Taxonomy: Nomenclature and Domains

Scientific Nomenclature

• Scientific names of organisms use binomial nomenclature.
• It consists of the Genus and species, written in italics.
• Only the Genus is capitalized (e.g., Escherichia coli).

Carl Woese's Classification System

• Carl Woese defined Archaea in 1977 based on ribosomal RNA gene sequence differences.
• Prokaryotes were separated into Bacteria and Archaea.
• Bacteria and Archaea are prokaryotes, characterized by a nucleoid and lacking a nucleus.
• Eukarya are eukaryotes, possessing a nucleus.

Comparison of Domains

• Archaea: Prokaryotic, cell wall lacks peptidoglycan, not known to cause disease, thrives in extreme environments, reproduces via binary fission.
• Bacteria: Prokaryotic, cell wall contains peptidoglycan, some cause disease, reproduces via binary fission.
• Eukarya: Eukaryotic, contains a nucleus and membrane-bound organelles, ribosomal RNA unique to this group, lacks peptidoglycan, unicellular or multicellular, size ranges from 5-50 micrometers.

Taxonomic Reference

• Bergey's Manual for Systematic Bacteriology serves as the reference for taxonomic descriptions of bacteria.

Light Microscopy

• Uses ocular (10x magnification) and objective lenses (10x to oil immersion magnification).
• Resolution refers to the ability to distinguish objects that are close together (0.2 microns or 200 nm).
• Contrast is the ability to distinguish objects from their background.
• Oil immersion (around 100x) improves resolution by preventing light refraction.
• Refraction occurs when light rays bend due to differences in the refractive index of different mediums.
• Same refractive index prevents image distortion.
• Types of microscopes increase contrast: bright field, dark field, phase contrast, and differential interference contrast (DIC).
• DIC provides a 3D image.

Electron Microscopy

• Uses electromagnetic lenses and electrons, with images displayed on a computer in a vacuum.
• Resolving power is the amount of detail visible on a specimen or between objects (0.3 nm).

Scanning Electron Microscopy (SEM)

• Used for viewing the surface of cells.
• Electrons scan over the surface.

Transmission Electron Microscopy (TEM)

• Used for viewing through the cell.
• Requires thin sectioning to observe internal details.
• Freeze fracturing/freeze etching techniques are used.

Usage Scenarios for Electron Microscopes

• TEM is used to examine the ultrastructure of cells at high magnification (up to 50 million times).
• SEM provides a detailed, three-dimensional view of a cell's outer structure.

Staining Microorganisms

• Staining improves contrast, making cells easier to observe.
• Common simple stains: methylene blue, crystal violet, safranin.
• Cells have a negative charge, so positively charged stains bind to them.

Simple vs. Differential Stains

• Simple stains use a single dye to improve contrast.
• Differential stains use multiple dyes to distinguish between different types of bacteria.

Gram Staining

• Relies on the decolorizing step and the age of the culture.
• Crystal violet is the primary stain, staining all cells purple.
• Iodine acts as a mordant, causing cells to remain purple.
• Decolorizing with alcohol (ethanol or acetone) differentiates cells.
• Gram-positive cells stay purple.
• Gram-negative cells become colorless.
• Safranin is used as a counterstain.
• Gram-positive cells remain purple.
• Gram-negative cells appear pink.
• Based on peptidoglycan layer differences.
• Gram-positive bacteria have a thick peptidoglycan layer that traps the purple stain.

Endospore Staining

• Primary stain: malachite green.
• Counterstain: safranin.
• Spores stain green, other cells stain pink.
• Used for identifying Bacillus and Clostridium species.

Acid-Fast Staining

• Used for cells that do not readily take up dyes, such as Mycobacterium species.
• Primary stain: red.
• Counterstain: blue.
• Acid-fast cells stain red; non-acid-fast cells stain blue.
• Used in clinical settings to identify Mycobacterium tuberculosis.

Bacterial Cell Morphology

• Coccus (spherical).
• Rod (bacillus).
• Vibrio.
• Spirillum.
• Spirochete (flexible cell wall).
• Pleomorphic (FLiPS), varying shapes.

Cytoplasmic Membrane

• Phospholipid bilayer with proteins.
• Hydrophobic tails face inward, hydrophilic heads face outward.
• Contains membrane proteins that act as selective gates, environmental sensors, and enzymes.
• Follows the fluid mosaic model.
• Similarities between Archaea and Bacteria but with different phospholipid compositions.
• Archaea have pseudo peptidoglycan.
• Lipid tails are fatty acids, linked differently to glycerol.
• Selective permeability allows gases, small hydrophobic molecules, and water (via aquaporins) to pass through.
• Simple diffusion moves molecules from high to low concentration.
• Water moves to hypertonic solutions (high solute concentration) via osmosis.
• Cell wall prevents cells from bursting due to water influx.
• Energy transformation occurs via the proton motive force.
• Protons move out of the cell through the electron transport chain and are used in various energy-requiring processes.
• Transport proteins ("permeases," "carriers") move solutes through the membrane.
• Passive transport requires no energy, while active transport requires energy (proton motive force or ATP).

