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4.2: Classifying Prokaryotes and Examples - Biology

4.2: Classifying Prokaryotes and Examples - Biology


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Learning Objectives

  • Explain how prokaryotes are classified what criteria are used to help group them into phylum
  • Highlight some interesting and diverse prokaryotes

Taxonomy and Systematics

Assigning prokaryotes to a certain species is challenging. They do not reproduce sexually, so it is not possible to 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 (particularly rRNA) 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). It can also be found as a living document, available through subscription, to try and keep it as up-to-date as possible.

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 earlier, 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, which lack a cell wall and therefore cannot retain the gram-stain reagents. 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. 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 this section.

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.

Using these two descriptions however, will only get small amounts of separation, so microbiologist turn to two other descriptions: the microbes interaction with or reliance on oxygen gas, and their main mode of gaining of nutrients (both more fully described in chapters 7 and 8). The classifications of prokaryotes are constantly changing as new species are being discovered and new information comes to light. Included in the next section are some highlights from the different major groups and phylum of the Bacterial and Archaeal domains.

Exercise (PageIndex{1})

What characteristics do scientists use to classify prokaryotes?

Proteobacteria

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 Bacteria based on the similarity of the nucleotide sequences in their genome.1 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.

Alphaproteobacteria include intracellular parasites

Among the Alphaproteobacteria are two taxa, chlamydias and rickettsias, that are obligate intracellular pathogens, meaning that part of their life cycle must occur inside other cells called host cells. When not growing inside a host cell, Chlamydia and Rickettsia are metabolically inactive outside of 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 (PageIndex{1})). 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. 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.

Chlamydia is another taxon of the Alphaproteobacteria. Members of this genus 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 (PageIndex{2}) illustrates the life cycle of Chlamydia. C. trachomatis is a human pathogen that causes trachoma, a disease of the eyes, often leading to blindness. 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.

Betaproteobacteria include other familiar infectious bacteria

Unlike Alphaproteobacteria, which survive on a minimal amount of nutrients, the class Betaproteobacteria are eutrophs (or copiotrophs), meaning that they require a copious amount of organic nutrients. Betaproteobacteria often grow between aerobic and anaerobic areas (e.g., in mammalian intestines). Some genera include species that are human pathogens, able to cause severe, sometimes life-threatening disease. 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.

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. 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 (PageIndex{3})).

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. 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).

Another famous member is 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, which perforates cellular membranes in the large intestine, causing bloody diarrhea and peritonitis (inflammation of the inner linings of the abdominal cavity). Other E. coli strains may cause traveler’s diarrhea, a less severe but very widespread disease. The genera Pasteruella, Legionella, Haemophilus and Salmonella.

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 nutrients for the bacteria to grow and the bacteria produce bioluminescence that protects the squid from predators (Figure (PageIndex{4})).

Deltaproteobacteria include potentially helpful a scattering of helpful bacteria

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 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 (PageIndex{5})), structures that are still being studied by biologists and bacterial ecologists.2 These bacteria can also form metabolically inactive myxospores.

Epsilonproteobacteria includes familiar GI pathogens

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 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 stomach and duodenum (Figure (PageIndex{6})). Studies have also shown that H. pylori is linked to stomach cancer.3 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.

Nonproteobacteria Gram-negative Bacteria and 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 three classes of gram-negative nonproteobacteria: 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.

Spirochetes

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. recurrens causes a condition known as relapsing fever.

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 (PageIndex{7})).

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 (PageIndex{8})), 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. 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.

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 (PageIndex{9})). 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 today.4 Cyanobacteria have other remarkable properties. Amazingly adaptable, they thrive in many habitats, including marine and freshwater environments, soil, and even rocks. They can live at a wide range of temperatures, even in the extreme temperatures of the Antarctic. 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.

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).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. 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.

Low G+C Gram-positive Bacteria Groups

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.

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. 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. 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. botulinum produces botulinum neurotoxin, the most 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. difficile is a common source of hospital-acquired infections (Figure (PageIndex{10})) 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.

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 (PageIndex{11})). 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.

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. 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 (PageIndex{12})). One other important species is B. thuringiensis. This bacterium produces a number of substances used as insecticides because they are toxic for insects.

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. Staphylococcus spp. are facultative anaerobic, halophilic, and nonmotile. The two best-studied species of this genus are S. epidermidis and S. aureus.

S. epidermidis, whose main habitat is the human skin, is thought to be nonpathogenic for humans with healthy immune systems, but in patients with immunodeficiency, it may cause infections in skin wounds and prostheses (e.g., artificial joints, heart valves). S. epidermidis is also an important cause of infections associated with intravenous catheters. This makes it a dangerous pathogen in hospital settings, where many patients may be immunocompromised.

Strains of S. aureus cause a wide variety of infections in humans, including skin infections that produce boils, carbuncles, cellulitis, or impetigo. Certain strains of S. aureus produce a substance called enterotoxin, which can cause severe enteritis, often called staph food poisoning. Some strains of S. aureus produce the toxin responsible for toxic shock syndrome, which can result in cardiovascular collapse and death.

Mycoplasmas

Although Mycoplasma spp. do not possess a cell wall and, therefore, are not stained by Gram-stain reagents, this genus is still included with the low G+C gram-positive bacteria. The genus Mycoplasma includes more than 100 species, which share several unique characteristics. They are very small cells, some with a diameter of about 0.2 μm, which is smaller than some large viruses. They have no cell walls and, therefore, are pleomorphic, meaning that they may take on a variety of shapes and can even resemble very small animal cells. Because they lack a characteristic shape, they can be difficult to identify. One species, M. pneumoniae, causes the mild form of pneumonia known as “walking pneumonia” or “atypical pneumonia.” This form of pneumonia is typically less severe than forms caused by other bacteria or viruses.

Clinical Focus - Resolution

Marsha’s sputum sample was sent to the microbiology lab to confirm the identity of the microorganism causing her infection. The lab also performed antimicrobial susceptibility testing (AST) on the sample to confirm that the physician has prescribed the correct antimicrobial drugs.

Direct microscopic examination of the sputum revealed acid-fast bacteria (AFB) present in Marsha’s sputum. When placed in culture, there were no signs of growth for the first 8 days, suggesting that microorganism was either dead or growing very slowly. Slow growth is a distinctive characteristic of M. tuberculosis.

