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Chemical transformations mediated by soil organisms

  • What is organic matter?

    Soil organic matter comprises carbon-containing compounds formed by biological processes which have either become part of the soil (e.g. as leaves of plants) or were formed in the soil (e.g. by soil microorganisms). Many different kinds of organic compounds are formed by animals, plants and microorganisms. They are either part of living cell structures or are used in cell function (catabolism and metabolism).

    Most of the organic material in a soil is dead and much of it comes from plants. The living portion of soil organic matter is made up of roots, microorganisms and soil animals.

    Because plants are the main contributors to soil organic matter, the amount of organic matter present in soil is related to the amount that is contained in plants. Plants obtain carbon from the atmosphere because they do not have access to the carbon stores in the soil. The carbon that plants fix during photosynthesis is used by heterotrophic microorganisms as they decompose fractions of soil carbon.

    As the amount of carbon fixed by plants influences the amount of carbon available to the soil biota, factors which affect plant growth can have unseen flow-on effects in the soil. For example, the duration and intensity of light during the day affects the capacity of plants to carry out photosynthesis and hence for them to obtain carbon. The availability of other nutrients in the soil also affects the ability of plants to grow. The inter-relationship between nutrients during the growth of plants is complex and different plant species need different relative quantities of nutrients for normal growth.

    Plants vary in shape and form reflecting the composition of their internal structures. Plant structure is based on organic molecules, mainly cellulose, hemicellulose and lignin all of which are based on carbon. Plants that have more molecules of lignin, e.g. lucerne, are physically stronger than other plants and they can grow larger because of their greater structural support.

    Only a small group of microorganisms, which produce specific enzymes, can decompose structurally complex molecules such as lignin and cellulose. These enzymes work by breaking the bonds that link the carbon atoms together within these molecules. Lignin is a more complex molecule than cellulose (Bettelheim and March 1991) and is broken down by different enzymes. Another complication is that lignin and cellulose are often combined in matrices within the cell walls of plants. Cellulose bound in this way is protected from degradation until the lignin complex is disrupted. This is one of the reasons that some components of organic matter remain in the soil for many years.

    Soil organisms are part of the soil organic matter and are rapidly broken down when they die because they do not contain structurally complex molecules such as lignin and cellulose. It is through the cycle of activities of microorganisms in breaking down plant, animal and microbial organic matter that humus is formed in soil.

    What is humus?

    The Oxford English Dictionary states that humus is ‘the organic component of soil, formed by the decomposition of leaves and other plant material” and that its Latin origin means ‘soil’. This simple definition hides the fact that humic substances are some of the most complex of all molecules. Furthermore, humic substances in soil are difficult to characterise and they are extremely diverse. Humic substances are formed as a result of the breakdown of organic matter in soil, and while these complex molecules have origins in decomposing plant organic matter, they are chemically integrated with molecules of microbial and soil faunal origin. The chemistry of humic acids and related molecules have been extensively studied, but the exact relationship between these molecules and soil processes is less well understood. Overall, it is agreed that the more humus in soil the better, and that humus plays a key role in the fertility of soil (Jackson 1993). It is very easy to lose this important component of the soil by using inappropriate management practices. Microbial processes are involved in both the stabilisation and destabilisation of very complex organic compounds in soil (Sollins et al. 1996)

    What are the stages in organic matter breakdown?

    Breakdown of organic matter commences with the decomposition of the plant parts that contain the simplest carbon molecules. There are many organic molecules in plants which are more easily broken down by soil organisms than lignin or cellulose. For example, starch and amino acids are simple organic molecules and are amongst the first molecules consumed during decomposition. Most bacteria and fungi have the enzymes necessary for this process. The decomposition of starch and amino acids provides much of the carbon and energy needs of soil microorganisms. In contrast, phenolic compounds, waxes and lignin are much more complex organic molecules and tend to remain in the soil without being degraded for the longest period of time.

    Generally and fairly obviously, the rate of plant breakdown depends on how complex their chemical structure is. For example, grass clippings decompose rapidly, whereas tree trunks decompose slowly. Similarly, leaves degrade more rapidly than the stems of the same plant. The main reason for these differences in the rates of decomposition is that parts like stems and tree trunks have a lot more lignin in their cell walls than parts like leaves.

