2. THE NITROGEN CYCLE Explore the cyclical interconversion of N 2 and its compounds via covering: Nitrogen fixation Nitrification Denitrification Nitrate assimilation Ammonification Ammonia assimilation

3. Recycling (oxidation and reduction) of chemical elements Biogeochemical Cycles

9. Food webs are feeding relationships among the members of a community. However, in addition to describing who eats who, they also illustrate: Energy flow through the community Functional feeding groups Potentially important ecological interactions Thus, food webs help us understand ecosystem ecology.

10. Geochemical Cycles About 25 of the 92 natural elements are known to be essential to life. Just four of these – carbon (C), oxygen (O), hydrogen (H), and nitrogen (N) – make up 96% of living matter.

12. Nitrogen Cycle N2N2 Nitrogen - fixation Ammonia (NH 3 ) Nitrate ion (NO 3 - ) Pseudmonas N2N2 Nitrite ion (NO 2 - ) Nitrobacter Nitrate ion (NO 3 - ) Ammonium ion (NH 4 + ) Nitrosomonas Nitrite ion (NO 2 - ) Amino acids (–NH 2 ) Microbial ammonification Ammonia (NH 3 ) Proteins and waste products Microbial decomposition Amino acids

13. Nitrogen What is Nitrogen? Nitrogen makes up approximately 78% of air (by weight) and is the second most abundant element in the human body. Although ecosystems receive an essentially inexhaustible influx of solar energy, chemical elements are available only in limited amounts and must be continually recycled. For nitrogen, this recycling process is known as the nitrogen cycle (illustrated below).

15. Formation of a Root Nodule Figure 27.5

16. The three components involved to make this happen are ammonia (NH³ or NH³+4), nitrite (NO²), and nitrate (NO³).

17. Nitrogen Cycle The nitrogen cycle of an aquarium is a chain reaction in nature resulting in the birth of various types of nitrifying bacteria, each with their own job to do. Each new bacteria born consumes the previous one, and in turn gives birth to the next bacteria.

18. The Nitrogen Cycle Figure 27.4

19. The Carbon Cycle Figure 27.3

20. The Nitrogen Cycle Figure 27.4

21. Nitrogen Cycle N2N2 Nitrogen - fixation Ammonia (NH 3 ) Nitrate ion (NO 3 - ) Pseudmonas N2N2 Nitrite ion (NO 2 - ) Nitrobacter Nitrate ion (NO 3 - ) Ammonium ion (NH 4 + ) Nitrosomonas Nitrite ion (NO 2 - ) Amino acids (–NH 2 ) Microbial ammonification Ammonia (NH 3 ) Proteins and waste products Microbial decomposition Amino acids

22. Formation of a Root Nodule Figure 27.5

23. The Sulfur Cycle Figure 27.7

24. Sulfur Cycle Proteins and waste productsAmino acids Microbial decomposition Amino acids (–SH) Microbial dissimilation H2SH2S H2SH2S Thiobacillus SO 4 2– (for energy) SO 4 2– Microbial & plant assimilation Amino acids

25. Primary producers in most ecosystems are photoautotrophs Primary producers in deep ocean and endolithic communities are chemoautotrophic bacteria Life Without Sunshine H2SH2SSO 4 2– Provides energy for bacteria which may be used to fix CO 2 CO 2 Sugars Provides carbon for cell growth Calvin Cycle

26. The Phosphorous Cycle

27. Natural organic matter is easily degraded by microbes Xenobiotics are resistant to degradation Degradation of Synthetic Chemicals

28. Decomposition by Microbes Figure 27.8

29. Decomposition by Microbes Bioremediation –Use of microbes to detoxify or degrade pollutants; enhanced by nitrogen and phosphorus fertilizer Bioaugmentation –Addition of specific microbes to degrade of pollutant Composting –Arranging organic waste to promote microbial degradation Figure 27.9

30. Decomposition by Microbes Figure 27.10

32. NITROGEN IS ESSENTIAL FOR LIFE Nitrogen is required for amino acids, proteins etc. The major reservoir for nitrogen on Earth is the atmosphere. N 2 is extremely stable N  N.

33. NITROGEN FIXATION The ability to use N 2 is of great ecological importance. Main types of N 2 fixing microbes: Free living bacteria e.g. Clostridium, Klebsiella that fix N 2 anaerobically. Rhizobium species in the root nodules of leguminous plants. Actinomycetes (Frankia) in root nodules of non-leguminous plants e.g. alder tree. Free-living cyanobacteria e.g. Anabaena. Symbiotic cyanobacteria (lichens). Free living aerobic microbes loosely associated with plant roots. e.g. Azotobacter

34. FACTORS INFLUENCING N 2 FIXATION Overall reaction: N 2 + 8H + + 8e -  2NH 3 + H 2 nitrogenase enzyme complex (MoFe protein) 1.Soil pH 2.Supply of carbon 3.Soil O 2 status 4.Addition of nitrogen fertiliser

35. Rhizobium nodules (arrowed) on the roots of young white Clover.

36. The legume/Rhizobium association 1.Legume sends out a chemical signal, lectin. 2.Invasion of legume root hair by Rhizobium. 3.Root cells/bacterial cells multiple to form nodule. 4.Rhizobial cells cease motile habit (bacteroid). 5.Leghaemoglobin protects the O 2 sensitive nitrogenase enzyme system.

