A. 9. Repairing the Soil Food Web

The soil food web is a complex, interdependent, mutually beneficial group of organisms ranging in size from bacteria, to fungi (the largest organisms on the planet) to protozoa, to nematodes, microarthropods, worms and beetles. The foodweb develops good soil structure by binding pieces of soil (clay, sand, silt, organic matter, roots) together and by building airways and passageways through the soil. Good movement of air and water are vital to the health of plants and the soil food web itself. While it seems contradictory, good soil structure both allows water to drain from too wet soil and helps soil to hold water when soils start to dry out.

When considering living organisms, it is true that "everything eats, everything excretes, and everything is food for something". Bacteria and fungi feed on plant residues, breaking them down and holding nutrients (e.g. nitrogen, calcium, iron, potassium, phosphorus, etc.) in their bodies, glued and bound to soil particles, preventing loss of nutrients through leaching. The nutrients bound in the bacteria and fungi are not available to plants, until protozoa, nematodes, small microarthropods, and earthworms consume individuals of bacteria and fungi and release nutrients in plant available forms. The nutrients are released when and where the plants need them, in the form and amounts that plants need. Plants excrete foods for bacteria and fungi from their roots, which are foods for the beneficial species, protecting the root from pathogen and pest attack.

In the process of feeding on plant materials and each other, these organisms also produce hormones that plants need, and consume or break down pollutants in the soil. The soil food web protects all plant surfaces from disease-causing organisms and other pests, often by out-competing them for food, sometimes simply by eating them, by occupying the plant surfaces so the pathogen cannot gain access, and at other times by altering the soil conditions so the disease-organisms cannot thrive.

So much of what modern agriculture has done is to destroy these beneficial organisms in the soil, and on plant surfaces. The goal was to destroy specific pathogen and pest organisms through the use of toxic chemicals, but the beneficial, protective organisms were also killed. And the boom-and-bust-life-style, disease-causing organisms came back faster from those toxic applications. It takes a number of toxic chemical applications, and typically several different kinds of toxic chemical applications have to be made, to wipe out the whole set of beneficial bacteria and fungi, protozoa and nematodes, but it has been done. In typical conventional agriculture fields, bacterial numbers have been reduced from several thousand billion in the root zone, to only a million per gram. Species diversity has been lost, and the disease-selected, the beneficials destroyed. No wonder disease and pests are impossible to control after 30 to 50 years of warfare against the normal set of organisms in soil.

But how do you fix the problem? We didn’t know we were harming things so badly, and so nearly everyone has inadvertently caused serious problems in their soils. How do we get the right biology back into the soil?

Step One: Bacterial Diversity Adequate?

Bacteria must be present to perform their functions of competing with disease-causing organisms, retaining nutrients and making microaggregates to improve soil structure. The “correct” density of bacteria, or amount of bacterial activity has just begun to be established, based on observation of what these levels are in different soils, climates, conditions, disturbances and plant species. Seasonal variations and the requirements of different plants appear to be the most important relative factors. The correct values for active bacterial biomass, and total bacterial biomass are given on a Soil Foodweb report, based on season, plant type, soil type and climate, in the row marked “desired range”.

1. When total bacterial biomass is too low, bacteria have to be added back to the soil, compost, compost tea or to the water, if working in hydroponics, for example. Add them back by using a healthy, aerobic compost, compost tea or commercial inoculum.
2. When total bacterial biomass is high, most of the time this means improved ability to perform bacterial functions, but if the balance between total bacteria and total fungi becomes inappropriate for the plant species, then the balance needs to be restored. However, you don’t kill off bacteria if they are higher than the desired ratio, you improve fungal biomass instead (see Ratios).
3. On rare occasions, total bacteria may compete with fungi for food resources, and in this case, reducing bacterial foods may be a good idea, to allow the fungi to have a chance to grow. Too high bacterial biomass, combined with too low active bacteria biomass may indicate anaerobic conditions occurred, because the bacteria grew very fast, used up the oxygen in the medium so the aerobic organisms went to sleep, but the anaerobes grew well. This can be very detrimental to the aerobic organisms, and actually kill them.

Step Two: Feed the Bacteria

Feed the bacteria, if bacterial activity is too low. Just like any other creature, bacteria require food. Plant roots often supply the simple carbon substrates that bacteria require, such as simple sugars, proteins, and carbohydrates. Bacteria need N, P, K, Ca, and all the other nutrients as well, and obtain those from organic matter and from inorganic sources as well. Various species of bacteria can solubilize mineral elements from the mineral components of soil, but no one species can effectively solubilize ALL minerals. Diversity of species to obtain all the needed nutrients is required.

