Download Organic matter and biological activity

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.
PLATE 1
With time, crop
residues that are left
on the soil surface will
be transformed into
organic material.
A.J. Bot
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.
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:
x composition of soil organisms,
x the physical environment (oxygen, moisture and temperature) and
x 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.
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
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.
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
Microfauna
< 100 μm
Mesoorganisms
100 μm - 2 mm
Macroorganisms
2 - 20 mm
Algae
Roots
10 μm
> 10 μm
Microorganisms
Macroorganisms
Plants
Bacteria
Fungi
Protozoa
Nematodes
Springtails
Mites
Earthworms
Millipedes
Woodlice
Snails and slugs
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).
PLATE 3
The burrowing effects of
earthworms create
macropores and
channels in the soil that
allow water infiltration
and air circulation.
FAO
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.
5
Number of P dissolving bacteria (*10 )
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).
40
Conventional tillage
Organic matter retention
30
20
10
0
Harvest
Sowing
Flowering
Harvest
Sowing
Flowering
Harvest
The decomposition of organic matter and the liberalization of carbon are aerobic
processes, which mean that the microorganisms need oxygen, and thus:
x
x
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
FIGURE 2
Effect of soil humidity on the occurrence of earthworms (Gassen
and Gassen, 1996).
Frequence of earthworms (%)
100
80
60
40
20
0
50
75
Soil humidity (%)
100
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.
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
x
mutualists: symbionts with plants
x
pathogens
x
chemoautotrophs
x
cyanobacteria
x
actinomycetes
x
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.
PLATE 4
Characteristic infection of
the roots of leguminous
crops with Rhizobium
bacteria.
R. Derpsch
1
+
Symbiotic Nitrogen fixation: N2 + O2 Æ Rhizobium Æ NH4
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):
x
decomposers
x
mutualists
x
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.
PLATE 5
Many plant roots have a
symbiotic association with
mycorrhizal fungi which provide
them with extra root surface.
R. Derpsch
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 diseasecausing 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:
x
Ecto-mycorrhiza
x
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
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):
x
arbuscules are thought to be the site where nutrient exchanges occur (between
fungus and plant)
x
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):
x
secretion of antibiotics that inhibit pathogens;
x
sheath acts as a physical barrier to penetration;
x
surplus nutrients in the root are utilised, thereby reducing the amount of nutrients
available to pathogens;
x
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
Beans, peas and other legumes
Flax
Sunflower
Maize and other warm season
cereals
Potatoes and other root crops
Most tropical plants and trees
Low dependency
Wheat and other cereals
Non hosts
Canola, mustard and other
brassicas
Lupins
Protozoa
Protozoa are one-celled, highly mobile organisms, several times larger than bacteria (5100 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:
x
ciliates
x
amoebae
x
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:
x
bacterial feeders
x
fungal feeders
x
predatory feeders
x
omnivores
x
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.
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
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
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
Potassium (ppm)
Phosphorus (ppm)
Calcium (me)
Organic matter (%)
Soil
62
0.5
0.6
4.4
Outside of heap
180
2.5
4.6
6.8
Centre of heap
>200
10.3
12.1
>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)
0- 5
5-10
10-15
15-20
20-25
25-30
Organic
matter (%)
5.8
3.8
3.3
2.7
2.4
2.2
Bothynus sp.
chambers
>9.4
pH
5.1
5.2
4.9
4.8
4.8
4.8
Al
(me/kg)
1.8
1.7
4.9
5.1
4.8
4.3
Ca
(me/kg)
57
55
22
12
10
10
Mg
(me/kg)
22
20
12
07
07
06
P
(ppm)
8.9
8.5
1.4
1.2
0.7
0.5
K
(ppm)
>200
164
162
104
84
66
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):
x Mucigel: a gel-like material, being a mixture of polysaccharides, proteins, lipids,
vitamins and plant hormones enveloping especially the root tips.
x A variety of organic acids, amino acids and simple sugars excreted by the root hairs.
x Cellular organic substances produced by senescence of root epidermis.
