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SOIL SCIENTIST
To understand why management practices make a difference to soil life, it helps to back up and examine the vast diversity of micro- and macro-organisms living in the soil and the critical roles they play in agriculture.
What Lives in Your Soil?
The soil ecosystem is tremendously varied - more-so than many above-ground plant and animal food webs. Each species has slightly different requirements. Aerobic microbes require oxygen. Anaerobes require the absence of oxygen. Some prefer either a high or a low pH, or high or low moisture. Many organisms can digest simple sugars, while only a few species have the enzymes to digest lignin, a major component of woody tissue.
At the microscopic level, soil conditions can change drastically from one point to the next, so a variety of organisms may be present in a single soil sample. Aerobes may live near anaerobes. Organisms requiring high pH may live near those preferring low pH.
Microbes differ greatly in how they get their energy. Most soil organisms are heterotrophs that get their energy and carbon from breaking down organic compounds. In contrast, the autotrophs use inorganic carbon (carbon dioxide). There are two groups of autotrophs. Phototrophs, such as plants and a few soil organisms, get their energy from light. Chemotrophs are a small, but important, group of soil bacteria that get their energy from oxidizing inorganic compounds including ammonium, nitrite, and sulfur compounds.
Macro-organisms, such as mites, beetles, and earthworms, are also tremendously varied in what they eat, their life cycle, and what agricultural conditions they will or will not tolerate. Each plays a different role in eating and breaking down plant residue and their fellow soil organisms.
What Do Soil Organisms Do?
Healthy soil is a jungle of rapacious organisms devouring everything in sight (including each other), processing their prey or food through their innards, and then excreting it. The value of these creatures to farmers lies in:
One of the important functions of the soil biological community is managing nutrients. Soil organisms continually transform nutrients among many organic and inorganic forms. (Organic compounds contain carbon. Inorganic compounds do not.) Plants primarily need simple inorganic forms of each nutrient. Soil organisms create many of these plant-available nutrients and help store nutrients in the soil as organic compounds.
Decomposition is the breakdown of plant and animal residue into different organic and inorganic compounds. Soil organisms decompose organic matter more quickly under warm, moist conditions than under cold or dry conditions. This is why it is easier to build up soil organic matter levels in the Midwest than in the southeastern part of the United States, where decomposition is rapid.
As part of the decomposition process, many bacteria and fungi produce humic acids. In the soil, these acids chemically combine with each other to form large molecules of stabilized organic matter. This formation of large molecules is both a biological and chemical process.
When soil organisms convert organic matter into inorganic, plant-available nutrients, they are said to be mineralizing nutrients. Protozoa and nematodes mineralize and excrete several hundred pounds of ammonium (NH[SUB]4[/SUB]+) per acre per day. Most is snatched up by other soil organisms, but some is used by plants.
The reverse of mineralization is immobilization - the conversion of inorganic compounds into organic compounds. Soil organisms consume inorganic molecules and incorporate them into their cells. Because immobilized nutrients are parts of soil organisms, they do not move easily through the soil and are unavailable to plants. Bacteria and fungi are responsible for large amounts of immobilization.
The previous paragraphs described three kinds of transformations performed by many soil organisms:
Nitrifying bacteria convert ammonia (NH3) into nitrate (NO3+). Plants prefer nitrate, but nitrate is easily leached from the soil. Some farmers apply "nitrification inhibitors" which reduce the activity of nitrifying bacteria and prevent the loss of fertilizer nitrogen from the soil.
Denitrifying bacteria convert nitrate into gases that are lost into the atmosphere. These species are anaerobic so denitrification occurs only in places in the soil where there is little or no oxygen. Anaerobic conditions are more common in compacted soils and in no-till soils.
Other soil bacteria are important for similar mineral transformations of sulfur, iron, and manganese.
Forming soil structure
Most crops grow best in crumbly soil that roots can easily grow through and that allows in water and air. Soil organisms play an important role in the formation of a good soil structure.
