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135 Cards in this Set
- Front
- Back
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Spirochaeta aurantia cell shape
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spiral
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Spirochaeta aurantia metabolic type
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facultative
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Spirochaeta aurantia phylogeny
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spirochetes
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Spirochaeta aurantia taxonomic classification
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spirochetes
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Spirochaeta aurantia metabolism
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Substrates:
electron donors: sugars (aerobic resp) sugars (fermentation) electron acceptors: o2(aerobic resp) acetyl coA (fermentation) Products: Oxidized Products: Co2 and acetate acetyl CoA (internal) + Co2 Reduced Products:H20 (aerobic) acetate, ethanol, H2 (fermentation) |
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Spirochaeta aurantia habitat
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mud and water of pond and marshes
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Spirochaeta aurantia ecological importance
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organic compounds to Co2 oxic and anoxic
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spirochetes: whats special about them.
morphology |
outer sheath, protoplasmic cylinder, periplasmic flagella(axial filaments)
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spirochetes:whats special about them
motility and flagellar rotation |
axial filaments that run outside of protoplasm, but inside outer sheath, allow them to move by rotating in place
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Caulobacter cell shape
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slightly curved rod with stalk or polar flagellum
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Caulobacter metabolic type
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aerobic chemoorganotroph
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Caulobacter phylogeny
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alpha proteobacteria
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Caulobacter taxonomic classification
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budding and/or appendaged bacteria
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Caulobacter metabolism
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Substrates:
Electron Donors: organic cmpds Electron Acceptors: O2 Products: Oxidized Products:CO2 Reduced Products: H20 |
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Caulobacter habitat
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widespread in aquatic habitats
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Caulobacter ecological importance
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O2 to H2o, oxic organic cmpds to Co2
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Caulobacter exploitation
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holdfast material
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caulobacter: whats special about it
how it divides |
swarmer vs stalk cell
swarmer just swims, stalk cell has DNA synthesis and cell division swarmer drops flagellum and grows stalk where flagellum used to be- grow flagellum on other side. divides- flagellum side is swarmer and starts process over again. stalk cell starts over again without dropping flagellum |
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Symbiodinium metabolic type
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oxygenic phototroph and/or aerobic chemoheterotroph
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Symbiodinium cell shape
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symbiotic form is spherical, free living form has transverse and longitudinal flagella
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Symbiodinium phylogeny
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dinoflagellate algae
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Symbiodinium metabolism
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energy from light or organic cmpds
electron donors: H20 organic compounds oxidized products: O2 Co2 Co2 fixation by calvin benson cycle |
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Symbiodinium habitats
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free living in seawater, endosymbiotic with marine cnidarians and molluscs
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Symbiodinium ecological importance
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symbiotic cells are responsible for the majority of primary production (co2 fixation) in coral reef ecosystems
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symbiodiniums' relationship with coral! where are they
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in the gastrodermal cells of the coral
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symbiodiniums' relationship with coral! nutrient recycling
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nitrogen goes from animal to algal symbiont as uric acid, symbiont changes it to ammonia, then amino acids for animal, takes photosynthetic carbon. gives carbon back to animal tissues
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agrobacterium tumefaciens lifestyle
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opportunistic plant pathogen
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agrobacterium tumefaciens genome size
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5,670kb
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agrobacterium tumefaciens anabolism
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can grow on minimal medium
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agrobacterium tumefaciens catabolism
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glycolysis, enter-doudoroff, TCA cycle, oxidative phosphorylation
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dbellovibrio life style
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obligate (with exceptions) periplasmic predators
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dbellovibrio genome size
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3,783 kb
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dbellovibrio anabolism
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precursors from prey
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dbellovibrio catabolism
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glycolysis, TCA cycle, oxidative phosphorylation
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rickettisa life style
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obligate intracellular parasite
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rickettisa genome size
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1,112 kb
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rickettisa anabolism
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limited
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rickettisa catabolism
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TCA cycle, oxidative phosphorylation, ATP from host
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chlamydia life style
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obligate intracelluar pathogen
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chlamydia genome size
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1,043
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chlamydia anabolism
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limited
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chlamydia catabolism
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aerobic resp of glutamate, also atp from host
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mycoplasma genitalium lifestyle
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urogenital pathogen, grows in mucous membranes and joints
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mycoplasma genitalium genome size
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580
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mycoplasma genitalium anabolism
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limited
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mycoplasma genitalium catabolism
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glycolysis
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carsonella life style
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obligate intracelluar symbiont of aphids
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carsonella genome size
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160
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carsonella anabolism
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limited. synthesizes essential amino acids for aphid
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carsonella catabolism
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glycolysis
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nanoarchaeum equitans life style
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extracellular parasite of certain crenarchaeota
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nanoarchaeum equitans
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491
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nanoarchaeum equitans anabolism
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limited
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nanoarchaeum equitans catabolism
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limited. simple atpases
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mitochondria life style
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organelles
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mitochondria genome size
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16
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Vibrio fischeri cell shape
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vibrio with polar flagella
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Vibrio fischeri metabolic type
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facultatively anaerobic chemoheterotroph. luminescent under aerobic conditions at high cell density
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Vibrio fischeri phylogeny
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gamma proteobacteria.
