Bacteria and Archaea:

Pre-Lecture Questions

  • Q1 (Gram Staining order): Which order reflects the correct procedure for Gram staining?

    • A. Alcohol/acetone – crystal violet – safranin – iodine

    • B. Crystal violet – alcohol/acetone – iodine – safranin

    • C. Crystal violet – iodine – alcohol/acetone – safranin

    • D. Iodine – safranin – crystal violet – alcohol/acetone

    • E. Alcohol/acetone – safranin – crystal violet – iodine

    • Answer: C

  • Q2 (Outcome of Gram stain): The outcome of the Gram stain is based on differences in the cell’s _.

    • a. wall

    • b. membrane

    • c. flagella

    • d. inclusions

    • e. ribosomes

    • Answer: a

  • Q3 (Gram-negative bacteria): Gram-negative bacteria __.

    • A. Are more susceptible to antibiotics that target peptidoglycan than Gram-positive organisms

    • B. Are less susceptible to antibiotics that target peptidoglycan than Gram-positive organisms

    • C. Stain purple in the Gram stain

    • D. Encompass all pathogens

    • E. None of these choices is correct

    • Answer: B

  • Q4 (Learning outcomes – Section 3.1): List the structures all bacteria possess. Identify three structures some but not all bacteria possess. Describe three major shapes of bacteria. Provide at least four terms to describe bacterial arrangements.

    • Answer: These are the core learning outcomes for Section 3.1.

  • Q5 (Overview): Bacteria and Archaea – overview: how organisms differ from Eukaryotes (DNA packaging, lack of nucleus/histones, peptidoglycan in cell walls, lack of membrane-bound organelles).

  • Q6 (Structure of bacterial cell): All bacterial cells possess a cytoplasmic membrane, cytoplasm, ribosomes, cytoskeleton, and one (or a few) chromosome(s). Most possess a cell wall and a glycocalyx.

Bacteria and Archaea: An Overview

  • Bacteria and Archaea are prokaryotes with key differences from Eukaryotes:

    • DNA packaging: lack of nucleus and histones

    • Cell wall composition: peptidoglycan presence varies; archaea have unique wall chemistries

    • Internal structures: lack membrane-bound organelles

  • Basic contrasts to review:

    • DNA packaging and organization (nucleoid vs nucleus)

    • Cell wall components and tolerance to environmental conditions

    • Ribosomal structure and translation differences (70S in prokaryotes)

The Structure of the Bacterial Cell

  • All bacterial cells possess:

    • Cytoplasmic membrane

    • Cytoplasm

    • Ribosomes

    • Cytoskeleton

    • One (or a few) chromosome(s)

  • Most bacterial cells possess:

    • Cell wall

    • A glycocalyx (surface coating)

  • Structures found in some bacteria (not all):

    • Flagella, pili, fimbriae

    • Outer membrane (in Gram-negative bacteria)

    • Nanowires / Nanotubes

    • Plasmids

    • Inclusions

    • Endospores

    • Microcompartments

  • Notes: Many of these structures are also observed in Archaea.

Bacterial Shapes and Arrangements

  • Typical size: about 1.0 \, ext{μm} in length for cocci; rods around 2.0 \, ext{μm} long and 1.0 \, ext{μm} wide.

  • Pleomorphism: variations in cell wall structure due to genetics or nutrition.

  • Major shapes:

    • Cocci: spherical or ovoid

    • Bacilli (rods): cylindrical

    • Variants: coccobacilli (short, plump rods)

    • Spirilla and Spirochetes: spiral forms (rigid or flexible, corkscrew-like)

  • Key examples:

    • Cocci: Staphylococcus (irregular clusters) – shown as a common example

    • Bacilli: Legionella pneumophila as an example image

    • Vibrios: single curved rod (Vibrio vulnificus)

    • Spirochetes: Campylobacter jejuni (periplasmic flagella)

    • Branched filaments: Streptomyces

Bacterial Shape 1: Cocci

  • Cocci (kokk-ous): spherical.

  • Cocci can be perfect spheres or vary to oval/bean-shaped/pointed forms.

  • Common arrangements:

    • Single

    • Diplococci (pairs)

    • Tetrads (groups of four)

    • Staphylo- or Micrococci (irregular clusters)

    • Streptococci (chains)

    • Sarcina (cubic packets of eight, sixteen or more)

Bacterial Shape 2: Bacilli (Rods)

  • Rods are cylindrical; there is a genus named Bacillus.

  • Shapes can be blocky, spindle-shaped, round-ended, long and thin, club-shaped, or drumstick-shaped.

  • Short, plump rods called cocco-bacilli.

