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Chapter 9 Soil organisms. (Section 4 Soil Biological and Biochemical Properties.

"Essentially, all life depends upon the soil.... There can be no life without soil and no soil without life; they have evolved together. " Charles E. Kellogg, USDA Yearbook of Agriculture, 1938

OVERVIEW

Soil without organisms or biological activity is little more than glorified support media. The soil is not inert, because clays and soil minerals have chemical activity, but a soil's full capacity to support plant life and other environmental processes (such as decomposition and gas exchange with the atmosphere) are not realized without its biology. In this chapter you will begin examining the biological properties of soil by examining the organisms that are present in it.

OBJECTIVES

After reading this chapter, you should be able to:

* Identify the organisms in soil.

* Determine how these organisms grow and live.

* Describe how these organisms interact with their environment.

* Identify the ecological roles these organisms have in soil.

* List the activities these organisms perform.

KEY TERMS

acellular

aerobes

ammensalism

archaea

autotroph

bacteriophage

bioturbation

chemotroph

drilosphere

ectomycorrhizae

encyst

endomycorrhizae

eukaryotes

fenestration

heterotroph

humification

lithotroph

macrofauna

mesofauna

microfauna

microorganisms

mycorrhiza (pl. mycorrhizae)

phototroph

prokaryotes

proteobacteria

redox potential

rhizosphere

symbiosis

synergism

WHAT ORGANISMS ARE PRESENT IN SOIL?
One way of classifying soil
organisms is by size and
complexity.


The soil is teeming with life. Some of it is visible but most of it is invisible. The easiest way to characterize these organisms is by size and complexity (Table 9-1). Soil organisms vary from large, multicellular insects you can catch in ajar to acellular viruses that require an electron microscope to see. One classification scheme (and there are many) is to divide soil organisms into the following groups, which become progressively smaller and less complex as you proceed: macrofauna, mesofauna, microfauna, microorganisms.

Macrofauna

Macrofauna are soil organisms that vary in width from 2 to 20 mm, and in length from 10 to > 80 mm. They can be transient, temporary, periodic, or permanent soil residents (Wallwork, 1970). Macrofauna are less directly affected by physical and chemical conditions in soil than are smaller, soil-dwelling organisms.

Insects and Arachnids
Crytozoans are
macrofauna that dwell
beneath rocks and litter.


Many of the insects found in the soil environment are cryptozoans, animals that dwell beneath rocks, bark, and debris and are easy to see when these shelters are disturbed. Typical cryptozoans include isopods (pillbugs, sowbugs, Figure 9-1) and diplopods (millipedes), which feed on dead and decaying plant material and leaf litter. Chilopods (centipedes) are generally predators, feeding on smaller soil insects.

The three most important insect groups in soils are the Isoptera, Hymenoptera, and Coleoptera. Isoptera (termites) are social insects that have a major impact on wood decay and soil restructuring. They are one of the three major groups of earth-moving invertebrates along with ants and earthworms. Lower termites have symbiotic associations with protozoa in their gut, which enables them to digest cellulose. Higher termites lack the protozoa, but form symbiotic associations with bacteria and fungi, which also allows them to consume wood and other cellulose-rich material for food.

[FIGURE 9-1 OMITTED]

[FIGURE 9-2 OMITTED]
Termites, ants and wasps,
and beetles are the three
most important insect
groups in soil.


Hymenoptera (ants and wasps) are social insects, although the ground-dwelling wasps are usually solitary. Ants, like termites, burrow and excavate nests and in so doing restructure the soil and contribute to nutrient redistribution (Figure 9-2). Collectively, ants are omnivorous, but individual species may have very selective feeding habits ranging from strictly carnivorous to cultivating fungi for food (leaf cutter or Attine ants).

Coleoptera (beetles) are the largest insect order (Figure 9-3). They range from strict predators to plant pests. Some groups, such as scarab beetles, play important roles by burying animal wastes and carcasses in soil.

Arachnids (spiders and scorpions) are major predators in leaf litter layers. The smallest arachnids (mites) are the only members that can truly be said to reside in soil.

[FIGURE 9-3 OMITTED]

Earthworms and Potworms
Lumbricus terrestris, the
common nightcrawler, is
actually a European
import.


Earthworms (annelids) and potworms (enchytraeids) are oligochaetesmultisegmented invertebrate animals. Potworms are much like miniaturized versions of earthworms, only 10 to 20 mm long. They feed on decaying plant material, humus, and fecal pellets deposited by larger organisms. Because of their size, they do not contribute much to restructuring soils. Earthworms, however, play a major role in restructuring and redistributing soil, a fact noted by Charles Darwin (1881). The most common earthworms you see in the United States, the Lumbricidae, are actually European invaders; most native earthworm species have been displaced and are only found in undisturbed environments.
Epigeic, endogeic, and
anecic are terms
describing where
earthworms reside in soil.


Earthworms can be grouped into three categories from an ecological perspective: epigeic, endogeic, and anecic, which also indicates how much they influence soil (Bouche, 1977). Epigeic earthworms live and feed in litter layers. Endogeic earthworms are rarely at the soil surface and form deep and continually extending burrows in soil. Anecic earthworms such as nightcrawlers (Lumbricus terrestris) travel between the soil and the soil surface (Figure 9-4). The organic debris that they carry to their burrows forms middens in cultivated fields.

Mesofauna

Mesofauna are soil animals that range in length from 0.2 to 10 mm. For the most part they are permanent soil residents. The major groups are rotifers, tartigrades, collembolans, mites and other microarthropods, and nematodes. Rotifers and tartigrades ("water bears") are very small saprophytic soil animals < 2 mm in length and usually much smaller. Collembolans (springtails) graze on soil bacteria and fungi. Mites are numerous and diverse members of the spider family. They are the most abundant microarthropods in soils. The most significant members of the mesofauna, however, are the nematodes, which have important roles in soil nutrient cycles, plant disease, and human health (Figure 9-5).

[FIGURE 9-4 OMITTED]

[FIGURE 9-5 OMITTED]

Nematodes

Nematodes (roundworms) are among the most numerous multicellular animals in soil and inhabit water-filled pore spaces and water films. Most nematodes are between 160 and 1300 [micro]m (1.3 mm) long. They are very simple animals with a smooth, tapered body cavity surrounding a digestive tract. At one end of the nematode is a distinctive mouth, which nematologists use to identify and place nematodes into one of several groups: bacterial feeders, fungal feeders, plant feeders, predators, and omnivores. Plant and fungal feeders, for example, are equipped with a specialized structure called a stylus that functions like a miniature hypodermic needle and lets nematodes stick and suck out the contents of their food. Predatory nematodes are equipped with a mouthful of teeth.
Although most nematodes
in soil are harmless
saprophytes, some are
serious human and plant
pathogens.


Most nematodes in soil are beneficial saprophytes. A few, such as soybean cyst nematode, are serious plant pathogens. Nematodes from human and animal wastes applied to soil are referred to as helminths, and are a major health concern.

Microfauna

The microfauna are the smallest soil animals, microscopic in size (20 to 100 [micro]m long), and require magnification to observe. Nematodes and the very smallest microarthropods are sometimes placed in this group. However, microfauna, for the most part, consist of the ciliated, flagellated, naked, and testacean protozoa.

