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1. The following slides are provided by Dr. Vincent O’Flaherty. Use the left mouse button to move forward through the show Use the right mouse button to view the slides in normal view, edit or print the slides

2. 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

3. 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

8. 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

9. 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

10. 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

11. 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

12. 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)

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

14. 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

15. 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

16. 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:

17. 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

18. 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

19. Microbial N-Fixation

20. Other Biogeochemical cycles P and S • Other major nutrient cycles include S and P • Sulfur cycle involves the cycling of elemental Sulfur (So), Sulphate (SO42-) and hydrogen sulphide (H2S) and organic matter (-SH)

21. 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

22. 3.Oxidation of H2S by chemolithotrophs to form sulfur (So) and sulfate (SO42-) • 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)

24. The Sulfur Cycle

25. 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

26. 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

27. 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