Soil organisms and The soil environment are responsible, to a varying degree depending on the system, for performing vital functions in the soil. Soil organisms make up the diversity of life in the soil (Figure A1.1). This soil biodiversity is an important but poorly understood component of ecosystems. Soil biodiversity is comprised of the organisms that spend all or a portion of their life cycles within the soil or on its immediate surface (including surface litter and decaying logs) (Table A1.1)
MICRO-ORGANISMS
These are the smallest organisms (<0.1 mm in diameter) and are extremely abundant and diverse. They include algae, bacteria, cyanobacteria, fungi, yeasts, myxomycetes and actinomycetes that are able to decompose almost any existing natural material. Micro-organisms transform organic matter into plant nutrients that are assimilated by plants. Two main groups are normally found in agricultural soils: bacteria and mycorrhizal fungi.
Bacteria
Bacteria are very small, one-celled organisms that can only be seen with a powerful light (1 000×) or electron microscope. They constitute the highest biomass of soil organisms. They are adjacent and more abundant near roots, one of their food resources. There are many types of bacteria but the focus here is on those that are important for agriculture, e.g. Rhizobium and actinomycetes.
Bacteria are important in agricultural soils because they contribute to the carbon cycle by fixation (photosynthesis) and decomposition. Some bacteria are important decomposers and others such as actinomycetes are particularly effective at breaking down tough substances such as cellulose (which makes up the cell walls of plants) and chitin (which makes up the cell walls of fungi). Land management has an influence on the structure of bacterial communities as it affects nutrient levels and hence can shift the dominance of decomposers from bacterial to fungal.
One group of bacteria is particularly important in nitrogen cycling. Free-living bacteria fix atmospheric N, adding it to the soil nitrogen pool; this is called biological nitrogen fixation and it is a natural process highly beneficial in agriculture. Other Nfixing bacteria form associations (in the form of nodules) with the roots of leguminous plants (Box A1.1).
The nodule is the place where the atmospheric N is fixed by bacteria and converted into ammonium that can be readily assimilated by the plant. The process is rather complicated but, in general, the bacteria multiply near the root and then adhere to it. Next, small hairs on the root surface curl around the bacteria and they enter the root. Alternatively, the bacteria may enter directly through points on the root surface. Once inside the root, the bacteria multiply within thin threads. Signals stimulate cell multiplication of both the plant cells and the bacteria. This repeated division results in a mass of root cells containing many bacterial cells. Some of these bacteria then change into a form that is able to convert gaseous N into ammonium nitrogen (they can “fix” N). These bacteria are then called bacteroids and present different properties from those of free cells. Most plants need very specific kinds of rhizobia to form nodules. A specific Rhizobium species will form a nodule on a specific plant root, and not on others. The shapes that the nodules form are controlled by the plant and nodules can vary considerably in size and shape.
Different types of nodules on leguminous roots: (1) soybean; (2) alfalfa; (3) pea; and (4) white clover (Soltner, 1978).
Source: FAO (2000)
Actinomycetes are a broad group of bacteria that form thread-like filaments in the soil. The distinctive scent of freshly exposed, moist soil is attributed to these organisms, especially to the nutrients they release as a result of their metabolic processes. Actinomycetes form associations with some non-leguminous plants and fix N, which is then available to both the host and other plants in the near vicinity.
Bacteria produce (exude) a sticky substance in the form of polysaccharides (a type of sugar) that helps bind soil particles into small aggregates, conferring structural stability to soils. Thus, bacteria are important as they help improve soil aggregate stability, water infiltration, and water holding capacity. However, in general their effect is less marked than that originated by large invertebrates such as earthworms.
Fungi
These organisms are responsible for the important process of decomposition in terrestrial ecosystems as they degrade and assimilate cellulose, the component of plant cell walls. Fungi are constituted by microscopic cells that usually grow as long threads or strands called hyphae of only a few micrometres in diameter but with the ability to span a length from a few cells to many metres. Soil fungi can be grouped into three general functional groups based on how they source their energy:
• Decomposers - saprophytic fungi - convert dead organic material into fungal biomass, CO2, and small molecules, such as organic acids. These fungi generally use complex substrates, such as the cellulose and lignin, in wood. They are essential for decomposing the carbon ring structures in some pollutants. Like bacteria, fungi are important for immobilizing or retaining nutrients in the soil.
