1. SOIL There are three major properties of of soil. There are three major properties of of soil. 1. physical – soil structure and texture 1. physical – soil structure and texture 2. chemical – chemical components; pH, nutrients 2. chemical – chemical components; pH, nutrients 3. biological – micro and macro fauna/flora 3. biological – micro and macro fauna/flora

2. LIVING ORGANISMS Contain five major groups of microorganisms 1.The bacteria 2.Actinomycetes 3.Fungi 4.Algae 5.Protozoa

3. All these microorganisms participate in the various activities that take place in the soil. Among the activities are; 1.Decomposition of organic matter 2.Nutrient Cycling 3.Nutrients transport/flow 4.Protection

4. Nutrient Cycling Essential plant nutrients There are at least 16 essential chemical elements for plant growth: the plant must have these nutrients to performance the various physiological functions Carbon (C), hydrogen (H), and oxygen (O), (from air and water) Nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), sulfur (S), iron (Fe), manganese (Mn), zinc (Zn), copper (Cu), boron (B), molybdenum (Mo), and chlorine (Cl) (from soil) Sodium (Na), silicon (Si), and nickel (Ni) Cobalt (Co) (required by certain plants)

5. Sources of plant nutrients in the soil 1) weathering of soil minerals 2) 2) decomposition of plant residues, animal remains, and soil microorganisms 3) application of fertilizers and liming materials, 4) 4) application of manures, composts, biosolids (sewage sludge) and other organic amendments

6. 5) N-fixation by legumes 6) ground rock powders or dusts including greensand, basalt, and rock phosphate 7) inorganic industrial byproducts 8) atmospheric deposition, such as N and S from acid rain or N-fixation by lightning discharges, 9) deposition of nutrient-rich sediment from erosion and flooding

8. Basic Plant Nutrient Cycle The basic nutrient cycle highlights the central role of soil organic matter and microorganmisms. The basic nutrient cycle highlights the central role of soil organic matter and microorganmisms. Cycling of many plant nutrients, especially N, P, S, and micronutrients, closely follows the Carbon Cycle. Cycling of many plant nutrients, especially N, P, S, and micronutrients, closely follows the Carbon Cycle. Plant residues and manure from animals that are fed forage, grain, and other plant-derived foods are returned to the soil.

9. This organic matter pool of carbon compounds becomes food for bacteria, fungi, and other decomposers. As organic matter is broken down to simpler compounds, plant nutrients are released in available forms for root uptake and the cycle begins again. Plant-available nutrients such as K, Ca, Mg, P, and trace metal micronutrients are also released when soil minerals dissolve. Plant-available nutrients such as K, Ca, Mg, P, and trace metal micronutrients are also released when soil minerals dissolve.

10. Decomposition of organic matter Definitions breakdown of dead plant and animal material and release of inorganic nutrients.

11. SOURCE OF ORGANIC MATTER 1.Plant remains 2.Animal tissues and excretory products 3.Cells of microorganisms However, plant is the main contributor to organic matter

12. ORGANIC CONSTITUENTS OF PLANTS 1.Cellulose, most abundant 15 to 60% of dry weight 2.Hemicelluloses, 10 to 30% 3.Lignin, 5 to 30% 4.Water soluble fraction include simple sugar, amino acids, and aliphatic acids, 5 to 30% of tisue weight 5.Ether and alcohol-soluble constituents; fats, oils, waxes, resins and a number of pigments 6.Proteins

13. WHY MICROORGANISMS DECOMPOSE ORGANIC MATTER 1.SUPPLYING ENERGY FOR GROWTH 2.SUPPLYING CARBON FOR NEW CELL SYNTHESIS The cells of most microorganisms commonly contain approximately 50% carbon. This is derived mainly from the substrates.

14. Why do we care about decomposition? Decomposition is important in releasing nutrients tied up in dead organic matter and return it back to the soil.

