Microbiology: A Systems

Approach, 2nd ed.

Chapter 4: “Prokaryotic” Profiles:

the Bacteria and Archaea

Chapter 5: Eukaryotic Microbes

4.1 Prokaryotic Form and Function
Structures common to all bacterial cells
• Cell (cytoplasmic) membrane
• Ribosomes
• Genetic Element [one or more chromosomes

• Cells are “filled” with cytoplasm

Figure 4.1
 Cell wall
• Typical Gram-positive cell wall
– Thick peptidoglycan (PG) layer (90%)
– Acidic polysaccharides
– (wall) teichoic acid and lipoteichoic acid

• Gram-negative cell wall

– Thin PG layer (10%)
– Outer membrane
– Lipopolysaccharide (LPS = “Endotoxin”)
– Porins
 Cell Membrane
• Also known as the cytoplasmic membrane
• Very thin (5-10 nm)
• Contain primarily phospholipids, proteins and
– Hopanes (hopanoids) or
– sterols (mycoplasmas)

• Functions
– Provides a site for functions such as energy
reactions, nutrient processing, and synthesis
– Regulates transport (selectively permeable
membrane)
– Facilitates communication
Transport systems are essential t o every
living cell.

They

(1) allow the entry of a ll essential nutrients into the cell and its
compartments,

(2) regulate the cytoplasmic concentrations of metabolites by excretion

mechanisms,

(3) provide physiological cellular concentrations of i ons that can differ by

several orders of magnitude from those in the external medium,

(4) export macromolecules such as complex carbohydrates, proteins, lipids,

and DNA,

(5) catalyze export and uptake of signaling molecules that mediate

intercellular communications,

(6) prevent toxic effects of drugs and toxins by mediating active efflux, and

(7) participate in biological warfare by exporting biological active agents

that insert into or permeate the membranes of target cells.

Transport is an essential aspec t of all life-endowing processes: catabolism,

biosynthesis, communication, reproduction, and both cooperative and
antagonistic inter-organismal behaviors.
 Practical Considerations of Differences
in Cell Envelope Structure

• OM - an extra barrier in Gram-negative bacteria

– Makes them impervious to some antimicrobials
– Generally, makes Gram-negative bacteria more
difficult to injure or kill than Gram-positive bacteria

• Cell wall and glycocalyx can interact with host

cell and tissues surfaces and facilitate infection
– Corynebacterium diphtheriae
– Streptococcus pyogenes
 4.4 Bacterial Internal Structure
• Cytoplasm
• Genetic element
• Inclusion bodies
• Actin
• Endospore
 Cytoplasm
• Contents of the Cell Cytoplasm
– Gelatinous solution
– Site for many biochemical and synthetic
activities
– 70%-80% water
– 20% - 30% nutrients, proteins, and genetic
material (i.e., chromatin, ribosomes,
macromolecular storage granules, and actin
strands)
 Bacterial Chromosome
• Circular or linear double strands of DNA
• Aggregated in a dense area of the cell - called
the nucleoid (chromosome)

Figure 4.17
 Plasmids
• extrachromosomal pieces of DNA
• Double-stranded circles or strands of DNA
• Often confer protective traits such as drug
resistance or the production of toxins and
enzymes
 Ribosomes
• Made of RNA and
protein
• Special type of RNA-
ribosomal RNA
(rRNA)
• Characterized by S
units- the prokaryotic
ribosome is 70S

Figure 4.18
 Inclusions
• Inclusions- also known as inclusion bodies

– Some bacteria accumulate polymer granules in

during periods of nutrient abundance

• Serve as a storehouse when nutrients become

depleted
• Serve as a storehouse when energy becomes
depleted
 Examples: Granules
• Contain crystals of inorganic compounds
• Are not enclosed by membranes
• Starch and glycogen granules
• Poly-hydroxybutyrate granules
• Sulfur granules accumulated by photosynthetic
bacteria (serve as storage for reductant)
• Polyphosphate granules of Corynebacterium
and Mycobacterium are called metachromatic
granules because they stain a contrasting color
in methylene blue; many other bacteria
accumulate poly~Pi
Figure 4.19
 Membrane-enclosed inclusions
• Protein membranes
– Some aquatic bacterial inclusions include gas
vesicles to provide buoyancy and flotation
– Some inclusions contain entire metabolic
pathways such as carbon fixation
(carboxysome) or polymer lysis (cellulosome)

