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Agricultural Chemistry

Agricultural Chemistry

Agricultural chemistry must be considered within the context of the soil ecosystem in which living and nonliving components interact in complicated cycles that are critical to all living things. Carbon inputs from photosynthetic organisms ultimately provide the fuel for many soil organisms to grow and reproduce. Soil organisms, in turn, promote organic carbon degradation and catalyze the release of nutrients required for plant growth. The stability and productivity of agricultural ecosystems rely on efficient functioning of these and other processes, whereby carbon and nutrients such as nitrogen and phosphorus are recycled. Human-induced perturbations to the system, such as those that occur with pesticide or fertilizer application, alter ecosystem processes, sometimes with negative environmental consequences.

Inorganic Components of the Agricultural Ecosystem

Soil is the primary medium in which biological activity and chemical reactions occur. It is a three-phase system consisting of solid, liquid, and gas. Approximately 50 percent of the volume in a typical agricultural soil is solid material classified chemically as either organic or inorganic compounds. Organic materials usually constitute 1 to 5 percent of the weight of the solid phase. The remainder of the soil volume is pore space that is either filled with gases such as CO2 and O2, or water.

Surface area and charge characteristics of the inorganic portion of the solid phase control chemical reactivity. Soil particles are classified based on their size, with sand-sized particles having diameters of 2 to 0.05 millimeters (0.08 to 0.002 inches) and silt-sized particles from 0.05 to 0.002 millimeters (0.002 to 0.00008 inches). Clay-sized materials of less than 0.002 millimeters (0.00008 inches) in diameter have the largest surface area per unit weight, reaching as much as 800 meters (2,625 feet) squared per gram. Because of large surface areas, clay-sized materials greatly influence the sorption of chemicals such as fertilizers and pesticides and play a major role in catalyzing reactions.

Crystalline layer silicates or phyllosilicates present in the clay-sized fraction are especially important because they function as ion exchangers. Most phyllosilicates have a net negative charge and thus attract cations. This cation exchange capacity (CEC) controls whether plant nutrients, pesticides, and other charged molecules are retained in soil or if they are transported out of the soil system. In contrast, aluminum and iron oxides also present in the clay-sized fraction typically possess a net positive charge or an anion exchange capacity (AEC). Soils in temperate regions are dominated most often by solid phase materials that impart a net CEC, whereas soils in tropical regions often contain oxides that contribute substantial AEC.

Organic Components of the Agricultural Ecosystem

Organic materials contained within the solid phase, although only a small percentage of the total soil weight, are extremely important in controlling chemical and physical processes in soil. Organic matter exists in the form of recognizable molecules such as proteins and organic acids, and in large polymers called humic materials or humus. Humus is dominated by acidic functional groups (OH and COOH) capable of developing a negative charge and contributing substantial CEC. These large polymers possess a three-dimensional conformation that creates hydrophobic regions important in retaining nonionic synthetic organic compounds such as pesticides. Nonionic pesticides partition into these hydrophobic regions, thereby decreasing off-site movement and biological availability (see Figure 1).

A wide variety of organisms live in soil, including microorganisms not visible to the naked eye such as bacteria, fungi, protozoa, some algae, and viruses. Bacteria are present in the largest numbers, but fungi produce more biomass per unit weight of soil than any other group of microorganisms. Much of agricultural chemistry as it relates to nutrient cycles, pesticide transformation, plant growth, and organic matter degradation involves the participation of microorganisms. Microorganisms produce both intracellular and extracellular enzymes that increase reaction rates, oxidize and reduce organic and inorganic compounds, and synthesize organic molecules that modify soil chemical and physical properties.

Additional organisms in soil such as insects, nematodes, and earthworms also alter the soil ecosystem in a manner that directly or indirectly affects chemical reactions. These organisms physically process plant-derived organic materials prior to biochemical degradation by microorganisms. Nutrient release from organic materials is thus accelerated because the meso- and macrofauna expose more organic matter surface area to microbial breakdown and redistribute such materials in soil to areas of intense microbial activity.

In addition, bioturbation may also cause physical changes to the soil structure that increase pore space or modify water movement. Changes in O2 concentration or soil water content will control biotic and abiotic reactions, altering rates of nutrient cycling and organic matter degradation.