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Vibrio fischeri taxonomic classification
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gram negative, bioluminescent marine vibrio, motile
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Vibrio fischeri metabolism
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Substrates:
Electron donors: organic compounds Electron acceptors: O2 organic intermediates Products: Oxidized products: CO2 +/- organic fermentation products Reduced products: H2O organic fermentation products |
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Vibrio fischeri habitat
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free living in sea water, symbiotic with fish and molluscs
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Vibrio fischeri ecological importance
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degradation of organic materials, including chitin
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Vibrio fischeri lab importance
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Model organsm for bacterial quorum sensing by acyl homoserine lactone signals
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luciferase reproductive advantage?
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takes all o2 so less free radicals form, metabolism changes at low o2 levels
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Quorum Sensing
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regulatory pathways that are controlled by the density of cells of their own kind
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homoserine lactone
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freely diffuses to out of the cell, if there are enough cells producing AHL, there will be high conc outside the cell. If there are enough, it trigger transcription of specific genes
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vibrio fishceri and quorum sensing
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enzyme called luciferase causes luminescence. Lux operons encode proteins involved are under control of LacR
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counter illumination
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organisms that use light bacteria hang out at the bottom in the dark during the day, then go eat at night. If it is moonlighty out, they can measure the amt of light shining down on them and emit the same light down so predators dont see there shadows
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Myxococcus cell shape
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vegetative cell: rod
spore: spherical forms fruiting bodies |
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Myxococcus metabolic type
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aerobic chemorganotroph
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Myxococcus phylogeny
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delta proteobacteria
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Myxococcus taxonomic classification
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fruiting myxobacteria
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Myxococcus metabolism
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Substrates:
Electron donors: proteins, peptides, amino acids, simple sugars Electron acceptors: O2 Products: Oxidized products: CO2 Reduced products: H2O |
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Myxococcus redox tower
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Redox pairs:
CO2/org cpds O2/H2O Redox potentials (volts): +0.82 |
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Myxococcus habitats
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soil
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Myxococcus ecological importance
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breakdown of polymeric substances
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How myxococcus hunt
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produce lysosomes that lyse prey cells
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how myxo feed
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eat cells, cellulose, proteins, so have to secrete specific enzymes. high cell density creates more secreted enzymes and creates small enough enzymes for metabolism
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how myxo move in a) individual cell b) social rafts and swarms
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a) slime gel, shoot gel out the back
b)retractile pili |
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how many signals in myxo are there and how did we find them
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5, through complementation
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what 2 signals in myxo do we know
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1) C signal- cell bound protein- signals cell to cell contact, makes spores
2) A signal- specific a.a. that gives indication of cell density, causes high cell density specific gene expression |
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Bdellovibrio cell shape
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tiny curved rod
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Bdellovibrio metabolic type
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aerobic chemoorganotroph
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Bdellovibrio phylogeny
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delta proteobacteria
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Bdellovibrio taxonomic classification
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aerobic or microaerophilic, motile, helical or vibroid Gram negative bacteria
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Bdellovibrio metabolism
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Substrates:
Electron donors: complex organic compounds Electron acceptors: O2 Products: Oxidized products: CO2 Reduced products: H2O |
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Bdellovibrio habitat
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soil, water, periplasmic space of other Gram negative bacteria
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how do bdello locate prey
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random collision
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how do attack phase bdello move
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very fast, with single flagella. high respiration rate and high catabolic and anabolic rates
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invasion phase of bdello: where are they?
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paraplasm, hard cuz bacteria pressurized
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prey requirements of bdello
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all gram negative bacteria
individual bdello have unique host ranges specific prey receptors unknown localized pili on the APC nose required (cant prey when knocked out) development of prey resistance is by acclimation |
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degradative modifications of bdelloplast envelope
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1) lipase- removes LPS
2)glycanase- solulize glycan 3)protease- removes lipoprotein 4) peptidase- cleaves cross bridges |
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biosynthetic modifications of bdello envelope
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1) addition of DAP to peptidoglycan goes again peptidoglycan
2) addition of fatty acids to peptioglycan goes against protease 3) deacetylation of peptidoglycan so glycanase cant reach it |
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unusual about bdello?
