In most ecosystems, more life and diversity exists underground than above. The soil is home to a vast array of organisms, including bacteria, cyanobacteria, algae, protozoa, fungi, nematodes and mites, insects of all sizes, worms, small mammals and plant roots.
Role of soil organisms
Soil organisms play critical roles in plant health and water dynamics. Processes that soil organisms contribute to include:
Water infiltration and water-holding capacity.
Degradation of pollutants.
Increasing the soil’s biological diversity.
Improving soil structure.
Soil biological processes are responsible for supplying approximately 75 percent of the plant-available nitrogen and 65 percent of the available phosphorus in the soil.
Like all organisms, those inhabiting soil need food and a favorable environment. Adequate organic matter content, ample aeration, moderate moisture, neutral pH and warm temperatures all favor increased microbial activity.
Benefits of organic matter
By maintaining a high soil organic matter content, food and a favorable habitat can be built for a diverse community of soil organisms. Not only does organic matter provide good habitat, but it also greatly benefits chemical and physical soil characteristics.
Moisture, pH, nutrient supply and the biological community are all more stable, or buffered, as soil organic matter increases. Organic material also helps maintain soil porosity, which is essential because most beneficial soil microbes and processes are aerobic, meaning they requiring oxygen.
Understanding soil biology
Most biological activity takes place in the top 8 to 12 inches in the soil profile. The rhizosphere, or rooting zone, is an area of intense microbial activity and is integral to plant and soil relationships.
Plant roots leak energy-rich carbon compounds, sugars and amino and organic acids called exudates. Every plant species leaks a unique signature of compounds from their roots. Different microbes are attracted to different chemical exudates. The plants grown play a large role in determining the microbial community in the soil below.
Bacteria are the smallest and most numerous of organisms in the soil. Collectively, there are billions of individuals in an ounce of soil. Some experts think less than half of the species of bacteria, and therefore their functions, have been identified.
Most bacterial species are decomposers that live on simple carbon compounds, root exudates and plant litter. They’re the first on the scene when nutrients and residue are added to the soil. They convert these compounds into forms readily available to the rest of the organisms in the food web.
Actinomycetes are an example of microbial decomposers (Figure 1). They grow hyphae like fungi, but are closer to bacteria in their evolutionary history. Actinomycetes arrive later in the decomposition process, and are responsible for the “earthy” smell of freshly tilled soil.
Other bacterial species form partnerships with plants. The most well-known of these are the nitrogen-fixing bacteria, rhizobium, which form symbiotic relationships with legumes, such as alfalfa, soybeans, edible beans and clover.
Rhizobium infect the roots of the host plant (Figure 2) and convert atmospheric nitrogen (N2) into plant-available ammonium (NH4+). In return for supplying the plant with all its nitrogen (N) needs, the host plant supplies the rhizobium with simple carbohydrates.
The plant can give up to 20 percent of its carbohydrate supply to the bacteria. However, if there’s a sufficient supply of nitrogen in the soil to meet the plant’s needs, the plant won’t engage in a relationship with the bacteria.
A healthy, well-nodulated legume crop can supply its own N needs. In addition, it can produce extra N which will be available for the next crop. This results in a “nitrogen credit,” which should be factored in when making N fertilizer recommendations.
It may be difficult to account for all of the sources that contribute to this credit. One source is nitrogen mineralized from the legume’s old roots and leaves. Another source is the beneficial microbial community created by the legume. Table 1 shows the nitrogen credits that can be expected from different legumes for first-year corn. Corn nitrogen credits are from the University of Minnesota Extension.
Table 1: Nitrogen credits in the first year of corn following a legume
|Legume crop||First-year nitrogen credit|
|Soybeans||30 pounds of N per acre|
|Alfalfa (credit depends on soil type, time of termination and stand age)||0-170 pounds of N per acre|
|Group 1 crops*||75 pounds of N per acre|
|Edible bean||20 pounds of N per acre|
|Field pea||20 pounds of N per acre|
*Group 1 crops include alsike clover, birdsfoot trefoil, grass-legume hay, grass-legume pasture, fallow and red clover.
Crop-specific rhizobium species
For each legume species there’s a corresponding rhizobium. For example, the rhizobium species for soybeans is Bradyrhizobium japonicum, while the species for alfalfa is Sinorhizobium meliloti.
To effectively inoculate the soil, you must use the rhizobium specific to the legume grown. If you introduce a legume into a soil that hasn’t previously been cropped to that species, it’s unlikely the soil will contain sufficient numbers of the correct rhizobia.
