Section 2 Flashcards
(154 cards)
1
Q
Nutritional requirements classified based on:
A
Energy source, carbon source, electron source and combing attributes
2
Q
Energy source
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Two types: Phototrophs and Chemotrophs
3
Q
Phototrophs
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Require photos (sunlight) e.g., anabaena spiroids (Cyanobacteria G-)
4
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Chemotrophs
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Break chemical bonds for energy
5
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Carbon source
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Two types: Autotrophs and heterotrophs
6
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Autotrophs
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Uses carbon dioxide (fix) as source to build large carbon structures into biomass
7
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Heterotrophs
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Degrade/decompose/consume organic biomass into small compounds, often liberating carbon dioxide or methane
8
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Electron source
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Two types: Lithographs and organotrophs
9
Q
Lithotrophs
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Donor-oxidize inorganic materials (N compounds, sulfur compounds, water)
10
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Organotrophs
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Donor-oxidize carbon-rich organic material, e.g., salmonella
11
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Prokaryotic growth
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- Binary fission
* Generation time: Nt=N0x2^n
12
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Detecting growth
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Grow in liquid media and measure “turbidity” using a spectrophotometer: absorbance/OD optical density), 1.0 OD600nm= ~108 colony forming units (CFU)/ml`
13
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Phases of prokaryotic growth
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Lag phase, early log (exponential) phase, late lag phase, stationary phase, and death phase
14
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Lag phase
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New gene expression, bacteria are preparing their cell machinery for growth
15
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Early log (exponential) phase and Late lag phase
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- Early log phase: Not “linear”
- Late log phase: Inflection point, change in metabolism, secondary metabolites, prep for stationary
- Growth approximates an exponential curve
16
Q
Stationary phase
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- Death=“Division”
* Cells stop growing and shut down their growth machinery while turning on stress responses to help retain viability
17
Q
Death phase
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- Death>Division
* Cells die with a “half-life” similar to that of radioactive decay, a negative exponential curve
18
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Environmental influences
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- Normal vs. Extremeophiles
* Environmental parameters: Temperature, pH, Osmolarity, Oxygen, and Pressure
19
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Temperature
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•Enzymatic rates vs membrane/enzyme stability
-Threshold effect, rate change with temperature, range vs. optimum
Hyperthermophile, thermophile, mesophile, psychrophile
20
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Hyperthermophile
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- Extreme thermophiles
- Growth above 80ºC+ optimum
- Saturated fatty acids and x-linked lipids
21
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Thermophile
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Growth between 50ºC and 80ºC optimum
22
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Mesophile
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Growth between 15ºC and 45ºC
23
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Psychrophile
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- Growth below 15ºC or less optimum
* Unsaturated fatty acids in lipid membranes=low temperature (flexible)
24
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pH
A
Alkaliphile, neutralophile, acidophile
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Alkaliphile
Growth above pH 9
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Neutralophile
Growth between pH 5 and pH 8
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Acidophile
* Growth below pH 3
* Acetobacter aceti (G-)
* Lactobacillus acidophilus (G+)
* Shape: rod
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Osmolarity
* Halophile
* Osmotic stress=Plasmolysis
* ”Normal”: 0.2-5% NaCl
* Osmotolerant (e.g., Staphyloccocus aureus (G+))
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Halophile
* Growth in high salt > 2 M NaCl
* Requires 3%+ NaCl
* Extreme halophile require 10-20% NaCl
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Oxygen
strict aerobe, facultative microbe, microaerophile, strict anaerobe
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Strict aerobe
Growth in only O2
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Facultative microbe
Growth with our without O2
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Microaerophile
Growth in small amounts of O2
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Strict anaerobe
Growth only without O2
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Presssure
Barophile and barotolerant
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Barophile
Growth at high temperature, greater than 380 atm
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Barotolerant
Growth between 10 and 500 atm
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2 distinct classifications of oxygem
“Use of” vs “response to” oxygen
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“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
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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
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Aerobic respiration
O2 terminal electron acceptor
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Anaerobic respiration
Other inorganic terminal electron acceptor
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“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
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Superoxide dismutase (SOD)
•Consumers superoxide but peroxides are formed
| 2O2^- + 2H^+ (reversible rxn) O2 + H2O2
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Catalase and peroxidase
•Consumes peroxides
2H2O2 (reversible rxn) 2H2O + O2
•O2 and H2O are stable and diffuse easily
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Use of and response to oxygen (cont.)
