Prokaryotes: Eubacteria and Archaea PDF

2.1 The Prokaryotes: Eubacteria and Archaea Organisms in Domain Eubacteria (commonly called bacteria) and Domain Archaea are prokaryotes. They are single-...

2.1 The Prokaryotes: Eubacteria and Archaea Organisms in Domain Eubacteria (commonly called bacteria) and Domain Archaea are prokaryotes. They are single-celled organisms, and they lack membrane-bound organelles. Prokaryotes are the smallest organisms on Earth (Figure 1) and some of the most important. Most prokaryote species are only 1 µm to 2 µm long—500 to 1000 of them would fit side by side across the dot of this letter “i.” a. b. c. LEARNiNg TIP Micrometres (µm) A micrometre, also known as a micron, is indicated by the symbol µm. It is a unit of length equal to one millionth of a metre. (a) (b) (c) m m. m Figure 1 Bacillus bacteria on the point of a pin. The images are magnified (a) 70, (b) 350, and (c) 14 000. Despite their small size, prokaryotes are dominant forms of life that live in every imaginable habitat. They live inside and on the surface of other organisms, in water and soil, deep within Earth, in boiling hot springs (Figure 2), and even in ice. For example, more than 100 trillion bacteria live on and within your body. These bacteria outnumber all the other cells in your body! In fact, prokaryotes vastly outnumber all living things on Earth. Their total mass exceeds that of animals and possibly all plant life on Earth. Everything we know so far about prokaryotes is based on a tiny fraction of the total number of species. Only about 10 000 prokaryote species have been isolated and identified, and this may represent as little as 1 % of the total number of species. Why have we identified so few species, and why are we not even sure how many prokary- Figure 2 Many prokaryotes inhabit extreme environments. Some species otes there might be? In order to identify and study prokaryotes, scientists must first live in the high temperatures found in find and collect live specimens, then grow them in the laboratory. Unfortunately this boiling hot springs. is extremely difficult, partly because many prokaryotes live in remote locations and in extreme conditions. why Prokaryotes Are Important Prokaryotes are extremely important organisms in many ways. Bacteria are the prokaryotic organisms most familiar to us. They are perhaps best known for their pathogen a disease-causing agent, often harmful effects. Bacteria are responsible for many diseases in humans and in other a virus or micro-organism organisms. Infectious bacteria are called pathogens and are responsible for many human deaths each year. Bacterial diseases include cholera, leprosy, typhoid fever, UNit tAsK BOOKMARK strep throat, salmonella poisoning, and tuberculosis. Bacteria also infect livestock Is your chosen group of species and crops and therefore threaten our primary food sources. threatened by pathogens? Are any It is important to keep in mind that from the perspective of the infected organism, other factors, such as climate change, pathogens are harmful. However, diseases that harm one species can benefit another. contributing to the threat? For example, diseases that weaken predators benefit their prey. 46 Chapter 2 The Prokaryotes, Viruses, and Protists NEL  Although some bacteria can be harmful, others play a very positive overall role on Earth, and without them we could not survive. Bacteria, and some archaea, play key roles in ecosystems. Many are decomposers, and others are producers. These micro- organisms also recycle nutrients and are vital to biogeochemical cycles. Bacteria fix, or convert, atmospheric nitrogen into chemical compounds that can be used by plants. Photosynthetic bacteria are the major producers in marine ecosystems and are therefore major producers of atmospheric oxygen. Bacteria are also important residents in the intestines of animals. For example, humans rely on bacteria in the large intestine to produce needed vitamins K and B12. So, although the bacteria benefit from living within the intestine, the individual also Figure 3 Yeast and bacteria are used benefits from the action of the bacteria. This type of relationship between two species in the process that produces chocolate from cacao (Theobroma cacao) beans. that are interdependent, where each benefits from the other, is known as mutualism. Bacteria also have many commercial uses. They are essential in the production of mutualism a relationship between two foods such as cheeses, yogurt, soy sauce, and chocolate (Figure 3)! Bacteria also species that live in very close association produce substances known as antibiotics, which can destroy or inhibit the growth of other with each other, whereby each benefits micro-organisms. Genetic engineers have even modified some