Protozoa
The most important
microfauna are the
protozoa.

There are four major
classes of protozoa.


Protozoa are characterized on the basis of their mobility and whether they have an external exoskeleton (Figure 9-6). Flagellated protozoa move through water films in soil by means of one or more whiplike appendages called flagella. Giardia lamblia is an example of a pathogenic flagellated protozoa. Cilliated protozoa are covered by numerous small hairs, or cilia. The cilia beat in unison to move the organism or transport food into its mouth. Paramecium is a classic example of a ciliated protozoa. Naked amoeba move by means of an elastic, flowing cell wall, which enables them to enter otherwise inaccessible soil pores. Testate amoebas (testaceans) have a hard exoskeleton with openings through which the cell contents exude. The protozoa are saprophytes and feed extensively on microorganisms. They are difficult to count because their populations constantly change in response to food availability and soil environmental conditions. Protozoa routinely become dormant (encyst) when soil conditions are unfavorable for growth.

[FIGURE 9-6 OMITTED]

Microorganisms
The microbial population
in soil is composed of
algae, fungi, bacteria, and
viruses.


Four groups make up the microbial population in soil: algae, fungi, bacteria, and viruses. Microorganisms are generally invisible to the eye, but this belies their critical role in soil processes. While the larger organisms you have read about play a major role in introducing organic matter to soil and influencing soil structure, it is the microorganisms that play the principal role in significant biochemical reactions and processes that occur in soil.

Algae

Algae are the smallest of the eukaryote plants. The algae in soil--green algae (chlorophyta), yellow-green algae (xanthophyta), and diatoms--can take atmospheric and dissolved C[O.sub.2] and convert it into sugars through photosynthesis. They begin the food chain in some soil systems. Algae are classified based on the type of photosynthetic pigments they have. Green algae, for example, contain chlorophyll. Yellow-green algae, in addition to chlorophyll, contain carotenoid pigments, which gives them their distinctive pigmentation. Diatoms are a unique algal group because they are surrounded by a hard, silica-rich shell called a frustule that often has an incredibly intricate and delicate structure. Algae are most noticeable in soil right after it rains, and algal blooms can often color the soil green.

Fungi

When you think of fungi in soil it is usually the most obvious manifestations of their growth to which you refer: mushrooms, toadstools, mildew, smuts, and mold (Figure 9-7). However, these fruiting bodies are not representative of the microscopic filaments and individual vegetative cells of fungi in the soil environment. These vegetative cells are 5 to 10 [micro]m in diameter. In the case of vegetative filaments, or mycelia, they can be either septate or aseptate (coenocytic). These terms refer to whether a cross wall is present (septate) or absent (coenoytic) in the hypha. The three major fungal groups in the soil are the ascomycetes, basidiomycetes, and zygomycetes.
The three major fungal
groups in soil are
ascomycetes,
basidiomycetes, and
zygomycetes.


Bacteria
The shape of bacteria is
an important basis for
their classification.


Bacteria are prokaryote microorganisms belonging to two groups, the proteobacteria and the archaea, which have distinctive physiological characteristics but similar shapes and sizes. Bacteria are usually found as rods (bacilli), spheres (cocci), vibrios (short spirals), and spirals of various length (spirilla and spirochaetes; Figure 9-8). Actinomycetes are members of the proteobacteria that can have filamentous growth, like fungi.

[FIGURE 9-7 OMITTED]

[FIGURE 9-8 OMITTED]

Bacteria are very small, usually 2 to 5 [micro]im in diameter. In contrast to fungi, which have great structural diversity, the bacteria have an incredibly rich array of biochemical transformations that they perform. Bacteria also have an incredibly rich variety of physiological capabilities that let them inhabit environments unsuitable for any other type of life. Bacteria can grow in extremes of temperature, pH, pressure, carbon availability, and airlessness; they can photosynthesize; they can metabolize inorganic and organic materials to reproduce and grow.

[FIGURE 9-9 OMITTED]

Viruses
Viruses are obligate
parasites; they need a
suitable host in order to
reproduce.


A virus is simply a nucleic acid core surrounded by a protein coat. Viruses are the smallest (< 0.1 [micro]m in diameter) and most numerous living organisms in soil (Figure 9-9). They are obligate parasites and rely on their hosts--all other larger organisms--to reproduce. The only organisms that viruses don't attack are other viruses because they are such simple organisms that they have lost their ability to reproduce without the assistance of a host. Viruses, also called phages, come in several shapes. Tailed viruses, which typically infect bacteria, have an icosahedral head (a structure with twenty faces), a tail, and a baseplate with appendages that attach to the surface of bacteria. Other viruses are cubic or cylindrical.

FOCUS ON ... TYPES OF SOIL ORGANISMS

1. Which of the macrofauna are mainly responsible for perturbing soil?

2. How does the habitat of earthworms affect their influence on soil structure?

3. What part of the nematode do you look at to characterize it, and why?

4. How do the four types of protozoa differ in terms of mobility?

5. How are fungi different from bacteria?

PHYSIOLOGICAL CHARACTERISTICS

You can characterize soil organisms based on size. You can also characterize soil organisms on the basis of basic cell characteristics such as whether they have a cell nucleus (eukaryotes vs. prokaryotes), or can hardly be considered cells at all (viruses). Proteobacteria, typical soil bacteria, can be distinguished from archaea based on the biochemistry of their cell wall and DNA composition. A classic approach to characterizing differences in soil bacteria is to determine whether they have a thick cell wall (Gram-positive bacteria) or a thin cell wall (Gram-negative bacteria) based on a differential staining procedure--the Gram stain.

What Do Soil Organisms Need for Growth?

All organisms in soil require the same basic factors to grow:

1. A favorable environment in terms of temperature, water availability, and pH

2. Basic elements such as H, O, N, P, and S to build the framework of organic compounds such as proteins, lipids, and high-energy molecules for growth; Ca, Mg, K, and Fe to facilitate metabolism and electron transport; micronutrients as metal cofactors for enzyme activity

3. Oxidized and reduced molecules suitable for oxidation and reduction reactions in the cell

4. Growth factors such as vitamins if the organisms are unable to synthesize them independently

5. A source of carbon (C)

6. A source of energy

To get at the heart of what soil organisms do in the soil environment, it is best to characterize them based on their carbon and energy requirements. This allows us to look at general physiological groups carrying out similar sorts of metabolism regardless of organism size or type.

Carbon and Energy Sources
You can characterize all
soil organisms based on
where they get their C and
their energy.


You can characterize all organisms based on where they get their energy and their carbon. If they get their energy from light through photosynthesis they are phototrophs. If they get their energy from oxidizing organic and inorganic molecules they are chemotrophs. For example, in these terms all plants and some bacteria are phototrophs, whereas all animals, fungi, and some bacteria are chemotrophs. Organisms that exclusively oxidize inorganic compounds are also called lithotrophs.

In terms of carbon, organisms that get their carbon from atmospheric or dissolved C[O.sub.2] are called autotrophs, and organisms that get their carbon from organic sources are called organotrophs or heterotrophs. Figure 9-10 outlines this scheme for you.

