Chris Maser

Organisms in the soil, such as bacteria, fungi, one-celled animals called protozoa, and worms, mites, spiders, centipedes, and insects of all kinds play critical roles in maintaining its health and fertility. These organisms perform various functions in the cycling of chemicals required as nutrients for the growth of green plants. Some of these functions are: (1) fixing nitrogen, which is the conversion of elemental nitrogen from the atmosphere by certain bacteria into organic combinations or forms readily usable in biological processes; (2) decomposing (recycling) plant material by bacteria and fungi; (3) improving the structure of the soil by such organisms as certain fungi that form a symbiotic relationship with the roots of certain plants—mycorrhizae—and produce a substance called "glycoprotein" (glomalin) and so increase soil aggregation1; (4) mediating the soil's pH, a determinant of what plants and animals can live where and what chemical reactions can take place where2; and (5) controlling disease-causing organisms through competition for resources and space. Without the organisms to perform these functions, the plant communities we see on the surface of the Earth (including agricultural fields) would not exist.

Lava and Volcanic Cinders Being Turned Gradually Into Soil That Whitebark Pine Can Inhabit in the Cascade Mountains of Oregon.

As the total productivity of an ecosystem increases, the biological diversity within the soil's food web also seems to increase. The greater the number of interactions among organisms that decompose organic material (decomposers), their predators, and the predators of the predators, the more nutrients there are retained in the soil. It is only through the belowground food web that plants can obtain the nutrients necessary for their growth; without the belowground food web, the aboveground food web—including us humans—would cease to exist. "The soil food web is every bit as complex as the aboveground web with the intricate connections to its aerial counterpart. In the subterranean world, ecology is writ small. The spatial, chemical and biological heterogeneity within a few cubic centimeters [cubic inches] of soil rivals that of a hectare [2.5 acres] of forest or coral reef."3

The development of soil in a forest or a grassland relies on self-reinforcing feedback loops, where organisms in the soil provide the nutrients for plants to grow, and plants in turn provide the carbon—the organic material—that selects for and alters the communities of soil organisms. One influences the other, and both determine the soil's development and health.

The soil food web is thus a prime indicator of the health of any terrestrial ecosystem. But soil processes can be disrupted by such things as: (1) decreasing bacterial or fungal activity, (2) decreasing the biomass of bacteria or fungi, (3) altering the ratio of fungal to bacterial biomass in a way that is inappropriate to the desired system, (4) reducing the number and diversity of protozoa, and (5) reducing the number of nematodes (roundworms as opposed to segmented worms like earthworms) and/or altering their community structure.4

The foregoing is about external food webs. There are, however, internal aspects to food webs as well. For example, the earthworm known to most people as a "nightcrawler" accelerates "weathering" of mineral clay. A combination of the low pH and bacteria-rich microenvironment in the gut of a nightcrawler radically accelerates the breakdown of existing minerals and their re-crystallization during the combined process of ingestion, digestion, and excretion.5

A model of a soil food web, composed of interactive strands, is enlightening because it shows that there are higher-level predators in the system whose function is to prevent the predators of bacteria and fungi from becoming too abundant and thus altering how the system functions. In turn, these higher-level predators serve as food for still higher-level predators.

In this way, mites, predatory roundworms, and small insects are eaten by organisms, which spend much of their time above ground. Thus predators in the third, fourth, and fifth upper strands of the food web are eaten by spiders, centipedes, and beetles, which in turn are eaten by salamanders, birds, shrews, and mice, which in turn are eaten by snakes, still other birds, weasels, foxes, and so on.

Biologists have for centuries studied the patterns of plant and animal diversity at continental scales. Until recently, similar studies were impossible to conduct for microorganisms, which arguably are the most diverse and abundant life forms on Earth. Although the diversity and species richness of bacterial communities differ among ecosystem types, these differences could be explained largely by soil pH, not by geography.

In a study of 98 soil samples from across North and South America, bacterial diversity was highest in neutral soils and lower in acidic soils; the most acidic soil was form the Peruvian Amazon, which also was most homogeneous. The biogeography of soil-dwelling microbial organisms is controlled primarily by edaphic variables (soil conditions) and thus differs fundamentally from the variables that account for the biogeographical distribution of macro-organisms. 6

Regardless of soil type, most of the terrestrial vegetation produced each year enters the decomposer system as dead organic matter, where the subsequent recycling of carbon and other nutrient-forming elements is a critical process for the functioning of ecosystems and the delivery of their goods and services. Within this paradigm, decomposition of litter from a particular species of plant changes greatly in the presence of diverse litter from coexisting species, even in the face of unaltered climatic conditions and litter chemistry. Most important, soil fauna determines the magnitude and directs the effects of decomposing litter from mixed species.