• Lipid membranes
– Magnetotactic bacteria contain granules with
iron oxide- give magnetic properties to the cell
 The Actin Cytoskeleton
• Long polymers of actin
• Arranged in helical ribbons around the cell
just under the cell membrane
• Contribute to cell shape
Actin is a protein fiber (cytoskeleton) present in some bacteria,
and is involved in maintaining cell shape.

Fig. 4.20 Bacterial cytoskeleton

 Bacterial Endospores: An
Extremely Resistant Resting Stage
• Dormant structures
produced by Bacillus,
Clostridium, and
Sporosarcina ==>
Gram-positive low G+C
bacteria

Figure 4.21
 Endospore-Forming Bacteria
• These bacteria have a two-phase life cycle
– Phase One - The vegetative cell
• Metabolically active and growing
• Can be induced by the environment to undergo
spore formation (sporulation)
 Phase Two: Endospore
• Many stimuli for sporulation- the depletion of
nutrients, heat, water shortage, UV, etc …
• Vegetative cell undergoes a conversion to a
sporangium
• Sporangium transforms in to an endospore
• Hardiest of all life forms
– Withstand extremes in heat, drying, freezing,
radiation, and chemicals
– Heat resistance - high content of calcium and
dipicolinic acid
– Some viable endospores have been found that were
more than 250 million years old
• Germination
– Breaking of dormancy
– In the presence of water and a specific
germination agent
– Quite rapid (1 ½ hours)
– The agent stimulates the formation of hydrolytic
enzymes, digest the cortex and expose the core
to water

• Medical Significance
– Several bacterial pathogens
• Bacillus anthracis
• Clostridium tetani
• Clostridium perfingensl; Clostridium botulinum
– Resist ordinary cleaning methods
 4.5 Bacterial Shapes,
Arrangements, and Sizes
• Three general shapes
– Coccus- roughly spherical
– Bacillus- rod-shaped
• Coccobacillus- short and plump
• Vibrio- gently curved
– Spirillum- curviform or spiral-shaped
• Pleomorphism- when cells of a single species
vary to some extent in shape and size
Figure 4.22
Figure 4.23
 Some bacteria (ex. Corynebacterium) have varied shapes called
pleomorphism.

Fig. 4.24 Pleomorphism in Corynebacterium

 Arrangement, or Grouping
• Cocci- greatest variety in arrangement
– Single
– Pairs (diplococcic)
– Tetrads
– Irregular clusters (staphylococci and micrococci)
– Chains (streptococci)
– Cubical packet (sarcina)
• Bacilli- less varied
– Single
– Pairs (diplobacilli)
– Chain (streptobacilli)
– Row of cells oriented side by side (palisades)
• Spirilla
– Occasionally found in short chains
Relative size of a bacterial cell compared to other cells and viruses.

Fig. 4.25 The dimension of bacteria

4.6 Classification Systems in the
“Prokaryotae”

• Phenotypic methods
• Molecular methods
• Taxonomic scheme
• Unique groups
 Phenotypic methods
• Cell morphology - staining & microscopy
• Biochemical test – enzyme test
 Classification
• One of the original classification systems- shape,
variations in arrangement, growth characteristics, and
habitat
• Definitive published source for bacterial classification
– Bergey’s Manual: Since 1923
– Early classification- the phenotypic traits of bacteria
– Current version - combines phenotypic information with
rRNA sequencing

• Modern Taxonomy is based on molecular methods,

i.e., comparing the nucleotide sequences in rRNA
 Molecular methods
Analyze:

• DNA sequence
• 16S rRNA sequence
• Protein sequence
 OLD Taxonomic Scheme
• Kingdom Prokaryotae - 4 divisions based
upon the nature of the cell wall
– Gracilicutes - Gram-negative
– Firmicutes - Gram-positive
– Tenericutes - lack cell wall
– Mendosicutes - the archaea
The methods of classification have allowed bacteria to be grouped
into different divisions and classes.