As spring turns to summer and the soil heats up, fungi grow long filaments called hyphae that surround soil particles and hold them together in soil aggregates. Some bacteria produce sticky substances that also help bind soil together.
Many soil aggregates between the diameters of 1/1000 and 1/10 of an inch (the size of the period at the end of this sentence) are fecal pellets. Arthropods and earthworms consume soil, digest the bacteria, and excrete a clump of soil coated with secretions from the gut. As beetles and earthworms chew and bury plant residue and burrow through the soil, they aerate the soil and create nutrient-lined channels for roots and water to move through.
Controlling disease and enhancing growth
Soil organisms have many methods for controlling disease-causing organisms. Protozoa, nematodes, insects, and other predatory organisms help control the population levels of their prey and prevent any single species from becoming dominant. Some bacteria and fungi generate compounds that are toxic to other organisms. Some organisms compete with harmful organisms for food or a location on a root.
In addition to protecting plants from disease, some organisms produce compounds that actually enhance the growth of plants. Plant roots may excrete compounds that attract such beneficial organisms.
How Do Soil Organisms and Plants Get Along?
The lives of plants and soil organisms are closely intertwined. Some plant and microbe species have developed symbioses, or mutually beneficial relationships. Rhizobium and other bacteria can invade roots and get sugars from the plant. In return, they fix atmospheric nitrogen into a form that plants can use.
Another group of friendly root-invaders are the mycorrhizal fungi. The fungal hyphae extend from inside the root, out into the soil, and often greatly expand the plants access to nutrients and (perhaps) water. Mycorrhizae improve phosphorus nutrition by producing acids that convert phosphorus into plant-available forms and transport the phosphorus back to the root. Most crop species depend on or benefit greatly from mycorrhizal associations.
Not all plant/microbe interactions are invasions. The rhizosphere (the narrow region surrounding each root) is rich in biological activity as bacteria and other microbes feed on the carbon compounds exuded by roots. Plants may exude compounds that attract certain species to the rhizosphere that protect the roots from disease-causing species.
When microbes and plants compete for soil nutrients, microbes have an advantage because they are often suspended in the soil solution while plants must pull the soil solution towards their roots.
In an ideal situation, microbes will tie-up (immobilize) nitrogen and prevent its loss from the rooting zone when plants are not growing, and then will release (mineralize) nitrogen when crops are actively growing. See Organic Matter Management (BU-7402 in this series) for more information about competition between microbes and plants for nitrogen.
When Do Soil Organisms Do Their Work?
The activity of organisms is constantly changing with temperature, moisture, pH, food supply, and other environmental conditions. Different species prefer different conditions, so even at maximum total activity levels only a minority of soil microbes are busily eating and respiring. The highest total activity is in late spring/early summer and in late summer/early fall when the soil is warm and moist. In early spring, some farmers see nutrient deficiency symptoms in their plants because not enough microbes are warm enough to convert organic compounds into plant-available nutrients. Leaching of excess nitrate often happens in early spring when the soil is too cool for either plants or microbes to grow and immobilize the nitrogen.
What Lives in the Soil and What Are They Doing?
Each type of organism fills a unique niche and plays a different role in the cycling of nutrients, the structure of soil, and in pest dynamics.
Why is Diversity Important?
Like the above-ground ecosystem, the soil community is not just a collection of individual species, but a complex, interacting food web. Decomposition of a single compound may require several organisms. The creation of aggregates involves a mix of physical and chemical processes and the activity of many types of organisms.
As the complexity of the food web increases, productivity of the soil tends to increase. It is not clear how much complexity is needed, but there are several reasons why complexity is thought to be beneficial.
First, the soil system may be more stable and resilient. If many organisms perform a similar role, the system is not dependent on just a few for that function. A soil disturbance (such as drought or tillage) might reduce the activity of some organisms, but in a complex system others will perform the same functions (such as providing ammonium or degrading a particular compound).
Other benefits of complexity may include improved nutrient cycling, decomposition, and disease control. When many different kinds of organisms are present, many organic compounds and potential pollutants can be degraded, and many competitors and predators are present to control pest populations.
