MICR 2420: Introduction to Microbiology COMPLETE EXAM
NOTES 2025 University of Guelph
• Anthrax (Bacillus anthracis) used as biological weapon in bioterrorism
RELATIONSHIPS BETWEEN MICROBES AND HIGHER ORGANISMS
• Bioluminescence: a biochemical emission of light by living organisms such as fireflies and
deep-sea fishes caused by light organ; Some symbiotic microorganisms carried within larger
organisms produce light
• Mycorrhiza is a microscopic fungus that attaches to the roots of plants and protects them
from infection
• Cellulose digestion: bacteria in gut of animals helpes them digest cellulose - these
bacteria secrete enzymes that break it down
FOOD
• Lots of fermented food is made by microorganisms giving it characteristic flavours; ex: beer,
bread, yogurt, cheese
WASTE RECYCLING
• Microorganisms important in geochemical cycling
• Plants use energy of the sun to grow --> plant fibre called cellulose converted from CO2
(most abundant organic molecule on earth) is turned into fermentable sugar and then into
ethanol (as well as CO2) by enzymes ---> cars also burn ethanol and release CO2
• CO2 is recycled
HUMAN MICROBIOME PROJECT
• There are 10 times more microorganisms in human body than there is human cells in each
individual
• Composition of gut bacteria generally remains constant and it is unique for each
person
SYNTHETIC BIOLOGY
• Construction of new biological functions or systems not found in nature usually by
genetic engineering of microorganisms
• Photographic film made using engineered bacteria that senses light
ASTROBIOLOGY/EXOBIOLOGY
• microogranisms are thought to be most versatile organisms, so likely that they would
survive on mars
• They can survive harsh cold or hot or dry conditions
INFECTIOUS DISEASES
• Antibiotic resistant microorganisms
, • Mobile - can spread all around the world
• WHO, US CDC, Public Health Agency of Canada
CLASSIFICATION
• Eukaryotes - have nucleus; example: fungi, algae, plants, animals, protists --->
eukarya
• Prokaryotes - don’t have nucleus; example: bacteria ---> archaea and bacteria
• 3 domains of life: eukarya, bacteria, archae
• VIRUSES ARE NOT LIVING SO THEY ARE NOT CLASSIFIED HERE - they cannot
reproduce on their own, they require a host
• Archae: hyperthermophiles (hot), methanogens (can’t live in oxygen), halophiles (like salt)
• In past, all prokaryotes were in Kingdom Monera, now in 2 different domains
NAMING
• 1st name is genus, second name is species
• Italics
• Genus first letter CAPITALS
• Some names don’t mean anything just named after person; other have meanings
• Escherichia coli causes diarrhea
• Yeast (used to make bread) = Saccharomyces cerevisiae
• Enterococcus faecalis = inhabit the gastrointestinal tracts of humans and other mammals
(from the word enteric and faecal). The Bacteria is cocci shape (spherical)
• Vibrio cholerae = causes cholera, a food poisoning disease and has comma shape (Vibrio =
comma shape bacteria)
• Thermus thermophilus = a microorganism that lives in high temperature environments
• Resolution is the smallest distance by which two objects can be separated and still be
distinguished
• Different micropscopes used for different sizes of microbes
• Eukaryotic microbes bigger than prokaryotic
• Eukaryotic = 10-100 um while prokaryotic = 0.4-10um
• Red blood cell = 8um
• Longest bacteria = up to 0.6mm and found in gut of Sturgeon fish
• Fixation and staining improve detection and resolution of cells under microscope
Fixation: cells are made to adhere to a fixed position Staining:
cells are given a distinct colour
- Most stains have conjugated double bonds or aromatic rings, and one or more
positive charges
- Simple stain gives dark colour specifically to cells but not the external medium or
surrounding tissue
- Most common stain is methylene blue
,- A differential stain will only stain one type of cell and not another; gram stain
differentiates between pink and purple bacteria
- Acid fast stain: Carbolfuchsin used to stain Mycobacterium species, wash with acid and then
counterstain with methylene blue (don’t stain well with gram stain) - acid-fast retain red
colour from carbol-fuchsin while non-acid fast get the blue colour since they lost initial dye
- Spore stain: Malachite green used to detect spores of Bacillus and Clostridium
- Negative stain: colours the background which makes capsules more visible
• Gram positive bacteria: retains crytsal violet colour due to thicker cell wall
• Gram negative bacteria: do not retain purple colour; instead are pink
GRAM STAINING PROCEDURE:
1) Both cells are fixed to a surface (BOTH ARE WHITE)
2) Crystal violet stain added to stain both (BOTH TURN PURPLE)
3) Add iodine, which binds stain to gram + bacteria only
4) Wash with ethanol (gram + remain purple while gram - lose colour completely)
5) Add safarin counter stain (gram + still purple while gram - turns pink)
TYPES OF MICROSCOPES
1) Bright field microscopy
- generates dark image overlight background
- improved visibility with contrast
- USED FOR STAINED CELLS (NOT LIVE) SINCE STAINING KILLS THEM; LIVE CELLS ARE
