jumpincactus
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I thought this was an excellent write up of the science and the terminology surrounding the study of soil biology and living soil for folks maybe new to these forums or maybe new to growing/farming/ organic farming in general. Great place to take the plunge if you are new, or even if you've been around a bit and want to better understand the world beneath your feet.
Soil Biology
Soil Biology is the study of the living component of soils – the bacteria, fungi, and soil animals which all have particular soil processing roles. It is distinct from, but linked to the processes involved in Soil Chemistry (nutrient processes) and Soil Physics (soil structure, texture, stability, water movement in soil).
Why is soil biology important?
The activities of the wide range of organisms in soil play a pivotal role in both natural and managed ecosystems. Their processes of organic matter breakdown contribute to the soil’s health – its stability, permeability, ability to retain nutrients and make them available for plant uptake.
Soil biological, physical and chemical processes are interrelated and all contribute to plant productivity. The level of soil biological activity is therefore affected by the soil type, but it also depends on the management practices used, particularly the management of organic matter, especially carbon. Changes that are made to the chemical and physical environment in soil will therefore influence the biological processes and subsequently the contribution they make to the soil’s fertility overall.
What are the issues associated with soil biology?
Knowledge of soil biological processes can support decision making aimed at achieving sustainable use of agricultural land. Soil biology is a complex field, however, and research continues to uncover new facts concerning the organisms themselves, their processes and factors that affect them. Additionally, management of soil biological processes is difficult to do precisely due to the differing parameters of each individual situation, such as soil type and land use. A certain land management practice may also affect one group of organisms, but not others. Consideration of the mass of microorganisms as a whole (microbial biomass) is therefore not sufficient for a complete interpretation of the effects of land management on soil biological fertility.
Measurement of soil health in terms of biological fertility is also a complex and at present, relatively expensive process. More attention has been usually given to the management of the soil chemical and physical environments. As a result, a host of inexpensive and simple tests are available to land managers. Incorporating soil biological processes into farming systems will require a more holistic and longer term approach to agricultural land management.
What are the benefits of understanding and managing soil biology?
Agricultural land management practices alter aspects of soil chemical and physical fertility with consequences for soil biological processes and vice versa. Both fauna and microorganisms contribute significantly to chemical transformations in the soil and influence their physical surroundings to various degrees. Organisms on and around plant roots have major influences on plant nutrient availability and some form specific associations with legumes, which greatly influence the C:N ratio of plant residues in soil. Associations between agricultural plants and fungi known as arbuscular mycorrhizas have the potential to increase the efficiency of use of phosphorus in agricultural ecosystems as well as improve soil structure.
Current research includes understanding some of the undesirable members of the biological population, such as root pathogens. The role of mycorrhizal fungi in preventing and reducing the effects of salinity is also being investigated. Stubble management is another area of research.
Soil Constituents and Formation
Soil is a dynamic medium made up of minerals, organic matter, water, air and living creatures including bacteria and earthworms. It was formed and is forever changing due to five major physical factors; the parent material, time, the climate, the organisms present and the topography. The way in which we manage soil is another major factor influencing the character of the soil. Note that the use of the term mineral describes the occurrence of crystals of quartz, mica, etc., and is not used to indicate plant nutrient elements.
Soil is not uniform on the surface, and it is not uniform with depth. It has layers or horizons. If you dig a pit to about 2 metres deep, you can observe these soil horizons. There is topsoil, or A horizon, where all the organic matter accumulates and is consequently the most fertile horizon. Some soils do not have an A horizon because it has been eroded away, for example, after a wind erosion event. Needless to say, these soils are often very infertile. Below the A horizon is the B horizon, or the subsoil. This is less fertile than the A horizon and usually has more clay, iron and aluminium compounds, as water has leached the finer particles down the profile. Below the subsoil is the parent material, the rock from which the soil has formed. Physical, chemical and biological weathering of this rock eventually leads to the formation of soil. Valley floor and plateau soils tend to be deeper than those on the slopes due to erosion removing the soil from the slopes. There is more time for soils to form in valleys and plateaux. Organisms add nutrients to the soil, aid in improving soil structure and help stabilise the soil against erosion, once again changing the soil.
Excerpt, with permission, from: Hunt, N. and Gilkes, R. (1992). Farm Monitoring Handbook. University of Western Australia. Nedlands; WA. 3.
Soil Organic Matter
What is organic matter?
Organic matter is anything that contains carbon compounds that were formed by living organisms. Examples include lawn clippings, leaves, stems, branches, moss, algae, any animal parts, manure, sawdust, insects, earthworms and microbes.
There are 3 main components of organic matter in soils:
Refer to "Soils are Alive" newsletter Volume 1 Number 4 "Living soil organic matter" by Dr Dan Murphy.
What is humus?
Organic matter that is so decomposed that it can no longer be recognised as individual components is known as humus. The highly complex compounds that make up humus are able to resist further decomposition, and therefore accumulate in the soil.
What is the impact of incorporating organic matter into the soil?
Incorporating organic matter into soil can alter the physical, chemical and biological balances in the soil. It can change the:
Nutrients taken up by plants in natural environments are derived largely from decomposition processes (Lavelle and Spain, 2001 p. 365). During organic matter decomposition, bacteria and fungi can use some of the energy or nutrients released by that process for their own growth. For example, during the break down of a protein, microbes will have access to the carbon, nitrogen and sulphur that become available for their own physiological processes and cell structure. If there are nutrients surplus to the microbes’ needs, they will be available for other soil organisms or plants to use. When microbes die, their cells are degraded and nutrients contained within them again become available to plants and other soil organisms.
Incorporating organic matter into soil can change the amount of nitrogen (and other nutrients) that is available to plants. Microbes can access nitrogen in the soil more quickly than plants. Depending on the C:N ratio of the organic matter they exploit, mineral N may be released during decomposition. However, the microbes will use some or all of the N first, or retain it in microbial tissues, rendering it temporarily unavailable for plant use. If there is insufficient N in the organic matter, most of the N may even be taken up from the soil by the microbes, leaving a lower amount for plant use; this is called ‘immobilisation’ (Lavelle and Spain, 2001 p.369).
Adding organic matter can also increase the activity of earthworms, which in turn can improve soil structure. Similarly, if the amount of fungi and bacteria associated with the breakdown of organic matter increases, soil structure will again benefit. Organic matter that is durable and less easily degraded will increase the microbial biomass over a longer period of time.
Organic Matter Breakdown: Releasing Nutrients for Uptake
How is organic matter broken down in the soil?
Organic matter break down is a biological process because it is the soil organisms (microorganisms, earthworms, microarthropods, ants, beetles etc) that perform the chemical and physical transformations. Break down of organic matter involves physical fragmentation, chemical alteration of organic matter and finally release of mineral nutrients. Different organisms are involved with the different stages of the decomposition.
Leaf and root systems are naturally colonised by microorganisms. Break down starts almost immediately after the organism, or part of it, dies. These colonies of microorganisms use enzymes to oxidise the organic matter to obtain energy and carbon (C). Earthworms and other larger soil animals, such as mites, collembola (springtails), and ants assist in the decomposition of organic matter by incorporating it into the sub-surface soil, where conditions are usually more favourable for decomposition than on the soil surface. The soil animals fragment the organic material, which increases its surface area and allows it to be further colonised and decomposed by microorganisms.
Can plants immediately take up nutrients released from decomposition?
Mineralisation is the biological process in which organic compounds are chemically converted to other simpler organic compounds or inorganic forms, such as ammonium or phosphate, by soil microorganisms. When microorganisms mineralise a protein molecule, for example, the molecule may undergo several changes to simpler organic molecules before the carbon is converted to carbon dioxide and the nitrogen, phosphorus and sulphur become readily available to plants as ammonium (NH4+), phosphate (PO43-) and sulphate (SO42-).
Bacteria and fungi are responsible for most of the mineralisation of organic matter in soil by releasing enzymes that oxidise organic compounds. This process releases energy and carbon, some of which is used by the microbes for constructing cellular components such as cell walls and membranes.
How long does organic matter take to break down?
The chemical compounds in organic matter undergo breakdown at different rates. The first organic compounds to be broken down are those that have simple cellular structures, such as amino acids and sugars. Cellulose breaks down more slowly and phenols, waxes and lignins will remain in the soil for the longest time. The chemical structures of these molecules are very complex; very strong chemical bonds hold the molecules together.
Stems and leaves do not break down at the same rate because they are made up of various combinations of molecules that differ in the strength of their chemical bonds. Specialised enzymes are required for their degradation. Leaves generally have more cellulose and less lignin than stems. Cellulose is a simpler, chain-like molecule that can be decomposed more rapidly than lignin which has a complex, folded structure. When lignin is linked with cellulose within plant cell walls, the cellulose becomes more difficult to degrade because it is less accessible to enzymes. Under most conditions it might take three times as long to degrade stems as it does to degrade leaves.
What is the C:N ratio of organic matter and why is it important?
The C:N ratio refers to the amount of carbon relative to the amount of nitrogen present in organic matter. There is always more carbon than nitrogen in organic matter. It is usually written as a single number, because it expresses how much more carbon than nitrogen there is. For example if the ratio is 20, this means that there are 20 atoms of carbon for each atom of nitrogen in that kind of organic matter. If the ratio is 100, it means that there are 100 atoms of carbon for each atom of nitrogen. When the number is low it means that the organic matter has a high concentration of N, while if the ratio is a large number, it means that there is considerably more carbon than nitrogen. The C:N ratio does not tell us what form the carbon and nitrogen are in, just the amounts of C relative to N.