Table 4.3 Major taxonomic groups of bacteria

 Diagnostic Scheme
• Many medical microbiologists prefer
• Informal working system
• See Table 4.2
 Species and Subspecies
• Common definition of species (“can produce viable
offspring only when it mates with others of its own kind”)
does not work for bacteria
• Bacteria do not exhibit a typical mode of sexual
reproduction
• For bacteria, a species is a collection of bacterial cells,
all of which share an overall similar pattern of traits
• Individual members of a bacterial species can show
variations
– Subspecies, Strain, or Isolate: bacteria of the same
species that have differing characteristics
• Biovar(iety) - representatives that have similar metabolism
• Pathovar(iety) - representative that cause a particular disease
• Serovar(iety) or serotype- representatives of a species that
stimulate a distinct pattern of immune responses in their hosts
 Unique groups of prokaryotes
• Intracellular parasites
• Photosynthetic bacteria
• Green and purple sulfur bacteria
• Gliding and fruiting bacteria
• Archaeobacteria (Archaea)
Obligate Intracellular Parasites
• Rickettsias
– Very tiny
– Gram-negative
– Atypical in lifestyle and other adaptations
• Most-pathogens that alternate between a mammalian
host and blood-sucking arthropods
• Cannot survive or multiply outside a host cell
• Cannot carry out metabolism completely on their own
– Human diseases
• Rocky Mountain Spotted Fever by Rickettsia rickettsii
• Endemic typhus by Rickettsia typhi
Intracellular bacteria must live in host cells in order to undergo
metabolism and reproduction.

Fig. 4.26 Transmission electron micrograph of Rickettsia.

• Chlamydias
– Genera Chalmydia and Chalmydophila
– Require host cells for growth and metabolism
(cannot synthesize ATP)
– Not closely related to Rickettsia
– Not transmitted by arthropods
– Human diseases
• Chlamydia trachomatis- causes a severe eye
infection and the STD
• Chlamydophila pneumonia- causes lung infections
• Chlamydia psittaci - heart inflammation
Free-Living Nonpathogenic Bacteria
• Photosynthetic Bacteria
– May or may not produce oxygen during
photosynthesis
– Some produce oxidized substances during
photosynthesis, such as sulfur granules or
sulfates
• Cyanobacteria: the Blue-Green Bacteria
– For many years, called Blue-Green Algae
– General prokaryotic structure
– Gram-negative cell wall
– Can be unicellular or can occur in colonial or
filamentous groupings
– Specialized adaptation- thylakoids
• Chlorophyll a
• Other photosynthetic pigments
– Gas inclusions
– Widely distributed in nature
Cyanobacteria are important photosynthetic bacteria associated
with oxygen production.

Fig. 4.27 Structure and examples of cyanobacteria

Green and Purple Sulfur Bacteria

• Green and Purple Sulfur Bacteria

– Photosynthetic
– Contain variety of pigments
– Different chlorophylls than cyanobacteria:
bacteriochlorophyll
– Do not give off oxygen (“anoxygenic”)
– Live in areas with low oxygen conditions but yet
where their pigments can absorb light
• Sulfur springs
• Freshwater lakes
• Swamps
 Green and purple sulfur bacteria are photosynthetic, do not give
off oxygen, and are found in sulfur springs, freshwater, and
swamps.

Fig. 4.28 Behavior of purple sulfur bacteria

An example of a fruiting body bacteria in which reproductive
spores are produced.

Fig. 4.29 Myxobacterium

 Archaea: The Other Prokaryotes
• Domain Archaea
• Prokaryotic in general structure
• Share many characteristics with bacteria
• Universal tree of life (based on ssu rRNA)
reveals that they are more closely related
to Domain Eukarya than to Domain
Bacteria; nevertheless, they are clearly a
different Domain by themselves …..
• How they differ from other cell types
– Unique rRNA sequences
– Unique membrane lipids and cell wall construction
– Not susceptible to antibiotics
– No nucleus
• Thought to be the least evolved of all life forms
• Many archaea live in habitats that share
conditions as the ancient earth
– Methane producers
– Hyperthermophiles
– Extreme halophiles
– Sulfur reducers

• ==> Thought to live only in extreme

environments and be most closely related to
the first cells that originated on earth -
wrong!!!!