Often soil tests will indicate that some nutrient is in low supply, but merely by adding the appropriate bacterial or fungal species, these organisms will convert plant unavailable nutrients into plant available forms. Diversity is the key, however, as well as feeding that diverse set of species so they will perform their functions.

1. If activity is low, then bacterial foods need to be added to increase growth rates and improve numbers. A diversity of foods needs to be added, and thus molasses is a much better choice than white sugar. Fish hydrolysate also adds fungal foods, and N and other micronutrients. Fruit juices can be used as well, but diversity is key.
2. If activity is higher than the desired, then try to balance the ratios of the organisms by improving the organism group that is too low.
3. If active bacterial biomass is low, but total bacterial biomass is high, this is a good indicator that anaerobic conditions have occurred. In rare instances, it may be because some environmental disturbance occurred that put the majority of the bacteria to sleep, but did not kill them.

Step Three: Fungal Biomass Adequate?

Fungi must be present to perform their functions of competing with the more difficult disease-causing organisms, retaining nutrients especially micronutrients like Ca, and making macroaggregates which form air passageways and hallways to allow air and water to move into the soil, and to allow good drainage. This is a critical step in improving soil structure, but cannot occur without the first step of good bacterial biomass.

The “correct” density of fungal biomass, or amount of fungal activity, has just begun to be established, based on observation of these levels in different soils, climates, conditions, disturbances and plant species. Seasonal variations and the requirements of different plants appear to be the most important relative factors. Again, the values for active fungal biomass and total fungal biomass are given for the season, plant type, soil type and climate in the row marked “desired range”.

1. When total fungal biomass is too low, fungi will need to be added back to the soil, compost, compost tea or to the water, in hydroponic situations, for example. Add them back by using a healthy, aerobic compost or compost tea. Alternatively, these fungi might be found in healthy soil, especially the humus layer of a healthy forest. But be careful not to destroy that resource by removing too much, or disturbing too much.
2. When total fungal biomass is high, most of the time this means improved ability to perform fungal functions, but if the balance between total bacteria and total fungi becomes inappropriate for the plant species, then the balance needs to be restored. However, you don’t kill off fungi if they are higher than the desired ratio, you improve bacterial biomass instead (see Ratios).
3. On rare occasions, total bacteria may compete with fungi for food resources, and in this case, reducing bacterial foods may be a good idea, to allow the fungi to have a chance to grow. High total fungal biomass, combined with too low active fungal biomass may indicate a fungal disease outbreak in progress. This can be confirmed by examining the roots for necrosis, galls, or other signs of fungal disease.
4. Beneficial fungi require aerobic conditions and if oxygen falls below 5.5 to 6 mg oxygen per liter, then the beneficial fungi may not survive. Anaerobic bacteria attack and consume fungi in these low oxygen conditions. Disease-causing fungi are benefited by anaerobic conditions, either because they no longer have competition from the beneficials, or because they require anaerobic conditions for best growth. In either case, anaerobic conditions select for and allow the disease-causing organisms to “win” in the fight for plant tissues.

Step Four: Fungal activity adequate?

Just like any other creature, fungi require food. Feed the beneficial fungi, if fungal activity is too low. Sloughed root cells and dead plant tissue often supply the more complex carbon substrates that fungi require, such as cellulose, cutins, lipopolysaccharides, complex protein-sugar-carbohydrate, and lignins. Fungi are good at condensing organic matter into ever more complex forms, such as fulvic to humic acids. Fungi need N, P, K, Ca, and all the other nutrients as well, and obtain those from organic matter and from inorganic sources as well. Many species of fungi can solubilize mineral elements from the mineral components of soil, but no one species effectively solubilizes ALL minerals. A diversity of species is needed to obtain all nutrients.

Often soil tests will indicate that some nutrient is in low supply, but merely by adding the appropriate bacterial or fungal species, these organisms will convert plant unavailable nutrients into plant available forms. Diversity is the key, however, as well as feeding that diverse set of species so they will perform their functions.