After four weeks, the lab microbiologist observed distinctive colorless granulated colonies (Figure (PageIndex{13})). The colonies contained AFB showing the same microscopic characteristics as those revealed during the direct microscopic examination of Marsha’s sputum. To confirm the identification of the AFB, samples of the colonies were analyzed using nucleic acid hybridization, or direct nucleic acid amplification (NAA) testing. When a bacterium is acid-fast, it is classified in the family Mycobacteriaceae. DNA sequencing of variable genomic regions of the DNA extracted from these bacteria revealed that it was high G+C. This fact served to finalize Marsha’s diagnosis as infection with M. tuberculosis. After nine months of treatment with the drugs prescribed by her doctor, Marsha made a full recovery.

Biopiracy and Bioprospecting

In 1969, an employee of a Swiss pharmaceutical company was vacationing in Norway and decided to collect some soil samples. He took them back to his lab, and the Swiss company subsequently used the fungus Tolypocladium inflatum in those samples to develop cyclosporine A, a drug widely used in patients who undergo tissue or organ transplantation. The Swiss company earns more than $1 billion a year for production of cyclosporine A, yet Norway receives nothing in return—no payment to the government or benefit for the Norwegian people. Despite the fact the cyclosporine A saves numerous lives, many consider the means by which the soil samples were obtained to be an act of “biopiracy,” essentially a form of theft. Do the ends justify the means in a case like this?

Nature is full of as-yet-undiscovered bacteria and other microorganisms that could one day be used to develop new life-saving drugs or treatments.5 Pharmaceutical and biotechnology companies stand to reap huge profits from such discoveries, but ethical questions remain. To whom do biological resources belong? Should companies who invest (and risk) millions of dollars in research and development be required to share revenue or royalties for the right to access biological resources?

Compensation is not the only issue when it comes to bioprospecting. Some communities and cultures are philosophically opposed to bioprospecting, fearing unforeseen consequences of collecting genetic or biological material. Native Hawaiians, for example, are very protective of their unique biological resources.

For many years, it was unclear what rights government agencies, private corporations, and citizens had when it came to collecting samples of microorganisms from public land. Then, in 1993, the Convention on Biological Diversity granted each nation the rights to any genetic and biological material found on their own land. Scientists can no longer collect samples without a prior arrangement with the land owner for compensation. This convention now ensures that companies act ethically in obtaining the samples they use to create their products.

Deeply Branching Bacteria

On a phylogenetic tree, the trunk or root of the tree represents a common ancient evolutionary ancestor, often called the last universal common ancestor (LUCA), and the branches are its evolutionary descendants. Scientists consider the deeply branching bacteria, such as the genus Acetothermus, to be the first of these non-LUCA forms of life produced by evolution some 3.5 billion years ago. When placed on the phylogenetic tree, they stem from the common root of life, deep and close to the LUCA root—hence the name “deeply branching.” (see chapter 1, section 4 for review)

The deeply branching bacteria may provide clues regarding the structure and function of ancient and now extinct forms of life. We can hypothesize that ancient bacteria, like the deeply branching bacteria that still exist, were thermophiles or hyperthermophiles, meaning that they thrived at very high temperatures. Acetothermus paucivorans, a gram-negative anaerobic bacterium discovered in 1988 in sewage sludge, is a thermophile growing at an optimal temperature of 58 °C.6 Scientists have determined it to be the deepest branching bacterium, or the closest evolutionary relative of the LUCA.

The class Thermotogae is represented mostly by hyperthermophilic, as well as some mesophilic (preferring moderate temperatures), anaerobic gram-negative bacteria whose cells are wrapped in a peculiar sheath-like outer membrane called a toga. The thin layer of peptidoglycan in their cell wall has an unusual structure; it contains diaminopimelic acid and D-lysine. These bacteria are able to use a variety of organic substrates and produce molecular hydrogen, which can be used in industry. The class contains several genera, of which the best known is the genus Thermotoga. One species of this genus, T. maritima, lives near the thermal ocean vents and thrives in temperatures of 90 °C; another species, T. subterranea, lives in underground oil reservoirs.

Finally, the deeply branching bacterium Deinococcus radiodurans belongs to a genus whose name is derived from a Greek word meaning terrible berry. Nicknamed “Conan the Bacterium,” D. radiodurans is considered a polyextremophile because of its ability to survive under the many different kinds of extreme conditions—extreme heat, drought, vacuum, acidity, and radiation. It owes its name to its ability to withstand doses of ionizing radiation that kill all other known bacteria; this special ability is attributed to some unique mechanisms of DNA repair.

Archaea

Like organisms in the domain Bacteria, organisms of the domain Archaea are all unicellular organisms. However, archaea differ structurally from bacteria in several significant ways. To summarize:

  • The archaeal cell membrane is composed of ether linkages with branched isoprene chains (as opposed to the bacterial cell membrane, which has ester linkages with unbranched fatty acids).
  • Archaeal cell walls lack peptidoglycan, but some contain a structurally similar substance called pseudopeptidoglycan or pseudomurein.
  • The genomes of Archaea are larger and more complex than those of bacteria.

Domain Archaea is as diverse as domain Bacteria, and its representatives can be found in any habitat. Some archaea are mesophiles, and many are extremophiles, preferring extreme hot or cold, extreme salinity, or other conditions that are hostile to most other forms of life on earth. Their metabolism is adapted to the harsh environments, and they can perform methanogenesis, for example, which bacteria and eukaryotes cannot. With few exceptions, archaea are not present in the human microbiota, and none are currently known to be associated with infectious diseases in humans, animals, plants, or microorganisms. However, many play important roles in the environment and may thus have an indirect impact on human health.

The size and complexity of the archaeal genome makes it difficult to classify. Most taxonomists agree that within the Archaea, there are currently five major phyla: Crenarchaeota, Euryarchaeota, Korarchaeota, Nanoarchaeota, and Thaumarchaeota. There are likely many other archaeal groups that have not yet been systematically studied and classified.

Crenarchaeota

Crenarchaeota is a class of Archaea that is extremely diverse, containing genera and species that differ vastly in their morphology and requirements for growth. All Crenarchaeota are aquatic organisms, and they are thought to be the most abundant microorganisms in the oceans. Most, but not all, Crenarchaeota are hyperthermophiles; some of them (notably, the genus Pyrolobus) are able to grow at temperatures up to 113 °C.7

Euryarchaeota

The phylum Euryarchaeota includes several distinct classes. Species in the classes Methanobacteria, Methanococci, and Methanomicrobia represent Archaea that can be generally described as methanogens. Methanogens are unique in that they can reduce carbon dioxide in the presence of hydrogen, producing methane. They can live in the most extreme environments and can reproduce at temperatures varying from below freezing to boiling. Methanogens have been found in hot springs as well as deep under ice in Greenland. Some scientists have even hypothesized that methanogens may inhabit the planet Mars because the mixture of gases produced by methanogens resembles the makeup of the Martian atmosphere.8

Methanogens are thought to contribute to the formation of anoxic sediments by producing hydrogen sulfide, making “marsh gas.” They also produce gases in ruminants and humans. Some genera of methanogens, notably Methanosarcina, can grow and produce methane in the presence of oxygen, although the vast majority are strict anaerobes.