These dead bristlecone pines on Mt. Charleston, in southern Nevada, are gradually becoming part of the organic material the nature reinvests in the formation and fertility of the soil out of which they are growing.

The species richness of the litter, coupled with the interactivity of soil macrofauna (such as earthworms, beetles, and mice), determines the rate of decomposition in temperate forests. Put differently, the species composition of the litter affects the species composition of the decomposer organisms, which in turn affects the cycling of carbon and nutrients. Thus, ecosystems, which support a well-developed, soil-macrofaunal community, play a fundamental role in altering decomposition in response to the changing diversity of litter-producing species, and this alteration in turn has important implications for biogeochemical cycles and the long-term functioning of ecosystems, at least within the temperate zone.7

If, therefore, part of the biological diversity of the belowground organisms is lost, the soil as a system will function differently and may not produce a chosen crop in a way that meets our economic expectations or may even produce a plant community not to our human liking, such as a hillside of shrubs instead of commercially valuable trees. If the predators in the soil are lost, which disrupts the governance of the soil, the mineral nitrogen in the soil may be lost, and the plants suffer and thus exhibit poor growth and produce fewer seeds. Conversely, too many predators can overuse the bacteria and fungi, which results in slower decomposition of organic material that is needed to fuel the system of nutrient uptake by the plants. A reduction or loss in any part of the food web affects at least two strands of the web at other levels. If we, as individuals and a society, poison the soil directly for whatever reason or otherwise damage its delicate infrastructure indirectly by condoning the pollution of our air and water, we help to destroy the stage on which life depends—including ours. It is much wiser, therefore, to work in harmony with the soil and the organisms that govern its infrastructure because they are responsible for the processes that in turn provide those nutrients to the plants.8

What's more, as long ago as 1998, agriculture fouled more than 173,000 miles of streams and rivers—a figure that does not include the hundreds of thousands of miles of ditches—with chemicals, erosion, and the runoff of animal wastes in commercial feedlots and poultry farms. It is also the largest overall source of pollution in U.S. waterways. According to the U.S. Environmental Protection Agency, farming is responsible for 70 percent of the pollution in streams and rivers in the United States, outstripping the combined discharges from sewage treatment plants, urban storm drains, and pollutants deposited by air.9


  1. Matthias C. Rillig, Sara E. Wright, Michael F. Allen, and Christopher B. Field. 1999. Rise in carbon dioxide changes soil structure. Nature 400:628.

  2. Noah Fierer and Robert B. Jackson. The Diversity and Biogeography of Soil Bacterial Communities. Proceedings of the National Academy of Sciences, 103 (2006):626-631.

  3. Andrew Sugden, Richard Stone, and Caroline Ash. Ecology in the Underworld. Science, 304 (2004):5677.

  4. (1) Elaine R. Ingham. Organisms in the Soil: The Functions of Bacteria, Fungi, Protozoa, Nematodes, and Arthropods. Natural Resource News, 5 (1995):10-12, 16-17; and (2) Andrew Sugden, Richard Stone, and Caroline Ash. Ecology in the Underworld. Science 304 (2004):1613-1620.

  5. S. J. Needham, R. H. Worden, and D.McIlroy. Animal-Sediment Interactions: The Effect of Ingestion and Excretion By Worms On Mineralogy. Biogeosciences, 1 (2004):113-121.

  6. The preceding two paragraphs are based on: Noah Fierer and Robert B. Jackson. The Diversity and Biogeography of Soil Bacterial Communities. Proceedings of the National Academy of Sciences, 103 (2006):626-631.

  7. Stephan Hättenschwiler and Patrick Gasser. Soil Animals Alter Plant Litter Diversity Effects on Decomposition. Proceedings of the National Academy of Sciences, 102 (2005):1519-1524.

  8. Elaine R. Ingham. Organisms in the Soil: The Functions of Bacteria, Fungi, Protozoa, Nematodes, and Arthropods. Natural Resource News,5 (1995):10-12, 16-17.

  9. Curt Anderson. Ag is the biggest river polluter. Corvallis Gazette-Times, Corvallis, OR. May 17, 1998.

Volcanic ash soils in the Painted Hills National Monument near the town of Mitchell in northcentral Oregon.

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