37. ADVANTAGE TO LEGUME 1.Fixed nitrogen from the atmosphere. ADVANTAGES TO Rhizobium 1.A habitat free of competition. 2.A steady supply of photosynthate carbon.

38. Root nodules on the common alder tree. Vesicles on the tips of hyphal filaments. Frankia nodules and cells Fig. 19.75

39. Fig. 12.80 Cyanobacteria

40. Fig. 19.54/5 Lichens

41. Azotobacter cells grown under a reduced oxygen concentration 2.5% Azotobacter cells grown in 21% oxygen. Fig. 17.71

42. NITRIFICATION Oxidation of NH 3, via NO 2 - to NO 3 - Carried out by chemolithotrophic bacteria Nitrosomonas and Nitrobacter. Energy yields Nitrosomonas – 8.8 ATP molecules per mole of NH 4 + Nitrobacter – 2.5 ATP molecules per mole of NO 2 - compare with A mole of glucose oxidizied aerobically yields 38 ATP molecules.

43. ENVIRONMENTAL CONSEQUENCES OF NITRIFICATION Nitrate  mobile anion (compare with) Ammonium  immobile cation 1.Leaching a.Eutrophication b.Hazardous to human health (50 ppm NO 3 - EEC legal limit for drinking water) ‘blue-baby disease/ methaemoglobinaemia Chemical Inhibitors Nitrapyrin – inhibits the activity of Nitrosomonas

44. DENITRIFICATION The process where nitrate replaces oxygen as the electron acceptor in soil microbial respiration. Facultative anaerobes, dominantly heterotrophic bacteria e.g. Pseudomonas and Alcaligenes. Nitrogen is lost either as N 2 or N 2 O ENVIRONMENTAL CONSEQUENCES OF DENITRIFICATION 1.Can reduce eutrophication. 2.Costly in agricultural terms.

45. NITRATE ASSIMILATION AND AMMONIA ASSIMILATION Bacteria and fungi require a source of N for growth. NO 3 - is reduced for use as a nutrient source i.e. assimilated. The formation of ammonia from dead organic nitrogen containing compounds. Rapidly recycled by microbes and plants! AMMONIFICATION

46. Summary: Fig. 19.29

47. Further Reading Brock Biology of Microorganisms Section 19.12 The Nitrogen Cycle Section 12.3 Nitrifying Bacteria Section 12.9 N 2 -fixing bacteria Section 19.22 Root nodule bacteria and symbiosis with legumes.

48. What is a Jaubert/Plenum Filter? Plenum is an integral part of a complete biological filter, The popular Live Sand Filter is the brain child of Dr. Dean Jaubert. This innovative filtration system consists of a Deep Sand Bed (DSB), a plenum and a protein skimmer. converting ammonia to nitrite, which is converted to nitrate (via aerobic bacteria), which is in turn converted to nitrogen (via anaerobic bacteria). A protein skimmer is the primary filter in a Jaubert Filter, removing a majority of the ammonia generating DOC's (Dissolved Organic Compounds), which are created by tank critter detritus, uneaten food and other decaying matter in the tank. Understanding the principles of foam fractionating (protein skimming) will greatly assist you as you design a new system or upgrade an existing one.

49. A protein skimmer is the primary filter in a Jaubert Filter, removing a majority of the ammonia generating DOC's (Dissolved Organic Compounds), which are created by tank critter detritus, uneaten food and other decaying matter in the tank. Understanding the principles of foam fractionating (protein skimming) will greatly assist you as you design a new system or upgrade an existing one

50. Biological filter media, providing surface area for beneficial nitrosoma and nitrobacter nitrifying bacteria to grow on. Gas barrier, keeping CO2 in the plenum and O2 the upper level of the Live Sand, allowing the filter to function properly.

51. Protein Skimmer To be as unscientific and as clear as possible, let's simply say that the air bubbles inside the skimmer's body strip the water of undesirable waste by-products

52. Protein Skimmer….How does this happen? Surface tension. Surface tension? The interaction between the oxygen bubble and the surrounding water creates a kind of friction between the two. This friction in turn "charges" the molecules in the water. Playing on the old Physics Law of "opposites attract", the charged gunk molecules "stick" to the bubbles, riding them up the column of water. Once the bubbles reach the surface air they burst, depositing their hitchhikers into a collection cup.

53. Plenum plenum is little more than a vacant space in the substrate, harboring anaerobic bacteria, which converts nitrates into nitrogen

54. Plenum The original Jaubert filters included a deep bed (4"-5") of live sand over the plenum, which essentially seals off the plenum from the oxygen rich water in the rest of the tank. The upper level of the live sand provides a home for the nitrifying bacteria, which converts the generated ammonia into nitrites, then nitrates, as well as a home for all of the sand stirring critters that keep the substrate clean.