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microbio unit 2 > week 8 > Flashcards

week 8 Flashcards

1
Q

axenic culture

A

pure culture - helps scientists understand microbial biology.

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2
Q

great plate count anomaly?

A
  • discrepancy between the number of microbial cells observed by microscopic examination and the number of colonies cultivated from the same natural sample.
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3
Q

how much microbes can actually grow in a lab? why can they not grow more?

A
  • Only 1-5% of microbes can be grown in the lab
  • Slow growing
  • Low abundance
  • Inhibition by other microbes in a mixed culture
  • Fastidious growth requirements
  • Cross-feeding or communication signals from other microbes are needed
  • Lacks trigger for growth or exists from a dormant state
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4
Q

what does an enrichment culture do/tell you?

A
  • Promotes growth of microorganisms, formerly restricted
  • Inhibits growth of other microbes
    Must understand the specific niche the microbes inhabit
  • Know features that set the microbes apart
  • Isolation and cultivation are needed before the analysis
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5
Q

how can you identify strains and subspecies?

A
  • Classical characteristics
    Morphological, physiological and ecological features
  • Biochemical characteristics
    Bacterial fatty acids/; lengths, degree of saturation, bacterial chains, and hydroxyl groups
    Proteins: mass spectrometry, 2D Gel electrophoresis
    DNA: RNA sequencing, DNA microarray
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6
Q

symbiosis? what is typically seen?

A
  • stable association of two or more organisms (host and symbiont), beneficial, neutral or negative impact
  • Genomic reduction typical in symbiotic relationships (genome gets very large and will start to cut costs to save energy)
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7
Q

faculitive and obligatory?

A

Facultative (aid each other - preferable but not required ) or obligatory (entirely independent - required )

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8
Q

mutualism?

A
  • usually obligatory; both partners benefit from each other
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9
Q

coevolution

A

evolved together - partners cannot grow without each other

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10
Q

what are two examples of mutaulaism?

A
  • Termites and the protist - Termites feed on wood (cellulose and lignocellulose) but can only degrade cellulose component. Protists in gut degrade the lignocellulose
    2. Tube worm
    Worm lacks a digestive tract and relies on bacteria to provide organic carbon
    Bacteria get delivery of carbon source, electron donor and acceptor
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11
Q

cooperation? 1 example

A
  • non-obligatory. Looser (indirect) interaction
  • Fungal highway
    the physical network of fungal hyphae grows toward nutrients
    Bacteria move along the hyphal surface to explore new environments
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12
Q

antagonism? three types

A
  • one organism negatively impacts another
    1. predation
    2. parasitism
    3. competition
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13
Q

what is predation? two strategies used?

A
  • killing - benefits after the victim is killed
    1. Epibiotic predators - attach to preys surface and lyse to release preys cytoplasmic contents (Vampirous lugosii - sucks contents.)
    2. Endnobiotic predators - invade victims’ cytoplasm, where they consume contents to get energy.
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14
Q

parasitism? benfits? gains what?

A
  • exploitation
  • Benefits while the victim is alive
  • It can involve nutrient acquisition, physical maintenance, or both
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15
Q

competition? two possible outcomes?

A
  • uneasy truce between microbes - Different organisms try to acquire the same resources
    1. Contact-independent growth inhibition - carried out by secretions of diffusible compounds (antibiotics)
    2. Contact-dependent growth inhibition - physical proximity for toxin delivery
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16
Q

syntrophy? example

A
  • when one species benefits from the metabolic products of another
  • Example - Methanotrophic archaea grow in association with sulfate-reducing bacteria
    – The archaea consume methane and produce by-products that the bacteria use, while the bacteria help the archaea by removing these by-products, benefiting both organisms
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17
Q

what are the two ways bacteria defend themselves?

