Lecture 2: Prokaryotes, Archaea and Bacteria Flashcards
Define taxonomy
the branch of science concerned with classification, especially of organisms; systematics.
Define taxon
is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit.
Define phylogeny
The history of the evolution of a species or group, especially in reference to lines of descent and relationships among broad groups of organisms
What are the advantages of the three domain system?
3 domain system differentiates better not only in the case of eubacteria and archae but also significantly subdivides protista. Also the 3 domain system is based on differences between rRNA gene as given by Woese et al.
Oxidoreductase
oxidation-reduction reactions
Transferase
Transfers functional groups
Hydrolase
Hydrolysis
Lyase
Removal of atoms without hydrolysis
Hydrolase
Hydrolysis
Isomerase
Rearrangement of atoms
Ligase
Joining of molecules; uses ATP
Rybozymes
RNA that cuts and splices RNA
What are the main factors influencing enzyme activity?
- Temperature
- pH
- Substrate concentration
- Inhibitors
How does temperature impact enzyme activity?
Temperatures that are too high can denature proteins.
How does pH impact enzyme activity?
- Most bacteria grow between pH 6.5 and 7.5
- Molds and yeasts grow between pH 5 and 6
- Acidophiles grow in acidic environments
What are the physical requirements of growth for bacteria?
- Temperature
- pH
- Osmotic pressure
What are the chemical requirements of growth for bacteria?
- Carbon
- Nitrogen, sulfur and phosphorous
- Trace elements
- Oxygen
- Organic growth factor
What are the minimum, optimum and maximum growth temperatures for psychrotrophs?
Minimum - 0 degrees C
Optimal - 15 degrees C
Maximum - 20 degrees C
Why is carbon a chemical requirement?
- Structural organic molecules, energy source
- Chemoheterotrophs use organic carbon sources
- Autotrophs use CO2
Why is nitrogen a chemical requirement?
- Found in amino acids and proteins
- Most bacteria decompose proteins
- Some bacteria use nitrate or ammonium
- A few bacteria use N2 nitrogen gas in nitrogen fixation
Why is sulfur a chemical requirement?
- In amino acids, thiamine and biotin
- Most bacteria decompose proteins
- Some bacteria use hydrogen sulfide and sulfate
Why is phosphorus a chemical requirement?
- Found in DNA, RNA, ATP and membranes
- Phosphate is a source of phosphorus
Why are trace elements important in growth?
- Inorganic elements are required in small amounts usually as enzyme cofactors
What are organic growth factors?
- Organic compounds obtained from the environment
- Vitamins, amino acids, purines and pyramidines
What are Capnophiles?
Microorganisms that thrive in the presence of high concentrations of carbon dioxide.
What does the rate of microbial death depend on?
- Number of microbes
- Environment (organic matter, temperature, biofilms)
- Time of exposure
- Microbial characteristics (eg. virulence)
How do microbial control agents kill microbes?
- Alter membrane permeability
- Damage proteins and nucleic acids
What are physical methods of microbial control?
- Heat
- Moist heat
- Pasteurization
- Dry Heat Sterilization
What is TDP (Thermal Death Point)?
Lowest temperature at which all cells in a culture are killed in 10 minutes.
What is TDT (Thermal Death Time)?
Time during which all cells in a culture are killed.
What is DRT (Decimal Reduction Time)?
Minutes to kill 90% of a population at a given temperature.
How does moist heat kill microorganisms?
- Denatures proteins
- Steam sterilization: steam must contact item’s surface
- Autoclave: steam under pressure
What are three different types of pasteurization?
1) 63 degrees C for 30 min
2) 72 degrees C for 15 sec
3) 140 degrees C for less than one second
What are the types of dry heat sterilization?
- Dry heat
- Flaming
- Incineration
- Hot air sterilization
How do we use low temps to inhibit microbial growth?
- Refrigeration
- Deep-freezing
- Lyophilization
How does filtration control microbes?
- Removes microbes > 0.3 um
- Membrane filtration removes microbes > 0.22 um
What are the different types of radiation uses to control microbial growth?
- Ionizing radiation (X-rays, gamma rays, electron beams) ionizes water to release hydroxide which damages DNA.
- Nonionizing radiation (UV 260nm) which damages DNA
- Microwaves Kill by heat, not especially antimicrobial
What are chemical methods of microbial control?
Factors related to effective disinfection such as:
- Concentration of disinfectant
- Organic matter
- pH
- Time
Types of disinfectants
1) Phenols and phenolics
2) Bisphenols
3) Biguanides
4) Halogens
5) Heavy metals
What do phenols and phenolics do?
Disrupt plasma membranes
What are some examples of bisphenols and what do they do?
- Hexachlorophane
- Triclosan
They disrupt plasma membranes
Give an example of a biguanide. What does it do?
- Chlorhexidine
Disrupts plasma membrane
Give some examples of halogens
Iodine - in aqueous alcohol or iodophors in organic molecules
Chlorine - found in bleach (hypochlorous acid)
What does iodine do?