The class Halobacteria (which was named before scientists recognized the distinction between Archaea and Bacteria) includes halophilic (“salt-loving”) archaea. Halobacteria require a very high concentrations of sodium chloride in their aquatic environment. The required concentration is close to saturation, at 36%; such environments include the Dead Sea as well as some salty lakes in Antarctica and south-central Asia. One remarkable feature of these organisms is that they perform photosynthesis using the protein bacteriorhodopsin, which gives them, and the bodies of water they inhabit, a beautiful purple color (Figure (PageIndex{15})).

Notable species of Halobacteria include Halobacterium salinarum, which may be the oldest living organism on earth; scientists have isolated its DNA from fossils that are 250 million years old.9 Another species, Haloferax volcanii, shows a very sophisticated system of ion exchange, which enables it to balance the concentration of salts at high temperatures

Clinical Focus: Resolution

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 (PageIndex{16})).

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.

Exercise (PageIndex{1})

  • What are some possible diseases that could be responsible for Marsha’s radiograph results?
  • Why did the doctor order Marsha to stay home for three months?

Summary

  • In recent years, the traditional approaches to classification of prokaryotes have been supplemented by approaches based on molecular genetics.
  • We separate the Phylum in the Bacterial and Archaeal domains by wall composition (Gram positive, Gram negative or other), their G+C percentage, how they get their energy, and how they react to oxygen gas.
  • Proteobacteria is a phylum of gram-negative bacteria discovered by Carl Woese in the 1980s based on nucleotide sequence homology. Proteobacteria are further classified into the classes alpha-, beta-, gamma-, delta- and epsilonproteobacteria, each class having separate orders, families, genera, and species.
  • Non-proteobacteria that are Gram negative include groups like the spirochetes and photosynthetic bacteria.
  • Actinobacteria are a group of high G+C Gram positive bacteria including Actinomyces and Mycobacterium.
  • Low G+C Gram positive bacteria include many smaller groups such as Clostridia, Lactobacillales, Bacilli and the highly variable Mycoplasma.
  • Deeply branching bacteria are phylogenetically the most ancient forms of life, being the closest to the last universal common ancestor.
  • Archaea are unicellular, prokaryotic microorganisms that differ from bacteria in their genetics, biochemistry, and ecology.
  • Some archaea are extremophiles, living in environments with extremely high or low temperatures, or extreme salinity.
  • Only archaea are known to produce methane. Methane-producing archaea are called methanogens.

Footnotes

  1. C.R. Woese. “Bacterial Evolution.” Microbiological Review 51 no. 2 (1987):221–271.
  2. H. Reichenbach. “Myxobacteria, Producers of Novel Bioactive Substances.” Journal of Industrial Microbiology & Biotechnology 27 no. 3 (2001):149–156.
  3. S. Suerbaum, P. Michetti. “Helicobacter pylori infection.” New England Journal of Medicine 347 no. 15 (2002):1175–1186.
  4. 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.
  5. J. Andre. Bioethics as Practice. Chapel Hill, NC: University of North Carolina Press, 2002
  6. G. Dietrich et al. “Acetothermus paucivorans, gen. nov., sp. Nov., a Strictly Anaerobic, Thermophilic Bacterium From Sewage Sludge, Fermenting Hexoses to Acetate, CO2, and H2.” Systematic and Applied Microbiology 10 no. 2 (1988):174–179.
  7. E. Blochl et al.“Pyrolobus fumani, gen. and sp. nov., represents a novel group of Archaea, extending the upper temperature limit for life to 113°C.” Extremophiles 1 (1997):14–21.
  8. R.R. Britt “Crater Critters: Where Mars Microbes Might Lurk.” www.space.com/1880-crater-cri...obes-lurk.html. Accessed April 7, 2015.
  9. H. Vreeland et al. “Fatty acid and DA Analyses of Permian Bacterium Isolated From Ancient Salt Crystals Reveal Differences With Their Modern Relatives.” Extremophiles 10 (2006):71–78.

Contributor

  • Nina Parker, (Shenandoah University), Mark Schneegurt (Wichita State University), Anh-Hue Thi Tu (Georgia Southwestern State University), Philip Lister (Central New Mexico Community College), and Brian M. Forster (Saint Joseph’s University) with many contributing authors. Original content via Openstax (CC BY 4.0; Access for free at https://openstax.org/books/microbiology/pages/1-introduction)


4.2: Classifying Prokaryotes and Examples - Biology

PART II. CORNERSTONES: CHEMISTRY, CELLS, AND METABOLISM

4. Cell Structure and Function

4.8. Prokaryotic and Eukaryotic Cells Revisited

Now that you have an idea of how cells are constructed, we can look at the great diversity of the kinds of cells that exist. You already know that there are significant differences between prokaryotic and eukaryotic cells.

Because prokaryotic (noneukaryotic) and eukaryotic cells are so different and prokaryotic cells show up in the fossil records much earlier, the differences between the two kinds of cells are used to classify organisms. Thus, biologists have classified organisms into three large categories, called domains. The following diagram illustrates how living things are classified:

The Domain Bacteria contains most of the microorganisms and can be found in a wide variety of environments. The Domain Archaea contains many kinds of microorganisms that have significant biochemical differences from the Bacteria. Many of the Archaea have special metabolic abilities and live in extreme environments of high temperature or extreme saltiness. Although only a few thousand Bacteria and only about 200 Archaea have been described, recent DNA studies of seawater and soil suggest that there are millions of undescribed species. In all likelihood, these noneukaryotic organisms far outnumber all the species of eukaryotic organisms combined. All other living things are comprised of eukaryotic cells.

Prokaryotic Cell Structure

Prokaryotic cells, the Bacteria and Archaea, do not have a typical nucleus bound by a nuclear membrane, nor do they contain mitochondria, chloroplasts, Golgi, or extensive networks of endoplasmic reticula. However, prokaryotic cells contain DNA and enzymes and are able to reproduce and engage in metabolism. They perform all of the basic functions of living things with fewer and simpler organelles. Although some Eubacteria have a type of green photosynthetic pigment and carry on photosynthesis, they do so without chloroplasts and use somewhat different chemical reactions.