The C:N ratio of the organic matter is important to consider in relation to the availability of nitrogen (and other nutrients) after breakdown has taken place. Incorporating organic matter that has a high C:N ratio into soil, for example, will probably cause some nitrogen deficiency in the crops/plants, at least in the short-term, unless additional N is added. If there is a shortage of nitrogen, the plants may suffer first because microorganisms can access nitrogen in soil more easily than plants. Legumes which are effectively nodulated can fix nitrogen to avoid the impact of nitrogen immobilisation.
Soil Aggregation
What are soil aggregates and soil pores?
Soil aggregates are ‘clumps’ of soil particles that are held together by moist clay, organic matter (such as roots), by organic compounds (from bacteria and fungi) and by fungal hyphae (pronounced “highfee”). Aggregates vary in size from about 2 thousandths of a millimetre across up to about 2 millimetres across, and are made up of particles of varying sizes. Some of these particles fit closely together and some do not and this creates spaces of many different sizes in the soil. These spaces, or pores, within and between soil aggregates are essential for storing air and water, microbes, nutrients and organic matter. Soils with many aggregates are called "well-aggregated". Such soils are more stable and less susceptible to erosion.
How could bacteria be involved in the formation of a soil aggregate?
There are two ways that bacteria could be involved in soil aggregation. One way is by producing organic compounds calledpolysaccharides. Bacterial polysaccharides are more stable than plant polysaccharides, resisting decomposition long enough to be involved in holding soil particles together in aggregates. The other way bacteria are involved in soil aggregation is by developing a small electrostatic charge that attracts the electrostatic charge on clay surfaces, bringing together small aggregates of soil.
How could fungal hyphae be involved in the formation of a soil aggregate?
Fungi grow in long, threadlike structures, called hyphae. The amount of aggregation in the soil has been found to relate to the length of fungal hyphae in the soil. Fungi help to form aggregates in the soil by enmeshing soil particles with their hyphae and forming cross-links between soil particles. Mycorrhizal fungi and fungi that colonise fresh organic matter are believed to be the most important for assisting with stabilisation of soil particles into aggregates.
Degradation of Pesticides
What happens to pesticides once they have been added to the soil?
Chemicals, such as pesticides, added to the soil are broken down in a similar way to organic matter. They are oxidised by the microorganisms that produce the appropriate enzymes. Pesticides generally have very complex structures and most are converted to several intermediate organic compounds before finally being converted to carbon dioxide and water.
When these kinds of chemicals are degraded metabolically, the microorganisms involved gain energy and carbon from the oxidation of the chemical. This allows the microorganisms to grow and multiply, and the size of the microbial population may increase as more of the chemical is degraded. Sometimes, microorganisms capable of degrading a particular chemical grow and multiply until there is a higher proportion of these microorganisms in the soil. When a community of microorganisms in the soil adapts in this way, the chemical can be broken down more rapidly than it would have previously. This can be a problem when rapid degradation of a pesticide may reduce its effectiveness against pests.
Some chemicals added to the soil are degraded by the microorganisms without any particular benefit to the organism such as nutrients or energy supply. The population of microorganisms remains constant while the concentration of the chemical in soil decreases. The different modes of interaction between synthetic chemicals and microorganisms are a result of the enormous diversity of organisms in soil.
Why are some chemicals easier to degrade than others?
The ease with which a chemical is degraded depends on the complexity of its structure. More complex structures degrade more slowly either because fewer microorganisms in the soil produce enzymes capable of degrading them or because of the inaccessibility to microbes.
The Nitrogen (N) Cycle
What are the major processes in the nitrogen cycle?
The nitrogen cycle describes how the different forms of nitrogen in the air, soil, water and living organisms are interconnected. It is described as a cycle because the nitrogen is never lost completely; it just changes form and is held in different places. There are 5 major processes involved:
1. Ammonification
Ammonification is the conversion of organic forms of nitrogen (for example, nitrogen in proteins in dead plants and soil animals) to ammonium. Ammonium is an inorganic form of nitrogen that has the symbol NH4+. A wide range of soil organisms carry out the ammonification process. Many different types of bacteria and fungi are involved. The organisms get carbon and energy from the breakdown of organic matter, while nitrogen is released at the same time.
2. Nitrification
Nitrification is the process where ammonium is converted to nitrite (NO2-) and then to nitrate (NO3-). The organisms involved in nitrification are a relatively small number of species in soil. They are autotrophic, which means they get energy from the chemical transformation of NH4+ to NO2-, while any needed carbon is obtained from CO2. One group of organisms converts ammonium to nitrite and another group of organisms converts nitrite to nitrate.
3. Denitrification
Denitrification is the process where oxides of nitrogen (e.g. nitrate and nitrite) are converted into gaseous nitrogen and are removed from the soil system. Examples are the gas nitrous oxide (NO2), and nitrogen gas (N2), which is the form of nitrogen most common in the atmosphere. Many species of microorganisms are capable of denitrification of soil. Denitrification occurs mainly when there is little or no oxygen in the soil, such as when the soil is waterlogged. However, if the waterlogging is only temporary, the denitrification process will stop when the soil dries.
4. Nitrogen fixation
Nitrogen fixation is the conversion of nitrogen gas (N2) to ammonium (NH4+)- either by free living bacteria in soil or water, or by bacteria in symbiotic association with plants (eg legume symbiosis).
5. Nitrogen immobilization
This is the process whereby nitrogen is incorporated into the microbial cells and ‘tied-up’ in the 'microbial pool' of nitrogen. Immobilisation occurs in parallel with ammonification.
Refer to “Soils are Alive’ newsletter Volume 2 Number 1: ‘Bacteria transform ammonium to nitrate in soil’ by Dr Nui Milton
The Living Soil
The Soil Habitat
Where are the organisms located in soil?
Most organisms are found in the top layers of soil, usually the top 2-3 centimetres, since this is typically where most of the organic matter is. Organisms do occur to depths of several kilometres below the soil surface, but the types of organisms that occur this far down are not the same as those close to the surface. The organisms in soil are often commonly found close to root surfaces in the rhizosphere, within living and dead roots, on soil particles, or amongst aggregates of soil particles.
Earthworms and other soil animals are able to move through most of the top layers of soil. Fungi can form a mat of hyphae, which can extend centimetres or even metres through the soil. They can also form a network of hyphae inside soil aggregates. Bacteria tend to accumulate inside soil aggregates because they are less likely to be eaten by soil animals such as protozoa and mites in this environment. Bacteria can be carried down further into the soil in water that is percolating downwards, but generally they do not move far.
Soils that are clayey often have more bacteria than sandy soils because the clay creates lots of small pores (spaces) which offer protection for bacteria. Sandy soils with fewer aggregates and small pores are less suitable habitats for bacteria and fungi unless a large amount of organic matter is added to the soil.
What are the main characteristics of the rhizosphere?
The rhizosphere is the region of soil that is immediately adjacent to and affected by plant roots. The rhizosphere is a very dynamic environment where plants, soil, microorganisms, nutrients and water meet and interact. The rhizosphere differs from the bulk soil because of the activities of plant roots and their effect on soil organisms.
A major characteristic of the rhizosphere is the release of organic compounds into the soil by plant roots. These compounds, called exudates, make the environment of the rhizosphere very different from the environment in the bulk soil. The exudates increase the availability of nutrients in the rhizosphere, and also provide a carbon source for heterotrophic microorganisms. The exudates cause the number of microorganisms to be far greater in the rhizosphere than in the bulk soil. Their presence attracts larger soil organisms that feed on microorganisms and the concentration of organisms in the rhizosphere can be up to 500 times higher than in the bulk soil. However, their growth and reproduction is even higher when grazing by predators is taken into account. This grazing helps release nutrients in microbial pool back into the soil. Thus the turnover of nutrients can be more important than the mount of microbes present at any point in time.
Another characteristic of the rhizosphere is the uptake of water and nutrients by plants. Water is drawn from the surrounding soil towards the roots. The balance between the movement of water and nutrients towards the roots and their removal from the soil by roots means that their concentration in the rhizosphere is usually very different from what it is in the bulk soil. This can affect microbial growth and activity.
What is the rhizoplane?
The rhizoplane is the surface of plant roots in the soil. The rhizoplane is the site of water and nutrient uptake and the release of exudates into the soil. Like the rhizosphere, the rhizoplane is a constantly changing environment. As roots grow they cast off dead cells and navigate around soil particles, making the rhizoplane highly irregular, blurring the dividing line between the root surface and the soil.
How do organisms in the rhizosphere influence plant roots?
The soil food web is a way of illustrating the way in which soil organisms relate to each other based on what they eat. The soil food web begins with organic matter, such as crop residues, pasture or any animal or plant material in the soil. Bacteria and fungi consume organic matter and are, in turn, consumed by nematodes, protozoa, earthworms, collembola and some mite species. Nematodes and protozoa are consumed by some mites. Mites and collembola are eaten by beetles and ants.
It is important to remember that the soil is a very complex habitat, in which the diversity of organisms is greater than that of the most diverse plant or animal community. This also means that it s not easy or accurate to generalize about all soil food web processes because the extent to which they occur will be different in different soils, at different times. The same processes (eg. mineralization) can be carried out by different groups of microorganisms.
Soil Animals
What are soil animals and what are the main types?
