Soil Organisms:
Why are they important?

by Dr. Elaine R. Ingham, Soil Foodweb, Inc.
Oregon State University
[Sep 2009: original source of article no longer available]

Past agricultural management practices have often resulted in a lack of beneficial organisms in the soil to compete against, inhibit, or consume disease-causing bacteria or fungi, or root-feeding nematodes. A second major problem is a lack of soil structure, resulting in a lack of oxygen in the soil, the production of plant toxins such as alcohol, which stress plants in a variety of ways. Lack of good soil structure results in water stress in late summer, because the soil cannot hold water even though vineyards may be irrigated daily.

Recent work (see "Reading List" for references) suggests that if a healthy foodweb is present in the soil, the foodweb supplies nutrients for plants. Plants release exudates from their roots, and so control the growth of bacteria and fungi around their roots. The exudates released by plants also stimulate the growth of mycorrhizal fungi that colonize roots. Thus the plant itself initiates and controls the processes of nutrient retention by bacteria and fungi, and nutrient solubilization, translocation and uptake back to the roots by mycorrhizal fungi. Of course, for the plant to obtain these benefits, these organisms must be present in soil. This requires that these organisms not be killed by toxic chemicals, many of which are pesticides, herbicides and inorganic fertilizers. And if they have been killed, then they need to be brought back to the soil.

Most of the nutrients that the plant needs, especially N, are converted into plant-available forms by protozoa and beneficial nematodes as these predators feed on bacteria and fungi. These inorganic forms of nutrients need good soil structure where water is held in water-filled pores to allow the plant-usable forms of the nutrients to diffuse easily back to the plant.

However, these functions can only occur if the correct types and biomass of bacteria, fungi, protozoa and beneficial nematodes are present in the soil. Many of our recent agricultural management practices have killed this soil life. Now that we realize that these organisms in soil play important roles in maintaining plant health, it is clear that we should incorporate appropriate management of these organisms into our agricultural practices, and delete, or at the very least alter or reduce usage of those practices that harm these beneficial organisms.

Managing Soil Organisms
First, determine what soil organisms are present in the soil. Determine which organism groups are missing or in too low number to benefit the plants in the system. Generally this means assessing the whole foodweb - total and active bacteria, total and active fungi, protozoa, nematodes and mycorrhizal fungal colonization of the root system (this last requires you send roots of the plant of interest).

Second, replace those organism groups that are missing by inoculating with a good diversity of species of that group. If a group of organisms is merely low in number or biomass, add food resources or living space for that group (see below under ADDING ORGANISMS and SOIL ORGANISM FOODS).

Third, once you've done something designed to increase soil organisms, check and make certain they HAVE been increased. This means doing a repeat of just the assays that showed missing or low organism biomass.

Problem areas - Most problem areas are prime candidates for using the soil foodweb to solve the problem. Some examples are given in the section below on PROBLEMS WITH FOODWEB SOLUTIONS.

Areas with particular problems need to be looked at more intensively than assessing generally healthy areas where the desire is to move away from expensive chemical inputs. More effort will be needed to get the foodweb back into balance in these problem areas than in areas where you just want to maintain productivity (although once the healthy foodweb is in place, crop quality typically increases and often production increases per expense of the inputs).

Sometimes the "how-to-fix" practices outlined below don't work with problem areas, because there is some chemical residue in the soil. These residues can be difficult to get rid of, but until they are decomposed by the soil organisms, it will never be possible to get good production in that area again, short of replacing all the soil.

There are two very different reasons to take samples. One is to determine whether the right foodweb is present and if it isn't present, what is needed to bring soil health back. The second reason is to determine the effect of a product or management practice on soil foodweb organisms, specifically to determine effects on total and active bacteria, total and active fungi, flagellates, amoebae and ciliates, nematodes and mycorrhizal fungal colonization of roots. While SFI offers microarthropod assessment, generally, you can do this yourself using pit-fall traps to catch these organisms. Generally, five to ten small cores, 0-3 inch depth of soil (remove any plant material, litter or mulch first) should be taken from the defined area of interest (see below on choosing your area). These cores should be mixed in a clean container, and a third of a sandwich-size Ziploc plastic baggie filled with this composite soil. All the easily picked out roots should be included too if mycorrhizal colonization is desired. Fill out a soil sample submission form which can be obtained from the SFI web site (, and send it and the soil sample by overnight mail to SFI (address is on the submission form).

