Download presentation
Presentation is loading. Please wait.
1
Introduction to Microbiology Lecture 2
“Small creatures, big impacts” Lecture 2
2
Previous lecture- questions?
Five reasons why microbes are important Differences between Prokaryotes and Eukaryotes Why are ribosomes important? Introduction to Microbiology
3
Introduction to Microbiology
Lecture outline The microbial cell (continued from Lecture 1) The history of microbiology Modern microscopy Microbial diversity Introduction to Microbiology
4
The microbial cell Common shapes of Prokaryotic cells Coccus Rod
Spirillum Spirochete Hypha Stalk Budding and appendaged bacteria Filamentous bacteria The microbial cell
5
The significance of being small
r = 1 µm r = 2 µm Surface area (4πr 2) = 12.6 µm2 Volume ( πr 3) = 4.2 µm3 Surface Volume = 3 Surface area = 50.3 µm2 Volume = 33.5 µm3 = 1.5 43 The microbial cell
6
The significance of being small
Smaller size = larger surface to volume ratio Exchange of nutrients and waste products easier Higher growth rate Same amount of nutrients greater cell density greater number of mutations Greater adaptability The microbial cell
7
The significance of being small
The microbial cell
8
History of Microbiology
9
History of Microbiology
Robert Hooke ( ) 1665: First description of microbes (mold growing on leather History of Microbiology
10
History of Microbiology
Antoni van Leeuwenhoek ( ) 1676: First description of bacteria History of Microbiology
11
History of Microbiology
Antoni van Leeuwenhoek ( ) First description of bacteria . . . my work, which I've done for a long time, was not pursued in order to gain the praise I now enjoy, but chiefly from a craving after knowledge, which I notice resides in me more than in most other men. And therewithal, whenever I found out anything remarkable, I have thought it my duty to put down my discovery on paper, so that all ingenious people might be informed thereof. Antony van Leeuwenhoek. Letter of June 12, 1716 History of Microbiology
12
History of Microbiology
Ferdinand Cohn ( ) Heat-resistant bacteria (Bacillus) and endospore formation Why boiling does not sterilize Large sulfur bacteria (Beggiatoa) History of Microbiology
13
History of Microbiology
Louis Pasteur ( ) Downfall of spontaneous generation Pasteurization Vaccines for anthrax, rabies, fowl cholera Beer! Steam forced out open end Nonsterile liquid poured into flask Neck of flask drawn out in flame Liquid sterilized by extensive heating Dust and microorganisms trapped in bend Open end Long time Liquid cooled slowly Liquid remains sterile indefinitely Short time Flask tipped so microorganism-laden dust contacts sterile liquid Microorganisms grow in liquid History of Microbiology
14
History of Microbiology
Robert Koch ( ) Germ theory of disease Pure cultures- use of potato slices, agar plates (still used today!) Koch’s postulates History of Microbiology
15
History of Microbiology
KOCH’S POSTULATES Tools: Diseased animal Healthy Red blood cell Observe blood/tissue under the microscope The Postulates: 1. The suspected pathogenic organism should be present in all cases of the disease and absent from healthy animals. 2. The suspected organism should be grown in pure culture. Suspected pathogen Microscopy, staining No organisms present Streak agar plate with sample from either diseased or healthy animal Colonies of suspected Laboratory culture 3. Cells from a pure culture of the suspected organism should cause disease in a healthy animal. Experimental animal Diseased animal Inoculate healthy animal with cells of suspected pathogen Remove blood or tissue sample and observe by microscopy Laboratory culture Laboratory reisolation 4. The organism should be reisolated and shown to be the same as the original. Pure culture (must be same organism as before) History of Microbiology
16
History of Microbiology
Robert Koch ( ) Germ theory of disease Pure cultures- use of potato slices, agar plates (still used today!) Koch’s postulates Discovered the cause for Tuberculosis Received Nobel Prize for Physiology or Medicine in 1905 History of Microbiology
17
Sergei Winogradsky (1856-1953)
“Winogradsky columns” Bacteria are important biogeochemical agents Chemolithotrophy (oxidation of inorganic compounds to make food from CO2) Nitrification (oxidation of ammonia to nitrate) Nitrogen fixation (nitrogen gas to ammonia) History of Microbiology
18
Sergei Winogradsky (1856-1953)
Chemolithotrophy Sulfide oxidation Nitrification Chemoautotrophy Nitrogen fixation Protein Nucleic acid ATP ADP + Pi History of Microbiology
19
Optional home exercises
How to make your own Winogradsky column! Read Microbe Hunters or Mikrobenjäger (Paul de Kruif) History of Microbiology
20
From the past to the future
