Teaming with Microbes

Go to the main page for this book

What Is the Soil Food Web, and Why Should Gardeners Care?

Given its vital importance to our hobby, it is amazing that most of us don't venture beyond the understanding that good soil supports plant life, and poor soil doesn't. You've undoubtedly seen worms in good soil, and unless you habitually use pesticides, you should have come across other soil life: centipedes, springtails, ants, slugs, ladybird beetle larvae, and more. Most of this life is on the surface, in the first 4 inches (10 centimeters); some soil microbes have even been discovered living comfortably an incredible two miles beneath the surface. Good soil, however, is not just a few animals. Good soil is absolutely teeming with life, yet seldom does the realization that this is so engender a reaction of satisfaction.

In addition to all the living organisms you can see in garden soils (for example, there are up to 50 earthworms in a square foot [0.09 square meters] of good soil), there is a whole world of soil organisms that you cannot see unless you use sophisticated and expensive optics. Only then do the tiny, microscopic organisms — bacteria, fungi, protozoa, nematodes — appear, and in numbers that are nothing less than staggering. A mere teaspoon of good garden soil, as measured by microbial geneticists, contains a billion invisible bacteria, several yards of equally invisible fungal hyphae, several thousand protozoa, and a few dozen nematodes.

The common denominator of all soil life is that every organism needs energy to survive. While a few bacteria, known as chemosynthesizers, derive energy from sulfur, nitrogen, or even iron compounds, the rest have to eat something containing carbon in order to get the energy they need to sustain life. Carbon may come from organic material supplied by plants, waste products produced by other organisms, or the bodies of other organisms. The first order of business of all soil life is obtaining carbon to fuel metabolism — it is an eat-and-be-eaten world, in and on soil.

Do you remember the children's song about an old lady who accidentally swallowed a fly? She then swallows a spider ("that wriggled and jiggled and tickled inside her") to catch the fly, and then a bird to catch the spider, and so on, until she eats a horse and dies ("Of course!"). If you made a diagram of who was expected to eat whom, starting with the fly and ending with the improbable horse, you would have what is known as a food chain.

Most organisms eat more than one kind of prey, so if you make a diagram of who eats whom in and on the soil, the straight-line food chain instead becomes a series of food chains linked and cross-linked to each other, creating a web of food chains, or a soil food web. Each soil environment has a different set of organisms and thus a different soil food web.

This is the simple, graphical definition of a soil food web, though as you can imagine, this and other diagrams represent complex and highly organized sets of interactions, relationships, and chemical and physical processes. The story each tells, however, is a simple one and always starts with the plant.

Plants are in control

Most gardeners think of plants as only taking up nutrients through root systems and feeding the leaves. Few realize that a great deal of the energy that results from photosynthesis in the leaves is actually used by plants to produce chemicals they secrete through their roots. These secretions are known as exudates. A good analogy is perspiration, a human's exudate.

Root exudates are in the form of carbohydrates (including sugars) and proteins. Amazingly, their presence wakes up, attracts, and grows specific beneficial bacteria and fungi living in the soil that subsist on these exudates and the cellular material sloughed off as the plant's root tips grow. All this secretion of exudates and sloughing-off of cells takes place in the rhizosphere, a zone immediately around the roots, extending out about a tenth of an inch, or a couple of millimeters (1 millimeter = 1⁄ 25 inch). The rhizosphere, which can look like a jelly or jam under the electron microscope, contains a constantly changing mix of soil organisms, including bacteria, fungi, nematodes, protozoa, and even larger organisms. All this "life" competes for the exudates in the rhizosphere, or its water or mineral content.

At the bottom of the soil food web are bacteria and fungi, which are attracted to and consume plant root exudates. In turn, they attract and are eaten by bigger microbes, specifically nematodes and protozoa (remember the amoebae, paramecia, flagellates, and ciliates you should have studied in biology?), who eat bacteria and fungi (primarily for carbon) to fuel their metabolic functions. Anything they don't need is excreted as wastes, which plant roots are readily able to absorb as nutrients. How convenient that this production of plant nutrients takes place right in the rhizosphere, the site of root-nutrient absorption.