[FIGURE 9-10 OMITTED]

For heterotrophic organisms the source of organic carbon for food can also be used as a defining characteristic. Organisms can be carnivores, herbivores, or omnivores, for example, depending on whether they consume animals, plants, or both. Another useful characterization is to distinguish between predators, which feed on living organisms, and saprophytes, which consume dead and decayed material.

Metabolism
Some soil organisms
ferment, but most respire
to produce their energy.


The organisms in soil can be divided into two groups based on metabolism: those that respire and those that ferment. Respiration, the process that humans carry out, requires oxidizing electron-rich (reduced) compounds. Oxidation removes the electrons from the reduced compounds and as they travel through the cell membrane they are used to make ATP. The electrons are ultimately used to convert [O.sub.2] into [H.sub.2]O. In anaerobic respiration other compounds besides [O.sub.2] are used to accept these electrons. In fermentation, reduced compounds are used to make a series of intermediates with high-energy phosphate bonds in a process called substrate-level phosphorylation. Respiration generates a lot more energy for growth than fermentation.
Numerous factors in soil
keep soil organisms from
reproducing as fast as
they could.


Growth takes energy, so the larger an organism is, the greater the energy it will take to move, grow, and reproduce. Bacteria, which are very small soil organisms, have the fastest growth rates in soil, as little as 0.5 hour per generation (Table 9-2). Earthworms, which are among the largest soil organisms, require almost a month to reproduce. If bacteria were allowed to grow uncontrollably, their mass would soon outweigh the entire mass of soil. This doesn't happen because bacterial growth is limited by the availability of carbon, nutrients, and other growth factors in soil.

FOCUS ON ... PHYSIOLOGY

1. What is the fundamental difference between eukaryotic and prokaryotic cells?

2. How do phototrophic and chemotrophic (or heterotrophic) soil organisms differ in the way they get their energy for growth?

3. What does it mean for a soil organism to be autotrophic?

4. What does a saprophyte use as food?

5. What does the Gram stain tell you?

ENVIRONMENTAL EFFECTS AND SOIL ORGANISMS
pH, temperature,
aeration, and water are
the most important
environmental factors
affecting soil organisms.


Environmental factors have a tremendous effect on the type, number, and activity of soil organisms. The most important environmental factors affecting soil organisms are pH, temperature, aeration, and available water. They most directly affect soil organisms, particularly microorganisms, which are permanent soil residents.

pH

Soil acidity and alkalinity are described by pH, the negative log of the H+ ion (technically speaking, the hydronium ion, [H.sub.3][O.sup.+]) concentration. Plant growth in most soils is optimal between a pH of 6.0 to 8.0. Soil organisms will also be most abundant in this neutral (slightly acid to slightly basic) pH range. Once you leave this optimal range the number and diversity of soil organisms begins to decline. Soils with a pH < 6.0 (acidic) or > 8.0 (alkaline) will have dramatically reduced biological populations for two reasons. First, as plant growth declines there will be progressively fewer large soil organisms, such as earthworms and insects, supported by the available plant growth. Second, microscopic soil organisms like protozoa and bacteria will be affected by the pH of the soil solution and its influence on the availability of essential nutrients such as phosphorus or the toxicity of elements such as aluminum and manganese (Figure 9-11). Third, fewer plants means less carbon for microbial growth.

[FIGURE 9-11 OMITTED]
Fungi dominate the soil
population in mildly acidic
conditions while
actinomycetes do so in
mildly alkaline conditions.


As a rule, only microorganisms such as bacteria and fungi predominate in acid or alkaline soils. In extremely acid (pH 1.0) or alkaline (pH 13.0) soils, bacteria alone can survive, although from the human perspective these soils would appear to be wastelands. In slightly acidic soil (pH 4.0 to 6.0) fungi, which are somewhat acid tolerant (acidophilic), will dominate the soil population. At alkaline pH (8.0 to 9.0) filamentous bacteria called actinomycetes will start to dominate the soil population because they are somewhat alkalophilic, or tolerant of basic conditions.

Some microbial processes such as N[H.sub.4.sup.+] or S oxidation will decrease the pH of the soil environment. This can affect nutrient transformations. For example, nitrification practically ceases at a soil pH < 4.0. Soil pH can also be managed to control soil organisms to some extent. For example, plant pathogenic actinomycetes, such as Streptomyces scabies, can be inhibited by acidifying the soils in which they grow. Some pathogenic fungi such as Fusarium oxysporum grow more poorly in well-buffered, neutral soils than acid soils.

Temperature
Soil organisms can thrive
in hot (thermophylic),
temperate (mesophylic), or
cold (cryophilic)
temperature regimes.


The temperature of the soil environment influences the growth and activity of soil organisms. The boundaries of biological activity in a soil environment range from 0 to 50[degrees]C (32 to 122[degrees]F). Within that range there are organisms that grow best when the temperature is < 10[degrees]C (< 50[degrees]F; cryophiles or psychrophiles), 10 to 40[degrees]C (50 to 104[degrees]F; mesophiles), and > 40[degrees]C (> 104[degrees]F; thermophiles). Compost piles are good examples of thermophilic environments in which the organisms responsible for decaying the organic material thrive where the temperature rises to 50 or 70[degrees]C (158[degrees]F).

Most soil organisms would be considered mesophiles. Small arthropods such as collembola, for example, will move deeper into the soil profile to avoid a source of light and heat at the soil surface. Although microorganisms, typically bacteria, can grow at temperatures below 0[degrees]C and close to 100[degrees]C (21[degrees]F) these would obviously not be environments permitting plant growth.
Microbial metabolism
increases as the
temperature rises, but
only to a point or limit.


As the soil temperature rises, the activity of soil organisms increases until an optimum temperature is reached. One reason soil organic matter is lower in the tropics than the tundra is because the decomposition rate is much higher. As a general rule for biological process in soil, the activity increases twofold for every 10[degrees]C rise in temperature until the optimum is reached. The optimum temperature varies depending on the typical soil temperature. Within the mesophilic range, for example, the optimum temperature for soil organisms that live in cool soils will be lower than the optimum temperature for soil organisms growing in warmer soils. These optimum temperatures can change on a seasonal basis for several nutrient transformations. For example, the optimum temperature for nitrification is higher in summer than it is in the spring.

Available Water
One of the most important
features of water in soil is
whether there is enough
to make continuous water
films for microbial
transport.


Water can help to moderate changes in soil temperature because it has a high heat capacity, which is one of the reasons that moist soils tend to be cooler than dry soils. Water is also important for permanent soil residents because they require moist environments in which to live, either because they are susceptible to desiccation, as are springtails and isopods, or because they depend on water films in the soil environment in which to move, or through which nutrients can diffuse to them. The latter case is particularly important for nonfilamentous organisms such as nematodes, protozoa, and bacteria. If the water content of the soil is excessive and the soil is flooded, it can drive soil organisms such as mites and springtails out of the soil pores. If the water content of the soil is limited, water films in the soil become discontinuous and isolate soil organisms.
Soil organisms have many
different approaches to
deal with water stress.


