Soil ecology

By Dr J Floor Anthoni (2000)
Soils, their living organisms, and the plant ecosystems rooted in them, have developed in close synchrony ever since plants evolved. Between them there exists a strange synergy, whose only purpose seems to be to sustain life to its maximum. Man's intervention, by cutting forests, seeding grassland and planting crops amounts to a major shock to this earthy world. Man's ignorance and unfriendliness towards the soil may lead to his own destruction. Knowing how the soil's ecosystem works, what it needs and how it likes to be treated, could save our soils for posterity. How does soil work? What happens in the soil? How are nutrients recycled in soil? What is the water cycle and how does the water cycle fertilise the soil? What lives in soil? What is the role of fungi? 
biosphere & carbon Life is about organic carbon compound, stored in the vegetation and animals, but also in the soil. Soil organisms' energy comes only from the various carbon compounds recycled to the soil.
internal cycles The nature of an ecosystem is to recycle the most precious building blocks of life, its nutrients, energy and water. These ecosystems have evolved over eons of time, long before the dawn of Man. The invisible ecosystem of the soil is what makes soil fertile.
external cycles The only way that nutrients can be cycled externally, is through the atmosphere. The cycles of water and carbon are well known, but there are others, all very important to life on Earth.
primary production Plants produce vegetable matter, but much of it is consumed by the invisible world in the soil, on which the plants depend. Primary production and the yield of crops depend on many invisible qualities.
soil biota Without the living circus in the soil, plants would not be able to live so well. The world above and that below,  provide for each other. Here we'll meet some of the many strange life forms that make up a large part of the world's biodiversity.
soil functioning Organisms ranging from a few times the size of a clay platelet to many thousands, find their places to live in the amazingly complicated micro structure of soil, where each contributes to its proper functioning. 

-- home -- environment -- issues -- Rev 20051121,20060712,20070211,

Carbon in the biosphere
what the biosphere containsPlanet Earth distinguishes itself by its biosphere (sphere of life), a thin layer of gases, soils and liquids within which all life exists. Imagine the planet (12,000km diameter) the size of a billiard or tennis ball. Then the thickness of the biosphere from the deepest abyss to the highest mountain amounts to no more than the thickness of a human hair (0.1mm). Within this ultra thin film, all life's processes occur, and also the horizontal movements of deep ocean currents, shallow ocean currents, the weather with its swirling winds and the high jet streams where air planes fly. But what is it composed of?
With a pressure of 1 atmosphere at the surface, almost equal to 1kg/cm2, a column of 10,000 kg of air towers above each square metre. Most of this is nitrogen (~8000kg) and oxygen (~2000kg) and a tiny 3 kg is carbondioxide (CO2) of which the carbon content is about 1kg. So there exists very little carbon overhead. For plants to be able to find it and catch it, is awesome.

The situation on the ground fares much better with about 15kg carbon for forests and 3kg for grassland. But the animal content is very small, amounting to only 50mg per square metre. By comparison, the soil contains most carbon, at 10kg. It is thus important for farmers to realise that their main concern should be with the life in the soil. But how would the carbon pools above and below the soil be distributed over the world?
what the biosphere containsThe diagram shown here combines data from various sources, in order to give an overview of how much carbon is stored above and below the surface, for the various main vegetation types of the world. From the top to the bottom the globe is traversed from the North Pole to the equator, with two odd biomes at the bottom. The lefthand column plots the amount of carbon in soils, the middle column their standing biomass and the righthand column their productivity in kg/m2/year. 'S'-curves can roughly be drawn around their contours. Note how grasslands store most of their carbon in their soils and forests have roughly equal amounts below and above, except for tropical rain forests. Note also that the lengths of each block represent the total areas of each biome, such that their sizes represent the total amounts of carbon stored in each biome. For an in-depth comparison of these biomes and their soil types, visit the soil and rock classification table where this diagram is also discussed.