Strict (obligate) aerobe, facultative anaerobe, aerotolerant anaerobe, microaerophile
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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
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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
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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
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Microaerophile
* Makes little SOD and little catalase/peroxidase
* Cannot detoxify effectively
* 2-10% O2 range
* Aerobic metabolism common
* Ex: Treponema Pallidum
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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
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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
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Metagenomic analysis (cont.)
* Consider new types of experiments: bovine rumen experiment
* New microbial therapies
* Ex: oral microbes promote intestinal inflammation
* Symbiotic compared to dysbiotic
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The bovine rumen
1. Digestion in the rumen and reticulum
2. Regurgitation and chewing of cud
3. Res wallowed cud moves to omasum
4. Digestion is completed in the abomasum
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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
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Wet succession: Biofilm formation
* Initiation: environmental signal, attachment, quorum sensing, Exopolysaccharide (EPS) formation
* Maturation and maintenance
* Dissolution
* 5 steps
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Biofilm development steps
1. Attachment to mono layer by flagella
2. Microcolonies
3. Exopolysaccharide (EPS) production
4. Mature biofilm
5. Dissolution and dispersal
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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
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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
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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
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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
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Biogeochemical cycling
* Broader perspective: Carbon, nitrogen and sulfur compounds are moved from one form to another by microbes, aiding the delicate balance of available compounds on earth
* Some materials cannot be accessed chemically and is available
* Microbes use their collective metabolism to convert chemical elements into various compounds, enabling other organisms to metabolize compounds
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Biogeochemical cycling (cont.)
* Cyanobacteria (G-) convert many CO2 into carbon rich organic biomass
* Soil microbes (G+) degrade organic biomass to release CO2 and complete to cycle
* Figure 22.3
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The carbon cycle
* Most abundant compound by weight, but not all carbon is in a form that can be used biochemically
* Concerns in greenhouse gases
* CO2 is a central available compounds, fixed into organic biomass or reduced to methane
* Aerobic, anaerobic, and methanogen types of carbons
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The carbon cycle: aerobic
* Above ground
* CO2 gas=available reservoir
* Transitions by Photoautotrophic
* Moved into new forms=biomass
* Photosynthesis generates O2, enabling the most efficient metabolism by heterotrophs, methanotrophs, and lithotrophs
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The carbon cycle: Anaerobic
* Below ground
* Biomass=available reservoir
* Transition by anaerobes
* Moved into diverse forms
* Photosynthesis generates only oxidized materials, supporting limited anaerobic respiration
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The carbon cycle: Methanogens
* Straddles ground
* Redox of single carbon
* Transitions by methanogens and methanotrophs
* Moved into diverse forms
* Fermentation generates organic carbon products, as well as CO2 and H2
* In the absence of oxygen, methanogens convert CO2 and H2 to CH4
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The Nitrogen cycle
* Nitrogen is an abundant compound, but not all nitrogen is in a form that be used biochemically
* Soil levels of available nitrogen for plant growth is dependent on microbes
* Plants use symbiotic microbe partners in their roots to convert: Nitrogen fixation, nitrification, and dentrification
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Nitrogen Fixation
* N2=NH4^+
* N2 is hard to break
* Nitrogenase in soil anaerobes (e.g., clostridium (G+))
* Nitrogenase also in water borne anaerobes
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Nitrification
* Oxidation of ammonia to nitrite or nitrate
| * Nitrosomonas coupled with nitrobacteri +/- nitrospira
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Denitrification
* Nitrate/Nitrite back to N2/NH4^+
| * Anaerobic reduction using nitrogen compounds as electron acceptors (e.g., pseudomonas)
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Soil microbiology
* Foundation of the soil food web
* Microenvironment around plant root is different than other soils of which is called the mycorrhizae
* Fungi that gather outsider the root but never invades the root is called the ectomycorrhizae
* Fungal hyphae extend outward to absorb and metabolize soil compounds
* Nitrogen-fixing microbes and plants have shared roles (rhizobia)
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Rhizobia in soil microbiology
