Bacteria & Archaea Cheatsheet

Cheatsheet Content

I. Bacteria: Occurrence, Habitat & Ecology Ubiquitous Distribution: Bacteria are the most abundant and diverse life forms on Earth, inhabiting virtually every niche imaginable, from the deepest oceans to the highest atmospheres, and from freezing glaciers to boiling hot springs. Diverse Habitats & Extremophiles: Mesophiles: The majority of bacteria, thriving in moderate temperatures ($20-45^\circ C$), like human body temperature or soil. Thermophiles: Grow optimally at high temperatures ($45-80^\circ C$), found in hot springs, compost piles. Hyperthermophiles: Extreme heat-loving, flourishing above $80^\circ C$, often in geothermal vents or volcanically active areas. Psychrophiles: Cold-loving organisms, growing best below $15^\circ C$, found in polar regions, deep oceans, and refrigerators. Halophiles: Require high salt concentrations (e.g., $NaCl > 0.2M$) for growth, found in salt lakes and curing brines. Acidophiles: Thrive in highly acidic environments (low pH, e.g., pH 1-5), such as acid mine drainage. Alkaliphiles: Prefer alkaline conditions (high pH, e.g., pH 9-11), found in soda lakes and soils rich in carbonates. Barophiles (Piezophiles): Grow optimally under high hydrostatic pressure, common in deep-sea environments. Radioresistant Bacteria: Can withstand extremely high levels of radiation (e.g., Deinococcus radiodurans ). Ecological Roles: Crucial for nutrient cycling (carbon, nitrogen, sulfur cycles), decomposition, primary production, and symbiotic relationships. II. Bacterial Morphology & Arrangements Basic Shapes: Cocci (Spherical/Ovoid): Monococcus: Single, independent spheres. Diplococcus: Pairs of cocci (e.g., Neisseria gonorrhoeae ). Streptococcus: Chains of cocci (e.g., Streptococcus pyogenes ). Staphylococcus: Irregular, grape-like clusters (e.g., Staphylococcus aureus ). Tetrad: Groups of four, forming a square. Sarcina: Cubical packets of eight (division in three perpendicular planes). Bacilli (Rod-shaped): Bacillus: Single rods (e.g., Escherichia coli ). Streptobacillus: Chains of rods (e.g., Bacillus anthracis when cultured). Coccobacillus: Very short, plump rods, appearing almost ovoid. Spirilla (Spiral/Helical): Spirillum: Rigid, wavy spirals with external flagella (e.g., Spirillum volutans ). Spirochete: Flexible, tightly coiled spirals with internal flagella (axial filaments) (e.g., Treponema pallidum , Borrelia burgdorferi ). Vibrio: Comma-shaped or curved rods (e.g., Vibrio cholerae ). Pleomorphic: Displaying a variety of shapes within a single culture or even individual cells, due to genetic programming or environmental factors (e.g., Mycoplasma , Corynebacterium ). Size: Typically $0.2 \mu m$ to $10 \mu m$, though some giant bacteria can be much larger (e.g., Thiomargarita namibiensis up to $750 \mu m$). III. Gram-Positive vs. Gram-Negative Bacteria: Key Differences The Gram stain differentiates bacteria based on cell wall composition, a critical diagnostic tool in microbiology. Feature Gram-Positive Bacteria Gram-Negative Bacteria Peptidoglycan Layer Very thick ($20-80$ nm), multilayered. Comprises $60-90\%$ of cell wall. Very thin ($2-7$ nm), single or few layers. Comprises $5-10\%$ of cell wall. Outer Membrane Absent. Present, external to peptidoglycan. Contains Lipopolysaccharide (LPS), phospholipids, and proteins (porins). Teichoic Acids Present (lipoteichoic acid and wall teichoic acid). Provide structural stability, adhesion, and antigenicity. Absent. Lipopolysaccharide (LPS) Absent. Present in the outer leaflet of the outer membrane. Acts as an endotoxin (Lipid A portion), responsible for fever and shock symptoms in infections. O-polysaccharide is antigenic. Periplasmic Space Absent or very small, between cell membrane and peptidoglycan. Prominent, between inner (cell) membrane and outer membrane. Contains enzymes (e.g., hydrolytic enzymes, $\beta$-lactamases) and transport proteins. Cell Membrane Single inner membrane. Inner (cytoplasmic) membrane and an outer membrane. Gram Stain Reaction Retain