• Mutualists - mycorrhizal fungi - colonize plant roots through a symbiotic relationship. The definition of symbiosis is a close, prolonged association between two or more different organisms of different species that may benefit each member. Mycorrhizae increase the surface area associated with the plant root, which allows the plant to reach nutrients and water that otherwise might not be available. Mycorrhizae essentially extend plant reach to water and nutrients, allowing plants to utilize more of the resources available in the soil. Mycorrhizae source their carbohydrates (energy) from the plant root they are living in/on and they usually help the plants by transferring phosphorus (P) from the soil into the root. Two major groups are identified: (i) ectomycorrhizae, that grow on the surface layers of the roots and are commonly associated with trees; and (ii) endomycorrhizae, such as arbuscular mycorrhizal fungi and vesicular mycorrhizal fungi, that grow within the root cells and are commonly associated with grasses, row crops, vegetables and shrubs. Arbuscular mycorrhizal fungi can also benefit the physical characteristics of the soil because their hyphae form a mesh to help stabilize soil aggregates. Vesicular-arbuscular mycorrhizae are the most widespread mycorrhizal fungi. Mycorrhizae are particularly important for phosphate uptake because P does not move towards plant roots easily. These organisms do not harm the plant, and in return, the plant provides energy to the fungus in the form of sugars. The fungus is actually a network of filaments that grows in and around the plant root cells, forming a mass that extends considerably beyond the root system of the plant (Figure A1.2).
• Pathogens or parasites cause reduced production or death when they colonize roots and other organisms. Root-pathogenic fungi, such as Verticillium, Pythium and Rhizoctonia, cause major economic losses in agriculture each year. Many fungi help control diseases, e.g. nematode-trapping fungi that parasitize disease-causing nematodes, and fungi that feed on insects may be useful as biocontrol agents.
CHEMICAL PROPERTIES
Many important chemical properties of soil organic matter result from the weak acid nature of humus. The ability of organic matter to retain cations for plant use while protecting them from leaching, i.e. the cation exchange capacity (CEC) of the organic matter, is due to the negative charges created as hydrogen (H) is removed from weak acids during neutralization. Many acid-forming reactions occur continually in soils. Some of these acids are produced as a result of organic matter decomposition by microorganisms, secretion by roots, or oxidation of inorganic substances. Commonly used N fertilizers through microbial conversion of NH4+ to NO3-. In particular, ammonium fertilizers, such as urea, and ammonium phosphates, such as monoammonium and diammonium phosphate, are converted rapidly into nitrate through a nitrification process, releasing acids in the process and thus increasing the acidity of the topsoil (Figure A2.4).
When acids or bases are added to the soil, organic matter reduces or buffers the change in pH. This is why it takes tonnes of limestone to increase the pH of a soil significantly compared with what would be needed to simply neutralize the free H present in the soil solution. All of the free hydrogen ions in the water in a very strongly acid soil (pH 4) could be neutralized with less than 6 kg of limestone per hectare. However, from 5 to more than 24 tonnes of limestone per hectare would be needed to neutralize enough acidity in that soil to enable acidsensitive crops to grow. Almost all of the acid that must be neutralized to increase soil pH is in organic acids, or associated with aluminium (Al) where the pH is very low.
However, with large values of soil organic matter, the pH will decrease less rapidly and the field will have to be limed less frequently. A lime application of 1-2 tonnes/ha every 2-3 years might be sufficient to regulate the acidity.
Organic matter may provide nearly all of the CEC and pH buffering in soils low in clay or containing clays with low CEC. In comparing conventional and conservation tillage in Brazil, the highest values of soil CEC and exchangeable calcium (Ca) and magnesium (Mg) were found in legume-based rotation systems with the highest organic matter content (Figure A2.5). In particular, systems with pigeon peas and lablab resulted in a 70-percent increase in CEC compared with a fallow/maize system.
Organic matter releases many plant nutrients as it is broken down in the soil, including N, phosphorus (P) and sulphur (S). Leguminous species are very important as part of a cereal crop rotation in view of their capacity to fix N from the atmosphere through symbiotic associations with rootdwelling bacteria. Again in Brazil, five years after starting an intensive system in which oats and clover were rotated with maize and cowpea, there was 490 kg/ha more total soil N in the 0-17.5-cm soil layer than under the traditional oats/maize system with conventional tillage. After nine years, no tillage in combination with the intensive cropping system had resulted in a 24-percent increase in soil N compared with conventional tillage. Although N uptake by plants was less in no-tillage systems, probably because of N immobilization and organic matter building, the maize yields under the different tillage systems did not differ. As the no-tillage system was more efficient in storing soil N from legume cover crops in the topsoil, in the long term this system can increase soil N available for maize production (Amado, Fernandez and Mielniczuk, 1998).
