Prokaryotic Diversity PDF

CHAPTER 4 Prokaryotic Diversity FIGURE 4.1 The bacterium Shewanella lives in the deep sea, where there is little oxygen diffused in the water. It is able to survive in this harsh environment by attaching to the sea floor and using long appendages, called “nanocables,” to sense oxygen. (credit a: modification of work by NASA; credit b: modification of work by Liza Gross) CHAPTER OUTLINE 4.1 Prokaryote Habitats, Relationships, and Microbiomes 4.2 Proteobacteria 4.3 Nonproteobacteria Gram-Negative Bacteria and Phototrophic Bacteria 4.4 Gram-Positive Bacteria 4.5 Deeply Branching Bacteria 4.6 Archaea INTRODUCTION Scientists have studied prokaryotes for centuries, but it wasn’t until 1966 that scientist Thomas Brock (1926–2021) discovered that certain bacteria can live in boiling water. This led many to wonder whether prokaryotes may also live in other extreme environments, such as at the bottom of the ocean, at high altitudes, or inside volcanoes, or even on other planets. Prokaryotes have an important role in changing, shaping, and sustaining the entire biosphere. They can produce proteins and other substances used by molecular biologists in basic research and in medicine and industry. For example, the bacterium Shewanella lives in the deep sea, where oxygen is scarce. It grows long appendages, which have special sensors used to seek the limited oxygen in its environment. It can also digest toxic waste and generate electricity. Other species of prokaryotes can produce more oxygen than the entire Amazon rainforest, while still others supply plants, animals, and humans with usable forms of nitrogen; and inhabit our body, protecting us from harmful microorganisms and producing some vitally important substances. This chapter will examine the diversity, structure, and function of prokaryotes. 4.1 Prokaryote Habitats, Relationships, and Microbiomes LEARNING OBJECTIVES By the end of this section, you will be able to: Identify and describe unique examples of prokaryotes in various habitats on earth Identify and describe symbiotic relationships Compare normal/commensal/resident microbiota to transient microbiota Explain how prokaryotes are classified 130 4 Prokaryotic Diversity CLINICAL FOCUS Part 1 Marsha, a 20-year-old university student, recently returned to the United States from a trip to Nigeria, where she had interned as a medical assistant for an organization working to improve access to laboratory services for tuberculosis testing. When she returned, Marsha began to feel fatigue, which she initially attributed to jet lag. However, the fatigue persisted, and Marsha soon began to experience other bothersome symptoms, such as occasional coughing, night sweats, loss of appetite, and a low-grade fever of 37.4 °C (99.3 °F). Marsha expected her symptoms would subside in a few days, but instead, they gradually became more severe. About two weeks after returning home, she coughed up some sputum and noticed that it contained blood and small whitish clumps resembling cottage cheese. Her fever spiked to 38.2 °C (100.8 °F), and she began feeling sharp pains in her chest when breathing deeply. Concerned that she seemed to be getting worse, Marsha scheduled an appointment with her physician. Could Marsha’s symptoms be related to her overseas travel, even several weeks after returning home? Jump to the next Clinical Focus box. All living organisms are classified into three domains of life: Archaea, Bacteria, and Eukarya. In this chapter, we will focus on the domains Archaea and Bacteria. Archaea and bacteria are unicellular prokaryotic organisms. Unlike eukaryotes, they have no nuclei or any other membrane-bound organelles. Prokaryote Habitats and Functions Prokaryotes are ubiquitous. They can be found everywhere on our planet, even in hot springs, in the Antarctic ice shield, and under extreme pressure two miles under water. One bacterium, Paracoccus denitrificans, has even been shown to survive when scientists removed it from its native environment (soil) and centrifuged it to 2.4 g, equivalent to the gravitational force on the surface of Jupiter. Prokaryotes also are abundant on and within the human body. It has been estimated that prokaryotes, especially 1 bacteria, outnumber nucleated human cells 10:1. More recent studies suggest the ratio could be closer to 1:1, but 2 even that ratio means that there are a great number of bacteria within the human body. Bacteria thrive in the human mouth, nasal cavity, throat, ears, gastrointestinal tract, and vagina. Large colonies of bacteria can be found on healthy human skin, especially in moist areas (armpits, navel, and areas behind ears). However, even drier areas of the skin are not free from bacteria. The existence of prokaryotes is very important for the stability and thriving of ecosystems. For example, they are a necessary part of soil formation and stabilization processes through the breakdown of organic matter and development of biofilms. One gram of soil contains up to 10 billion microorganisms (most of them prokaryotic) belonging to about 1,000 species. Many species of bacteria use substances released from plant roots, such as acids and carbohydrates, as nutrients. The bacteria metabolize these plant substances and release the products of bacterial metabolism back to the soil, forming humus and thus increasing the soil’s fertility. In salty lakes such as the Dead Sea (Figure 4.2), salt-loving halobacteria decompose dead brine shrimp and nourish young brine shrimp and flies with the products of bacterial metabolism. 1 R. Sender et al. "Revised Estimates for the Number of Human and Bacteria Cells in the Body." PLoS Biology 14 no. 8 (August 19, 2016): https://doi.org/10.1371/journal.pbio.1002533. 2 A. Abbott. “Scientists Bust Myth That Our Bodies Have More Bacteria Than Human Cells: Decades-Old Assumption about Microbiota Revisited.” Nature. http://www.nature.com/news/scientists-bust-myth-that-our-bodies-have-more-bacteria-than-human-cells-1.19136. Accessed June 3, 2016. Access for free at openstax.org 4.1 Prokaryote Habitats, Relationships, and Microbiomes 131 FIGURE 4.2 (a) Some prokaryotes, called halophiles, can thrive in extremely salty environments such as the Dead Sea, pictured here. (b) The archaeon Halobacterium salinarum, shown here in an electron micrograph, is a halophile that lives in the Dead Sea. (credit a: modification of work by Jullen Menichini; credit b: modification of work by NASA) In addition to living in the ground and the water, prokaryotic microorganisms are abundant in the air, even high in the atmosphere. There may be up to 2,000 different kinds of bacteria in the air, similar to their diversity in the soil. Prokaryotes can be found everywhere on earth because they are extremely resilient and adaptable. They are often metabolically flexible, which means that they might easily switch from one energy source to another, depending on the availability of the sources, or from one metabolic pathway to another. For example, certain prokaryotic cyanobacteria can switch from a conventional type of lipid metabolism, which includes production of fatty aldehydes, to a different type of lipid metabolism that generates biofuel, such as fatty acids and wax esters. Groundwater bacteria store complex high-energy carbohydrates when grown in pure groundwater, but they metabolize these molecules when the groundwater is enriched with phosphates. Some bacteria get their energy by reducing sulfates into sulfides, but can switch to a different metabolic pathway when necessary, producing acids and free hydrogen ions. Prokaryotes perform functions vital to life on earth by capturing (or “fixing”) and recycling elements like carbon and nitrogen. Organisms such as animals require organic carbon to grow, but, unlike prokaryotes, they are unable to use inorganic carbon sources like carbon dioxide. Thus, animals rely on prokaryotes to convert carbon dioxide into organic carbon products that they can use. This process of converting carbon dioxide to organic carbon products is called carbon fixation. Plants and animals also rely heavily on prokaryotes for nitrogen fixation, the conversion of atmospheric nitrogen into ammonia, a compound that some plants can use to form many different biomolecules necessary to their survival. Bacteria in the genus Rhizobium, for example, are nitrogen-fixing bacteria; they live in the roots of legume plants such as clover, alfalfa, and peas (Figure 4.3). Ammonia produced by Rhizobium helps these plants to survive by enabling them to make building blocks of nucleic acids. In turn, these plants may be eaten by animals—sustaining their growth and survival—or they may die, in which case the products of nitrogen fixation will enrich the soil and be used by other plants. 132 4 Prokaryotic Diversity FIGURE 4.3 (a) Nitrogen-fixing bacteria such as Rhizobium live in the root nodules of legumes such as clover. (b) This micrograph of the root nodule shows bacteroids (bacterium-like cells or modified bacterial cells) within the plant cells. The bacteroids are visible as darker ovals within the larger plant cell. (credit a: modification of work by USDA) Another positive function of prokaryotes is in cleaning up the environment. Recently, some researchers focused on the diversity and functions of prokaryotes in manmade environments. They found that some bacteria play a unique 3 role in degrading toxic chemicals that pollute water and soil. Despite all of the positive and helpful roles prokaryotes play, some are human pathogens that may cause illness or infection when they enter the body. In addition, some bacteria can contaminate food, causing spoilage or foodborne illness, which makes them subjects of concern in food preparation and safety. Less than 1% of prokaryotes (all of them bacteria) are thought to be human pathogens, but collectively these species are responsible for a large number of the diseases that afflict humans. Besides pathogens, which have a direct impact on human health, prokaryotes also affect humans in many indirect ways. For example, prokaryotes are now thought to be key players in the processes of climate change. In recent years, as temperatures in the earth’s polar regions have risen, soil that was formerly frozen year-round (permafrost) has begun to thaw. Carbon trapped in the permafrost is gradually released and metabolized by prokaryotes. This produces massive amounts of carbon dioxide and methane, greenhouse gases that escape into the atmosphere and contribute to the greenhouse effect. CHECK YOUR UNDERSTANDING In what types of environments can prokaryotes be found? Name some ways that plants and animals rely on prokaryotes. Symbiotic Relationships As we have learned, prokaryotic microorganisms can associate with plants and animals. Often, this association results in unique relationships between organisms. For example, bacteria living on the roots or leaves of a plant get nutrients from the plant and, in return, produce substances that protect the plant from pathogens. On the other hand, some bacteria are plant pathogens that use mechanisms of infection similar to bacterial pathogens of animals and humans. Prokaryotes live in a community, or a group of interacting populations of organisms. A population is a group of individual organisms belonging to the same biological species and limited to a certain geographic area. Populations can have cooperative interactions, which benefit the populations, or competitive interactions, in which one population competes with another for resources. The study of these interactions between microbial populations and their environment is called microbial ecology. Any interaction between different species that are associated with each other within a community is called symbiosis. Such interactions fall along a continuum between opposition and cooperation. Interactions in a 3 A.M. Kravetz “Unique Bacteria Fights Man-Made Chemical Waste.” 