I marine archaea are so abundant that a teaspoon of seawater contains a population equivalent to that of a large human city. c. If lined up end to end, all the bacteria and archaea alive today would make a chain longer than the Milky Way galaxy. 2. They are found in every possible environment. 3. They are very diverse, and we are still discovering entire new phyla. B. Medical importance 1. Some bacteria are pathogenic, meaning that they cause disease. (Table 28.2) 2. Koch's postulates: Koch proposed that four criteria had to be met to prove that a specific microbe causes a certain disease. a. The microbe must be present in individuals suffering from the disease and absent in healthy individuals. b. The microbe must be isolated and grown in pure culture.

2 c. Injection of the microbe (from the pure culture) into a healthy animal should cause the disease symptoms to appear. d. The microbe should be isolatable again from the diseased animal and shown to be identical in size, shape, and color to the original microbe. e. Koch demonstrated that all four postulates were true for anthrax. 3. The germ theory of disease a. The germ theory is based on Koch s postulates. b. The germ theory states that infectious diseases are caused by microbes (microscopic organisms). c. The germ theory's immediate impact was in improving sanitation, greatly reducing mortality due to infectious disease. (Fig. 28.2) 4. What makes some bacterial cells pathogenic? a. Virulence, or the ability to cause disease, is a heritable trait that varies among individuals in a population. b. Current research is identifying the genes responsible for virulence in a wide variety of bacteria. 5. Antibiotics are molecules that kill bacteria. a. Since their development in the late 1920s, antibiotics have been very useful in combating infectious disease. b. Unfortunately, many pathogens are evolving resistance to antibiotics. C. Role in bioremediation 1. Some of the most serious pollutants are hydrophobic compounds that accumulate in sediment and in the bodies of living organisms. 2. Bioremediation strategies use bacteria to break down these compounds. a. Fertilization of contaminated sites encourages the growth of whatever existing bacteria are already on site. These bacteria often degrade the toxic compounds. (Fig. 28.3) b. Seeding adds specific bacteria that are known to use that pollutant as a food source, producing a nontoxic by-product. D. Extremophiles 1. Extremophiles are bacteria that live in unusual environments. a. For example, there are bacteria that live at 121 C, at a ph less than 1.0, in seawater deeper than 2500 m, and in salt-saturated seawater with no oxygen. 2. Studying extremophiles may help us understand the origin of life, since life probably evolved in a high-temperature, anoxic environment. 3. Astrobiologists use extremophiles as model organisms in the search for extraterrestrial life. 4. Extremophiles are useful in certain commercial and research applications. a. For example, the heat-tolerant enzyme that is necessary for PCR (the DNA-copying technique fundamental to most genetic research)

3 is from an extremophile found in hot springs in Yellowstone National Park. II. How Do Biologists Study Bacteria and Archaea? A. Using enrichment cultures 1. Enrichment cultures provide a specific set of living conditions (food, temperature, etc.) and can grow large populations of certain bacteria and archaea. 2. Most bacteria and archaea species were discovered when they were grown in a culture in a lab. 3. Example: discovering bacteria from the depths of Earth. (Fig. 28.4) a. Samples were taken from meters below Earth s surface, where temperatures reach 85ºC. b. Scientists hypothesized that if anything were living down there, it would produce magnetite as a by-product of cellular respiration. c. Magnetite did appear in cultures, and microscopy confirmed the presence of previously unidentified thermophiles (bacteria that grow at only high temperatures). 4. Students should be able to design an enrichment culture that will isolate species that can be used to clean up oil spills. B. Using direct sequencing 1. Direct sequencing allows biologists to name and characterize organisms that have never been seen. 2. DNA is sequenced directly from a small sample from a habitat (soil, water, etc.). The DNA sequences are then compared to known sequences to determine whether any previously undiscovered species exist in the sample. (Fig. 28.5) 3. Direct sequencing has changed the way we think about archaea. a. Entire new lineages were discovered, showing that archaea cannot be classified into the four simple categories that had previously been used. 4. Students should be able to design a study to identify the bacterial and archaeal species present in a soil sample near the biology building on your campus. C. Evaluating molecular phylogenies (Fig. 28.6) 1. Ribosomal RNA sequences have shown that the tree of life has three major lineages: Bacteria, Archaea, and Eukarya. a. Archaea are more closely related to Eukarya than to Bacteria. 2. Further analysis has identified several monophyletic groups within each of these domains. III. What Themes Occur in the Diversification of Bacteria and Archaea? A. Morphological diversity 1. Size, shape, and motility (Fig. 28.7) a. Bacteria vary greatly in size. For example, more than a billion of the smallest bacterium could fit inside the largest bacterium. b. Bacteria may be filaments, spheres, rods, chains, or spirals. c. Many bacteria can swim or glide. 2. Cell wall composition and the Gram stain (Fig. 28.8)

