03/28/2011

Chapter 6: Microbial Growth

* Refer to pictures
The Requirements for Growth
 Physical requirements
o Temperature
 Minimum growth temperature
 Optimum growth temperature
 Maximum growth temperatue
o pH
o osmotic pressure
 Chemical Requirements
o C,N, S, P, trace elements, oxygen, organic growth factor
 Plasmolysis (Fig. 6.4)
Psychropiles/psychotrophes
 Grow between 0-15C and 10-25C
 Cause food spoilage
pH
 Most bacteria grow bw pH 6.5-7.5
 Molds and yeasts grow bw pH 5-6
 Acidophiles grow in acidic environment
Osmotic Pressure
-Hypertonic environments or an increase in slat or sugar cause plasmolysis
-Extreme or obligate halophiles require high osmotic pressure (ie 30% salt – Great Sea, Red Sea)
-Facultative halophiles can tolerate high osmotic pressure (2%-15% salt)
What would happen if cell put into distilled water?
Plasmolysis*

Chemical Requirements for Bacterial Growth

Carbon
 Structural organic molecules, energy source
 Chemoheterotrophs use organic carbon sources
 Autotrophs use CO2
Nitrogen
 Amino acids and proteins
 Most bacteria decompose proteins (recycle)
 Some bacteria use ammonium ions NH4 or nitrate ions
 A few bacteria(cyanobacteria) use N2 in nitrogen fixation
Sulfur
 In amino acids, thiamine, and biotin
 Most bacteria decompose proteins to get sulfur
 Some bacteria use SO4-2 or H2S
 Phosporus
 In DNA, RNA, ATP and membranes
 PO43- is a source of phosporus
Trace Elements
 Inorganic elements required in small amounts
 Usually as enzyme cofactors
The Effect of Oxygen on Microbial Growth (Table 6.1)
A. obligate aerobe- needs oxygen to survive
B. facultative anaerobe- retain the ability to ferment to undergo anaerobic metabolism. Organisms not on
top are facultative anaerobe. eg. E.Coli
C. obligate anaerobe- cannot use molecule oxygen, but they can use oxygen from water eg. Plastrinium-
causes tetanus and botulism
D. Aerotolerant anaerobe-they don’t use oxygen but can still grow in the presence of it.
E. Microaerophile-can only grow in a very SPECIFIC level of oxygen

Toxic Oxygen
Singlet oxygen: O2- boosted to a higher energy state
Superoxide radicals O2-
 When you use oxygen as an electron acceptor
 Try to grab electrons from nearest molecule
 SOD (enzyme)* o
O2-2+ O2-2 +2H+  * H2O2 +O2
Peroxide anion O2-2
 catalase or peroxidase – neutralize H2O2
 catalase- produce H2O and O2
 peroxidase- H2O
Hydroxyl radical (OH-)
 Happens in cytoplasm
 Through ionizing radiation
 All of these could be toxic to humans or bacteria
Organic Growth Factors
-Organic compounds obtained from the environment. Varies from organism to organism
-Vitamins, amino acids, purines, and pyramidines

Biofilms (Fig 6.5)