2012. http://www.livescience.com/25181-bacteria-strain-cleans-up- toxins-nsf-bts.html. Accessed March 9, 2015. Access for free at openstax.org 4.1 Prokaryote Habitats, Relationships, and Microbiomes 133 symbiotic relationship may be beneficial or harmful, or have no effect on one or both of the species involved. Table 4.1 summarizes the main types of symbiotic interactions among prokaryotes. Types of Symbiotic Relationships Type Population A Population B Mutualism Benefitted Benefitted Amensalism Harmed Unaffected Commensalism Benefitted Unaffected Neutralism Unaffected Unaffected Parasitism Benefitted Harmed TABLE 4.1 When two species benefit from each other, the symbiosis is called mutualism (or syntropy, or crossfeeding). For example, humans have a mutualistic relationship with the bacterium Bacteroides thetaiotaomicron, which lives in the intestinal tract. Bacteroides thetaiotaomicron digests complex polysaccharide plant materials that human digestive enzymes cannot break down, converting them into monosaccharides that can be absorbed by human cells. Humans also have a mutualistic relationship with certain strains of Escherichia coli, another bacterium found in the gut. E. coli relies on intestinal contents for nutrients, and humans derive certain vitamins from E. coli, particularly vitamin K, which is required for the formation of blood clotting factors. (This is only true for some strains of E. coli, however. Other strains are pathogenic and do not have a mutualistic relationship with humans.) A type of symbiosis in which one population harms another but remains unaffected itself is called amensalism. In the case of bacteria, some amensalist species produce bactericidal substances that kill other species of bacteria. The microbiota of the skin is composed of a variety of bacterial species, including Staphylococcus epidermidis and Propionibacterium acnes. Although both species have the potential to cause infectious diseases when protective barriers are breached, they both produce a variety of antibacterial bacteriocins and bacteriocin-like compounds. S. epidermidis and P. acnes are unaffected by the bacteriocins and bacteriocin-like compounds they produce, but these compounds can target and kill other potential pathogens. In another type of symbiosis, called commensalism, one organism benefits while the other is unaffected. This occurs when the bacterium Staphylococcus epidermidis uses the dead cells of the human skin as nutrients. Billions of these bacteria live on our skin, but in most cases (especially when our immune system is healthy), we do not react to them in any way. S. epidermidis provides an excellent example of how the classifications of symbiotic relationships are not always distinct. One could also consider the symbiotic relationship of S. epidermidis with humans as mutualism. Humans provide a food source of dead skin cells to the bacterium, and in turn the production of bacteriocin can provide an defense against potential pathogens. If neither of the symbiotic organisms is affected in any way, we call this type of symbiosis neutralism. An example of neutralism is the coexistence of metabolically active (vegetating) bacteria and endospores (dormant, metabolically passive bacteria). For example, the bacterium Bacillus anthracis typically forms endospores in soil when conditions are unfavorable. If the soil is warmed and enriched with nutrients, some B. anthracis endospores germinate and remain in symbiosis with other species of endospores that have not germinated. A type of symbiosis in which one organism benefits while harming the other is called parasitism. The relationship between humans and many pathogenic prokaryotes can be characterized as parasitic because these organisms invade the body, producing toxic substances or infectious diseases that cause harm. Diseases such as tetanus, diphtheria, pertussis, tuberculosis, and leprosy all arise from interactions between bacteria and humans. Scientists have coined the term microbiome to refer to all prokaryotic and eukaryotic microorganisms and their genetic material that are associated with a certain organism or environment. Within the human microbiome, there 134 4 Prokaryotic Diversity are resident microbiota and transient microbiota. The resident microbiota consists of microorganisms that constantly live in or on our bodies. The term transient microbiota refers to microorganisms that are only temporarily found in the human body, and these may include pathogenic microorganisms. Hygiene and diet can alter both the resident and transient microbiota. The resident microbiota is amazingly diverse, not only in terms of the variety of species but also in terms of the preference of different microorganisms for different areas of the human body. For example, in the human mouth, there are thousands of commensal or mutualistic species of bacteria. Some of these bacteria prefer to inhabit the surface of the tongue, whereas others prefer the internal surface of the cheeks, and yet others prefer the front or back teeth or gums. The inner surface of the cheek has the least diverse microbiota because of its exposure to oxygen. By contrast, the crypts of the tongue and the spaces between teeth are two sites with limited oxygen exposure, so these sites have more diverse microbiota, including bacteria living in the absence of oxygen (e.g., Bacteroides, Fusobacterium). Differences in the oral microbiota between randomly chosen human individuals are also significant. Studies have shown, for example, that the prevalence of such bacteria as Streptococcus, 4 Haemophilus, Neisseria, and others was dramatically different when compared between individuals. There are also significant differences between the microbiota of different sites of the same human body. The inner surface of the cheek has a predominance of Streptococcus, whereas in the throat, the palatine tonsil, and saliva, there are two to three times fewer Streptococcus, and several times more Fusobacterium. In the plaque removed from gums, the predominant bacteria belong to the genus Fusobacterium. However, in the intestine, both Streptococcus and Fusobacterium disappear, and the genus Bacteroides becomes predominant. Not only can the microbiota vary from one body site to another, the microbiome can also change over time within the same individual. Humans acquire their first inoculations of normal flora during natural birth and shortly after birth. Before birth, there is a rapid increase in the population of Lactobacillus spp. in the vagina, and this population serves as the first colonization of microbiota during natural birth. After birth, additional microbes are acquired from health- care providers, parents, other relatives, and individuals who come in contact with the baby. This process establishes a microbiome that will continue to evolve over the course of the individual’s life as new microbes colonize and are eliminated from the body. For example, it is estimated that within a 9-hour period, the microbiota of the small 5 intestine can change so that half of the microbial inhabitants will be different. The importance of the initial Lactobacillus colonization during vaginal child birth is highlighted by studies demonstrating a higher incidence of diseases in individuals born by cesarean section, compared to those born vaginally. Studies have shown that babies born vaginally are predominantly colonized by vaginal lactobacillus, whereas babies born by cesarean section are more frequently colonized by microbes of the normal skin microbiota, including common hospital-acquired pathogens. Throughout the body, resident microbiotas are important for human health because they occupy niches that might be otherwise taken by pathogenic microorganisms. For instance, Lactobacillus spp. are the dominant bacterial species of the normal vaginal microbiota for most females. lactobacillus produce lactic acid, contributing to the acidity of the vagina and inhibiting the growth of pathogenic yeasts. However, when the population of the resident microbiota is decreased for some reason (e.g., because of taking antibiotics), the pH of the vagina increases, making it a more favorable environment for the growth of yeasts such as Candida albicans. Antibiotic therapy can also disrupt the microbiota of the intestinal tract and respiratory tract, increasing the risk for secondary infections and/or promoting the long-term carriage and shedding of pathogens. CHECK YOUR UNDERSTANDING Explain the difference between cooperative and competitive interactions in microbial communities. List the types of symbiosis and explain how each population is affected. Taxonomy and Systematics Assigning prokaryotes to a certain species is challenging. They do not reproduce sexually, so it is not possible to 4 E.M. Bik et al. “Bacterial Diversity in the Oral Cavity of 10 Healthy Individuals.” The ISME Journal 4 no. 8 (2010):962–974. 