Microbiology Basic Notes

● Define and compare the terms of magnification and resolution.
Resolution: the ability to distinguish two adjacent objects as distinct and separate,
governs our abilities to see really small
Magnification: Enlarging the image.
● Magnification:
Ocular lens - 10-20X
Objective lenses - 10-100X
At 100X, objects 0.2 micrometer in diameter can just be resolved.
● What is the useful upper limit of magnification for a bright-field microscope? Why is this
so?
2000X, resolution does not approve above this magnification.
● Immersion oil-
It increases the light-gathering ability of a lens by allowing some of the light rays
emerging from the specimen at angles (that would otherwise be lost to the objective
lens) to be collected and viewed.
● Why is resolution a limiting factor?

Although magnification can be increased virtually without limit, resolution cannot,
because resolution is a function of the physical properties of light.
● Types of light microscopes:

bright-field
phase-contrast
differential interference contrast
dark-field
fluorescence
● Bright-field microscope:
specimens are visualized because of the slight differences in contrast that exist between
them and their surrounding medium. Contrast differences arise because cells absorb or
scatter light to varying degrees.
● Compound light microscope:

the microscopes are called
compound because they contain two lenses, objective and ocular,
that function in combination to form the image.
● Why are bacterial cells typically difficult to see well with the bright-field microscope?
Because the cells themselves lack significant contrast with their surrounding medium.
(Pigmented microorganisms are an exception because the color of the organism itself
adds contrast, thus improving visualization).
● Numerical aperture:
resolution is a function of the wavelength of light used and a characteristic of the
objective lens known as its numerical aperture, a measure of light-gathering ability.
● What is the correlation between the magnification of a lens and its numerical aperture?
Lenses with higher magnification typically have higher numerical apertures.
The diameter of the smallest object resolvable by any lens is equal to 0.5
lambda/numerical aperture, which is the wavelength of light used.
(Based on this formula, resolution is highest when blue light is used to illuminate a
specimen and the object has a very high numerical aperture).
● What is the highest resolution possible in a compound light microscope?

0.2 micrometer.
This means that two objects that are closer together than 0.2 micrometer cannot be
resolved as distinct and separate.
Dyes-
● Examples of basic dyes include:

methylene blue, crystal violet, and
safranin.
(Basic dyes are positively charged so they bind strongly to negatively charged cell
components, such as nucleic acids, acidic polysaccharides and also cell surfaces).
● What is differential stain?

Stains that render different kinds of cells different colors are called differential stains. e.g
Gram stain.
● Limiting factor of staining:

It can kill cells and can distort their features.
● Solution -
Phase-Contrast microscopy and Dark-Field microscopy improve image contrast without
the use of stain, and thus do not kill cells. These are
● Phase-contrast microscopy-
* Is based on the principle that cells
differ in refractive index (a factor by which light is slowed as it passes through a material)
from their surroundings.
* Light passing through a cell thus differs in phase from light passing through the
surrounding liquid.
* This subtle difference is amplified by a device in the objective lens of the
phase-contrast microscope called the phase ring, resulting in a dark image on a light
background.
* The ring consists of a phase plate that amplifies the minute variation in phase.
● Dark-field microscope-
* Is a light microscope in which light reaches the specimen from the sides only.
* The only light that reaches the lens is scattered by the specimen, and thus the
specimen appears light on a dark background.
* Resolution by dark-field microscopy is somewhat better than by light microscopy.
* Dark-field microscopy is also an excellent way to observe microbial motility.
● Fluorescence microscope-
* Is used to visualize specimens that fluoresce—that is, emit light of one color.
Cells fluoresce either because they contain naturally fluorescent substances such as–
● chlorophyll
● other fluorescing components, a phenomenon called autofluorescence
● a fluorescent dye
● DAPI
*(4',6-diamidino-2-phenylindole)
* Is a widely used fluorescent dye, staining cells bright blue because it complexes with
the cell’s DNA.
* DAPI can be used to visualize cells in various habitats, such as soil, water, food, or a
clinical specimen.
* Fluorescence microscopy using DAPI or related stains is therefore widely used in–
● clinical diagnostic microbiology
● microbial ecology for enumerating bacteria in a natural environment
● in a cell suspension
● How can cells be made to use fluoresce?

