Soil

The soil is home to a large proportion of the world's biodiversity. The links between soil organisms and soil functions are observed to be incredibly complex. The interconnectedness and complexity of this soil ‘food web’ means any appraisal of soil function must necessarily take into account interactions with the living communities that exist within the soil. We know that soil organisms break down organic matter, making nutrients available for uptake by plants and other organisms. The nutrients stored in the bodies of soil organisms prevent nutrient loss by leaching. Microbial exudates act to maintain soil structure, and earthworms are important in bioturbation. However, we find that we don't understand critical aspects about how these populations function and interact. The discovery of glomalin in 1995 indicates that we lack the knowledge to correctly answer some of the most basic questions about the biogeochemical cycle in soils. We have much work ahead to gain a better understanding of how soil biological components affect us and the biosphere

In balanced soil, plants grow in an active and steady environment. The mineral content of the soil and its heartiful structure are important for their well-being, but it is the life in the earth that powers its cycles and provides its fertility. Without the activities of soil organisms, organic materials would accumulate and litter the soil surface, and there would be no food for plants. The soil biota includes:

· Mega fauna: size range - 20 mm upward, e.g. moles, rabbits, and rodents.

· macrofauna: size range - 2 to 20 mm, e.g. woodlice, earthworms, beetles, centipedes, slugs, snails, ants, and harvestmen.

· Mesofauna: size range - 100 micrometers to 2 mm, e.g. tardigrades, mites and springtails.

· Micro fauna and Microflora: size range - 1 to 100 micrometers, e.g. yeasts, bacteria (commonly actinobacteria), fungi, protozoa, roundworms, and rotifers.

Of these, bacteria and fungi play key roles in maintaining a healthy soil. They act as decomposers that break down organic materials to produce detritus and other breakdown products. Soil detritivores, like earthworms, ingest detritus and decompose it. Saprotrophs, well represented by fungi and bacteria, extract soluble nutrients from delitro. The ants (macrofaunas) help by breaking down in the same way but they also provide the motion part as they move in their armies. Also the rodents, wood-eaters help the soil to be more absorbent

Bacteria

Bacteria are single-cell organisms and the most numerous denizens of agriculture, with populations ranging from 100 million to 3 billion in a gram. They are capable of very rapid reproduction by binary fission (dividing into two) in favourable conditions. One bacterium is capable of producing 16 million more in just 24 hours. Most soil bacteria live close to plant roots and are often referred to as rhizobacteria. Bacteria live in soil water, including the film of moisture surrounding soil particles, and some are able to swim by means of flagella. The majority of the beneficial soil-dwelling bacteria need oxygen (and are thus termed aerobic bacteria), whilst those that do not require air are referred to as anaerobic, and tend to cause putrefaction of dead organic matter. Aerobic bacteria are most active in a soil that is moist (but not saturated, as this will deprive aerobic bacteria of the air that they require), and neutral soil pH, and where there is plenty of food (carbohydrates and micronutrients from organic matter) available. Hostile conditions will not completely kill bacteria; rather, the bacteria will stop growing and get into a dormant stage, and those individuals with pro-adaptive mutations may compete better in the new conditions. Some gram-positive bacteria produce spores in order to wait for more favourable circumstances, and gram-negative bacteria get into a "nonculturable" stage. Bacteria are colonized by persistent viral agents (bacteriophages) that determine gene word order in bacterial host.

From the organic gardener's point of view, the important roles that bacteria play are:

The nitrogen cycle (Turkish)

Nitrification

Nitrification is a vital part of the nitrogen cycle, wherein certain bacteria (which manufacture their own carbohydrate supply without using the process of photosynthesis) are able to transform nitrogen in the form of ammonium, which is produced by the decomposition of proteins, into nitrates, which are available to growing plants, and once again converted to proteins.

