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CHAPTER 16

Microbial : Prokaryotes and

Chapter Objectives

Prokaryotes 16.1 Describe the diversity, abundance, and importance of prokaryotic life. 16.2 Compare the different shapes, walls, and projections of prokaryotes. 16.3 Explain how can evolve quickly and how bacteria can survive stressful environments. 16.4 Describe the types of nutritional diversity found in prokaryotes. 16.5 Explain why are unique and potentially dangerous to human health. 16.6 Explain how prokaryotes are employed to address the needs of human society. 16.7 Compare the three domains of life based on differences in cellular and biochemical traits. 16.8 Describe the diverse types of living in extreme and more moderate environments. 16.9 Distinguish between the five subgroups of the Bacteria, noting the particular structure, special features, and habitats of each group. 16.10 Describe some of the diseases associated with bacteria. Distinguish between exotoxins and en- dotoxins, noting examples of each. 16.11 Describe the four parts of Koch’s postulates. Explain how Marshall was able to demonstrate that the bacterium Helicobacter pylori can cause gastritis.

Protists 16.12 Describe the basic types of protists. Explain why biologists currently think that they represent many . 16.13 Explain how primary endosymbiosis and secondary endosymbiosis led to further cellular diversity. 16.14 Describe and compare the groups that together form the supergroup SAR. 16.15 Explain how cultured may be used as renewable fuels and the current challenges that re- main. 16.16–16.18 Describe and distinguish between the , Unikonta, and groups. 16.18 Describe the life cycle of Ulva, noting each form in the alternation of generations and how each is produced. 16.19 Describe the ancestors of , , and fungi. Explain how each ancestral protist group is similar to its most likely descendants.

Copyright © 2015 Pearson Education, Inc. 1 Outline

I. Introduction 1. residing in and on your body outnumber your own cells 10 to 1—100 trillion bacteria, archaea, and protists call your body home. 2. Scientists hypothesize that disrupting our microbial communities may a. increase diseases, b. predispose us to certain cancers, and c. contribute to conditions such as asthma and other allergies, , Crohn’s disease, and autism. II. Prokaryotes A. 16.1 Prokaryotes are diverse and widespread 1. Prokaryotic cells are smaller than eukaryotic cells. a. Prokaryotes range from 1 to 5 µm in diameter. b. range from 10 to 100 µm in diameter. 2. The collective of prokaryotes is at least 10 times that of all eukaryotes. 3. Prokaryotes live in habitats a. too cold, b. too hot, c. too salty, d. too acidic, and e. too alkaline for eukaryotes to survive. 4. Some bacteria are causing disease. 5. But most bacteria on our bodies are benign or beneficial. 6. Our consists of the community of microorganisms that live in and on our bodies. 7. Each of us harbors several hundred different species and genetic strains of prokaryotes, including a few positive effects that are well studied. a. Some intestinal bacteria supply essential vitamins and enable us to extract nutrition from food mole- cules that we can’t otherwise digest. b. Many of the bacteria that live on our skin perform helpful housekeeping functions such as decom- posing dead skin cells. c. Other prokaryotes guard against pathogenic intruders. 8. Prokaryotes in help to decompose dead organisms and other organic waste material, which return vital chemical elements to the environment. 9. If prokaryotes were to disappear, a. the chemical cycles that sustain life would halt and b. all forms of eukaryotic life would be doomed. 10. There are two very different kinds of prokaryotes, which are classified in different domains. a. Archaea b. Bacteria B. 16.2 External features contribute to the success of prokaryotes 1. Prokaryotic cells have three common cell shapes. a. Cocci are spherical prokaryotic cells. They sometimes occur in chains that are called streptococci. b. Bacilli are rod-shaped prokaryotes. Bacilli may also be threadlike, or filamentous. c. Spiral prokaryotes are like a corkscrew. i. Short and rigid prokaryotes are called spirilla. ii. Longer, more flexible cells are called spirochetes.

