Soil Biological Properties

Soil Biota

The soil contains a vast array of life forms ranging from submicroscopic (the viruses), to earthworms, to large burrowing animals such as gophers and ground squirrels. Microscopic life forms in the soil are generally called the "soil microflora" (though strictly speaking, not all are plants in the true sense of the word) and the larger animals are called macrofauna.

Microorganisms can be found in your compost pile . . . Microorganisms can be found in your yard . . .

Soil animals, especially, the earthworms and some insects tend to affect the soil favorably through their burrowing and feeding activities which tend to improve aeration and drainage through structural modifications of the soil solum. In general, they affect soil chemical properties to a lesser extent though their actions indirectly enhance microbial activities due to creation of a more favorable soil environment.

Soil Microorganisms

Soil microorganisms occur in huge numbers and display an enormous diversity of forms and functions. Major microbial groups in soil are bacteria (including actinomycetes), fungi, algae (including cyanobacteria) and protozoa.

Because of their extremely small cell size (one to several micrometers), enormous numbers of soil microbes can occupy a relatively small volume, hence space is rarely a constraint on soil microbes. Soil microbes can occur in numbers ranging up to several million or more in a gram of fertile soil (a volume approximately that of a red kidney bean). Note that the bacteria are clearly the most numerous of the soil microbes. Perhaps more important than the numbers of the various soils microbes is the microbial biomass contributed by the respective groups. It is the soil fungi which tend to contribute the most biomass among the microbial groups. In fact, it is because of their large contribution to the biomass that they are generally regarded as being the dominant decomposer microbes in the soil. You might find it surprising that there are literally "tons" of microbes beneath your feet as you walk across a grassland in Africa or Australia or through a cornfield in the American Midwest. Interesting­ly, a fungus discovered in the state of Michigan may be one of the largest living organ­isms on the planet.

A fungus, Armillaria bulbosa, discovered in the U.S. in the state of Michigan, could turn out to be earth's largest creature or at least among the largest. Scientists discovered the fungus growing among the roots of hardwood trees in a forest. The microscopic, branched filaments (called hyphae) of the fungus occupy a 14.8 ha (37-acre) area of land. Careful genetic analysis has shown the filaments constitute a single organism. Fungi generally radiate outward in a circular pattern as they grow through the soil. In fact, the fairy rings of mushrooms (named because ancient peoples thought they represented the paths of fairies dancing in the night) often seen in lawns or on golf courses actually represent the outer boundary of a developing fungus. Scientists estimate that the portion of the Michigan fungus they have been able to identify may weigh as much as 100 tons, slightly less than a blue whale. Imagine the biochemical capacity of a soil microorganism this large!

What would happen if decomposer organisms such as fungi didn’t exist?

The significance of these large amounts of microbial biomass in the soil lies not only in their large biochemical capacity, but in the phenomenal diversity of biochemical reactions attributed to the soil microbial population. It is worth remembering that soil microbes not only interact with other members of their own group, they also interact with other microbial groups. It is quite common to find, for example, that degradation of plant materials occurs much more quickly in the presence of the mixed soil population than it does when one or more groups of soil microbes have been eliminated from the system.

Soil life can be divided into trophic (i.e. feeding) levels. At the base of the trophic levels lies the soil microbial population which degrades plant, animal and microbial bodies, and also serves as the food source for some of the levels above it. For example, soil protozoa consume enormous numbers of bacteria and even some fungal spores. These in turn are consumed by still larger soil animals (nematodes, mites, etc.) which in turn are eaten by still larger animals (e.g. worms and insects). Thus, nutrients flow through this microbial food web which lies at the heart of controlling soil fertility and plant productivity in the absence of external inputs such as fertilizers. In fact, the role of soil microbes in degrading organic materials and thereby regenerating a supply of carbon dioxide for plants is perhaps their most vital global function.

Nutrient Cycling by Soil Microbes

Soil microbes exert much influence in controlling the quantities and forms of various chemical elements found in soil. Most notable are the cycles for carbon, nitrogen, sulfur and phosphorus, all of which are elements important in soil fertility, and as we know today, may be involved in global environmental phenomena. The mineralization (i.e. the conversion of organic forms of the elements to their inorganic forms) of organic materials by soil microbes liberates carbon dioxide, ammonium (which is rapidly converted to nitrate by soil microbes), sulfate, phosphate and inorganic forms of other elements. This is the basis of nutrient cycling in all major ecosystems of the world. John Burroughs once said, "Without death and decay, how could life go on?" No doubt, he was referring to the mineralization of nutrients from dead animals and plants. We now know that soil microbes accomplish this task with remarkable zeal and that in the process a substantial part (perhaps as much as one third) of the decomposing materials are converted to the bodies of soil microbes. This pool of microbial biomass constitutes a portion of the soil organic matter which turns over (cycles) fairly quickly and therefore represents a "fertility buffer" in the soil. Don't forget that the liberation of carbon dioxide through microbial respiration makes possible the continued photosynthesis (i.e. carbon dioxide fixation) by algae and green plants which in turn produce more organic materials which may ultimately reach the soil, thereby completing the cycle.

