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Test 2 - Flashcards

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Class:BIOL 473 - ECOLOGY-MICROORGANISM
Subject:BIOLOGY
University:New Mexico State University-Main Campus
Term:Spring 2012
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R strategy
  • Do well when population numbers are low
  • High nutrient concentration, few competitors
  • High Km enzymes, low affinity for substrate
K strategy
  • Do better when population numbers are high
  • Low nutrient concentration, high population number
  • Low Km enzymes, higher Vmax
Primary Succession
  • Initial colonization of a previously devoid area, ie newborn intestine or after a volcano.
  • Carried out by pioneer organisms

Autotrophic sucession
  • Bare inorganic material, Fix N2 and CO2 (cyanobacteria)
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Heterotrophic succession
  • Already and organic source of carbon available
P/R Ratio
  • P (photosynthesis), R (respiration)
  • When P exceeds R organic carbon builds up
  • Ratio of P/R >1 then stable, if <1 unstable community
Example of succession in Biofilms
  1. Macromolecular film of organic chemicals
  2. Bacteria/Fungi adhere to the surface
  3. Bacterial growth, release of extracellular polysacharides (EPS) for sticking to each other
  4. Protozoa move in to graze on bacteria/fungi
Quorum sensing
  • Ability to detect levels of population and express certain genes when there is a high enough population
Generated by Koofers.com
Cystic Fibrosis
  • Infection in lungs by pseodomonas aeruginosa with population.
  • With poulation growth levels of homoserine lactone go up then alginate genes turn on "sticks" causes biofilm (fibrous)
Biofilms on medical implants
  • Huge public health problem. 10million a year, microbes in biofilm are generally antibiotic resistant.
Conjugation, transformation, transduction (Horzontal transfer)
  • Conjugation - pili exchange of DNA
  • transformation - environmental takeup
  • Transduction - virus, bacteriophage
  • Vertical transfer is transfer across generations (mother to daughter) 
Hg Study Containing amalgum
  • silver filling in chimps
  • Bacteria in gut had Hg resistance and antibiotic resistance plasmid pBSK plasmid
Generated by Koofers.com
Shannon Index
  • Measure of ecological diversity.  Species richness and eventness
In a 10 grams of soil
  • 4000 - 10000 species of microflora
Microcosm
  • A microbial ecosystem
Batchmicrocosms
  • Closed systems, only work short term
  • No new nutrient flow, goes anaerobic
Generated by Koofers.com
Flow through systems
  • Nutrients in, waste out
  • Chemostat - keeps the chemistry constant
Animal Model (Experimental Ecosystems)
  • A host for the microbial community
  • Gnotobiotic animal as a control (bacteria free)
  • Eg. Vibrio cholorea becomes inactive outside of host, inject in animal and revive 
in Situ Work
  • In field measure of community structure/function
Oligotrophic vs Eutrophic
  • Oligo - low nutrient concentration (K)
  • Eu - high nutrient concentration (r)
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Microbes vs Macrobes dominated
  • Under nutrient sufficient conditions, macrobes (animals and plants) dominate
  • Under nutrient deficient conditions microbes dominate
Tularosa Basin Desert Crusts
  • Dominated by microcoleus (cyanobacteria)
  • Secrets an EPS forms a biofilm of bacterial growth
  • W/ desiccation, dry out, brittle and forms crust, prevents soil loss by wind and water w/ rainfall organisms revive and colonize more surface soil.
Media Choices (for winogradsky selection)
  • Defined media - C source, N source are all identified
  • Complex media - undefined (BHI; brain-heart infusion)
  • Selective media - select for a specific trait
Phenotypic detection methods
