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Joe Bradford -Soil Microbiology and Organic Matter in Crop Production


Soil Microbiology and Organic Matter in Crop Production


Soil Microbiology and Fertility Research Results

Gebert Pecan Orchard 2008



We took soil samples in March and analyzed them for several characteristics that give us a snapshot of the changes after six years to soil biology caused by some of the organic treatments tested. These are compared to the conventional fertility practices the Geberts have used in the past. This comparison treatment is called “Conventional (no compost tea)” in all the figures below. Please note the differences in responses between the top 2 inches and the next 4 inches of the soil. These differences occur because most of the treatments are applied to the surface of the soil, and some time is needed for their effects to be seen in the lower part of the soil horizon. There are several cases, however, that show a pronounced effect in the lower part of the soil layers tested. These differences may have important, long-term effects on soil health and tree productivity.


Soil Organic Carbon.


Soil organic carbon is the element that is quantified in the laboratory. It converts to an “organic matter” estimate by multiplying the organic carbon by 1.72. Clear increases in soil carbon are seen with both the compost and compost + poultry litter treatments. Much of the increases in those treatments is due to the compost, which has a longer lasting effect on soil organic matter because it is lower in energy than poultry litter.

Lower amounts of organic carbon show up in the Kinsey Organic, Kinsey Synthetic and Poultry litter treatments. These either have high energy content (poultry litter) or result from smaller amounts of organic matter sources being added. However, even these lower application rate treatments have increased soil carbon over the comparison standard treatment. Increases in organic carbon in many of these treatments indicates that the soil is in much better condition to support both tree health and nut production as well as providing lasting support for microbial populations in the soil. Note that most soils used for agriculture in this part of the world contain about 1% organic carbon.


Similarly, results for organic nitrogen show increases with organic amendments to the soil. Nitrogen is a major fertility nutrient for crop production in any system, but requires critical attention in organic systems because it is not quite as simple as adding more nitrogen if the crop needs it. It is best to plan for the trees’ nitrogen needs in advance. The nitrogen levels seen here are not immediately available to the crop. Only during decomposition of the organic carbon does the nitrogen in organic matter become available to the trees. The amount released is usually the same percentage of the amount of carbon decomposed in a growing season, as explained in the earlier section. Note the relatively lower amounts of organic nitrogen in the Conventional (no compost tea) treatment. Little accumulation is possible in that treatment because there is no added carbon to help tie-up any extra nitrogen from the chemical fertilizer treatment. Carbon is needed to tie up extra nitrogen into soil microbial biomass and other organic forms which can be used later for the crop. Note also that most soils used for agriculture in this part of the world contain about 0.1% organic nitrogen.


Determining how much decomposition will occur during the year is often difficult. The percentage is affected by rainfall and temperature, and we all know how predictable those are. Another factor is also important. To estimate how much of the nutrients in an organic source is made available during the growing season, we must also look at the relative amounts of carbon and nitrogen in the amendment, the carbon-to-nitrogen ratio (C:N). If the carbon is too high, the imbalance can lead to nitrogen tie-up by the microbes, which makes it unavailable to the crop. If the carbon in too low, excessive nitrogen may be produced and wasted when crops don’t need that much. Other problems with plant health may also result, such as luxury consumption leading to high nitrate levels in some crops.

The C:N ratio of the Gebert pecan soils ranges from just over 14 to around 12. These numbers indicate a number of things, but we must remember that the ratio does not necessarily address issues of quantity of each element, but issues that are more important to availability of the nutrients to crops. Most native soils have a C:N ratio between 10 and 12. One might conclude that the organic treatments tried in the Gebert orchard have not improved the soil much, since the highest is 14. In this case, higher is not better. When the system reached equilibrium between nutrients in and nutrients out, the ratio should be at or near the usual range. A fertile organically-managed soil may have the same C:N ratio as a depleted, synthetically-managed soil (note the ratio of the Conventional (no compost tea) treatment. The difference is in the energy content of the organic carbon. We can be very sure that the carbon is low energy and the nitrogen is poorly available in that treatment. These results indicate that a balanced increase in the organic component of soil has occurred. The balance helps prevent  a disconnect between natural forces of balancing plant nutrient requirements and plant nutrient provision driven by soil microbial activity, and promotes healthy relationships between the crop, soil and microbes in the system.  


The energy content of organic matter is used by microbes to cycle nutrients to crops. Therefore, there must be enough energy in the organic amendments to carry this out. One method of determining the effects of organic amendments on microbial populations to measure the amount of microbial activity that results from adding organic matter to the soil.   Dehydrogenase is a microbially-produced enzyme that is a general indicator of microbial activity in the soil. We can see that the amount of microbial activity is much higher in those treatments where large amounts of compost or poultry litter are added. Microbes use the high energy carbon in those materials to power the entire nutrient cycling processes in the soil.


