4 Chapter Preview and Key Concepts 4.1 1.1 DiversityThe Beginnings among theof Microbiology Bacteria and Archaea 1.1. •The BacteriaThe are discovery classified of microorganismsinto several Cell Structure wasmajor dependent phyla. on observations made with 2. theThe microscope Archaea are currently classified into two 2. •major phyla.The emergence of experimental 4.2 Cellscience Shapes provided and Arrangements a means to test long held and Function beliefs and resolve controversies 3. Many bacterial cells have a rod, spherical, or 3. MicroInquiryspiral shape and1: Experimentation are organized into and a specific Scientificellular c arrangement. Inquiry in the Bacteria 4.31.2 AnMicroorganisms Overview to Bacterialand Disease and Transmission Archaeal 4.Cell • StructureEarly epidemiology studies suggested how diseases could be spread and 4. Bacterial and archaeal cells are organized at be controlled the cellular and molecular levels. 5. • Resistance to a disease can come and Archaea 4.4 External Cell Structures from exposure to and recovery from a mild 5.form Pili allowof (or cells a very to attach similar) to surfacesdisease or other cells. 1.3 The Classical Golden Age of Microbiology 6. Flagella provide motility. Our planet has always been in the “Age of Bacteria,” ever since the first 6. (1854-1914) 7. A glycocalyx protects against desiccation, fossils—bacteria of course—were entombed in rocks more than 3 billion 7. • The germ theory was based on the attaches cells to surfaces, and helps observations that different microorganisms years ago. On any possible, reasonable criterion, bacteria are—and always pathogens evade the immune system. have been—the dominant forms of life on Earth. have distinctive and specifi c roles in nature 4.5 8.The • Cell EnvelopeAntisepsis and identifi cation of the —Paleontologist Stephen J. Gould (1941–2002) 8. causeBacterial of animal cell walls diseases help reinforcedmaintain cell the shape germ theoryand protect the cell membrane from rupture. 9.9. •Archaeal cellKoch's walls postulates have crystalline provided layers. a way to 10. Molecules and ions cross the cell membrane “Double, double toil and trouble; Fire burn, and cauldron bubble” is the identify a specifi c microorganism as causing a specifiby facilitated c infectious diffusion disease or active transport. refrain repeated several times by the chanting witches in Shakespeare’s 10.11. •Archaeal membranesLaboratory scienceare structurally and teamwork unique. Macbeth (Act IV, Scene 1). This image of a hot, boiling cauldron actu- 4.6 Thestimulated Cell Cytoplasm the discovery and Internal of additional ally describes the environment in which many bacterial, and especially Structuresinfectious disease agents archaeal, species happily grow! For example, some species can be iso- 11.12. •The nucleoidViruses contains also can the cause cell’s diseaseessential 12. • Many benefi cial bacteria recycle lated from hot springs or the hot, acidic mud pits of volcanic vents genetic information. 13. nutrientsPlasmids incontain the environment nonessential genetic ( FIGURE 4.1 ). information. When the eminent evolutionary biologist and geologist Stephen J. Gould 14. Ribosomes, microcompartments, and wrote the opening quote of this chapter, he as well as most microbiologists inclusions carry out specific intracellular had no idea that embedded in these “bacteria” was another whole domain functions. 15. Cytoskeletal proteins regulate cell division of organisms. Thanks to the pioneering studies of Carl Woese and his col- and help determine cell shape. leagues, it now is quite evident there are two distinctly different groups of 4.7 The Bacteria/Eukaryote Paradigm— “prokaryotes”—the Bacteria and the Archaea (see Chapter 3). Many of the Revisited organisms Woese and others studied are organisms that would live a happy 16. Cellular processes in bacterial cells can be life in a witch’s cauldron because they can grow at high temperatures, produce similar to those in eukaryatic cells. MICROINQUIRY 4: The Prokaryote/Eukaryote methane gas, or survive in extremely acidic and hot environments—a real Model cauldron! Termed extremophiles, these members of the domains Bacteria 97 © Jones and Bartlett Publishers, LLC. NOT FOR SALE OR DISTRIBUTION. 62582_CH04_097_130.indd 97 1/26/10 2:20 PM 98 CHAPTER 4 Cell Structure and Function in the Bacteria and Archaea (A) (B) FIGURE 4.1 Life at the Edge. Bacterial and archaeal extremophiles have been isolated from the edges of natural cauldrons, including (A) the Grand Prismatic Spring in Yellowstone National Park, Wyoming, where the water of the hot spring is over 70ºC, or (B) the mud pools surrounding sulfurous steam vents of the Solfatara Crater in Pozzuoli, Italy, where the mud has a very low pH and a temperature above 90º. »» How do extremophiles survive under these extreme conditions? and Archaea have a unique genetic makeup and As more microbes have had their complete genomes have adapted to extreme environmental conditions. sequenced, it now is clear that there are unique as In fact, Gould’s “first fossils” may have been well as