April 21, 2004 | General

Soil Chemistry And The Quality Of Humus

Richard Stehouwer
BioCycle April 2004, Vol. 45, No. 4, p. 41

Final uses for most of the organic materials processed by BioCycle readers are directed to soil-based application intended to improve the capacity of those soils to support plant growth. Composted organic products, for example, may be used to cover the soil surface, to augment natural soil organic matter, to supply plant nutrients or to blend with other materials to create manufactured soil products.
The first article of this four part series (“Soil Quality Fundamentals,” October 2003) introduced the concept of soils as natural bodies that are undergoing constant change. Part II (see “Soil Quality Fundamentals – Water and Air Essentials,” November 2003) described soil physical properties and processes that control water, air, and heat movement and exchange in soil. This article will focus on chemical properties and processes in soil, and the last will cover soil biology. Separating soil physics, chemistry, and biology is one way to simplify and help us understand complex soil systems. But such separation is artificial. In reality, it is the intricate interplay of these properties and processes that accounts for the dynamic nature of soils.
Soil chemistry is fundamentally the chemical reactions that occur in soil water and at the interface between soil water and the surfaces of soil particles. But in contrast to the simple pure chemical systems often studied in research laboratories, soils are very complex chemical systems. Soil water is more accurately called soil solution because many different inorganic and organic chemical constituents are dissolved in the water. Each of these soil solution constituents can undergo reactions with each other and with the surfaces of soil solids. There is a diverse array of surfaces in soils, each with characteristics that influence how they react with soil solution constituents. Thus a very large number of different chemical reactions can occur in soil as these chemical constituents strive to achieve a state of equilibrium with each other and with clay and organic matter surfaces. True chemical equilibrium is never achieved in soil systems because the soil environment is constantly changing due to microbial activity, nutrient removal by roots, wetting and drying cycles, and leaching losses. Part III of this Soil Quality Fundamental series takes a closer look at soil solution, soil surfaces and a few soil chemical processes that are fundamental to the function of soils as plant growth media.
Inorganic constituents in the soil solution are contributed by the gradual dissolution of soil minerals, and by human activities such as fertilizer application. Most of the inorganic constituents carry an electric charge and are called ions. Those with a positive charge are cations; those with a negative charge are called anions. The cations include the important macronutrients – ammonium (a nitrogen source), potassium, calcium and magnesium – and micronutrients such as cobalt, copper, iron, nickel, sodium and zinc. Important anions in the soil solution include the plant macronutrients nitrate, phosphate and sulfate; micronutrients include chloride, borate, bromide, iodide, manganate and molybdate. Carbonate and bicarbonate are important soil anions because of their effect on pH. Also important in determining pH is aluminum, which exists as a cation at low pH and as an anion at high pH. The soil solution also contains naturally occurring organic constituents that include dissolved organic matter, organic molecules produced during decomposition of fresh organic material, or organic exudates from plant roots or soil microorganisms. Human activities such as spreading manure or pesticide application also add organic molecules to the soil solution. Some organic molecules also may carry an electric charge and thus behave like anions or cations.
In addition to being the source of water for plant growth, the soil solution is the immediate source of almost all nutrients taken up by terrestrial plants. (A very small amount of nutrients can be absorbed through plant leaves.) Plant roots are only able to absorb nutrients that are dissolved in the soil solution. Although soil solution is a complex mixture, it is also a relatively weak or dilute solution and plant nutrients would quickly be exhausted if they were not constantly replenished from some reserve. Furthermore, if all plant nutrients and other essential soil chemical constituents were dissolved in the soil solution, they would easily be lost in percolating rainfall or irrigation water. Fortunately this is not the situation as the solid part of soil serves as a large reservoir of plant nutrients and other constituents of the soil solution.
The first article in this series described the vast surface area per unit weight of clays and humus and their importance to soil structure and water holding capacity. The surface area of clay and humus also allows these particles to function like a soil chemical bank in that they retain and release soil chemical constituents. Soils contain many different kinds of clay, each with unique mineralogy that influences what chemical constituents it will react with, how strongly they will be held, and how much can be held. Likewise, soil humus is made up of many different molecular structures that determine the extent and nature of its reactions with soil chemical constituents.