crystal violet-iodine complex, appear purple/blue . Crystal violet-iodine complex is washed out, counterstained by safranin, appear pink/red . Exotoxins/Endotoxins Primarily produce exotoxins (proteins secreted by living cells). Produce endotoxins (LPS, released upon cell lysis) and some exotoxins. Antibiotic Sensitivity Generally more susceptible to penicillin and lysozyme due to exposed peptidoglycan. More resistant to penicillin, lysozyme, and detergents due to outer membrane barrier. Often more sensitive to streptomycin, chloramphenicol, tetracycline. IV. Method of Gram Staining A differential staining technique developed by Hans Christian Gram in 1884. Preparation: A thin smear of bacterial culture is made on a clean glass slide and heat-fixed (kills bacteria, adheres them to slide). Primary Stain (Crystal Violet): The smear is flooded with crystal violet solution for $\sim 1$ minute. Crystal violet is a basic dye that stains all cells purple. Mordant (Gram's Iodine): The crystal violet is rinsed off, and Gram's iodine solution is applied for $\sim 1$ minute. Iodine acts as a mordant, forming a large crystal violet-iodine (CV-I) complex within the cytoplasm of both Gram-positive and Gram-negative cells. Decolorization (Alcohol/Acetone): The slide is rinsed with alcohol (ethanol) or acetone for $10-20$ seconds. This is the critical step: Gram-Positive: The thick peptidoglycan layer of Gram-positive cells becomes dehydrated, shrinking and trapping the large CV-I complex within the cell. Cells remain purple. Gram-Negative: The alcohol dissolves the outer membrane of Gram-negative cells, and the thin peptidoglycan layer cannot retain the CV-I complex. The complex is washed out, leaving Gram-negative cells colorless. Counterstain (Safranin): The slide is rinsed, and safranin (a red dye) is applied for $\sim 1$ minute. Gram-Positive: Remain purple, as they are already intensely stained by crystal violet. Gram-Negative: Absorb the safranin and appear pink or red . Rinsing and Drying: The slide is rinsed with water and blotted dry before microscopic examination. V. Bacterial Cell Structure (Prokaryotic Cell) Bacteria are prokaryotes, meaning they lack a membrane-bound nucleus and other membrane-bound organelles. Cell Wall: Function: Provides structural integrity, maintains cell shape, protects against osmotic lysis, and can contribute to pathogenicity. Composition: Primarily peptidoglycan (murein) – a polymer of $N$-acetylglucosamine (NAG) and $N$-acetylmuramic acid (NAM) cross-linked by short peptide chains. Variations: Gram-positive (thick peptidoglycan, teichoic acids) vs. Gram-negative (thin peptidoglycan, outer membrane with LPS). Atypical Cell Walls: Mycobacterium (mycolic acid layer outside peptidoglycan, making them acid-fast); Mycoplasma (lack cell walls, stabilized by sterols in membrane). Cell (Cytoplasmic) Membrane: Structure: Phospholipid bilayer with embedded proteins (fluid mosaic model). Lacks sterols (except Mycoplasma ). Function: Selectively permeable barrier, regulates transport of substances, site of ATP synthesis (electron transport chain), DNA replication initiation, cell wall synthesis, and secretion. Cytoplasm: Composition: Semifluid substance filling the cell, primarily water, proteins, carbohydrates, lipids, and inorganic ions. Contents: Nucleoid, ribosomes, inclusion bodies, metabolic enzymes. Nucleoid: Structure: Irregularly shaped region containing the bacterial chromosome. Not enclosed by a membrane. Chromosome: Typically a single, circular, double-stranded DNA molecule, highly supercoiled and condensed. Ribosomes: Structure: Prokaryotic ribosomes are $70S$ (composed of $50S$ and $30S$ subunits). Function: Sites of protein synthesis (translation). Plasmids: Structure: Small, circular, extrachromosomal, double-stranded DNA molecules. Replicate independently of the chromosome. Function: Carry non-essential but often advantageous genes (e.g., antibiotic resistance genes (R factors), virulence factors, genes for conjugation (F factors), metabolic capabilities). Used