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BIOL 447- ENV MICROBIOLOGY > Midterm 1 > Flashcards

Midterm 1 Flashcards

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Biology 101 flashcards
1
Q

Where should the samples be from for an ideal sampling? And the common sampling methods?

A
  1. ) Taking Depth profiles to include both limnetic and profundal zone (bottle sampler)
  2. ) sampling around littoral region (Bottle sampler)
  3. )separate methods for sampling benthic zone including sediment (Core sampler- cylindrical)
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2
Q

What are the two characteristics that should be considered when sampling aquatic microbiology?

A

Morphometric: The dimensions, depth, geology around the water body
Physiochemical: The temperature, pH, light and oxygen level

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3
Q

What is it called when areas of the lake are sampled most frequently?

A

Hot spots and they are often associated with industrial sites

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4
Q

Give an example of the one Great Lakes area of concern

A

Deer Lake: Due to effluent from iron industry which contained a high level of mercury, bioconcentrated in fishes. Reproduction problems of many wildlife in the area such as bald eagles. Eutrophication from untreated or partially treated sewage from the city led to a depletion in oxygen dead where aquatic organisms can not survive.

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5
Q

What happened to Lake Erie?

A

lake Erie is the shallowest and smallest in volume out of all the great lakes - most likely to show “sickness” first. Eutrophication due to industrial and city waste and agricultural run off containing high levels of organic and inorganic nutrients such as P led to extensive algal bloom, the death of these phytoplankton and other biota settles on the sediment and decomposition of these by heterotrophs utilizes oxygen leading to oxygen depletion. Eventually lead to dead zones, hypoxic *very low oxygen level

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6
Q

What are the two reactions in photosynthesis?

A 
Light reaction happens on thylakoid membrane ( PSI and PSII (chlorophyll a P680)), splits water and forms the reducing power of ATP abd NADPH from ADP and NADP+
Dark reaction (co2 fixation) - happens inbetween the thylakoid spaces, where rubisco is the key enzyme in catalyzing the fixation of carbon dioxide to carbohydrates. This reaction requires the reducing power from the light reaction
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7
Q

Would phytoplankton or terrestrial plants have more accessory pigments?

A

Phytoplankton beceause of green light (450-550nm) can penetrate the deepest into the water column. These pigments help harvest the light energy from green light and funnel it to P680.

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8
Q

True/ False: All oxygen evolving photosynthesizing organisms have chlorophyll a

A

True

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9
Q

What are the three things the pigments are useful for?

A

Estimation of biomass, identification of a particular phototroph and determining the phytoplankton community based on pigments

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10
Q

What are the three main methods of estimating algal biomass?

A
  1. ) Counting the algal cells (filtering a suitable volume of water) and examine under fluorescence microscopy to count (chlorophyll autofluorescence red)- convert to biomass
  2. ) Most sensitive: Extract the chlorophyll a using acetone and determine chlorophyll a content using fluorimetry or spectrophotometry - convert to biomass
  3. ) Combustion of the alagal cells to co2 and examine cC content using atomic absorption spectroscopy
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11
Q

For measuring the chlorophyll content (most common), what is the ratio often used?

A

Algal C to chlorophyll content is 50: 1

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12
Q

What are the main hold backs with measuring algal biomass?

A

Differing cell sizes, dependent upon light and temperature. Therefore just estimates

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13
Q

What are the three main methods for measuring the rate of photosynthesis?

A
  1. ) Light-opaque bottle (oxygen level)
  2. ) Light- opaque bottle (carbon level- Primary productivity)
  3. ) Measuring fluorescence
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14
Q

What are the steps in the Light-opaque bottle (oxygen level)?

A

Place equal volumes of water into clear and opaque bottles, measure initial oxygen content using oxygen probe, incubate under conditions similar to sample origin, or in situ, for appropriate time and measure oxygen content

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15
Q

What are the results of clear-opaque bottle (oxygen level)?