-Microbial communities
-form slime or hydrogels
 bacteria attracted by chemicals via quorum sensing: communication between one cell and another.
Drugs to block the quorum sensing receptors.
 “place gets too crowded, people have to leave.”
 Important in digestive systems of cows. Need to digest cellulose.
 Grow upwards to increase surface area. Causes bacterial infections.
-share nutrients
-sheltered from harmful factors
- patients with indwelling catheters received contaminated heparin.
 -bacterial numbers in contaminated heparin were too low to cause infection
-84-421 after exposure, patients developed pseudomonas infection
-Pseudomonas fluorescens were cultured from catheters.
-What happened?
 They grew and multiplied by themselves.
 They are antibiotic resistance.
 Heparin might signal biofilm growth
Table 6.2: A chemically defined medium for growing a typical chemoheterotroph, such as E.Coli
Table 6.4: Composition of Nutrient Agar, a Complex medium for the growth of heterotrophic bacteria
Culture Media
-Culture Media: nutrients prepared for microbial growth.
-Sterile: no living microbes
-Inoculum: introductions of microbes intro mediums
-Culture: microbes growing in/on culture medium
Growing a Culture
-nutrients
-pH
-moisture
-oxygen
-initially sterile
Agar
-Complex polysaccharide
-Used as solidifying agent for culture media in Petri plates, slants, and deeps
-Generally not metabolized by microbes
-Liquefies at 100C
-Solidifies at ~40C
Culture Media (Table 6.2, 6.4)
-Chemically defined media: exact chemical composition is known
-complex media: you don’t know the exact compositions. Include extracts and digests of yeasts, meats or
plants
 Nutrient Broth
 Nutrient Agar
Anaerobic Culture Methods
 Anaerobic jar (fig. 6.6)
 Anaerobic chamber (fig. 6.8)
Reducing media
-Contains chemicals (thioglycolate or oxyrase) that combine O2.
-Heated to drive off O2.
 Figure 6.6, 6.7
Capnophiles
-microbes that require high CO2 conditions
-CO2 packet
-Candle jar
-multiple methods present
Biosafety Level
1:No special precautions
2: Lab coats, gloves, eye protection
3: Biosafety cabinets to prevent airborne transmission
4: Sealed, negative pressure
Selective Media
-suppress unwanted microbes and encourage desired microbes.
-chemically defined: salt media is preventing some bacterial species while allowing others to grow
-Staphylococcus aureus- metabolizes manatose to make acidic environment (yellow)
- Staphylococcus epidermidis- growing but basic
Differential Media
-make it easy to distinguish colonies of different microbes
Enrichment Culture
-encourages growth of desired microbe
-assume a soil sample contains a few phenol-degrading bacteria and thousands of other bacteria
 inoculate phenol-containing culture medium with soil and incubate
 transfer 1 mL to another flask of the phenol medium, and incubate
 transfer 1 mL to another flask of the phenol medium and incubate
 only phenol-metabolizing bacteria will grow after much dilutions later.
Binary Fission (Fig 6.12A)
 Cell Division
Bacterial Growth Curve

Obtaining Pure Cultures

-A pure culture contains only one species or strain
-A colony is a population of cells arising from a single cell or spore or from a group of attached cells.
-A colony is often called a colony-forming unit (CFU)
-The streak plate method is used to isolate pure cultures
Preserving Bacterial Cultures
-deep freezing: -50C to -95C
-Lyophilization (freeze-drying): frozen (-54 to 72C) and dehydrated in a vacuum.
The Growth of Bacterial Culture
Reproduction in Prokaryotes
 Binary fission
 Budding
 Conidiospores (actinomycetes)-chains when they reproduce
 Fragmentation of filaments
 Bacterial growth happens exponentially- based on generation number and binary fission can figure out
how many cells are being made.
Generation Time
 If 100 cells growing for 5 hours produced 1,720,320 cells:
o Number of generation= [log #of cells (end) –log #cells (beg)]/(0.301)  log of 2
o Generation time= (60min x 5hours)/ number of generations= 21 min/generation.
 Bacterial Growth Curve
Phases of Growth (log graph, not linear)
1. Lag phase
-not much bacterial growth
-no exponential growth
2. Log phase
-exponential growth
-assuming optimal conditions
-reaches point of capacity
3. Stationary phase
-# cells growing = # cells dying
-no exponential growth
4. Death phase
-nutrients have been used up
-exponential decrease
Direct Measurement of Microbial Growth
1. Serial Dilutions
1:10 – 9 mL broth in each tube
1:100
1:1000
1:10,000
1:100,000
2. Plate Counts
a) pour plate method
b) the spread plate method
3. Plate Counts
 After incubation, count colonies on plates that have 25-250 colonies (CFUs)
4. Counting Bacteria by Membrane Filtration
Fig 6.18
5. Direct Microscopic Count
-Serial dilution must be performed
-number of bacteria/mL= #of cells counted/ volume of area counted
6. Turbidity
Direct Methods Indirect Methods
-plate counts -turbidity
-filtration -metabolic activity
-MPN -dry weight
-direct microscopic count
 03/28/2011
The terminology of microbial control
-Sepsis-microbial contamination
-Asepsis- the absence of significant contamination
-Aseptic surgery-prevent microbial contamination of wounds
Sterilization- removing all microbial life
Commercial sterilization- killing C. botulinum endospores
Disinfection- removing pathogens
Antisepsis- removing pathogens from living tissue
Degerming- removing microbes from a limited area
Sanitization- lowering microbial counts on eating utensils
Biocide/germicide- kills microbes
Bacteriostasis- inhibiting growth, NOT killing