A
  1. Restriction modification - chemically distinguish viral and host DNA and hydrolyses viral DNA
  2. CPISPR/Cas system - recognizes viral DNA by comparing samples from previous encounters to identify and degrade viral genomes
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18
Q

what are the four ways we can investigate macro and micro diversity in a natural community ?

A
  1. Species richness - the number of different species in the environment
  2. Population - a group of microorganisms within a single species
  3. Guild - a group of microbes defined by physiological activity
  4. Microbial community - microorganisms that share a common habitat
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19
Q

what are communities dependent on?

A

Energy source (nurteint)
Terminal electron acceptor
Sunlight

20
Q

Phototrophs -
Chemotroph -
Lithotrophs -
Organitrophs -
Heterotrophs -
autotroph s -

A

Phototrophs - light
Chemotroph - chemicals
Lithotrophs - inorganic
Organitrophs - organic
Heterotrophs - carbon
autotroph s - CO2

21
Q

what state does water exist in? what are they considered as?

A
  • dissolved
  • Microbial versatility = consumption/use of variety of molecules
22
Q

carbon cycle ? what can it be reduced into? found where? release off? fraction ? global?

A
  • carbon is continuously transferred from one to another
  • Plants and microbes fix CO2
  • CO2 can be reduced anaerobically to methane, which itself can be oxidized
  • Methane can be found in rice paddies, coal mines, etc
  • Release of CO2 and biomass production
  • A small fraction of decomposed plant material remains in the soil as SOM
  • Balancing global CO2 levels, minimizes climate change
23
Q

nitrogen cycle: Nitrogen fixation? carried out by? ratio? affects?

A
  • reduction of inorganic N2 to organic form (ammonia)
  • Carried out by some bacteria and archaea
  • It can be carried out under both oxic and anoxic conditions
  • Carbon to nitrogen ratio is important for soil quality
  • It affects plant growth, microbial activity, and decomposition
24
Q

Denitrification

A

nitrate to nitrogen gas
retunes nitrogen to the atmosphere
N availability in ecosystems -> plant growth and agricultural

25
Q

phosphorus cycle
required in? excess released in? moves to? nutrints?

A
  • Phosphorus is required for ATP, nucleic acids, lipids, and polysaccharides.
  • Commonly short supply in soils dependent on soil pH
  • When the soil has bound all phosphorus, the excess is released by soil erosion
  • Moves to lakes, streams, and estuaries where it can stimulate the growth of microorganisms
  • Nutreninet availability and microbes in soil and water
  • Binding to soil depend on soil pH
26
Q

sulfur cycle
reduction?
depending on?
?->?

A
  • Reduction of sulfate for use in amino acids and protein biosynthesis
  • depending on the oxidation of Sulfur species, it can serve as electron donors and acceptors or both
    SO4^2- -> H2S in anaerobic (dissimilatory sulfate reduction)
27
Q

iron cycle
- used in?
- important for?
- element ?
- avalibility for?

A
  • respiration/photosynthesis
  • Free iron is an essential component
  • Fe3+ can serve as a terminal electron acceptor during anaerobic respiration in a range of bacteria and archaea (redox reaction)
  • Iron availability to plants and algae
28
Q

maganese cycle

A

Mn2+ as an electron donor —- reduction(anoxic) ——> MnO2 e- acceptor
<—– oxidation (oxic)

29
Q

mercury cycle
biomagnifcation?
reduction?
does?

A
  • Biomagnification - anaerobic bacteria feed into the food chain and accumulate
  • Demethylation of methylmercury -> Hg^0/reduction
  • Microbes can either facilitate toxic transformations or detoxify mercury/preventution of bioaccumilation
30
Q

what is the ocean adapted to ?

A

nutrient liimitation

31
Q

what is the purpose of the microbial loop?

A
  • key to surviving in the photic zone
  • Recycling of nutrients rather than letting them sink to the seafloor
32
Q

what does the microbial loop include? DOM? POM?