shared characteristics between species in the archaeal species. Many microbiologists believe the domains Bacteria and Archaea. ancestors of today’s archaeal species might represent In this chapter, we examine briefly some of the a type of organism that first inhabited planet Earth organisms in the domains Bacteria and Archaea. when it was a young, hot place (see MicroFocus 2.1). However, because almost all known “prokaryotic” These unique characteristics led Woese to propose pathogens of humans are in the domain Bacteria, these organisms be lumped together and called the we emphasize structure within this domain. As we Archaebacteria (archae = “ancient”). see in this chapter, a study of the structural features Since then, the domain name has been of bacterial cells provides a window to their activi- changed to Archaea because (1) not all members ties and illustrates how the Bacteria relate to other are extremophiles or related to these possible living organisms. ancient ancestors and (2) they are not As we examine bacterial and archaeal cell Bacteria—they are Archaea. Some might also structure, we can assess the dogmatic statement debate using the term prokaryotes when refer- that these cells are characterized by a lack of a ring to both domains, as organisms in the two cell nucleus and internal membrane-bound organ- domains are as different from each other as they elles. Before you finish this chapter, you will be are from the Eukarya. equipped to revise this view. 4.1 Diversity among the Bacteria and Archaea In this section, we discuss bacterial and archaeal bacterial and archaeal species and a suspected diversity using the current classification scheme, 10 million species. In this section, we will high- which is based in large part on nucleotide light a few phyla and groups using the phyloge- sequence data. There are some 7,000 known netic tree in FIGURE 4.2 . © Jones and Bartlett Publishers, LLC. NOT FOR SALE OR DISTRIBUTION. 62582_CH04_097_130.indd 98 1/26/10 2:20 PM 4.1 Diversity among the Bacteria and Archaea 99 ARCHAEA BACTERIA (2 major phyla) (>70 major phyla) Chlamydia Euryarchaeota Spirochaetes Extreme Methanogens halophiles Proteobacteria Crenarchaeota Gram-positive Eukarya bacteria Hyperthermophiles UNIVERSAL ANCESTOR FIGURE 4.2 The Phylogenetic Tree of Bacteria and Archaea. The tree shows several of the bacterial and archaeal phyla discussed in this chapter. »» What is common to the branch base of both the Bacteria and Archaea? The Domain Bacteria Contains Some springs, the fringes of space, and the tissues of ani- of the Most Studied Microbial mals. Bacterial species, along with their archaeal Organisms relatives, have so completely colonized every part KEY CONCEPT of the Earth that their mass is estimated to out- 1. The Bacteria are classified into several major phyla. weigh the mass of all plants and animals com- bined. Let’s look briefly at some of the major phyla There are about 18 phyla of Bacteria identified from and other groups. culturing or nucleotide sequencing. It should come Proteobacteria. The Proteobacteria (proteo = as no shock to you by now to read that the vast “first”) contains the largest and most diverse group majority of these phyla play a positive role in nature of species and includes many familiar gram-negative (MICROFOCUS 4.1). Although not unique to just genera, such as Escherichia ( FIGURE 4.3A ). The phylum the bacterial phyla, they digest sewage into simple also includes some of the most recognized human chemicals; they extract nitrogen from the air and pathogens, including species of Shigella, Salmonella, make it available to plants for protein production; Neisseria (responsible for gonorrhea), Yersinia they break down the remains of all that die and (responsible for plague), and Vibrio (responsible recycle the carbon and other elements; and they pro- for cholera). It is likely that the mitochondria duce oxygen gas that we and other animals breathe. of the Eukarya were derived through endosym- Of course, we know from Chapter 1 and per- biosis from an ancestor of the Proteobacteria (see sonal experience that some bacterial organisms are MicroInquiry 3). harmful—many human pathogens are members The group also includes the rickettsiae (sing., of the domain Bacteria. Certain species multiply rickettsia), which were first described by Howard within the human body, where they disrupt tissues Taylor Ricketts in 1909. These tiny bacterial cells or produce toxins that result in disease. can barely be seen with the most powerful light The Bacteria have adapted to the diverse envi- microscope. They are transmitted among humans ronments on Earth, inhabiting the air, soil, and primarily by arthropods, and are cultivated only Arthropods: water, and they exist in enormous numbers on in living tissues such as chick embryos. Different Animals having jointed appendages and the surfaces of virtually all plants and animals. species cause a number of important diseases, segmented body (e.g., ticks, They can be isolated from Arctic ice, thermal hot including Rocky Mountain spotted fever and lice, fleas, mosquitoes).