Plant roots also modify soil by producing a zone of intense biological activity called the rhizosphere. This is a region of soil influenced by the root, most often delineated by comparing microbial numbers at greater distance from the root surface. Carbon compounds exuded or sloughed off from roots are used as a food source by microorganisms, thereby causing increased growth and activity. Microbial numbers above those of the bulk soil, which displays no root influence, indicate that the rhizosphere extends to 5 millimeters (0.2 inches) or less. Rhizosphere microorganisms that capitalize on carbon from the plant root interact physically and biochemically with the root, potentially producing positive or negative effects on plant growth.

Soil Chemistry

Biological availabilities and transport phenomena of ions and molecules in soil are controlled by the type of bonding that occurs with the solid phase. Ions such as those typically formed when amending soils with inorganic fertilizers interact with high surface area clay and humic colloids to form either outer- or inner-sphere complexes (see Figure 1). Outer-sphere complexes result when ions, electrostatically attracted to an oppositely charged colloidal surface, retain their shell of hydrating water molecules. These loosely held ions satisfy the excess positive or negative charge of the colloid, but are separated from the colloid's surface by one or more layers of water. In contrast, inner-sphere complexes form when the ion loses its hydration water to form a much stronger covalent bond with the colloid. Nutrient ions held in outer-sphere complexes are plant-available because they may be exchanged with ions of the same charge, but nutrients held by an inner-sphere mechanism are not available until the covalent bond is broken.

Most soils contain a net CEC often reported in centimoles of charge per kilogram of soil (cmolc/kg). Biological and physical characteristics of the soil are controlled by the amount of CEC and the specific cations involved. Soils dominated by high surface area clays or humus display the highest CECs, whereas soils with large amounts of sand or silt, and only small amounts of humus, exhibit much lower CECs. Highly charged cations with small hydrated radii such as Al3+ are more tightly held on the CEC and less likely to exchange than larger, less highly charged cations such as Na+. This general relationship is superseded when a specific inner-sphere complex forms such as between Cu2+ and humus, or K+ and clay. An even more dramatic example is that of two plant nutrients, NO3 and PO43. Negatively charged NO3 readily leaches out of soil, but PO43 is retained quite strongly because it forms an inner-sphere complex (see Figure 1).

The percentage of the CEC occupied by specific cations influences soil pH and associated characteristics relevant to plant growth and soil biological activity. Only the most strongly held cations remain in soils in high rainfall areas. Al3+ dominates the CEC, hydrolyzing when released from the solid phase to the soil solution to form acidic soils with pH values often below 5.

Al3+ + H2O AlOH2+ + H+

In contrast, soils located in lower rainfall areas accumulate less tightly bound cations such as Ca2+, Mg2+, K+, and Na+ and have higher pH values between 5 and 7. In the most arid regions, large amounts of OH-generating sodium and calcium salts accumulate, causing soil pH values to exceed 7. Plant growth is optimal in soils having pH values between 5.5 and 6.5 because aluminum toxicity occurring at lower pH values, and nutrient limitations caused by higher pH values, are avoided.

Soil Microbiology and Biochemistry

Biochemical transformations catalyzed largely by microorganisms are required for the sustained productivity of all ecosystems. Nutrients sequestered in organic materials and added in the form of fertilizers are cycled by microorganisms

in their quest for energy, reducing equivalents, and carbon. Microorganisms grow and reproduce by oxidizing organic or inorganic materials, thereby releasing electrons. The electrons are passed down a series of carriers aligned in a thermodynamic gradient designed to capture energy in the form of adenosine triphosphate (ATP) . Additional electrons originating from organic or inorganic materials are used to provide reducing equivalents necessary for synthesizing cell constituents. Carbon for cell growth is obtained from the organic materials being oxidized or captured in the form of CO2 if inorganic materials are being oxidized.

Reduction-oxidation processes are therefore central to agricultural chemistry because oxidation of the electron source and reduction of the electron sink profoundly modify the respective element's chemical characteristics, and thus its behavior and biological availability in the environment. For example, microbial oxidation processes convert organic compounds to CO2, a gas, and NH4+, a cation, to NO3, an anion. Electrons obtained in these oxidations are passed on to a terminal electron acceptor. Microorganisms use terminal electron acceptors in a sequence that maximizes energy yield starting with O2 and proceeding through NO3, Mn4+, Fe3+, SO42, and finally CO2, which upon reduction yield H2O, N2, Mn2+, Fe2+, H2S, and CH4, respectively.

