1. Introduction and Review Flashcards
Microbiology is the study of
Microbes
Microbes are
living organisms that are too small to be observed by the naked eye.
what is required for the study & observation of microbes.
Microscopes
A bacterium may weigh approximately
1x10^-11g
collectively microbes constitute about what % of the earth’s biomass?
60%
Microbes on earth for almost
4 billion years
Microbes Impacts
environment and higher life forms
there are Extremely high microbial numbers and diversity on earth
thereare Trillion of microbe Species on Earth with 5 million trillion trillion or 530 (5,000,000,000,000,000,000,000,000,000,000)
bacterial cells
Human body has ~3.0 X 10^ 13 cells and how many bacterial cells?
Human body has ~3.0 X 10^13cells and 3.8 X 10^13 bacterial cells
Microbes play a critical role in state of
health
Rhizosphere may contain >10 billion bacteria per
per gram of soil
Microbiological processes in the rhizosphere, phyllosphere and within plant impact tremendously on
health and productivity of plants
What are the theories of the origin of life on earth? (5)
1) Primordial soup theory
2) clay theory
3) spontaneous generation theory
4) pansermia
5) Directed Panspermia
4600 millions of years ago
planet earth formed
4300 - 3800 millions of years ago
indirect evidence of life on earth
3500 - 3400 millions of years ago
microbial life present evidenced by stromatolites
2800 - 2400 millions of years ago
cyanobacteria capable of oxygen evolving photosynthesis
2000 - 1800 millions of years ago
oxygen begins to accumulate in the atmosphere
evolution of eukaryotes
1400 millions of years ago
microbial assemblages of relatively large unicells
800 - 700 millions of years ago
rock deposits containing about 20 different taxa of eukaryotes, including probable protozoa and filamentous green algae
640 millions of years ago
oxygen reaches 3% of present atmospheric level
650 - 570 millions of years ago
the oldest fossils of multicellular animals, including primitive arthropods
570 millions of years ago onwards
the first evidence of plentiful living things in the rock record
400 millions of years ago onwards
development of the land flora
200 millions of years ago
mammals, flowering plants, social insects appear
The science of classification is known as
taxonomy
Each specific group or category used in classification is known as a
TAXON (plural TAXA)
Who was credited with founding the science of taxonomy
Carolus Linnaeus (1707-1778), the 18th century Swedish botanist
Linnaeus devised the binomial nomenclature system that is still used today to name organisms
the 5 kingdom classification systems
- Kingdom of protists (protozoans, algae)
- kingdom of prokaryotes / monerans (bacteria)
- kingdom of fungi (mushrooms, yeasts, mold)
- kingdom of plants (trees, fern, moss)
- kingdom of animals (insects, earthworm, sponge etc)
Proposed by Woese (1990) that a taxonomic category called DOMAIN placed above the level of
KINGDOM
taxonomic category called DOMAIN placed above the level of KINGDOM Based largely on
ancestral relationship derived from molecular sequence data.
Proposal spurred on by the discovery and study of organism representing a different cell type – archaeobacteria.
All living organisms evolve from a UNIVERSAL COMMON ANCESTOR
All living organisms evolve from a
UNIVERSAL COMMON ANCESTOR
The Cell Theory, formulated by Schleiden & Schwann, states that
cells are the fundamental units of all living organisms
All living organisms are classified as either
prokaryotic or eukaryotic
Prokaryotic
a combination of the Greek words pro (before) and karyon (nucleus).
These cells therefore lack a nucleus and other membrane-bound organelles
Eukaryotic
a combination of the Greek words eu (true) and karyon (nucleus).
These cells therefore contain a true membrane-bound nucleus as well as a host of membrane-bound organelles
DIAGRAM OF PROKARYOTIC CELL STRUCTURE
DIAGRAM OF EUKARYOTIC CELL STRUCTURE
Size of cells in Prokaryotes and Eukaryotes
Prokaryotes are smaller- typically 0.2-2.0 um in diameter
Eukaryotes are bigger - typically 10-100 um in diameter
membrane enclose organelles in Prokaryotes and Eukaryotes
absent in prokaryotes and present in eukaryotes (eg- lysosomes, golgi complex, endoplasmic reticulum, mitochondria and chloroplasts.