  • Based on lips nucleic acids or cells
  • Lipid profiles - membrane chemistry, fatyacid methyl ester analysis FAME; they need to be methylated in order to be detected via gas chromotography
  • Phospholipids fatty acids profiles (PFLA) ; branched phospholipids
Generated by Koofers.com
Direct microscopic methods
  • Laser confocal microscopy
  • Staining techniques - acridine orange; intercalate DNA -> fluorescence.  Binds between two strands
  •  Direct counts of all cells is 10x higher than plate counts
  • Vital stains - distinguish live from dead
Genotypic Detection
  • Purify nucleic acid - direct extraction, lyse cells and purify.
  • Analyse by: gene probe analysis, PCR, sequencing DNA rDNA or chromosome, denaturing gradient gel electrophoresis, reporter genes.
DGGE
  • Allows you to differentiate different sequences with a gel electrophoresis; High G-C content goes further
Reporter Genes
  • Use of genes to discover when a gene is turned on, downstream of a promoter
  • Eg, petroleum waste -> napthalene, when nah genes are turned on
  • Other reporter genes: lux genes, LacZ
  • When napthalene concentration goes up so does light (lux) goes up
Generated by Koofers.com
Lebig Law of the Minimum
  • The growth and final yield is determined by the nutrient that is present in the lowest concentrations
  • Cell formula - C5H7O2NP.2
  • C:N:P 10:3:1
Shelfords law of Tolerance
  • For survival of organism - require a complex set of conditions that must remain withing what that organism can tolerate
Autecology
  • Individual species 1 at a time in pure culture
Synecology
  • Interactions of different species in a community populations that exist close to upper or lower limits are more vunerable to competition
Generated by Koofers.com
Soluble vs Precipitated vs Surface Sorbed
  • Soluble is available
  • precipitated is not
  • Surface sorbed may be depending, bonded to clay, may still be toxic or mobilize into aquifers
  • Metal solubility is effected by pH, high pH (ppt), low pH soluble
  • Oxidized and reduced also changes solubility, U oxidized is soluble, Fe oxidized is (ppt) 
Shewanella and cyanobacterial production of nanowires
  • Insoluble Fe causes synthesis of fimbriae many times 10-100 the cell length.
  • They allow electron flow to distant.  Ppt (pyrite) acts as a electron acceptor = amorphous Fe.  
  • Are electrically conductive nanowires
  • Anaerobic respiration, Fe3+ to Fe2+ as final electron acceptor
Kinds of Extremophiles
  • Thermophile - heat loving; psychrophiles - cold loving
  • Low pH - acidophiles; high pH - alkylophiles
  • High irradiation: deinococcus radiodurans, resits 1.5mil rads of radiations
  • Taq polymerase - isolated from thermus aquaticus grows in yellowstone hot springs
Ability to grow @ low substrate levels
  • Hyphomicrobium, oligotrophic
  • In nutrient sufficient conditions spherical, in nutrient deficient hyphal like growth
Generated by Koofers.com
Ability to become inactive but survive
  • Reducing proteins/biochemicals that use limiting nutrient
  • induction of high affinity transport systems (low Km)
  • reducing growth rate
  • Formation of ultramicrobacteria (low metabolism and resist stress).  Less than .3um
  • Stringent response - in response to low [aa] unusual metabolites of phosporolated quanosine molecules are produced which reduced rRNA and tRNA production.
Temperature Stress
  • Chaperone proteins - repair high temperature damage to proteins via a tunnel that refolds the protein
  • As temperature goes up microbe increases saturated fatty acid content of the membrane (at low temperature unsaturated is up)
  • Archaea have FA glycerol bilayers and tetraether monolayers (biphantyl) which allow it to grow in boiling water
  • Spore production can allow a bacteria to survive higher temperatures