bacteria to produce from the association medically valuable compounds, including insulin and human growth hormone. antibiotic a substance that can kill or Archaea are a group of prokaryotes that were discovered only about 40 years ago. weaken micro-organisms; natural antibiotics Scientists do not know as much about archaea as they do about bacteria, but we do are produced by bacteria or fungi, whereas know that these species play key roles in many ecosystems. Archaea live in some synthetic antibiotics are manufactured of the most extreme environments on Earth, such as hot springs, Arctic ice floes, and highly acidic waters. They also live in the intestines of some animals, including cAREER lInK humans. No species from Domain Archaea are known to cause disease. Cheese Maker To learn more about careers in the The Domain eubacteria cheese-making industry, Fossil evidence shows that prokaryotes have lived on Earth for more than 3.5 billion go t o N ELsoN s c i EN c E years. Although fossils cannot provide information about how Eubacteria evolved, genetic studies suggest that species in this domain diversified early. Classification and Phylogeny The Domain Eubacteria has more than 12 separate evolutionary branches, or groups. Figure 4 shows six particularly important groups of bacteria. proteobacteria green bacteria cyanobacteria Eubacteria Gram-positive bacteria spirochetes chlamydias common ancestor of all present-day euryarchaeota organisms crenarchaeota Archaea korarchaeota eukaryotes Eukaryotes Figure 4 This phylogenetic tree shows the relationships among the three domains of life: Eubacteria, Archaea, and Eukaryotes. For simplicity, only the six major groups of bacteria are shown here. These six groups of bacteria are extremely diverse. They vary dramatically in how they obtain energy and nutrients, in their ecological roles, and in their importance to humans. NEL 2.1 The Prokaryotes: Eubacteria and Archaea 47  Table 1 lists the key features of each group of bacteria. Three of these major groups are photosynthetic. Proteobacteria and green bacteria, however, use a process that is very different from photosynthesis in plants. They do not use water or release oxygen, and they use different forms of chlorophyll. Table 1 Key Features of the Six Major Groups of Bacteria Group Key features proteobacteria Some are photosynthetic but use a form of photosynthesis that differs from (purple that of plants. bacteria) Ancient forms of these bacteria were the likely ancestors of eukaryotic mitochondria. Some are nitrogen fixing. They are responsible for many diseases, including bubonic plague, gonorrhea, dysentery, and some ulcers. green bacteria They use a form of photosynthesis that differs from that of plants. They are usually found in salt-water environments or hot springs. cyanobacteria They use a form of photosynthesis similar to plants and other eukaryotes. (blue-green Ancient forms of these bacteria were the likely ancestors of eukaryotic chloroplasts. algae) They play major roles as producers and nitrogen fixers in aquatic ecosystems. They form symbiotic relationships with fungi. Gram-positive They cause many diseases, including anthrax, strep throat, bacterial bacteria pneumonia, and meningitis. They are used in food production (for example, lactobacillus is used in yogurt and probiotic products). Some have lost their cell wall. One type—mycoplasmas—are the smallest known cells (0.1 µm to 0.2 µm). spirochetes Their spiral-shaped flagellum is embedded in their cytoplasm. They move with a corkscrew motion. They cause syphilis. Symbiotic spirochetes in termite intestines digest wood fibre. chlamydias All are parasites that live within other cells. They cause chlamydia, one of the most common sexually transmitted infections. They cause trachoma, the leading cause of blindness in humans. Characteristics Images of bacteria taken with a standard electron microscope typically show little more than a cell wall and a plasma membrane surrounding cytoplasm (Figure 5). However, these prokaryotic cells are relatively complex. A bacterium’s chromosome is a single loop of DNA (deoxyribonucleic acid) that is found in a region called the nucleoid. Ribosomes, which are used in protein synthesis, are scattered throughout the cyto- plasm. Bacteria often have one or more flagella for movement and small hair-like struc- tures called pili (singular: pilus). The pili are made of stiff proteins and help the cell attach to other cells or surfaces. Figure 6 shows the structure of a typical bacteria cell. condensed DNA molecule pili cytoplasm (in the nucleoid) containing ribosomes flagellum plasma membrane peptidoglycan layer cell wall outer membrane plasmid capsule Figure 5 Bacterial cells do not have membrane-bound organelles. Figure 6 A