Study Guide: Bacteria and Archaea (Campbell Biology, Chapter 27)

Bacteria and Archaea

Introduction

Prokaryotes, which include the domains Bacteria and Archaea, were the first organisms to inhabit Earth. They are single-celled organisms that have adapted to a wide range of environments, including some of the most extreme conditions on the planet. Prokaryotes are the most abundant organisms on Earth and play essential roles in ecological and evolutionary processes.

Structural and Functional Adaptations of Prokaryotes

Cell Size and Shape

• Prokaryotic cells are typically 0.5–5 μm in diameter, much smaller than most eukaryotic cells (which are usually 10–100 μm).

• Common shapes include:

  • Cocci (spherical)

  • Bacilli (rod-shaped)

  • Spirilla (spiral-shaped)

• These shapes are adaptations that can influence motility, nutrient uptake, and colonization.

Cell Wall Structure

• The cell wall maintains cell shape, protects the cell, and prevents it from bursting in hypotonic environments.

• In hypertonic environments, prokaryotes lose water and may undergo plasmolysis (shrinking of the cytoplasm away from the cell wall).

• Salt is used as a preservative because it causes water loss in prokaryotes, inhibiting their growth.

Composition of Cell Walls

• Most bacterial cell walls contain peptidoglycan, a network of sugar polymers cross-linked by polypeptides.

• Archaeal cell walls contain a variety of polysaccharides and proteins but lack peptidoglycan.

• Plant cell walls (for comparison) are made of cellulose; fungal cell walls are made of chitin.

Gram Stain and Cell Wall Types

• The Gram stain is a technique used to classify bacteria based on cell wall composition.

• Gram-positive bacteria have thick peptidoglycan layers and stain purple.

• Gram-negative bacteria have thinner peptidoglycan layers and an additional outer membrane; they stain pink/red.

• Gram-negative bacteria are generally more resistant to antibiotics because of their outer membrane.

Feature	Gram-Positive	Gram-Negative
Peptidoglycan Layer	Thick	Thin
Outer Membrane	Absent	Present
Antibiotic Resistance	Lower	Higher

Surface Structures

• Capsule: A sticky layer of polysaccharide or protein that surrounds the cell wall, aiding in adherence, protection from dehydration, and evasion of the host immune system.

• Fimbriae: Hairlike appendages that help prokaryotes stick to surfaces or each other.

• Pili (sex pili): Longer than fimbriae, these structures pull two cells together prior to DNA transfer during conjugation.

• Endospores: Metabolically inactive, highly resistant structures formed by some bacteria to survive harsh conditions.

Motility

• About half of all prokaryotes are capable of taxis, movement toward or away from a stimulus (e.g., chemotaxis for chemicals).

• Flagella are the most common structures used for movement; prokaryotic flagella differ from eukaryotic flagella in structure and mechanism.

Internal Organization and DNA

• Prokaryotes lack membrane-bound organelles and a nucleus.

• Their DNA is located in a region called the nucleoid.

• Most have a single circular chromosome; some have small rings of DNA called plasmids.

• Differences in DNA replication, transcription, and translation between prokaryotes and eukaryotes are exploited by antibiotics.

Reproduction

• Prokaryotes reproduce asexually by binary fission, often every 1–3 hours under optimal conditions.

• Key features: small size, rapid reproduction, and short generation times.

Genetic Diversity in Prokaryotes

Sources of Genetic Variation

• Rapid reproduction and large population sizes increase the chance of mutations.

• Mutation rates are low per division but accumulate quickly due to rapid reproduction.

• Genetic recombination (combining DNA from two sources) occurs via transformation, transduction, and conjugation.

• Horizontal gene transfer is the movement of genes between different species.

Mechanisms of Genetic Recombination

• Transformation: Uptake of foreign DNA from the environment.

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

• Conjugation: Direct transfer of DNA between two cells, often mediated by a pilus and requiring the F factor (fertility factor).

• Plasmids can carry genes for antibiotic resistance (R plasmids) and can be transferred between cells, spreading resistance.

Nutritional and Metabolic Adaptations

Major Nutritional Modes

Prokaryotes are classified by how they obtain energy and carbon:

Mode	Energy Source	Carbon Source	Example Organisms
Photoautotroph	Light	CO2	Cyanobacteria, plants
Chemolithoautotroph (Chemoautotroph)	Inorganic chemicals	CO2	Some prokaryotes (e.g., Sulfolobus)
Photoheterotroph	Light	Organic compounds	Some aquatic prokaryotes
Chemoheterotroph	Organic compounds	Organic compounds	Many prokaryotes, animals, fungi

Oxygen and Metabolism

• Obligate aerobes require O2 for cellular respiration.