Population Death Rate is Constant

A Microbial Death Curve (fig 7.1 A)

Actions of Microbial Control Agents

 alternation of membrane permeability
 damage to proteins
 damage to nucleic acids
Heat
 Thermal death point (TDP)-lowest temperature at which all cells in a culture are killed in
10 min.
 Thermal death time (TDT)- time during which all cells in a culture are killed.
Decimal Reduction Time (DRT)
 Minutes to kill 90% of a population at a given temperature (fig 7.2)
Moist Heat Sterilization
 Moist heat denatures proteins
 Autoclave: steam under pressure
Steam Sterilization
 Steam must contact item’s surface
Pasteurization
 Reduces spoilage organisms and pathogens
 Equivalent treatments
 63 C for 30 min
 High temperature short time- 72C for 15 sec
 Ultra high temp- 140 C for <1 sec
 Thermoduric organisms survive
Dry Heat Sterilization
 Kills by oxidation
o Dry heat
o Flaming
o Incineration
o Hot-air sterilization

Hot Air Autoclave

Equivalent treatments 170 C, 2 hr 121 C, 15 min
Filtration
 HEPA removes microbes > 0.3 uM
 Membrane filtration removes microbes > 0.22 uM
Physical Methods of Microbial Control
 Low temp inhibit microbial growth
o Refrigeration
o Deep freezing
o Lyophilization
 High pressure denatures proteins
 Dessication prevents metabolism
 Osmotic Pressure causes plasmolysis
Radiation
 Ionizing radiation (X rays, gamma rays, electron beams)
o Ionizes water to release OH
o Damages DNA
 Nonionizing radiation (UV, 260 nm)
 o Damages DNA
 Microwaves
o Kill by heat; not especially antimicrobial
Principles of Effective Disinfection
 Concentration of disinfectant
 Organic matter
 Time
 pH
Use Dilution Test
 Metal rings dipped in test bacteria are dried
 Dried cultures are placed in disinfectant for 10 minutes @ 20C.
 Rings are transferred to culture media to determine whether bacteria survived treatment.
Disk Diffusion Method
Phenols and Phenolics
 Disrupt plasma membranes
Bisphenols
 Hexacholorphene triclosan
o Disrupt plasma membranes
Biguanides
 Chlorhexidine
o Disrupt plasma membranes
Halogens
 Iodine
o Tinctures: in aq. Solution
o Iodophors: in organic molecules
o Alter protein synthesis and membranes
 Chlorine
o Bleach: HOCl (hypochlorous acid)
o Chloramine: chlorine + ammonia
o Oxidizing agents
 03/28/2011
TRANSCRIPTION-NUCLEUS
Fig. 8.10
Eukaryotes: nucleus
Prokaryotes: cytoplasm

Fig 8.11 : RNA Processing in Eukaryotes

DNA  RNA transcript  mRNA
Exons- are expressed
Introns- intervening sequences
 Has to be removed
 In order to be translated for protein synthesis
 snRNPs

TRANSLATION- CYTOPLASM
Fig 8.2
-mRNA is translated in codons (three nucleotides)
-translation of mRNA begins at start codon: AUG (meth)
-Translation ends at nonsense codons: UAA, UAG, UGA
-64 sense codons on mRNA encode the 20 amino acids
the genetic code is degenerate
tRNA carries the complementary anticodon
 The Genetic Code (fig 8.8)
 Note the degeneracy
Simultaneous Transcription and Translation (fig 8.10)
 Cannot happen in eukaryotes
 DNA/RNA stuck in nucleus

