Ch. 26: Bacteria and Archaea

Introduction to Bacteria and Archaea

Bacteria and Archaea are two of the three domains of life, both consisting of unicellular, prokaryotic organisms. Despite their similarities, they differ significantly in cell structure, molecular machinery, and evolutionary history.

• Unicellular & Prokaryotic: Both domains lack a nucleus and membrane-bound organelles.

• Cell Wall & Membrane Differences:

  • Bacteria: Have a plasma membrane similar to eukaryotes and a unique cell wall made of peptidoglycan.

  • Archaea: Possess unique phospholipids in their plasma membrane (isoprenes instead of fatty acids) and cell walls made of different polysaccharides (not peptidoglycan).

• Molecular Machinery:

  • Bacteria: Unique DNA polymerases, 70S ribosomes, and "naked" DNA (no histones).

  • Archaea: DNA polymerases and ribosomes more similar to eukaryotes (80S ribosomes), and DNA associated with histone proteins.

Key similarities: Both have cell walls (of different composition) and a phospholipid bilayer plasma membrane.

Why Study Bacteria and Archaea?

Bacteria and Archaea are ancient, abundant, and ecologically vital. They are found in nearly every environment on Earth and play crucial roles in global cycles and human health.

• Biological Impact:

  • Oldest known fossils (~3.7 billion years ago); only life forms for over 1.8 billion years.

  • Extremely abundant: >5 x 1030 alive today, containing half of all carbon and most nitrogen and phosphorus.

  • Ubiquitous: Found in diverse habitats, including extreme environments (anaerobic, hot springs, deep-sea vents, Antarctic ice, salt flats, deep rock).

• Extremophiles: Prokaryotes that thrive in extreme conditions (high temperature, salinity, pressure, or low pH). Studying them helps us understand the origin of life, search for extraterrestrial life, and develop commercial applications (e.g., Taq polymerase for PCR).

• Medical Importance:

  • Pathogens: Disease-causing microbes. Most bacterial pathogens are in Domain Bacteria; only one known archaeal pathogen.

  • Koch’s Postulates: Four criteria to link a specific microbe to a disease:

    1. Microbe present in all cases of the disease, absent in healthy individuals.

    2. Isolate and culture the microbe.

    3. Inoculate a healthy host; disease should appear.

    4. Re-isolate the same microbe from the newly diseased host.

  • Germ Theory of Disease: Infectious diseases are caused by transmission and reproduction of certain bacteria and viruses. Foundation for modern medicine and sanitation.

  • Virulence: The ability to cause disease, often due to specific genes (e.g., E. coli strains with toxin genes).

  • Antibiotics: Molecules that kill or inhibit bacteria, discovered in 1928 (penicillin). Overuse has led to antibiotic resistance, a major medical challenge.

• Bioremediation: Use of prokaryotes to degrade environmental pollutants. Strategies include fertilizing sites to encourage natural decomposers and "seeding" with specific species.

How Do Biologists Study Bacteria and Archaea?

• Enrichment Cultures: Growing microbes under specific conditions to isolate particular species.

• Metagenomics: Analyzing DNA from environmental samples to identify species that cannot be cultured. Based on sequencing specific genes.

• Human Microbiome: The collection of microbes living in and on the human body (e.g., gut, skin, mouth). Benefits include digestion, synthesis of vitamins and amino acids, and even influencing mood.

Themes in the Diversification of Bacteria and Archaea

Morphological Diversity

Bacteria and Archaea display a wide range of sizes, shapes, and structural features.

• Size: Most are ~1 μm in diameter, but range from 0.5 μm to 0.1 mm.

• Shape:

  • Coccus: Spherical (single, diplo-, strepto- (chains), staphylo- (clusters)).

  • Bacillus: Rod-shaped (single or chains).

  • Spirillum: Spiral or corkscrew-shaped.

  • Filamentous: Long, thread-like (e.g., some cyanobacteria).

• Motility: Some are motile via flagella or gliding.

• Cell Wall Structure:

  • Gram-positive: Thick peptidoglycan wall, stains bluish-purple.

  • Gram-negative: Thin peptidoglycan wall plus outer phospholipid bilayer, stains reddish-pink.

• Capsules: Thick gel-like layer outside cell wall, common in pathogens.

• Endospores: Tough, dormant structures for survival under harsh conditions (resist heat, radiation, antibiotics).

Variation in Reproduction

• Asexual Reproduction: Binary fission produces genetically identical daughter cells.