Soil animals are an extremely diverse group of organisms. Soil animals are grouped roughly according to their size, into three groups. The first group is the microfauna. These are the smallest of the soil animals ranging from 20 - 200µm. The main soil animals in this group are protozoa. The mesofauna is the next largest group and range in size from 200µm - 10mm. The most important animals in this group are mites, collembola (or spring tails) and nematodes. The macrofauna contain the largest soil animals such as earthworms, beetles and termites. Generally, the most common soil animals are protozoa, nematodes, mites and collembola.
Why are soil animals important?
Soil animals perform several functions in soil that make them a vital part of all ecosystems, including agriculture. Soil animals are involved in:
Soil animals contribute directly to nutrient cycling in soil when they release mineralised nutrients in their excreta. However, most of their contributions are indirect, by:
Soil animals have an important role in the formation of soil structure. Soil animals improve soil structure by forming channels and pores, concentrating fine soil particles together into aggregates and by fragmenting and mixing organic matter through soil.
What do soil animals need to survive in soil?
Soil animals are found in almost every environment on earth, including Antarctica! Different species require different conditions to grow and survive but all soil animals, require sufficient carbon and nutrients, moisture, oxygen and an optimum pH and temperature. The optimum pH and temperature levels vary between species. Some organisms do not survive dry or very cold conditions, but they may leave eggs in the soil that hatch when conditions become more favourable. Other soil animals remain in the soil in an inactive state and become active again when conditions become favourable. Larger soil animals such as earthworms may live deeper in the soil when there are unfavourable conditions near the soil surface.
Refer to "Soils are Alive" newsletter Volume 1 Number 1: "Mites in your soil" by Dr Graeme Osler
Soil Fungi
What are fungi?
Fungi are primarily organisms that cannot synthesise their own food and are dependent on complex organic substances for carbon. Specialized fungi can be pathogenic on the tissues of plants, while others form mutually beneficial relationships with plants and assist in direct nutrient supply to the plants (e.g. mycorrhizal associations).
Many fungi play a very important role in the recycling of important chemical elements that would otherwise remain locked up in dead plants and animals. In the decomposition of plant debris, certain fungi are particularly important because of their ability to derive their carbon and energy requirements from the break down of dead and decaying plant cell walls, cellulose and lignin. They are much less dependent on water than other microorganisms, but interactions with other microbes, temperature and nutrient availability will have an effect on their activity. Fungal activity is greatest in decomposing leaves and wood, and tends to diminish in the later stages of decomposition when bacteria become more dominant.
What are mycorrhizal fungi?
Mycorrhizas are associations between fungi and plant roots that can be beneficial to both the plant and the fungi. The fungi link the plant with soil by acting as agents of nutrient exchange. The fungi receive carbohydrates as energy from the host plant root whilst nutrients such as phosphorus and zinc are passed back into the plant roots from the soil. Mycorrhizal associations may also reduce attack from root pathogens and increase the tolerance of the plant to adverse conditions such as heavy metals, drought, and salinity. In general, mycorrhizas play an important role in sustainable plant productivity and maintenance of soil structure.
Mycorrhizal associations occur on almost all terrestrial plants and are not as plant-specific as other plant-microbe associations that formed between some plants (e.g. legumes) and bacteria (e.g. rhizobia).
“Some plant species, such as crucifers (i.e. broccoli) are unusual in that mycorrhizal symbioses are absent. Species with fine root hairs and many root hairs are not as dependent on mycorrhizae as species with well-defined tap roots” (Coyne, 1999).
Are there different types of mycorrhizal associations and what plants are involved with them?
There are four main kinds of mycorrhizal fungi: arbuscular, ectomycorrhizal, ericoid and orchid mycorrhiza. Most agricultural plants, vegetables and orchard plants form arbuscular mycorrhizal associations. Ectomycorrhizal associations are less common in disturbed ecosystems and are more common on perennial plants than annuals. Ornamental plants form associations from each of the four groups and orchid mycorrhizal associations are formed only by orchids.
What are Vesicular Arbuscular Micorrhizae?
The most common type of mycorrhizas are the arbuscular mycorrhizas. They are found in natural ecosystems as well as in agricultural areas, are common on both perennials and annuals, and form associations with most agricultural plants. Two exceptions among agricultural crops are canola (oilseed rape) and lupin.
Arbuscules are believed to be the major site where the carbon and nutrient exchange between plant and fungus occurs. Named because of their "tree-like" structure, arbuscules are created by repeated branching of hyphae once they enter a cell within a plant root.
Vesicles are structures formed inside a cell within the plant’s roots. They can be regular or irregular in shape and many times wider than the hyphae on which they form. Therefore, vesicles are usually very distinctive and in some species can resemble spores. These structures are known as a place for storing nutrients. Only three of the fivegenera of arbuscular mycorrhizas (Glomus, Acaulospora and Entrophosphora) form vesicles.
The fungi are grouped according to the size, shape and wall structure of their spores. The spores are approximately spherical or ovoid in shape and usually have thick walls which allow them to survive harsh environmental conditions. When soil conditions are favourable, the spores germinate and hyphae grow from the spore, entering roots and establishing mycorrhizal associations.
Spores are between 30 and 500 micrometres in size - this is between 30 thousandths of a millimetre and half a millimetre. Identifying and classifying the spores is therefore something that must be done with the aid of a microscope.
What are the benefits of mycorrhizal associations?
Mycorrhizal fungi are characterised by very thin hyphae, which are between 1 and 10 thousandths of a millimetre in width. These hyphae explore the soil for nutrients, transport them back to the host-plant, and help bind soil particles into aggregates. The hyphae form networks between neighbouring soil particles, between roots and soil particles, between roots on the same plant, and between roots of different plants (even different types of plants). They also form networks inside the roots they colonize. These networks of hyphae are also referred to as mycelium.
Mycorrhizas extend the volume of soil explored by the plant, a characteristic that is especially important for phosphorous which does not move in the soil solution as nitrogen does. There is some evidence that the fungi may help the plants tolerate drought. When phosphorus is scarce in soil, plants that have developed mycorrhizas on their root systems have greater access to and take up more phosphorus others. Trace elements, copper and zinc behave in a similar way to phosphorus in soil and plant roots must explore the soil to intercept them.
Although arbuscular mycorrhizas can enhance plant growth in phosphorous deficient soils, the extent to which this occurs in the field in agricultural and natural environments is difficult to measure.
Refer to ‘Soils are Alive’ newsletters Volume 1 Number 2 “Arbuscular mycorrhizal fungi” by Professor Lyn Abbott andVolume 3 Number 2“Mycorrhizas and Olive Trees: Letting nature takes it course” by Tom Ganz, Professor Stan Kailis and Professor Lyn Abbott.
Where do plant pathogenic fungi come from?
Disease-causing microorganisms have always been inherent members of any living community. In natural ecosystems, characterised by uncontrolled and changeable conditions, their population growth is impeded by the scattered distribution of host plants and, in the case of fungal pathogens, by their dependence on rainfall at the time of spore germination. In managed systems, however, such as agriculture and horticulture, monocultures of crop plant species provide an unconstrained food supply for a pathogen. Irrigated systems also provide a constant supply of water which can enable spores to germinate and cause disease in accessible host plants.
What are the most important fungal soil pathogens in Australia?
Climatic patterns can affect the types of fungal pathogens that are dominant in a region. For example, low fertility soils favour necrotrophicpathogens over biotrophic pathogens. Necrotrophic pathogens are distinguished from biotrophs because they kill host tissue prior to colonisation. Biotrophic pathogens include powdery mildew, downy mildew, rust, nematodes and viruses. Biotrophs live on living tissue and die when the host plant dies.
What soil conditions favour the growth of fungal pathogens?
The soil conditions that exist at the opening of the cropping season (warm-moist soils and low microbial activity) can favour the growth of a pathogen.
How do cultural practices affect the incidence or spread of fungal pathogens?
Reduced tillage practices help maintain infested residues at the surface of soil, increasing the damage to young seedlings. Conventional cultivations bury this inoculum source which gets broken-down more rapidly by soil microorganisms than when on the soil surface. Rotations with susceptible hosts can increase the inoculum potential of the pathogen in soil. Certain herbicides also increase the disease severity (e.g: the disease caused by the Take-all fungus and root rot caused by Rhizoctonia).
Soil Bacteria
What do bacteria look like?
Most bacteria in soil are about one micron in length or diameter (there are a thousand microns in a millimetre). Some are slightly larger than this, up to several microns, and in rare cases even larger. Their size varies with their environment. Bacteria in environments that have high levels of nutrients may be larger than those in nutrient poor conditions.
The majority of bacteria in soil usually occur as single cells. Bacteria sometimes join together in chains or clusters. They mainly have one of two shapes - spheres (called cocci) and rods (called bacilli). Other bacteria have more varied shapes including spirals and long thin hyphae (although these are less common).
What do bacteria do in soil?
Bacteria are able to perform an extremely wide range of chemical transformations, including degradation of organic matter, disease suppression, disease, and nutrient transformations inside roots (e.g. reducing bacteria in roots, bacteria cause nitrogen fixation).
Azobacter, for example, is a genus of free-living bacteria that converts atmospheric nitrogen into ammonium, making it available for plant use. This process may only take place, however, if the following conditions are met:
In general, bacteria are the organisms in soil that are mainly responsible for transforming inorganic constituents from one chemical form to another. Their system of external digestion means that some of the metabolites released by the use of extracellular enzymes may be used by other organisms, such as plants. The bacteria gain nutrients and energy from these processes and provide other organisms with suitable forms of chemicals they require for their own processes. For example, in the conversions of nitrate to nitrite, sulphate to sulphide and ammonium to nitrite.
