Conservation of natural resources for sustainable Agriculture
what you should know about…
Organic matter
and biological activity
What it is and what it does
Plant nutrient release through biological activity
How does OM build soil structure
Need to continuously feed soil biota
Conclusion
References
What it is and what it does Soil organisms (biota), including microorganisms, use the plant and animal residues and derived organic matter as food. As they break down the residues and organic matter, any excess nutrients (nitrogen, phosphorus and sulphur) are released into the soil in forms that plants can use (nutrient availability). The waste products produced by microorganisms contribute to the called soil organic matter. This waste material is less easy to break down than the original plant and animal material, but can be used by a large number of organisms. By breaking down residues and storing the carbon into their own biomass or rebuilding new carbon structures, soil biota play the most important role in nutrient cycling processes and thus in the ability of a soil to provide the crop with sufficient nutrients to harvest a healthy product. Continual addition of plant residues and other organic matter, together with their transformation by soil organisms, provides soil with a capacity for self-recuperation of damaged soil architecture. Sticky substances on the skin of earthworms and those produced by fungi and bacteria help bind particles together. Earthworm casts are also more strongly aggregated (bound together) than the surrounding soil from the mixing of organic matter and soil mineral material, as well as the intestinal mucus of the worm. The living part of the soil thus is responsible for keeping available air and water, providing plant nutrients, breaking down pollutants and maintaining the soil structure. This contributes to restoration of its porosity through the burrowing and gum-forming processes associated with the biological activity. Consequently, the soil can store more water and acts as a sink for carbon dioxide. Organic materials (plant residues) above and on the surface of the soil can provide physical ‘buffering’ against raindrop impact and direct insolation. The decomposition of dead roots provides downward-penetrating channels, through which rainwater can quickly reach lower levels of the root-zone. Meso-Oorganisms such as worms and termites (the so-called macrofauna) create burrows with the same effect. If the soil has been so mis-managed that the formation of such macro-pores is hindered or halted, the water-cycle within the soil ecosystem is diminished in effectiveness. In conventional systems of agriculture, if insufficient time and input is given for complete biological restoration of damage caused by tillage or trampling, soil fertility - and its productivity as assessed from the yields of plants – will decline. Restoration of soil porosity by mechanical means is less satisfactory than by biological means.
PLATE 1 With time, crop residues that are left on the soil surface will be transformed into organic material. A.J. Bot
Plant nutrient release through biological activity Decomposition of organic matter is a biological process that occurs naturally. Its rate is determined by three major factors:
composition of soil organisms, the physical environment (oxygen, moisture and temperature) and the quality of the organic matter.
The organisms and the interactions among organisms make up the soil food web. The energy needed for all food webs is generated by primary producers: plants, lichens, moss, photosynthetic bacteria and algae that use sunlight to transform carbon dioxide (CO2) from the atmosphere into carbohydrates. Most other organisms depend on the primary producers for their energy and nutrients: they are called consumers. Microorganisms, such as bacteria, and large invertebrates, such as earthworms and insects, help break down crop residues and manures by ingesting them and mixing them with the mineral matrix of the soil, and in the process recycle energy and plant nutrients. The living part of soil includes a wide variety of microorganisms such as bacteria, fungi, protozoa , nematodes,. viruses and algae. Macroorganisms in soils include vertebrates, such as moles, and invertebrates (those organisms that lack a backbone and rely on an external covering). This group of organisms includes arthropods, ranging from mites to larger beetles, millipedes, and termites, and earthworms, slugs and snails. They are visible to the naked eye, although a microscope or magnifying glass might be needed to identify the species.
PLATE 2 Crop residues are being incorporated in the soil by white grubs. If no alternative is present, they will attack the crop. C. Pruett
Plants, represented by their roots and litter accumulated on the soil surface, form the macroflora of the soil. The different groups of soil organisms can be classified according to their size, as shown in table 1. Table 1 Classification of soil organisms (Adapted from Swift et al., 1979)
Microflora < 5 μm Bacteria Fungi Microorganisms
Microfauna < 100 μm Protozoa Nematodes
Mesoorganisms 100 μm - 2 mm Springtails Mites
Macroorganisms Macroorganisms 2 - 20 mm
Earthworms Millipedes Woodlice Snails and slugs
Algae 10 μm Plants Roots > 10 μm NB. Clay particles are smaller than 2 μm. They all have their own role in the nutrient cycling processes. In general, bacteria decompose the easy-to-use substrates; simple carbon compounds such as root exudates and fresh plant litter. The waste products produced by bacteria become soil organic matter. This waste material is less decomposable than the original plant and animal material, but can be used by a large number of other organisms. A number of decomposers can even break down pesticides and pollutants in the soil. Decomposers are especially important in immobilising or retaining nutrients in their cells, and thus preventing the loss of nutrients from the rooting zone. Fungi break down the more resistant organic matter, retain the resulting nutrients in the soil as fungal biomass and release carbon dioxide (CO2). The less resistant material is broken down first, whereas the breakdown of the more resistant material, such as lignin and some proteins, takes place in several stages. Many of the secondary waste products are organic acids, so fungi help increase the accumulation of organic matter rich in humic acid, resistant to further degradation. The decomposers are also important for breaking down the carbon ring structures in some pollutants. In agricultural soils, protozoa are the major producers of plant-available nitrogen. Between 40 and 80 percent of the nitrogen in plants can come from the predator-prey interaction of protozoa with bacteria. The nitrogen released by protozoa is in the form of ammonium (NH4
+) and thus readily available to plant roots and other organisms. Nematodes have even lower nitrogen contents than protozoa, between 10 and 100 times less than bacteria, or between 5 and 50 times less than fungal hyphae. Thus when bacterial- or fungal-feeding nematodes eat bacteria or fungi, nitrogen is released as ammonium (NH4
+), making the nitrogen available for plant growth or other soil organisms. Earthworms promote the activity of microorganisms by fragmenting organic matter and increasing the surface area accessible to fungi and bacteria. They also stimulate extensive root growth in the subsoil because of higher nitrogen availability in the casts (up to four times more total nitrogen than the topsoil) and the ease of root penetration through existing channels. Shredders chew plant leaf material, roots, stems and trunks of trees into smaller pieces, as they feed on the bacteria and fungi on the surface. The most abundant shredders are
millipedes and termites, as well as sowbugs, certain mites and roaches. Shredders can become pests in agricultural fields, attacking live plant roots when there is not enough dead plant material available (Moldenke, 2000). Another important role of arthropods that live on or in the soil is consuming or competing with various plant pests. Where a healthy population of generalist predators is present, these plant pests can be adequately controlled. But a population of predators can only be maintained between pest outbreaks if other kinds of prey are present; this is the case in a healthy food web with high diversity. Organisms depend on their food source (which in turn is seasonal dependent) and therefore are neither uniformly distributed through the soil nor uniformly present all year. Each species and group exists where they can find appropriate food supply, space, nutrients and moisture. They occur wherever organic matter is present and therefore soil organisms are concentrated around roots; in litter; on humus; on the surface of soil aggregates and in spaces between aggregates. For this reason they are most prevalent in forested areas and cropping systems that leave a lot of biomass on the surface. The activity of soil organisms follows seasonal as well as daily patterns. Not all organisms are active at the same time. The majority is barely active or even dormant. Availability of food is an important factor that influences the level of activity of soil organisms and thus is related to land use and management.