    Soil organisms are present throughout the soil. Therefore, organic matter deposited on the soil surface provides a source of carbon and energy within reach of many bacteria and fungi. Soil animals such as mites help to break up organic matter into smaller particles, increasing the surface area available for bacteria and fungi to work on.

    Soil organisms can only decompose organic material if other environmental conditions are suitable. Straw or forest litter on a soil surface will not decompose without moisture and the rate of breakdown may be slowed by factors such as low soil pH, low temperature and low nitrogen availability.

    What is mineralisation?

    The process of decomposition of organic material is called mineralisation. During mineralisation, elements that were part of the structure of organic molecules are oxidised into less complex forms. They may at first be combined with other organic molecules but are eventually transformed into inorganic molecules. For example, nitrogen is present in organic molecules such as protein. When protein is degraded, nitrogen is eventually released as ammonium ions, which is an inorganic form of nitrogen.

    It is the process of mineralisation, where the chemical bonds that hold the organic molecules together are broken, that provides the carbon and energy needed by microorganisms. Carbon is used by microorganisms to construct molecules such as proteins and other constituents of their cells such as cell walls. The level of microorganism activity during the breaking down of organic matter is controlled by the extent to which they can capture the carbon and energy that is released.

    As the carbon is released during mineralisation, other elements also become available. This provides both the microorganisms and plants, via their roots, with a source of phosphorus, sulphur, nitrogen and other elements. Microorganisms need a specific range of nutrients for their growth. However, if the organic molecules do not contain the required proportion of elements, microorganisms can absorb elements from the soil solution if they are present. If there is more of an element such as nitrogen or phosphorus in the organic matter than is required for the growth of the microorganism, the excess may either be released into the surrounding soil or accumulate in microbial cells.

    Mineralisation of plant organic matter releases nutrients incorporated into plant cells. The quantity of each element released is proportional to its concentration in the decomposing plant material, but the rates of release depends on the degree to which they are incorporated into complex molecules, such as lignin.

    What is immobilisation?

    A complementary process to mineralisation is immobilisation which is the accumulation of nutrients within the cells of soil organisms so they are temporarily unavailable to plants. When organic matter is decomposed, nutrients in the soil are taken into the living cells of soil organisms; this may be supplemented by uptake of ions from the soil solution. In this way, nutrients accumulate in soil microbial biomass.

    The immobilisation of nitrogen by soil organisms can pose a significant problem for plants. Nitrogen is an important element for all organisms since it is needed to form proteins, nucleic acids and a variety of other molecules. Plants require large quantities of nitrogen for their growth relative to other elements such as phosphorus and zinc, but plants are dependent on other organisms to supply their nitrogen needs. For example, legumes and some other plant species (e.g. the treeAlnus) form symbiotic associations with bacteria that convert atmospheric nitrogen to a form that plants can use. Because of this symbiotic relationship these plants can grow in extremely nitrogen deficient soils. However, most plants do not form symbiotic associations and rely entirely on nitrogen in the soil, the main source of which comes from the decomposition of organic matter. If this nitrogen becomes immobilised within soil microorganisms then it is not available for plant growth.

    Why can the breakdown of organic matter be a slow process?

    The quantity of carbon that is fixed by plants during photosynthesis each year is substantial. Once organic carbon is returned to soil as dead or dying leaf, root or other plant material, a considerable proportion persists in various states of decomposition for a long time. Soil organic matter is naturally composed of material in different states of decomposition.

    One method for measuring the rate of breakdown of organic matter added to soil is to use isotopes of common elements to distinguish between recently added material from existing material in the soil. An isotope is a form of an element with a particular atomic weight so that the different isotopes of the same element can be distinguished from one another. Isotopes of nitrogen and carbon are primarily used in tracking the origin and break down of organic matter (Staddon 2004). Plants are grown in soil that has been enriched with a specific isotope to increase its abundance in the plant material. The release of the enriched isotope during decomposition can be monitored and the rate of breakdown of the element can be assessed.

    The breakdown of plant material enriched with carbon (14C) in relation to unlabelled material occurs at different rates (Russell 1973). After 10 years, the majority of the plant material labelled with 14C disappeared from soil, being released as carbon dioxide. However, during the same period, there was little change in the total amount of unlabelled material in the soil. There was a large reserve of organic carbon in this soil. About half of the freshly added organic matter disappeared from the soil within the first two years. The rest would have remained in soil for extremely long periods, contributing to the slowly degrading component of soil organic matter including the humus fraction.