extensively in genetic engineering. Glycocalyx (Capsule and Slime Layer): Structure: Polysaccharide (most common) or polypeptide layer external to the cell wall. Capsule: Well-organized, tightly attached to the cell wall. Can be visualized by negative staining. Slime Layer: Unorganized, diffuse, loosely attached. Function: Protection against phagocytosis by host immune cells, desiccation, viral infection; aids in adhesion to surfaces (biofilm formation), nutrient reserve. Flagella: Structure: Long, helical protein filaments (flagellin) extending from the cell surface. Anchored by a basal body and connected by a hook. Function: Motility (propulsion by rotation, like a propeller), enabling chemotaxis (movement in response to chemical stimuli) and phototaxis. Arrangements: Monotrichous: Single flagellum at one pole. Amphitrichous: Single flagellum at each pole. Lophotrichous: Tuft of multiple flagella at one pole. Peritrichous: Flagella distributed over the entire cell surface. Pili (Fimbriae): Structure: Shorter, thinner, and more numerous protein appendages than flagella. Made of pilin protein. Function: Fimbriae: Primarily for adhesion to host cells or surfaces (important for colonization and biofilm formation). Sex Pili (F pilus): Longer, less numerous. Involved in conjugation for genetic exchange. Inclusion Bodies (Storage Granules): Structure: Intracellular aggregates of various substances (e.g., poly-$\beta$-hydroxybutyrate (PHB) for carbon/energy, glycogen, polyphosphate/volutin granules, sulfur granules). Function: Storage of nutrients, energy reserves, or metabolic byproducts. Endospores: Structure: Highly resistant, dormant structures formed intracellularly by certain Gram-positive bacteria (e.g., Bacillus , Clostridium ) in response to nutrient depletion or adverse conditions. Contain a core with DNA, ribosomes, dipicolinic acid, and calcium, surrounded by cortex and spore coats. Function: Survival mechanism, resistant to heat, radiation, chemicals, desiccation. Can germinate back into metabolically active vegetative cells when conditions improve. VI. Bacterial Reproduction & Genetic Exchange A. Asexual Reproduction: Binary Fission This is the primary mode of bacterial proliferation, resulting in two genetically identical daughter cells. Process: Cell Elongation & DNA Replication: The cell grows in size, and the circular bacterial chromosome replicates, usually starting from a single origin of replication. Chromosome Segregation: The two identical chromosomes move to opposite ends of the elongating cell, often aided by attachment to the cell membrane. Septum Formation: A new cell wall and cell membrane begin to grow inward from the periphery, forming a transverse septum in the middle of the cell. Cell Division: The septum completes its formation, dividing the parent cell into two separate, genetically identical daughter cells. Growth Rate: Under optimal conditions, bacteria can divide very rapidly (e.g., E. coli every $20$ minutes). B. Genetic Recombination (Horizontal Gene Transfer - HGT) While not sexual reproduction in the eukaryotic sense, HGT allows bacteria to acquire new genetic material from other bacteria, leading to genetic diversity and adaptation. 1. Conjugation ("Bacterial Mating"): Definition: Direct transfer of genetic material (plasmid or chromosomal DNA) from a donor bacterium to a recipient bacterium through direct cell-to-cell contact. Mechanism: Requires a sex pilus (encoded by the F factor or fertility plasmid) on the donor cell. The donor cell ($F^+$) extends a pilus to attach to an $F^-$ (recipient) cell. The pilus retracts, bringing the cells into close contact. A conjugation bridge (pore) forms between the cells. One strand of the F plasmid DNA is transferred from $F^+$ to $F^-$ through rolling circle replication. Both cells then synthesize the complementary DNA strand, resulting in two $F^+$ cells. Hfr (High-Frequency Recombination) Cells: Occur when the F plasmid integrates into the bacterial chromosome. Hfr cells can transfer portions of their chromosome, along with the integrated F factor, to an $F^-$ recipient. F-prime (F') Conjugation (Sexduction): If an integrated F plasmid excises imperfectly from the chromosome, it can carry adjacent chromosomal genes with it, forming an F' plasmid. This F' plasmid can then be transferred to other cells, introducing these chromosomal genes. 