It is well beyond the scope of this article to delve into the mineralogy and chemistry of the hundreds of clay minerals found in soils. For simplicity, just three broad groupings of clay will be described – the layer silicate clays, iron and aluminum oxides, and allophone type clays.
This group is the dominant type of clay in most soils, especially soils of temperate regions. These clays consist of layers or sheets of highly ordered crystalline arrangements of oxygen and hydrogen packed around primarily aluminum and silicon atoms. The exact composition and arrangement of these sheets is what gives rise to the many different kinds of layer silicate clays and their differing chemical behavior. Figure 1 is a diagram that depicts the structure of a layer silicate clay particle. In reality, these layers may be flat as indicated in the diagram, or they can be curled and folded into various arrangements. The layer clays have both external surface area that makes up the outside of the particle, and internal surface area – surfaces that face each other between the layers or sheets. This internal surface area greatly increases the adsorptive capacity of these clays. In some clays, the distance between sheets is fixed, while in others, it can expand and contract with the addition or removal of water. Soils with an abundance of such expansive clays shrink and swell as water is removed or added. Large cracks open up in these soils when they dry out. Conversely, pressure is exerted when these soils absorb water and swell, potentially crushing foundation walls of buildings or heaving roads and sidewalks.
A unique feature of layer silicate clays is that atoms other than aluminum or silicon may get inserted into the clay mineral when it forms. This disrupts the electrical balance of the mineral and a permanent negative charge results. The amount of this substitution of atoms ranges from very little in some layer silicates such as kaolinite, to very extensive in others such as vermiculite. The permanent negative charge in these clay layers must be satisfied by an equal number of positive charges. This is accomplished when cations (positively charge ions) in the soil solution are attracted to the negatively charged clay surface.
Cations are held on the surface due to the electrostatic attraction of the opposite charges as depicted in Figure 2. These cations are held with varying degrees of strength depending on the size and charge of the cation, and the crystalline structure and amount and location of the negative charges in the clay layer. However, the cations are not held permanently and do not become part of the structure of the clay. Therefore they can be exchanged with other cations in the soil solution. For example, as a soil gradually acidifies due to natural weathering processes, hydrogen and aluminum ions become more abundant and will exchange with cations on clay surfaces such as calcium or magnesium. Conversely, if an acid soil is limed thereby adding large amounts of calcium, the calcium will exchange with adsorbed cations such as hydrogen or aluminum. This process, known as cation exchange, is one of the most important chemical processes in soils for storing and supplying plant nutrients.
However, not all cations are exchanged equally. Due to differences in the sizes and charges of cations and the geometry of the clay surfaces, certain clays will exhibit a strong preference for certain cations, i.e., some cations will be held much more strongly than others and consequently their concentration in soil solution will be much lower. Fortunately for plant nutrition, the cations that plants need the most of (ammonium, potassium, calcium, magnesium) tend to be held less strongly and consequently are more available to plants. Conversely, cations that plants need in only small amounts and that can be toxic in larger amounts (copper, nickel, zinc) tend to be held strongly and are less available to plants. These metals are also present at far lower total concentrations than macronutrients like ammonium, potassium, calcium and magnesium.
Allophane type clays are chemically similar to the layer silicate clays, but do not have a highly ordered crystalline structure and do not have the permanent negative charge in the clay layers. Allophane type clays are abundant in soils derived from volcanic ash. The iron and aluminum oxide clays do not have the layered, sheet-like structure of the silicates. Some oxide clays occur as well ordered crystals and others do not. Oxides are abundant in highly weathered soils of the humid tropics and subtropical regions. In humid, warm temperate regions like the southeastern United States, oxide clays frequently occur as coatings on other soil clays, giving these soils their characteristic red and yellow colors. Like the allophanes, oxides also do not carry a permanent negative charge in their structure.
