Carbon Cycle

Soil organic matter

The organic matter subjected to microbial decay in soil comes from several sources like plant remains, forest litter, incorporation of plant tissues, animal, microbial cells and excretory products. The chemistry of organic matter is clearly very complex, and investigations of the transformations and the responsible organisms have therefore been extremely interesting.

Soil organic matter comprises residues of plant and animals and these compounds occur in soil in close combination with inorganic substances. Animals and plant residues are made up of complex carbohydrates, simple sugars, starch, cellulose, hemicellulose, pectins, gums, mucilage, proteins fats, oils, waxes, resins, alcohols, aldehydes , ketones, organic acids, lignin, phenols, tannins, hydrocarbons, alkaloids, pigments etc.

The relationship between organic matter and plant growth may be direct or indirect.

• Organic matter is a natural substrate for saprophytic micro organism and provides nutrition to plants indirectly through the activity of soil microorganisms
• It is essential for the formation of soil aggregates and hence soil structure which ultimately determines the soil aeration and rooting habit of plants
• Organic matter helps in the conservation of soil nutrients by preventing erosion and surface run off of nutrients.

Microbes in decomposition

Microorganisms present in soil play an important role in the decomposition. Bacteria are the dominant group – mostly heterotrophic organisms (use energy from organic sources such as sugars, starch, cellulose and protein) – are involved. Autotrophic organism which occupy a small portion of the biomass in soil (and use inorganic sources such as Fe and S) are not directly involved in organic matter decomposition. Actinomycetes grow on complex substances such as keratin, chitin and other complex polysaccharides and play active role in humus formation. Soil fungi are mostly heterotrophos and use organic residues and decomposes easily. Soil algae contribute a small amount of organic matter through their biomass, but they do not have any active role in organic matter decomposition. Organic matter decomposition serves two important functions a) Provide energy for growth; b) Supply carbon for the formation of new cell materials.

During the decomposition of organic matter three parallel process occur

• Degradation of plant and animal remains by microbial enzymes –Mineralization.
• Increase in biomass of microorganisms which comprises polysaccharides and proteins-immobilization.
• Accumulation or liberation of end products –Index of microbial activity.

Changes during organic matter decomposition

As a result of development of mixed flora on chemically complex natural products, some components quickly disappear while others are less susceptible to microbial enzymes and persist. The water soluble fraction contains the least resistant plant components and is thus the first to be metabolized. Cellulose and hemicellulose on the other hand disappear not as quickly as water soluble substances, but their persistence usually is not too great. The lignins are highly resistant and consequently become relatively more abundant in the residual, decaying organic matter.

• At aerobic conditions when carbonaceous substrates are incorporated into soil, immediate drop in O₂ and an increase in CO₂ content of soil air occurs.
• Change in (O) (H) oxidation reduction potential (En) – it is shifted to a more reduced condition (fall in oxidation reduction potential).

The end products of decomposition

• CO₂, H₂O_, NO₃, SO₄, CH₄, NH₄ and H₂S depending on the availability of air.

Importance of organic matter decomposition

• Important function is the breakdown of organic matter by which CO₂ available for photosynthesis is replenished
• Any compound that is synthesized biologically is subject to destruction by soil inhabitants, otherwise the compounds would have accumulated in vast amounts on the earth’s surface
• Since, organic matter degradation is a property of all heterotrophs, it is commonly used to indicate the level of microbial activity.

Methods to evaluate the decomposition rate

• Measurement of CO₂ evolution or O₂ uptake
• Determination of decrease in organic matter either chemically or by weight loss
• Observations on disappearance of specific constituents such as cellulose, hemicellulose or lignin.

Anaerobic decay / decomposition of organic matter

In the absence of O₂ organic carbon is incompletely metabolized, intermediary substances accumulate, and abundant quantities of CH₄ and smaller amounts of H₂ are evolved. Energy yield during anaerobic fermentation is low, resulting in fewer microbial cells per unit of organic carbon degraded. Consequently, organic matter breakdown is consistently slower under total anaerobiosis than in environments containing adequate O₂. The rate in water logged soils is intermediate between the two extremes.

When a soil is water logged or flooded there is a shift from aerobic to anaerobic transformation. The primary microbial colonisers initially breakdown the complex CH₂O and proteins into organic acids and alcohols. Formation and accumulation of organic acids viz., acetic, formic, butyric, lactic and succinic acids appear too, these are frequently detrimental to root development. At a later stage, the methane bacteria which are strict anaerobes begin to act upon the secondary substrate chiefly lactic and butyric acids and ferment them into CH₄ and CO₂.The an aerobic carbon transformation are thus characterized by the formation of organic acids, alcohols, CH₄ and CO₂ as major end products.