TRANSPARENT
2) Dark field microscopy
- enables microbes to be visualized as halos of bright light against a dark background
- used for bacteria with distinct shape to ensure it’s not a spec of dust or something
- the object scatters light that is collected by microscope objective lens - no staining
only optics and well focused
- light that pass through the medium does not reach the objective lens while light
scattered by the specimen (cells) enters the objective lens
- USED FOR LIVE CELLS AND CELLULAR ORGANISMS
3) Phase contrast microscopy
- Phase contrast microscopy is an optical microscopy technique that converts phase shifts
in light passing through a transparent specimen to brightness changes in the image
- destructive interference = dark = half a wavelenght out of phase
- reveals differences in refractive index as patterns of light and dark
, - the cells and their internal structures appear darker than the surrounding medium
- Phase contrast microscopy is based on the principle that light passing through a dense
object like a cell will be slowed. This refraction leads to destructive interference (waves are
out of phase with incident light) therefore cellular structures appear darker (lower intensity)
than the surrounding media
- CAN SEE INTERIOR
- USED FOR LIVE CELLS AND CELLULAR ORGANISMS
4) Fluorescence microscope
- incident light is absrobed by the specimen and reemitted at a lower energy, thus longer
wavelength
- visualize cells in 3D (confocal)
- need specific fluorescent stains or tags
- The specimen is illuminated with light of a specific wavelenght which is absorbed by the
fluorophores, causing them to emit light of longer wavelengths
- different protein flouresce at different wavelengths: ex neurons each have different
protein so different colour
- USED FOR OBSERVATION OF LIVE MICROBES
5) Electron microscopy
- electrons behave like waves
- VERY GOOD RESOLUTION
- use this for viruses
- STAIN = heavy metal salt
- smaller wavelenght than light
- Need dyes that are electron rich like uranium so they can deflect electrons when you pass
electrons through them - this lets us determine the structure
- sample must absorb electrons and are coated in heavy metal
- electron beam and sample in vacuum
- lenses are magentic fields
a) TEM - Transmission electron microscopy
- electrons pass through the specimen
- reveals internal structures in 2D such as layers
b) SEM - Scanning electron microscopy
- electron scan the specimen surface
- reveals external structures in 3D
SAMPLE PREPARATION
- For SEM, it is not sliced
NOTES 2025 University of Guelph
• Anthrax (Bacillus anthracis) used as biological weapon in bioterrorism
RELATIONSHIPS BETWEEN MICROBES AND HIGHER ORGANISMS
• Bioluminescence: a biochemical emission of light by living organisms such as fireflies and
deep-sea fishes caused by light organ; Some symbiotic microorganisms carried within larger
organisms produce light
• Mycorrhiza is a microscopic fungus that attaches to the roots of plants and protects them
from infection
• Cellulose digestion: bacteria in gut of animals helpes them digest cellulose - these
bacteria secrete enzymes that break it down
FOOD
• Lots of fermented food is made by microorganisms giving it characteristic flavours; ex: beer,
bread, yogurt, cheese
WASTE RECYCLING
• Microorganisms important in geochemical cycling
• Plants use energy of the sun to grow --> plant fibre called cellulose converted from CO2
(most abundant organic molecule on earth) is turned into fermentable sugar and then into
ethanol (as well as CO2) by enzymes ---> cars also burn ethanol and release CO2
• CO2 is recycled
HUMAN MICROBIOME PROJECT
• There are 10 times more microorganisms in human body than there is human cells in each
individual
• Composition of gut bacteria generally remains constant and it is unique for each
person
SYNTHETIC BIOLOGY
• Construction of new biological functions or systems not found in nature usually by
genetic engineering of microorganisms
• Photographic film made using engineered bacteria that senses light
ASTROBIOLOGY/EXOBIOLOGY
• microogranisms are thought to be most versatile organisms, so likely that they would
survive on mars
• They can survive harsh cold or hot or dry conditions
INFECTIOUS DISEASES
• Antibiotic resistant microorganisms
, • Mobile - can spread all around the world
• WHO, US CDC, Public Health Agency of Canada
CLASSIFICATION
• Eukaryotes - have nucleus; example: fungi, algae, plants, animals, protists --->
eukarya
• Prokaryotes - don’t have nucleus; example: bacteria ---> archaea and bacteria
• 3 domains of life: eukarya, bacteria, archae
• VIRUSES ARE NOT LIVING SO THEY ARE NOT CLASSIFIED HERE - they cannot
reproduce on their own, they require a host
• Archae: hyperthermophiles (hot), methanogens (can’t live in oxygen), halophiles (like salt)
• In past, all prokaryotes were in Kingdom Monera, now in 2 different domains
NAMING
• 1st name is genus, second name is species
• Italics
• Genus first letter CAPITALS
• Some names don’t mean anything just named after person; other have meanings