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1) extremely high complement of transport systems and hydrolytic enzymes
2) complete gene systems for respiratory catabolism/ATP synthesis |
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adaptations of p. aeruginosa in CF lung
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1) loss of motility functions
2) loss of LPS O-antigens 3) alginate overproduction 4) amino acid auxotrophy |
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transcriptomics
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looking at expression level of mRNA using microarray technology
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proteomics
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the study of the protein complement of the genome
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metagenomics
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assaying the genomic content of environmental samples- can be used to mine DNA for enzymes/functions
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how to separate and identify a protein
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protein mixture- use 2D-SDS-PAGE to make individual proteins- use spot cutting, digestion, and trypsin to make peptides- use mass spec to find peptide mass use database search to identify protein
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2D gel electrophoresis
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1 dimension- separate based on size
second dimension- separate based on protein charge |
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olavius algarvensis
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worm with no digestive tract or mouth, uses bacterial symbionts for nutrients
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olavius algarvensis metagenomic analysis
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4 genomes- 2 unknown, 1 gamma and 1 delta found to have sulfur oxidizing and sulfate reducing qualities
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key gradients in a biofilm
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1) nutrients
2) signaling molecules 3) toxic compounds 4) chemical gradients |
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what influences gradients
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1)microbial metabolic activity
2) spatial distribution of populations 3) biofilm extracellular matrix 4)physical factors |
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FISH and biofilm
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ammonia oxidizing bacteria
NH4->NO2 nitrite oxidizing bacteria NO2->NO3 from top to bottom: O2 goes down NH4 goes down NO3 goes up NO2 goes up, then down |
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Wsp signal transduction system
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moldulates c-di-GMP (intracellular messenger) synthesis in pseudomonas- downregulates motility, increased cell surface adhesiveness, important for biofilms, resistant to antimicrobials, wrinkly colony formation
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GGDEF domain
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2 GTP -> cyclic di GMP
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EAL domain
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cyclic di GMP -> 2 GMP
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how bdellovibrio get out of the host cell
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produce special glycanase that they have the ability to produce the whole time. don't know what triggers it
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strange things about bdellos genome
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there are 6 amino acids it can neither make nor degrade. 47% of its genome is of unknown function
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Agrobacterium TDNA: what is in it
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oncogenes, octopine metabolism genes, plant hormones
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agrobacterium vir genes: what is in it and how does it work
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plant phenols that are produced from a wound stimulates virA, which phosphorylats virG, which induces transcription of virB, which helps with the gene transfer of tDNA. VirG also starts virC D and E. virD is an endonuclease that nics tDna so that it comes loose and virE produces single stranded Dna binding proteins so that it stays away from plasmid
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what is an octopine
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a modified amino acid that only agrobacterium can use- arginine + pyruvate + NADPH
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elementary body of chlamydia
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domant/resistant to desiccation, airborne
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reticulate body of chlamydia
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stage where it grows inside cells
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donor/recipient experiment in myxo
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donor has:
a- (no adventurous motility) s- (no pilA) tg1+ recipient has a- s- (tg1-) pilA+ donor gives tg+ to recipient and rescues its social motility |
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are methanogens parasites of the ruminant host?
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use H2 and Co2 or acetate (cow uses acetate also) but they consume H2 (interspecies H2 transfer), also provide protein for cow
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trophosome
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giant tube worms at hydrothermal vents with no digestive tracts have these full of sulfide oxidizers
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special hemoglobin of giant tube worms
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provides sulfur and o2
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giant tube worms and sulfide oxidizers- obligate or facultative?
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obligate
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cnidarians and zooxanthallae- obligate or facultative
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facultative
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function of mycorrhizae associations b/w fungal and plant roots?
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1) increases absorptive S.A.
2) can create nutritional internet |
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flatworm convoluta and tetraselmis
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adult flatworm loses mouth and digestive tract with algae teraselmis in it, born algae free
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aphids and buchnera
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buchnera provide a.a. for aphid
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mycetocytes
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cells in the aphid that buchnera are kept in
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evolutionary different about buchnera and aphids?
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cospeciation- aphids began because of the symbiosis
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photorhabdus luminescens
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live in nemotodes- when nemotode infects an insect, they go into haemocoel of it and produce exoenzymes, antibiotics, pigments. and glow!
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host induced oxidative stress in the bobtail squid
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1) NO present in spithelial mucous
2) NO present in ciliated ducts 3) halide peroxidases induced deep in crypt |
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how vibrio get inside the squid
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a) in response to gram - or + bacteria, squid secretes mucous
b)gram - form aggregations because of mucous c)v fischeri compete other gram - and become dominant d)migrate thru pores and into ducts |
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advantages of dumping 90% of its symbionts to bobtail squid
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1) pure culture
2)continuous enrichment |
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why luciferase is energetically beneficial
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acts as an e- sink- it has enough affinity for o2 the be present in the crypts, allows TCA cycle
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purpose of halide perioxidases in the squid
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they are host induced to select for vibrio fischeri. they create oxidative stress that only luciferase can cope with
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what does the large tube worm use its symbionts for?
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carbon fixation
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what does cnidarians use zooxanthellae for?
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carbon fixation (photosynthesis)
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