In these cases, a yield response to seed inoculation is likely. Where such inoculation is properly carried out, nodule senescence at the end of the growing season will return large numbers of rhizobia to the soil.
This should ensure inoculation in future years won’t be necessary. However, there’ve been benefits from inoculation if the crop hasn’t been grown in the last three to five years in that field.
Rhizobium are easily applied to the seed, and the preferred inoculant for any legume is a sterile peat-based culture. However, you can also supply inoculants in a non-sterile peat, as a liquid or frozen concentrate or as a clay-based or granulated peat preparation.
In the United States, more than one strain is generally included in an inoculant, but in Australia, Canada and France, the inoculant usually contains only a single strain. Control of inoculant quality is also more formalized in Australia and Canada than in the United States.
Nitrifying bacteria, Nitrosomonas and Nitrobacter, convert ammonium (NH4+) to nitrite (NO2-) and then to nitrate (NO3-). Nitrate is the preferred form of nitrogen by row crops.
Strategies to avoid leaching
However, nitrate is also the nitrogen form that’s most easily leached out of the root zone.
Only make fall applications of anhydrous ammonia after the soil temperature at a 6-inch depth is 50 degrees Fahrenheit or below. Nitrifying bacteria have very low activity below this temperature, reducing the risk of nitrate leaching losses from overwintering.
In addition, the very low vapor pressure of ammonia below 50 degrees virtually eliminates direct loss of ammonia during or after application. Table 2 lists the time it takes nitrifying bacteria to convert different N fertilizers to nitrate-N. Source: Laboski (2006).
Table 2: Conversion rate of different fertilizer sources to nitrate-N
|Fertilizer material||Conversion time to nitrate|
|Ammonium sulfate (10-34-0, MAP, DAP)||1-2 weeks|
|Anhydrous ammonia||3-8 weeks|
|Ammonium nitrate||Nitrate (50%) = 0 weeks
Ammonium (50%) = 1-2 weeks
|Urea-ammonium nitrate (UAN)||Urea (50%) = 1.5-3 weeks
Ammonium (25%) = 1-2 weeks
Nitrate (25%) = 0 weeks
Some bacteria can live without oxygen or in anaerobic conditions. Denitrifying bacteria are an example of anaerobic bacteria that convert nitrate (NO3-) to nitrous oxide gas (N2O) and then to nitrogen gas (N2).
Once the nitrogen is in a gaseous form, it’s no longer available for plant uptake and will escape back to the atmosphere. There are 13 different species of bacteria responsible for this process. They become active when the soil has at least 50 percent of its pore space filled with water, and are most active when the soil is saturated.
Denitrifying bacteria under saturated conditions can convert 2 to 4 pounds of nitrate to a gaseous form per acre per day. Commercial products can reduce the potential for nitrogen loss from either volatilization or leaching. The two most popular choices are described below.
The goal for all fall applications of N fertilizer should be to keep as much nitrogen as possible in the ammonium (NH4+) form going into the winter. With this strategy, only small amounts are present in the nitrate (NO3-) form and, thus, not subject to spring losses caused by leaching and denitrification.
Nitrapyrin, a nitrification inhibitor, selectively inhibits Nitrosomonas spp. bacteria (Figure 3), which in turn slows or stops the conversion of ammonium to nitrite. Two commercially available formulations of nitrapyrin are N-Serve and Instinct II.
N-Serve is typically added to anhydrous ammonia and other solid fertilizers to prevent the conversion of ammonium to nitrate, but it must be incorporated to be effective. Instinct II is formulated for use with liquid fertilizers and manure.
An Illinois study found that the earlier ammonia is applied in the fall, the more ammonia is converted to nitrate, increasing the potential for leaching (Table 3). Adding a nitrification inhibitor decreased the conversion rate, but didn’t entirely stop it.
Values in table 3 are shown by application date, and with and without a nitrification inhibitor in northern Illinois in 2004. Source: Hoef
Table 3: Rate of conversion of anhydrous ammonia to nitrate by May 25
|Application date||Ammonia without N inhibitor||Ammonia with N inhibitor|
|Nov. 1, 2003||85% conversion to nitrate||55% conversion to nitrate|
|Dec. 1, 2003||60% conversion to nitrate||45% conversion to nitrate|
|March 15, 2004||50% conversion to nitrate||20% conversion to nitrate|
|April 1, 2004||35% conversion to nitrate||15% conversion to nitrate|
Effect on corn yield
Another study conducted in Waseca sought to look at the effects of a nitrification inhibitor on corn yield over a 14-year period. Average corn yields showed that yield from spring-applied anhydrous ammonia by itself and fall-applied anhydrous ammonia with a nitrification inhibitor was equal.
