MODULE D1 - SOIL ORGANISMS

INTRODUCTION
Soil organisms are the living portion of the soil which includes animals, plants, fungi, bacteria
and actinomycetes. While plant life is easily seen, most people would be surprised to discover
that the kinds and numbers of animals and microbes living in the soil far outnumber the plants
living on the soil surface. Together, the various soil organisms influence important factors
governing crop growth including tilth, drainage, fertility and disease.

ANIMALS (FAUNA)
Soil animals can be divided into the general categories of macrofauna and microfauna.
Macrofauna are the large, visible animals which include burrowing mammals, birds, worms,
slugs and insects. Microfauna are those which are only clearly visible under a microscope.

Macrofauna
Macrofauna affect soil mainly by burrowing through it. The movement of everything from
gophers to insects involves mixing and churning activities that loosen soils and create channels
which become pathways for air, water and roots. Some macrofauna may move substantial
amounts over organic matter deeper into the soil by feeding on vegetation at the soil surface
and excreting their wastes into the subsoil. Most soil animals move only tiny amounts of soil at
any one time, but the combined effect is equivalent to a complete mixing of topsoils every few
decades.
Earthworms are among the most important soil animals. Earthworms ingest a mixture of dead
organic matter and soil particles as they move through the soil. The mixture is partially digested
in their gut then excreted as castings. The castings are high in available nutrients and improve
soil structure by acting as a glue to increase aggregate stability.
Some animals have both beneficial and negative effects. Slugs, snails and some insects may
feed on living plant tissue. When the living food source is a farmer’s crop, the animal is
considered to be a crop pest.

Microfauna
The most important microfauna are protozoa and nematodes. Protozoa are single celled
animals which feed on tiny organisms such as bacteria and algae. They contribute in a small
way to the production of soil humus through the excretion of wastes and ultimately in their own
death.
Nematodes (sometimes called threadworms) include a vast array of tiny worm-like creatures
which feed on living or dead tissue. They are barely visible, varying in length from 0.5 to 4 mm.
Nematodes are generally a beneficial organism feeding on other microbes and the larvae of
insects. However, root knot nematodes cause serious damage to the roots of vegetable crops
including peas and carrots when present in high numbers.

PLANTS (FLORA)
Plants (flora) are unique organisms which contain chlorophyll that allows them to convert light
energy into chemical energy compounds via photosynthesis. Plants have a greater effect on soil
conditions than all other soil organisms. Macroflora impact the soil directly through the physical
and chemical actions of their roots. They also affect soils indirectly by contributing organic
matter when their life cycle is complete. Microflora (plants only visible with a microscope) affects
soils, but to a much lesser degree.

Macroflora
Plant roots explore the soil, exerting tremendous forces on the soil aggregates they encounter.
The growing roots shape the soil structure by creating a network of channels and by pressing
soil particles together into new arrangements. For example, fibrous roots of grasses will create a
porous, granular structure in compacted soils in only a few years by the exploring activity of their
roots.
The chemical activity of microflora is equally important in affecting soils. Macroflora take up
soluble inorganic nutrients such as nitrates and phosphates and convert them into organic
compounds as part of their tissues. Plants contribute important chemical compounds to the soil
in the rhizosphere (the area within about 1 mm of the root surface). Acids excreted from their
roots dissolve minerals which can then be taken up as a nutrients. The pH in the rhizosphere is
often as much as 2 pH units lower than the surrounding soil.
Organic compounds such as sugars, proteins, growth promoters and toxins are released into
the rhizosphere by plants. Sugars and proteins are in important food source for microbes, some
of whom are helpful in obtaining food for growing plants, while some others may secrete special
compounds that are toxins competing soil organisms. Most of the complex interactions between
plant roots and microbial organisms are only vaguely understood.

Microflora
The main microflora in soils are the chlorophyll containing algae which live near the soil surface,
where they can obtain light to be converted into energy compounds. Algae prefer moist fertile
soils. Algae has a relatively small impact on the total production of soil organic matter compared
to macro plants. However, they are very important in some soils by working symbiotically with
specific soil microbes to convert atmospheric nitrogen to plant available forms.