15. Who are the decomposers? A. Soil fauna (e.g., earthworms, arthropods): physical A. Soil fauna (e.g., earthworms, arthropods): physical fragmentation (comminution) increases surface area, distributes organic matter within soil profile, doesn’t alter litter chemistry fragmentation (comminution) increases surface area, distributes organic matter within soil profile, doesn’t alter litter chemistry B. Soil microorganisms: heterotrophic bacteria and fungi derive energy, carbon, and nutrients from dead organic matter; in the process they release CO2 thru respiration; RESPONSIBLE FOR BULK OF DECOMPOSITION!!

16. Decomposition processes There are three main processes 1. Assimilation = conversion of substrate materials into protoplasmic materials. Eg. Organic matter carbon to microbial carbon. Protein to microbial protein. 2. Mineralization = conversion of organic substance to inorganic form. Eg. Protein from the organic matter will be converted to inorganic nitrogen in the soil. 3. Immobilization = conversion of inorganic form into organic form. Eg. Inorganic nitrogen NH 4 from the soil converted into microbial protein.

17. Factors Affecting Rate of Decomposition Environmental Factors Temperature - Microbial activity responds exponentially to increased temperature until enzymes denature, etc. Moisture Microbial activity has optimum moisture - Low moisture = dessication, slow diffusion (microbes live in water films) - High moisture = low O2 availability; no lignin degradation pH - most microbes exhibit optimum acitivty near pH 7. -fungi most active in acid soil and bacteria in moderate soil pH.

18. Substrate quality: Carbon Substrate quality: Carbon - different carbon compounds are decomposed at different rates. Eg. - different carbon compounds are decomposed at different rates. Eg. Cellulose faster Cellulose faster Lignin slower decomposition as compared to cellulose. Lignin slower decomposition as compared to cellulose. - C:N of the organic matter determine the rate: - C:N of the organic matter determine the rate: high slower, this is due to insufficient of N for microorganisms to assimilate carbon; low faster, nitrogen is sufficient for rapid assimilation of carbon.

19. The C:N ratio is the most commonly used in soils because N is the most limiting element. Knowing the impact of litter decomposition on available N is therefore very important. Microbes can easily out-compete plants for available N

20. C:N OF SOME ORGANIC MATTER Oraganic matter C:N ratio legumes 13 – 25:1 manure 20 - 30:1 straw80:1 sawdust 400 – 600:1 microorganisms 5 – 10:1

21. In genaral, for every gram carbon used for microbial biomass, another 2gram will be respired as CO 2. A microbe with a C:N ratio of 8:1 would require organic matter with a C:N ratio of 24:1. Because there is a suite of microorganism and organic matter quality, generally we can predict whether mineralization or immobilization will take place base on the C:N ration range 1. C:N > 30 = Nett N immobilization 2. C:N > 20 but < 30 N immobilization = N mineralization 3. C:N < 20 = Nett N mineralizarion

22. CARBON CYCLE Carbon is an element fundamental to all life as we know it. Nature has devised a way to recycle this element, which is called the carbon cycle. Carbon is an element fundamental to all life as we know it. Nature has devised a way to recycle this element, which is called the carbon cycle. Plants take in carbon as carbon dioxide through the process of and convert it into sugars, starches and other materials necessary for the plant's survival. From the plants, carbon is passed up the food chain to all the other organisms. This occurs when animals eat plants and when animals eat other animals. Plants take in carbon as carbon dioxide through the process of photosynthesis and convert it into sugars, starches and other materials necessary for the plant's survival. From the plants, carbon is passed up the food chain to all the other organisms. This occurs when animals eat plants and when animals eat other animals.

23. Both animals and plants release waste carbon dioxide. This is due to a process called cell respiration where the cells of an organism break down sugars to produce energy for the functions they are required to perform. The equation for cell respiration is as follows: Glucose + Oxygen --> Energy + Water + Carbon Dioxide i.e. C6H12O6 + 602 --> Energy + 6H2O + 6CO2

25. Carbon dioxide is returned to the atmosphere when plants and animals die and decompose. The decomposers release carbon dioxide back into the atmosphere where it will be absorbed again by other plants during photosynthesis. In this way the cycle of carbon dioxide being absorbed from the atmosphere and being released again is repeated over and over. In the carbon cycle the amount of carbon in the environment always remains the same. However, in the last 200 years the burning of fossil fuels and deforestation has increased the amount of atmospheric carbon dioxide by an estimated 28%. If humans had not used fossil fuels or altered the amount of plant life, through deforestation, then the amount of carbon dioxide in the atmosphere would not have changed.