Human Manipulation of Agricultural Ecosystems

Food and fiber production are typically optimized by carefully managing the agricultural ecosystem. Synthetic organic compounds are often applied

to control plant pests including weeds, insects, nematodes, and fungal pathogens. Pesticide fate is controlled by sorption to the solid phase and degradation rate. Because most soils have a CEC, cationic pesticides are so strongly held by soil that they are typically biologically unavailable. Weak acid pesticides containing carboxyl, phenolic hydroxyls, or aminosulfonyl functional groups are weakly retained by soil and thus most likely to leach or move off-site (see Figure 1). Weak bases, which may exist as positively charged or uncharged molecules, and nonionic compounds, are intermediate in their susceptibility to move off-site and cause environmental contamination. However, rapid degradation of some pesticides to form benign products eliminates the time available for transport, decreasing the potential for environmental problems. Both biotic and abiotic mechanisms catalyze degradative reactions, the rate of which is controlled by the pesticide's chemical structure.

With the advent of molecular techniques and the ability to transfer genes, an additional area of concern has emerged: the introduction of foreign genes into plant species for enhanced crop productivity. In addition, we have the ability to produce a variety of pharmaceutical chemicals in genetically modified plants using what has been termed "pharm crops." David Suzuki and Holly Dressel in From Naked Ape to Superspecies have commented on such genetic manipulations, addressing the risks of placing genes from one species into another. Not only is direct gene transfer from one living organism to another possible, but extracellular DNA preserved in soil systems is also potentially available for transfer, further increasing environmental risks.

Agricultural chemistry is most often linked to food and fiber production, specifically for human consumption. Jared Diamond in Guns, Germs, and Steel argues quite convincingly that it was our ability to domesticate crops and eliminate the need for hunting and gathering that allowed for the establishment of permanent settlements and the development of technologically advanced societies. The ensuing increase in human population has led to tremendous pressure to produce additional food from finite resources. Increased agricultural production, in combination with additional resource consumption and waste generation, has caused environmental degradation. By understanding key concepts in agricultural chemistry, we can utilize the soil resource to produce an adequate food supply and protect the environment.

see also Fertilizer; Herbicides; Insecticides.

Matthew J. Morra


Brady, Nyle C., and Weil, Ray R. (2002). The Nature and Properties of Soils, 13th edition. Upper Saddle River, NJ: Prentice Hall.

Diamond, Jared M. (1997). Guns, Germs, and Steel: The Fates of Human Societies. New York: Norton.

Hillel, Daniel (1991). Out of the Earth: Civilization and the Life of the Soil. New York: Free Press.

Suzuki, David, and Dressel, Holly (1999). From Naked Ape to Superspecies: A Personal Perspective on Humanity and the Global Eco-crisis. New York: Stoddart.

Sylvia, David M.; Fuhrmann, Jeffry J.; Hartel, Peter G.; and Zuberer, David A., eds. (1998). Principles and Applications of Soil Microbiology. Upper Saddle River, NJ: Prentice Hall.

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Agricultural Biotechnology

Agricultural Biotechnology

Biotechnology is the use of living organismsmicrobes, plants, or animalsto provide useful new products or processes. In a broad sense, biotechnology continues a process that is thousands of years old. Using traditional plant breeding techniques, humans have altered the genetic composition of almost every crop by only planting seeds from plants with desired traits, or by controlling pollination. As a result, most commercial crops bear little resemblance to their early relatives. Current maize varieties are so changed from their wild progenitors that they cannot survive without continual human intervention.

The 1970s heralded recombinant DNA technology, which gave researchers the ability to cut and recombine DNA fragments from different sources to express new traits. Genes and traits previously unavailable through traditional breeding became available through DNA recombination.


Modern plant genetic engineering involves transferring desired genes into the DNA of some plant cells and regenerating a whole plant from the transformed tissue. New DNA may be introduced into the cell via biological or physical means.

The most widely used biological method for transferring genes into plants capitalizes on a trait of a naturally occurring soil bacterium, Agrobacterium tumefaciens, which causes crown gall disease. This bacterium, in the course of its natural interaction with plants, has the ability to infect a plant cell and transfer a portion of its DNA into a plant's genome . This leads to an abnormal growth on the plant called a gall. Scientists take advantage of this natural transfer mechanism by first removing the disease-causing genes and then inserting a new beneficial gene into A. tumefaciens. The bacteria then transfer the new gene into the plant.

Another gene transfer technique involves using a "gene gun" to literally shoot DNA through plant cell walls and membranes to the cell nucleus, where the DNA can combine with the plant's own genome. In this technique, the DNA is made to adhere to microscopic gold or tungsten particles and is then propelled by a blast of pressurized helium.


