Chapter 2: The Prokaryotes (Domains Bacteria and Archaea) PDF

Chapter 2: The Prokaryotes (Domains Bacteria and Archaea) Jason M. Madronero, MEd BIO 313 (Microbiology and Parasitology) The Prokaryotes Prokaryotes are unicellular organisms without a nucleus or other membrane-bound organelles. They represent two of the three domains of life: Bacteria and Archa...

Chapter 2: The Prokaryotes (Domains Bacteria and Archaea) Jason M. Madronero, MEd BIO 313 (Microbiology and Parasitology) The Prokaryotes Prokaryotes are unicellular organisms without a nucleus or other membrane-bound organelles. They represent two of the three domains of life: Bacteria and Archaea. 2 The Prokaryotes These organisms are incredibly diverse, both in their genetic makeup and in their ecological niches, thriving in environments ranging from the human gut to deep-sea hydrothermal vents. 3 Domains of Prokaryotes Domain Bacteria: Includes a wide range of prokaryotic microorganisms that are found in various environments. They have significant roles in nutrient cycling, human health, and biotechnology. 4 Domains of Prokaryotes Domain Archaea: Comprises prokaryotes that often live in extreme environments (extremophiles) such as hot springs, salt lakes, and anaerobic environments. Archaea have unique biochemical and genetic traits that differentiate them from bacteria. 5 Prokaryotic Cells Size Prokaryotic cells are typically small, ranging from 0.2 to 2.0 µm in diameter and 2 to 8 µm in length. Their small size allows for a high surface-area- to-volume ratio, which is advantageous for nutrient uptake and waste elimination. 6 Prokaryotic Cells Shape Prokaryotic cells exhibit various shapes, including: Coccus (spherical): These bacteria can be found singly (coccus), in pairs (diplococci), chains (streptococci), clusters (staphylococci), or tetrads (groups of four). Bacillus (rod-shaped): Bacilli can occur as single rods, pairs (diplobacilli), or chains (streptobacilli). Spiral: These include spirilla (rigid spiral structures), spirochetes (flexible spiral structures), and vibrios (comma-shaped bacteria). 7 8 9 Prokaryotic Cells Shape The shape of a bacterium is determined by heredity. Most bacteria are monomorphic, maintaining a single, consistent shape. Environmental conditions can sometimes alter the shape of bacteria, making identification challenging. Some bacteria, like Rhizobium and Corynebacterium, are pleomorphic, meaning they can exhibit multiple shapes. 10 Prokaryotic Cells Arrangement The arrangement of cells can vary depending on the plane of division and whether the cells remain attached after division. This can result in distinctive patterns like chains (strepto-), clusters (staphylo-), or pairs (diplo-). 11 12 13 Structures External to the Cell Wall Glycocalyx Composition and Types: The glycocalyx (meaning sugar coat) is a sticky, gelatinous polymer composed of polysaccharides, polypeptides, or both. It is located outside the cell wall and can exist in two forms: Capsule: A neatly organized and firmly attached layer that protects bacteria from phagocytosis. Slime Layer: An unorganized and loosely attached layer that allows bacteria to adhere to surfaces, forming biofilms. 14 Structures External to the Cell Wall Glycocalyx Functions: Protects cells from desiccation. Helps in the formation of biofilms, which are protective communities of bacteria that adhere to surfaces like teeth, medical devices, and river rocks. Enhances bacterial virulence by protecting pathogenic bacteria from the host's immune system. 15 16 Structures External to the Cell Wall Flagella Structure: Flagella are long, filamentous appendages that protrude from the cell surface and are responsible for motility. They consist of three parts: Filament: The long, helical structure made of the protein flagellin. Hook: A curved structure that connects the filament to the basal body. Basal Body: A complex structure anchored in the cell wall and plasma membrane, consisting of a rod and several rings that rotate to propel the bacterium. 17 Structures External to the Cell Wall Archaella Archaella (singular: archaellum) are the motility structures found in archaea, analogous to bacterial flagella but distinct in structure and mechanism. Like flagella, archaella allow archaea to move in liquid environments, aiding in chemotaxis and adaptation to extreme habitats. 