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Soil Microbiology > Lecture 2 - Exam 1 > Flashcards

Lecture 2 - Exam 1 Flashcards

1
Q

What is soil?

A

Soil is the unconsolidated, thin, variable layer of mineral and organic material that covers most of the Earth’s land surface. It’s usually biologically active. Particle size is smaller than 2mm (any particle larger is not considered soil).

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2
Q

If there is no life, can we consider it soil?

A

No.

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3
Q

What are the components of soil?

A

Half occupied by soil solids, and the other half is pore space.
The solid space is made up of 45% mineral and 5% organic material. The pore space is made up of 20-30% air and 20-30% water.

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4
Q

What are the three phases that soil can be in?

A

Solid, liquid, and gas. All three are represented in the pi chart that shows the components of the soil.

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5
Q

Soil solids: Mineral fraction. What are the two kinds of minerals, what is the soil particle size, and what is the soil texture?

A

Primary and secondary minerals. Primary minerals are present in rock, and are unweathered & once it ends up in the soil it stays the same. Ex: Sand
Secondary minerals undergo the weathering process, they change into clay minerals during weathering. Ex: types of clays.
Soil particle size:
Sand : 2 - 0.05 mm
Silt : 0.05 - 0.002 mm
Clay : < 0.002 mm
Soil texture: relative portions of different size particles determines soil texture.

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6
Q

What are the soil textures?

A

If there is 80% silt in the soil, then that particular soil has a silt texture. If there is 85% sand in the soil, then that particular soil has texture of sand. If the soil has 40% clay particle in it, then the soil texture class is clay. Clay influences the texture more.

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7
Q

Soil solids: Organic fraction.

A

Carbon makes up 58% of soil organic matter (SOM).
Organic C content = 58% x organic matter content
Organic matter content = 1.724

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8
Q

Soil solids: Charges of soil particles.

A

Type: Negative charge (that’s why they can contain nutrients - cations)
Sources: Isomorphous substitution, broken edge of clay minerals, and organic matter (R-COOH).
There is CEC and AEC. CEC: cation exchange capacity
AEC: anion exchange capacity

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9
Q

Is it possible for soil to carry a net positive charge?

A

Yes. It would be in acidic soils like in the tropics where aluminum and elemental oxide is present. They retain a lot of anions instead of cations.

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9
Q

Soil Solids : What is particle and bulk denisty?

A

Particle density: dry mass of soil per unit volume of soil solids
Bulk density: dry mass of soil per unit bulk volume of a soil. (takes into account both solids and pores) It is always lower than particle density.

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10
Q

Soil water is important for…?

A

In terms of oxygen in the soil, soil pH, and concentrations of soil solutions (& chemical reactions in general)

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11
Q

Soil Water: Soil water content.

A

Mass water content and Volumetric water content.

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12
Q

Soil water content: Mass water content.

A

Thetam = mass of water/soil dry mass.

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13
Q

Soil water content: Volumetric water content.

A

Theta = water vol./dry soil vol
or
Theta = thetam x bulk density
(NOTE: thetam is just theta of mass water content)

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14
Q

Soil Water: Soil water potential.

A

Relative energy level of water in a given amount of soil, indicate tendency of soil water to move, soil water potential is positively related to theta, and units are kilopascal (or bar)
NOTE: 1kPa = 0.01 bar

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15
Q

Soil water moves from ______ potential to ______ potential.

A

High ; low

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16
Q

When the soil is dry, the soil potential is usually…?

A

Negative

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17
Q

When the soil is saturated (like standing water), then the soil potential is usually…?

A

Positive

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18
Q

Soil Water: Water held on soil particles and availability: What are the three different types of water that are possible in the soil?

A

Hygroscopic water, capillary water, gravitational water.

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19
Q

What is Hygroscopic water?

A

Thin layer of water and this layer of water interacts with the soil particles through adhesion force.
Water potential is < -31 bar

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20
Q

What is Capillary water?

A

This water does not interact directly with soil particles, they interact with each other via hydrogen bonding (or cohesion force). Part of the capillary water is available for the plant and microbes to use.
Water potential is -31 bar < potential < -0.33 bar

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21
Q

T or F. Microbes cannot extract more water from the soil than plants.

A

False. They can!

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22
Q

What is Gravitational water?