2 Copyright © 2015 Pearson Education, Inc. 2. Nearly all prokaryotes have a . Cell walls a. provide physical protection and b. prevent the cell from bursting in a hypotonic environment. 3. When stained with Gram stain, cell walls of bacteria are either a. gram-positive, with simpler cell walls containing peptidoglycan, or b. gram-negative, with less peptidoglycan. These bacteria are more complex and more likely to cause disease. 4. The cell wall of many prokaryotes is covered by a capsule, a sticky layer of polysaccharides or . 5. The capsule a. enables prokaryotes to adhere to their substrate or to other individuals in a and b. shields pathogenic prokaryotes from attacks by a ’s immune system. 6. Some prokaryotes have external structures that extend beyond the cell wall. a. Flagella are adaptations that enable them to move about in response to chemical or physical signals in their environment. b. Hairlike projections called fimbriae enable prokaryotes i. to stick to a surface or each other or ii. latch onto the host cells they colonize. C. 16.3 Populations of prokaryotes can adapt rapidly to changes in the environment 1. Prokaryote population growth a. occurs by binary , b. can rapidly produce a new generation within hours, and c. can generate a great deal of genetic variation by spontaneous mutations, increasing the likelihood that some members of the population will survive changes in the environment. 2. The of a prokaryote typically a. has about one-thousandth as much DNA as a eukaryotic genome and b. is one long, circular chromosome packed into a distinct region of the cell. 3. Many prokaryotes also have additional small, circular DNA molecules called plasmids, which replicate independently of the chromosome. 4. Some prokaryotes form specialized cells called endospores that remain dormant through harsh condi- tions. 5. Endospores can survive extreme heat or cold. 6. When the endospore receives environmental cues that conditions have improved, it a. absorbs water and b. resumes growth. D. 16.4 Prokaryotes have unparalleled nutritional diversity 1. Prokaryotes exhibit much more nutritional diversity than eukaryotes, allowing them to inhabit almost every nook and cranny on Earth. 2. Two sources of energy are used. a. capture energy from sunlight. b. Chemotrophs harness the energy stored in chemicals.

Copyright © 2015 Pearson Education, Inc. CHAPTER 16 Microbial Life: Prokaryotes and Protists 3 3. Two sources of carbon are used by prokaryotes. a. obtain carbon atoms from carbon dioxide. b. obtain their carbon atoms from the organic compounds present in other organisms. 4. The terms that describe how prokaryotes obtain energy and carbon are combined to describe their modes of nutrition.

a. Photoautotrophs obtain energy from sunlight and use CO2 for carbon. b. Photoheterotrophs obtain energy from sunlight but get their carbon atoms from organic sources.

c. Chemoautotrophs harvest energy from inorganic chemicals and use carbon from CO2 to make or- ganic molecules. d. Chemoheterotrophs acquire energy and carbon from organic molecules. E. 16.5 CONNECTION: Biofilms are complex associations of microbes 1. Biofilms are highly organized colonies that attach to surfaces. 2. Biofilms consist of one or several species of prokaryotes and may also include protists and fungi. 3. Biofilms can form on most any support, including rocks, soil, organic material, or the surface of stag- nant water. 4. formation begins when prokaryotes secrete signaling molecules that attract nearby cells into a cluster. 5. Once the cluster becomes sufficiently large, the cells produce a gooey coating that glues them to the support and to each other, making the biofilm extremely difficult to dislodge. 6. Biofilms a. communicate by chemical signals, b. coordinate a division of labor, and c. collectively defend against invaders. 7. Channels in the biofilm allow a. nutrients to reach cells in the interior, b. wastes to leave, and c. a variety of environments to develop within it. F. 16.6 CONNECTION: Prokaryotes help clean up the environment 1. Prokaryotes are useful for cleaning up contaminants in the environment because prokaryotes a. have great nutritional diversity, b. are quickly adaptable, and c. can form biofilms. 2. Bioremediation is the use of organisms to remove pollutants from a. soil, b. air, or c. water. 3. Prokaryotic decomposers are the mainstays of treatment facilities. a. Raw sewage is first passed through a series of screens and shredders. b. Solid matter then settles out from the liquid waste, forming sludge. c. Sludge is gradually added to a culture of anaerobic prokaryotes, including bacteria and archaea. d. The microbes decompose the organic matter into material that can be placed in a landfill or used as fertilizer. 4. Liquid wastes are treated separately from the sludge. a. Liquid wastes are sprayed onto a thick bed of rocks. b. Biofilms of aerobic bacteria and fungi growing on the rocks remove much of the dissolved organic material. c. Fluid draining from the rocks is sterilized and then released, usually into a river or .