The process of Translation (fig 8.9)

AUG codon  tRNA anticodon ribosomal units attaches
EPA sites
New protein

The Regulation of Gene Expression

Regulation
-Constitutive genes are expressed at fixed rate
~60-80% of genes
-Other genes are expressed only as needed
 Repressible genes
 Inducible genes
 Catabolite repression
Operon
Fig 8.12
DNA Regulatory gene  Promoter*  Operator*
 *Not genes: causes polymerase to bind
 Operator: acts as a stop light
Structural Genes: Z Y A enzymes that ferments lactose (E. Coli)
Regulatory gene: also a repressible protein (turns on AND off)
Induction
-Fig 8.12
-Lac operon when there is no lactose.
-RNA polymerase binds at promoter, repressor binds the operator
- Lac operon when there is lactose PRESENT
 Allolactose binds the repressor protein shape- no longer binds the operator.
 RNA polymerase can go ahead and make structural genes Z Y A
Repression
-Fig 8.13
-Structural genes: E D C BA
 encoding for different genes: tryptophan synthesis
 Repressor protein is ALWAYS on
o Cannot bind at O, operator site
Once tryptophan is made
 Binds inactive repressor protein
  Blocking RNA polymerase
 Tryptophan: co repressor
 Allolactose: co- inducer
Catabolite Repression
Fig 8.14a & b
- Constitutively active genes
-Preference energy source is GLUCOSE
 growth rate is much faster than LACTOSE
-When glucose runs out, cAMP builds up
 cAMP= alarm mode
 Lag time
 Then, metabolizes LACTOSE
Lactose PRESENT, no GLUCOSE
cAMP  Inactive CAP Active CAP Promoter (extra red flag encouraging RNA polymerase
to bind there: promoting lactose metabolism)
 Fig. 8.15
LACTOSE +GLUCOSE Present
 Inactive CAP
 RNA polymerase cannot bind
 Inducer- allolactose

Mutation
 -A change in the genetic material
-Mutations can be neutral, beneficial, or harmful
 Neutral: Triplet code codes for the same amino acid
o Non-gene encoding regions: neither beneficial or harmful
-Mutagen: agent that causes mutations
-Spontaneous mutations: occurs in the absence of mutagen.

Fig 8.17a, b,c,d

Base substitution (point mutation)- change in one base
 Sickle cell disease
Missense mutation- Constitutively active genes result in change in amino acid
Nonsense mutation- results in a nonsense codon. Peptide sequence cuts short, protein isn’t being
made.
Frameshift mutation- insertion or deletion of one or more nucleotide pairs
 Huntington’s Disease: accumulates in nerve cells
The Frequency of Mutation
 Spontaneous mutation rate = 1 in 10^9 replicated base pairs or 1 in 10^6 replicated genes.
 Mutagens increase to 10^-5 or 10^-3 per replicated gene
Chemical Mutagen (fig 8.19a)
 Nitrous Acid
 Nucleotide analog: looks like correct DNA base but they are NOT
Radiation
 Ionizing radiation (X rays and gamma rays) causes the formation of ions that can react with
nucleotides and the deoxyribose-phospate backbone
 Wave that breaks covalent bonds
UV Radiation and Repair (fig 8.20)
 Photolyases separate thymine dimmers
 Nucleotide excision repair
 DNA polymerase makes the repair
Selection*
Positive (direct) selection detects mutant cells because they grow or appear different.
Negative (indirect) selection detects mutant cells because they do not grow
 Replica plating- (recorded)
 Fig 8.21- Looking for a auxotrophic mutation- being able to metabolize something
Ames Test for Chemical Carcinogens
Fig 8.22
Amount of mutation that forms- increased incidents of cancer
Media lacking histidine  Incubation into Colonies of revertant bacteria
 Salmonella + Rat liver extract
Genetic Recombination
-Vertical gene transfer: occurs during reproduction between generations of cells
-horizontal gene transfer: Gene transfer between organisms without reproduction
-Exchange of genes between two DNA molecules
 Crossing over occurs when two chromosomes break and rejoin
 Fig 8.23
Fig 8.25
-Circular chromosome
-DNA gets into the bacterial cell
-One piece of DNA will replace the other
-Result: Genetically transformed cell
Fig 8.24 Griffith Experiment
-Bacteria was encapsulated
-Injected encapsulated bacteria into mouse dies.
-injected nonencapsulated bacteria into mouse  sick.
-dead bacteria into mouse  lives
-Mixed bacteria  mouse dies due to genetic transformation
Fig 8.26 Bacterial Conjugation
-One bacteria on one species can contact another species and can change genetic material
Fig 8.27a.b,c Conjugation of E. Coli
 F+ (has f factor), F-, Hfr (f+ recombined with chromosome)
 Hfr + F-  Hfr cell + Recombinant F- cell
Fig 8.28 Transduction by a Bacteriophage
-Usually talks about viruses
-Transfers DNA from one host to another