A

Outer layer that does not stay in the soil for long periods. When it rains and the soil pores are saturated, and the soil water moves down to the lower soil profile, that is gravitational water.
Note: Dry soil will have low potential.

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23
Q

What is the optimal water potential for microbial activity?

A

-0.1 bar (-10 kPa), which is at field capacity

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24
Q

What is the water potential range for field capacity? What is field capacity?

A

-0.1 - -0.3 bar (-10 - -30 kPa)
Field capacity is the amount of water held by the soil about 24 hours after it rains.

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25
Q

What is the permanent wilting point for water potential?

A

-15 bar (-1500 kPa)

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26
Q

Unsaturated soil has a potential value of…? How about saturated?

A

Unsaturated: negative value
Saturated: 0

27
Q

Soil Air: What are the gases commonly found in the soil, and what are the differences between atmosphere and soil air?

A

Nitrogen, oxygen, and carbon dioxide.
N2: Atmosphere and Soil air have an equal amount (78%)
O2: Atmosphere air has more than soil air (atmosphere = 21% and soil air = 18-20%)
CO2: Soil air has more than atmosphere air (atmosphere = 0.042% and soil air = 0.07-1%)

28
Q

Why is there more O2 in the atmosphere air than soil air?

A

Aerobes consume O2 and that comes from diffusion from the atmosphere, and diffusion cannot keep up with consumption.

29
Q

Why is there more CO2 in soil air than atmosphere air?

A

Because CO2 cannot diffuse out.

30
Q

What are the two types of heterogeneity of soil?

A

Physical and chemical heterogeneity

31
Q

What is the consequence of physical heterogeneity?

A

Soil restricts movement of microorganisms.

32
Q

What does chemical heterogeneity consist of?

A

Silica based minerals, carbon based organic minerals, and large organic molecules.
For example, a leaf falling onto the soil will begin to break down into simpler beings, like CO2 and H2O via chemical reaction.

33
Q

What is biological heterogeneity?

A

Means that there are several million species, consists of phototrophs & chemotrophs, autotrophs (use inorganic carbon) & heterotroph (use organic carbon), copiotroph (like a lot of nutrients) & oligotroph (can’t tolerate rich nutrients), organisms have different tolerance levels to pH, Eh, temperature, and salinity, and each organisms has different physiological states (actively growing, resting, etc)

34
Q

How does moisture affect the growth and activities of microorganisms?

A

Control gas exchange, buffer temperature fluctuations, affect movement and concentrations of nutrients (mass flow: microbes and water move together, and diffusion: solute moving from high to low concentration), and alter composition of microbial community (bacteria are more sensitive than fungi to water stress & total microbial activity is reduced if soil is too dry or too wet)

35
Q

What is the relationship between water potential and water film thickness?

A

Water film thickness decreases as water potential decreases.

36
Q

Moisture is one of the physical/chemical factors affecting growth and activities of microorganisms. What are the other three?

A

Aeration, temperature, pH, and osmotic potential & salinity.

37
Q

Oxidation-reduction (redox) potential has a _____ correlation w/ oxygen content.

A

Positive

38
Q

What is the Eh in well-drained soils?

A

0.4-0.8V.

39
Q

Do aerobes and anaerobes operate side by side in the soil?

A

Yes!

40
Q

Aerobes and anaerobes are classified based on?

A

O2 requirement.

41
Q

What are the three different aerobes and what do they require to survive?

A

Obligate aerobes: Require O2 to survive and use O2 as their electron acceptor.
Facultative aerobes: Can use O2 as electron acceptor, but when O2 is not around they can switch their mode of metabolism & use nitrate as electron acceptor.
Microaerophilic organisms: Grow at low O2 concentrations

42
Q

What are the two different anaerobes and what do they require to survive?

A

Aerotolerant anaerobes: Don’t use O2 as electron acceptor, but low traces of O2 don’t kill them. They do not switch their mode of metabolism, they use organic compounds as electron acceptor and donor.
Obligate anaerobes: Are sensitive to O2, it it toxic to them. They are sulfate-reducing, methanogenic and acetogenic bacteria

43
Q

O2 concentration in the soil/air is _________ correlated to soil pH.

A

Positively

44
Q

Why do aerobes need oxygen?