Both bacteria and fungi are important in holding nutrients in the soil when they would otherwise leach into deeper soil layers, and into ground water. The importance of microbes in forming soil structure and preventing erosion is well-known, but in order to hold the nutrients in soil, bacteria and fungi must turn them into biomass, which is not-leachable as long as the glues and strands that the fungi and bacteria use to hold themselves on any surface are not destroyed.

1. If activity is low, then fungal foods need to be added to increase growth rates and improve numbers. A diversity of foods needs to be added, and thus dead leaf material is a much better choice than purified cellulose. Fish hydrolysate also adds bacterial foods, and N and other micronutrients. Wood, sawdust, bark, paper and cardboard can be used as well, but diversity is key.
2. If activity is higher than the desired, then try to balance the ratios of the organisms by improving the organism group that is too low.
3. If active fungal biomass is low, but total fungal biomass is high, this is a good indicator that disease is either rampant, or about to be rampant. Add BENEFICIAL fungal foods and build soil structure as rapidly as possible to compete with the disease, and protect the plant roots from the disease.
4. In rare instances, it may be because some environmental disturbance occurred that put the majority of the fungi to sleep, but did not kill them.

Step Five: Roots colonized by the “goods guys”?

Mycorrhizal fungi are needed by some plants, absolutely critical for other plants, and are probably detrimental for other plants. You need to know what kind of plant you have, but in general, very early successional plant species, such as many (weeds, brassicas, mustards and kale crops do not require mycorrhizal fungal and may be harmed by mycorrhizal fungi. Annual vegetables, flowers, grasses and row crops or broadacre crops need vesicular-arbuscular mycorrhizal fungi. Most evergreen plants require ectomycorrhizal fungi, and blueberry and ericoid plants require ericoid mycorrhizal fungi.

The percentage of the root system that must be colonized has not been fully established in the mycorrhizal literature, mostly because determining benefit is relative. Mycorrhizal fungi can protect the roots from disease organisms, through simple spatial interference, by improving nutrient uptake, and by producing glomulin and other metabolites that inhibit disease. Stress in plants can be reduced because the mycorrhizal fungi can solubilize mineral nutrients from plant not-available forms to plant available forms, and translocate those nutrients to the root system in exchange for sugars provided by the plant.

Given that mycorrhizal fungi can influence so many aspects of plant growth, and documenting all these benefits is usually extremely expensive and difficult, they have not been documented. Therefore, probably the best that can be done is to say that perhaps as low as 12% colonization might be documented to be beneficial (work by Moore and Reeves in the mid-1990’s), but more likely a minimum level of 40% colonization is required, as suggested by Mosse, and St. John in various publications and comments.

Early researchers found colonization as high as 80% in root systems, but most likely because they did not differentiate false-arbuscular and vesicular structures produced by disease-causing fungi from true VAM structures. Thus, colonization is rarely as high as 80% is not commonly found now that we recognize these non-mycorrhizal forms.

In the last 10 years, some researchers have suggested that some mycorrhizal fungi do not produce vesicles under all conditions, and so VA mycorrhizal fungi should be called arbuscular mycorrhizal fungi, not vesicular-arbuscular mycorrhizal fungi. Just be aware that sometimes, people say VAM, sometimes AM. Whatever.