deforestation and soil degradationThe most serious degradation of soils happens slowly and invisibly as quality is lost, as illustrated by this diagram and the curve of fertility underneath. For any soil to remain sustainable, the recycling of minerals from soil to plant to animal to soil must be near-perfect, such that losses can be made up from the natural weathering of the rock (shown in grey) below. The pictures show the main soil layers (rock, subsoil, top soil, humus) and the carbon pools above and below the surface.
When the forest is burnt, the total amount of carbon (and thus minerals) lost is about 50% in the first two years. During these years, the soil is highly productive, giving farmers the false impression that this will last forever. But after about ten years , depending on the soil's slope, a considerable amount of carbon is lost. Often lighter grazing animals such as sheep replace the heavier cattle. At this level of fertility, the soils may last about 50 years, after which they begin to degrade rapidly, eventually losing all their carbon and minerals. After the point of no return, fertilisation will be in vain and soil erosion will be almost impossible to halt.
Fertilisers need to be used to keep the soils from travelling down this path of total degradation, and when applied carefully, they will be able to raise fertility to their original levels. This depends critically on the slope of the land, to such extent that any farmland steeper than 10% will not be sustainable.
Note that the example shown here relates to a permanent crop like pasture (grass). But when the land is ploughed, degradation proceeds much more rapidly as the soil's carbon is consumed by soil organisms under the influence of increased oxygenation. See the sustainability chapter for more discussion.

Internal cycles
food cycle on the farmNutrient cycling is at the heart of any ecosystem. As this picture shows, it is a very sensitive process. The carbon dioxide in the air is taken up by plants to feed the farm animals. They use the energy for living, moving and growing. Their respired carbon dioxide re-enters the atmosphere, cycling back into the plants that feed the animals. The predator (man) eats the meat and uses its energy for living, moving and growing. His respiration also enters the pool of carbon in the atmosphere, ready to recycle to the plants.
But plants need nutrients before they can convert carbon dioxide into plant matter. Here is where the soil plays its major role. The animal's excrements that contain most of the nutrients, is recycled and made ready for the plants again. Some new nutrients arrive from below, where the soil weathers. The excrement of the predator follows the same path.

Because a grazing farm animal uses only a small part of its food for growing (see soil/dependence), it has to eat 10-20 times its weight in order to double it. Thus the nutrient cycle is rather large, compared with the amount of live matter in the grazing stock. The organisms in the soil, which process this large amount of recyclable material, must thus form a large living body or work faster, or do both.
Due to rain and poor farming practices, some of the nutrients are washed from the farm, ending up in the sea, where they cause plankton to bloom. The plankton feeds the fish and the nutrients become part of the cycles in the sea, but they won't return to the land. If only a small percentage of the nutrients is lost, like 10%, it could mean that the equivalent of one or two animals is lost for each one raised. As one can see, the task of retaining nutrients, while reducing their losses, is not trivial.
Recycling on the farmLet's follow what happens in the soil in more detail. When a grazing animal urinates, the soil where it lands, changes almost immediately, to start the conversion processes needed to turn urine into nitrate fertiliser. It is a three step process, in which first the urine is broken into ammonia fragments, then oxygenated to nitrite and nitrate. For each step a different microbe (bacterium) is required. The last step cannot be done before the one before it and so on. But something else happens as well - time delay. A sudden delivery is gradually spread out into a slow release of fertiliser, at the rate that plants can use.

If an animal urinated pure nitrate (which animals can't do), the rather sudden delivery would be too fast for plants to absorb. The process of making plant matter from nutrients, water and carbon dioxide is a rather slow and lengthy one, requiring plenty of water and sunlight. In the meantime, the highly soluble nutrients would wash away. Instead, after delivery, the urine is first soaked up by the pores in the soil, swelling the slime that is left there by bacteria and slithering organisms. Then the first army of bacteria arrives, not because it lay there dormant or by marching to the spot, but because bacteria can multiply so quickly. They are the hard workers in any ecosystem.