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
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.
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 carbohydrates,
carbohydrates 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.
Polysaccharides 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 lipids 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 amino
acids, nucleic acids and
amino acids
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:
x
dissolve, mobilise and transport metals and organics in soils and waters, i.e. nutrient
availability, especially those present at microconcentrations only, or
x
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:
x
Fulvic acids: the fraction of humus that is soluble in water under all pH conditions.
Their colour is commonly light yellow to yellow-brown.
x
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.
x
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).
FIGURE 3
Organic matter content of a soil under different tillage regimes
(Balota et al., 1996a).
Organic matter content (%)
Soil depth (cm)
0
0.5
1
1.5
2
0-3
3-13
13-26
Direct seeding
26-52
Minimum tillage
Conventional tillage
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.
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.
FIGURE 4
Carbon cycle showing nitrogen uptake and release by
microorganisms.
Crop
residues
Decomposition
Crop
NH4+
NO 3-
Microorganisms
and soil biota
Nutrients
CO2 + H2O
Humus
Mineralization
Immobilization
NH 4+
NO3-
Proteins and
polysaccharides
Soil
structure
Table 5 Carbon-nitrogen relationships of different crop residues.
Crop residue
Legumes and grass
Vegetative residues without legumes
Straw (crop residues after harvest)
Leaves (when falling)
C/N ratio
10-20
10-15
60-150
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).
PLATE 8
Cover crops and crop
residues will
continuously provide
the soil biota with
enough energy.
R. Derpsch
FIGURE 5
Microbial biomass (C and N) under conventional tillage and
conservation agriculture (Balota et al., 1996a)
Microbial biomass (ug g -1 soil)
300
Conv entional tillage
Conserv ation agriculture
200
100
0
T otal C-CO2
T otal N
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.
FIGURE 6
Microbial biomass as a function of different cover crops under conventional tillage (CT) and
direct seeding (DS) (Balota et al., 1996b)
-1
Microbial biomass (ug C-CO2 g soil)
600
Conventional tillage
Direct seeding
500
400
300
200
100
0
Fallow
Hairy vetch
Lupin
Lathyrus
Wheat
Rye
Italian
ryegrass
Oats
Oil radish
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
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.
Population size Bradyrhizobium (# cells *100)
FIGURE 7
Population size of root nodule bacteria with different crop rotations
(S=soya; W=wheat; M=maize) (Voss and Sidirias, 1985).
60
50
40
30
20
10
0
S/W/M
S/W
M/W
S/W/M
S/W
M/W
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).
Average root colonization (%)
FIGURE 8
Infestation of crop roots with Mycorrhizal fungi (Venzke Filho, et al.,
1999).
70
Maize
60
Soya
50
40
30
20
10
0
Natural
vegetation
Conventional Conservation Conservation
tillage (1 year) agriculture
agriculture
(10 years)
(20 years)
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
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.
3
Number of earthworm burrows per m
FIGURE 9
Number of earthworm burrows (diameter of t1.5 mm) in clayey soils
under conservation agriculture and conventional tillage (Pauletti,
1999).
1200
Conventional tillage
Conservation agriculture
1000
800
600
400
200
0
10
20
30
Soil depth (cm)
40
50
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.
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:
ƒ incorporation and reduction of residues
ƒ increase in microbial activity and thus the recycling of nutrients
ƒ mixing and gluing of soil particles
ƒ nitrogen fixation from the atmosphere
ƒ carbon sequestration (storage as soil C)
ƒ mobilization of nutrients in the profile
ƒ 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
Flagellates
Bactivorous Nematodes
Fungivorous Nematodes
Oribatid mites
Non Oribatids
Bactivorous Mites
Fungivorous Collembola
Enchytraeids
32.4
1.9
17.3
1.2
0.01
0.03
0.003
0.8
3.2
Predatory Nematodes
Predatory mites
Nematophagous mites
19.1
0.3
0.2
Predatory Collembola 0.
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