Autochthonous vs Allochthonous
  • Auto - normal inhiabitant of an ecosystem
  • Allo - foreign introduced into the ecosystem

Lakes
  • Freshwater environments (limnology)
  • Surface -  organisms at the air-water interface grow as pellicles.  Use H2O tension to attach and colonize.  Caulobacter important due to fimbriae production; better O2
  • Water column - 3 Levels: In photic zone where light can penetrate, green algae (400-650nm) and purple bacteria (<400 or above 650nm) resource partition.  Heterotrophs below the autotrophic zone.  Sediments is where anaerobes reside and make H2S + CH4.  Methanogens make CH4 and methanotrophs live above them

Generated by Koofers.com
Rivers
  • Lotic Zones
  • Flowing -> no stratification
  • Sediment deposition - irregular pattern, nutrients are taken up and released upon death get taken up again
  • Rivers are self cleaning.
  • Eg Sewage contamination; Increase in C leads to a decrease in O2 until the C is used up.  When C becomes low again O2 recovers as C is used upstream.

Soil (General)
  • Large scale looks homogenous, small looks heterogeneous
  • Chemical composition -  depends on the rock
  • Particles and aggregates are the habitats for microbes
  • AS you go further in the particle you get less and a less oxygen, leading to a microanaerobic environment at the inside layers of the particle
  • Minerals 1/2 Matter; Organic .1-30% of the matter (5% in praries .1% in desert).  Air and H20 makes up the balance

Cation Exchange (Soil)
  • Higher CEC -> more binding to cations

Humic materials
  • Random polymers of aromatic and hetero-cyclic peptides
  • Formation by microbial action
  • Released polymer components linked by chemical rather than biological reactions
  • Many side groups as well as porous material, absorbs nearly everything.

Generated by Koofers.com
Peter Herman's Experiments
  • Hypothesis: microbial numbers will follow nutrient differences in the landscape.  Nutrient islands caused by the mesquite vs grasslands.
  • Found that most microbes were concentrated at shrubs and much lower in the soil between shrubs.  Whereas grasslands had a homogenous distribution throughout
  • This is an example of the Rhizosphere effect
  • Microflora reflect above ground macroflora

Mesquite vs Creosote
  • Resource partitioning
  • Mesquite has long deep roots that get deep ground water and they normally grow only in warmer months; on hill
  • Creosote has near surface roots and grows all year round; below hill

Atmosphere as habitat
  • Air currents provide means by which microbes are dispersed
  • Spores: Temp and environmentally resistant non growing forms.  Germination in favorable environment.
  • Viruses behave like spores

Spore dispersal mechanisms
  • Raindrop drops into a spore cup of the birds nest fungus causing ejection of the spore which adheres to nearby grass by a spore thread.  The spores use kinetic energy of the raindrop to drive ejection
  • Pilobus spore clusters adhere to a drop of H20 and are expelled towards light where there is more likely to be wind (so called the hat thrower).  Spore hat on top of the face water drop

Generated by Koofers.com
Hazards to air travel
  • Dessication -  most microbes die of thirst in minutes (Chlorea after 6min)
  • Thick walled spore can survive years
  • UV inactivation - without protection microbes are inactivated by light.  Pigments protect from light (melanin).  Also particles can be adhered to by microbes to "shade them"

Micrococcus Luteus
  • Has a strong yellow pigment
  • Under UV light (aerobic) it cannot survive without its pigment
  • But if you put it in an anaerobic environment without its pigment it can still survive UV light
  • Because of photo-oxidation is killing the bacteria.  By removing O2 you remove the short term killing mechanism (may still have long term damage ie mutageneisis)

Generated by Koofers.com

List View: Terms & Definitions

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 R strategy
  • Do well when population numbers are low
  • High nutrient concentration, few competitors
  • High Km enzymes, low affinity for substrate
 K strategy
  • Do better when population numbers are high
  • Low nutrient concentration, high population number
  • Low Km enzymes, higher Vmax
 Primary Succession
  • Initial colonization of a previously devoid area, ie newborn intestine or after a volcano.
  • Carried out by pioneer organisms

