4 BIO-GEO-CHEMICAL CYCLING The cyclic movements of chemical elements between living organism and the environment (soil, air, water) is referred to as a * Bio-geo-chemical cycle. Microbes play an essential role in the transformation of various chemicals like Carbon, Hydrogen, Oxygen, Nitrogen, Sulphur and fron. Plants absorb N,P,K because these elements are readily available in the soil. They move from one biotic community to another through the food chain. Bio-geo-chemical cycles include two phases : (i) Organic phase (ii) Abiotic phase : Flowing of chemicals through the food chain is the organic phase, Abiotic phase is’ the major reservoir for all nutrients. There are two classes of abiotic phases in bio-geo-chemicdl.cycles, These are (a) Sedimentary phase (b) Atmospheric phase ‘ { : . Bio-geo-chemical cycles that have dominant atmospheric ‘phases are called atmospheric reservoir cycles; those whose sedimentary phases are dominant are called sedimentary reservoir cycles,Bio-Geo-Chemical Cycling 47 in gaseous cycles, the main reservoir of nutrients is the atmosphere and the ocean. In sedimentary cycles, the main reservoir is the soil and sedimentary rocks. Both involve biotic: and abiotic agents, both are driven by the flow of energy and are tied to the water cycle. Water Cycle (Hydrologic Cycle) A cyclic movement of water between living organisms and the environment or Biosphere is referred to as the Water cycle, Water is not evenly distributed throughout the earth. Almost 95% of the total water on earth is chemically bound into rocks. Water forms a very significant part of environment and without the cycling of water, bio-geo-chemical cycles cannot exist, the ecosystem cannot function and life cannot be maintained. Water is a solvent; it is the medium by which nutrients are introduced into autotrophic organisms. The chemically-bound rock water does not cycle, but fresh water can move through the hydrologic cycle. The hydrologic cycle covers oceans, ice caps, fresh water lakes, saline lakes, rivers etc. Water circulates through evaporation, transpiration, surface run-off, evapo-transpiration and ground. Water is evaporated directly from any surface other than a plant. This process is referred to as. evaporation e.g., animal skin, soil * surface, lake, etc. H20 Cycle 4 Evapotranspiration of water (land) from earth surface L Formation of clouds 4 Precipitation L Surface runoff (ground water) 4 Return of water oe y ee * 1 © via streams Sea2 Introduction to Soil and Agricultural Microbiology The Process of water evaporating from the surface of leaves of plants is called transpiration. Nutrients that have accumulated in the soil can be eroded by streams, removed altogether from a local eco-system and carried by soil seepage into surface water. Ground water saturates in either sediment or rock below the water surface. Gaseous Cycle It includes Carbon, Oxygen and Nitrogen. Carbon Cycle Carbon exists in the form of inorganic and organic compounds. The concentration of CO, in atmosphere is only 0.003% which is less that what is required to build the organic world. The carbon cycle invglves the transfer of carbon dioxide and organic carbon in the atmosphere where carbon occurs as inorganic CO,, Hydrosphere and lithosphere contains varying concentrations of organic and inorganic carbon compounds. Sometimes CO, can react with water to form carbonates and bicarbonates. Carbon can be present in reduced forms for example methane (CH,) and organic . matter, and in more oxidised forms such as CO and CQ,. Carbon fixation occurs through the activities of photo-autotrophic and chemo-autotrophi o-organisms. The CO, is released into the atmosphere as a by-product of plants respiration. It is then used by plants in photosynthesis. Through the decomposition process, carbon is released back into the carbon cycle. The carbon compounds that are lost to the food chain after fermentation, such as methane, are readily oxidized to CO, by inorganic reactions in the atmosphere. By mict I iti cellulose, lignin and Hemicellulose .are most readily broken down by micro-organisms resulting it thé formation of carbon compounds. Several other carbon compounds such as gum, inulin and related substances present in plant and animal tissues, eventually reach the soil, These substances are attacked by soil