Water availability, or potential, is more important than water content in determining biological activity of microorganisms in soil. Because water flows from high (e.g., -1 kPa) to low (e.g., -100 kPa) potential, microorganisms must maintain an internal water potential the same as or slightly lower than their external environment or they risk becoming desiccated. Depending on the water content of the environment in which they are found, microorganisms use several strategies to ensure that this happens. Organisms that grow in relatively wet environments will take up solutes from the environment in response to decreased water availability. These organisms are susceptible to further drying because if they accumulate too many external solutes they begin to impair their own metabolism. This response is typical of most protozoa.

In progressively drier environments typical of most soils, some microorganisms can respond to reduced water availability by synthesizing solutes to lower their internal water potential. This response is typical of most Gram-negative bacteria. In the driest or most saline environments the microorganisms have adapted by continuously producing internal solutes. This response is typical of Gram-positive bacteria and many fungi.

Biological activity in soil is highest when the water potential is between -0.1 and -1.0 Mpa (or -1.0 to -10.0 atmospheres tension). Activity declines steeply when the water potential drops below this optimum, and becomes negligible below -6.0 Mpa, although some fungi can maintain activity at water potentials as low as -400 Mpa (Table 9-3).

When soils dry many soil organisms can persist because they enter a dormant state or because they encyst--surround themselves with an impermeable coating and become inactive until water is available again. Protozoa typically encyst. Bacteria and fungi can also produce spores that can persist for long periods.

Oxygen and Aeration
Water is also important
because it slows the
diffusion of O2.


In addition to moderating soil temperatures, serving as a substrate in enzyme reactions, acting as a solvent, and facilitating transport through soil, water plays a critical role by affecting soil aeration. Because [O.sub.2] diffusion is 10,000 times slower through water than air, and because water can only hold a small amount of dissolved [O.sub.2] (approximately 8 mg/L at room temperature), it does not take long in a saturated soil for all of the available [O.sub.2] to be consumed, to the detriment of those organisms that require [O.sub.2] for growth. This is one important reason why, as Figure 9-12 demonstrates, soil activity can actually decline when the water potential is greater than -0.1 Mpa.

[FIGURE 9-12 OMITTED]

[FIGURE 9-13 OMITTED]
In the absence of O2 some
soil organisms can use
other compounds for
respiration.


With the exception of fungi, some of which are capable of fermentation, all eukaryotic organisms are obligate aerobes--they require [O.sub.2] for growth and metabolism. Many bacteria are obligate anaerobes--they do not require [O.sub.2] and are actually killed by [O.sub.2]. Between these two extremes are facultative anaerobes. They will preferentially grow when [O.sub.2] is present but have the ability, or faculty, to grow in the absence of [O.sub.2], often by using other compounds to take the place of [O.sub.2] during anaerobic metabolism. This is very important because as a soil changes from being well-aerated to poorly aerated, from aerobic to anaerobic, the products of metabolizing these alternatives to [O.sub.2] start to be produced and can be used to estimate the redox potential of the soil environment (Figure 9-13). Furthermore, as these products are produced they can affect the chemistry of the soil environment and can result in the loss of gaseous C and N from the soil (see Chapter 10).

FOCUS ON ... ENVIRONMENTAL EFFECTS ON SOIL ORGANISMS

1. What are some of the consequences if soil pH falls outside a neutral range?

2. In what kinds of soil environments would you expect thermophiles to live?

3. Oxygen is important for soil organisms, so how does good or poor soil aeration affect different groups of soil organisms?

4. Why is diffusion important for soil organisms?

5. Will fertilizing a soil make water more available or less available to soil organisms?

SOIL ORGANISMS AND THEIR DISTRIBUTION

The distribution of soil organisms is not uniform. It is affected by the soil structure, to which the soil organisms contribute, and it is affected by the distribution of available carbon and energy that the soil organisms require for growth.

Distribution and Porosity
Pore size is an important
determinant of predation
and food availability
in soil.


Soil is a porous media composed of various-sized sand, silt, and clay particles. Within these different sized aggregates are innumerable pores forming a continuum from the very small (< 20 [micro]m) to the very large (> 250 [micro]m). The size of the aggregates and the size of the pores determine the kind of organisms that can be found there. The smallest pores have few if any organisms and they will be microscopic. One advantage to inhabiting small pores is that larger predatory soil organisms are unable to get in. One disadvantage is that the smallest aggregates with the smallest pores have the least available food for growth and the pores tend to be water-filled and poorly aerated. Consequently, most soil organisms are found in larger soil aggregates that have a mixture of water- and air-filled pores and abundant food sources.

Distribution and Depth
Soil organisms can be
found throughout the soil
profile, but most are found
close to the soil surface.


The soil is a thin, biologically active skin surrounding Earth. Even in that skin, the zone where soil organisms are found is quite limited, usually in the first meter (40 inches) or so. If you confine yourself to the nonburrowing organisms, then the biologically active layer shrinks even further to approximately 30 cm (12 inches), or the approximate plant rooting depth. Photosynthetic soil organisms will be active only at the soil surface where there is enough light to generate energy. As the soil depth increases, the number of bacteria significantly decreases, and this is true for most soils. For example, Table 9-4 shows results of a study in Nebraska that examined the distribution of soil bacteria by depth. If you look at the column for nutrient agar medium, 77 percent of the bacteria were in the first 30 cm of soil.

Soil organisms accumulate at the soil surface because most soil organisms are saprophytes and only grow where there is available organic matter, which tends to accumulate at the soil surface where plants occur. Tillage management practices, such as no-tillage or conservation tillage, that do not return organic matter into the soil accentuate this stratification (Table 9-5).

Occasionally microbial populations can be observed to increase within the soil profile. This is usually because there is an intervening layer such as clay or organic matter that has more nutrients, more water, or more available carbon for growth than soil immediately above or below it, thus resulting in a more favorable environment in which organisms can grow. Soil organisms can be found at great depths in soil but this does not mean that they are active. Their presence could simply reflect their transport through soil channels from the soil surface to deeper depths.

Distribution and Plant Roots
The rhizosphere, which
surrounds plant roots, is
an important microbial
habitat in soil.


One of the most dramatic influences on the distribution of soil organisms is the presence of plant roots. The soil zone immediately around the plant root and influenced by the growth and exudates of the plant root is called the rhizosphere. Because plant roots represent an abundant food source for saprophytes and parasites and the organisms that prey on them, the population of soil organisms immediately adjacent to the plant root, in the rhizosphere, is much greater than the surrounding soil, as Table 9-6 illustrates. Notice how quickly the number and diversity of bacteria decreases in this example. As you move away from the plant root the population of soil organisms exponentially declines and does so at a much faster rate than it does as you move through the soil by depth.

Soil organisms can be characterized by whether they grow preferentially in the root zone or bulk soil. The R/S (rhizosphere/soil) ratio is the ratio of the mass or number of organisms in the rhizosphere relative to that in the bulk soil several cm away. Organisms with a high R/S ratio grow preferentially in the vicinity of the rhizosphere. This includes many Gram-negative bacteria and the protozoa and nematodes that feed on them. Organisms with a low R/S ratio are not influenced by the rhizosphere or grow preferentially in the bulk soil. This includes lithotrophic organisms that get their energy from oxidizing inorganic compounds rather than organic carbon. It also includes many Gram-positive bacteria that can't compete for readily available carbon in the root zone but can successfully compete for lessavailable carbon in the bulk soil.