Most Bacteria are surrounded by a capsule, or slime layer, which is composed of a variety of compounds. In certain bacteria, this layer is responsible for their ability to stick to surfaces, forming biofilms (e.g., the film of bacteria on teeth), and to resist phagocytosis. Many bacteria also have fimbriae, hairlike protein structures, which help the cell stick to objects. Those with flagella are capable of propelling themselves through the environment. Below the capsule is the rigid cell wall, comprised of a unique protein/carbohydrate complex called peptidoglycan. This gives the cell the strength to resist osmotic pressure changes and gives it shape. Just beneath the wall is the plasma membrane. Thinner and with a slightly different chemical composition from that of eukaryotes, the plasma membrane carries out the same functions as the plasma membrane in eukaryotes. Most bacteria are either rod-shaped (bacilli), spherical (cocci), corkscrew-shaped (spirilla), or comma-shaped (vibrio). The genetic material within the cytoplasm is DNA in the form of a loop.

The Archaea share many characteristics with the Bacteria. Many have a rod or spherical shape, although some are square or triangular. Some have flagella and have cell walls, but the cell walls are made of a different material than that of bacteria.

One significant difference between the cells of Bacteria and Archaea is in the chemical makeup of their ribosomes. The ribosomes of Bacteria contain different proteins from those found in the cells of Eucarya or Archaea. Bacterial ribosomes are also smaller. This discovery was important to medicine, because many cellular forms of life that cause common diseases are bacterial. As soon as differences in the ribosomes were noted, researchers began to look for ways in which to interfere with the bacterial ribosome’s function, but not interfere with the ribosomes of eukaryotic cells. Antibiotics, such as streptomycin, are the result of this research. This drug combines with bacterial ribosomes and causes bacteria to die because it prevents production of the proteins essential to survival of bacteria. Because eukaryotic ribosomes differ from bacterial ribosomes, streptomycin does not interfere with the normal function of the ribosomes in human cells.

Eukaryotic Cell Structure

Eukaryotic cells contain a true nucleus and most of the membranous organelles described earlier. Eukaryotic organisms can be further divided into several categories, based on the specific combination of organelles they contain. The cells of plants, fungi, protozoa and algae, and animals are all eukaryotic. The most obvious characteristic that sets plants and algae apart from other organisms is their green color, which indicates that the cells contain chlorophyll in chloroplasts. Chlorophyll is necessary for photosynthesis—the conversion of light energy into chemical-bond energy in food molecules. Another distinguishing characteristic of plant and algal cells is that their cell walls are made of cellulose (table 4.2).

The fungi are a distinct group of organisms that lack chloroplasts but have a cell wall. However, the cell wall is made from a polysaccharide, called chitin, rather than cellulose. Organisms that belong in this category of eukaryotic cells include yeasts, molds, mushrooms, and the fungi that cause such human diseases as athlete’s foot, jungle rot, and ringworm.

Eukaryotic organisms that lack cell walls and chloroplasts are placed in separate groups. Organisms that consist of only one cell are called protozoans—examples are Amoeba and Paramecium. They have all the cellular organelles described in this chapter except the chloroplast therefore, protozoans must consume food as do fungi and multicellular animals.

TABLE 4.2. Comparison of Various Kinds of Cells

Note: Viruses are not included in this classification system, because viruses are not composed of the basic cellular structural components. They are composed of a core of nucleic acid (DNA or RNA, never both) and a surrounding coat, or capsid, composed of protein. For this reason, viruses are called acellular or noncellular.

The Cell—The Basic Unit of Life

Although the differences in these groups of organisms may seem to set them worlds apart, their similarity in cellular structure is one of the central themes unifying the field of biology. One can obtain a better understanding of how cells operate in general by studying specific examples. Because the organelles have the same general structure and function, regardless of the kind of cell in which they are found, we can learn more about how mitochondria function in plants by studying how mitochondria function in animals. There is a commonality among all living things with regard to their cellular structure and function. The fact that all eukaryotic organisms have the same cellular structures is strong evidence that they all evolved from a common ancestor.

17. List five differences in structure between prokaryotic and eukaryotic cells.

18. What two types of organisms have prokaryotic cell structure?

The concept of the cell has developed over a number of years. Initially, only two regions, the cytoplasm and the nucleus, could be identified. At present, numerous organelles are recognized as essential components of both noneukaryotic and eukaryotic cell types. The structure and function of some of these organelles are compared in table 4.3. This table also indicates whether the organelle is unique to noneukaryotic or eukaryotic cells or is found in both.

The cell is the common unit of life. Individual cells and their structures are studied to discover how they function as individual living organisms and as parts of many-celled beings. Knowing how prokaryotic and eukaryotic organisms resemble each other and differ from each other helps physicians control some organisms dangerous to humans.

There are several ways in which materials enter or leave cells. These include diffusion and osmosis, which involve the net movement of molecules from an area of high to low concentration. In addition, there are several processes that involve activities on the part of the cell to move things across the membrane. These include facilitated diffusion, which uses carrier molecules to diffuse across the membrane active transport, which uses energy from the cell to move materials from low to high concentration and endocytosis and exocytosis, in which membrane-enclosed packets are formed.

TABLE 4.3. Summary of the Structure and Function of the Cellular Organelles


Cooperation between Bacteria and Eukaryotes: Nitrogen Fixation

Nitrogen is a very important element to living things, because it is part of nucleotides and amino acids that are the building blocks of nucleic acids and proteins, respectively. Nitrogen is usually the most limiting element in terrestrial ecosystems, with atmospheric nitrogen, N2, providing the largest pool of available nitrogen. However, eukaryotes cannot use atmospheric, gaseous nitrogen to synthesize macromolecules. Fortunately, nitrogen can be “fixed,” meaning it is converted into a more accessible form—ammonia (NH3)—either biologically or abiotically.

Abiotic nitrogen fixation occurs as a result of physical processes such as lightning or by industrial processes. Biological nitrogen fixation (BNF) is exclusively carried out by prokaryotes: soil bacteria, cyanobacteria, and Frankia spp. (filamentous bacteria interacting with actinorhizal plants such as alder, bayberry, and sweet fern). After photosynthesis, BNF is the most important biological process on Earth. The overall nitrogen fixation equation below represents a series of redox reactions (Pi stands for inorganic phosphate).

The total fixed nitrogen through BNF is about 100 to 180 million metric tons per year, which contributes about 65 percent of the nitrogen used in agriculture.