bacteria and fungi through their co-enzymes which are also adaptive enzymes. : Micro-organisms which are capable of utilizing pectic substances as carbon and energy sources are abundant in soil and plant surface. Examples of such micro-organisms are Bacillus, Pseudomonas, Erwinia. These micro-organisms readily produce the p\ ses.Bio-Geo-Chemical Cycling 49 Proto ectinase. Pectinmethyl esterase i: Protopectin Eocene Pectin ————> Peete acid For example, starch serves as a storage product of plants e.g., tubers, bulbs, rhizomes. It contains two components namely amylose and amylope ectin. Aerobically the microbes fully utilize the starch to produce CO, and anaerobically (Fermentation) to yield methane, acetic acid, lactic acids, The organisms like Bacteria and Fungi utilize starch aS a carbon source for growth and multiplication. Amylase a-glucosidase = Starch Maltose Glucose Some specific groups of bacteria are particularly effective in reducing carbon compounds to form lactic, butyric and acetic acids. \t gtucose is acted upon by micro-organisms under aerobic conditions, then CgHg0 + 60 —— 6800, + 6H,0 ‘Glucose Is formed It it is attacked anaerobically by yeasts and bacteria then © OgHiOg ——> 2C3H,0, ‘Lactic acid is formed An increase in CO,, as a result of decomposition of plant and animal residues added to the soil, leads to an increase in the CO, content of the soil atmosphere. This results in a rise in the hydrogen ion yn concentration of the soil. The mi ms regulate the CO, in the atmosphere and in plants. If they do not act on organic matter, the limited supply of CO, in the atmosphere will be exhausted and green Plants will cease to manufacture carbohydrates. If the micro-organisms are over-active, then all the organic matter will be reduced to CO, and the soil will not be fit for plant growth. Thus:the micro-organisms do a balancing act. The carbon cycle is largely maintained by the balanced action of the micro-organisms in the soil. (Fig. 4.1). The fossil fuels, sich as coal and petroleum, are not actively cycled through the activities of micro-organisms. Burning of fossil fuels also adds CO, to the atmosphere. This has led to a general rise in the concentration of atmospheric CO, resulting in the rise in global temperature. This phenomenon is known as the Greenhouse effect.Introduction ta Soil and Agricultural Microbiology Atmosphere co, fj} air) MICROBIAL CELLS! & Dissolves: Combustion aco) a ee [Punt — ANIMAL § Ld | 8 € ‘| 3 “y Lithosphere (Soll) HYDROSPHERE (Water) iRespi- | | | Respiration ere 3% 7 2 D iN % %, Respiration Y et dt : Fig. 4.1: The Carbon Cycle Nitrogen Cycle Nitrogen is the most abundant substance present in the atmosphere. Micro-organisms utilize N, in the form of'NHj, NO3 and NO as well as organic nitrogen such as amino acids and proteins. The concentration of Nitrogen in the atmosphere is 79%. It is an essential constituent of proteins and chlorophyll found in organisms. The process of Biogeochemical cycling of N, are : (aj Nitrogen Fixation (b) Ammonification (c) Nitrification (d) DenitrificationJH IES, Bio-Geo-Chamical Cycling ' NITROGEN (Atmosphere) DENITRIFICATION (PSEUDOMONAS) N, FIXATION NITRATE SYMBIOTIC No, (Rhizobium) ASYMBIOTIC (Azotobacter) PLANT, ANIMAL, ORGANIC (N,) NITRIFICATION (NITROBACTER) \ * ete DEAD ORGANIC WASTE NITRIFICATION (NITROSOMONAS) : oe 2 * 4.2 The Nilfogen Cycle (a) Nitrogen Fixation Nitrogen fixation is a process in which the gaseous form of nitrogen is converted into organic form (NH,) by micro-organisms like bacteria and Cyanobacteria. Among bacteria the N, fixation process is carried by Rhizobium (Symbiotic) and Azotobacter (Asymbiotic). Among Cyanobacteria the N, fixation process is carried by Nostoc and Anabaena in both symbiotic and asymbiotic form. (Fig. 4.2). The bio-chemical reactions are as follows : . HY HY No 2H une NH 2H, N= NH, ea ONN, 2e 2e 2e (Dinitrogen) (Di-imide) " (Hydrazine) (Ammonia) (b) Ammonification The process of formation of Ammonia by micro-organisms, plants and animals, where organic amino nitrogen is converted into NH, is known as Ammonification. The dead organic waste in the soil forms amino acids and is then converted into Ammonia. The enzyme, Deaminases transfers the nitrogen from organic to inorganic forms.52 introduction to Soil and Agricultural Microbiology There are