We walk upon a thin and fragile crust of broken and chemically weathered rock mixed with organic and animate matter—soil. It is the life-support substance on which all earthly living organisms depend. It is disappearing under our feet, largely because of human activity. Consider the following:

  • Human-induced soil degradation by wind, water, and pollution affects about 24% of the inhabited land area of the globe.
  • In this century alone, some 10% of the world’s soil has been lost through deforestation, erosion, urban development, and other human-induced abuses of the land.
  • In the last 40 years, approximately 30% of the world’s arable cropland has been abandoned because of severe erosion.
  • In the United States, soil is being lost at 17 times the rate it is being formed.

This loose mantle of minerals and organic matter teems with life. According to Elaine Ingham, Ph.D., a soil biologist and president of Soil Foodweb Inc. in Corvallis, OR, a teaspoon of typical healthy soil contains 600 million or more individual bacteria, 10,000 to 100,000 protozoa, five to 500 beneficial nematodes, and in a square foot of soil, several hundred microarthropods. Fungal mass in healthy soil is astonishing: one thimbleful of soil can contain several thousand feet of mycorrhizal filament.

Soil organisms play a fundamental role in the sustainability of life on earth, and yet we know so little about them. Says Ingham, “There are seven to nine major groups of organisms present in healthy soil, including viruses, worms, insects, arthropods, protozoa, nematodes, bacteria, fungi, and mycorrhizal fungi. Different soils have different numbers of individuals, numbers of species, and total biomass.” In a fertile soil, biomass may exceed 20 tonnes/ha. Although there are far too many species to list, here is a tour of the most important players and a glimpse at their day-to-day activities.

Bacteria are decomposers of easy-to-use substrates and a few plant pathogens. They often live in colonies of thousands or millions of individuals, all of the same species. Many of these colonies produce substances that act as glue to hold soil particles together. Some bacteria fix atmospheric nitrogen and convert it into a form that is available to plants, while some change ammonium to nitrate and others turn nitrate into nitrous oxide or nitrogen gas that returns to the atmosphere. Some bacteria also play a role in liberating phosphorus from minerals, or turn phosphorus into swamp gas.

Anaerobic bacteria are one group of detrimental bacteria that harms plant roots. Actually, the organism itself isn’t harmful, it’s the waste metabolites they make that are harmful to plants. Humans consume certain kinds of anaerobic metabolites, such as wine made by anaerobic yeasts and yogurt made with lactobacilli, but alcohol and volatile organic acids produced by anaerobic bacteria kill plant roots at very low concentrations.

The beneficial bacteria for plants are all aerobic, but some bacteria have a Dr. Jekyll and Mr. Hyde personality. They switch from heroes to villains when oxygen concentration is reduced. They are aerobic and can be quite beneficial when there’s plenty of oxygen, but they start making alcohols and nasty organic acids when oxygen is reduced. We call these bacteria facultative anaerobes. You don’t want to kill them because they are so beneficial when they grow aerobically. Just don’t let oxygen levels in soil drop lower than 14-16%. Oxygen diffusion in soil becomes limiting when soil is compacted or when bacterial growth is very rapid.

Actinomycetes are bacteria that use some of the more complex substrates. They are famous for producing the characteristic “smell” of soil, as well as antibiotics and other compounds that inhibit other organisms. According to Ted St. John, a restoration consultant based in Menifee, CA, and an expert on mycorrhizal fungi, “Since they are filamentous, like fungi, it is believed that they might have a role in soil structure at smaller aggregate-size scales. Some can fix nitrogen and form symbiotic partnerships with many nonleguminous plants.”