5 C.C. Booijink et al. “High Temporal and Intra-Individual Variation Detected in the Human Ileal Microbiota.” Environmental Microbiology 12 no. 12 (2010):3213–3227. Access for free at openstax.org 4.1 Prokaryote Habitats, Relationships, and Microbiomes 135 classify them according to the presence or absence of interbreeding. Also, they do not have many morphological features. Traditionally, the classification of prokaryotes was based on their shape, staining patterns, and biochemical or physiological differences. More recently, as technology has improved, the nucleotide sequences in genes have become an important criterion of microbial classification. In 1923, American microbiologist David Hendricks Bergey (1860–1937) published A Manual in Determinative Bacteriology. With this manual, he attempted to summarize the information about the kinds of bacteria known at that time, using Latin binomial classification. Bergey also included the morphological, physiological, and biochemical properties of these organisms. His manual has been updated multiple times to include newer bacteria and their properties. It is a great aid in bacterial taxonomy and methods of characterization of bacteria. A more recent sister publication, the five-volume Bergey’s Manual of Systematic Bacteriology, expands on Bergey’s original manual. It includes a large number of additional species, along with up-to-date descriptions of the taxonomy and biological properties of all named prokaryotic taxa. This publication incorporates the approved names of bacteria as determined by the List of Prokaryotic Names with Standing in Nomenclature (LPSN). LINK TO LEARNING The 7th edition (published in 1957) of Bergey’s Manual of Determinative Bacteriology is now available (https://openstax.org/l/22mandeterbact). More recent, updated editions are available in print. Classification by Staining Patterns According to their staining patterns, which depend on the properties of their cell walls, bacteria have traditionally been classified into gram-positive, gram-negative, and “atypical,” meaning neither gram-positive nor gram-negative. As explained in Staining Microscopic Specimens, gram-positive bacteria possess a thick peptidoglycan cell wall that retains the primary stain (crystal violet) during the decolorizing step; they remain purple after the gram-stain procedure because the crystal violet dominates the light red/pink color of the secondary counterstain, safranin. In contrast, gram-negative bacteria possess a thin peptidoglycan cell wall that does not prevent the crystal violet from washing away during the decolorizing step; therefore, they appear light red/pink after staining with the safranin. Bacteria that cannot be stained by the standard Gram stain procedure are called atypical bacteria. Included in the atypical category are species of Mycoplasma and Chlamydia. Rickettsia are also considered atypical because they are too small to be evaluated by the Gram stain. More recently, scientists have begun to further classify gram-negative and gram-positive bacteria. They have added a special group of deeply branching bacteria based on a combination of physiological, biochemical, and genetic features. They also now further classify gram-negative bacteria into Proteobacteria, Cytophaga-Flavobacterium- Bacteroides (CFB), and spirochetes. The deeply branching bacteria are thought to be a very early evolutionary form of bacteria (see Deeply Branching Bacteria). They live in hot, acidic, ultraviolet-light-exposed, and anaerobic (deprived of oxygen) conditions. Proteobacteria is a phylum of very diverse groups of gram-negative bacteria; it includes some important human pathogens (e.g., E. coli and Bordetella pertussis). The CFB group of bacteria includes components of the normal human gut microbiota, like Bacteroides. The spirochetes are spiral-shaped bacteria and include the pathogen Treponema pallidum, which causes syphilis. We will characterize these groups of bacteria in more detail later in the chapter. Based on their prevalence of guanine and cytosine nucleotides, gram-positive bacteria are also classified into low G+C and high G+C gram-positive bacteria. The low G+C gram-positive bacteria have less than 50% of guanine and cytosine nucleotides in their DNA. They include human pathogens, such as those that cause anthrax (Bacillus anthracis), tetanus (Clostridium tetani), and listeriosis (Listeria monocytogenes). High G+C gram-positive bacteria, which have more than 50% guanine and cytosine nucleotides in their DNA, include the bacteria that cause diphtheria (Corynebacterium diphtheriae), tuberculosis (Mycobacterium tuberculosis), and other diseases. The classifications of prokaryotes are constantly changing as new species are being discovered. We will describe them in more detail, along with the diseases they cause, in later sections and chapters. 136 4 Prokaryotic Diversity CHECK YOUR UNDERSTANDING How do scientists classify prokaryotes? MICRO CONNECTIONS Human Microbiome Project The Human Microbiome Project was launched by the National Institutes of Health (NIH) in 2008. One main goal of the project is to create a large repository of the gene sequences of important microbes found in humans, helping biologists and clinicians understand the dynamics of the human microbiome and the relationship between the human microbiota and diseases. A network of labs working together has been compiling the data from swabs of several areas of the skin, gut, and mouth from hundreds of individuals. One of the challenges in understanding the human microbiome has been the difficulty of culturing many of the microbes that inhabit the human body. It has been estimated that we are only able to culture 1% of the bacteria in nature and that we are unable to grow the remaining 99%. To address this challenge, researchers have used metagenomic analysis, which studies genetic material harvested directly from microbial communities, as opposed to that of individual species grown in a culture. This allows researchers to study the genetic material of all microbes 6 in the microbiome, rather than just those that can be cultured. One important achievement of the Human Microbiome Project is establishing the first reference database on microorganisms living in and on the human body. Many of the microbes in the microbiome are beneficial, but some are not. It was found, somewhat unexpectedly, that all of us have some serious microbial pathogens in our microbiota. For example, the conjunctiva of the human eye contains 24 genera of bacteria and numerous pathogenic 7 species. A healthy human mouth contains a number of species of the genus Streptococcus, including pathogenic 8 species S. pyogenes and S. pneumoniae. This raises the question of why certain prokaryotic organisms exist commensally in certain individuals but act as deadly pathogens in others. Also unexpected was the number of organisms that had never been cultured. For example, in one metagenomic study of the human gut microbiota, 174 9 new species of bacteria were identified. Another goal for the near future is to characterize the human microbiota in patients with different diseases and to find out whether there are any relationships between the contents of an individual’s microbiota and risk for or susceptibility to specific diseases. Analyzing the microbiome in a person with a specific disease may reveal new ways to fight diseases. 4.2 Proteobacteria LEARNING OBJECTIVES By the end of this section, you will be able to: Describe the unique features of each class within the phylum Proteobacteria: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, and Epsilonproteobacteria Give an example of a bacterium in each class of Proteobacteria 6 National Institutes of Health. “Human Microbiome Project. Overview.” http://commonfund.nih.gov/hmp/overview. Accessed June 7, 2016. 7 Q. Dong et al. “Diversity of Bacteria at Healthy Human Conjunctiva.” Investigative Ophthalmology & Visual Science 52 no. 8 (2011):5408–5413. 8 F.E. Dewhirst et al. “The Human Oral Microbiome.” Journal of Bacteriology 192 no. 19 (2010):5002–5017. 9 J.C. Lagier et al. “Microbial Culturomics: Paradigm Shift in the Human Gut Microbiome Study.” Clinical Microbiology and Infection 18 no. 12 (2012):1185–1193. Access for free at openstax.org 4.2 Proteobacteria 137 In 1987, the American microbiologist Carl Woese (1928–2012) suggested that a large and diverse group of bacteria that he called “purple bacteria and their relatives” should be defined as a separate phylum within the domain 10 Bacteria based on the similarity of the nucleotide sequences in their genome. This phylum of gram-negative bacteria subsequently received the name Proteobacteria. It includes many bacteria that are part of the normal human microbiota as well as many pathogens. The Proteobacteria are further divided into five classes: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, and Epsilonproteobacteria (Appendix D). Alphaproteobacteria The first class of Proteobacteria is the Alphaproteobacteria, many of which are obligate or facultative intracellular bacteria. Some species are characterized as oligotrophs, organisms capable of living in low-nutrient environments such as deep oceanic sediments, glacial ice, or deep undersurface soil. Among the Alphaproteobacteria are rickettsias, obligate intracellular pathogens, that require part of their life cycle to occur inside other cells called host cells. When not growing inside a host cell, Rickettsia are metabolically inactive outside the host cell. They cannot synthesize their own adenosine triphosphate (ATP), and, therefore, rely on cells for their energy needs. Rickettsia spp. include a number of serious human pathogens. For example, R. rickettsii causes Rocky Mountain spotted fever, a life-threatening form of meningoencephalitis (inflammation of the membranes that wrap the brain). R. rickettsii infects ticks and can be transmitted to humans via a bite from an infected tick (Figure 4.4). FIGURE 4.4 Rickettsias require special staining methods to see them under a microscope. Here, R. rickettsii, which causes Rocky Mountain spotted fever, is shown infecting the cells of a tick. (credit: modification of work by Centers for Disease Control and Prevention) Another species of Rickettsia, R. prowazekii, is spread by lice. It causes epidemic typhus, a severe infectious disease common during warfare and mass migrations of people. R. prowazekii infects human endothelium cells, causing inflammation of the inner lining of blood vessels, high fever, abdominal pain, and sometimes delirium. A relative, R. typhi, causes a less severe disease known as murine or endemic typhus, which is still observed in the southwestern United States during warm seasons. Table 4.2 summarizes the characteristics of important genera of Alphaproteobacteria. 10 C.R. Woese. “Bacterial Evolution.” Microbiological Review 51 no. 2 (1987):221–271. 