Characterizing and Classifying Prokaryotes

         and Classifying Prokaryotes Characterizing Coccus Spirillum Coccobacillus Spirochete Bacillus Pleomorphic Vibrio Star ­ ­ Prokaryotes are by far the most numerous and diverse group of cellular microbes. Scientists estimate there are more than 5 * 1030 prokaryotes on Earth. If laid end to end, they would more than encircle the entire Milky Way galaxy. They thrive in every habitat: from Antarctic glaciers to thermal hot springs to the dry sands of deserts, from the colons of animals to the cytoplasm of other prokaryotes, from distilled water to supersaturated brine, and from disinfectant solutions to basalt rocks thousands of meters below the Earth’s surface. Among this great diversity of prokaryotes, a very few have enzymes, toxins, or cellular structures that enable them to colonize humans or cause diseases. We begin this chapter by examining general prokaryotic characteristics and conclude with a survey of specific prokaryotic taxa, briefly mentioning human pathogens throughout the chapter. (More detailed discussions of disease-causing prokaryotes appear in Chapters 19–24.) SEM difference between a spirillum and a spirochete? ­ ­ In this section, we consider shapes of prokaryotic cells, the ability of some prokaryotes to form endospores that allow them to survive unfavorable conditions, some reproduction strategies, and spatial arrangements of prokaryotic cells. (Chapters 3 and 5–7 consider other general characteristics of prokaryotic cells, including cellular structure, metabolism, growth, and genetics.) ▲ FIGURE 11.1 Typical prokaryotic morphologies. What is one Figure 11.1 Generally, spirilla are stiff, whereas spirochetes are flexible. General Characteristics of Prokaryotic Organisms 10 µm Morphology of Prokaryotic Cells LE A R N I N G O U TC O M E LE A R N I N G O UTC O M E 11.2 Describe the formation and function of bacterial endospores. The Gram-positive bacteria Bacillus (ba-sil’ŭs) and Clostridium (klos-trid’ē-ŭm) produce endospores, which are important for several reasons, including their durability and potential pathogenicity. Endospores constitute a defensive strategy: They are stable resting stages that barely metabolize in hostile or unfavorable conditions, and they germinate when conditions improve. Though some people refer to endospores as “spores,” endospores should not be confused with reproductive spores, such as those of algae and fungi. A single bacterial cell, called a vegetative cell to distinguish it from an endospore, transforms into only one endospore, which reactivates to grow into a single vegetative cell; therefore, endospores are not reproductive structures. No new cells are produced from endospores. The process of endospore formation, called sporulation, requires 8 to 10 hours and proceeds in seven steps (see Chapter 3, Figure 3.25). Depending on the species, a vegetative cell forms an endospore either centrally, subterminally (near one end), or terminally (at one end) (FIGURE 11.2). Endospore formation is a concern to food processors, health care professionals, and governments. Endospores are difficult to kill; moreover, many endospore-forming bacteria produce deadly toxins that cause fatal diseases, such as anthrax, tetanus, and gangrene. ­ ­ ­ ­ Prokaryotic cells exist in a variety of shapes, or morphologies (FIGURE 11.1). The three basic shapes are coccus (kok’ŭs; roughly spherical; plural: cocci, kok’sī), bacillus (ba-sil’ŭs; rod shaped; plural: bacilli, bă-sil’ī), and spiral. Cocci are not all perfectly spherical; for example, there are pointed, kidney-shaped, and oval cocci. Similarly, bacilli vary in shape; for example, some bacilli are pointed, others are spindle shaped, and still others are threadlike (filamentous). Spiral-shaped prokaryotes are either spirilla, which are stiff, or spirochetes (spī’rō-kētz), which are flexible. Curved rods are vibrios. The term coccobacillus is used to describe cells that are intermediate in shape between cocci and bacilli; that is, it is difficult to ascertain whether a coccobacillus is an elongated coccus or a short bacillus. In addition to these basic shapes, there are star-shaped, triangular, and rectangular prokaryotes as well as prokaryotes that are pleomorphic1 (plē-ō-mōr’fik), that is, vary in shape and size. ­ ­ 11.1 Identify six basic shapes of prokaryotic cells. Endospores 1From Greek pleon, meaning “more,” and morphe, meaning “form.” M11_BAUM7206_05_SE_C11.indd 322 11/23/16 3:03 AM Vegetative cell Endospore       P General Characteristics of rokaryotic Organisms Endospore 1 Cell replicates its DNA; both molecules are attached to the cytoplasmic membrane. Cell wall Cytoplasmic membrane Replicated DNA 2 The cytoplasmic membrane elongates, separating DNA molecules. (a) LM 5 µm LM (b) 3 Cross wall forms; membrane invaginates. 10 µm ▲ FIGURE 11.2 Locations of endospores. (a) Central endospores of Bacillus. (b) Subterminal endospores of Clostridium botulinum. The enlarged endospores have swollen the vegetative cells that produced them. 4 Cross wall forms completely. Reproduction of Prokaryotic Cells LE A R N I N G O U TC O M E S 11.3 List three common types of reproduction in 5 Daughter cells may separate. prokaryotes. 11.4 Describe snapping division as a type of binary fission. ­ ­ ­ ­ A variation of binary fission called snapping division occurs in some Gram-positive bacilli (FIGURE 11.4) . In snapping division, only the inner portion of a cell wall is deposited across the dividing cell. As the cells grow and the new cross wall thickens, they put tension on the outer layer of the old cell wall, which still holds the two cells together. Eventually, as the tension increases, the outer wall breaks at its weakest point with a snapping movement that tears it most of the way around. The daughter cells then remain hanging together almost side by side, held at an angle by a small remnant of the original outer wall that acts like a hinge. M11_BAUM7206_05_SE_C11.indd 323 ­ Some prokaryotes have other methods of reproduction in which a parental cell retains its identity. For example, the actinomycetes (ak’ti-nō-mī-sētz) produce reproductive cells called spores at the ends of filamentous cells (FIGURE 11.5). These are true spores and should not be confused with endospores. Each actinomycete spore contains complete genetic information and can develop into a clone of the original organism. Other prokaryotes reproduce by fragmentation into small motile filaments with a full complement of DNA that glide away from the parental strand. Still others, such as the bacterium Planctomyces (plank-tō-mī’sēz), reproduce by budding, in which an outgrowth of the original cell (a bud) receives a copy of DNA and enlarges. Eventually the bud is cut off from the parental cell, typically while it is still quite small (FIGURE 11.6). Epulopiscium (ep’yoo-lō-pis’sē-ŭm), a giant bacterium that lives inside surgeonfish, and many of its relatives have a truly unique method of reproduction among prokaryotes: They give “birth” to as many as 12 live offspring that emerge from ­ Growth: Overview ▲ FIGURE 11.3 Binary fission. ­ All prokaryotes reproduce asexually; none reproduce sexually. The most common method of asexual reproduction is binary fission, which proceeds as follows (FIGURE 11.3): 1 The cell replicates its DNA by semiconservative replication, meaning that each molecule of DNA consists of one strand of original DNA and one strand of new DNA (see Chapter 7). Each DNA molecule remains attached to the cytoplasmic membrane. 2 The cell grows, and as the cytoplasmic membrane elongates, it moves the daughter molecules of DNA apart. 3 The cell forms a cross wall, invaginating the cytoplasmic membrane. 4 The cross wall completely divides daughter cells. 5 The daughter cells may or may not separate. The parental cell disappears with the formation of progeny. ▶ ANIMATIONS: Bacterial 11/23/16 3:03 AM r 11    Characterizing and Classifying rokaryotes P p te ha       C Newer, inner portion of cell wall Older, outer portion of cell wall DNA, which is attached to the cytoplasmic membrane, is replicated. Cell elongates to form a bud; the expanding cytoplasmic membrane carries one attached DNA molecule into the bud. (a) Young bud Ruptured remains of old cell wall Daughter cell ▲ FIGURE 11.6 Budding. How does budding differ from binary fission? Figure 11.6 In binary fission, the parent cell disappears with the formation of two equal-sized offspring; a bud, in contrast, is often much smaller than its parent, and the parent remains to produce more buds. Hinge (b) TEM 0.5 µm ­ ▲ FIGURE 11.4 Snapping division, a variation of binary fission. (a) Only the inner portion of the cell wall forms a cross wall. (b) As the daughter cells grow, tension snaps the outer portion of the cell wall, leaving the daughter cells connected by a hinge of old cell wall material. Spores Filamentous vegetative cells LM 100 μm ▲ FIGURE 11.7 Viviparity in Epulopiscium. Multiple offspring ­ simultaneously develop inside a mother cell. ­ ▲ FIGURE 11.5 Spores of actinomycetes. Filamentous vegetative cells produce long, filamentous cells and chains of spores, shown here in Streptomyces. LE A R N I N G O UTC O M E 11.5 Draw and label nine arrangements of prokaryotes. The arrangements of prokaryotic cells result from two aspects of division during binary fission: the planes in which cells divide and whether or not daughter cells remain attached to each other. Cocci that remain attached in pairs are diplococci (FIGURE 11.8a), and long chains of cocci are called streptococci2 ­ the body of their dead mother cell (FIGURE 11.7). The production of live offspring within a mother is called viviparity, and this is the first documented case of viviparous behavior in the prokaryotic world. In these bacteria, formation of internal offspring proceeds in a manner similar to the early stages of endospore formation. Arrangements of Prokaryotic Cells ­ 2.5 µm ­ SEM M11_BAUM7206_05_SE_C11.indd 324 2From Greek streptos, meaning “twisted,” because long chains tend to twist. 11/23/16 3:03 AM Plane of division       P General Characteristics of rokaryotic Organisms Diplococci Single bacillus LM (a) LM (a) 10 µm Streptococci 10 µm Diplobacilli LM (b) LM (b) 10 µm 10 µm Tetrads Streptobacilli LM (c) 10 µm LM (c) Sarcinae LM (d) 10 µm Palisade 10 µm Staphylococci V-shape LM (d) deo r attached as either pairs or chains (FIGURE 11.9a–c). Because the cells of Corynebacterium diphtheriae (kŏ-rī’nē-bak-tēr’ē-ŭm difthi’rē-ī), the causative agent of diphtheria, divide by snapping division, t he daughter cells remai n at tac hed to for m V-shapes and a side-by-side arrangement called a palisade5 (FIGURE 11.9d). Descriptive words can be used to refer either to a general shape and/or arrangement or to a specific genus. Thus, the characteristic shape of the genus Bacillus is a rod-shaped bacterium, and the characteristic arrangement of bacteria in the genus Sarcina (sar’si-nă) is cuboidal. In such potentially confusing 3Latin 4From ­ ­ for “bundles.” Greek staphyle, meaning “bunch of grapes.” M11_BAUM7206_05_SE_C11.indd 325 5From ­ planes to form cuboidal packets called sarcinae 3 (sar’si-nī) (FIGURE 11.8d). Clusters called staphylococci4 (staf’i-lo-kok-sī), which look like bunches of grapes, form when the planes of cell division are random (FIGURE 11.8e). Bacilli are less varied in their arrangements than cocci because bacilli divide transversely—that is, across their long axis. Daughter bacilli may separate to become single cells or stay ­ ­ (FIGURE 11.8b). Some cocci divide in two planes and remain attached to form tetrads (FIGURE 11.8c); others divide in three ­ ­ ­ Streptococcus pneumoniae. (b) The streptococci of Streptococcus pyogenes. (c) Tetrads, in this case of Micrococcus luteus. (d) The genus Sarcina is characterized by sarcinae. (e) The staphylococci of Staphylococcus aureus. Vi Tu to ▲ FIGURE 11.8 Arrangements of cocci. (a) The diplococci of ­ 10 µm ▲ FIGURE 11.9 Arrangements of bacilli. (a) A single bacillus of Escherichia coli. (b) Diplobacilli in a young culture of Bacillus cereus. (c) Streptobacilli in an older culture of Bacillus cereus. (d) V-shapes and palisades of Corynebacterium diphtheriae. ­ LM (e) 10 µm Latin palus, meaning “stake,” referring to a fence made of adjoining stakes. 11/23/16 3:03 AM r 11    Characterizing and Classifying rokaryotes P matter of opinion and judgment, and not all taxonomists agree. Legitimately differing views often change as more information is uncovered and examined, so Bergey’s Manual is merely a consensus of experts at a given time. More information about Bergey’s Manual can be found on the textbook website at www .masteringmicrobiology.com. In the following sections, we examine representative prokaryotes of major phyla. We begin our exploration of prokaryotic diversity with a survey of archaea. ­ ­ ­ cases, the meaning can be distinguished because genus names are always capitalized and italicized. In other cases, the arrangement uses the plural form, whereas a genus name is singular; thus, streptococci—spherical cells arranged in a chain—are characteristic of the genus Streptococcus (strep-tō-kok’ŭs). Spirilla, spirochetes, and star-shaped, triangular, and pleomorphic prokaryotes are typically singular. Rectangular and square prokaryotes often form sheets of cells. ­ p te ha       C TELL ME WHY TELL ME WHY Why does binary fission produce chains of cocci in some species but clusters of cocci in other species? ­ Why are taxonomic names and categories in our current taxonomic scheme different from those in 1990? Modern Prokaryotic Classification LE A R N I N G O U TC O M E S 11.6 Explain the general purpose of Bergey’s Manual of LE A R N I N G O UTC O M E 11.8 Identify the common features of microbes in the domain Archaea. ­ Systematic Bacteriology. 