Cyanobacteria are also bacteria, although for a long time they were thought to be “blue-green” algae. Because they are photosynthetic, they inhabit the uppermost layer of the soil and play a vital role in binding soil particles in desert soils. “Among the most resistant organisms on earth to onslaughts such as drought, salinity, and heat, they are quickly destroyed by physical disturbance. This is truly nature’s erosion control blanket,” says St. John. Cyanobacteria are the first arrivals in the complex assemblage known as the “microphytic crust,” and within a few years of their presence, they are joined by mosses, lichens, and other primitive plants. “These crusts,” says St. John, “are credited with wonderful powers. They definitely hold the soil together and prevent the formation of mineral crusts—crusts made by physical cementing and interlocking of particles that prevent water penetration and lead to erosive runoff. Biological crusts may favor the development of mycorrhizal roots in the underlying soils too and, according to some, may inhibit weed growth while favoring natives.”

Fungi are also decomposers, although they play almost every other functional role in the soil as well. There may be as many 1.5 million species of fungi, and estimates are that only 5% of these species are even identified. “Reckoned by number of species, most fungi are decomposers,” states St. John, “but reckoned by biomass, most fungi are mycorrhizal.”

The fungal decomposers can be ranked based on what kinds of foods they use. There are “sugar fungi” that attack substrates such as simple sugars found in bread or fruit juices; there are those that attack less simple, harder-to-break-down substrates such as hemicellulose, fats, and oils; while slower growing fungi (such as mushroom-formers) attack difficult organic residues, including lignin and tannin. “Part of the secret of these very specialized fungi is their transport system consisting of strands and aggregates that may be several feet long,” describes St. John. “They can move energy from an established area to a log or dead root that they are starting to attack. Only with this starter energy are they able to carry out the energetically improbable transformations of these difficult plant compounds.”

There are fungi that cause serious plant diseases, such as Pythium, Phytopthora, Rizoctonia, Fusarium, or Verticillium. All of these are caused by fungi that like to use the simple foods exuded by plants. But fighting these diseases are other fungi that compete with these “heavies” for the same foods or for space, preventing the disease from taking over. Some beneficial fungi produce antibiotics or other inhibitory compounds while others, such as Trichoderma or Gliocladium, parasitize the disease-causing fungi, keeping them in control. Unfortunately, chemical control methods kill the beneficials to a greater extent than the disease-causing fungi.

One group of fungi that has been the center of attention for many years is the mycorrhizal fungi. They form mutualistic associations with plant roots and draw all, or almost all, of their energy from the host plant. Their growth can be so extensive that in some forest soils they make up the bulk of the microbial biomass. In return for the supply of energy from the host plant, they take up phosphorus and other nutrients from the soil and pass them to the plant. “On their ramblings through the soil, fungi bind soil particles together and contribute a major fraction of what is known as soil structure,” St. John points out. “The biomass, ubiquity, and energy resources of mycorrhizal fungi are so much greater than those of other soil organisms that they essentially ‘call the tune’ to which the rest of the soil dances. Soil that is full of mycorrhizal mycelium has mostly ‘good bugs,’ while soil lacking in it has many more ‘bad bugs.’ They promote plant growth mostly through improved uptake of phosphorus, they make many plants more resistant to drought, they greatly improve plant diversity, they hold the soil together, and they protect against plant pathogens.”

Nematodes are tiny, round worms—the largest of which are just barely visible to the naked eye—that have a role in most soil processes from decomposition to plant pathology. Some nematodes consume bacteria and release nitrogen, phosphorus, and other nutrients in plant-available forms. They can function as biological controls of disease-causing bacteria. Some nematodes consume disease-causing fungi; some eat other nematodes and are especially noted for their ability to consume the “black sheep” of the nematode family—root-eating nematodes. If the bacterial-feeding, fungal-feeding, and predatory nematodes are present in normal, healthy numbers, root-feeding nematodes have a very difficult time. In fact, they generally can’t be found. But if nematicides, insecticides, fumigants, or even some herbicides have been used, the beneficial nematodes will be killed, and the nasty, root-eating nematodes can take over.