However, the yield from fall-applied nitrogen without a nitrification inhibitor was lower for only six of the 14 years. Therefore, there’s no guarantee that using an inhibitor with anhydrous ammonia (82-0-0) in the fall will increase yields.
Key takeaways: Nitrification inhibitors
Nitrogen loss is a complex relationship and not an exact science. It’s based on the:
Timing of nitrogen application.
Rainfall totals and intensity.
Both of these studies stress that using a nitrification inhibitor must be viewed as an insurance policy, not a guarantee.
Urease enzyme inhibitors, such as Agrotain, are designed to delay ammonia volatilization when applied with urea or urea-containing fertilizers, such as ammonium nitrate (UAN). This delay allows more time to get the urea incorporated into the soil through rainfall before N losses occur.
You’ll get the greatest benefit from these inhibitors if you surface-apply urea-based fertilizers or if the fertilizer isn’t fully incorporated, such as in a no-till system.
An Illinois evaluation found that, in most studies, combining Agrotain with urea gave greater yield increases (average 14 bushels per acre) than using Agrotain with UAN (average of 7 bushels per acre).
Researchers observed the greatest yield benefit (30 bushels per acre) from Agrotain when applied with urea to corn in a corn-soybean rotation. Yield decreases with Agrotain application also occurred; 7 percent of the sites saw yield reductions of 10 bushels per acre or more.
Consistent crop yield increases aren’t expected every year or on all fields. Benefits will likely occur 30 to 40 percent of the time, with negative impacts on yield 5 to 10 percent of the time.
Overall, these data highlight that when conditions for N loss exist, Agrotain can help prevent N loss. However, yield gains won’t necessarily be realized every year.
Fungi are a critical contributor to decomposition and nutrient cycling. Fungal activity is often slower to develop than bacteria and is more active on relatively high carbon-to-nitrogen ratio (C:N) and lignin-containing materials, such as corn residue.
Fungi, more so than bacteria, enhance soil physical structure and add chemical compounds that bind soil aggregates and serve as building blocks for organic matter (Figure 4).
Although most fungi are beneficial, several species are notorious as pathogens, including:
Sclerotinia, also known as white mold (Figure 5).
Arbuscular mycorrhizae (AM)
One particularly beneficial and important type of fungi is arbuscular mycorrhizae (AM). These fungi form a mutually beneficial relationship with 80 percent of all land plants, including most agricultural crops (Figure 6).
Role in crop growth
AM fungi are critical in the early establishment and growth of corn and most cereal crops. They’re also important to sunflower, soybeans, flax and potatoes.
Mycorrhizal hyphae are one-tenth the size of root hairs and extend throughout the plant’s soil-mobilizing nutrients (Table 4). In exchange, the fungi receive food from the plant in the form of carbohydrates.
Similar to the relationship between a leguminous plant and a bacterial rhizobium, colonization of plant roots by AM will be inhibited if the plant has sufficient levels of soil phosphorus.
Values in table 4 are for when no phosphorus is applied. Source: Lambert, Baker, & Cole (1979).
Table 4: Nutrients taken up by corn plants with and without AM infection
|Element||No Mycorrhizae||With Mycorrhizae|
|Phosphorus||750 micrograms per plant||1,340 micrograms per plant|
|Potassium||6,000 micrograms per plant||9,700 micrograms per plant|
|Calcium||1,200 micrograms per plant||1,600 micrograms per plant|
|Magnesium||430 micrograms per plant||630 micrograms per plant|
|Zinc||28 micrograms per plant||95 micrograms per plant|
|Copper||7 micrograms per plant||14 micrograms per plant|
|Manganese||72 micrograms per plant||101 micrograms per plant|
|Iron||80 micrograms per plant||147 micrograms per plant|
Due to the hyphal density of the fungi on the plant root, AM are known to increase resistance of the host plant to root diseases by acting as a physical barrier. Figure 7 shows the direct effect of hyphae on a nematode. Additionally, AM can increase water efficiency and drought tolerance in times of low soil moisture.
Keys to survival
Fungi need oxygen, nutrients, neutral pH and a host to survive. Crops that are non-hosts and therefore don’t support AM establishment are canola, sugarbeet, mustard, lupines and other brassicas.