Nitrogen fixation

In another part of the cycle, the process of nitrogen fixation constantly puts additional nitrogen into biological circulation. This is carried out by free-living nitrogen-fixing bacteria in the soil or water such as Azotobacter, or by those that live in close symbiosis with leguminous plants, such as rhizobia. These bacteria form colonies in nodules they create on the roots of peas, beans, and related species. These are able to convert nitrogen from the atmosphere into nitrogen-containing organic substances.[2]

Denitrification

While nitrogen fixation converts nitrogen from the atmosphere into organic compounds, a series of processes called denitrification returns an approximately equal amount of nitrogen to the atmosphere. Denitrifying bacteria tend to be anaerobes, or facultatively anaerobes (can alter between the oxygen dependent and oxygen independent types of metabolisms), including Achromobacter and Pseudomonas. The purification process caused by oxygen-free conditions converts nitrates and nitrites in soil into nitrogen gas or into gaseous compounds such as nitrous oxide or nitric oxide. In excess, denitrification can lead to overall losses of available soil nitrogen and subsequent loss of soil fertility. However, fixed nitrogen may circulate many times between organisms and the soil before denitrification returns it to the atmosphere. The diagram above illustrates the nitrogen cycle.

Actinobacteria

Actinobacteria are critical in the decomposition of organic matter and in humus formation, and their presence is responsible for the sweet "earthy" aroma associated with a good healthy soil. They require plenty of air and a pH between 6.0 and 7.5, but are more tolerant of dry conditions than most other bacteria and fungi.

Fungi

A gram of garden soil can contain around one million fungi, such as yeasts and moulds. Fungi have no chlorophyll, and are not able to photosynthesise. They cannot use atmospheric carbon dioxide as a source of carbon, therefore they are chemo-heterotrophic, meaning that, like animals, they require a chemical source of energy rather than being able to use light as an energy source, as well as organic substrates to get carbon for growth and development.

Many fungi are parasitic, often causing disease to their living host plant, although some have beneficial relationships with living plants, as illustrated below. In terms of soil and humus creation, the most important fungi tend to be saprotrophic; that is, they live on dead or decaying organic matter, thus breaking it down and converting it to forms that are available to the higher plants. A succession of fungi species will colonise the dead matter, beginning with those that use sugars and starches, which are succeeded by those that are able to break down cellulose and lignins.

Fungi spread underground by sending long thin threads known as mycelium throughout the soil; these threads can be observed throughout many soils and compost heaps. From the mycelia the fungi is able to throw up its fruiting bodies, the visible part above the soil (e.g., mushrooms, toadstools, and puffballs), which may contain millions of spores. When the fruiting body bursts, these spores are dispersed through the air to settle in fresh environments, and are able to lie dormant for up to years until the right conditions for their activation arise or the right food is made available.

Mycorrhizae

Those fungi that are able to live symbiotically with living plants, creating a relationship that is beneficial to both, are known as Mycorrhizae (from myco meaning fungal and rhiza meaning root). Plant root hairs are invaded by the mycelia of the mycorrhiza, which lives partly in the soil and partly in the root, and may either cover the length of the root hair as a sheath or be concentrated around its tip. The mycorrhiza obtains the carbohydrates that it requires from the root, in return providing the plant with nutrients including nitrogen and moisture. Later the plant roots will also absorb the mycelium into its own tissues.

Beneficial mycorrhizal associations are to be found in many of our edible and flowering crops. Shewell Cooper suggests that these include at least 80% of the brassica and solanum families (including tomatoes and potatoes), as well as the majority of tree species, especially in forest and woodlands. Here the mycorrhizae create a fine underground mesh that extends greatly beyond the limits of the tree's roots, greatly increasing their feeding range and actually causing neighbouring trees to become physically interconnected. The benefits of mycorrhizal relations to their plant partners are not limited to nutrients, but can be essential for plant reproduction: In situations where little light is able to reach the forest floor, such as the North American pine forests, a young seedling cannot obtain sufficient light to photosynthesise for itself and will not grow properly in a sterile soil. But, if the ground is underlain by a mycorrhizal mat, then the developing seedling will throw down roots that can link with the fungal threads and through them obtain the nutrients it needs, often indirectly obtained from its parents or neighbouring trees.