18 19 Structures External to the Cell Wall Flagella Types of Flagellar Arrangements Monotrichous: A single flagellum at one end of the cell. Lophotrichous: A cluster of flagella at one or both ends of the cell. Amphitrichous: A single flagellum or cluster of flagella at both ends of the cell. Peritrichous: Flagella distributed over the entire surface of the cell. 20 21 Structures External to the Cell Wall Flagella Rotation: Counterclockwise Rotation: Typically results in a "run," where the bacterium moves forward in a straight line. Clockwise Rotation: Causes the bacterium to "tumble," changing its direction randomly. 22 Structures External to the Cell Wall Flagella Motility and Taxis: Flagella enable bacteria to move toward or away from stimuli (taxis). Chemotaxis refers to movement in response to chemical stimuli, and phototaxis refers to movement in response to light. 23 24 Structures External to the Cell Wall Axial Filaments Axial Filaments are specialized structures used for motility in spirochetes, a unique group of spiral-shaped bacteria. Also known as endoflagella, these structures allow spirochetes to move in a corkscrew motion, enabling them to navigate through viscous environments, such as mucus or host tissues. 25 Structures External to the Cell Wall Axial Filaments The unique motility provided by axial filaments is crucial for the pathogenicity of some spirochetes, as it allows them to penetrate host tissues and evade immune responses. For example, in Treponema pallidum, the causative agent of syphilis, uses its corkscrew motion to penetrate mucous membranes and tissues. 26 27 Structures External to the Cell Wall Fimbriae and Pili Fimbriae: Short, hair-like structures that are involved in attachment to surfaces and other cells. Fimbriae play a crucial role in the formation of biofilms and in the adherence of pathogens to host tissues, facilitating infection. 28 29 Structures External to the Cell Wall Fimbriae and Pili Pili Longer than fimbriae and usually fewer in number, pili are involved in the transfer of DNA between bacterial cells during a process called conjugation. This transfer of genetic material can contribute to the spread of antibiotic resistance. 30 31 The Cell Wall Composition: The bacterial cell wall is primarily composed of peptidoglycan, a mesh-like polymer of sugars and amino acids that provides structural strength and shape to the cell. Peptidoglycan consists of repeating units of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM), which are linked by short peptide chains. 32 33 The Cell Wall Functions: Maintains the cell shape and protects against osmotic lysis (bursting due to water intake). Anchors the flagella and serves as a site for some antibiotic action, as certain antibiotics (e.g., penicillin) target the synthesis of peptidoglycan, weakening the cell wall and leading to cell death. 34 The Cell Wall Gram-Positive vs. Gram-Negative Bacteria Gram-Positive Bacteria: Have a thick peptidoglycan layer that is interspersed with teichoic acids, which provide rigidity and contribute to the cell's antigenic specificity. The absence of an outer membrane makes gram-positive bacteria more susceptible to antibiotics that target peptidoglycan synthesis. 35 36 The Cell Wall Gram-Positive vs. Gram-Negative Bacteria Gram-Negative Bacteria: Have a thin peptidoglycan layer located between the inner plasma membrane and an outer membrane. The outer membrane contains lipopolysaccharides (LPS), which contribute to the structural integrity and protect against certain antibiotics. 37 The Cell Wall Gram-Positive vs. Gram-Negative Bacteria Gram-Negative Bacteria: The presence of an outer membrane also serves as a barrier to environmental threats, but it makes gram-negative bacteria less susceptible to antibiotics that target peptidoglycan. 38 39 The Gram Stain Mechanism The Gram stain is a differential staining technique developed by Hans Christian Gram in 1884. It is one of the most important techniques in microbiology for distinguishing between gram-positive and gram-negative bacteria based on differences in cell wall structure. 