Prokaryotic Diversity: Structure, Function, and Genetics

Prokaryotic Diversity

Eubacteria & Archaea

Prokaryotes, which include Eubacteria and Archaea, are among the most diverse and successful organisms on Earth. They inhabit a wide range of environments, from the human body to extreme habitats such as deep-sea vents and acidic hot springs.

The Three Domains of Life

Domain Classification

All life is classified into three domains: Bacteria, Archaea, and Eukarya. Both Bacteria and Archaea are prokaryotic, lacking a nucleus and membrane-bound organelles, while Eukarya includes all eukaryotic organisms.

• Extremophiles: Many archaea are extremophiles, thriving in environments too harsh for other organisms.

• Thermophiles: Live in hot springs and deep-sea vents.

• Halophiles: Thrive in high-salt environments (e.g., Great Salt Lake).

• Methanogens: Obligate anaerobes that produce methane; found in environments devoid of oxygen.

Diversity and Ecological Roles

Habitat and Biomass

Prokaryotes are found in nearly every habitat on Earth and have a biomass greater than that of eukaryotes. There are approximately 20,000 known species, but millions more are likely undiscovered.

• Some are pathogenic (parasitic symbiosis), while others are harmless or beneficial.

• Beneficial prokaryotes aid in digestion, vitamin production, and protection against harmful microorganisms.

• Critical for chemical recycling as decomposers in ecosystems.

• Engage in mutualistic symbioses with eukaryotes, such as mitochondria and chloroplasts (endosymbiotic theory).

Examples of Symbiosis

• Vibrio fischeri: Lives in the light organ of flashlight fish, providing bioluminescence for signaling and attracting prey; receives nutrients from the fish (mutualistic symbiosis).

• Rhizobium: Forms nodules in legume roots, fixing atmospheric nitrogen ($N_2$) into ammonia ($NH_3$) usable by plants; plants provide energy to the bacteria (mutualistic symbiosis).

Common Prokaryotic Shapes

Cell Morphology

Prokaryotes exhibit several characteristic shapes:

• Spherical (cocci)

• Rod-shaped (bacilli)

• Spiral (spirochetes)

Most prokaryotes are small (1–5 μm), but some, such as Thiomargarita namibiensis, can reach up to 0.75 mm.

Prokaryotic Structure

Cell Organization

Most prokaryotes are unicellular, though some form colonies with specialized cells (e.g., myxobacteria). Nearly all have a cell wall that provides protection, maintains shape, and prevents bursting in hypotonic environments. However, cell walls do not prevent plasmolysis in hypertonic conditions.

Prokaryotic Cell Walls

Composition and Gram Staining

• Bacterial cell walls contain peptidoglycan, a polymer of modified sugars crosslinked by short polypeptides.

• Archaeal cell walls have other polysaccharides and proteins, but no peptidoglycan.

• Gram stain distinguishes between gram positive (thick peptidoglycan layer) and gram negative (thin peptidoglycan layer and outer lipopolysaccharide membrane) bacteria.

Gram Positive vs. Gram Negative

• Gram negative bacteria are often pathogenic due to lipopolysaccharides (endotoxins) that provoke immune responses.

• The outer membrane protects against host defenses and antibiotics targeting peptidoglycan crosslinking.

Additional Cell Surface Structures

Capsules and Pili

• Capsule: Sticky polysaccharide or protein layer that helps cells adhere to surfaces, protects against dehydration and host defenses.

• Attachment pili (fimbriae): Small, numerous structures for attachment.

• Sex pili: Larger, less numerous structures used for DNA exchange during conjugation.

Motility

Movement Mechanisms

About half of bacterial species are capable of taxis, movement toward or away from stimuli (chemotaxis, phototaxis, magnetotaxis).

• Flagella: Rotate like a propeller, powered by proton motive force (PMF), not membrane-bound as in eukaryotes. Can reach speeds up to 100 μm/sec.

• Spirochetes: Move by corkscrew motion.

• Some filamentous prokaryotes glide along slime-coated threads.

Internal Structure

Genetic Material and Membranes

• No membrane-bound organelles; DNA is in the cytoplasm as a single closed circular chromosome, bundled with proteins in a nucleoid.

• Plasmids: Small, autonomously replicating DNA molecules carrying genes for fertility, antibiotic resistance, etc.

• Complex infoldings of plasma membrane house electron transport systems (ETS) and ATP synthase, similar to mitochondrial cristae.

• Cyanobacteria have thylakoid membranes for photosynthesis.

Reproduction

Binary Fission and Endospores

• Prokaryotes reproduce by binary fission, a rapid process under optimal conditions (as short as 20 minutes).

• Generation times are limited by resources and environmental factors.

• Some bacteria produce endospores: highly resistant, dormant cells that survive extreme conditions and can remain viable for centuries.

Bacillus anthracis (anthrax) and Clostridium botulinum produce endospores, making them potential biowarfare agents.

Genetic Recombination

Mechanisms of Genetic Exchange

• Transformation: Uptake of DNA from the environment; can result in new phenotypes (e.g., Griffith's experiment with pneumococcus).

• Transduction: Transfer of DNA via bacteriophages (viruses that infect bacteria).

• Conjugation: Direct transfer of DNA between cells via sex pili and a cytoplasmic mating bridge; involves F-plasmid and can result in high-frequency recombination (hfr) cells.

Conjugation & Transfer of Genetic Material

F Plasmid and R Plasmids

• Cells with F (fertility) plasmid are F+ and can form sex pilus to attach to F− cells.

• F plasmid is copied and transferred, making both cells F+.

• R plasmids carry antibiotic resistance genes, which can spread rapidly among bacteria, even across species.

Major Nutritional Modes

Energy and Carbon Sources

Prokaryotes exhibit diverse nutritional strategies, classified by their energy and carbon sources.

Mode of Nutrition	Energy Source	Carbon Source	Types of Organisms
Photoautotroph	Light	CO2	Photosynthetic prokaryotes (e.g., cyanobacteria), plants, certain protists (e.g., algae)
Chemoautotroph	Inorganic chemicals	CO2	Certain prokaryotes (e.g., Sulfolobus)
Photoheterotroph	Light	Organic compounds	Certain prokaryotes (e.g., Rhodobacter, Chloroflexus)
Chemoheterotroph	Organic compounds	Organic compounds	Many prokaryotes (e.g., Clostridium), protists, fungi, animals, some plants

Metabolic Cooperation and Biofilms

Specialized Functions and Community Living

• Some prokaryotes, such as colonial cyanobacterium Anabaena, exhibit metabolic cooperation. Specialized cells (heterocysts) fix nitrogen while others perform photosynthesis.

• Biofilms: Surface-coating colonies of prokaryotes that engage in metabolic cooperation and provide protection to the community.

Molecular Systematics and Major Bacterial Groups

Classification and Diversity

• Modern classification uses molecular systematics to group prokaryotes based on genetic similarities.

• Major bacterial groups include Proteobacteria, Chlamydias, Spirochetes, Cyanobacteria, and Gram-positive bacteria.

Additional info: Some details inferred from standard biology textbooks to clarify mechanisms and terminology.