David Attenborough points out the plant, fungi, animal relationship that creates a "Three way harmonious trio" to be found in forest ecosystems, wherein the plant/fungi symbiosis is enhanced by animals such as the wild boar, deer, mice, or flying squirrel, which feed upon the fungi's fruiting bodies, including truffles, and cause their further spread (Private Life Of Plants, 1995). A greater understanding of the complex relationships that pervade natural systems is one of the major justifications of the organic gardener, in refraining from the use of artificial chemicals and the damage these might cause.[citation needed]

Recent research has shown that arbuscular mycorrhizal fungi produce glomalin, a protein that binds soil particles and stores both carbon and nitrogen. These glomalin-related soil proteins are an important part of soil organic matter.[3]

Earthworms, ants, and termites

Earthworms, ants and termites mix the soil as they burrow, significantly affecting soil formation. Earthworms ingest soil particles and organic residues, enhancing the availability of plant nutrients in the material that passes through and out their bodies. By aerating and stirring the soil, and by increasing the stability of soil aggregates, these organisms help assure the ready infiltration of water.

soil organism, any organism inhabiting the soil during part or all of its life. Soil organisms, which range in size from microscopic cells that digest decaying organic material to small mammals that live primarily on other soil organisms, play an important role in maintaining fertility, structure, drainage, and aeration of soil. They also break down plant and animal tissues, releasing stored nutrients and converting them into forms usable by plants. Some soil organisms are pests. Among the soil organisms that are pests of crops are nematodes, slugs and snails, symphylids, beetle larvae, fly larvae, caterpillars, and root aphids. Some soil organisms cause rots, some release substances that inhibit plant growth, and others are hosts for organisms that cause animal diseases.

Since most of the functions of soil organisms are beneficial, earth with large numbers of organisms in it tends to be fertile; one square metre of rich soil can harbour as many as 1,000,000,000 organisms.

Soil organisms are commonly divided into five arbitrary groups according to size, the smallest of which are the protists—including bacteria, actinomycetes, and algae. Next are the microfauna, which are less than 100 microns in length and generally feed upon other microorganisms. The microfauna include single-celled protozoans, some smaller flatworms, nematodes, rotifers, and tardigrades (eight-legged invertebrates). The mesofauna are somewhat larger and are heterogeneous, including creatures that feed on microorganisms, decaying matter, and living plants. The category includes nematodes, mites, springtails (wingless insects so called for the springing organ which enables them to leap), the insectlike proturans, which feed on fungi, and the pauropods.

The fourth group, the macrofauna, are also quite diverse. The most common example is the potworm, a white, segmented worm that feeds on fungi, bacteria, and decaying plant material. The group also includes slugs, snails, and millipedes, which feed on plants, and centipedes, beetles and their larvae, and the larvae of flies, which feed on other organisms or on decaying matter.

Megafauna constitute the largest soil organisms and include the largest earthworms, perhaps the most important creatures that live in the topsoil. Earthworms pass both soil and organic matter through their guts, in the process aerating the soil, breaking up the litter of organic material on its surface, and moving material vertically from the surface to the subsoil. This is extremely important to soil fertility, and it develops the structure of the soil as a matrix for plants and other organisms. It has been estimated that earthworms completely turn over the equivalent of all the soil on the planet to a depth one inch (2.5 cm) every 10 years. Some vertebrates are also in the megafauna category; these include all sorts of burrowing animals, such as snakes, lizards, gophers, badgers, rabbits, hares, mice, and moles.

One of the most important roles of soil organisms is breaking up the complex substances in decaying plants and animals so that they can be used again by living plants. This involves soil organisms as catalysts in a number of natural cycles, among the most prominent being the carbon, nitrogen, and sulfur cycles.