40 41 The Gram Stain Mechanism Steps of the Gram Stain Procedure 1. Primary Stain (Crystal Violet): Crystal violet is applied to a heat-fixed smear of bacterial cells. Both gram-positive and gram-negative cells are initially stained purple. 42 The Gram Stain Mechanism Steps of the Gram Stain Procedure 2. Mordant (Iodine Solution) Iodine is added as a mordant, forming a crystal violet-iodine complex (CV-I) within the cells, which is larger and more insoluble than crystal violet alone. 43 The Gram Stain Mechanism Steps of the Gram Stain Procedure 3. Decolorization (Alcohol or Acetone): The decolorizing agent (usually ethanol or acetone) is added, which dehydrates the thick peptidoglycan layer in gram-positive cells, trapping the CV-I complex. In gram-negative cells, the alcohol dissolves the outer membrane and disrupts the thin peptidoglycan layer, allowing the CV-I complex to escape, rendering the cells colorless. 44 The Gram Stain Mechanism Steps of the Gram Stain Procedure 4. Counterstain (Safranin): Safranin, a red counterstain, is applied, staining the now colorless gram-negative cells pink. Gram-positive cells remain purple due to the retained crystal violet. 45 The Gram Stain Mechanism Interpretation of Gram Stain Results Gram-Positive Bacteria: Appear purple due to the retention of the crystal violet stain in the thick peptidoglycan layer. Gram-Negative Bacteria: Appear pink or red after the counterstain because the decolorization step removes the initial crystal violet stain. 46 Gram-Negative Bacteria Gram-Positive Bacteria 47 Atypical Cell Walls Mycoplasma Mycoplasmas are a group of bacteria that lack a cell wall entirely. They have only a plasma membrane that contains sterols, which provide added strength and rigidity to the membrane. Clinical Relevance: Mycoplasma pneumoniae is known to cause atypical pneumonia. The absence of a cell wall makes Mycoplasma resistant to antibiotics like penicillin that target cell wall synthesis. 48 49 Atypical Cell Walls Acid-Fast Bacteria Mycobacteria and Nocardia: These bacteria have a cell wall with a high lipid content, specifically mycolic acids (waxy, long-chain fatty acids), which make the cell wall impermeable to many stains and chemicals. 50 Atypical Cell Walls Acid-Fast Bacteria Acid-Fast Staining Acid-fast bacteria retain the primary stain (carbolfuchsin) even after decolorization with acid-alcohol due to the mycolic acid layer. Non- acid-fast bacteria do not retain the stain and are counterstained with methylene blue. 51 52 Atypical Cell Walls Acid-Fast Bacteria Acid-Fast Staining Clinical Relevance: Mycobacterium tuberculosis (causes tuberculosis) and Mycobacterium leprae (causes leprosy) are notable acid-fast bacteria 53 Acid-fast stain of Mycobacterium tuberculosis 54 Atypical Cell Walls Archaea Cell Walls Archaeal cell walls do not contain peptidoglycan. Instead, they have unique structures: Pseudopeptidoglycan: Composed of polysaccharides and proteins similar to peptidoglycan but with different chemical linkages. S-layers: Made of protein or glycoprotein, providing structural support and protection. 55 Atypical Cell Walls Archaea Cell Walls Adaptations: These variations allow archaea to survive in extreme environments, such as high temperatures, acidity, or salinity. 56 57 Structures Internal to the Cell Wall Plasma (Cytoplasmic) Membrane Structure: The plasma membrane is a phospholipid bilayer with embedded proteins. It serves as a selective barrier that regulates the entry and exit of substances into and out of the cell. In bacteria, the plasma membrane lacks sterols (found in eukaryotic membranes) but may contain hopanoids, which help in stabilizing the membrane. 58 59 Structures Internal to the Cell Wall Plasma (Cytoplasmic) Membrane Functions: Involved in energy production (e.g., via the electron transport chain in respiration) and contains enzymes necessary for metabolic processes such as ATP synthesis. Regulates the movement of materials in and out of the cell via processes like diffusion, facilitated diffusion, osmosis, and active transport. 