11.7 Discuss the veracity and limitations of any taxonomic scheme. Survey of Archaea • Archaea lack true peptidoglycan in their cell walls. • Their cytoplasmic membrane lipids have branched or ringform hydrocarbon chains, whereas bacterial membrane lipids have straight chains. • The initial amino acid in their polypeptide chains, coded by the AUG start codon, is methionine (as in eukaryotes and in contrast to the N-formylmethionine used by bacteria). M11_BAUM7206_05_SE_C11.indd 326 ­ ­ Archaea are currently classified in two major phyla— Crenarchaeota (kren-ar’kē-ō-ta) and Euryarchaeota (yŭr-ēar’kē-ō-ta)—and three minor phyla, which each contain only one or a few described species. Researchers discovered these minor phyla by analyzing rRNA sequences. They have cultured few of the archaeal species from the minor phyla. Archaea reproduce by binary fission, budding, or fragmentation. Known archaeal cells are cocci, bacilli, spirals, or pleomorphic (FIGURE 11.11). Archaeal cell walls vary among taxa and are composed of a variety of compounds, including proteins, glycoproteins, lipoproteins, and polysaccharides; all lack peptidoglycan. Another surprising feature for an entire domain of life is that to date microbiologists have not discovered any archaeon that causes disease. The first archaea identified were found in extreme environments considerably hostile to most life; these archaea are extremophiles, which we discuss next. Other archaea are methanogens (discussed shortly). We now know that most archaea live in moderate environmental conditions, including the mouths of people. It should be noted that some bacteria are also extremophiles. ­ ­ ­ ­ ­ ­ ­ Scientists called taxonomists group similar organisms into categories called taxa (see p. 334). At one time, the smallest taxa of prokaryotes (i.e., genera and species) were based solely on growth habits and the characteristics we considered in the previous section, especially morphology and arrangement. More recently, the classification of living things has been based more on genetic similarities. Accordingly, modern taxonomists place all organisms into three domains—Archaea (ar’kē-ă), Bacteria, and Eukarya—which are the largest, most inclusive taxa. Scientists recognize bacterial and archaeal (both prokaryotic) taxa primarily on the basis of similarities in RNA, DNA, and protein sequences. The vast majority of prokaryotes—perhaps as many as 99.5%, and probably millions of species—have never been isolated or cultured and are known, if at all, only from their ribosomal (rRNA) “fingerprints”; that is, they are known only from sequences of rRNA that do not match any known rRNA sequences. In light of this information, taxonomists now construct modern classification schemes of prokaryotes based primarily on the relative similarities of rRNA sequences found in various prokaryotic groups (FIGURE 11.10). An authoritative reference in modern prokaryotic systematics is Bergey’s Manual of Systematic Bacteriology, which classifies prokaryotes into 29 phyla—5 in Archaea and 24 in Bacteria. The five volumes of the second edition of Bergey’s Manual discuss the great diversity of prokaryotes based in large part (but not exclusively) on their possible evolutionary relationships, as reflected in their rRNA sequences. Our examination of prokaryotic diversity in this text is for the most part organized to reflect the taxonomic scheme that appears in Bergey’s Manual, but it is important to note that as authoritative as Bergey’s Manual is, it is not an “official” list of prokaryotic taxa. The reason is that taxonomy is partly a Scientists originally identified archaea as a distinct type of prokaryote on the basis of unique rRNA sequences. Archaea also share other common features that distinguish them from bacteria: 11/23/16 3:03 AM       Survey of Archaea PHYLUM CHLOROFLEXI (green nonsulfur) BACTERIA PHYLUM DEINOCOCCUS-THERMUS Thermophilic bacteria BACT ERIA DEEPLY BRANCHING BACTERIA GRAM-NEGATIVE BACTERIA PHYLUM PROTEOBACTERIA Purple nonsulfur (c) Rickettsias (c) Nitrogen fixing (c) ARC HAE Nitrifying (d) PHYLUM AQUIFICAE Myxobacteria (f) (b) Zetaproteobacteria (1) Campylobacteria (g) PHYLUM CHLOROBI (green sulfur) TIME Gammaproteobacteria (i) Neisserias (d) PHYLUM PLANCTOMYCETES ARCHAEA PHYLUM THAUMARCHAEOTA PHYLUM NANOARCHAEAOTA PHYLUM SPIROCHAETES Low G+C Gram-positive PHYLUM FIRMICUTES the ut o b g n a on tio s am a l e cu ip Spetionsh er tim v a l o e r ups gro PHYLUM CYANOBACTERIA PHYLUM FIBROBACTERES PHYLUM CHLAMYDIAE PHYLUM BACTEROIDETES A PHYLUM CRENARCHAEOTA PHYLUM FUSOBACTERIA PHYLUM KORARCHAEOTA PHYLUM EURYARCHAEOTA Methanogens Halophiles Clostridia Mycoplasmas Selenomonas Bacilli, lactobacili, cocci Streptomyces Atopobium Arthrobacter GRAM-POSITIVE BACTERIA Thermophilic archaea Corynebacterium Mycobacterium Nocardia PHYLUM ACTINOBACTERIA High G+C Gram-positive (a) P LE A R N I N G O U TC O M E 11.9 Compare and contrast the two kinds of extremophiles discussed in this section. Extremophiles are microbes that require what humans consider to be extreme conditions of temperature, pH, pressure, and/or salinity to survive. There are extremophilic bacteria (mentioned later) as well as archaea. Prominent among extremophiles are thermophiles and halophiles. M11_BAUM7206_05_SE_C11.indd 327 Thermophiles Thermophiles6 are prokaryotes whose DNA, RNA, cytoplasmic membranes, and proteins do not f unction properly at temperatures lower than about 45°C. Prokaryotes that require temperatures over 80°C are called hyperthermophiles. Most thermophilic archaea are in the phylum Crenarchaeota, though some are also found in the phylum Euryarchaeota. Two representative genera of thermophilic archaea are Thermococcus (ther-mō-kok’-us) and Pyrodictium (pī-rō-dik’tē-um; ­ Extremophiles ­ I R R ▲ FIGURE 11.10 Prokaryotic taxonomy. (a) This scheme is based on relatedness according to r NA sequences. The closer together the disks, the more similar are the r NA sequences of the species within the group. The sizes of disks are proportional to the number of species known for that group. Note that archaea are distinctly separate from bacteria. The discussion in this chapter is based largely on the scheme depicted in this figure. Not all phyla are shown. ( n phylum roteobacteria, classes are indicated by a Greek letter: a = alpha, b = beta, g = gamma, d = delta, e = epsilon, and z = zeta.) (b) The exact relationships between and among groups over time are speculative. (Adapted from Road Map to Bergey’s. 2002, Bergey’s Manual Trust.) 6From Greek thermos, meaning “heat,” and philos, meaning “love.” 11/23/16 3:03 AM r 11    Characterizing and Classifying rokaryotes P p te ha       C TEM (a) 0.5 µm ▲ FIGURE 11.12 Some hyperthermophilic archaea live in hot springs. Orange archaea thrive along the edge of this steaming pool in P Yellowstone National ark. Halophiles ­ of flagella. (b) Pyrodictium, which has disk-shaped cells with filamentous extensions. ­ ­ ­ see Figure 11.11). These microorganisms live in acidic hot springs such as those found in deep ocean rifts and similar terrestrial volcanic habitats (FIGURE 11.12). Geogemma (jē’ō-jem-ă) is the current record holder for surviving high temperatures—it can survive two hours at 130°C! The cells of Pyrodictium, which live in deep-sea hydrothermal vents, are irregular disks with elongated protein tubules that attach them to grains of sulfur that they use as final electron acceptors in respiration. Scientists use thermophiles and their enzymes in recombinant DNA technology applications because thermophiles’ cellular structure and enzymes are stable and functional at temperatures that denature most proteins and nucleic acids and kill other cells. DNA polymerase from hyperthermophilic archaea makes possible the automated amplification of DNA in thermocyclers (see Chapter 8). Heat-stable enzymes are also ideal for many industrial applications, including their use as additives in laundry detergents. M11_BAUM7206_05_SE_C11.indd 328 ­ ▲ FIGURE 11.11 Archaea. (a) Thermococcus, which has a tuft ­ 1 µm ­ TEM (b) ­ ­ Halophiles7 are organisms that inhabit extremely saline habitats, such as the Dead Sea, the Great Salt Lake, and solar evaporation ponds used to concentrate salt for use in seasoning and for the production of fertilizer (FIGURE 11.13). Halophiles can also colonize and spoil such foods as salted fish, sausages, and pork. Halophilic archaea are classified in the phylum Euryarchaeota. The distinctive characteristic of halophiles is their absolute dependence on a salt concentration greater than 9% to maintain the integrity of their cell walls. Most halophiles grow and reproduce within an optimum range of 17% to 23% salt, and many species can survive in a saturated saline solution (35% sodium chloride). Many halophiles contain red to orange pigments that probably play a role in protecting them from intense sunlight. A well-studied halophile is Halobacterium salinarum (hā’lō-bak-tēr’ē-ŭm sal-ē-nar’ŭm), which is an archaeon despite its name. It is a photoheterotroph, using light energy to drive the synthesis of ATP while deriving carbon from organic compounds. Halobacterium lacks photosynthetic pigments— chlorophylls and bacteriochlorophylls. Instead, it synthesizes purple proteins, called bacteriorhodopsins (bak-tēr’ē-ō-rōdop’sinz), that absorb light energy to pump protons across the cytoplasmic membrane to establish a proton gradient. Cells use the energy of proton gradients to produce ATP (see Chapter 5). Halobacterium also rotates its flagella with energy from the proton gradient so as to position itself at the proper water depth for maximum light absorption. Methanogens LE A R N I N G O UTC O M E 11.10 List at least four significant roles that methanogens play in the environment. 7From Greek halos, meaning “salt.” 11/23/16 3:03 AM       Survey of Bacteria moderate habitats and don’t produce methane. For example, archaea make up about a third of the prokaryotic biomass in coastal Antarctic water, providing food for marine animals. TELL ME WHY Why is it that archaea don’t seem to cause disease of humans, plants, or animals? Survey of Bacteria ­ ­ ­ ­ ­ ­ Methanogens are obligate anaerobes that convert CO2, H2, and organic acids into methane gas (CH4), which is the major component of natural gas. These microbes constitute the largest known group of archaea in the phylum Euryarchaeota. A few thermophilic methanogens are known. For example, Methanopyrus 8 (meth’a-nō-pī’rŭs) has an optimum growth temperature of 98°C and grows well in 110°C seawater around submarine hydrothermal vents. Scientists have also discovered halophilic methanogens. Methanogens play significant roles in the environment by converting organic wastes in pond, lake, and ocean sediments into methane. Other methanogens living in the colons of animals are one of the primary sources of environmental methane. Methanogens dwelling in the intestinal tract of a cow, for example, can produce 400 liters of methane a day. Sometimes the production of methane in swamps and bogs is so great that bubbles rise to the surface as “swamp gas.” Methane is a so-called greenhouse gas; that is, methane in the atmosphere traps heat, which adds to global warming. It is about 25 times more potent as a greenhouse gas than carbon dioxide. Methanogens have produced about 10 trillion tons of methane—twice the known amount of oil, natural gas, and coal combined—that lies buried in mud on the ocean floor. If all the methane trapped in ocean sediments were released, it would wreak havoc with the world’s climate. Methanogens also have useful industrial applications. An important step in sewage treatment is the digestion of sludge by methanogens, and some sewage treatment plants burn methane to heat buildings and generate electricity. T houg h we have concent rated ou r d isc ussion on extremophiles and methanogens, most archaea live in more 8From Greek pyrus, meaning “fire.” M11_BAUM7206_05_SE_C11.indd 329 Deeply Branching and Phototrophic Bacteria LE A R N I N G O UTC O M E s often contain red-to-orange pigments, possibly to protect them from intense solar energy. Different colors in the ponds indicate the presence of different species and numbers of halophiles. ­ ▲ FIGURE 11.13 The habitat of halophiles: highly saline water. These are solar evaporation ponds near San Francisco. Halophiles ­ ­ As we noted previously, our survey of prokaryotes in this chapter reflects the classification scheme that is featured in the second edition of Bergey’s Manual. Whereas the classification scheme for bacteria in the first edition of the Manual emphasized morphology, Gram reaction, and biochemical characteristics, the second edition bases its classification of bacteria largely on differences in 16S rRNA sequences. We begin our survey of bacteria by considering the deeply branching and phototrophic bacteria. 