Because bacteria are so small, having no internal organs, but a primitive cell structure (prokaryote), they can reproduce faster than any of the cells with a more complicated structure (eukaryotes). And while not wasting any energy on moving or pumping body fluids around within themselves, they are capable of metabolising thousands of times more rapidly than higher organisms. That makes them the living chemical factories of the world, the most important organisms on Earth, without whom life on the planet could not exist. But they have needs too.

In order to be able to live, bacteria need water and energy (like animals, they are heterotrophs). The soil must stay moist. A soil that dries up, kills or stunts its soil biota, an effect far worse than the loss of water that caused it. Bacteria need energy, lots of it because they work so fast. Living underground, sunlight is not an option. The energy must come from eating other organisms, or carbohydrates freely available in the soil. Often they live in associations of many diverse bacteria, each providing what the other needs.

While converting urine to nitrates, the substance becomes part of a bacterium's body and is not easily washed out, until it has been processed and released for the next step.

What happens to the more solid wastes, the dung, is far more complicated than described above, requiring many different kinds of bacteria, fungi and soil organisms. But the ecological principles remain similar: waste is absorbed into the pores of the soil, and its chemical constituents in the bodies of soil organisms, and it is processed such, that nutrients are released slowly enough to be absorbed and used by plants. Without a healthy soil, full of soil organisms, a soil loses its fertility very rapidly.

Slush and symbiotic decomposition
In 2005, the author of this web site, Dr J Floor Anthoni discovered that something very important had been overlooked in understanding the role of decomposers in ecosystems. Decomposers are all heterotrophs, deriving the energy for living entirely from the solar energy stored in the chemical bonds of biomolecules. Scientists made the mistake thinking that this could happen without any friction, as in a perpetuum mobilae - movement without friction. But the second law of thermodynamics insists that there are conversion losses when converting chemical energy to other forms of energy, and also bacteria must spend energy living, growing and reproducing. The short of it is that decomposition CANNOT complete and an intermediate substance remains, that Dr Anthoni named slush (as in incompletely molten snow).
Slush is a short biomolecule that is neither food for decomposers, nor nutrients for plants. It is a harmless and useless molecule. The world would be awash in slush if there were no way of using it. Here is where symbiotic decomposition comes in. If plants donate a little bit of high energy food (like sugar) to the bacteria, they can overcome the energy conversion deficit, and decomposition can complete. Thus plant and bacteria working together, can tap the resource of slush. Without this co-operation, most life would not be possible on this planet.
The discovery of slush and symbiotic decomposition as an essential part of any ecosystem is thus an important discovery if it weren't for the fact that this should have been predicted over a century ago, based on elementary laws of physics. For now it will be remembered as one of the sorriest bloopers of contemporary science.
Read more about this in the chapter of the Dark Decay Assay (DDA): www.seafriends.org.nz/dda/

External cycles
water cycleWater
The water cycle is the largest of all. With an average of 1m of rainfall each year, the sheer mass transported this way is beyond imagination. The diagram shows how water flows between atmosphere, land and ocean. Most water evaporates from the ocean, while a large part also rains back into it. Most of what rains on the land is evaporated back into the atmosphere or is respired by plants in the process of photosynthesis. Only a small part returns to the sea by river. 

Various nutrient sourcesNourishment
In many places on Earth, the fertility of the soil is renourished from the cauldron of minerals under the crust, during volcanic eruptions. Apart from the laval flows which are strictly local, a volcano can belch ash clouds tens of km into the atmosphere, accompanied by loads of sulphur, nitrogen and phosphorus compounds. These rain out of the atmosphere over months, fertilising soils sometimes half a globe away. Although such events are sporadic, their influence is nonetheless noticeable.

Locally, down-hill soils can be renourished from nutrient losses up-hill, resulting in fertile river valleys, flood plains and deltas. Flooded valleys by the sea once harboured rich estuarine life, buried under layers of sediment. As the sea retreated, the flooded valleys became fertile and easily workable cropland. With the rhythm of the ice ages, such processes repeated themselves.

Where seas are rich in plankton, sustaining high densities of sea life, sea birds cycle nutrients, particularly nitrates and phosphates from the sea to the places where they roost. Resulting in dense deposits of the coveted guano fertiliser, now becoming a threatened resource.