Gram-Positive Cell Walls

• Very thick peptidoglycan layer.
• Teichoic acids weave through the peptidoglycan, carrying a negative charge and binding ions like Mg+.

Gram-Negative Cell Walls

• Thin peptidoglycan layer.
• Outer membrane contains LPS (lipopolysaccharide) with Lipid A and O Antigen.
• O Antigen recognized as foreign invaders.
• Contains porins and secretion systems.
• Periplasm is a gel-like substance between the cytoplasmic membrane and outer membrane.

Effects of Antibacterial Substances on Peptidoglycan

• Penicillin prevents cross-linking in peptidoglycan synthesis.
• Lysozyme breaks the glycan chain (NAM and NAG bonds).
• Penicillin kills actively growing cells.
• Lysozyme kills cells at any stage of growth.

Mycoplasma Characteristics

• Lack a cell wall.
• Pleomorphic.
• Small (0.2-0.3 microns).
• Contain sterols in the membrane for strength.
• Not affected by penicillin or lysosome.

Pili Functions

• Fimbriae: used for attachment to surfaces.
• Sex pilus: facilitates genetic exchange between bacteria.

Endospores

• Designed for survival.
• Produced by bacteria like Clostridium and Bacillus.
• Resistant to heat, chemicals, UV light, and boiling water.
• Sporulation is triggered by starvation, such as carbon or nitrogen limitation.
• Cortex keeps the core dehydrated.
• Core contains calcium dipicolinate for protection.
• Germination is triggered by heat or chemical exposure.

Endospores in the Food Industry

• Endospores can survive canning processes.
• Clostridium botulinum causes botulism.
• Bacillus cereus causes food poisoning.

Enzyme Structure and Activity

• Competitive inhibition: binds to the active site, often with a structure similar to the substrate.
• Non-competitive (allosteric) control: binds to a site other than the active site.
• Feedback inhibition: enzyme activity controlled by binding to an allosteric site.

Enzyme Function

• Enzymes speed up reactions by lowering the activation energy.
• Biological catalysts accelerate the conversion of substrates into products.
• Enzyme names typically end in "-ase".

Factors Influencing Enzyme Activity

• Temperature.
• Salt concentration.
• pH.
• Enzymes function best at low salt concentrations, around pH 7, and optimal temperatures.

Glycolysis

• Breakdown of glucose to pyruvate.
• Produces 2 ATP (net) .
• Importance: First step in glucose metabolism, provides energy and intermediates for other pathways.
• ATP Produced: 2 ATP .
• Precursor Metabolites:
  • Pyruvate.
  • G3P (Glyceraldehyde-3-phosphate).

Transition Step

• Pyruvate is converted to Acetyl-CoA.
• Generates 1 NADH per pyruvate and releases 1 CO₂.
• Importance: Links glycolysis to the TCA cycle, important for energy production.
• ATP Produced: 0 ATP
• Precursor Metabolites: Acetyl-CoA (used in TCA cycle).

TCA Cycle

• Acetyl-CoA is oxidized to CO₂.
• Produces 3 NADH, 1 FADH₂, and 1 GTP (ATP equivalent).
• Importance: Major ATP-producing cycle, provides key intermediates for biosynthesis.
• ATP Produced: 2 ATP (1 GTP, which is equivalent to ATP).
• Precursor Metabolites:
  • Acetyl-CoA (enters the cycle).
  • Citrate (formed in the cycle, can be used for biosynthesis).

Pentose Phosphate Pathway

• Produces NADPH and ribose-5-phosphate.
• NADPH is used in anabolic reactions, ribose-5-phosphate is used for nucleic acid synthesis.
• Importance: Provides reducing power and precursors for nucleotide biosynthesis.
• ATP Produced: 0 ATP.
• Precursor Metabolites:
  • Ribose-5-phosphate (for nucleotide synthesis).
  • Erythrose-4-phosphate (for aromatic amino acid synthesis).
  • NADPH (used in biosynthesis).

Oxidation-Reduction

• Oxidation is the loss of electrons, reduction is the gain of electrons.
• Hydrogenation is a reduction, dehydrogenation is an oxidation.

Electron Transport and Chemiosmosis

• Electron Transport: NADH and FADH₂ donate electrons to the electron transport chain (ETC), which creates a proton gradient across the mitochondrial membrane.
• Chemiosmosis: Protons flow back into the matrix through ATP synthase, driving the production of ATP from ADP and inorganic phosphate.