Plasmids
Conjugative plasmid-carries genes for sex pilli and transfer of the plasmid
Dissimilation plasmids-
R factors-

R factors, a Type of Plasmid (fig 8.29)

 Origin of replication
 Similar map to bacterial chromosome- like a clock
Transposons (Fig 8.30a b c)
 Segments of DNA that can move from one region of DNA to another
 Contain insertion sequences for cutting and resealing DNA (transposase)
 Complex transposons carry other genes
Chapter 9 03/28/2011
Biotechnology and Recombinant DNA
 Biotechnology- use of microorganisms, cells, or cell components, to make product
o Foods, antibiotics, vitamins, enzymes
 Vector- self replicating DNA used to carry the desired gene to a new cell
 Clone- population of cells arising from one cell, each carries the new gene
 Recombinant DNA
o Insertion or modification of genes to produce desired proteins.
Fig 9.1 : A Typical Genetic Modification Procedure
1. Vector, such as plasmid is isolated (human insulin gene)
2. GO back into the bacteria
3. Make many copies
 OR Protein products of gene
 GMOs, or foods, hormones
Table 9.2 : Used in pharmaceutical industry
Interesting Facts
Restriction Enzymes
 Cut specific
PCR
Inserting Foreign DNA into cell
 DNA can be inserted into a cell by
o Transformation
 o Electroporation
o Protoplast fusion fig 9.5b
o Gene Gun
o Microinjection fig 9.6, 9.7
o
Obtaining DNA
 Complementary DNA (cDNA) is made from mRNA by reverse transcriptase (fig 9.9)
 Synthetic DNA is made by a DNA synthesis machine
 Selecting a Clone (fig 9.11)
o Putting obtained DNA into a special vector
o Vector inserted into bacteria
o Grown in a special plate
o Grows in certain color/ certain environment
o Obtain DNA of sequence
Making a Product (vector for gene expression or the gene itself)
 E.Coli
o Used because it is easily grown and its genomics are known
o Cells must be lysed to get product
 Sacchromyces cerevisiae
o Used because it is easily grown and its genomics are known.
o May express eukaryotic genes easily
 Plant cells and whole plants
o May express eukaryotic genes easily
o Plants are easily grown
 Mammalian cells
o May express eukaryotic genes easily
o Harder to grow
Therapeutic Applications
Human enzymes and other proteins
Subunit vaccines
Non pathogenic viruses carrying genes for pathogen’s antigens as DNA vaccines
Gene therapy to replace defective or missing genes

RNA Interference (RNAi)