FUNGI, BACTERIA AND ACTINOMYCETES

In addition to plants, most of the remaining soil organisms are bacteria, fungi and
actinomycetes. Because they are generally visible, these organisms are not easily appreciated.
In fact, one teaspoon of soil may contain 500 million bacterial cells, over 1 million actinomycetes
and 25 meters of fungal mycelia (threadlike structures). Each of these classes of organisms are
made up of thousands of different species. This has allowed them to adapt to a tremendous
variety of food sources and soil conditions. Together they are involved in the decomposition of
dead organisms and the transformations of literally millions of different chemical compounds
into simple products used to build up new plant structures.
Besides feeding on dead organisms, some of them feed on living plants or animals as well,
causing disease. Others work in special symbiotic (mutually beneficial) relationships with plant,
providing some specific benefit to the plant in return for food.
Fungi
Fungi are the huge group of organisms that we associate with decomposition. Molds, mildews,
smuts, rusts and mushrooms are all visible examples of fungi. Fungi are single celled or
multicellular organisms which do not contain chlorophyll. Because they are unable to use the
sun’s energy to produce food, fungi must obtain their energy from other organisms, either dead
or alive.
Fungi are a very diverse group of organisms which are adapted to survival across a diverse set
of conditions. In general, fungi prefer an environment that is moist, well aerated and rich in fresh
organic matter. Fungi do well in soils with pH values between 6 and 8 but some are adapted to
pH levels well below 5. Fungi attack fresh organic matter by spreading threadlike structures
called hyphae throughout the food source and slowly devouring it. The hyphae are the
structures that can be seen on rotting materials.
Some fungi feed on living tissues and are responsible for common crop disease. Examples of
fungal diseases include rust, smut, leaf wilt, powdery mildew, leaf spots and root rust found on a
wide variety of crop on plants. Prevention of fungal diseases usually involves crop rotations to
non-susceptible plants in order to avoid the buildup of the particular fungus involved.
Mycorrhiza are a specific group of fungi that are of great benefit to plant growth. Mycorrhizae
form symbiotic relationships with plant roots. They attach to root cells where they obtain
nutrients from the plant. In return the fungi send out fine, threadlike filaments into the
surrounding soil to obtain nutrients, especially phosphorus which is given to the plant root.
Mycorrhizal fungi are believed to benefit a wide variety of crop plants including forage grasses,
legumes, cereals and many vegetables and fruits. A variety of Mycorrhizae exist in most soils,
but sometimes need to reintroduced to soils that have been fumigated or to soils where a crop
has been introduced for the first time.

Bacteria
Bacteria are among the smallest of all living organisms. They are made of single cells in the
shape of a rod, sphere or spiral less than 1 micron (1 millionth of a meter) in length. This means
that more than 10,000 bacteria could be lined up end to end in one centimeter.
Despite their small size, bacteria are so numerous and diverse that some type will be present
and functioning in virtually any environment. Bacteria have very short reproductive cycles which
allow them to double their populations in as little as thirty minutes. When environmental
conditions are unsuitable, they assume a dormant form which may be viable for many years
until suitable conditions for growth and reproduction return.
One of they ways of classifying bacteria is to group them as either autotrophs or heterotrophs
according to their source of carbon. Carbon is the primary element needed to create every kind
of organic compound in all living things.
1. Autotrophs take carbon directly from CO2 in the air and derive their energy by
oxidizing inorganic substances, including nitrogen and Sulphur compounds. Specific
autotrophic bacteria are responsible for the conversion of nitrites [NO2-] (which are
toxic to most plants) into nitrates [NO3-] which are the form of nitrogen preferred by
most plants. Another type of autotrophic bacteria converts elemental Sulphur S into
sulphate [SO2--] which can be used by plant.
2. Heterotrophs feed on organic carbon derived from dead or living organisms.
 Heterotrophic bacteria, along with fungi, are the main organisms involved in the
decomposition of organic structures, they free up nutrients which are ultimately
recycled for use by growing plants.
Another way of classifying bacteria is to group them as aerobic (require oxygen) or anaerobic
(do not require oxygen). The majority of the heterotrophs are aerobic, which is why
decomposition in a compost heap occurs at a faster rate when it is turned or stirred regularly to
allow fresh air to enter. Some decomposition will occur even under water, however, because of
the action of the anaerobic bacteria.
The gases released from decomposition by aerobic and anaerobic bacteria can be very
different. Aerobic bacteria evolve mostly CO2 and H2O. Anaerobic bacteria release large
amounts of carbon monoxide [CO] and methane [CH4] which are toxic to both plants and people
when they are present in high concentrations. Some of these toxic end products contribute to
putrid smell that comes from materials that have been decomposing in a closed space or deep
inside an unturned compost heap.
Rhizobium bacteria are a special kind of aerobic heterotrophs which “fix” atmospheric nitrogen
by converting N2 into ammonia [NH3]. In the soil this ammonia is quickly changed into
ammonium [NH4+], a nitrogen form that plants can use. The conversion from N2 to ammonia is
called nitrogen fixation. Rhizobium bacteria live symbiotically with the group of plants known as
legumes.
Rhizobium infect root cells, causing the formation of nodules within which they reproduce. The
plant supplies the nodules with carbohydrates as an energy source, and in return the rhizobium
converts N2 from the soil atmosphere into NH3 which is given to the plant. Legume crops are
commonly inoculated with potent varieties of rhizobium at seeding time to improve the level of
nitrogen fixation. Healthy legume crops will fix anywhere from 50 - 250 lbs of available N per
acre of crop per year. Typical rates of N fixation found in various legumes are given below.