  • Example: Legionella pneumophila image.

Bacterial Shape 3: Vibrios

  • Singly occurring rods that are gently curved are vibrio.

  • Example image: Vibrio vulnificus.

Bacterial Shape 4: Spirillum

  • Slightly curved or spiral-shaped body.

  • Rigid helix twisted along its axis (corkscrew-like).

  • Example: Campylobacter jejuni.

Bacterial Shape 5: Spirochete

  • Slender, flexible spiral with periplasmic flagella; more flexible than spirilla.

  • Example: Spirochetes.

Bacterial Shape 6: Branching Filaments

  • Some bacteria produce multiple branches off a basic rod structure (branching filaments).

  • Example: Streptomyces.

Bacterial Arrangements: Cocci

  • Arrangements by division planes:

    • Division in one plane: diplococcus

    • Division in two perpendicular planes: tetrad

    • Division in several planes: irregular clusters (staphylococci, micrococci)

    • Streptococcus: chains

    • Sarcina: cubic packets (8–64+ cells)

Bacterial Arrangements: Bacilli

  • Arrangements:

    • Single

    • Diplobacilli: pair with ends attached

    • Strepotbacilli: chain of several cells

    • Palisades: chain cells remain partially attached at ends ( Corynebacterium species )

Bacterial Arrangements: Spirilla and Spirochetes

  • Spirilla: occasionally found in short chains

  • Spirochetes: rarely remain attached after cell division

Concept Check (1)

  • Which structures are possessed by some but not all prokaryotes?

    • A. Ribosomes

    • B. Cell membrane

    • C. One or more chromosomes

    • D. Flagella

  • Answer: D (Flagella) is not universal; others are common to most prokaryotes.

Learning Outcomes Section 3.2: External Structures

  • Exterior appendages include:

    • Motility: flagella and axial filaments

    • Attachment points or channels: fimbriae, pili, and nanotubes/nanowires

  • Flagellum: primary function is motility; three distinct parts: filament, hook (sheath), basal body

Flagellum of a Gram-Negative Cell

  • The flagellum structure and chemotaxis signaling involve interactions with rotor proteins (e.g., CheY) to control rotation direction.

  • Image reference shows Gram-negative flagella and associated chemotaxis signaling.

Arrangement of Flagella

  • Polar arrangement: flagella at one or both ends

    • Monotrichous: single flagellum

    • Lophotrichous: small bunches or tufts from the same site

    • Amphitrichous: flagella at both poles

  • Peritrichous: flagella dispersed randomly over the surface

Types of Flagellar Arrangements (illustrations)

  • Visual examples show various arrangements across species.

Fine Points of Flagellar Function

  • Chemotaxis: movement toward chemical signals

    • Positive chemotaxis: toward favorable chemical stimulus

    • Negative chemotaxis: away from repellents

  • Run: flagellum rotates counterclockwise, producing smooth linear movement

  • Tumble: reversal of flagellar rotation, causing the cell to stop and change direction

Operation of Flagella (motility patterns)

  • General motility of a single flagellum (straight path; tumble)

  • Peritrichous motility (many flagella): a run followed by tumbles to navigate gradients

Key: Chemotaxis in Bacteria (schematic)

  • Run (R) and Tumble (T) cycles in response to attractant gradients

  • In attractant gradients, runs become more frequent and tumbles decrease to favor movement toward the attractant

Appendages for Attachment or Channel Formation: Fimbriae

  • Fimbriae are small, bristle-like fibers aiding tight adhesion to epithelial cells and host tissues; promote colonization and infection

Appendages: Pili and Nanotubes

  • Pili (pili):

    • Used in conjugation between bacterial cells

    • Well characterized in Gram-negative bacteria

    • Type IV pili can transfer genetic material, assist in attachment, and function like flagella to promote motility

  • Nanotubes / Nanowires: thin tubular extensions used as channels to transfer amino acids or shuttle electrons for energy acquisition (e.g., respiration with iron-rich substances)

Conjugating Process (diagrammatic)

  • Interaction between fimbriae and pili involved in bacterial conjugation; genetic exchange mechanisms

S Layer and Glycocalyx

  • S layer: single layer of thousands of copies of a single protein; produced in hostile environments; forms protective lattice

  • Glycocalyx: repeating polysaccharide or glycoprotein units forming a coating

    • Slime layer: loose, protects against water and nutrient loss

    • Capsule: dense, tightly bound; sticky/mucoid colonies on agar

Position of Bacterial S Layer

  • S layer sits outside the cytoplasmic membrane and peptidoglycan; can be associated with the glycoprotein external coating

Encapsulated Bacteria

  • Capsule or glycocalyx presence often correlates with virulence, evasion of phagocytosis, and environmental resilience

Concept Check (2)

  • Which of the following bacterial appendages is not used for attachment?

