Chapter 1-7 Microbiology Review: Prokaryotes, Archaea, Bacteria, and Viruses
Major metabolic modes and oxygen dependence
Oxygen importance in biology
Oxygen is not a direct part of nutrition (it's not a food source), but it is essential for many organisms to extract energy efficiently from nutrient molecules. This efficiency is due to its role as a highly electronegative final electron acceptor in cellular respiration.
In animals (us) and many microbes, mitochondria (in eukaryotes) or specialized membranes (in prokaryotes) use oxygen to produce ATP via aerobic respiration. This process, specifically the electron transport chain, generates a large proton gradient, driving ATP synthesis.
Aerobic respiration yields significantly more ATP (e.g., up to 32 ATP per glucose molecule) than anaerobic processes (like fermentation, which yields 2 ATP, or anaerobic respiration) because oxygen allows for a complete oxidation of fuel molecules.
Definitions of metabolic categories (for oxygen use)
Obligate aerobes: strictly require oxygen to survive. They exclusively use aerobic respiration for energy production and lack the metabolic pathways for anaerobic survival. Examples include Mycobacterium tuberculosis.
Obligate anaerobes: cannot tolerate oxygen at all; exposed to oxygen, they die (often due to accumulation of toxic oxygen radicals like superoxide and hydrogen peroxide, which they lack enzymes like superoxide dismutase and catalase to neutralize). They rely solely on anaerobic respiration or fermentation. Examples include methanogens and Clostridium botulinum.
Facultative anaerobes: are highly versatile; they can use oxygen when present (preferring aerobic respiration due to higher ATP yield) but can switch to anaerobic metabolism (fermentation or anaerobic respiration) in low-oxygen or oxygen-free environments. Escherichia coli is a classic example.
Some eukaryotes and prokaryotes can tolerate low levels of oxygen (microaerophiles) or switch metabolic modes, but obligate aerobes die in oxygen-free environments, highlighting the strict requirement.
Cellular energy production in prokaryotes vs eukaryotes
Prokaryotes lack membrane-bound organelles. Therefore, respiration-associated proteins, including components of the electron transport chain and ATP synthase, may reside on the plasma membrane or on internal membrane invaginations (mesosomes or lamellar structures) but are not enclosed by a double-membrane organelle like mitochondria.
Membranes with respiratory proteins in prokaryotes are functional sites of respiration, not organelles; they are extensions or specialized regions of the cellular membrane.
Photosynthetic prokaryotes (e.g., cyanobacteria) use specialized internal membranes called thylakoid membranes to host photosynthetic pigments (e.g., chlorophyll, phycobilins). These are similar in function to chloroplast thylakoids in eukaryotes but are not enclosed within a chloroplast organelle.
Photosynthesis (PS) generates oxygen in many organisms (oxygenic photosynthesis), releasing it into the atmosphere. PS pigments embed in these thylakoid membranes rather than inside mitochondria or chloroplasts.
The term PS here refers to photosynthesis; thylakoid membranes house photosynthetic pigments like chlorophyll, which absorb light energy to drive the synthesis of ATP and NADPH.
Photosynthetic pigments and names
Chlorophyll is a key photosynthetic pigment enabling oxygenic photosynthesis in many organisms (plants, algae, cyanobacteria). It effectively captures light energy for conversion into chemical energy.
Some prokaryotes perform photosynthesis that does not generate oxygen (anoxygenic photosynthesis). These organisms use electron donors other than water, such as H_2S, and different types of bacteriochlorophylls. This class primarily covers oxygen-producing photosynthesis, so we’ll focus on oxygenic forms, especially in cyanobacteria.
Result of oxygen-based metabolism
Oxygen allows for a much more efficient and complete oxidation of metabolic fuels, leading to significantly more ATP production. This larger energetic dividend provides aerobic organisms with a greater capacity for growth, movement, and complex cellular processes, influencing their ecological success.
Major metabolic categories based on energy and carbon sources
Photoautotroph: An organism that uses light as its energy source and carbon dioxide (CO_2) as its main carbon source (e.g., plants, algae, cyanobacteria).