11.11 Provide a rationale for the name deeply branching bacteria. 11.12 Explain the function of heterocysts in terms of both photosynthesis and nitrogen fixation. Deeply Branching Bacteria The deeply branching bacteria are so named because their rRNA sequences and growth characteristics lead scientists to conclude that these organisms are similar to the earliest bacteria; that is, they appear to have branched off the “tree of life” at an early stage. For example, the deeply branching bacteria are autotrophic, and early organisms must have been autotrophs because heterotrophs by definition must derive their carbon from autotrophs. Further, many of the deeply branching bacteria live in extreme habitats similar to those some scientists think existed on the early Earth—hot, acidic, anaerobic, and exposed to intense ultraviolet radiation from the sun. One representative of these microbes—the Gram-negative Aquifex (ăk’wē-feks), a bacterium in the phylum Aquificae— is considered to represent the earliest branch of bacteria. It is chemoautotrophic, hyperthermophilic, and microaerophilic, deriving energy and carbon from inorganic sources in very hot habitats containing little oxygen. Another representative of deeply branching bacteria is Deinococcus (dī-nō-kok’ŭs), in phylum Deinococcus-Thermus, which grows as tetrads of Gram-positive cocci. Interestingly, the cell wall of Deinococcus has an outer membrane similar to that of Gram-negative bacteria, but the cells stain purple like typical Gram-positive microbes. Deinococcus is extremely resistant to radiation because of the way it packages its DNA, the 11/23/16 3:03 AM P       Chapter 11    Characterizing and Classifying rokaryotes presence of radiation-absorbing pigments, unique lipids within its membranes, and high cytoplasmic levels of manganese that protect its DNA repair proteins from radiation damage. Even when exposed to 5 million rad of radiation, which shatters its chromosome into hundreds of fragments, Deinococcus has enzymes that repair the damage. Not surprisingly, researchers have isolated Deinococcus from sites severely contaminated with radioactive wastes. Vegetative cell Akinete Phototrophic Bacteria Heterocyst ­ ­ Phototrophic bacteria acquire the energy needed for anabolism by absorbing light with pigments located in thylakoids called photosynthetic lamellae. They lack the membrane-bound thylakoids seen in eukaryotic chloroplasts. Most phototrophic bacteria are also autotrophic—they produce organic compounds from carbon dioxide. Phototrophs are a diverse group of microbes that are taxonomically confusing. Based on their pigments and their source of electrons for photosynthesis, phototrophic bacteria can be divided into five groups (though classified in four phyla based on 16S rRNA sequencing). • • • • • LM (a) 10 µm Sheath (glycocalyx) Blue-green bacteria (phylum Cyanobacteria) Green sulfur bacteria (phylum Chlorobi) Green nonsulfur bacteria (phylum Chloroflexi) Purple sulfur bacteria (phylum Proteobacteria) Purple nonsulfur bacteria (phylum Proteobacteria) We consider them together in the following sections because of their common phototrophic metabolism. (b) LM 5 µm (c) LM 10 µm ­ ▲ FIGURE 11.14 Examples of cyanobacteria with different growth habits. (a) Anabaena, which grows as a filament of cocci with H ­ ­ differentiated cells. eterocysts fix nitrogen; akinetes are reproductive cells. (b) Merismopedia, which grows as a flat sheet of cocci surrounded by a gelatinous glycocalyx. (c) Oscillatoria, which forms a filament of tightly appressed disk-shaped cells within a sheath. light 12H2O + 6CO2 ¡ C6H12O6 + 6H2O + 6O2 (1) ­ ­ For this reason, cyanobacteria were formerly called blue­green algae; however, the name cyanobacteria properly emphasizes their true bacterial nature: They are prokaryotic and have peptidoglycan cell walls. Additionally, they lack membranous cellular organelles such as nuclei, mitochondria, and chloroplasts. Photosynthesis by cyanobacteria is thought to have transformed the anaerobic atmosphere of the early Earth into our oxygen-containing one, and according to the endosymbiotic theory, chloroplasts developed from cyanobacteria. Indeed, M11_BAUM7206_05_SE_C11.indd 330 chloroplasts and cyanobacteria have similar rRNA and structures, such as 70S ribosomes and photosynthetic membranes. Nit rogen is a n essent ia l element i n protei n s a nd nucleic acids. Though nitrogen constitutes about 79% of the atmosphere, relatively few organisms can utilize the element in gaseous form. A few species of filamentous cyanobacteria as well as some proteobacteria (discussed later in the chapter) reduce nitrogen gas (N2) to ammonia (NH3) via a process called nitrogen fixation. Nitrogen fixation is essential for life on Earth because nitrogen fixers not only are able to enrich their own growth but also provide nitrogen in a usable form to other organisms. Because the enzyme responsible for nitrogen fixation is inhibited by oxygen, nitrogen-fixing cyanobacteria are faced with a problem—how to segregate nitrogen fixation, which is inhibited by oxygen, from oxygenic photosynthesis, which produces oxygen. Nitrogen-fixing cyanobacteria solve this problem ­ ­ ­ ­ ­ ­ Cyanobacteria Cyanobacteria are Gram-negative phototrophs that vary greatly in shape, size, and method of reproduction. They range in size from 1 mm to 10 mm in diameter and are typically coccoid or disk shaped. Coccal forms can be single or arranged in pairs, tetrads, chains, or sheets (FIGURE 11.14a, b); disk-shaped forms are often tightly appressed end to end to form filaments that can be either straight, branched, or helical and are frequently contained in a gelatinous glycocalyx called a sheath (FIGURE 11.14c). Some filamentous cyanobacteria are motile, moving along surfaces by gliding. Cyanobacteria generally reproduce by binary fission, with some species also reproducing by motile fragments or by thick-walled spores called akinetes (ā-kin-ēts’; see Figure 11.14a). Like plants and algae, cyanobacteria utilize chlorophyll a and are oxygenic (generate oxygen) during photosynthesis: 06/03/2018 10:05       Survey of Bacteria ­ Comparing Prokaryotes and Eukaryotes light (2) LE A R N I N G O UTC O M E 11.13 Discuss the lack of cell walls in mycoplasmas. 11.14 Identify significant beneficial or detrimental effects of the genera Clostridium, Bacillus, Listeria, Lactobacillus, Streptococcus, and Staphylococcus. 11.15 Describe the difference between low and high G + C content. Now we turn our attention to various groups of Gram-positive bacteria and to a different characteristic of microbes that is used in the classification of Gram-positive bacteria—G + C content. This is the percentage of all base pairs in a genome that are guanine-cytosine base pairs, and it is a useful criterion in classifying Gram-positive bacteria. Those with G + C content below 50% are considered “low G + C bacteria”; the remainder are considered “high G + C bacteria.” Because taxonomists have discovered that Gram-positive bacteria with low G + C content have similar sequences in their 16S rRNA and that those with high G + C content also have rRNA sequences in common, they have assigned low G + C bacteria and high G + C bacteria to different phyla. We discuss the low G + C bacteria first. The low G + C Gram-positive bacteria are classified within phylum Firmicutes (fer-mik’ū-tēz), which includes three groups: clostridia, mycoplasmas, and other low G + C Gram-positive bacilli and cocci. Next, we consider these three groups in turn. ­ 12H2S + 6CO2 ¡ C6H12O6 + 6H2O + 12S Low G + C Gram-Positive Bacteria s ­ ­ ­ ­ ­ Green and Purple Phototrophic Bacteria Green and purple bacteria differ from plants, algae, and cyanobacteria in two ways: They use bacteriochlorophylls for photosynthesis instead of chlorophyll a, and they are anoxygenic; that is, they do not generate oxygen during photosynthesis. Green and purple phototrophic bacteria commonly inhabit anaerobic muds rich in hydrogen sulfide at the bottoms of ponds and lakes. These microbes are not necessarily green and purple in color; rather, the terms refer to pigments in some of the better-known members of the groups. As previously indicated, the green and purple phototrophic bacteria include both sulfur and nonsulfur forms. Whereas nonsulfur bacteria derive electrons for the reduction of CO2 from organic compounds such as carbohydrates and organic acids, sulfur bacteria derive electrons from the oxidation of hydrogen sulfide to sulfur, as follows: by photosynthetic plants. It was initially thought that oxygen was derived from carbon dioxide, but a comparison of photosynthesis in cyanobacteria (Equation 1) with that in sulfur bacteria (Equation 2) provided evidence that free oxygen is derived from water. Whereas green sulfur bacteria are placed in phylum Chlorobi, green nonsulfur bacteria are members of phylum Chloroflexi. The purple bacteria (both sulfur and nonsulfur) are placed in three classes of phylum Proteobacteria, which is composed of Gram-negative bacteria and is discussed shortly. TABLE 11.1 on p. 332 summarizes the characteristics of phototrophic bacteria. ▶ ANIMATIONS: Photosynthesis: ­ in one of two ways. Most cyanobacteria isolate the enzymes of nitrogen fixation in specialized, thick-walled, nonphotosynthetic cells called heterocysts (see Figure 11.14a). Heterocysts transport reduced nitrogen to neighboring cells in exchange for glucose. A few types of cyanobacteria photosynthesize during daylight hours and fix nitrogen at night, thereby separating nitrogen fixation from photosynthesis in time rather than in space. ­ ­ Green sulfur bacteria deposit the resultant sulfur outside their cells, whereas purple sulfur bacteria deposit sulfur within their cells (FIGURE 11.15). At the beginning of the 20th century, a prominent question in biology concerned the origin of the oxygen released Clostridia ­ Clostridia are rod-shaped, obligate anaerobes, many of which form endospores. The group is named for the genus Clostridium,9 which is important both in medicine—in large part because its members produce potent toxins, which cause a variety of diseases in humans—and in industry because their endospores enable them to survive harsh conditions, including many types of disinfection and antisepsis. Examples of clostridia include C. tetani (te’tan-ē, which causes tetanus), C. perfringens (perfrin’jens; gangrene), C. botulinum (bo-tū-lī’num; botulism), and LM 2 µm ­ ▲ FIGURE 11.15 Deposits of sulfur within purple sulfur bacteria. These bacteria oxidize H2S to produce the granules of elemental sulfur evident inside the cells. Where do green sulfur bacteria deposit sulfur grains? Figure 11.15 Green sulfur bacteria deposit sulfur grains externally. M11_BAUM7206_05_SE_C11.indd 331 9From Greek kloster, meaning “spindle.” 11/23/16 3:03 AM TABLE 11.1 r 11    Characterizing and Classifying rokaryotes P p te ha       C Characteristics of the Major Groups of Phototrophic Bacteria Phylum Chlorobi Chloroflexi Proteobacteria Proteobacteria Class Cyanobacteria Chlorobia Chloroflexi Gammaproteobacteria Alphaproteobacteria and one genus in Betaproteobacteria Common Name(s) Blue-green bacteria (“blue-green algae”) Green sulfur bacteria Green nonsulfur bacteria Major Photosynthetic Pigments Chlorophyll a Bacteriochlorophyll a plus c, d, or e Bacteriochlorophylls a and c Bacteriochlorophyll a or b Bacteriochlorophyll a or b Types of Photosynthesis Oxygenic Anoxygenic Anoxygenic Anoxygenic Anoxygenic Electron Donor in Photosynthesis H 2O H2, H2S, or S Organic compounds H2, H2S, or S Organic compounds Sulfur Deposition None Outside cell None nside cell None I urple sulfur bacteria urple nonsulfur bacteria P P Cyanobacteria Nitrogen Fixation Some species None None None None Motility Nonmotile or gliding Nonmotile Gliding Motile with polar or peritrichous flagella Nonmotile or motile with polar flagella ­ ­ ­ ­ C. difficile (di’fe-sēl, severe diarrhea). (Chapters 22 and 24 examine these pathogens and the diseases they cause in greater detail.) Microbes related to Clostridium include Epulopiscium, a giant bacterium that “gives birth” (discussed on pp. 323–324); sulfate-reducing microbes, which produce H2S from elemental sulf ur duri ng a naerobic respirat ion; a nd Selenomonas (sĕ-lē’nō-mō’nas), a genus of vibrio-shaped bacteria that includes members that live as part of the biofilm (plaque) that forms on the teeth of warm-blooded animals. Selenomonas is unusual because even though it has a typical Gram-positive rRNA sequence, it has a negative Gram reaction—it stains pink. Researchers have linked one species of Selenomonas to obesity. for attachment to eukaryotic cells and that gives the bacterium a pearlike shape. They require organic growth factors, such as cholesterol, fatty acids, vitamins, amino acids, and nucleotides, which they acquire from their host or which must be added to laboratory media. When growing on solid media, most species form a distinctive “fried egg” appearance because cells in the center of the colony grow into the agar while those around the perimeter only spread across the surface (FIGURE 11.16). In animals, mycoplasmas colonize mucous membranes of the respiratory and urinary tracts and are associated with Mycoplasmas ­ A second group of low G + C bacteria are the mycoplasmas10 (mī’kō-plaz’mas). These facultative or obligate anaerobes lack cell walls, meaning that they stain pink when Gram stained. Indeed, until their nucleic acid sequences proved their similarity to Gram-positive organisms, mycoplasmas were classified as Gram-negative microbes instead of in phylum Firmicutes with other low G + C Gram-positive bacteria. Mycoplasmas are able to survive without cell walls in part because they colonize osmotically protected habitats, such as animal and human bodies, and because they have tough cytoplasmic membranes, many of which contain lipids called sterols that give the membranes strength and rigidity. Because they lack cell walls, they are pleomorphic. They were named “mycoplasmas” because their filamentous forms resemble the filaments of fungi. Mycoplasmas have diameters ranging from 0.2 mm to 0.8 mm, making them the smallest free-living cells, and many mycoplasmas have a terminal structure that is used LM 0.1 mm ▲ FIGURE 11.16 The distinctive “fried egg” appearance of 10From Greek mycos, meaning “fungus,” and plassein, meaning “to mold.” M11_BAUM7206_05_SE_C11.indd 332 Mycoplasma colonies. This visual feature is unique to some species of this genus of bacteria when growing on an agar surface. 