26. Nitrogen Cycle

27. Nitrogen cycle involves several processes: Nitrogen fixation Ammonification Nitrification Denitrification

28. Nitrogen Fixation This is the first step in the N Cycle - conversion of nitrogen gas (N2) into NH3 or organic nitrogen. This is the first step in the N Cycle - conversion of nitrogen gas (N2) into NH3 or organic nitrogen. defined as the reduction of atmospheric nitrogen gas (N2) to ammonia (NH3) defined as the reduction of atmospheric nitrogen gas (N2) to ammonia (NH3) can only be done biologically by a small and highly specialized group of microorganisms in the presence of the enzyme nitrogenase which catalyzes the reduction of dinitrogen gas (in the atmosphere) to ammonia. --- can only be done biologically by a small and highly specialized group of microorganisms in the presence of the enzyme nitrogenase which catalyzes the reduction of dinitrogen gas (in the atmosphere) to ammonia. --- N2 + 6 e- + 8H+ ---Nitrogenase-- & Fe, Mo-----> 2 NH3 + H2 The ammonia is now combined with organic acids to form amino acids and proteins

29. Nitrogen fixation can be biological or non-biological Nitrogen fixation can be biological or non-biological Non Biological Fixation Non Biological Fixation lightning + N2 + O2 --------------> 2 NO (nitrous oxide) lightning + N2 + O2 --------------> 2 NO (nitrous oxide) The nitrous oxide formed combines with oxygen to form nitrogen dioxide. The nitrous oxide formed combines with oxygen to form nitrogen dioxide. 2 NO + O2 ---------------> 2NO2 Nitrogen dioxide readily dissolves in water to produce nitric and nitrous acids; Nitrogen dioxide readily dissolves in water to produce nitric and nitrous acids; 2 NO2 + H2O -------> HNO3 + HNO2 These acids readily release the hydrogen, forming nitrate and nitrite ions. The nitrate can be readily utilized by plants and micro-organisms. These acids readily release the hydrogen, forming nitrate and nitrite ions. The nitrate can be readily utilized by plants and micro-organisms. HNO3 --------> H+ + NO3- (nitrate ions) & HNO2 --------> H+ + NO2- (nitrite ions) HNO3 --------> H+ + NO3- (nitrate ions) & HNO2 --------> H+ + NO2- (nitrite ions)

30. Biological Fixation Is the association between microorganisms and plant roots; example Rhizobium and legume plant roots carbon source (energy) for nitrogen fixation Heterotrophic (need to assimilate pre-formed organic carbon) example is the bacteria, Rhizobium. Autotrophic (make their own C by fixing CO 2 in photosynthesis) example is anabaena.

31. Biological Nitrogen Fixing Associations Free living N fixers --(they fix N 2 on their own). Free living nitrogen fixers that generate ammonia for their own use (e.g. bacteria living in soil but not associated with a root) include the bacteria, Azospirillum, Azotobacter spp. and Clostridium spp. (30 % of all N2 fixed in world) Symbiotic N fixers --example is bacteria (Rhizobium) and plant (soybean) (70 % of all N 2 fixed in world). Symbiotic nitrogen fixers are associated with plants and provide the plant with nitrogen in exchange for the plant's carbon and a protected home.

32. Nodule Formation

33. Factors affecting N fixation When soil nitrogen (NO 3 - or NH 4 +) levels are high, the formation of nodules is inhibited. Also, anything that impacts the carbohydrate production will effect the amount of N fixed. In order for the nitrogen to be used by succeeding crops, the nodules and plant must be incorporated into the soil, or no nitrogen will be gained. Harvesting for animal feed reduces the chances for a net nitrogen gain, unless the manure is returned to the soil.