Chemoautotroph: An organism that obtains energy by oxidizing inorganic chemical compounds and uses carbon dioxide (CO_2) as its main carbon source (e.g., some bacteria and archaea found in deep-sea vents).
Photoheterotroph: An organism that uses light as its energy source but obtains carbon from organic compounds (e.g., purple non-sulfur bacteria).
Chemoheterotroph: An organism that obtains both energy and carbon from organic chemical compounds (e.g., animals, fungi, most bacteria, and protozoa). Includes Decomposers, which are organisms that break down dead organic matter.
Prokaryotes and domains: Archaea vs Bacteria
Domain Archaea
Name “archaea” reflects early ideas of ancient life, suggesting they were primitive; discovered in the late 1970s by Carl Woese based on ribosomal RNA sequencing, challenging the two-domain system of life.
They inhabit extreme and unusual environments (e.g., Yellowstone hot springs (thermophiles), highly saline lakes (halophiles), highly acidic conditions (acidophiles), and deep-sea vents (barophiles)). These extremophilic adaptations define much of their known diversity.
They are prokaryotic but are not typically pathogenic to humans. Their unique biochemistry makes them generally unsuitable for infecting human cells.
Only a subset is discussed in depth here; the course suggests broader reading for more archaeal diversity, which includes different metabolic strategies and ecological roles.
A key group discussed: methanogens, strict anaerobes that produce methane (CH_4) as a byproduct of their metabolism, often found in anaerobic sediments and the guts of ruminants.
Domain Bacteria
Bacteria are prokaryotic and include many medically important organisms (pathogens causing infectious diseases), beneficial decomposers in nutrient cycling, and vital symbionts.
Bacteria have cell walls in nearly all members, providing structural integrity and protection. Peptidoglycan (also known as murein) is the hallmark polymer of most bacterial cell walls, distinguishing them from Archaea and Eukaryotes.
Bacteria can be visually diverse in shape (e.g., cocci, bacilli, spirilla) and arrangement (e.g., chains, clusters); images used in lectures are often false-color scanning electron micrographs (SEM images) to enhance visualization of surface features.
General contrast between Archaea and Bacteria
Archaea can have variable cell wall composition, including pseudopeptidoglycan, S-layers (surface layers of protein/glycoprotein), or other polysaccharide layers; some lack walls entirely (naked cells). This diversity contrasts with the consistent peptidoglycan of most bacteria.
Bacterial cell walls consistently feature peptidoglycan, a unique polymer of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) subunits cross-linked by short peptides. Archaeal walls do not contain peptidoglycan.
Archaea are not known to be human pathogens in this lecture; many bacterial lineages, however, notably include significant human pathogens (e.g., Staphylococcus, Streptococcus, Salmonella).
Another key difference is membrane lipids: Bacteria have ester-linked fatty acids, while Archaea have ether-linked branched hydrocarbons (isoprenoids), which can form monolayers, providing structural stability in extreme conditions.
Key terms to know
70S ribosomes in bacteria and archaea (vs 80S in most eukaryotes): Ribosomes are responsible for protein synthesis and differ in size. Prokaryotic ribosomes are 70S (composed of a 50S large subunit and a 30S small subunit), while eukaryotic ribosomes are 80S (composed of a 60S large subunit and a 40S small subunit). This difference is a target for some antibiotics.
Nucleoid: The region within a bacterial or archaeal cell where the circular chromosome (often a single, double-stranded DNA molecule) is located. It is not a true nucleus because it lacks a nuclear membrane and is not compartmentalized from the cytoplasm.
Fimbriae: Short, hair-like protein structures on the surface of some bacteria (e.g., Neisseria gonorrhoeae) that are thinner and more numerous than flagella. They are primarily used for adherence to host mucosal surfaces or other cells/surfaces, facilitating colonization and biofilm formation.