1. If the plant does not require mycorrhizal colonization, there probably is no reason to assess the roots for mycorrhizal colonization. Although the Allens showed that one way for certain plants to exclude non-mycorrhizal plants from a community was to make sure the mycorrhizal fungi were present, because the mycorrhizal fungi pulled nutrients from the non-mycorrhizal plants. This is a probable mechanism for mycorrhizal crop plants being able to out compete weeds and earlier successional plant species.
2. When mycorrhizal colonization is low, or less than the desired range, given that the desired plant requires VAM or ectomycorrhizal colonization or ericoid mycorrhizal fungi, then check how low the colonization is.
1. If less than perhaps 10 to 15%, then addition of mycorrhizal spores would be a good idea. If it is an annual plant, placing VAM spores near or on the seed or seed pieces is the simplest way to get the roots colonized as soon as the roots area produced.
   1. With permanent turf, adding VAM spores into the compost mixWed into the aeration cores gets the VAM spores into the root system without destroying the turf.
   2. With perennial plants, verti-mulching and adding the VAM or ecto- spores into the compost mixed in the vertimulch is the simplest way to get the spores next to the root system. In cases where we have added inoculum in this fashion, roots have gone from 0% colonization to 25 to 30% within a year, and to 50 to 60% in two years, with addition of humic acids through the season to help the mycorrhizal fungi grow rapidly (see next section)
2. If colonization is between 15% and 40%, then all that is needed is additional fungal foods to help the mycorrhizal fungi improve plant growth, reduce plant stress, and improve root protection.
1. There is a dose response relationship to humic acids additions. Typically addition of 2 to 4 pounds of dry product, or 1 to 2 gallons of liquid product per acre are adequate to improve fungal growth. But, if there are toxic chemical residues to overcome, additional humics of fulvics may be needed. It is best to check periodically to see that colonization is improving as desired.
2. Be aware that that most humic acid products contain 10 to 12% humic acids. If the product you are considering is less expensive, please check the concentration of humic acid. Half the concentration of the humic acid means they can drop the price, but your fungi get less benefit.
3. Check colonization periodically to make sure the fungi are growing and colonization is increasing. Weather can cause problems with colonization, and severe drought, floods, burns, compaction causing by over-grazing, heavy machinery, herds of people walking on the lawns or turf can reduce colonization. If that happens, additional applications of fungal foods will be needed to help resuscitate the damage. Fungi are just like any other organism. If they are harmed, they need care to recover. Triage for fungi includes adding foods they love (humic acid is like chocolate to a choc-a-holic, but they’ll also accept any woody, wide C:N ratio fungal food), and putting on a mulch or litter layer on the soil surface.
3. If colonization is above 40%, then the plants are getting the help they need from the fungi. Periodically check to make sure nothing has harmed them.
4. What if colonization seems too high? This is extremely rare, but does happen, and seems to be associated with the fungi taking more than their fair share of the plant’s resources. Stop applying fungal foods. Consider helping the bacteria compete with the fungi for a bit.
   

Steps Six, Seven, Eight: Adequate protozoa to cycle nutrients?

Make air passageways? Flagellates (Six), Amoebae (Seven), Ciliates (Eight). These are the three groups of protozoa and they are critical in a bacterial-dominated soil, because the plants need a way to access all the wonderful nutrients tied up in the bacteria. Nutrients within the bacteria cannot be obtained by plant roots, so something has to eat the bacteria to release those nutrients. That’s what protozoa do. Protozoa also help build the larger soil pores by pushing aggregates around as the protozoa search for and try to reach the bacteria tucked away around soil particles.

1. 1. If the protozoa are too low in number, the nutrients remain tied up in bacterial and fungal bodies. Even if the bacteria and fungi die, they may not release the nutrients in their bodies until the protozoa come along. In many early microbial studies, microbiologists doing plate counts did not recognize that the protozoa were still in their “pure cultures”, and it was the protozoa “mineralizing” nutrients, not the bacteria themselves. When protozoa are too low, and nematodes are too low as well, then inorganic fertilizer will have to be added in order to supply N, P, S etc to the plant. This is expensive and a large proportion of these nutrients will likely be lost from the soil, either by leaching or by volatilization. Until the protozoa are inoculated and brought to desired numbers, nutrient loss will continue to be a problem. Protozoa inocula are available in the form of good compost, good compost tea, or from a commercial source, Holmes Environmental, holmesenviro@attbi.com
2. If the protozoa are within the desired range, nutrients will be made available for the plants are minimal amounts over time. How much will be made available? That will be discussed in the section on Plant Available N made available to plants (see below). But reductions in fertilizer applications should be possible if protozoa are in good range.
3. If protozoa numbers are extremely high, or the different groups are very un-balanced, then nutrient cycling will be variable, and there may be periods when pulses of ammonium or nitrate may accumulate. These forms are subject to leaching and loss through gas production, and may result in weeds having the nitrate they need to germinate, grow and outcompete the crop or desired plant species.
4. If ciliates are too high, then the soil is either compacted or water-logged, and lacking oxygen. Ciliates are aerobic organisms, but prefer to consume anaerobic bacteria. They tolerate reduced oxygen conditions better than the other protozoa, so high numbers of ciliates indicate problems with the movement of oxygen into the soil, which needs to be fixed. Of course, it the soil gets too anaerobic, all three groups of protozoa will be low.
5. When ciliates are high, but flagellates and amoebae are also high suggests that one of three things may be happening:
   1. The sample has just become compacted, or flooded, and the anaerobic conditions have just been initiated. Generally the number of ciliates is not extremely high.
   2. The sample has aggregates, which are anaerobic inside the aggregates. The high ciliate signal comes from the internal parts of those aggregates where anaerobic conditions exist, but outside those aggregates, aerobic conditions exist, and thus flagellate and amoebae numbers are typically high as well. Both anaerobes and aerobes co-exist, but in very different places within the spatial structure of this sample. This is very typical of good worm compost, particularly worm compost high in castings.
   3. The sample has been anaerobic in the past, but is just becoming aerobic. Flagellates and amoebae are growing because aerobic bacteria have begun to grow. Generally, ciliate numbers will be fairly high, while flagellate and amoebae are just barely in good range. Quite often this will result in nitrate pulses and germination of weed seeds.
6. When flagellates are high and amoebae low, or flagellates low and amoebae high indicates an imbalance in nutrient cycling, with pulses of nitrate being produced, resulting in weeds being able to out-compete the desired plants.
7. What do you feed protozoa? Bacteria. So, if you have taken care of step one and two, the bacteria should be there for the protozoa to eat.