To understand why management practices make a difference to soil life, it helps to back up and examine the vast diversity of micro- and macro-organisms living in the soil and the critical roles they play in agriculture.
What Lives in Your Soil?
The soil ecosystem is tremendously varied - more-so than many above-ground plant and animal food webs. Each species has slightly different requirements. Aerobic microbes require oxygen. Anaerobes require the absence of oxygen. Some prefer either a high or a low pH, or high or low moisture. Many organisms can digest simple sugars, while only a few species have the enzymes to digest lignin, a major component of woody tissue.
At the microscopic level, soil conditions can change drastically from one point to the next, so a variety of organisms may be present in a single soil sample. Aerobes may live near anaerobes. Organisms requiring high pH may live near those preferring low pH.
Microbes differ greatly in how they get their energy. Most soil organisms are heterotrophs that get their energy and carbon from breaking down organic compounds. In contrast, the autotrophs use inorganic carbon (carbon dioxide). There are two groups of autotrophs. Phototrophs, such as plants and a few soil organisms, get their energy from light. Chemotrophs are a small, but important, group of soil bacteria that get their energy from oxidizing inorganic compounds including ammonium, nitrite, and sulfur compounds.
Macro-organisms, such as mites, beetles, and earthworms, are also tremendously varied in what they eat, their life cycle, and what agricultural conditions they will or will not tolerate. Each plays a different role in eating and breaking down plant residue and their fellow soil organisms.
What Do Soil Organisms Do?
Healthy soil is a jungle of rapacious organisms devouring everything in sight (including each other), processing their prey or food through their innards, and then excreting it. The value of these creatures to farmers lies in:
- Cycling nutrients.
- Enhancing soil structure, which improves water and air movement.
- Controlling disease and enhancing plant growth.
One of the important functions of the soil biological community is managing nutrients. Soil organisms continually transform nutrients among many organic and inorganic forms. (Organic compounds contain carbon. Inorganic compounds do not.) Plants primarily need simple inorganic forms of each nutrient. Soil organisms create many of these plant-available nutrients and help store nutrients in the soil as organic compounds.
Decomposition is the breakdown of plant and animal residue into different organic and inorganic compounds. Soil organisms decompose organic matter more quickly under warm, moist conditions than under cold or dry conditions. This is why it is easier to build up soil organic matter levels in the Midwest than in the southeastern part of the United States, where decomposition is rapid.
As part of the decomposition process, many bacteria and fungi produce humic acids. In the soil, these acids chemically combine with each other to form large molecules of stabilized organic matter. This formation of large molecules is both a biological and chemical process.
When soil organisms convert organic matter into inorganic, plant-available nutrients, they are said to be mineralizing nutrients. Protozoa and nematodes mineralize and excrete several hundred pounds of ammonium (NH[SUB]4[/SUB]+) per acre per day. Most is snatched up by other soil organisms, but some is used by plants.
The reverse of mineralization is immobilization - the conversion of inorganic compounds into organic compounds. Soil organisms consume inorganic molecules and incorporate them into their cells. Because immobilized nutrients are parts of soil organisms, they do not move easily through the soil and are unavailable to plants. Bacteria and fungi are responsible for large amounts of immobilization.
The previous paragraphs described three kinds of transformations performed by many soil organisms:
- decomposition: turning organic compounds into other organic compounds
- mineralization: turning organic matter into inorganic compounds that may be used by plants
- immobilization: turning inorganic compounds into organic compounds. Farmers depend on bacteria for one more transformation:
- mineral transformation: turning inorganic matter into other inorganic compounds
Nitrifying bacteria convert ammonia (NH3) into nitrate (NO3+). Plants prefer nitrate, but nitrate is easily leached from the soil. Some farmers apply "nitrification inhibitors" which reduce the activity of nitrifying bacteria and prevent the loss of fertilizer nitrogen from the soil.