138 4 Prokaryotic Diversity Class Alphaproteobacteria Genus Microscopic Unique Characteristics Morphology Agrobacterium Gram-negative bacillus Plant pathogen; one species, A. tumefaciens, causes tumors in plants Bartonella Gram-negative, Facultative intracellular bacteria, transmitted by lice and fleas, pleomorphic, flagellated cause trench fever and cat scratch disease in humans coccobacillus Brucella Gram-negative, small, Facultative intracellular bacteria, transmitted by contaminated flagellated coccobacillus milk from infected cows, cause brucellosis in cattle and humans Caulobacter Gram-negative bacillus Used in studies on cellular adaptation and differentiation because of its peculiar life cycle (during cell division, forms “swarm” cells and “stalked” cells) Ehrlichia Very small, gram- Obligatory intracellular bacteria; can be transported from cell to negative, coccoid or cell; transmitted by ticks; cause ehrlichiosis (destruction of ovoid bacteria white blood cells and inflammation) in humans and dogs Hyphomicrobium Gram-negative bacilli; Similar to Caulobacter grows from a stalk Methylocystis Gram-negative, coccoid Nitrogen-fixing aerobic bacteria or short bacilli Rhizobium Gram-negative, Nitrogen-fixing bacteria that live in soil and form symbiotic rectangular bacilli with relationship with roots of legumes (e.g., clover, alfalfa, and rounded ends forming beans) clusters Rickettsia Gram-negative, highly Obligate intracellular bacteria; transmitted by ticks; may cause pleomorphic bacteria Rocky Mountain spotted fever and typhus (may be cocci, rods, or threads) TABLE 4.2 CHECK YOUR UNDERSTANDING What is a common characteristic among the human pathogenic Alphaproteobacteria? Betaproteobacteria Betaproteobacteria are a diverse group of bacteria. The different bacterial species within this group utilize a wide range of metabolic strategies and can survive in a range of environments. Some genera include species that are human pathogens, able to cause severe, sometimes life-threatening disease. The genus Neisseria, for example, includes the bacteria N. gonorrhoeae, the causative agent of the STI gonorrhea, and N. meningitides, the causative agent of bacterial meningitis. Access for free at openstax.org 4.2 Proteobacteria 139 Neisseria are cocci that live on mucosal surfaces of the human body. They are fastidious, or difficult to culture, and they require high levels of moisture, nutrient supplements, and carbon dioxide. Also, Neisseria are microaerophilic, meaning that they require low levels of oxygen. For optimal growth and for the purposes of identification, Neisseria spp. are grown on chocolate agar (i.e., agar supplemented by partially hemolyzed red blood cells). Their characteristic pattern of growth in culture is diplococcal: pairs of cells resembling coffee beans (Figure 4.5). FIGURE 4.5 Neisseria meningitidis growing in colonies on a chocolate agar plate. (credit: Centers for Disease Control and Prevention) The pathogen responsible for pertussis (whooping cough) is also a member of Betaproteobacteria. The bacterium Bordetella pertussis, from the order Burkholderiales, produces several toxins that paralyze the movement of cilia in the human respiratory tract and directly damage cells of the respiratory tract, causing a severe cough. Table 4.3 summarizes the characteristics of important genera of Betaproteobacteria. Class Betaproteobacteria Example Microscopic Unique Characteristics Genus Morphology Bordetella A small, gram-negative Aerobic, very fastidious; B. pertussis causes pertussis (whooping coccobacillus cough) Burkholderia Gram-negative bacillus Aerobic, aquatic, cause diseases in horses and humans (especially patients with cystic fibrosis); agents of nosocomial infections Leptothrix Gram-negative, Aquatic; oxidize iron and manganese; can live in wastewater sheathed, filamentous treatment plants and clog pipes bacillus Neisseria Gram-negative, coffee Require moisture and high concentration of carbon dioxide; oxidase bean-shaped coccus positive, grow on chocolate agar; pathogenic species cause forming pairs gonorrhea and meningitis Thiobacillus Gram-negative bacillus Thermophilic, acidophilic, strictly aerobic bacteria; oxidize iron and sulfur TABLE 4.3 CHECK YOUR UNDERSTANDING Why are Neisseria classified as microaerophilic? 140 4 Prokaryotic Diversity CLINICAL FOCUS Part 2 When Marsha finally went to the doctor’s office, the physician listened to her breathing through a stethoscope. He heard some crepitation (a crackling sound) in her lungs, so he ordered a chest radiograph and asked the nurse to collect a sputum sample for microbiological evaluation and cytology. The radiologic evaluation found cavities, opacities, and a particular pattern of distribution of abnormal material (Figure 4.6). What are some possible diseases that could be responsible for Marsha’s radiograph results? FIGURE 4.6 This anteroposterior radiograph shows the presence of bilateral pulmonary infiltrate (white triangles) and “caving formation” (black arrows) present in the right apical region. (credit: Centers for Disease Control and Prevention) Jump to the next Clinical Focus box. Go back to the previous Clinical Focus box. Gammaproteobacteria The most diverse class of gram-negative bacteria is Gammaproteobacteria, and it includes a number of human pathogens. For example, a large and diverse family, Pseudomonaceae, includes the genus Pseudomonas. Within this genus is the species P. aeruginosa, a pathogen responsible for diverse infections in various regions of the body. P. aeruginosa is a strictly aerobic, nonfermenting, highly motile bacterium. It often infects wounds and burns, can be the cause of chronic urinary tract infections, and can be an important cause of respiratory infections in patients with cystic fibrosis or patients on mechanical ventilators. Infections by P. aeruginosa are often difficult to treat because the bacterium is resistant to many antibiotics and has a remarkable ability to form biofilms. Other representatives of Pseudomonas include the fluorescent (glowing) bacterium P. fluorescens and the soil bacteria P. putida, which is known for its ability to degrade xenobiotics (substances not naturally produced or found in living organisms). The Pasteurellaceae also includes several clinically relevant genera and species. This family includes several bacteria that are human and/or animal pathogens. For example, Pasteurella haemolytica causes severe pneumonia in sheep and goats. P. multocida is a species that can be transmitted from animals to humans through bites, causing infections of the skin and deeper tissues. The genus Haemophilus contains two human pathogens, H. influenzae and H. ducreyi. Despite its name, H. influenzae does not cause influenza (which is a viral disease). H. influenzae can cause both upper and lower respiratory tract infections, including sinusitis, bronchitis, ear infections, and pneumonia. Before the development of effective vaccination, strains of H. influenzae were a leading cause of more invasive diseases, like meningitis in children. H. ducreyi causes the STI known as chancroid. The order Vibrionales includes the human pathogen Vibrio cholerae. This comma-shaped aquatic bacterium thrives in highly alkaline environments like shallow lagoons and sea ports. A toxin produced by V. cholerae causes hypersecretion of electrolytes and water in the large intestine, leading to profuse watery diarrhea and dehydration. V. parahaemolyticus is also a cause of gastrointestinal disease in humans, whereas V. vulnificus causes serious and potentially life-threatening cellulitis (infection of the skin and deeper tissues) and blood-borne infections. Another representative of Vibrionales, Aliivibrio fischeri, engages in a symbiotic relationship with squid. The squid provides Access for free at openstax.org 4.2 Proteobacteria 141 nutrients for the bacteria to grow and the bacteria produce bioluminescence that protects the squid from predators (Figure 4.7). FIGURE 4.7 (a) Aliivibrio fischeri is a bioluminescent bacterium. (b) A. fischeri colonizes and lives in a mutualistic relationship with the Hawaiian bobtail squid (Euprymna scolopes). (credit a: modification of work by American Society for Microbiology; credit b: modification of work by Margaret McFall-Ngai) The genus Legionella also belongs to the Gammaproteobacteria. L. pneumophila, the pathogen responsible for Legionnaires disease, is an aquatic bacterium that tends to inhabit pools of warm water, such as those found in the tanks of air conditioning units in large buildings (Figure 4.8). Because the bacteria can spread in aerosols, outbreaks of Legionnaires disease often affect residents of a building in which the water has become contaminated with Legionella. In fact, these bacteria derive their name from the first known outbreak of Legionnaires disease, which occurred in a hotel hosting an American Legion veterans’ association convention in Philadelphia in 1976. FIGURE 4.8 (a) Legionella pneumophila, the causative agent of Legionnaires disease, thrives in warm water. (b) Outbreaks of Legionnaires disease often originate in the air conditioning units of large buildings when water in or near the system becomes contaminated with L. pneumophila. (credit a: modification of work by Centers for Disease Control and Prevention) Enterobacteriaceae is a large family of enteric (intestinal) bacteria belonging to the Gammaproteobacteria. They are facultative anaerobes and are able to ferment carbohydrates. Within this family, microbiologists recognize two distinct categories. The first category is called the coliforms, after its prototypical bacterium species, Escherichia coli. Coliforms are able to ferment lactose completely (i.e., with the production of acid and gas). The second category, noncoliforms, either cannot ferment lactose or can only ferment it incompletely (producing either acid or gas, but not both). The noncoliforms include some notable human pathogens, such as Salmonella spp., Shigella spp., and Yersinia pestis. E. coli has been perhaps the most studied bacterium since it was first described in 1886 by Theodor Escherich (1857–1911). Many strains of E. coli are in mutualistic relationships with humans. However, some strains produce a potentially deadly toxin called Shiga toxin. Shiga toxin is one of the most potent bacterial toxins identified. Upon entering target cells, Shiga toxin interacts with ribosomes, stopping protein synthesis. Lack of protein synthesis leads to cellular death and hemorrhagic colitis, characterized by inflammation of intestinal tract and bloody diarrhea. In the most severe cases, patients can develop a deadly hemolytic uremic syndrome. Other E. coli strains may cause traveler’s diarrhea, a less severe but very widespread disease. 