    Termites have specific types of microorganisms in their guts. The microorganisms produce enzymes that are necessary to decompose woody material. Termites in agricultural soils also degrade plant debris, increasing the rate of breakdown of complex plant material.

    The mineralisation of dead microorganisms and animals is generally less complex than the mineralisation of dead plants. The decomposition of microorganisms and most parts of soil animals (excluding exoskeletons of insects and bones) generally occurs quickly because there are no complex molecules such as lignin and cellulose. However, some fungi and insects have molecules such as chitin in their cell walls, which are very complex structurally and degrade extremely slowly. Very few organisms produce the enzymes necessary to degrade them.

    What is the significance of the ratio of carbon to nitrogen (C : N) in organic matter?

    Plant species have characteristic quantities of carbon relative to nitrogen in their cell walls. For example, legumes have a higher proportion of nitrogen than do grasses. As a result, the ratio of carbon to nitrogen is low for legumes and high for grasses. There are quite large differences in the C:N ratio between different types of organic matter and understanding this is useful for predicting how organic matter can be retained in soil (Robertson and Thorburn 2007).

    Differences in C:N of plant material influences the cycling of nitrogen (and other nutrients) in the soil. Organic matter with a high C:N provides insufficient nitrogen relative to carbon to meet the needs of microorganisms for growth. In contrast, organic matter made up of plants with a low C:N, such as legumes, provides more than the required amount of nitrogen relative to carbon for growth of microorganisms. Consequently, the breakdown of legume residues leads to an increase in soil nitrogen, but the breakdown of cereal straw leads to a decrease in soil nitrogen.

    The extent to which the release or immobilisation of nitrogen influences plants depends on the total supply of ammonium or nitrate in the soil. If sufficient nitrogen in the soil is already available to meet the growth requirements of plants relative to other nutrients, the mineralisation of soil organic matter will not affect plant growth in the short term. In contrast, if there is insufficient nitrogen in the soil for the plant, even if other nutrients do not limit plant growth, immobilisation of nitrogen can reduce plant growth. Plants are generally not efficient at competing with microorganisms for soil nitrogen.

    The mineralisation of nutrients in organic matter that has recently been added to soil is a significant component of the carbon and nitrogen cycles in soil. The process is driven by both the availability of carbon to the microorganisms and the suitability of the conditions for the growth of these organisms. Immobilisation occurs simultaneously, but as explained above, the impact of this for plant growth depends on the quantity and form of nitrogen already in the soil.

    What happens as organic matter breaks down?

    The process of breaking down organic matter involves much of the soil community, although in sequence rather than simultaneously. As decomposition proceeds, the communities involved changes. For example, soil animals play a major role by incorporating organic matter into soil and in the initial stages of its breakdown. Once the organic matter is part of the soil, other soil organisms begin to further breakdown the material.

    During the breakdown of organic matter, the involvement of soil organisms can be direct or indirect.

    Directly involved organisms include:

    • Bacteria and fungi colonise and help breakdown leaves. Although there are some microorganisms already on the leaves before they fall to the ground, different communities colonise the material once it is on the ground.

    • Earthworms feed directly on organic matter which is relatively high in nitrogen. During the passage of organic matter and soil through the earthworm gut, the organic matter is decomposed to some extent by bacteria and fungi. But, because the material only takes about 24 hours to pass through the earthworm little decomposition occurs. When the material is returned to the soil in an earthworm cast, soil bacteria and fungi further degrade the material.

    • Mites, springtails and larger soil animals also feed on organic matter. In doing so these animals fragment the organic matter, exposing a greater surface area for colonisation by bacteria and fungi, thereby increasing the rate of decomposition.

    Indirectly involved organisms include:

    • Many soil organisms are affected by the changes in the soil environment during the decomposition process. If acids are released by soil organisms, soil pH may decrease and the availability of inorganic nutrients may be altered. Such a change in the chemical environment may either stimulate or inhibit the growth of some soil organisms. Moreover, the activity of nitrifying bacteria can be stimulated by the release of ammonium from organic nitrogen molecules during decomposition. Furthermore, colonisation of sections of organic matter by some organisms can make them unsuitable for colonisation by others. This colonisation process may include both a physical and chemical change to the environment of other organisms.