Capsule: An extracellular polysaccharide layer (or sometimes polypeptide) surrounding some bacteria, lying outside the cell wall. It provides protection against phagocytosis by host immune cells and aids in adhesion, but is not deeply discussed here.
Plasma membrane: The selectively permeable lipid bilayer that lies inside the cell wall, regulating the passage of substances into and out of the cell. Bacterial cell wall lies outside the plasma membrane and provides structural support, protection from osmotic lysis, and shape maintenance.
Important note on visualization
SEM (Scanning Electron Microscopy) images show bacteria in false color. This means the color observed in these images is not the original color of the bacterium in nature but is artificially added during image processing to enhance contrast, highlight specific features, and improve visualization for study.
Prokaryotic cell structure (typical features in bacteria)
Cell wall
All bacteria have a cell wall primarily composed of peptidoglycan (a polymer of protein and carbohydrate components), which is crucial for structural integrity and protection.
The peptidoglycan layer provides structural strength to resist osmotic pressure, preventing the cell from bursting (lysis) in hypotonic environments, and helps maintain the cell's characteristic shape.
Outer structures
Fimbriae (pili): Short, numerous, hair-like protein projections on the cell surface, primarily for attachment to host tissues or surfaces. A specialized type, the sex pilus, is involved in bacterial conjugation (transfer of genetic material).
Flagella: Longer, whip-like appendages used for locomotion, enabling bacteria to move towards attractants or away from repellents (chemotaxis). Prokaryotic flagella are structurally different from eukaryotic flagella: they are simpler, primarily made of a single protein (flagellin), rotate like a propeller driven by a proton motive force, and lack the 9+2 microtubule arrangement found in eukaryotic flagella.
Cytoplasm and nucleoids
Nucleoid: The irregular-shaped region in the cytoplasm where the bacterial chromosome resides. It is not membrane-bound, distinguishing it from the true nucleus of eukaryotes. The chromosome is typically a single, circular, double-stranded DNA molecule, often supercoiled.
Ribosomes: Bacteria have 70S ribosomes functioning in protein synthesis within the cytoplasm. Each 70S ribosome is composed of a 50S large subunit and a 30S small subunit. This size difference is exploited by many antibiotics that target bacterial, but not host, ribosomes.
Internal organization
No true membrane-bound organelles like mitochondria, chloroplasts, or endoplasmic reticulum are present. Essential metabolic functions, such as respiration and photosynthesis, occur on the plasma membrane or on internal membrane systems (e.g., thylakoids, chromatophores) in some specialized bacteria. These internal membranes are invaginations of the plasma membrane, not enclosed in double membranes like eukaryotic organelles.
Gram staining basics (diagnostic tool)
The Gram stain is a differential staining technique developed by Hans Christian Gram, widely used to classify bacteria based on their cell wall structure, which correlates with differences in antibiotic susceptibility.
Gram-positive bacteria: Possess a very thick peptidoglycan layer and lack an outer membrane. During staining, they retain the crystal violet-iodine complex, appearing purple (dark blue) after the Gram staining procedure and decolorization with alcohol. Their thick cell wall prevents the trapped dye complex from being washed out.
Gram-negative bacteria: Have a thin peptidoglycan layer located in the periplasmic space, sandwiched between the inner plasma membrane and an outer membrane. The outer membrane contains lipopolysaccharide (LPS), which includes endotoxin (Lipid A), and porin proteins for nutrient passage. Due to the thin peptidoglycan layer and the outer membrane, the crystal violet-iodine complex is easily washed out by alcohol. They then take up the counterstain (safranin) and appear red/pink.
The Gram stain helps distinguish bacteria by cell wall structure and correlates with antibiotic susceptibility in many cases because antibiotics targeting peptidoglycan (e.g., penicillin) are generally more effective against Gram-positive bacteria, while the outer membrane of Gram-negative bacteria provides an additional barrier.
Notable Gram-positive and Gram-negative examples mentioned
Gram-positive example: Mycobacterium tuberculosis is often classified as Gram-positive-like, but due to its unique waxy outer layer (rich in mycolic acid), it does not stain well with the Gram stain and requires the acid-fast stain. This waxy layer contributes to its hardiness and antibiotic resistance. It forms tubercles in the lungs during infection.
