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BM211: Introduction to Microbiology > Block B Lecture 3 - Environmental Microbiology > Flashcards

Block B Lecture 3 - Environmental Microbiology Flashcards

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Biology 101 flashcards
1
Q

When studying a microbe, why is isolating it in a pure culture important?

A

Detailed studies in a controlled laboratory environment
Biotechnology applications
(Part 1, Slide 2)

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2
Q

Why is isolation in a pure culture difficult?

A

As microorganisms live in communities in the environment
(Part 1, Slide 3)

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3
Q

What is a biofilm?

A

A gathering of bacterial cells adhered to a surface and enclosed in an adhesive matrix excreted by the cells
(Part 1, Slide 4)

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4
Q

What do biofilms do?

A

They trap nutrients for microbial growth and help prevent detachment of cells in flowing systems
(Part 1, Slide 4)

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5
Q

What do biofilms resist?

A

Physical forces which sweep away unattached cells, phagocytosis by immune system cells and penetration of toxins (e.g antibiotics)
(Part 1, Slide 4)

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6
Q

What 2 things do biofilms allow to happen?

A

Allows cells to remain in a favourable niche and allows bacterial cells to live in close association with one each other
(Part 1, Slide 4)

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7
Q

What does the direct isolation method of isolating a microbe from the environment involve?

A

Extracting microbes from a sample, use eluent to release from solid matrix, then dilute and plate out
(Part 1, Slide 5)

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8
Q

What is eluent?

A

A liquid used to removed an absorbed surface by washing with a solvent
(Part 1, Slide 5)

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9
Q

What is the direct isolation method of isolating a microbe from its environment used for?

A

Enumeration
(Part 1, Slide 5)

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10
Q

What is enumeration?

A

The process of counting or listing items of interest such as cells, bacteria, viruses etc.
(Part 1, Slide 5)

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11
Q

What is involved in the enrichment culture method of isolating microbes from their environment?

A

Extract microbes from sample, enrich, dilute and plate out
(Part 1, Slide 5)

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12
Q

What is the enrichment culture method of microbial isolation useful for?

A

Isolation (biotechnology) and risk assessment
(Part 1, Slide 5)

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13
Q

When trying to isolate an organism using a direct culture, what medium and incubation conditions should be established?

A

Ones that are selective for the desired organism and are de-selective for undesired organisms
(Part 1, Slide 6)

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14
Q

What are 3 ways in which pure cultures can be obtained?

A

Streak Plate
Agar shake
Liquid dilution
(Part 1, Slide 6)

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15
Q

What is the agar shake-tube method?

A

For anaerobic bacteria - Dilution of mixed cultures in tubes of molten agar
(Part 1, Slide 8)

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16
Q

What are 3 disadvantages of direct counting?

A

Answers Include:
Can’t distinguish between live and dead cells without special staining

Small cells can be overlooked

Precision is difficult to achieve

Phase-contrast microscope is required if a stain is not used

Cell suspension of low density (<10^6 cells/ml) hard to count

Motile Cells need to be immortalised

Debris in sample can be mistaken for cells
(Part 2, Slide 2)

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17
Q

What is a viable cell count?

A

A measurement of living, reproducing population
(Part 2, Slide 3)

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18
Q

What are the 2 main methods of performing a plate viable cell count?

A

Spread-plate method
Pour-plate method
(Part 2, Slide 3)

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19
Q

What should always be done in order to obtain the appropriate colony number when doing a viable cell count?

A

The sample to be counted should always be diluted
(Part 2, Slide 3)

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20
Q

How is the most probable number (MPN) obtained?

A

Serial dilution of inoculum in liquid medium until the final tube shows no growth, repeat this several times , then the approximate cell count can then be estimated from the cultures with growth / no growth in them
(Part 2, Slide 4)

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21
Q

What are 4 ways purity should be checked?

A

Microscopy
Colony characteristics on plate
Test for growth in other media
Check for contamination (i.e failure to grow in media in which the organism should grow poorly)
(Part 2, Slide 4)

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22
Q

What 2 rates does an organism need to balance?