Flagella in Prokaryotes and Eukaryotes
Prokaryotes flagella consists of two protein building blocks
Eukaryotes flagella is complex and consists of multiple microtubules
glycocoalyx in Prokaryotes and Eukaryotes
prokaryotes - present as a capsule or slime layer
Eukaryotes- present in some cells that lack a cell wall
Cell wall in Prokaryotes and Eukaryotes
Prokaryotes - usually present; chemically complex (typically bacterial cell wall includes peptidoglycan
Eukaryotes - when present, chemically simple
Plasma membrane in Prokaryotes and Eukaryotes
Prokaryotes- plasma membrane has no carbohydrates and generally lacks sterols
Eukaryotes - plasma membrane has sterols and carbohydrates that serve as receptors
Cytoplasm in Eukaryotes
Eukaryotes - cytoskeleton; cytoplasmic streaming
Ribosomes in Prokaryotes and Eukaryotes
Prokaryotes - smaller size ribosomes
Eukaryotes - larger size; smaller size in organelles
Chromosome (DNA) in Prokaryotes and Eukaryotes
Prokaryotes - chromosomes usually single circular chromosome; typically lacks histones
Eukaryotes - multiple linear chromosomes with histones
Cell Division in Prokaryotes and Eukaryotes
Prokaryotes - Cell division by binary fission
Eukaryotes - cell division involves mitosis
Sexual Recombination in Prokaryotes and Eukaryotes
Prokaryotes - no sexual recombination; only transfer of DNA fragments only
Eukaryotes - sexual recombination involves meiosis
The prokaryotes comprise the domains
Archaea and Bacteria
How are the two domains distinguished from each other?
Archaea and Bacteria differ primarily in the following characteristics
Cell Wall
Membrane Lipids
Antibiotic Sensitivity
First Amino Acid in Protein Synthesis
There are three (3) major groups of Archaea recognized:
Methanogens
Extreme Halophiles
Extreme Thermoacidophiles
Extreme halophiles
Generally obligate aerobes
Thrive in highly saline environments such as the Dead Sea, the Great Salt Lake & surfaces of salt-preserved foods
Extreme halophiles Generally obligate
aerobes
Extreme halophiles thrive in
highly saline environments such as the Dead Sea, the Great Salt Lake & surfaces of salt-preserved foods
Extreme thermoacidophiles
Optimum growth temperatures usually exceed 80°C
They possess heat-stable enzymes known as extremozymes
Usually colonise hot-springs, hydrothermal vents, etc
Extreme thermoacidophiles optimum growth usually exceed
80°C
Extreme thermoacidophiles possess heat-stable enzymes known as
extremozymes
Diameter of bacteria
Bacteria are typically between 0.5 – 2.0µm in diameter
Human red blood cells measure at about 7.5µm in diameter
Human red blood cells measure at about
7.5µm in diameter
Bacteria have a large surface-to-volume ratio because of
Their small size.
The large surface-to-volume ratio of bacteria means that no internal structure is far from the cell surface allowing rapid access to nutrients from the exterior
Bacteria reproduce by
binary fission
Bacteria are classified according to a number of different criteria:
Morphology
Staining
Nutrition
Growth Characteristics
Physiology
Biochemistry
Genetics
Serology
Phage typing
rRNA sequencing
Protein electrophoretic profiles
Bacteria show a variety of different shapes, however three basic shapes exist
Spherical
Rod-like
Spiral
Coccus bacteria are what shape
Spherical
Bacillus
rod shaped
Spirillium
Spiral-shaped
Coccobacillus shape are
Short rods (intermediate between coccus and bacillus)
Vibrio
comma shaped
Spirochete
Corkscrew-shaped
pleomorphism.
when bacteria demonsrate minor variations in shape within a single species, however some species show major variations in morphology
After cell-division bacteria adopt different cellular arrangements:
Diplococci – bacteria remain in pairs after dividing
Streptococci – bacteria remain attached in a chain-like pattern
Tetrads – bacteria divide in two planes and remain in groups of four
Sarcinae – bacteria divide in three planes and remain in groups of eight
Staphyllococci – bacteria divide in multiple planes and remain in clusters
Diplococci
– bacteria remain in pairs after dividing
Streptococci
bacteria remain attached in a chain-like pattern
Tetrads
bacteria divide in two planes and remain in groups of four
Sarcinae
bacteria divide in three planes and remain in groups of eight
Staphyllococci –
bacteria divide in multiple planes and remain in clusters
Staining involves
colouring the cells with certain dyes that emphasize different features and cellular structures
before staining cells must be
fixed to the slide
Stains are usually
organic salts comprising negative and positive ions, one of which is coloured
Basic dyes are dyes in which
the positive ion is coloured
Acidic dyes are those in which
the negative ion is coloured
Three basic staining techniques are used to classify and identify bacteria:
- Simple Staining
- Differential Staining
- Special Staining
Simple Staining are either
aqueous or alcohol solutions of a single basic dye
the purpose of simple staining is to
visualise the entire microorganism making cellular structure and morphology identifiable
what chemical additive is usually added to simple staining
A chemical additive called a mordant is usually applied to:
Intensify the stain
Increase the affinity of the stain for the specimen
Act as a coating
Examples of simple stains include
crystal violet,
methylene blue &
safrinin
Differential Staining have the advantage of distinguishing between
between different types of bacterial cells since they react variably
Multiple dyes are used in differential staining (the first dye is used to
create the primary stain and a subsequent counterstain is performed using another dye
The two most common differential stains used for bacterial preparations are:
The Gram stain
The Acid-fast stain
The Gram Stain technique is used to
distinguish between two main groups of bacteria and is based on the nature of bacterial cell walls.
Gram-positive bacteria have
cell walls comprising a thick layer of peptidoglycan.