Depending on which genes are transferred, agricultural biotechnology can protect crops from disease, increase their yield, improve their nutritional content, or reduce pesticide use. In 2000, more than half of American soybeans and cotton and one-fourth of American corn crops were genetically modified by modern biotechnology techniques. Genetically modified foods may also help people in developing countries. One in five people in the developing world do not have access to enough food to meet their basic nutritional needs. By enhancing the nutritional value of foods, biotechnology can help improve the quality of basic diets.

"Golden rice" is a form of rice engineered to contain increased amounts of vitamin A. Researchers are also developing rice and corn varieties with enriched protein contents, as well as soybean and canola oils with reduced saturated fat. Other potential benefits include crops that can withstand drought conditions or high salinity, allowing populations living in harsh regions to farm their land.

Agricultural biotechnology also provides benefits for the manufacture of pharmaceutical products. Because plants do not carry human diseases, plant-made vaccines and antibodies require less screening for bacterial toxins and viruses. In addition to plants, animals may also be engineered to produce beneficial genes. In order to produce large quantities of monoclonal antibodies for research on new therapeutic drugs, several companies have genetically engineered cows and goats to secrete antibodies into their milk. One company has inserted a spider gene into dairy goats. The spider silk extracted from the goat's milk is expected to produce fibers for bulletproof vests and medical supplies, such as stitch thread, and other applications where flexible and extremely strong fibers are required.


Despite the benefits of genetic engineering, there are concerns about whether recombinant DNA techniques carry greater risks than traditional breeding methods. Consumer acceptance of food derived from genetically engineered crops has been variable. Many individuals express concerns regarding the environmental impact and ethics of the new technology, and about food safety. One of the major food safety concerns is that there is a risk that crops expressing newly inserted genes may also contain new allergens .

Some groups have expressed concern that widespread use of plants engineered for specific types of pest resistance could accelerate the development of pesticide-resistant insects or have negative effects on organisms that are not crop pests. Another environmental concern is that transgenic, pest-protected plants could hybridize with neighboring wild relatives, creating "superweeds" or reducing genetic biodiversity .


To address these concerns, agricultural biotechnology products are regulated by a combination of three federal agencies: the U.S. Department of Agriculture (USDA), the Environmental Protection Agency (EPA), and the Food and Drug Administration (FDA). Together, these agencies assess genetically modified crops, as well as products that use those crops. They test the crops and products for safety to humans and to the environment, and for their efficacy and quality.

see also Biopesticides; Genetically Modified Foods; Plant Genetic Engineer; Transgenic Animals; Transgenic Microorganisms; Transgenic Plants.

Barbara Emberson Soots


Ferber, Dan. "Risks and Benefits: GM Crops in the Cross Hairs." Science 286 (1999): 1662-1666.

Internet Resources

Agricultural Biotechnology. U.S. Department of Agriculture. <>.

Transgenic Plants and World Agriculture. Royal Society of London, U.S. National Academy of Sciences, Brazilian Academy of Sciences, Chinese Academy of Sciences, Indian National Science Academy, Mexican Academy of Sciences, and Third World Academy of Sciences. <>.

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Agricultural Ecosystems

Agricultural Ecosystems

An agricultural ecosystem, which is also known as an agroecosystem, is a place where agricultural productiona farm, for exampleis understood as an ecosystem . When something like a farm field is examined from an ecosystem viewpoint, food production can be understood as part of a whole, including the complex kinds of materials entering the system, or inputs, and the materials leaving the system, or outputs. At the same time, the ways that all of the parts of the system are interconnected and interact are of great importance.

Humans alter and manipulate ecosystems for the purpose of establishing agricultural production, and in the process, can make the resulting agroecosystem very different from a natural ecosystem. At the same time, however, by understanding how ecosystem processes, structures, and characteristics are modified, management of an agricultural system can become more stable, less dependent on inputs brought in from outside the system, and more protective of the natural resources with which it may interact.

Scientists who study agricultural systems as ecosystems are known as agroecologists, and the field they work in is known as agroecology. An agroecologist applies the concepts and principles of ecology to the design and management of sustainable agroecosystems. Sustainability refers to the ability to preserve the productivity of agricultural land over the long term, protect the natural resources upon which that productivity depends, provide farming communities with a fair and prosperous way of life, and produce a secure and healthy food supply for people who do not live on the farms. The challenge these scientists face is developing agroecosystems that achieve natural ecosystem-like characteristics while maintaining a harvest output. With a goal of sustainability, a farm manager strives as much as possible to use the ecosystem concept in designing and managing the agroecosystem. In doing so, the following four key traits of ecosystems are included.