Alters protein synthesis and membranes
What does chlorine do?
It is an oxidizing agent
What does alcohol (ethanol, isopropanol) do?
Denatures protein, dissolves lipids, requires water
Give some examples of heavy metals that can be used to kill bacteria?
Ag
- Silver nitrate may be used to treat gonorrhoeal opthalmia neonatorum
- Silver sulfadiazine is used as a topical cream on burns
Cu
- Copper sulfate is an algicide
Hg (in past)
- Mercuric chloride was used to kill pests
- Mercurous iodide kills bacteria on the skin
Give examples of surfactants (surface-active agents) and what they do.
1) Soap is degerming.
2) Acid-anionic detergents are sanitizing
2) Quaternary ammonium compounds (cationic detergent) kill bacteria, denature proteins and disrupt plasma membranes.
What is taxonomy and why is it useful?
- The science of classifying organisms
- It provides universal names for organisms
- Provides a reference for identifying organisms
What is phylogeny (systematics)?
The study of the evolutionary history of organisms.
What is the three domain system?
The three domain system includes bacteria, archaea and eukarya.
What is binomial nomenclature?
- Genus
- Specific epithet (species)
Honors Edwin Klebs + disease name
Klebsiella pneumoniae
Honors Lois Pfiester + disease in fish
Pfiesteria piscicida
Salmonella typhimurium
Honors Daniel Salmon + stupor (typh) in mice (muri)
Chains of cells + pus (pyo)
Streptococcus pyogenese
Tuftlike (penicill) + produces yellow pigment (chryso)
Penicillium chrysogenum
Borer, body, honours Oswaldo Cruz
Trypanosoma cruzi
What is the taxonomic hierarchy?
A series of subdivisions developed by Linnaeus to classify plants and animals.
Eukaryotic species
a group of closely related organisms that breed among themselves
Dumb Kings Play Chess On Fine Green Sand (Definitely Kinky People Come Over For Group Sex)
Domain Kingdom Phylum Class Order Family Genus Species
Prokaryotic species
a population of cells with similar characteristics
Culture
grown in laboratory media like agar
Clone
a population of cells derived from a single cell
Strain
genetically different cells within a clone
Animalia
multicellular, no cell walls, chemoheterotrophic
Plantae
multicellular, cellulose cell walls, usually photoautotrophic
Fungi
chemoheterotrophic, unicellular or multicellular, cell walls of chitin, develop from spores or hyphal fragments
Protista
catchall kingdom for eukaryotic organisms that do not fit other kingdoms (grouped into clades based on rRNA)
Classification
placing organisms in groups of related species
Classification of viral species
population of viruses with similar characteristics that occupies a particular ecological position
Identification
matching characteristics of an “unknown” organism to lists of known organisms
Morphological characteristics
useful for identifying eukaryotes
Bacteria that can ferment lactose and sucrose
E. coli O157
Bacteria that ferment lactose but not sucrose
Escherichia spp.
Ferment lactose, citric acid sufficient carbon source
Citrobacter
Ferment lactose, citric acid sufficient carbon source and produce acetoin
Enterobacter
Cannot ferment lactose but can use citric acid as sole carbon source
Salmonella (produce hydrogen sulfide)
Cannot ferment lactose, need other carbon sources besides citric acid
Shigella (produces lysine decarboxylase)
Slide agglutination test
Combine known antiserum plus unknown bacterium and check for agglutination
ELISA
Enzyme-linked immunosorbent assay
- Known antibodies
- Unknown bacterium
- Antibodies linked to enzyme
- Enzyme substrate
Western blot
identify specific amino-acid sequences in proteins
Flow cytometry
- Uses differences in electrical conductivity between species
- Fluorescence of some species
- Cells selectively stained with antibody plus fluorescent dye
DNA base composition
Percentage of guanine + cytosine moles present
DNA fingerprinting
Electrophoresis of restriction enzyme digests
Other types of genetic identification
- rRNA sequencing
- PCR (polymerase chain reaction)
FISH
Fluorescent in situ hybridization (add DNA probe for S. aureus)
Prokaryote with pseudomurein rRNA signature
Domain archaea
Prokaryote with peptidoglycan rRNA signature
Domain bacteria
Types of Gram-positive bacteria
- Firmicutes (low g + c)
2. Actinobacteria (high g + c)
Main subtypes of gram negative bacteria
- Proteobacteria
2. Nonproteobacteria
Types of Proteobacteria
A. Alphaproteobacteria B. Betaproteobacteria C. Gammaproteobacteria D. Deltaproteobacteria E. Epsilonproteobacteria