Protozoa, tiny one-celled creatures, are also predators of bacteria and other soil organisms. In agricultural soils, they are the major way that nitrogen is turned into a plant-available form. Without these creatures in your soil, you have to use inorganic fertilizers, and you run a huge risk of contaminating drinking water with nitrates because nitrate moves the most rapidly with wetting fronts and is easily lost from the soil. Protozoa work at a pace determined by the rate at which plants put out exudates-foods that the plant uses to grow the right kind of bacteria and fungi around the root. These bacteria and fungi are protective of the root because that root is feeding them. These beneficial bacteria and fungi prevent disease-causing bacteria and fungi from being able to detect the root. This increase in bacteria and fungi brings the protozoa and the beneficial nematodes to feed, and in feeding, nutrients are released in plant-available forms.

Ciliates are a type of protozoa that prefer feeding on anaerobic bacteria rather than aerobic bacteria. Thus, in soil with compaction or limited oxygen movement where anaerobic bacteria are beginning to dominate, ciliate numbers will be very high. “This is an observation that we have just started to recognize,” notes Ingham, “and a great deal more work needs to be performed to figure out the relationship between anaerobic bacteria and ciliates. Certainly when oxygen becomes very limiting and rotten-egg smells come from the material (hydrogen-sulfide production), ciliates will be killed. So they seem to be useful as an indicator of the early stages of conversion to anaerobic conditions.”

Arthropods are visible to the naked eye, but you need a microscope to identify which one you are looking at in most cases. These organisms range from mites to larger beetles, centipedes, and wood lice. Their role in the soil depends on what their mouths allow them to do. Those with sucking mouth parts tend to attack plants by sucking plant juices or sap. Those with little jaws attack fungi, while those with bigger jaws eat the fungal-feeders, including protozoa and nematodes. The ones with big mouth parts eat the critters that attack plants or eat fungi. None of them spits out bacteria in its food though. For the most part, arthropods are not decomposers; that is, they don’t make the enzymes that allow them to digest plant material. However, they do break up dead plant material while foraging for their fungal dinner. This fragmentation exposes fresh surfaces to attack by bacteria and fungi and accelerates the process of decomposition. Arthropods such as ants and termites, along with nematodes and protozoa, are important tunnelers—they make air passages in soil and form channels for movement of water, roots, and other soil animals.
Holding It All Together
The soil is held together by roots and associated microorganisms, especially mycorrhizal fungi. Newly graded ground has no structure to it because it lacks the living organisms and their intricate interactions with roots and each other. Soil mineral particles are bound together into larger units by natural forces, roots, bacterial glues, and fungi tying the bits together like a tangled mass of string. The way these aggregates are arranged together is what characterizes a soil’s structure.In a recent study for the California Department of Transportation (Caltrans) by V.P. Claassen and M.P. Hogan of the University of California at Davis, the authors looked at the complex and diverse factors that contribute to the formation of water-stable soil aggregates and concluded that sustained and vigorous plant growth is the most important factor in the maintenance of soil structure. Citing work carried out by J.M. Tisdall and J.M. Oades, the study relates that microorganisms contribute about half of the microbial biomass associated with microaggregates 2 to 20 microns in diameter (for comparison, a human hair is about 75 microns in diameter). Larger microaggregates, from 20 to 250 microns in diameter, are characterized by encrustation around plant debris. “The accumulated microbial residues continue to hold the aggregates together,” the study points out. They are “…most easily developed by amendment with organic residues. However, it is not merely the amendment with organics, but the decomposition of the organics by microbes (and subsequent mucilage production) that generates and stabilizes the aggregate structure.” When we move up to the next category of aggregates, greater than 250 microns up to 10 mm in diameter, the study states, “roots and mycorrhizal hyphae are important structural components of this size of aggregate.” These larger aggregate structures are more susceptible to disruption than are the microaggregates and must be maintained by continuous plant growth and the presence of mycorrhizal fungi.”It’s more complex than one thinks,” says St. John. “Fungal hyphae not only play a role in the aggregrates of 250 microns and more, they also have influence on bacteria that have influence on the smaller-size aggregates.” Claassen points out that they also have a key role to play in water extraction. The role of microorganisms, fungal mycelium, and plant roots in stabilizing the soil, whether on a microscopic or visible level, is crucial. “No organisms, no soil structure, no retention of nutrients,” says Ingham. “You need to tie-up nitrates.” High nitrate levels set the stage for weeds (hungry feeders) and for fungal diseases. “Indeed,” comments St. John, “if there is a lot of readily available nitrogen on a site, you’ll have a devil of a time getting the plants you want rather than weeds.” Adds Ingham, “You need to ‘suck up’ that excess nitrate.”But how do you do that? “Grow fungi and bacteria that take it up, dropping soil nitrate levels below 10 parts per million,” St. John advises. Add bacterial foods such as sugar, plant extracts, or fulvic acids. Add fungal foods such as humic acid, straw, hay, brown leaves, stems, kelps, and rock dust. However, be careful not to add too much of these things and tie up all of your nitrogen. You can kill all the plants in a field if you do! This will give the slower-growing plants time to fill the soil with their own roots and mycorrhizal hyphae. We want the nitrogen on-site, but we want it sequestered in forms that will make it available only over a long period of time.”
“Nitrogen is essential to regenerate various parts of the plant-soil community,” the Caltrans study concludes, “including shoots, roots, litter, and microbial biomass. Insufficient amendments of nitrogen result in inadequate development of some or all of these plant-soil community components..” By far the most valuable source of nitrogen is the organic nitrogen in soil organic matter. Because its nitrogen is released slowly through decomposition and microbial activity, the nutrients are stored safely until they can be used and are made available to plants right where they need them—in the root zone.One promising development is the use of polymerization technology to lock up the nitrogen in enhanced amendment fertilizers used in revegetation projects. Neil Anderson, president of ReForestation Technologies International in Monterey, CA, explains, “Through the polymer technology, the only way the nitrogen can be released through this material is by biological activity. Biological activity usually correlates with vegetative development activity. We may have just developed the first nonpolluting fertilizer nitrogen product available because it just can’t release the nitrogen unless microbial activity is present, and as that is so closely tied to plant growth, the possibility of leaching is practically nil.”

