Chapter 22 Prokaryotes: Bacteria and Archaea

History and Development of Microbiology

• Microbial Invisibility: For the vast majority of human history, prokaryotic cells remained undiscovered due to their microscopic size.

• Early Hypotheses: In 1546, Girolamo Fracastoro, an Italian physician, was among the first to suggest that diseases were caused by "unseen organisms."

• Enabling Technologies: The scientific study of microbes developed through two primary strands:

  • Microscopy: Used for the direct visualization of organisms.

  • Infectious Disease Investigations: Tracking the spread and causes of illness.

• Antony van Leeuwenhoek: He was the first individual to observe and provide an accurate description of microbial life.

• Louis Pasteur: Conducted famous experiments that refuted the long-held idea of spontaneous generation.

• Robert Koch: Known for his work on anthrax (caused by the bacterium $Bacillus\,anthracis$ ), he proposed four postulates to establish a causal relationship between a microorganism and a disease:

  1. The microorganism must be present in every case of the disease and consistently absent from healthy individuals.

  2. The suspected (putative) causative agent must be isolated from the host and grown in a pure culture.

  3. The same disease must result when the isolated, cultured microorganism is used to infect a healthy host.

  4. The same microorganism must be isolated again from the newly diseased host.

• Modern Microscopy: The development of the electron microscope allowed for the detailed study of internal cell substructures.

Prokaryotic Diversity and Habitat

• General Characteristics: Prokaryotes are the oldest, structurally simplest, and most abundant forms of life on Earth. They existed for over a billion years before the emergence of eukaryotes.

• Discovery Gap: It is estimated that between $90\%$ and $99\%$ of prokaryotic species remain unknown and undescribed. Less than $1\%$ are known to cause disease.

• Taxonomic Domains: Prokaryotes fall into two distinct domains:

  • Bacteria: Also known as Eubacteria.

  • Archaea: Formerly known as Archaebacteria. This group includes many extremophiles, which are organisms that live in extreme environments.

• Extreme Environments:

  • The Morning Glory Pool (Yellowstone National Park): This hot spring reaches very high temperatures; its vivid blue color is produced by the specific prokaryotes thriving there.

  • The Dead Sea: This is a hypersaline environment where salt-tolerant "halobacteria" (salt-loving bacteria) form bacterial mats.

• Stromatolites:

  • Living stromatolites can be found in Shark Bay, Australia.

  • Fossilized stromatolites in Glacier National Park, Montana, date back nearly $1.5 \times 10^9$ years.

• Ancient Atmosphere: Cyanobacteria found in hot springs (such as those in Yellowstone) are responsible for early oxygen production. They are often green, with color intensity increasing alongside cell density, particularly in cooler water at the edges of the stream.

Ecology and Development of Biofilms

• Biofilm Development: Biofilms are complex associations of prokaryotes that follow five distinct stages of development:

  • Stage 1 (Initial Attachment): Bacteria adhere to a solid surface through weak van der Waals interactions (forces caused by induced electrical interactions between atoms).

  • Stage 2 (Irreversible Attachment): Bacteria use hairlike appendages called pili to permanently anchor themselves to the surface.

  • Stage 3 (Maturation I): The biofilm grows via cell division and the recruitment of other bacteria. It is held together by an extracellular matrix made mostly of polysaccharides.

  • Stage 4 (Maturation II): The biofilm continues to grow, developing a complex shape.

  • Stage 5 (Dispersal): The matrix is partially broken down, and some bacteria escape to colonize new surfaces.

• Case Study: $Pseudomonas\,aeruginosa$ is frequently studied in the context of these five developmental stages.

Fundamental Differences Between Prokaryotes and Eukaryotes

• Unicellularity: Prokaryotes are single-celled organisms, whereas only eukaryotes can be multicellular. Prokaryotes may form colonies or biofilms but remain distinct individuals.

• Cell Size: Most prokaryotes are less than $1\,mm$ (specifically, usually much smaller than eukaryotes, often cited in the micrometer range).

• Nucleoid: Prokaryotic DNA is a single, circular, double-stranded molecule located in the nucleoid region, rather than a membrane-bound nucleus. They also frequently contain smaller loops of DNA called plasmids.

• Cell Division and Recombination:

  • Prokaryotes divide primarily by binary fission, which does not involve the mitosis seen in eukaryotes.

  • They exchange genetic material extensively through horizontal gene transfer rather than sexual reproduction.

• Internal Compartmentalization: Prokaryotes lack membrane-bounded organelles and a defined internal compartment.