Gram-negative example: Escherichia coli (E. coli) is a major gut bacterium, typically a commensal, but includes pathogenic strains that produce toxins (e.g., Shiga toxin in EHEC) causing severe foodborne illness.
A well-known Gram-negative group includes cyanobacteria (e.g., Anabaena), which are photosynthetic, often called blue-green algae in common language, and were instrumental in oxygenating Earth's early atmosphere.
Notable prokaryotes, their lifestyles, and ecological roles
Bacillus anthracis (endospores)
Produces endospores: highly resistant, metabolically dormant forms that allow survival in extremely harsh environments (e.g., drying, heat, radiation, disinfectants, nutrient depletion) for extended periods.
Endospore structure: They are thick-walled, dehydrated, and contain dipicolinic acid, which helps with heat resistance. They are metabolically dormant and can remain viable for decades or even centuries. When conditions improve, they can rapidly germinate into a vegetative (actively growing) cell.
Pathogenic: Causes anthrax, a severe disease affecting animals and humans. It has three main forms based on the route of exposure: cutaneous (skin, least severe), gastrointestinal (ingestion, rare but can be severe), and inhalational (lung, highly dangerous and often fatal if untreated due to widespread toxin production and sepsis).
Historical note: Involved in bioterrorism concerns (e.g., 2001 anthrax attacks in the US); inhalational exposure is particularly dangerous due to its high mortality risk and rapid progression.
Tuberculosis: Mycobacterium tuberculosis
Gram-positive-like cell wall with an outer lipid-rich layer (mycolic acid), making it waxy and impermeable, hence it does not stain well with Gram stain and is classified as acid-fast. This waxy layer provides protection against host defenses and many antibiotics. It forms characteristic granulomas called tubercles in the lungs, which can encapsulate the bacteria but also serve as sites of chronic infection.
Tuberculosis (TB) can be fatal if untreated, and some strains display multi-drug antibiotic resistance (MDR-TB, XDR-TB), complicating treatment and global health efforts.
Tuberculin skin test (PPD test, detecting delayed-type hypersensitivity reaction) and X-ray findings (showing lung lesions, cavitation, or tubercle gaps) are key diagnostic clues for infection. Further tests like sputum culture confirm active disease.
Lyme disease: Borrelia burgdorferi
Spirochete bacterium: Characterized by a distinctive helical shape and internal flagella (endoflagella) located in the periplasmic space, which provide a corkscrew-like motility. This allows it to burrow through viscous tissues.
Transmitted by ticks (genus Ixodes, commonly known as deer ticks or blacklegged ticks) during a blood meal (vector transmission). This makes it a zoonotic disease.
Causes Lyme disease, a multi-stage illness. It often presents with a characteristic target-like rash called erythema migrans in many cases (though not all). Early antibiotic treatment (e.g., doxycycline) is highly effective if started promptly, preventing progression to later, more severe stages affecting joints, heart, and nervous system.
Nitrogen fixation and Rhizobium symbiosis
Rhizobium: A genus of soil bacteria that forms a mutualistic symbiosis with leguminous plants (e.g., soybeans, peas, clover). This is a vital process in the global nitrogen cycle.
In soybean roots, Rhizobium resides within specialized structures called root nodules, which are created by the plant in response to bacterial signals. The plant supplies carbon compounds (sugars from photosynthesis) to the bacteria.
In return, Rhizobium fixes atmospheric nitrogen (N2) into a form usable by the plant (ammonia, NH3, which is then incorporated into organic nitrogen compounds like amino acids). This mutualism is a classic example of nutrient cycling in ecosystems, enhancing soil fertility naturally.