Soil Depth
As long as there are no unusual inclusions, compacted zones, hardpans, or buried horizons in the soil, by knowing what is going on in the 0-3 inch depth, we can predict soil organism numbers down to the bottom of the rooting zone, and often on beyond that. If there are unusual layers in the soil horizon, then sampling may need to be done at these points in the soil. With compaction zones, mostly we need to know how deep it is so we can concentrate efforts on that depth to build soil structure and get rid of the problem. Choose your sampling area Factors that should be kept the same when you are taking a sample:

When to sample
When assessing soil foodweb organism health, use plant phenology to help choose sample dates. For example, sample at one of the following on an annual basis. Develop a database on your soils and soil organisms, and how they vary from year-to-year, from season to season, and with changes in management practices. For example, sample at first true-leaf plant stage to assess immediate effects, at bud formation or bud break when working with perennial plants, or at flowering, fruit set, at harvest or at start of fall rains to determine what management could be performed during the winter to get the foodweb in shape for crop growth next spring.

When assessing the effect of a management practice, the immediate effect on bacteria should be assessed at 3 to 7 days, but the direct effect on fungi or protozoa should be assessed at 5 to 10 days. Effects on nematodes and mycorrhizal fungi should be assessed one month after the treatment is applied. In general, though, the immediate, direct effect of any product or management on soil organisms is not usually of primary interest. More important is the ultimate effect on plant health, and so sampling at 7, 21 and 35 days following treatment for bacteria, fungi, protozoa and nematodes (and mycorrhizal colonization at 35 days) is generally useful to assess the full effect of the management on soil foodweb dynamics.

Bacteria and fungi may need to be inoculated, and there are commercial inocula available. There appears to be some degree of specificity for soil types, or climate in the commercial products available. In some cases, it is wisest if several inocula are tested, and the ones that give the best result should be used until a good level of bacteria and fungi have been returned to the soil. When these organisms are inoculated, or if their numbers are low, food must be added to the soil for them to consume.

One danger exists with adding food for these organisms. As bacteria and fungi grow, they will take-up and immobilize nutrients in their biomass and if so much food is added for them that they tie-up most of the nutrients, plants can be severely stressed, and indeed, killed, by the lack of nutrients. The organisms that convert the nutrients immobilized in bacteria and fungi must be present to prevent this from occurring. Thus, when first starting this process, addition of small increments of bacterial and fungal foods is wisest, or the proper number of protozoa, nematodes and microarthropods should be inoculated into the soil about three days after bacterial food is added, or two to three weeks after fungal food is added. This will start the nutrient cycling process of making nutrients available to plants.

Protozoa can be obtained by placing alfalfa, fresh grass material or hay in water and letting a broth of protozoa 'soup' grow up in four to five days, and then using this in the irrigation system. Care must be taken to make certain no pesticides have been used on the plant material, and that no pesticide sprays (or even copper sulfate sprays) are used following application until the protozoan populations become well-established.

Nematode cultures are being developed, but are not yet commercially available. Alternatively, a small amount of aerobic compost (good soil smell, no stink!) can be spread along the rows just along the grape row, or a compost tea can be made and used as a foliar and soil spray through the irrigation system.

If mycorrhizal colonization of the root is shown to be lacking, the roots should be inoculated. There are some excellent VAM and ectomycorrhizal products, but there are some non-effective products on the market as well. There is some specificity between plants and the mycorrhizal species that colonize it, and an effort should be made to double-check several sources of information about the plant you want to grow, and the type of mycorrhizal fungi that colonize it's root system. In general, grape needs to start off colonized by VAM. The specificity seems to be more with respect to the micro-climate conditions that the VAM fungus tolerates, rather than limitations in host-range. Buying grape stock already colonized with VAM, or placing the inoculum of a mixture of species of VAM as spores at the bottom of the planting hole, seems to work best.

There are a number of products that help resuscitate different organisms in the foodweb (see below under Soil Organism Foods).