several factors which influences the ammonification of proteins in the soil. Many organisms utilize urea to liberate ammonia. N, ————> NH, (organic amino) (c) Nitrification The process of oxidation of ammonium ions (oxidation level = -3) to-nitrate ions (oxidation level = +3) and subsequently to nitrate ions. (oxidation level = +5) is known as Nitrification. Nitrification is an example of aerobic respiration. The process of Nitrification is carried out by two different types of Nitrifying bacteria. in this process Ammonium is firs’ converted to ?ydroxylamine 4 (NH,OH) and then to nitrite. by the bacteria Nitrosomonas, Nitrosococcus, Nitrosolobus The Nitrite is converted into Nitrate by Nitrobacter, Nitrococcus NH, ———~> NH,OH ———> NO; NO; ——— NO; ~ Normally nitrification is carried out by autotrophic bacteria. But there are some heterotrophic bacteria and fungi which also take part in nitrification. For example, Nitrosomonas, Aspergillus flavus. *(d) Denitrification The microbial reduction of Nitrite to Nitrate with the liberation of molecular Nitrogen dnd Nitrous oxide (N, + NO) is called Denitrification. It is carried out by bacteria such as Bacillus, Pseudomonas, Paracoccus, Chromobacterium etc. The biochemical reactions can be summed up as : 2NOj + 10H ———> Ne + 4H,O + 20H" 2NO; +6H = ——— Ne + 2H,0 + 20H N,O+2H ———> N,+H,0 This is the reverse process of nitrification i.e, nitrate is reduced to nitrites and then to nitrogen gas and Ammonia. Denitrification normally takes place in anaerobic soils, But some aerobic organisms such as Pseudomonas denitrificans also seem to reduce nitrate under certain ' conditions.Bio-Geo-Chemical Cycling Sedimentary Cycles , it he There are different kinds of sedimentary cycles, aoe i kinds of elements, but two cycles are significant in a ecosystem, ¢ Sulphur cycle and the Phosphorus cycle. (i) Sulphur cycle (ii) Phosphorus cycle (i) Sulphur cycle : The cyclic movement of sulphur between the organis: environment is called the sulphur cycle. The sulphur cycle is both sedimentary and gaseous. The sedimentary phase of sulphur cycle is long-term and in this sulphur is tied up in organic and inorganic deposits, The gaseous phase of sulphur cycle'ls less et and permits the circulation of sulphur on a global scale. [ Sulphur is an essential nutrient of plants and animals. It is most abundant in earth's crust in dW concentration where it is unavailable to plants. Sulphur enters the soil as plant and animal residues, chemical fertilizers and rain water, Organic and inorganic sulphur compoi'nds are microbiolonically metabolised in the soil through different transformation Processes such as mineralization, immobilization, sulphur oxidation and sulfate reduction. Initially, sulphur enters the atmosphere as HS through several Sources such as combustion of fossil fuels, volcanic eruption which quickly oxidizes into SO,. Atmospheric SO,, soluble in water, is carried back to earth through rainwater as weak H,SO,. In its soluble form, sulphur mostly appears as sulphate (SO,). It is absorbed by the plant roots and converted into certain Organic molecules, (Aminoacids) The bacteria capable of oxidizing inorganic sulphur compounds could either be aerobic or anaerobic, For example, Thiobacillus thiooxidans, EE looxidans Several fungi and actinomycetes are also sulphur oxidizers, For example, Aspergillus, Penicillium, Microsporum Similarly, bacteria like Desulfovibrio Cesulfuri i fur Sulphate into hydrogen sulphide, (Fig. 4.3) a organic (a) Oxidation S. +0, + 2,0 —_, 2H,S0, HS +20, —, 50, , oHHMrOGUCE Hyd Iphid (Oxidation) 5 ph {, rogen sulphide ——__——— Sulphal - a ree : (Thiobacillus) . (b) Reduction ATP : _]. 7 Desulfovibrio) (i) so? Soe Sullite Thiosulfate The sulphur containing aminoacids are enzymatically attacked by micro-organisms to produce H,S. In an aerobic environment, the H.S is oxidised to sulphate by bacteria. The sulphate produced can be re-used by the autotrophs. COMBUSTION BACTERIAL (FOSSIL FUELS) OXIDATION . g 9 33 : Use 233 aes bas : oa BS « 258 g38 °& az3 g & MICROBIAL, DEGRADATION SULPHATES IN SOIL Fig. 4.3 The Sulphur Cycle (ii) The Phosnbams Cycle: The cyclic movement of phosphorus between the living organisms and the environment is referred to as the Phosphorus cycle. Phosphorus is an essential element in all living systems. It is present in the protoplasm of all living things. It ts found in a huge amount as a calcium phosphate and in many minerals. The framework of plants and animals also consists of calcium phosphate.55 6 0 & Bip-Goo-Chomical Gygling « . . 