A

Clear bottle have higher oxygen content (presuming net community production (NCP) is greater than zero) and opaque bottles have less. Assume respiration happens in both bottles.

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16
Q

Under what circumstance would you use the radio-labelled Carbon bottle method?

A

Because the oxygen level measurement is not very sensitive, it can not be accurately used for oligotrophic lakes

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17
Q

What are the steps in the clear-opaque bottle (carbon level)?

A

Place equal volumes of water into clear and opaque bottles, add radio-labled carbon in the form of NH4CO3. Incubate under conditions similar to sample origin, or in situ, for appropriate time (not too long or respiration products will accumulate) and filter through the water using 0.45 micrometer filters and place filter in scintillation fluid and radioactivity level to be measured using liquid scintillation counter

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18
Q

What is the ratio used in measuring rate of photosynthesizing using the oxygen level?

A

Respiratory Quotient, for every molecule of oxygen used, 0.9 moles of CO2 is produced

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19
Q

What value does measuring with carbon level provide?

A

Somewhere in between the net and gross primary production because some carbon is lost

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20
Q

What are three main ways that labeled carbon is unaccounted?

A

Respiration, excretion and uptake of excretion product by heterotrophs which passes through the filtered but are not measured

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21
Q

What are the bacteria responsible for dark fixation?

A

Heterotrophs - dominate surface to near surface water, 3-5% of cellular C from fixation
C1 microbes- unique combination of auto- and heterotrophy because assimilate 30-90% of C from atm but can metabolize small low wight organic compounds such as methane and formate
Chemolithotrophs - dominate in certain environments such as anoxic env, oxidize reduced compounds such as H2S, H2

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22
Q

Where do you mostly find C1 microbes and Chemolithotrophs?

A

oxic and anoxic interface (water column and sediment interface)

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23
Q

What do changes in primary productivity mean?

A

Short term changes (hours to weeks) - seasonal changes or diet changes (such as snow melt)
-physical alterations such as vertical mixing
-reflect shift in plant community, its composition and activity
Long term Changes (years, decades to Millenia)
- indicative of ecological, geochemical, climatic changes, useful indicators of ecosystem alterations

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24
Q

How can Fv and photochemical efficiency value be determined?

A 
Fv= Fm-Fo 
Efficiency= Fv/Fm
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25
Q

What is the basic idea of fluorescence?

A

Energy from photosynthesis is divided into three components heat, or work, or fluorescence (competing demands)
→ changes in one must be reflected by opposing changes in the others

26
Q

What are the three main methods of measuring bacterial biomass?

A

1.) “dark fixation” value; CO2 uptake in absence of light
known that heterotrophic CO2 fixation usually accounts for ~5-7% of the total biomass and can use formula for oxic waters (i.e., no anaerobes functioning), approximation for calculation of estimated bacterial production:
biomass =( dark fixation of CO2 x 100 gC/L/day)/
6

  1. ) Count the cells
  2. ) biochemical components
27
Q

What is the protocol in counting the cells to determine bacterial cell biomass?

A

Filter a suitable volume through nucleopore filter (not weaves like typical filter, therefore cells do not get stuck, lies on of the filter). Add fluorescence dye, such as DAPiI and examine under epifluroresence microscope and convert

28
Q

What is the protocol in biochemical components to determine bacterial cell biomass?

A

Find a suitable assay for example phospholipid fatty acids, where “marker” fatty acids are used such as, fatty acids methyl esters, these are then measured using G.C

29
Q

What is the main component of epifluorescence microscope that make it different from normal microscope?

A

Dichroic mirror module, which is opaque to short wavelengths of light such as UV but allows long wavelength of light to pass through such as those in visible spectrum so can see the slide

30
Q

What are the 4 methods of measuring microbial activity?

A
  1. ) direct increase in cell numbers on membrane filters or incorporation of radiolabelled substrates
  2. ) FISH (Fluorescent in situ hybridization)
  3. ) CARD- FISH (Catalyzed Reporter Disposition)
  4. ) FISH-MAR (Microautoradiography)
31
Q

What does incorporation of radiolabelled thymidine measure and leucine measure?