A

Growth and death rates
(Part 2, Slide 5)

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23
Q

What are the 2 methods that an organism can used to balance growth and death rates?

A

Oligotrophs
Copiotrophs
(Part 2, Slide 5)

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24
Q

What are oligotrophs?

A

Microbes that grow continuously but at low levels of activity. They have nutrient uptake enzymes with low specificity but high affinity

^ both these things help them grow in environments with low nutrients
(Part 2, Slide 5)

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25
Q

What are copiotrophs?

A

Microbes that exist primarily in a resting phase but have brief periods of activity. They have nutrient uptake enzymes with low specificity but high affinity.

^ this helps them thrive in environments with high nutrient concentrations
(Part 2, Slide 5)

26
Q

What are viable but nonculturable (VBNC) bacteria?

A

Bacteria in a state of very low metabolic activity which do not divide, cannot grow on standard growth media, are morphologically smaller and have reduced nutrient transport, respiration and synthesis of macromolecules
(Part 2, Slide 6)

27
Q

What are macromolecules?

A

Large complex molecules composed of monomer subunits (E.g proteins, nucleic acids, carbohydrates, lipids etc..)

(Part 2, Slide 6)

28
Q

What causes viable but nonculturable (VBNC) bacteria to arise?

A

Stress factors such as:
Lack of nutrients
Temperature
Osmotic conditions
Lack of oxygen
Light conditions
(Part 2, Side 6)

29
Q

How are potential antibiotic producers tested?

A

The suspected antibiotic producer is streaked across one side of an agar plate and is then is incubated to allow growth. The antibiotic will diffuses into the agar. The agar is then cross-streaked with test organisms and then incubated again. The zones where test organisms did and didn’t grow are then examined
(Part 2, Slide 7)

30
Q

Why is rediscovery a problem when looking for potential antibiotic producers?

A

As there are so many microbes in such a small amount of soil, making rediscovery likely
(Part 2, Slide 7)

31
Q

What should a well designed drug screening do?

A

Hit a novel target such as a:
Natural product
Synthetic target
Semi-synthetic target
(Part 2, Side 7)

32
Q

What is a zone of inhibition?

A

A zone of inhibition refers to the clear area surrounding an antimicrobial agent on a culture plate where microbial growth is inhibited
(Part 2, Slide 8)

33
Q

What does a larger zone of inhibition indicate?

A

Greater antimicrobial activity and therefore a stronger inhibition of microbial growth
(Part 2, Slide 8)

34
Q

What is a lawn of indicator organism?

A

A lawn of indicator organism refers to a dense and uniform growth of a specific type of microorganism, known as an indicator organism, that covers the entire surface of an agar plate and is used to provide a consistent background of microbial growth for various purposes
(Part 2, Slide 8)

35
Q

What is an agar plug method of testing a antibiotic producing organism?

A

It refers to a small piece of agar containing a colony or culture of a microorganism that is capable of producing a specific compound or substance of interest. The antibody then diffuses into the agar which creates an antimicrobial gradient which then creates zones of inhibition. It is used to isolate and culture microorganisms which produce bioactive compounds (e.g antibiotics, enzymes or metabolites)
(Part 2, Slide 8)

36
Q

What occurs in the filter paper disk soaked in test compound method?

A

The antibiotic you are testing is dissolved in a suitable solvent / medium and a filter disk is then soaked in it. The filter disk is then placed onto the surface of a coated agar plate so that the test compound diffuses into the agar, this creates zones of inhibitory where the test organism doesn’t grow
(Part 2, Slide 8)

37
Q

What is the minimum inhibitory concentration (MIC)?

A

The lowest concentration of the antibiotic that inhibits visible growth of the bacterial isolate (test organism) under standardized conditions
(Part 2, Slide 9)

38
Q

What does the minimum inhibitory concentration (MIC) measure?

A

The sensitivity of a bacterial isolate to an antibiotic
(Part 2, Slide 9)

39
Q

How is the minimum inhibitory concentration (MIC) calculated?