• Ribosomes: Prokaryotic ribosomes are different in size and structure from eukaryotic ribosomes.

• Flagella: Prokaryotic flagella are simple in structure and distinct from those found in eukaryotes.

• Metabolic Diversity: Prokaryotes exhibit vast metabolic capability, including oxygenic and anoxygenic photosynthesis and chemolithotrophy (the ability to utilize energy stored in the bonds of inorganic molecules).

Structural and Molecular Classification of Bacteria

• Basic Shapes:

  • Cocci: Spherical.

  • Bacilli: Rod-shaped.

  • Spirilli: Spiral-shaped.

• Traditional Classification: Historically relied on observable phenotypes:

  1. Photosynthetic vs. nonphotosynthetic.

  2. Motile vs. nonmotile.

  3. Unicellular, colony-forming, or filamentous.

  4. Spore formation vs. transverse binary fission.

  5. Pathogenicity to humans.

• Modern Molecular Classification:

  • Amino acid sequences of key proteins.

  • Percent Guanine-Cytosine ($G+C$) content.

  • Nucleic acid hybridization (measuring base pairing between species).

  • Gene and RNA sequencing (particularly ribosomal RNA/rRNA).

  • Whole-genome sequencing.

• Bergey’s Manual of Systematic Bacteriology: The primary reference for bacterial classification; random sampling suggests the vast majority of bacteria have never been cultured or studied.

Comparing Bacteria and Archaea

• Common Ancestry: Archaea are believed to be more closely related to Eukarya than to Bacteria. An ancestor of modern Archaea is thought to have given rise to the Domain Eukarya.

• Plasma Membranes:

  • Bacteria: Lipids are unbranched and use ester bonds.

  • Archaea: Use a glycerol skeleton with ether linkages (not ester). Hydrocarbons may be branched or contain rings. Some possess tetraether polymers that form a monolayer, allowing them to withstand extreme heat.

• Cell Walls:

  • Bacteria: Possess peptidoglycan.

  • Archaea: Lack peptidoglycan but have a similar structural molecule.

• DNA Replication: Both have a single origin, but the process in Archaea is more similar to that of eukaryotes.

• Gene Expression: Archaeal enzymes used for transcription and translation are more similar to eukaryotic enzymes than bacterial ones.

Major Groups and Phyla of Prokaryotes

• Proteobacteria: A major phylum of Gram-negative bacteria divided into five classes (Alpha, Beta, Gamma, Delta, and Epsilon).

  • Gamma Proteobacteria: Includes beneficial human gut symbionts and pathogens like $Escherichia\,coli$, $Salmonella$ (food poisoning/typhoid), $Yersinia\,pestis$ (plague), $Vibrio\,cholerae$ (cholera), and $Pseudomonas\,aeruginosa$ (lung infections). Also includes sulfur-oxidizing bacteria like $Chromatium$.

  • Delta Proteobacteria: Includes $Myxobacteria$, which generate spore-forming fruiting bodies, and $Desulfovibrio\,vulgaris$ (anaerobic sulfate-reducer).

  • Epsilon Proteobacteria: Found in animal digestive tracts and deep-sea hydrothermal vents. Examples include $Campylobacter$ (blood poisoning) and $Helicobacter\,pylori$ (stomach ulcers).

• Cyanobacteria: Often called "blue-green algae." They are photosynthetic and ubiquitous. Eukaryotic chloroplasts are thought to be derived from this group. $Prochlorococcus$ is perhaps the most abundant photosynthetic organism on Earth, generating half the world's oxygen.

• Gram-positive Bacteria:

  • Low G/C: Examples include $Bacillus$ (anthrax) and $Clostridium$ (botulism, tetanus, and $C.\,difficile$ which causes diarrhea during antibiotic therapy).

  • High G/C: Examples include $Streptomyces$, the source of many antibiotics like streptomycin.

  • Mycoplasmas: The smallest known bacteria; they lack a cell wall.

• Other Groups: Includes Chlamydias and Spirochetes.

Special Internal and External Structures

• Cell Wall and Gram Stain:

  • Gram-positive: Thick peptidoglycan layer that retains purple dye.

  • Gram-negative: Thin peptidoglycan layer that does not retain purple dye; appears pink after counterstaining.

  • The cell wall maintains shape and protects against hypotonic environments.

• S-layer: A rigid paracrystalline layer found outside the peptidoglycan or outer membrane in some bacteria and Archaea; it often aids in adhesion.