Cyanobacteria are the most important nitrogen fixers in aquatic environments. In soil, members of the genera Clostridium and Azotobacter are examples of free-living, nitrogen-fixing bacteria. Other bacteria live symbiotically with legume plants, providing the most important source of fixed nitrogen. Symbionts may fix more nitrogen in soils than free-living organisms by a factor of 10. Soil bacteria, collectively called rhizobia, are able to symbiotically interact with legumes to form nodules , specialized structures where nitrogen fixation occurs (Figure 1). Nitrogenase, the enzyme that fixes nitrogen, is inactivated by oxygen, so the nodule provides an oxygen-free area for nitrogen fixation to take place. The oxygen is sequestered by a form of plant hemoglobin called leghemoglobin, which protects the nitrogenase, but releases enough oxygen to support respiratory activity.

Symbiotic nitrogen fixation provides a natural and inexpensive plant fertilizer: It reduces atmospheric nitrogen to ammonia, which is easily usable by plants. The use of legumes is an excellent alternative to chemical fertilization and is of special interest to sustainable agriculture, which seeks to minimize the use of chemicals and conserve natural resources. Through symbiotic nitrogen fixation, the plant benefits from using an endless source of nitrogen: the atmosphere. The bacteria benefit from using photosynthates (carbohydrates produced during photosynthesis) from the plant and having a protected niche. In addition, the soil benefits from being naturally fertilized. Therefore, the use of rhizobia as biofertilizers is a sustainable practice.

Why are legumes so important? Some, like soybeans, are key sources of agricultural protein. Some of the most important legumes consumed by humans are soybeans, peanuts, peas, chickpeas, and beans. Other legumes, such as alfalfa, are used to feed cattle.

Figure 1: Nitrogen-fixation nodules on soybean roots. Soybean (Glycine max) is a legume that interacts symbiotically with the soil bacterium Bradyrhizobium japonicum to form specialized structures on the roots called nodules where nitrogen fixation occurs. (credit: USDA)

OCR A-level Biology A Module 4.2.2 REVISION (Classification and evolution)

A Science teacher by trade, I've also been known to be found teaching Maths and PE! However, strange as it may seem, my real love is designing resources that can be used by other teachers to maximise the experience of the students. I am constantly thinking of new ways to engage a student with a topic and try to implement that in the design of the lessons.

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This revision resource has been designed with the simple aim of motivating the students whilst they assess their understanding of the content found in module 4.2.2 (Classification and evolution) of the OCR A-level Biology A specification. This module is often brushed over by students which leads to misconceptions and therefore time has been taken to explain the important concepts so that key points are recalled and retained. The resource includes a detailed and engaging Powerpoint (85 slides) and associated worksheets, some of which are differentiated to allow students of differing abilities to access the work.

The range of activities have been designed to cover as much of the content as possible but the following sub-topics have been given particular attention:

  • The biological classification of a species
  • Classification hierarchy
  • The three-domain and five-kingdom classification
  • The features of the five kingdoms
  • Phylogenetic trees
  • Anatomical, physiological and behavioural adaptations
  • Calculating the standard deviation
  • Continuous and discontinuous variation

In addition to these topics, some topics from other modules such as cell division and prokaryotic cells are tested in order to challenge the students on their ability to make links between the modules. The range of activities include exam questions and understanding checks as well as quiz competitions to maintain student engagement.

Get this resource as part of a bundle and save up to 57%

A bundle is a package of resources grouped together to teach a particular topic, or a series of lessons, in one place.

OCR A-Level Biology A REVISION LESSONS

Each of the 20 revision lessons included in this bundle has been designed to motivate and engage the students whilst they are challenged on their knowledge of the content of the OCR A-Level Biology A specification. The detailed PowerPoints contain a wide range of activities which include exam questions with explained answers, differentiated tasks and quiz competitions that are supported by the accompanying worksheets. The modules covered in this bundle are: Module 2.1.1: Cell structure Module 2.1.2: Biological molecules Module 2.1.3: Nucleotides and nucleic acids Module 2.1.4: Enzymes Module 2.1.5: Biological membranes Module 2.1.6: Cell division, cell diversity and cellular organisation Module 3.1.2: Transport in animals Module 3.1.3: Transport in plants Module 4.1.1: Communicable diseases, disease prevention and the immune system Module 4.2.1: Biodiversity Module 4.2.2: Classification and evolution Module 5.1.2: Excretion as an example of homeostatic control Module 5.1.3: Neuronal communication Module 5.1.4: Hormonal communication Module 5.1.5: Plant and Animal responses Module 5.2.1: Photosynthesis Module 5.2.2: Respiration Module 6.1.1: Cellular control Module 6.1.2: Pattens of inheritance Module 6.1.3: Manipulating genomes Helpful hints are provided throughout the lessons to help the students with exam technique and in structuring their answers. These lessons are suitable for use throughout the course and can be used for revision purposes at the end of a module or in the lead up to mocks or the actual A LEVEL exams

OCR A-level Biology A AS REVISION LESSONS

Each of the 11 revision lessons which are found in this bundle have been written to include a range of activities that will motivate the students whilst they assess their understanding of the content in the AS modules of the OCR A-level Biology A specification. The following modules are covered: 2.1.1: Cell structure 2.1.2: Biological molecules 2.1.3: Nucleic acids 2.1.4: Enzymes 2.1.5: Biological membranes 2.1.6: Cell division, cell diversity and cellular organisation 3.1.2: Transport in animals 3.1.3: Transport in plants 4.1.1: Communicable diseases 4.2.1: Biodiversity 4.2.2: Classification and evolution

OCR A-Level Biology A Module 4 REVISION LESSONS

This bundle of 4 revision lessons have been designed to provide the students with lots of opportunities to evaluate their understanding of the topics found in module 4 of the OCR A-level Biology A specification. The bundle includes lessons which cover the three sub modules 4.1.1 (Communicable diseases), 4.2.1 (Biodiversity) and 4.2.2 (Classification and evolution) as well as a lesson to cover all of module 4 (Biodiversity, evolution and disease). As this module is often taught near to the end of the AS year, it doesn't always receive the time that the other modules do. With this in mind, each of the lessons has been written to include a wide range of activities that allow the important details to be covered and any misconceptions addressed.


114 Beneficial Prokaryotes

By the end of this section, you will be able to do the following:

  • Explain the need for nitrogen fixation and how it is accomplished
  • Describe the beneficial effects of bacteria that colonize our skin and digestive tracts
  • Identify prokaryotes used during the processing of food
  • Describe the use of prokaryotes in bioremediation

Fortunately, only a few species of prokaryotes are pathogenic! Prokaryotes also interact with humans and other organisms in a number of ways that are beneficial. For example, prokaryotes are major participants in the carbon and nitrogen cycles. They produce or process nutrients in the digestive tracts of humans and other animals. Prokaryotes are used in the production of some human foods, and also have been recruited for the degradation of hazardous materials. In fact, our life would not be possible without prokaryotes!

