Chapter 4

Classification of Microbes

 Prokaryotes

Prokaryotes lack a nucleus.
Includes bacteria and archaea.
Archaea are distinct from bacteria despite both being prokaryotic.
Prokaryotes are smaller cells compared to eukaryotes.

 Eukaryotes

Eukaryotes have a nucleus.
Contain membrane-bound organelles.
More compartmentalized than prokaryotic cells.
Cellular structure includes nucleus and membrane-bound organelles.

 Acellular Microbes

Not composed of cells.
Viruses fall under this category.
Viruses do not meet the criteria for being alive.
Characteristics of life differentiate living from non-living entities.

Characteristics of Life

 Key Characteristics

Growth: All living things increase in size.
Reproduction: Capacity to reproduce at a species level.
Responsiveness: Ability to respond to environmental changes.
Metabolism: Involves chemical reactions within cells.
Cellular organization: Living things are composed of cells.
Development, regulation, homeostasis, heredity, and adaptation are vital.

 Living vs. Non-Living

Life defined by a set of shared characteristics.
Living entities exhibit all key characteristics.
Viruses meet only a few life criteria.
Prokaryotes and eukaryotes fulfill all life requirements.

Cellular Morphology

 Common Morphologies

Bacillus: Rod-shaped cells, varying in size.
Cocci: Spherical cells resembling circles under a microscope.
Spiral: Long, thin cells resembling a corkscrew.
Spiral subtypes: Vibrio and Spirillum.

 Less Common Morphologies

Spiral cells have flagella extending away or wrapping around.
Vibrio cells are slightly curved bacilli.
Cell morphology varies in shape and structure.

Ø Bacterial Cell Morphology

 Cell Shapes

Spiral Cut Cells: Flagellum wraps around the cell (e.g., Vibrio).
Barella Cells: Flagellum extends away from the cell.
Filamentous Cells: Long, thin, hair-like structures.
Coco Bacillus Cells: Unique morphology resembling a circle squared or a rounded bacillus.

 Cell Arrangements

Diplo Arrangement: Cells paired together.
Strepto Arrangement: Long chains of bacteria.
Staphylo Arrangement: Clustered cells resembling grapes.
Tetrad Arrangement: Four spherical cells forming a square.
Sarcina Arrangement: Two tetrads stacked, totaling eight cells.
Palisade Arrangement: Bacilli cells aligned at angles to each other.

Cellular Arrangement and Morphology

 Cellular Arrangement

Diplo arrangement involves paired cells.
Strepto arrangement forms long chains of bacteria.
Staphylo arrangement clusters cells like grapes.
Tetrad arrangement creates a square with four spherical cells.
Sarcina arrangement stacks two tetrads for eight cells.
Palisade arrangement aligns bacilli cells at angles.

 Biofilms and Bacterial Behavior

Biofilms are microbial habitats with diverse species in cooperative associations.
Biofilms provide protection, food, and water for organisms within.
Bacteria in biofilms adhere to surfaces and exhibit quorum sensing.
Quorum sensing triggers gene expression for biofilm formation.
Bacteria in biofilms secrete an extracellular matrix for stability.
Some bacteria may leave biofilms to swim freely and form new biofilms.

External Structures of Bacterial Cells

 Flagella

Flagellum extends from the cell for movement.
Anchored to the cell membrane and wall.
Used to propel bacterial cells along.
Essential for bacterial motility and navigation.

 Pili

Hair-like appendages for attachment and conjugation.
Facilitate bacterial adhesion to surfaces.
Involved in genetic exchange between bacterial cells.
Play a role in bacterial pathogenicity.

 Glycocalyx

Outer coating of polysaccharides or proteins.
Protects bacteria from desiccation and immune responses.
Contributes to biofilm formation and virulence.
Can be capsule (well-organized) or slime layer (loose).

Structures of Bacterial Cells

 Flagella

Flagella are extensions from bacterial cells used for movement.
Consist of basal body, filament, and hook unique to prokaryotes.
Powered by a hydrogen ion gradient.
Bacterial flagella vary in arrangement: mono-, lopho-, amphi-, and peritrichous.
Endoflagella found in spiral bacteria cause corkscrew movement.
Chemotaxis and phototaxis guide bacterial movement in response to stimuli.

