Soil Biodiversity

Soil Life - Who Lives Where?

Here we'll get to know what soil biodiversity is, which organisms we find in soil, how many of them there are, and where they live? Let’s first take a look at a living soil and try to see as many different organisms as possible.

Where:

So, what did you see here? From the top to the bottom of the profile we see fresh litter, partly degraded litter and mineral soil. Now where do we see the soil biota? I am sure you spotted these, the worms. The big ones are earthworms and the much smaller ones, white in color, are potworms, also called enchytraeids. They have no legs! In the soil there are even smaller worms that you can only see with a microscope.Those are nematodes. Did you see more soil animals? Walking around with legs? Like this one This is an isopod. And perhaps you also noticed small dots moving around on the leaves. These are tiny soil fauna, barely visible to the naked eye,  but here is an enlarged picture these are springtails and mites . Did you also see the growth of the white threads on and between leaves?These are hypha of fungi growing on and in the leaves. They are  also living organisms and use the nutrients in the leaves for growing their hypha. The smallest organisms in picture, that were also feeding on the leaves, are bacteria. You could not see them because they are too small for observation with the human eye.

What:

What do we really mean by soil biodiversity? Soil biodiversity refers to all the life in soil. That comprises both the organisms we can see and those that are too small to be seen by the naked eye. If you use a microscope you can also see the smallest ones. What are examples of the large, macroscopic organisms, that are visible to the human eye? Indeed animals without legs like earthworms and potworms and animals with legs like isopods, but also millipedes and centipedes all belong to the group of ‘large organisms’ in the soil. The microorganisms comprise bacteria and fungi and also small animals like nematodes which are little roundworms.

How Many:

But how diverse is this soil life?

If we now take a look below ground, how much diversity do we find in one square meter of a grassland?

To really answer this question, it is very useful to look at the different groups of soil organisms according to their body widths. From top to bottom we have the larger to the smaller sized soil organisms. Looking at the number of individuals we can find per meter square of soil this way,

we see, for just the top layer of soil alone, about 100 earthworms, about 1000-10 --> 000 spring tails and mites, 10 --> 000-100 000 nematodes and 50 km of fungal hypha along with an immense amount of bacteria. Now if we look at the number of different species, or the diversity, we can see the smaller the organisms the more different species there are, ranging from 10 species of earthworms to thousands of species of bacteria and fungi.

Clearly soil life is very diverse indeed! Finally, Let’s take a look into the soil to see where we can find all this soil life.

In this drawing we basically see 1 square centimetre of soil and we can see big irregular structures which are mineral particles such as this one. In between the solid particles we have spaces filled with air, where small soil fauna with legs crawl around. Depending on the size of the pore, larger or smaller fauna fit in. In the pores there is also water. Depending on how much it has rained recently or how much the soil was irrigated, the pores can be totally or partially filled with water. Typically we would find at least a water film around the soil mineral and organic particles. And that’s where soil organisms without legs live and move around like this nematode and this ciliate. So you can see that the soil and the structure of the soil provide a home for many different soil organisms. Now that you know where they live, you may not be surprised that soil life is sensitive to what we people and nature do to the soil. Soil life is sensitive to disturbance and compaction of soil, because that affects the amount of space and air available for plant roots and other soil biota. It is also sensitive to chemicals that end up in the soil water or pollution like oil spills that block the access to food, air and water.

Biological Soil Processes and Functions:

Did you know: soils provide a habitat for a quarter of the world’s total biodiversity! That in itself is already a function - harbouring so much biodiversity. But why should you care? All the soil organisms together carry out a range of processes that are important for the functioning of the soil and both in natural and agricultural ecosystems.

Soil life thus provides important services to humans. You may know that the soil food web is essential for recycling nutrients and carbon locked up in plant residues or animal manure. But there is more. For example, many soil organisms also contribute to the formation of soil structure, and that is very important for soil functioning. Plant roots and other organisms need a structure soil because the spaces between the solid soil particles determine the availability of air and water. Soil biota that eat plant pests and diseases are very helpful to us as they provide biological control of pests and diseases.

Plant roots and their interactions with certain soil micro-organisms also provide key functions. They regulate the uptake of nutrients from the soil and thereby the supply of nutrients for plants to grow.

