Chapter 22: Prokaryotes — Bacteria and Archaea

Antony van Leeuwenhoek (1600s)

• Dutch shopkeeper and skilled lens maker

• First to observe and describe single-celled organisms

• Called them “animalcules”

• Used simple microscopes with very high-quality lenses

• Discovered bacteria and protozoa in the 1670s

• His work laid the foundation for microbiology

Robert Koch

• German physician who developed pure culture techniques

• Introduced:

  • Staining methods

  • Growth media (liquid broth and solid agar)

• Koch studied Mycobacterium tuberculosis

Microorganisms are grown by:

• Placing them on media with needed nutrients

• Incubating at proper temperature

Koch’s Postulates

Used to link a specific organism to a disease:

1. Organism is found in all infected individuals

2. Organism can be isolated and grown in culture

3. Cultured organism causes disease in a healthy host

➡ Still widely used in medicine today

Prokaryotic Diversity

• Prokaryotes are:

  • Oldest life forms on Earth

  • Structurally simplest

  • Most abundant

• Existed over 1 billion years before eukaryotes

• 90–99% of prokaryotes are unknown

• Less than 1% cause disease

• Found in two domains:

  • Bacteria (Eubacteria)

  • Archaea

Extremophiles

• Many Archaea are extremophiles

• Live in extreme environments:

  • High salt (halophiles)

  • High heat

  • High acidity

• Example: Halobacteria in the Dead Sea

Early Prokaryotic Life

Microbial Mats

• Likely earliest form of life (~3.5 billion years ago)

• Multi-layered sheets of bacteria and archaea

• Found where different environments meet (air/water, water/sediment)

• Different metabolic pathways create layered colors

Stromatolites

• Rock-like structures formed by microbial mats

• Created when minerals precipitate due to prokaryotic activity

• Provide fossil evidence of early life

Why Prokaryotes Are So Successful

• Have evolved many adaptations to harsh environments

• Can survive where most life cannot

• This makes them the most abundant organisms in land and water ecosystems

Prokaryotes vs. Eukaryotes

Cell Organization

• Prokaryotes:

  • Unicellular

  • No multicellular forms

  • Can form biofilms or colonies

• Eukaryotes:

  • Can be multicellular

Cell Size

• Prokaryotes are much smaller

• Usually less than 1 μm in diameter

Genetic Material

• Single, circular, double-stranded DNA

• Located in the nucleoid (not a nucleus)

• Often contain plasmids

Cell Division

• Divide by binary fission

• No mitosis

• Exchange genes through horizontal gene transfer

• Genetic recombination is not reproduction

Internal Structure

• No membrane-bound organelles

• Ribosomes differ from eukaryotic ribosomes

Flagella

• Simple structure

• Different from eukaryotic flagella

Metabolic Diversity

• Can perform:

  • Oxygenic photosynthesis

  • Anoxygenic photosynthesis

  • Chemolithotrophy (using inorganic chemicals for energy)

Bacteria vs. Archaea

Although both are prokaryotes, they are placed in separate domains.

• Archaea are believed to be closely related to eukaryotes

• An ancestral archaeon likely gave rise to Eukarya

Plasma Membranes

• Different lipid composition

• Archaeal membranes are more stable in extreme environments

Cell Walls

• Bacteria: contain peptidoglycan

• Archaea: no peptidoglycan

 DNA Replication

• Both have a single origin of replication

• Archaeal DNA replication is more similar to eukaryotes

Gene Expression

• Archaeal transcription and translation resemble eukaryotes

• Similar enzymes used in both processes

Big Picture Takeaways

• Prokaryotes were the first life on Earth

• They are incredibly diverse, adaptable, and abundant

• Only a small fraction cause disease

• They are essential to:

  • Nutrient cycles

  • Human health

  • Food production

  • Environmental cleanup

Basic Bacterial Shapes

• Cocci: spherical bacteria (may form pairs or clusters)

• Bacilli: rod-shaped bacteria

• Spirilli: spiral-shaped bacteria

Shape does not determine phylum; bacteria in the same phylum can be any shape.