• Genetic Variation: Mainly from mutations, but also from:

  • Conjugation: DNA transfer via sex pilus (plasmid transfer).

  • Transduction: DNA transfer by viruses.

  • Transformation: Uptake of DNA from the environment.

Metabolic Diversity

Prokaryotes exhibit remarkable diversity in how they obtain energy and carbon, far exceeding that of eukaryotes.

• Energy Sources for ATP Production:

  • Phototrophs: Use light energy.

  • Chemoorganotrophs: Use organic molecules (e.g., sugars).

  • Chemolithotrophs: Use inorganic molecules (e.g., NH3, CH4).

• Carbon Sources:

  • Autotrophs: Use CO2 or CH4 to build organic molecules (carbon fixation).

  • Heterotrophs: Use preformed organic molecules from the environment.

• Cellular Respiration: Prokaryotes use a variety of electron donors (H2, H2S, NH3, CH4) and acceptors (SO42-, NO3-, CO2, Fe3+), unlike eukaryotes which use sugars and O2.

• Fermentation: Prokaryotes can ferment a wide range of substrates, not just glucose.

• Photosynthesis: Some prokaryotes use H2O as an electron source (oxygenic), others use H2S or Fe2+ (anoxygenic). They possess diverse pigments for absorbing light.

Ecological Diversity and Global Impacts

• Oxygen Revolution:

  • For the first 2.3 billion years, Earth's atmosphere lacked free O2.

  • Cyanobacteria were the first oxygenic photosynthesizers (~2.7 billion years ago), producing O2 as a byproduct.

  • O2 enabled aerobic respiration, multicellularity, and large body size.

• Nitrogen Fixation and the Nitrogen Cycle:

  • Nitrogen is essential for proteins and nucleic acids, but most organisms cannot use atmospheric N2 due to its triple bond.

  • Usable forms: Ammonia (NH3), nitrate (NO3-).

  • Nitrogen fixation: Conversion of N2 to NH3 by the enzyme nitrogenase (requires anaerobic conditions), found only in select prokaryotes.

  • Examples:

    • Rhizobium: Terrestrial, mutualistic in legume root nodules.

    • Anabaena: Aquatic cyanobacterium, fixes nitrogen in heterocysts.

  • Other bacteria complete the nitrogen cycle (e.g., nitrification, denitrification).

  • Nitrogen pollution: Excess fertilizer leads to nitrate runoff, causing algal blooms and dead zones in aquatic systems.

Key Terms and Definitions

• Prokaryote: Unicellular organism lacking a nucleus and membrane-bound organelles.

• Extremophile: Organism that thrives in extreme environmental conditions.

• Pathogen: Disease-causing organism.

• Virulence: The degree to which a pathogen can cause disease.

• Antibiotic: Substance that kills or inhibits the growth of bacteria.

• Bioremediation: Use of organisms to remove or neutralize pollutants.

• Enrichment Culture: Laboratory technique to grow specific microbes by providing optimal conditions.

• Metagenomics: Study of genetic material recovered directly from environmental samples.

• Microbiome: The community of microorganisms living in a particular environment, such as the human body.

• Binary Fission: Asexual reproduction in prokaryotes, producing two identical cells.

• Conjugation: Transfer of genetic material between bacteria via direct contact.

• Transduction: Transfer of bacterial genes by viruses.

• Transformation: Uptake of free DNA from the environment by bacteria.

• Phototroph: Organism that uses light as an energy source.

• Chemoorganotroph: Organism that uses organic molecules for energy.

• Chemolithotroph: Organism that uses inorganic molecules for energy.

• Autotroph: Organism that synthesizes its own organic molecules from CO2 or CH4.

• Heterotroph: Organism that obtains organic molecules from the environment.

• Oxygenic Photosynthesis: Photosynthesis that produces O2 as a byproduct.

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

• Nitrogenase: Enzyme complex that catalyzes nitrogen fixation.

Table: Comparison of Bacteria and Archaea

Table: Bacterial Shapes and Arrangements

Key Equations

• Photosynthesis (oxygenic):

• Nitrogen Fixation:

Summary

• Bacteria and Archaea are ancient, diverse, and essential to Earth's ecosystems.

• They differ in cell structure, molecular machinery, and ecological roles.

• Prokaryotes exhibit remarkable metabolic and morphological diversity, enabling them to inhabit nearly every environment.

• They play key roles in global cycles (carbon, nitrogen) and have significant medical and industrial importance.