FIGURE 1 Large fluctuations in microbial biomass at different stages of crop development in conventional agriculture compared to systems with residue retention and high organic matter input (Balota, 1996).
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Harvest Sowing Flowering Harvest Sowing Flowering Harvest
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Conventional tillageOrganic matter retention
PLATE 3 The burrowing effects of earthworms create macropores and channels in the soil that allow water infiltration and air circulation. FAO
The decomposition of organic matter and the liberalization of carbon are aerobic processes, which mean that the microorganisms need oxygen, and thus:
the residues on the soil surface slow down the carbon cycle, because they are exposed to less microorganisms and thus wane more slowly, resulting in the production of humus which is more stable and liberate less carbon dioxide to the atmosphere when ploughed the residues are incorporated in the soil together with air and come into contact with many microorganisms, which accelerates the carbon cycle. The decomposition is faster, resulting in the formation of less stable humus and an increased liberalization of carbon dioxide to the atmosphere, and thus a reduction of organic matter
Soil moisture is one of the most important factors that define the presence of earthworms in the soil. Through conservation of soil cover, evaporation is reduced and organic matter in the soil is increased, which in turn can hold more water. Figure 2 shows the frequency of occurrence of earthworms at different humidity levels. Optimal living conditions are created with a soil humidity of 78-80 percent. As is discussed in one of the other modules, conservation agriculture creates optimal conditions for soil moisture storage (Soil moisture module). The conservation of residues on the surface not only provides ample feed for soil organisms, but protects the soil from direct insolation, which in turn regulates the soil temperature. High temperatures adversely affect growth and development of both soil organism populations and root growth development. Depending on the chemical structure of crop residues and organic matter, decomposition is rapid (sugars, starches and proteins), slow (cellulose, fats, waxes and resins) or very slow (lignin). More attractive scenarios, for increased numbers and activity of soil organisms, will include reduced or zero till with stubble retention; providing minimum disturbance of burrows and living chambers with an almost continuous food supply.
FIGURE 2 Effect of soil humidity on the occurrence of earthworms (Gassen and Gassen, 1996).
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50 75 100Soil humidity (%)
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The active, or easily decomposed, fraction of soil organic matter is the main supply of food for various organisms living in the soil. The active fraction is strongly influenced by weather conditions, moisture status of the soil, growth stage of the vegetation, addition of organic residues, and cultural practices, like tillage. About 35-55 percent of the non-living part of organic matter is humus. It is an important buffer, reducing fluctuations in soil acidity and nutrient availability. Compared to simple organic molecules, humic substances are large, with high molecular weights, and very complex. The characteristics of the well-decomposed part of the organic matter, the humus, are very different from those of simple organic molecules. While much is known about their general chemical composition, the relative significance of the various types of humic materials to plant growth is still not established.
Bacteria Bacteria are one-celled organisms, somewhat longer than wide, with an average size of 1μm. W hat they lack in size, they make up in numbers. Bacteria often live in colonies of thousands or millions of individuals, all of the same species. Many of these colonies produce substances that act as glue to hold soil particles together. Six functional groups can be distinguished:
decomposers mutualists: symbionts with plants pathogens chemoautotrophs cyanobacteria actinomycetes
The largest group of bacteria is formed by the decomposers. The second group, the mutualists, form partnerships with plants. An association in which a mutual benefit exists is called a symbiosis. One of the best known groups of bacteria comprises the nitrogen fixers that infect the roots of leguminous plants: Rhizobium bacteria. When a root hair comes into contact with a bacterium, the root hair curls and the cell walls dissolve under the influence of enzymes, thus forming a nodule. Once inside the nodule the bacteria obtain their necessary nutrients (carbon compounds) and oxygen from the host plant and in turn the host plant receives nitrogen compounds produced by the bacteria from nitrogen gas in the soil atmosphere. This process is called symbiotic nitrogen fixation1. When the roots of the host plant decompose the nitrogen compounds become available to other microorganisms and plants.