Some previous landmarks van Leeuwenhoek, 1687 (first bacteria) Pasteur, 1861 (spontaneous generation) Koch, 1886 (Koch’s postulates) Watson/Crick,1953 (DNA structure) Phylogenetic stains (Norman Pace) Community sampling of ribosomal RNA genes reveals enormous diversity of bacteria in nature (Norman Pace) Discovery of marine Archaea (Jed Fuhrman and Ed Delong) First genome sequence (Craig Venter and Hamilton Smith) First large scale metagenomics project (Craig Venter) 2010 2004 1995 1992 Year Era of environmental genomics, proteomics and transcriptomics 1987 1986 History of Microbiology
21
Modern Microscopy
22
Microscopy: important concepts
Visualization of microbes: Light or Electron microscopy Magnification: in theory unlimited increase Resolution: Ability to distinguish two neighboring objects Property of the wave Diameter of smallest object resolvable: directly proportional to wavelength Increase is limited by properties of light / electrons Contrast Modern microscopy
23
The importance of resolution & contrast
Modern microscopy 5 X 5 X
24
Light microscopy Modern microscopy Maximum resolution = 0.2 μm
Ocular Objective Stage Condenser Focusing knobs Light source None Specimen on glass slide 10, 40, or 100 (oil) 10 100, 400, 1000 Magnification Light path Visualized image Eye Eyepiece (ocular) lens Intermediate image (inverted from that of the specimen) Objective lens Specimen Condenser lens Field diaphragm [“Light source” in (a)] Modern microscopy
25
Light microscopy Modern microscopy Staining increases contrast
100 Slide Dry in air Flood slide with stain; rinse and dry Place drop of oil on slide; examine with 100 objective lens Spread culture in thin film over slide Pass slide through flame to heat fix Oil I. Preparing a smear III. Microscopy II. Heat fixing and staining Modern microscopy
26
Gram-staining Modern microscopy Step 1 Step 2 Step 3 Step 4 Result:
Gram-positive cells are purple; gram-negative cells are colorless Step 1 All cells remain purple Step 2 Step 3 Step 4 Counterstain with safranin for 1–2 min G– G+ All cells purple (G+) cells are purple; gram-negative (G–) cells are pink to red Decolorize with alcohol briefly — about 20 sec Add iodine solution for 1 min Modern microscopy
27
Bright-field, Phase contrast & Dark-field
Special ring in objective lens Enhances differences in refractive index View cells without staining Dark-field: Light incident from sides Improves contrast Modern microscopy Light-field Phase-contrast Dark-field
28
Fluorescence microscopy
Cyanobacteria-light Fluorescence: Incident light of one wavelength causes specimen to emit light at a different wavelength Natural or “auto- fluorescence” (AF) Fluorescent dyes Modern microscopy Cyanobacteria-AF DAPI stain
29
Modern microscopy DIC & AFM DIC: AFM
Differential interference contrast Polarized light AFM Atomic force microscopy Weak repulsive atomic forces between sample and probe DIC Modern microscopy AFM
30
Modern microscopy Electron Microscopy
Electron beams; Maximum resolution = 0.2 nm TEM: Transmission electron microscopy Intracellular details Thin sections, Heavy metal salts SEM Scanning electron microscopy Gold coating Surface only Modern microscopy
31
Electron Microscopy: TEM & SEM
DNA (nucleoid) Cell wall Cytoplasmic membrane TEM of viruses Modern microscopy TEM of bacterial cell SEM of bacteria
32
Microbial diversity
33
Microbial diversity Evolution Phylogeny
“Change in a line of descent over time leading to new species and varieties” Phylogeny Evolutionary relationships between organisms Microbial diversity
34
Phylogenetic trees Microbial diversity http://tolweb.org/tree/
35
Phylogenetic trees Microbial diversity
36
Phylogenetic trees Microbial diversity Ribosomal RNA
Present in all living organisms Ribosomal DNA: used widely to construct phylogenetic relationships Introduced by Carl Woese (1977) Microbial diversity Aligned rRNA gene sequences Generate phylogenetic tree Sequence analysis DNA sequencing PCR Gene encoding ribosomal RNA DNA Isolate Cells
37
The tree of life: 3 domains
Eukaryotic “Crown species” BACTERIA EUKARYOTES PROKARYOTES EUKARYA ARCHAEA Animals Fungi Plants Slime molds Flagellates Giardia Extreme halophiles Methanogens Hyperthermophiles Gram-positive bacteria Proteobacteria Mitochondrion Cyanobacteria Chloroplast Root of the tree Microbial diversity
38
Microbial diversity
39
Types of diversity Microbial diversity
Microbial cells- nearly 4 million years of evolution Diversity Cell size and morphology Metabolic strategies (physiology) Adaptation to extreme environments Reproductive biology Developmental biology Interactions with other organisms Microbial diversity
40
Metabolic diversity Microbial diversity Chemoorganotrophs
Chemicals Phototrophy Chemoorganotrophs Light Chemotrophy Chemolithotrophs Phototrophs (light) (H2 + O2 H2O) CO2 + H2O) (glucose + O2 Organic chemicals Inorganic (glucose, acetate, etc.) (H2, H2S, Fe2+, NH4+, etc.) Microbial diversity
41
Metabolic diversity Microbial diversity All cells require C
