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2) Introductory Microbiology COPY > Soil Microbiology > Flashcards

Soil Microbiology Flashcards

1
Q

Give 3 examples in which microbes play a critical role in the recycling of elements in living systems.

A
  • Carbon cycle
  • Nitrogen cycle
  • Sulfur cycle
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2
Q

What is soil?

A

The loose outer material of Earth’s surface; distinct from bedrock

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3
Q

Soil can be divided into two broad groups, what are they and what are they derived from?

A
  • Mineral soils: derived from rock weathering and other inorganic materials
  • Organic soils: derived from sedimentation in bogs and marshes
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4
Q

What are soils composed of?

A
  • Inorganic mineral matter (40% of soil volume)
  • Organic matter (5%)
  • Air and water (50%)
  • Living organisms
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5
Q

What is humus? What is its function?

A
  • Dead plant material that is resistant to decomposition

- Keeps water and nutrients in the soil

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6
Q

Where does most microbial growth take place?

A

On the surface of soil particles

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7
Q

How does the availability of water differ in sand, slit, and clay?

A
  • Sand: water drains quickly
  • Slit: retains water to the right extent
  • Clay: water retained too well; soil becomes anoxic
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8
Q

What is the most important factor in subsurface environments?

A

Nutrient availability

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9
Q

What microorganisms are contained in the top few centimeters of soil?

A
  • Bacteria/Archaea
  • Fungi
  • Protozoan
  • Algae
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10
Q

What are the 4 functions of Prokaryotes in soil?

A
  • Production of humus
  • Release of minerals from soil particles
  • Cycling of nutrients (C, N, S)
  • Nitrogen fixation
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11
Q

What is the rhizosphere?

A

Soil that surrounds plant roots and receives plant secretions

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12
Q

What is mycorrhizae?

A

Association of fungi with plant roots

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13
Q

Can all Prokaryotes fix nitrogen?

A
  • No

- A lot of energy is required because of the triple bond

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14
Q

What happens in the absence of fertilizers?

A

Other organisms are dependent on nitrogen fixers

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15
Q

Nitrogen fixers can be ________, and others are _________

A

free-living

symbiotic

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16
Q

What is nitrogen fixation catalyzed by?

A

Nitrogenase complex (metal cofactors)

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17
Q

How many electrons are required for nitrogen fixation? From what? How many are lost?

A
  • 8 electrons from Pyruvate

- 2 are lost as H2

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18
Q

What is the final product of nitrogen fixation? What is it used for?

A

Ammonia; used to produce amino acids, etc.

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19
Q

Give examples of free-living nitrogen fixers.

A

Azotobacter, Beijerinckia, and Clostridium

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20
Q

What kind of soil do free-living nitrogen fixers require?

A
  • Widespread in soil

- Soil rich in organic matter to provide energy for nitrogen fixation

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21
Q

How does ammonia become ammonium?

A

Ammonia dissolves in water to produce ammonium

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22
Q

What are the enzymes of Azobacter protected from oxygen by?

A
  • By a very high rate of O2 consumption, which keeps the intracellular environment anaerobic
  • Oxygen cannot accumulate in the intracellular environment
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23
Q

Are all species of cyanobacteria capable of N2 fixation?

A

Only some species

24
Q

Which organism is a major nitrogen-fixing organism in nature?

A

Cyanobacteria

25
Q

How does cyanobacteria produce energy?

A
  • By oxygenic photosynthesis

- Oxygen is produced in the cell

26
Q

Where does nitrogen fixation occur in cyanobacteria? Why is that structure particular

A

In specialized anaerobic cells (heterocysts), which lack Photosystem II (do not produce O2)

27
Q

What is the structure of the cell wall of heterocysts?

A

Thick cell wall that slows down the diffusion of O2

28
Q

What is the form of carbohydrate found in heterocysts?

A

Pyruvate

29
Q

What is one of the most important symbiotic relationships known?