Approximate Amounts of Nitrogen Fixed by Various Legumes Under Ideal Conditions

LEGUME CROP lb/ace of N FIXED PER GROWING SEASON

alfalfa 200

sweet clover 160

red clover 115

beans 40

Actinomycetes
Actinomycetes are somewhere between bacteria and fungi in structure. They are single celled,
yet they form branched structures with long filaments like some fungi. Actinomycetes are mainly
decomposers of organic matter and generally thrive in warm moist soils with neutral pH. They do
not tolerate acid soils the way fungi do, but they survive better in very dry conditions than fungi
or bacteria.
Actinomycetes are known to form symbiotic N-fixing relationships with a diverse range of plants.
These plants include alders, as well as many other species of trees and shrubs. The rice plant is
also known to benefit from nitrogen provided by specific actinomycetes. The N- fixing capacity of
actinomycetes is less well known that the rhizobium bacteria because it affects relatively few
crop plants, but it is very important to natural ecosystem. The establishment of plant life on the
barren surfaces left after glaciation was likely led by plants that received their nitrogen from
symbiotic relationships with these microbes.
Actinomycetes have become of the greatest interest to medical scientists since it was
discovered that they produce valuable antibiotics. Hundreds of antibiotics have been isolated
from actinomycete cultures including streptomycin.

OPTIMUM CONDITIONS FOR FUNGI, BACTERIA AND ACTINOMYCETES

Fungi, bacteria and actinomycetes are a very diverse group of organisms that include millions of
different species. The tremendous variation between them allows each to find their special niche
in an ecosystem where they are able to compete and survive. The diversity of their food
requirements and environmental adaptation ensures that some forms of organisms will be
present and functioning in nearly any soil condition imaginable.
While optimum conditions will vary between species, the factors of temperature, moisture, pH
and available food source are the main influences on microbial life in the soil.

Temperature
Microbial activity increases as temperatures rise. Most soil microbes found in western Canadian
soils do not function at temperatures below 5c and reach an optimum activity between 20c and
40c. Some special organisms are adapted to temperatures much colder or warmer than this.

pH
Most microbes function best in soils with a pH of near 7. A pH range between 6 and 8 is
acceptable for most microbes. Fungi and some specialized bacteria are comfortable at pH levels
below 5.

Food Source
Specific microbes feed on specific food sources among the variety of organic and inorganic
materials that are present in soils. In general, however, the presence of fresh organic material in
the soil provides suitable conditions for the greatest number of organisms.

Water
Aerobic organisms including the fungi, actinomycetes and most bacteria prefer moist, well
drained soils. Anaerobic organisms will become more active under flooded conditions where
aerobic organisms die or become dormant.

