Ch 4 - Microscopy & Identification

Relative Sizes

What other kind of metric measurements will you do?

Volume - liter (dl, ml, l)

what is the equivalent of 1 cc?

Mass - grams (mg, g)

To get a sense of scale, look for “powers of ten” on the Web

http://micro.magnet.fsu.edu/primer/java/scienceopticsu/powersof10/

van Leuwenhoek’s simple microscope

early compound microscope

Light microscope

See 4.7 for how it works

Fluorescent

with dye-antibodies

With dye

Phase-contrast Confocal

Creates very thin “slices” by using precise laser lighting & computer-processing

Transmission electron microscope (TEM)

Scanning electron microscope (SEM)

(images are colorized)

STEM: Rec A protein credit card hologram surface

AFM: toxin from C. perfringens CD surface

Scanned-Probe Microscopy

Wet mount, no stain

Hanging drop: for living, moving microbes

Preparing a smear

Simple stain (crystal violet)

Use a basic/ alkalinedye

(chromo-phore is positively charged)

Negative stain

Use an acid dye

(chromophore is negatively charged)

Differential stains

Gram stain - the most important one to know

Acid-fast stain

Mycobacterium or Nocardia

Endospore stain

Capsule stain with counterstain

Just capsule stain

flagellar stain

Other prokaryotic internal structures (inclusions)

lipid

carboxysomes

sulfur

magnetite

“Bt” toxin

Air bubbles & dirt

Basic Methods

1. collect(see also App. B)

2. amplify

3. inspect

4. identify

Bacterial colonies

Biochemical tests

Serological tests

(Bacterio)phage typing

DNA-based tests

%G+C (%GC)

hybridization-based

“fingerprinting” (restriction fragment polymorphisms)

sequence-based

Dichotomous key (animated description at The Microbiology Place)

taxonomy

phylogeny

How many kingdoms of life?

Two vs. Three vs. Five vs. Six KingdomsProkaryota Bacteria Monera (bacteria) Bacteria

Archaea ArchaeaEukarya Eukarya Protista Protista

Plants PlantsFungi FungiAnimals Animals

Modern Linnaean Taxonomy

(largely based on his ideas)

Domain

(2 mnemonics)

How are organisms actually named? binomial nomenclature (invented by Gaspard Bauhin and Johann Bauhin; Linnaeus (1753) was the first to “popularize”)

species name = genus name + specific epitheteg: Staphylococcus aureus OR

Staphylococcus aureus Capitalized lower case

eg: Homo sapiens

“A species of” = genus name + sp.eg: Staphylococcus sp.

“several species of” = genus name + spp.eg: Homo spp.

Note: Usually can’t say S. aureus or H. sapiens, etc. without 1st using entire name