Microbiology: Prokaryotes, Eukaryotes and Domains

• The exam is worth 100 points and includes 25 multiple-choice questions (3 points each), 10 fill-in-the-blank questions (1 point each), and 3 short answer questions (choose 3 of 5, worth 5 points each)

Course Overview & the History of Microbiology

• Microbes are organisms needing a microscope to be seen, existing as single cells or in colonies, including bacteria, viruses, fungi, or protozoa
• Microbes have profoundly affected human history, as exemplified by COVID-19, smallpox, tuberculosis, and the Black Plague
• All life forms fall into one of the three categories of Bacteria, Archaea, or Eukarya on the phylogenetic tree of life
• Bacteria are simple, single-celled microbes like E. coli
• Archaea are single-celled microbes thriving in extreme environments
• Eukarya includes complex-celled organisms like protists, fungi, plants, and animals
• Prokaryotes (Bacteria & Archaea) exhibit greater diversity in energy acquisition and survival compared to eukaryotes
• Eukaryotes (Plants, Animals, Fungi, Protists) are more complex, with specialized cells and organelles
• Prokaryotes have more metabolic variety, while eukaryotes have more structural complexity
• Endosymbiosis is how prokaryotes contributed to eukaryotic evolution
• Eukaryotic cells evolved when larger cells engulfed smaller bacteria, which later became mitochondria (for energy), and chloroplasts (for photosynthesis)

Observing the Microbial Cell

• Light microscopes are useful for basic cell shapes, while electron microscopes are for detailed structures
• Gram staining differentiates bacterium types; fluorescent stains highlight specific cell parts
• Microbes can be grown on agar plates or in liquid media to study colonies
• PCR detects microbial DNA; sequencing identifies species
• Biochemical Tests can be used to identify microbes based on nutrient or chemical processing
• Gram-positive bacteria have a thick peptidoglycan layer and no outer membrane
• Gram-negative bacteria have a thin peptidoglycan layer and an outer membrane for extra protection
• Microbial cell membranes are made of a phospholipid bilayer with embedded proteins in both Bacteria & Eukarya. Archaea have unique ether-linked lipids for stability in extreme conditions
• The microbial cell membrane functions as barrier which controls what enters and exits the cell
• The microbial cell membrane functions in energy production via the electron transport chain in prokaryotes
• The microbial cell membrane functions in nutrient uptake and waste removal using proteins
• The microbial cell membrane functions to detect signals from the environment via receptors and to maintain cell shape and interact with the cell wall
• In bacteria, antibiotics like polymyxins target the membrane, disrupting its function. In archaea, unique membranes allow survival in extreme heat, acidity, and salinity

Membrane fluidity

• Unsaturated fatty acids (bent tails) increase fluidity, saturated fatty acids (straight tails) decrease fluidity
• High temperatures increase fluidity, while low temperatures decrease it
• Cholesterol (eukaryotes) and hopanoids (bacteria) help stabilize fluidity
• Short lipid chains increase fluidity; long chains decrease it
• Membrane Proteins can adjust local fluidity
• Gram-positive bacteria are more susceptible to penicillin because they have a thick peptidoglycan wall but no outer membrane to block the substance
• Gram-negative bacteria are more resistant due to their outer membrane protecting their thin peptidoglycan layer

Microbial cell structure and function

• In prokaryotes, transcription and translation occurs simultaneously due to the absence of a nucleus
• Faster growth occurs because proteins are made quickly
• Quick response allows cells to adapt fast to changes
• More mutation effects cause mistakes to affect proteins right away and act as an antibiotic target, where some drugs block this process to kill bacteria
• Thylakoids help photosynthetic bacteria capture light for energy
• Carboxysomes store enzymes to help bacteria use CO2 efficiently
• Storage Granules save nutrients for survival in tough conditions
• Pili help bacteria stick to surfaces or share DNA
• Flagella help bacteria move toward food or away from danger

Nutrition, Growth, and Development

• Macronutrients (large amounts) such as Carbon, Nitrogen, Phosphorus, Sulfur, Oxygen, and Hydrogen build cells and make energy
• Micronutrients (small amounts) such as Iron, Magnesium, and Zinc enable enzymes to work
• Vitamins and Amino Acids are growth factors some microbes can't make and must obtain from the environment
• Small molecules (O2, CO2) can enter freely via passive diffusion
• Transport proteins help move molecules without energy via facilitated diffusion
• Active transport utilizes energy to pull in nutrients
• Group Translocation modifies nutrients as they enter
• Siderophores help microbes grab iron from the environment
• Endocytosis (only in eukaryotes) engulfs large particles
• Heterotrophs eat organic food (e.g., animals, fungi)
• Autotrophs use CO2 to make food (e.g., plants, some bacteria)
• Photoautotrophs use light + CO2 (e.g., plants, cyanobacteria)
• Chemoautotrophs use chemicals + CO2 (e.g., deep-sea bacteria)
• To culture microbes, keep it sterile using aseptic techniques for prevent contamination
• To culture microbes, transfer them onto a growth medium (inoculate) and incubate at the right temperature to grow
• Defined culture media has exact ingredients are known, complex culture media contains unknown nutrient amounts (e.g., nutrient broth)
• Selective culture media allows only certain microbes to grow (e.g., MacConkey agar)
• Differential culture media shows differences between microbes (e.g., blood agar)
• Enriched culture media has extra nutrients for picky microbes (e.g., chocolate agar)
• In the bacterial growth curve & stages, during the lag bacteria adjust but don't grow yet, and during the log bacteria multiply quickly
• During the stationary phase, growth slows as food runs out and waste builds up
• During the death phase, bacteria die as conditions become toxic