Cooperation between Bacteria and Eukaryotes: Nitrogen Fixation

Nitrogen is a very important element to living things, because it is part of nucleotides and amino acids that are the building blocks of nucleic acids and proteins, respectively. Nitrogen is usually the most limiting element in terrestrial ecosystems, with atmospheric nitrogen, N2, providing the largest pool of available nitrogen. However, eukaryotes cannot use atmospheric, gaseous nitrogen to synthesize macromolecules. Fortunately, nitrogen can be “fixed,” meaning it is converted into a more accessible form—ammonia (NH3)—either biologically or abiotically.

Abiotic nitrogen fixation occurs as a result of physical processes such as lightning or by industrial processes. Biological nitrogen fixation (BNF) is exclusively carried out by prokaryotes: soil bacteria, cyanobacteria, and Frankia spp. (filamentous bacteria interacting with actinorhizal plants such as alder, bayberry, and sweet fern). After photosynthesis, BNF is the most important biological process on Earth. The overall nitrogen fixation equation below represents a series of redox reactions (Pi stands for inorganic phosphate).

The total fixed nitrogen through BNF is about 100 to 180 million metric tons per year, which contributes about 65 percent of the nitrogen used in agriculture.

Cyanobacteria are the most important nitrogen fixers in aquatic environments. In soil, members of the genera Clostridium and Azotobacter are examples of free-living, nitrogen-fixing bacteria. Other bacteria live symbiotically with legume plants, providing the most important source of fixed nitrogen. Symbionts may fix more nitrogen in soils than free-living organisms by a factor of 10. Soil bacteria, collectively called rhizobia, are able to symbiotically interact with legumes to form nodules , specialized structures where nitrogen fixation occurs ((Figure)). Nitrogenase, the enzyme that fixes nitrogen, is inactivated by oxygen, so the nodule provides an oxygen-free area for nitrogen fixation to take place. The oxygen is sequestered by a form of plant hemoglobin called leghemoglobin, which protects the nitrogenase, but releases enough oxygen to support respiratory activity.

Symbiotic nitrogen fixation provides a natural and inexpensive plant fertilizer: It reduces atmospheric nitrogen to ammonia, which is easily usable by plants. The use of legumes is an excellent alternative to chemical fertilization and is of special interest to sustainable agriculture, which seeks to minimize the use of chemicals and conserve natural resources. Through symbiotic nitrogen fixation, the plant benefits from using an endless source of nitrogen: the atmosphere. The bacteria benefit from using photosynthates (carbohydrates produced during photosynthesis) from the plant and having a protected niche. In addition, the soil benefits from being naturally fertilized. Therefore, the use of rhizobia as biofertilizers is a sustainable practice.

Why are legumes so important? Some, like soybeans, are key sources of agricultural protein. Some of the most important legumes consumed by humans are soybeans, peanuts, peas, chickpeas, and beans. Other legumes, such as alfalfa, are used to feed cattle.

The commensal bacteria that inhabit our skin and gastrointestinal tract do a host of good things for us. They protect us from pathogens, help us digest our food, and produce some of our vitamins and other nutrients. These activities have been known for a long time. More recently, scientists have gathered evidence that these bacteria may also help regulate our moods, influence our activity levels, and even help control weight by affecting our food choices and absorption patterns. The Human Microbiome Project has begun the process of cataloging our normal bacteria (and archaea) so we can better understand these functions.

A particularly fascinating example of our normal flora relates to our digestive systems. People who take high doses of antibiotics tend to lose many of their normal gut bacteria, allowing a naturally antibiotic-resistant species called Clostridium difficile to overgrow and cause severe gastric problems, especially chronic diarrhea ((Figure)). Obviously, trying to treat this problem with antibiotics only makes it worse. However, it has been successfully treated by giving the patients fecal transplants from healthy donors to reestablish the normal intestinal microbial community. Clinical trials are underway to ensure the safety and effectiveness of this technique.

Scientists are also discovering that the absence of certain key microbes from our intestinal tract may set us up for a variety of problems. This seems to be particularly true regarding the appropriate functioning of the immune system. There are intriguing findings that suggest that the absence of these microbes is an important contributor to the development of allergies and some autoimmune disorders. Research is currently underway to test whether adding certain microbes to our internal ecosystem may help in the treatment of these problems, as well as in treating some forms of autism.

Early Biotechnology: Cheese, Bread, Wine, Beer, and Yogurt

According to the United Nations Convention on Biological Diversity, biotechnology is “any technological application that uses biological systems, living organisms, or derivatives thereof, to make or modify products or processes for specific use.” 1 The concept of “specific use” involves some sort of commercial application. Genetic engineering, artificial selection, antibiotic production, and cell culture are current topics of study in biotechnology and will be described in later chapters. However, humans were using prokaryotes before the term biotechnology was even coined. Some of the products of this early biotechnology are as familiar as cheese, bread, wine, beer, and yogurt, which employ both bacteria and other microbes, such as yeast, a fungus ((Figure)).

Cheese production began around 4,000 to 7,000 years ago when humans began to breed animals and process their milk. Fermentation in this case preserves nutrients: Milk will spoil relatively quickly, but when processed as cheese, it is more stable. As for beer, the oldest records of brewing are about 6,000 years old and were an integral part of the Sumerian culture. Evidence indicates that the Sumerians discovered fermentation by chance. Wine has been produced for about 4,500 years, and evidence suggests that cultured milk products, like yogurt, have existed for at least 4,000 years.

Using Prokaryotes to Clean up Our Planet: Bioremediation

Microbial bioremediation is the use of prokaryotes (or microbial metabolism) to remove pollutants. Bioremediation has been used to remove agricultural chemicals (e.g., pesticides, fertilizers) that leach from soil into groundwater and the subsurface. Certain toxic metals and oxides, such as selenium and arsenic compounds, can also be removed from water by bioremediation. The reduction of SeO4 -2 to SeO3 -2 and to Se 0 (metallic selenium) is a method used to remove selenium ions from water. Mercury (Hg) is an example of a toxic metal that can be removed from an environment by bioremediation. As an active ingredient of some pesticides, mercury is used in industry and is also a by-product of certain processes, such as battery production. Methyl mercury is usually present in very low concentrations in natural environments, but it is highly toxic because it accumulates in living tissues. Several species of bacteria can carry out the biotransformation of toxic mercury into nontoxic forms. These bacteria, such as Pseudomonas aeruginosa, can convert Hg +2 into Hg 0 , which is nontoxic to humans.