Nitrogen fixation reaction (conceptual):
This complex biological process is catalyzed by the enzyme nitrogenase, which reduces chemically inert atmospheric dinitrogen (N2) to ammonia (NH3). A simplified representation of the overall reaction, requiring significant energy (ATP) and reducing power (electrons and protons), is:
N2 + 8 e^- + 8 H^+ + 16 ATP \rightarrow 2 NH3 + H2 + 16 ADP + 16 Pi
The nitrogenase enzyme is very sensitive to oxygen, which irreversibly inactivates it. This explains why nitrogen fixation and oxygenic photosynthesis are often spatially or temporally segregated in separate cells or organisms. In legume nodules, the plant produces leghemoglobin, a protein that binds free oxygen, creating an anaerobic microenvironment essential for nitrogenase activity while still allowing plant respiration.
Cyanobacteria (photosynthetic prokaryotes)
Also known as blue-green algae, they are a diverse group of photosynthetic bacteria. They perform oxygenic photosynthesis, leading to significant contributions to environmental oxygen production and serving as primary producers in many ecosystems.
Some cyanobacteria form colonies or filaments (e.g., Anabaena, Nostoc) and may exhibit division of labor, a primitive form of multicellularity. For example, Anabaena contains specialized cells called heterocysts for nitrogen fixation and vegetative cells that perform photosynthesis.
Heterocysts (literally “different cell”) are thickened-walled cells where nitrogen fixation occurs. They lack Photosystem II (which produces oxygen) and have increased respiratory activity to consume internal oxygen, thereby providing an anaerobic microenvironment necessary for the oxygen-sensitive enzyme nitrogenase.
Cyanobacteria can form chains (filaments) such as in the genus Anabaena or Cylindrospermum. Many cyanobacteria are large enough to be readily visualized with light microscopy in many cases.
Role of Archaea and Bacteria in ecology
Archaea include methanogens: strict anaerobes that produce methane (CH4) as a metabolic byproduct from the reduction of CO2 or other carbon compounds. Methane is a potent greenhouse gas, contributing significantly to climate change.
Methanogens commonly inhabit anoxic environments like swamps, wetlands, anaerobic sediments, sewage treatment plants, and the gullet guts of ruminants (e.g., cows, sheep).
Ruminant animals (e.g., cows) rely heavily on their gut microbiota to break down plant cellulose (which they cannot digest themselves due to lacking cellulase enzymes) through microbial fermentation in specialized stomach chambers like the rumen. They host vast populations of methanogens in the rumen, where microbial digestion occurs, leading to substantial methane emissions.
Humans also harbor gut microbiota, including potential methanogens, but their prevalence and contribution to methane production are generally lower than in ruminants.
Cellulose digestion is largely carried out by diverse microbial symbionts (bacteria, archaea, fungi, protists) rather than by the host animal itself; humans lack cellulases required to break down cellulose, highlighting the importance of microbial-host mutualism.
Koalas have specialized gut morphology (a long cecum) and microbiota enabling their highly specialized, plant-only (eucalyptus leaf) diets; their digestive systems are adapted for extensive fermentative digestion of tough plant material.
Symbiotic nitrogen fixation in legumes is a broader example of mutualism that supports plant growth in nutrient-poor soils, reducing the need for artificial fertilizers and promoting ecosystem productivity.
Symbiosis and ecological interactions (types and examples)
Mutualism: A symbiotic relationship where both partners benefit from the interaction. Examples include Rhizobium-legume root nodules (plant gets nitrogen, bacterium gets carbon and habitat); gut microbiota providing essential vitamins (e.g., Vitamin K) or aiding digestion in humans; lichens (fungus provides structure, algae/cyanobacteria provide photosynthates).
Commensalism: One partner benefits without harming or helping the other. Examples include certain epiphytic organisms (e.g., bacteria or fungi) living harmlessly on the bark of trees; specific gut bacteria that benefit from the host environment without significantly impacting host health.
Parasitism: One partner (the parasite) benefits at the expense of the other (the host), causing harm. Examples include pathogens such as Borrelia burgdorferi causing Lyme disease; many bacterial toxins directly damaging host cells; viruses like HIV exploiting host cell machinery.