60 Structures Internal to the Cell Wall Plasma (Cytoplasmic) Membrane Cytoplasm The cytoplasm is the gel-like substance inside the plasma membrane that contains water, enzymes, nutrients, waste products, and gases. It is the site of many metabolic reactions and houses the cell's genetic material (nucleoid) and ribosomes. 61 62 Structures Internal to the Cell Wall Nucleoid The nucleoid is the region in the cytoplasm where the bacterial chromosome resides. Unlike eukaryotic cells, bacteria lack a true nucleus, and their DNA is not enclosed by a membrane. The bacterial chromosome is typically a single, circular DNA molecule that contains the genetic information required for the cell's functions and replication. 63 64 Structures Internal to the Cell Wall Plasmids Plasmids are small, circular, double-stranded DNA molecules that are separate from the chromosomal DNA. They often carry genes that provide advantageous traits, such as antibiotic resistance, and can be transferred between bacteria through conjugation. 65 66 Structures Internal to the Cell Wall Ribosomes Prokaryotic ribosomes (70S) are composed of two subunits (30S and 50S) and are the sites of protein synthesis. These ribosomes are targeted by certain antibiotics (e.g., tetracycline, erythromycin), which inhibit protein synthesis by binding to the bacterial ribosome. 67 68 Structures Internal to the Cell Wall Inclusions Intracellular structures that serve as storage deposits for nutrients and other substances. Allow bacteria and archaea to store essential compounds when they are in excess and utilize them when needed. Help cells survive fluctuating environmental conditions and contribute to the efficiency of cellular metabolism by minimizing osmotic pressure. 69 Structures Internal to the Cell Wall Inclusions Metachromatic Granules (Volutin) Function: Store inorganic phosphate for ATP synthesis and nucleic acid production. Occurrence: Found in bacteria like Corynebacterium diphtheriae and Mycobacterium tuberculosis. 70 Structures Internal to the Cell Wall Inclusions Polysaccharide Granules Function: Store glycogen and starch as energy reserves. Occurrence: Present in bacteria such as Escherichia coli and Clostridium species. 71 Structures Internal to the Cell Wall Inclusions Lipid Inclusions Function: Store lipids, particularly poly-β-hydroxybutyrate (PHB), for carbon and energy. Occurrence: Found in bacteria like Bacillus megaterium and Mycobacterium species. 72 Structures Internal to the Cell Wall Inclusions Sulfur Granules Function: Store sulfur for energy production in sulfur-oxidizing bacteria. Occurrence: Seen in bacteria such as Thiobacillus and Beggiatoa species. 73 Structures Internal to the Cell Wall Inclusions Carboxysomes Function: Contain RuBisCO enzyme for carbon fixation in autotrophic bacteria. Occurrence: Found in cyanobacteria and nitrifying bacteria like Nitrosomonas. 74 Structures Internal to the Cell Wall Inclusions Gas Vacuoles Function: Provide buoyancy to aquatic bacteria, allowing optimal light and nutrient positioning. Occurrence: Present in photosynthetic bacteria, such as cyanobacteria (Anabaena, Microcystis). 75 Structures Internal to the Cell Wall Inclusions Magnetosomes Function: Contain magnetite or greigite crystals to help bacteria orient along the Earth’s magnetic field. Occurrence: Found in magnetotactic bacteria like Magnetospirillum. 76 77 Structures Internal to the Cell Wall Endospores Formation and Function: Endospores are highly durable, dormant structures formed by certain gram-positive bacteria (e.g., Bacillus and Clostridium) as a survival mechanism under adverse conditions. They are resistant to extreme heat, desiccation, radiation, and chemicals. 78 Structures Internal to the Cell Wall Endospores Sporulation The process by which a vegetative cell forms an endospore. This involves the replication of the cell's DNA, the formation of a spore septum, and the deposition of protective layers around the DNA. 79 Structures Internal to the Cell Wall Endospores Germination When favorable conditions return, the endospore germinates, returning to its vegetative state and becoming metabolically active. 80 81 Classification of Microorganisms Three Domains Based on genetic analysis, particularly rRNA sequences. 1. Bacteria: True bacteria, prokaryotic cells with peptidoglycan in their cell walls. 