142 4 Prokaryotic Diversity The genus Salmonella, which belongs to the noncoliform group of Enterobacteriaceae, is interesting in that there is still no consensus about how many species it includes. Scientists have reclassified many of the groups they once thought to be species as serotypes (also called serovars), which are strains or variations of the same species of bacteria. Their classification is based on patterns of reactivity by animal antisera against molecules on the surface of the bacterial cells. A number of serotypes of Salmonella can cause salmonellosis, characterized by inflammation of the small and the large intestine, accompanied by fever, vomiting, and diarrhea. The species S. enterobacterica (serovar typhi) causes typhoid fever, with symptoms including fever, abdominal pain, and skin rashes (Figure 4.9). FIGURE 4.9 Salmonella typhi is the causative agent of typhoid fever. (credit: Centers for Disease Control and Prevention) Table 4.4 summarizes the characteristics of important genera of Gammaproteobacteria. Class Gammaproteobacteria Example Microscopic Unique Characteristics Genus Morphology Beggiatoa Gram-negative Aquatic, live in water with high content of hydrogen disulfide; can bacteria; disc-shaped cause problems for sewage treatment or cylindrical Coxiella Small, gram-negative Obligatory intracellular bacteria; cause Q fever; potential for use as bacillus biological weapon Enterobacter Gram-negative Facultative anaerobe; cause urinary and respiratory tract infections bacillus in hospitalized patients; implicated in the pathogenesis of obesity Erwinia Gram-negative Plant pathogen causing leaf spots and discoloration; may digest bacillus cellulose; prefer relatively low temperatures (25–30 °C) Escherichia Gram-negative Facultative anaerobe; inhabit the gastrointestinal tract of warm- bacillus blooded animals; some strains are mutualists, producing vitamin K; others, like serotype E. coli O157:H7, are pathogens; E. coli has been a model organism for many studies in genetics and molecular biology Hemophilus Gram-negative Pleomorphic, may appear as coccobacillus, aerobe, or facultative bacillus anaerobe; grow on blood agar; pathogenic species can cause respiratory infections, chancroid, and other diseases TABLE 4.4 Access for free at openstax.org 4.2 Proteobacteria 143 Class Gammaproteobacteria Example Microscopic Unique Characteristics Genus Morphology Klebsiella Gram-negative Facultative anaerobe, encapsulated, nonmotile; pathogenic species bacillus; appears may cause pneumonia, especially in people with alcoholism rounder and thicker than other members of Enterobacteriaceae Legionella Gram-negative Fastidious, grow on charcoal-buffered yeast extract; L. pneumophila bacillus causes Legionnaires disease Methylomonas Gram-negative Use methane as source of carbon and energy bacillus Proteus Gram-negative Common inhabitants of the human gastrointestinal tract; motile; bacillus (pleomorphic) produce urease; opportunistic pathogens; may cause urinary tract infections and sepsis Pseudomonas Gram-negative Aerobic; versatile; produce yellow and blue pigments, making them bacillus appear green in culture; opportunistic, antibiotic-resistant pathogens may cause wound infections, hospital-acquired infections, and secondary infections in patients with cystic fibrosis Serratia Gram-negative Motile; may produce red pigment; opportunistic pathogens bacillus responsible for a large number of hospital-acquired infections Shigella Gram-negative Nonmotile; dangerously pathogenic; produce Shiga toxin, which can bacillus destroy cells of the gastrointestinal tract; can cause dysentery Vibrio Gram-negative, Inhabit seawater; flagellated, motile; may produce toxin that causes comma- or curved hypersecretion of water and electrolytes in the gastrointestinal tract; rod-shaped bacteria some species may cause serious wound infections Yersinia Gram-negative Carried by rodents; human pathogens; Y. pestis causes bubonic bacillus plague and pneumonic plague; Y. enterocolitica can be a pathogen causing diarrhea in humans TABLE 4.4 CHECK YOUR UNDERSTANDING List two families of Gammaproteobacteria. Deltaproteobacteria The Deltaproteobacteria is a small class of gram-negative Proteobacteria that includes sulfate-reducing bacteria (SRBs), so named because they use sulfate as the final electron acceptor in the electron transport chain. Few SRBs are pathogenic. However, the SRB Desulfovibrio orale is associated with periodontal disease (disease of the gums). Deltaproteobacteria also includes the genus Bdellovibrio, species of which are parasites of other gram-negative bacteria. Bdellovibrio invades the cells of the host bacterium, positioning itself in the periplasm, the space between 144 4 Prokaryotic Diversity the plasma membrane and the cell wall, feeding on the host’s proteins and polysaccharides. The infection is lethal for the host cells. Another type of Deltaproteobacteria, myxobacteria, lives in the soil, scavenging inorganic compounds. Motile and highly social, they interact with other bacteria within and outside their own group. They can form multicellular, macroscopic “fruiting bodies” (Figure 4.10), structures that are still being studied by biologists and bacterial 11 ecologists. These bacteria can also form metabolically inactive myxospores. FIGURE 4.10 Myxobacteria form fruiting bodies. (credit: modification of work by Michiel Vos) Table 4.5 summarizes the characteristics of several important genera of Deltaproteobacteria. Class Deltaproteobacteria Genus Microscopic Morphology Unique characteristics Bdellovibrio Gram-negative, comma- Obligate aerobes; motile; parasitic (infecting other shaped rod bacteria) Desulfovibrio Gram-negative, comma- Reduce sulfur; can be used for removal of toxic and (formerly shaped rod radioactive waste Desufuromonas) Myxobacterium Gram-negative, coccoid Live in soil; can move by gliding; used as a model bacteria forming colonies organism for studies of intercellular communication (swarms) (signaling) TABLE 4.5 CHECK YOUR UNDERSTANDING What type of Deltaproteobacteria forms fruiting bodies? Epsilonproteobacteria The smallest class of Proteobacteria is Epsilonproteobacteria, which are gram-negative microaerophilic bacteria (meaning they only require small amounts of oxygen in their environment). Two clinically relevant genera of 11 H. Reichenbach. “Myxobacteria, Producers of Novel Bioactive Substances.” Journal of Industrial Microbiology & Biotechnology 27 no. 3 (2001):149–156. Access for free at openstax.org 4.2 Proteobacteria 145 Epsilonproteobacteria are Campylobacter and Helicobacter, both of which include human pathogens. Campylobacter can cause food poisoning that manifests as severe enteritis (inflammation in the small intestine). This condition, caused by the species C. jejuni, is rather common in developed countries, usually because of eating contaminated poultry products. Chickens often harbor C. jejuni in their gastrointestinal tract and feces, and their meat can become contaminated during processing. Within the genus Helicobacter, the helical, flagellated bacterium H. pylori has been identified as a beneficial member of the stomach microbiota, but it is also the most common cause of chronic gastritis and ulcers of the 12 stomach and duodenum (Figure 4.11). Studies have also shown that H. pylori is linked to stomach cancer. H. pylori is somewhat unusual in its ability to survive in the highly acidic environment of the stomach. It produces urease and other enzymes that modify its environment to make it less acidic. FIGURE 4.11 Helicobacter pylori can cause chronic gastritis, which can lead to ulcers and stomach cancer. Table 4.6 summarizes the characteristics of the most clinically relevant genera of Epsilonproteobacteria. Class Epsilonproteobacteria Example Microscopic Unique Characteristics Genus Morphology Campylobacter Gram-negative, Aerobic (microaerophilic); often infects chickens; may infect humans via spiral-shaped undercooked meat, causing severe enteritis rod Helicobacter Gram-negative, Aerobic (microaerophilic) bacterium; can damage the inner lining of the spiral-shaped stomach, causing chronic gastritis, peptic ulcers, and stomach cancer rod TABLE 4.6 CHECK YOUR UNDERSTANDING Name two Epsilonproteobacteria that cause gastrointestinal disorders. 12 S. Suerbaum, P. Michetti. “Helicobacter pylori infection.” New England Journal of Medicine 347 no. 15 (2002):1175–1186. 146 4 Prokaryotic Diversity 4.3 Nonproteobacteria Gram-Negative Bacteria and Phototrophic Bacteria LEARNING OBJECTIVES By the end of this section, you will be able to: Describe the unique features of nonproteobacteria gram-negative bacteria Give an example of a nonproteobacteria bacterium in each category Describe the unique features of phototrophic bacteria Identify phototrophic bacteria The majority of the gram-negative bacteria belong to the phylum Proteobacteria, discussed in the previous section. Those that do not are called the nonproteobacteria. In this section, we will describe four classes of gram-negative nonproteobacteria: Chlamydia, the spirochetes, the CFB group, and the Planctomycetes. A diverse group of phototrophic bacteria that includes Proteobacteria and nonproteobacteria will be discussed at the end of this section. Chlamydia C. trachomatis is a human pathogen that causes trachoma, a disease of the eyes, often leading to blindness. C. trachomatis also causes the sexually transmitted disease lymphogranuloma venereum (LGV). This disease is often mildly symptomatic, manifesting as regional lymph node swelling, or it may be asymptomatic, but it is extremely contagious and is common on college campuses. Members of the genus Chlamydia are gram-negative, obligate intracellular pathogens that are extremely resistant to the cellular defenses, giving them the ability to spread from host to host rapidly via elementary bodies. The metabolically and reproductively inactive elementary bodies are the endospore-like form of intracellular bacteria that enter an epithelial cell, where they become active. Figure 4.12 illustrates the life cycle of Chlamydia. Access for free at openstax.org 4.3 Nonproteobacteria Gram-Negative Bacteria and Phototrophic Bacteria 147 FIGURE 4.12 Chlamydia begins infection of a host when the metabolically inactive elementary bodies enter an epithelial cell. Once inside the host cell, the elementary bodies turn into active reticulate bodies. The reticulate bodies multiply and release more elementary bodies when the cell dies after the Chlamydia uses all of the host cell’s ATP. (credit: modification of work by Centers for Disease Control and Prevention) Spirochetes Spirochetes are characterized by their long (up to 250 μm), spiral-shaped bodies. Most spirochetes are also very thin, which makes it difficult to examine gram-stained preparations under a conventional brightfield microscope. Darkfield fluorescent microscopy is typically used instead. Spirochetes are also difficult or even impossible to culture. They are highly motile, using their axial filament to propel themselves. The axial filament is similar to a flagellum, but it wraps around the cell and runs inside the cell body of a spirochete in the periplasmic space between the outer membrane and the plasma membrane (Figure 4.13). 