A

The mutualistic relationship between leguminous plants and nitrogen-fixing bacteria

30
Q

Which nitrogen-fixing bacteria is know to engage in symbioses with legumes?

A

Rhizobium

31
Q

What is the symbiotic relationship between nitrogen fixers and legumes?

A

Colonization of legume roots by nitrogen-fixing bacteria leads to the formation of root nodules that fix nitrogen

32
Q

What are the 6 steps to nodule formation?

A

1) Recognition and attachment of bacterium to root hairs
2) Excretion of nod factors by the bacterium
3) Bacterial invasion of the root hair
4) Travel to the main root via the infection thread
5) Formation of bacteroid state within plant cell
6) Continued plant and bacterial division, forming the mature root nodule

33
Q

What is the infection thread composed of?

A

Cellulose

34
Q

What are oxygen levels controlled by in nodule formation? What is it produced by?

A
  • By the O2-binding protein leghemoglobin

- Produced by the plant cells

35
Q

Which structure in nodules cannot be shed in the environment?

A

Bacteroids are a terminal structure, and cannot be shed in the environment

36
Q

Why do nodules contain regular Rhizobium cells?

A

To inoculate the environment

37
Q

Most plants will use nitrogen compounds produced by what?

A
  • Free-living nitrogen fixers

- Other organisms during ammonification (urine)

38
Q

Is nitrate or ammonium more soluble?

A

Nitrate is more soluble than ammonium and is more readily available to plants

39
Q

What reaction do nitrifying bacteria catalyze?

A

NH3 –> NO2- –> NO3-

40
Q

What promotes denitrification?

A

If the soil is poorly drained and becomes waterlogged, the soil becomes anaerobic, which promotes denitrification

41
Q

What is denitrification?

A

NO3- –> NO2- –> NO –> N2O –> N2

42
Q

What do anaerobic conditions promote? What toxic plant compound does that produce?

A

Promote sulfur and sulfate reduction, which produces H2S (toxic for plants)

43
Q

Where do you find high richness, low abundance environments?

A

Good environments

44
Q

Where do you find low richness, high abundance environments?

A

Extreme environments

45
Q

What are the 4 layers of soil?

A

O horizon
A horizon
B horizon
C horizon

46
Q

What is the O horizon?

A

Layer of undecomposed plant materials

47
Q

What is the A horizon?

A
  • Surface soil

- Plants and microorganisms in large numbers

48
Q

What is the B horizon? Is there a little or a lot of organic material?

A
  • Subsoil (minerals, humus)
  • Little organic material
  • Lower microbial activity than A
49
Q

What is the C horizon?

A
  • Soil bed; develops directly from underlying bedrock

- Microbial activity is very low

50
Q

Which horizon contains the most plants and microorganisms?

A

A

51
Q

How do sand, silt, and clay vary based on size?

A

Sand > Silt > Clay

52
Q

Is nitrogen oxidized or reduced in nitrogen fixation? To what?

A

N2 is reduced to NH3 (ammonia)

53
Q

What is nitrogen fixation inhibited by? How?

A
  • Oxygen

- Dinitrogenase reductase is inhibited by the presence of oxygen

54
Q

What is the function heterocysts in cyanobacteria?

A
  • Does nitrogen fixation
  • Lacks photosystem II, so it does not produce O2
  • Heterocysts have a very thick wall that inhibits the diffusion of O2
55
Q

What is the benefit of the symbiotic relationship with Rhizobium?

A
  • Higher yield of the plant

- Plants can go in nutrient poor soils

56
Q

What are bacteroids?

A
  • Nitrogen fixer variants of Rhizobium
  • They don’t grow; they only provide nitrogen compounds to the plant
  • They cannot be shed in the environment
57
Q

What is the final electron acceptor of nodules? What does photosynthesis provide? What does it produce?

A

Final electron acceptor: O2
Photosynthesis: sugars –> organic acids
N2 –> NH3 –> Glutamine and Asparagine

2) Introductory Microbiology COPY (24 decks)

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