    • As bacteria and fungi colonise organic matter, the numbers of soil animals which feed on them increases. This predation can substantially limit the numbers of bacteria and fungi, despite the ready availability of nutrients from decomposition. This is a common occurrence and is part of the dynamic nature of the soil community.

    The organisms responsible for organic matter decomposition change over time depending on the type of material and the stage of decomposition. In a study of the breakdown of wheat straw, fungi in the genus Trichoderma were common on degrading straw but they were less common at some times of the year than at others (Robinson et al. 1994). In contrast, the fungus Epicoccum nigrum was most abundant in when Trichoderma species were more abundant.

    Although only a few microorganisms produce the enzymes needed to break down cellulose or lignin, fungi that cannot degrade these molecules may compete for the breakdown products. Therefore, organisms that degrade complex molecules may not be the only beneficiaries of the degraded molecules.

    Overall, the soil community forms a complex food-web, which is a term used to describe all the feeding links between different organisms. Although some animals are involved in the physical break down of organic material they may also feed on the fungi and bacteria, which have already colonised the organic matter. Other animals predate on smaller animals or feed directly on bacteria and fungi: these predators are not directly involved in the decomposition of plant organic matter but do contribute to the overall cycling of material through the soil.

    Is nutrient cycling the same under all soil conditions?

    Nutrient cycling pathways differ according to the environmental conditions. Different species of microorganisms can be dominant in acid and saline soils for example. Furthermore, decomposition processes in aerobic and anaerobic soil may follow different biochemical pathways, with different end products produced. For example, in a waterlogged soil, decomposition may produce methane and sulphur-containing molecules with unpleasant smells whereas these compounds are not released during decomposition of the same organic matter when the soil is aerobic.

    What is the significance of microbial biomass to nutrient cycling?

    For many years researchers have measured total organic carbon in soil and observed that it changed little even when plant residues were incorporated into the soil over long periods of time. A common conclusion was that it was not possible to increase the organic carbon in soil, and hence burning the stubble was often continued as an acceptable practice. Stubble burning provided a convenient way of removing excessive material that interfered with agricultural machinery during cultivation and sowing.

    In the landmark study by Powlson et al. (1987), the long-term effect of incorporating straw into soil compared with burning was assessed from a soil biological perspective. The comparative effects of stubble incorporation and stubble burning on total and microbial carbon, phosphorus and nitrogen were assessed.

    In this study, incorporating straw into soil over many years had a negligible effect on the total soil organic carbon, whereas it increased the biomass of microbial carbon by 45%. Thus, although the total amount of organic carbon in the soil remained relatively constant, there was an important change in the form of carbon in the soil. This resulted from an increase in the quantity of living organisms. The nutrients held within the soil organisms are more readily degraded after the organisms die than are nutrients bound in plant material. The nutrients in microbial biomass are therefore an important pool of nutrients in soil because they can be recycled rapidly.

    Continual input of organic material into soils in natural ecosystems arises from leaf fall, tree debris and root loss. Large or sudden inputs of organic matter occur due to fire or severe storms (Bauhus et al. 1993). The incorporation of nutrients into the microbial biomass is rapid if environmental conditions favour mineralisation. Addition of organic matter itself can change the physical and chemical environment of soil organisms.

    Immobilisation of nutrients may occur at an inappropriate time for plant production in soils that have not had regular inputs of organic matter. Soils that have received long-term inputs of organic matter are less likely to require large quantities of nitrogen fertiliser to compensate for immobilisation of nitrogen by microorganisms. In any environment, immobilisation of nutrients provides a store and has the potential to reduce losses through leaching.

    The rapid release of nitrogen through mineralisation of dead microbial biomass can provide a valuable supply of nitrogen to plants if it is not leached below the root zone. A large and active microbial community in soil is more likely to immobilise nitrogen and prevent its loss through leaching (if it is not taken up by plants) than is a less developed microbial community. Therefore, the retention of plant organic matter can be beneficial in minimising loss of nutrients even if this is not reflected in increased plant growth. It should eventually be reflected in the reduced need for nutrient inputs.

    What is composting?