4 a. Gram-positive bacteria have a cell wall with abundant peptidoglycan, which stains dark purple when exposed to a Gram stain. b. Gram-negative bacteria have a cell wall with a thin layer of peptidoglycan surrounded by a phospholipid bilayer. They stain light pink. c. Gram stain analysis can predict sensitivity to certain drugs. (1) Gram-positive bacteria are often sensitive to penicillin-like drugs that disrupt peptidoglycan synthesis. (2) Gram-negative bacteria are more likely to be affected by drugs that target bacterial ribosomes. B. Metabolic diversity 1. Bacteria and archaea are astonishingly diverse in the ways they acquire energy to make ATP and the carbon compounds they can use as building blocks. 2. There are three ways to acquire energy to produce ATP: (Table 28.3) a. Phototrophs use light energy to energize electrons, producing ATP by photophosphorylation (light reactions of photosynthesis). b. Chemoorganotrophs oxidize organic molecules with high potential energy, such as sugars (cellular respiration, fermentation). c. Chemolithotrophs oxidize inorganic molecules with high potential energy, such as ammonia or methane (usually via cellular respiration). 3. There are two ways to acquire carbon: (Table 28.3) a. Autotrophs use carbon dioxide or methane to build their own carbon-containing compounds. Example: Calvin cycle. b. Heterotrophs acquire carbon-containing compounds from other organisms. 4. Overall, there are six major "feeding strategies" (the six possible combinations of three methods of acquiring energy and two methods of acquiring carbon). a. Plants, animals, fungi, and other eukaryotes use only two strategies. b. Bacteria and archaea use all six. (Table 28.4) c. Students should be able to match the six example species described in Table 28.3 to the appropriate categories in Table Producing ATP via cellular respiration: variation in electron donors and acceptors a. In cellular respiration, electrons are moved from molecules with high potential energy and gradually "stepped down" to a molecule with low potential energy, using the released energy to make ATP. (Fig. 28.9) b. Eukaryotes are chemoorganotrophs that use a sugar like glucose as the electron donor and oxygen as the final electron acceptor.

5 c. Many bacteria and archaea are chemolithotrophs that use an electron donor that is not a sugar and often an electron acceptor that is not oxygen. (Table 28.5) (1) The electron donor may be hydrogen molecules, hydrogen sulfide, ammonia, or methane. (2) The electron acceptor may be sulfate, nitrate, carbon dioxide, or ferric ions. 6. Producing ATP via fermentation: variation in substrates a. Fermentation is a strategy for making ATP from organic molecules that requires a separate electron acceptor. b. Fermentation is less efficient than respiration in making ATP. c. Some bacteria ferment glucose to either ethanol or lactic acid. d. Other bacteria use a variety of other organic compounds as fermentable substrates. Examples: ethanol, fatty acids, complex carbohydrates, proteins, amino acids, lactose. 7. Producing ATP via photosynthesis: variation in electron sources and pigments a. There are three forms of photosynthesis: (1) Light activates a pigment that transports protons across a membrane, driving the synthesis of ATP via chemiosmosis. (2) Geothermal radiation can be used instead of light. (3) Light can be absorbed by pigments that raise electrons to highenergy states. The electrons are stepped down with electron transport chains, and the energy released is used to make ATP. b. The form of photosynthesis that uses electron transport chains requires a source of electrons. (1) Plants and cyanobacteria use oxygenic photosynthesis. This means they use water as the source of electrons and produce oxygen as a by-product. (2) Many bacteria use anoxygenic photosynthesis, using a molecule other than water as the source of electrons. Examples: hydrogen sulfide, ferrous iron. (They also produce by-products other than oxygen.) 8. Obtaining building-block compounds: variation in pathways for fixing carbon a. Autotrophs can build their own carbon compounds. (1) Plants (and cyanobacteria) fix CO 2 with the enzymes of the Calvin cycle. (2) Some bacteria also fix CO 2 but use different enzymatic pathways to do so that is, not the Calvin cycle. (3) Some bacteria use a molecule other than CO 2 as the starting point. Examples: methane, carbon monoxide, methanol. b. Heterotrophs obtain organic compounds from other organisms. (1) Animals, fungi, and many bacteria and archaea use this strategy.