Steps Nine, Ten, Eleven: Adequate nematodes numbers, and are they the right kinds to help nutrient cycling, and build passageways to let water and air into the soil?

Bacterial-feeding nematodes (9), Fungal-feeding nematodes (10) and Predatory nematodes (11). The beneficial nematodes consume their prey groups, and in the case of bacterial- and fungal-feeders, release N, P, S, and micronutrients that would now be available to plants, if the majority of the cycling occurs in the root system. These nematodes also interfere with the ability of the root-feeding nematodes finding the root. The higher number of these organisms, the more nutrient cycling is occurring.

Step Twelve: The bigger critters home?

Earthworms, Microarthropods.
If earthworms and/or microarthoropods are present, then the full food web is present, and if everything is in a good biomass or numbers of individual organisms, then plant health is pretty much assured, because all the processes will be functioning.

How much do I add to fix any group?

In any case, just an inoculum is required, since all of these organisms will multiply, resulting in increased numbers. Of course, the higher the initial number of individuals added, the faster the return to health. Addition of foods for the organisms will increase the rate of return to health as well.

If toxic chemicals are present in the soil, or litter material, then these materials have to be consumed by the organisms before the twelve step program can be performed. Addition of foods to help consumption by organisms will increase the rate of return to health.

Bacteria – add bacterial foods, such as simple sugars, simple proteins, simple carbohydrates. Molasses, fruit juice, fish emulsion and green plant material high in cellular cytoplasmic material feeds bacteria. The more kinds of sugars and simple substrates added, the greater the diversity of species of bacteria, and the more likely the full range of beneficials will be present.

Bacterial AND fungal inocula can be found in most good AEROBIC composts, or compost teas made with compost documented not to contain E. coli, or other human pathogens.

There are some “starter” bacterial inocula that are useful as well. What you need to look for are maximum diversity in the bacterial species. Unless you are trying to make fermentative compost, you need to avoid inocula containing anaerobic bacterial species.

Fungi – add fungal foods, such as complex sugars, amino sugars, complex proteins, soy bean meal, fish hydrolysate, fish oils, cellulose, lignin, cutins, humic acids, fulvic acids, wood, paper or cardboard. The more kinds of fungal foods that are present, the greater the diversity of fungal species will grow.

There are no fungal inocula on the market. Yeasts are rarely useful fungal species in soil, or at least there is little data to support their usefulness. Some effort needs to expended to show the veracity of this view point.

Protozoa – consume bacteria, and thus to improve protozoan numbers, bacterial biomass needs to be enhanced. Protozoa inocula are compost, compost tea, and some commercially available protozoan cultures.

Nematodes – consume bacteria, fungi and each other. Inocula of certain entomopathogenic nematodes are available, for control of certain insect species, such as root grubs and root weevils. Compost and compost tea are the only source of inocula for the beneficial nematodes.

Mycorrhizal fungi – need roots to germinate and grow successfully. Humic acids can improve germination, but then the germinated fungus has to rapidly find a root to colonize or it will die. Spore inocula exist for all kinds of mycorrhizal fungi. Make sure you have the kind needed for your plant. Make certain to get the spores into the root system of the plant, such as injecting the spore, or adding compost mix into the soil, filling soil cores with a mix of compost and spores.

This is just a start to understanding how to get the right biology back into the soil. You need to test your soil and figure out where your soil is, with respect to the right biology, and then make a plan on how to get the right biology back. Once you think you have achieved the goal, test again to see if you have achieved a healthy soil condition for your plants.

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