The Living Soil
The
Living Soil
When soil
organisms and roots go about their normal functions of getting energy for
growth from organic molecules, they “respire”—using oxygen and releasing carbon
dioxide to the atmosphere. (Of course, as we take our essential breaths of air,
we do the same.) An entire field can be viewed as breathing as if it is one
large organism. The soil is like a living being in another way, too—it may get “sick”
in the sense that it becomes incapable of supporting healthy plants.
The organisms living in the
soil, both large and small, play a significant role in maintaining a healthy
soil system and healthy plants. One of the main reasons we are interested in
these organisms is because of their role in breaking down organic residues and
incorporating them into the soil. Soil organisms influence every aspect of
decomposition and nutrient availability. As organic materials are decomposed,
nutrients become available to plants, hummus is produced, soil aggregates are
formed, channels are created for water infiltration and better aeration, and
those residues originally on the
surface are brought deeper into the soil.
We classify soil
organisms in several different ways. Each can be discussed separately or all
organisms that do the same types of things can be discussed as a group. We also
can look at soil organisms according to their role in the decomposition of
organic materials. For example, organisms that use fresh residues as their source
of food are called primary (1°), or first-level, consumers of organic materials
(see figure 4.1). Many of these primary consumers break down large pieces of
residues into smaller fragments. Secondary (2°) consumers are organisms that
feed on the primary consumers themselves or their waste products. Tertiary (3°)
consumers then feed on secondary consumers. Another way to treat organisms
is by general size, such as very small, small, medium, large, and very large.
This is how we will discuss soil organisms in this chapter.
There is
constant interaction among the organisms living in the soil. Some organisms
help others, as when bacteria that live inside the earthworm’s digestive
Soil organisms and
their role in decomposing residues. Modified from D.L. Dindal (1972).
system help decompose
organic matter. Although there are many examples of such mutually beneficial,
or symbiotic, relationships, an
intense competition occurs among most
of the diverse organisms in healthy soils. Organisms may directly compete with
each other for the same food. Some organisms naturally feed on others— nematodes
may feed on fungi, bacteria, or other nematodes, and some fungi trap and kill
nematodes. There are also fungi and bacteria that parasitize nematodes and
completely digest their content.
Some soil organisms can harm
plants, either by causing disease or by being parasites. In other words, there
are “good” as well as “bad” bacteria, fungi, nematodes, and insects. One of the
goals of agricultural production
systems should be to create
conditions that enhance the growth of beneficial organisms, which are the vast
majority, while decreasing populations of those few that are potentially
harmful.
SOIL
MICROORGANISMS
Microorganisms are very small forms of life
that can sometimes live as single cells, although many also form colonies of
cells. A microscope is usually needed to see individual cells of these
organisms. Many more microorganisms exist in topsoil, where food sources are
plentiful than in subsoil. They are especially abundant in the area
immediately next to plant roots (called the rhizosphere), where sloughed-off
cells and chemicals released
by roots provide ready food sources. These
organisms are primary decomposers of organic matter, but they do other things,
such as provide nitrogen through fixation to help grow plants, detoxify
harmful chemicals (toxins), suppress disease organisms and produce products
that might stimulate plant growth. Soil microorganisms have had another direct
importance for humans—they are the source of most of the antibiotic medicines
we use to fight diseases.
Bacteria
Bacteria live in almost any
habitat. They are found inside the digestive system of animals, in the ocean
and freshwater, in compost piles (even at temperatures over 130°F), and in
soils. Although some kinds of bacteria live in flooded soils without oxygen,
most require well-aerated soils. In general, bacteria tend to do better in
neutral pH soils than in acid soils.
In addition to
being among the first organisms to begin decomposing residues in the soil,
bacteria benefit plants by increasing nutrient availability. For example, many
bacteria dissolve phosphorus, making it more available for plants to use.
Bacteria are
also very helpful in providing nitrogen to plants, which they need in large
amounts but is often deficient in agricultural soils. You may wonder how soils
can be deficient
in nitrogen when we are surrounded by it—78% of the air we breathe is composed
of nitrogen gas. Yet plants, as well as animals, face a dilemma similar to that
of the Ancient Mariner, who was adrift at sea without fresh water: “Water,
water, everywhere nor any drop to drink.” Unfortunately, neither animals nor
plants can use nitrogen gas (N2) for their nutrition. However, some types of
bacteria are able to take nitrogen gas from the atmosphere and convert it into
a form that plants can use to make amino acids and proteins.
This conversion
process is known as nitrogen fixation.