FOCUS ON ... THE HABITATS OF SOIL ORGANISMS

1. What are three ways to look at the distribution of soil organisms?

2. How does porosity affect the distribution of soil organisms?

3. Where in soil would you expect to find the most soil organisms?

4. What is the rhizosphere?

5. How do you calculate the R/S ratio and what does it mean?

NUMBERS AND MASS OF SOIL ORGANISMS

Soil organisms make up part of the solid fraction of soil, the organic matter. The living organisms in soil are generally referred to as biomass. As a general rule, the greater the biomass, the greater the activity and productivity of soil.

Mass versus Numbers
Bacteria may be more
numerous than soil fungi,
but fungi make up most
of the soil biomass.


There is a direct relationship between the numbers and mass of soil organisms (Table 9-7). Sheer numerical superiority does not necessarily mean that an organism will play a significant role in soil. Two earthworms may have a greater impact on soil structure and function than all the viruses combined; bacteria may outnumber fungi 100 to 1, but it is the fungi that make up the greatest fraction of biomass in most soils.

Enumeration and Estimation
A variety of techniques
are used to extract or trap
macrofauna in soil.


The size and mobility of soil organisms has a tremendous influence on the techniques used to enumerate them. The very largest soil organisms, such as insects and earthworms, can be directly extracted by digging up a known soil volume and physically removing each specimen. Alternately, noxious compounds can be added to the soil, such as a weak formalin solution, which will drive these macrofauna to the soil surface, where they can be collected.

Small insects and mesofauna that are too small to be individually picked can be harvested in traps. Typically, a volume of soil is placed on top of a trap and some stimulus, such as a heat and light source, is used to drive the soil organisms through the soil and into the traps below (Figure 9-14).

[FIGURE 9-14 OMITTED]
Soil microorganisms are so
numerous that they first
have to be diluted before
they can be counted.


Isolating smaller soil organisms most frequently makes use of their growth on specific prey or substrates. Because these organisms are so numerous in soil, one of the first procedures is to dilute the soil sample so that only a portion of the total population is estimated. Thereafter, the organisms are grown in a selective culture medium that only supports the growth of some organisms. This makes use of physiological specificity that increasingly becomes important as soil organisms get smaller. For bacteria and fungi, each individual cell, spore, or fragment can multiply and rapidly form a mass of cells called a colony. The individual colonies that develop on selective media, therefore, tell what the population of the organism is and the morphological differences between colonies tell something about the individual species present in the soil sample (Figure 9-15).

Viruses are particularly difficult to enumerate because of their size. The most common strategy is to grow their specific host and infect them with a solution containing the virus. For bacteriophage, the host cells are distributed over the surface of a selective media that permits the host growth. As the host grows, however, the viruses replicate, are released, and spread to surrounding hosts, infecting and killing them as well. Eventually you are left with a lawn of cells pocketed with cleared zones, called plaques, indicative of where individual viruses developed and were released.

[FIGURE 9-15 OMITTED]

FOCUS ON ... THE NUMBERS

OF SOIL ORGANISMS

1. What is the relationship between size and numbers of organisms in soil?

2. What organism represents the greatest fraction of biomass in soil?

3. Why can you use traps to collect some soil organisms?

4. Which kinds of protozoa are most important in terms of biomass?

5. Why is serial dilution important?

SOIL ORGANISMS AND THEIR ECOLOGICAL ROLES

Everything you have read about in terms of soil organisms pales in comparison to what these organisms do in soil, and how they are essential to the structure and function of soil systems. Soil organisms have an active role in developing soil architecture and an even more important role in decomposing, transforming, and distributing nutrients in the soil environment (Hendrix et al., 1990).

Developing Soil Structure
Soil organisms play
crucial roles in developing
soil structure.


In many soils, aggregation of minerals and organic matter into clay-, silt-, and sand-sized particles depends on biological activity. At this scale it is the microbial populations that are paramount. Microbial exudates and decomposing cells help to bind particles into packets > 2 [micro]m in diameter. Living bacteria and fungal hyphae help to bind these packets into larger aggregates > 20 [micro]m in diameter. Fungal hyphae and plant roots help to bind these small aggregates into even larger aggregates > 200 to 2000 [micro]m in diameter (Tisdale and Oades, 1982). Mycorrhizal fungi produce a compound called glomalin, which is thought to have significant soil aggregation properties. In no-tillage soils much of the aggregation is due to fungal growth and activity, because networks of fungal hyphae are not disturbed by soil tillage (Beare et al., 1994a; Beare et al., 1994b). In tilled soils bacteria appear to be the most significant influence on soil aggregates.

The larger soil organisms influence soil structure through processes collectively called bioturbation. Burrowing animals make large openings in the soil while small insects make small cavities. Termites and carpenter ants create large mounds of excavated soil material. Earthworms, ants, and termites all burrow vertically and laterally in soil, which affects water infiltration. Earthworms consume soil for its organic material and produce wastes called casts, helping to improve soil stability because these casts, in addition to being a rich source of soil enzymes and nutrients, are also more water stable than surrounding soil aggregates. Burrowing earthworms also line the channels they form with a layer of polysaccharides that can influence the surrounding soil. These earthworm-influenced zones in soil are called the drilosphere.

Fenestration and Soil Mixing
Without the activity
of macrofauna, rates
of plant litter
incorporation into soil
would be very slow.


There is a direct relationship between the surface area of organic debris and the rate at which it will decompose. Before plant material and other organic debris is readily available to microorganisms and other saprophytes it must first be broken down. Fenestration, which is carried out by soil insects, isopods, and mollusks, is a process in which plant material is fenestrated or opened to reveal the interior and allow soft tissues to be attacked by bacteria and fungi. In addition, the burrowing activity of insects and other macrofauna helps to bring the organic material into the soil, where it is mixed with other soil material and becomes even more accessible to decomposition and promotes humification. If macrofauna are excluded from the process of fenestration and mixing, the overall decomposition rates slow, as illustrated in Figure 9-16. This figure shows that when mesh bags fine enough to exclude most macrofauna are used, the overall leaf decomposition is retarded.

[FIGURE 9-16 OMITTED]

Mineralization and Decay
Mineralization by soil
organisms recycles
organic matter back into
plant nutrients.


Algae are a small but significant contributor to the primary productivity of many soils, particularly soils that are just in the process of forming and that do not yet have more developed plant life. In most soils, higher plants supply the organic carbon and nitrogen to soil, and it is the activity of saprophytic fungi and bacteria that makes this material available to other soil organisms: first as it is converted to new microbial growth, then as that new microbial growth is eaten or dies and releases the carbon and nitrogen to the soil environment. Bacteria rapidly metabolize much of the readily available carbon and nitrogen in organic debris, compounds such as sugars, proteins, and lipids. Much of this material, however, is composed of resistant compounds such as cellulose and lignin, which give plants their structural strength. These compounds are best decomposed by saprophytic lignin and cellulose-digesting fungi. Fungi, in fact, are the main agents responsible for decomposing fallen trees and limbs.

