Lecture 10

1 Soil
 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 matter (~40% of soil volume)
Organic matter (~5%)
Air and water (~50%)
Living organisms
 O horizon is surface layer of undecomposed plant materials, A horizon is very active part, has
many organic material, dark in colour, many microorganisms live here, B horizon has low organic
material, chemolethotroph lives there, characterized by lots of humus, C horizon is the rock
crust, just mineral stuff (like mars surface)
 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 [big amount]
Silt: retains water to the right extent
Clay: water retained too well soil becomes anoxic. [small amount, too much water so it will
denitrate]
 Nutrient availability is the most important factor in subsurface environments.
2 Microorganism in soil
 Top few centimeters contains the most microorganisms:
Bacteria/Archaea: up to 2.5x109
Fungi, Protozoa, Algae
 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
 Around the roots in the soil is rhizosphere: soil that surrounds plant roots and receive plant
secretions. [so there will be lot of microorganisms performing mutualistic relation] ex)
Mycorrhizae: association of fungi with plant roots
3 Nitrogen fixation [converting nitrogen to ammonia] [less oxygen is needed to do this but need oxygen
for aerobic respiration to get many energy]
 Only certain prokaryotes can fix nitrogen (N2); a lot of energy is required because to break 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).
 Dinitrogenase reductase is inhibited by the presence of oxygen.
 [1 ATP is needed to convert one nitrogen to two ammonia]
 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. [some of them will leak
out of the soil]
4 Free-living Nitrogen fixers
 Azotobacter, Beijerinckia and Clostridium. [all of them are chemoheterotroph so they will make
many organic matter]
 Widespread in soil, require a soil rich in organic matter 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. [only do fermentation]
 Azotobacter: strict aerobe. The enzyme is protected by a very high rate of O 2 consumption,
which keeps the intracellular environment anaerobic. [high metabolic rate so they burn any
oxygen that goes in]
 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.
Nitrogen fixation occurs in specialized anaerobic cells (heterocysts), which lack
Photosystem II (does not produce O2). just do cyclic photophosphorylation so produce mass
ATP
The heterocysts have a thick cell wall that slow down the diffusion of O2.
The regular cells provide the heterocysts with carbohydrate (pyruvate).
The normal cells produce pyruvate
5 Symbiotic nitrogen fixers
 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. [let plants
grow bigger and better]
 Colonization of legume roots by nitrogen- fixing bacteria leads to the formation of root nodules
that fix nitrogen. [plants will share organic material with the N-fixing bacteria]
6 Nodule formation
 Step 1: Recognition and attachment of bacterium to root hairs
 Step 2: Excretion of nod factors by the bacterium [to ask plants to let them enter]
 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)
[rhizobium cells that changed to n-fixing cell]
 Step 6: Continued plant and bacterial division, forming the mature root nodule
 Oxygen levels are controlled by the O2-binding protein leghemoglobin, produced by plant cells.
 Bacteroids (fix N2 and provide amino acids to the plant) are a terminal structure and cannot be
shed in the environment. The nodules contain regular Rhizobium cells that serve to inoculate the
environment.
 Part of the plant’s role is to give organic acid and to control amount of oxygen using
leghemoglobin to allow just enough oxygen inside bacteria
7 Implication for agriculture
 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 → NO2- → NO3-.
 If the soil is poorly drained and becomes waterlogged, the soil becomes anaerobic, which
promotes denitrification: NO3 -→ NO2- → NO → N2O → N2.
 Anaerobic conditions also promote sulfur and sulfate reduction which produce H 2S (toxic for
plants).