The carbon cycle was shown in the first picture on this page, and more of it will be discussed in the section on global problems and global warming.

The plankton itself also plays an important role in recycling nutrients back onto the land. In the late 70s it was discovered by scientist James Lovelock, that sulphur is generated by some phytoplankton organisms as dimethyl sulfide (CH3.S.CH3), a gas easily diffused out of the ocean's waters. In the atmosphere, this gas, because of its polarity and similarity to the water molecule (H.O.H), attracts water vapour and encourages it to condensate around a nucleus of only one molecule dimethyl sulfide. This property makes it one of the most potent cloud-forming agents known, playing an important role in both the water cycle and the sulfur cycle. Dimethyl sulfide rained onto soil, is easily incorporated into the soil structure.
Because plankton has been shown to affect cloud formation and thus Earth's albedo (reflectance), it is thought that it plays an important role in the temperature regulation of the planet and a strong counteractive force against global warming. This will be discussed in more detail in the section on global warming. Other such cycles may exist for micro nutrients.

As we have seen in the chapter on soil formation, the macronutrient (important nutrient) nitrogen is in short supply in the rocks and minerals of Earth's crust, but it is the main component of the atmosphere (79%). Here it is found as the very stable gas molecule (N2), which is not easily broken apart. In the upper atmosphere it can be separated into (N+.N+) radicals by ultraviolet radiation,  immediately combining with oxygen into various nitric oxides (2NO, NO, NO2), and later with water to form the fertile nitric acid (3NO2 + 3H2O = 2HNO3 + NO). These compounds are also formed inside rain clouds by the high energy discharges of lightning.

In 1914 the Nobel prize winning German scientists Fritz Haber and Carl Bosch invented an industrial nitrogen fixation process by which pure nitrogen and hydrogen are combined to form ammonia (NH4) from methane (CH4), while using fossil fuel as energy source. Some of the ammonia is reacted with carbon dioxide to produce urea, a slow-release fertiliser. The remaining ammonia is converted to ammonium nitrate (NH3.NO3), a very powerful quick-release fertiliser. Because of the low cost of fossil fuel, these new artificial fertilisers have powered the green revolution, together with high yield cultivars. (See the chapter soil/fertility)

No plant or animal is capable of fixing nitrogen, but some bacteria do. Where soil is healthy and moist, bacteria can be found that produce nitrogenous fertiliser from atmospheric nitrogen. In rice paddies, associated with a small water fern (Azolla), live nitrogen-fixing cyanobacteria that make paddies about ten times more productive than common soil (both by repetitive cycling and by increased nitrogen levels). In lakes, estuaries and oceans, live blue-green algae (these are bacteria) capable of fixing nitrogen with solar energy. In the roots of legumes (peas, beans) live nitrogen-fixing bacteria (Rhizobium) that convert nitrogen to ammonia (2N2 + 6H2O = 4NH3 + 3O2), using the plant's sugars as energy. Some of the ammonia is used by the plant to assimilate amino acids, the building blocks of protein (example for glycine: 2NH3 + 2H2O + 4CO2 = 2CH2.NH2.COOH + 3O2).

Here are some of the nitrogen processes, their chemical reactions and associated organisms.

Process Chemical reaction Energy
Fixation 2N2 + 6H2O = 4NH3 + 3O2 in Rhizobium, Azobacter, 
Gloeocapsa, Plectonema
Amino acid synth 2NH3 + 2H2O + 4CO2 = 2CH2.NH2.COOH + 3O2 in Many bacteria and others
Nitrification 2NH4+ + 3O2 = 2NO2- + 4H+ + 2H2O out Nitrosomonas
Nitrification 2NO2- + O2 = 2NO3- out Nitrobacter
Denitrification 4NO3- + 2H2O = 2N2 + 5 O2 + 4OH- out Pseudomonas
Denitrification 5S + 6KNO3 + 2CaCO3 = 3K2SO4 + 2CO2 + 3N2 out Thiobacillus denitrificans
Denitrification C6H12O6 + 6NO3- = 6CO2 + 3H2O + 6OH- + 3N2.0 out Many. N2O is a very potent greenhouse gas, 280 times more potent than CO2.