One of the most useful and interesting examples of the use of prokaryotes for bioremediation purposes is the cleanup of oil spills. The significance of prokaryotes to petroleum bioremediation has been demonstrated in several oil spills in recent years, such as the Exxon Valdez spill in Alaska (1989) ((Figure)), the Prestige oil spill in Spain (2002), the spill into the Mediterranean from a Lebanon power plant (2006), and more recently, the BP oil spill in the Gulf of Mexico (2010). In the case of oil spills in the ocean, ongoing natural bioremediation tends to occur, since there are oil-consuming bacteria in the ocean prior to the spill. In addition to these naturally occurring oil-degrading bacteria, humans select and engineer bacteria that possess the same capability with increased efficacy and spectrum of hydrocarbon compounds that can be processed. Bioremediation is enhanced by the addition of inorganic nutrients that help bacteria to grow.

Some hydrocarbon-degrading bacteria feed on hydrocarbons in the oil droplet, breaking down the hydrocarbons into smaller subunits. Some species, such as Alcanivorax borkumensis, produce surfactants that solubilize the oil (making it soluble in water), whereas other bacteria degrade the oil into carbon dioxide. Under ideal conditions, it has been reported that up to 80 percent of the nonvolatile components in oil can be degraded within one year of the spill. Other oil fractions containing aromatic and highly branched hydrocarbon chains are more difficult to remove and remain in the environment for longer periods of time.

Section Summary

Pathogens are only a small percentage of all prokaryotes. In fact, prokaryotes provide essential services to humans and other organisms. Nitrogen, which is not usable by eukaryotes in its plentiful atmospheric form, can be “fixed,” or converted into ammonia (NH3) either biologically or abiotically. Biological nitrogen fixation (BNF) is exclusively carried out by prokaryotes, and constitutes the second most important biological process on Earth. Although some terrestrial nitrogen is fixed by free-living bacteria, most BNF comes from the symbiotic interaction between soil rhizobia and the roots of legume plants.

Human life is only possible due to the action of microbes, both those in the environment and those species that call us home. Internally, they help us digest our food, produce vital nutrients for us, protect us from pathogenic microbes, and help train our immune systems to function properly.

Microbial bioremediation is the use of microbial metabolism to remove pollutants. Bioremediation has been used to remove agricultural chemicals that leach from soil into groundwater and the subsurface. Toxic metals and oxides, such as selenium and arsenic compounds, can also be removed by bioremediation. Probably one of the most useful and interesting examples of the use of prokaryotes for bioremediation purposes is the cleanup of oil spills.

Review Questions

Which of these occurs through symbiotic nitrogen fixation?

  1. The plant benefits from using an endless source of nitrogen.
  2. The soil benefits from being naturally fertilized.
  3. Bacteria benefit from using photosynthates from the plant.
  4. All of the above occur.

Synthetic compounds found in an organism but not normally produced or expected to be present in that organism are called _____.

Bioremediation includes _____.

  1. the use of prokaryotes that can fix nitrogen
  2. the use of prokaryotes to clean up pollutants
  3. the use of prokaryotes as natural fertilizers
  4. All of the above

In addition to providing yogurt with its unique flavor and texture, lactic acid-producing bacteria also provide which additional benefit during food production?

  1. Providing xenobiotics
  2. Lowering the pH to kill pathogenic bacteria
  3. Pasteurizing milk products
  4. Breaking down lactose for lactose-intolerant individuals

Critical Thinking Questions

Your friend believes that prokaryotes are always detrimental and pathogenic. How would you explain to them that they are wrong?

Remind them of the important roles prokaryotes play in decomposition and freeing up nutrients in biogeochemical cycles remind them of the many prokaryotes that are not human pathogens and that fill very specialized niches. Furthermore, our normal bacterial symbionts are crucial for our digestion and in protecting us from pathogens.

Many people use antimicrobial soap to kill bacteria on their hands. However, overuse may actually increase the risk of infection. How could this occur?

Soap indiscriminately kills bacteria on skin. This kills harmful bacteria, but can also eliminate “good” bacteria from the skin. When the non-pathogenic bacteria are eliminated, pathogenic bacteria can colonize the empty surface.

Footnotes

Glossary


Features of Prokaryotes

Prokaryotes have a semi-rigid cell wall and a flexible membrane that encloses their cytoplasm, the medium that supports the processes of life. They contain one or more loops of DNA within the cytoplasm and protein manufacturing regions called ribosomes. They may have rudimentary internal membranes, but the environment within the cell is essentially uniform. That is, the cytoplasm contains a certain level of salinity, pH and chemical distribution, and all the processes of the cell occur in that environment.


4.2: Classifying Prokaryotes and Examples - Biology

Introduction to Prokaryotes
Prokaryotes are usually single-celled organisms, it has been around for billions of years and it can be found in air, water and soil. Some can cause serious diseases. They can thrive in habitats not suitable for any eukaryotes &ndashExtreme heat, cold, acidity, salinity. Prokaryotes have plasma membrane surrounding the cell but no membrane bound organelles such as the mitochondria, nucleus or Golgi bodies.

Bacteria Cell Wall
Bacteria cell wall is a layered structure which surrounds the protoplasm of the cell to protect cells from the environment. The lipid bilayer cell membrane of most of the Gram-positive bacteria is covered by a porous peptidoglycan layer which does not exclude most antimicrobial agents. Gram-negative bacteria are surrounded by two membranes. The outer membrane functions as an efficient permeability barrier because it contains lipopolysaccharides and proteins. Bacteria cell wall is made up of a unique peptidoglycan (a polymer of disaccharide which is cross linked to amino acids) called Murein. Its basic structure is a carbohydrate backbone of alternating units of N-acetyl glucosamine and N-acetyl muramic acid. Bacteria lacking a cell wall are called mycoplasma, which usually inhabit osmotically protected environments and have sterol like compounds in their membranes.

Organelles and Inclusions
Cytoplasm contains chromosomes and ribosomes. A chromosome is usually a circular DNA molecule. Enzymes are attached to the plasma membrane. Often distinct granules are found in cytoplasm for storage of fat, glycogen and enzymes. Ribosomes are the only cytoplasmic organelles in prokaryotes.

Mobility , Response to Stimuli and Reproduction
Bacteria have rotating rings that gives it propeller movement to allow move to different environments. Some bacteria have short hair like structures to help the bacteria to adhere to each other and to surfaces. A special pilli are involved in bacterial reproduction &ndash Sex Pilli.