The degradation of pollutants in soil by microbes, that is called bioremediation. And, soil biodiversity as an important source of medicine! That is a very important function which many people are not aware of. Scientists observed that microbes in soil produce different compounds to fight other micro-organisms and those compounds are a continuous source of novel antibiotics. Now you may wonder: who are these hidden heroes and how do they do what they do? Let’s find out. The functions that soil organisms provide in the soil depend on

1) their body size.

2) where they live in the soil.

3) what they feed on.

4) their mobility.

Bacteria and fungi are the primary decomposers. They control the flow of carbon and nutrients through the decomposition of organic matter. The microfauna make up a small proportion of the total soil biomass, but they have a key role in the mineralization of nutrients through their feeding on bacteria and fungi. Their mobility is very limited because they are so small. The mesofauna feed on microbes and other soil animals, and some feed on litter. Their feeding releases nutrients and regulates pests and diseases. They have some ability to burrow through soil but if you want mobile soil fauna you better take a look at the soil macrofauna. The macrofauna are mobile, they either live and feed in the litter layer, or dig down to seek food and protection in the mineral soil layer.

Species that feed on plant litter, the detritivores, are important for the fragmentation and decomposition of organic residues is attributed to them. We call them ‘litter transformers’.

The carnivores among the macrofauna can be important for biological pest regulation, for example predatory ants and beetles. The most abundant groups, however, are the termites, the ants and earthworms. They are famous for their role in soil formation and bioturbation.

We call them the soil ecosystem engineers. Now what makes them so special? Well, they physically rework the soil making changes to its abiotic and biotic state. This means that they produce physical structures by which they create and modify habitats for themselves and for other soil organisms.

Doing this they modify the availability or accessibility of resources. Ecosystem engineers also increase habitat diversity in soils which can in turn increase the diversity of the soil communities.

Want some examples? OK - first the termites! Termites are a diverse group of social insects. They live in tropical and subtropical soils and can translocate large amounts of plant residues and soil, which they transport to their nests or mounds. Their networks enhance soil porosity and increases water infiltration. This species of termites grows its own food. Like we have an allotment they have fungal gardens. The special fungi help the termites to digest recalcitrant, or hard to degrade plant materials and provide a nutritious food.

The other important group of engineers, known in temperate and humid tropical regions, are the earthworms. They may look rather slow and inactive, but is that true? Earthworms live on plant residues in different stages of decomposition. Indeed, the earthworms incorporated the litter into the soil. At the same time something is happening to the soil too, as they burrow through it. Yes, the earthworms mix the soil. That process of mixing soil by living organisms, we call bioturbation.

We have seen that soil organisms, small and large, participate in different processes that are essential to the functioning of soils and ecosystems. These include: recycling of organic residues and carbon, nutrient cycling, soil structure formation, biological regulation for ecosystem stability and pest and disease control. A special group are the ecosystem engineers. They have the ability to physically modify the soil habitat and resource availability for soil biota through abiotic and biotic changes.

The soil below our feet is a factory with heroes at work! – to keep soil fit for life!

Threats to Soil Biodiversity and Their Effects:

Soil life is alive so, just like you and me, it needs: air, water and food. All in the right proportion.

Any idea of what these proportions might be?

Well, in a healthy soil we have: 45% of the volume made up of mineral particles and then 25% of the volume is filled with water. The water forms films around the solid particles and fills soil pores in part or completely. The pores that are not filled with water contain air. In a healthy soil the proportion of air is about 25% as well. Together that makes 95% of the volume. The last component is organic matter, and even though it’s a small percentage of the whole volume, it is very important to healthy soil. We typically have 5% organic matter, in orange on the drawing. This percentage of about 5% of the volume holds for arable soil; in grassland soils and especially in peatlands the percentage of organic matter is much higher. Now that we know what soil life needs it’s not very difficult to think of threats. Let’s start with water. What can happen with water? Indeed we can have too much or too little!

When there is too much water we have saturation and as a result there is too little air left in the soil for the organisms to breath. Also when there is more rain than the soil can absorb the water will runoff and can end up taking soil and organic matter with it, we call that erosion. This threatens the whole living environment for our soil biodiversity.

Now when there is too little water for a prolonged period, what happens then?

The organisms dry out. As you can imagine, the species that live in the water phase are more sensitive to drought than the species that live in the air phase. Of course plants will wilt too. Water quality in the soil is also important, and pollution of that water also threatens soil biodiversity. For example, when the soil water becomes too salty, through what is called soil salinization. This is often the result of irrigation with high salt content water in arid areas. Plants take up part of the water and another part evaporates from the soil, but the salt stays behind. When the soil water or solution get too salty, plants cannot grow well and soil life will also be much reduced. Want to know why? Think about pickled food. Not much can grow on pickled food and also not in saline soils because salt disrupts the cells of organisms. But there’s more than salt that threatens soil biota via soil water.