Lichens illustrate a complex symbiotic relationship between a fungal partner (mycobiont) and a photosynthetic partner (photobiont, usually green algae or cyanobacteria). The fungus provides protection, water, and minerals, while the photobiont provides organic nutrients through photosynthesis.
Toxins and pathogenicity in prokaryotes
Pathogenic bacteria may produce toxins, which are virulence factors harming the host and contributing to disease symptoms. They can be categorized as:
Exotoxins: Proteins secreted by living bacteria into their environment. They are highly potent, specific in their action, and can target specific host cells or processes (e.g., neurotoxins like botulinum toxin affecting nerves, enterotoxins like cholera toxin affecting the gut, cytotoxins killing cells). They are often heat-labile and can be toxoided (inactivated but still immunogenic) for vaccine development.
Endotoxins: Components of the outer membrane of Gram-negative bacteria, specifically the Lipid A portion of lipopolysaccharide (LPS). Endotoxins are released primarily when bacteria die or are lysed (e.g., by antibiotics or host immune responses). They are less specific, heat-stable, and trigger a generalized inflammatory response, leading to fever, shock, and potentially death in high concentrations.
Pathogenic bacteria have historically caused significant human disease epidemics; some have been engineered or weaponized for harmful purposes (bioterrorism), raising biosecurity concerns.
Viruses: the non-cellular parasites
Fundamental characteristics
Viruses are obligate intracellular parasites; they are not cells (lacking cellular machinery like ribosomes, cytoplasm, and metabolism) and cannot reproduce on their own. They absolutely require a host cell (prokaryotic or eukaryotic) to replicate.
Host range varies: The range of host species, tissues, or cells a virus can infect is determined by specific interactions between viral surface proteins and host cell receptors. Some viruses have a narrow host range (e.g., bacteriophages specific to certain bacterial strains), while others have broader ranges (e.g., influenza virus can infect multiple species).
Viruses cause damage by manipulating host cellular processes, diverting host resources for viral replication. They often release hydrolytic enzymes or express proteins that aid viral replication, assembly, and eventual release, frequently leading to host cell lysis or dysfunction (cytopathic effects).
They can carry or encode enzymes/toxins that affect the host environment, such as neuraminidase in influenza, which helps viral release, or enzymes that degrade host DNA.
Genome and structure
Viruses do have genomes, but they are relatively very small and compact compared to cellular organisms, encoding only essential viral functions.
Viral genomes can be remarkably diverse: they can be either DNA or RNA, and can be single-stranded (ss) or double-stranded (ds). This genomic diversity is key to their classification and replication strategies:
DNA viruses: Can be double-stranded (e.g., Adenovirus, Herpesviruses) or single-stranded (e.g., Parvoviruses).
RNA viruses: Can be double-stranded (e.g., Rotavirus) or single-stranded, with ssRNA genomes further classified as positive-sense (+ssRNA like Poliovirus, acting directly as mRNA) or negative-sense (-ssRNA like Influenza, requiring an RNA polymerase to make mRNA).
A key structural component is the capsid, a protein shell built from repeating subunits called capsomeres. The capsid protects the viral genome and aids in attachment to host cells.
Examples of viral capsids include shapes seen in tobacco mosaic virus (helical), adenovirus (icosahedral), influenza (helical enveloped), and bacteriophages (complex, often with an icosahedral head and helical tail, visually resembling spaceships under electron microscopy).
Retroviruses (like HIV) are a specific type of RNA virus that carry an enzyme called reverse transcriptase. This enzyme allows them to synthesize a DNA copy from their RNA genome, which is then integrated into the host cell's chromosome, a unique replication strategy (RNA \rightarrow DNA \rightarrow RNA \rightarrow Protein); relevance to human disease and treatment with antiretroviral drugs.
Many animal viruses are also enveloped, possessing an outer lipid bilayer membrane derived from the host cell's membrane upon budding. This envelope typically contains viral glycoproteins essential for host cell recognition and entry.