representative bacterial cell 48 Chapter 2 The Prokaryotes, Viruses, and Protists NEL  In addition to a single chromosome, many bacteria have one or more plasmids in their cytoplasm. A plasmid is a small loop of DNA that usually carries a small number plasmid a small loop of DNA often found of genes. The genes are not essential for cellular functions but often provide some in prokaryotic cells; usually contains a advantage to the cell. For example, genes that give bacteria resistance to antibiotics small number of genes are often found on plasmids. Bacteria have complex cell walls composed primarily of peptidoglycan, a large molecule that forms long chains. These chains become cross-linked, making the cell wall strong and rigid. Some bacteria are also surrounded by a sticky capsule. The capsule an outer layer on some bacteria; capsule reduces water loss, resists high temperatures, and helps keep out antibiotics provides some protection for the cell and viruses. coccus a round bacterial cell Bacteria cells vary considerably in shape. Three common shapes are coccus (plural: bacillus a rod-shaped bacterial cell cocci), or round; bacillus (plural: bacilli), or rod shaped; and spirillum (plural: spirilli), or spiral (Figure 7(a) to (c)). Bacteria cells often occur in particular arrangements, spirillum a spiral or corkscrew-shaped such as pairs, clumps, or strings. The prefixes diplo-, staphylo-, and strepto- are used bacterial cell to describe these arrangements (Figure 7(d)). Many species names are based on these easily recognizable characteristics. For example, the species of bacteria responsible for strep throat is Streptococcus pyogenes. diplococci staphylococci (a) (b) (c) (d) streptococci 1.0 m 3.0 m 2.0 m Figure 7 Bacteria cells have three common shapes: (a) cocci, (b) bacilli, and (c) spirilla. (d) They often occur in pairs (diplo), clumps (staphylo), or strings (strepto). MeTABOlISM Bacteria are extremely diverse in the ways they get nutrients and energy from their inorganic chemical a chemical that has surroundings. Autotrophic bacteria make their own food. They assemble complex an abiotic origin; some simple substances carbon molecules from simple inorganic chemicals—substances such as carbon that are produced by organisms are also dioxide, water, and minerals that are part of the abiotic environment. Heterotrophic classified as inorganic bacteria get their nutrients from carbon containing organic chemicals found in other organic chemical in biology, any living organisms or their remains. chemical that contains carbon and is The two primary sources Ontario Biology of energy for 11 U SB living things are sunlight and chemical produced by living things; carbon dioxide energy. We are most familiar0176504311 with the chemical energy contained in organic chemicals is an exception—it is produced during such as sugars, fats, and proteins. FN Many bacteria can also get energy from inorganic C02-F03-OB11USB respiration but is classified as inorganic chemicals such as hydrogen, COsulfur, and iron compounds. Crowle Art Group All animals and plants are obligate aerobes: Ontario they needBiology oxygen, 11 U SB through the obtained obligate aerobe an organism that cannot process of respiration, in order to get energy0176504311 from food. Some bacteria are obligate survive without oxygen Pass 4th pass aerobes, and others are facultative aerobes. These FN bacteria perform aerobic respiration C02-F04-OB11USB facultative aerobe an organism that can in the presence of oxygenApproved and anaerobic respiration, or anaerobic fermentation, when live with or without oxygen CO Crowle Art Group oxygen is absent. Still other bacteria Not are obligate anaerobes: they cannot live in environ- Approved fermentation an anaerobic process that ments where oxygen is present. Ontario Biology 11 U SB Pass 4th pass releases chemical energy from food RePRODUCTIOn 0176504311 obligate anaerobe an organism that Approved Prokaryotes normally reproduce asexually. FN In this process, a parent cell divides by C02-F05-OB11USB cannot survive in the presence of oxygen Not Approved binary fission, producing two daughter CO cells. Each daughter cell receives Crowle Art Group an exact binary fission the division of one parent copy of the genetic material from the parent cell—its chromosome and plasmids. cell into two genetically identical daughter Sometimes mistakes are made when the genetic material is copied. cells; a form of asexual reproduction Pass 4th pass NEL Approved 2.1 The Prokaryotes: Eubacteria and Archaea 49 Not Approved  Copying errors result in mutations, or changes in the genetic makeup of the cell. Bacteria reproduce very quickly, so they mutate more often than organisms that reproduce more slowly. A bacterial gene mutates roughly 1000 times