148 4 Prokaryotic Diversity FIGURE 4.13 Spirochetes are typically observed using darkfield microscopy (left). However, electron microscopy (top center, bottom center) provides a more detailed view of their cellular morphology. The flagella found between the inner and outer membranes of spirochetes wrap around the bacterium, causing a twisting motion used for locomotion. (credit “spirochetes” micrograph: modification of work by Centers for Disease Control and Prevention; credit “SEM/TEM”: modification of work by Guyard C, Raffel SJ, Schrumpf ME, Dahlstrom E, Sturdevant D, Ricklefs SM, Martens C, Hayes SF, Fischer ER, Hansen BT, Porcella SF, Schwan TG) Several genera of spirochetes include human pathogens. For example, the genus Treponema includes a species T. pallidum, which is further classified into four subspecies: T. pallidum pallidum, T. pallidum pertenue, T. pallidum carateum, and T. pallidum endemicum. The subspecies T. pallidum pallidum causes the sexually transmitted infection known as syphilis, the third most prevalent sexually transmitted bacterial infection in the United States, after chlamydia and gonorrhea. The other subspecies of T. pallidum cause tropical infectious diseases of the skin, bones, and joints. Another genus of spirochete, Borrelia, contains a number of pathogenic species. B. burgdorferi causes Lyme disease, which is transmitted by several genera of ticks (notably Ixodes and Amblyomma) and often produces a “bull’s eye” rash, fever, fatigue, and, sometimes, debilitating arthritis. B. recurrens causes a condition known as relapsing fever. Appendix D lists the genera, species, and related diseases for spirochetes. CHECK YOUR UNDERSTANDING Why do scientists typically use darkfield fluorescent microscopy to visualize spirochetes? Cytophaga, Fusobacterium, and Bacteroides The gram-negative nonproteobacteria of the genera Cytophaga, Fusobacterium, and Bacteroides are classified together as a phylum and called the CFB group. Although they are phylogenetically diverse, bacteria of the CFB group share some similarities in the sequence of nucleotides in their DNA. They are rod-shaped bacteria adapted to anaerobic environments, such as the tissue of the gums, gut, and rumen of ruminating animals. CFB bacteria are avid fermenters, able to process cellulose in rumen, thus enabling ruminant animals to obtain carbon and energy from grazing. Access for free at openstax.org 4.3 Nonproteobacteria Gram-Negative Bacteria and Phototrophic Bacteria 149 Cytophaga are motile aquatic bacteria that glide. Fusobacteria inhabit the human mouth and may cause severe infectious diseases. The largest genus of the CFB group is Bacteroides, which includes dozens of species that are prevalent inhabitants of the human large intestine, making up about 30% of the entire gut microbiome (Figure 4.14). One gram of human feces contains up to 100 billion Bacteroides cells. Most Bacteroides are mutualistic. They benefit from nutrients they find in the gut, and humans benefit from their ability to prevent pathogens from colonizing the large intestine. Indeed, when populations of Bacteroides are reduced in the gut—as often occurs when a patient takes antibiotics—the gut becomes a more favorable environment for pathogenic bacteria and fungi, which can cause secondary infections. FIGURE 4.14 Bacteroides comprise up to 30% of the normal microbiota in the human gut. (credit: NOAA) Only a few species of Bacteroides are pathogenic. B. melaninogenicus, for example, can cause wound infections in patients with weakened immune systems. CHECK YOUR UNDERSTANDING Why are Cytophaga, Fusobacterium, and Bacteroides classified together as the CFB group? Planctomycetes The Planctomycetes are found in aquatic environments, inhabiting freshwater, saltwater, and brackish water. Planctomycetes are unusual in that they reproduce by budding, meaning that instead of one maternal cell splitting into two equal daughter cells in the process of binary fission, the mother cell forms a bud that detaches from the mother cell and lives as an independent cell. These so-called swarmer cells are motile and not attached to a surface. However, they will soon differentiate into sessile (immobile) cells with an appendage called a holdfast that allows them to attach to surfaces in the water (Figure 4.15). Only the sessile cells are able to reproduce. FIGURE 4.15 (a) Sessile Planctomycetes have a holdfast that allows them to adhere to surfaces in aquatic environments. (b) Swarmers are motile and lack a holdfast. (credit: modification of work by American Society for Microbiology) 150 4 Prokaryotic Diversity Table 4.7 summarizes the characteristics of some of the most clinically relevant genera of nonproteobacteria. Nonproteobacteria Example Microscopic Morphology Unique Characteristics Genus Chlamydia Gram-negative, coccoid or ovoid Obligatory intracellular bacteria; some cause bacterium chlamydia, trachoma, and pneumonia Bacteroides Gram-negative bacillus Obligate anaerobic bacteria; abundant in the human gastrointestinal tract; usually mutualistic, although some species are opportunistic pathogens Cytophaga Gram-negative bacillus Motile by gliding; live in soil or water; decompose cellulose; may cause disease in fish Fusobacterium Gram-negative bacillus with Anaerobic; form; biofilms; some species cause disease pointed ends in humans (periodontitis, ulcers) Leptospira Spiral-shaped bacterium Aerobic, abundant in shallow water reservoirs; infect (spirochetes); gram negative-like rodents and domestic animals; can be transmitted to (better viewed by darkfield humans by infected animals’ urine; may cause severe microscopy); very thin disease Borrelia Gram-negative-like spirochete; B. burgdorferi causes Lyme disease and B. recurrens very thin; better viewed by causes relapsing fever darkfield microscopy Treponema Gram-negative-like spirochete; Motile; do not grow in culture; T. pallidum (subspecies T. very thin; better viewed by pallidum pallidum) causes syphilis darkfield microscopy TABLE 4.7 CHECK YOUR UNDERSTANDING How do Planctomycetes reproduce? Phototrophic Bacteria The phototrophic bacteria are a large and diverse category of bacteria that do not represent a taxon but, rather, a group of bacteria that use sunlight as their primary source of energy. This group contains both Proteobacteria and nonproteobacteria. They use solar energy to synthesize ATP through photosynthesis. When they produce oxygen, they perform oxygenic photosynthesis. When they do not produce oxygen, they perform anoxygenic photosynthesis. With the exception of some cyanobacteria, the majority of phototrophic bacteria perform anoxygenic photosynthesis. One large group of phototrophic bacteria includes the purple or green bacteria that perform photosynthesis with the help of bacteriochlorophylls, which are green, purple, or blue pigments similar to chlorophyll in plants. Some of these bacteria have a varying amount of red or orange pigments called carotenoids. Their color varies from orange to red to purple to green (Figure 4.16), and they are able to absorb light of various wavelengths. Traditionally, these bacteria are classified into sulfur and nonsulfur bacteria; they are further differentiated by color. Access for free at openstax.org 4.3 Nonproteobacteria Gram-Negative Bacteria and Phototrophic Bacteria 151 FIGURE 4.16 Purple and green sulfur bacteria use bacteriochlorophylls to perform photosynthesis. The sulfur bacteria perform anoxygenic photosynthesis, using sulfites as electron donors and releasing free elemental sulfur. Nonsulfur bacteria use organic substrates, such as succinate and malate, as donors of electrons. The purple sulfur bacteria oxidize hydrogen sulfide into elemental sulfur and sulfuric acid and get their purple color from the pigments bacteriochlorophylls and carotenoids. Bacteria of the genus Chromatium are purple sulfur Gammaproteobacteria. These microorganisms are strict anaerobes and live in water. They use carbon dioxide as their only source of carbon, but their survival and growth are possible only in the presence of sulfites, which they use as electron donors. Chromatium has been used as a model for studies of bacterial photosynthesis since the 13 1950s. The green sulfur bacteria use sulfide for oxidation and produce large amounts of green bacteriochlorophyll. The genus Chlorobium is a green sulfur bacterium. These bacteria use at least four types of chlorophyll for photosynthesis. The most prevalent of these, bacteriochlorophyll, is stored in special vesicle-like organelles called chlorosomes. Purple nonsulfur bacteria are similar to purple sulfur bacteria, except that they use hydrogen rather than hydrogen sulfide for oxidation. Among the purple nonsulfur bacteria is the genus Rhodospirillum. These microorganisms are facultative anaerobes, which are actually pink rather than purple, and can metabolize (“fix”) nitrogen. They may be valuable in the field of biotechnology because of their potential ability to produce biological plastic and hydrogen 14 fuel. The green nonsulfur bacteria are similar to green sulfur bacteria but they use substrates other than sulfides for oxidation. Chloroflexus is an example of a green nonsulfur bacterium. It often has an orange color when it grows in the dark, but it becomes green when it grows in sunlight. It stores bacteriochlorophyll in chlorosomes, similar to Chlorobium, and performs anoxygenic photosynthesis, using organic sulfites (low concentrations) or molecular hydrogen as electron donors, so it can survive in the dark if oxygen is available. Chloroflexus does not have flagella but can glide, like Cytophaga. It grows at a wide range of temperatures, from 35 °C to 70 °C, thus can be thermophilic. Another large, diverse group of phototrophic bacteria compose the phylum Cyanobacteria; they get their blue-green color from the chlorophyll contained in their cells (Figure 4.17). Species of this group perform oxygenic photosynthesis, producing megatons of gaseous oxygen. Scientists hypothesize that cyanobacteria played a critical role in the change of our planet’s anoxic atmosphere 1–2 billion years ago to the oxygen-rich environment we have 15 today. 13 R.C. Fuller et al. “Carbon Metabolism in Chromatium.” Journal of Biological Chemistry 236 (1961):2140–2149. 