• Escherichia coli causes diarrhea
• Yeast (used to make bread) = Saccharomyces cerevisiae
• Enterococcus faecalis = inhabit the gastrointestinal tracts of humans and other mammals
(from the word enteric and faecal). The Bacteria is cocci shape (spherical)
• Vibrio cholerae = causes cholera, a food poisoning disease and has comma shape (Vibrio =
comma shape bacteria)
• Thermus thermophilus = a microorganism that lives in high temperature environments
• Resolution is the smallest distance by which two objects can be separated and still be
distinguished
• Different micropscopes used for different sizes of microbes
• Eukaryotic microbes bigger than prokaryotic
• Eukaryotic = 10-100 um while prokaryotic = 0.4-10um
• Red blood cell = 8um
• Longest bacteria = up to 0.6mm and found in gut of Sturgeon fish
• Fixation and staining improve detection and resolution of cells under microscope
Fixation: cells are made to adhere to a fixed position Staining:
cells are given a distinct colour
- Most stains have conjugated double bonds or aromatic rings, and one or more
positive charges
- Simple stain gives dark colour specifically to cells but not the external medium or
surrounding tissue
- Most common stain is methylene blue
,- A differential stain will only stain one type of cell and not another; gram stain
differentiates between pink and purple bacteria
- Acid fast stain: Carbolfuchsin used to stain Mycobacterium species, wash with acid and then
counterstain with methylene blue (don’t stain well with gram stain) - acid-fast retain red
colour from carbol-fuchsin while non-acid fast get the blue colour since they lost initial dye
- Spore stain: Malachite green used to detect spores of Bacillus and Clostridium
- Negative stain: colours the background which makes capsules more visible
• Gram positive bacteria: retains crytsal violet colour due to thicker cell wall
• Gram negative bacteria: do not retain purple colour; instead are pink
GRAM STAINING PROCEDURE:
1) Both cells are fixed to a surface (BOTH ARE WHITE)
2) Crystal violet stain added to stain both (BOTH TURN PURPLE)
3) Add iodine, which binds stain to gram + bacteria only
4) Wash with ethanol (gram + remain purple while gram - lose colour completely)
5) Add safarin counter stain (gram + still purple while gram - turns pink)
TYPES OF MICROSCOPES
1) Bright field microscopy
- generates dark image overlight background
- improved visibility with contrast
- USED FOR STAINED CELLS (NOT LIVE) SINCE STAINING KILLS THEM; LIVE CELLS ARE
TRANSPARENT
2) Dark field microscopy
- enables microbes to be visualized as halos of bright light against a dark background
- used for bacteria with distinct shape to ensure it’s not a spec of dust or something
- the object scatters light that is collected by microscope objective lens - no staining
only optics and well focused
- light that pass through the medium does not reach the objective lens while light
scattered by the specimen (cells) enters the objective lens
- USED FOR LIVE CELLS AND CELLULAR ORGANISMS
3) Phase contrast microscopy
- Phase contrast microscopy is an optical microscopy technique that converts phase shifts
in light passing through a transparent specimen to brightness changes in the image
- destructive interference = dark = half a wavelenght out of phase
- reveals differences in refractive index as patterns of light and dark
, - the cells and their internal structures appear darker than the surrounding medium
- Phase contrast microscopy is based on the principle that light passing through a dense
object like a cell will be slowed. This refraction leads to destructive interference (waves are
out of phase with incident light) therefore cellular structures appear darker (lower intensity)
than the surrounding media
- CAN SEE INTERIOR
- USED FOR LIVE CELLS AND CELLULAR ORGANISMS
4) Fluorescence microscope
- incident light is absrobed by the specimen and reemitted at a lower energy, thus longer
wavelength
- visualize cells in 3D (confocal)
- need specific fluorescent stains or tags
- The specimen is illuminated with light of a specific wavelenght which is absorbed by the
fluorophores, causing them to emit light of longer wavelengths
- different protein flouresce at different wavelengths: ex neurons each have different
protein so different colour
- USED FOR OBSERVATION OF LIVE MICROBES
5) Electron microscopy
- electrons behave like waves
- VERY GOOD RESOLUTION
- use this for viruses
- STAIN = heavy metal salt
- smaller wavelenght than light
- Need dyes that are electron rich like uranium so they can deflect electrons when you pass
electrons through them - this lets us determine the structure
- sample must absorb electrons and are coated in heavy metal
- electron beam and sample in vacuum
- lenses are magentic fields
a) TEM - Transmission electron microscopy
- electrons pass through the specimen
- reveals internal structures in 2D such as layers
b) SEM - Scanning electron microscopy
- electron scan the specimen surface
- reveals external structures in 3D
SAMPLE PREPARATION
- For SEM, it is not sliced