Population Control
Macro-, meso-, and
microfauna all help keep
microbial populations
under control.


Unrestricted growth of soil organisms rarely if ever occurs because of the limitation of necessary growth factors, or because predator populations keep growth in control. One of the principal ecological roles of the mesofauna and microfauna--the nematodes, protozoa, and microarthropodsis--to consume the bacteria and fungi that grow as a result of organic matter decomposition. The same is also true of some of the insects, which serve to control the populations of herbivorous and saprophytic microfauna such as collembolas and rotifers.

Nutrient Supply

Decomposing microbial biomass represents the largest and most readily available source of nutrients in soil. Because fungi make up the largest fraction of the biomass they also represent the largest single source of readily available nutrients. Protozoa also represent a large supply of readily available nutrients since the protozoa populations in soil are thought to turnover as much as ten times a year (Beare et al., 1992). Dung-burying beetles in environments with considerable animal waste play a significant role in adding organic nitrogen to soil. As much as 75 percent of cattle feces in some instances is buried by beetles, representing an annual nutrient addition of approximately 175 kg N per hectare (Fincher et al., 1981).
Symbiotic bacteria and
fungi help acquire
plant-available N and P.


Bacteria also contribute to nutrient cycling through symbiotic and asymbiotic nitrogen fixation, and enhanced P uptake by mycorrhizal fungi. Bacteria along with fungi also contribute to the steady dissolution of soil minerals, which releases elements, particularly Ca and P, that are otherwise slowly available.

Parasitism

Viruses are the arch parasites in the soil environment. Through their activity they help keep other soil populations in control. Some bacteria are also parasites. There are several nematode-trapping fungi in soil that increase and develop specialized structure to ensnare, trap, and otherwise infect nematodes (Figure 9-17).

FOCUS ON ... ECOLOGICAL ROLES

1. How do macrofauna and microorganisms contribute to soil structure?

2. What evidence suggests that macrofauna contribute to organic matter decomposition?

3. What is probably the most important ecological role of fungi?

4. Although protozoa aren't the largest fraction of the soil biomass, they make a significant contribution to nutrient cycling. How?

5. What is the major ecological role of viruses in soil?

[FIGURE 9-17 OMITTED]

ECOLOGICAL INTERACTIONS
There are seven distinct
kinds of ecological
interactions among
organisms in soil.


There are several ways in which soil organisms interact. Neutralism occurs when soil organisms have little influence on one another because they are separated spatially, temporally, or occupy different ecological niches. Competition is when two organisms directly compete for the same scarce resources to the detriment of both. Commensalism occurs when the activities of one organism are beneficial to the growth of another. Ammensalism occurs when the activities of one organism are detrimental to the growth of another. Predation and parasitism happen when one organism is the prey or host of another. Mutualism is the condition when the growth of two organisms is mutually beneficial. Mutualism takes several forms. One is synergism, in which two organisms growing together will grow better than either organism alone. Another is symbiosis, in which the union of two organisms is essential for either the survival or certain physiological processes to occur.

Symbioses
Only bacteria are actually
capable of N-fixation.


Three types of symbioses stand out as contributing significantly either to the fertility of soil systems, and consequently to their productivity, or to the initial development of soil in harsh environments: the legume/rhizobia and woody shrub/Frankia [N.sub.2]-fixing symbiosis, the mycorrhizal symbiosis, and the symbiosis between algae and fungi to produce lichens.

Legume/Rhizobia

Because atmospheric [N.sub.2] is relatively inert, and soil nitrogen is the most limiting nutrient in most soil systems, symbiotic [N.sub.2]-fixation is a critical path by which plant-available N can enter the soil. The symbiotic association is relatively specific. Forage and seed-bearing legumes form symbiotic associations with bacteria from the genera Rhizobium, Bradyrhizobium, and Azorhizobium. Rhizobium and Bradyrhizobium form root nodules while Azorhizobium forms stem nodules in which the fixation occurs. Bacteria in the soil invade root or stem tissue and the plant host, in turn, creates a specialized structure in which the bacteria are housed. In exchange for converting [N.sub.2] into N[H.sub.3], which plants can use, the bacteria are provided with shelter, nutrients, and carbon (Figure 9-18). Only bacteria can fix [N.sub.2], and although they can be made to do so apart from the host, they normally do not.

[FIGURE 9-18 OMITTED]

Woody Shrub/Frankia

Members of the genus Frankia are actinomycetes that also have the ability to infect plant tissue and fix NZ in a symbiotic relationship with their host. Frankia infect woody shrubs such as Alnus, Alder, and Ceanothus. They form nodules that can be the size of baseballs. This association, the actinorhizal association, is important in cool, moist environments, forest soils, and soils developing in adverse conditions. Frankia can be grown apart from their host only with great difficulty.

Mycorrhizae

Mycorrhizae are fungi that infect the plant roots of nearly all plants. The symbiosis is almost as ancient as are terrestrial plants. The most significant role associated with mycorrhizae is in plant nutrition, particularly phosphorus nutrition, although additional roles have been ascribed to enhanced drought tolerance, improved disease resistance, and improved soil structure (Figure 9-19). There are two broad categories of mycorrhizae: ectomycorrhizae and endomycorrhizae.
Mycorrhizae means
"fungus root," and refers
to the symbiosis between
plant roots and certain
fungi.


Ectomycorrhizae

Ectomycorrhizae infect most deciduous plants and shrubs. They form a characteristic structure called the "Hartig net" in which the fungal mycelium surrounds the plant root and penetrates between plant cells. The roots themselves develop a stunted and stubby appearance (Figure 9-20). Ectomycorrhizal species are numerous and the fungus can grow apart from the host, but it is usually a poor competitor with other soil fungi.

Endomycorrhizae

Endomycorrhizae, characterized by the genus Glomus, are critical symbionts with most agriculturally important plants. The endomycorrhizae are obligate symbionts and cannot grow apart from their host. Endomycorrhizae usually form two distinct structures that develop in the plant root: an arbuscle, which is a very fine, highly branched invagination into the cell, and a vesicle, which is a spherical structure forming between cells (Figure 9-21). The arbuscles are the site of nutrient exchange between plant and mycorrhizae and the vesicle is a fungal storage organ.

[FIGURE 9-19 OMITTED]

[FIGURE 9-20 OMITTED]

[FIGURE 9-21 OMITTED]

Lichens
Lichens help to initiate
the physical and chemical
weathering of rocks, the
first step in soil formation.


Lichens are obligate and transitory symbioses between algae and fungi or cyanobacteria (photosynthetic, [N.sub.2]-fixing bacteria) and fungi. Lichens appear in deserts, on rocks, and in soils undergoing the first stages of development. Crustose lichens are small and colorful and frequently appear on bare rock (Paul and Clark, 1996; Figure 9-22). Foliose lichens form colorful ruffled mats, usually in moist environments or on trees. Fruticose lichens are stalked and bushy in appearance.