Where do bacteria live in soil?
Bacteria are aquatic organisms that live in the water-filled pore spaces within and between soil aggregates. As such, their activities are directly dependent on relatively high soil water contents (Lavelle and Spain, 2001, p. 211).
Bacteria are normally found on the surfaces of mineral or organic particles or congregate around particles of decaying plant and animal debris. Most are unable to move and hence, their dispersion is dependent on water movement, root growth or the activity of soil and other organisms (Lavelle and Spain, 2001, p. 212).
What are rhizobia?
Rhizobia are one of the groups of microorganisms living in soil. They are single celled bacteria, approximately one thousandth of a millimetre in length. Rhizobia belong to a family of bacteria called Rhizobiaceae. There are a number of groups (genera and species) of bacteria in this family.
Rhizobia belong to a specific group of bacteria that form a mutually beneficial association, or symbiosis, with legume plants. These bacteria take nitrogen from the air (which plants cannot use) and convert it into a form of nitrogen called ammonium (NH4+), which plants can use. The nitrogenase enzyme controls the process, called nitrogen fixation, and these bacteria are often called "nitrogen fixers".
Rhizobia are found in soils of many natural ecosystems. They may also be present in agricultural areas where they are associated with both crop legumes (like soybean) and pasture legumes (like clover). Usually, the rhizobia in agricultural areas have been introduced at sowing by applying an inoculum to the exterior of the seeds as liquid formations or pellets.
Refer to ‘Soils are Alive’ newsletter Volume 1 Number 3 “Rhizobia” by Dr Krys Haq.
How are nodules formed on the roots of legumes?
The nodulation process is a series of events in which rhizobia interact with the roots of legume plants to form a specialised structure called a root nodule. These are visible, ball-like structures that are formed by the plant in response to the presence of the bacteria.
The process involves complicated signals between the bacteria and the host roots. In the first stages, the bacteria multiply near the root and then adhere to it. The small hairs on the root's surface curl around the bacteria and they enter the root. Alternatively, the bacteria may enter directly through points on the root surface. The method of entry of the bacteria into the root depends on the type of plant. Once inside the root, the bacteria multiply within thin threads. Signals stimulate cell multiplication of both the plant's cells and the bacteria and this repeated division results in a mass of root cells containing many bacterial cells. Some of these bacteria then change into a form that is able to convert gaseous nitrogen into ammonium nitrogen (that is, they can "fix" nitrogen). These bacteria are then called bacteroids.
The shape of the nodules is controlled by the plant and nodules can vary considerably - both in size and shape.
Most plants need specific kinds of rhizobia to form nodules. The rhizobia that form nodules on peas, for example, cannot form nodules on clover.
Nodulation can be impeded by low pH, Al toxicity, nutrient deficiencies, salinity, waterlogging, and the presence of root parasites such as nematodes or genetic incompatibility with the plant host (Lavelle and Spain, 2001 p.439).
Why are nodules pink inside?
The nitrogenase enzyme is extremely sensitive to oxygen and is only active at low oxygen levels or anaerobic conditions. The physical structure of the nodule acts as a barrier to oxygen and the enzyme leghaemaglobin binds oxygen and transports it away from nitrogenase to respiratory sites. Leghaemoglobin gives the inside of nodules their reddish-pink colouring.
What are some of the other plant-bacterial associations that fix atmospheric nitrogen?
Associations between bacteria and plants that fix atmospheric nitrogen include an association between species of Frankia bacteria and several tree species such as those of the genera Casuarina and Allocasuarina. Another example is between that of Azospirillum and grasses.
Fungi vs Bacteria: Their Different Roles in Decomposition of Organic Matter
Even though a high proportion of both fungi and bacteria are decomposers in the soil, they degrade plant residues differently and have different roles in the recycling of nutrients. This is partly due to their different choice of habitats within the soil and the different types of organic matter they consume.
Fungi are generally much more efficient at assimilating and storing nutrients than bacteria. One reason for this higher carbon (C) storage by fungi lies in the chemical composition of their cell walls. They are composed of polymers of chitin and melanin, making them very resistant to degradation. Bacterial membranes, in comparison, are phospholipids, which are energy-rich. They degrade easily and quickly and function as a food source for a wide range of microorganisms.
The different proportions of C and N (i.e. different C:N ratios) of bacteria and fungi might also play a role in the mineralisation and immobilisationprocesses of nutrients in the soil. Due to their structure and C:N ratio between 7:1 and 25:1, fungi need a greater amount of carbon to grow and reproduce and will therefore 'collect' the required amount of carbon available for this from the soil organic matter. Bacteria, however, have a lower C:N ratio (between 5:1 and 7:1) and a higher nitrogen requirement and take more nitrogen from the soil for their own requirements.
Refer to ‘Soils are Alive’ newsletter Volume 3 Number 3 “The fungal-bacterial ratio: Tipping the balance for soil health” by Florian Wichern.
Measuring and Identifying Soil Organisms
How can the amount of microorganisms in a soil be measured?
The whole mass of living organisms in soil is called its microbial biomass. It can be estimated by measuring the amount of carbon, nitrogen, phosphorus or sulfur that is present in the microorganisms, small animals and algae in the soil. There are a number of different ways of measuring microbial biomass.
For example:
The number of individual soil animals in the soil is enormous. In all but the driest environments there are billions of protozoa per square metre (m2), millions of nematodes/m2 and 100 000’s of mites/m2. Data from east Beverley in Western Australia indicates that there were approximately 800 million protozoa/m2, 900 000 nematodes/m2 and 130 000 mites/m2 in a soil under pasture.
What techniques are used for identifying soil organisms?
Soil organisms are identified by looking at:
How are rhizobia identified?
Rhizobia are bacteria which can grow and multiply on artificial food sources. They are very difficult to identify from their shape or size alone because all forms are extremely small, short rods with rounded ends.
Recently, new methods of rhizobia characterisation have been developed using DNA patterns from known rhizobia grown under laboratory conditions. Comparisons are made between sections of the known DNA molecule that code for particular functions (eg. nitrogen fixation) with samples of DNA from soil or from a root nodule. This tells the scientists whether there are genes for that function in the soil sample or root nodule.
Serological techniques can also be used to identify rhizobia. Samples of known bacteria are injected into an animal under specific laboratory conditions. The animal's body produces antibodies against the bacteria. (A process that is similar to vaccination). The component of the blood containing the antibodies is the serum and this is separated from the red blood cells. This is called antiserum.
The antiserum produced by the animal can be collected and used to help locate bacteria in a sample. The antibodies in the antiserum can be joined to a fluorescent dye or to an enzyme with an attached dye. When the antibody is added to the corresponding bacteria it attaches firmly. The bacteria can then be identified using a fluorescence microscope or in a solution that contains a molecule that can interact with the enzyme and cause a colour change in the solution. This method is called the ELISA method.
The antiserum can be chosen to be very specific for particular types of rhizobia, so it is a good way to identify whether those rhizobia are present in a root nodule. It is often important to know whether the rhizobia that were added with the seed have actually been responsible for forming the nodules on the legume or whether other rhizobia already in the soil formed the nodules.
Glossary
Lewis, 1973)
Lewis, 1973)
Bettleheim and March, 1991)
References
Bettleheim, Frederick A., and March, Jerry (1991) Introduction to General, Organic and Biochemistry (Third edition) p. 516. Saunders College Publishing, USA.
Coyne, Mark (1999) Soil Microbiology: An Exploratory Approach. pp. 337-347. Delmar Publishers, New York.
Lavelle, P. and Spain, A.V. (2001) Soil Ecology, pp 201-356 Kluwer Academic Publishers, The Netherlands.
Lewis, D.H. (1973) Concepts in fungal nutrition and the origin of biotrophy. Biol. Rev. 48, 261-278.
http://www.soilhealth.see.uwa.edu.au/components/measuring
Soil Biology
Soil Biology is the study of the living component of soils – the bacteria, fungi, and soil animals which all have particular soil processing roles. It is distinct from, but linked to the processes involved in Soil Chemistry (nutrient processes) and Soil Physics (soil structure, texture, stability, water movement in soil).
Why is soil biology important?
The activities of the wide range of organisms in soil play a pivotal role in both natural and managed ecosystems. Their processes of organic matter breakdown contribute to the soil’s health – its stability, permeability, ability to retain nutrients and make them available for plant uptake.
Soil biological, physical and chemical processes are interrelated and all contribute to plant productivity. The level of soil biological activity is therefore affected by the soil type, but it also depends on the management practices used, particularly the management of organic matter, especially carbon. Changes that are made to the chemical and physical environment in soil will therefore influence the biological processes and subsequently the contribution they make to the soil’s fertility overall.
What are the issues associated with soil biology?
Knowledge of soil biological processes can support decision making aimed at achieving sustainable use of agricultural land. Soil biology is a complex field, however, and research continues to uncover new facts concerning the organisms themselves, their processes and factors that affect them. Additionally, management of soil biological processes is difficult to do precisely due to the differing parameters of each individual situation, such as soil type and land use. A certain land management practice may also affect one group of organisms, but not others. Consideration of the mass of microorganisms as a whole (microbial biomass) is therefore not sufficient for a complete interpretation of the effects of land management on soil biological fertility.
Measurement of soil health in terms of biological fertility is also a complex and at present, relatively expensive process. More attention has been usually given to the management of the soil chemical and physical environments. As a result, a host of inexpensive and simple tests are available to land managers. Incorporating soil biological processes into farming systems will require a more holistic and longer term approach to agricultural land management.