The carbon cycle begins in plants, which combine carbon dioxide from the atmosphere with water to make plant tissues such as leaves, stems, and fruits. Animals eat the plants and convert the tissues into animal tissues. The cycle is completed when the animals die and their decaying tissues are eaten by soil organisms, a process that releases carbon dioxide.

Proteins are the basic stuff of organic tissues, and nitrogen is an essential element of all proteins. The availability of nitrogen in forms that plants can use is a basic determinant of the fertility of soils; the role of soil organisms in facilitating the nitrogen cycle is therefore of great importance. When a plant or animal dies, soil organisms break up the complex proteins, polypeptides, and nucleic acids in their bodies and produce ammonium, ions, nitrates, and nitrites that plants then use to build their body tissues.

Both bacteria and blue-green algae can fix nitrogen directly from the atmosphere, but this is less vital to plant development than the symbiotic relationship between the bacteria genus Rhizobium and leguminous plants and certain trees and shrubs. In return for secretions from their host that encourage their growth and multiplication, Rhizobia fix nitrogen in nodules of the host plant’s roots, providing nitrogen in a form usable by the plant.

Soil organisms also participate in the sulfur cycle, mostly by breaking up the naturally abundant sulfur compounds in the soil so that this vital element is available to plants. The smell of rotten eggs so common in swamps and marshes is due to the hydrogen sulfide produced by these microorganisms.

Though soil organisms have become less important in agriculture due to the development of synthetic fertilizers, they play a vital role in woodlands, especially in the creation of humus, a finely separated complex of organic materials composed of decaying leaves and other vegetable matter.

When a leaf falls it cannot be eaten by most animals. After the water-soluble components of the leaf are leached out, fungi and other microflora attack its structure, making it soft and pliable. Now the litter is palatable to a wide variety of invertebrates, which fragment it into a mulch. The multipedes, wood lice, fly larvae, springtails, and earthworms leave the litter relatively unchanged organically, but they create a suitable substrate for the growth of the primary decomposers that break it into simpler chemical compounds. There is also a group called secondary decomposers (some creatures, such as the springtails, are in both groups), which break it down even further.

So the organic matter of leaves is constantly being digested and redigested by waves of increasingly smaller organisms. Eventually the humic substance that remains may be as little as one-fourth of the original organic matter of the litter. Gradually this humus is mixed into the soil by burrowing animals (such as moles, rabbits, etc.) and by the action of the earthworms.

Though some soil organisms can become pests—especially when a single crop is grown repeatedly in the same field, encouraging the proliferation of organisms that prey on their roots—by and large they are essential elements in the process of life, death, and decay, which rejuvenates the environment.

Micro-Organisms

Bacteria are organisms that have only one cell and are therefore microscopic. But don't let their size fool you! There are anywhere from  100 MILLION to 1BILLION bacteria in just 1TEASPOON of soil!!!! They are decomposers, eating dead plant material and organisms' waste. By doing this, the bacteria release nutrients that other organisms could not access. The bacteria do this by changing the nutrients into a form that can be used. Do you know what soil smells like? Well actinomycetes, a unique type of bacteria, cause that smell, and it is a good sign of healthy soil. Actually, people have been smelling soil for many, many years as a way to judge if the land is good for planting.

Fungi are organisms. They are not plants, nor are they animals. They group themselves into strings called hyphae.  The hyphae then form groups called mycelium. They are less than an inch wide but can get as long as several meters. They are helpful but could also be harmful to soil organisms. Fungi are helpful because they have the ability to break down nutrients that other organisms cannot. Fungi release them into the soil, and other organisms get to use them. Fungi can attch themselves to plant roots. Most plants grow much better when this happens. This is a good relationship called mycorriza. The fungi help the plant by giving it those needed nutrients, and the fungi get food from the plant, the same food that plants give to humans. On the other hand, fungi can get food by being parasites, attaching themselves to plants or other organisms, but for selfish reasons. 