Denitrifying bacteria convert nitrate into gases that are lost into the atmosphere. These species are anaerobic so denitrification occurs only in places in the soil where there is little or no oxygen. Anaerobic conditions are more common in compacted soils and in no-till soils.
Other soil bacteria are important for similar mineral transformations of sulfur, iron, and manganese.
Forming soil structure
Most crops grow best in crumbly soil that roots can easily grow through and that allows in water and air. Soil organisms play an important role in the formation of a good soil structure.
As spring turns to summer and the soil heats up, fungi grow long filaments called hyphae that surround soil particles and hold them together in soil aggregates. Some bacteria produce sticky substances that also help bind soil together.
Many soil aggregates between the diameters of 1/1000 and 1/10 of an inch (the size of the period at the end of this sentence) are fecal pellets. Arthropods and earthworms consume soil, digest the bacteria, and excrete a clump of soil coated with secretions from the gut. As beetles and earthworms chew and bury plant residue and burrow through the soil, they aerate the soil and create nutrient-lined channels for roots and water to move through.
Controlling disease and enhancing growth
Soil organisms have many methods for controlling disease-causing organisms. Protozoa, nematodes, insects, and other predatory organisms help control the population levels of their prey and prevent any single species from becoming dominant. Some bacteria and fungi generate compounds that are toxic to other organisms. Some organisms compete with harmful organisms for food or a location on a root.
In addition to protecting plants from disease, some organisms produce compounds that actually enhance the growth of plants. Plant roots may excrete compounds that attract such beneficial organisms.
How Do Soil Organisms and Plants Get Along?
The lives of plants and soil organisms are closely intertwined. Some plant and microbe species have developed symbioses, or mutually beneficial relationships. Rhizobium and other bacteria can invade roots and get sugars from the plant. In return, they fix atmospheric nitrogen into a form that plants can use.
Another group of friendly root-invaders are the mycorrhizal fungi. The fungal hyphae extend from inside the root, out into the soil, and often greatly expand the plants access to nutrients and (perhaps) water. Mycorrhizae improve phosphorus nutrition by producing acids that convert phosphorus into plant-available forms and transport the phosphorus back to the root. Most crop species depend on or benefit greatly from mycorrhizal associations.
Not all plant/microbe interactions are invasions. The rhizosphere (the narrow region surrounding each root) is rich in biological activity as bacteria and other microbes feed on the carbon compounds exuded by roots. Plants may exude compounds that attract certain species to the rhizosphere that protect the roots from disease-causing species.
When microbes and plants compete for soil nutrients, microbes have an advantage because they are often suspended in the soil solution while plants must pull the soil solution towards their roots.
In an ideal situation, microbes will tie-up (immobilize) nitrogen and prevent its loss from the rooting zone when plants are not growing, and then will release (mineralize) nitrogen when crops are actively growing. See Organic Matter Management (BU-7402 in this series) for more information about competition between microbes and plants for nitrogen.
When Do Soil Organisms Do Their Work?
The activity of organisms is constantly changing with temperature, moisture, pH, food supply, and other environmental conditions. Different species prefer different conditions, so even at maximum total activity levels only a minority of soil microbes are busily eating and respiring. The highest total activity is in late spring/early summer and in late summer/early fall when the soil is warm and moist. In early spring, some farmers see nutrient deficiency symptoms in their plants because not enough microbes are warm enough to convert organic compounds into plant-available nutrients. Leaching of excess nitrate often happens in early spring when the soil is too cool for either plants or microbes to grow and immobilize the nitrogen.
What Lives in the Soil and What Are They Doing?