What are the benefits of understanding and managing soil biology?
Agricultural land management practices alter aspects of soil chemical and physical fertility with consequences for soil biological processes and vice versa. Both fauna and microorganisms contribute significantly to chemical transformations in the soil and influence their physical surroundings to various degrees. Organisms on and around plant roots have major influences on plant nutrient availability and some form specific associations with legumes, which greatly influence the C:N ratio of plant residues in soil. Associations between agricultural plants and fungi known as arbuscular mycorrhizas have the potential to increase the efficiency of use of phosphorus in agricultural ecosystems as well as improve soil structure.
Current research includes understanding some of the undesirable members of the biological population, such as root pathogens. The role of mycorrhizal fungi in preventing and reducing the effects of salinity is also being investigated. Stubble management is another area of research.
Soil Constituents and Formation
Soil is a dynamic medium made up of minerals, organic matter, water, air and living creatures including bacteria and earthworms. It was formed and is forever changing due to five major physical factors; the parent material, time, the climate, the organisms present and the topography. The way in which we manage soil is another major factor influencing the character of the soil. Note that the use of the term mineral describes the occurrence of crystals of quartz, mica, etc., and is not used to indicate plant nutrient elements.
Soil is not uniform on the surface, and it is not uniform with depth. It has layers or horizons. If you dig a pit to about 2 metres deep, you can observe these soil horizons. There is topsoil, or A horizon, where all the organic matter accumulates and is consequently the most fertile horizon. Some soils do not have an A horizon because it has been eroded away, for example, after a wind erosion event. Needless to say, these soils are often very infertile. Below the A horizon is the B horizon, or the subsoil. This is less fertile than the A horizon and usually has more clay, iron and aluminium compounds, as water has leached the finer particles down the profile. Below the subsoil is the parent material, the rock from which the soil has formed. Physical, chemical and biological weathering of this rock eventually leads to the formation of soil. Valley floor and plateau soils tend to be deeper than those on the slopes due to erosion removing the soil from the slopes. There is more time for soils to form in valleys and plateaux. Organisms add nutrients to the soil, aid in improving soil structure and help stabilise the soil against erosion, once again changing the soil.
Excerpt, with permission, from: Hunt, N. and Gilkes, R. (1992). Farm Monitoring Handbook. University of Western Australia. Nedlands; WA. 3.
Soil Organic Matter
What is organic matter?
Organic matter is anything that contains carbon compounds that were formed by living organisms. Examples include lawn clippings, leaves, stems, branches, moss, algae, any animal parts, manure, sawdust, insects, earthworms and microbes.
There are 3 main components of organic matter in soils:
- dead and decaying forms of organic material - mainly dead plant parts
- living plant parts - mostly roots
- living microbes and soil animals
Refer to "Soils are Alive" newsletter Volume 1 Number 4 "Living soil organic matter" by Dr Dan Murphy.
What is humus?
Organic matter that is so decomposed that it can no longer be recognised as individual components is known as humus. The highly complex compounds that make up humus are able to resist further decomposition, and therefore accumulate in the soil.
What is the impact of incorporating organic matter into the soil?
Incorporating organic matter into soil can alter the physical, chemical and biological balances in the soil. It can change the:
- amount of nitrogen that is available to plants
- amount of other nutrients available
- way the soil holds together (soil aggregation)
- number and type of organisms present in the soil
Nutrients taken up by plants in natural environments are derived largely from decomposition processes (Lavelle and Spain, 2001 p. 365). During organic matter decomposition, bacteria and fungi can use some of the energy or nutrients released by that process for their own growth. For example, during the break down of a protein, microbes will have access to the carbon, nitrogen and sulphur that become available for their own physiological processes and cell structure. If there are nutrients surplus to the microbes’ needs, they will be available for other soil organisms or plants to use. When microbes die, their cells are degraded and nutrients contained within them again become available to plants and other soil organisms.
Incorporating organic matter into soil can change the amount of nitrogen (and other nutrients) that is available to plants. Microbes can access nitrogen in the soil more quickly than plants. Depending on the C:N ratio of the organic matter they exploit, mineral N may be released during decomposition. However, the microbes will use some or all of the N first, or retain it in microbial tissues, rendering it temporarily unavailable for plant use. If there is insufficient N in the organic matter, most of the N may even be taken up from the soil by the microbes, leaving a lower amount for plant use; this is called ‘immobilisation’ (Lavelle and Spain, 2001 p.369).
Adding organic matter can also increase the activity of earthworms, which in turn can improve soil structure. Similarly, if the amount of fungi and bacteria associated with the breakdown of organic matter increases, soil structure will again benefit. Organic matter that is durable and less easily degraded will increase the microbial biomass over a longer period of time.
Organic Matter Breakdown: Releasing Nutrients for Uptake
How is organic matter broken down in the soil?
Organic matter break down is a biological process because it is the soil organisms (microorganisms, earthworms, microarthropods, ants, beetles etc) that perform the chemical and physical transformations. Break down of organic matter involves physical fragmentation, chemical alteration of organic matter and finally release of mineral nutrients. Different organisms are involved with the different stages of the decomposition.
Leaf and root systems are naturally colonised by microorganisms. Break down starts almost immediately after the organism, or part of it, dies. These colonies of microorganisms use enzymes to oxidise the organic matter to obtain energy and carbon (C). Earthworms and other larger soil animals, such as mites, collembola (springtails), and ants assist in the decomposition of organic matter by incorporating it into the sub-surface soil, where conditions are usually more favourable for decomposition than on the soil surface. The soil animals fragment the organic material, which increases its surface area and allows it to be further colonised and decomposed by microorganisms.
Can plants immediately take up nutrients released from decomposition?
Mineralisation is the biological process in which organic compounds are chemically converted to other simpler organic compounds or inorganic forms, such as ammonium or phosphate, by soil microorganisms. When microorganisms mineralise a protein molecule, for example, the molecule may undergo several changes to simpler organic molecules before the carbon is converted to carbon dioxide and the nitrogen, phosphorus and sulphur become readily available to plants as ammonium (NH4+), phosphate (PO43-) and sulphate (SO42-).
Bacteria and fungi are responsible for most of the mineralisation of organic matter in soil by releasing enzymes that oxidise organic compounds. This process releases energy and carbon, some of which is used by the microbes for constructing cellular components such as cell walls and membranes.
How long does organic matter take to break down?
The chemical compounds in organic matter undergo breakdown at different rates. The first organic compounds to be broken down are those that have simple cellular structures, such as amino acids and sugars. Cellulose breaks down more slowly and phenols, waxes and lignins will remain in the soil for the longest time. The chemical structures of these molecules are very complex; very strong chemical bonds hold the molecules together.
Stems and leaves do not break down at the same rate because they are made up of various combinations of molecules that differ in the strength of their chemical bonds. Specialised enzymes are required for their degradation. Leaves generally have more cellulose and less lignin than stems. Cellulose is a simpler, chain-like molecule that can be decomposed more rapidly than lignin which has a complex, folded structure. When lignin is linked with cellulose within plant cell walls, the cellulose becomes more difficult to degrade because it is less accessible to enzymes. Under most conditions it might take three times as long to degrade stems as it does to degrade leaves.
What is the C:N ratio of organic matter and why is it important?
The C:N ratio refers to the amount of carbon relative to the amount of nitrogen present in organic matter. There is always more carbon than nitrogen in organic matter. It is usually written as a single number, because it expresses how much more carbon than nitrogen there is. For example if the ratio is 20, this means that there are 20 atoms of carbon for each atom of nitrogen in that kind of organic matter. If the ratio is 100, it means that there are 100 atoms of carbon for each atom of nitrogen. When the number is low it means that the organic matter has a high concentration of N, while if the ratio is a large number, it means that there is considerably more carbon than nitrogen. The C:N ratio does not tell us what form the carbon and nitrogen are in, just the amounts of C relative to N.
The C:N ratio of the organic matter is important to consider in relation to the availability of nitrogen (and other nutrients) after breakdown has taken place. Incorporating organic matter that has a high C:N ratio into soil, for example, will probably cause some nitrogen deficiency in the crops/plants, at least in the short-term, unless additional N is added. If there is a shortage of nitrogen, the plants may suffer first because microorganisms can access nitrogen in soil more easily than plants. Legumes which are effectively nodulated can fix nitrogen to avoid the impact of nitrogen immobilisation.
Soil Aggregation
What are soil aggregates and soil pores?
Soil aggregates are ‘clumps’ of soil particles that are held together by moist clay, organic matter (such as roots), by organic compounds (from bacteria and fungi) and by fungal hyphae (pronounced “highfee”). Aggregates vary in size from about 2 thousandths of a millimetre across up to about 2 millimetres across, and are made up of particles of varying sizes. Some of these particles fit closely together and some do not and this creates spaces of many different sizes in the soil. These spaces, or pores, within and between soil aggregates are essential for storing air and water, microbes, nutrients and organic matter. Soils with many aggregates are called "well-aggregated". Such soils are more stable and less susceptible to erosion.
How could bacteria be involved in the formation of a soil aggregate?
There are two ways that bacteria could be involved in soil aggregation. One way is by producing organic compounds calledpolysaccharides. Bacterial polysaccharides are more stable than plant polysaccharides, resisting decomposition long enough to be involved in holding soil particles together in aggregates. The other way bacteria are involved in soil aggregation is by developing a small electrostatic charge that attracts the electrostatic charge on clay surfaces, bringing together small aggregates of soil.