11/23/16 3:03 AM       Survey of Bacteria Listeria Another pathogenic low G + C Gram-positive rod is Listeria monocytogenes (mo-nō-sī-tah’je-nēz), which can contaminate milk and meat products. This microbe, which does not produce endospores, is notable because it continues to reproduce under refrigeration and because it can survive inside phagocytic white blood cells. Listeria rarely causes disease in adults, but it can kill a fetus in an infected woman when it crosses the placental barrier. It also causes meningitis11 and bacteremia12 when it infects immunocompromised patients, such as the aged and patients with AIDS, cancer, or diabetes. Lac tobac illus Organisms in the genus Lactobacillus are non-spore-forming rods normally found growing in the human mouth, stomach, intestinal tract, and vagina. These organisms rarely cause disease; instead, they protect the body by inhibiting the growth of pathogens—a situation called microbial antagonism. Lactobacilli are used in industry in the production of yogurt, buttermilk, pickles, and sauerkraut. (The Beneficial Microbes: Probiotics box on p. 301 discusses the potential role of Lactobacillus in promoting human health.) ­ ­ Bacillus The genus Bacillus includes endospore-forming aerobes and facultative anaerobes that typically move by means of peritrichous flagella. The genus name Bacillus should not be confused with the general term bacillus. The latter refers to any rod-shaped cell of any genus. Numerous species of Bacillus are common in soil. Bacillus thuringiensis (thur-in-jē-en’sis) is beneficial to farmers and gardeners. During sporulation, this bacterium produces a crystalline protein that is toxic to caterpillars that ingest it (FIGURE 11.17). Gardeners spray Bt toxin, as preparations of the bacterium and toxin are known, on plants to protect them from caterpillars. Scientists have achieved the same effect, without the need of spraying, by introducing the gene for Bt toxin into plants’ chromosomes. Other beneficial species of Bacillus include B. polymyxa (po-lē-miks’ă) and B. licheniformis (lī-ken-i-for’mis), which synthesize the antibiotics polymyxin ­ ­ ­ ­ A third group of low G + C Gram-positive organisms is composed of bacilli and cocci that are significant in environmental, industrial, and health care settings. Among the genera in this group are Bacillus, Listeria (lis-tēr’ē-ă), Lactobacillus (lak’tōbă-sil’ŭs), Streptococcus, Enterococcus (en’ter-ō-kok’ŭs), and Staphylococcus (staf’i-lō-kok’ŭs). (Chapters 19–24 discuss the pathogens in these genera in greater detail.) ­ Other Low G + C Gram-Positive Bacilli and Cocci and bacitracin, respectively. (Chapter 10 discusses the production and effects of antibiotics in more detail.) Bacillus anthracis (an-thrā’sis), which causes anthrax, gained notoriety in 2001 as an agent of bioterrorism. Its endospores either can be inhaled or can enter the body through breaks in the skin. Each endospore germinates and becomes a vegetative cell producing toxins that kill surrounding tissues. Untreated cutaneous anthrax is fatal in 20% of patients; untreated inhalational anthrax is generally 100% fatal without prompt, aggressive treatment. Refrigeration of food prevents excessive growth of this and many other bacterial contaminants (see Chapter 9). ­ pneumonia and urinary tract infections. (Chapters 22 and 24 discuss pathogenic mycoplasmas and the diseases they cause more fully.) Bt toxin Streptococcus and Enterococcus The genera Streptococcus and Enterococcus are diverse groups of Gram-positive cocci associated in pairs and chains (see Figure 11.8a and b). They cause numerous human diseases, including pharyngitis, scarlet fever, impetigo, fetal meningitis, wound infections, pneumonia, and diseases of the inner ear, skin, blood, and kidneys. In recent years, health care providers have become concerned over strains of multidrug-resistant enterococci and streptococci. Of particular concern are so-called flesh­eating streptococci (see Disease in Depth on pp. 560–561), which produce toxins that destroy muscle and fat tissue; and enterococci, which are leading causes of healthcare-associated (nosocomial) infections. ­ ­ Bacillus thuringiensis Staphylococcus Among the common inhabitants of humans is Staphylococcus aureus13 (o’rē-ŭs), which is typically found growing harmlessly in clusters in the nasal passages. SEM 1 µm ▲ FIGURE 11.17 Crystals of Bt toxin, produced by the endospore-forming Bacillus thuringiensis. The crystalline protein ­ kills caterpillars that ingest it. M11_BAUM7206_05_SE_C11.indd 333 of the membranes covering the brain and spinal cord; from Greek meninx, meaning “membrane.” 12The presence of bacteria, particularly those that produce disease symptoms, in the blood. 13From Latin aurum, meaning “gold” because it produces yellow pigments. 11Inflammation 06/03/2018 09:06 P       Chapter 11    Characterizing and Classifying rokaryotes TABLE 11.2 Characteristics of Selected Gram-Positive Bacteria Phylum/Class G + C Percentage Representative Genera Special Characteristics Low (less than 50%) Clostridium Obligate anaerobic rod; endospore former Diseases Clostridia T Firmicutes etanus, botulism, Selenomonas art of oral biofilm on human teeth; stains like Gram-negative bacteria (pink) Dental caries Mycoplasma Lacks cell walls; pleomorphic; smallest free-living cell; stains like Gram-negative bacteria (pink) Facultative anaerobic rod; endospore former Listeria Contaminates dairy products roduces yogurt, buttermilk, pickles, sauerkraut P P Bacillus Lactobacillus severe diarrhea neumonia, urinary tract infections A Low (less than 50%) gangrene, nthrax Listeriosis R Bacilli Low (less than 50%) Giant rod P Mollicutes Epulopiscium are blood infections Streptococcus Cocci in chains Strep throat, scarlet fever, and others Staphylococcus Cocci in clusters Bacteremia, food poisoning, and others Corynebacterium Snapping division; metachromatic granules in cytoplasm Diphtheria Mycobacterium Waxy cell walls (mycolic acid) Actinomyces Filaments Nocardia Filaments; degrade pollutants High G + C Gram-Positive Bacteria LE A R N I N G O U TC O M E S 11.16 Explain the slow growth of Mycobacterium. 11.17 Identify significant beneficial or detrimental properties of the genera Corynebacterium, Mycobacterium, Actinomy­ ces, Nocardia, and Streptomyces. Taxonomists classify Gram-positive bacteria with a G + C percentage greater than 50% in the phylum Actinobacteria. The phylum includes species with rod-shaped cells (many of which M11_BAUM7206_05_SE_C11.indd 334 T A ctinomycosis are sinus infections are significant human pathogens) and filamentous bacteria, which resemble fungi in their growth habit and in the production of reproductive spores. Here, we examine briefly some prominent high G + C Gram-positive bacteria. (Chapters 19–24 discuss the numerous pathogens in this group more fully.) Corynebacterium Members of the genus Corynebacterium are pleomorphic—though generally rod-shaped—aerobes and facultative anaerobes. They reproduce by snapping division, which often causes the cells to form V-shapes and palisades (see Figures 11.4 and 11.9d). Corynebacteria are also characterized by their stores of phosphate within inclusions called metachromatic granules, which stain differently from the rest of the cytoplasm when the cells are stained with methylene blue or toluidine blue. The bestknown species is C. diphtheriae, which causes diphtheria. ­ A variety of toxins and enzymes allow some strains of S. aureus to invade the body and cause such diseases as bacteremia, pneumonia, wound infections, food poisoning, toxic shock syndrome, and diseases of the joints, bones, heart, and blood. Horizontal gene transfer, in which genes are shared between and among neighboring cells (discussed in Chapter 7), results in many different strains of S. aureus. Strains vary widely in their capacity to make toxins and harmful enzymes, some making one or a few and others generating dozens. Further, strains of S. aureus can become resistant to multiple antibiotics. This is especially true of the infamous methicillin-resistant S. aureus (MRSA), which is resistant to penicillin and cephalosporin antimicrobial drugs. The characteristics of the low G + C Gram-positive bacteria are summarized in the first part of TABLE 11.2. Next, we consider Gram-positive bacteria that have high G + C ratios. roduce antibiotics uberculosis and leprosy Lesions R Streptomyces P igh (greater than 50%) ­ Actinobacteria H Actinobacteria Mycobacterium The genus Mycobacterium (mī’kō-bak-tēr’ē-ŭm) is composed of aerobic species that are slightly curved or straight rods that sometimes form filaments. Mycobacteria grow very slowly, often requiring a month or more to form a visible colony on an agar surface. Their slow growth is partly due to the time and energy required to enrich their cell walls with high concentrations of long carbon-chain waxes called mycolic acids, which make the cells resistant to desiccation and to staining with water-based dyes. Microbiologists developed the 06/03/2018 09:07       Survey of Bacteria filaments that make them resemble fungi. Nocardia is notable because it can degrade many pollutants of landfills, lakes, and streams, including waxes, petroleum hydrocarbons, detergents, benzene, polychlorinated biphenyls (PCBs), pesticides, and rubber. Some species of Nocardia cause lesions in humans, particularly in the brain and skin, though they can occur in other organs and tissues as well. ­ Spores ­ Streptomyces Bacteria in the genus Streptomyces (strep-tō-mī’sēz) are important in several realms. Ecologically, they recycle nutrients in the soil by degrading a number of carbohydrates, including cellulose, lignin (the woody part of plants), and chitin (the outer skeletal material of insects and crustaceans). They can also degrade latex, aromatic chemicals (organic compounds containing a benzene ring), and keratin (the protein that forms hair, nails, and horns). The metabolic by-products of Streptomyces give soil its musty smell. Medically, Streptomyces species produce most of the important antibiotics, including chloramphenicol, erythromycin, and tetracycline (discussed in Chapter 10). 10 µm ­ LM ▲ FIGURE 11.18 The branching filaments of actinomycetes. This photograph shows filaments of a colony of Streptomyces sp. growing on agar. How do the filaments of actinomycetes compare to the filaments of fungi? ­ Figure 11.18 Filaments of actinomycetes are thinner than those of fungi, and they are composed of prokaryotic cells. Actinomycetes ­ ­ Actinomycetes (ak’ti-nō-mī-sētz) are high G + C Gram-positive bacteria that form branching filaments resembling fungi (FIGURE 11.18). Of course, in contrast to fungi, the filaments of actinomycetes are composed of prokaryotic cells. As we have seen, some actinomycetes also resemble fungi in the production of chains of reproductive spores at the ends of their filaments. These spores should not be confused with endospores, which are resting stages and not reproductive cells. Actinomycetes may cause disease, particularly in immunocompromised patients. Among the important actinomycete genera are Actinomyces (which gives this group its name), Nocardia, and Streptomyces. 