4 Copyright © 2015 Pearson Education, Inc. 5. Bioremediation is becoming a useful tool for cleaning up toxic chemicals released into the soil and wa- ter. 6. Environmental workers may change the natural environment to accelerate the activity of naturally oc- curring prokaryotes capable of metabolizing pollutants. G. 16.7 Bacteria and Archaea are the two main branches of prokaryotic 1. New studies of representative of prokaryotes and eukaryotes strongly support the three-do- main view of life. a. Eukaryotes belong to the domain Eukarya. b. Prokaryotes are now classified into two domains: i. Bacteria and ii. Archaea. H. 16.8 Archaea thrive in extreme environments—and in other habitats 1. Archaeal inhabitants of extreme environments have unusual and other molecular adaptations that enable them to metabolize and reproduce effectively. a. Extreme halophiles thrive in very salty places. b. Extreme thermophiles thrive in i. very hot water, such as geysers, and ii. acid pools. 2. Methanogens a. live in anaerobic environments, b. give off methane as a waste product from i. the digestive tracts of cattle and deer and ii. decomposing materials in landfills. I. 16.9 Bacteria include a diverse assemblage of prokaryotes. 1. The domain Bacteria is currently divided into five groups, based on comparisons of genetic sequences. a. i. are all gram-negative, ii. share a particular rRNA sequence, and iii. represent all four modes of nutrition. iv. Thiomargarita namibiensis is a type of photoautotrophic species of proteobacteria that

(I) uses H2S to generate organic molecules from CO2 and (II) produces sulfur wastes, seen as small greenish globules in Figure 16.9A. v. Proteobacteria also include Rhizobium species that (I) live symbiotically in nodules of legumes and (II) convert atmospheric nitrogen gas into a form usable by their legume host. vi. is a close association between organisms of two or more species.

Copyright © 2015 Pearson Education, Inc. CHAPTER 16 Microbial Life: Prokaryotes and Protists 5 vii. Endosymbiosis refers to one species, called the , living within another. (I) Rhizobium is an endosymbiont. b. Gram-positive bacteria i. Gram-positive bacteria rival proteobacteria in diversity and include the actinomycetes common in soil. ii. Streptomyces are often cultured by pharmaceutical companies as a source of many antibiotics, including streptomycin. c. i. Cyanobacteria are the only group of prokaryotes with plantlike, oxygen-generating photosynthe- sis. ii. Some species, such as Anabaena, have specialized cells that fix nitrogen. d. i. Chlamydias live inside eukaryotic host cells. ii. trachomatis (I) is a common cause of blindness in developing countries and (II) causes nongonococcal urethritis, the most common sexually transmitted disease in the United States. e. Spirochetes are i. helical bacteria and ii. notorious pathogens, causing (I) and (II) Lyme disease. J. 16.10 CONNECTION: Some bacteria cause disease 1. All organisms are almost constantly exposed to . 2. Most often, our body’s defenses prevent pathogens from affecting us. 3. Most bacteria that cause illness do so by producing a poison. a. Exotoxins are proteins that bacterial cells secrete into their environment. b. Endotoxins are components of the outer membrane of gram-negative bacteria that are released when the cell dies or is digested by a defensive cell. 5. All endotoxins induce the same general symptoms: fever, aches, and sometimes a dangerous drop in blood pressure. 6. Bacillus anthracis forms hardy endospores that have been used as biological weapons. 7. The weapon form of C. botulinum is the exotoxin it produces, botulinum, which is the deadliest poison known. 8. Botulinum blocks transmission of the nerve signals that cause muscle contraction, resulting in paralysis of the muscles required for breathing. This effect is also responsible for a more benign use of botulinum—relaxing facial muscles that cause wrinkles. K. 16.11 SCIENTIFIC DISCOVERY: Stomach microbiota affect health and disease 1. How do scientists determine which bacteria cause disease? 2. To the hypothesis that a certain bacterium is the cause of a disease, a researcher must satisfy four conditions. 3. For a human disease, the researcher must be able to a. find the candidate bacterium in every case of the disease; b. isolate the bacterium from a person who has the disease and grow it in pure culture;