as often as a eukaryotic gene. These mutations increase the genetic diversity in populations of bacteria (Figure 8(a)). conjugation a form of sexual Bacteria also increase their genetic diversity by gaining new DNA. This may reproduction in which two cells join to happen when a bacterium is infected by a virus or through conjugation and exchange genetic information transformation. In conjugation, one bacterial cell passes a copy of a plasmid to a nearby cell through a hollow pilus (Figure 8(b)). This can benefit the recipient transformation a process in which a cell if the plasmid provides beneficial genes. Conjugation is considered a form bacterial cell takes in and uses pieces of of sexual reproduction, because two different cells are sharing genetic informa- DNA from its environment tion. Transformation occurs when a cell picks up a loose fragment of DNA from its horizontal gene transfer the transfer of surroundings and uses it. These DNA fragments may have been released into the genetic information from one species into a environment when other cells died. If the new DNA came from a different species, different species the process is called horizontal gene transfer. (a) (b) endospore a dormant structure that Figure 8 (a) The E. coli (Escherichia coli) cell on the top is dividing by binary fission. (b) Pairs of forms inside certain bacteria in response bacteria are joined by a pilus and are undergoing conjugation. One cell is transferring a copy of a to stress; protects the cell’s chromosome plasmid to another cell. from damage As you observed in the mini investigation at the beginning of this chapter, organisms that can double their population size in only 1 h can produce millions of individuals in a matter of hours. This fast reproduction can have dramatic ecological consequences, such as “algal blooms” in aquatic ecosystems (Figure 9). Algal blooms can reduce the oxygen content of water bodies and threaten other organisms, including fish. Some bacteria have a unique strategy for surviving unfavourable conditions: they produce endospores. An endospore is a highly resistant structure that forms around the chromosome when the cell is under stress. Endospores can withstand extreme conditions and remain dormant until conditions improve, often for many years. Figure 9 Cyanobacteria, or blue-green Living bacterial endospores that are thousands of years old have been recovered from algae, create an “algal bloom.” Egyptian mummies! Research This Biofilms SKILLS Skills: Researching, Analyzing, Evaluating HANDBOOK A2.1, A5.1 Under certain conditions, some bacteria form large colonies that 3. Research why biofilms are of particular interest to humans. stick together and to surfaces, forming biofilms. Dental plaque is A. How and why do biofilms form? T/I a familiar example of a biofilm. In this activity you will research B. What are some ecological roles and benefits of biofilms? T/I the characteristics and roles of biofilms. C. What are examples of biofilms that are harmful or damaging 1. Use the Internet and other resources to find out why some to property? T/I bacteria form biofilms. D. Why are biofilms of medical interest? T/I 2. Research why forming these colonies is advantageous to bacteria. GO T O NELSON SC I EN C E 50 Chapter 2 The Prokaryotes, Viruses, and Protists NEL Bacterial Diseases Table 2 Human Bacterial Diseases Bacteria are responsible for many diseases ranging in severity from minor ear infec- Disease Bacteria species tions, which affect individuals, to the bubonic plague wiped out entire populations. Table 2 lists a few bacterial diseases and examples of species that cause them. cholera Vibrio cholerae Some infectious bacteria cause disease by producing and releasing toxins. For diphtheria Corynebacterium example, botulism food poisoning is caused by the toxin released by the bacterium diphtheriae Clostridium botulinum, which grows in poorly preserved foods. The toxin, botulin, is one of the most poisonous substances known. Botulin causes muscle paralysis that Lyme disease Borrelia can be fatal if the muscles that control breathing are affected. burgdorferi Other bacteria contain toxic compounds that are not released unless the cell pertussis Bordetella dies. These toxins have different effects depending on the bacterial species and site pertussis of infection. One example of this type of bacteria is the E. coli strain O157:H7. This strain causes severe food poisoning and was responsible for the water contamination Rocky Mountain Rickettsia spotted fever rickettsii tragedy in Walkerton, Ontario, in 2000. Unlike other E. coli, this deadly strain has an additional piece of DNA with instructions for making the toxin. Evidence strongly scarlet fever Streptococcus suggests that this is a case of horizontal