34. Ammonification Second step in N cycle The biochemical process whereby ammoniacal nitrogen is released from nitrogen- containing organic compounds. Soil bacteria decompose organic nitrogen forms in soil to the ammonium form. This process is referred to as ammonification. The amount of nitrogen released for plant uptake by this process is most directly related to the organic matter content. The initial breakdown of a urea fertilizer may also be termed as an ammonification process

35. In the plant, fixed nitrogen that is locked up in the protoplasm (organic nitrogen) of N 2 fixing microbes has to be released for other cells. This is done by the process of ammonification with the assistance of deaminating enzymes. In the plant=Alanine(an amino acid) + deaminating enzyme --------> ammonia + pyruvic acid, or in the soil=RNH 2 (Organic N) + heterotrophic (ammonifying) bacteria ---------> NH 3 (ammonia) + R. In soils NH 3 is rapidly converted to NH4+ when hydrogen ions are plentiful (ph< 7.5)

36. Fate of Ammonium Ammonium has several divergent pathways from this point forth. Plants and algae can assimilate ammonia and ammonium directly for the biosynthesis. The remaining bulk of decomposed byproducts is utilized by bacteria in a process called nitrification. Some are used by hetertroph for further asimilation of organic carbon Some are fixed by clay particles and made unavaialble or other uses.

37. Nitrification This is the third step in nitrogen cycle Nitrification- conversion of ammonium to nitrate (NO 3 -) Performed by several species of nitrifying bacteria that live in the soil – NH 4 + --> NO 3 - (nitrate)

39. The nitrification process is primarily accomplished by two groups of autotrophic nitrifying bacteria that can build organic molecules using energy obtained from inorganic sources, in this case ammonia or nitrite.

40. In the first step of nitrification, ammonia-oxidizing bacteria oxidize ammonia to nitrite according to equation (1). NH 3 + O 2 ® NO 2 -+ 3H+ + 2e- (1) Nitrosomonas is the most frequently identified genus associated with this step, although other genera, including Nitrosococcus, and Nitrosospira. Some subgenera, Nitrosolobus and Nitrosovibrio, can also autotrophically oxidize ammonia (Watson et al. 1981).

41. In the second step of the process, nitrite-oxidizing bacteria oxidize nitrite to nitrate according to equation (2). NO 2 - + H 2 O ® NO 3 - + 2H+ +2e- (2) Nitrobacter is the most frequently identified genus associated with this second step, although other genera, including Nitrospina, Nitrococcus, and Nitrospira can also autotrophically oxidize nitrite.

42. ENVIRONMENTAL INFLUENCES Physical and chemical factors affect the rate of ammonium oxidation. Aciditty: acid environ rate slower, due to effect on the responsible species. Enhanced by liming Oxygen, since it is oxidation process, oxygen is necessary, effect the microorganisms involved Water level, water logging can create anaerobic cond. temperature

43. NITRATE POLLUTION Excessive nitrification may lead to undesirable conditions Excessive nitrification may lead to undesirable conditions 1.Eutrophication 2.Infant & animal methemoglobinemia 3.Formation of nitrosamines

44. Denitrification Fourth and last step of N Cycle Involves conversion of NO3- to N2 gas in the presence of low oxygen levels. C 6 H 12 O 6 + 4NO 3 - --> 6CO 2 + 6H 2 O + 2N 2 (gas) + NO + NO 2 Bacterial denitrification is the microbial reduction of NO 3 - to NO 2 - or N. For example Pseudomonas Use NO 3 - instead of O 2 as a terminal electron acceptor.

45. Denitrification is accelerated under anaerobic (flooded or compacted) conditions and high nitrogen inputs. Denitrification results in environmental pollution (destroys ozone) and also contributes to global warming since nitrous oxides do have a minor effect as a greenhouse gas. Through nitrification and denitrification 10 - 20 % of the applied N is lost.