6 Copyright © 2015 Pearson Education, Inc. c. show that the cultured bacterium causes the disease when transferred to a healthy subject (usually an ); and d. isolate the bacterium from the experimentally infected subject. 4. Australian microbiologist Barry Marshall hypothesized that chronic gastritis (an of the stomach lining that can lead to ulcers) was caused by a bacterium called Helicobacter pylori. a. Over the course of several years, Marshall satisfied the first two requirements, but his efforts to in- fect animals failed to produce results. b. At last, Marshall decided to take a radical course of action—he would experiment on himself. c. He concocted a nasty brew of H. pylori and swallowed it. d. Several days later, he became ill from gastritis (step 3 of Koch’s postulates). e. His stomach lining proved to be teeming with H. pylori (step 4). Marshall then cleared up his infec- tion with antibiotics. f. He continued to make progress in his research, and other scientists followed up with further studies. g. Several years after Marshall’s big gulp, antibiotics became a standard treatment for ulcer patients. 5. Since Marshall’s breakthrough work, scientists have learned that our relationship with H. pylori is an- cient—at least 50,000 years old—and it’s complicated. a. Only a particular genetic strain causes ulcers; other strains are harmless members of our microbiota. b. Some scientists hypothesize that the absence of H. pylori can cause problems. c. Researchers are investigating a possible connection between this decline and the high rate of obe- sity. III. Protists A. 16.12 Protists are an extremely diverse assortment of eukaryotes 1. Protists a. are a diverse collection of mostly unicellular eukaryotes, b. may constitute multiple kingdoms within the Eukarya, and c. refer to eukaryotes that are not i. plants, ii. animals, or iii. fungi. 2. Protists obtain their nutrition in many ways. Protists include a. autotrophs, called algae, producing their food by , b. heterotrophs, called protozoans, eating bacteria and other protists, c. heterotrophs, called parasites, deriving their nutrition from a living host, which is harmed by the interaction, and d. , using photosynthesis and heterotrophy. 3. Protists are found in many habitats, including a. anywhere there is moisture and b. the bodies of host organisms. 4. Recent molecular and cellular studies indicate that nutritional modes used to categorize protists do not reflect natural clades. 5. Protist phylogeny remains unclear.

Copyright © 2015 Pearson Education, Inc. CHAPTER 16 Microbial Life: Prokaryotes and Protists 7 6. One hypothesis, used here, proposes four monophyletic supergroups. a. “SAR” (includes Stramenopila, Alveolata, and ), b. Excavata, c. Unkonta, and d. Archaeplastida. B. 16.13 EVOLUTION CONNECTION: Secondary endosymbiosis of unicellular algae is the key to much of protist diversity 1. The endosymbiont theory explains the origin of mitochondria and . a. According to this theory, oxygen-using prokaryotes established residence within other, larger pro- karyotes. b. These evolved into mitochondria, giving rise to heterotrophic eukaryotes. 2. Autotrophic eukaryotes later arose through primary endosymbiosis: a. A heterotropic engulfed an autotrophic cyanobacterium. i. If the cyanobacterium continued to function within its host cell, its photosynthesis would have provided a steady source of food and given it a significant selective advantage. ii. Further, because the cyanobacterium had its own DNA, it could reproduce within the host cell. iii. Finally, cyanobacteria could be passed on when the host reproduced. b. Over time, the descendants of the original cyanobacterium evolved into chloroplasts. c. The -bearing lineage of eukaryotes later diversified into the autotrophs and . 3. In secondary endosymbiosis, an autotrophic eukaryotic protist became endosymbiotic in a heterotrophic eukaryotic protist. a. Green algae and red algae became endosymbionts following ingestion by different heterotrophic eu- karyotes. The heterotrophic host cells enclosed the algal cells in food . b. But the algae—or parts of them—survived and became cellular . C. 16.14 The “SAR” supergroup represents the range of protist diversity 1. The SAR supergroup a. is considered to be monophyletic on the basis of genomic studies, b. forms a huge and extremely diverse group, and c. stands for three clades: i. Stramenopila ii. Alveolata, and iii. Rhizaria 2. Autotrophic include and . a. Diatoms i. are unicellular algae that are one of the most important photosynthetic organisms on Earth, ii. have a unique glassy cell wall containing silica, and iii. live in freshwater and marine environments. b. Brown algae i. are large and complex, ii. owe their characteristic brownish color to some of the pigments in their chloroplasts, iii. are all multicellular and mostly marine, and iv. include , which, attached to the seafloor, may reach 60 meters in length.