gene transfer. The strain was created when pyogenes DNA was transferred to E. coli from the bacteria Shigella dysenteriae, the cause of tetanus Clostridium tetani dysentery. Antibiotics are the most successful and widely used treatment of bacterial infections. With E. coli O157:H7, however, the deadly toxin is released when the cell dies. A dose of antibiotics can kill many of the bacteria at once, causing a dangerous amount of the toxin to be released. Antibiotics and Antibiotic Resistance Prokaryotes and fungi are often in direct competition with each other for food and resources, and they produce antibiotic substances as a form of chemical warfare. Imagine a piece of fruit that has just fallen from a tree and come in contact with fungi and bacteria on the ground. Both types of microbes would benefit from the nutrients in the fruit. By producing and releasing an antibiotic into the surroundings, one of the microbes may be able to kill the other and get the fruit. Antibiotics are immensely valuable to humans (Figure 10). By mass-producing a wide variety of antibiotics, we can often kill bacteria where they are unwanted. Unfortunately, though antibiotics have saved many millions of lives, they may not be so effective in the future. The overuse of antibiotics can cause bacteria to adapt and become resistant, so that the antibiotics are no longer effective (Figure 11). Figure 10 Penicillin killed the bacterium Resistant bacteria on the left by weakening its cell wall. exposure to make up more of exposure to antibiotics the population. antibiotics Resistant bacteria are more likely to Bacteria may Some bacteria survive and reproduce. become more have some resistant, making resistance to the antibiotics antibiotics. ineffective. Figure 11 The process by which many bacteria develop antibiotic resistance C02-F06-OB11USB The Domain Archaea Archaea are fascinating organisms, although little is known about them. These tiny prokaryotes were originally thought of as unusual types of true bacteria. They are now known to be unlike any other living thing. Their cell membranes and walls have a unique chemical makeup, and most lack peptidoglycan. Archaea also have genetic information that distinguishes them from bacteria and eukaryotes. NEL 2.1 The Prokaryotes: Eubacteria and Archaea    51  One characteristic of archaea is that many inhabit extreme environments (Figure 12). Some can even survive being boiled in strong detergents! Their cell membranes and cell walls are much more resistant to physical and chemical disrup- tions than those of other organisms. There are three branches in Domain Archaea (see Figure 4, page 47). Table 3 describes some examples of archaea from the group Euryarchaeota and highlights the diversity of organisms in this domain. Table 3 Representative Archaea from the Group Euryarchaeota Figure 12 The sulfur-rich water of Emerald Hole in Yellowstone National Park Euryarchaeota subgroup Key features has very high temperatures. Archaea can use foul smelling H2S as a food source in methanogens They live in low-oxygen environments, including this environment. sediments of swamps, lakes, marshes, and sewage lagoons digestive tracts of some mammals (including humans) and some insects They generate energy by converting chemical compounds into methane gas, which is released into the atmosphere. halophiles They are salt-loving organisms that can live in highly saline environments including the Dead Sea and foods preserved by salting. Most are aerobic and get energy from organic food molecules. Some use light as a secondary energy source. extreme thermophiles They live in extremely hot environments including hot springs and hydrothermal vents on the ocean floor. Their optimal temperature range for growth is 70 °C to 95 °C. psychrophiles They are cold-loving organisms found mostly in the Antarctic and Arctic oceans, and cold ocean depths. Their optimal temperature range for growth is 10 °C to 20 °C. Research This Prokaryotes and environmental Change SKILLS Skills: Researching, Analyzing, Evaluating, Communicating HANDBOOK A2.1, A5.1 Organisms as small as prokaryotes can be influenced by 3. If you have chosen an effect of environmental change, environmental changes. For example, some bacterial diseases may conduct research about the following topics: be able to spread more effectively in warmer climates. Prokaryotes (i) the nature and cause of the environmental change might also be useful in combating environmental change and (ii) the ways in which the environmental change is damage. For example, cyanobacteria might be used to mass- affecting the organism produce a “green” source of fuel. In this activity you will work with (iii) the likely consequences of the effects on the organism, a partner to research