10. Soil Microbiology

Question 1

Mineral soil vs. organic soil

Answer 1

– Mineral soils: derived from rock weathering and other inorganic materials.
– Organic soils: derived from sedimentation in bogs and marshes.

Question 2

Humus

Answer 2

Dead plant material that is resistant to decomposition. Keep water and nutrients in the soil.
»hard to digest materials in B horizons

Question 3

proportion of different particles in the soil determine the amount of water can be detained in the soil.

Answer 3

– Sand: water drains quickly
– Silt: retains water to the right
extent
– Clay: water retained too well soil becomes anoxic.

Question 4

Rhizosphere vs. Mycorrhizae

Answer 4

• Rhizosphere: soil that surrounds plant roots and receive plant secretions.
  »get nutrient from the plants, particular microbes biomass near the roots
• Mycorrhizae: association of fungi with plant roots.
  »symbiotic relationship:
  microbes provides certain nutrient for plants whereas plants secrets juices

Question 5

Prokaryotes are largely responsible for:____?

Answer 5

– the production of the humus
– release of minerals from soil particles
– cycling of nutrients (C, N, S)
– nitrogen fixation.

Question 6

Nitrogen fixation

- Only certain prokaryotes can fix nitrogen (N2) because___?

Answer 6

a lot of energy is required because of the triple bond (N≡N).
»16-24 ATP is required for N2 reduction

Question 7

In the absence of fertilizers, other organisms are dependent on__?

Answer 7

nitrogen fixers.
-Some nitrogen fixers are free-living (ex.: Cyanobacteria)
and others are symbiotic (ex.: Rhizobium).

Question 8

Nitrogen fixation

-Reaction is catalyzed by __?

Answer 8

• Reaction is catalyzed by nitrogenase complex (metal cofactors)
• 8 electrons (from pyruvate) are required, 2 are lost as H2 in the process. (4H–>2H–>2H)

N≡N—>HN=NH—>H2N-NH2—>2NH3
- Ammonia is the final product which used ti produce AA

Question 9

Nitrogen fixation is inhibited by___ ??

Answer 9

Nitrogen fixation is inhibited by: 1)oxygen
aerobic respiration –>produce oxygen
2)oxygenic photosynthesis—> reduce oxygen

because Dinitrogenase reductase is inhibited by the presence of oxygen.

Question 10

Free-living Nitrogen fixers

Answer 10

1) Azotobacter: strict aerobe.
»The enzyme is protected by a very high rate of O2 consumption, which keeps the intracellular environment anaerobic.
2) Beijerinckia
3) Clostridium: strict anaerobe
**only some species of Cyanobacteria are capable of nitrogen fixation. MAJOR nitrogen- fixing organisms in nature. Cyanobacteria produce energy by oxygenic photosynthesis, oxygen is produced in the cell.

Question 11

Cyanobacteria

- heterocyst?

Answer 11

• specialized anaerobic cells where Nitrogen fixation occurs
• lack Photosystem II (does not produce O2).
• have a thick cell wall that slow down the diffusion of O2.
  • The regular cells provide the heterocysts with carbohydrate (pyruvate).
  »Heterocyst: only doing N fixation
  »vegetative cell: doing oxygenic photosynthesis

Question 12

Symbiotic nitrogen fixers

e.g. Rhizobium

Answer 12

• mutualistic relationship between leguminous plants and nitrogen-fixing bacteria
  e. g. Rhizobium

Question 13

Nodules

- leghemoglobin

Answer 13

Colonization of legume roots by nitrogen- fixing bacteria leads to the formation of root nodules that fix nitrogen.
- Leghemoglobin: the O2-binding protein produced by plant cell to control Oxygen levels
»so bacteria can do oxygenic respiration without interfere N fixation
» because citric cycle and photosynthesis both requires enzymes: succinate, malate, fumerate
- Bacteroids: terminal structure and cannot be shed in the environment.

Question 14

Nodule formation

Answer 14

• Step 1: bacterium recognize and attach to root hair
• Step 2: bacterium excrete nod factor
• Step 3: Bacterial invade the root hair
• Step 4: Travel to the main root via the infection thread (tube composed of cellulose)
• Step 5: Bacteroid state formed within plant cell (swollen and misshapen bacteria - fix N2)
• Step 6: Continued plant and bacterial division, forming the mature root nodule

Question 15

Anaerobic conditions promote nitrification OR denitrification?

Answer 15

•  anaerobic promotes denitrification: 
NO3- --> NO2--->NO-->N2O-->N2.
•  Nitrifying bacteria: requires oxygen
NH3-->NO2- --> NO3-.
•  Nitrate is more soluble than ammonium and is more readily available to plants.

Anaerobic conditions also promote sulfur and sulfate reduction which produce H2S (toxic for plants).