Allophanes and oxides do have a pH dependent charge that results primarily from hydroxyl chemical groups (one oxygen and one hydrogen atom) that occur at the edges of the clay structures. When the soil pH is somewhat acidic, there is no charge on the clay. But as pH increases to neutral and higher, more and more of the hydroxyl groups become dissociated, meaning they lose a positively charged hydrogen ion. This leaves a negative charge on the site and other cations in the soil solution can be held and exchanged on these negatively charged sites. However, the amount of negative charge per unit weight of clay is much less than in most clays with permanent charge. If soil pH decreases well into the acid range, a second hydrogen ion may attach to the hydroxyl group thereby giving it a positive charge. In this situation, anions such as phosphate, sulfate, or chloride can be held and exchanged by the clays.
Oxides and allophane clays also react with and hold certain anions very tightly, as opposed to an exchange type reaction that is easily reversible. This occurs very readily with phosphate, which is significant because of its impact on phosphorus fertility. Phosphate reacts with oxide and allophane surfaces by replacing a hydroxyl group and is then held by a rather strong chemical bond. In some cases, phosphate may replace two hydroxyl groups and is then held on the clay surface by two strong chemical bonds. This reaction is sometimes called chemical fixation because once phosphate reacts with the clay surface it tends not to go back into solution, or does so very slowly. The layer silicate clays also will react in this way with phosphate, but in general they have a much smaller capacity to fix phosphate than the allophane and oxide clays. These types of reactions explain why large amounts of phosphorus fertilizer must be added in many soils to achieve much smaller increases in plant available phosphorus.
Humus particles consist of large complex organic molecules made up of carbon chains and rings that tend to twist and fold in highly convoluted patterns. Connected to this carbon backbone are numerous and varied chemical structures, many of which contain or consist of hydroxyl groups. Although humus has very little permanent charge, it has a large amount of pH dependent charge resulting from essentially the same mechanism that produces negative charges on allophane and oxide clays. At low pH, very few hydroxyl groups are dissociated so there are few negatively charged sites on the humus molecules. As pH increases, more and more hydroxyls become dissociated leading to more and more negatively charged sites that can hold and exchange soil cations. Because there are so many hydroxyl groups in the organic molecules that make up humus, at near neutral and higher pH humus has many more negative charges per unit weight than clay. It is important to emphasize that fresh organic material such as manure or plant residues are very different from soil humus and have much less capacity to exchange cations.
Humus, like the clays, will hold some cations more strongly than others. In particular, aluminum and heavy metals like copper, nickel, lead and zinc are held much more strongly than cations such as ammonium, calcium, potassium, sodium or magnesium. In acidic soils, aluminum is often toxic to plants. This is why adding organic matter to an acidic soil can greatly reduce toxicity and allow plants to grow even if the soils remains at relatively low pH.
The total amount of cation exchangeable sites found in soil clays and humus constitutes the cation exchange capacity or CEC of the soil. CEC is an important property of soil because it measures the capacity of soil to retain and supply many important plant nutrients. The exchange of cations between soil surfaces and soil solution, and between soil solution and plant roots is essential for sustained plant growth. CEC has traditionally been reported in units of milliequivalents per 100 g of soil (meq/100 g) but now is often reported in units of centimoles of charge per kg of soil (cmolc/kg). Although the units are different, the numeric values are equivalent in each system; that is 1 meq/100g is equal to 1 cmolc/kg.
Worldwide, the CEC of topsoils spans a wide range. Highly weathered soils in the humid tropics typically have low CECs in the range 2 to 6 cmolc/kg. The CECs of most temperate region soils fall in the range of 8 to 25 cmolc/kg, though certain mineral soils that contain a large amount of permanent layer charge clays can have CECs of 35 cmolc/kg or more. In the U.S., soils in the East tend to have lower CEC than those in the Midwest and West. Organic or “muck” soils with very high organic matter levels ( In general, the higher a soil’s CEC, the greater its capacity is to meet plant nutritional needs without frequent, small fertilizer additions. Thus high CEC is desirable in soils used for agronomic production or for low maintenance landscapes where it is not possible or feasible to make frequent fertilizer applications. High CEC allows these soils to retain nutrients applied in large fertilizer applications or released during decomposition of added manures or plant residues. Since soil CEC is largely a function of clay and organic matter content and pH, increasing one or more of these factors will increase CEC. In most cases adding clay to soil is technically and economically not a viable management option. Furthermore, addition of enough clay to have a marked effect on CEC would likely have adverse effects on soil structure, water infiltration and percolation, and the soil’s ability to withstand compaction forces.