Heterotrophs C from organic compounds Depend on other organisms to make the organic compounds Chemoorganotrophs Autotrophs CO2 is the C source Known as “primary producers” Most Chemolithotrophs, almost all Phototrophs Microbial diversity
42
Bacterial diversity Microbial diversity Spirochetes Green sulfur
Proteobacteria Aquifex Gram-positive bacteria Thermotoga Deinococcus Planctomyces Chlamydia Cyanobacteria Green sulfur Green nonsulfur OP2 Spirochetes Microbial diversity
43
Bacterial diversity Microbial diversity Bacteria: all known pathogens
Proteobacteria Largest division (Phylum) of Bacteria Chemoorganotrophs, e.g. Escherichia coli Phototrophs, e.g. Purple sulfur bacteria Oxidize H2S instead of H2O during photosynthesis Produce SO42- instead of O2 Microbial diversity
44
Purple sulfur bacteria
Proteobacteria Purple sulfur bacteria Purple S bacteria Microbial diversity
45
Bacterial diversity Microbial diversity Bacteria: all known pathogens
Proteobacteria Largest division (Phylum) of Bacteria Chemoorganotrophs, e.g. Escherichia coli Phototrophs, e.g. Purple sulfur bacteria Oxidize H2S instead of H2O during photosynthesis Produce SO42- instead of O2 Chemoautotrophs e.g. Beggiatoa Large gliding bacterial filaments Oxidize H2S and uses energy to make organic C from CO2 Microbial diversity
46
Proteobacteria Microbial diversity Beggiatoa
Proteobacteria Beggiatoa Microbial diversity
47
Bacterial diversity Microbial diversity Gram-positive bacteria
Stain purple with Gram staining process Examples: Bacillus- spore forming Streptococcus : some are pathogenic Microbial diversity Streptococcus Bacillus
48
Bacterial diversity Microbial diversity Cyanobacteria
Oxygen producing photoautotrophs First oxygenic phototrophs on Earth- made the atmosphere oxygen rich Some can fix nitrogen (N2 -> NH3) Microbial diversity Filamentous cyanobacteria Modern-day stromatolites
49
Bacterial diversity Microbial diversity
Green sulfur bacteria, e.g. Chlorobium Photoautotrophs Green non-sulfur bacteria, e.g. Chloroflexus Hot springs, stratified microbial mats Microbial diversity Chlorobium Chloroflexus
50
Microbial diversity Bacterial diversity
Early branching lineages: Aquifex, Thermotoga Growth at very high temperatures (near boiling point of water) Early Earth was much warmer- descendents of ancient bacteria Microbial diversity
51
Microbial diversity Archaeal diversity
Two main subdivisions: Euryarchaeota, Crenarchaeota Thermoplasma Euryarchaeota Crenarchaeota Desulfurococcus Methanopyrus Pyrolobus Thermoproteus Pyrococcus Methanocaldococcus Methanobacterium Sulfolobus Halobacterium Natronobacterium Methanosarcina Marine group Halophilic methanogens Microbial diversity
52
Microbial diversity Archaeal diversity Many Archaea are extremophiles:
High temperatures, extreme pH E.g. Pyrolobus (optimum temperature : 106˚C at deep-sea Hydrothermal vent) Microbial diversity
53
Microbial diversity Archaeal diversity All Archaea are chemotrophs
Many are chemolithotrophs (H2 : common energy source) Exception: Halobacterium can make food from light Salt-loving (live in salt-lakes) No chlorophyll but rhodopsin Microbial diversity
54
Microbial diversity Archaeal diversity
Euryarchaeota are metabolically diverse Extremely high and extremely low pH Some need oxygen Some are poisoned by oxygen (strict anaerobes), e.g. Methanogens Degrade organic matter, reduce CO2 to CH4 Produce almost all of Earth’s methane Found 3 km deep in Earth’s subsurface! Microbial diversity
55
Microbial Eukaryotic (Protist) diversity
Flagellates Slime molds Trichomonads Diplomonads Early-branching, lack mitochondria Brown algae Diatoms Ciliates Animals Green algae Plants Red algae Fungi Microbial diversity
56
Microbial Eukaryotic (Protist) diversity
Algae Photoautotrophic (chlorophyll); have cell walls Major primary producers (produce food) Soil, freshwater and marine environments Phytoplankton, e.g. Diatoms: microscopic algae in the ocean: basis of food chain Microbial diversity
57
Microbial Eukaryotic (Protist) diversity
Fungi Unicellular (yeast) Filamentous (molds) Biodegradation and recycling of nutrients Have cell walls Microbial diversity
58
Microbial Eukaryotic (Protist) diversity
Lichens Symbiosis between fungi and algae/ cyanobacteria Rock weathering Extreme environments- deserts, glaciers, etc. Microbial diversity
59
Microbial Eukaryotic (Protist) diversity
Protozoans Lack cell wall Heterotrophic: consumers, decomposers Important food source for higher organisms E.g. Ciliates (Paramecium) Amoeboids Microbial diversity
60
Protozoans relevant to Geologists
Foraminiferans Amoeboid Shells or “tests” made of calcium carbonate or agglutinated sediment Fossil record: Cambrian- present Biostratigraphy Limestone formation Microbial diversity
61
Protozoans relevant to Geologists
Radiolarians Amoeboid Shells made of silica Important fossil record Siliceous ooze Microbial diversity
Similar presentations