2. Transformation: Definition: The uptake of naked (free) DNA from the environment by a competent recipient bacterial cell. Competence: The ability of a cell to take up exogenous DNA. Can be natural (e.g., Bacillus , Streptococcus ) or induced artificially in the lab (e.g., E. coli treated with $CaCl_2$ and heat shock). Mechanism: Free DNA fragments (e.g., from lysed bacterial cells) bind to specific receptors on the competent cell surface, are transported across the membrane, and can be integrated into the recipient's chromosome via homologous recombination. 3. Transduction: Definition: Transfer of bacterial genetic material from one bacterium to another via a bacteriophage (a virus that infects bacteria). Mechanism: Generalized Transduction: During lytic phage replication, host bacterial DNA is accidentally packaged into phage capsids instead of phage DNA. These "defective" phages can then inject the bacterial DNA into a new host cell. Any part of the bacterial chromosome can be transferred. Specialized Transduction: Occurs with lysogenic phages (prophages). When a prophage excises from the host chromosome, it sometimes takes adjacent bacterial genes with it. These genes are then transferred to a new host during subsequent infection. Only specific genes located near the prophage integration site can be transferred. VII. Bacterial Nutrition & Metabolism Bacteria exhibit vast metabolic diversity, categorized by their energy and carbon sources. Nutritional Type Energy Source Carbon Source Description & Examples Photoautotrophs Light $CO_2$ (inorganic) Use light energy to fix $CO_2$ into organic compounds. Primary producers. E.g., Cyanobacteria (oxygenic photosynthesis), Purple/Green sulfur bacteria (anoxygenic photosynthesis). Photoheterotrophs Light Organic compounds Use light energy, but cannot fix $CO_2$. Obtain carbon from pre-formed organic molecules. E.g., Purple non-sulfur bacteria, Green non-sulfur bacteria. Chemoautotrophs (Chemolithoautotrophs) Chemical reactions (oxidation of inorganic compounds) $CO_2$ (inorganic) Derive energy by oxidizing inorganic substances (e.g., $NH_3, NO_2^-, H_2S, Fe^{2+}$) and fix $CO_2$. Key in biogeochemical cycles. E.g., Nitrifying bacteria ( Nitrosomonas, Nitrobacter ), Sulfur-oxidizing bacteria, Hydrogen bacteria, Iron bacteria. Chemoheterotrophs (Chemoorganoheterotrophs) Chemical reactions (oxidation of organic compounds) Organic compounds Obtain both energy and carbon from organic molecules. The largest group, including most pathogenic bacteria, decomposers, and fermenters. E.g., E. coli , Staphylococcus aureus , Fungi, Animals. Detailed Comparison: Phototrophic vs. Chemoautotrophic Bacteria Phototrophic Bacteria: Energy Source: Utilize solar energy (photons). Pigments: Possess light-absorbing pigments like chlorophylls (in cyanobacteria) or bacteriochlorophylls (in other phototrophs). Photosynthesis: Oxygenic Photosynthesis: (e.g., Cyanobacteria) Use water ($H_2O$) as an electron donor, producing oxygen ($O_2$) as a byproduct. Equation: $CO_2 + H_2O + \text{light} \to (\text{CH}_2\text{O})_n + O_2$. Anoxygenic Photosynthesis: (e.g., Purple and Green bacteria) Use electron donors other than water (e.g., $H_2S$, organic acids), thus not producing $O_2$. Equation: $CO_2 + 2H_2S + \text{light} \to (\text{CH}_2\text{O})_n + 2S$. Carbon Source: Can be $CO_2$ (photoautotrophs) or organic compounds (photoheterotrophs). Ecological Role: Major primary producers, especially cyanobacteria, which were instrumental in oxygenating Earth's early atmosphere. Chemoautotrophic Bacteria: Energy Source: Obtain energy by oxidizing inorganic chemical compounds. Electron Donors: Use diverse inorganic substrates as electron donors, such