 Pili

Short bristle fibers aiding in attachment rather than movement.
More numerous and shorter than flagella.
Primarily made of protein and used for adherence to surfaces or biofilm formation.
Special type called F pili facilitates DNA transfer during conjugation.

 Surface Coatings

Include S layer, slime layer, and capsule for protection and adherence.
S layer consists of linked proteins for environmental protection.
Slime layer loosely protects from water loss, while capsule tightly binds and organizes.
Capsules and glycolyxes can form biofilms due to their sticky nature.

Bacterial Capsules and Biofilms

 Capsules and Glycocalyx

Capsules are visible as cleared areas around encapsulated bacteria, aiding in biofilm formation.
Glycocalyx, including glycol classes, contributes to the stickiness of capsules.
Capsules can be slippery to immune cells, aiding bacterial escape from the immune system.
Pathogenic cells often utilize capsules for biofilm formation, causing issues in medical devices like catheters.
Dental plaque is an example of a biofilm formed by bacteria, impacting oral health.

Bacterial Cell Envelope

 Gram Stain and Cell Wall Differentiation

Gram stain differentiates bacteria into gram-positive (purple) and gram-negative (pink/red) based on cell wall composition.
Gram-positive cell walls have a thick layer of peptidoglycan, while gram-negative cell walls have a thin layer and an outer membrane.
Cell wall structure determines bacterial shape, provides support, and protects against osmotic pressure changes.
Peptidoglycan, unique to bacteria, forms a flexible framework with alternating Nam and Nag subunits.

 Gram-Negative Cell Wall and Outer Membrane

Gram-negative cell walls have an outer membrane containing lipopolysaccharide (LPS) and proteins.
LPS, or endotoxin, acts as a cell marker and receptor, triggering immune responses.
Outer membrane proteins facilitate molecule transport and defense against antibiotics.
Gram-negative bacteria are more resistant to antimicrobials due to their outer membrane.

 Cytoplasmic Membrane Structure

The cytoplasmic membrane in bacteria is a lipid bilayer with embedded proteins, facilitating various functions.
Energy reactions, nutrient processing, synthesis, and transport occur within the cytoplasmic membrane.
It is selectively permeable, allowing controlled movement of molecules in and out of the cell.
Cytoplasmic membranes prevent water and small polar molecules from freely crossing due to their hydrophobic nature.

Internal Structures of Bacterial Cells

 Cytoplasm and Cytosol

Cytoplasm contains cytosol, a gelatinous solution where biochemical activities occur.
Cytosol comprises 70-80% water with sugars, amino acids, salts, and cellular components like chromatin, ribosomes, granules, and cytoskeleton.
Biochemical and synthetic activities take place in the cytoplasm due to its non-compartmentalized nature.
Cytosol also houses essential cellular components necessary for various functions.

 Bacterial Chromosome and Plasmids

Most bacteria contain a single circular DNA chromosome within the cytoplasm.
Chromosome lacks a membrane and is tightly coiled around proteins in the nuclear region.
Plasmids are small circular DNA pieces with non-essential genes providing advantages like antibiotic resistance and virulence.
Plasmids can be duplicated, spread to offspring, and passed via conjugation for horizontal transfer.

Ribosomes and Inclusion Bodies

 Ribosomes in Bacterial Cells

Ribosomes, the only true organelles in prokaryotic cells, are not membrane-bound.
Composed of ribosomal RNA and proteins, ribosomes are essential for protein synthesis.
Consist of large and small subunits that come together to build proteins.
Bacterial ribosomes are measured in Svedberg units, with a size of 70s.

 Inclusion Bodies and Cytoskeleton

Inclusion bodies are nutrient droplets within the cytoplasm, aggregating excess nutrients.
Cytoskeleton in bacteria consists of long protein polymers, aiding in maintaining cell shape.
Cytoskeleton proteins are arranged in helical ribbons under the cytoplasmic membrane.
Some bacteria form endospores as survival structures under hostile conditions, not for reproduction.