 Autotrophic sucession
  • Bare inorganic material, Fix N2 and CO2 (cyanobacteria)
 Heterotrophic succession
  • Already and organic source of carbon available
 P/R Ratio
  • P (photosynthesis), R (respiration)
  • When P exceeds R organic carbon builds up
  • Ratio of P/R >1 then stable, if <1 unstable community
 Example of succession in Biofilms
  1. Macromolecular film of organic chemicals
  2. Bacteria/Fungi adhere to the surface
  3. Bacterial growth, release of extracellular polysacharides (EPS) for sticking to each other
  4. Protozoa move in to graze on bacteria/fungi
 Quorum sensing
  • Ability to detect levels of population and express certain genes when there is a high enough population
 Cystic Fibrosis
  • Infection in lungs by pseodomonas aeruginosa with population.
  • With poulation growth levels of homoserine lactone go up then alginate genes turn on "sticks" causes biofilm (fibrous)
 Biofilms on medical implants
  • Huge public health problem. 10million a year, microbes in biofilm are generally antibiotic resistant.
 Conjugation, transformation, transduction (Horzontal transfer)
  • Conjugation - pili exchange of DNA
  • transformation - environmental takeup
  • Transduction - virus, bacteriophage
  • Vertical transfer is transfer across generations (mother to daughter) 
 Hg Study Containing amalgum
  • silver filling in chimps
  • Bacteria in gut had Hg resistance and antibiotic resistance plasmid pBSK plasmid
 Shannon Index
  • Measure of ecological diversity.  Species richness and eventness
 In a 10 grams of soil
  • 4000 - 10000 species of microflora
 Microcosm
  • A microbial ecosystem
 Batchmicrocosms
  • Closed systems, only work short term
  • No new nutrient flow, goes anaerobic
 Flow through systems
  • Nutrients in, waste out
  • Chemostat - keeps the chemistry constant
 Animal Model (Experimental Ecosystems)
  • A host for the microbial community
  • Gnotobiotic animal as a control (bacteria free)
  • Eg. Vibrio cholorea becomes inactive outside of host, inject in animal and revive 
 in Situ Work
  • In field measure of community structure/function
 Oligotrophic vs Eutrophic
  • Oligo - low nutrient concentration (K)
  • Eu - high nutrient concentration (r)
 Microbes vs Macrobes dominated
  • Under nutrient sufficient conditions, macrobes (animals and plants) dominate
  • Under nutrient deficient conditions microbes dominate
 Tularosa Basin Desert Crusts
  • Dominated by microcoleus (cyanobacteria)
  • Secrets an EPS forms a biofilm of bacterial growth
  • W/ desiccation, dry out, brittle and forms crust, prevents soil loss by wind and water w/ rainfall organisms revive and colonize more surface soil.
 Media Choices (for winogradsky selection)
  • Defined media - C source, N source are all identified
  • Complex media - undefined (BHI; brain-heart infusion)
  • Selective media - select for a specific trait
 Phenotypic detection methods
  • Based on lips nucleic acids or cells
  • Lipid profiles - membrane chemistry, fatyacid methyl ester analysis FAME; they need to be methylated in order to be detected via gas chromotography
  • Phospholipids fatty acids profiles (PFLA) ; branched phospholipids
 Direct microscopic methods
  • Laser confocal microscopy
  • Staining techniques - acridine orange; intercalate DNA -> fluorescence.  Binds between two strands
  •  Direct counts of all cells is 10x higher than plate counts
  • Vital stains - distinguish live from dead
 Genotypic Detection
  • Purify nucleic acid - direct extraction, lyse cells and purify.
  • Analyse by: gene probe analysis, PCR, sequencing DNA rDNA or chromosome, denaturing gradient gel electrophoresis, reporter genes.
 DGGE
  • Allows you to differentiate different sequences with a gel electrophoresis; High G-C content goes further
 Reporter Genes
  • Use of genes to discover when a gene is turned on, downstream of a promoter
  • Eg, petroleum waste -> napthalene, when nah genes are turned on
  • Other reporter genes: lux genes, LacZ
  • When napthalene concentration goes up so does light (lux) goes up
 Lebig Law of the Minimum
  • The growth and final yield is determined by the nutrient that is present in the lowest concentrations
  • Cell formula - C5H7O2NP.2
  • C:N:P 10:3:1
 Shelfords law of Tolerance
  • For survival of organism - require a complex set of conditions that must remain withing what that organism can tolerate
 Autecology
  • Individual species 1 at a time in pure culture
 Synecology
  • Interactions of different species in a community populations that exist close to upper or lower limits are more vunerable to competition
 Soluble vs Precipitated vs Surface Sorbed
  • Soluble is available
  • precipitated is not
  • Surface sorbed may be depending, bonded to clay, may still be toxic or mobilize into aquifers
  • Metal solubility is effected by pH, high pH (ppt), low pH soluble
  • Oxidized and reduced also changes solubility, U oxidized is soluble, Fe oxidized is (ppt) 
 Shewanella and cyanobacterial production of nanowires
  • Insoluble Fe causes synthesis of fimbriae many times 10-100 the cell length.
  • They allow electron flow to distant.  Ppt (pyrite) acts as a electron acceptor = amorphous Fe.  
  • Are electrically conductive nanowires
  • Anaerobic respiration, Fe3+ to Fe2+ as final electron acceptor
 Kinds of Extremophiles
  • Thermophile - heat loving; psychrophiles - cold loving
  • Low pH - acidophiles; high pH - alkylophiles
  • High irradiation: deinococcus radiodurans, resits 1.5mil rads of radiations
  • Taq polymerase - isolated from thermus aquaticus grows in yellowstone hot springs
 Ability to grow @ low substrate levels
  • Hyphomicrobium, oligotrophic
  • In nutrient sufficient conditions spherical, in nutrient deficient hyphal like growth
 Ability to become inactive but survive
  • Reducing proteins/biochemicals that use limiting nutrient
  • induction of high affinity transport systems (low Km)
  • reducing growth rate
  • Formation of ultramicrobacteria (low metabolism and resist stress).  Less than .3um
  • Stringent response - in response to low [aa] unusual metabolites of phosporolated quanosine molecules are produced which reduced rRNA and tRNA production.
 Temperature Stress
  • Chaperone proteins - repair high temperature damage to proteins via a tunnel that refolds the protein
  • As temperature goes up microbe increases saturated fatty acid content of the membrane (at low temperature unsaturated is up)
  • Archaea have FA glycerol bilayers and tetraether monolayers (biphantyl) which allow it to grow in boiling water
  • Spore production can allow a bacteria to survive higher temperatures