Respiration

• A process to produce ATP by breaking down glucose (or other molecules) in the presence (aerobic) or absence (anaerobic) of oxygen.

Aerobic vs. Anaerobic Respiration

• Aerobic Respiration: Uses oxygen as the final electron acceptor in the electron transport chain, producing up to 38 ATP (from 1 glucose molecule).
• Anaerobic Respiration: Uses other electron acceptors (not oxygen, e.g., sulfate, nitrate, carbon dioxide) and produces less ATP (typically around 2 ATP).

Alternative Electron Acceptors

• In Anaerobic Respiration: Organisms can use alternative electron acceptors.
• Nitrate (NO₃⁻).
• Sulfate (SO₄²⁻).
• Carbon dioxide (CO₂).

Fermentation

• No terminal electron acceptor or ETC.
• ATP from substrate-level phosphorylation.
• Pyruvate acts as a terminal electron acceptor
• Crucial to recycle NADH, so NAD+ can return to glycolysis.
• Starts with glucose, produces minimal ATP.
• Two common pathways: lactic acid and ethanol.
• Fermentation products vary useful for identification and commercial purposes
• Lactic acid: yogurt.
• Ethanol.
• Butyric acid.
• Propionic acid.
• Mixed acids.
• 2,3-butanediol.
• Acids produced during fermentation slow food spoilage.

Carbon and Energy Source Classification

• Heterotroph: organic carbon source.
• Autotroph: inorganic carbon source.
• Phototroph: energy from light.
• Chemotroph: energy from chemicals.

Chemolithotrophs

• Energy source: reduced inorganic chemicals.
• Carbon source: carbon dioxide.
• Unique to prokaryotes.
• Four main groups: hydrogen bacteria, sulfur bacteria (non-photosynthetic), iron bacteria, nitrifying bacteria.
• Thrive in extreme environments.
• Sulfur-rich habitats (metal sulfides).
• Hydrothermal vents (thermophilic chemolithotrophs).

Photosynthesis

• Radiant energy converted into chemical energy.

Anoxygenic Photosynthetic Bacteria

• Single photosystem.
• Hydrogen sulfide or hydrogen gas as electron donor.
• Byproduct: sulfur rather than molecular oxygen. examples include
  • Purple Sulfur bacteria
  • Purple Non-Sulfur Bacteria

Anaerobic Chemolithotrophs: Methanogens

• Methane-producing archaea.
• Oxidize H₂ gas to generate ATP, producing methane.
• Can use formate, methanol, or acetate as alternative energy sources.
• CO₂ as terminal electron acceptor.
• Found in swamps, marine sediments, cows, and intestinal tracts.
• Sensitive to oxygen.

Lithotrophy: Dehalorespiration

• Halogenated organic molecules serve as electron acceptors for H₂.
• Chlorine removed as a chloride anion replaced by H, requiring 2e⁻ from H₂.
• Dechlorinates compounds such as chlorobenzene, perchloroethylene, and polyvinyl chloride (PVC).
• Example genus: Dehalococcoides CBDB1 can reductively dechlorinate chlorobenzene.

Anaerobic Chemoorganotrophs

• Energy source: organic compounds (glucose).
• Sulfur or sulfate as common electron acceptors.
• Sulfur and sulfate-reducing bacteria produce hydrogen sulfide.
• Desulfovibrio is the most studied.

Aerobic Chemolithotrophs

• Oxidize reduced inorganic chemicals.
• O₂ as terminal electron acceptor.
• Sulfur-oxidizing bacteria generate sulfuric acid.
• Filamentous forms store sulfur as intracellular granules.
• Unicellular forms include Acidithiobacillus.
• Acidithiobacillus oxidizes metal sulfides (biomining).

Facultative Anaerobes

• Prefer aerobic respiration but can ferment if oxygen is unavailable.
• Enterobacteriaceae (enterics or enterobacteria) are Gram-negative rods found in the intestinal tract of humans and animals.
• Lactose fermenters are termed "coliforms," including E. coli, an indicator of possible fecal pollution.

Anoxygenic Phototrophs: Purple Bacteria

• Photosynthetic machinery in the cytoplasmic membrane.
• Gas vesicles control depth.
• Store sulfur as intracellular granules.
• Hydrogen sulfide for reducing power.
• Strict photosynthetic anaerobes, can grow in the absence of light using inorganic or organic compounds for energy.
• Purple non-sulfur bacteria use organic molecules rather than hydrogen sulfide as a source of electrons.

Anoxygenic Phototrophs: Green Bacteria

• Gram-negative, green or brown.
• Use H₂S, form sulfur granules outside of the cell.
• Accessory pigments located in chlorosomes. Metabolically diverse, Chloroflexus aurantiacus can use reduced sulfur compounds.