At the center of any viable soil food web are plants. Plants control the food web for their own benefit, an amazing fact that is too little understood and surely not appreciated by gardeners who are constantly interfering with Nature's system. Studies indicate that individual plants can control the numbers and the different kinds of fungi and bacteria attracted to the rhizosphere by the exudates they produce. During different times of the growing season, populations of rhizosphere bacteria and fungi wax and wane, depending on the nutrient needs of the plant and the exudates it produces.

Soil bacteria and fungi are like small bags of fertilizer, retaining in their bodies nitrogen and other nutrients they gain from root exudates and other organic matter (such as those sloughed-off root-tip cells). Carrying on the analogy, soil protozoa and nematodes act as "fertilizer spreaders" by releasing the nutrients locked up in the bacteria and fungi "fertilizer bags." The nematodes and protozoa in the soil come along and eat the bacteria and fungi in the rhizosphere. They digest what they need to survive and excrete excess carbon and other nutrients as waste.

Left to their own devices, then, plants produce exudates that attract fungi and bacteria (and, ultimately, nematodes and protozoa); their survival depends on the interplay between these microbes. It is a completely natural system, the very same one that has fueled plants since they evolved. Soil life provides the nutrients needed for plant life, and plants initiate and fuel the cycle by producing exudates.

Soil life creates soil structure

The protozoa and nematodes that feasted on the fungi and bacteria attracted by plant exudates are in turn eaten by arthropods (animals with segmented bodies, jointed appendages, and a hard outer covering called an exoskeleton). Insects, spiders, even shrimp and lobsters are arthropods. Soil arthropods eat each other and themselves are the food of snakes, birds, moles, and other animals. Simply put, the soil is one big fast-food restaurant. In the course of all this eating, members of a soil food web move about in search of prey or protection, and while they do, they have an impact on the soil.

Bacteria are so small they need to stick to things, or they will wash away; to attach themselves, they produce a slime, the secondary result of which is that individual soil particles are bound together (if the concept is hard to grasp, think of the plaque produced overnight in your mouth, which enables mouth bacteria to stick to your teeth). Fungal hyphae, too, travel through soil particles, sticking to them and binding them together, thread-like, into aggregates.

Worms, together with insect larvae and moles and other burrowing animals, move through the soil in search of food and protection, creating pathways that allow air and water to enter and leave the soil. Even microscopic fungi can help in this regard. The soil food web, then, in addition to providing nutrients to roots in the rhizosphere, also helps create soil structure: the activities of its members bind soil particles together even as they provide for the passage of air and water through the soil.

Soil life produces soil nutrients

When any member of a soil food web dies, it becomes fodder for other members of the community. The nutrients in these bodies are passed on to other members of the community. A larger predator may eat them alive, or they may be decayed after they die. One way or the other, fungi and bacteria get involved, be it decaying the organism directly or working on the dung of the successful eater. It makes no difference. Nutrients are preserved and eventually are retained in the bodies of even the smallest fungi and bacteria.When these are in the rhizosphere, they release nutrients in plant-available form when they, in turn, are consumed or die.

Without this system, most important nutrients would drain from soil. Instead, they are retained in the bodies of soil life. Here is the gardener's truth: when you apply a chemical fertilizer,a tiny bit hits the rhizosphere, where it is absorbed, but most of it continues to drain through soil until it hits the water table. Not so with the nutrients locked up inside soil organisms, a state known as immobilization; these nutrients are eventually released as wastes, or mineralized. And when the plants themselves die and are allowed to decay, the nutrients they retained are again immobilized in the fungi and bacteria that consume them.

The nutrient supply in the soil is influenced by soil life in other ways. For example, worms pull organic matter into the soil, where it is shredded by beetles and the larvae of other insects, opening it up for fungal and bacterial decay. This worm activity provides yet more nutrients for the soil community.