    Composting of garden or other plant residues involves similar processes to those which occur naturally in the soil when organic matter is degraded by soil organisms (Insam et al. 2002). The difference is that the composting process concentrates organic matter, increasing the level of activity of soil organisms to levels beyond that normally found in soil. The greatly increased activity of the soil organisms leads to the temperatures within the compost rising considerably. Subsequently, the relative abundance of organisms changes, and those that survive and grow at the higher temperatures become dominant. Some bacteria and fungi are killed during this process (including some pathogenic organisms) so that organisms that are most important in degrading the material when it is concentrated in a compost differ from to those that are important in breaking down organic matter in the soil. The type of organic matter that is added to the compost also alters the relative abundance of organisms within it. As with decomposition of organic matter in soil, the breakdown of organic matter in compost is carried out by a succession of organisms which changes as the conditions in the compost change.

    Composting illustrates how an increase in readily decomposable organic matter would stimulate the activity of soil organisms. Organisms are always present in the soil, air or on the organic matter itself; but it is not until conditions change with an increase in organic matter that their activity is stimulated. Management of a compost, by the addition of lime or nitrogen for example, is a way to speed the rate and type of decomposition by manipulating the environment of the degrading organisms. Disturbance of the compost to maintain adequate oxygen also affects the biochemical pathways of decomposition. Anaerobic decomposition of organic matter is less effective than organic decomposition.

    What is nitrification?

    Nitrification is the conversion of ammonium to nitrate. The ammonium may form during the mineralisation of organic matter or as nitrogen added to soil in fertilisers or animal waste. Autotrophic bacteria commonly function as nitrifiers but nitrification by heterotrophic bacteria can also occur in acid soils, especially in forest ecosystems. Two groups of autotrophic nitrifying bacteria are involved in nitrification. The first group converts ammonium to nitrite, and the second group converts the nitrite to nitrate. Only a small number of bacterial species is involved in these transformations. Enzymes produced by the bacteria release energy during the transformation of ammonium to nitrite and from nitrite to nitrate.

    Autotrophic nitrifying bacteria are a small group of bacteria and they are very difficult to isolate and grow in laboratory conditions. This hinders study of nitrification under controlled (laboratory) conditions. Some fungi can also function as nitrifiers.

    Mineralisation of organic matter can increase nitrification, even though autotrophic nitrifying bacteria are not dependent on the organic matter as a source of either carbon or energy (Gupta and Roper 1994). This is because the ammonium released during mineralisation of organic matter provides a form of nitrogen readily used by nitrifying bacteria as an energy source. In this study, retention of stubble increased by ten times the number of nitrifying bacteria present at one time of sampling. However, all these organisms remain inactive in soil unless a source of ammonium (and subsequently nitrite) is available.

    What is denitrification?

    Denitrification involves the conversion of oxides of nitrogen to gaseous products that are released into the atmosphere (Firestone et al. 1980), which can lead to loss of nitrogen from soil. This process usually occurs in soil that has little or no oxygen. Many different species of bacteria are capable of denitrification when soil conditions are highly anaerobic (i.e. lacking in oxygen). For example, some legume root nodule bacteria (rhizobia) can denitrify when conditions are very wet, although they are most commonly known for their ability to fix atmospheric nitrogen (Garcia-Plazaola 1993).

    Anaerobic soils are often a result of waterlogging. When the soil dries out, oxygen levels increase and the soil becomes aerobic again. The organisms that denitrified oxides of nitrogen in the waterlogged soil alter their physiology to perform different metabolic and catabolic processes in the drier, aerobic soil. This illustrates the versatility of soil organisms and their ability to change in response to their environment.

    What is nitrogen fixation?

    Some bacteria can convert nitrogen gas into nitrogen-based compounds; this is known as biological nitrogen fixation. These nitrogen-based compounds are in a form that other microorganisms and plants can use. There are three main groups of bacteria with the capacity to fix nitrogen: one group lives independently as part of the general soil microbial community, another group lives in a loose association with root surfaces and may colonise the outer cells of roots, and a third group forms highly specific, symbiotic associations with roots. Molecular tools are available to detect bacteria capable of nitrogen fixation in many environments.

    Although bacteria associated with legume roots are the best known, other associations are formed between plants and nitrogen-fixing organisms. Additional information on symbiotic nitrogen fixation is provided in Part 3.

    How do soil organisms transform inorganic molecules?

    Certain bacteria can transform many elements in the soil from one inorganic state to another (see Alexander 1977; Coyne 1999). These autotrophic processes occur in all habitats and are particularly important in deeper layers of the regolith.

