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The following slides are provided by Dr. Vincent O’Flaherty.

Symbiotic nitrogen fixation

1. Legume symbioses

Most NB examples of nitrogen-fixing symbioses are the root nodules of legumes (peas, beans, clover, etc.).

Bacteria are Rhizobium species, but the root nodules of soybeans, chickpea and some other legumes are formed by small-celled rhizobia termed Bradyrhizobium

Bacteria "invade" the plant and cause the formation of a nodule by inducing localised proliferation of the plant host cell

Chemicals called lectins act as signal molecules between Rhizobium and its plant host - v. specific

Bacteria form an “infection thread” and eventually burst into the plant cells - cause cells to proliferate - form nodules

Bacteria always separated from the host cytoplasm by being enclosed in a membrane

In nodules - plant tissues contain the oxygen-scavenging molecule - leghaemoglobin

Function of this molecule is to reduce the amount of free O2, protects the N-fixing enzyme nitrogenase, which is irreversibly inactivated by oxygen

Bacteria are supplied with ATP (80%), substrates and an excellent growth environment by the plant -carry out N-fixation

Bacteria provide plant with fixed N - major advantage in nutrient poor soils

Other symbiotic associations

2. Frankia form nitrogen-fixing root nodules (sometimes called actinorhizae) with several woody plants of different families, such as alder

3. Cyanobacteria often live as free-living organisms in pioneer habitats such as desert soils (see cyanobacteria) or as symbionts with lichens in other pioneer habitats

The nitrogen cycle

Diagram shows an overview of the nitrogen cycle in soil or aquatic environments

At any time a large proportion of the total fixed nitrogen will be locked up in the biomass or in the dead remains of organisms

So, the only nitrogen available to support new growth will be that which is supplied by NITROGEN FIXATION from the atmosphere (pathway 6)

or by the release of ammonium or simple organic nitrogen compounds through the decomposition of organic matter (pathway 2 (AMMONIFICATION/MINERALISATION)

Other stages in this cycle are mediated by specialised groups of microorganisms - NITRIFICATION AND DENITRIFICATION

Nitrification

Nitrification - conversion of ammonium to nitrate (pathway 3-4)

Brought about by the nitrifying bacteria, specialised to gain energy by oxidising ammonium, while using CO2 as their source of carbon to synthesise organic compounds (chemoautotrophs)

The nitrifying bacteria are found in most soils and waters of moderate pH, but are not active in highly acidic soils

Found as mixed-species communities (consortia) because some - Nitrosomonas sp. - are specialised to convert ammonium to nitrite (NO2

-) while others - Nitrobacter sp. - convert nitrite to nitrate (NO3

-)

Accumulation of nitrite inhibits Nitrosomonas, so depends on Nitrobacter to convert this to nitrate, and Nitrobacter depends on Nitrosomonas to generate nitrite

Nitrate leaching from soil is a serious problem in Ireland

Denitrification

Denitrification - process in which nitrate is converted to gaseous compounds (nitric oxide, nitrous oxide and N2).

Several types of bacteria perform this conversion when growing on organic matter in anaerobic conditions

Use nitrate in place of oxygen as the terminal electron acceptor. This is termed anaerobic respiration and can be illustrated as follows:

In aerobic respiration (as in humans), organic molecules are oxidised to obtain energy, while oxygen is reduced to water:

C6H12O6 + 6 O2 = 6 CO2 + 6 H2O + energy

In the absence of oxygen, any reducible substance such as nitrate (NO3

-) could serve the same role and be reduced to nitrite, nitric oxide, nitrous oxide or N2

Conditions in which we find denitrifying organisms: (1) a supply of oxidisable organic matter, and (2) absence of oxygen but availability of reducible nitrogen sources

Common denitrifying bacteria include several sp. of Pseudomonas, Alkaligenes and Bacillus. Their activities result in substantial losses of N into the atmosphere, roughly balancing the amount of nitrogen fixation that occurs/year

Microbial N-Fixation

Other Biogeochemical cycles P and S

Other major nutrient cycles include S and P

Sulfur cycle involves the cycling of elemental Sulfur (So), Sulphate (SO4

2-) and hydrogen sulphide (H2S) and organic matter (-SH)

The Sulfur Cycle

Some major steps in the sulfur cycle include:

1.Assimilative reduction of sulfate (SO42-) into -

SH groups in proteins (cysteine) carried out by virtually all bacteria

2.Release of -SH to form H2S during excretion and decomposition

3.Oxidation of H2S by chemolithotrophs to form sulfur (So) and sulfate (SO4

2-)

4.Dissimilative reduction of sulfate (SO42-) by

anaerobic respiration of sulfate-reducing bacteria.

5.Anerobic oxidation of H2S and S by anoxygenic phototrophic bacteria (purple and green bacteria)

The Sulfur Cycle

The sulfur cycle includes more steps. Sulfur compounds undergo some interconversions due to chemical and geologic processes (slow flux)

Human impact on the S-cycle is through the production of SO2 through fossil fuel combustion

The Phosphorus Cycle

The major reservoir of P is locked in a slow geochemical flux between rocks n sediments and soils release slowly over millennia

The ecosystem phase of the phosphorus cycle moves faster than the sediment phase. All organisms require phosphorus for synthesizing phospholipids, NADPH, ATP, nucleic acids, and other compounds. Plants absorb phosphorus v. quickly, and herbivores get phosphorus by eating plants

Carnivores get phosphorus by eating herbivores. Eventually both of these organisms will excrete phosphorus as a waste

Then DECOMPOSITION will release phosphorus into the soil. Plants absorb the phosphorus from the soil and they recycle it within the ecosystem