In the world's agricultural soils, the source of our food supply, mineralization of nitrogen by soil microbes is a most important process. In those soils not receiving external inputs of fertilizer nitrogen (e.g. most forested lands and many grasslands) the liberation of ammonium from organic debris makes possible the continued growth of new plant matter. Therefore, it is the soil microbial population which controls the productivity of these soils if other environmental factors (moisture, temperature) are suitable. In fact, fertilization of a soil represents our attempt to balance the competition between plants and soil microbes for available soil nitrogen. Nitrogen tied-up (assimilated into cell constituents) in microbial cells is not available for plants or other microbes until that tissue has been decomposed by other microbes. In other words, nitrogen contained in tissues is said to be immobilized. Microbes are the keys for the remobilization of these nutrients. These mineralization/immobilization phenomena are common to all the elements but typically they are only agriculturally important for the macronutrients such as nitrogen, phosphorus and sulfur.

Aside from their role in controlling the rates of production of inorganic forms of nitrogen and sulfur, soil microbes, in particular soil bacteria, can control the forms of the ions in which these nutrients occur. For example, ammonium (NH4+) in the soil is usually rapidly oxidized by bacteria first to nitrite (NO-) and then to nitrate (NO3-) which may readily leach through soil. Ammonium is oxidized to nitrite and then to nitrate by the bacteria Nitrosomonas and Nitrobacter, respectively. Thus, bacteria can influence the form and, thereby, the retention of nitrogen in the soil. Similarly, reduced sulfur compounds such as thiosulfate, elemental sulfur and even iron pyrite (FeS2, "Fool's Gold") can be oxidized to sulfuric acid by soil bacteria. The bacteria which accomplish the oxidation of reduced nitrogen and sulfur compounds use these materials as energy sources to drive their metabolism. Unlike the decomposer microbes which use organic carbon compounds from organic matter for energy and to make cell matter (e.g. they are called heterotrophs), these specialized bacteria called chemoautotrophs obtain their carbon for cell synthesis from carbon dioxide or from dissolved carbonate.

There are many genera of bacteria that can oxidize reduced sulfur compounds. However, much of this activity, especially the oxidation of sulfur and pyrite, can be attributed to bacteria of the genus Thiobacillus (thio = sulfur; bacillus = rod-shaped bacterium). Thiobacillus thiooxidans can oxidize elemental sulfur to sulfuric acid. Sulfur, therefore, can be used to decrease the pH of an alkaline soil. Thiobacillus ferrooxidans attacks both the iron and sulfur in iron pyrite, generating sulfuric acid and dissolved iron in the process. This is also the basis of acid mine drainage associated with the mining of coal throughout the world.

The long-term application of ammonium-based fertilizers can likewise result in the acidification of agricultural soils through bacterial nitrification (the conversion of ammonium to nitrate with the concurrent production of acidity). Thus, we see that certain environmental problems can arise from the activities of these chemoautotrophic soil bacteria.

Another important aspect of nutrient cycling is that under certain circumstances nitrogen and sulfur may be converted to gaseous forms (volatilized) and lost to the atmosphere. Nitrogen in the form of nitrate can be converted to gases such as nitrous oxide (N2O) and dinitrogen (N2) through the process of denitrification (the bacterial reduction of NO3- to N2O or N2) by soil bacteria under anaerobic conditions. A consequence of denitrification is that nitrogen, a precious nutrient for plants, is lost from the soil. On the other hand, this process is a useful way to remove excess nitrate from wastewater.

Sulfur in the form of sulfate (SO4-2) is used by anaerobic bacteria like the genus Desulfovibrio which convert it to hydrogen sulfide gas (H2S). Hydrogen sulfide reacts with metal ions and forms very insoluble metallic sulfides like pyrite (Fe2S). In fact, it is probable that the pyrites associated with coal seams were deposited by the action of these bacteria eons ago. The black color of salt marsh soils and the rotten egg smell associated with them are a result of the activities of the sulfate-reducing bacteria in these habitats. They attest to the occurrence of anaerobic conditions. Sulfur volatilization from soil represents loss of a plant nutrient as well as a contribution of atmospheric sulfur which may contribute to the phenomenon of acid precipitation.

We mentioned above that nitrogen can be lost from agricultural soils as well as from other ecosystems. Fortunately, this "leak" in the terrestrial nitrogen cycle can be at least partially replaced through another important biological process called biological nitrogen fixation. In this process, which is unique to bacteria and a few other mi­crobes, notably the cyanobacteria (blue-green algae), atmospheric dinitrogen (N2) is captured and converted to plant-available forms. Biological nitrogen fixation is carried out by free-living bacteria and cyanobacteria and by symbiotic microorganisms in a wide variety of mutualistically symbiotic associations with higher plants.