 Interference with RNA, cannot be used for translation
 Transcript control: cleaved. A way to gene silencing vs. gene knock out
The Human Genome Project
 Nucleotides have been sequenced
  Human Proteome Project may provide diagnostics and treatments
o Reverse genetics: block a gene to determine its function
Scientific Applications
 Understanding DNA
 Sequencing organisms’ genomes
 DNA fingerprinting for identification (fig 9.17)
Forensic Microbiology
 PCR
 Primers for a specific organism will cause amplification if that organism is present
 Reverse-trancription (RT-PCR): Reverse transcriptase makes DNA from viral RNA or
mRNA. Real time PCR is different
Chapter 10: Classification 03/28/2011
Taxonomy
  The science of classifying organisms
 Provides universal names for organism
 Provides a reference for identifying organisms
Systematics, or Phylogeny
 The study of evolutionary history of organisms
 All Species inventory (2001-2005)
o To identify all species of life on Earth.
o Identify which of those species might have diagnostic use and evolutionary history.
Placing Bacteria
1735 Kingdoms Plantae and Animalia
1857 Bacteria and fungi put in Kingdom, Plantae – “Flora”
1866 Kingdom Protista proposed for bacteria, protozoa, algae, and fungi
1959 Kingdom Fungi
1961 Prokaryote defined as cell in which nucleoplasm is not surrounded by a nuclear membrane
1968 Kingdom Prokaryotae proposed
1978 Two types of prokaryotic cells (Bacteria and Archea) found- 3 Domain classification
recommended
 Fig 10.1/ Table 10.1
The 3-domain System (fig 10.1)
Endosymbiotic Theory
 Pre-eukarya looked like prokaryote
 Plasma membrane invaginated DNA
Fossilized Prokaryotes
 Determine common ancestors thru imprints of bones and shells
 Microorganisms are hard to find in fossilized form
o Black rock: Filamentous bacteria
o Upper right: cyanobacteria ~3 bil years ago
Phylogenetics
 Each species retains some characteristics of its ancestors
 Grouping organisms according to common properties implies that a group of organisms
evolved from a common ancestor
o Anatomy
o Fossils
o rRNA
Scientific Nomenclature
 Common Names
o Vary with language and geography
 Binomial Nomenclature (genus + specific epithet)
o Used worldwide
o Escheria coli
o Homo sapiens- same all-knowing
Taxonomic Hierarchy
Domain (bacteria is a domain not a Kingdom)
 Kingdom* no kingdoms for bacteria
o Phylum
 Class
 Order
 Family
o Genus
 Species
The Taxonomic Hierarchy
 Fig 10.5 Appreciate Taxonomic Hierarchy- not inclusive
Classification of Prokaryotes
 Prokaryotic species: a population of cells with similar characteristics
o Culture: grown in laboratory media
o Clone: Population of cells derived from a single cell
o Strain: genetically different cells within a clone. Same species, but specific subtype
Phylogenetic Relationships of Prokaryotes
 Fig 10.6
Classification of Eukaryotes
 Eukaryotic species: a group of closely related prganisms that breed among themselves
o Animalia
 Multicellular, no cell walls, chemoheterotrophic
o Plantae
  Multicellular, cellulose cell walls, usually photoautotrophic
o Fungi
 Chemoheterotrophic; unicellular OR multicellular, cell walls of chitin,
develop from spores or hyphal fragments.
o Protista
 A catchall kingdom for eukaryotic organisms that do not fit other kingdoms
 Grouped into clades based on rRNA
Classification of Viruses
 Viral species: population of viruses with similar characteristics that occupies a particular
ecological niche. They do not fit in Domain, not living organism. Has its own classification
system.
Classification and Identification
 Classification- placing organisms in groups of related species. Lists of characteristics of
known organisms.
 Identification- Matching characteristics of “unknown” organisms to lists of known
organisms.
o Clinical lab ID
o Seen in hospitals