8 Copyright © 2015 Pearson Education, Inc. c. Water are heterotrophic unicellular stramenopiles that i. typically decompose dead plants and animals and ii. live in freshwater habitats. 3. () a. includes unicellular autotrophs, heterotrophs, and mixotrophs and b. are common components of marine and freshwater 4. Blooms—population explosions—of autotrophic dinoflagellates sometimes cause warm coastal waters to turn pinkish orange, a phenomenon known as “.” 5. Alveolata also includes , which are a. unicellular protists including heterotrophs and mixotrophs and b. named for their use of cilia to move and to sweep food into their mouth. 6. The common freshwater protist is often studied in a biology lab. 7. The two largest groups of Rhizaria, foraminiferans and radiolarians, are among the organisms referred to as . a. Amoebas move and feed by means of , temporary extensions of the cell. b. Foraminiferans i. are found in and in , ii. have porous shells, called tests, composed of calcium carbonate, and iii. have pseudopodia that function in feeding and locomotion. c. Radiolarians i. are mostly marine and ii. produce a mineralized internal made of silica. D. 16.15 CONNECTION: Can algae provide a renewable source of energy? 1. Fossil fuels are the organic remains of organisms that lived hundreds of millions of years ago. a. Diatoms are thought to be the main source of oil. b. Coal was formed from primitive plants. 2. Lipid droplets in diatoms and other algae may serve as a renewable source of energy. 3. If unicellular algae could be grown on a large scale, this oil could be harvested and processed into bio- diesel. 4. Numerous technical hurdles remain before industrial-scale production of biofuel from algae becomes a reality. E. 16.16 Some excavates have modified mitochondria 1. Excavata has recently been proposed as a on the basis of molecular and morphological similarities. 2. The name refers to an “excavated” feeding groove possessed by some members of the group. 3. Excavates a. have modified mitochondria that lack functional electron transport chains and b. use anaerobic pathways such as glycolysis to extract energy. 4. Excavates include a. heterotrophic endosymbionts, b. autotrophic species, c. mixotrophs such as , d. the common waterborne parasite intestinalis, e. the parasite vaginalis, which causes 5 million new each year of human re- productive tracts, and f. the parasite , which causes sleeping sickness in humans. F. 16.17 Unikonts include protists that are closely related to fungi and animals 1. Unikonta is a controversial grouping joining a. amoebozoans and