• Most live in temperate environments!!!

Archaea are found in hot springs (thermophiles) and high salt
content areas (halophiles) as well in temperate environments.

Fig. 4.30 Halophile

around the world
Archaea Also come in very different sizes and engage in
symbiotic associations with one another and with other organisms.
 5.1 The History of Eukaryotes
• First eukaryotic cells emerged on Earth
approximately 2 billion years ago
• Evidence points to these eukaryotic cells evolving
from prokaryotic organisms through intercellular and
intracellular symbioses
– First eukaryotes- single-celled and independent
– Thought to be a merger of an Archaeon engulfed by a
Bacterium
– Eventually formed colonies
– Cells within colonies became specialized
– Eukaryotic organelles originated from prokaryotic cells
trapped inside of them
– Evolved in to multicellular organisms
• Extant (“today’s”) Eukaryotes have many levels of
cellular complexity
 5.2 Form and Function of the
Eukaryotic Cell: External Structures

Figure 5.2
 Locomotor Appendages:
Cilia and Flagella
• Eukaryotic flagella are much different from
those of prokaryotes
– 10X thicker
– Structurally more complex
– Covered by an extension of the cell
membrane
• A single flagellum contains regularly
spaced microtubules along its length
– 9 pairs surrounding a single pair
– The 9 + 2 arrangement
 9+2