How could fungal hyphae be involved in the formation of a soil aggregate?
Fungi grow in long, threadlike structures, called hyphae. The amount of aggregation in the soil has been found to relate to the length of fungal hyphae in the soil. Fungi help to form aggregates in the soil by enmeshing soil particles with their hyphae and forming cross-links between soil particles. Mycorrhizal fungi and fungi that colonise fresh organic matter are believed to be the most important for assisting with stabilisation of soil particles into aggregates.
Degradation of Pesticides
What happens to pesticides once they have been added to the soil?
Chemicals, such as pesticides, added to the soil are broken down in a similar way to organic matter. They are oxidised by the microorganisms that produce the appropriate enzymes. Pesticides generally have very complex structures and most are converted to several intermediate organic compounds before finally being converted to carbon dioxide and water.
When these kinds of chemicals are degraded metabolically, the microorganisms involved gain energy and carbon from the oxidation of the chemical. This allows the microorganisms to grow and multiply, and the size of the microbial population may increase as more of the chemical is degraded. Sometimes, microorganisms capable of degrading a particular chemical grow and multiply until there is a higher proportion of these microorganisms in the soil. When a community of microorganisms in the soil adapts in this way, the chemical can be broken down more rapidly than it would have previously. This can be a problem when rapid degradation of a pesticide may reduce its effectiveness against pests.
Some chemicals added to the soil are degraded by the microorganisms without any particular benefit to the organism such as nutrients or energy supply. The population of microorganisms remains constant while the concentration of the chemical in soil decreases. The different modes of interaction between synthetic chemicals and microorganisms are a result of the enormous diversity of organisms in soil.
Why are some chemicals easier to degrade than others?
The ease with which a chemical is degraded depends on the complexity of its structure. More complex structures degrade more slowly either because fewer microorganisms in the soil produce enzymes capable of degrading them or because of the inaccessibility to microbes.
The Nitrogen (N) Cycle
What are the major processes in the nitrogen cycle?
The nitrogen cycle describes how the different forms of nitrogen in the air, soil, water and living organisms are interconnected. It is described as a cycle because the nitrogen is never lost completely; it just changes form and is held in different places. There are 5 major processes involved:
1. Ammonification
Ammonification is the conversion of organic forms of nitrogen (for example, nitrogen in proteins in dead plants and soil animals) to ammonium. Ammonium is an inorganic form of nitrogen that has the symbol NH4+. A wide range of soil organisms carry out the ammonification process. Many different types of bacteria and fungi are involved. The organisms get carbon and energy from the breakdown of organic matter, while nitrogen is released at the same time.
2. Nitrification
Nitrification is the process where ammonium is converted to nitrite (NO2-) and then to nitrate (NO3-). The organisms involved in nitrification are a relatively small number of species in soil. They are autotrophic, which means they get energy from the chemical transformation of NH4+ to NO2-, while any needed carbon is obtained from CO2. One group of organisms converts ammonium to nitrite and another group of organisms converts nitrite to nitrate.
3. Denitrification
Denitrification is the process where oxides of nitrogen (e.g. nitrate and nitrite) are converted into gaseous nitrogen and are removed from the soil system. Examples are the gas nitrous oxide (NO2), and nitrogen gas (N2), which is the form of nitrogen most common in the atmosphere. Many species of microorganisms are capable of denitrification of soil. Denitrification occurs mainly when there is little or no oxygen in the soil, such as when the soil is waterlogged. However, if the waterlogging is only temporary, the denitrification process will stop when the soil dries.
4. Nitrogen fixation
Nitrogen fixation is the conversion of nitrogen gas (N2) to ammonium (NH4+)- either by free living bacteria in soil or water, or by bacteria in symbiotic association with plants (eg legume symbiosis).
5. Nitrogen immobilization
This is the process whereby nitrogen is incorporated into the microbial cells and ‘tied-up’ in the 'microbial pool' of nitrogen. Immobilisation occurs in parallel with ammonification.
Refer to “Soils are Alive’ newsletter Volume 2 Number 1: ‘Bacteria transform ammonium to nitrate in soil’ by Dr Nui Milton
The Living Soil
The Soil Habitat
Where are the organisms located in soil?
Most organisms are found in the top layers of soil, usually the top 2-3 centimetres, since this is typically where most of the organic matter is. Organisms do occur to depths of several kilometres below the soil surface, but the types of organisms that occur this far down are not the same as those close to the surface. The organisms in soil are often commonly found close to root surfaces in the rhizosphere, within living and dead roots, on soil particles, or amongst aggregates of soil particles.
Earthworms and other soil animals are able to move through most of the top layers of soil. Fungi can form a mat of hyphae, which can extend centimetres or even metres through the soil. They can also form a network of hyphae inside soil aggregates. Bacteria tend to accumulate inside soil aggregates because they are less likely to be eaten by soil animals such as protozoa and mites in this environment. Bacteria can be carried down further into the soil in water that is percolating downwards, but generally they do not move far.
Soils that are clayey often have more bacteria than sandy soils because the clay creates lots of small pores (spaces) which offer protection for bacteria. Sandy soils with fewer aggregates and small pores are less suitable habitats for bacteria and fungi unless a large amount of organic matter is added to the soil.
What are the main characteristics of the rhizosphere?
The rhizosphere is the region of soil that is immediately adjacent to and affected by plant roots. The rhizosphere is a very dynamic environment where plants, soil, microorganisms, nutrients and water meet and interact. The rhizosphere differs from the bulk soil because of the activities of plant roots and their effect on soil organisms.
A major characteristic of the rhizosphere is the release of organic compounds into the soil by plant roots. These compounds, called exudates, make the environment of the rhizosphere very different from the environment in the bulk soil. The exudates increase the availability of nutrients in the rhizosphere, and also provide a carbon source for heterotrophic microorganisms. The exudates cause the number of microorganisms to be far greater in the rhizosphere than in the bulk soil. Their presence attracts larger soil organisms that feed on microorganisms and the concentration of organisms in the rhizosphere can be up to 500 times higher than in the bulk soil. However, their growth and reproduction is even higher when grazing by predators is taken into account. This grazing helps release nutrients in microbial pool back into the soil. Thus the turnover of nutrients can be more important than the mount of microbes present at any point in time.
Another characteristic of the rhizosphere is the uptake of water and nutrients by plants. Water is drawn from the surrounding soil towards the roots. The balance between the movement of water and nutrients towards the roots and their removal from the soil by roots means that their concentration in the rhizosphere is usually very different from what it is in the bulk soil. This can affect microbial growth and activity.
What is the rhizoplane?
The rhizoplane is the surface of plant roots in the soil. The rhizoplane is the site of water and nutrient uptake and the release of exudates into the soil. Like the rhizosphere, the rhizoplane is a constantly changing environment. As roots grow they cast off dead cells and navigate around soil particles, making the rhizoplane highly irregular, blurring the dividing line between the root surface and the soil.
How do organisms in the rhizosphere influence plant roots?
- Organisms in the rhizosphere can affect the plant roots by altering the movement of carbon compounds from roots to shoots. This alteration occurs when organisms compete with root cells for carbon that is fixed by photosynthesis.
- The burrows of earthworms in soil provide an easy route for plants roots as they grow through the soil.
- Various root microorganism associations can increase nutrient uptake by plants in nutrient poor environments, such as symbiotic (e.g. mycorrhizal) and other specific (e.g. nitrogen fixing) associations and rhizobia.
- Some soil organisms are pathogenic and attack living plant roots.
- Azospirillum is a bacterium that commonly lives in the rhizosphere of grasses. Some strains of this organism produce hormones that stimulate plant growth. Other strains of Azospirillum fix atmospheric nitrogen and may or may not make it available to the grass.
The soil food web is a way of illustrating the way in which soil organisms relate to each other based on what they eat. The soil food web begins with organic matter, such as crop residues, pasture or any animal or plant material in the soil. Bacteria and fungi consume organic matter and are, in turn, consumed by nematodes, protozoa, earthworms, collembola and some mite species. Nematodes and protozoa are consumed by some mites. Mites and collembola are eaten by beetles and ants.
It is important to remember that the soil is a very complex habitat, in which the diversity of organisms is greater than that of the most diverse plant or animal community. This also means that it s not easy or accurate to generalize about all soil food web processes because the extent to which they occur will be different in different soils, at different times. The same processes (eg. mineralization) can be carried out by different groups of microorganisms.
Soil Animals
What are soil animals and what are the main types?
Soil animals are an extremely diverse group of organisms. Soil animals are grouped roughly according to their size, into three groups. The first group is the microfauna. These are the smallest of the soil animals ranging from 20 - 200µm. The main soil animals in this group are protozoa. The mesofauna is the next largest group and range in size from 200µm - 10mm. The most important animals in this group are mites, collembola (or spring tails) and nematodes. The macrofauna contain the largest soil animals such as earthworms, beetles and termites. Generally, the most common soil animals are protozoa, nematodes, mites and collembola.
Why are soil animals important?
Soil animals perform several functions in soil that make them a vital part of all ecosystems, including agriculture. Soil animals are involved in:
- degradation of organic matter and mineralisation of nutrients,
- controlling populations of pathogens,
- improving and maintaining soil structure and
- mixing organic matter through the soil.
