Section 2 Flashcards
Nutritional requirements classified based on:
Energy source, carbon source, electron source and combing attributes
Energy source
Two types: Phototrophs and Chemotrophs
Phototrophs
Require photos (sunlight) e.g., anabaena spiroids (Cyanobacteria G-)
Chemotrophs
Break chemical bonds for energy
Carbon source
Two types: Autotrophs and heterotrophs
Autotrophs
Uses carbon dioxide (fix) as source to build large carbon structures into biomass
Heterotrophs
Degrade/decompose/consume organic biomass into small compounds, often liberating carbon dioxide or methane
Electron source
Two types: Lithographs and organotrophs
Lithotrophs
Donor-oxidize inorganic materials (N compounds, sulfur compounds, water)
Organotrophs
Donor-oxidize carbon-rich organic material, e.g., salmonella
Prokaryotic growth
- Binary fission
* Generation time: Nt=N0x2^n
Detecting growth
Grow in liquid media and measure “turbidity” using a spectrophotometer: absorbance/OD optical density), 1.0 OD600nm= ~108 colony forming units (CFU)/ml`
Phases of prokaryotic growth
Lag phase, early log (exponential) phase, late lag phase, stationary phase, and death phase
Lag phase
New gene expression, bacteria are preparing their cell machinery for growth
Early log (exponential) phase and Late lag phase
- Early log phase: Not “linear”
- Late log phase: Inflection point, change in metabolism, secondary metabolites, prep for stationary
- Growth approximates an exponential curve
Stationary phase
- Death=“Division”
* Cells stop growing and shut down their growth machinery while turning on stress responses to help retain viability
Death phase
- Death>Division
* Cells die with a “half-life” similar to that of radioactive decay, a negative exponential curve
Environmental influences
- Normal vs. Extremeophiles
* Environmental parameters: Temperature, pH, Osmolarity, Oxygen, and Pressure
Temperature
•Enzymatic rates vs membrane/enzyme stability
-Threshold effect, rate change with temperature, range vs. optimum
Hyperthermophile, thermophile, mesophile, psychrophile
Hyperthermophile
- Extreme thermophiles
- Growth above 80ºC+ optimum
- Saturated fatty acids and x-linked lipids
Thermophile
Growth between 50ºC and 80ºC optimum
Mesophile
Growth between 15ºC and 45ºC
Psychrophile
- Growth below 15ºC or less optimum
* Unsaturated fatty acids in lipid membranes=low temperature (flexible)
pH
Alkaliphile, neutralophile, acidophile
Alkaliphile
Growth above pH 9
Neutralophile
Growth between pH 5 and pH 8
Acidophile
- Growth below pH 3
- Acetobacter aceti (G-)
- Lactobacillus acidophilus (G+)
- Shape: rod
Osmolarity
- Halophile
- Osmotic stress=Plasmolysis
- ”Normal”: 0.2-5% NaCl
- Osmotolerant (e.g., Staphyloccocus aureus (G+))
Halophile
- Growth in high salt > 2 M NaCl
- Requires 3%+ NaCl
- Extreme halophile require 10-20% NaCl
Oxygen
strict aerobe, facultative microbe, microaerophile, strict anaerobe
Strict aerobe
Growth in only O2
Facultative microbe
Growth with our without O2
Microaerophile
Growth in small amounts of O2
Strict anaerobe
Growth only without O2
Presssure
Barophile and barotolerant
Barophile
Growth at high temperature, greater than 380 atm
Barotolerant
Growth between 10 and 500 atm
2 distinct classifications of oxygem
“Use of” vs “response to” oxygen
“Use of” oxygen
•Energy production with or without O2
•Obtain energy from light or chemical compounds
•Remove electrons from chemical compounds
-More electron from donors or other sources to final acceptors
•Microbe dependent variable
•Mechanisms: Aerobic respiration, anaerobic respiration and fermentation
Respiration (aerobic and anaerobic)
•Use of electron transport system/chain (ETS/ETC) to make protein motive force (PMF)
-Oxidative phosphorylation
•ATP synthase uses PMF to make ATP
Aerobic respiration
O2 terminal electron acceptor
Anaerobic respiration
Other inorganic terminal electron acceptor
“Response to Oxygen”
•O2= reactive oxygen species (ROS)
-Toxic byproducts “oxidative stress”
-Avoid hydroxyl formation and reductions. How?