    Sulphur is an essential element for the growth of living organisms. It is present in the soil in different states and the transformation of sulphur compounds occurs in both aerobic and anaerobic environments. Inorganic sulphur compounds are transformed by a number of different types of bacteria, but the most common genus is Thiobacillus. Species of Thiobacillus vary considerably in their tolerance of environmental conditions such as pH and alkalinity.

    Iron can exist in different oxidation states, depending on the degree of acidity of the soil. The bacterium Thiobacillus feroxidans transforms iron at acidic (low pH) levels. The oxidation of iron has a distinctive effect in some soils due to the colour of the iron compounds formed. Under anaerobic and waterlogged conditions, a grey colouring is produced when iron is reduced. In contrast, under aerobic conditions, iron can be oxidised to produce the distinctive reddish coloration observed in some soil profiles. These processes result from activity of similar bacteria under different environmental conditions.

    Siderophores are molecules produced by some bacteria that have a strong capacity to bind iron. If siderophores are formed around roots, they may alter the capacity of roots and microorganisms to take up iron (Höfte 1993).

    Some bacteria convert manganese from Mn2+ to Mn4+ by the process of oxidation. This occurs in the rhizosphere and may change the availability of manganese to plants.

    Some microorganisms transform inorganic forms of phosphorus in soil. This process is dependent on the excretion of organic molecules by bacteria that change soil pH and alter the rate of dissolution of phosphate. This may solubilise phosphorus that is adsorbed to soil particles or in rock phosphate.

    The capacity of soil organisms to solubilise inorganic phosphate was exploited many years ago for the production of the ‘biological’ phosphate fertiliser – ‘Biosuper’ (Jones and Field 1976). This fertiliser was a combination of rock phosphate, sulphur and the bacterium Thiobacillus. Under warm and moist conditions, the bacteria transformed sulphur to sulphuric acid that dissolved the phosphate rock. The outcome was a slow release of phosphate for use by plants. However, the success of this biological-based fertiliser was short-lived because the bacteria required particular conditions for their activity and these were not always available. At low temperatures, the activity of the bacteria was restricted and only small quantities of phosphorus were released from the rock phosphate.

    What is biodegradation?

    Biodegradation refers to the detoxification of organic compounds, such as chemicals used as pesticides, oil (and other hydrocarbons) and industrial wastes, that were either intentionally or accidentally added to the environment.

    These complex polluting organic molecules are transformed into other organic forms in several stages and are eventually completely broken down into water and simple carbon molecules, such as carbon dioxide (Helweg 1993). Many different microorganisms are involved, some of which also degrade complex plant molecules such as lignin. The key necessary factor is the ability to produce the enzymes required to carry out the transformations.

    The rate of biodegradation of a chemical depends on its structure as well as environmental conditions. Biodegradation usually occurs more quickly in an aerobic environment than in one where oxygen is limited. This is because oxygen is used during the mineralisation process. Alternatively, when conditions are anaerobic conditions in the soil, some microorganisms can use nitrate (NO3-), sulphate (SO42+) or iron (Fe2+) instead of oxygen during mineralisation.

    Biological degradation of pollutants can reduce their toxicity to plants, but this is not always the case. The products of the degradation process may themselves have toxic properties. For example, the transformation of some pesticides leads to the formation of intermediate molecules with greater persistence and different toxicity to the original compounds. The breakdown of a pesticide in soil or ground water could cause the accumulation of toxic substances that may remain undetected if soil samples are only tested for the original molecule. This demonstrates the importance of understanding the complete mineralisation process of potentially toxic substances released into the environment (Somasundram and Coates 1991).

    How does biodegradation occur?

    Only a small proportion of organisms in soil are able to degrade the complex structures of some industrial organic chemicals. These specialised microorganisms are the dominant biological degraders of pesticides, but small animals and plants can also be involved. Pesticides are biologically degraded in two ways: (i) compounds are mineralised by microorganisms into smaller molecules or (ii) molecules are transformed slightly in a way that reduces their toxicity.

    The process of degradation to smaller molecules is a mineralisation process similar to the breakdown of organic matter. Microorganisms may or may not gain energy and carbon from the transformation. Transformations that occur without providing energy or carbon are said to be incidental to the growth of the microorganisms; this process of transformation has been called co-metabolism.