Frequently, saturated soils or black fallow will dramatically decrease the number of AM. Other agents that’ll decrease their populations are ammonia present in alkaline soils, aluminum and possibly tannins from leaf litter.
Similar to rhizobium, AM fungi inoculants often benefit crops when low populations of the correct species or strains are present in the soil.
Generally, inoculated organisms won’t last long if the environment isn’t suitable. If the environment is suitable, the organisms are probably there anyway. Good organic matter content along with good moisture and aeration are all that most beneficial microbes need.
Unlike rhizobium, AM aren’t easily applied to the seed. Mycorrhizae can’t be grown in artificial medium and must be cultured on plant roots.
This is why the seed is coated with clay granules that contain the appropriate strain of AM. Because of this process, inoculation of AM is difficult and economical only for horticulture crops, turf grass or high-value crops.
Nematodes are microscopic, worm-like organisms that are very abundant in the soil. Nematodes are beneficial because they enhance the rate of nutrient cycling by grazing on bacteria and other microorganisms, or by eating organic matter and debris.
A few nematodes are plant parasites, such as the soybean cyst nematode (Figure 8). Root-feeding nematodes use their stylets to puncture the thick cell wall of plant root cells and siphon off the internal contents.
How nematodes work
Bacteria and fungi are high in protein that, in turn, is high in nitrogen. When these nematodes eat bacteria or fungi, they digest the protein and excrete nitrogen into thin a form that becomes available to plants.
Nematodes are a biological control agent of armyworms, root weevil, black cutworm, grubs, Japanese beetles, ants, fleas and more than 250 other soil-dwelling pests.
When nematodes come into contact with their prey, they attack by entering through body openings or simply by boring through the body wall. Once inside, the nematode releases mutualistic bacteria from its gut that kills the host organism within 24 to 48 hours. Such nematodes will feed and reproduce before exiting in search of fresh prey.
Beneficial and infective nematodes
Beneficial soil nematodes are usually more abundant in crop management systems that include multiple crop sequences, reduced cultivation and the addition of organic amendments.
Infective juveniles are compatible with most, but not all, agricultural chemicals under field conditions. Many chemicals recognized to be toxic to nematodes only have a transient effect, and nematodes recover quickly after exposure.
It’s important to remember the general philosophy that beneficial soil organisms need to be needed.
That is, if the farm system depends on and supports their activities, more biomass and positive activities will develop. If the farm system solely depends on chemical inputs instead of biological inputs, beneficial biomass and activities will decline.
Some fertilizers and agrochemicals negatively impact soil microbes. Anhydrous ammonia, some nematicides and ammonia-rich and sulfur-rich fertilizers can directly harm soil life or indirectly hamper their growth by decreasing soil pH (acidification).
Increased pest and pathogen problems are often caused by insufficient rotation interval between crops. This is at least partially due to reduced biological diversity and weakened communities of beneficial organisms.
If the soil microbes aren’t working for you they are more likely to work against you. Soil biota includes hundreds of pathogens, which are more likely to dominate the soil community if beneficial organisms have declined. When beneficials dominate the community, they suppress pathogens by competition and predation, and act as a physical protective barrier for plant roots.
Effect of tillage
Tillage directly affects soil porosity and the placement of residues. Porosity determines the amount of air and water the soil can hold. Residue placement affects the soil surface temperatures, evaporation rate and water content, nutrient loading and rate of decay.
In other words, tillage collapses the pores and changes the soil’s water-holding, gas and nutrient exchange capacity. Reducing soil disturbance increases the diversity and population of soil organisms. These soils gradually release nutrients and have better soil structure than full-width tillage systems.
A more diverse soil community results in a more flexible soil. This means a soil has the ability to successfully grow a number of crops and is resilient in drought, low-nutrient conditions and after a disturbance. Agricultural practices such as tillage, crop rotations and fertilizer inputs affect the soil community’s numbers, diversity and functioning.
Organic matter from roots, plant biomass, manure and compost provide the food energy to support the biological community. Cover crops and green manure crops increase the length of time that plants are actively growing in a soil, providing a steady influx of food for soil microbial populations.
Cover crops also aid in reducing soil erosion. Diverse crop rotations can also help disrupt some pathogen cycles.
How to promote soil biodiversity
Regularly add organic matter (cover crops, green and livestock manures).
Diversify the type of plants across the landscape (crop rotation, grass waterways and Conservation Reserve Program).
Maintain residue cover.
Avoid excessive soil disturbance (intensive and secondary tillage, compaction, heavy use of pesticides).
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Reviewed in 2018