• Obligate anaerobes are poisoned by O2 and use fermentation or anaerobic respiration.

• Facultative anaerobes can use O2 if present or switch to anaerobic metabolism if not.

Nitrogen Metabolism

• Nitrogen fixation: Some prokaryotes convert atmospheric N2 to ammonia (NH3), making nitrogen available to other organisms.

• Nitrogen is essential for amino acids and nucleic acids.

Metabolic Cooperation

• Some prokaryotes cooperate in colonies or biofilms to utilize resources more efficiently.

• In Anabaena, specialized cells called heterocysts fix nitrogen, while other cells perform photosynthesis.

• Biofilms are surface-coating colonies that facilitate nutrient sharing and protection but can cause problems such as chronic infections and industrial corrosion.

Prokaryotic Diversity and Evolution

Phylogeny and Classification

• Prokaryotes are divided into two domains: Bacteria and Archaea.

• Genomic analysis and techniques like PCR and metagenomics have revealed extensive diversity, with many species yet to be named.

• Horizontal gene transfer has played a major role in prokaryotic evolution, resulting in genomes that are mosaics of genes from different sources.

Major Groups of Bacteria

• Proteobacteria: Includes photoautotrophs, chemoautotrophs, and heterotrophs; some are pathogens (e.g., Neisseria gonorrhoeae).

• Chlamydias: Parasitic bacteria with gram-negative cell walls lacking peptidoglycan (e.g., Chlamydia trachomatis).

• Spirochetes: Helical heterotrophs, some are pathogens (e.g., Treponema pallidum causes syphilis).

• Cyanobacteria: Photoautotrophs; ancestors of chloroplasts via endosymbiosis.

• Gram-positive bacteria: Includes actinomycetes (soil decomposers), Staphylococcus, Bacillus anthracis, and Streptomyces (antibiotic producers).

Major Groups of Archaea

• Extreme halophiles: Thrive in highly saline environments.

• Extreme thermophiles: Thrive at very high temperatures.

• Methanogens: Produce methane as a metabolic by-product; obligate anaerobes found in diverse environments.

• Major clades include Euryarchaeota (halophiles, methanogens, some thermophiles) and the TACK supergroup (Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota).

• Asgard archaea: Recently discovered, closely related to eukaryotes, may provide insight into eukaryotic origins.

Characteristic	Bacteria	Archaea	Eukarya
Nuclear envelope	Absent	Absent	Present
Membrane-bound organelles	Absent	Absent	Present
Peptidoglycan in cell wall	Present	Absent	Absent
Membrane lipids	Unbranched hydrocarbons	Some branched hydrocarbons	Unbranched hydrocarbons
RNA polymerase	One kind	Several kinds	Several kinds
Initiator amino acid for protein synthesis	Formyl-methionine	Methionine	Methionine

Prokaryotes in the Biosphere

Chemical Recycling

• Prokaryotes decompose dead organisms and wastes, releasing carbon and other elements.

• Autotrophic prokaryotes produce oxygen and fix carbon; nitrogen-fixing bacteria make nitrogen available to other organisms.

Ecological Interactions

• Symbiosis: Close ecological relationship between two species; includes mutualism, commensalism, and parasitism.

• Some ecosystems, such as hydrothermal vents, depend on prokaryotes for primary production.

Prokaryotes and Humans

Beneficial Interactions

• Human intestines host hundreds of bacterial species, many of which are mutualists aiding in digestion and nutrient synthesis (e.g., Bacteroides thetaiotaomicron).

• Prokaryotes are used in food production (cheese, yogurt, fermented foods) and biotechnology (gene cloning, PCR, CRISPR-Cas9).

Pathogenic Bacteria

• Bacteria cause about half of all human diseases (e.g., tuberculosis, Lyme disease).

• Pathogenic bacteria may produce exotoxins (secreted proteins) or endotoxins (lipopolysaccharides released upon cell death).

• Horizontal gene transfer can spread virulence genes to nonpathogenic strains.

Antibiotic Resistance

• Antibiotic resistance has evolved rapidly due to overuse and misuse of antibiotics.

• Resistance genes spread quickly via horizontal gene transfer and plasmids.

• New antibiotics and alternative treatments are being developed, but resistance remains a major public health challenge.

Prokaryotes in Research and Technology

• Prokaryotes are used in genetic engineering, production of biodegradable plastics, biofuels, and bioremediation (removal of pollutants from the environment).