Copyright © 2015 Pearson Education, Inc. CHAPTER 16 Microbial Life: Prokaryotes and Protists 9 b. a group that includes animals and fungi, addressed at the end of this unit on Protists. 2. Amoebozoans have lobe-shaped pseudopodia and include a. many species of free-living amoebas, b. some parasitic amoebas, and c. slime molds. 3. Plasmodial slime molds a. are common where there is moist, decaying organic matter and b. consist of a single, mass of undivided by plasma membranes, called a . 4. Cellular slime molds a. are common on rotting logs and decaying organic matter and b. usually exist as solitary amoeboid cells, but when food is scarce, amoeboid cells i. swarm together, forming a slug-like aggregate that wanders around for a short time, and then ii. form a stock supporting an asexual reproductive structure that produces . G. 16.18 Archaeplastids include red algae, green algae, and land plants 1. Almost all the members of the supergroup Archaeplastida are autotrophic. 2. Archaeplastids include a. red algae, b. green algae, and c. land plants. 3. Red algae a. are mostly multicellular, b. contribute to the structure of reefs, and c. are commercially valuable. 4. Green algae may be unicellular, colonial, or multicellular. a. is a colonial green algae, and b. Chlamydomonas is a unicellular alga propelled by two flagella. 5. Ulva, or lettuce, is a multicellular green alga with a complex life cycle that includes an alternation of generations that consists of a multicellular diploid (2n) form, the sporo- phyte, that alternates with a multicellular haploid (1n) form, the gametophyte. H. 16.19 EVOLUTION CONNECTION: Multicellularity evolved several times in eukaryotes 1. The origin of the eukaryotic cell led to an evolutionary radiation of new forms of life. 2. Unicellular protists are much more diverse in form than simpler prokaryotes. 3. Multicellular organisms (seaweeds, plants, animals, and most fungi) are fundamentally different from unicellular organisms. a. All of life’s activities occur within a single cell in unicellular organisms. b. A has various specialized cells that perform different functions and are interdependent. 4. Multicellular organisms have evolved from three different lineages: a. stramenopiles (brown algae), b. unikonts (fungi and animals), and c. archaeplastids (red algae and green algae). 5. One hypothesis states that two separate unikont lineages led to fungi and animals, which diverged more than one billion years ago. 6. A combination of morphological and molecular evidence suggests that are the closest-living protist relative of animals.

10 Copyright © 2015 Pearson Education, Inc. Key Terms

alga (plural, algae) dinoflagellates photoautotroph alternation of generations endospore photoheterotroph Alveolata endotoxins plasmodial slime amoebozoan Excavata plasmodium Archaea exotoxins proteobacteria Archaeplastida extreme halophiles protists bacillus (plural, bacilli) extreme thermophiles protozoan (plural, ) biofilms fimbriae pseudopodium (plural, pseudopodia) bioremediation foraminiferans radiolarians brown algae gametophyte red algae cellular slime molds Gram stain Rhizaria chemoautotroph gram-positive bacteria secondary endosymbiosis chemoheterotroph green algae spirochetes chlamydias kelp sporophyte ciliates methanogens Stramenopiles coccus (plural, cocci) microbiota symbiosis cyanobacteria mixotrophs Unikonta diatoms peptidoglycan water molds

Word chemo- = chemical; auto- = self; -troph = food (chemoautotroph: an organism that obtains both energy and carbon from inorganic chemicals, making its own organic compounds from CO2 without using light energy); hetero- = different (chemoheterotroph: an organism that obtains both energy and carbon from organic molecules) cyan- = dark blue (cyanobacteria: photoautotrophic prokaryotes with plantlike, oxygen-generating photosynthesis. These bacteria are sometimes called blue-green algae.) endo- = inner, within (endospore: a thick-coated protective cell produced within a bacterial cell that can become dormant to survive harsh environmental conditions; endotoxin: a poisonous component of the outer membrane of gram-negative bacteria, released only when the bacteria die) exo- = outside (exotoxin: a poisonous protein secreted by certain bacteria) -gen = produce (methanogen: Archaea that produce methane as a metabolic waste product) halo- = salt; -philos = loving (extreme halophile: a that in a highly saline environment) hetero- = different (chemoheterotroph: an organism that obtains both energy and carbon from organic molecules) photo- = light; auto- = self; -troph = food, nourish (photoautotroph: an organism that obtains energy from sunlight and carbon from CO2) -phyte = (gametophyte: the multicellular haploid form in the life cycle of organisms undergoing alternation of generations) pseudo- = false; -podium = foot (pseudopodium [plural, pseudopodia]: a temporary extension of an amoeboid cell that functions in moving and feeding) sym- = with, together; -bios = life (symbiosis: a close association between organisms of two or more species) thermo- = heat; -philos = loving (extreme thermophile: a microorganism that thrives in a hot environment)

Copyright © 2015 Pearson Education, Inc. CHAPTER 16 Microbial Life: Prokaryotes and Protists 11