Some nitrogen-fixing bacteria form mutually benefit-
social associations with
plants. One such symbiotic relationship that is very important to agriculture
involves the nitrogen-fixing rhizobia group of bacteria that live inside
nodules formed on the roots of legumes. These bacteria provide nitrogen in a
form that leguminous plants can use, while the legume provides the bacteria
with sugars for energy.
People eat some
legumes or their products, such as peas, dry beans, and tofu made from
soybeans. Soybeans, alfalfa, and clover are used for animal feed. Clovers and
hairy vetch are grown as cover crops to enrich the soil with organic matter, as
well as nitrogen, for the following crop. In an alfalfa field, the bacteria may
fix hundreds of pounds of nitrogen per acre each
year. With peas, the amount
of nitrogen fixed is much lower, around 30 to 50 pounds per acre.
The
actinomycetes, another group of bacteria, break large lignin molecules into
smaller sizes. Lignin is a large and complex molecule found in plant tissue,
especially stems, that is difficult for most organisms to break down. Lignin
also frequently protects other molecules like cellulose from decomposition.
Actinomycetes have some characteristics similar to those of fungi, but they are
sometimes grouped by themselves and given equal billing with bacteria and
fungi.
Root heavily infected with
mycorrhizal fungi (note round spores
at the end of some hyphae). Photo by Sara Wright.
Fungi
Fungi are another type of soil microorganism.
Yeast is a fungus used in baking and in the production of alcohol. Other fungi
produce a number of antibiotics. We have all probably let a loaf of bread sit
around too long only to find fungus growing on it. We have seen or eaten mushrooms,
the fruiting structures of some fungi. Farmers know that fungi cause many plant
diseases, such as downy mildew, damping-off, various types of root rot,
and apple scab. Fungi also
initiate the decomposition of fresh organic residues. They help get things
going by softening organic debris and making it easier for other organisms to
join in the decomposition process. Fungi are also the main decomposers of
lignin and are less sensitive to acid soil conditions than bacteria. None are
able to function without oxygen. Low soil disturbance resulting from reduced
tillage systems tends to promote organic residue accumulation at and near the
surface. This tends to promote fungal growth, as happens in many natural
undisturbed ecosystems.
Many plants
develop a beneficial relationship with fungi that increases the contact of
roots with the soil. Fungi infect the roots and send out rootlike structures
called hyphae (see figure 4.2). The
hyphae of these mycorrhizal fungi
take up water and nutrients that can
then feed the plant. The hyphae are very thin, about 1/60 the diameter of a
plant root, and are able to exploit the water and nutrients in small spaces in
the soil that might be inaccessible to roots. This is especially important for
phosphorus nutrition of plants in low-phosphorus soils. The hyphae help the
plant absorb water and nutrients, and in return, the fungi receive energy in the
form of sugars, which the plant produces in its leaves and sends down to the
roots. This symbiotic
interdependency between
fungi and roots is called a mycorrhizal relationship. All things considered, it’s
a pretty good deal for both the plant and the fungus. The hyphae of these fungi
help develop and stabilize larger soil aggregates by secreting a sticky gel
that glues mineral and organic particles together.
Algae
Algae, like crop plants, convert sunlight into
complex molecules like sugars, which they can use for energy and to help build
other molecules they need. Algae are found in abundance in the flooded soils of
swamps and rice paddies, and they can be found on the surface of poorly drained
soils and in wet depressions. Algae may also occur in relatively dry soils, and
they form mutually beneficial relationships with other organisms. Lichens
found on rocks are an association between a fungus and an alga.
on the root, sometimes cause
greater disease severity and more damage than the nematode itself. A number of
plant-parasitic nematodes vector important and damaging plant viruses of
various crops. However, there are many beneficial nematodes that help in the
break-down of organic residues and feed on fungi, bacteria, and protozoa as
secondary consumers. In fact, as with the protozoa, nematodes feeding on fungi
and bacteria help convert nitrogen into forms for plants to use. As much as 50%
or more of mineralized nitrogen comes from nematode feeding. A number of
nematodes alone or with special bacteria parasitize and kill insects such as
the larvae of the cabbage looper and the grubs of the Japanese beetle. Finally,
several nematodes infect animals and humans, causing serious diseases such as
river blindness and heartworm.
Protozoa
Protozoa are single-celled
animals that use a variety of means to move about in the soil. Like bacteria
and many fungi, they can be seen only with the help of a microscope. They are
mainly secondary consumers of organic materials, feeding on bacteria, fungi,
other protozoa, and organic molecules dissolved in the soil water. Protozoa—through
their grazing on nitrogen-rich organisms and excreting wastes—are believed to
be responsible for mineralizing (releasing nutrients from organic molecules)
much of the nitrogen in agricultural soils.