[FIGURE 9-22 OMITTED]

FOCUS ON ... SYMBIOSES

1. What are several types of ecological interactions in soil?

2. What are the three types of nodule-forming bacteria?

3. What are mycorrhizae?

4. What is the difference between ectomycorrhizae and endomycorrhizae?

5. What are lichens composed of?

SUMMARY

In this chapter you examined eight key features of soil organisms. The soil organisms can be divided into basic groups by size: macrofauna (insects, arachnids, earthworms, and potworms), mesofauna (nematodes and microarthropods), microfauna (protozoa), and microorganisms (algae, fungi, bacteria, and viruses). Soil organisms can be characterized as prokaryotes or eukaryotes and by where they get their energy and carbon for growth. They can be grouped based on how they are affected by environmental factors such as temperature and pH.

The nutritional requirements of soil organisms and the most important chemical elements required for their growth were discussed. The enormous diversity of soil organisms was examined. You looked at how the soil structure affects the habitats and distribution of soil organisms, and also how it influences their biomass and numbers. You also looked at the various ways in which soil organisms reproduce and are distributed. Finally, you surveyed important ecological roles of soil organisms and how they interact in relationships, like symbioses, with higher plants and animals.

In the next chapter you will take a closer look at how soil organisms are involved in important biogeochemical cycles in soil and the transformation and availability of important soil elements.

END OF CHAPTER QUESTIONS

1. Draw a scale showing the relative sizes of soil organisms. How does cell complexity change as the size of the organism increases or decreases?

2. How does size affect the ecological roles of soil organisms and the locations in soil where they can exist?

3. In terms of C and energy requirements, how would you classify an organism that grew on C[O.sub.2] as its C source while metabolizing iron for energy?

4. Draw a graph showing the change in population of an obligate anaerobe as the [O.sub.2] content in soil increases.

5. What is the H+ ion concentration when the pH is 4, and what soil organisms are most likely to compete at this pH?

6. Draw a graph that illustrates the change in population of cryophilic, mesophilic, and thermophilic bacteria as the temperature rises from 5 to 75[degrees]C.

7. If a soil sample is serially diluted 1000-fold before bacteria are enumerated and 1.6 x 102 bacteria are subsequently observed, what was the starting population?

8. Using the data in Table 9-4, what depth would account for approximately 50 percent of the bacteria?

9. What is the R/S ratio for a ciliated protozoa if its population in the bulk soil is 1.6 x 103 g-1 and its population in the rhizosphere is 3.0 x 104 9 1?

10. Draw a graph showing what would happen to the population of a soil organism if an ammensal organism were introduced into its environment.

FURTHER READING

Coleman, D. C., and D. A. Crossley. 1996. Fundamentals of soil ecology. San Diego, CA: Academic Press.

(An excellent and brief examination of soil organisms from an ecological perspective. It has excellent chapters on the various macro-, meso-, and microfaunal groups, where they are found, and how they can be collected and enumerated.)

Coyne, M. S. 1999. Soil microbiology: An exploratory approach. Clifton Park, NY: Thomson Delmar Learning.

(Examines soil organisms in greater depth but still maintains an introductory level for the reader new to the topic.)

Paul, E. A., and F. E. Clark. 1996. Soil microbiology and biochemistry, 2nd ed. San Diego, CA: Academic Press.

(A graduate-level text. It has good introductions to looking at soil systems in terms of biological modeling.)

REFERENCES

Beare, M. H., R. W. Parmelee, P. F. Hendrix, W. Cheng, D. C. Coleman, and D. A. Crossley. 1992. Microbial and faunal interactions and effects on litter nitrogen and decomposition in agroecosystems. Ecological Monographs 62: 569-571.

Beare, M. H., M. L. Cabrera, P. F. Hendrix, and D. C. Coleman. 1994a. Aggregate-protected and unprotected pools of organic matter in conventional and no-tillage ultisols. Soil Science Society of America Journal 58: 787-795.

Beare, M. H., P. F. Hendrix, and D. C. Coleman. 1994b. Water stable aggregates and organic matter fractions in conventional and no-tillage soils. Soil Science Society of America Journal 58: 777-786.

Bouche, M. B. 1977. Strategies lombriciennes. Ecol. Bull. 25: 122-132. Coleman, D. C., and D. A. Crossley. 1996. Fundamentals of soil ecology. San Diego, CA: Academic Press.

Darwin, C. 1881. The formation of vegetable mold, through the action of worms, with observations on their habits. London: Murray.

Doran, J. W., and D. M. Linn. 1994. Microbial ecology of conservation management systems. In J. L. Hatfield and B. A. Stewart (ed.), Soil biology effects on soil quality. Advances in soil science, Lewis Publ. Boca Raton, FL., pp. 1-27.

Fincher, G. T., W. G. Monson, and G. W. Burton. 1981. Effects of cattle feces rapidly buried by dung beetles on yield and quality of coastal Bermuda grass. Agronomy Journal 73: 775-779.

Harris, R. F. 1981. Effect of water potential on microbial growth and activity. In L. F. Elliot et al. (eds.), Water potential relations in soil microbiology. Madison, WI: Soil Science Society of America, pp. 23-95.

Hendrix, P. F., D. A. Crossley, J. M. Blair, and D. C. Coleman. 1990. Soil biota as components of sustainable agroecosystems. In C. A. Edwards et al. (eds.), Sustainable agricultural systems. Ankeny, IA: Soil and Water Conservation Society, pp. 637-654.

Paul, E. A., and F. E. Clark. 1996. Soil microbiology and biochemistry. San Diego, CA: Academic Press.

Phillipson, J. 1968. Ecological energetics. Edward Arnold Publishing, Ltd. Great Britain.

Putnam, J. J. 1913. The bacteria of Nebraska soil. Ph.D. dissertation, University of Nebraska. Lincoln, NE: The Woodruff Press.

Tisdale, J. M., and J. M. Oades. 1982. Organic matter and water stable aggregates in soil. Journal of Soil Science 32: 141-163.

Wallwork, J. A. 1970. Ecology of soil animals. London: McGraw-Hill.

THE GRAM STAIN-A CLASSIC APPROACH TO CHARACTERIZING BACTERIA

The Gram stain is a simple laboratory staining procedure that is used to categorize bacteria into two basic groups. The procedure itself is simple. Bacteria are deposited onto the surface of a glass slide, heat treated to kill and permanently fix them to the slide surface, and then stained with a series of stains. First, crystal violet is added. Second, Gram's iodine solution is added to precipitate the crystal violet. Third, the stained cells are briefly decolorized with ethanol. Fourth, the cells are counterstained with safranin. Gram-positive bacteria will appear purple under a microscope after counter staining and Gram-negative bacteria will appear red. The usefulness of the staining procedure entirely depends on bacteria having different thicknesses of cell walls. Gram-positive bacteria have a thick cell wall compared to Gram-negative bacteria. As a general rule, Gram-positive bacteria grow more slowly than Gram-negative bacteria but are more tolerant of adverse soil conditions and low available nutrients. Gram-negative bacteria are able to grow much quicker and respond rapidly to available food, but tend to die quicker if environmental conditions deteriorate.