o Helps with classification ( p. 283 )
 Dichotomous Keys
Identification Methods
 Morphological characteristics- useful for identifying eukaryotes
 differential staining- gram staining, acid-fast staining
 biochemical tests- determines presence of bacterial enzymes
Identifying a Gram- Negative, Oxidase – Negative Rod (fig 10.8 )
Numerical Identification (fig 10.9)
 More Methods of Identification
Serology- use of antibiotics for testing purposes
 Aggluntination, ELISA, Western Blotting
o Based on how they are detected
Phage Typing
 Plate with lawn of bacteria. Each square of grid, add a different phage.
 Observe virus clearing of bacterial lawn- what type of viruses can infect this particular cell
Fatty Acid Profiles- FAME (fatty acid methyl ester)
Flow Cytometry
 Machine with microscopic probe. Solution sucked into a tube, passed into a laser picture.
 Take cell then use electrical conductivity- size, shape, density (more or less organelles,
inclusions), cell surface
 Fluorescence- pick out one cell at a time
DNA Base Composition- GC, AT ratio can be figured out. Indicative of relation.
DNA Fingerprinting- RFLP’s (chapter 9) restriction length polymorphisms are regions of DNA
that has repeats in them. takes advantage of knowing DNA sequence.
PCR- increasing frequency for amplification.
Nucleic Acid Hybridization
 Southern Blotting, DNA Chip, FISH
Building a Cladogram
The Prokaryotes (check pic)
Domain Bacteria
 Phylum Proteobacteria:
o gram-negative, chemoheterotrophic
 Class:
o Alphaproteobacteria
o Betaproteobacteria
o Gammaproteobacteria
o Deltaproteobacteria
o Epsilonproteobacteria
The Gammaproteobacteria
 Pseudomonadales
o Pseudomonas
 Opportunistic pathogens
 Metabolically diverse
 Polar flagella
 Vibrionales
o Found in coastal water
 Vibrio cholerae causes cholera
 V. parahaemolyticus causes gastroenteritis
 Enterobacteriales (enterics)
o Petrichous flagella; facultatively anaerobic
 Enterobacter
  Erwinia
 Escherichia
 Klebsiella
 Proteus
 Salmonella
 Serratia
 Shigella
 Yersinia
The Epsilonproteobacteria
 Slender gram-negative rods
 Helicobacter
o Multiple flagella
o Peptic ulcer
o Stomach cancer
 Campylobacter
o One polar flagella
o Gastroenteritis
Nonproteobacteria Gram- Negative Bacteria
 Photosynthesizing bacteria
 Oxygenic Photosynthetic Bacteria: Phylum- Cyanobacteria
o Gliding motility
 o Fix nitrogen
 Anoxygenic Photosynthetic Bacteria
o Purple sulfur, Purple nonsulfur: proteobacteria
o Green sulfur, Green nonsulfur
Phototropic
 Oxygenic photosynthesis
 Anoxygenic photosynthesis
The Gram-Positive Bacteria
 Phylum: Firmiculates
o Low G+ C
o Gram +
 Phylum: Acitnobacteria
o High G+C
o Gram +
o Pleomorphic (many shapes)
o Actinomyces, Corynebacterium, Frankia, Gardnerella, Mycobacterium, Nocardia,
Propionibacterium, Streptomyces
o They look like protista but they are BACTERIA
Nonproteobacteria Gram- Negatives
 Planctomycetes
o Gemmata obscuriglobus
 Double internal membrane around DNA ( fig 11.23)
 Life Cycle of the Chlamydias (fig 11.24a)
 Sprochetes- note axial filaments
o Borrelia
o Leptospira
o Treponema
 Fusobacteria
o Fusobacterium
 Are found in the mouth
 May be involved in dental disease
 Looks like toothpick
Domain Archaea
 Extremophiles
o Hyperthermophiles
 Pyrodictium
 Sulfolobus
o Methanogens
 Methanobacterium
o Extreme halophiles
 Halobacterium
Microbial Diversity
 Bacteria size range
o Thiomargarita (750 uM)
o Nanobacteria (0.02uM) in rocks
 PCR indicates up to 10,000 bacteria per gram of soil
 Many bacteria have not been identified because they
o Haven’t been cultured
o Need special nutrients
o Are a part of complex food chains requiring the products of other bacteria
o Need to be cultured to understand their metabolism and ecological role.
 03/28/2011
Focus on Phyla- What distinguishes one phyla from another.