Primary production
primary productionPlants produce plant matter from soil nutrients, water and carbon dioxide, using the energy of light. It is called primary production. The diagram shows the carbon flows (is equal to energy flows). At left one sees a plant receiving light and CO2 from the air and returning oxygen. At night, when there is no sunlight, plants respire like animals do, taking up oxygen and returning CO2. Surprisingly, a large proportion of a plant's primary production (50%) disappears underground, where it grows the root system and feeds soil organisms. Only 50% is used for above-ground growth. Of this, between 10 and 40% is used for growing, depending on plant type, age and kind of harvesting. If the plant is grazed regularly, the grown biomass will be grazed, amounting to no more than 40%. The remaining 10% is lost by leaf drop. This leaf litter is decomposed by fungi and bacteria, contributing energy to the soil biota, while returning nutrients to the plant.

It is remarkable that plants sacrifice so much of their primary production to the soil organisms, but it is the only way these will be able to obtain the energy needed to do the many tasks required of them, including the maintenance and growth of a deep, porous soil. It is part of a mutually benefiting system that evolved over eons of time, a system that is easily disrupted and destroyed by farming.

At this point it can be seen that the productive soils of the world are in desperate need of a source of energy, the carbon in plant litter. It comes as no surprise then that 'green-finger' gardeners apply copious amounts of compost to their soils in order to get results. Farmers are often not aware that the soil needs so much green manure. One of the effects of overgrazing is that not enough organic matter in the form of decayed leaves, returns to the soil. The soil organisms starve and cannot deliver their services. The top soil diminishes. Nutrients are lost and washed out. The soil is bared through lack of cover. The soil dries out. Soil organisms diminish further, and so on. It is a certain path to soil degradation that cannot be reversed after the point of no return. Then the soil becomes similar to that found in deserts.
soil degradationThe picture shows four scenarios that lie on the path of soil degradation. The figures show the amount of life, measured as kg carbon per square metre. At the bottom, a conceptual graph is shown of the fertility of the land and how it degrades. Most fertile agricultural soils were once fertile forests. In such forests, the amount of carbon in stems and foliage is 15 kg/m2 and the soil and leaf litter account for 10 kg/m2. The soil carbon is found in the dark brown A and O horizons. Immediately after clear felling, burning and resowing, the situation above ground changes, but the soil itself not as much. At the cost of losing 14 kg carbon per square metre into the air, the soil remains highly productive. But grassland is not the same as forest and the soil degrades, as shown above, from lack of carbon inputs.

After another ten years, five more units of carbon are lost, most from the soil which is adapting to the new situation. If at this point the soil is fertilised, enough wastes and foliage can be generated to maintain it. Without fertiliser, pasture becomes less productive and cattle is eventually replaced by sheep. After some 50 years, the point of no return is reached, when fertiliser application is no longer able to raise productivity. By 100 years, the soil has lost its structure, having been eroded to its bedrock. Many of our hill pastures have reached the point of no return, because soil degrades faster where it is steeper. At the point of no return, it is still possible to plant trees, which will not be possible at stage four.

It is important to note that soil fertilisation is an important weapon in retaining soil and preventing its loss. Indeed, the first course of action to fight erosion, is a generous application of fertiliser. This is not only cheaper than any other method, but works immediately and is the most effective course of action. See the chapter soil/erosion for more detail and other solutions. Also see rock&soil/carbon to compare productivity, carbon storage above ground and underground for various terrestrial ecosystems.
catabolic processesAs we have seen, the breaking-down function of soil (catabolic process) is its most important one, but it requires time. The summary shows a few important points.
The carbon returned by plants to the soil comes in various classes. Most voluminous and amounting to nearly 40% of a plant's primary production, goes into hair roots, which can be eaten or broken down in a matter of days. Coarse roots take years and whole stems and branches decades. Each has its place and purpose and benefits. Where leaf litter cannot be buried by soil organisms, decomposition is about 5 times slower.