14Meaning that they grow best with a relatively high concentration of carbon dioxide. M11_BAUM7206_05_SE_C11.indd 335 ­ Actinomyces Species of Actinomyces (ak’ti-nō-mī’sēz) are facultative capneic 14 filaments that are normal inhabitants of the mucous membranes lining the oral cavity and throats of humans. Actinomyces israelii (is-rā’el-ē-ē) growing as an opportunistic pathogen in humans destroys tissue to form abscesses and can spread throughout the abdomen, consuming every vital organ. Gram-Negative Proteobacteria Phylum Proteobacteria15 constitutes the largest and most diverse group of bacteria. Scientists have identified over 2000 species of proteobacteria. Though they have a variety of shapes, reproductive strategies, and nutritional types, they are all Gram-negative and share common 16S rRNA nucleotide sequences. The G + C percentage of Gram-negative species is not critical in delineating taxa of most Gram-negative organisms, so we will not consider this characteristic in our discussion of these bacteria. There are six distinct classes of proteobacteria, designated by the first six letters of the Greek alphabet—alpha, beta, gamma, delta, epsilon, and zeta. These classes are distinguished by minor differences in their rRNA sequences. Here, we will focus our attention on species with novel characteristics as well as species with practical importance. Class Alphaproteobacteria LE A R N I N G O UTC O M E s  ­ ­ acid­fast stain for mycobacteria because they are difficult to stain by standard staining techniques such as the Gram stain (see ­Chapter 4). Though some mycobacteria are free-living, the most prominent species are pathogens of animals and humans, including Mycobacterium tuberculosis (too-ber-kyū-lō’sis) and Mycobacterium leprae (lep’rī), which cause tuberculosis and leprosy, respectively. Mycobacteria should not be confused with the low G + C mycoplasmas discussed earlier. Nocardia Species of Nocardia (nō-kar’dē-ă) are soil- and waterdwelling aerobes that typically form aerial and subterranean Table 11.2 includes a summary of the characteristics of the genera of high G + C Gram-positive bacteria (phylum Actinobacteria) discussed in this chapter. To this point, we have discussed archaea and deeply branching, phototrophic, and Gram-positive bacteria. Now we turn our attention to the Gram-negative bacteria that are grouped together within the phylum Proteobacteria. 11.18 Describe the appearance and function of prosthecae in alphaproteobacteria. 11.19 Describe three genera of nitrogen-fixing alphaproteo- bacteria and their association with crops or biofuels. 11.20 Describe nitrification, and name a nitrifying bacterium. 11.21 Name two diseases caused by alphaproteobacteria. 15Named for the Greek god Proteus, who could assume many shapes. 11/23/16 3:03 AM r 11    Characterizing and Classifying rokaryotes P Flagellum Prostheca TEM 1 µm ▲ FIGURE 11.19 A prostheca. This extension of an ▲ FIGURE 11.20 Nodules on pea plant roots. Rhizobium, a alphaproteobacterial cell increases surface area for absorbing nutrients and serves as an organ of attachment. ­ ­ nitrogen-fixing alphaproteobacterium, stimulates the growth of such nodules. hydrogen, forming hydrogen gas (H2), which can be used as a clean-burning fuel. Biofuel producers such as R. palustris may help relieve the world’s dependence on oil and gas. Nitrifying Bacteria Organisms need a source of electrons for redox reactions of metabolism (see Chapters 5 and 6). Bacteria that derive electrons from the oxidation of nitrogenous compounds are called nitrifying bacteria. These microbes are important in the environment and in agriculture because they convert reduced nitrogenous compounds, such as ammonia (NH3), into nitrate (NO3)—a two-step process called nitrification. Nitrate moves more easily through soil and is therefore more available to plants. The first step in nitrification is the oxidation of ammonia into nitrite (NO2); the second step is further oxidation of nitrite into nitrate (NO3): - N2 + 8H + 8e ¡ 2NH3 + H2 (3)  + ­ ­ Azospirillum associates with the outer surfaces of roots of tropical grasses, such as sugarcane. In addition to supplying nitrogen to the grass, this bacterium also releases chemicals that stimulate the plant to produce numerous root hairs, increasing a root’s surface area and thus its uptake of nutrients. Rhizobium grows within the roots of leguminous plants, such as peas, beans, and clover, stimulating the formation of nodules on their roots (FIGURE 11.20). Rhizobium cells within the nodules make ammonia available to the plant, encouraging growth. Scientists are actively seeking ways to successfully insert the genes of nitrogen fixation into plants such as corn, which requires large amounts of nitrogen. Rhodopseudomonas palustris (rō-dō’soo-dō-mō′ nas pal-us’tris) is another nitrogen-fixing alphaproteobacterium. Scientists are actively studying this bacterium because it can also reduce M11_BAUM7206_05_SE_C11.indd 336 2NH3 + 3O2 S 2NO2- + 2H2O + 2H + 2NO2- + O2 ¡ 2NO3-  ­ ­ Nitrogen Fixers Two genera of nitrogen fixers in the class Alphaproteobacteria—Azospirillum (ā-zō-spī’ril-ŭm) and Rhizobium (rī-zō’bē-ŭm)—are important in agriculture. They grow in association with the roots of plants, where they make atmospheric nitrogen available to the plants as ammonia (NH3), which is one kind of fixed nitrogen:  ­ Alphaproteobacteria are typically aerobes capable of growing at very low nutrient levels. Many have unusual methods of metabolism, as we will see shortly. They may be rods, curved rods, spirals, coccobacilli, or pleomorphic. Many species have unusual extensions called prosthecae (pros-thē’kē), which are composed of cytoplasm surrounded by the cytoplasmic membrane and cell wall (FIGURE 11.19). They use prosthecae for attachment and to increase surface area for nutrient absorption. Some prosthecate species produce buds at the ends of the extensions. ­ p te ha       C (4a) (4b) No microbe can perform both reactions. Nitrifying alphaproteobacteria include species of Nitrobacter (nī-trōbak’ter), which perform the second step of nitrification. The first step of nitrification is performed either by archaea or by betaproteobacteria. Purple Nonsulfur Phototrophs With one exception (the betaproteobacterium Rhodocyclus), purple nonsulfur phototrophs are classified as alphaproteobacteria. Purple nonsulfur bacteria grow in the upper layer of mud at the bottoms of lakes and ponds. As we discussed earlier, they harvest light as an energy source by using bacteriochlorophylls, and they do not generate oxygen during photosynthesis. Morphologically, they may be rods, curved rods, or spirals; some species are prosthecate. 11/23/16 3:03 AM       Survey of Bacteria Refer to Table 11.1 on p. 332 to review the characteristics of all phototrophic bacteria. Rock or other substrate 1 Pathogenic Alphaproteobacteria Notable pathogens among the alphaproteobacteria include Rickettsia (ri-ket’sē-ă) and Brucella (broo-sel’lă). Rickettsia is a genus of small, Gram-negative, aerobic rods that live and reproduce inside mammalian cells. Outside a host cell, rickettsias are unstable and quickly die; therefore, they require a vector for transmission from host to host. They are transmitted through the bites of arthropods (fleas, lice, ticks, and mites). Rickettsias cause a number of human diseases, including typhus and Rocky Mountain spotted fever. Brucella is a coccobacillus that causes brucellosis, a disease of mammals characterized by spontaneous abortions and sterility in animals. In contrast, infected humans suffer chills, sweating, fatigue, and fever. Brucella is notable because it survives phagocytosis by white blood cells—normally an important step in the body’s defense against disease. Flagellum 2 3a Swarmer cell Cell doubles in size 3b 4a or 4b ­ Other Alphaproteobacteria Other alphaproteobacteria are important in industry and the environment. For example, Acetobacter (a-sē’tō-bak-ter) and Gluconobacter (gloo-kon’ōbak-ter) are used to synthesize acetic acid in the production of vinegar. Caulobacter (kaw’lō-bak-ter) is a common prosthecate rod-shaped microbe that inhabits nutrient-poor seawater and freshwater; it can also be found in laboratory water baths. Caulobacter has a unique reproductive strategy (FIGURE 11.21). A cell that has attached to a substrate with its prostheca 1 grows 2 until it has doubled in size, at which time it produces a flagellum at its apex; it then divides by asymmetric binary fission 3 . The flagellated daughter cell, which is called a swarmer cell, then swims away. The swarmer cell can either attach to a substrate with a new prostheca that replaces the flagellum 4a or attach to other swarmer cells to form a rosette of cells 4b . The process of reproduction repeats about every two hours. Beneficial Microbes: A Microtube of Superglue on p. 338 examines an amazing property of Caulobacter prosthecae. Scientists are very interested in the usefulness of another alphaproteobacterium, Agrobacterium (ag’rō-bak-tēr’ē-um), which infects plants to form tumors called galls (FIGURE 11.22). The bacterium inserts a plasmid (an extrachromosomal DNA molecule) that carries a gene for a plant growth hormone through a pilus-like hollow filament into a plant cell, which then makes extra growth hormone. Growth hormone causes the cells of the plant to proliferate into a gall and to produce nutrients for the bacterium. Scientists have discovered that they can insert almost any DNA sequence into the plasmid, making it an ideal vector for genetic manipulation of plants. Characteristics of selected members of the alphaproteobacteria are listed in Table 11.4 on p. 344. Prostheca Rosette TEM 1.5 µm ▲ FIGURE 11.21 Growth and reproduction of Caulobacter. ­ ­ 1 A cell attached to a substrate by its prostheca. 2 Growth and production of an apical flagellum. 3 Division by asymmetrical binary fission to produce a flagellated daughter cell called a swarmer cell. 4a Attachment of a swarmer cell to a substrate by a prostheca that replaces the flagellum. 4b Swarmer cells can attach to one another to form rosettes. Class Betaproteobacteria LE A R N I N G O U TC O M E 11.22 Name three pathogenic, three useful, and one problem- atic betaproteobacteria. M11_BAUM7206_05_SE_C11.indd 337 ­ Betaproteobacteria are another diverse group of Gramnegative bacteria that thrive in habitats with low levels of nutrients. They differ from alphaproteobacteria in their rRNA sequences, though metabolically the two groups overlap. One example of such metabolic overlap is seen with Nitrosomonas (nī-trō-sō-mō’nas), an important nitrifying soil bacterium that performs the first reaction of nitrification—the conversion of ammonia into nitrite (Equation 4a on p. 336). In this section, we will discuss a few other interesting betaproteobacteria. Pathogenic Betaproteobacteria Species of Neisseria (nī-se’rē-ă) are Gram-negative diplococci that inhabit the mucous membranes of mammals and cause such diseases as gonorrhea, meningitis, pelvic inflammatory disease, and inflammation of the cervix, pharynx, and external lining of the eye. 11/23/16 3:03 AM r 11    Characterizing and Classifying rokaryotes P p te ha       C herbicides, and gasoline additives. (Chapters 22 and 24 discuss pathogenic betaproteobacteria in more detail.) ­ ­ ­ Other Betaproteobacteria Members of the genus Thiobacillus (thī-ō-bă-sil’ŭs) are colorless sulfur bacteria that are important in recycling sulfur in the environment by oxidizing hydrogen sulfide (H2S) or elemental sulfur (S0) to sulfate (SO42- ). Miners use Thiobacillus to leach metals from low-grade ore, though the bacterium does cause extensive pollution when it releases metals and acid from mine wastes. (Chapter 26 discusses the sulfur cycle.) Sewage treatment supervisors are interested in Zoogloea (zō’ō-glē-ă) and Sphaerotilus (sfēr-ō’til-us), two genera that form flocs—slimy, tangled masses of bacteria and organic matter in sewage (FIGURE 11.23). Zoogloea forms compact flocs that settle to the bottom of treatment tanks and assist in the purification process (see Figure 11.23). Sphaerotilus, in contrast, forms loose flocs that float, impede the proper flow of water, and can overflow onto walkways, creating a hazard to staff and interfering with proper function of the treatment plant. The characteristics of the genera of betaproteobacteria discussed in this section are summarized in Table 11.4 on p. 344. Class Gammaproteobacteria LE A R N I N G O UTC O M E Other pathogenic betaproteobacteria include Bordetella (bōr-dĕ-tel’ă), which is the cause of pertussis (whooping cough; see Emerging Disease Case Study: Pertussis on p. 341), and Burkholderia (burk-hol-der’ē-ă), which can colonize moist environmental surfaces (including laboratory and medical equipment) and the respiratory passages of patients with cystic fibrosis. Burkholderia can be beneficial as when it recycles organic compounds contaminating soil, such as crude oil, s  I ▲ FIGURE 11.22 A plant gall. nfecting cells of Agrobacterium have inserted into a plant chromosome a plasmid carrying a plant growth hormone gene. The hormone causes the proliferation of undifferentiated plant cells. These gall cells synthesize nutrients for the bacteria. 11.23 Describe the gammaproteobacteria. 11.24 Describe the metabolism of the largest group of gammaproteobacteria. 