Chemicals that kill soil biota can come in different forms and from different sources. For example: pesticides, use of too many nutrients, heavy metals, and oil spills. Oil may not be directly toxic but it covers soil particles and soil organisms and blocks water, air and food access. So, many organisms will die after some time. Interestingly some soil micro-organisms can help to clean up the soil contaminants. Places with high levels of pollutants are waste dumps and mining sites. Now from water we move to air. What could a threat be there?

Indeed, not having enough air! an extreme cause of insufficient air is soil sealing. The soil is covered by asphalt or concrete and air cannot be exchanged. We see a lot of soil sealing in road infrastructures and also in cities. A less drastic, but still very serious cause of reduced soil air availability is compaction. Think of heavy machines driving on soil, like this tractor. What happens? The weight of the machine presses on the soil. And the soil that was first this volume now fits in a smaller soil volume - because as it was compressed the air spaces were reduced. And it is not just machinery that can do this, livestock can also cause soil compaction - especially if they are at high stocking density.

Now let's take a closer look at what compaction means for soil life.

On the left is a non-compacted soil and on the right a compacted soil. Do you see the main difference? Yes, more pore space in the non-compacted soil – and less space with soil compaction. That means space and air for the soil biota, of all sizes in the non-compacted soil – and less soil biota and only small-sized biota in soil with compaction. Perhaps you guessed, there is more to it than just air and space. Both soil sealing and compaction have an impact on soil water too. Water flows more easily through open, non-compacted soil, while in sealed or compacted soil it stays on the soil surface. With good water regulation in soil, the soil biota are happy and that also shows aboveground with fruiting bodies of fungi and plant growth. However, when water cannot get into the soil, which can happen from soil sealing, compaction or reduced wettability, the life and function of soil biota come under threat. That brings me to our third and last major need for soil life: food! The food for soil life is directly or indirectly derived from plants. As plants die, the litter falls on the soil.

And root exudates and dead roots collect in the soil, and together they form a pool of carbohydrates and nutrients for the soil biota to feed on. But, just like you and me, they do not turn all the food into new biomass. They also excrete part of it as mineral nutrients. And that again is food for the plants, what a great collaboration! Apart from plant inputs other organic matter is often added to soil to ‘feed’ the soil, for example, compost and manure and that can be added as either green manure or brown manure. Now, organic matter that is added or left in the soil doesn’t only serve as food for soil biota, it is also important for soil water because soil organic matter acts like a sponge, it can absorb a lot of water so the soil does not dry out as fast.

Now you know where food for the soil biota comes from, what do you think could be food related threats?

Indeed - not having enough food! And the main cause of that is: Loss of vegetation cover, like through deforestation or slash and burn management in which vegetation is cut and burned to make space for agricultural land. Also overgrazing is a serious threat in this regard, like we see in the picture. Vegetation can only support a limited number of grazers if the plants are to regrow. If vegetation is overgrazed the plants will not be able to regrow and may even completely disappear. This results in bare soil and desertification. Having vegetation on and in soil is not only essential for soil life, a bare soil also has a high risk of erosion and drought, which we have already discovered: those are also other threats to soil biodiversity.

Prevention and Remediation:

Globally many soils are being degraded due to human activity, to a degree ranging from low to very severe. According to the FAO, 33% of the soils globally are in a degraded state. As a result, soil biota diversity and abundance are reduced and the functions they generate are impaired. Part of this is because they are deprived of the water, air and nutrients or food that they need. So what can we do to counteract that?

Prevention! The restoration of soil and biodiversity requires much more time and effort than the rate at which soils degrade, so protecting healthy soils from becoming degraded is much better. How do we do that?

By doing some things and not doing some other things, for example do manage soil nutrients wisely.

Well, we need to compensate the nutrients that are extracted with the harvest, yet we should not overload the soil with nutrients. So wisely means aiming for a balance of outputs and inputs. Otherwise a nutrient overload acts as a pollutant. Another smart thing to do to feed the soil biota and indirectly the plants is returning organic matter to soil. In contrast to mineral fertilizers, organic matter is composed of carbon compounds and nutrients in organic form. Part of this diverse blend of compounds is eaten and mineralised by the soil life and the other part becomes soil organic matter in more stable forms.