It is usually much more feasible to increase soil organic matter. As a rule of thumb, for every one percent increase in soil humus (by weight), the soil CEC will increase by 2 cmolc/kg. Soil organic matter can be increased by adding organic materials such as composts or manures and recycling plant residues into the soil. Remember though, that compost, manure or plant residues are not the equivalent of stable soil humus. The CEC of stable, mature compost is only about one-fourth that of soil humus and that of fresh organic material is even lower. Thus a one percent addition of compost to soil (on a dry weight basis) can be expected to increase soil CEC by only about 0.5 cmolc/kg. Clearly large amounts of compost are required to measurably increase soil CEC, and the benefits of such additions must be weighed against possible negative effects. The second article in this series discussed how large additions of organic materials could adversely affect soil quality. Over the long-term soils tend to reach a steady state organic matter level where organic inputs equal organic matter decomposition. Thus building up and maintaining soil organic matter levels requires management practices that increase organic inputs and decrease decomposition rates. This can be accomplished by recycling plant residues into the soil and decreasing soil tillage and cropping intensity.
Liming soil to increase pH is an option for increasing CEC of low pH soils. The cation exchange capacity of soil humus will typically increase from around 100 cmolc/kg at pH 4 to 200 cmolc/kg at pH 7. The CEC of oxide clays is zero at pH 4 and increases to about 5 cmolc/kg at pH 7. The CEC increase per unit increase in pH will obviously depend on how much of the soil’s exchange capacity is due to humus and oxide and allophane type clays. Again, the benefits of increased CEC must be weighed against other factors affected by pH. For most agronomic and vegetable crops and turf, the ideal soil pH range is 6.5 to 7.5, the range where pH will be near maximum. Many ornamentals and some trees prefer a lower pH in the range 4.5 to 6 where soil CEC could be considerably lower.
The ideal CEC for soil depends on soil function. Intensively managed soils, such as golf course fairways and athletic fields, function well with relatively low CEC (2 to 5 mmolc/kg) because these soils can be fertilized regularly. It is critical for these soils to maintain rapid water infiltration and drainage even when heavily trafficked. Adding clay or organic matter to increase CEC would also tend to decrease water infiltration and internal drainage. Higher CEC (10 to 20 cmolec/kg) is desirable for soils that are not intensively managed and will not be regularly fertilized, such as production agriculture fields, low traffic lawn areas and garden beds.
Soil pH is often referred to as the master chemical variable in soils because of its major influence on so many other chemical processes. The plant availability of most plant macronutrients is greatest near neutral pH and decreases as pH increases or decreases. Elements such as aluminum, iron and manganese are most soluble and can become toxic to plants at low pH. Plant micronutrients, especially metals such as copper, nickel and zinc, are most available at low pH and largely unavailable to plants at high pH. Cation exchange capacity of organic matter and of some clays is controlled by pH as are many dissolution and precipitation reactions. Technically, pH is a measure of the hydrogen ion activity in the soil solution, expressed in negative log units. The pH scale ranges from 0 (extremely acidic) to 14 (extremely alkaline) with 7 being neutral. Most mineral surface soils are in the pH range 5 to 9, though humid region forest soils can have pH less than 5 and salt affected arid region soils can have pH greater than 9.