A
  • Carbon fixation by phytoplankton
  • Heterotrophic microbes consume dissolved organic matter (DOM) released by resident microbes
  • Particulate organic matter (POM) - microbial cells, insoluble detritus and other solid organic matter
  • Marine snow is a shower of organic material falling from upper waters to the deep ocean
  • Material consumed by zooplankton enters the food chain
33
Q

what happens when CO2 is high in the ocean? what role do viruses have in water?

A
  • If CO2 is high, microbial growth in open ocean that is limited by nitrogen
  • Viruses are important members of marine and freshwater microbial communities
  • Virus-like particles (VLPs) are now recognized as the most abundant microbes on earth
34
Q

what are important physical factors in water?

A

Temperature
pH
Light penetration
Osmotic conditions
Dissolved oxygen
Water potential

35
Q

Lotic systems vs Lentic

A

Lotic systems - free-running waters (streams and rivers)
Lentic systems - free-standing waters (ponds, lakes, marshes, and slow-moving rivers)

36
Q

what are the two types of lentic systems?

A
  • Dominated by planktonic microbes and invertebrates
    1. Oligotrophic lakes - mountain lakes fed from infertile land - why lakes tend to be clear
    2. Eutrophic lakes - low-level lakes that catch water from fertile, cultivated soils
    High level of planktonic growth - appear turbid
37
Q

what are esturaies ?

A
  • This is where the river (freshwater) meets the sea (saltwater). These are likely to be halotolerant.
  • Planktonic microbes and invertebrates dominate microbes in lakes.
38
Q

what are three adaptions that have allowed for success of terrestrial ecosystems and problems it might cause?

A

1.) In deep, hot biosphere, bacteria and archea live in biofilms kilometers below the earth’s crust. Genomic studies suggest the presence of N2 fixation and denitrifixation from subterranean
2. Some bacteria have the ability to fix atomospheric nitrogen into a form that plants can use and therefore can form commensual or mutalistic relationships with plants
However microbes can be plant pathogen and harm a host
3. Microbial diversity in soil exceed that of any other habitat on earth
Roles of degradation of hydrocarbons, plant materials, and soil humus. Micro habitats created by interdependent biological , physical and chemical factors

39
Q

greenhouse gases ?

A
  • trapped heat reflected from earths surface in the atmosphere, rather than allowing it to radiate into space
  • Gases accumulate if the rate they enter the atmosphere exceeds the rate by which the natural carbon and nitrogen cycle can remove them
40
Q

what are the consequences of disrupting carbon and nitrogen cycel?

A

Global climate change
Surface temperature on land and sea and in the atmosphere
Rates of precipitation
Frequency of extreme weather

41
Q

oceanography and limnology

A

Oceanography - the study of marine systems and related biological, geographical and chemical factors
Limnology - investigations of aquatic systems within continental boundaries

42
Q

what affect does solar radition have on water? thermoclone ? photic zone ? phytoplankton? nutrinets?

A
  • Warm water is less dense than cool water
  • As water layers mix, nutrients swell up
  • Thermocline - warm water floating on top of cooler water
  • Photic zone - Upper 100 meters of the open ocean
  • A diverse collection of microbes
  • Phytoplankton - a major source of organic matter
  • Nutrient levels are extremely low
43
Q

pelagic and benthic zone

A

Pelagic - upper layers of water
Benthic = bottom of a body of water
- the microbes here are very slow - doubling times a hundred years

44
Q

rainfall? mineral soil? organic soil?

A
  • Well aggregate soil changed to isolated pockets of water
    Waterlogged soils can become anoxic
    Gas fluxes can change CO2 concentration
  • Contains less than 20% organic carbon
    Most of earths soil is in this category
  • Possess at least 20% organic carbon
    Soil organic matter (SOM)
    Retains nutrients and water
    Maintain soil structure
45
Q

what are the three roles microbes have in soil?

A

Provide nutrients for other organisms
Promotion of plant growth
Associative nitrogen fixation

microbio unit 2 (6 decks)

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