prokaryotes and environmental change. including how other species may be affected 1. Work with a partner. Decide who will research a possible effect 4. If you have chosen to research a beneficial use of a of environmental change on a prokaryote and who will research prokaryote, conduct research about the following topics: a possible use of prokaryotes to protect the environment. (i) the characteristics of the prokaryote 2. Conduct some initial research to find one or two examples (ii) the benefits that the prokaryote provides or could provide that interest you. Check your choices with your teacher (iii) the current status of technology before continuing your research. A. Share your summarized findings with your partner. T/I A B. Share your findings with the class. Discuss the overall relationship between environmental change and prokaryotes. T/I A go t o N E LsoN sc iE Nc E 52 Chapter 2 The Prokaryotes, Viruses, and Protists NEL  2.1 Summary Investigation 2.1.1 Bacteria are extremely abundant and play keys roles in ecosystems as Observing Bacteria (page 68) producers, decomposers, and pathogens. Now that you have read about the different types of bacteria, you can Bacteria are used in the production of some types of antibiotics and many complete Investigation 2.1.1. different foods. In this observational study you Bacteria are characterized by the presence of peptidoglycan in their cell walls will observe and identify basic types and have diverse metabolic processes. of bacteria and document your Bacteria reproduce asexually by binary fission and increase their genetic findings with biological drawings. diversity by conjugation and transformation. The ability of bacteria to develop antibiotic resistance is a serious concern. Archaea are an important but not well understood group of prokaryotes. Archaea are found in a variety of habitats including many extreme environments and the intestines of mammals. Archaea have unique cell membranes, cell walls, and genetic information. 2.1 Questions 1. List three ways in which prokaryotes are important to (b) Conduct research to check your prediction. Were you humans and the environment. K/U correct? Where are these bacteria found in nature? 2. Which major groups of eubacteria perform photosynthesis? 12. Describe three extreme environments that are inhabited by Which group uses a form of photosynthesis most similar to archaea. A plants? K/U 13. Although bacteria are typically unicellular, one group, the 3. Describe and state the function of each of the following: K/U Myxobacteria, or “slime bacteria,” form colonies containing (a) nucleoid (d) peptidoglycan millions of cells (Figure 13). Conduct research to determine (b) pili (e) capsule how these bacteria benefit from forming such large (c) plasmid (f) endospore associations. T/I 4. Create labelled sketches of the three common shapes of 100 m bacterial cells. K/U C 5. Distinguish between the following terms: K/U (a) inorganic and organic chemicals (b) obligate and facultative aerobes (c) conjugation and transformation 6. Conduct research to determine how the botulin toxin, released by Clostridium botulinum, is used in the cosmetics industry. What are the benefits and risks of this use? T/I A 7. Explain the role horizontal gene transfer is thought to have played in making the E. coli strain O157:H7 so dangerous. K/U 8. What is the benefit to one kind of bacteria of producing antibiotics that kill other types of bacteria? K/U Figure 13 Colonies of Myxobacteria can contain millions of cells. 9. (a) Describe the process by which many bacteria have 14. Imagine that you overheard someone say, “Bacteria cause developed resistance to antibiotics. disease. It would be good if we could eliminate all bacteria (b) How has their ability to reproduce rapidly influenced on Earth.” Would you agree with this statement? Explain this process? K/U T/I A your reasoning. T/I A 10. Describe two examples of symbiosis involving bacteria. K/U 15. Certain species of bacteria are the only organisms known to 11. Many genetic technologies rely on the ability to make copies be able to feed on crude oil. These bacteria play an important of DNA molecules in the laboratory. This involves using role in cleaning up major oil spills. Use the Internet and other chemicals that operate at high temperatures without being sources to find out more about these bacteria. How are these altered or destroyed. One of these chemicals is produced species used? How do they clean up oil spills? Do they occur by the bacterium Thermus thermophilus. T/I A naturally, or are they applied to the spill by clean-up crews? (a) Do you predict this bacterium to live in cold, moderate, or T/I A hot environments? go to nels on s c i en c e NEL 2.1 The Prokaryotes: Eubacteria and Archaea    53