The soil organic matter is important for soil water, nutrient and carbon retention in the soil, all of which are important for soil biota as well as other things.

What else can we do?

Do promote crop rotation and keep soil surfaces vegetated. The vegetation not only provides food for the soil biota, it also helps to prevent or at least reduce soil erosion. Of course at some point, you may want to change your crop. And to do so you will need to rework your soil a bit.

How would you do that on a hilly slope like in the picture and still prevent the soil from getting eroded?

By using a practice called contour farming. This is working the soil in line with the slope but across the slope. Another very useful thing to do to conserve soil, the life in it and crop growth in hilly places is terracing, creating horizontal platforms to keep the soil and soil life in place. And now some other things we need to avoid to keep the soil healthy and prevent threats to soil life. Soil compaction, for example by using designated driving paths and sparing the rest of the soil, also soil salinization should be avoided by practicing good irrigation and drainage management; and loss of soil wettability by monitoring it and managing it. Keeping the soil surface covered with mulch can help with several of these goals and also provide food for the soil biota. And of course we want to avoid pollution as much as possible. So that’s prevention. But what if the soil is already in a degraded state, what to do then?

Now we are talking about remediation. In the case of pollution the source of pollution needs to be removed, and to do that it is important to know what the pollutants are. In case of organic pollutants, sanitation by bioremediation can be a good option. Especially bacteria and fungi can help, if you have the right species, they can biodegrade the pollutant, which is what is going on in this picture of an oil spill being degraded by soil fungi.

Plants and plant-soil biota interactions can also help remediate polluted soils via different strategies, depending on the pollutant and plant species. We call this phytoremediation.  We can have phyto-extraction and phyto-stabilisation. With phyto-extraction, the plant takes up the pollutant which is then removed with the plant. Or when the pollutants are made less mobile via interaction with root exudates, then we have phytostabilization. Two other possibilities are phyto-degradation and phyto-stimulation. Plant species used for phyto-degradation produce enzymes that degrade the compounds in their root cells. And with phyto-stimulation the plants stimulate the soil biota to degrade the contaminants in the rhizosphere, so it is also called rhizodegradation.

What is needed to restore eroded soil so it is again a good environment for soil life?

Vegetation! Yes! But there is a major problem, we need fertile soil to grow vegetation and with erosion we usually also get nutrient depletion. A good first step is to restore the pool of organic matter in soil by adding compost, manure or crop residue, mulch, together with soil biota that will make the nutrients available through decomposition mineralization and so then, they can support plant growth and also stimulate other soil biota. Planting trees that can root deeply, stabilize the soil and get water from deep in the soil is also good for creating a healthy and stable environment for soil organisms. Cover crops to cover the soil surface and that root throughout the top soil are also valuable. But is erosion just a problem in hilly landscapes? Definitely not!

For example, in a slash and burned area the soil is very exposed and the risk of erosion by wind and water is high. It is also important to realise that after fire the soil is usually bare and often becomes water repellent, making it even more prone to erosion and nutrient depletion. In these situations, fast restoration of soil cover is warranted to reduce the risk of soil degradation. For restoration, we need several steps, and different plant species and soil biota are used depending on the limiting conditions.

Imagine your degraded soil is nitrogen poor and that is the reason for limited plant growth. Which plant species would you then choose to grow? I think you have heard of these special plants before...

Indeed, nitrogen-fixing plants! Like for example this pigeon pea. Thanks to the symbiotic associations between nitrogen fixing bacteria in the plant roots, these plants can use nitrogen from the air and bring extra nitrogen into the soil. Plant growth provides soil shading and improves water infiltration into the soil. It also adds organic matter to the soil. All together this stimulates the build-up of soil organic matter and the soil food web. In turn this facilitates the establishment of shrubs and trees which can lift water and nutrients from deeper in the soil up to the top soil. Finally, the soil biology, chemistry and physics are such that soil organisms can live and function well to support good crop growth. We have seen several key threats to soil biodiversity now, like pollution, erosion and nutrient depletion, and also some ways to prevent and remediate them. Now especially if you live in a city you may be aware of another main threat to soil life: I bet you can imagine what the issue is here. Indeed, soil sealing! To remediate that there are actually some simple solutions. Even a very small urban park could be the beginning of something bigger!