14 T.T. Selao et al. “Comparative Proteomic Studies in Rhodospirillum rubrum Grown Under Different Nitrogen Conditions.” Journal of Proteome Research 7 no. 8 (2008):3267–3275. 15 A. De los Rios et al. “Ultrastructural and Genetic Characteristics of Endolithic Cyanobacterial Biofilms Colonizing Antarctic Granite Rocks.” FEMS Microbiology Ecology 59 no. 2 (2007):386–395. 152 4 Prokaryotic Diversity FIGURE 4.17 (a) Microcystis aeruginosa is a type of cyanobacteria commonly found in freshwater environments. (b) In warm temperatures, M. aeruginosa and other cyanobacteria can multiply rapidly and produce neurotoxins, resulting in blooms that are harmful to fish and other aquatic animals. (credit a: modification of work by Dr. Barry H. Rosen/U.S. Geological Survey; credit b: modification of work by NOAA) Cyanobacteria have other remarkable properties. Amazingly adaptable, they thrive in many habitats, including marine and freshwater environments, soil, and even rocks. Roseli Ocampo-Friedmann and Imre Friedman identified photosynthetic cyanobacteria living within rocks in Antarctica's Dry Valleys, a barren, snowless region of with extremely low perceiptiation and an average temperature of -15 degrees Celsius. The discovery was the basis for new theories and practices in the area of astrobiology (both researchers went on to work for NASA), considering that Earth's polar deserts have conditions resembling those on Mars, which may provide a home to organisms similar to cyanobacteria. They can live as unicellular organisms or in colonies, and they can be filamentous, forming sheaths or biofilms. Many of them fix nitrogen, converting molecular nitrogen into nitrites and nitrates that other bacteria, plants, and animals can use. The reactions of nitrogen fixation occur in specialized cells called heterocysts. Photosynthesis in Cyanobacteria is oxygenic, using the same type of chlorophyll a found in plants and algae as the primary photosynthetic pigment. Cyanobacteria also use phycocyanin and cyanophycin, two secondary photosynthetic pigments that give them their characteristic blue color. They are located in special organelles called phycobilisomes and in folds of the cellular membrane called thylakoids, which are remarkably similar to the photosynthetic apparatus of plants. Scientists hypothesize that plants originated from endosymbiosis of ancestral 16 eukaryotic cells and ancestral photosynthetic bacteria. Cyanobacteria are also an interesting object of research in 17 18 19 biochemistry, with studies investigating their potential as biosorbents and products of human nutrition. Unfortunately, cyanobacteria can sometimes have a negative impact on human health. Genera such as Microcystis can form harmful cyanobacterial blooms, forming dense mats on bodies of water and producing large quantities of toxins that can harm wildlife and humans. These toxins have been implicated in tumors of the liver and diseases of 20 the nervous system in animals and humans. Table 4.8 summarizes the characteristics of important phototrophic bacteria. 16 T. Cavalier-Smith. “Membrane Heredity and Early Chloroplast Evolution.” Trends in Plant Science 5 no. 4 (2000):174–182. 17 S. Zhang, D.A. Bryant. “The Tricarboxylic Acid Cycle in Cyanobacteria.” Science 334 no. 6062 (2011):1551–1553. 18 A. Cain et al. “Cyanobacteria as a Biosorbent for Mercuric Ion.” Bioresource Technology 99 no. 14 (2008):6578–6586. 19 C.S. Ku et al. “Edible Blue-Green Algae Reduce the Production of Pro-Inflammatory Cytokines by Inhibiting NF-κB Pathway in Macrophages and Splenocytes.” Biochimica et Biophysica Acta 1830 no. 4 (2013):2981–2988. 20 I. Stewart et al. Cyanobacterial Poisoning in Livestock, Wild Mammals and Birds – an Overview. Advances in Experimental Medicine and Biology 619 (2008):613–637. Access for free at openstax.org 4.4 Gram-Positive Bacteria 153 Phototrophic Bacteria Phylum Class Example Genus Common Oxygenic or Sulfur or Species Name Anoxygenic Deposition Cyanobacteria Cyanophyceae Microcystis Blue-green Oxygenic None aeruginosa bacteria Chlorobi Chlorobia Chlorobium Green sulfur Anoxygenic Outside bacteria the cell Chloroflexi Chloroflexi Chloroflexus Green Anoxygenic None (Division) nonsulfur bacteria Alphaproteobacteria Rhodospirillum Purple Anoxygenic None nonsulfur bacteria Betaproteobacteria Rhodocyclus Purple Anoxygenic None Proteobacteria nonsulfur bacteria Gammaproteobacteria Chromatium Purple sulfur Anoxygenic Inside the bacteria cell TABLE 4.8 CHECK YOUR UNDERSTANDING What characteristic makes phototrophic bacteria different from other prokaryotes? 4.4 Gram-Positive Bacteria LEARNING OBJECTIVES By the end of this section, you will be able to: Describe the unique features of each category of high G+C and low G+C gram-positive bacteria Identify similarities and differences between high G+C and low G+C bacterial groups Give an example of a bacterium of high G+C and low G+C group commonly associated with each category Prokaryotes are identified as gram-positive if they have a multiple layer matrix of peptidoglycan forming the cell wall. Crystal violet, the primary stain of the Gram stain procedure, is readily retained and stabilized within this matrix, causing gram-positive prokaryotes to appear purple under a brightfield microscope after Gram staining. For many years, the retention of Gram stain was one of the main criteria used to classify prokaryotes, even though some prokaryotes did not readily stain with either the primary or secondary stains used in the Gram stain procedure. Advances in nucleic acid biochemistry have revealed additional characteristics that can be used to classify gram- positive prokaryotes, namely the guanine to cytosine ratios (G+C) in DNA and the composition of 16S rRNA subunits. Microbiologists currently recognize two distinct groups of gram-positive, or weakly staining gram-positive, prokaryotes. The class Actinobacteria comprises the high G+C gram-positive bacteria, which have more than 50% guanine and cytosine nucleotides in their DNA. The class Bacilli comprises low G+C gram-positive bacteria, which have less than 50% of guanine and cytosine nucleotides in their DNA. 154 4 Prokaryotic Diversity Actinobacteria: High G+C Gram-Positive Bacteria The name Actinobacteria comes from the Greek words for rays and small rod, but Actinobacteria are very diverse. Their microscopic appearance can range from thin filamentous branching rods to coccobacilli. Some Actinobacteria are very large and complex, whereas others are among the smallest independently living organisms. Most Actinobacteria live in the soil, but some are aquatic. The vast majority are aerobic. One distinctive feature of this group is the presence of several different peptidoglycans in the cell wall. The genus Actinomyces is a much studied representative of Actinobacteria. Actinomyces spp. play an important role in soil ecology, and some species are human pathogens. A number of Actinomyces spp. inhabit the human mouth and are opportunistic pathogens, causing infectious diseases like periodontitis (inflammation of the gums) and oral abscesses. The species A. israelii is an anaerobe notorious for causing endocarditis (inflammation of the inner lining of the heart) (Figure 4.18). FIGURE 4.18 (a) Actinomyces israelii (false-color scanning electron micrograph [SEM]) has a branched structure. (b) Corynebacterium diphtheria causes the deadly disease diphtheria. Note the distinctive palisades. (c) The gram-variable bacterium Gardnerella vaginalis causes bacterial vaginosis. This micrograph shows a Pap smear from a person with vaginosis. (credit a: modification of work by “GrahamColm”/Wikimedia Commons; credit b: modification of work by Centers for Disease Control and Prevention; credit c: modification of work by Mwakigonja AR, Torres LM, Mwakyoma HA, Kaaya EE) The genus Mycobacterium is represented by bacilli covered with a mycolic acid coat. This waxy coat protects the bacteria from some antibiotics, prevents them from drying out, and blocks penetration by Gram stain reagents (see Staining Microscopic Specimens). Because of this, a special acid-fast staining procedure is used to visualize these bacteria. The genus Mycobacterium is an important cause of a diverse group of infectious diseases. M. tuberculosis is the causative agent of tuberculosis, a disease that primarily impacts the lungs but can infect other parts of the body as well. It has been estimated that one-third of the world’s population has been infected with M. tuberculosis and millions of new infections occur each year. Treatment of M. tuberculosis is challenging and requires patients to take a combination of drugs for an extended time. Complicating treatment even further is the development and spread of multidrug-resistant strains of this pathogen. Another pathogenic species, M. leprae, is the cause of Hansen’s disease (leprosy), a chronic disease that impacts peripheral nerves and the integrity of the skin and mucosal surface of the respiratory tract. Loss of pain sensation and the presence of skin lesions increase susceptibility to secondary injuries and infections with other pathogens. Bacteria in the genus Corynebacterium contain diaminopimelic acid in their cell walls, and microscopically often form palisades, or pairs of rod-shaped cells resembling the letter V. Cells may contain metachromatic granules, intracellular storage of inorganic phosphates that are useful for identification of Corynebacterium. The vast majority of Corynebacterium spp. are nonpathogenic; however, C. diphtheria is the causative agent of diphtheria, a disease that can be fatal, especially in children (Figure 4.18). C. diphtheria produces a toxin that forms a pseudomembrane in the patient’s throat, causing swelling, difficulty breathing, and other symptoms that can become serious if untreated. The genus Bifidobacterium consists of filamentous anaerobes, many of which are commonly found in the gastrointestinal tract, vagina, and mouth. In fact, Bifidobacterium spp. constitute a substantial part of the human gut microbiota and are frequently used as probiotics and in yogurt production. The genus Gardnerella, contains only one species, G. vaginalis. This species is defined as “gram-variable” because its small coccobacilli do not show consistent results when Gram stained (Figure 4.18). Based on its genome, it is Access for free at openstax.org 4.4 Gram-Positive Bacteria 155 placed into the high G+C gram-positive group. G. vaginalis can cause bacterial vaginosis; symptoms are typically mild or even undetectable, but can lead to complications during pregnancy. Table 4.9 summarizes the characteristics of some important genera of Actinobacteria. Additional information on Actinobacteria appears in Appendix