Calegari and Alexander (1998) noted that the P content (both inorganic P and total P) of the surface layer (0-5 cm) was higher in the plots with cover crops after nine years. Cover crops were shown to have an important P-recycling capacity, especially when the residues were left on the surface. This was especially clear in the fallow plots, where the conventional tillage plots had a P content 25 percent lower than the no-tillage plots. Depending on the cover crop, the increase was between 2 and almost 30 percent. Even more important is the effect of land preparation on the increase of P availability in the soil (Figure A2.6).
PHYSICAL PROPERTIES
Organic matter influences the physical conditions of a soil in several ways. Plant residues that cover the soil surface protect the soil from sealing and crusting by raindrop impact, thereby enhancing rainwater infiltration and reducing runoff. Increased organic matter also contributes indirectly to soil porosity (via increased soil faunal activity).
Fresh organic matter stimulates the activity of macrofauna such as earthworms, which create burrows lined with the glue-like secretion from their bodies and intermittently filled with worm cast material. Surface infiltration depends on a number of factors including aggregation and stability, pore continuity and stability, the existence of cracks, and the soil surface condition.
Organic matter also contributes to the stability of soil aggregates and pores through the bonding or adhesion properties of organic materials, such as bacterial waste products, organic gels, fungal hyphae and worm secretions and casts. Moreover, organic matter intimately mixed with mineral soil materials has a considerable influence in increasing moisture holding capacity.
The quality of the crop residues, in particular its chemical composition, determines the effect on soil structure and aggregation.
BENEFITS OF SOIL ORGANIC MATTER
As noted above, the benefits of a soil that is rich in organic matter and hence rich in living organisms are many. Direct organic matter amendments include:
• compost;
• animal manure;
• use of compost;
• use of waste sludge.
Benefits of soil organic matter for farmers include:
• Reduced input costs: reduced fertilizer needs owing to improved nutrient cycling and reduced leaching from the rootzone; reduced pesticide needs owing to pest-predator interactions among organisms and natural biocontrol; reduced tillage costs owing to reliance on biotillage by macrofauna under conservation agriculture approaches.
• Improved yield and crop quality: soil organic matter and soil biodiversity contribute to improved soil structure, root growth and mycorrhizal development, access to water and nutrients and hence improved root and tuber development and aboveground plant production. Improved soil and crop health reduce impacts of disease-causing organisms (pathogens and viruses and harmful bacteria).
• Pollution prevention: soil organic matter enhances biological activity of soil organisms that detoxify and absorb excess nutrients that would otherwise become pollutants to groundwater and surface water supplies. Soil organic matter is an important means of C sequestration, and organic matter management practices contribute to C storage (up to 0.5 tonnes/ha/year) and reduced greenhouse gas emissions.
SOIL ORGANIC MATTER AND DECOMPOSITION
Soil organic matter consists of living parts of plants (principally roots), dead forms of organic material (principally dead plant parts), and soil organisms (micro-organisms and soil animals) in various stages of decomposition. It has great impact upon the chemical, physical and biological properties of the soil. Organic matter in the soil gives the soil good structure, and enables the soil to absorb water and retain nutrients. It also facilitates the growth and life of the soil biota by providing energy from carbon compounds, N for protein formation, and other nutrients. Some of the nutrients in the soil are held in the organic matter, comprising almost all the N, a large amount of P and some S. When organic matter decomposes, the nutrients are released into the soil for plant use. Therefore, the amount and type of organic matter in the soil determines the quantity and availability of these nutrients in the soil. It also affects the colour of the soil.
Dead matter constitutes about 85 percent of all organic matter in soils. Living roots make up about another 10 percent, and microbes and soil animals make up the remainder.
Organic matter that has fully undergone decomposition is called humus. The origins of the materials after formation of humus cannot be recognized. Humus is dark in colour and very rich in plant nutrients. It is usually found in the top layers of a soil profile. The dark colour of humus absorbs heat from the sun, thereby improving soil temperature for plant growth and microbial activity under cooler climatic conditions.
Some of the most important functions of organic matter in the soil are:
• It increases soil fertility as it retains cations and conserves nutrients in organic forms and slowly releases required nutrients for plant uptake and growth.
• It binds soil particles together; the cementing and aggregation functions improving soil structure and aeration.
• It acts as a sponge in the soil, retaining soil moisture. Soils with high organic matter content can hold more water than those low in organic matter.
• It provides food for micro-organisms living in the soil.