SMALL AND MEDIUM-SIZE SOIL ANIMALS Nematodes
Nematodes are simple multicellular soil
animals that resemble tiny worms but are nonsegmented. They tend to live in the
water films around soil aggregates. Some types of nematodes feed on plant roots
and are well-known plant pests. Fungi such as Pythium and Fusarium,
which may enter nematode-feeding wounds
Earthworms
Earthworms are every bit as
important as Charles Darwin believed they were more than a century ago. They
are keepers and restorers of soil fertility. Different types of earthworms,
including the nightcrawler, field (garden) worm, and manure (red) worm, have
different feeding habits. Some feed on plant residues that remain on the soil
surface, while other types tend to feed on organic matter that is already mixed
with the soil.
The
surface-feeding night crawlers fragment and mix fresh residues with soil
mineral particles, bacteria, and enzymes in their digestive system. The
resulting material is given off as worm casts. Worm casts are generally higher
in available plant nutrients, such as nitrogen, calcium, magnesium, and
phosphorus, than the surrounding soil and, therefore, contribute to the
nutrient needs of plants. They also bring food down into their burrows, thereby
mixing organic matter deep into the soil. Earthworms feeding on debris that is
already below the surface continue to decompose organic materials and mix them
with the soil minerals.
A number of types of earthworms, including the
surface-feeding nightcrawler, make burrows
that allow rainfall to easily infiltrate the soil. These worms usually burrow
to 3 feet or more, unless the soil is saturated or very hard. Even those types
of worms that don’t normally produce channels to the surface help loosen the
soil, creating channels and cracks below the surface that help aeration and
root growth. The number of earthworms in the soil ranges from close to zero to
over a million per acre. Just imagine, if you create the proper conditions for
earthworms, you could have 800,000 small channels per acre that conduct water
into your soil during downpours.
Earthworms do
some unbelievable work. They move a lot of soil from below up to the surface—from
about 1 to 100 tons per acre each year. One acre of soil 6 inches deep weighs
about 2 million pounds or 1,000 tons. So 1 to 100 tons is the equivalent of
about .006 of an inch to about half an inch of soil. A healthy earthworm
population may function as nature’s plow and help replace the need for tillage
by making channels and bringing up subsoil and mixing it with organic residues.
Earthworms do
best in well-aerated soils that are supplied with plentiful amounts of organic
matter. A study in Georgia showed that soils with higher amounts of organic
matter contained higher numbers of earth-worms. Surface feeders, a type we
would especially like to encourage, need residues left on the surface. They are
harmed by plowing or disking, which disturbs their burrows and buries their
food supplies. Worms are usu-ally more plentiful under no-till practices than
under conventional tillage systems. Although many pesticides have little effect
on worms, some insecticides are very harmful to earthworms.
Diseases or insects that
overwinter on leaves of crops can sometimes be partially controlled by high
earthworm populations. The apple scab fungus—a major pest of apples in humid
regions—and some leaf miner insects can be partly controlled when worms eat the
leaves and incorporate the residues deeper into the soil.
Although the nightcrawler is certainly
beneficial in farm fields, this European introduction has caused problems in
some northern forests. As fishermen have discarded unused worms near forest
lakes, nightcrawlers have become adapted to the forests. They have in some
cases reduced the forest litter layer almost completely, accelerating nutrient
cycling and changing the species composition of the understory vegetation. So some
forest managers view this organism, considered so positively by farmers, as a
pest!
Insects and
Other Small to Large Soil Animals
Insects are another group of
animals that inhabit soils. Common types of soil insects include termites,
spring-tails, ants, fly larvae, and beetles. Many insects are secondary and
tertiary consumers. Springtails feed on fungi and animal remains, and in turn, they themselves are food for predacious mites. Many beetles, in particular,
eat other types of soil animals. Some beetles feed on weed seeds in the soil.
Termites, well-known feeders of woody material, also consume decomposed organic
residues in the soil.
Other medium-size to large
soil animals include millipedes, centipedes, mites, slugs, snails, and spiders.
Millipedes are primary consumers of plant residues, whereas centipedes tend to
feed on other organisms. Mites may feed on food sources like fungi, other
mites, and insect eggs, although some feed directly on residues. Spiders feed
mainly on insects and keep insect pests from developing into large populations.
VERY LARGE
SOIL ANIMALS
Very large soil animals,
such as moles, rabbits, woodchucks, snakes, prairie dogs, and badgers, burrow
in the soil and spend at least some of their lives below ground. Moles are
secondary consumers, their diet consisting mainly of earthworms. Most of the
other animals exist on vegetation. In many cases, their presence is considered
a nuisance for agricultural production or lawns and
gardens.