    If organisms benefit from the mineralisation of a complex toxic substance through the supply of energy and carbon, the number of microorganisms in the soil will increase in parallel with the disappearance of the pesticide (Torstensson 1980). In contrast, if the transformation is incidental, there will be no correlation between the number of organisms degrading the chemical and its disappearance from the soil (Torstensson 1980). Consequently, incidental degradation may be slow due to the presence of low numbers of organisms required to be involved in the process.

    The chemical structure of a molecule may severely limit its rate of breakdown even if the organisms involved gain carbon and energy. This is why some harmful pesticides such as DDT are so persistent in the environment.

    The chemical structure of a molecule may severely limit its rate of breakdown even if the organisms involved gain carbon and energy. This is why some harmful pesticides such as DDT are so persistent in the environment.

    There may be a lag period before a pesticide or other complex molecules begin to break down. This delay can result from two processes: (i) the number of microorganisms in the soil that are able to degrade the chemical may need to increase before there is an noticeable effect and (ii) the microorganisms may need to adapt their physiological processes in response to the presence of the chemical so that appropriate enzymes are activated.

    Once these processes begin, further addition of the same or similar substance to the soil may lead to its breakdown without a lag period.

    A minor difference in the structure of a molecule can have a major influence on its susceptibility to degradation by microorganisms. For example, the inclusion of a single chlorine atom alters the chemical structure of the relatively degradable 2,4-D molecule to the highly recalcitrant molecule 2,4,5-T.

    Toxic substances are likely to be degraded by a succession of organisms that produce enzymes acting on different parts of the molecule. The suite of enzymes formed by lignin-degrading organisms has been shown to be effective in degrading toxic industrial chemicals.

    Deep in the regolith, contaminants are likely to degrade slowly because of the low abundance of soil organisms. Furthermore, organisms that degrade the contaminants at depth by co-metabolism may require an additional carbon source (e.g. phenol) for their growth before they can effectively degrade the contaminant.

    What is ‘accelerated’ pesticide degradation?

    Some pesticides are broken down quickly because the soil community adapts rapidly to their presence, whereas other chemicals can be extremely persistent in the soil. The rapid degradation of some pesticides can make them ineffective if they need to persist for a certain length of time to damage their target, e.g. herbicides for weeds.

    Summary Points (2.1)

    • The role of soil organisms in nutrient cycling is a key biological process in all ecosystems.

    • The rate of breakdown of organic matter depends on its structure, particularly the quantities of lignin and cellulose present.

    • Mineralisation of organic matter is the process that converts elements from organic to inorganic forms.

    • Immobilisation of nutrients occurs when soil organisms retain elements released during mineralisation, or take up nutrients from soil during mineralisation in order to meet their physiological needs (e.g. to achieve the appropriate balance between C and N, or C and P etc).

    • A high proportion of organic matter can remain in soil for many years because it is not easily degraded by enzymes produced by microorganisms.

    • An ecological succession of organisms is involved in the mineralisation of organic matter.

    • Soil animals form part of the food-web and contribute directly to degradation of organic matter by breaking it into smaller fragments, and indirectly by predation on the bacteria and fungi associated with mineralisation.

    • A very wide range of species of soil organisms are involved in mineralisation of organic matter.

    • A small number of species of soil organisms are involved in nitrification.

    • A wide range of organisms in soil are involved in denitrification, usually under anaerobic conditions.

    • Nitrogen fixation transforms atmospheric nitrogen to a form that plants or other organisms can use, and is carried out either by free living bacteria, by bacteria that form loose associations with roots or by specific bacteria in symbiosis with plants.

    • Inorganic nutrient transformations of sulphur, iron, manganese and phosphorus provide energy for autotrophic microorganisms.

    • Microbial nitrogen and phosphorus are important pools of nutrients in many environments.

    • Some soil organisms have the ability to produce enzymes that degrade complex industrial chemicals.

    • The rate of degradation of toxic chemicals depends on the physiological processes that the organisms use, the structure of the chemical, and the number of organisms present.

    • Some organisms use complex chemicals that are introduced into the environment as a source of carbon and energy.

    • Some organisms incidentally degrade complex chemicals by the process of co-metabolism without gaining carbon or energy for their growth, and require other organic molecules for their source of carbon and energy.

    • Organisms in soil can develop the capacity for accelerated degradation of pesticides (e.g. herbicides) if the soil community adapts during long-term application of the same or a related chemical. The adaptation can be due to a genetic shift or a physiological change.


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