D. Actinobacteria: High G+C Gram-Positive Example Genus Microscopic Unique Characteristics Morphology Actinomyces Gram-positive Facultative anaerobes; in soil, decompose organic matter; in the bacillus; in colonies, human mouth, may cause gum disease shows fungus-like threads (hyphae) Arthrobacter Gram-positive Obligate aerobes; divide by “snapping,” forming V-like pairs of bacillus (at the daughter cells; degrade phenol, can be used in bioremediation exponential stage of growth) or coccus (in stationary phase) Bifidobacterium Gram-positive, Anaerobes commonly found in human gut microbiota filamentous actinobacterium Corynebacterium Gram-positive Aerobes or facultative anaerobes; form palisades; grow slowly; bacillus require enriched media in culture; C. diphtheriae causes diphtheria Frankia Gram-positive, Nitrogen-fixing bacteria; live in symbiosis with legumes fungus-like (filamentous) bacillus Gardnerella Gram-variable Colonize the human vagina, may alter the microbial ecology, thus coccobacillus leading to vaginosis Micrococcus Gram-positive coccus, Ubiquitous in the environment and on the human skin; oxidase- form microscopic positive (as opposed to morphologically similar S. aureus); some clusters are opportunistic pathogens Mycobacterium Gram-positive, acid- Slow growing, aerobic, resistant to drying and phagocytosis; fast bacillus covered with a waxy coat made of mycolic acid; M. tuberculosis causes tuberculosis; M. leprae causes leprosy Nocardia Weakly gram-positive May colonize the human gingiva; may cause severe pneumonia bacillus; forms acid- and inflammation of the skin fast branches Propionibacterium Gram-positive Aerotolerant anaerobe; slow-growing; P. acnes reproduces in the bacillus human sebaceous glands and may cause or contribute to acne TABLE 4.9 156 4 Prokaryotic Diversity Actinobacteria: High G+C Gram-Positive Example Genus Microscopic Unique Characteristics Morphology Rhodococcus Gram-positive Strict aerobe; used in industry for biodegradation of pollutants; R. bacillus fascians is a plant pathogen, and R. equi causes pneumonia in foals Streptomyces Gram-positive, Very diverse genus (>500 species); aerobic, spore-forming fungus-like bacteria; scavengers, decomposers found in soil (give the soil its (filamentous) bacillus “earthy” odor); used in pharmaceutical industry as antibiotic producers (more than two-thirds of clinically useful antibiotics) TABLE 4.9 CHECK YOUR UNDERSTANDING What is one distinctive feature of Actinobacteria? Low G+C Gram-positive Bacteria The low G+C gram-positive bacteria have less than 50% guanine and cytosine in their DNA, and this group of bacteria includes a number of genera of bacteria that are pathogenic. CLINICAL FOCUS Part 3 Based on her symptoms, Marsha’s doctor suspected that she had a case of tuberculosis. Although less common in the United States, tuberculosis is still extremely common in many parts of the world, including Nigeria. Marsha’s work there in a medical lab likely exposed her to Mycobacterium tuberculosis, the bacterium that causes tuberculosis. Marsha’s doctor ordered her to stay at home, wear a respiratory mask, and confine herself to one room as much as possible. He also said that Marsha had to take one semester off school. He prescribed isoniazid and rifampin, antibiotics used in a drug cocktail to treat tuberculosis, which Marsha was to take three times a day for at least three months. Why did the doctor order Marsha to stay home for three months? Jump to the next Clinical Focus box. Go back to the previous Clinical Focus box. Clostridia One large and diverse class of low G+C gram-positive bacteria is Clostridia. The best studied genus of this class is Clostridium. These rod-shaped bacteria are generally obligate anaerobes that produce endospores and can be found in anaerobic habitats like soil and aquatic sediments rich in organic nutrients. The endospores may survive for many years. Clostridium spp. produce more kinds of protein toxins than any other bacterial genus, and several species are human pathogens. C. perfringens is the third most common cause of food poisoning in the United States and is the causative agent of an even more serious disease called gas gangrene. Gas gangrene occurs when C. perfringens endospores enter a wound and germinate, becoming viable bacterial cells and producing a toxin that can cause the necrosis (death) of tissue. C. tetani, which causes tetanus, produces a neurotoxin that is able to enter neurons, travel to regions of the central nervous system where it blocks the inhibition of nerve impulses involved in muscle contractions, and cause a life-threatening spastic paralysis. C. botulinum produces botulinum neurotoxin, the most Access for free at openstax.org 4.4 Gram-Positive Bacteria 157 lethal biological toxin known. Botulinum toxin is responsible for rare but frequently fatal cases of botulism. The toxin blocks the release of acetylcholine in neuromuscular junctions, causing flaccid paralysis. In very small concentrations, botulinum toxin has been used to treat muscle pathologies in humans and in a cosmetic procedure to eliminate wrinkles. C. difficile is a common source of hospital-acquired infections (Figure 4.19) that can result in serious and even fatal cases of colitis (inflammation of the large intestine). Infections often occur in patients who are immunosuppressed or undergoing antibiotic therapy that alters the normal microbiota of the gastrointestinal tract. Appendix D lists the genera, species, and related diseases for Clostridia. FIGURE 4.19 Clostridium difficile, a gram-positive, rod-shaped bacterium, causes severe colitis and diarrhea, often after the normal gut microbiota is eradicated by antibiotics. (credit: modification of work by Centers for Disease Control and Prevention) Lactobacillales The order Lactobacillales comprises low G+C gram-positive bacteria that include both bacilli and cocci in the genera Lactobacillus, Leuconostoc, Enterococcus, and Streptococcus. Bacteria of the latter three genera typically are spherical or ovoid and often form chains. Streptococcus, the name of which comes from the Greek word for twisted chain, is responsible for many types of infectious diseases in humans. Species from this genus, often referred to as streptococci, are usually classified by serotypes called Lancefield groups, and by their ability to lyse red blood cells when grown on blood agar. S. pyogenes belongs to the Lancefield group A, β-hemolytic Streptococcus. This species is considered a pyogenic pathogen because of the associated pus production observed with infections it causes (Figure 4.20). S. pyogenes is the most common cause of bacterial pharyngitis (strep throat); it is also an important cause of various skin infections that can be relatively mild (e.g., impetigo) or life threatening (e.g., necrotizing fasciitis, also known as flesh eating disease), life threatening. FIGURE 4.20 (a) A gram-stained specimen of Streptococcus pyogenes shows the chains of cocci characteristic of this organism’s morphology. (b) S. pyogenes on blood agar shows characteristic lysis of red blood cells, indicated by the halo of clearing around colonies. (credit a, b: modification of work by American Society for Microbiology) The nonpyogenic (i.e., not associated with pus production) streptococci are a group of streptococcal species that are not a taxon but are grouped together because they inhabit the human mouth. The nonpyogenic streptococci do not belong to any of the Lancefield groups. Most are commensals, but a few, such as S. mutans, are implicated in the development of dental caries. 158 4 Prokaryotic Diversity S. pneumoniae (commonly referred to as pneumococcus), is a Streptococcus species that also does not belong to any Lancefield group. S. pneumoniae cells appear microscopically as diplococci, pairs of cells, rather than the long chains typical of most streptococci. Scientists have known since the 19th century that S. pneumoniae causes pneumonia and other respiratory infections. However, this bacterium can also cause a wide range of other diseases, including meningitis, septicemia, osteomyelitis, and endocarditis, especially in newborns, the elderly, and patients with immunodeficiency. Bacilli The name of the class Bacilli suggests that it is made up of bacteria that are bacillus in shape, but it is a morphologically diverse class that includes bacillus-shaped and cocccus-shaped genera. Among the many genera in this class are two that are very important clinically: Bacillus and Staphylococcus. Bacteria in the genus Bacillus are bacillus in shape and can produce endospores. They include aerobes or facultative anaerobes. A number of Bacillus spp. are used in various industries, including the production of antibiotics (e.g., barnase), enzymes (e.g., alpha-amylase, BamH1 restriction endonuclease), and detergents (e.g., subtilisin). Two notable pathogens belong to the genus Bacillus. B. anthracis is the pathogen that causes anthrax, a severe disease that affects wild and domesticated animals and can spread from infected animals to humans. Anthrax manifests in humans as charcoal-black ulcers on the skin, severe enterocolitis, pneumonia, and brain damage due to swelling. If untreated, anthrax is lethal. B. cereus, a closely related species, is a pathogen that may cause food poisoning. It is a rod-shaped species that forms chains. Colonies appear milky white with irregular shapes when cultured on blood agar (Figure 4.21). One other important species is B. thuringiensis. This bacterium produces a number of substances used as insecticides because they are toxic for insects. FIGURE 4.21 (a) In this gram-stained specimen, the violet rod-shaped cells forming chains are the gram-positive bacteria Bacillus cereus. The small, pink cells are the gram-negative bacteria Escherichia coli. (b) In this culture, white colonies of B. cereus have been grown on sheep blood agar. (credit a: modification of work by “Bibliomaniac 15”/Wikimedia Commons; credit b: modification of work by Centers for Disease Control and Prevention) The genus Staphylococcus also belongs to the class Bacilli, even though its shape is coccus rather than a bacillus. The name Staphylococcus comes from a Greek word for bunches of grapes, which describes their microscopic appearance in culture (Figure 4.22). Staphylococcus spp. are facultative anaerobic, halophilic, and nonmotile. The two best-studied species of this genus are S. epidermidis and S. aureus. Access for free at openstax.org 4.4 Gram-Positive Bacteria 159 FIGURE 4.22 This SEM of Staphylococcus aureus illustrates the typical “grape-like” clustering of cells. (credit:

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