The amount of microbial biomass in soil is an indicator of soil health. Biomass increases when the environmental conditions favor biological activity, and is also directly related to the amounts and quality of organic amendments added to the soil. In March of this year the microbes were already active and had produced or maintained enough biomass to start the process of making nutrients available to the crop. Note that this was occurring before trees had leafed out. One might be concerned about wasting those nutrients before they were needed by the trees, but the analysis indicates that the rates of activity were just beginning to increase, and by the time the trees leafed out, trees would have a good supply to start the year. Note that the synthetic treatments are lagging behind somewhat from the other treatments.


Overall, significant changes in the soils have resulted from the treatments tested in this experiment. The organic treatments have increased the content of organic nutrients in the soil that will become a storehouse for future crop cycles. The annual additions of high-energy organic matter sources may be adjusted in the future to ensure an appropriate amount of microbial activity and nutrient cycling. Added to that, the maintenance of the balance for other nutrients such as calcium, magnesium and sulfur may be adjusted as necessary to meet crop needs and to maintain soil health.


Larry Zibilske USDA-ARS

Weslaco, Texas

Researcher, Soil Microbiology and Organic Matter

The amazing increase in demand for organic foods has attracted the interest of many growers. They are exploring the possibility of growing organically by evaluating how they might change their current methods in order to produce for organic markets. There are certainly many things to consider, starting from the ground up.


Transitioning to organic production requires thinking in terms of the system. As we explore all the aspects of organic growing, we begin to realize that all these issues, including soil biology and fertility, plant biology, the environment, and pest dynamics and economics are related and our thinking probably needs to reflect that. Transitioning to organic production is not just a process of exchanging one set of inputs for another. As we consider all these things, we begin to appreciate the complexity of organic systems, but then the decisions take on a complexity to match, and this may become frustrating. Fortunately, before confusion gets the best of us, we also begin to recognize that organic systems are very flexible. This means that established organic systems deal with natural stresses, and our mistakes, much better than conventional systems. They are generally more forgiving.


So where do we start our thinking? What steps do we take to transition to organic production? The first item on everyone’s the list should be the soil. Soil is the foundation of the organic system. If we get the soil right, system flexibility will be good; allowing greater latitude in piecing together the rest of the components into an organic system that is appropriate for a particular grower’s situation.


To start the process, we should pay particular attention to soil microbes and organic matter. Soil microbes are the engine and organic matter is the fuel in organic systems. Microbes decompose organic matter and trap some of the energy for their own use and release excess nutrients which become available to crops. This is the centerpiece of soil microbial function in organic systems. Organic systems rely on soil microbes to do the heavy lifting when it comes to providing nutrients to the crop, but they also play vital roles in protecting plants from diseases and pests. Microbes are natural partners of all plants and organic systems are designed to exploit their beneficial activities that support healthy crop production and protection.



Soil Microbes


How do we know if we have the correct microbes in our system? And if we don’t what can be done about it? The fact is that we know absolutely nothing about 99% of the bacteria in the soil. For fungi, the number is about 83%. These numbers come from soil surveys carried out using powerful genetic tools, and from an accounting for the differences between what we see under the microscope and what we see growing on agar plates in the laboratory. As more tools are developed and applied to soil habitats, we’ll certainly know more in the future than we do now. Right now, a grower can spend a lot of money to determine if the “right” microbes are present in the soil, and what to do about adding more microbes. Alternatively, the grower might consider spending that money to increase soil organic matter by using varied sources of organic materials. Doing so will virtually ensure “inoculation” of many beneficial microbes that will thrive in the soil and become permanent residents. This is not to say that adding specific microbes is without merit. There are several plant protective microbes on the market that have been successfully incorporated into organic systems. The real trick is to maintain their populations at high enough numbers to control diseases or pests, or accept adding them as a regular procedure in the system. Soil is a hotly competitive place for microbes. In deciding whether to add microbes just remember that, if they are to be effective, the newcomers must compete with those microbes already in the system.


Soil Organic Matter


 As introduced above, organic matter is the basis of fertility for the crop in organic systems and also provides nutrients and energy to soil microbes. Soil organic matter is a mixed pool of materials that is made up mainly of decaying plant residues and microbially modified organic residues. It contains most, if not all of the nutrients needed by plants and microbes. As soil microbes decompose organic matter, they use the energy contained in the chemical bonds of the organic matter to drive many beneficial processes. An appropriate amount of soil organic matter is indicative of soil health. The question is, how do we reach an “appropriate” level of soil organic matter?