Underground organisms, all need a carbon source and oxygen to live. Oxygen penetrates the soil through the many tunnels of soil-burrowing organisms, of which the earth worm is very important. Where soils are waterlogged, such as in marshes, swamps and bogs, soil organisms die and organic matter accumulates, often creating an acidic environment. It is interesting to note that in cold climates, soil organisms slow down in winter to such an extent that they require hardly any oxygen. The suffocating snow cover and winter rains won't harm them in this state, and as soon as spring arrives, they can resume their tasks undiminishedly.

Decomposition rates also depend on temperature. The comparative figures show 50 years for mountain pine, 4 years for temperate pine, 2 years for deciduous maple forest, a quarter year for tropical rain forest.

An important point to mention here is that decomposition also depends on the amount of oxygen supplied. When a farmer ploughs his land, the soil suddenly becomes intensely exposed to oxygen, causing the soil organisms to do their work so fast, that valuable organic humus is 'burned' by them, resulting in poorer soils. Humus is organic matter in the form of humic acids, fats, resins, waxes, cellulose and more, that covers each and every soil particle, colouring the A horizon deep brown or black. It contributes to a loose, friable and porous soil structure. Solutions to this problem are to plough less (reduced tilling), to leave stubble and plant litter on the field through winter and to plough in the beginning of spring, when soil organisms are still inhibited by the cold, and to return more plant litter to the soil.

Autotrophic and catabolic processes
energy process chemical reaction energy 
hydrogen sulphide oxydation:
1) H2S oxidation
2) S oxidation
3) carbohydrate synthesis
2H2S + O2 = 2H2O + 2S + 527 kJ
3O2 + 2S + 2H2O = 2SO4 + 4H + 410 kJ
6H2 + 2O2 + CO2 + energy = (CH2O) + 5H2O
410 kJ
autotroph blue-green algae, Beggiatoa.
photosynthesis 6CO2 + 6H2O + light energy = 6(CH2O) + 6O2 in
2816 kJ
all plants with chlorophyll
combustion 6(CH2O) + 6O2 = 6H20 + 6CO2 + 2816 kJ out
2816 kJ
all animals
decomposition 2(CH2O) = CH4 + CO2
2(CH2O) + O2 = 2CO + 2 H2O
2CH4 + 3O2 = 2CO + 4H2O
2CO + O2 = 2CO2
out various decomposition paths, producing methane and carbon monoxide, carbon dioxide and oxide
fermentation C6H12O6 = 2(C2H5OH) + 2CO2 + 75 kJ out
75 kJ

Soil biota
The soil is a most amazing and largely undiscovered realm with over 2 million species. Although it forms part of the terrestrial ecosystems, it is nonetheless an entirely separate environment, not or hardly mixing with any of the other, the terrestrial, fresh water and oceanic realms. Soil species are biologically very varied because they cannot travel easily. Rivers, lakes, mountains and seas form impassable barriers, leading to intensive variation and specialisation. In a small country like New Zealand, for instance, over 280 indigenous earth worms are found that occur nowhere else.

The zone of the soil where by far most of its species live, the A horizon, is no more than a foot deep (0.3m), covering only part of the land. Some soil organisms have been discovered in sedimental rock, to depths where temperature kills ordinary organisms. Indeed, the fossil oil and natural gas we consume so prodigiously, may have been formed by such micro-organisms.
soil biota - groupsThe picture contains text only, challenging your imagination. All groups shown are consumers, deriving their energy from the breaking down of organic matter. They also eat one another. The weights shown are dry matter per square metre and are typical, but large variations occur. Surprisingly, the farm stock represents only 50g, with earth worms in the same league and fungi far outweighing it.
Although the soil biota receive a large part of the plant's primary production, and also the droppings from grazers and finally their bodies as well when these die, their collective biomass is surprisingly high. In natural ecosystems, soil biomass often exceeds that of the vegetation above. How is this possible, since the soil organisms cannot make food themselves, relying entirely on what the plants provide? Normally one would expect the biomass of consumers to be 5-15% of the plant biomass on which they graze. 
The answer to this enigma must be found in the way they differ from land animals:

In the above slide, the groups of organisms have been arranged by size, the smallest on top. The smaller an organism, the higher their numbers and the faster they reproduce. Surprisingly, viruses are shown. These are not important in the animal and plant world, where they cause disease, but in the soil they play a critical role. By infecting and killing bacteria, they contribute to the cycling of edible, even absorbable, organic matter. Their volume is very small, for they do not posses the skin and machinery of a living cell.

Bacteria are probably the most important group. They are the chemical factories that convert one substance into another. Associations of many species group together, each doing what it does best. Their mass of 50g, equivalent to the grazing stock, is astounding for they can metabolise and grow thousands of times faster than sheep. Because bacteria multiply so fast, they can respond quickly to varying circumstances, making it seem as if the soil behaves like a single organism. Bacteria are recognisable by the slime they produce, a substance that is beneficial to soil by preventing dissolved nutrients from leaching away.
Sometimes a film of blue-green algae is found on the surface of the soil where light is available. Near roots and often inside root nodules, living symbiontically with them, one finds cyanobacteria capable of fixing nitrogen. The ones living inside the roots derive their energy direct from the plant's sugars and are therefore the most efficient. But nitrogen fixation can occur throughout the soil by other cyanobacteria. In the guts of all higher soil organisms like nematodes, worms and arthropods, decomposing bacteria are found, including bacteria capable of breaking down persistent woody matter like lignin and cellulose.

The fungi are more advanced than bacteria (eukaryotes) but still primitively single-celled, although having multiple nuclei. By extending their cells as thin, long threads (hypha) that enlarge their surface area considerably without enlarging their mass, they are able to absorb substances efficiently. They do so by secreting decomposing enzymes outside their bodies and absorbing the decomposed products through their cell walls. Their long hypha act as nutrient highways through the soil. Fungi are capable of storing soil nutrients, an important factor in soil fertility.

Amoeba are single-celled animals capable of moving around in liquids. They prey on bacteria and fungi and form food for the larger animals. They are found in permanent or semi-permanent pools and puddles.

common soil animals
(Drawings adapted from H Pauline McColl: An illustrated guide to common soil animals. DSIR, 1981)

Nematodes are tiny round worms, which are quite mobile. They hunt amoeba, attack roots and eat fungi.

The arthropods are insect or spider like, eating all of the organisms above. Many species occur, but those living entirely in the soil are the tardigrades, collembolas, mites, hoppers and slaters Their functions are not sufficiently known.

Earth worms have been proved to be very beneficial to soil. They drill tunnels, aerating the soil for all other organisms and making it capable of absorbing heavy rain. They eat soil and leaf litter. They rotate the soil in the A-horizon, such that leaf litter and other materials become buried, eventually migrating slowly to the base of the A-horizon. They can be found even in deeper horizons.
soil biota by sizeThis diagram classifies soil organisms by size, covering a range of five decades! Organisms are classified by body width, which is relevant because many are worm-shaped, and their widths are more important than their lengths. As is generally the case in ecosystems, larger organisms eat smaller ones, because these form no risk to their health (can't defend themselves) and are bite-sized. The background colours divide this world up by size in micro- (small), meso- (middle) and macro- (large) fauna. D C Coleman & D A Crossley in 'Fundamentals of soil ecology, 1996, assign functions and influence on nutrient cycling and soil structure to these groups in the following ways:

Nutrient cycling Soil strucure
(bacteria + fungi)
Catabolise organic matter. Mineralise and immobilise nutrients. Produce organic compounds that bind aggregates. Hyphae entangle particles onto aggregates.
microfauna Regulate bacterial and fungal populations. Alter nutrient turnover. May affect aggregate structure through interactions with microflora.
mesofauna Regulate fungal and microfaunal populations. Alter nutrient turnover. Fragment plant residues. Produce fecal pellets. Create biopores. Promote humification.
macrofauna Fragment plant residues. Stimulate microbial activity. Mix organic and mineral particles. Redistribute organic matter and microorganisms. Create biopores. Promote humification. Produce fecal pellets.