•Detoxification: Superoxide dismutase and catalase and peroxidase
Superoxide dismutase (SOD)
•Consumers superoxide but peroxides are formed
2O2^- + 2H^+ (reversible rxn) O2 + H2O2
Catalase and peroxidase
•Consumes peroxides
2H2O2 (reversible rxn) 2H2O + O2
•O2 and H2O are stable and diffuse easily
Use of and response to oxygen (cont.)
Strict (obligate) aerobe, facultative anaerobe, aerotolerant anaerobe, microaerophile
Strict (obligate) aerobe
- Only aerobic respiration: Oxygen required for growth
- Cannot respire anaerobically
- Makes high levels of SOD and catalase/peroxidase (detoxify)
- Only grows at the bottom
- Ex: mycobacterium tuberculosis, Nesseria gonorrheae, many Cyanobacteria
Facultative anaerobe
- Prefers aerobic respiration: with oxygen for growth (efficient)
- Can respire anaerobically or ferment
- Makes SOD and some catalase/peroxidase
- Can grow anywhere without oxygen
- Ex: Staphylococcus Aureus, bacillus anthracite, salmonella typhimurium, e.coli
Aerotolerant anaerobe
- Cannot respire
- Can only ferment
- Makes SOD and catalase/peroxide
- Oxygen levels do not change growth patterning effect
- Ex: streptococcus pyogenes, lacto bacillus acidophiles
Microaerophile
- Makes little SOD and little catalase/peroxidase
- Cannot detoxify effectively
- 2-10% O2 range
- Aerobic metabolism common
- Ex: Treponema Pallidum
Metagenomic analysis
•Characterize communities (microbiomes) genetically
-16S rRNA sequences in database identify
-Presence (+/-)
-Proportion (%)
•Experimental design: controls vs. experimental, use dependent variables, correlated or associated, many analysis possible
•Results=Correlation
Metagenomic analysis key experiment
- Do gut bacteria determine phenotype regardless of genotype?
- Transfer fecal microbes from humans into germ-free mice
- Results: microbes from obese humans transferred obese phenotype to mice
- Gut microbes over-ride genetics/diet
Metagenomic analysis (cont.)
- Consider new types of experiments: bovine rumen experiment
- New microbial therapies
- Ex: oral microbes promote intestinal inflammation
- Symbiotic compared to dysbiotic
The bovine rumen
- Digestion in the rumen and reticulum
- Regurgitation and chewing of cud
- Res wallowed cud moves to omasum
- Digestion is completed in the abomasum
Microbial/food webs
•Simplest view: cycling of materials
(Basic>[production]>Accumulated>[break down]>Basic)
•Ecosystem=[materials+organisms+abiotic conditions]
•Microbes play a vital role in any ecosystem, allowing chemical compounds to be modified into forms used by multiple other organisms
Wet succession: Biofilm formation
- Initiation: environmental signal, attachment, quorum sensing, Exopolysaccharide (EPS) formation
- Maturation and maintenance
- Dissolution
- 5 steps
Biofilm development steps
- Attachment to mono layer by flagella
- Microcolonies
- Exopolysaccharide (EPS) production
- Mature biofilm
- Dissolution and dispersal
Microbial ecology history
- Sergei Winogradsky (1856-1953)
- Focus on microbes from aquatic environments
- Water-column model demonstrates roles for both Phototrophs and chemolithotrophs
- Foundation for microbial geochemical cycles
- Study interactions, rather than isolated species
Microbial ecology
Top: water surface; highest, most sunlights production of Photoautotrophic
-Cyanobacteria
-Purple sulfur bacteria
-Green sulfur bacteria
-Sulfate-reducing bacteria
Lower: underwater; lowest specific protons, carbon rich debris, other substances
Marine and aquatic microbiology: Microbes in fresh water
•Surface: full spectrum photons and high oxygen, Photoautotrophic aerobes at surface (neuston)
•Deeper: only longer wavelengths; little oxygen, microbe pigments reflect
photon penetration, lower depths require longer wavelengths, colder (thermocline), few nutrients
Marine and aquatic microbiology: microbes in bodies of fresh water
•Environmental changes impact microbes
-Seasonal with temperature (abiotic)
-Run off with specific potential nutrients (abiotic or biotic, aiding growth of
certain microbes)
-Climate change and related environmental effects on temperatures,
currents, hassles and other factors