Since pH affects so many soil processes, it is an important variable for soil managers to monitor and control. It is important to remember that soil pH is a measure of the acidity or alkalinity in soil solution – the so-called active acidity or alkalinity. Soil solution pH is controlled by the much larger reserve or residual acidity or alkalinity held by certain constituents in the solid part of the soil. Reserve soil acidity is due mainly to aluminum and hydrogen ions held on mineral and organic matter. When these ions move from the solids into soil solution they generate acidity, either directly in the case of hydrogen or indirectly when aluminum reacts with water to produce hydrogen ions. The aluminum and hydrogen held on soil surfaces buffer soil solution pH – they resist change in pH. If acidity in a low pH soil solution is neutralized thus increasing solution pH, some aluminum or hydrogen will dissociate from the soil surface to generate additional acidity in the soil solution and push the pH back down again.
Reserve alkalinity in soils is most often in the form of calcium or magnesium carbonates (limestone and dolomite). Many arid region soils and some limestone-derived soils in more humid regions contain these carbonates. When carbonates dissolve into the soil solution, they react with and neutralize acidity. If acid is added to a high pH soil solution, it reacts with alkalinity and decreases pH. This prompts dissolution of carbonates, thereby adding alkalinity to soil solution and bringing the pH back up to its former level.
To actually increase or decrease soil pH, a large amount of the reserve soil acidity or alkalinity must be neutralized. Soil acidity is most commonly neutralized by the addition of ground agricultural limestone, often referred to as “lime.” Pure limestone is calcium carbonate (CaCO3) and goes by the mineral name calcite and is often referred to as “high cal lime. ” Many limestones also contain some magnesium carbonate (MgCO3) and are referred to as “dolomitic lime.” Dolomite is the mineral name for limestone that has a 1:1 ratio of calcium to magnesium. In all these materials, it is the carbonate part of the molecule that reacts with and neutralizes acidity. The calcium and magnesium, known as base cations, will exchange with aluminum and hydrogen displacing these acid cations and increase the soil base saturation. The term base saturation refers to the percentage of total CEC that is occupied by calcium and magnesium. All liming materials are very insoluble and thus react very slowly when present as rock or stone. To increase their rate of reaction they must be very finely ground. However, even finely ground liming materials may require several weeks to months to completely react in soil. Thus liming materials ideally should be applied well in advance of planting pH sensitive crops.
Soil alkalinity is neutralized by adding materials that generate acids when added to soil. Acidic plant residues – particularly needles, bark and sawdust from coniferous trees – generate organic acids as they decompose and will lower pH. Several inorganic chemicals also are used, such as ferrous sulfate (FeSO4), elemental sulfur (S), and ammonium containing fertilizers such as ammonium sulfate [(NH4)2SO4]. With each of these, oxidation of iron, sulfur, or nitrogen by soil bacteria generates acidity that in turn reacts with soil alkalinity to decrease pH. These microbially mediated reactions take time to occur so the pH change may take several weeks. On a weight basis, elemental sulfur generates the most acidity and is usually the least expensive option. However, if iron is needed for plant nutrition, ferrous sulfate may be a better option and it also tends to react faster than sulfur. Ammonium fertilizers are generally not used to acidify soils because the amount required for acidification would far exceed the amount of nitrogen needed for soil fertility. However, these fertilizers will generate acidity and with continued use, will gradually decrease soil pH.
It is important to remember that a soil pH test measures only active acidity in the soil solution – not the amount of reserve acidity or alkalinity in the soil. Thus while a pH test indicates if a soil is too acidic or alkaline, it provides no indication of how much lime or acidifying agent such as elemental sulfur is needed to adjust soil pH to the desired level. Liming or acidifying recommendations provided by soil testing laboratories to achieve a desired pH change are based on tests that measure some or all of the soil reserve acidity, and have been calibrated with soil response to liming or addition of acidifying agents such as elemental sulfur.
These are some of the key sol chemical properties and processes that influence plant growth. There are others that were not discussed (i.e. salinity) and much more could have been said about those that were mentioned. Although this article has focused on soil chemistry, it is clear that soil physical properties (clays, humus) and processes (water movement) strongly influence soil chemistry. Likewise, several chemical processes were described as being biologically mediated. The final article in this series will focus on soil biology.
Richard Stehouwer is in the Crop and Soil Sciences Department at Penn State University in University Park, Pennsylvania. His e-mail is

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