Microbial Diversity; Optical

Tools
BOD- Bacillus calmette-guerin
BCG Live
Anticancer drug,
notably Bladder
cancer
Acts as a super
antigen
 Energy Classification
Chemoorganotrophs-energy from organic
sources (glucose, acetate, amino acids,
etc.)
Chemolithotrophs- energy from inorganic
compounds (H2, H2S, Fe2+, N2O, NH4+)
Phototrophs-Energy derived from light
Growth at the Extremes
Thermophiles-Growth
typically 45C to 70C
Hyperthermophile-
growth above 100C
(120C current max)
Thermo vents
Acidophiles-pH below
3 Volcanic hot springs
Psycrophiles- Growth around 4C
Sea Ice-Mostly Bacteria
 Mesophiles
Growth in the middle
temperatures-10 C to
42 C
Alkaliphiles-pH above 10- Soda
Lakes
Acidophiles
Halophiles-25% NaCl- Desert
Lakes
-Mostly Archaea
Tree of Life-The Domains of Carl
Woese
 Domain-Bacteria
Two main divisions
Proteobacteria
Contain all known
pathogens
Most bacteria that we
generally think of
belong here
Odd organisms too
Cyanobacter
Photosynthetic
bacterium
 Other unusual Bacteria groups
Planctomyces-Stalked aquatic bacteria
Green Sulfur/ Purple Sulfur bacteria-
Contains photosynthetic pigments
Chlamydia- Obligate intercellular parasites
Deinococcus-
Aquifex/Thermotoga-thermophylic bacteria
Rickettsia-
Mycoplasma-no cell wall
Domain Bacteria (Eubacteria)
 Archaea-Generally Extremophiles
Methanogens-Methanococcus,
Methanobacterium, etc.
Halophiles-Halobacterium
Therophiles-Pyrococcus
Sulfur utilizing archaeas-Desulfurococcus
Archaea
Light Microscope
Magnification 10X to
1000X with oil
Why oil objectives?
Properties of light
Theoretical limit of
magnification 0.2 m
Dark Phase
Dark background
Light refracts through
organism light source
on the side.
Can visualize live
bacteria, more
typically used for
larger organisms
Phase Contrast
Specimen appears
dark
Useful for live
specimens.
Useful to visualize
flagellum in bacteria
Requires a special
objective
Bright-field
Need a specimen with
high contrast.
For bacteria need to
mount and stain.
Brightness
Subject is in focus
Contrast
Resolution
Determining Size of a Specimen
A known scale is used
to measure the
diameter of the FOV
of an objective
Once you have the
FOV of one objective
lens, the FOV's for
the other objectives
are proportional
 For example, the FOV for
the image to the left is 4.5
mm (4500m) using a 4x
objective.
Using a 40x objective the
FOV of the image would
be 0.45 mm (450m),
which is a 10 times
increase in
magnification, and a 10
times decrease in the
diameter of the FOV
Subject size Determination
Size of a feature is
worked out by
dividing the FOV by
the number of times
that the feature will fit
across the FOV.
FOV for 4x obj = 4.5
mm or 4500 m
With the 10X Objective
then
FOV for 10x obj = (4 /10 ) x
4.5
= 1.8 mm or 1800m
Lining Cell A up would be
~2.5 times across the
diameter of the FOV,
therefore, the size of the cell
is 1.8 mm divided by 2.5.
1.8 / 2.5 = 0.72 mm
OR
1800 / 2.5 = 720m
Transmission Electron Microscope
Electrons pass
through thin specimen
Contrast electron
dense and thin areas
Specimen is prepared
by immobilization and
is shaved thin
Point resolution of 5
Angstroms or better
Scanning Microscope
Specimen coated in metal
(Osmium alloy, Gold, etc)
Electron beam deflected
off specimen
Magnification 15X to
100,000X
Only the surface of
organisms can be seen.
Scanning Tunnel Electron
Microscope
shows three-
dimensional images
of a sample.
Can see DNA
structure