Healthy soil food webs control disease

A healthy food web is one that is not being destroyed by pathogenic and disease-causing organisms. Not all soil organisms are beneficial, after all. As gardeners you know that pathogenic soil bacteria and fungi cause many plant diseases. Healthy soil food webs not only have tremendous numbers of individual organisms but a great diversity of organisms. Remember that teaspoon of good garden soil? Perhaps 20,000 to 30,000 different species make up its billion bacteria — a healthy population in numbers and diversity.

A large and diverse community controls troublemakers. A good analogy is a thief in a crowded market: if there are enough people around, they will catch or even stop the thief (and it is in their self-interest to do so). If the market is deserted, however, the thief will be successful, just as he will be if he is stronger, faster, or in some other way better adapted than those that would be in pursuit.

In the soil food web world, the good guys don't usually catch thieves (though it happens: witness the hapless nematode that started this all for us); rather, they compete with them for exudates and other nutrients, air, water, and even space. If the soil food web is a healthy one, this competition keeps the pathogens in check; they may even be outcompeted to their death.

Just as important, every member of the soil food web has its place in the soil community. Each, be it on the surface or subsurface, plays a specific role. Elimination of even just one group can drastically alter a soil community.Birds participate by spreading protozoa carried on their feet or dropping a worm taken from one area into another. Too many cats, and things will change. Dung from mammals provides nutrients for beetles in the soil. Kill the mammals, or eliminate their habitat or food source (which amounts to the same thing), and you won't have as many beetles. It works in the reverse as well. A healthy soil food web won't allow one set of members to get so strong as to destroy the web. If there are too many nematodes and protozoa, the bacteria and fungi on which they prey are in trouble and, ultimately, so are the plants in the area.

And there are other benefits. The nets or webs fungi form around roots act as physical barriers to invasion and protect plants from pathogenic fungi and bacteria. Bacteria coat surfaces so thoroughly, there is no room for others to attach themselves. If something impacts these fungi or bacteria and their numbers drop or they disappear, the plant can easily be attacked.

Special soil fungi, called mycorrhizal fungi, establish themselves in a symbiotic relationship with roots, providing them not only with physical protection but with nutrient delivery as well. In return for exudates, these fungi provide water, phosphorus, and other necessary plant nutrients. Soil food web populations must be in balance, or these fungi are eaten and the plant suffers.

Bacteria produce exudates of their own, and the slime they use to attach to surfaces traps pathogens. Sometimes, bacteria work in conjunction with fungi to form protective layers, not only around roots in the rhizosphere but on an equivalent area around leaf surfaces, the phyllosphere. Leaves produce exudates that attract microorganisms in exactly the same way roots do; these act as a barrier to invasion, preventing disease-causing organisms from entering the plant's system.

Some fungi and bacteria produce inhibitory compounds, things like vitamins and antibiotics, which help maintain or improve plant health; penicillin and streptomycin, for example, are produced by a soil-borne fungus and a soilborne bacterium, respectively.

All nitrogen is not the same

Ultimately, from the plant's perspective anyhow, the role of the soil food web is to cycle down nutrients until they become temporarily immobilized in the bodies of bacteria and fungi and then mineralized. The most important of these nutrients is nitrogen — the basic building block of amino acids and, therefore, life. The biomass of fungi and bacteria (that is, the total amount of each in the soil) determines, for the most part, the amount of nitrogen that is readily available for plant use.

It wasn't until the 1980s that soil scientists could accurately measure the amount of bacteria and fungi in soils. Dr. Elaine Ingham at Oregon State University along with others started publishing research that showed the ratio of these two organisms in various types of soil. In general, the least disturbed soils (those that supported old growth timber) had far more fungi than bacteria, while disturbed soils (rototilled soil, for example) had far more bacteria than fungi. These and later studies show that agricultural soils have a fungal to bacterial biomass (F:B ratio) of 1:1 or less, while forest soils have ten times or more fungi than bacteria.

Ingham and some of her graduate students at OSU also noticed a correlation between plants and their preference for soils that were fungally dominated versus those that were bacterially dominated or neutral. Since the path from bacterial to fungal domination in soils follows the general course of plant succession, it became easy to predict what type of soil particular plants preferred by noting where they came from. In general, perennials, trees, and shrubs prefer fungally dominated soils, while annuals, grasses, and vegetables prefer soils dominated by bacteria.