    • A. Slime layer

    • B. Flagellum

    • C. Pilus

    • D. Fimbriae

  • Answer: B (Flagellum) is not primarily an attachment structure.

Learning Outcomes Section 3.3: Bacterial Envelopes

  • Goals: Differentiate two main envelope types; justify why Gram-positive cell walls are stronger; name a substance in the envelope that can cause severe symptoms; discuss clinical implications

  • The cell envelope lies outside the cytoplasm and typically consists of:

    • Cell wall

    • Cytoplasmic membrane

    • Outer membrane (in some bacteria)

The Cell Envelope: Overview

  • Gram-positive vs Gram-negative comparison (reference images)

  • Outer envelope components and their roles influence antibiotic susceptibility and permeability

The Cell Wall

  • Functions:

    • Helps determine bacterial shape

    • Provides strong structural support to resist osmotic lysis

    • Targeted by certain antibiotics that disrupt integrity causing cell lysis

  • Relative rigidity arises from peptidoglycan

  • Structure features:

    • Cross-linked glycan chains connected by peptide bridges

    • Alternating sugar units: N-acetylglucosamine (G) and N-acetylmuramic acid (M)

    • Peptide cross-links and interbridges stabilize the mesh

  • Drug targets: penicillin and related antibiotics interact with peptide cross-links

Gram-Positive Cell Wall

  • Structure: thick, homogeneous peptidoglycan layer (approx. 20 ext{-}80 \, ext{nm} thick)

  • Teichoic acids and lipoteichoic acids contribute to cell wall maintenance and anionic surface charge

Gram-Negative Cell Wall

  • Structure: a thin peptidoglycan layer (approx. 1 ext{-}3 \, ext{nm} thick)

  • Outer membrane adds an extra barrier to many chemicals; contributes to increased susceptibility to lysis when compromised by detergents

  • Outer membrane components:

    • Lipopolysaccharide (LPS): signaling molecules, receptors, endotoxin

    • Porin proteins: channels allowing selective entry

  • Cytoplasmic membrane under the cell wall: lipid bilayer with embedded proteins; energy reactions, nutrient processing, synthesis, and transport; selectively permeable with specific carrier mechanisms

Differences in Cell Envelope Structure

  • Outer membrane in Gram-negative bacteria adds barriers: more resistant to many antimicrobials; harder to inhibit/kill than Gram-positive bacteria

  • Alcohol swabs dissolve lipids in the outer membrane, damaging Gram-negative cells; treatment may require drugs that cross the outer membrane

Concept Check (3)

  • The statement: The outer membrane contributes an extra barrier in Gram-positive bacteria that makes them impervious to some antimicrobial chemicals, so they are generally more difficult to inhibit or kill than Gram-negative bacteria.

    • A True

    • B False

  • Answer: B (False) — outer membrane is a feature of Gram-negative bacteria, not Gram-positive

Learning Outcomes Section 3.4 The Cytoplasm

  • Identify seven structures that may be contained in bacterial cytoplasm

  • Detail the causes and mechanisms of sporulation and germination

The Cytoplasm

  • Composition:

    • 70–80% water

    • A complex mix of sugars, amino acids, and salts

  • Bacterial chromosomes and plasmids:

    • Hereditary material primarily in the bacterial chromosome within the nucleoid region

    • Plasmids are nonessential DNA pieces that confer traits like drug resistance, toxin production, and enzymes

  • Ribosomes:

    • Site of protein synthesis

    • Composition: RNA ~60% and protein ~40%

    • Subunits: small 30S, large 50S; whole ribosome is 70S

    • Archaea have 70S ribosomes with archaeal features; Eukaryotes have 80S ribosomes

  • Inclusions and microcompartments:

    • Food storage, gas vesicles, iron oxide storage (magnetic properties)

    • Microcompartments have protein shells and enzymes organized for specific pathways

  • Cytoskeleton:

    • Protein polymers forming helical ribbons that contribute to cell shape; present in some bacteria and archaea; potential antibiotic target

  • Endospores and sporulation:

    • Dormant bodies produced by Bacillus, Clostridium, and Sporosarcina

    • Endospores resist heat, desiccation, freezing, radiation, and chemicals; survive harsh conditions

  • Maturation and release of enveloped viruses (context):

    • Endospores are dormant; vegetative cells are metabolically active; sporulation is environmentally induced

Sporulation and Germination (Bacillus spp.)