1 Symbiotic Nitrogen fixation: N2 + O2 Rhizobium NH4
+
PLATE 4 Characteristic infection of the roots of leguminous crops with Rhizobium bacteria. R. Derpsch
The third group, the pathogens, are mainly anaerobic bacteria (bacteria that do not need oxygen) that harm plant roots. Actually, the organism itself is not harmful; their waste products are harmful to plants. Some bacteria of this group can be beneficial for plant growth when there is enough oxygen in the soil. However, they produce alcohols and organic acids that harm plant tissue when oxygen is lacking. The chemoautotrophs obtain their energy for growth and development from other chemical elements such as nitrogen, sulphur, iron or hydrogen, instead from carbon compounds. Some of these bacteria are important for nitrification in which ammonium is changed into nitrate (Nitrosomonas and Nitrobacter), and further denitrification of nitrate to nitrous oxide and nitrogen gas. Others are important for the degradation of pollutants. Cyanobacteria -for a long time they were thought to be 'blue-green' algae- form a special group. They are photosynthetic and therefore live at soil surface. They play a vital role in binding soil particles in desert soils. In general, cyanobacteria are the first organisms to infect under harsh conditions or on fresh sediments and form so-called microphytic crusts. These bacteria fix atmospheric carbon and nitrogen, produce small amounts of organic matter and thus initiate nitrogen and carbon cycling processes in the soil. Within a few years they are joined by mosses, lichens and other primitive plants. These organisms inhibit the formation of mineral crusts: the cementing of soil particles that would prevent water infiltration and enhance runoff. Actinomycetes are bacteria that are responsible for the characteristic musty smell of soil and compost. Like fungi, they form threads or hyphae. They decompose a wide variety of organic substrates, but more important, they decompose the more complex compounds, such as chitin and cellulose, at high pH levels. Fungi degrade these at low pH. Besides decomposing organic matter, actinomycetes such as Streptomyces produce a number of antibiotics. As bacteria feed on organic compounds such as sugars and proteins, they are concentrated in the green litter of younger plants, and in the rhizosphere, the area around the roots, where they feed on dead cells and organic substances released by the roots (exudates).
Fungi Fungi are microscopic organisms that usually grow as long threads or hyphae, which sometimes group into masses called mycelium, or thick root-like structures. The most well-known fungi are those that produce fruiting structures, mushrooms. Some fungi, like yeast, perform important services for human food production. The thousands of species that are active in the soil, but are not seen, perform functions that are as important as those of yeast. Fungi are aerobic organisms and will die when a soil becomes anaerobic, for instance through water logging or compaction. Like bacteria, soil fungi can be divided into different groups according to their sources of energy (Ingham, 2000):
decomposers mutualists pathogens and parasites
Decomposers of lignin are active around woody plant tissue.
The roots of most plants are infected with mycorrhizal fungi, the mutualists. These fungi form a network of mycelium threads on the roots of plants and trees and thus extend the surface area of the roots. The fungi obtain carbon from the plant and in exchange the plants obtain nutrients such as phosphorus, nitrogen, micronutrients and water from the soil. This symbiotic association extends the root system of the plant. The potential benefits of effective association include protection against some root pathogens, increased disease tolerance, drought tolerance and reduction of soil toxicity and high temperature problems. The third group, the pathogens or parasites, cause reduced production or death when they colonise roots or other organisms. Soil fungi such as Pythium, Verticillium, Phytophthora, Fusarium and Rizoctonia cause serious plant diseases that result in major economic losses in agriculture. All these fungi prefer to use the simple organic substrates that are exuded by plant roots. However, not all fungi in this group are harmful. Some species compete with disease-causing organisms for food or space, and thus reduce the incidence of the disease. Some beneficial fungi produce antibiotics or other inhibitory compounds, while others, such as Trichoderma or Gliocladium, parasitise disease-causing fungi. Some nematode-trapping fungi parasites root-feeding nematodes, while others feed on insects.
Mycorrhizae fungi Mycorrhizae fungi can be divided into two groups:
Ecto-mycorrhiza Endo- mycorrhiza
Ectomycorrhiza. The hyphae of these fungi form a dense sheath on the outside of the root. A few hyphae penetrate and grow between the root cortical cells. They do not enter
PLATE 5 Many plant roots have a symbiotic association with mycorrhizal fungi which provide them with extra root surface. R. Derpsch
the cells, and generally do not penetrate beyond the cortex. The hyphal mantles are often visible to the naked eye. This type of mycorrhizae is associated with trees. Endomycorrhiza are localised between and within root cortical cells and do not produce a hyphal sheath around the root. Some are called vesicular-arbuscular mycorrhizae (VAM):
arbuscules are thought to be the site where nutrient exchanges occur (between fungus and plant) vesicles are the storage organs at the end of the hyphae
VAM fungi increase the effective nutrient absorbing surface. The endomycorrhiza are associated with grasses, agricultural crops, vegetables and shrubs. Mycorrhizae protect plants through several mechanisms (Linderman, 1994):
secretion of antibiotics that inhibit pathogens; sheath acts as a physical barrier to penetration; surplus nutrients in the root are utilised, thereby reducing the amount of nutrients available to pathogens; sheath supports a protective microbial population in the rhizosphere.
