10- Microbiology of soil

Question 1

What is soil composed of? 2 broad groups; definition

Answer 1

• The loose outer material of Earth’s surface, distinct from bedrock.

• Soil can be divided into two broad groups:
– Mineral soils: derived from rock weathering and other inorganic materials.
– Organic soils: derived from sedimentation in bogs and marshes.

• Soils are composed of
– Inorganic mineral macer (~40% of soil volume)
– Organic macer (~5%)
– Air and water (~50%)
– Living organisms

Question 2

What are the 4 soil horizons?

Answer 2

1) O horizon
2) A horizon
3) B horizon
4) C horizon

Question 3

Soil; made of whut

Answer 3

• Most microbial growth takes place on the surfaces of soil
particles

• The availability of water is the most important factor influencing microbial activity in surface soils
– Sand: water drains quickly
– Silt: retains water to the right
extent
– Clay: water retained too well soil becomes anoxic.

• Nutrient availability is the most important factor in subsurface environments.

Question 4

Microorganisms in soil; top cm; prokaryote; rhizosphere; mycorrhizae

Answer 4

• Top few centimeters:
– Bacteria/Archaea: up to 2.5 x 109
– Fungi: up to 2 x 105
– Protozoa: up to 3 x 104
– Algae: up to 2.5 x 104

• Prokaryotes are largely responsible for:
– the production of the humus
– release of minerals from soil particles (production of acids from organic compounds solubilize the minerals)
– cycling of nutrients (C, N, S)
– nitrogen fixation.

Rhizosphere: soil that surrounds plant roots and receive plant secretions.

Mycorrhizae: association of fungi with plant roots.

Question 5

Explain nitrogen fixation

Answer 5

• Only certain prokaryotes can fix nitrogen (N2); a lot of energy is required because of the triple bond (N≡N).
• Nitrogen fixation is one of the most important microbial processes on earth. In the absence of fertilizers, other organisms are dependent on nitrogen fixers.
• Some nitrogen fixers are free-living (ex.: Cyanobacteria) and others are symbiotic (ex.: Rhizobium).

Question 6

Nitrogen fixation; catalyzed by?; electrons; final product

Answer 6

• Reaction is catalyzed by nitrogenase complex (metal
cofactors)

• 8 electrons (from pyruvate) are required, 2 are lost as H2 in the
process.

• Ammonia is the final product and is used to produce amino acids, etc.

• Dinitrogenase reductase is inhibited by the presence of
oxygen.

Question 7

Explain free-living nitrogen fixers; Clostridium; Azotobacter; Cyanobacteria;

Answer 7

• Azotobacter, Beijerinckia and Clostridium.
• Widespread in soil, require a soil rich in organic macer to provide energy for nitrogen fixation.
• Produce ammonia that can be used by plants (NH3, dissolves in water to produce ammonium NH4).
• Clostridium: strict anaerobe.
• Azotobacter: strict aerobe. The enzyme is protected by a very high rate of O2 consumption, which keeps the intracellular environment anaerobic.
• Cyanobacteria: only some species are capable of N2 fixation. MAJOR nitrogen fixing organisms in nature. Cyanobacteria produce energy by oxygenic photosynthesis, oxygen is produced in the cell.

Question 8

Explain cyanobacteria; heterocyst

Answer 8

• Nitrogen fixation occurs in specialized anaerobic cells (heterocysts), which lack Photosystem II (does not produce O2).
• The heterocysts have a thick cell wall that slow down the diffusion of O2.
• The regular cells provide the heterocysts with carbohydrate (pyruvate).

Question 9

Explain symbiotic nitrogen fixers

Answer 9

• The mutualistic relationship
between leguminous plants and nitrogen-fixing bacteria is one of the most important symbioses known.

• Examples of legumes include soybeans, clover, alfalfa, beans, and peas.
• Rhizobium is the best-known nitrogen-fixing bacteria engaging in these symbioses
• Colonization of legume roots by nitrogen-fixing bacteria leads to the formation of root nodules that fix nitrogen.

Question 10

Explain nodule formation (6 steps)

Answer 10

• Step 1: Recognition and attachment of bacterium to root hairs
• Step 2: Excretion of nod factors by the bacterium
• Step 3: Bacterial invasion of the root hair
• Step 4: Travel to the main root via the infection thread (tube composed of cellulose)
• Step 5: Formation of bacteroid state within plant cell (swollen and misshapen bacteria - fix N2)
• Step 6: Continued plant and bacterial division, forming the mature root nodule

Question 11

Nodule formation; O2 levels; bacteroids

Answer 11

• Oxygen levels are controlled by the O2-binding protein leghemoglobin, produced by plant cells.

• Bacteroids are a terminal structure and cannot be shed
in the environment. The nodules contain regular

Rhizobium cells that serve to inoculate the environment.

Question 12

Explain implication for agriculture

Answer 12

• Most plants will use nitrogen compounds produced by free-living nitrogen fixers or by other organisms during ammonification (e.g. urine).
• Nitrate is more soluble than ammonium and is more readily available to plants.
• Nitrifying bacteria: NH3 à NO2- à NO3
• If the soil is poorly drained and becomes waterlogged, the soil becomes anaerobic, which promotes denitrification: NO3 - à NO2 - à NO à N2O à N2.
• Anaerobic conditions also promote sulfur and sulfate reduction which produce H2S (toxic for plants).