Bacterial Endospores

 Formation of Endospores

Bacterial cells commit 6-8 hours to produce endospores, a major time investment.
Triggered by hostile environments, a bacterial cell replicates its DNA and forms two separate DNA molecules.
Chromosomes are positioned in different areas of the cell, leading to endospore formation.
Cell thickens the endospore wall by adding layers of cytoplasm and cell wall until the rest of the cell dies.

 Germination of Endospores

Endospores germinate into new vegetative cells when exposed to water or germination agents.
Hydrolytic enzymes break down the endospore wall, allowing rehydration and nutrient uptake.
Germination process takes about 1.5 hours, leading to the growth of a new vegetative cell.
Endospores aid bacteria in surviving harsh conditions and can remain viable for extended periods.

 Pathogenic Implications

Pathogenic species like Bacillus anthracis and Clostridium botulinum produce endospores.
Endospores, resistant to normal cleaning methods, can contaminate the environment and cause diseases like anthrax and botulism.
Improperly canned food may lead to endospore germination, resulting in food poisoning.
Endospores, akin to biofilms, pose challenges due to their resistance and ability to survive for years.

Archaea

 Genetic and Structural Features

Archaea are genetically closer to Eukarya than Bacteria, sharing unique ribosomal RNA sequences.
Distinct DNA compaction method, unique lipids, and cell wall composition set Archaea apart.
Morphologically, Archaea exhibit diverse shapes like square, needle-like, and irregular cells.
External structures include flagella powered by ATP, unique membrane called hami, and distinct cell wall compositions.

 Cellular Components of Archaea

Archaeal cell walls lack peptidoglycan, with gram-negative forms devoid of LPs and having a protein layer.
Cell membranes feature a bilayer with sections of single layers linked by ether linkages.
Archaeal cytoplasm lacks a nucleus, contains 70S ribosomes, and exhibits a cytoskeleton similar to bacteria.
Archaea show similarities to Eukarya in certain cellular components, enhancing their uniqueness.

Archaea Characteristics

 Unusual Cell Walls

Archaea have chemically distinct cell walls lacking peptidoglycan.
Majority of archaea species thrive in moderate climates.
Some archaea species inhabit extreme environments with high heat, salt, acid, and pressure.
Notable archaea types include methane producers, hyperthermophiles, extreme halophiles, and sulfur reducers.

 Distinct Archaea Groups

Methanogens convert CO2 and H2 into methane, found in anaerobic environments like swamp mud and animal digestive systems.
Extreme halophiles require high salt concentrations to grow, surviving in salt levels that would destroy most cells.
Hyperthermophiles thrive in very high temperatures, living in volcanic waters and submarine vents.
Archaea classification serves practical and academic purposes, aiding in species differentiation and evolutionary studies.

Classification of Prokaryotes

 Historical Classification Methods

Early microbiology classified microorganisms based on shape, cellular morphology, arrangement, growth characteristics, and habitat.
Newer methods like biochemistry and genetics provide faster and more detailed classification.
Evolutionary relatedness is determined by comparing highly conserved DNA sequences, like RNA sequences.
Sources like Bergey's Manual and Bergey's Manual of Systematic Bacteriology aid in bacterial and archaeal classification.

 Taxonomic Divisions

Prokaryotes are divided into four major groups: Gracilicutes (gram-negative), Firmicutes (gram-positive), Tenericutes (lack cell walls), and Mendosicutes (archaea).
Classification schemes often start by determining if the cell is gram-positive, gram-negative, or lacks a cell wall, leading to further categorization based on cell shape, arrangement, and other traits.

Chapter 4: Classification of Microbes

Prokaryotes

Lack a nucleus
Includes bacteria and archaea
Archaea are distinct from bacteria
Smaller cells compared to eukaryotes

Eukaryotes

Have a nucleus
Contain membrane-bound organelles
More compartmentalized than prokaryotic cells
Cellular structure includes nucleus and organelles

Acellular Microbes

Not composed of cells
Includes viruses
Viruses do not meet all criteria for life