Mycorrhizae grow in the younger roots, as in mature roots the cortex is broken away. Fine roots are the primary sites of mycorrhizal development as they are the most active sites for nutrient uptake. Mycorrhizae also improve soil structure by binding soil particles into more stable aggregates through hyphae. The hyphae clump individual clay particles into aggregates, thereby allowing more oxygen to reach the root zone. This promotes the rapid multiplication of beneficial aerobic bacteria, which fix nitrogen, dissolve phosphorus, and process other elements into plant-available forms. As the fungi are also aerobic organisms, this forming of clay soil into a granular texture will improve aeration and thus their own oxygen supply. The fungal hyphae will also clump together sand, which then becomes an ideal moisture-holding environment for plant roots and bacteria. It seems that the fungi do not only search soil for nutrients, but can form a hyphae-linked underground network to transport nutrients from older trees to young seedlings. Similarly, in arid areas the fungi convey scarce water from moist pockets in the soil to the plants. Most trees and agricultural crops depend on mycorrhizal fungi or benefit from them. However, some plants do not form mycorrhizal associations, such as lupin and many members of the Cruciferae family (mustard, oil radish, and broccoli) (Ingham, 2000). Table 2 gives an overview of the relationship between VAM fungi and some plant species. Table 2 Relationship with some plants and VAM fungi
High dependency Low dependency Non hosts Beans, peas and other legumes Wheat and other cereals Canola, mustard and other
brassicas Flax Lupins
Sunflower Maize and other warm season
cereals
Potatoes and other root crops Most tropical plants and trees
Protozoa Protozoa are one-celled, highly mobile organisms, several times larger than bacteria (5-100 µm in diameter). They are predators and feed on bacteria, other protozoa, and sometimes fungi, although they can also ingest soluble organic matter. Because protozoa have 5 to 10-fold times lower nitrogen contents than bacteria, nitrogen compounds are released when protozoa eat bacteria. The released nitrogen is then available for plants. Based on their shape, three groups of protozoa can be distinguished:
ciliates amoebae flagellates
Ciliates are the largest of the protozoa and the least numerous. They move by means of hair-like structures (cilia) along their bodies. They feed on the other types of protozoa and on bacteria, especially anaerobic bacteria rather than aerobic ones, and thus their numbers are quite high in compacted soils. Amoebae are also rather large and move by means of a temporary foot (which is called pseudopodium). One group of amoebae feeds on fungi including disease-causing fungi, the way vampires feed on their victims. After drilling round holes through the fungal cell walls of the hyphae, the amoebae suck the fungal cells dry. Flagellates are the smallest protozoa and move by means of a push-pull movement generated by one or two whip-like tails (flagella). As protozoa mainly feed on bacteria, they are particularly active in the rhizosphere, where the highest concentration of bacteria occurs. They need moisture to move, so the available water content of the soil will determine the type of protozoa that are active. In general, the smaller protozoa (flagellates and naked amoebae) dominate in clayey soils, while sandy soils contain more large flagellates, amoebae and ciliates. Another role of protozoa is regulating bacteria populations. By feeding or grazing on bacteria, bacterial growth is stimulated and thus the decomposition rate of organic matter in the soil. Besides this, protozoa are an important food source for other soil organisms.
Nematodes Nematodes are tiny, round worm-like, multicellular animals, which live in the maze of pores in the soil. They move in the films of water that adhere to soil particles. The largest, which are barely visible to the eye, are 50 microns (µm) in diameter and 1 mm in length. They play an important role in most soil processes, from decomposition to plant pathology. Although they are generally considered as pests in agriculture most nematode species are beneficial, but little is known about them. Beneficial nematodes eat bacteria, fungi and other nematodes. The few plant disease-causing species have received most attention. Based on their food source, nematodes can be divided into five groups:
bacterial feeders fungal feeders predatory feeders omnivores root-feeders
Predatory nematodes eat all types of nematodes and protozoa. The smaller ones are swallowed as a whole and the larger ones are injured until the internal body parts can be extracted. Omnivores consist of a group of nematode species that may have a different diet in each life stage (Ingham, 2000). Root-feeding nematodes are not free-living in the soil, but attached to plant roots. This is probably the best-known group, as they cause root diseases in plants. Major plant parasitic nematodes include root-knot nematodes, cyst nematodes, sting nematodes and root-lesion or meadow nematodes (Yepsen, 1984). When bacterial-feeding, fungal-feeding and predatory nematodes are present in normal healthy numbers, root-feeding nematodes have a difficult time to establish themselves and are hardly found. Besides releasing plant nutrients, nematodes help distribute bacteria and fungi through the soil and along roots by carrying live and dormant microorganisms on their surfaces and in their digestive system. Nematodes are eaten by other predators, such as predatory nematodes, microarthropods and insects. Some fungi also trap nematodes As all other organisms, nematodes are concentrated near their food source. This means that bacterial feeders are concentrated in the root zone, where the highest concentration of bacteria occurs. Fungal feeders occur close to fungal biomass; root-feeding nematodes concentrate near plants in stressed conditions and predatory nematodes are more likely to be abundant in soils with large numbers of nematodes and protozoa.
EARTHWORMS Worldwide there are 3670 described species of earthworms (Fragoso et al. 1999), although the number is expected to be double, that vary in length from 5 cm to 90 cm (Edwards, 2000). Through their activities earthworms ingest soil and mix plant material into the soil. By passing soil through their bodies, earthworms digest fungi, protozoa, nematodes and microarthropods. Besides that, organic material is fragmented and mixed with mucus produced in their guts and inoculated with microorganisms. The activity of microorganisms is favoured by the trigging effect of this mixing and higher numbers are found in earthworm faeces or casts than on the organic matter before consumption. These microorganisms continue their activity in fresh casts and provide other microorganisms with food and thus facilitate the cycling of nutrients. According to Bouché (1972) three groups of earthworms can be distinguished, based on their feeding and burrowing activity: epigeic earthworms, endogeic earthworms and anecic earthworms. Epigeic earthworms live in the superficial soil layers and feed on undecomposed plant litter. These worms are usually small and produce new generations rapidly. They are well adapted to the changing moisture and temperature regimes that occur in the topsoil. Endogeic species forage below the soil surface in horizontal, branching burrows. These species ingest large amounts of soil, with a preference for soil rich in organic matter. Endogeics may have a major impact on the decomposition of dead plant roots, but are not important in the incorporation of surface litter. Their burrows are not permanent, but
constantly filled with cast material. There are three subgroups of endogeic earthworms owing to the quality of organic matter ingested (Lavelle et al. 1981): oligo- , meso- and polyhumic endogeics for low, medium and high quality of organic matter, repectively. Anecic earthworms build long-lastingor semi-permanent vertical burrows that extend deep into the soil (sometimes several meters). This type of worm comes to the surface to feed on manure, leaf litter, and other organic matter; in some cases these earthworms ingest other surface earthworm casts (Mariani et al. 2001). Anecics have profound effects on decomposition of organic matter and the formation of soil.