Oxygenic Phototrophs: Cyanobacteria

• Water as a source of electrons, generating O₂.
• Gas vesicles facilitate movement through the water column.
• Photosystems similar to land plants.
• Pigments: chlorophyll and phycobiliproteins.

Cyanobacteria Blooms

• Nutrient-rich (N, P) water from wastewater treatment plants and agricultural runoff.
• Microcystis produces microcystin (hepatotoxin).
• Binding to type 1 and 2A protein phosphatase (PP1 and PP2A) in the liver, resulting in excessive phosphorylation.

Extremophiles: Thermus and Deinococcus

• Thermus is thermophilic with heat-stable enzymes, staining Gram-negative.
• Deinococcus is highly radiation-resistant with an unusual cell wall.

Extreme Halophiles (Salt-Loving)

• Grow in 32% NaCl, require at least 9% NaCl.
• produce red patches on salted fish, pink blooms in saltwater ponds.
• Aerobic or facultative anaerobic chemoheterotrophs.
• Obtain additional energy from light via bacteriorhodopsin.
• Representative genera: Halobacterium, Halorubrum, Natronobacterium, Natronococcus.

Extreme Thermophiles

• Found near volcanic vents and fissures that release sulfurous gases, and hydrothermal vents.
• Methane-generating hyperthermophiles such as Methanothermus species.

Sulfur-Reducing Hyperthermophiles

• Obligate anaerobes that use S as terminal electron acceptors.
• Generate H₂S.

Thermophilic Extreme Acidophiles

• Thermoacidophilic such as Sulfolobus species oxidize sulfur compounds and generate sulfuric acid.
• Thermoplasma, Picrophilus grow optimally at pH 2, tolerate even more acidic conditions.

Microbial Growth

• Cells divide by binary fission and undergo exponential growth.
• Generation time varies among species and medium.

Growth Curves

• Lag phase: active but not dividing.
• Exponential (log) phase: constant growth rate.
• Stationary phase.
• Death phase.

Environmental Factors

• Temperature.
• Closed system growth curve is in a flask with limited resources.

Additional Nutritional Factors

• Trace elements.
• Growth factors.
• Fastidious bacteria have complex nutritional requirements.

Culture Media

• Complex medium: peptone (amino acids and peptides), beef extract (vitamins and minerals).
• Chemically defined medium: slower growth.

Selective and Differential Media

• Selective media: inhibits growth of certain microbes.
• Differential media: microbes change in an observable way.
• MacConkey Agar: Selective and Differential for enteric, Gram-negative bacteria.

MacConkey Agar

• Selective for enteric Gram-negative bacteria.
• Kills Gram-positive and non-enteric Gram-negative.
• Differential with lactose (carbon source) and neutral red (pH indicator).
• Lactose fermentation drops pH and changes color.

Enrichment Cultures

• Uses media that favor growth of a particular microbe over others.
• Enriches for species present at very low abundance in a mixed population.

Bifidobacterium Longum

• Member of the gut microbiome.
• Used as a probiotic.
• Gram-positive, rod-shaped, micro aerotolerant anaerobe.

Proteus Mirabilis

• Gram-negative bacteria, rod-shaped, related to E. coli.
• Opportunistic pathogen causing urinary tract infections.
• Forms a bullseye on agar due to swimmer to swarmer cell differentiation.

Escherichia Coli

• Gram-negative bacteria.
• Facultative anaerobe.
• Found in the lower intestine of warm-blooded organisms.
• Model organism.
• Member of Enterobacteriaceae.

Thermus Aquaticus

• Isolated from hot springs at Yellowstone National Park.
• Grows between 50–80°C (122–176°F).
• Source of DNA polymerase (Taq polymerase) used in PCR.

Geobacter Metallireducens

• Gram-negative.
• Metal-reducing proteobacterium.
• Strict anaerobe.
• Anaerobic respiration: dissimilatory metal reduction.
• Uses Fe(III) as electron acceptor ("iron reducing").
• Used for bioremediation of U-contaminated water.

Pryolobus Fumarii

• Archeal species.
• Isolated from black smoker hydrothermal vent.
• Chemolithotroph: H₂ or sulfur as energy source.

Dehalococcoides

• Very small, grows very slow.
• Anaerobic respiration = “organohalide respiration’
• Degrades toxic halogenated compounds such as tetrachloroethene (PCE).
• Used for bioremediation of contaminated groundwate

Learn about scientific nomenclature, including binomial nomenclature. Explore Carl Woese's classification system, which divides life into Bacteria, Archaea, and Eukarya based on ribosomal RNA differences. Compare the key characteristics of these three domains.