Energy Flow

Energy flows into an ecosystem as a result of the capture of solar energy from the Sun by plants, and most of this energy is stored as biomass or used to maintain the internal processes of the system. But removing energy-rich biomass from the system causes changes. Human energy (considered renewable) as labor, and industrial energy (considered nonrenewable) from fossil fuels, become necessary. Agroecologists look for ways to increase the efficiency of the capture of energy from the Sun and increase the use of renewable energy, achieving a better balance between the energy needed to maintain internal processes and that which is needed for harvest export.

Nutrient Cycling

Many nutrients are cycled through ecosystems. Biomass is made up of organic compounds manufactured from these nutrients, and as organisms die and decompose, the nutrients return to the soil or the atmosphere to be recycled and reused again. Agricultural ecosystems lose nutrients with harvest removal, and because of their more simplified ecological structure, lose a greater proportion of nutrients to the air or by leaching in rain and irrigation water. Humans must return these nutrients in some form. In a well-designed agroecosystem, the farmer strives to keep nutrient cycles as closed as possible, reducing nutrient losses while searching for sustainable ways of returning exported nutrients to the farm.

Regulation of Populations

Complex interactions between organisms regulate their numbers in natural ecosystems. Competition, mutualisms , and other types of interactions are promoted by the organization and structure of the system. Growing one or very few crops in modern agriculture eliminates many of these interactions, often removing natural control mechanisms and allowing pest outbreaks. An agroecological alternative seeks to reintroduce more complex structures and species arrangements, often including both crop and noncrop species, in order to reduce the use of pesticides and enhance natural controls.

System Stability and Change

Ecosystems maintain themselves over time and have the ability to recover from natural disturbances such as a fire or a hurricane. In agricultural ecosystems, disturbance from cultivation, weeding, harvest, and other agricultural activities is much more intense and frequent. It is difficult to maintain any equilibrium in the system with this disturbance, requiring constant outside interference in the form of human labor and external human inputs. By incorporating ecosystem qualities such as diversity, stability, recovery, and balance, the maintenance of an ecological foundation for long-term sustainability can be established.

Agroecologists use the idea of an agricultural ecosystem as a focus for the study of farming systems that are converting from single crops and synthetic inputs to ecologically based design and management. Ecological concepts and principles are applied for the development of alternative practices and inputs. A good example is research done by Sean Swezey and his colleagues on apples in California. After three years of using organic farming techniques, an apple orchard had begun to show a reduction in the use of fossil fuel energy. Nutrients were supplied from compost and annual cover crops planted in the rows between the trees during the winter season. Nutrient recycling and storage in leaves and branches within the apple agro-ecosystem improved soil conditions, reduced the need for fertilizer, and even led to increased yields. Insect pests normally controlled by synthetic pesticides were reduced instead by beneficial predatory insects that were attracted to the organic orchard by mustard and fava-bean flowers in the rows between apple trees. Cover crop species smothered weeds so that herbicides were not needed. In the spring when the cover crop was mowed and cultivated into the soil, microorganism abundance and diversity increased, acting as a biological barrier to the outbreak of diseases in the soil. As the use of external human inputs for the control of the ecological processes in the apple system was reduced, a shift to the use of natural ecosystem processes and interactions and locally derived materials took place. Such an ecological foundation is an important way of determining the sustainability of the agricultural ecosystems of the future.

see also Agriculture, Modern; Agriculture, Organic; Ecosystem.

Stephen R. Gliessman


Altieri, Miguel A. Agroecology: The Science of Sustainable Agriculture. Boulder, CO: Westview Press, 1995.

Gliessman, Stephen R. Agroecology: Ecological Processes in Sustainable Agriculture. Chelsea, MI: Ann Arbor Press, 1998.

Lowrance, Richard, Ben R. Stinner, and Gar J. House. Agricultural Ecosystems: Unifying Concepts. New York: John Wiley & Sons, 1984.

National Research Council. Alternative Agriculture. Washington, DC: National Academy Press, 1989.

Odum, Eugene P. Ecology: A Bridge Between Science and Society. Sunderland, MA: Sinauer Associates.

Swezey, Sean L., Jim Rider, Matthew Werner, Marc Buchanan, Jan Allison, and Stephen R. Gliessman. "Granny Smith Conversions to Organic Show Early Success." California Agriculture 48 (1994): 36-44.

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agro-ecosystem An agricultural ecosystem, e.g. a cereal crop.

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"agro-ecosystem." A Dictionary of Ecology. . 25 May. 2017 <>.

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agro-ecosystem An agricultural ecosystem, e.g. a cereal crop.

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