11.25 Contrast gammaproteobacterial nitrogen fixers with alphaproteobacterial nitrogen fixers. The gammaproteobacteria make up the largest and most diverse class of proteobacteria; almost every shape, arrangement of R I I I BENEF C AL M C OBES A Microtube of Superglue Caulobacter crescentus ­ ­ I ­ spot of glue the size of a .S. quarter. And remember, this bacterium lives in water, so its glue works even when submerged. Scientists are researching the biophysical and chemical mechanisms that give this biological glue such incredible gripping power. One critical component of the glue is N-acetylglucosamine, one of the sugar subunits of peptidoglycan found in bacterial cell walls. Scientists are struggling to characterize the other molecules that make up the glue. The problem? They cannot pry the glue free to analyze it. Some potential applications of such a bacterial superglue include use as a biodegradable suture in surgery, as a more durable dental adhesive, or to stick anti-biofilm disinfectants onto surfaces such as medical devices and ships’ hulls. ­ µm 11µm U SEM SEM A swarmer cell of the Gram-negative alphaproteobacterium Caulobacter crescentus attaches itself to an environmental substrate by secreting an organic adhesive from its prostheca as if it were a tube of glue. This polysaccharide-based bonding agent is the strongest known glue of biological origin, beating out such contenders as barnacle glue, mussel glue, and the adhesion of gecko lizard bristles. One way scientists gauge adhesive strength is to measure the force required to break apart two glued objects. Commercial superglues typically lose their grip when confronted with a shear force of 18 to 28 newtons (N) per square millimeter.a Dental cements bond with strengths up to 30 N/mm2, but Caulobacter glue is more than twice as adhesive. t maintains its grip up to 68 N/mm2! That is equivalent to being able to hang an adult female elephant on a wall with a M11_BAUM7206_05_SE_C11.indd 338 a1 newton is the amount of force needed to accelerate a 1-kg mass 1 meter per second. 11/23/16 3:04 AM       Survey of Bacteria ▲ FIGURE 11.23 Flocs—slimy, tangled masses of bacteria (a) LM 5 µm and organic matter. Sphaerotilus forms flocs that float and can clog sewage treatment plant pipes. Zoogloea forms “good” flocs that settle, as in the beaker on the right. Purple sulfur bacteria ­ cells, metabolic type, and reproductive strategy are represented in this group. Ribosomal studies indicate that gammaproteobacteria can be divided into several subgroups: • • • • Purple sulfur bacteria Intracellular pathogens Methane oxidizers Facultative anaerobes that utilize Embden-Meyerhof glycolysis and the pentose phosphate pathway • Pseudomonads, which are aerobes that catabolize carbohydrates by the Entner-Doudoroff and pentose phosphate pathways Here, we will examine some representatives of these groups. ­ Purple Sulfur Bacteria Whereas the purple nonsulfur bacteria are distributed among the alpha- and betaproteobacteria, purple sulfur bacteria are all gammaproteobacteria (FIGURE 11.24a). Purple sulfur bacteria are obligate anaerobes that oxidize hydrogen sulfide to sulfur, which they deposit as internal granules. They are found in sulfur-rich zones in lakes, bogs, and oceans. Some species form intimate relationships with marine worms, covering the body of a worm like strands of a rope (FIGURE 11.24b). Intracellular Pathogens Organisms in the genera Legionella (lē-jŭnel’lă) and Coxiella (kok-sē-el’ă) are pathogens of humans that avoid digestion by white blood cells, which are normally part of a body’s defense; in fact, they thrive inside these defensive cells. Legionella derives energy from the metabolism of amino acids, which are more prevalent inside cells than outside. Cox­ iella grows best at low pH, such as is found in the phagolysosomes of white blood cells. The bacteria in these genera cause Legionnaires’ disease and Q fever, respectively. M11_BAUM7206_05_SE_C11.indd 339 Roundworm (b) SEM 10 µm ▲ FIGURE 11.24 Purple sulfur bacteria. (a) These bacteria deposit sulfur granules internally. (b) Numerous bacteria on the surface of a nematode (roundworm, colored yellow) give the appearance of a rope. Methane Oxidizers Gram-negative bacteria that utilize methane as a carbon source and as an energy source are called methane oxidizers. Like archaeal methanogens, bacterial methane oxidizers inhabit anaerobic environments worldwide, growing just above the anaerobic layers that contain methanogens, which generate methane. Methane is one of the so-called greenhouse gases that retains heat in the atmosphere, but methane oxidizers can digest methane in their local environment, ideally before it can adversely affect the world’s climate. Glycolytic Facultative Anaerobes The largest group of gammaproteobacteria is composed of Gram-negative, facultatively anaerobic rods that catabolize carbohydrates by glycolysis and the pentose phosphate pathway. This group, which is divided into three families (TABLE 11.3 on p. 340), contains numerous human pathogens. 11/23/16 3:04 AM TABLE 11.3 r 11    Characterizing and Classifying rokaryotes P p te ha       C Representative Glycolytic Facultative Anaerobes of the Class Gammaproteobacteria Special Characteristics Representative Genera Typical Human Diseases Enterobacteriaceae Straight rods; oxidase negative; peritrichous flagella or nonmotile Escherichia Gastroenteritis Enterobacter ( arely pathogenic) Serratia ( arely pathogenic) Salmonella Enteritis Yersinia Klebsiella R U rinary tract infection Shigellosis P Shigella P Proteus R Family lague neumonia Vibrionaceae Vibrios; oxidase positive; polar flagella Vibrio Cholera Pasteurellaceae Cocci or straight rods; oxidase positive; nonmotile Haemophilus Meningitis in children, middle ear infections, pneumonia ­ Members of the family Enterobacteriaceae live in the guts of animals and can be harmless, beneficial, or pathogenic. Because of their effect on human health, scientists have studied enterobacteria, particularly Escherichia coli (esh-ĕ-rik’ē-ă ko’lī), more than any other bacteria. Researchers frequently use enterobacteria for laboratory studies of metabolism, genetics, and recombinant DNA technology. (Chapter 23 examines several pathogenic gammaproteobacteria in detail.) ­ Pseudomonads Bacteria called pseudomonads are Gramnegative, aerobic, flagellated, straight or slightly curved rods that catabolize carbohydrates by the Entner-Doudoroff and pentose phosphate pathways. These organisms are noted for their ability to break down numerous organic compounds; some strains can catabolize more than 80 different organic compounds, including oil, rubber, and plastic. Many pseudomonads are important pathogens of humans and animals and are involved in the spoilage of refrigerated milk, eggs, and meat because they can grow and catabolize proteins and lipids at 4°C. The pseudomonad group is named for its most important genus, Pseudomonas (soo-dō-mō’nas) (FIGURE 11.25), which causes diseases such as urinary tract infections, external otitis (swimmer’s ear), and lung infections in cystic fibrosis patients. Other pseudomonads, such as Azotobacter (ā-zō-tō-bak’ter) and Azomonas (ā-zō-mō’nas), are soil-dwelling, nonpathogenic nitrogen fixers; however, in contrast to nitrogen-fixing alphaproteobacteria, these gammaproteobacteria do not associate with the roots of plants. The characteristics of the members of the gammaproteobacteria discussed in this section are summarized in TABLE 11.4 on p. 344. 0.5 µm LE A R N I N G O U TC O M E 11.26 List several members of the deltaproteobacteria. The deltaproteobacteria are not a large assemblage, but, like other proteobacteria, they include a wide variety of metabolic types. M11_BAUM7206_05_SE_C11.indd 340 ­ ­ Desulfovibrio (dē’sul-fō-vib’rē-ō) is a sulfate-reducing microbe that is important in recycling sulfur in the environment. It is also an important member of bacterial communities living in the sediments of polluted streams and sewage treatment lagoons, where its presence is often apparent by the odor of hydrogen sulfide that it releases during anaerobic respiration. Hydrogen sulfide reacts with iron to form iron sulfide, so sulfate-reducing bacteria, such as Desulfovibrio, play a primary role in the corrosion of iron pipes in heating systems, sewer lines, and other structures. Bdellovibrio (del-lō-vib’rē-ō) is another deltaproteobacterium. It attacks and destroys other Gram-negative bacteria in a complex and unusual way (FIGURE 11.26a): 1. A free Bdellovibrio swims rapidly through the medium until it attaches via fimbriae to a Gram-negative bacterium. 2. It rapidly drills through the cell wall of its prey by secreting hydrolytic enzymes and rotating in excess of 100 revolutions per second (FIGURE 11.26b). ­ Class Deltaproteobacteria ▲ FIGURE 11.25 Pseudomonas has notable polar flagella. ­ ­ ­ ­ TEM 11/23/16 3:04 AM       Survey of Bacteria U I I R EME G NG D SEASE CASE ST DY Pertussis A bacterium, Bordetella pertussis, causes pertussis, commonly known as whooping cough. The disease is usually considered a childhood ailment, though it can strike adults. Older patients seldom develop the severe symptoms or characteristic “whooping” sound associated with gasping inhalation, but in Jeeyun’s case, the severity and length of the coughing led to a speedy diagnosis. mmunization is the only way to control pertussis, but adults have been lax in vaccinating children and receiving boosters for themselves. As a result, whooping cough is reemerging as a major problem in the industrialized world. nfected people spread Bordetella in respiratory droplets to their neighbors. (For more about pertussis, see p. 688.) I I I Jeeyun was coughing again. She had been coughing off and on for two weeks. f she had thought of it, she might have noticed that the coughing spells began soon after her return from New York, where she had visited her grandmother. Within a week of arriving home in California, she had developed coldlike signs—runny nose, sneezing, and a slight fever—but she didn’t remember these things. What she did know was that the coughing was worse; her chest hurt from the constant hacking. Then the coughing broke two ribs. The surprising pain caused Jeeyun to involuntarily urinate. When the coughing stopped, she vomited and fainted in a heap on the floor. This was no ordinary cough! Jeeyun’s roommate called 911. Later, emergency room staff at the hospital bandaged her chest to stabilize the broken ribs and diagnosed the cough as pertussis. 1. Why might adults neglect to get a pertussis booster shot for themselves? 2. Why might parents leave their children unimmunized against pertussis? 3. Why is immunization a societal and not merely a personal decision? Bdellovibrio Gram-negative bacterial prey 1 Outer membrane 10 minutes Periplasmic space 2 5 10 seconds later 20 minutes later Cytoplasmic membrane 3 20 minutes later 4 150–210 minutes later (b) TEM 0.5 µm (a) ▲ FIGURE 11.26 Bdellovibrio, a Gram-negative pathogen of other Gram-negative bacteria. (a) Life cycle, including the elapsed times between events. (b) Bdellovibrio invading the periplasmic space of its host. M11_BAUM7206_05_SE_C11.indd 341 11/23/16 7:18 PM r 11    Characterizing and Classifying rokaryotes P p te ha       C 3. Once inside, Bdellovibrio lives in the periplasmic space—the space between the cytoplasmic membrane and the outer membrane of the cell wall. It kills its host by disrupting the host’s cytoplasmic membrane and inhibiting DNA, RNA, and protein synthesis. 4. The invading bacterium uses the nutrients released from its dying prey and grows into a long filament. 5. Eventually, the filament divides into as many as nine smaller cells at once, each of which, when released from the dead cell, produces a flagellum and swims off to repeat the process. Undergoing multiple fissions to produce many offspring is a rare form of reproduction. The life cycle of myxobacteria can be summarized as follows (FIGURE 11.27a): ­ ­ 1. Vegetative myxobacteria glide on slime trails through their environment, digesting yeasts and other bacteria or scavenging nutrients released from dead cells. When nutrients and cells are plentiful, the myxobacteria divide by binary fission; when nutrients are depleted, however, they aggregate by gliding into a mound of cells. 