Prokaryotes: Bacteria and Archaea

Three Domains of Life

The classification of life is based on cellular structure and genetic differences, resulting in three domains: Bacteria, Archaea, and Eukarya. Prokaryotes include Bacteria and Archaea, while Eukarya encompasses plants, fungi, animals, and protists.

Prokaryotic Diversity and Abundance

Prokaryotes are found in nearly every environment, including extreme conditions. Their small size (0.5–5 µm) is offset by their vast numbers and rapid reproduction, which allows for quick evolution and adaptation.

Prokaryotic Cell Structure

Cell Shapes

Prokaryotic cells exhibit three main shapes:

• Cocci: Spherical

• Bacilli: Rod-shaped

• Spirillum: Spiral

Cell Wall Composition

Nearly all prokaryotes have a cell wall that maintains shape, protects the cell, and prevents lysis in hypotonic environments. The composition differs between domains:

• Bacterial cell walls contain peptidoglycan, a polymer of sugars and amino acids.

• Archaean cell walls lack peptidoglycan and instead contain polysaccharides and proteins.

• Eukaryotic cell walls (plants/fungi) are made of cellulose or chitin.

Gram Staining and Bacterial Classification

The Gram stain is used to classify bacteria based on cell wall structure:

• Gram-positive bacteria: Thick peptidoglycan layer, stain blue/purple.

• Gram-negative bacteria: Thin peptidoglycan layer and an outer membrane, stain red/pink. The outer membrane can be toxic and contributes to antibiotic resistance.

Prokaryotic Adaptations

Endospores

Some bacteria, especially Gram-positive species, form endospores—dormant, resistant cells that survive extreme conditions. Endospores can remain viable for centuries and are resistant to heat, drying, and chemicals.

Motility and Taxis

Many prokaryotes move using flagella, which are structurally different in bacteria, archaea, and eukaryotes. Motile bacteria exhibit taxis, moving toward or away from stimuli (e.g., chemotaxis).

• Chemoattractant: Movement toward a chemical stimulus.

• Chemorepellent: Movement away from a chemical stimulus.

Cell Surface Structures

Prokaryotes may have additional structures such as capsules (protection and adhesion), fimbriae (attachment), and pili (DNA transfer).

Genetic Organization and Variation

Prokaryotic Genome

Prokaryotes have a smaller genome than eukaryotes, typically consisting of a single circular chromosome located in the nucleoid region. They may also possess plasmids, which are small, circular DNA molecules carrying non-essential genes (e.g., antibiotic resistance).

• Binary fission: Asexual reproduction method; rapid division leads to quick accumulation of mutations.

• Genetic diversity arises from rapid reproduction, mutation, and horizontal gene transfer (transformation, transduction, conjugation).

*Additional info: Horizontal gene transfer allows prokaryotes to acquire genes from unrelated species, contributing to their adaptability and evolution.*

Antibiotic Resistance

Mechanisms and Impact

Genes for antibiotic resistance are often carried on R plasmids. Antibiotic-resistant bacteria survive treatment and pass resistance genes to offspring, leading to increased prevalence of resistant strains.

*Additional info: Natural selection favors bacteria with resistance traits in environments exposed to antibiotics.*

Metabolic Diversity

Nutritional Types

Prokaryotes are classified by how they obtain energy and carbon:

• Autotrophs: Use inorganic carbon (CO2) as a carbon source.

• Heterotrophs: Require organic nutrients (e.g., glucose) as a carbon source.

*Additional info: Prokaryotes display diverse metabolic pathways, including photosynthesis, chemosynthesis, and fermentation.*

Metabolic Cooperation

Some prokaryotes form colonies (biofilms) and cooperate metabolically. For example, cyanobacteria exchange products between photosynthetic and nitrogen-fixing cells.

*Additional info: Biofilms facilitate nutrient exchange and waste removal among different species.*

Oxygen and Nitrogen Metabolism

Prokaryotes vary in their oxygen requirements:

• Obligate aerobes: Require O2 for respiration.

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

• Facultative anaerobes: Can survive with or without O2.

Some prokaryotes perform nitrogen fixation, converting atmospheric N2 to ammonia (NH3), which is essential for amino acid and nucleic acid synthesis.

Prokaryotic Diversity and Evolution

Phylogeny and Horizontal Gene Transfer

Genomic studies reveal extensive diversity among prokaryotes. Horizontal gene transfer has played a significant role in their evolution, allowing gene acquisition from distantly related species.

*Additional info: The TACK supergroup within Archaea is closely related to eukaryotes, providing insight into the origin of eukaryotic cells.*

Ecological Roles of Prokaryotes

Decomposition and Nutrient Cycling

Prokaryotes are essential decomposers, recycling nutrients such as nitrogen, phosphorus, and potassium. Cyanobacteria contribute to atmospheric O2 production and carbon fixation.

Symbiotic Relationships

Prokaryotes engage in various symbiotic relationships:

• Commensalism: One organism benefits, the other is unaffected.

• Mutualism: Both organisms benefit (e.g., Rhizobium in legume roots).

• Parasitism: One organism benefits at the expense of the other; pathogens cause disease.

*Additional info: Over 150 bacterial species live on the human body, many as commensals or mutualists.*

Prokaryotes and Human Health

Beneficial and Harmful Impacts

Human intestines host hundreds of bacterial species, many of which aid digestion and nutrient absorption. Pathogenic bacteria cause diseases by releasing exotoxins or endotoxins.

*Additional info: E. coli is a common mutualist in mammalian intestines, while Lyme disease is caused by a spirochete bacterium.*

Prokaryotes in Research and Technology

Bioremediation and Biotechnology

Prokaryotes are used in bioremediation to remove pollutants and in biotechnology to produce plastics, vitamins, antibiotics, hormones, and biofuels. They are also involved in food production (e.g., cheese, yogurt, fermented foods).

*Additional info: Engineered bacteria can produce insulin and other medically important proteins.* ----------------------------------------