ARTHROPODS Arthropods are organisms that have jointed (arthros) legs (podos). They include not only insects (beetles, springtails, ants and termites), but also arachnids (spiders and mites), crustaceans (sowbugs), centipedes and millipedes, and scorpions, and .they have several functions in the soil ecosystem. Based on their functions and feeding habits they can be divided into shredders, predators, herbivores and fungal feeders. Predators can be generalists, feeding on many different organisms, or specialists, hunting only a single species (Evans, 1984). They include ants, certain mites, spiders, centipedes, ground beetles and scorpions. Many predators eat crop pests and some are used as biological control agents such as parasitic wasps. Soil herbivores are usually insects that pass part of their lives in the soil and feed on roots. Some herbivores turn to other plant parts when they appear in large numbers and the population is not controlled by other organisms. They include cicadas, mole crickets, rootworms, larvae of some beetles (white grubs) and symphylans. Fungal feeders, including most springtails, some mites and silverfish, scrape and consume fungi, and to a lesser extent bacteria, off root surfaces. This stimulates the growth of these bacteria and fungi and thus, the decomposition rate of organic matter is favoured. By reducing organic material in size, the arthropods make it easier for bacteria and fungi to find the food they like on the new surfaces. The arthropods can increase
PLATE 6 White grubs, one of the most feared crop pests can turn into a friend of the farmer, when a more ecological approach is chosen. C. Pruett
decomposition rates by 2 to 100 times, although if the bacteria and fungi are lacking, the decomposition rate will not increase. In many cases however, the arthropods carry around an inoculum of bacteria and fungi, so that their preferred kinds of prey are inoculated on the newly exposed surfaces. As the C/N ratio of arthropods is 100 times higher than the bacteria and fungi they feed upon, they release nitrogen, which then is available for plant growth. Several ecological studies suggest that in tropical environments, termites play a role similar to that of earthworms in temperate regions. Termites of importance for agriculture live in the soil and construct hills and subterraneous tunnels. Some species feed on leaves, seeds or roots, but most species consume organic material. They feed on cellulose and accelerate the decomposition of organic matter and formation of humus, and thus play an important role in the recycling of nutrients. The opening of channels in the soil, the burying of organic matter and the concentration of nutrients and organic matter in termite heaps, which is several times higher than in the surrounding soil (Table 3), make them very useful for agriculture. Table 3 Nutrient content of termite heaps (Cornitermes cumulans) compared to surrounding soil (Gassen, 1999) Element Soil Outside of heap Centre of heap Potassium (ppm) 62 180 >200 Phosphorus (ppm) 0.5 2.5 10.3 Calcium (me) 0.6 4.6 12.1 Organic matter (%) 4.4 6.8 >9.4 Insects, such as Bothynus sp. dig channels up to 40-100 cm. During summer and autumn the larvae of this insect transport and collect residues inside the channels, which is later consumed. This species does not feed on plant parts, not even when there are no residues left on the soil. As with earthworms, excrements are left in wide spaces at the end of the channels and consequently these areas are high in nutrients and organic matter and have a higher pH than the surrounding soil (Table 4). Table 4 Nutrient content and acidity of Bothynus sp. chambers compared to the surrounding soil (Gassen, 1999) Soil depth (cm)
Organic matter (%)
pH Al (me/kg)
Ca (me/kg)
Mg (me/kg)
P (ppm)
K (ppm)
0- 5 5.8 5.1 1.8 57 22 8.9 >200 5-10 3.8 5.2 1.7 55 20 8.5 164 10-15 3.3 4.9 4.9 22 12 1.4 162 15-20 2.7 4.8 5.1 12 07 1.2 104 20-25 2.4 4.8 4.8 10 07 0.7 84 25-30 2.2 4.8 4.3 10 06 0.5 66 Bothynus sp. chambers
>9.4 5.3 1.7 93 37 7.6 >200
Besides the positive influence on nutrient cycling, the feeding behaviour of arthropods is important for the formation of soil aggregates. In most soils, every particle in the topsoil has gone through the intestines of numerous soil fauna where it is mixed with organic substances. Soil aggregates of 2.5 Mm to 2.5 mm generally are faecal pellets of soil fauna. The abundance and diversity of soil fauna diminishes with depth in the soil and as a general rule, the size of the arthropods also diminishes with depth. The larger organisms are active on the soil surface, in the litter layer. The organisms that dwell in deeper soil layers often lack pigmentation and eyesight and their size allows them to squeeze through soil micropores.
Plant roots and algae Plant roots and algae represent the flora in the soil. Plants and algae are the primary producers (through the process of photosynthesis they convert CO2 taken from the air and H2O from the air and the soil with the energy of sun into carbohydrates that are available to other organisms). Roots are influenced by the soil in which they live. When the soil is compact or has low nutrient contents or limited water, or other problems, plants will not grow well. But plants also influence the soil in which they grow. The physical pressure of roots growing through the soil helps form aggregates by bringing particles closer together. Decayed roots leave pores and channels in the soil that improve water and air exchange. When plant material is returned to the soil, it becomes the primary food source for bacteria and fungi. Plant roots also create a distinct ecosystem that can profoundly influence plant growth. This often neglected ecosystem is the rhizosphere, which is the outer part of the root and its immediately surrounding area (Lynch, 1988). A large number of microorganisms, mainly bacteria and protozoa, are concentrated around the surfaces of plant roots. They are attracted to the root surface because of carbon compounds exuded by live roots, which are vital sources of food and energy for bacteria. These compounds are called root exudates and can be distinguished into three groups (Jackson, 1993):
Mucigel: a gel-like material, being a mixture of polysaccharides, proteins, lipids, vitamins and plant hormones enveloping especially the root tips. A variety of organic acids, amino acids and simple sugars excreted by the root hairs. Cellular organic substances produced by senescence of root epidermis.