* Rhizobia are attracted by plant Nod flavonoid proteins
* Rhizobia release factors to promote root hair growth/curl
* Plant creates infections thread, allowing rhizobia access into cortical cells
* Rhizobia grows cells to form nitrogen-fixing bacteroids in nodules
* Rhizobia moves from root hair through infection threads, forming bacteroids in nodules of internal plants cells
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Marine and aquatic microbiology
* Microbes move both carbon and sulfur into forms used by predators/partners
* Primary microbial production and microbial mutualism
* Heat and materials provide unique environment
* Carbon and sulfur based cycling
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Microbial relationships
Mutualism, commensalism, ammensalism, and paratism
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Mutualism
Both benefit in relationship to some degree
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Commensalism
One clearly benefits while the other other is not affected
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Ammensalism
One benefits at the expense of all others
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Paratism
One clearly benefits at the expense of another (1 on 1)
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Another type of relationship
1. First microbe thrives in a environment, releasing metabolic products that alter the environment
2. Second microbe thrives in the altered environment, while the first microbe fades (does not co-exist)
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Fermentation
* Organic terminal electron acceptor
| * No ETS/ETC
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Microbial succession
* Microbes compete for nutrients/resources
* Microbes constantly attack competitors
* Some microbes take advantage of metabolic activities of others, moving into environments after pioneers
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Microbial Succession: Raw milk example
Lactococcus lactis, lactobacillus, yeasts and molds, and putrefying bacteria
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lactococcus lactis
* Starts at day 1 at pH of 6.8 to day 5
* Peak of # of organism, pH is 4 (day 2)
* Environmental change
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Lactobacillus sp.
* Starts at day 1 at pH of 6.8 to day 11
* Ferments and becomes more acidic
* Peak of # of organism, pH is 3 (day 5-6)
* Environment changes more, organism are dying
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Yeasts and molds
* Starts at day 5-6 at pH of 3 to day 14
* Peak of # of organism, pH is 5.5 (day 10)
* No sugar remains
* Works on other substrates like fats and proteins
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Putrefying bacteria
* Starts at day 8 at pH of 4 to day (beyond 14 days)
* Peak of # of organism, pH is 6.8 (day 14)
* Slow and eats protein since there’s no sugar
* Breaks down organism that others cant
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Hydrologic cycle and wastewater treatment
* Used to limit contamination of freshwater sources with microbes that would alter these environments
* Distribution of carbon rich nutrients to an ecosystem alters the potential for aerobic microbes to metabolize and consume dissolved oxygen, fouling the water
* Biochemical oxygen demand (BOD) is a measurement of the potential for aerobic metabolism of a given sample
* Sewage must be processed to reduce BOD before effluent can be released back to a water source
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Hydrologic cycle and wastewater treatment cycle
Preliminary, primary, secondary, anaerobic, digestion, tertiary, effluent
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Preliminary
Treatment removes solid debris
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Primary
Treatment sediments insoluble material
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Secondary
Treatment uses aerobic metabolism to remove organic material and dramatically reduce BOD; biofilms or flocs may form that sediment
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Tertiary
Treatment may involve anaerobic digestion and mineralization of compounds, ultimately treated with volatile Cl to sanitize
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End results
Fresh water with limited potential to cause microbial blooms and solids for use in agriculture
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Solid waste and compost
* Early stages ion composting: aerobic decomposes of polysaccharide and cellulose-rich materials liberate heat, raising the temperature to 50-60ºC
* Thermphilic microbes take over
* Final product is use foil soil amendment with available nutrients, acceptable smell and limited toxicity
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Solid waste and compost stages
Primary stage: Aerobic thermophiles (150ºF), gets lots of oxygen
Secondary stage:sieve and grind to increase surface area, mounds for anaerobic digestion
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Bioremediation
•Microbes can metabolizes toxic compounds in soil, such as herbicide 2,4-dichlorophenoxyacetic acid but cannot degrade toxic materials such as 2,4,5-trichlorophenoxyacetic acid because there’s extra Cl and blocks enzyme
•Microbes can be manipulated in several ways to promote degradation of unwanted compounds, including biostimulation:
-Co-metabolism: stimulating one set of microbes that also metabolize toxins
-Ex:methanotrophs degrade trichloroethylene
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Host-microbe interactions
•Constant contact with microbes in the environment
•Various relationships with microbes