Soil animals contribute directly to nutrient cycling in soil when they release mineralised nutrients in their excreta. However, most of their contributions are indirect, by:
- grazing on the microbial biomass, which alters the rate at which organic matter breaks down
- fragmenting organic matter and increasing its surface area for attack by microorganisms,
- controlling the grazing pressure of nematodes on microorganisms,
- mixing soil and organic matter and
- introducing microorganisms onto fresh organic matter.
Soil animals have an important role in the formation of soil structure. Soil animals improve soil structure by forming channels and pores, concentrating fine soil particles together into aggregates and by fragmenting and mixing organic matter through soil.
What do soil animals need to survive in soil?
Soil animals are found in almost every environment on earth, including Antarctica! Different species require different conditions to grow and survive but all soil animals, require sufficient carbon and nutrients, moisture, oxygen and an optimum pH and temperature. The optimum pH and temperature levels vary between species. Some organisms do not survive dry or very cold conditions, but they may leave eggs in the soil that hatch when conditions become more favourable. Other soil animals remain in the soil in an inactive state and become active again when conditions become favourable. Larger soil animals such as earthworms may live deeper in the soil when there are unfavourable conditions near the soil surface.
Refer to "Soils are Alive" newsletter Volume 1 Number 1: "Mites in your soil" by Dr Graeme Osler
Soil Fungi
What are fungi?
Fungi are primarily organisms that cannot synthesise their own food and are dependent on complex organic substances for carbon. Specialized fungi can be pathogenic on the tissues of plants, while others form mutually beneficial relationships with plants and assist in direct nutrient supply to the plants (e.g. mycorrhizal associations).
Many fungi play a very important role in the recycling of important chemical elements that would otherwise remain locked up in dead plants and animals. In the decomposition of plant debris, certain fungi are particularly important because of their ability to derive their carbon and energy requirements from the break down of dead and decaying plant cell walls, cellulose and lignin. They are much less dependent on water than other microorganisms, but interactions with other microbes, temperature and nutrient availability will have an effect on their activity. Fungal activity is greatest in decomposing leaves and wood, and tends to diminish in the later stages of decomposition when bacteria become more dominant.
What are mycorrhizal fungi?
Mycorrhizas are associations between fungi and plant roots that can be beneficial to both the plant and the fungi. The fungi link the plant with soil by acting as agents of nutrient exchange. The fungi receive carbohydrates as energy from the host plant root whilst nutrients such as phosphorus and zinc are passed back into the plant roots from the soil. Mycorrhizal associations may also reduce attack from root pathogens and increase the tolerance of the plant to adverse conditions such as heavy metals, drought, and salinity. In general, mycorrhizas play an important role in sustainable plant productivity and maintenance of soil structure.
Mycorrhizal associations occur on almost all terrestrial plants and are not as plant-specific as other plant-microbe associations that formed between some plants (e.g. legumes) and bacteria (e.g. rhizobia).
“Some plant species, such as crucifers (i.e. broccoli) are unusual in that mycorrhizal symbioses are absent. Species with fine root hairs and many root hairs are not as dependent on mycorrhizae as species with well-defined tap roots” (Coyne, 1999).
Are there different types of mycorrhizal associations and what plants are involved with them?
There are four main kinds of mycorrhizal fungi: arbuscular, ectomycorrhizal, ericoid and orchid mycorrhiza. Most agricultural plants, vegetables and orchard plants form arbuscular mycorrhizal associations. Ectomycorrhizal associations are less common in disturbed ecosystems and are more common on perennial plants than annuals. Ornamental plants form associations from each of the four groups and orchid mycorrhizal associations are formed only by orchids.
What are Vesicular Arbuscular Micorrhizae?
The most common type of mycorrhizas are the arbuscular mycorrhizas. They are found in natural ecosystems as well as in agricultural areas, are common on both perennials and annuals, and form associations with most agricultural plants. Two exceptions among agricultural crops are canola (oilseed rape) and lupin.
Arbuscules are believed to be the major site where the carbon and nutrient exchange between plant and fungus occurs. Named because of their "tree-like" structure, arbuscules are created by repeated branching of hyphae once they enter a cell within a plant root.
Vesicles are structures formed inside a cell within the plant’s roots. They can be regular or irregular in shape and many times wider than the hyphae on which they form. Therefore, vesicles are usually very distinctive and in some species can resemble spores. These structures are known as a place for storing nutrients. Only three of the fivegenera of arbuscular mycorrhizas (Glomus, Acaulospora and Entrophosphora) form vesicles.
The fungi are grouped according to the size, shape and wall structure of their spores. The spores are approximately spherical or ovoid in shape and usually have thick walls which allow them to survive harsh environmental conditions. When soil conditions are favourable, the spores germinate and hyphae grow from the spore, entering roots and establishing mycorrhizal associations.
Spores are between 30 and 500 micrometres in size - this is between 30 thousandths of a millimetre and half a millimetre. Identifying and classifying the spores is therefore something that must be done with the aid of a microscope.
What are the benefits of mycorrhizal associations?
Mycorrhizal fungi are characterised by very thin hyphae, which are between 1 and 10 thousandths of a millimetre in width. These hyphae explore the soil for nutrients, transport them back to the host-plant, and help bind soil particles into aggregates. The hyphae form networks between neighbouring soil particles, between roots and soil particles, between roots on the same plant, and between roots of different plants (even different types of plants). They also form networks inside the roots they colonize. These networks of hyphae are also referred to as mycelium.
Mycorrhizas extend the volume of soil explored by the plant, a characteristic that is especially important for phosphorous which does not move in the soil solution as nitrogen does. There is some evidence that the fungi may help the plants tolerate drought. When phosphorus is scarce in soil, plants that have developed mycorrhizas on their root systems have greater access to and take up more phosphorus others. Trace elements, copper and zinc behave in a similar way to phosphorus in soil and plant roots must explore the soil to intercept them.
Although arbuscular mycorrhizas can enhance plant growth in phosphorous deficient soils, the extent to which this occurs in the field in agricultural and natural environments is difficult to measure.
Refer to ‘Soils are Alive’ newsletters Volume 1 Number 2 “Arbuscular mycorrhizal fungi” by Professor Lyn Abbott andVolume 3 Number 2“Mycorrhizas and Olive Trees: Letting nature takes it course” by Tom Ganz, Professor Stan Kailis and Professor Lyn Abbott.
Where do plant pathogenic fungi come from?
Disease-causing microorganisms have always been inherent members of any living community. In natural ecosystems, characterised by uncontrolled and changeable conditions, their population growth is impeded by the scattered distribution of host plants and, in the case of fungal pathogens, by their dependence on rainfall at the time of spore germination. In managed systems, however, such as agriculture and horticulture, monocultures of crop plant species provide an unconstrained food supply for a pathogen. Irrigated systems also provide a constant supply of water which can enable spores to germinate and cause disease in accessible host plants.
What are the most important fungal soil pathogens in Australia?
Climatic patterns can affect the types of fungal pathogens that are dominant in a region. For example, low fertility soils favour necrotrophicpathogens over biotrophic pathogens. Necrotrophic pathogens are distinguished from biotrophs because they kill host tissue prior to colonisation. Biotrophic pathogens include powdery mildew, downy mildew, rust, nematodes and viruses. Biotrophs live on living tissue and die when the host plant dies.
What soil conditions favour the growth of fungal pathogens?
The soil conditions that exist at the opening of the cropping season (warm-moist soils and low microbial activity) can favour the growth of a pathogen.
How do cultural practices affect the incidence or spread of fungal pathogens?
Reduced tillage practices help maintain infested residues at the surface of soil, increasing the damage to young seedlings. Conventional cultivations bury this inoculum source which gets broken-down more rapidly by soil microorganisms than when on the soil surface. Rotations with susceptible hosts can increase the inoculum potential of the pathogen in soil. Certain herbicides also increase the disease severity (e.g: the disease caused by the Take-all fungus and root rot caused by Rhizoctonia).
Soil Bacteria
What do bacteria look like?
Most bacteria in soil are about one micron in length or diameter (there are a thousand microns in a millimetre). Some are slightly larger than this, up to several microns, and in rare cases even larger. Their size varies with their environment. Bacteria in environments that have high levels of nutrients may be larger than those in nutrient poor conditions.
The majority of bacteria in soil usually occur as single cells. Bacteria sometimes join together in chains or clusters. They mainly have one of two shapes - spheres (called cocci) and rods (called bacilli). Other bacteria have more varied shapes including spirals and long thin hyphae (although these are less common).
What do bacteria do in soil?
Bacteria are able to perform an extremely wide range of chemical transformations, including degradation of organic matter, disease suppression, disease, and nutrient transformations inside roots (e.g. reducing bacteria in roots, bacteria cause nitrogen fixation).
Azobacter, for example, is a genus of free-living bacteria that converts atmospheric nitrogen into ammonium, making it available for plant use. This process may only take place, however, if the following conditions are met:
- An easily degradable carbon source is available
- Any nitrogen compounds such as ammonium or nitrate, are not already in present in substantial concentrations
- Soil pH levels are between 6 and 9
- High levels of phosphorus are present
- Very low levels of oxygen are present
In general, bacteria are the organisms in soil that are mainly responsible for transforming inorganic constituents from one chemical form to another. Their system of external digestion means that some of the metabolites released by the use of extracellular enzymes may be used by other organisms, such as plants. The bacteria gain nutrients and energy from these processes and provide other organisms with suitable forms of chemicals they require for their own processes. For example, in the conversions of nitrate to nitrite, sulphate to sulphide and ammonium to nitrite.
Where do bacteria live in soil?