Decomposition is the general process whereby dead organic materials are transformed into simpler states with the concurrent release of energy and their contained biological nutrient and other elements in inorganic forms. Such forms are directly assimilable by micro-organisms and plants, and the remaining soil organic matter may be stabilized through physical and chemical processes or further decomposed (Lavelle and Spain, 2001). These transformations of dead organic materials into assimilable forms involve the simultaneous and complementary processes of mineralization and humification:
• Mineralization is the process through which the elements contained in organic form within biological tissues are converted to inorganic forms such as nitrate, phosphate and sulphate ions.
• Humification is an anabolic process where organic molecules are condensed into degradation-resistant organic polymers, which may persist almost unaltered for decades or even centuries.
Decomposition is essentially a biological process. Nutrients taken up by plants are derived largely from the decomposition process. Micro-organisms are by far the major contributors to soil respiration and are responsible for 80-95 percent of the total carbon dioxide (CO2) respired and, consequentl,y of the organic C respired (Satchell, 1971; Lamotte, 1989). Therefore, decomposition is a process determined by the interactions of three factors: organisms, environmental conditions (climate and minerals present in the soil); and the quality of the decomposing resources (Swift, Heal and Anderson, 1979; Anderson and Flanagan, 1989). These factors operate at different spatial and temporal scales (Lavelle et al., 1993).
Living organisms are made up of thousands of different compounds. Thus, when organisms die, there are thousands of compounds in the soil to be decomposed. As these compounds are decomposed, the organic matter in soil is gradually transformed until it is no longer recognizable as part of the original plant. The stages in this process are:
1. Breakdown of compounds that are easy to decompose, e.g. sugars, starches and proteins.
2. Breakdown of compounds that take several years to decompose, e.g. cellulose (an insoluble carbohydrate found in plants) and lignin (a very complicated structure that is part of wood).
3. Breakdown of compounds that can take up to ten years to decompose, e.g. some waxes and the phenols. This stage also includes compounds that have formed stable combinations and are located deep inside soil aggregates and are therefore not accessible to soil organisms.
4. Breakdown of compounds that take tens, hundreds or thousands of years to decompose. These include humus-like substances that are the result of integration of compounds from breakdown products of plants and those generated by microorganisms.
The easily decomposable sugars, starches and proteins are quick and easy for fungi and bacteria to decompose, hence the C and energy they provide is readily available. Most of the microbes living in the soil can secrete the enzymes needed to break up these simple chemical compounds. The larger mites and small soil animals often help in this first stage of degradation by breaking up the organic matter into smaller pieces, thereby exposing more of the material to colonization by bacteria and fungi.
Some of the energy or nutrients released by the breakdown of molecules by enzymes can be used by the bacteria and fungi for their own growth. For example, when an enzyme stimulates the breakdown of a protein, a microbe may be able to use the C, N and S for its own physiological processes and cell structure. If there are nutrients that the microbes do not use, they will be available for other soil organisms or plants to take up and use. When microbes die, their cells are degraded and the nutrients contained within them become available to plants and other soil organisms.
The second stage of decomposition involves the breakdown of more complicated compounds by many fungal and bacteria species. These compounds take longer to decompose because they are larger and are made up of more complicated units. Specific enzymes, not commonly produced by most micro-organisms, are required to break down these compounds.
Decomposition only takes place where conditions are suitable. Abiotic conditions have a considerable effect on the rate of breakdown. There must be some moisture available, soil temperatures must be suitable (usually between 10 and 35 °C) and the soil must not be too acidic or alkaline. Decomposition also occurs at higher temperatures, as in composts, or under waterlogged conditions through anaerobic processes. Thus, the types of organisms involved in breaking down the organic matter also depend on the conditions.
The type of organic matter, the way it is applied or incorporated into soil and the way it is decomposed influence the physical, chemical and biological balances in the soil and determine the various impacts. It can change:
• the amount of N available to plants;
• the amount of other nutrients available;
• how the soil binds together (soil aggregation);
• the number and type of organisms present in the soil.
Micro-organisms can access N in the soil more easily than plants. This means that where there is not enough N for all the soil organisms, the plants will probably be N deficient. When soils are low in organic matter content, application of organic matter will increase the amount of N (and other nutrients) available to plants through enhanced microbial activity. The number of microbes in the soil will also multiply, as they can use the organic matter as a source of energy. Where the number of fungi and bacteria associated with the breakdown of organic matter increases, there may be some improvements to the soil structure. Adding organic matter can also inc
Posted in 