A

DNA synthesis and protein synthesis which are both scaled to growth

32
Q

What is FISH useful for ?

A

Track and identifying specific an organism or organisms in a particular phylogenetic domain.

33
Q

What does FISH use?

A

RNA/DNA oligonucleotides probe with fluorescent dye that penetrates the cell and hybridize with target Gene or rRNA. For example if hybridizing with rRNA in ribosomes, because these are scattered through out the cell, the entire cell fluoresces

34
Q

What is FISH- CARD useful for ?

A

Measuring gene expression - targets mRNA

35
Q

What is the difference between FISH and FISH-CARD?

A

CARD- have enzyme, peroxidase conjugated instead o fluorescent dye. After hybridization, stain with tyramide (Fluorescence dye) and the enzyme will activate multiple tyramide and amplification occurs. Even if mRNA is low in abundance will still be visible

36
Q

What is MAR- FISH useful for?

A

The physiological function of organisms. The FISH identifies the organism and the MAR identifies their activity. For understanding the activity of microbial ecosystem and guiding enrichment cultures

37
Q

What does MAR-FISH use?

A

Cells exposed to radio-labeled substrate and incubate (heterotroph vs phototroph) and cells are affixed on slide and dipped into photographic emulsion and kept in the dark for silver grains to form in emulsion

38
Q

What technique identifies all the gene pool of a bacterial community?

A

Metagenome

39
Q

What is the difference between community sampling approach and environmental genetics approach?

A

Community sampling approach- phylogenetic tree which provides only a snapshot of the community and can discover new phylotypes
environmental genetics approach- metagenome, discovers new genes and link genes to phylotypes

40
Q

Who is most abundant in the make-up of freshwater lake bacterioplankton communities?

A

Most abundant: Actinobacteria in epilimnia. From metagenome shows that they are very small size, cell wall composition help discouraging grazers. Harbour rhodopsin-like genes to harvest light energy BUT not used for photosynthesis. Possibly heterotrophic due to nucleic acid and amino acid metabolic pathways
pH, particle attachment, C substrate preferences important in differentiating clades

41
Q

What are the characteristics of Bacteroidetes?

A

Very diverse, ften abundant in environments with high organic load, or during periods after cyanobacterial blooms – a “copiotrophic” lifestyle

  • don’t seem to show any seasonal &/or lake-specific occurrence patterns; instead their presence seems ~sporadic, stochastic (as are occurrences of cyanobacterial blooms)
  • Experience top-down control , but in bodies of water where there is a high grazing pressure, there is a shift in morphology from organisms that tend to be rod shaped (tend to be grazed upon) to filamentous form (too big to eat).
42
Q

True/False: For cyanobacteria, all N fixing ones produce heterocyst?

A

False

43
Q

What are the three groups that Proteobacteria are broken down into?

A

Alpha- numerically dominant in marine system but not in freshwater. Non- cultured from freshwater – almost no info on them. Competitive under low nutrient/low substrate conditions (i.e., oligotrophic) but also capable of degrading complex organic compounds, widely distributed in lakes all over globe

Beta (best cultured and studied excluding cyano)- numerically-dominant in freshwater epilimnia.Niche preferrance can be used to distinguish different closely- related species. Because nutrient loving- easy to grow. Also back to size matters due to top-down control

Gamma - Example how wrong we are to assume bacterial commnity on land and in water would be the same. not particularly abundant in freshwaters (generally more abundant in saline waters). - patchy recovery of sequences suggests they may be transient members of lake communities (e.g., enterics), or common members existing at low abundances

44
Q

What are the characteristics of Verrucomicrobia?

A

ubiquous but can’t be cultured!

45
Q

What is the difference between DOM/POM?