2. Myxobacteria within the mound differentiate to form a macroscopic fruiting body ranging in height from 50 mm to 700 mm. ­ 3. Some cells within the fruiting body develop into dormant myxospores that are enclosed within walled structures called sporangia (singular: sporangium) (FIGURE 11.27b). ­ ­ ­ 4. The sporangia release the myxospores, which can resist desiccation and nutrient deprivation for a decade or more. ­ ­ ­ Myxobacteria are Gram-negative, aerobic, soil-dwelling bacteria with a unique life cycle for prokaryotes in that individuals cooperate to produce differentiated reproductive structures. In fact, myxobacteria demonstrate many features that scientists previously thought were only found in eukaryotes, such as moving as a group, cell differentiation, and cell-to-cell communication via hormones. Not surprisingly, the genome of a myxobacterium can be over 10 million bp in size. Binary fission (nutrients plentiful) ­ 5. When nutrients are again plentiful, the myxospores germinate and become vegetative cells. Mounding when nutrients are depleted 1 Vegetative cells Mound of cells Slime trail 2 Formation of fruiting body Sporangium Myxospores Sporangium 5 Myxospores germinate to form vegetative cells once nutrients are restored 4 3 Myxospores Fruiting body (a) (b) SEM 20 µm ­ ­ ▲ FIGURE 11.27 Life cycle of myxobacteria. (a) (1) Vegetative myxobacteria divide by binary fission when nutrients are plentiful. They aggregate in mounds when nutrients are depleted. (2) The mound forms fruiting bodies. (3) Some cells in a fruiting body develop into dormant myxospores within a sporangium. The sporangia release the myxospores (4), which remain dormant until nutrients are again plentiful, at which time they germinate and become vegetative cells (5). (b) Fruiting body. M11_BAUM7206_05_SE_C11.indd 342 11/23/16 3:04 AM       Survey of Bacteria ­ Class Epsilonproteobacteria of Bergey’s Manual into nine phyla that are grouped together for convenience rather than because of genetic relatedness. Species in six of the nine phyla are of relatively minor importance. Here, we discuss representatives from the three phyla that are either of particular ecological concern or significantly affect human health: the chlamydias (phylum Chlamydiae), the spirochetes (phylum Spirochaetes), and the bacteroids (phylum Bacteroidetes). ­ Myxobacteria live worldwide in soils that have decaying plant material or animal dung. Though certain species live in the Arctic and others in the tropics, most myxobacteria live in temperate regions. diseases. The class Epsilonproteobacteria includes Gram-negative rods, vibrios, or spirals. Important genera are Campylobacter (kam’pilō-bak’ter), which causes blood poisoning and inflammation of the intestinal tract, and Helicobacter (hel’ĭ-kō-bak’ter), which causes ulcers. (Chapter 23 examines these pathogens more fully.) Class Zetaproteobacteria LE A R N I N G O U TC O M E 11.28 Describe both the discovery of zetaproteobacteria and the type of metabolism most zetaproteobacteria use. ­ ­ ­ ­ Researchers discovered the new class, Zetaproteobacteria, in the mid-2000s based on DNA sequences. Discoveries of never-before-identified microbes are becoming common occurrences as modern scientists use metagenomic sequenc­ ing—sequencing of all the DNA from a site to discover all of the microbes present, not just the 1–2% that can be currently grown in the lab. Subsequent to the discovery of zetaproteobacteria as DNA sequences, scientists successfully cultured at least two of the organisms in the laboratory, with one species formally named, Mariprofundus ferrooxydans (mĕ-rē-prō-fun’dus fĕ-rō-oks’ē-danz). The name reflects the fact that these organisms oxidize iron as an energy source and use oxygen as the final electron acceptor. Based on their DNA sequences, most zetaproteobacteria appear to be autotrophic, using carbon dioxide as a carbon source. Scientists have discovered DNA from zetaproteobacteria in oceans around the world, so it is likely these bacteria play an important role in Earth’s iron cycle. The characteristics of the delta-, epsilon-, and zetaproteobacteria are summarized in Table 11.4 on p. 344. Chlamydias Microorganisms called chlamydias (kla-mid’ē-ăz) are small, Gram-negative cocci that grow and reproduce only within the cells of mammals, birds, and a few invertebrates. The smallest chlamydias—0.2 mm in diameter—are smaller than the largest viruses; however, in contrast to viruses, chlamydias have both DNA and RNA, cytoplasmic membranes, functioning ribosomes, reproduction by binary fission, and metabolic pathways. Like other Gram-negative prokaryotes, chlamydias have two membranes, but unlike most prokaryotes, they lack peptidoglycan. Because chlamydias and rickettsias share an obvious characteristic—both have a requirement for intracellular life—these two types of organisms were grouped together in a single taxon in the first edition of Bergey’s Manual. Now, however, the rickettsias are classified with the alphaproteobacteria, and the chlamydias are in their own phylum. Chlamydias cause neonatal blindness, pneumonia, and a sexually transmitted disease called lymphogranuloma venereum; in fact, chlamydias are the most common sexually transmitted bacterium in the United States. (Chapter 24 examines chlamydial diseases. Figure 24.9 illustrates the chlamydial life cycle.)  ­ 11.27 List two epsilonproteobacteria that cause human ­ LE A R N I N G O U TC O M E spirochetes. 11.30 Describe the ecological importance of bacteroids. In the final section of this chapter we consider an assortment of Gram-negative bacteria that are classified in the second edition M11_BAUM7206_05_SE_C11.indd 343 Bacteroids Bacteroids are yet another diverse group of Gram-negative microbes that are grouped together on the basis of similarities in their rRNA nucleotide sequences. The group is named for Bacteroides (bak-ter-oy’dēz), a genus of obligately anaerobic rods that normally inhabit the digestive tracts of humans and animals. Bacteroids assist in digestion by catabolizing substances such as cellulose and other complex carbohydrates ­ 11.29 Describe the unique features of chlamydias and Spirochetes (also spelled spirochaetes) are unique helical bacteria that are motile by means of axial filaments composed of flagella that lie within the periplasmic space (see Figure 3.8). When an axial filament rotates, the entire cell corkscrews through the medium. Spirochetes have a variety of types of metabolism and live in diverse habitats. They are frequently isolated from the human mouth, marine environments, moist soil, and the surfaces of protozoa that live in termites’ guts. In the latter case, they may coat the protozoan so thickly that they look and act like cilia. The spirochetes Treponema (trep-ō-ne’mă) and Borrelia (bō-rē’lē-ă) cause syphilis and Lyme disease, respectively, in humans. ­ LE A R N I N G O U TC O M E s Other Gram-Negative Bacteria Spirochetes 11/23/16 3:04 AM TABLE 11.4 r 11    Characterizing and Classifying rokaryotes P p te ha       C Characteristics of Selected Gram-Negative Bacteria Phylum/Class Representative Members Special Characteristics Azospirillum Nitrogen fixer Diseases Proteobacteria Nitrifying bacterium Purple nonsulfur bacteria Anoxygenic phototrophs Rickettsia ntracellular pathogen Typhus and ocky Mountain spotted fever Brucella Coccobacillus Brucellosis Acetobacter, Gluconobacter Synthesize acetic acid Caulobacter rosthecate bacterium Agrobacterium Causes galls in plants; vector for gene transfer in plants Nitrosomonas Nitrifying bacterium Neisseria Diplococcus P Bordetella Burkholderia ertussis Lung infection of cystic fibrosis patients Thiobacillus Colorless sulfur bacterium Zoogloea Forms beneficial flocs in sewage treatment Sphaerotilus Floating flocs can block sewage treatment pipes Legionella Coxiella I urple sulfur bacteria I P Gammaproteobacteria Gonorrhea and meningitis ntracellular pathogen Legionnaires’ disease ntracellular pathogen Q fever Methylococcus Oxidizes methane Glycolytic facultative anaerobes: Facultative anaerobes that catabolize carbohydrates via glycolysis and the pentose phosphate pathway See Table 11.3 on p. 340 Pseudomonas Aerobe that catabolizes carbohydrates via EntnerDoudoroff and pentose phosphate pathways rinary tract infections, external otitis Azotobacter Nitrogen fixers not associated with plant roots Escherichia, Enterobacter, Serratia, Salmonella, Proteus, Shigella, Yersinia, Klebsiella, Vibrio, Haemophilus U Betaproteobacteria R Nitrogen fixer I Rhizobium Nitrobacter P Alphaproteobacteria Azomonas Bdellovibrio Myxobacteria Epsilonproteobacteria Sulfate reducer P Desulfovibrio R Deltaproteobacteria athogen of Gram-negative bacteria eproduces by forming differentiated fruiting bodies Campylobacter Curved rod Gastroenteritis Helicobacter Spiral Gastric ulcers Mariprofundus Oxidize iron Chlamydia ntracellular pathogen; lacks peptidoglycan Neonatal blindness and lymphogranuloma venereum Treponema Motile by axial filaments Syphilis Borrelia Motile by axial filaments Lyme disease “Bacteroidia”a Bacteroides Anaerobe that lives in animal colons Abdominal infections “Sphingobacteria” Cytophaga Digests complex polysaccharides Zetaproteobacteria Chlamydiae I Chlamydiae Spirochaetes Spirochaetes Bacteroidetes aThe names of taxa within quotation marks are not officially recognized. M11_BAUM7206_05_SE_C11.indd 344 11/23/16 3:04 AM       Chapter Summary and oxygen levels. Organisms in Cytophaga differ from other gliding bacteria, such as cyanobacteria and myxobacteria, in that they are nonphotosynthetic and do not form fruiting bodies. The characteristics of these groups of Gram-negative bacteria are listed in Table 11.4. TELL ME WHY Why are bacteria all classified in the same domain (Bacteria) despite their widely divergent oxygen tolerance, sizes, shapes, and nutritional requirements? ­ that are indigestible by mammals. Between 5% and 50% of the bacteria isolated from various humans’ feces are Bacteroides. Some species cause abdominal, pelvic, blood, and other infections. They are the most common anaerobic human pathogen, causing diarrhea, fever, foul-smelling lesions, gas, and pain. Bacteroids in the genus Cytophaga (sī-tof’ă-gă) are aquatic, gliding, rod-shaped aerobes with pointed ends. These bacteria degrade complex polysaccharides, such as agar, pectin, chitin, and cellulose, so they cause damage to wooden boats and piers; they also play an important role in the degradation of raw sewage. Their ability to glide allows these bacteria to position themselves at sites with optimum nutrients, pH, temperature, ­ ­ 1. The cattle likely became infected after ingesting B. anthracis ­ endospores in the soil. How could ingestion of endospores by the cattle lead to an infection with vegetative cells of B. anthracis in the cattle? 2. What is one hypothesis to explain how the ranchers became infected from the cattle? I ­ When Dr. Emerson removes the gauze from Alejandro’s arm, she doesn’t find blisters, but she does see dry, crusty lesions. As part of her initial examination, she swabs the lesions and sends them for lab analysis. Since the lesions aren’t inflamed and don’t appear to be infected and Alejandro doesn’t have any other obvious signs of infection, Dr. Emerson instructs him to treat the lesions with a topical antibiotic. The next day, Dr. Emerson calls Alejandro to come into the office as soon as possible to discuss the results of the lab analysis. The urgency of Dr. Emerson’s request worries Alejandro and Mary—what could be so bad that she couldn’t tell him the results over the phone? Dr. Emerson tells Mary and Alejandro that the results of the lab analysis have indicated that Alejandro’s lesions are due to Bacillus anthracis. Mary and Alejandro can’t believe it—he has anthrax! Dr. Emerson explains that Alejandro has a type called cutaneous anthrax—the most common and the least severe form of anthrax. t is not contagious, and with proper antibiotics Alejandro should be f ine. Dr. Emerson prescribes a 10-day course of ciprofloxacin, and Alejandro makes a complete recovery. Dr. Emerson also notif ies public health authorities of the anthrax infection. The cattle at Alejandro’s ranch and neighboring ranches are tested for anthrax. Four other ranch workers are found with lesions on their arms, neck, or face; all recover with antibiotic treatment. ltimately, 63 cattle die on two of the ranches. Diseased cattle are confirmed as the source of infection for the ranchers. ­U Simply Spider Bites? CHAPTER SUMMARY ­ 1. Three basic shapes of prokaryotic cells are spherical cocci, rod-shaped bacilli, and spirals. Spirals may be stiff (spirilla) or flexible (spirochetes). 2. Other variations in shapes include vibrios (slightly curved rods), coccobacilli (intermediate to cocci and bacilli), and pleomorphic (variable shape and size). M11_BAUM7206_05_SE_C11.indd 345 ­ 3. Environmentally resistant endospores are produced within vegetative cells of the Gram-positive genera Bacillus and Clostridium. Depending on the species in which they are formed, the endospores may be terminal, subterminal, or centrally located. ­ ­ General Characteristics of Prokaryotic Organisms (pp. 322–326) 4. Prokaryotes reproduce asexually by binary fission, snapping division (a type of binary fission), spore formation, and budding. ▶ ANIMATIONS: Bacterial Growth: Overview 11/23/16 3:04 AM r 11    Characterizing and Classifying rokaryotes P 6. Clostridia include the genus Clostridium (pathogenic bacteria that cause gangrene, tetanus, botulism, and diarrhea), Epulopiscium (which is large enough to be seen without a microscope), and Selenomonas (often found in dental plaque). 2. The most authoritative reference in modern prokaryotic systematics is Bergey’s Manual of Systematic Bacteriology, second edition. Currently, there are five known phyla of Archaea and 24 phyla of Bacteria. The organization of this text’s survey of prokaryotes largely follows Bergey’s classification scheme. Survey of Archaea (pp. 326–329) 1. The domain Archaea includes extremophiles, microbes that require extreme conditions of temperature, pH, pressure, and/or salinity to survive. 2. Thermophiles and hyperthermophiles (in the phyla Crenarchaeota and Euryarchaeota) live at temperatures above 45°C and 80°C, respectively, because their DNA, membranes, and proteins do not function properly at lower temperatures. 3. Halophiles (phylum Euryarchaeota) depend on high concentrations of salt to keep their cell walls intact. Halophiles such as Halobacterium salinarum synthesize purple proteins called bacteriorhodopsins that harvest light energy to synthesize ATP. 4. Methanogens (phylum Euryarchaeota) are obligate anaerobes that produce methane gas and are useful in sewage treatment. Survey of Bacteria (pp. 329–345) 1. Deeply branching bacteria have rRNA sequences thought to be similar to those of earliest bacteria. They are autotrophic and live in hot, acidic, and anaerobic environments, often with intense exposure to sun. 2. Phototrophic bacteria trap light energy with photosynthetic lamellae. The five groups of phototrophic bacteria are cyanobacteria, green sulfur bacteria, green nonsulfur bacteria, purple sulfur bacteria, and purple nonsulfur bacteria. 