2. Archaea: Prokaryotic cells without peptidoglycan, often extremophiles. 3. Eukarya: Eukaryotic cells, including protists, fungi, plants, and animals. Classification of Microorganisms Taxonomic Hierarchy Domain Kingdom Phylum Class Order Family Genus Species Classification of Microorganisms Five-Kingdom System Prior to the three-domain system, organisms were classified into five kingdoms: Monera (prokaryotes) Protista (unicellular eukaryotes) Fungi Plantae Animalia Prokaryote Diversity Prokaryotes are divided into two domains: Bacteria and Archaea. These microorganisms are distinguished based on differences in their rRNA sequences, membrane lipid structure, and other molecular characteristics. 85 Domain Bacteria Gram-Negative Bacteria Proteobacteria This is the largest phylum of gram-negative bacteria, including a wide variety of pathogenic and non-pathogenic species. Members of this phylum include: Alphaproteobacteria Betaproteobacteria Gammaproteobacteria Deltaproteobacteria Epsilonproteobacteria 86 Domain Bacteria Phylum Proteobacteria Class Alphaproteobacteria Characteristics: This class consists of bacteria that are often oligotrophic (capable of growing in low-nutrient environments). They include both free-living and intracellular symbionts. 87 Domain Bacteria Phylum Proteobacteria Class Alphaproteobacteria Notable Genera Rickettsia: Obligate intracellular parasites transmitted by arthropods; responsible for diseases like typhus and Rocky Mountain spotted fever. Rhizobium: Nitrogen-fixing bacteria forming symbiotic relationships with legumes, contributing to soil fertility. 88 Rickettsia Rhizobium 89 Domain Bacteria Phylum Proteobacteria ClassBetaproteobacteria Characteristics: Betaproteobacteria are generally aerobic or facultatively anaerobic, and they include pathogens and environmental bacteria. 90 Domain Bacteria Phylum Proteobacteria Class Betaproteobacteria Notable Genera Neisseria: Includes pathogens like Neisseria gonorrhoeae (causing gonorrhea) and Neisseria meningitidis (causing meningitis). Bordetella: Bordetella pertussis is the causative agent of whooping cough. 91 Neisseria gonnorhoeae Bordetella pertussis 92 Domain Bacteria Phylum Proteobacteria Class Gammaproteobacteria Characteristics: This is the largest class within Proteobacteria, comprising a wide variety of physiological types, including many medically significant pathogens. 93 Domain Bacteria Phylum Proteobacteria Class Gammaproteobacteria Notable Genera Escherichia: Escherichia coli is a model organism in research and can also be pathogenic, causing foodborne illnesses. Salmonella: Pathogens responsible for foodborne illnesses and typhoid fever. Vibrio: Includes Vibrio cholerae, the causative agent of cholera. Pseudomonas: Known for their metabolic diversity, Pseudomonas species are often involved in infections, especially in immunocompromised individuals. 94 Escherichia coli Salmonella typhi 95 Vibrio cholerae Pseudomonas aeruginosa 96 Domain Bacteria Phylum Proteobacteria Class Deltaproteobacteria Characteristics: This group includes bacteria that are primarily involved in the sulfur cycle and some that are predators of other bacteria. 97 Domain Bacteria Phylum Proteobacteria Class Deltaproteobacteria Notable Genera Bdellovibrio: Preys on other gram-negative bacteria by invading their periplasmic space. Desulfovibrio: Sulfate-reducing bacteria that play a role in the sulfur cycle by reducing sulfate to hydrogen sulfide. 98 Bdellovibrio Desulfovibrio desulfuricans 99 Domain Bacteria Phylum Proteobacteria Class Epsilonproteobacteria Characteristics: This group includes bacteria that are often microaerophilic and are found in the digestive tract of animals. 100 Domain Bacteria Phylum Proteobacteria Class Epsilonproteobacteria Notable Genera Campylobacter: Includes species like Campylobacter jejuni, a common cause of foodborne gastrointestinal infections. Helicobacter: Helicobacter pylori is associated with peptic ulcers and stomach cancer. 101 Campylobacter jejuni Helicobacter pylori 102 Domain Bacteria Nonproteobacteria Gram-Negative Bacteria Phylum Cyanobacteria Characteristics: Photosynthetic bacteria, formerly known as blue- green algae, capable of oxygenic photosynthesis. They are important contributors to oxygen production and nitrogen fixation in aquatic environments. 