Nevertheless, their burrows may help conduct water away from the surface during
downpours and thus decrease erosion. In the southern U.S., the burrowing action
of crawfish, abundant in many somewhat poorly drained soils, can have a large
effect on soil structure. (In Texas and Louisiana, some rice fields are “rotated”
with crawfish production
PLANT ROOTS
Healthy plant roots are essential for good
crop yields. Roots are clearly influenced by the soil in which they live and
are good indicators of soil quality. If the soil is compact, is low in
nutrients or water, includes high populations of root pathogens, or has other
problems, plants will not grow well. On the other hand, plants also influence
the soil in which they grow. The physical pres-sure of roots growing through
soil helps form aggregates by bringing particles closer together. Small roots
also help bind particles together. In addition, many organic compounds are
given off, or exuded, by plant roots and provide nourishment for soil organisms
living on or near the roots. The zone surrounding roots is one of especially
great numbers and activity of organisms that live off root exudates and
sloughed-off cells. This increased activity by microorganisms, plus the slight
disruption caused as roots grow through the soil, enhances the use of active (“dead”)
organic matter by organisms—also enhancing nutrient availability to the plant.
A sticky layer surrounding roots, called the mucigel, provides close contact
between microorganisms, soil minerals, and the plant (figure 4.3). Plant roots
also contribute
The soil population must be considered from the point of
view of a biological complex; it is not sufficient to separate it into
different constituent groups.
greatly to organic matter
accumulation. They are usually well distributed in the soil and may be slower
to decompose than surface residues, even if incorporated by plowing or
harrowing.
For plants with
extensive root systems, such as grasses, the amount of living tissue below the ground may actually weigh more than the amount of leaves and stems we see above
ground.
BIOLOGICAL
DIVERSITY, ABUNDANCE, AND BALANCE
A diverse biological community in soils is
essential to maintaining a healthy environment for plant roots. There may be
over 100,000 different types of organisms living in soils. Most are providing
numerous functions that assist plants, such as making nutrients more available,
producing growth-stimulating chemicals, and helping form soil aggregates. In a
teaspoon of agricultural soils, it
is estimated that there are
from 100 million to 1 billion bacteria, several yards of fungi, and several
thousand protozoa. It may hold 10 to 20 bacterial-feeding nematodes and a few
fungal-feeding and plant-parasitic nematodes. Arthropods can number up to 100
per square foot, and earthworms from 5 to 30 per square foot.
Of all the organisms in
soils, only a small number of bacteria, fungi, insects, and nematodes might
harm plants in any given year. Diverse populations of soil organisms maintain a
system of checks and balances that can keep disease organisms or parasites from
becoming major plant problems. Some fungi kill nematodes, and others kill
insects. Still, others produce antibiotics that kill bacteria. Protozoa feed on
bacteria and may attack fungi. Some bacteria kill harmful insects. Many
protozoa, springtails, and mites feed on disease-causing fungi and bacteria.
Beneficial organisms, such
as the fungus Trichoderma and the
bacteria Pseudomonas fluorescens,
colonize plant roots and protect them from attack by harmful organisms. Some
of these organisms, isolated from soils, are now sold commercially as
biological control agents. The
effects of bacteria and
fungi that suppress plant disease organisms are thought to arise from
competition for nutrients, production of antagonistic substances, and/ or
direct parasitism. In addition, a number of beneficial soil organisms induce
the immune systems of plants to defend the plants (systemic acquired resistance; see discussion in chapter 8). Also, the roots of agronomic crops usually have their own characteristic microbial
communities with numerous interactions.
Soil management
can have dramatic effects on soil 
biological composition (see figure 4.4 for
manage-
biological composition (see figure 4.4 for
manage-
ment effects on organisms).
For example, the less a soil is disturbed by tillage, the greater the
importance of fungi relative to bacteria. Thus, the promotion of cropping practices
that encourage abundance and diversity of soil organisms encourages healthy
soil. Crop rotations of plants from different families are recommended to keep
microbial diversity at its maximum and to break up any potential damaging pest
cycles. Additional practices that promote the diversity and activity of soil
organisms include low amounts of soil disturbance, the use of cover crops,
maintaining pH close to neutral, and routine use of organic sources of
slow-release fertility.
SUMMARY
Soils are alive with a
fantastic number of many types of organisms, most of which help to grow healthy
plants and protect them from pests. The food for all the soil’s organisms
originates with crop residues and organic materials added from off the field.
These provide the fuel that powers the underground life that has such a
positive effect on the soil’s chemical and physical properties, as well as, of
course, maintaining a system of equilibrium that helps regulate the populations
of organisms. Soil