Bacterial Food Resources

  1. Simple sugars such as table sugar, syrups or molasses. The question always becomes how much sugar in what volume of liquid. Dosages need to be worked out, but generally, try an increasing gradient of concentration. Start with a syrup that is 1 gram of sugar in 100 ml (1% sugar) and apply to a 1 meter square area. Apply a solution of 10 grams in 100 ml (10%) to another area, and a solution of 20 g in 100 ml (20%) to another area. Wait a week, perhaps two, and test to see if this was effective in increasing bacterial biomass. Be aware that too high a concentration of sugar will cause a bacterial bloom, and will cause symptoms of N-deficiency in the plants. Avoid concentrations that result in plant yellowing.
  2. Molasses - there are some humic materials in molasses, which gives the molasses the dark color. Blackstrap molasses contains more of these humic materials than less thick and dark molasses suspensions. Test as above for rate.
  3. Plant extracts usually contain the sap of the plant material, which are combinations of simple sugars, protein, carbohydrates. a) Yucca extract is a product that appears to enhance 'stickiness', selecting for bacteria which produce extracellular slime. b) Nettle extract contains an unknown compound with antibiotic-like qualities.
  4. Fulvic acids appear to be a food resources for bacteria. The molecular weight of these 'humics' is less than that of humic acid, and at least in some cases, supply food for bacteria more than fungi. More work is needed to understand the difference in microbial communities selected by fulvic versus humic acids.
  5. Yeast provides vitamins for bacterial growth. The kind of yeast is important, as Baker's yeast provides quite different sets of vitamins than Brewer's yeast, or champagne yeast, as examples.
Fungal Food Resources
  1. Cellulose which is the structural element of plant cell walls is a food resource for fungi more than bacteria. Often, however, there are some simple sugars, proteins and carbohydrates left in plant leaves, stems etc., to result in some initial bacterial growth. Newspaper, wood chips, hay, straw, or dead, brown leaves all contain high percentages of cellulose.
  2. Leaves also contain tannins, terpenes, and phenols, which are recalcitrant precursors to humic acids. Some tannins and phenols are toxic, preventing plant germination or growth as times. Some care is needed to make certain the more volatile of these terpenes and phenols are gone, or consumed by the fungi before using the material with growing plants. Fresh pine chips, cedar chips, even fresh peat, contain high concentrations of terpenes that kill many plants.
  3. Lignin is one of the major breakdown products from microbial decomposition of plant material. This is a structurally very complex molecule, with a mixture of very hard-to-break down (recalcitrant) chemical bonds embedded in the material. Only fungi can use this material.
  4. Humic acids, the long molecular weight, long chain portion of humics. Again, the condensation of the chains of materials make enzymatic attack of this material difficult, just as difficult as lignin. Only fungi can use this material, and for the most part, only fungi produce the long molecular weights chains as metabolic by-products of their metabolism. The action of extra-cellular fungal enzymes also produce humic acids from smaller chain materials in soil. These reactions resulting in the building of ever-more complex molecules are called condensation reactions, and result in the most recalcitrant, most difficult to break down soil organic matter. Its 'half-life' in soil may be 300 to 3000 years. Only fungi have the enzymatic abilities to consume this material. As a saving account, it can't be beat, but the more nasty and condensed the material, the less likely it is to be a source of food that will result in improved fungal growth. Be careful of the color and smell of humic acids. The nasty, impossible to use humic acids smell like tar or petroleum products (which is what petroleum is - really old humic acids). Use the brown to dark brown, NOT BLACK, humic products.
Protozoa Food
  1. Bacteria are what protozoa eat. Therefore, anything that grows more bacteria will result in more protozoa eventually. The lag between more bacteria growing and the protozoa "noticing" this increase in food resource is about 2 weeks in the spring, about 4 weeks in the winter (not-frozen soil), and about a week in a warm, moist soil in the early summer. When soil moisture is below wilting point, the protozoa may never notice until soil moisture increases.
Nematode Food Resources
  1. Nematodes come as four types: bacterial-feeders, fungal-feeders, root-feeders and predatory nematodes. Predatory nematodes eat other nematodes and are great at controlling root-feeders a great deal of the time. Like protozoa, when the organisms that the nematodes eat increase, then nematodes have more food, and you see an increase in nematode numbers. The lag between more food and more nematodes is greater than for protozoa. Protozoa can begin to increase their reproductive rate in 24 hours, but nematodes require a 2 week to 1 year growth cycle, depending on the type of nematode.
  2. The only good sources of beneficial nematodes are good compost (which you MUST check to make sure it is good stuff. There's a lot of organic material out there being sold as compost. Or use a soil that has been tested for nematodes and shown to have only good guys. Old growth forest soil typically has just the beneficials. But be careful - old growth forests that have been disturbed can have very sick soil. It can take ten years for the trees to start showing the effects of a compacted soil, or fertilizer impacts, or atmospheric pollution. Test the soil first to make certain it's ok.