Notable examples mentioned
HIV: Human Immunodeficiency Virus; an enveloped RNA retrovirus that carries reverse transcriptase. It specifically targets T-helper lymphocytes, leading to AIDS (Acquired Immunodeficiency Syndrome). Primarily sexually transmitted, but also via blood and from mother to child.
Influenza: An enveloped RNA virus with a segmented genome (typically 8 segments for influenza A and B). This segmentation facilitates antigenic shift (major changes) through reassortment, leading to new pandemic strains. Multiple strains circulate globally, causing seasonal epidemics.
Tobacco mosaic virus (TMV): A plant virus with a simple helical capsid and a +ssRNA genome. It was one of the first viruses discovered and serves as a classic model in virology to study viral structure and replication in plants.
Bacteriophages: Viruses that infect bacteria. They exhibit diverse morphologies (e.g., T-even phages like T4, lambda phage). Examples include phages isolated from environmental samples; used in demonstrations of phage morphology and genome sequencing, and explored for therapeutic uses (phage therapy) against antibiotic-resistant bacterial infections.
Interaction with hosts
Viruses disrupt cellular processes and can cause a wide range of diseases, from acute (e.g., common cold) to chronic (e.g., HIV) and oncogenic (e.g., HPV). They may also be used as tools in molecular biology (e.g., viral vectors for gene therapy) and biotechnology (e.g., producing vaccines).
Phages illustrate a natural predator–prey relationship in microbial ecosystems, specializing in bacterial hosts. Their role in regulating bacterial populations is significant in many environments, including the human gut.
Connections to foundational principles and real-world relevance
Energy and metabolism
The distribution of aerobic vs anaerobic metabolic strategies explains why many organisms rely on oxygen for high-energy yield (aerobic respiration is far more efficient in ATP production) and why some environments, particularly anoxic ones, favor anaerobes or facultative anaerobes (e.g., methanogens in wetlands).
The separation of photosynthesis and nitrogen fixation in some filamentous cyanobacteria (e.g., Anabaena with its heterocysts and vegetative cells) demonstrates how microbial life solves the challenge of oxygen-sensitive enzymes (like nitrogenase) by spatially segregating metabolic processes. This cellular differentiation enables simultaneous operation of oxygenic photosynthesis and anaerobic nitrogen fixation within the same
Key Terms and Definitions
Photoautotroph: An organism that uses light as its energy source and carbon dioxide (CO_2) as its main carbon source (e.g., plants, algae, cyanobacteria).
Chemoautotroph: An organism that obtains energy by oxidizing inorganic chemical compounds and uses carbon dioxide (CO_2) as its main carbon source (e.g., some bacteria and archaea found in deep-sea vents).
Photoheterotroph: An organism that uses light as its energy source but obtains carbon from organic compounds (e.g., purple non-sulfur bacteria).
Chemoheterotroph: An organism that obtains both energy and carbon from organic chemical compounds (e.g., animals, fungi, most bacteria, and protozoa).
Aerobe: An organism that requires oxygen to survive and for efficient energy production (e.g., obligate aerobes).
Anaerobe: An organism that does not require oxygen for survival and may be harmed by its presence (e.g., obligate anaerobes).
Obligate: A descriptor meaning strictly necessary or required (e.g., obligate aerobes strictly require oxygen, obligate anaerobes cannot tolerate oxygen).
Facultative: A descriptor meaning capable of switching metabolic modes depending on environmental conditions (e.g., facultative anaerobes can use oxygen if present but can also survive without it).
Gram +/-: Refers to bacteria classified by the Gram stain based on cell wall structure: Gram-positive bacteria have a thick peptidoglycan layer and stain purple/dark blue; Gram-negative bacteria have a thin peptidoglycan layer and an outer membrane, staining red/pink.
Nucleoid: The irregular-shaped region within a bacterial or archaeal cell where the circular chromosome is located. It is not membrane-bound.
Fimbriae: Short, hair-like protein structures on the surface of some bacteria, primarily used for adherence to host mucosal surfaces or other cells/surfaces.