There are beautiful mushrooms, shown below. This is only one part of the fungus; its mycelium are growing underground. The mushrooms form when the fungus is trying to reproduce.

Protozoa are organisms that have only one cell, and are microscopic, but larger than bacteria. They behave like animals in how they move, but they are not animals. They are a type of simple organism. There can be millions found in a square meter of soil. They are grouped by the ways they move: amoebae use a psuedo (fake) foot, ciliates have cilia (short hair) and move them very fast, and flagellates have one or more flagella (whips) and move them very fast. Protozoa eat bacteria which actually helps keep the bacteria population growing. Protozoa help other soil organisms and plants by releasing a usable form of nitrogen into the soil. These other organisms and plants cannot do this by themselves.

Nematodes are worms that do not have any segments in their body. You may have seen these before, but there are actually 22,000 differnt species of nematods. There are LOTS of them living in the soil, about 10 to 20 MILLION in a square meter! They are small, microscopic even, but they can grow up to a meter long. Nematodes can be  helpful and sometimes can become pests in the soil. They eat plants, fungi, and bacteria. This can be good or bad. It is good because when the small nematods eat bacteria and fungi, they release some of the bacteria's and fungi's good nutrients into the soil. When there are too many nematodes they can over-eat and will throw-off the natural balance of the bacteria's and fungi's population. Predatory nematodes help with this by eating some of the smaller nematodes. Although it sounds strange, this keeps the populations in check.

Arthropods are bugs that have jointed (arthro) legs (pods) and an exoskeleton.   They include insects, mites, spiders, ants, termites, beetles, cockroaches, all the bugs that creep many of us out! There are over a MILLION different species.They can be microscopic to several inches long. In a square meter, there could be 500 to 200,000 arthropds (not close to the number of nematods). Some arthropds feed on plants (herbivores), some on dead plants (decomposers), some on other animals (carnivores), some on fungi and bacteria. The more the fungi and bacteria are eaten, the more they continue to grow. It is a strange idea, but it is true. They release nutrients from the bacteria and fungi into the soil and air. Without them, other organisms would not have acccess to the nutrients. They help bacteria get around in the soil by transporting them on their exoskeletons. They also feed the bacteria and fungi when they give off waste. 

 

Mullusks include slimy snails and slugs, and many shellfish. There are over 100,000 species. Many, obviously live in water environments, but they are special in the soil because they are able to digest a material in plants, cellulose, that most other organisms cannot. Therefore, they eat living and dead plants.

Did you know that sea snails provide the seashells that wash-up at the beach. Those shells then become the homes of hermit crabs, who live in several seashells throughout their lives. Snails only use one shell for their entire lives. They just keep adding more chitin to make it bigger. When they roll into their shell they give-off material that creates a door so no predators can get in.

Oligochaeta are segmented worms. There are about 7000 species of eathworms, which can be anywhere from 1 inch to about 2 meters long. Imagine seeing a worm that long! In a square meter, there could be anywhere from 50 to 500 worms depending on the climate. If there are earthworms in your garden, then you are in luck! We discussed why it is good for soil organisms to eat bacteria and fungi, and earthworms feed on them too. Earthworms mainly help the soil when they burrow through it.  While doing this, they create tunnels. Other organisms use that space to travel, making it easier for them to get around and do their business. These tunnels also give the rain somewhere to go, which gives the plants' roots more access to the water. While burrowing, the earthworms steadily eat and process soil and dead plant material. They release their waste throughout the soil, but it is so rich with nutrients and bacteria that their waste is like a fertilzer. Actually, you can buy wormcasts form plant stores to put into your own garden!

Soil Food WebThe following diagram shows how all of the organisms that are discussed above are dependent on each other for survival. Even though some of them are microscopic, they still need food, even plants. This is called a food web. Can you figure out where the humans would fit into this food web? What do humans eat in order to survive? Don't forget that people from other parts of the world may eat different things that you don't eat!