Prokaryotes: Structure, Diversity, and Roles in the Biosphere

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Prokaryotes: Structure, Diversity, and Roles in the Biosphere

Overview of Prokaryotes

Prokaryotes are single-celled organisms classified into the domains Bacteria and Archaea. They are the most abundant and diverse organisms on Earth, thriving in a wide range of environments, including extreme conditions.

Unicellular, but some species form colonies.
Cell size: 0.5–5 µm (smaller than most eukaryotes).
Shapes: spheres (cocci), rods (bacilli), spirals.

Cell-Surface Structures

The cell wall is a critical structure for prokaryotes, maintaining cell shape, protecting against environmental stress, and preventing lysis in hypotonic environments.

Bacterial cell walls contain peptidoglycan, a network of sugar polymers cross-linked by polypeptides.
Archaeal cell walls lack peptidoglycan; instead, they contain various polysaccharides and proteins.
Eukaryotic cell walls are made of cellulose (plants) or chitin (fungi).

Gram Staining

The Gram stain is used to classify bacteria based on 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.
Gram-negative bacteria are generally more resistant to antibiotics.

Capsules and Slime Layers

Many prokaryotes have a sticky layer of polysaccharide or protein outside the cell wall.
Capsule: Dense and well-defined.
Slime layer: Less organized.
Functions: Adherence, protection from dehydration, defense against host immune system.

Endospores

Some bacteria form metabolically inactive endospores when conditions are harsh.
Endospores can survive extreme conditions for centuries.

Fimbriae and Pili

Fimbriae: Hairlike appendages for attachment.
Pili (sex pili): Longer, used for DNA exchange between cells.

Motility

About half of prokaryotes exhibit taxis, movement toward or away from stimuli (e.g., chemotaxis).

Flagella: Most common motility structure; differs from eukaryotic flagella in structure and function.
Bacterial flagella are composed of a motor, hook, and filament, evolved through exaptation.

Internal Organization and DNA

Prokaryotes lack complex compartmentalization but may have specialized membrane infoldings for metabolic functions.

DNA: One circular chromosome located in the nucleoid (no membrane).
May also have plasmids: Small, independently replicating DNA rings.
Differences in DNA replication, transcription, and translation allow antibiotics to target bacteria without harming human cells.

Reproduction and Genetic Diversity

Prokaryotes reproduce rapidly by binary fission, leading to large populations and short generation times.

Three key features: Small size, binary fission, short generation times.
Rapid reproduction and mutation promote genetic diversity.

Genetic Recombination

Genetic recombination combines DNA from two sources, increasing diversity.

Transformation: Uptake of foreign DNA from surroundings.
Transduction: DNA transfer via bacteriophages (phages).
Conjugation: DNA transfer between cells via a pilus and mating bridge.
Horizontal gene transfer: Movement of genes between different species.

F Factor and Plasmids

F factor: Required for pilus production; can be a plasmid or chromosomal segment.
F+ cells: DNA donors; F– cells: recipients.
R plasmids: Carry antibiotic resistance genes and genes for pilus formation, enabling rapid spread of resistance.

Nutritional and Metabolic Adaptations

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.

Mode	Energy Source	Carbon Source	Example
Photoautotroph	Light	CO2	Cyanobacteria
Chemoautotroph	Inorganic chemicals	CO2	Thiomargarita namibiensis
Photoheterotroph	Light	Organic compounds	Rhodobacter
Chemoheterotroph	Organic compounds	Organic compounds	Most bacteria

Role of Oxygen in Metabolism

Obligate aerobes: Require O2 for respiration.
Obligate anaerobes: Poisoned by O2; use fermentation or anaerobic respiration.
Facultative anaerobes: Can use O2 or not, depending on availability.

Nitrogen Metabolism

Nitrogen is essential for amino acids and nucleic acids.
Some prokaryotes perform nitrogen fixation: Conversion of atmospheric N2 to NH3.

Metabolic Cooperation

Prokaryotes may cooperate to use resources unavailable to individual cells.
Example: Anabaena cyanobacteria have specialized cells (heterocysts) for nitrogen fixation, while other cells perform photosynthesis.
Biofilms: Surface-coating colonies with cooperative interactions; can cause industrial and medical problems.