1. Cellulose

It is a polymer of glucose, bound by β-linkage at carbon 1 and 4 of the sugar molecule and is might abundant organic material in nature changes with age and type of plants. It has a linear chain of several hundred to thousands of D-Glucose units. Woody materials have more cellulose and succulent tissues had poor, but the concentration increases as the plant matures. Cellulose breakdown in soil is influenced by several environmental factors.

• Aerobic organism convert cellulose to 2 major products: CO₂ + cell substance, but certain group releases small amount of organic acids. It is however resistant to microbial decomposition. When cellulose is associated with pentosans (xylan, mannans) it undergoes rapid decomposition. When associated with lignin, the decomposition rate is very low.
• Cellulases are the enzyme system composed of endoglucanase, exoglucanase and β glucosidase (collectively called cellobiase ) are involved in decomposition.
• Theses enzymes have distinct roles in cleaving various bonds ,which causes disruption of crystalline structure, followed by depolymerization into short glucose chains.

Simplified mechanisms of decomposition

The decomposition of cellulose occurs in two stages: (i) in the first stage the long chain of cellulase is broken down into cellobiose and then into glucose by the process of hydrolysis in the presence of enzymes cellulase and cellobiase, and (ii) in second stage glucose is oxidized and converted CO₂ and water.

Cellulase Cellobiase

1. Cellulose → Cellobiose → Glucose

Hydrolysis hydrolysis

Oxidation Oxidation

2. Glucose → Organic Acids → CO₂ + H₂O

The intermediate products formed/released during enzymatic hydrolysis of cellulose (eg. cellobiose and glucose) are utilized by the cellulose-decomposing organisms or by other organisms as source of energy for biosynthetic processes. The cellulolytic microorganisms responsible for degradation of cellulose through the excretion of enzymes (cellulase & Cellobiase) by fungi, bacteria and actinomycetes.

Mechanisms of enzyme action

• Cellobiohydrolases (CBHs) are exoglucanases (cellulases) that cleave disaccharide units from the reducing or non-reducing end (type I or type II enzymes, respectively) of the cellulose molecule.
• β-glucosidase (cellobiases) cleaves the disaccharides into glucose monomers.
• Endoglucanases (EGs) (cellulases ) cleave bonds in the amorphous region of cellulose, generating ends that act as CBH substrates.

Cellulolytic organisms

• Trichoderma, Aspergillus,Chetomium ,Fusarium
• Cellulomonas,Cellovirio,Pseudomonas,
• Bacillus,Clsotridium,Bacteroids

Most cellulolytic bacteria do not excrete significant amounts of cellulase but fungi are found to excrete these enzymes. The soluble sugars released by enzymatic hydrolysis are later utilized by the same or other micro organism for biosynthetic purpose.

2. Hemicellulose

Polymer of simple sugars such as pentose, hexose and uronic acids. May be either homo or hetero polymers. In addition to glucose, the other structural components in hemicelluloses are xylose, galactose, mannose, rhamnose, and arabinose. Hemicellulose has shorter chains of 500 and 3000 sugar units with a branched structure. It is a major plant constituents second only in quantity of cellulose, and sources of energy and nutrients for soil microflora.

When subjected to microbial decomposition, hemicelluloses degrade initially at faster rate and are first hydrolyzed to their component sugars and uronic acids. The hydrolysis is brought about by number of hemicellulolytic enzymes known as "hemicellulases" excreted by the microorganisms. On hydrolysis hemicelluloses are converted into soluble monosaccharide/sugars (eg. xylose, arabinose, galactose and mannose) which are further convened to organic acids, alcohols, CO₂ and H2O and uronic acids are broken down to pentoses and CO₂. Various microorganisms including fungi, bacteria and actinomycetes both aerobic and anaerobic are involved in the decomposition of hemicelluloses.

organisms involved in decomposition :

• Aspergillus, Chetomium, Penecillium
• Rhizopus, Trichoderma,Fusarium
• Bacillus, Erwinina,Arthrobacter and vibrio

3. Lignin

Third most abundant constituent of plant tissues accounts about 10-30 percent of the dry matter of mature plant materials. Lignin content of young plants is low and gradually increases as the plant grows old. It consists of heterocyclic aromatic organic molecules containing C, H and O. The degradation is very slow and rate of decomposition depends on the presence of other compounds such as cellulose and hemicellulose. Lignin is highly resistant to microbial degradation. Degradation is a complex process. Complete oxidation of lignin result in the formation of aromatic compounds such as syringaldehydes, vanillin and ferulic acid. The final cleavages of these aromatic compounds yield organic acids, carbon dioxide, methane and water.