The microorganisms that inhabit the rhizosphere are a mixture of beneficial, neutral and harmful organisms. The majority of the microorganisms are beneficial. The microbes in the rhizosphere extract nutrients and energy from the root and its products. In return, the microorganisms release plant nutrients for direct uptake by the roots, and some of the waste products of the microorganisms regulate plant growth. The pool of compounds around the root is large and varied: the mix depends on the species of the plant, its age and on environmental conditions. The cycling of carbon in the ecosystem depends largely on this deposition of compounds. The process is strongly influenced by environmental factors.
PLATE 7 Plant roots explore the soil for nutrients. Roots from different plant species use different soil layers to extract their nutrients and thus create distinct ecosystems at different soil depths. J. Clapperton
How does organic matter build soil structure When plant residues are returned to the soil, various organic compounds undergo decomposition. Decomposition is a biological process where the physical breakdown and biochemical transformation of complex organic molecules of dead material result into simpler organic and inorganic molecules (Juma, 1998). Crop residues contain mainly complex carbon compounds originating from cell walls. These carbon chains, with varying amounts of attached oxygen, hydrogen, nitrogen, phosphorus, and sulphur, are the basis for both simple sugars and amino acids. Successive decomposition of dead material and modified organic matter results in the formation of a more complex organic matter, called humus. Humus affects the soil properties, as it colours the soil darker; increases soil aggregation and aggregate stability; increases the cation exchange capacity; and contributes nitrogen, phosphorus, and other nutrients as it slowly decomposes. Humus consists of complex organic substances suche as Humic substances (humic acids and humins, fulvic acids) that remain in the soil after decomposition of the residues. Humus also plays an important role in soil structure. Without humus, soils with high lime or clay content would compact easily when worked. Polysaccharides are the actual substances that glue the soil particles together; the more resistant soil organic matter (humic acids) hold together the microaggregates while fulvic acids bond the microaggregates into macroaggregates. Sugars, amino acids and phospholipids are the sources for nitrogen, phosphorus and sulphur for microorganisms and plant growth. The burrowing activity of earthworms provides channels for air entrance and passage of water, which has an important effect on oxygen diffusion in the root zone and drainage. Shallow-dwelling earthworms create numerous channels throughout the topsoil, when residues are conserved on the soil surface, which increases overall porosity. The large vertical channels created by the deep-burrowing earthworms greatly increase water infiltration under intense rainfall or waterlogged conditions. Earthworms enhance soil aggregation.
NON-HUMIC SUBSTANCES: SIGNIFICANCE AND FUNCTION Non-humic, organic molecules directly released from cells of fresh residues, such as proteins, amino acids, sugars, and starches, are also considered part of organic matter. There are many different types of organic molecules in soil. Some are simple molecules that have come directly from plants or other living organisms. These relatively simple chemicals, like sugars, amino acids, and cellulose are readily consumed by many organisms. For this reason they do not stay in the soil for a long time. Other chemicals such as resins and waxes also come directly from plants, but are more difficult for soil organisms to break down. This part of soil organic matter is the active, or easily decomposed, fraction. This active fraction of soil organic matter is the main supply of food for various organisms living in the soil. The active fraction is strongly influenced by weather conditions, moisture status of the soil, growth stage of the vegetation, addition of organic residues, and cultural practices, like tillage.
The carbohydratescarbohydratescarbohydratescarbohydrates, like simple sugars, cellulose and hemicellulose, etc., constitute 5 to 25 percent of the organic matter in most soils. Carbohydrates occur in the soil in three main forms: free sugars in the soil solution, complex polysaccharides and polymeric molecules of various sizes and shapes that are strongly attached to clay colloids or humic substances. As there are many microorganisms that use them, these compounds generally do not last long in the soil. The microorganisms in turn synthesise most of the soil polysaccharides (repeating units of sugar-type molecules connected in longer chains), as they decompose fresh residues. PolysaccharidesPolysaccharidesPolysaccharidesPolysaccharides promote better soil structure through their ability to bind inorganic soil particles into stable aggregates. The more complex polysaccharide molecules are more important in promoting aggregate stability and water infiltration than the simpler molecules. Some sugars may stimulate seed germination and root elongation. Other soil properties affected by polysaccharides include cation exchange capacity, anion retention and biological activity. [insert link to BA p13 biol. properties] The soil lipidslipidslipidslipids form a very diverse group of materials. Of these fats, waxes and resins make up two to six percent of soil organic matter. The significance of lipids arises from the ability of some compounds to act as growth hormones. Others may have a depressing effect on plant growth. Soil nitrogen occurs mainly (>90%) in organic forms as amamamamino acidsino acidsino acidsino acids, nucleic acids and amino sugars. Small amounts exist in the form of amines, vitamins, pesticides and their degradation products, etc. The rest is present as NH4
+ and is held by clay minerals.
COMPOUNDS AND FUNCTION OF HUMUS Humus or humified organic matter is the remaining part of organic matter that has been used and transformed by many different soil organisms. It is a relatively stable component formed by humic substances, including humic acids, fulvic acids, hymatomelanic acids and humins. It is probably the most widely distributed organic carbon-containing material in terrestrial and aquatic environments. Humus cannot be readily decomposed because of its intimate interactions with soil minerals and it is chemically too complex to be used by most organisms. One of the most striking characteristics of humic substances is their ability to interact with metal ions, oxides, hydroxides, minerals and organics, including toxic pollutants, to form water-soluble and water-insoluble complexes. Through the formation of these complexes, humic substances can:
dissolve, mobilise and transport metals and organics in soils and waters, i.e. nutrient availability, especially those present at microconcentrations only, or accumulate in certain soil horizons, i.e. a reduction of toxicity, for instance of aluminium in acid soils, or the capture of pollutants - herbicides such as Atrazine or pesticides such as Tefluthrin - in the cavities of the humic substances.