5 4 Phosphorus is found in organic form in the following substances — (a) Nucleic acids (DNA and RNA) and nucleoproteins (b) Nuclear and cytoplasmic enzymes. (c) NAD, NADP, FAD, FMN, ATP, GTP, UTP and other co-en- zymes (d) Thiamine pyrophosphate, pyrophosphate (e) Phospholipids, Glycerophosphatides (f) Phosphorylated sugars (g) Phosphoproteins like phosphoarginine, phosphocreatinine etc., (h) Vacuoles and internal buffers as in organic orthophosphate. ORGANIC. PHOSPHATES. (Animals, Man) DEATH : (Bones) : MICROBIAL DEGRADATION SOLUBLIZED INORGANIC SOLUBLE INORGANIC PHOSPHATES oe PHOSPHATES MICROBIAL PRODUCTION ROCK MICROBIAL PHOSPHATES ACTIVITY INSOLUBLE «INORGANIC PHOSPHORUS ! OCEAN Fig. 4.4 The Phosphorus Cycle Phosphorus is rare in the atmosphere. It is present in the soil and water. Phosphorus_has its physiological importance, when ‘accumulated and liberated trom energy during tellular metabolism. Phosphorus is added to the soil in the form of chemical fertilizers or residues of dead plants and animals of phosphate ion POT or HPOy or HPO, and primary phosphates like NaH,PO,.25 Introduction to and Ag Micro-organisms are involved in tne transformation of Phosphorus in four ways, as follows: 1. Altering Solubility of Inorganic Phosphate In the Phosphorus cycle, the alteration is mainly between insoluble and soluble, inorganic and organic forms. Micro-organisms are involved in the solubilization of inorganic. phosphorus. Species of Pseudomonas, Mycobacterium, Micrococcus, Penicillium and Aspergillus bring the insoluble inorganic phosphates into solutions. These micro-organisms produce acids like nitric and sulfuric acids. For example, Calcium phosphate is an insoluble inorganic phosphate, It reacts with H,SO, or HNO, to form calcium hydrogen phosphate in the following reactions. Ca,(PO,)2 + HSO, ———————> CaHPO, + CaSO, Ca,(PO,)2 + HNO, ———————> CaHPO, + Ca(NO,), Calcium hydrogen phosphate ionizes as follows: CaHPO, ——-——> Cap + HPOy (ionic phosphate) 2. Converting Inorganic Phosphate into Organic » Phosphate The plants absorb the soluble inorganic phosphate through the root system. The inorganic form is converted into organic form. For-example, the Inorganic phosphates react with ADP to form ATP. They also react with glucose to form glucose 6-phosphate. This is very important in bone formation of animals. 3. Mineralizing Organic Phosphates In the soil, the organic phosphates cannot be utilized directly by plants. Decomposers like bacteria, fungi convert the organic Phosphorus into inorganic form, Minerals and raw materials are released during this process. This phenomenon is known as mineralization. The process ig catalyzed by‘Phosphatas® etrzymes. ' Micro-organisms like bacteria and fungi produce an enzyme called pytase. It releases soluble inorganic phosphate from phytic acid, (Inositol hexophosphate) Inositol hexophosphate + 64,0 —-—————> Inositol + 6PO; The inorganic phosphate can be readily absorbed by plants for recycling. (Fig. 4.4). :Bio-Geo-Chemical Cycling 57 4. Oxidation - Reduction Reactions A number of heterotrophic bacteria, fungi and actinomycetes utilize phosphite as the sole source of phosphorus in culture media They oxidize the phosphite within the cell to organic phosphate compounds For example, Clostridium butyricum and E. coli. Other Cycling Processes ; The Iron Cycle: The Iron cycle is very important in terms of microbial functioning. The cycling of iron compounds has a marked effect on its availability for other organisms, Iron is transformed belween the ferrous (Fe™ *) and Ferme ) oxidation states by micro-organisms. (Fig. 4.5) Iron ] (Oxi) pata be (Aerobic) (hiobacitius) (AEROBIC) For (ANAEROBIC) Fer fron (red) Bn Fig, 4.5 tron Cycle : Pr : The major genera that carry'out iron oxidations are Thiobacillus Leptospirillum and Sulfolobus. \ron reduction occurs under anaerobic conditions resulting in the accumylation of ferrous ions. Some of the micro-organisms reduce small amount of iron during their metabolism. Different microbial groups carry out the oxidation of ferrous ion, depending on environmental conditions. gaqQ