as ammonia ($NH_3$), nitrites ($NO_2^-$), hydrogen sulfide ($H_2S$), ferrous iron ($Fe^{2+}$), hydrogen gas ($H_2$). Carbon Source: Fix atmospheric $CO_2$ (or bicarbonates) into organic matter, similar to plants, but using chemical energy instead of light. Ecological Role: Crucial for biogeochemical cycles (nitrogen, sulfur, iron cycles). Often found in environments where light is absent (e.g., deep-sea hydrothermal vents, subsurface soils) and inorganic compounds are abundant. VIII. Economic Importance of Bacteria A. Beneficial Roles 1. Ecological Contributions: Decomposition & Nutrient Cycling: Saprophytic bacteria break down dead organic matter, recycling essential nutrients (carbon, nitrogen, phosphorus, sulfur) back into the ecosystem, making them available for plants. Nitrogen Fixation: Convert atmospheric nitrogen ($N_2$), which is unusable by most organisms, into ammonia ($NH_3$) or other nitrogen compounds (e.g., nitrates) that can be assimilated by plants. This is carried out by free-living bacteria (e.g., Azotobacter, Azospirillum ) and symbiotic bacteria (e.g., Rhizobium in legume root nodules). Bioremediation: Utilize bacteria's metabolic capabilities to degrade pollutants (e.g., petroleum hydrocarbons in oil spills, pesticides, heavy metals, plastics) into less harmful substances. 2. Industrial & Biotechnological Applications: Food Production: Fermentation processes to produce dairy products (yogurt, cheese, kefir - Lactobacillus, Streptococcus ), alcoholic beverages, vinegar ( Acetobacter ), sauerkraut, pickles, sourdough bread. Pharmaceuticals: Antibiotics: Many antibiotics are produced by bacteria (e.g., Streptomyces species produce streptomycin, tetracycline, erythromycin). Vaccines: Used in the production of subunit vaccines or as vectors for gene delivery. Recombinant Proteins: Genetically engineered bacteria (e.g., E. coli ) produce human insulin, growth hormone, enzymes, and other therapeutic proteins. Chemicals & Enzymes: Production of organic acids (e.g., lactic acid, acetic acid), amino acids, vitamins, ethanol (biofuel), and various industrial enzymes (e.g., amylase, protease). Mining (Bioleaching): Used to extract metals (e.g., copper, uranium) from low-grade ores using chemosynthetic bacteria (e.g., Thiobacillus ferrooxidans ). 3. Human & Animal Health: Gut Microbiota: Commensal bacteria in the human gut aid in food digestion, synthesize essential vitamins (e.g., Vitamin K, B vitamins), train the immune system, and protect against pathogens by competitive exclusion. Probiotics: Live bacteria (e.g., Lactobacillus, Bifidobacterium ) consumed for their beneficial effects on gut health. B. Harmful Roles 1. Pathogenesis: Human Diseases: Cause a wide range of infectious diseases (e.g., tuberculosis - Mycobacterium tuberculosis , cholera - Vibrio cholerae , tetanus - Clostridium tetani , pneumonia, strep throat). Animal Diseases: Affect livestock and pets (e.g., anthrax, brucellosis). Plant Diseases: Cause crop damage (e.g., bacterial blights, soft rots, galls). 2. Food Spoilage: Bacteria decompose food products, leading to undesirable changes in taste, smell, texture, and appearance, making them unfit for consumption. Can produce toxins in food (e.g., Clostridium botulinum toxin). 3. Biodeterioration: Damage to materials such as textiles, wood, paper, and metals (e.g., microbial corrosion of pipelines). IX. Actinomycetes: General Characteristics Actinomycetes are a group of Gram-positive bacteria known for their filamentous, fungus-like growth and significant ecological and industrial roles. Taxonomic Classification: Belong to the phylum Actinobacteria, which is a major group of Gram-positive bacteria. Morphology: Filamentous Growth: Characteristically grow as branching filaments (hyphae) that form a mycelial colony, resembling molds (fungi). This gives them their name "ray fungi." Non-septate Hyphae: Unlike true fungi, their hyphae are typically non-septate (lack cross-walls). Spores: Reproduce by forming asexual spores (conidia) on aerial hyphae. These are