About 35-55 percent of the non-living part of organic matter is humus. It is an important buffer, reducing fluctuations in soil acidity and nutrient availability. Compared to simple organic molecules, humic substances are large, with high molecular weights, and very complex. The characteristics of the well-decomposed part of the organic matter, the humus, are very different from those of simple organic molecules. While much is known
about their general chemical composition, the relative significance of the various types of humic materials to plant growth is still not established. Humus consists of different humic substances:
Fulvic acids: the fraction of humus that is soluble in water under all pH conditions. Their colour is commonly light yellow to yellow-brown. Humic acids: the fraction of humus that is soluble in water, except for conditions more acid than pH 2. Common colours are dark brown to black.
The term acid is used to describe humic materials because humus behaves like weak acids.
Humin: the fraction of humus that is not soluble in water at any pH and that cannot be extracted with a strong base, such as sodium hydroxide (NaOH). Commonly, black in colour.
Humic and fulvic substances enhance plant growth directly through physiological and nutritional effects. Some of these substances function as natural plant hormones (auxines and gibberillins) and are capable of improving seed germination, root initiation, uptake of plant nutrients and can serve as sources of nitrogen, phosphorus and sulphur. Indirectly, they may affect plant growth through modifications of physical , chemical and biological properties of the soil, for example increased soil water holding capacity and cation exchange capacity, and improved tilth and aeration through good soil structure. Fulvic and humic acids are complex mixtures of large molecules. Humic acids are larger than fulvic acids. For a long time it was thought that fulvic acids were converted to humic acids, but nowadays, it appears that there is not such a process. The different substances are only differentiated from each other on the basis of their water solubility. Fulvic acids are produced in the earlier stages of humus formation. The relative amounts of humic and fulvic acids in soils vary with soil type and management practices. The humus of forest soils is characterised by a high content of fulvic acids while the humus of agricultural and grassland areas contain more humic acids.
Need to continuously feed soil biota The reduction of soil disturbance and biomass increase through cover crops, like in conservation agriculture, result in preservation of crop residues on the soil surface, and thus in an improvement of soil health. The greater production of foliage in a system with cover crops and reduced or zero tillage compared to monocrop cultures with conventional tillage, provides a protective blanket of leaves, stems and stalks from the previous crops on the surface. In this way organic matter can be built up on the soil surface, which creates favourable conditions for the activity and the population development of the microorganisms. Organic matter is accumulated mainly in the topsoil layers (figure 3). In turn, conventional tillage results in homogeneous mixing of organic matter and soil up to a depth of 20 cm and because of the absence of soil cover, bigger fluctuations in temperature and humidity occur (see Physical properties) and in turn result in fluctuations in microbial development, as is shown in figure 1. The microorganisms that decompose the crop residues need carbon as their energy source and for building their cells, but even more important, big quantities of nitrogen are needed for growth and multiplication. In residues with low nitrogen content (like straw), the activity of microorganisms will be reduced because of lack of nitrogen, resulting in low decomposition rate. During the first years of conservation agriculture on poor soils, the nitrogen of the residues is not sufficient, so the microorganisms also use the nitrogen that is stored in the soil. This process is called immobilization of nitrogen (figure 4) and can lead to a nitrogen deficiency in the crops, resulting in chlorotic appearance of the leaves. It is always advisable to keep in mind the carbon-nitrogen (C/N) ratio of the residues and if necessary correct with fertilizers. Once the system is stabilized, and there is enough organic matter that provides the nitrogen for the microbial development, no additional fertilization is needed to correct this process. During the decomposition process, CO2 is liberated and the C/N ratio decreases; this way the microorganisms release (mineralize) nitrogen as ammonium (NH4) to the soil. Other microorganisms quickly convert the ammonium into nitrate (NO3), which is then easily available for uptake by plant roots.
FIGURE 3 Organic matter content of a soil under different tillage regimes (Balota et al., 1996a).
����������������������������������������������������������������������������������������������������������������������������������������0 0.5 1 1.5 2
0-3
3-13
13-26
26-52
����Direct seeding
����Minimum tillage
����Conventional tillage
Organic matter content (%)
Soil depth (cm)
Table 5 shows C/N ratios of a number of crops. In order to avoid problems, the C/N ratio should be 30 or less. Table 5 Carbon-nitrogen relationships of different crop residues. Crop residue C/N ratio Legumes and grass 10-20 Vegetative residues without legumes 10-15 Straw (crop residues after harvest) 60-150 Leaves (when falling) 20-60 The higher the production of green manure or crop biomass, the higher will be the microbial population of the soil. Agricultural production systems, in which residues are left on the soil surface, like direct seeding and the use of cover crops therefore stimulate the development and activity of soil microorganisms. The microbial biomass is higher under conservation agriculture conditions, regardless of the season. After 19 years of experimentation this resulted in 129 percent increase of microbial carbon biomass and 48 percent increase of microbial nitrogen biomass (figure 5).
FIGURE 4 Carbon cycle showing nitrogen uptake and release by microorganisms.
