CH.27: Bacteria and Archaea

Overview of Prokaryotes

Prokaryotes, comprising the domains Bacteria and Archaea, are single-celled organisms that thrive in diverse and extreme environments. They are the most abundant organisms on Earth, capable of reaching huge population sizes due to their unique structural and functional adaptations.

• Adaptation: Prokaryotes are found in environments ranging from hot springs to deep-sea vents.

• Abundance: Their rapid reproduction and mutation rates contribute to their evolutionary success.

Structural and Functional Adaptations

Prokaryotes were the first organisms to inhabit Earth. Most are unicellular, though some form colonies. Their cells are typically 0.5–5 µm, much smaller than eukaryotic cells (10–100 µm), and exhibit a variety of shapes:

• Cocci: Spherical

• Bacilli: Rod-shaped

• Spirals: Spiral-shaped

Cell Wall Composition

• Bacterial cell walls: Contain peptidoglycan, a network of sugar polymers cross-linked by polypeptides.

• Archaeal cell walls: Composed of polysaccharides and proteins, lacking peptidoglycan.

• Eukaryotic cell walls: Made of cellulose or chitin.

• Gram stain: Used to classify bacteria by cell wall composition.

• Gram-positive bacteria: Thick peptidoglycan layer, simpler walls.

• Gram-negative bacteria: Thin peptidoglycan layer, complex walls with an outer membrane containing lipopolysaccharides.

Capsules and Slime Layers

Many prokaryotes have a sticky layer of polysaccharide or protein surrounding the cell wall, called a capsule (dense and well-defined) or slime layer (not well organized). These structures:

• Enable adherence to substrates or other cells

• Prevent dehydration

• Protect against the host’s immune system

Endospores

Some bacteria form metabolically inactive endospores when water or nutrients are lacking. The cell copies its chromosome and surrounds it with a multilayered structure, allowing survival in extreme conditions for centuries.

Fimbriae and Pili

• Fimbriae: Hairlike appendages for adherence to substrates or other cells.

• Pili (sex pili): Longer appendages used to pull cells together for DNA exchange.

Motility and Flagella

About half of prokaryotes exhibit taxis, moving toward or away from stimuli (e.g., chemotaxis). Flagella are the most common structures for movement, either scattered or concentrated at cell ends.

• Bacterial flagella: Composed of motor, hook, and filament; evolved through exaptation.

Internal Organization and DNA

Prokaryotic cells lack complex compartmentalization but may have specialized membranes for metabolic functions (e.g., infoldings of the cell membrane).

• DNA: One circular chromosome located in the nucleoid (no membrane).

• Plasmids: Small rings of independently replicating DNA.

Genetic Diversity in Prokaryotes

Rapid Reproduction, Mutation, and Genetic Recombination

Three factors contribute to high genetic diversity:

1. Rapid reproduction: Binary fission allows division every 1–3 hours under optimal conditions.

2. Mutation: Low rates, but accumulate rapidly due to short generation times and large populations.

3. Genetic recombination: Combining DNA from two sources via transformation, transduction, or conjugation.

Transformation

Prokaryotic cells incorporate foreign DNA from their surroundings, potentially acquiring new traits (e.g., pathogenicity).

Transduction

Bacteriophages (viruses that infect bacteria) transfer prokaryotic genes from one host cell to another, usually as an unintended result of the phage replicative cycle.

Conjugation and Plasmids

• Conjugation: DNA transfer between two prokaryotic cells, typically one-way.

• Pilus: Attaches donor to recipient, retracts to bring cells together, DNA transferred via "mating bridge".

• F factor: Required for pilus production, can exist as plasmid or chromosomal segment.

R Plasmids and Antibiotic Resistance

• R plasmids: Carry resistance genes, often for multiple antibiotics.

• Enable rapid spread of resistance via horizontal gene transfer.