Sustainable ecosystem development can only be accomplished by establishment of self-sustaining and healthy plant growth. “You need the nutrients, the organics, and the biological activity. There’s such a close synergy between the microbial activity and vegetation. If you take it full circle, the vegetation is actually producing the material that will create the mineralization that will feed those bacteria in the long term,” says Anderson.

“Rebuilding drastically disturbed soils into vibrant organic matter rich in living organisms is the prime objective of the Native Plants Trust team,” says Peter McRae, president of Quattro Environmental in Coronado, CA, and a founding member of the Native Plants Trust. “We recognize that the key to establishing sustainable native plant growth on drastically disturbed sites is not merely growing plants per se; instead we focus on firing up the natural cycling processes of the soil’s ‘biological engine.’ This amounts to setting the stage for natural reestablishment of mycorrhizal fungi via the medium of growing early seral state plants-pioneer species that act as soil builders-in tandem with the incorporation of certain organic complexes of enzymes and bacteria as well as protein-rich, organic-fiber nutrients into the seedbed. We are growing soil more than we are growing plants.to ultimately reestablish climax native plant species.”

“You get healthier and longer-lasting vegetation and more stable soils when you can enhance the diversity of the soil ecosystem,” says Holden. “You want the vegetation to establish quickly and keep going, and you have to get that nutrient cycling going in the soil in order to do that.”

Perhaps it is time we take a holistic approach to the health of the soil, realizing that it does indeed have a reality independent of and greater than the sum of its parts.