Compost is a great source of ALL the organisms AND the food the organisms need to do their jobs. A great diversity of bacteria, fungi, protozoa and beneficial nematodes occur in good compost. But beware! There is quite a bit of organic matter sold under the name of compost, and it's not worth the money spent on it. Improperly composted material can kill plants (phytotoxicity), and can add all kinds of nasty organisms, from fungal pathogens to root-feeding nematodes. Test the compost first, and know the conditions of composting before you buy the material. A good compost can grow grass directly seeded into 100% compost, and you will never see grass grow more beautifully. But so much of what is sold has serious salt, heavy metal and toxic anaerobic problems that care must be taken. See the Biocycle column papers that appear in the ARTICLES section of the website.

Areas with obvious disease problems. Especially if the disease is known, this helps pin-point the "out-of-balance" aspect of the foodweb. For example, root rots suggest compaction and high nitrate are both problems. Compaction results in anaerobic zones where metabolic products from anaerobic bacterial growth are released. Anaerobic metabolic products kill roots and allow root rot fungi to have the advantage over all the beneficial fungi. The Foodweb solution is to get oxygen moving back into the soil by opening up compacted zones. This can be done by getting the organisms that make soil structure back into the soil. Even if you plow, or deep rip, the problem won't be solved, because without the organisms to build structure, plowed soil just re-compacts over the next four to five watering events (rain or irrigation).

It is important to know whether it is a lack of bacteria or fungi that is preventing the formation of the building-block aggregates in the soil. Once that is established, and fixed by adding back in the food and organisms that are lacking, then determining whether the organisms that build the spaces in soil, the beneficial nematodes and microarthropods, are lacking.

Nematode samples need to be sent to us to assess, but microarthropods are best assessed by placing small cups flush with the surface of the soil, putting a little antifreeze in the cup, and letting the cup remain undisturbed for 24 hours. If there are adequate arthropods, you'll find 10 to 50 little critters in the antifreeze. If you don't have any, you need to talk with us about how to encourage them to come back.

Compost and compost teas are a great way to get all the organisms and the foods to feed them back into the soil. But, be aware that many things that people call compost ARE NOT COMPOST!!!! If the material stinks, is black in color, is dry, then it is not good compost. Stinky, smelly organic matter is not compost - it is putrefying organic matter, and will kill you plants quite often. One of the earlier speakers at the conference said that compost will kill plants, but clearly the person did not differentiate good compost from putrefying organic matter (POM). There are no plant-toxic materials in good compost - there are in POM.

Areas with low fertility. Plants lacking green color mean stress of some kind. It could be lack of nitrogen, or lack of any of a number of micronutrients. A soil chemistry test may let you know what that limiting nutrient is, but if no limiting nutrient is apparent, it is a problem with making the nutrients plant-available, not a lack of having the nutrient in soil.

Again, a step-wise approach can be taken. First, make sure there are plenty of bacteria and fungi to keep those nutrients in the soil. If the soil has poor structure and poor organic matter levels, there's no CEC to hold the nutrients in the soil. The only way to build that is to get the bacteria back. Determine whether the soil lacks bacteria and/or fungi. Add products to bring back these organisms. Then the soil will hold those nutrients. Then check for protozoa and beneficial nematodes. If either group is lacking, the nutrients held by the bacteria and fungi will not be made into plant-available nutrients. Check for mycorrhizal fungi. If these are lacking, then micronutrients will not be easily transported to the plant in plant-available forms. With adequate saprophytic fungi, this transport will occur, but the plant has much less direct control over these saprophytic fungi than of the mycorrhizal fungi. If both kinds of fungi are lacking, the plant will be stressed, and the only way to solve the problem right now is to apply fertilizer, or do foliar micronutrient sprays. Bring back these organisms to the right levels for the plant you want to grow, and the process will begin again without you having to constantly apply fertilizer.

Areas where water puddles on the surface during rainy periods. Again, this is a compaction problem, but the compaction is probably deeper than the 0-3 inches that we typically ask for, and you'll have to take cores down to the depth where the compaction is occurring, and take samples from that depth for us to look at. After determining what the organism group is that is out-of-balance, getting that organism to that depth can be a problem. We will generally send you to another business that specializes in applying that organism group at that depth, and have you work with them to get that organism where it needs to be.

Areas where there is no soil structure (the 'soil' runs through your fingers like sand when it's dry). Here, everything is lacking from the foodweb. Before even taking a foodweb sample, start getting the organisms back and adding food for them. After the management is begun to bring back soil life, take samples to make sure the foodweb is building the way it should for that plant.

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