Major Groups of Prokaryotes

Archaea

• Includes groups like Euryarchaeota

• Many are extremophiles

Bacteria

• Chlamydias – obligate intracellular parasites

• Gram-positive bacteria

  • Low G/C content (example: Bacillus, Clostridium)

  • High G/C content (example: Streptomyces)

• Spirochetes – spiral-shaped bacteria

• Photosynthetic bacteria – cyanobacteria

• Proteobacteria – includes E. coli, Pseudomonas, Salmonella

  • Subdivided into Alpha, Beta, Gamma, Delta, Epsilon classes

Plasma Membrane Differences: Bacteria vs. Archaea

• Bacteria:

  • Lipids are unbranched

  • Lipids linked by ester bonds

• Archaea:

  • Lipids may be branched or have rings

  • Lipids linked by ether bonds

  • Tetraether polymers allow extremophiles to survive heat

Cell Wall Structure and Function

• Found outside the plasma membrane

• Provides shape, rigidity, and protection

• Prevents osmotic lysis

• Bacteria:

  • Made of peptidoglycan

  • Contains D-amino acids (D-glutamic acid, D-alanine)

  • Targeted by antibiotics

• S-layer proteins: found in both Bacteria and Archaea

Gram-positive vs. Gram-negative

• Gram-positive: thick peptidoglycan layer, no outer membrane

• Gram-negative: thin peptidoglycan layer, outer membrane with lipopolysaccharides and proteins (porins)

Prokaryotic Cell Features

• Capsule: gelatinous layer

  • Helps in attachment

  • Protects against immune system

• Flagella:

  • Helical, rigid, made of flagellin

  • Spins like a propeller for movement

• Pili:

  • Short, hairlike

  • Found in Gram-negative bacteria

  • Used for attachment and conjugation

• Nucleoid:

  • Contains circular chromosome

  • May have plasmids

• Ribosomes:

  • Smaller than eukaryotic

  • Targeted by some antibiotics

Prokaryotic Reproduction

• Divide by binary fission

• Steps:

  • DNA replication of circular chromosome

  • Cell enlarges

  • Cell divides into two identical clones

• No sexual reproduction

• Genetic variation achieved through horizontal gene transfer:

  • Conjugation: DNA via pilus

  • Transduction: DNA via bacteriophage

Transformation: DNA from environment

Horizontal Gene Transfer

1. Transformation: uptake of DNA from environment

2. Transduction: DNA delivered by virus

3. Conjugation: DNA transferred via pilus bridge

These processes occur in both Bacteria and Archaea

Prokaryotic Metabolism & Macronutrients

• Essential macronutrients (CHONPS):

  • Carbon (C) – 50% of cell; for proteins, lipids, nucleic acids

  • Hydrogen (H), Oxygen (O) – for water and biomolecules

  • Nitrogen (N) – 12% of cell; for proteins and nucleic acids

  • Phosphorus (P) – for nucleotides and phospholipids

  • Sulfur (S) – in amino acids (cysteine, methionine) and vitamins

• Other important ions:

  • Potassium (K), Magnesium (Mg), Calcium (Ca), Sodium (Na)

  • Needed in smaller amounts but crucial for cell function

Prokaryotic Metabolism: Environmental Requirements

• Need for nutrients: Energy source, carbon source, and other micronutrients

• Environmental adaptability: Can survive in various temperatures, pH levels, and salinity

• Micronutrients (Trace Elements):

  • Iron (Fe) – needed for cytochromes in electron transport

  • Boron, Chromium, Manganese – enzyme cofactors

  • Required in tiny amounts but essential for cell processes

Types of Prokaryotic Energy Sources

• Phototrophs:

  • Use light to produce ATP

  • Some use bacterial rhodopsin (not true photosynthesis)

• Chemotrophs:

  • Get energy from chemicals

  • Chemoorganotrophs – organic compounds

  • Chemolithotrophs – inorganic compounds (e.g., sulfur, iron)

• Can be aerobic or anaerobic

• Important in carbon and nitrogen cycles

Carbon Sources

• Autotrophs – use CO2

  • Photoautotrophs – energy from sunlight

  • Chemolithoautotrophs – energy from inorganic chemicals

• Heterotrophs – use organic molecules

  • Photoheterotrophs – light for energy but carbon from other organisms

  • Chemoheterotrophs – energy and carbon from organic compounds

  • Humans are chemoheterotrophs

Prokaryotes and the Carbon Cycle

• Prokaryotes help move carbon between inorganic and organic forms across land, water, atmosphere, and biomass

• CO2 removal: Plants and marine prokaryotes

• CO2 return: Respiration by chemoorganotrophs, fungi, animals

• Roles in ecosystem:

  • Producers – plants and photosynthetic bacteria

  • Consumers – animals and heterotrophs

  • Decomposers – bacteria and fungi

• In anoxic sediments, archaea produce methane, which methane-oxidizing bacteria turn back to CO2

Prokaryotes and the Nitrogen Cycle

• Nitrogen is vital for proteins and nucleic acids

• Prokaryotes recycle nitrogen through ammonia, nitrite, nitrate, and nitrogen gas

Key Steps

1. Nitrogen Fixation – converts N2 gas → ammonia (NH3)

   • Carried out by Azotobacter and Rhizobium

   • Ammonia is used by plants

2. Ammonification – decomposers release ammonia from organic nitrogen

3. Nitrification – converts NH4+ → NO2− → NO3−

   • Carried out by Nitrosomas and Nitrobacter

4. Denitrification – reverses nitrification: NO3− → N2 or N2O

   • Releases nitrogen gas back into atmosphere

Prokaryotes are key players in both carbon and nitrogen cycles

Human Bacterial Disease

• Some bacteria are pathogens, causing disease and historical plagues

• Before modern science, disease was thought to be spiritual punishment

• Epidemiologists study how diseases spread and affect populations

• Endemic disease – always present at low levels

• Epidemic – sudden rise in cases above normal

Disease History

• Infectious diseases recorded since 3000 B.C.

• Pandemics caused major declines in cities and nations

• Even today, infectious diseases are a leading cause of death worldwide

• Pathogen requirements to cause disease:

  • Must reproduce in the host

  • Must cause harm

Historical Bacterial Diseases

Plague of Athens (430 B.C.)

• Killed ¼ of Athenian troops

• Caused by Salmonella enterica serovar Typhi → typhoid fever

  • Gram-negative, rod-shaped, gamma proteobacterium

  • Symptoms: intestinal hemorrhage, high fever, delirium, dehydration

• Spread through fecal contamination

• Modern stats: 16–33 million cases annually, 200,000+ deaths

• Carriers may be asymptomatic

• Famous case: Mary Mallon (“Typhoid Mary”) infected 50+ people, 3 deaths

Bubonic Plagues

• Plague of Justinian (541-750) & Black Death (1346-1361)

  • Killed up to 50% of populations in Europe and Eastern Mediterranean

• Spread via fleas on rats

• Yersinia pestis = causative bacterium

• Symptoms: swollen lymph nodes (buboes) and tissue necrosis

• Modern treatment: antibiotics reduce mortality

• Only 1,000–3,000 cases/year today; sylvatic plague exists in American Southwest

Emerging & Re-emerging Diseases

• Emerging disease: new to a population or increasing rapidly

• Re-emerging disease: returning after a period of control

• About 75% of new diseases are zoonotic (from animals)

• Examples:

  • Zoonotic: brucellosis, necrotizing fasciitis (flesh-eating bacteria)

  • Re-emerging: tuberculosis, bubonic plague

• WHO monitors: dengue fever, yellow fever, Zika (viral); diphtheria, cholera, bubonic plague (bacterial)

• Fight against infectious disease is ongoing with no end in sight

Antibiotics and Resistance

• Antibiotics: chemicals that kill bacteria

• Overuse in humans and livestock → antibiotic resistance

• Resistant bacteria survive, reproduce, and spread resistance genes

• Leads to “superbugs” → infections harder to treat

MRSA (Methicillin-Resistant Staphylococcus aureus)

• Resistant to multiple antibiotics (methicillin, amoxicillin, penicillin, oxacillin)

• Can cause infections in:

  • Skin

  • Bloodstream

  • Lungs

  • Urinary tract

Beneficial Prokaryotes

Environmental Roles

• Most bacteria are non-pathogenic

• Decomposers: recycle atoms from dead organisms

• Photosynthesizers: fix carbon into sugars, produce oxygen

• Nitrogen fixers: convert N2 → NH3

  • Examples: Anabaena (aquatic), Rhizobium (soil)

Food Production & Biotechnology

• Ancient fermentation produced:

  • Cheese, bread, wine, beer, yogurt

• Bacteria act as biofactories:

  • Produce chemicals like insulin and antibiotics

• Used in bioremediation:

  • Remove pollutants from water, soil, air

  • Biostimulation/bioenhancement: add nutrients to encourage growth of microbes

  • Example: Exxon Valdez oil spill cleanup