Each type of organism fills a unique niche and plays a different role in the cycling of nutrients, the structure of soil, and in pest dynamics.
| Description | Size | Diet | Typical amt in ag soils | Action in soil |
| Bacteria Usually one-celled | 1 um (0.001 mm) | Organic matter, especially simple carbon compounds | 100 mil. to 1 bil. in a teaspoon | Decompose organic matter. Immobilize nutrients in the rooting zone. Rhizobium and other genera fix nitrogen from air. Convert ammonium to nitrate, and nitrate to nitrogen gasses. Actinomycetes, which grow as filaments, are important in decomposition at moderate-to-high pH. Create substances that help bind soil aggregates. |
| Fungi Grow in long filaments calleed hyphae | A few um wie, yards or miles long | Organic matter, especially simple carbon compounds. Also, living plants | Several yards in a teaspoon | Decompose organic matter. Immobilize nutrients in the rooting zone. Mycorrhizal fungi form mutually beneficial associa- tions with roots. They release acids that help make phosphorus more available to plants. Help stabilize soil aggregates. |
| Protozoa One-celled animals | 5-500 um | Bacteria, primarily | Several thousand in a teaspoon | Stimulate and control growth of bacteria. Release ammonium. |
| Nematodes Roundworms. Not segmented as are earthworms | 50 um wide, 1 mm long | Bacteria, fungi, protozoa, other nematodes, and roots | Ten to twenty in a teaspoon | Control many disease-causing organisms. Root-feeders may cause root diseases. Release ammonium. |
| Arthropods Include insects, mites, spiders, springtails, & millipedes | Microscopic to inches | All other organisms | Several hundred in a cubic foot | Shred plant residue, making it more accessible to bacteria and fungi. Enhance soil structure by creating fecal pellets, and by burrowing. Control populations of other organisms. |
| Earthworms | Inch or more long | Bacteria, fungi, and organic matter | Five to thirty in a cubic foot | Shred plant residue. Enhance soil structure by burrowing, mixing, and creating fecal pellets. Transport and stimulate growth of bacteria. |
Like the above-ground ecosystem, the soil community is not just a collection of individual species, but a complex, interacting food web. Decomposition of a single compound may require several organisms. The creation of aggregates involves a mix of physical and chemical processes and the activity of many types of organisms.
As the complexity of the food web increases, productivity of the soil tends to increase. It is not clear how much complexity is needed, but there are several reasons why complexity is thought to be beneficial.
First, the soil system may be more stable and resilient. If many organisms perform a similar role, the system is not dependent on just a few for that function. A soil disturbance (such as drought or tillage) might reduce the activity of some organisms, but in a complex system others will perform the same functions (such as providing ammonium or degrading a particular compound).
Other benefits of complexity may include improved nutrient cycling, decomposition, and disease control. When many different kinds of organisms are present, many organic compounds and potential pollutants can be degraded, and many competitors and predators are present to control pest populations.
| Nematodes: Good Guys or Bad Guys? Nematodes are a group of tiny roundworms that demonstrate the wide diversity and the inextricable food web that exists in a healthy soil. Twenty thousand species have been described, but half a million species may exist. Most soil nematodes eat bacteria, fungi, protozoa, and other nematodes, making them important in nutrient cycling. Others are plant parasites and cause disease symptoms such as malformed or dwarfed plants, or root structures with deformities such as galls and cysts. The root knot nematode, for instance, stimulates parasitized plants to form root galls. The galls choke off the flow of water and nutrients to the above-ground portion of the plant. Plants infected by root gall nematodes may live through the season but crop yields will be dramatically reduced. One way to respond to nematode problems is to rotate crops to remove the nematodes food source. Another highly effective approach is to build up soil organic matter. The increased organic matter might initially increase nematode populations, but it will also create an explosion of nematode predators such as fungi, mites, and other nematodes. Fungi prey on nematodes in a number of ways. They trap them with their sticky appendages or squeeze them (like a boa constrictor) in fungal mechanical ring traps. Some fungi exude a toxin to quiet their struggling prey. (Think of these vicious dramas next time you are riding safely in your tractor cab!) Some nematodes eat undesirable residents of farm fields. Cut worms, for instance, are hunted down by one species of carnivorous nematode. These nematodes (N. carpocapsae) are available from some biological supply catalogues to control cut worms and other crop-damaging underground caterpillars and beetle larva. Nematodes are not simply pests, but a diverse group of species that play many roles in the soil system. |
Okay just wanted to know what I should do.