EFFECT OF SOIL MANAGEMENT PRACTICES ON SOIL ORGANISMS

Any field practices that disturb the soil or adds material to it will affect the organisms living there.
The impact of these field practices may be positive, negative or a mixture of both. The farming
practices that have the greatest impact are drainage, tillage, crop residue management and
fertilizer use.
Drainage
Well-drained soils contain less water and more oxygen than soils which drain poorly. Improving
the runoff of rainwater from the surface of poorly drained soils or bringing down high water
tables with subsurface drainage has a positive impact on the total life of the soil. Aeration
increases plant growth and consequently increases the amount of organic matter added as the
plants die. This organic matter provides a rich source of food for the aerobic decomposers
(fungi, actinomycete and many bacteria) which quickly convert the dead material into simple
plant nutrients
Poorly drained soils tend to be less productive before improvements are made. Anaerobic
bacteria thrive in warm, poorly drained soils convert available nitrogen and Sulphur nutrients into
gasses that are lost from the soil.

Tillage
Tillage practices darken the soil surface while incorporating oxygen and crop residues into the
soil. This leads to faster decomposition of organic matter. When summer fallow is practiced, soil
remains dark, aerated and most throughout one growing season and no new plant material is
added to the soil. Soil organic matter levels are normally lower on fields where summer fallow is
regularly practiced.
Research on zero tillage farming, where no cultivation is practiced, indicates that the amounts
and diversity of soil organisms increases dramatically when tillage is avoided. Earthworm
populations, for example, may increase by as much as a hundred times under zero tillage
conditions.

Crop Residue Management

Microbial activity is increased by the incorporation of crop residues beneath the surface.
Sometimes straw and chaff are removed from a field by grazing, baling or burning. When this
happens, the microbial food supply and long-term fertility of a soil may be reduced. Crop
rotations have a marked impact on the amounts and diversity of soil organisms since they
provide a more varied food source to the soil environment. Monocultures will favor the
development of a narrower range of soil organisms and may lead to the selection of specific
crop pests including disease and insects.

Fertilizer
The use of organic or inorganic fertilizers increases the amount of food for microbes and
increases their ability to provide simple nutrients for plant growth. Organic fertilizers like manure
and compost provide compostable food for the microbes which break it down into available
nutrients for plants. Inorganic fertilizers provide nutrients directly to the plants. This produces
more crop growth and consequently increases the amount of organic matter that is returned into
the soil after harvest.
PRACTICE QUESTIONS MODULE D1
1. What positive effect do earthworms have on soils?
Earthworm castings are rich in plant nutrients and also act as glues to form stable soil
aggregates.

2. Describe two main ways in which microplants affect soils.

Macro Plants shape soil structure with the tremendous forces of growing roots. They also affect
soil chemistry in rhizosphere, providing food for microbes and increasing the plant availability of
some nutrients.

3. What is the main function of fungi, bacteria and actinomycetes in soil systems?
Fungi, bacteria and actinomycetes are essentially involved in the decomposition of dead
organisms to provide simple chemical products used to build up new plant structures.

4. How do mycorrhizae and rhizobium benefit plant growth?

Mycorrhizae attach to the roots of some plants to increase their uptake of phosphorus.
Rhizobium live in nodules on the roots of legume plants where they “fix” atmospheric nitrogen
into a plant available form.

5. Define
a) macro animal - large animals which may burrow in soils
b) nematode - a microscopic thread-like worm which may be a parasite of some root caps
c) rhizosphere - the area immediately surrounding a plant root
d) mycorrhizae - a specific fungus which forms a symbiotic relationship with plant roots
e) rhizobium - a type of bacteria able to convert atmospheric N2 into NH3 in root nodules of
legume plants
f) nitrogen fixation - the conversion of atmospheric N2 into NH3 which is available to plants
g) autotroph - an organism able to use CO2 as a source of carbon
h) heterotroph - an organism that relies on organic matter to supply its carbon requirements
i) anaerobic - an organism which does not require O2 to survive

6. Name the four factors which are the main influence on microbial life in the soil.
Temperature, pH, food source, water.

7. Explain how tillage effects soil organisms.

Tillage incorporates oxygen and organic matter into the soil. This stimulates microbes that
decompose organic matter, but tend to reduce the diversity of organisms found in soils.