6 9. Students should be able to defend the claim that, in terms of metabolism, bacteria and archaea are much more sophisticated than eukaryotes. C. Ecological diversity and global change 1. Bacteria and archaea have altered the chemical composition of the oceans, the atmosphere, and terrestrial environments for billions of years. 2. The oxygen revolution a. No free O 2 existed in Earth's atmosphere for 2.3 billion years. b. Cyanobacteria were the first organisms to perform oxygenic photosynthesis, and they are responsible for the appearance of oxygen in Earth's atmosphere. (Fig ) (1) The fossil record shows that cyanobacteria first became numerous in oceans billion years ago. (2) Oxygen concentrations began to increase billion years ago. c. Once O 2 was abundant, other organisms could use it as an electron acceptor. The evolution of aerobic respiration was a crucial event in the history of life. (Fig ) 3. Nitrogen fixation and the nitrogen cycle (Fig ) a. Plant growth is often limited by the availability of nitrogen, but plants cannot use molecular nitrogen (N 2 ) from the atmosphere. (1) Some bacteria absorb N 2 from the atmosphere and fix or reduce it to NH 3, ammonia, a form that plants can use. (2) Other bacteria and archaea convert ammonia to nitrates and nitrites, resulting in a complex nitrogen cycle. (Fig ) 4. Nitrate pollution a. Most farmers use synthetic fertilizers, which often contain ammonia, to add nitrogen to soils and increase crop yields. b. Bacteria convert the ammonia in fertilizer runoff into nitrates. c. This has led to worldwide pollution of aquatic ecosystems with excessive nitrates, which causes overgrowth of algae and results in anoxic "dead zones." (Fig ) IV. Key Lineages of Bacteria and Archaea A. Bacteria. At least 16 major phyla now known; 6 are featured here. 1. Firmicutes: low-gc Gram-positives (Fig ) a. Traits: Most are rod shaped or spherical. b. Human and ecological impact: They are very common in the human gut. Some cause anthrax, botulism, tetanus, gangrene, strep throat, and other diseases. Lactobacillus is used to ferment milk to make yogurt or cheese. 2. Spirochaetes (spirochetes) (Fig ) a. This lineage branches near the base of the bacterial phylogenetic tree. b. Traits: They have a unique corkscrew shape, with flagella housed in a sheath. Most make ATP via fermentation.

7 c. Human and ecological impact: They cause syphilis and Lyme disease. Many live in freshwater and marine habitats, some in anaerobic conditions. 3. Actinobacteria: high-gc Gram-positives (Fig ) a. Traits: They form rods, filaments, and sometimes mycelia. Many are heterotrophs. Some are parasitic. b. Human and ecological impact: They cause tuberculosis and leprosy. Many antibiotics have been isolated from Streptomyces. One species is important for making Swiss cheese. Species in this group live in plant roots and fix nitrogen. 4. Chlamydiae (Fig ) a. Traits: They are spherical and tiny. All are endosymbionts and live in hosts. b. Human and ecological impact: Chlamydia trachomatis infections cause blindness and urogenital tract infections in humans. 5. Cyanobacteria ("blue-green algae") (Fig ) a. Traits: They are highly diverse in morphology. Some form colonies. All perform oxygenic photosynthesis, and some can fix nitrogen. b. Human and ecological impact: They produce much of the oxygen and nitrogen that other species need. A few species live with fungi, forming lichens. 6. Proteobacteria (Fig ) a. This very diverse lineage is divided into five subgroups designated by the Greek letters α, β, γ, δ, and ε. b. Traits: Their morphology is very diverse. They use every metabolic strategy except oxygenic photosynthesis. c. Human and ecological impact: They cause Legionnaire s disease, cholera, food poisoning, dysentery, ulcers, diarrhea, and other diseases. Rhizobium live in the root nodules of legumes and fix nitrogen. Escherichia coli, the best-studied bacterium, is in this group. B. Archaea. At least three major phyla are known. 1. Crenarchaeota, are perhaps the oldest lineage of archaeans. (Fig ) a. Traits: They have highly diverse morphology and metabolism. b. Human and ecological impacts: Some are extremophiles and may be the only life-form present in certain environments, such as extremely acid ph and extremely deep sea. 2. Euryarchaeota (Fig ) a. Traits: They have highly diverse morphology and metabolism. Many species produce methane (methanogens). They are found in every conceivable habitat. b. Human and ecological impact: Ferroplasma live in piles of waste rocks near abandoned mines and produce acids that pollute nearby streams. Methanogens live in the mammalian gut.

8 3. Korarcheaota were recently discovered through direct sequencing. Almost nothing is known about them, and they have never been grown in culture. Chapter Vocabulary To emphasize the functional meanings of these terms, the list is organized by topic rather than by first occurrence in the chapter. It includes terms that may have been introduced in earlier chapters but are important to the current chapter as well. It also includes terms other than those highlighted in bold type in the chapter text. Bacteria Archaea unicellular prokaryotic microbe microbiology universal tree tree of life monophyletic group kingdom phylum (plural: phyla) germ theory of disease pathogen Koch s postulates antibiotic bioremediation seeding anoxic enrichment culture direct sequencing Gram-positive bacteria Gram-negative bacteria Gram stain cell wall peptidoglycan phototroph chemoorganotrophs chemolithotroph autotroph heterotroph cellular respiration aerobic respiration anaerobic respiration electron donor electron acceptor fermentation photosynthesis oxygenic photosynthesis anoxygenic photosynthesis Calvin cycle methanotroph nitrogen cycle nitrogen fixation nitrate pollution dead zone Firmicutes/low-GC Gram-positives spore Spirochaetes Spirochetes Actinobacteria/high- GC Gram-positives mycelium (plural: mycelia) Chlamydiae endosymbiont Cyanobacteria Proteobacteria Crenarchaeota Euryarchaeota Korarcheaeota halophile sulfate reducer methanogen thermophile extremophile