Prokaryotes have the ability to move toward environmental stimuli. They can also respond to light, oxygen and magnets. Prokaryotes reproduce asexually by Binary fission, or sexually by conjugation.

Classification of Prokaryotes
Classification can be based on oxygen requirement, Nutrition, Photosynthetic Capacity, Chemosynthetic Capacity, Feeding of Organic Matter, Staining and Shape. Based on nutrition, bacteria can be classified as heterotrophs, chemosynthetic and photosynthetic bacteria. Archaea is also called Archaebacteria they are more closely related to eukaryotes than prokaryotes. In a 3-dimensional system, it contains Archaea, bacteria and eukaryotes.

Protists
Protists are all eukaryotes and therefore all have cell organelles, most of them are single-celled but multi-celled form exists. Protists contain three groups: algae, slime molds (fungi) and protozoa. Algae include three groups: red algae, brown algae and green algae. Protozoa have contractile vacuoles which collect excess water and pump it outside the cell body. Amoeba is a typical protozoa. Protozoa can reproduce via sexual and asexual pathway. They can form cysts during harsh conditions.

Prokaryotes are usually single-celled organisms. They have plasma membrane surrounding the cell but no membrane bound organelles such as the mitochondria, nucleus or Golgi bodies. Their only cytoplasm organelle is ribosome, the metabolism enzymes are attached to the plasma membrane which encompasses the cell. Bacteria have cell walls to protect them from the environment. They have rotating rings that gives it propeller movements to allow move to different environments. Some bacteria have short hair like structures to help the bacteria to adhere to each other and to surfaces. Bacteria classification can be based on oxygen requirement, Nutrition, Photosynthetic Capacity, Chemosynthetic Capacity, Feeding of Organic Matter, Staining and Shape. Protists are all eukaryotes and therefore all have cell organelles, most of them are single-celled but multi-celled form exists. Protists contain three groups: algae, slime molds (fungi) and protozoa. Protozoa can reproduce via sexual and asexual pathway. They can form cysts during harsh conditions.

  • Colorful text boxes for explicit demonstration of concepts
  • Elegant drawing and graphics for vivid explanation and classification
  • Schematic presentation for easy understanding
  • Flow chart and tables are used for summarization
  • Importance of Cell Wall
  • Cell Wall of Gram Positive and Negative Bacteria
  • Chemical Composition
  • Biopolymer
  • Mycoplasma

Inclusions and Organelles

  • Cytoplasm of Prokaryotes
  • Location of Enzymes
  • Inclusion Organelles
  • Ribosomes

Classification of Bacteria

  • Oxygen Requirements
  • Nutrition
  • Photosynthetic Capacity
  • Chemosynthetic Capacity
  • Feeding of Organic Matter
  • Staining
  • Shape
  • Characteristics
  • Features
  • Evolution of Protists
  • Heterotrophs: Algae, Water Molds, Slime Molds, Protozoa, Fungi
  • Adaptations
  • Disease Causing Protists
  • Symbiotic Relationship

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Examples of data based questions

There are many data based questions in IB exams. These questions are found in section A of paper two and also in Section B of paper three, the option paper.

This page list a number of examples of data based questions which can be found in this InThinking Biology website.
There are also data based questions in each of the IB style end ot topic tests in the assessment and revision section.

Data analysis questions about cancer and the digestive tract

Try this data analysis activity about mitosis. This link to mitosis is not immediately obvious, this is the sort of question which tests a students ability to work out what is happening in a specific biological study which they haven't seen before.

The evidence in the study supports the concept of mitosis which has become deregulated in the small intestines, which may cause cancer.

To answer the questions precisely it's important to understand the command terms commonly found in data based questions.


Scientists have observed the following types of recombination in nature:

    • Homologous (general) recombination: As the name implies, this type occurs between DNA molecules of similar sequences. Our cells carry out general recombination during meiosis.
      • Nonhomologous (illegitimate) recombination: Again, the name is self-explanatory. This type occurs between DNA molecules that are not necessarily similar. Often, there will be a degree of similarity between the sequences, but it’s not as obvious as it would be in homologous recombinations.
        • Site-specific recombination: This is observed between particular, very short, sequences, usually containing similarities.
        • Mitotic recombination: This doesn’t actually happen during mitosis, but during interphase, which is the resting phase between mitotic divisions. The process is similar to that in meiotic recombination, and has its possible advantages, but it’s usually harmful and can result in tumors. This type of recombination is increased when cells are exposed to radiation.

        Prokaryotic cells can undergo recombination through one of these three processes:

          • Conjugation is where genes are donated from one organism to another after they have been in contact. At any point, the contact is lost and the genes that were donated to the recipient replace their equivalents in its chromosome. What the offspring ends up having is a mix of traits from different strains of bacteria.
            • Transformation: This is where the organism acquires new genes by taking up naked DNA from its surroundings. The source of the free DNA is another bacterium that has died, and therefore its DNA was released to the environment.
            • Transduction is gene transfer that is mediated by viruses. Viruses called bacteriophages attack bacteria and carry the genes from one bacterium to another.

            Cell Theory, Form, and Function: Prokaryotes and Eukaryotes

            Two structurally distinct types of cells have evolved that vary greatly in their internal complexity. Prokaryote cells are the simplest type and are evolutionary precursors to eukaryote cell types. What is thought to be the earliest known fossilized cells were discovered by paleontologists working near the Great Lakes in North America. They discovered microfossil evidence with enough detail to classify the cells as prokaryote. How did they know they were prokaryote?

            Although both prokaryote and eukaryote cells can have a cell wall and a cell membrane to enclose the cellular cytoplasm, the structural similarities end there. Inside a typical prokaryote cell, such as a bacteria cell, there are no membrane-bound organelles. An organelle is a subcellular structure that has a specific function. Even the genetic material, although often contained and cornered inside the cell, is not bound by a membrane. Eukaryotic cells, which basically include every cell type except bacteria, are characterized by internal organelles surrounded by a membrane, which helps to increase their organization and efficiency. In contrast to prokaryotes, in eukaryotes the chromosomes are made of distinct lengths of DNA and are stored within a nuclear membrane. Because prokaryotes are simpler, lacking membrane-bound organelles, they are also much smaller (1 to 10 micrometers) than eukaryotes, which range from 10 to 100 micrometers in size.


            Watch the video: Prokaryotic Cells - Introduction and Structure - Post 16 Biology A Level, Pre-U, IB, AP Bio (July 2022).


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