Cells can fluoresce because they contain fluorescent substances such as chlorophyll or
other fluorescing components , which is called autofluorescence or the cells have been
stained with a fluorescent dye.
● Differential interference contrast (DIC) microscopy-

* Is a form of light microscopy that employs a polarizer in the condenser to produce
polarized light (light in a single plane).
* The polarized light then passes through a prism that generates two distinct beams.
* These beams traverse the specimen and enter the objective lens where they are
recombined into one.
* Because the two beams pass through different substances with slightly different
refractive indices, the combined beams are not totally in phase but instead create an
interference effect.
* This effect visibly enhances subtle differences in cell structure.
* Thus, by DIC microscopy, cellular structures such as the nucleus of eukaryotic cells, or
endospores, vacuoles, and granules of bacterial cells, appear more 3-dimensional.
● Atomic force microscopy (AFM)-
* A tiny stylus is positioned extremely close to the specimen such that weak repulsive
forces are established between the probe on the stylus and atoms on the surface of the
specimen.
* During scanning, the stylus surveys the specimen surface, continually recording any
deviations from a flat surface.
* The pattern that is generated is processed by a series of detectors that feed the digital
information into a computer, which then outputs an image.
● How does AFM differ from general electron microscopes?

AFM has the advantage that the specimen does not have to be treated with fixatives or
coatings. The AFM thus allows living specimens to be viewed, something that is
generally not possible with electron microscopes.
● Confocal Scanning Laser microscope (CSLM)-

* Is a computerized microscope that couples a laser source to a fluorescent microscope.
* This generates a three-dimensional image and allows the viewer to profile several
planes of focus in the specimen.
* The laser beam is precisely adjusted such that only a particular layer within a specimen
is in perfect focus at one time.
* By precisely illuminating only a single plane of focus, the CSLM eliminates stray light
from other focal planes.
* Cells in CSLM preparations are typically stained with fluorescent dyes to make them
more distinct.
* CSLM is particularly useful anywhere thick specimens are assessed for microbial
content with depth.
* E.g microbial biofilm, various layers can be observed by adjusting the plane of focus of
the laser beam.
● Can CSLM improve resolution?

Using CSLM it has been possible to improve on the 0.2 micrometer resolution of the
compound light microscope to a limit of about 0.1 micrometer.
● Electron microscopes-
* It uses electrons instead of visible light (photons) to image cells and cell structures.
* Electromagnets function as lenses in the electron microscope, and the whole system
operates in a vacuum. * Electron microscopes are fitted with cameras to allow a
photograph, called an electron micrograph, to be taken.
● The Transmission Electron microscope (TEM)-

* It is used to examine cells and cell structure at very high magnification and resolution.
* The resolving power of a TEM is much greater than that of the light microscope, even
enabling one to view structures at the molecular level.
* This is because the wavelength of electrons is much shorter than the wavelength of
visible light, and wavelength affects resolution.
● Can electron beams penetrate like visible light?

Unlike visible light, however, electron beams do not penetrate very well; even a single
cell is too thick to reveal its internal contents directly by TEM.
● Do specimens need to be prepared to be observed under TEM?

Special techniques of thin sectioning (20–60 nm) are needed to prepare specimens.
These specimens are cut into many thin slices which are then examined individually by
TEM.
● To obtain sufficient contrast, the preparations are treated with stains such as-
* osmic acid,
* permanganate,
* uranium,
* lanthanum,
* lead salts.
(Because these substances are composed of atoms of high atomic weight, they scatter
electrons well and thus improve contrast).
● Negative staining- the results yield a clear cell with a dark background.
● Scanning Electron microscopy (SEM)-

* Here the specimen is coated with a thin film of a heavy metal, such as gold.
* An electron beam then scans back and forth across the specimen.
* Electrons scattered from the metal coating are collected and activate a viewing screen
to produce an image. * In the SEM, even fairly large specimens can be observed, and
the depth of field (the portion of the image that remains in sharp focus) is extremely
good.
* A wide range of magnifications can be obtained with the SEM, from as low as 15X up
to about 100,000X.
● Limiting factor of SEM-

Only the surface of an object is typically visualized by SEM.

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● Define and compare the terms of magnification and resolution.

● Why is resolution a limiting factor?

● Types of light microscopes:

● Compound light microscope:

● What is the highest resolution possible in a compound light microscope?

● Examples of basic dyes include:

● What is differential stain?

● Limiting factor of staining:

● How can cells be made to use fluoresce?

● Differential interference contrast (DIC) microscopy-

● How does AFM differ from general electron microscopes?

● Confocal Scanning Laser microscope (CSLM)-

● Can CSLM improve resolution?

● The Transmission Electron microscope (TEM)-

● Can electron beams penetrate like visible light?

● Do specimens need to be prepared to be observed under TEM?

● Scanning Electron microscopy (SEM)-

● Limiting factor of SEM-

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