Prokaryotes and Microbial Diversity: Bacteria, Archaea, and Pathogens

Prokaryotes

The oldest and most abundant form of life on Earth, existing for over 3.8 billion years.

Bacteria

One of the two domains of prokaryotes.

Archaea

The second domain of prokaryotes.

Nucleus

Prokaryotes do not have a nucleus; their genetic material is located in a single, circular chromosome within a nucleoid region.

Membrane-bound organelles

Prokaryotes lack membrane-bound organelles; processes like energy production occur in the cytoplasmic membrane.

Binary fission

The method of cell division in prokaryotes that produces genetically identical offspring.

Size of Prokaryotes

Most prokaryotes measure 0.5-5 micrometers.

Diverse metabolism

Prokaryotes are capable of photosynthesis, respiration, or fermentation under varied conditions.

Classification

Based on phenotypic and genotypic traits, with modern classification relying heavily on rRNA sequences and molecular data.

Species

A group of organisms that share high genetic similarity and common characteristics, e.g., Escherichia coli.

Subspecies

Minor genetic or physiological variation, e.g., Bacillus subtilis subsp. spizizenii.

Strain

Specific isolate or variant of a species, e.g., E. coli K-12 vs E. coli O157:H7.

Serotype

Differ by surface antigens, e.g., Salmonella enterica serovar Typhi.

Coccus

Spherical prokaryotes that may appear alone or in clusters.

Bacillus

Rod-shaped prokaryotes that are cylindrical and often longer than wide.

Vibrio

Curved rod-shaped prokaryotes that are slightly curved or comma-shaped.

Spirillum

Rigid spiral-shaped prokaryotes with external flagella.

Spirochete

Flexible spiral-shaped prokaryotes with internal axial filaments.

Pleomorphic

Prokaryotes with variable shape depending on the environment.

Diplococci

Cocci that appear in pairs.

Streptococci

Cocci that appear in chain-like formations.

Tetrads

Cocci that appear in groups of four.

Sarcinae

Cocci that appear in cubelike groups of eight.

Staphylococci

Cocci that appear in grapelike clusters.

Bacilli

Rod-shaped bacteria that divide across their short axis.

Single bacillus

A single rod-shaped bacterium.

Diplobacillus

Bacilli that occur in pairs after division.

Streptobacilli

Bacilli that form chain-like arrangements.

Coccobacillus

Bacilli that are oval and resemble cocci.

Palisades

Cells of a chain that remain partially attached by a small hinge region at the ends.

Spiral bacteria

Bacteria that have one or more twists.

Spirillum/Spirilla

Bacteria with a slightly curled or spiral-shaped body.

Monomorphic

Most bacteria that maintain a single shape.

Pleomorphism

Variations in cell wall structure caused by slight genetic or nutritional differences.

Prokaryotic Cell

Cells that lack a nucleus and histones, have a unique cell wall makeup, and lack membrane-bound organelles.

Cell Envelope

Includes all layers surrounding the cytoplasm: cytoplasmic membrane, cell wall, and outer membrane (in Gram-negative bacteria).

Cytoplasmic Membrane

A selectively permeable barrier that controls what enters and leaves the cell, made of a phospholipid bilayer with embedded proteins.

Gram-Positive Bacteria

Bacteria with a thick peptidoglycan layer (20-80 nm) and no outer membrane.

Gram-Negative Bacteria

Bacteria with a thin peptidoglycan layer (2-7 nm) and an outer membrane containing lipopolysaccharide (LPS).

Lipopolysaccharide (LPS)

An endotoxin found in the outer membrane of Gram-negative bacteria that acts as a powerful antigen and can trigger strong immune responses.

Acid-Fast Bacteria

Bacteria with atypical cell walls that have a peptidoglycan layer surrounded by a thick coat of waxy mycolic acids, making them extremely resistant to drying, disinfectants, and many antibiotics.

Acid-fast stain

A staining technique used for bacteria with waxy layers that prevent standard Gram staining.

Mycobacterium tuberculosis

A bacterium that causes tuberculosis.

Mycoplasma

A type of prokaryote that lacks a cell wall, making it resistant to antibiotics like penicillin.

Mycoplasma pneumoniae

A bacterium that causes atypical or 'walking' pneumonia.

L-forms

Prokaryotes that have a temporary or permanent loss of the cell wall.

Pseudomurein

A wall material found in Archaea that is similar but chemically distinct from peptidoglycan.

S-layers

Crystalline sheets of protein or glycoprotein that form the outermost cell covering in many prokaryotes.

Glycocalyx

A sticky layer of polysaccharide and protein outside the cell wall, existing in capsule and slime layer forms.