  • Sporulation sequence is a developmental program triggered by stress; results in endospore formation

  • Germination occurs when favorable conditions return, returning the spore to a metabolically active vegetative cell

Medical Significance of Bacterial Endospores

  • Pathogens associated with endospores:

    • Bacillus anthracis: agent of anthrax

    • Clostridium tetani: tetanus

    • Clostridium perfringens: gas gangrene

    • Clostridium botulinum: botulism

    • Clostridioides difficile: C. diff infection

Concept Check (4)

  • Where in a bacterial cell would you find the genetic material?

    • A. Nucleus

    • B. Nucleolus

    • C. Nucleocapsid

    • D. Nucleoid

  • Answer: D

Learning Outcomes Section 3.5 Archaea, Bacteria, and Eukarya

  • Compare and contrast the major features of these three cellular domains

Archaea: Overview and Distinctions

  • A third cell type in a separate superkingdom; more closely related to Eukarya in some respects than to Bacteria

  • Similarities with Eukarya in certain transcription/translation features; differences from Bacteria in rRNA sequences

  • Unique aspects:

    • Novel DNA compaction strategies

    • Distinct membrane lipids, cell-wall components, and pilin proteins

  • Extremophiles: many live in extreme temps, high salt, acidity, or sulfur/methane environments; some colonize humans and may cause disease

Comparison Across Domains (Bacteria, Archaea, Eukarya)

  • Chromosomes: Bacteria – single/circular; Archaea – single/circular; Eukarya – multiple, linear

  • Ribosomes: Bacteria – 70S; Archaea – 70S (with some archaeal features); Eukarya – 80S

  • 70S signature: shared among Bacteria and Archaea; all have 70S ribosomes but with domain-specific features

  • Cell wall: Bacteria – peptidoglycan present varies by group; Archaea – often lack peptidoglycan; Eukarya – none (in general, except some algae/plants with cell walls of different chemistry)

  • Cytoplasmic membranes: Bacteria – fatty acids with ester linkages; Archaea – ether linkages with unique core lipids; Eukarya – ester linkages; sterols may be present in some membranes

  • Nucleus/organelles: Eukarya – present; Bacteria and Archaea – absent

  • Flagella: Bacteria – bacterial flagellum; Archaea – archaellum; Eukarya – eukaryotic flagellum

Concept Check (5)

  • Which of the following do members of the domains Bacteria and Archaea both possess?

    • A. Linear DNA

    • B. Nucleus

    • C. 70S ribosomes

    • D. Fatty acids with ether linkages

  • Answer: C

Learning Outcomes Section 3.6 Bergey’s Manual: Systematic vs Determinative

  • Bergey’s Manual of Systematic Bacteriology:

    • Comprehensive view of bacterial and archaeal relatedness; based on rRNA sequencing

  • Bergey’s Manual of Determinative Bacteriology:

    • Based on phenotypic characteristics; used for categorization in clinical, teaching, and research settings (shape, metabolism, etc.)

Taxonomic Scheme and Divisions

  • Four major divisions based on cell-wall nature:

    • Gracilicutes: Gram-negative with thin cell walls

    • Firmicutes: Gram-positive with thick, strong cell walls

    • Tenericutes: Lack a cell wall and are soft

    • Mendosicutes: Archaea with unusual walls and nutritional habits

Species and Subspecies in Bacteria and Archaea

  • Bacterial species: a collection of cells sharing overall similar trait patterns; should share at least 95\% of their genes as matches

  • Subspecies, strain, or type: same species but differing characteristics

  • Serotype: representatives of a species that stimulate distinct antibody responses due to unique surface molecules

Concept Check (6)

  • You identify a bacterium as Gram-negative using Gram-stain; in Bergey’s Manual of Determinative Bacteriology, this bacterium belongs to which division?

    • A. Gracilicutes

    • B. Firmicutes

    • C. Tenericutes

    • D. Mendosicutes

  • Answer: A

Notes on Form and Connection

  • The Gram stain, cell envelope structure, and cytoplasmic components are foundational for understanding bacterial taxonomy, antibiotic targeting, and pathogenic mechanisms.

  • The three-domain framework (Bacteria, Archaea, Eukarya) emphasizes both shared features (e.g., 70S ribosomes in Bacteria and Archaea) and fundamental divergences (e.g., membrane lipid chemistry, cell-wall composition, and genetic organization).

  • Practical implications include antibiotic design (cell wall synthesis targets), Gram-stain interpretation in clinical diagnostics, and recognition of non-traditional organisms (acid-fast bacteria, archaea) that may challenge standard staining or culturing methods.