103 Domain Bacteria Nonproteobacteria Gram-Negative Bacteria Phylum Cyanobacteria Ecological Role: Cyanobacteria are pivotal in aquatic ecosystems, forming the base of the food chain and contributing to nutrient cycles. 104 Cyanobacteria 105 Domain Bacteria Nonproteobacteria Gram-Negative Bacteria Phylum Chlamydiae Characteristics: Obligate intracellular pathogens with a unique developmental cycle, including an infectious elementary body and a replicative reticulate body. 106 Domain Bacteria Nonproteobacteria Gram-Negative Bacteria Phylum Chlamydiae Notable Species: Chlamydia trachomatis: Causes chlamydia, a common sexually transmitted infection, and trachoma, a leading cause of blindness. 107 Chlamydia trachomatis 108 Domain Bacteria Nonproteobacteria Gram-Negative Bacteria Phylum Spirochaetes Characteristics: Spiral-shaped bacteria with axial filaments allowing them to move in a corkscrew motion. They are often found in aquatic environments and as pathogens in hosts. 109 Domain Bacteria Nonproteobacteria Gram-Negative Bacteria Phylum Spirochaetes Notable Species: Treponema: Includes Treponema pallidum, the causative agent of syphilis. Borrelia: Known for causing Lyme disease, transmitted by ticks. 110 Treponema pallidum Borrelia burgdorferi 111 Domain Bacteria Nonproteobacteria Gram-Negative Bacteria Phylum Bacteroidetes Characteristics: A diverse group of gram-negative bacteria, commonly found in the intestines of humans and animals. 112 Domain Bacteria Nonproteobacteria Gram-Negative Bacteria Phylum Bacteroidetes Notable Species: Bacteroides: Dominant bacteria in the human colon, involved in digesting complex molecules. 113 Bacteroides fragilis 114 Domain Bacteria Nonproteobacteria Gram-Negative Bacteria Phylum Fusobacteria Characteristics: Gram-negative anaerobic bacteria often involved in human infections, particularly in the oral cavity. 115 Domain Bacteria Nonproteobacteria Gram-Negative Bacteria Phylum Fusobacteria Notable Species: Fusobacterium nucleatum: Associated with periodontal disease and has been linked to colorectal cancer. 116 Bacteroides fragilis 117 Domain Bacteria Gram-Positive Bacteria Phylum Firmicutes Characteristics: This phylum includes bacteria with a low G+C content in their DNA, many of which are gram-positive. They are known for forming endospores, which are resistant to harsh conditions. 118 Domain Bacteria Gram-Positive Bacteria Phylum Firmicutes Notable Species: Clostridium: Includes pathogens such as Clostridium botulinum (causing botulism), Clostridium tetani (causing tetanus), and Clostridium difficile (associated with severe colitis). Bacillus: Known for species like Bacillus anthracis (causing anthrax) and Bacillus subtilis, a model organism for studying bacterial cell processes. 119 Domain Bacteria Gram-Positive Bacteria Phylum Firmicutes Notable Species: Staphylococcus: Includes Staphylococcus aureus, a common cause of skin infections, and Staphylococcus epidermidis, often associated with medical device-related infections. Lactobacillus: Important in the food industry for the production of yogurt, cheese, and other fermented products. 120 Domain Bacteria Gram-Positive Bacteria Phylum Firmicutes Notable Species: Streptococcus: Includes Streptococcus pyogenes (causing strep throat) and Streptococcus pneumoniae (causing pneumonia). 121 Clostridium botulinum Bacillus anthracis 122 Staphylococcus aureus Lactobacillus acidophilus 123 Streptococcus pyogenes 124 Domain Bacteria Gram-Positive Bacteria Phylum Tenericutes Characteristics: Tenericutes lack a cell wall, making them unique among bacteria. They only have a plasma membrane, which contains sterols for added rigidity and stability. They are pleomorphic (variable in shape) due to the absence of a rigid cell wall. In Gram Stain, they do not retain crystal violet and appear gram-negative due to the lack of a cell wall. 125 Domain Bacteria Gram-Positive Bacteria Phylum Tenericutes Notable Species: Mycoplasma pneumoniae causes atypical pneumonia (often referred to as "walking pneumonia"). Mycoplasma genitalium is associated with urogenital tract infections, including urethritis in men and cervicitis in women. 