 Autochthonous vs Allochthonous
  • Auto - normal inhiabitant of an ecosystem
  • Allo - foreign introduced into the ecosystem

 Lakes
  • Freshwater environments (limnology)
  • Surface -  organisms at the air-water interface grow as pellicles.  Use H2O tension to attach and colonize.  Caulobacter important due to fimbriae production; better O2
  • Water column - 3 Levels: In photic zone where light can penetrate, green algae (400-650nm) and purple bacteria (<400 or above 650nm) resource partition.  Heterotrophs below the autotrophic zone.  Sediments is where anaerobes reside and make H2S + CH4.  Methanogens make CH4 and methanotrophs live above them

 Rivers
  • Lotic Zones
  • Flowing -> no stratification
  • Sediment deposition - irregular pattern, nutrients are taken up and released upon death get taken up again
  • Rivers are self cleaning.
  • Eg Sewage contamination; Increase in C leads to a decrease in O2 until the C is used up.  When C becomes low again O2 recovers as C is used upstream.

 Soil (General)
  • Large scale looks homogenous, small looks heterogeneous
  • Chemical composition -  depends on the rock
  • Particles and aggregates are the habitats for microbes
  • AS you go further in the particle you get less and a less oxygen, leading to a microanaerobic environment at the inside layers of the particle
  • Minerals 1/2 Matter; Organic .1-30% of the matter (5% in praries .1% in desert).  Air and H20 makes up the balance

 Cation Exchange (Soil)
  • Higher CEC -> more binding to cations

 Humic materials
  • Random polymers of aromatic and hetero-cyclic peptides
  • Formation by microbial action
  • Released polymer components linked by chemical rather than biological reactions
  • Many side groups as well as porous material, absorbs nearly everything.

 Peter Herman's Experiments
  • Hypothesis: microbial numbers will follow nutrient differences in the landscape.  Nutrient islands caused by the mesquite vs grasslands.
  • Found that most microbes were concentrated at shrubs and much lower in the soil between shrubs.  Whereas grasslands had a homogenous distribution throughout
  • This is an example of the Rhizosphere effect
  • Microflora reflect above ground macroflora

 Mesquite vs Creosote
  • Resource partitioning
  • Mesquite has long deep roots that get deep ground water and they normally grow only in warmer months; on hill
  • Creosote has near surface roots and grows all year round; below hill

 Atmosphere as habitat
  • Air currents provide means by which microbes are dispersed
  • Spores: Temp and environmentally resistant non growing forms.  Germination in favorable environment.
  • Viruses behave like spores

 Spore dispersal mechanisms
  • Raindrop drops into a spore cup of the birds nest fungus causing ejection of the spore which adheres to nearby grass by a spore thread.  The spores use kinetic energy of the raindrop to drive ejection
  • Pilobus spore clusters adhere to a drop of H20 and are expelled towards light where there is more likely to be wind (so called the hat thrower).  Spore hat on top of the face water drop

 Hazards to air travel
  • Dessication -  most microbes die of thirst in minutes (Chlorea after 6min)
  • Thick walled spore can survive years
  • UV inactivation - without protection microbes are inactivated by light.  Pigments protect from light (melanin).  Also particles can be adhered to by microbes to "shade them"

 Micrococcus Luteus
  • Has a strong yellow pigment
  • Under UV light (aerobic) it cannot survive without its pigment
  • But if you put it in an anaerobic environment without its pigment it can still survive UV light
  • Because of photo-oxidation is killing the bacteria.  By removing O2 you remove the short term killing mechanism (may still have long term damage ie mutageneisis)

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