Capsule

A well-organized and firmly attached form of glycocalyx.

Fimbriae

Hair-like structures that help bacteria adhere to surfaces.

Pili

Structures that facilitate genetic exchange between bacteria.

Flagella

Long, whip-like structures that provide motility to bacteria.

Axial filaments

Specialized structures that enable movement or communication in certain prokaryotes.

Alcohol-based compounds

Substances that can dissolve lipids in the outer membrane of Gram-negative bacteria, damaging the cell.

External structures

Extensions or coatings that project from or surround the cell wall in many bacteria and archaea.

Polysaccharides

Carbohydrates that can be part of the cell wall materials in Archaea.

Glycoproteins

Proteins that can be part of the wall materials in Archaea.

S-layers in Archaea

Often the only wall structure in Archaea, providing rigidity and osmotic protection in extreme environments.

Slime Layer

A loose and irregular form of glycocalyx.

Functions of Glycocalyx

Prevents desiccation, shields cells from phagocytosis, promotes adhesion, and starts biofilm formation.

Conjugation Pili

Pili that connect cells for DNA transfer.

Flagellum

A structure with three distinct parts: filament, hook (sheath), and basal body.

Polar Arrangement of Flagella

Flagella attached at one or both ends of the cell.

Monotrichous

A flagellar arrangement with a single flagellum.

Lophotrichous

A flagellar arrangement with small bunches or tufts of flagella emerging from the same site.

Amphitrichous

A flagellar arrangement with flagella at both poles of the cell.

Peritrichous Arrangement

Flagella are dispersed randomly over the surface of the cell.

Movement (Motility)

Powered by rotating flagella acting like tiny propellers.

Run

Flagella rotate in one direction, causing the cell to move straight.

Tumble

Rotation reverses, causing the cell to reorient.

Chemotaxis

Directed movement in response to chemical signals.

Attractants

Nutrients that cause longer runs and fewer tumbles.

Repellents

Toxins that increase tumbles and random reorientation.

Periplasmic Flagella

Internal flagellum enclosed in the space between the cell wall and the cytoplasmic membrane.

Spirochetes

Corkscrew-shaped bacteria with a wriggly mode of locomotion caused by periplasmic flagella.

Sex Pilus

Forms a bridge between bacterial cells for DNA transfer during conjugation.

Type IV Pili

Pili that extend and retract for twitching or gliding movement and aid in adhesion and biofilm formation.

Nanotubes

Structures that connect neighboring cells to exchange nutrients, waste products, or signals.

Archaella

Archaeal motility structures that rotate for movement, similar in function to bacterial flagella but made of different proteins.

Hami

Grappling-hook-like appendages in some archaea used for strong surface attachment.

Internal Organization of Prokaryotic Cells

Prokaryotic cells lack membrane-bound organelles but maintain high internal organization.

Cytoplasm

The gel-like matrix that fills the cell interior, composed mostly of water, along with enzymes, ions, ribosomes, and macromolecules.

Nucleoid

Region containing the bacterial chromosome, a single, circular molecule of DNA, not surrounded by a membrane.

Plasmids

Small, circular DNA molecules separate from the main chromosome that carry nonessential genes providing advantages such as antibiotic resistance or virulence traits.

Ribosomes

Sites of protein synthesis composed of rRNA and protein subunits (30S + 50S = 70S ribosome), smaller than eukaryotic (80S) versions.

Inclusions

Specialized internal structures for storage and adaptation that allow cells to conserve energy and resources for changing conditions.

Glycogen or Starch Granules

Types of inclusions that serve as carbon and energy storage.

Polyphosphate Granules

Inclusions that store phosphate for ATP and nucleic acids.

Sulfur Granules

Energy source for sulfur-oxidizing bacteria.

Lipid Inclusions

Long-term energy reserves in prokaryotic cells.

Gas Vesicles

Structures that confer buoyancy and allow cells to position themselves in regions of the water column that best suit their metabolisms.

Magnetosomes

Inclusions that contain magnetite particles, allowing cells to align with Earth's magnetic field.

Endospores

Dormant, highly resistant cell forms produced by some Gram-positive bacteria, serving as survival structures.

Germination

The process of an endospore converting back to a vegetative cell rapidly.

Cytoskeleton

A structure in prokaryotic cells that maintains cell shape, aids cell division, and organizes internal contents.

Methanogens

Major group of Archaea that produce methane.

Halophiles

Major group of Archaea that thrive in high salt concentrations.

Thermophiles

Major group of Archaea that thrive in extreme and moderate temperatures.

Microbial Dark Matter

The portion of archaeal diversity that remains uncultured.