Diversity of Nutritional and Metabolic Adaptations

Energy and Carbon Sources

Prokaryotes are classified by how they obtain energy and carbon:

• Phototrophs: Energy from light

• Chemotrophs: Energy from chemicals

• Autotrophs: Carbon from CO2 or related compounds

• Heterotrophs: Carbon from organic nutrients

Role of Oxygen in Metabolism

• Obligate aerobes: Require O2 for cellular respiration

• Obligate anaerobes: Poisoned by O2, use fermentation or anaerobic respiration

• Facultative anaerobes: Can use O2 or carry out fermentation/anaerobic respiration

Nitrogen Metabolism

• Nitrogen fixation: Conversion of atmospheric N2 to ammonia (NH3)

• Essential for amino acid and nucleic acid production

Metabolic Cooperation

Prokaryote cells may cooperate to use resources unavailable to individual cells. In Anabaena, cells specialize for nitrogen fixation (heterocysts) or photosynthesis, exchanging nutrients.

Biofilms

Cells of one or more prokaryote species cooperate to form surface-coating colonies called biofilms.

• Cells secrete sticky proteins and polysaccharides

• Channels allow nutrient and waste transport

• Biofilms cause corrosion, contamination, tooth decay, and chronic infections

Diversity and Evolution of Prokaryotes

Lineages and Phylogeny

Prokaryotes date back 3.5 billion years and inhabit every environment supporting life. Genetic analysis divides prokaryotes into Bacteria and Archaea. Horizontal gene transfer has played a key role in their evolution, resulting in mosaic genomes.

Major Groups of Bacteria

• Proteobacteria: Gram-negative, includes photoautotrophs, chemoautotrophs, heterotrophs, and pathogens.

• Chlamydias: Parasitize animal cells, gram-negative, lack peptidoglycan.

• Spirochetes: Helical, gram-negative, free-living or pathogenic.

• Cyanobacteria: Gram-negative photoautotrophs, likely ancestors of plant chloroplasts.

• Gram-positive bacteria: Diverse, includes pathogens and soil decomposers.

Archaea

Archaea share traits with both bacteria and eukaryotes.

• Extremophiles: Live in extreme environments (halophiles, thermophiles).

• Methanogens: Obligate anaerobes producing methane.

• TACK supergroup: Includes Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota.

• Lokiarchaeotes: Closely related to eukaryotes, may shed light on eukaryotic origins.

Prokaryotes in the Biosphere

Ecological Roles

Prokaryotes are essential for recycling chemical elements between living and nonliving components.

• Decomposers: Break down dead organisms and wastes, releasing carbon and other elements.

• Autotrophs: Produce sugars and O2 consumed by other organisms.

• Nitrogen-fixers: Transform atmospheric nitrogen into usable forms.

Ecological Interactions

• Symbiosis: Close relationship between two species (mutualism, commensalism, parasitism).

• Mutualism: Both organisms benefit.

• Commensalism: One benefits, other unaffected.

• Parasitism: Parasite harms host, often causing disease (pathogens).

Prokaryotes and Humans

Beneficial and Harmful Impacts

• Mutualistic bacteria: Human intestines host 500–1,000 species, aiding digestion and nutrient synthesis.

• Pathogenic bacteria: Cause about half of all human diseases (e.g., tuberculosis, Lyme disease).

• Exotoxins: Proteins secreted by bacteria causing disease even if bacteria are absent.

• Endotoxins: Lipopolysaccharide components released when bacteria die.

• Antibiotic resistance: Rapid evolution and horizontal gene transfer spread resistance genes.

Prokaryotes in Research and Technology

• Food production: Cheese, yogurt, beer, wine, fermented foods.

• DNA technology: E. coli used in gene cloning; DNA polymerase from Pyrococcus furiosus used in PCR.

• CRISPR-Cas9: Gene editing tool derived from prokaryotic defense systems.

• Bioplastics: Bacteria synthesize PHA, used for biodegradable plastics.

• Biofuel production: Engineering bacteria to produce ethanol from agricultural waste.

• Bioremediation: Use of bacteria to remove pollutants (e.g., oil spills).

Summary Table: Comparison of the Three Domains of Life

Additional info: This table summarizes key differences among the three domains, highlighting structural and molecular distinctions.