One implication of these findings, for the gardener, has to do with the nitrogen in bacteria and fungi. Remember, this is what the soil food web means to a plant: when these organisms are eaten, some of the nitrogen is retained by the eater, but much of it is released as waste in the form of plant-available ammonium (NH4). Depending on the soil environment, this can either remain as ammonium or be converted into nitrate (NO3) by special bacteria. When does this conversion occur? When ammonium is released in soils that are dominated by bacteria. This is because such soils generally have an alkaline pH (thanks to bacterial bioslime), which encourages the nitrogen-fixing bacteria to thrive. The acids produced by fungi, as they begin to dominate, lower the pH and greatly reduce the amount of these bacteria. In fungally dominated soils, much of the nitrogen remains in ammonium form.

Ah, here is the rub: chemical fertilizers provide plants with nitrogen, but most do so in the form of nitrates (NO3). An understanding of the soil food web makes it clear, however, that plants that prefer fungally dominated soils ultimately won't flourish on a diet of nitrates. Knowing this can make a great deal of difference in the way you manage your gardens and yard. If you can cause either fungi or bacteria to dominate, or provide an equal mix, then plants can get the kind of nitrogen they prefer, without chemicals, and thrive.

Negative impacts on the soil food web

Chemical fertilizers negatively impact the soil food web by killing off entire portions of it. What gardener hasn't seen what table salt does to a slug? Fertilizers are salts; they suck the water out of the bacteria, fungi, protozoa, and nematodes in the soil. Since these microbes are at the very foundation of the soil food web nutrient system, you have to keep adding fertilizer once you start using it regularly. The microbiology is missing and not there to do its job, feeding the plants.

It makes sense that once the bacteria, fungi, nematodes, and protozoa are gone, other members of the food web disappear as well. Earthworms, for example, lacking food and irritated by the synthetic nitrates in soluble nitrogen fertilizers, move out. Since they are major shredders of organic material, their absence is a great loss. Without the activity and diversity of a healthy food web, you not only impact the nutrient system but all the other things a healthy soil food web brings. Soil structure deteriorates, watering can become problematic, pathogens and pests establish themselves and, worst of all, gardening becomes a lot more work than it needs to be.

If the salt-based chemical fertilizers don't kill portions of the soil food web, rototilling will. This gardening rite of spring breaks up fungal hyphae, decimates worms, and rips and crushes arthropods. It destroys soil structure and eventually saps soil of necessary air. Again, this means more work for you in the end. Air pollution, pesticides, fungicides, and herbicides, too, kill off important members of the food web community or "chase" them away. Any chain is only as strong as its weakest link: if there is a gap in the soil food web, the system will break down and stop functioning properly.

Healthy soil food webs benefit you and your plants

Why should a gardener be knowledgeable about how soils and soil food webs work? Because then you can manage them so they work for you and your plants. By using techniques that employ soil food web science as you garden, you can at least reduce and at best eliminate the need for fertilizers, herbicides, fungicides, and pesticides (and a lot of accompanying work).You can improve degraded soils and return them to usefulness. Soils will retain nutrients in the bodies of soil food web organisms instead of letting them leach out to God knows where. Your plants will be getting nutrients in the form each particular plant wants and needs so they will be less stressed. You will have natural disease prevention, protection, and suppression. Your soils will hold more water.

The organisms in the soil food web will do most of the work of maintaining plant health. Billions of living organisms will be continuously at work throughout the year, doing the heavy chores, providing nutrients to plants, building defense systems against pests and diseases, loosening soil and increasing drainage, providing necessary pathways for oxygen and carbon dioxide. You won't have to do these things yourself.

Gardening with the soil food web is easy, but you must get the life back in your soils. First, however, you have to know something about the soil in which the soil food web operates; second, you need to know what each of the key members of the food web community does. Both these concerns are taken up in the rest of Part 1.