• Capsule: A gelatinous outer layer that aids in attachment and protects the bacterium from the host's immune system.

• Flagella: Rigid, helical structures made of the protein flagellin; they spin like a propeller for locomotion.

• Pili: Short, hairlike structures in Gram-negative bacteria used for attachment and the process of conjugation.

• Endospores: Highly resistant, thick-walled structures containing the genome and a small amount of cytoplasm. They develop under environmental stress (especially heat) and can germinate when conditions improve. Examples: Tetanus, botulism, and anthrax.

• Internal Membranes: Invaginated regions of the plasma membrane that function in respiration or photosynthesis (e.g., carboxysomes in $Halothiobacillus\,neapolitanus$).

Prokaryotic Metabolism and Genetics

• Metabolic Categories (Carbon and Energy Source):

  • Autotrophs: Use inorganic $CO_2$.

    • Photoautotrophs: Energy from the Sun.

    • Chemolithoautotrophs: Energy from oxidizing inorganic substances.

  • Heterotrophs: Use organic molecules.

    • Photoheterotrophs: Use light for energy but must obtain organic carbon from other organisms.

    • Chemoheterotrophs: Obtain both energy and carbon from organic molecules (includes humans and many bacteria).

• Horizontal Gene Transfer (HGT): There are three types, all observed in both Bacteria and Archaea:

  • Conjugation: Requires cell-to-cell contact via a pilus. In $E.\,coli$, this involves the F plasmid (fertility factor). F+ cells transfer a copy of the plasmid to F- cells via rolling circle replication, resulting in two F+ cells.

  • Transduction: DNA transfer by bacteriophages (viruses).

  • Transformation: The uptake of DNA directly from the environment.

    • Natural Transformation: Occurs in some species when DNA from a dead cell is picked up by a live cell.

    • Artificial Transformation: Accomplished in laboratories (e.g., for molecular cloning in $E.\,coli$).

• Plasmids and Variation:

  • R (Resistance) Plasmids: Encode antibiotic resistance (e.g., in $Staphylococcus\,aerus$ / MRSA).

  • Virulence Plasmids: Encode traits for pathogenicity (e.g., $E.\,coli\,O157:H7$).

  • Auxotrophs: Nutritional mutants studied using replica plating.

Human Impact and Bacterial Diseases

• Historical Perspective: In the early 20th century, infectious diseases killed $20\%$ of children under age 5. Sanitation and antibiotics significantly improved this.

• Tuberculosis (TB): Caused by $Mycobacterium\,tuberculosis$; it affects the respiratory system and is easily transmitted through the air. Multidrug-resistant (MDR) strains are a major concern.

• Dental Caries: Plaque is a biofilm. $Streptococcus\,sobrinus$ ferments sugar into lactic acid, causing tooth enamel degeneration.

• Peptic Ulcers: Primarily caused by $Helicobacter\,pylori$ and treated with antibiotics.

• The Great Plague of London: Caused by $Yersinia\,pestis$; killed approximately $200,000$ people ($20\%$ of the city). Transmitted by fleas from rodents.

• Lyme Disease: Caused by the spirochete $Borrelia$. Transmitted by ticks from mice/deer. Named after Lyme, Connecticut (1995 outbreak), but found in "Ötzi the Iceman" from $5,300$ years ago.

• E. coli Outbreak (Germany, 2011): Strain $O104:H4$ from organic vegetable sprouts killed $32$ people and sickened $3,800$. It produces Shiga toxin, which inhibits protein synthesis, destroys red blood cells, and can lead to kidney failure ($845$ patients).

Beneficial Roles of Prokaryotes

• Environment: Decomposers release atoms from dead organisms back into the environment.

• Fixation:

  • Carbon Fixation: Photosynthesizers turn $CO_2$ into sugars.

  • Nitrogen Fixation: Reducing $N_2$ to $NH_3$ (ammonia). Examples: $Anabaena$ (aquatic) and $Rhizobium$ (soil/plant roots).

• Biotechnology and Food: Used in early biotechnology to produce cheese, wine, beer, bread, and yogurt. Modern "biofactories" produce insulin and antibiotics.

• Bioremediation: Using microbes to remove pollutants from the air, water, and soil (e.g., cleaning the Exxon Valdez oil spill).

• Symbiosis:

  • Mutualism: Both benefit (e.g., nitrogen-fixing bacteria on roots; cellulose-producers in animal guts).

  • Commensalism: One benefits, the other is unaffected.

  • Parasitism: One benefits, the other is harmed.