Comparing Growth Curves

• In fast log phase bacteria grow quickly
• In long lag phase, bacteria take longer to adjust
• In long stationary phase, some bacteria survive longer
• In rapid death phase, harsh conditions kill bacteria quickly
• The time for bacteria to double in number is the doubling time
• Final Bacteria Count: N=N0×2nN=N0×2n
• NO = Starting bacteria
• n = Number of times they double
• N = Final bacteria count

Environmental factors and microbial growth

• Psychrophiles (Cold lovers) prefer 0-20°C
• Mesophiles (Moderate lovers) prefer 20–45°C (human pathogens)
• Thermophiles (Heat lovers) prefer 45–80°C
• Hyperthermophiles (Extreme heat lovers) prefer 80°C+
• Obligate Aerobes need oxygen to survive
• Obligate Anaerobes die in oxygen
• Facultative Anaerobes prefer oxygen but can grow without it
• Aerotolerant Anaerobes ignore oxygen
• Microaerophiles need low oxygen
• Acidophiles (Acid lovers) prefer pH < 5
• Neutrophiles (Neutral lovers) prefer pH ~7 (most human pathogens)
• Alkaliphiles (Base lovers) prefer pH > 9
• Halophiles need salt
• Halotolerant tolerate salt
• Cold-loving microbes have flexible membranes and antifreeze proteins
• Heat-loving microbes Have heat-stable enzymes and stronger membranes
• Deep-sea microbes strengthen membranes and proteins to survive high pressure
• Acid-lovers pump out extra acid and use acid-resistant enzymes
• Base-lovers use special ion pumps to keep pH balanced
• No-oxygen microbes use fermentation instead of respiration
• Oxygen-using microbes have enzymes to remove toxic oxygen byproducts
• Salt-loving microbes store special solutes to prevent water loss, and freshwater microbes control solutes to prevent too much water from entering
• Heat (boiling, autoclaving, or pasteurization) kills microbes versus cold (refrigeration and freezing) slow growth but don't always kill
• Chemicals (bleach, alcohol, and antibiotics) destroy microbes
• Salt & Sugar dry out microbes, stopping their growth (e.g., pickling, curing meat)
• Acids & Bases (vinegar, lemon juice, and alkaline cleaners) kill bacteria
• Some bacteria die when exposed to oxygen and radiation (UV light and X-rays) damages DNA, killing microbes

Microbial diversity

• Bacteria are simple, single-celled microbes without a nucleus (e.g., E. coli)
• Archaea are single-celled microbes that live in extreme places (e.g., hot springs)
• Eukarya are complex cells with a nucleus, including plants, animals, fungi, and protists
• DNA & RNA studies show bacteria, archaea, and eukaryotes are very different
• Cell structure of archaea feature unique membranes not found in bacteria or eukaryotes
• Metabolism & genes in archaea are a mix of bacteria and eukaryotes in how they function
• Bacteria & Archaea are both prokaryotes (no nucleus), but archaea have unique membranes and live in extreme environments
• Eukaryotes are larger, more complex, and have a nucleus
• Bacteria & Archaea both reproduce by binary fission and have circular DNA
• Archaea & Eukaryotes share similar gene processing (e.g., introns, RNA polymerase)
• Phylogenetic trees uses a diagram shows how organisms are related by evolution

How to Read Phylogenetic Trees:

• Root represents the earliest ancestor of all organisms in the tree
• Branches show how species split and evolve
• Nodes are where branches meet, showing a common ancestor
• Leaves (Tips) are the organisms being compared
• Closer branches are closely related, longer branches means more genetic changes over time, and shared nodes mean a common ancestor between species

Examples of Microbal Phyla

• Bacteria includes Proteobacteria ( E. coli and Salmonella), Firmicutes (Bacillus and Staphylococcus), Actinobacteria (Streptomyces and Mycobacterium), Cyanobacteria (Anabaena), Spirochaetes (Treponema and Borrelia)
• Archaea includes include Euryarchaeota (methanogens and halophiles), Crenarchaeota (thermophiles)
• Eukarya includes Ascomycota (Yeast), Amoebozoa (Amoeba)
• Cyanobacteria created Earth's oxygen-rich air through photosynthesis
• Nitrogen-fixing bacteria give plants nutrients, bacteria & fungi break down dead matter, returning nutrients to the soil, and methanogens produce methane
• Microbes improve soil health, help plant roots grow, and release particles that make rain clouds
• Stromatolites are layered rocks made by ancient bacteria, microfossils are tiny fossilized bacteria found in old rocks, and carbon Isotopes features chemical signs in rocks that show microbial activity

Lines of Geological Evidence for Early Earth

• Banded Iron Formations consist of layers of iron in rocks prove that early microbes made oxygen and organic molecules appear in old rocks contain ancient biological molecules from microbes

Microbial Genetic Changes

• Mutations are random DNA changes that create new traits
• Gene Swapping is how microbes share DNA using plasmids or viruses
• DNA Rearrangement is how genes get copied or shuffled, leading to new functions
• Helpful changes allow microbes survive and grow (e.g., antibiotic resistance)
• Harmful changes kill microbes and neutral changes have no effect now but night help later
• The molecular clock estimates when species evolved by tracking DNA changes over time
• The molecular clock uses the idea that mutations happen at a steady rate
• More mutations means more time passed (more genetic differences and thus older spit)
• Different genes change at different speeds so scientists choose the right gene for each study
• The molecular clock is used to find out when species evolved, track viruses & diseases, and study common ancestors in evolution
• Vertical transfer is generation to generation (like parents to children) and horizontal transfer is between unrelated microbes (like bacteria swapping genes)