A

DOM are fine particulates that passes through the 0.2 microfilter and this also includes viruses and small bacteria as they are able to pass through as well
POM: Are organic matter that are too coarse to pass through 0.2 filter

46
Q

What are some other potential roles for the microbial loop?

A

Trophic upgrading by improving the quality of food. Ex. algivorous ciliates vs bacterivorous ciliates, rotifer would prefer to eat the algivorous ciliates because they have a higher level of PFA and sterols that rotifers need as they graze on algae which are high in sterols and PFA as well. thus enhances the food quality.

Upgrading of food by detoxifying them. Ex Microcystis aeruginosa→ Paraphysomonas sp. (detoxify and de novo synthesis of PUFA and sterols)→ Daphnia magna

47
Q

Why are river channels significant and how are they mainly formed?

A

River channels derives from atm precipitation (rain water) therefore not much ions dissolved, but the river evolves due to terrestrial runoff and other sources of input. They are significanty because they delivery of water across continents, they contribute to erosion and weathering of geologic material. Habitat for aquatic organisms

48
Q

What is there when you have oxic and anoxic interface (water column and sediment)?

A

Gradient of energy: denitrification –> sulfate reduction –> least favourable methanogensis. Will sequence in what electron acceptors are used

49
Q

What is the sediment like?

A

High biological activity and the biogeochemical gradients develop that controls the type of microbes and microbial activities found in the region

50
Q

Nitrogen decomposition happens where?

A

In the sediment and generates ammonia (assimilated by planktonic and sediment organisms) OR nitrification of ammonia as a nitrogen source by chemoautotrophs (oxidize ammonia to nitrate)

51
Q

Where does nitrification typically occur?

A

At the oxic and anxoic interface as require oxygen but ammonia released by decomposers

52
Q

What is the role of Fermentative bacteria in the sediment?

A

Metabolize DOM into organic acids and carbon dioxide, where strictly anaerobic group of microbes can use, organic acid acts as electron donor and carbon dioxide cats as electron acceptor, generating methane

53
Q

When was it historically that there was a realization that there was a serious consequence to chemical pollution?

A

Silent Spring- Rachel Carson→ eventual recognition of serious consequences of chemical pollution of soil, water (human health-related, economic, environmental) → est $1 trillion or more to clean-up or remediate contaminated sites in USA

54
Q

What was Madsen’s 5 core concepts?

A
  1. ) The house of env micro: evolution, diverse habitat, physiology, ecology and thermodynamics
  2. ) Prime directive for microbial life (i.e repro, survival)
  3. ) Link between microbial genotype and environment (diversity)
  4. ) Advances require convergent of independent lines of study using many measurement procedures such as biomarkers etc
  5. ) Recognize that the field is dynamic, methods driven; each methodology has its own set of strengths, weaknesses and potential artiacts
55
Q

What is the Earth most covered in?

A

Water and the majority of this is seawater

56
Q

True/False: Freshwater is evenly distributed between countries but undeveloped countries just don’t have the facility to access the clean water?

A

False - The majority of the freshwater is in developed countries

57
Q

What is the two most prolonged issue with water between developed and undeveloped countries?

A

huge disparity in availability & quality of potable water
2-pronged issue
(i) available water resources,
(ii) adequate sanitation (e.g., toilet, WWT facilities) to ensure that water is clean, safe to consume

58
Q

A lot of our water is considered to be fossil or renewable water?

A

Fossil water, which means once we take it out, it wont be coming back

59
Q

True/ False: Sanitation is getting worse?

A

True: many people moving to the cities which is not constructed to accommodate this large volume of water

60
Q

What is an example of over extraction draw of water?

A

land subsidence in Mexico City
a result of massive over-extraction of groundwater from the Mexico City aquifer over last ~100 yrs
city is built on an ancient lakebed (soft clay) which is shrinking & collapsing as water is pumped from it
in some areas the land has sunk 9 meters or more

BIOL 447- ENV MICROBIOLOGY (1 decks)

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