A

That’s their electron acceptor and some enzymes and other growth factors require O2. Ex: Oxygenases

45
Q

What are the toxic forms of oxygen (reactive oxygen species?

A

Hydrogen peroxide, superoxide anion, hydroxyl radical.

46
Q

There is an overall reaction for the formation of reactive oxygen species. What are they?

A

O2 + 4e + 4H+ -> 2H2O
4 separate reactions that lead to this

47
Q

What are the detoxification mechanisms?

A

Catalase (responsible for removing H2O2), peroxidase (responsible for removing H2O2), and superoxide dismutase (catalyzes the reaction between two superoxide anions).

48
Q

Why are some anaerobes susceptible to O2?

A

Need low Eh for flavin enzymes and they lack detoxification mechanisms.

49
Q

The sensitivity to oxygen varies for anaerobes. Why can aerotolerant anaerobes tolerate O2?

A

They have a protein-free Mn2+ complex for O2 removal.
Pyrococcus furiosus has superoxide reductase.

50
Q

_______ life is possible on the surface soil.

A

Aerobic

51
Q

What is the temperature quotient equation? What does it tell us?

A

Q10 = kt/kt-10
approx = 2
The reaction rates of biochemical reactions double for every 10 degrees C increase in temperature.

52
Q

What are the optimum temperatures for the different classes of organisms?

A

Psychrophiles or cryophiles: 0-20
Mesophiles: 20-40
Thermophiles: 40 - <80
Hyperthermophiles: 80-110 (max of 121C)

53
Q

pH: What are the causes of soil acidity?

A

Warm temperatures, and a lot of rainfall. Cations such as calcium and magnesium, leak out of the upper part of the soil profile. Also, sulfur-oxidizing bacteria produce sulfuric acid so that’s also a source of natural acidity.
Human causes: air pollution cause acid rain and fertilizer (ammonium NH4 fertilizer)

54
Q

How do we modify the soil pH?

A

Lime the soil and the pH will increase.
Add sulfur to the soil and the pH will decrease.

55
Q

What are the direct and indirect impacts pH on microorganisms?

A

Direct: Hydrogen ion concentration effects microorganisms directly because enzymes in the soil can be denatured if the pH is too high or too low.
Indirect impacts: Has to do with toxicity of metal irons, especially aluminum and iron, and manganese.

56
Q

What are the classes of organisms based on pH tolerance?

A

Acidophiles (pH 1-6), Neutrophiles (pH 6-8), and Alkalophiles (pH >8)

56
Q

What is the range for most known bacteria?

A

4-9

57
Q

What is the pH range for different microbial groups?

A

Bacteria: 1-9 (opt: 7)
Actinobacteria (produce antibiotics): 6-8 (opt:7)
Fungi: 2-7 (opt: 5)
Protozoa: 5-8 (opt: 7)
Note: Fungi handle acidity better than some bacteria.

57
Q

What’s the significance of all this information?

A

In potato growing regions, there is an actinobacteria that causes potato scab. Farmers will lower the soil pH because they know the actinobacteria prefer neutral pH and apply sulfur to get rid of the scab problem.

58
Q

How can microbes influence soil pH?

A

Produce organic acids (producing CO2 & it dissolves in water, lowering the pH), sulfur oxidations, nitrification, and sulfate reduction.
Many anaerobic metabolisms will lead to an increase in soil pH.

59
Q

What is osmotic potential?

A

It is the portion of total water potential due to the presence of solutes. This helps maintain cell turgor. If the osmotic potential is high in a cell, then the cell will lose water.

60
Q

Osmotic potential is influenced by what?

A

Salt concentration

61
Q

What are the classifications based on salt requirement?

A

Halotolerant/slightly halophilic: require 1-6% salt for growth
Moderate halophilic: require 6-15% salt for growth.
Extreme halophilic: require >15% salt for growth. (ex: Halobacterium salinarum)
Salt concentration in the ocean is 3%, so those microbes are halotolerant.
Dead sea is 29%, microbes here are extreme halophiles

62
Q

If you have 20g of moist soil and Om = 0.2, what is the soil dry weight?

A

Om = water / dry weight
0.2 = (20g - x) / x
1.2x = 20 g
x = 16.7 g

Soil Microbiology (10 decks)

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