Many organic producers add some form of organic matter to the soil. Crop residues, manures, and composts are commonly used, and in some systems cover crops are used to increase soil organic matter. These not only add energy and nutrients to the soil, but they improve several characteristics of the soil, such as water holding capacity and soil structure, that promote crop growth and soil health. The amount of organic amendment needed depends on balancing crop needs and soil needs.


Objectives of Adding Organic Matter. In transitioning to organic production, there are two main objectives we are trying to address by adding organic materials to soil.


1.  Provide adequate nutrition for the crop. Crops need certain amounts of nutrients to thrive. The blessing (and curse) of using organic sources is that they contain lower concentrations of nutrients and that the nutrients are metered out over time. This means nutrients become available to crops only as the organic material is decomposed by microbes. This can take place over a period of weeks or months, depending on the quality of the organic amendment. Quality is a combination of two ideas. One is whether the material has the appropriate balance of nutrients in the organic amendment (does it contain the correct amounts of all the nutrients needed to support microbial decomposition of the amendment?). The other, very important idea is the energy content of the material. Energy is needed to promote the microbial activity necessary to transform the crop nutrients into crop available forms.


Example 1. Adding 50 lbs. of nitrogen in chemical fertilizer form results in 50 lbs. of nitrogen being immediately available for crops, whether that much is needed immediately or not. In common circumstances, at least 50% of fertilizer nitrogen does not end up in the crop (25 lbs. is lost). Contrast this with compost containing 3% organic nitrogen. This equals 60 lbs. of nitrogen per ton. If two tons are added to the soil, those 120 lbs. of nitrogen become available only as fast as microbes can decompose the compost. Commonly, only about 20% of compost is decomposed in one growing season because it has “low energy”. This means that, 120 lbs. times 20% decomposition = 24 lbs. of nitrogen made available to crops in one season. However, because it becomes more slowly available to the crop, there is a greater efficiency in the absorption of that nitrogen. These 24 lbs. would almost certainly result in better crop use than the 25 lbs. in the first example.


Example 2. Some organic sources, such as manures, decompose faster than composts and offer an opportunity to combine sources to allow for better matching of crop nutrient needs to nutrient supply. For example, manure might contain 12% nitrogen which equals 240 lbs. of nitrogen per ton. Decomposition of manures is commonly 70% in a growing season, faster than composts because they contain higher energy. Adding one-half ton provides 120 lbs. of nitrogen times 80% decomposition = 96 lbs. of nitrogen that becomes crop available in a growing season. Combining composts and manures could be done in such a way to meet high crop nitrogen demands quickly (from the manure) and provide a lasting organic effect (from the compost).


There are other questions that bear on the deliberations of which materials to use, how much of them to use, and how often to use them. Cost can vary widely, availability varies, which application methods are best, timing the applications during the year, and environmental considerations may significantly affect these decisions. These examples illustrate guiding principles but cannot cover every situation. Grower experimentation and “trial and error” are the useful approaches. Remember, the forgiving nature of organic systems allows us some latitude to try things.


2.  Improve soil quality and the microbial component of the soil. The nutrient needs of microbes will most often be met as growers address objective 1. What microbes need in addition to that revolves around the concept of soil habitat. There is normally a great range in microbial habitats in the soil which allow many different kinds of microbes to thrive there at the same time. For instance, there are aerobic parts of the soil, anaerobic parts, and degrees between the two extremes. This allows for the growth of anaerobic microbes, aerobic microbes and many microbes in between; all at the same time. The diversity of soil habitats has great ecological impact because with diverse habitats comes diverse microbial populations, and these combine to increase the stability of the system. The more stable the system, the more predictable it is.


Diversify inputs. To promote different thriving microbial populations, diversify organic inputs. Using compost, some manure, and perhaps other organic sources of nutrients (i.e. fish emulsions, kelp, feather meals) further diversify soil microbial habitats and populations.


Use balanced inputs. Soils have limited capacity to hold nutrients. Loading up with one nutrient, such as calcium, limits how much magnesium and potassium the soil can accept. This also results in other problems with the crop because an unbalanced relationship among soil nutrients contributes to unhealthy crops. Keep an eye on soil nutrients by soil testing on a regular basis.


Timing and Frequency. Microbial population rise and fall naturally during the year. It may be worth considering adding more organic amendments through the year. This might help stabilize populations. This is an area of current research.


Soil Quality. Over time, organically managed soils show improvements in characteristics that support microbes and crops. Soil water properties change. Tight, clayey soils become more permeable; sandy soils gain the capacity to retain water better. Soils show improved structure, which improves aeration of the soil, benefiting crop root systems. Soil quality improvement generally just happens. In organic systems, as soil organic matter levels increase, so do many other soil properties that support




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