EGGS AND GELATIN

Why do high and low temperatures kill soil organisms? At high temperatures the principle mechanisms are desiccation and denaturation. At low temperatures, freezing is a problem. Denaturation and freezing disrupt the lipids and proteins that are essential for cells to function. This is best illustrated by what happens to gelatin when it is frozen and eggs when they are boiled. Ice crystals that form in the gelatin as it freezes prevent the orderly arrangement of the proteins in the gelatin. Hardboiled eggs are a good example of how heat causes cell proteins and lipids to coagulate (denature). Because most soil organisms reflect the temperature of their environment (unlike mammals, which maintain a relatively constant body temperature regardless of the external temperature) they are susceptible to temperature extremes. Unless they have time to adapt, drastic temperature changes will kill them. That is one reason why you never freeze a soil sample that you are going to use to examine biological activity.

A CLOSER LOOK AT SERIAL DILUTION

Serial dilution is one of the most important techniques in soil biology. It is a process of reproducibly diluting soil or water samples containing millions of organisms so that one examines only a few representative organisms. In serial dilution a soil or water sample is dispensed into a buffered solution called a diluent and agitated to release as many organisms as possible. A known volume of this agitated sample is collected and added to more diluent (usually in a 1 to 10 ratio). Further dilution is repeated until the organisms present are diluted almost to extinction. The diluted sample is then evenly dispensed on a solid growth medium (plating) or added to broth in a flask that permits growth. Based on the number of colonies that form on the medium, or the evidence of growth in broth and the extent to which the original sample was diluted, you can calculate how many organisms were originally present.
TABLE 9-1 Characterizing soil organisms by size.

Organism           Example           Typical Dimensions ([micro]m)

Troglodyte/
  cave dweller     Homo sapiens      2 x [10.sup.6]
Earthworm          Lumbricus         1 x [10.sup.5]
Insects            Hymenoptera       1 x [10.sup.4] - 1 x [10.sup.5]
Nematodes          Pratylenchus      20 - 3000
Protozoa           Euglena           15 x 50 (20 to 2000)
Algae              Chlorella         5 x 13
Fungi              Mucor             8.0 (diameter do hypha)
                                     1 x [10.sup.6] to 1 x [10.sup.9]
                                     (fruiting bodies or hyphal
                                     spread)
Bacteria
  Actinomycete     Streptomyces      0.5 - 2.0 (up to 10,000)
  Proteobacteria   Pseudomonas       0.5 x 1.5 (up to 1000)
  Archaea          Methanobacillus   0.5 x 1.5
  Mycoplasmas                        0.1 - 0.3
Virus              TMV (tobacco      0.02 - 0.30
                   mosaic virus)

TABLE 9-2 Generation times of various soil organisms. (Adapted from
Coleman and Crossley, 1996)

                            Minimum Generation   Number of Generations
Organism                       Time (hours)           per Season

Earthworm                          720                     3
Potworm                            170                     ?
Mites                              720                    2-3
Springtails (collembola)           720                    2-3
Nematodes (microbivorous)          120                    2-4
Protozoa                           2-4                    10
Fungi                              4-8                    0.75
Bacteria                           0.5                    2-3

TABLE 9-3 Influence of water potential on soil organisms.
(Adapted from Harris, 1981)

Water Potential
([PSI])

MPa     Bars    Example         Activity in Soil

-0.03   -0.3    Ciliates        Movement of protozoa, bacteria
-0.1    -1.0    Flagellates     Movement of protozoa, bacteria
-0.5    -5.0    Naked amoeba    Movement of protozoa, bacteria
                Spirillum
-1.5    -15.0   Nitrosomonas    [NH.sub.4.sup.+] and S oxidation
                                  affected
                                Wilting point of many plants affected
                                Gram-negative bacteria affected
-2.5    -25.0   Pseudomonas
-4.0    -40.0   Basidiomycete   Phycomycete fungal growth
                  yeasts
                                [NH.sub.4.sup.+] and S oxidation cease
                Archrobacter    Gram-positive bacteria affected
                Streptococcus
-6.0    -60.0                   Fungal growth
-10     -100    Saccharomyces   Fungal growth

TABLE 9-4 Number of bacteria in air-dried soils from Nebraska sampled
by soil depth. (Data from Putnam, 1913)

                               Growth Media (a)

        Depth           Nutrient Agar   Ashby's Medium

5.1 cm       2 inches       2,500,000          610,000
10.2 cm      4 inches         660,000          458,000
30.5 cm      1 foot           290,000          417,000
61.0 cm      2 feet           282,000          250,000
91.4 cm      3 feet            69,000          185,000
1.2 meter    4 feet            77,000          210,000
1.5 m        5 feet            56,000          114,000
1.8 m        6 feet            66,000           47,000
2.2 m        7 feet            11,000            2,000
2.4 m        8 feet             7,400            7,100
2.7 m        9 feet               700              300
3.0 m       10 feet             1,200            1,000
3.3 m       11 feet             4,700            2,700
3.6 m       12 feet             1,200            2,600
4.0 m       13 feet            26,500          116,000
4.2 m       14 feet                50                0
4.6 m       15 feet                 0                0
4.9 m       16 feet                 0                0
5.5 m       18 feet                 0                0
5.8 m       19 feet                 0                0
6.1 m       20 feet                 0                0

(a) Nutrient agar is a complex, protein-rich medium. Ashby's medium
is an example of a minimal medium, it contains mannitol (a sugar) as
a carbon source and other essential growth elements but no growth
factors, so the bacteria that grow must be able to synthesize
everything for themselves.

TABLE 9-5 The ratio of various soil biological parameters in untilled
and tilled soils. (Adapted from Doran and Linn, 1994)

                                   Untilled/Tilled by Depth

                                  0-7.5 cm     7.5-15.0 cm

Organic C                           1.4            1.0
Mineralizable N                     1.4            1.0
Microbial biomass                   1.5            1.0
Fungi                               1.4            0.6
Aerobic bacteria                    1.4            0.7
Obligate anaerobic bacteria         1.3            1.1

TABLE 9-6 The effect of the rhizosphere on bacteria populations and
diversity. (Adapted from Paul and Clark, 1996)

Distance from           Population           Distinct Morphological
  Root (mm)     (x [10.sup.9] [cm.sup.-3])           Types

     0-1                   120                         11
     1-5                    96                         12
     5-10                   41                          5
    10-15                   34                          2
    15-20                   13                          2

TABLE 9-7 Size, mass, and numerical relationships among soil
rganisms. (Adapted from Coleman and Crossley, 1996)

                                                     Individuals
                 Approximate   Approximate Biomass   Per 1000 Cubic
Organisms        Length (mm)   (kg dw [ha.sup.-1])   [cm.sup.3] (a)

Earthworm        15-85              25-50            2
Potworm          1.0-60.0           1-8              50
Arthropods       1-30                                100
Nematodes        0.2-2.0            1.5-4.0          30,000
Mites            1.0                2-8              2,000
Collembola       0.5                0.2-0.5          1,000
Protozoa                                             1,000,000,000
  Naked amoeba   0.03               47.5
  Flagellates    0.01               2.5
Ciliates         0.08               <0.5
Fungi                               700-2700         Billions
Bacteria                            500-750          Billions

(a) 1000 [cm.sup.3] has the same volume as a cube of soil 4 inches
on each side.
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