-Few damage the host (pathogens)
-Examples of symbiotic relationships
-Normal microbiota includes microbes on surface
•Changes in the host status can alter their relationships
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Host-pathogen interactions
•First step: Binding and colonization
-Binding and est. are key events of which beneficial microbes may
compete locally
-Defenses work to compete against binding: mucus lining epithelial cells
-Colonization is replication but not established
•Infection may or may not lead to disease
-Signs can be sub-clinical or unapparent
•Disease=loss of function
-Differentiates from colonization, infection
-Can have related disease; often in a sequence
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Pathogens
•Primary or frank pathogens: presence of pathogen like salmonella, causes a diarrheal disease
•Opportunistic infections: HIV infected patients progress to AIDS by die of opportunistic infections
-Reduced immunity allows microbes to take advantage and invade where
they could not previously
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Principles of infection: Diseases have varying time courses
•Acute: Starts to increase, reaches its peak then reduces and goes
away (e.g., rhinovirus)
•Chronic: starts to increase, reaches its peak and stays till death (e.g.,
hepatitis B)
•Latent: Starts to increase, reaches its peak then reduces but stays chronic
until death (Herpes virus or HIV)
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Principles of infection: distribution
•Localized: one area/location
•Systemic or disseminated: pertaining to multiple areas or whole body
-Includes: bacteremia, toxemia, and septicemia
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Bacteremia
Bacteria in blood
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Toxemia
Bacterial product (toxins) in blood
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Septicemia
* Both in blood, often lethal
| * Intravascular coagulation
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Virulence factors: capacity for disease
•Early stages critical: pathogen virulence vs. host defense
- Adherence (binding): adhesions as virulence factors
- Adherence confer host cell tropsim/range
- Ex: enteropathic E. Coli (EPEC) vs. other E. Coli
- Colonization:
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Virulence factors: exotoxins
•Exotoxins subvert host cells secreted, forced response favors microbe, may also diminish host immunity
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Classes of microbial toxins
Hemolysis, block function (AB), and Cholera toxin (AB)
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Hemolysis
* Spore forming
* Damage cellular membranes
* Lysis RBC to open hole/pore (cylinder) until cell death
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Block function (AB)
* Inhibit protein synthesis
| * Pathogens have AB toxins, B binds and A delivers
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Cholera (AB)
* Activate 2nd messenger pathways
| * Bins to a receptor, locks into “on” position
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AB toxins example: anthrax alpha toxin
Step 1: Protective antigen binds
Step 2: Human cell protease cleaves PA
Step 3: Pa’s self-assemble into cylinder
Step 4: Lethal factor (LF) and edema factor (EF) bind and enter by endocytosis
Step 5: LF and EF release into cytoplasm
Step 6: EF blocks cAMPL regulation of ion channels
Step 7: LF blocks distress signal sent from cell while blocking cell division
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Survival within host
•Survival within host cell entry: e.g., salmonella G-
-Avoid immunity (WBC and/or blood proteins)
-Thrive in hostile environments
-If captured, escape: block WBC action and use WBC as camouflage/altered
surface
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Fungal pathogens: fungi
* Most common in the environment
* Some colonize healthy, immunocompetent individuals
* Opportunists invade immuno-compromised hosts
•Candida Albicans causes thrush seen in young adults, elderly, genetics defects in immune function, HIV-infected AIDS patients
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More pathogens: Eukaryotes
* Some use insect “vectors” to move from one ghost to host—unique forms to regional insects
* Bites colonize healthy, immunocompetent individuals—malnutrition is on risk factor
* Ex: plasmodium ssp. common cause of malaria—parasite lysis RBC, causing anemia and clots
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Life cycle of malaria
Step 1: Mosquito salivary gland transmits sporozoites to human blood stream
Step 2: Sporozoites travel to the liver
-Schizogony: mitosis to form numerous merozoites
-Gamogony: mitosis and maturation of gametes
Step 3: Merozoites repeatedly invade RBC
Step 4: Gametocytes firm and are transmitted to mosquito
Step 5: Fertilization
Step 6: Zygote undergoes meiosis to form sporozoites
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Sexually-transmitted infections
•Urogenital transmission most-common, based on selective pressure on “fragile” microbes: temperature, humidity, pH, competition, and high binding affinity for epithelial cells
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Types of STI’s
Chlamydia trachomatis, Human papilloma virus (HPV), Treponema pallidum, Nesseria gonorrheae, Trichomonas vaginalis, and Herpes simplex virus (HSV-2)
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Chlamydia trachomatis classification
* Genus species: Chlamydia trachomatis
| * Chyamydia is a protozoan
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Chlamydia trachomatis: In healthy individuals?