Diversity and Classification of Prokaryotes

Prokaryotes have radiated into diverse lineages, inhabiting every environment that supports life.

Divided into Bacteria and Archaea.
Horizontal gene transfer has played a major role in prokaryotic evolution.

Bacteria

Include most familiar prokaryotes.
Major groups:
- Proteobacteria: Gram-negative; diverse nutrition; includes pathogens (e.g., Neisseria gonorrhoeae, Vibrio cholerae).
- Chlamydias: Animal cell parasites; gram-negative, lack peptidoglycan (e.g., Chlamydia trachomatis).
- Spirochetes: Helical, gram-negative; some are pathogens (e.g., Treponema pallidum, Borrelia burgdorferi).
- Cyanobacteria: Gram-negative photoautotrophs; ancestors of plant chloroplasts.
- Gram-positive bacteria: Diverse; includes actinomycetes (soil decomposers), pathogens (Staphylococcus aureus, Bacillus anthracis).

Archaea

Share traits with both bacteria and eukaryotes; many unique features.
Extremophiles: Live in extreme environments.
- Extreme halophiles: Saline environments.
- Extreme thermophiles: High temperatures.
- Methanogens: Produce methane; obligate anaerobes.
Major clades: Euryarchaeota (halophiles, methanogens), TACK (Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota), Lokiarchaeotes (closely related to eukaryotes).

Archaeal Group	Environment	Key Features
Extreme halophiles	Saline	Tolerate/require high salt
Extreme thermophiles	High temperature	Stable DNA/proteins
Methanogens	Anaerobic	Produce methane
Lokiarchaeotes	Various	Related to eukaryotes

Prokaryotes in the Biosphere

Prokaryotes are essential for chemical recycling and ecological interactions.

Decomposers: Break down dead organisms and wastes, releasing nutrients.
Autotrophic prokaryotes: Produce sugars and O2 for other organisms.
Nitrogen-fixing bacteria: Make nitrogen available to plants.
Can immobilize nutrients by using them within their cells.

Ecological Interactions

Symbiosis: Close association between two species.
Mutualism: Both benefit.
Commensalism: One benefits, other unaffected.
Parasitism: One harms the other; pathogens cause disease.
Some ecosystems (e.g., hydrothermal vents) depend on prokaryotes.

Prokaryotes and Humans

Prokaryotes have both beneficial and harmful impacts on humans.

Mutualistic bacteria: Human intestines host hundreds of species; aid in digestion and nutrient synthesis.
Pathogenic bacteria: Cause many diseases (e.g., tuberculosis, Lyme disease).
Exotoxins: Secreted proteins causing disease (e.g., cholera).
Endotoxins: Lipopolysaccharides released when bacteria die (e.g., Salmonella).
Horizontal gene transfer can spread virulence and antibiotic resistance.

Antibiotic Resistance

Resistance has evolved rapidly since the 1940s.
Resistance genes spread quickly via horizontal gene transfer.
Drug-resistant strains of tuberculosis and other pathogens are a major concern.
New antibiotics (e.g., malacidins) and virus-like particles are being developed to combat resistance.

Prokaryotes in Research and Technology

Used in food production (cheese, yogurt, beer, wine, sauerkraut, soy sauce).
Advances in DNA technology (gene cloning, PCR, CRISPR-Cas9).
Production of biodegradable plastics (e.g., PHA).
Bioengineering for ethanol production.
Bioremediation: Removal of pollutants from soil, air, water (e.g., oil spill cleanup).

Key Terms and Concepts

Binary fission: Asexual reproduction in prokaryotes.
Plasmid: Small, circular DNA molecule.
Peptidoglycan: Structural molecule in bacterial cell walls.
Gram stain: Technique to classify bacteria.
Horizontal gene transfer: Movement of genes between species.
Biofilm: Cooperative colony of prokaryotes.
Exaptation: Evolutionary process where structures acquire new functions.

Important Equations

Nitrogen fixation:

Example: Anabaena cyanobacteria exchange carbohydrates and fixed nitrogen between specialized cells, demonstrating metabolic cooperation.

Additional info: Some content expanded for clarity and completeness, including examples and definitions of key terms.