Lignin → coniferyl ether → coniferyl alcohol → coniferyl aldehyde → vanillin → vannillic acid → protocatechuic acid → ring cleavage → organic acids, carbon dioxide, methane and water

Brown rot, white rot fungi and soft rot fungi are mainly involved in degradation. Brown rot fungi degrades cellulosic component and white rot degrade the lignin component of ligno celluloses. ligninases, perxoidases and polyphenol oxidases are the enzymes involved in degradation. Phanerochaete chrysosporium, chaetomium are the degrading fungus

Influence of C:N ratio on organic matter decomposition

• Nitrogen is a key nutrient substance for microbial growth. For every eight part of carbon, one part of nitrogen is needed. If N content of the substrate is high it is readily utilized and decomposition is faster. If N is poor decomposition is slower, needs additional N. If N is not sufficient they look for scavenging N from soil which leads to N deficiency for the crop. Protein rich substrates are readily decomposed.
• Low N or wide C:N ratio results slow decay and the optimum level of C:N ratio for maximum decomposition is 20-25 (1.4-1.7% N). Less than this range (More of N is available ) more microbial cells are produced leads to faster mineralization and it likely exceeds immobilization. Wider the ratio, lesser microbial cells (due to lesser quantity of N) are produced which slows down the immobilization and mineralization increases gradually, resulting in accumulation of Ammonia and Nitrates. At optimum level, there must be an equilibrium between Mineralization and Immobilization
• Hence the soil N level constrains the maintenance of C:N (organic carbon /soil organic matter) ration, which ultimately affects the decomposition.

Humus formation

Compost, like humus, is made of decomposed organic material. Compost usually refers to material created by people from leftover foods and yard waste. Humus usually refers to the natural decay of material such as leaves in the soil's top layer.

What is Humus?

A dark coloured and fairly stable soil organic matter with known and unknown physical and chemical properties is called humus .It is an integral part of the organic matter complex in soil.

Humus can be defined as lingo protein complex containing approximately 45 % lignin compounds; 35% amino acids; 11% carbohydrates; 4% cellulose; 7% Hemicellulose; 3% fats, wax, resins; 6% other miscellaneous substances, including plant growth substances and inhibitors.

The organic fraction of soil, often termed humus. It is a product of synthetic and decomposing activities of the microflora. Since it contains the organic C and N needed for microbial development, it is the dominant food reservoir. Because humus is both a product of microbial metabolism and an important food source, the organic fraction is of special interest.

Age and composition of the humus are dependent on its origin and environment. Bacterial and algal protoplasm contribute a good deal to the nutritive value of humus. Soil micro organism take part in humus formation. Some fungi such as Penicillium, Aspergillus and actinomycetes produce dark humus like substances which serve as structural units for the synthesis of humic substances.

Benefits of humic substances

• Improved seed germination, root growth, uptake of minerals by plants and other physiological effects on plant growth
• Increases the enzyme activities involved in plant metabolism. Since humic acid serves as hydrogen acceptors.
• Increases the cytochrome oxidase activity in root systems results in growth stimulatory effect (on roots)
• Exhibits chelating effect on trace elements by which enhances the Fe uptake by roots
• Enhances the vigour and yield of plants
• Humic acid known to influence the growth and proliferation of micro organism.

How the Humus is formed?

• Once the plant or animal remains fall on or are incorporated into the soil, they are subjected to decomposition by the microorganisms in the soil body
• From the original residues, a variety of products are formed through decomposition and new microbial cells are synthesized
• As the original materials and the initial products undergo further decomposition, they are converted to brown or black organic complexes. The thick brown or black substance that remains after most of the organic litter has decomposed is called humus. At this stage no trace of the original remains are there. Earthworms often help mix humus with minerals in the soil.
• Humus contains many useful nutrients for healthy soil. One of the most important is nitrogen. Nitrogen is a key nutrient for most plants.

Composition in terms of specific elements

The organic fraction contains compounds of C, H, O, N, P, S and small amounts of other elements. Only a small portion of the total is soluble in water, but much can be brought into solution by alkali.

Composition in terms of type of compounds

Humus contains a number of polymerized substances, aromatic, molecules, polysaccharides, ascorbic acids, polymers of uronic acids and P containing compounds. No definite composition can be assigned. It should be considered as a portion of the soil that is composed of a heterogeneous group of substances, most having an unknown parentage and an unknown chemical structure.

Lignin and lignin derived molecules have long been considered to be of significance in the formation of humus. It is possible either that simple aromatics released in the microbial attack on lignin polymerize to yield constituents of the soil organic fraction or that partially altered lignin itself give rise to humus constituents. The monomeric portions of humus are similar to the constituents of lignin.