metabolically dormant but not as resistant as bacterial endospores. Gram Stain: Universally Gram-positive. Habitat: Abundant in soil, where they play a crucial role in decomposition of organic matter. Responsible for the characteristic "earthy" smell of soil (due to production of geosmin). Metabolism: Primarily chemoheterotrophic. Most are strict aerobes, but some are facultative or strict anaerobes. Industrial Importance: Antibiotic Production: The genus Streptomyces is the most prolific natural producer of antibiotics, responsible for more than two-thirds of all natural antibiotics (e.g., streptomycin, tetracycline, erythromycin, chloramphenicol). Enzyme Production: Produce various enzymes used in industry. Pathogenicity: Some genera can cause diseases in humans and animals: Actinomyces: Causes actinomycosis (chronic granulomatous infections). Nocardia: Causes nocardiosis (pulmonary and systemic infections). Mycobacterium: While not typically filamentous, it is closely related and causes tuberculosis and leprosy. X. Archaebacteria (Archaea): General Characteristics Archaea represent a distinct domain of life, separate from Bacteria and Eukarya. They share some features with bacteria (prokaryotic cell structure) but are fundamentally different in biochemistry and genetics, with some similarities to eukaryotes. Evolutionary Position: Considered to be more closely related to Eukaryotes than to Bacteria, based on ribosomal RNA gene sequences and other genetic markers. They represent a distinct, ancient lineage. Prokaryotic Structure: Lack a true membrane-bound nucleus and other membrane-bound organelles. Possess a single, circular chromosome (like bacteria). Have $70S$ ribosomes, but their rRNA sequences and protein components are distinct from bacteria. Unique Cell Wall Composition: Absence of Peptidoglycan: Unlike bacteria, archaea never contain peptidoglycan in their cell walls. Diverse Cell Wall Types: Pseudopeptidoglycan (Pseudomurein): Found in some archaea (e.g., methanogens). Similar in structure to peptidoglycan but has $N$-acetyltalosaminuronic acid instead of NAM and $\beta(1,3)$ glycosidic bonds instead of $\beta(1,4)$. Not sensitive to lysozyme or penicillin. S-Layers: Most common type, composed of a paracrystalline array of proteins or glycoproteins. Other materials: Some have cell walls made of polysaccharides or proteins. Unique Cell Membrane Lipids: Ether Linkages: Membrane lipids feature ether linkages between glycerol and branched hydrocarbon chains (isoprenoids), instead of ester linkages found in bacteria and eukaryotes. Branched Chains: The hydrocarbon chains are branched, not straight. Monolayers: Some hyperthermophilic archaea have lipid monolayers instead of bilayers, providing extreme stability at high temperatures. Function: These unique lipid structures contribute to their ability to withstand extreme temperatures and pH. Metabolic Diversity: Methanogens: A unique group of archaea that produce methane ($CH_4$) as a metabolic byproduct, strictly anaerobic. Found in anoxic sediments, rumens of animals, and sewage treatment plants. Extremophiles: Many archaea are famous for thriving in extreme environments: Extreme Halophiles: (e.g., Halobacterium ) Require very high salt concentrations (up to $30\%$ $NaCl$). Extreme Thermophiles/Hyperthermophiles: (e.g., Pyrolobus fumarii ) Grow at temperatures above $80^\circ C$, some even above $100^\circ C$. Extreme Acidophiles: (e.g., Picrophilus ) Thrive at very low pH (e.g., pH 0-1). Some are mesophilic and found in less extreme environments (e.g., soil, oceans). Genetic Characteristics: RNA Polymerase: More complex than bacterial RNA polymerase, resembling eukaryotic RNA polymerase II. Introns: Some archaeal genes contain introns (non-coding regions), a feature common in eukaryotes but rare in bacteria. Histones: Some archaea possess histone-like proteins that compact their DNA, similar to eukaryotes. Pathogenicity: No known archaeal pathogens of humans, animals, or plants. They are generally considered benign or beneficial.