126 Mycoplasma pneumoniae Mycoplasma genitalium 127 Domain Bacteria Gram-Positive Bacteria Phylum Actinobacteria Characteristics: This phylum is characterized by a high G+C content in their DNA and includes bacteria that are important both in medicine and the environment. 128 Domain Bacteria Gram-Positive Bacteria Phylum Actinobacteria Notable Genera: Streptomyces: Known for their role in producing a wide range of antibiotics, including streptomycin, tetracycline, and erythromycin. Mycobacterium: Includes Mycobacterium tuberculosis (causing tuberculosis) and Mycobacterium leprae (causing leprosy). 129 Domain Bacteria Gram-Positive Bacteria Phylum Actinobacteria Notable Genera: Corynebacterium: Includes Corynebacterium diphtheriae, the causative agent of diphtheria. Nocardia: Soil-dwelling bacteria, some species of which can cause pulmonary and cutaneous infections in humans. Propionibacterium: Involved in the production of propionic acid in cheese-making and includes Propionibacterium acnes, associated with acne. 130 Streptomyces Mycobacterium leprae 131 Corynebacterium diphtheriae Nocardia asteroides Propionibacterium acnes 132 Domain Archaea 133 Domain Archaea Major Groups of Archaea Methanogens Characteristics: Methanogens are a unique group of archaea that produce methane as a byproduct of their metabolic processes. They are obligate anaerobes, meaning they can only survive in environments devoid of oxygen. 134 Domain Archaea Major Groups of Archaea Methanogens Ecological Role: Methanogens play a crucial role in the carbon cycle by breaking down organic material in anaerobic environments, such as wetlands, landfills, and the digestive tracts of ruminants (e.g., cows). This process produces methane, a potent greenhouse gas. 135 Domain Archaea Major Groups of Archaea Methanogens Notable Genera: Methanobacterium, Methanococcus, and Methanosarcina are examples of methanogens that contribute to methane production in various environments. 136 Methanococcus jannaschii Methanosarcina acetivorans 137 Domain Archaea Major Groups of Archaea Extreme Halophiles Characteristics: Extreme halophiles thrive in environments with high salt concentrations, such as salt lakes, salt mines, and salt pans. These archaea require high levels of sodium chloride (NaCl) for growth. 138 Domain Archaea Major Groups of Archaea Extreme Halophiles Adaptations: To survive in such hypertonic environments, extreme halophiles have developed unique adaptations, including the production of compatible solutes like potassium chloride (KCl) to balance osmotic pressure. 139 Domain Archaea Major Groups of Archaea Methanogens Notable Genera: Halobacterium and Halococcus are examples of extreme halophiles, often found in places like the Dead Sea and Great Salt Lake. 140 Halococcus salifonidae Halobacterium salinarum 141 Domain Archaea Major Groups of Archaea Hyperthermophiles Characteristics: Hyperthermophiles are archaea that thrive in extremely high-temperature environments, often exceeding 80°C. These environments include hydrothermal vents, hot springs, and geothermal soils. 142 Domain Archaea Major Groups of Archaea Hyperthermophiles Enzyme Stability: The proteins and enzymes of hyperthermophiles are highly stable at elevated temperatures, making them of great interest for industrial applications, such as in PCR (polymerase chain reaction) where heat-stable DNA polymerases are required. 143 Domain Archaea Major Groups of Archaea Hyperthermophiles Notable Genera: Thermococcus, Pyrococcus, and Sulfolobus are examples of hyperthermophiles. Sulfolobus species are often found in sulfur-rich hot springs and are capable of both aerobic and anaerobic respiration. 144 Sulfolobus acidocaldarius Pyrococcus furiosus 145 Domain Archaea Major Groups of Archaea Acidophiles and Alkaliphiles Characteristics: Some archaea are adapted to extreme pH environments, thriving in either highly acidic or highly alkaline conditions. 146 Domain Archaea Major Groups of Archaea Acidophiles and Alkaliphiles Acidophiles: These organisms grow optimally at a pH below 3. Sulfolobus is an example, often found in sulfuric hot springs. Alkaliphiles: These archaea thrive at a pH above 9 and are often found in alkaline soils and soda lakes. 147