Cropresidues
Humus
Immobilization
Proteins andpolysaccharides
Mineralization
Nutrients
Crop
Soilstructure
Microorganismsand soil biota
CO2 + H2O
Decomposition
NH4+
NO3-
NH4+
NO3-
PLATE 8 Cover crops and crop residues will continuously provide the soil biota with enough energy. R. Derpsch
Figure 6 shows that although in general, under direct seeding the microbial biomass is higher than under conventional tillage, it is the type of cover crop that determines the differences in microbial biomass. Highest microbial biomass production is found when oil radish is sown as cover crop under no-tillage. However, highest increases in microbial biomass are found under hairy vetch and rye (respectively 135 and 115 percent), comparing direct seeding and conventional tillage. For zero tillage systems in southern Brazil, differences of about 50% in soil biomass and rhizobial populations, compared to conventional tillage were reported (Hungria, et al. 1997). Evaluations have demonstrated that some crop rotations and zero tillage favour Bradyrhizobia populations, nodulation and thus nitrogen fixation and yield (Voss and
FIGURE 6 Microbial biomass as a function of different cover crops under conventional tillage (CT) and direct seeding (DS) (Balota et al., 1996b)
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100
200
300
400
500
600
Fallow Hairy vetch Lupin Lathyrus Wheat Rye Italianryegrass
Oats Oil radish
Micr
obial
biom
ass (
ug C
-CO 2
g-1 so
il)
��Conventional tillage
��Direct seeding
FIGURE 5 Microbial biomass (C and N) under conventional tillage and conservation agriculture (Balota et al., 1996a) ������������ ����
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0
100
200
300
T otal C-CO2 T otal N
Micro
bial b
iomas
s (ug
g-1
soil)
���Conv entional tillage
���Conserv ation agriculture
Sidirias, 1985, Hungria, et al., 1997, Ferreira, et al., 2000). Figure 7 indicates a 200-300 percent increase in population size when applying zero tillage, compared to conventional tillage. The presence of Soya bean in the crop rotation resulted even in a 5-10 times higher increase of population size. The roots of most plants are infected with Mycorrhizae, fungi that form a network of mycelia or threads on the roots and extend the surface area of the roots. Infestation of crop roots with mycorrhizal fungi is enhanced with conservation agriculture as is shown in figure 8 (Venzke Filho, et al., 1999). With time infestation with mycorrhizal fungi increases, resulting in a 287 percent increase after 20 years of conservation agriculture in maize and 305 percent in soya, compared to infestation under natural vegetation. Fine roots are the primary sites of mycorrhizal development as they are the most active site for nutrient uptake. This
FIGURE 7 Population size of root nodule bacteria with different crop rotations (S=soya; W=wheat; M=maize) (Voss and Sidirias, 1985).
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50
60
S/W/M S/W M/W S/W/M S/W M/W
Popu
lation
size
Bra
dyrh
izobiu
m (#
cells
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)
FIGURE 8 Infestation of crop roots with Mycorrhizal fungi (Venzke Filho, et al., 1999). ������� ���
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0
10
20
30
40
50
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Naturalvegetation
Conventionaltillage (1 year)
Conservationagriculture(10 years)
Conservationagriculture(20 years)
Aver
age r
oot c
oloniz
ation
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����Maize
��������Soya
explains partly the increase under conservation agriculture: rooting conditions are far better than under conventional tillage, which in turn creates ideal conditions for mycorrhizal colonization. Other factors that might affect mycorrhizal development positively are the increase of organic carbon, the absence of mixing the soil and the rotation of crops with cover crop/green manure species. By implementing conservation agriculture, the earthworm population will be increased (Figure 9). Earthworms, like other soil inhabiting organisms, rarely come to the soil surface, except certain ecological categories (only epigeic and anecic worms), due to their physical characteristics: photophobia -afraid of light-, body without pigment (in the case of endogeic earthworms), but resistant to periods of submergence during rainfall and resistant to carbon dioxide. Tanck and Santos (1995) observed an earthworm population of 112 individuals per m2
under conservation agriculture, compared to hardly 2 under conventional tillage. Residues on the soil surface force earthworms to come to the surface in order to incorporate the residues in the soil. One of the consequences of an increased earthworm population is the formation of channels and pores. The burrowing activity of earthworms provides channels for air and water, which vehas an important effect on the oxygen diffusion in the root zone, and the drainage of water from it. Furthermore nutrients and amendments can be distributed easily and the root system can develop, especially in acid subsoil in the existing casts. The burrows are an easy-to-use indicator while monitoring in the field.
FIGURE 9 Number of earthworm burrows (diameter of 1.5 mm) in clayey soils under conservation agriculture and conventional tillage (Pauletti, 1999).
��������������������������
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0
200
400
600
800
1000
1200
10 20 30 40 50Soil depth (cm)
Numb
er o
f ear
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rm b
urro
ws p
er m3
���Conventional tillage
���Conservation agriculture
Conclusion Soil organisms of all shapes and sizes from microbes to macrofauna, are of great importance for plant health and nutrition as they interact directly in the biogeochemical cycles of nutrients (figures 4). They influence moisture and nutrient availability and mobility in the soil profile. Certain species can also become pests and pathogens due to a population imbalance and resulting loss of critical interactions in the soil food web. Microorganisms are responsible for the mineralization and immobilization of nitrogen, phosphorus and sulphur, among others, through the decomposition of organic matter and contribute to the gradual and continuous liberation of plant nutrients. Therefore agronomic practices that influence nutrient cycling, especially mineralization and immobilization result in immediate productivity gain or loss which are reflected in the profitability of the agricultural system. Application of the principles of conservation agriculture, will improve the habitat and increase the population of soil organisms, which in turn will result in:
incorporation and reduction of residues increase in microbial activity and thus the recycling of nutrients mixing and gluing of soil particles nitrogen fixation from the atmosphere carbon sequestration (storage as soil C) mobilization of nutrients in the profile creation of burrows, which improve porosity, water infiltration and water retention capacity
On the other hand, when a soil ecosystem is not well managed, species tend to disappear which will result in a reduction of the above effects and a domination of certain species with negative consequences. Table 6 illustrates the reduction in nitrogen mineralization when a certain group of species disappears from the system. Table 6 Reduction in Nitrogen mineralisation if a group is absent what are the units?(Clapperton, 2003) Amoebae 32.4 Flagellates 1.9 Bactivorous Nematodes 17.3 Fungivorous Nematodes 1.2 Oribatid mites 0.01 Non Oribatids 0.03 Bactivorous Mites 0.003 Fungivorous Collembola 0.8 Enchytraeids 3.2 Predatory Nematodes 19.1 Predatory mites 0.3 Nematophagous mites 0.2 Predatory Collembola 0.
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