A

Typically, multiple culture mediums with varying concentrations of the antibiotic are prepared and then inoculated with the test organism. If growth (turbidity) is observed in the culture medium, then the concentration of the bacteria was not sufficient to inhibit bacteria growth and therefore the antibiotic concentration was below the MIC, anything with no growth contained an antibiotic concentration either equal to or above the MIC
(Part 2, Slide 9)

40
Q

What do sulphides form with metals?

A

Insoluble minerals
(Part 3, Slide 2)

41
Q

When is mining low-grade ores economically feasible?

A

Only if the metal can be concentrated
(Part 3, Slide 2)

42
Q

How are valuable metals removed from low-grade ores?

A

By microbial activity in a process called microbial leaching
(Part 3, Slide 2)

43
Q

What happens in microbial leeching?

A

Low-grade ore is dumped in a large pile called the leech dump and sulfuric acid is added. Then the liquid emerging from the bottom of the pile is enriched in dissolved metals and is transported to a precipitation plant.
(Part 3, Slide 2)

44
Q

What plays a major role in bacterial leeching?

A

Bacterial oxidation of Fe2+ is critical as Fe3+ itself can oxidise metals in the ores
(Part 3, Slide 2)

45
Q

What is bioremediation?

A

The use of microbes to clean up contaminated soil or water
(Part 3, Slide 3)

46
Q

How can bacteria be used in the bioremediation of uranium contaminated water?

A

As some bacteria can reduce U6+ to U4+.
U6+ is water soluble whereas U4+ is not.
(Part 3, Slide 3)

47
Q

Is uranium removed in bioremediation?

A

No, it is contained
(Part 3, Slide 3)

48
Q

What are 2 bacterial genera which can reduce U6+ to U4+?

A

Geobacter and Shewanella
(Part 3, Slide 3)

49
Q

What spills can prokaryotes be used to bioremediate?

A

Crude oil spill
(Part 3, Slide 4)

50
Q

Why can prokaryotes be used in the bioremediation of crude oil spills?

A

As organic pollutants (like those found in crude oil) can be completed degraded to CO2 by some microbes
(Part 3, Slide 4)

51
Q

Some bacteria, fungi and green algae can oxidise petroleum products aerobically, when is this oil-oxidising activity best?

A

If temperature and inorganic nutrient concentrations are optimal
(Part 3, Slide 4)

52
Q

How do hydrocarbon-degrading bacteria work in the context of oil bioremediation?

A

They attach to oil droplets and decompose the oil and disperse the slick (the thin layer of oil which spreads on the surface of the water)
(Part 3, Slide 4)

53
Q

What are xenobiotic compounds?

A

Synthetic compounds which are not naturally occurring
(Part 3, Slide 5)

54
Q

Generally how fast do synthetic compounds degrade?

A

Extremely slowly
(Part 3, Slide 5)

55
Q

What are 3 toxic materials included in the xenobiotic compound category?

A

Herbicides, Insecticides and Fungicides
(Part 3, Slide 5)

56
Q

What can some xenobiotic compounds be used for?

A

Some can be used as carbon sources by microorganisms and some can be used as electron donors
(Part 3, Slide 5)

57
Q

Why are xenobiotics degrading very slowly a problem?

A

As plastic of various types are xenobiotics that are not readily degraded by microorganisms
(Part 3, Slide 6)

58
Q

What has recalcitrance (resistance of a substance to be degraded) of plastics fueled?

A

Research of biodegradable alternatives
(Part 3, Slide 6)

59
Q

What are polyhydroxyalkanoates (PHAs)?

A

They are linear polymers used as storage compounds by bacteria. They are biodegradable and are used in the production of bioplastics
(Part 3, Slide 6)

60
Q

What enzyme biodegrades PHA?

A

PHA depolymerase of several bacteria
(Part 3, Slide 6)

61
Q

What does biodegradation of PHA under aerobic and anaerobic conditions result in?

A

Results in CO2 and water in aerobic conditions and CO2 and CH4 in anaerobic conditions
(Part 3, Slide 6)

BM211: Introduction to Microbiology (21 decks)

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