Earthworms are, in effect, predators of everything they can put in their mouths. They aren’t picky eaters. By passing soil through their bodies, earthworms digest fungi, protozoa, nematodes, and microarthropods, as well as the associated bacteria. What comes out of the other end of an earthworm is great stuff for the rapid growth of nearly everything—from new bacterial populations to plants. It contains high amounts of organic nitrogen and nitrates. Earthworms play an important role in promoting soil fertility, plant production, and the rehabilitation of degraded soils. By burrowing through the soil, they create channels that improve aeration and drainage.

“Every group in the soil food web performs many complex functions. It depends on who is home, what the habitat is, and what food is available to determine just who is doing the work and when,” explains Ingham. “In every group, there are good and bad guys. It’s relative too—a good guy this week could be a bad guy next week. Within all of these groups, some cause disease and some prevent disease.” In fact, about 99% of soil organisms are beneficial.

Soil biota, or the life in the soil, is extremely important in the regulation of plant nutrient uptake and release and in organic-matter decomposition, as well as to the formation of stable soil aggregates, porosity, and the infiltration of water. A healthy soil is soil in which the right kinds of soil organisms are present in the right numbers at the normal level of activity. Natural disturbances (freeze, thaw, drought, flooding) as well as human disturbances (fire, compaction, and use of pesticides, herbicides, and salt fertilizers) can kill critical organisms in the soil.

What can be done to increase the underground population or to establish new communities? “Increase the kind of foods for the beneficial organisms in the soil with more organic matter, as great as a variety as you can manage,” suggests Ingham. “Plow or disk to the minimum degree necessary. Let a good soil profile develop. Then you’ll have the right habitat for the right organisms to help the plant you want to grow.” In other words, feed and house them so they will flourish.

“You need to understand organisms,” says Ingham. “They are like people. If you want a full diversity, you must provide them with the habitats they will be comfortable in.” Adding organic material is the logical first step, but using the right organic matter—one that will most rapidly rebuild the groups of soil organisms—is even better. Compost that has been composted correctly is the best organic food source because it naturally contains the entire range of species for recolonization—some 15,000 or more species of bacteria in most ag soils and a diversity of fungi, protozoa, nematodes, and other organisms. Returning organic matter to the soil—whether plant residues, manures, or compost—and care in cultivation promote the good life for soil organisms.

A key factor to keep in mind is the ratio of carbon to nitrogen of the amendment material. Craig Holden, president of Natural Fertilizers of America in Cannon Falls, MN, manufacturer of Suståne explains, “If you put straight carbon on a soil, it can immobilize any soil-applied or free nitrogen that might be there already. Microorganisms need both carbon and nitrogen—carbon as a source of carbohydrates and nitrogen as a source of protein. The law of the soil is that microorganisms desire a carbon-to-nitrogen ratio of around 11-to-1, so if a farmer goes out and dumps hundreds of tons of straw that he wants to get rid of on the soil, the microorganisms will be overloaded with carbonaceous materials. They’ll still require nitrogen sources to metabolize that, and they’ll take all the free nitrogen in the soil. The inverse is also true: If you put down too much nitrogen, they will oxidize the organic material in the soil, and that will kill the soil too.”

St. John continues, “Above all, give them what they want to eat. Decomposers need organic detritus. Mineralizers need decomposers. Mycorrhizal fungi need roots. Cyanobacteria need sunlight. The most important factor here is a healthy, diverse plant community. This will directly and indirectly produce everything from roots and detritus to bird droppings—all great material for the soil community.”

There are many commercial products available that provide some part of the food source or push things in the right direction for different organisms. Commercial inocula for bacteria and fungi are widely available. However, the decision as to which specific set of bacterial or fungal species to use depends on complex criteria, and it is wise to consult the experts in these matters. “There are lots of magic bug potions out there,” remarks Holden. “Most microbiologists probably agree, though, that if you’re simply applying a microbial soup, the probability of those microorganisms surviving without the right food source is very, very low.”

About the Author

Kate Goff

Author Kate Goff writes on a variety of solid waste—related issues.