Bacteria are aquatic organisms that live in the water-filled pore spaces within and between soil aggregates. As such, their activities are directly dependent on relatively high soil water contents (Lavelle and Spain, 2001, p. 211).
Bacteria are normally found on the surfaces of mineral or organic particles or congregate around particles of decaying plant and animal debris. Most are unable to move and hence, their dispersion is dependent on water movement, root growth or the activity of soil and other organisms (Lavelle and Spain, 2001, p. 212).
What are rhizobia?
Rhizobia are one of the groups of microorganisms living in soil. They are single celled bacteria, approximately one thousandth of a millimetre in length. Rhizobia belong to a family of bacteria called Rhizobiaceae. There are a number of groups (genera and species) of bacteria in this family.
Rhizobia belong to a specific group of bacteria that form a mutually beneficial association, or symbiosis, with legume plants. These bacteria take nitrogen from the air (which plants cannot use) and convert it into a form of nitrogen called ammonium (NH4+), which plants can use. The nitrogenase enzyme controls the process, called nitrogen fixation, and these bacteria are often called "nitrogen fixers".
Rhizobia are found in soils of many natural ecosystems. They may also be present in agricultural areas where they are associated with both crop legumes (like soybean) and pasture legumes (like clover). Usually, the rhizobia in agricultural areas have been introduced at sowing by applying an inoculum to the exterior of the seeds as liquid formations or pellets.
Refer to ‘Soils are Alive’ newsletter Volume 1 Number 3 “Rhizobia” by Dr Krys Haq.
How are nodules formed on the roots of legumes?
The nodulation process is a series of events in which rhizobia interact with the roots of legume plants to form a specialised structure called a root nodule. These are visible, ball-like structures that are formed by the plant in response to the presence of the bacteria.
The process involves complicated signals between the bacteria and the host roots. In the first stages, the bacteria multiply near the root and then adhere to it. The small hairs on the root's surface curl around the bacteria and they enter the root. Alternatively, the bacteria may enter directly through points on the root surface. The method of entry of the bacteria into the root depends on the type of plant. Once inside the root, the bacteria multiply within thin threads. Signals stimulate cell multiplication of both the plant's cells and the bacteria and this repeated division results in a mass of root cells containing many bacterial cells. Some of these bacteria then change into a form that is able to convert gaseous nitrogen into ammonium nitrogen (that is, they can "fix" nitrogen). These bacteria are then called bacteroids.
The shape of the nodules is controlled by the plant and nodules can vary considerably - both in size and shape.
Most plants need specific kinds of rhizobia to form nodules. The rhizobia that form nodules on peas, for example, cannot form nodules on clover.
Nodulation can be impeded by low pH, Al toxicity, nutrient deficiencies, salinity, waterlogging, and the presence of root parasites such as nematodes or genetic incompatibility with the plant host (Lavelle and Spain, 2001 p.439).
Why are nodules pink inside?
The nitrogenase enzyme is extremely sensitive to oxygen and is only active at low oxygen levels or anaerobic conditions. The physical structure of the nodule acts as a barrier to oxygen and the enzyme leghaemaglobin binds oxygen and transports it away from nitrogenase to respiratory sites. Leghaemoglobin gives the inside of nodules their reddish-pink colouring.
What are some of the other plant-bacterial associations that fix atmospheric nitrogen?
Associations between bacteria and plants that fix atmospheric nitrogen include an association between species of Frankia bacteria and several tree species such as those of the genera Casuarina and Allocasuarina. Another example is between that of Azospirillum and grasses.
Fungi vs Bacteria: Their Different Roles in Decomposition of Organic Matter
Even though a high proportion of both fungi and bacteria are decomposers in the soil, they degrade plant residues differently and have different roles in the recycling of nutrients. This is partly due to their different choice of habitats within the soil and the different types of organic matter they consume.
Fungi are generally much more efficient at assimilating and storing nutrients than bacteria. One reason for this higher carbon (C) storage by fungi lies in the chemical composition of their cell walls. They are composed of polymers of chitin and melanin, making them very resistant to degradation. Bacterial membranes, in comparison, are phospholipids, which are energy-rich. They degrade easily and quickly and function as a food source for a wide range of microorganisms.
The different proportions of C and N (i.e. different C:N ratios) of bacteria and fungi might also play a role in the mineralisation and immobilisationprocesses of nutrients in the soil. Due to their structure and C:N ratio between 7:1 and 25:1, fungi need a greater amount of carbon to grow and reproduce and will therefore 'collect' the required amount of carbon available for this from the soil organic matter. Bacteria, however, have a lower C:N ratio (between 5:1 and 7:1) and a higher nitrogen requirement and take more nitrogen from the soil for their own requirements.
Refer to ‘Soils are Alive’ newsletter Volume 3 Number 3 “The fungal-bacterial ratio: Tipping the balance for soil health” by Florian Wichern.
Measuring and Identifying Soil Organisms
How can the amount of microorganisms in a soil be measured?
The whole mass of living organisms in soil is called its microbial biomass. It can be estimated by measuring the amount of carbon, nitrogen, phosphorus or sulfur that is present in the microorganisms, small animals and algae in the soil. There are a number of different ways of measuring microbial biomass.
For example:
- The fumigation-incubation technique: Two samples of soil are collected. One is not treated; this is called the untreated soil. The other sample is treated with fumigant to kill all the organisms in it. Living organisms are then added back into the fumigated soil and the sample is left to incubate. During incubation, the living organisms degrade a proportion of the dead organisms. The difference between the amount of carbon dioxide released from the untreated soil and the treated soil samples is used to estimate the amount of respiration that has occurred during the degradation process. Respiration is then used to estimate the amount of carbon degraded which correlates to a certain biomass of microbes. (Only a proportion of the organisms will be degraded, so this is taken into account).
- The fumigation-extraction method: Two soil samples are collected, one remains untreated and the other is fumigated to kill all the organisms. Chemical tests are done on the fumigated soil to extract the ninhydrin-positive compounds. Carbon, nitrogen, or phosphorus that has been released from the dead microorganisms is then measured to determine microbial levels.
- The substrate-induced respiration method: Two soil samples are collected, one remains untreated and the other is fumigated to kill all the organisms. A source of energy (eg sugar) is added to the other sample, so that the organisms in the soil can be more active. When they are more active, they respire (breathe) more and so release more carbon dioxide into the soil. The amount of carbon dioxide released by the organisms in the treated soil is then compared to the untreated soil to calculate the probable mass of microorganisms in the soil.
- Using ATP or enzyme activity: ATP is the name given to one of the molecules that carries energy inside living things. Enzymes are proteins that help reactions to go faster. The amounts of ATP and specific enzymes in soil indicate how many organisms are in that soil.
The number of individual soil animals in the soil is enormous. In all but the driest environments there are billions of protozoa per square metre (m2), millions of nematodes/m2 and 100 000’s of mites/m2. Data from east Beverley in Western Australia indicates that there were approximately 800 million protozoa/m2, 900 000 nematodes/m2 and 130 000 mites/m2 in a soil under pasture.
What techniques are used for identifying soil organisms?
Soil organisms are identified by looking at:
- Morphology (their structure and shape)
- Physiology (what happens inside them)
- Genetic characteristics (their DNA structure)
- Ecological characteristics (where they live, how they interact with other living things), and
- Molecular characteristics (whether they have particular parts of genes and the type of proteins or molecules they produce)
How are rhizobia identified?
Rhizobia are bacteria which can grow and multiply on artificial food sources. They are very difficult to identify from their shape or size alone because all forms are extremely small, short rods with rounded ends.
Recently, new methods of rhizobia characterisation have been developed using DNA patterns from known rhizobia grown under laboratory conditions. Comparisons are made between sections of the known DNA molecule that code for particular functions (eg. nitrogen fixation) with samples of DNA from soil or from a root nodule. This tells the scientists whether there are genes for that function in the soil sample or root nodule.
Serological techniques can also be used to identify rhizobia. Samples of known bacteria are injected into an animal under specific laboratory conditions. The animal's body produces antibodies against the bacteria. (A process that is similar to vaccination). The component of the blood containing the antibodies is the serum and this is separated from the red blood cells. This is called antiserum.
The antiserum produced by the animal can be collected and used to help locate bacteria in a sample. The antibodies in the antiserum can be joined to a fluorescent dye or to an enzyme with an attached dye. When the antibody is added to the corresponding bacteria it attaches firmly. The bacteria can then be identified using a fluorescence microscope or in a solution that contains a molecule that can interact with the enzyme and cause a colour change in the solution. This method is called the ELISA method.
The antiserum can be chosen to be very specific for particular types of rhizobia, so it is a good way to identify whether those rhizobia are present in a root nodule. It is often important to know whether the rhizobia that were added with the seed have actually been responsible for forming the nodules on the legume or whether other rhizobia already in the soil formed the nodules.
Glossary
Lewis, 1973)
Lewis, 1973)
Bettleheim and March, 1991)
References
Bettleheim, Frederick A., and March, Jerry (1991) Introduction to General, Organic and Biochemistry (Third edition) p. 516. Saunders College Publishing, USA.
Coyne, Mark (1999) Soil Microbiology: An Exploratory Approach. pp. 337-347. Delmar Publishers, New York.
Lavelle, P. and Spain, A.V. (2001) Soil Ecology, pp 201-356 Kluwer Academic Publishers, The Netherlands.
Lewis, D.H. (1973) Concepts in fungal nutrition and the origin of biotrophy. Biol. Rev. 48, 261-278.
http://www.soilhealth.see.uwa.edu.au/components/measuring
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