3. Many cyanobacteria reduce atmospheric N2 to NH3 via a process called nitrogen fixation. Cyanobacteria must separate (in either time or space) the metabolic pathways of nitrogen fixation from those of oxygenic photosynthesis because nitrogen fixation is inhibited by the oxygen generated during photosynthesis. Many cyanobacteria fix nitrogen in thick-walled cells called heterocysts. ­ 4. Green and purple bacteria use bacteriochlorophylls for anoxygenic photosynthesis. Nonsulfur forms derive electrons from organic compounds; sulfur forms derive electrons from H2S. ▶ ANIMATIONS: Photosynthesis: Comparing Prokaryotes and Eukaryotes 5. The phylum Firmicutes contains bacteria with a G + C content (the percentage of all base pairs that are guanine-cytosine base pairs) of less than 50%. Firmicutes includes clostridia, mycoplasmas, and other low G + C cocci and bacilli. M11_BAUM7206_05_SE_C11.indd 346 8. Low G + C Gram-positive bacilli and cocci important to human health and industry include Bacillus (which contains species that cause anthrax and food poisoning and includes beneficial bacteria that produce Bt toxin), Listeria (which causes bacteremia and meningitis), Lactobacillus (used to produce yogurt and pickles), Streptococcus, Enterococcus, and Staphylococcus, each of which causes a number of human diseases. 9. High G + C Gram-positive bacteria (Corynebacterium, Mycobacterium, and actinomycetes) are classified in phylum Actinobacteria. 10. Bacteria in Corynebacterium store phosphates in metachromatic granules; C. diphtheriae causes diphtheria. 11. Members of the genus Mycobacterium, including species that cause tuberculosis and leprosy, grow slowly and have unique, resistant cell walls containing waxy mycolic acids. 12. Actinomycetes resemble fungi in that they produce spores and form filaments; this group includes Actinomyces (normally found in human mouths), Nocardia (useful in degradation of pollutants), and Streptomyces (produces important antibiotics). 13. Phylum Proteobacteria is a very large group of Gram-negative bacteria divided into five classes—the alpha-, beta-, gamma-, delta-, and epsilonproteobacteria. 14. The alphaproteobacteria include a variety of aerobes, many of which have unusual cellular extensions called prosthecae. Azospirillum and Rhizobium are nitrogen fixers that are important in agriculture. 15. Some members of the alphaproteobacteria are nitrifying bacteria, which oxidize NH3 to NO3 via a process called nitrification. Nitrifying alphaproteobacteria are in the genus Nitrobacter. ­ 1. Living things are now classified into three domains—Archaea, Bacteria, and Eukarya—based largely on genetic similarities. ­ Modern Prokaryotic Classification (p. 326) 7. Mycoplasmas are Gram-positive, pleomorphic, facultative anaerobes and obligate anaerobes that lack cell walls and therefore stain pink with Gram stain. They are frequently associated with pneumonia and urinary tract infections. ­ r 16. Most purple nonsulfur phototrophs are alphaproteobacteria. 17. Pathogenic alphaproteobacteria include Rickettsia (typhus and Rocky Mountain spotted fever) and Brucella (brucellosis). 18. There are many beneficial alphaproteobacteria, including Acetobacter and Gluconobacter, both of which are used to synthesize acetic acid. Caulobacter is of interest in reproductive studies, and Agrobacterium is used in genetic recombination in plants. ­ deo Vi Tu to 6. Bacilli are found singly, in pairs, in chains, or in a palisade arrangement. 19. The betaproteobacteria include the nitrifying Nitrosomonas and pathogenic species such as Neisseria (gonorrhea), Bordetella (whooping cough), and Burkholderia (which colonizes the lungs of cystic fibrosis patients). 20. Other betaproteobacteria include Thiobacillus (ecologically important), Zoogloea (useful in sewage treatment), and Sphaerotilus (hampers sewage treatment). ­ 5. Cocci may typically be found in groups, including long chains (streptococci), pairs (diplococci), foursomes (tetrads), cuboidal packets (sarcinae), and clusters (staphylococci). 21. The gammaproteobacteria constitute the largest class of proteobacteria; they include purple sulfur bacteria, intracellular pathogens, methane oxidizers, facultative anaerobes that ­ p te ha       C 11/23/16 3:04 AM       R Questions for eview 27. The epsilonproteobacteria include some important human pathogens, including Campylobacter and Helicobacter. utilize glycolysis and the pentose phosphate pathway, and pseudomonads. 28. Scientists discovered zetaproteobacteria using metagenomic sequencing, which entails sequencing all the DNA from a site so as to ascertain all microbes present. Zetaproteobacteria oxidize iron in marine environments. 22. Both Legionella and Coxiella are intracellular, pathogenic gammaproteobacteria. 23. Methane oxidizers are anaerobic bacteria that use methane for both carbon and energy. 29. Chlamydias are Gram-negative cocci typified by the genus Chlamydia; they cause neonatal blindness, pneumonia, and a sexually transmitted disease. ­ ­ 24. Numerous human pathogens are facultatively anaerobic gammaproteobacteria that catabolize carbohydrates by glycolysis. ­ ­ 25. Pseudomonads, including pathogenic Pseudomonas and nitrogenfixing Azotobacter and Azomonas, utilize the Entner-Doudoroff and pentose phosphate pathways for catabolism of glucose. 31. Bacteroids include Bacteroides, an obligate anaerobic rod that inhabits the digestive tract, and Cytophaga, an aerobic rod that degrades wood and raw sewage. I EV EW R I U Q EST ONS FO R 26. The deltaproteobacteria include Desulfovibrio (important in the sulfur cycle and in corrosion of pipes), Bdellovibrio (pathogenic to bacteria), and myxobacteria. The latter form stalked fruiting bodies containing resistant, dormant myxospores. 30. Spirochetes are flexible, helical bacteria that live in diverse environments. The pathogens Treponema (syphilis) and Borrelia (Lyme disease) are important spirochetes. Answers to the Questions for Review (except Short Answer questions) begin on p. A-I. 1.                    All prokaryotes reproduce sexually. 2.                    A bacillus is a bacterium with a slightly curved rod shape. 3.                    If you were to view staphylococci, you should expect to see clusters of cells. 4.                    Chlamydias have peptidoglycan cell walls. 5.                    Archaea are classified into phyla based primarily on tRNA sequences. 6.                    Halophiles inhabit extremely saline habitats, such as the Great Salt Lake. 7.                    Pigments located in thylakoids in phototrophic bacteria trap light energy for metabolic processes. 8.                    Most cyanobacteria form heterocysts in which nitrogen fixation occurs. 5. How is Halobacterium salinarum distinctive? a. It is absolutely dependent on high salt concentrations to maintain its cell wall. b. It is found in terrestrial volcanic habitats. c. It photosynthesizes without chlorophyll. d. It can survive 5 million rad of radiation. 6. Photosynthetic bacteria that also fix nitrogen are a. mycoplasmas c. bacteroids b. spirilla d. cyanobacteria . 7. Which genus is the most common anaerobic human pathogen? a. Bacteroides c. Chlamydia b. Spirochetes d. Methanopyrus 8. Flexible spiral-shaped prokaryotes are . a. spirilla c. vibrios b. spirochetes d. rickettsias                    9.                    A giant bacterium that is large enough to be seen without a microscope is Selenomonas. 4. Endospores . a. remain alive for decades b. can remain alive in boiling water c. exist in a state of suspended animation d. All of the above are correct.                 For each of the following statements that is true, write “true” in the blank. For each statement that is false, write the word(s) that should be substituted for the underlined word(s) to make the statement correct. 3. Which of the following terms best describes stiff, spiral-shaped prokaryotic cells? a. cocci c. spirilla b. bacilli d. spirochetes                    Modified True/False 10.                    When environmental nutrients are depleted, myxobacteria aggregate in mounds to form fruiting bodies. 9. Bacteria that convert nitrogen gas into ammonia are . a. nitrifying bacteria c. nitrogen fixers b. nitrogenous d. nitrification bacteria             Multiple Choice                    2. The thick-walled reproductive spores produced in the middle of cyanobacterial filaments are called . a. akinetes c. metachromatic granules b. terminal endospores d. heterocysts 10. The presence of mycolic acid in the cell wall characterizes . a. Corynebacterium c. Nocardia b. Listeria d. Mycobacterium                                       1. The type of reproduction in prokaryotes that results in a palisade arrangement of cells is called . a. pleomorphic division c. snapping division b. endospore formation d. binary fission M11_BAUM7206_05_SE_C11.indd 347 11/23/16 3:04 AM r 11    Characterizing and Classifying rokaryotes P p te ha       C Matching 7. How is Agrobacterium used in recombinant DNA technology? Match the bacterium on the left with the term with which it is most closely associated. 8. Name and describe five distinct classes of phylum Proteobacteria. 9. Explain why organisms formerly known as blue­green algae are now called cyanobacteria. 1.       Bacillus anthracis A. wood damage 2.       Selenomonas B. dental biofilm (plaque) 3.       Clostridium perfringens C. gangrene 4.       Clostridium botulinum D. botox VISUALIZE IT! 5.       Bacillus licheniformis E. anthrax 1. Label the shapes of these prokaryotic cells. 6.       Streptococcus F. lymphogranuloma venereum 7.       Streptomyces G. leprosy 8.       Corynebacterium H. tetracycline 9.       Gluconobacter I. vinegar 10.       Bordetella J. yogurt 11.       Zoogloea K. impetigo 12.       Rhizobium L. bacitracin 13.       Desulfovibrio M.iron pipe corrosion 14.       Chlamydia N. pertussis 15.       Cytophaga O. nitrogen fixation P. floc formation 12. stiff a. ___________________ b. ___________________ e. ___________________ flexible f. ___________________ c. ___________________ g. ___________________ Q. diphtheria d. ___________________ Short Answer 1. Whereas the first edition of Bergey’s Manual relied on morphological and biochemical characteristics to classify microbes, the new edition focuses on ribosomal RNA sequences. List several other criteria for grouping and classifying bacteria. 2. Describe the location of these endospores within their cells. 2. What are extremophiles? Describe two kinds, and give examples. 3. Name and describe three types of bacteria mentioned in this chapter that “glide.” 13. Endospores Endospore 4. Name three groups of low G + C Gram-positive bacteria. 5. Compare and contrast bacterial and archaeal cells. 6. A student was memorizing the arrangements of bacteria and noticed that there are more arrangements for cocci than for bacilli. Why might this be so? (a) (b) I I I RI C T CAL TH NK NG 1. A microbiology student described “deeply branching bacteria” as having a branched filamentous growth habit akin to Streptomyces. Do you agree with this description? Why or why not? 2. Iron oxide (rust) forms when iron is exposed to oxygen, particularly in the presence of water. Nevertheless, iron pipes typically corrode more quickly when they are buried in moist anaerobic soil than when they are buried in soil containing oxygen. Explain why this is the case. M11_BAUM7206_05_SE_C11.indd 348 3. Why is it that Gram-positive species don’t have axial filaments? 4. Even though Clostridium is strictly an anaerobic bacterium, it can be isolated easily from the exposed surface of your skin. Explain how this can be. 5. Louis Pasteur said, “The role of the infinitely small in nature is infinitely large.” Explain what he meant, using examples of the roles of microorganisms in health, industry, and the environment. 11/23/16 3:04 AM       Questions for Review 6. How are bacterial endospores different from the spores of actinomycetes? 7. A scientist who discovers a prokaryote living in a hot spring at 100°C suspects that it belongs to the archaea. Why does she think it might be archaeal? How could she prove that it is not bacterial? 8. Contrast the processes of nitrogen fixation and nitrification. 9. What do the names Desulfovibrio and Bdellovibrio tell you about the shape of these deltaproteobacteria? 10. How do scientists know there are millions of species of bacteria and of archaea, if most have never been cultured in a lab? 11. Why might soil-dwelling organisms such as Pseudomonas have large genomes and be highly metabolically flexible? CONCEPT MAPPING Using the following terms, fill in the following map that describes the domain Archaea. Methane Methanogens Peptidoglycan Prokaryotes Sewage treatment Thermophiles Extremophiles Great Salt Lake Halophiles Hydrothermal vents Hyperthermophiles Low pH 45°C 80°C 17–25% salt Acidophiles Animal colons Disease Domain Archaea are lack 1 2 include 4 Methanogens such as 5 grow best at >45ºC M11_BAUM7206_05_SE_C11.indd 349 do not cause 3 produce 11 inhabit (in part) 12 participate in 13 8 Hyperthermophiles grow best at inhabit 6 7 9 grow best at grow best at Low pH 17–25% salt inhabit 10 06/03/18 4:53 PM