Chapter 16: Microbial Life: Prokaryotes and Protists

General Characteristics of Prokaryotes and Eukaryotes

• Size Comparisons:

  • Prokaryotic cells typically range from $1-5\,\mu m$ in diameter.

  • Eukaryotic cells range from $10-100\,\mu m$ in diameter.

• Biomass: The collective biomass of all prokaryotes is estimated to be at least $10$ times greater than the collective biomass of all eukaryotes.

• Environmental Range: Prokaryotes thrive in habitats that are often lethal to eukaryotes, including environments that are exceptionally cold, hot, salty, acidic, or alkaline.

• Symbiosis and Pathogenicity:

  • Pathogens: Some bacteria are pathogenic, meaning they cause disease.

  • Beneficial Bacteria: Most bacteria residing on or in the human body are benign or beneficial. Hundreds of species decompose dead skin cells, supply essential vitamins, and protect against pathogenic organisms.

  • Ecological Role: Prokaryotes in soil act as decomposers, recycling vital chemicals through ecosystems.

External Features and Morphology of Prokaryotes

• Common Shapes:

  • Cocci: Spherical cells. When they occur in chains, they are referred to as streptococci.

  • Bacilli: Rod-shaped cells. These may be filamentous (threadlike).

  • Spiral Prokaryotes: Corkscrew-shaped cells.

    • Spirilla: Short and rigid cells.

    • Spirochetes: Longer, more flexible cells.

• Cell Walls:

  • Nearly all prokaryotes possess a cell wall providing physical protection and preventing lysis in hypotonic environments.

  • Gram Stain Classification:

    • Gram-positive: Simpler cell walls with a relatively thick layer of peptidoglycan.

    • Gram-negative: More complex cell walls with less peptidoglycan; these are often more likely to be pathogenic.

• Capsules: A sticky layer composed of polysaccharides or proteins. The capsule allows the cell to adhere to substrates or other colony members and protects pathogenic species from a host's immune system.

• Appendages:

  • Flagella: Distinct from eukaryotic flagella, these enable movement.

  • Fimbriae (Pili): Hair-like projections that allow cells to attach to surfaces or each other.

Population Growth, Genetics, and Survival Strategies

• Reproduction: Prokaryotes reproduce asexually via binary fission. This process can produce a new generation within hours.

• Genetic Variation: Despite asexual reproduction, substantial genetic variation occurs via spontaneous mutations, allowing for rapid adaptation to environmental changes.

• Genetics:

  • The prokaryotic genome has approximately one-thousandth as much DNA as a eukaryotic genome.

  • The genome consists of one long, circular chromosome located in a distinct cell region.

  • Plasmids: Small, circular DNA molecules that replicate independently of the primary chromosome. These are often used for horizontal gene transfer.

• Endospores: Specialized, dormant cells produced by some prokaryotes. Endospores are capable of surviving extreme conditions, such as intense heat or cold.

Nutritional Diversity in Prokaryotes

• Energy Sources:

  • Phototrophs: Capture energy from sunlight.

  • Chemotrophs: Extract energy from chemical compounds.

• Carbon Sources:

  • Autotrophs: Use carbon dioxide ($CO_2$) as a carbon source.

  • Heterotrophs: Obtain carbon from organic compounds in other organisms.

• Combined Modes of Nutrition:

  • Photoautotrophs: Use sunlight for energy and $CO_2$ for carbon (e.g., Oscillatoria).

  • Photoheterotrophs: Use sunlight for energy and organic compounds for carbon (e.g., Rhodopseudomonas).

  • Chemoautotrophs: Extract energy from inorganic chemicals and use $CO_2$ for carbon (e.g., "rock-eating" bacteria).

  • Chemoheterotrophs: Use organic molecules for both energy and carbon (e.g., Bdellovibrio).

Biofilms and Bioremediation

• Biofilms:

  • Complex surface-coating colonies of one or more species (may include protists and fungi).

  • Microbes in biofilms communicate via chemical signals to coordinate defense and division of labor.

  • Channels facilitate nutrient distribution and waste removal.

  • Impact: Biofilms clog pipes, corrode industrial equipment, and cause medical infections.

• Bioremediation: The use of organisms to remove pollutants from soil, air, or water.

• Sewage Treatment:

  • Prokaryotes decompose organic matter in sewage plants.

  • Sludge Treatment: Anaerobic bacteria and archaea decompose solid matter.

  • Liquid Treatment: Liquid is sprayed over a rock bed coated in aerobic biofilms (bacteria and fungi) to remove dissolved organics.

Prokaryotic Phylogeny and Domains

• The Three-Domain View: Life is divided into Bacteria, Archaea, and Eukarya.

• Comparison of Domains:

  • rRNA Sequences: Bacteria have some unique to the domain; Archaea have some unique and some matching Eukarya; Eukarya have some unique and some matching Archaea.

  • RNA Polymerase: Bacteria have one kind (small/simple); Archaea and Eukarya have several kinds (complex).

  • Introns: Rare in Bacteria; present in some genes in Archaea; present in Eukarya.