Basal Apparatus: The motor portion of a bacterial flagellum, a complex structure embedded in the cell envelope that powers the rotation of the flagellar filament.
Filament: A strand-like structure; in bacteria, this can refer to chains of cells (e.g., in cyanobacteria) or the long, whip-like part of the bacterial flagellum.
Bacteria: Prokaryotic organisms characterized by cell walls containing peptidoglycan, including many pathogens, decomposers, and symbionts.
Archaea: Prokaryotic organisms that inhabit extreme environments, not typically pathogenic to humans, and have diverse cell wall compositions lacking peptidoglycan.
Eukarya: The domain of life comprising organisms whose cells contain membrane-bound organelles and a true nucleus, contrasting with prokaryotic Bacteria and Archaea.
Methanogen: Strict anaerobes belonging to Archaea that produce methane (CH4) as a metabolic byproduct from the reduction of CO2 or other carbon compounds.
E. Coli: Escherichia coli, a major gut bacterium (Gram-negative), typically a commensal but includes pathogenic strains, and is a classic example of a facultative anaerobe.
Endospore: Highly resistant, metabolically dormant forms produced by some bacteria (e.g., Bacillus anthracis) that allow survival in extremely harsh environments for extended periods.
Peptidoglycan: A unique polymer of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) subunits cross-linked by short peptides, forming the hallmark of most bacterial cell walls.
B. anthracis: Bacillus anthracis, a pathogenic bacterium that produces endospores and causes anthrax, a severe disease affecting animals and humans.
Mycobacterium: A genus of bacteria, including Mycobacterium tuberculosis, characterized by a waxy outer layer rich in mycolic acid, making them acid-fast rather than reliably Gram-staining.
Tuberculosis: A severe disease caused by Mycobacterium tuberculosis, characterized by the formation of granulomas (tubercles) in the lungs and often resistant to multiple drugs.
Cyanobacteria: Also known as blue-green algae, these are diverse photosynthetic prokaryotes that perform oxygenic photosynthesis, contributing significantly to environmental oxygen production.
Anabaena: A genus of filamentous cyanobacteria that exhibits cellular differentiation, containing specialized cells called heterocysts for nitrogen fixation and vegetative cells for photosynthesis.
Heterocyst: Thickened-walled cells in some cyanobacteria (e.g., Anabaena) where nitrogen fixation occurs, providing an anaerobic microenvironment necessary for oxygen-sensitive nitrogenase.
N2 Fixation: Nitrogen fixation, a complex biological process catalyzed by the enzyme nitrogenase, which reduces chemically inert atmospheric dinitrogen (N2) to ammonia (NH3), making nitrogen usable by organisms.
Symbiosis: A close and often long-term interaction between two different biological organisms.
Mutualism: A symbiotic relationship where both partners benefit from the interaction (e.g., Rhizobium-legume root nodules).
Commensalism: A symbiotic relationship where one partner benefits without harming or helping the other (e.g., specific gut bacteria benefiting from the host environment).
Parasite: An organism that benefits at the expense of its host, causing harm.
Decomposer: An organism that breaks down dead organic matter, obtaining both energy and carbon from these compounds.
Pathogen: An agent that causes disease, especially a microorganism like a bacterium or virus.
Borrelia: Referring to Borrelia burgdorferi, a spirochete bacterium with a helical shape and internal flagella, transmitted by ticks, and causing Lyme disease.
Vector: An organism (e.g., a tick in Lyme disease) that transmits a pathogen from one host to another.
Exotoxin: Proteins secreted by living bacteria into their environment, which are highly potent, specific in their action, and often heat-labile.
Endotoxin: Components of the outer membrane of Gram-negative bacteria (specifically the Lipid A portion of lipopolysaccharide, LPS) released primarily when bacteria die, triggering a generalized inflammatory response, and are heat-stable.
Capsid: A protein shell built from repeating subunits called capsomeres that protects the viral genome and aids in attachment to host cells
Host Range: The range of host species, tissues, or cells a virus can infect, determined by specific interactions between viral surface proteins and host cell receptors.