No, It is passed sexually from person to person
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Chlamydia trachomatis: Stages
1)Pathogen binds to the epithelial cell, 2)then it begins to colonize inside of the cytoplasm of which begins to reproduce via binary fission, 3)Microbe take nutrients from host cell, killing the cell
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Chlamydia trachomatis: Time course
Physical symptoms can start showing at week 1 to 3 or even a few weeks later
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Chlamydia trachomatis: Symptoms
Painful urination, genital discharge, bleeding, testicular pain in men, pain during intercourse
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Chlamydia trachomatis: treatments
Oral antibiotics
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Human papilloma virus (HPV): Classification
Papillomavirriidae
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Human papilloma virus: In healthy individuals?
Yes, most HPV infections are asymptomatic
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Human papilloma virus: Stages/Binding, colonization, and infection
The virus is spread through sexual intercourse of which it then attacks healthy epithelial cells. After binding, it will colonize and replicate and continues to attack host cells
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Human papilloma virus: Time course
The virus can last a few months to two year
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Human papilloma virus: Symptoms
Genital warts and cancer symptoms (if cancer occurs post-HPV)
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Human papilloma virus: Treatments
* Salicylic acid to remove layers of wart
* Imiquimod to enhance immune system
* Vaccination
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Treponema pallidum: Classification
Spirochete bacteruim
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Treponema pallidum: In healthy individuals?
No, it is sexually transmitted
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Treponema pallidum: Stages/Binding, colonization, and infection
1) Infection with the bacteria, 2) Binding of T. Syphilis within the epithelial cells, 3) It can spread to surrounding tissues, 4) Latent stage—remain dormant of which can later cause organ failure and CNS damage
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Treponema pallidum: Time course
* Primary stage can occurs 3 weeks after exposure
* Secondary stage can occur 3 months after exposure
* Latent, it can go away but most likely can dormant of which—
* Tertiary stage can be seen as early as a year
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Treponema pallidum: Symptoms
* Skin rash
* Sores
* Fever
* Swollen glands
* Weight loss
* Hair loss
* Headache
* Fatigue
* Muscle aches
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Treponema pallidum: Treatments
Single injection of benzathine penicillin antibiotic
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Neisseria gonorrheae: Classification
Betaproteobacteria
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Neisseria gonorrheae: In healthy individuals?
Yes/no, it can be asymptomatic
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Neisseria gonorrheae: Stages/Binding, colonization, and infection
1) The virus binds to epithelial cells, 2) this then colonizes and reproduces, 3) this infects the body by releasing its viral genomic properties
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Neisseria gonorrheae: Time course
Symptoms can show within the 5 to 28 day or even longer or never
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Neisseria gonorrheae: Symptoms
Abnormal genital discharge and painful urination
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Neisseria gonorrheae: Treatments
Oral and injected antibiotics
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Trichomonas Vaginalis: Classification
Protozoan
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Trichomonas Vaginalis: In healthy individuals?
No, it is transmitted via sex
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Trichomonas Vaginalis: Stages/Binding, colonization, and infection
1)Binding by adhesion, 2)colonization with reproduction, 3) infection by detaching and releasing its genomic material
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Trichomonas Vaginalis: Time course
Incubation time goes from 4 to 28 days
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Trichomonas Vaginalis: Symptoms
* Vaginal discharge
* Pruritus
* Dysuria
* Dyspareunia
* Itching
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Heroes Simplex Virus: Classification
Herpesviridae
150
Herpes simplex virus: In healthy individuals?
No, transmitted through sexual intercourse
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Herpes simplex virus: Stages/Binding, colonization, infection
1) Virus binds to the epithelial cells, 2) colonization by replicating, 3) after being reactivated, it spreads to other tissues
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Herpes simplex virus: Time course
Incubation is 2 to 12 days
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Herpes simplex virus: Symptoms
Lesions that turn into ulcers
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Herpes simplex virus: Treatments
Antiviral medications
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Trichomonas Vaginalis: Treatments
Oral metronidazole or tinidazole pills