Soil functioning
soil aggregationThe amazingly fine structure of healthy soil and how it works, is revealed by this drawing, containing five successive enlargements, from a 2mm soil crumb to a square of 0.2µm. It is remarkable how much pore space with air and liquid is found, not only between crumbs (peds) but also inside them. In a ten times enlargement (second image), fine hair roots (yellow) easily penetrate the loose soil particles and so do the hypha of fungi (purple). Most action happens where the three meet (picture 3).

Picture three shows part of a soil particle, with the hypha surrounded by bacteria and bacterial debris (both organic and inorganic, and slime). Compared to bacteria (green), a hypha is rather large, but its enzymes extend outside, mixing with bacterial debris composed from decayed bacteria and their food and wastes, while also interacting with the bacteria. On this scale, the hypha obtains its food. 

Picture four shows in detail the microbial and fungal debris encrusted with inorganic and persistent organic material (humus). Around these particles, one finds the clay platelets, shown in detail in the last picture. These platelets are charged, binding and holding inorganic nutrients (mainly cations K+, Ca+ and so on), organic polymers and other substances. Because of these bonds, nutrients are not easily leached out, but plants can't easily sequester them either, partly also because their smallest roots (hair roots) are far too big on this scale. Persistent humus exerts even stronger bonds on both cations and anions.

In the environment of picture three, the interaction between humus, clay platelets, bacteria and hypha, the acidity is high, enabling bacteria to draw nutrients from the clay and humus particles. Hypha then transport these towards the hair roots. Without an army of bacteria and fungi, a soil appears infertile, reason why it is important to manage it with care.
soil activity - the drilosphereChemical decomposing activity can be found throughout the soil, but it is most active in five special areas. They are the arenas where activity concentrates.
The drilosphere is the workplace of earth worms. As can be seen from the top right drawing, worms leave a funnel-shaped business end on top of previous funnels. Earth is cast on top and to the side, covering leaf litter in a loose fashion. In the oxygen-rich moisture, other organisms find shelter or actively take part in some of the process. Rainwater dissolves nitrates, DOC (Dissolved Organic Carbon) and transports it down the worm hole.
The detritusphere works where leaf litter is moist and rich in oxygen. Here fungi can work efficiently, decomposing cellulose while taking oxygen in and respirating carbon dioxide. Inside anoxic corners of leaf structure, bacteria convert nitric oxides to nitrogen.

porosphere, aggregatusphere, rhizosphereWhere masses of young roots are found, activity is high in the porosphere of the soil. Pores are necessary to hold water and to transport oxygen and carbon dioxide. Aggregates of soil are pierced by hair roots (yellow) and covered in hyphae of fungi (purple). By the transport channels from worms and other organisms, water, nitrates, phosphorus and dissolved organic carbon compounds leach from the top down.
In the aggregatusphere, sand and clay particles form enclosed workshops for bacteria. Many chemical processes happen here, producing nitrates (NO3-), ammonia (NH4+), carbon dioxide (CO2), nitric oxides and more. Many compounds are transported by the fine hyphae to other places.

The rhizosphere is the area directly around hair roots. This is a special place because hair roots bring food and oxygen, enabling the micro organisms to work faster than anywhere else. A continuous flow of water is caused, as water is absorbed by these roots, drawing with it dissolved substances. As these hair roots grow, they intrude into other aggregatuspheres, find nutrients, get eaten, and other fine roots take their place. The soil is in a continuous state of decomposition, provided moisture and oxygen are available.

Reader, please note that in the above drawings, false colours have been used to identify the various objects. In reality, all look brownish to whitish and hyphae are not purple; roots not yellow. Note also that the precise interaction of soil organisms is a field of recent study, which will take many decades to evolve. However, what is known today will already be of enormous benefit towards farming sustainably.

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