Types of Nonproteobacteria (Gram negative)
A. Anoxygenic photosynthetic bacteria B. Bacteroidetes C. Chlamydia trachomatis D. Deinococci E. Planctomycetes F. Fusobacterium G. Spirochetes
Alphaproteobacteria that are human pathogens
- Bartonella (B. henselae)
- Brucella (brucellosis)
- Ehrlichia (tickborne)
Alphaproteobacteria that are obligate intracellular parasites
- Ehrlichia: tickborne
- Rickettsia: arthropod-borne, spotted fevers
- R. prowazekii; epidemic tyhpus
- R. typhi; endemic murine typhus
- R. rickettsii; Rocky Mountain spotted fever
Alphaproteobacteria with prosthecae
Caulobacter - stalked bacteria found in lakes
Hyphomicrobium - budding bacteria found in lakes
Alphaproteobacteria plant pathogens
Agrobacterium - inserts a plasmid into plant cells, inducing a tumor
Chemoautotrophic Alphaproteobacteria
- Oxidize nitrogen for energy
- Fix CO2
- Nitrobacter
- Nitrosomonas
Nitrogen-fixing alphaproteobacteria
- Azospirillum
Name as many betaproteobacteria as you can
- Bordetella (chemoheterotrophic; rods, B. pertussis causes whooping cough)
- Burkholderia (nosocomial infections)
- Neisseria
- Aerobic, gram negative cocci (gonorrhea and meningitis)
Pseudomonas (Gammaproteobacteria)
Gram-negative, aerobic, opportunistic pathogen, polar flagella
Pseudomonadales
- Pseudomonas
- Moraxella (Conjunctivitis)
- Azotobacter and Azomonas (nitrogen-fixing)
Legionellales (Gammaproteobacteria)
- Legionella (Found in streams, warm-water pipes, cooling towers)
- L. pneumophilia
- Coxiella: Q fever transmitted via aerosols or milk
Vibrionales (Gammaproteobacteria)
- Found in coastal water
- Vibrio cholerae (cholera)
- Vibrio parahaemolyticus causes gastroenteritis
Enterobacteriales (enterics)
- Peritrichous flagella; facultatively anaerobic
- Enterobacter
- Escherichia
- Klebsiella
- Proteus
- Salmonella
- Shigella
- Yersinia
Pasteurellales
- Pasteurella (causes pneumonia and septicemia)
- Haemophilus (requires X heme group and V NAD/NADP factors)
Deltaproteobacteria
Desulfovibrionales (use Sulfulr instead of O2 as final electron acceptor)
Epsiolonproteobacteria
- Campylobacter (one polar flagellum, gastroenteritis)
- Helicobacter (multiple flagella, peptic ulcers, stomach cancer)
Anoxygenic photosynthetic bacteria
- Purple sulfur
- Purple nonsulfur
- Green sulfur
- Green nonsulfur
Bacteroidetes
Anaerobic, found in the mouth and large intestine
Cytophaga degrade cellulose in soil
Chlamydia (Nonproteobacteria)
- Chlamydia trachomatis
(Trachoma, STI, urethritis) - Chlamydophila pneumoniae
- Chlamydophila psittaci (psittacosis)
Deinococci
Deinococcus radiodurans (more resistant to radiation than endospores) Thermus aquaticus (found in hot springs, source of Taq polymerase)
Planctomycetes
Gemmata obscurglobus (double internal membrane around DNA)
Fusobacterium
- Found in the mouth
- May be involved in dental disease
Spirochetes - types
- Trepanoma pallidum - pathogenic bacteria that causes syphilis
- Borrelia - causes Lyme disease, transmitted by ticks
- Leptospira - leptospirosis disease spread to humans by contaminated water
Spirochetes - general characteristics
- Obligate intracellular parasites
- Helically coiled
- Corkscrew shaped cells with flagella
Firmicutes
Low G + C Gram-positive bacteria - includes spore forming bacteria
Lactobaccilus
Type of firmicute that is not pathogenic
Types of Firmicutes
A. Lactobacillales
B. Bacillales
C. Clostridiales
D. Mycoplasmatales
Lactobacillales
Generally aerotolerant anaerobes; lack an electron transport chain
- Lactobacillus
- Streptococcus
- Enterococcus
- Listeria
Bacillales
Gram-positive rods and cocci
- Baccilus (endospore producing rods)
- Staphylococcus (S. aureus)
Clostridiales
Clostridium - endospore producing, obligate anaerobes
Mycoplasmatales
- Lack cell wall, pleomorphic
- Small size (0.1 - 0.24um)
- M. pneumoniae
Types of actinobacteria
Draw diagram
- Actinomyces
- Corynebacterium
- Frankia
- Gardnerella
- Mycobacterium
- Nocardia
- Propionibacterium
- Streptomyces
Domain Archaea
- Hyperthermophiles
- Pyrodictium
- Sulfolobus - Methanogens
- Methanobacterium - Extreme halophiles
- Halobacterium
Microbial Diversity
Bacteria size range (Thiomargarita 750 um)
Metagenomics (study of genetic material recovered from environmental sample)
Why have many bacteria not been identified?
- Have not been cultured
- Need special nutrients
- Part of complex food chains requiring the products of other bacteria
- Need to be cultured to understand their metabolism and ecological role