  • Peptidoglycan: Present in Bacteria cell walls; absent in Archaea and Eukarya.

  • Histones: Absent in Bacteria; present in some Archaea species; present in Eukarya.

Domain Archaea

• Archaea often inhabit extreme environments:

  • Extreme Halophiles: Thrive in highly saline environments.

  • Extreme Thermophiles: Thrive in very hot water (e.g., geysers) or acidic pools.

  • Methanogens: Live in anaerobic environments (e.g., landfills, digestive tracts of cattle) and release methane ($CH_4$) as waste.

Domain Bacteria Groups

1. Proteobacteria: All are Gram-negative and share specific rRNA sequences. Includes Thiomargarita namibiensis (up to $100-300\,\mu m$ diameter, uses $H_2S$) and Rhizobium (nitrogen-fixing endosymbionts in legume root nodules).

2. Gram-Positive Bacteria: High diversity. Includes Actinomycetes in soil and Streptomyces, a source of various antibiotics.

3. Cyanobacteria: Known as "blue-green algae" (though they are not true algae). They perform plant-like, oxygen-generating photosynthesis. Some, like Anabaena, have specialized nitrogen-fixing cells.

4. Chlamydias: Obligate intracellular parasites of eukaryotic cells. Chlamydia trachomatis causes blindness and is the most common STI in the U.S.

5. Spirochetes: Helical pathogens. Examples include Treponema pallidum (syphilis) and Borrelia sp. (Lyme disease).

Bacterial Diseases and Pathogenicity

• Toxins:

  • Exotoxins: Proteins secreted into the environment; extremely powerful (e.g., Botulism, Tetanus).

  • Endotoxins: Lipid components (lipopolysaccharides) of the Gram-negative outer membrane (e.g., Salmonella, Vibrio cholerae).

• Koch’s Postulates: Criteria to prove a bacterium causes a disease:

  1. Find the bacterium in every case.

  2. Isolate and grow it in pure culture.

  3. Induce the disease in a healthy subject using the culture.

  4. Re-isolate the bacterium from the infected subject.

  • Note: Used to prove Helicobacter pylori causes peptic ulcers.

• Biological Weapons: Bacillus anthracis (anthrax), Yersinia pestis (plague), and Clostridium botulinum (the botulinum exotoxin is the deadliest poison on earth, blocking nerve signals)..

Protists: The Diversification of Eukaryotes

• Protists: Diverse collection of primarily unicellular eukaryotes that are not plants, animals, or fungi.

• Nutritional Modes:

  • Algae: Autotrophic (photosynthetic).

  • Protozoans: Heterotrophic (consume bacteria/protists).

  • Parasites: Heterotrophic (derive nutrition from living hosts).

  • Mixotrophs: Use both photosynthesis and heterotrophy (e.g., Euglena).

• Endosymbiont Theory: Proposes that mitochondria and chloroplasts originated as small prokaryotes living inside larger host cells.

  • Secondary Endosymbiosis: An autotrophic eukaryotic protist was engulfed by a heterotrophic eukaryotic protist, leading to further diversity.

Major Protist Supergroups

1. Chromalveolates:

   • Diatoms: Unicellular algae with silica (glass) walls. Fossilized remains form fossil fuels.

   • Dinoflagellates: Marine plankton; can be autotrophs, heterotrophs, or mixotrophs.

   • Brown Algae: Large multicellular autotrophs (e.g., Kelp).

   • Water Molds: Unicellular heterotrophs.

   • Ciliates: Use cilia for movement/feeding (e.g., Paramecium).

   • Parasites: Includes Plasmodium (causes malaria).

2. Rhizaria: Includes amoebas with threadlike pseudopodia.

   • Foraminiferans: Have porous calcium carbonate shells (tests).

   • Radiolarians: Mostly marine with internal silica skeletons.

3. Excavata: Grouped by molecular/morphological similarities. Many have modified mitochondria and use anaerobic glycolysis.

   • Includes Giardia intestinalis, Trichomonas vaginalis, and Trypanosoma (sleeping sickness).

4. Unikonta:

   • Amoebozoans: Have lobe-shaped pseudopodia.

   • Slime Molds:

     • Plasmodial: A single multinucleate mass called a plasmodium.

     • Cellular: Exist as solitary cells but swarm to form a slug-like aggregate when food is scarce.

5. Archaeplastids:

   • Red Algae: Multicellular, found in coral reefs; used for Nori and Agar.

   • Green Algae: Unicellular (Chlamydomonas), colonial (Volvox), or multicellular (Ulva).

   • Alternation of Generations: Features a diploid sporophyte ($2n$) and a haploid gametophyte ($1n$).

The Evolution of Multicellularity

• Multicellularity evolved independently in three lineages:

  1. Brown Algae: From chromalveolates.

  2. Fungi and Animals: From unikonts.

  3. Red and Green Algae: From archaeplastids.

• Ancestry: Evidence suggests choanoflagellates are the closest living protist relatives of animals, while nucleariids are the closest relatives of fungi.