The most useful and probably the most widely recognized example of symbiotic nitrogen fixation is that of the Rhizobium - legume root-nodule symbiosis. Soil bacteria belonging to the genera Rhizobium and Bradyrhizobium (and a few others) are capable of inducing the formation of nodules on roots of specific legumes (plants like peas, beans, peanuts, soybeans, alfalfa etc.) and fixing large quantities of nitrogen in these structures. In the nodule, the bacteria are supplied with carbon sources (photosynthate from the plant) that they need in order to fix nitrogen. In return for this carbon, the bacteria fix atmospheric nitrogen which is converted to amino acids used by the plant for growth. The result of this unique plant-microbe partnership is that many legumes are self-sufficient for nitrogen, that is, they are nearly independent of a supply of nitrogen from the soil. It is no wonder that these plants are cultivated all over the world as sources of food, fiber and forage. Nearly two-thirds of the world's nitrogen supply is from biological nitrogen fixation. Legumes have been used since the beginning of recorded history as "soil improving" crops known as "green manures". Green manuring is the practice of growing a legume species for the sole purpose of returning it to the soil to serve as a source of nitrogen for an ensuing crop.

Soil Microbes and Bioremediation

Drop of oil. Oil drums.

We have touched on the remarkable metabolic diversity and capacity of the soil microflora. This capacity is increasingly being harnessed and put to good use by humans. A most beneficial spin-off from our understanding of the metabolism of soil microbes has been the development of methods for the bioremediation of soils contaminated by hazardous wastes or spilled petroleum products both on land and sea. Bioremediation may be defined as the controlled use of microorganisms for the destruction of chemical pollutants. A large number of processes have been developed to handle various wastes and for the cleanup of spilled organic materials. At the heart of all of these processes lies the premise that the metabolic activities of bacteria or fungi can be used to degrade many of the organic chemicals of commerce (solvents, pesticides, hydrocarbon fuels, etc.).

Either of two forms of bioremediation is commonly employed. In biostimulation the environment into which the material has been spilled or otherwise introduced is made favorable for the rapid development of microbes. Typically, this process involves adding sufficient nitrogen and phosphorus fertilizer to overcome nutrient limitations to microbial growth and providing some mechanism for increased aeration of the system. These practices encourage development of the indigenous microbial population which usually contains microbes able to degrade the compounds of interest. In the practice of bioaugmentation, an external microbial population is added in order to speed up the degradation process. Numerous microbes have been developed for such purposes. However, the full measure of the usefulness of such microbial products is not yet known. Some inoculants have reportedly enhanced the remediation process and others have had little or no effect on the process. It is probable that in due time useful microbial products or processes will be developed for use in the clean-up of oil or other chemical spills. What is certain is that successful bioremediation will require detailed knowledge of the factors which make some microbes more competitive than others in a given environment. Only when these details are established will we know how to use sound ecological principles to add microbes to these complex environments to insure their establishment and function in the clean-up process.

In March 1989, the Exxon Valdez oil tanker hit a reef in Prince William Sound, Alaska (USA) and released over 40 million liters of crude oil into the Sound within a 5-hour period. Over 1500 km (932 miles) of shoreline in the Sound and the Gulf of Alaska were contaminated to varying degrees by crude oil. The Exxon Valdez oil spill was a historic event because of the magnitude of the spill, the vastness and isolation of the area to be treated, and the large number of personnel and vehicles ultimately involved. The success of bioremediation, particularly in a climate as cold as Alaska’s, prompted regulatory agencies in the United States to view bioremediation much more favorably over previous strategies of physical or chemical “entombment” (storage in cement tombs).

Because oil is inherently high in carbon and low in nitrogen and phosphorus, a portion of the shoreline was selected for biostimulation. After several potential fertilizer candidates were evaluated, a microemulsion, Inipol EAP22 (henceforth, Inipol), was selected. Inipol (an “oleophilic” fertilizer) is a stable water-in-oil formulation that yields an N-P-K ratio of 7.3:0.8:0. The nitrogen source is urea and the phosphorus source is trilaureth (4)-phosphate. At room temperature, Inipol has the consistency and appearance of honey, and it must be heated to 90oC (194oF) before it can be sprayed on the soil. Inipol was applied as a thin coat to the shore at a rate of 306 ml m-2 (0.27 quart per square yard). As the microemulsion mixed with the weathered crude oil, the crude oil destabilized Inipol to release its urea-N. In addition, a surface-active organic material (oleic acid) in Inipol served as a readily degradable carbon and energy source to increase the activity and number of indigenous hydrocarbon-degrading bacteria. When the oleic acid was depleted, the increased biomass of hydrocarbon-degrading bacteria supported enhanced biodegradation of the petroleum. Visual observations and chemical assays showed dramatic evidence that biostimulation contributed to the remediation of the site. Although passive bioremediation also undoubtedly occurred in the absence of the fertilizer nitrogen and phosphorus, the accelerated rate of biodegradation observed with Inipol was critical to a successful bioremediation effort.

Why has biostimulation generally proven more successful than bioaugmentation?

Lesson 8. Plant Essential Nutrients


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