Gram-negative bacteria have
cell walls comprising a thin layer of peptidoglcan sandwiched between the plasma membrane and an outer membrane. (inter-membrane space is known as the periplasm).
Diagram of gram positive bacteria
Diagram of gram negative bacteria
difference between gram positive and negative bacteria diagram
the gram staining procedure
- crystal violet (20 seconds)
- wash (2 seconds)
- grams iodine (1 minute)
- de-colorize with alcohol (until solvent flows colorlessly)
- wash (2 seconds)
- safranin (20 seconds)
- wash (2 seconds)
- blot dry
diagram colour changes that occur at each step in the gram staining process
no colour change for heat fixed cells
colour change for crystal violet and grams iodine
gram positive have a colour change with alcohol
while gram negative is colourless
with safranin gram positive keeps colour change and gram negative turns into a different colour
The Acid-fast Stain is Used to
observe bacteria with high lipid content in cell wall eg Mycobacterium
diagram of acid fast bacteria
The Acid-fast Stain is Mainly used to identify bacteria in the genus Mycobacterium
bacteria in the genus Mycobacterium
The acid-fast stain makes use of the dye
arbol-fuchsin which binds strongly to lipids in the cell wall of these and related bacteria
how does the acid fast stain work
The acid-fast stain makes use of the dye carbol-fuchsin which binds strongly to lipids in the cell wall of these and related bacteria
The fixed bacterial smear is washed with carbol-fuchsin and heated for several minutes to allow penetration into the cells
After cooling, acid alcohol is used to decolourise cells that are not acid-fast and therefore cannot retain the dye
Acid-fast cells are able to retain
the red dye since carbol-fuchsin is more soluble in the waxy lipid components of the cell wall than in alcohol
Counterstaining with methylene blue allows visualisation of
non-acid-fast bacteria
what allows visualisation of non-acid-fast bacteria
Counterstaining with methylene blue
Special Stains are stains that are
very specific and used to identify certain features of microbial cells
Examples of special stains include:
Capsule staining- mostly use of negative staining techniques
Flagella staining
Endospore staining
NEGATIVE STAINING can be used to
detect the presence of diffuse capsules surrounding bacteria
negative staining uses acidic stains such as
negrosin or India ink
Since these negative stains are negatively charged they
cannot penetrate the cells
The surface of bacterial cells is negatively charged
The unstained cells will be easily discernible against the coloured background
advantages of negative staining
No fixing required
Enables visualisation of bacteria that are difficult to stain
diagram of endospore staining - process of sporulation in bacillus
in ENDOSPORE STAINING The spore stain uses
two different reagents
Typical staining procedures do not work for endospore staining due to
the impervious nature of the spore coat
Malachite green is applied to the bacterial smear and heat is applied
How is endospore staining done
Malachite green is applied to the bacterial smear and heat is applied
Both the spore as well as the cell pick up the green stain
Tap water is used as a decolourizing agent, however the endospore retains the green stain since the stain does not have a strong affinity for the vegetative cell components
Safrinin is used as a counterstain
diagram of the bacterial growth curve
bacterial growth curve is
a graph indicating the growth of a bacterial population over time
During batch culture, a typical bacterial growth curve shows five distinct phases of growth:
lag phase, the delay before the start of exponential growth;
exponential phase, where cell division proceeds at a constant rate;
stationary phase, when conditions become unfavorable for growth and bacteria stop replicating
death phase, when cells lose viability; and, finally, long-term stationary phase, which can extend for years
what is the primordial soup theory
the primordial soup contained small organic molecules (monomers) and complex organic molecules (polymers) formed from inorganic materials in the primitive atmosphere.
what is clay theory
A theory that is based on the fact that growing crystals are able to pass on traits to new crystal generations, and that clay crystals may have acted as precursors to genetic genetic material
examples of microbes that can be seen
mushrooms
endospores are bacteria but NOT
Fungi
endospores are resistant structures produced by gram positive bacteria
spontaneous generation theory
aristotle concept that all life on earth originated spontaneously from inorganic matter
organisms that are considered microbes
fungi
bacteria
microscopic algae
nemotodes
virues
protozones
parasites
virolos
satelite viruses
pansermia theory
all life originated from the comits that crashed on earth
direct pansermia
crashed onto earth- directed by some intelligent being
which experiment disproved the spontaenous generation theory
meat in test tube
what type of reaction was used for energy by the earliest microorganisms
anaerobic because oxygen was not present in the atmosphere (it was present in the rocks)
Chemotrophic respiration under anaerobic conditions- the earth was largely inorganic at that time
the earliest photosynthetic organisms were using
sulfur compounds
what were the electron donors used by the earliest photosynthetic micoorganisms on earth
hydrogen and sulfur compounds but later on cyanobacteria
so now water is used as a donor which allowed oxygen to accumulate into the atmosphere
with simple staining, if stained with crystal violet all the cells would appear
purple
with simple staining, if stained with safronin all the cells would appear
pink
simple staining does not
differentiate between the different types of bacterial cells.