Figure 5.3
• Cilia- similar to flagella but some
differences
– Shorter
– More numerous
– Can also function as feeding and filtering
structures
 The Glycocalyx
• Most eukaryotic cells have this outermost boundary
that comes into direct contact with the environment
• Usually composed of polysaccharides
• Appears as a network of fibers, a slime layer, or a
capsule
• Functions
– Protection
– Adhesion
– Reception of signals
• The layer beneath the glycocalyx varies among
eukaryotes
– Fungi, plants and most algae have a thick, rigid cell wall
– Protozoa and animal cells do not have this cell wall
Form and Function of the Eukaryotic
Cell: Boundary Structures
• Cell Wall
– Rigid
– Provide support and shape
– Different chemically from prokaryotic cell walls
– Fungi
• Thick, inner layer of chitin or cellulose
• Thin outer layer of mixed glycans
– Algae
• Varied in chemical composition
• May contain cellulose, pectin, mannans, and
minerals
Figure 5.5
• Cytoplasmic (plasma) Membrane
– Bilayer of phospholipids with protein
molecules embedded
– Also contain sterols
• Gives stability
• Especially important in cells without a cell wall
– Selectively permeable
 5.3 Form and Function of the
Eukaryotic Cell: Internal Structures
• The Nucleus: The Control Center
– Separated from the cytoplasm by a nuclear double
membrane
• Two parallel membranes separated by a narrow space
• Perforated with nuclear pores
– Filled with nucleoplasm
– Contains area of dense NAs, called the nucleolus
• rRNA synthesis
• High density of ribosomal subunits
– Chromatin
• Comprises the chromosomes
– Long, linear DNA molecules
– Bound to histone proteins
– Visible during mitosis
 Endoplasmic Reticulum (ER):
A Passageway in the Cell
• Microscopic series of tunnels
• Used in transport and storage
• Two kinds
– Rough endoplasmic reticulum (RER)
• Extension of the outer membrane of the nuclear
envelope
• Extends through the cytoplasm
• Spaces in the RER - cisternae - transport materials
from the nucleus to the cytoplasm
• “Rough” because of ribosomes attached to its surface
• Proteins synthesized by the ribosomes shunted into the
lumen of the RER and held for later sorting, targeting
and transport
 Golgi Apparatus: A Packaging
Machine
• Where proteins are modified and sent to their final
destinations
• A stack of cisternae
• Do not form a continuous network
• Closely associated with ER both in location and
function
– The ER buds off transitional vesicles (packets of
protein) where it meets the Golgi apparatus
– The Golgi apparatus picks up the transitional vesicles
– The proteins are often modified by addition of
polysaccharides and lipids
– Then the apparatus pinches off condensing vesicles
• Sent to lysosomes
• Or transported outside the cell
Figure 5.10
Mitochondria: Energy Generators
• Cellular activities require a constant supply of energy
• The bulk of this energy generated by mitochondria
• Smooth, continuous outer membrane
• Inner folded membrane (folds are cristae)
– Cristae hold enzymes and electron carriers of aerobic
respiration
– Spaces inside the cristae filled with a matrix
• Ribosomes
• DNA
• Enzymes and other compounds involved in the metabolic cycle
• Divide independently of the cell
• Contain circular strands of DNA
• Contain prokaryotic-sized 70S ribosomes
 Ribosomes: Protein Factories
• Some scattered in the cytoplasm and
cytoskeleton
• Others associated with (R)ER
• Often found in chains of polyribosomes
(polysomes)
• Composed of large and small subunits of
ribonucleoprotein
• Larger 80S variety, composed of 60S and
40S subunits
The Cytoskeleton: A Support Network
• Flexible framework of molecules criss-
crossing the cytoplasm
• Several functions
– Anchoring organelles
– Moving RNA and vesicles
– Permitting shape changes and movement in
some cells
• Two types: Microfilaments and microtubules
 5.4 The Kingdom of the Fungi
• Myceteae
• Great variety and complexity
• Approximately 100,000 species
• Can be divided in to two groups
– Macroscopic fungi
– Microscopic fungi
• Yeasts
– Round oval shape
– Unique mode of asexual reproduction
• Hyphae
– Long, threadlike cells
• Some are dimorphic
• Majority are unicellular or colonial
• Some form a pseudohypha
 Fungal Nutrition
• Heterotrophic
• Acquire nutrients from substrates
• Most fungi are saprophytes (saprotrophs)
• Can be benign, parasitic, pathogenic
• General method of obtaining nutrition
– Penetrates the substrate
– Secretes enzymes
– Breaks down the polymers into small molecules
– Absorbs the small molecules
• Can absorb a wide variety of substrates
• Large medical and agricultural importance
Organization of Microscopic Fungi
• Most grow in loose associations or colonies
• Yeasts: unicellular, uniform texture and appearance
• Molds (Filamentous fungal colonies): cottony, hairy, or
velvety textures
• Mycelium- the woven, intertwining mass of hyphae that
makes up the body or colony of a mold
• Unique organizational features of hyphae
– Septa- divide the hyphae in to segments (most fungi
have so called septate hyphae)
– Nonseptate hypha (coenocytic) - long, continuous cell
• Functions of hyphae
– Vegetative hyphae (mycelium): visible mass of growth
on the substrate surface; penetrates the substrate to
digest and absorb nutrients
– Reproductive (fertile) hyphae: form vegetative hyphae;
responsible for the production of spores
Figure 5.18
 5.5 The Protists
• Traditionally contains the algae and
protozoa
• Two major taxonomic categories
– Subkingdom Algae
– Subkingdom Protozoa
• Any unicellular or colonial organism that
lacks true tissues
 The Algae: Photosynthetic
protists
• Vary in length from a few micrometers to 100 meters
• Unicellular, colonial, and filamentous forms
• Larger forms can possess tissues and simple organs
• Exhibit all eukaryotic organelles
• Chloroplasts contain chlorophyll as well as other
pigments
• One of the main components of plankton
• Rarely infectious
• Primary medical threat: shellfish exposed to red tide
 Biology of the Protozoa
• About 65,000 species
• Most are harmless, free-living inhabitants
of water and soil
• Few are parasites
Important Protozoan Pathogens
 5.6 The Parasitic Helminths
• Tapeworms, flukes, and roundworms
• Adults large enough to be seen with the
naked eye
• From 1 mm to 25 m in length
• Microscope is necessary to identify eggs
and larvae
• Two major groups: Flatworms and
Roundworms
 Distribution and Importance of
Parasitic Worms
• About 50 species parasitize humans
• Distributed in all areas of the world
• Yearly estimate of worldwide infections- in
the billions