The Soil Food Web
Contributed by: paraniodpete
THE SOIL FOOD WEB
Unseen beneath our feet, there dwells a teeming microscopic
universe of complex living organisms that few humans ever consider. In
one teaspoon of soil alone, there may he over 600 million bacterial
cells. These bacterial cells exist in complex predator-prey
relationships with countless other diverse organisms. This topsoil food
web forms the foundation for healthy soil, healthy plants, and
ultimately, a healthy planet.
The soil food web is the community of organisms living all or part
of their lives in the soil. The food web has a basic set of expected
organisms groups, but the numbers of organisms and different species in
each group can vary significantly by plant and soil type.
Photosynthesizing living plant material provides the initial energy to
the soil food system through their roots. Living plant roots exude many
types of complex high-energy nutrient molecules into the surrounding
soil. Dead plant material is decomposed by bacteria and fungi, building
up even greater numbers of these organisms and their metabolic
products. As a plant grows, photosynthesis supplies much more than the
individual plant’s carbohydrate requirements. It has been documented
that plant roots can exude over 50 percent of the carbon fixed through
photosynthesis in the form of simple sugars, proteins, amino acids,
vitamins, and other complex carbohydrates.
pho•to•syn•the•size - synthesis of chemical compounds with the
aid of radiant energy and especially light; : formation of
carbohydrates from carbon dioxide and a source of hydrogen (as water)
in the chlorophyll-containing tissues of plants exposed to light
ORGANIC SOIL STRUCTURE
Around plant roots, bacteria form a slimy layer. They produce waste
products that glue soil particles and organic matter together in small,
loose clumps called aggregates. Threading between these aggregates and
binding them together are fine ribbon-like strands of fungal hyphae,
which further define and stabilize the soil into macro aggregates. It
is this aggregated soil structure, which looks a bit like spongy
chocolate cake that effectively resists compaction and erosion and
promotes optimal plant and microbial growth. Water and air are also
stored in the aggregate pores until needed.
Mycorrhizal fungi are especially effective in providing nutrients
to plant roots. These are certain types of fungi that actually colonize
the outer cells of plant roots, but also extend long fungal threads, or
hyphae, far out into the rhizosphere, forming a critical link between
the plant roots and the soil. Mycorrhizae produce enzymes that
decompose organic matter, solubilize phosphorus and other nutrients
from inorganic rock, and convert nitrogen into plant available forms.
They also greatly expand the soil area from which the plant can absorb
water. In return for this activity, mycorrhizae obtain valuable carbon
and other nutrients from the plant roots. This is a win-win mutualism
between both partners, with the plant providing food for the fungus and
the fungus providing both nutrients and water to the plant. The
importance of mycorrhizae in plant productivity and health has often
been overlooked. EXAMPLE Pines are not native to Puerto Rico and
therefore the appropriate mycorrhizal fungi were absent in the soil.
For years, people unsuccessfully tried to establish pines on the
island. The pine seeds would germinate well and grow to heights of 8 to
10 cm but then would rapidly decline. In 1955, soil was taken from
North Carolina pine forests, and the Puerto Rico plantings were
inoculated. Within one year, all inoculated seedlings were thriving,
while the un-inoculated control plants were dead. Microscopic analysis
showed that the healthy seedlings were well colonized by a vigorous
mycorrhizal population. While the benefits of mycorrhizae is not always
as dramatic, it has been well documented that mycorrhizal plants are
often more competitive and better able to tolerate environmental
The symbiotic association of the mycelium of a fungus with the roots of a seed plant.
hyphae (plural of hypha)
The microscopic, non-photosynthetic branching filaments that
collectively form the feeding structure of a fungus called the
The soil surrounding and directly influenced by plant roots and micro-organisms.
Compost in particular can improve soil nutritional availability and
soil tilth because of its complex microbial population. Composts bring
with them a wide array of bacteria, fungi, protozoa, nematodes and
micro arthropods, along with the food resources needed to feed these
organisms. However, not all composts have the same beneficial effects.
There are many different types of composts, as determined by their
original ingredients and their degree of maturity. The greater the
diversity of food resources in the original composted material, the
greater the diversity of microorganisms that can grow in that compost.
Soil from potted plants may be composted in the fall and used again the
following year. It is advantageous to leave the roots in the soil
rather than removing them, fostering the presence of beneficial
In general, the largest soil organisms are the first damaged by
soil compaction and disturbance. These include earthworms and small
insects, which are at the top of the soil food web and are essential to
keeping microbial populations in balance. When these organisms are
lost, an otherwise undisturbed soil will have the tendency to shift
from being fungal dominated to being more bacterially dominated. This
will alter nutrient availability and soil structure, effectively
limiting the types of plants that can grow. Some species of anaerobic
bacteria thrive in a soil deprived of oxygen and can produce chemical
metabolites, such as alcohols, aldehydes, phenols and ethylene, that
are toxic to plant roots and to other microorganisms. As compaction
continues to eliminate pore space, plant roots have difficulty
obtaining sufficient water, air and nutrients, placing them under
considerable stress. This stress, added to the shift in beneficial
organisms, will create a situation where plant pathogens may increase
rapidly and cause serious problems. No-till gardening methods can be
very useful in minimizing soil disturbance. When re-potting plants of
any kind, minimal disturbance to the root structure and soil is
Dr. Ingham and others in her field have found that plant roots,
well colonized by a mixture of different bacterial and fungal species,
are far more resistant to pathogenic attack. Mycorrhizal fungi form an
impenetrable physical barrier on the surface of plant roots, varying in
thickness, density and fungal species, according to the plant species,
plant health and soil conditions.
This layer of beneficial fungi plays a powerful role in disease
suppression, both through simple physical interference as well as
through the production of inhibitory products. Some species of fungi
that parasitize other fungi, such as Trichoderma, have been observed
physically attacking and destroying pathogenic fungi. Dr. William
Albrecht reported that Fusarium, a fungal species often maligned in its
role in many plant diseases, could actually be one of the most common
beneficial saprophytes in a healthy soil. He stated that the dividing
line between beneficial symbiosis and parasitism could be very narrow.
When Fusarium encounters a root that is poorly nourished or is under
stress, it can become rapidly pathogenic.
In healthy soil, unaltered by the application of lethal
agricultural chemicals, “microherds” groups of microbes colonize the
root zone or the rhizosphere of the plant. Most are beneficial bacteria
and fungi; they do not damage living plant tissue and are critical to
making essential minerals available to the plant. These microbes retain
large amounts of nitrogen, phosphorous, potassium, sulfur, calcium,
iron and many micronutrients in their bodies, preventing these
nutrients from being leached or removed by water runoff. Ideally, they
out-compete pathogenic species and form a protective layer on the
surface of living plant roots. It is usually only when the beneficial
species of bacteria and fungi are killed by continuous soil disturbance
and toxic chemicals that pathogenic species have an advantage.
As part of her research, Dr. Ingham has shown that herbicides,
pesticides and fertilizers have many non-target effects. The most
common pesticides are fairly broad spectrum; that is, they kill much
more than the target species. Residual pesticides that accumulate in
soil over many years may recombine and form new, unintentional
chemicals that have additional and often synergistic negative effects.
Out of the 650 active ingredients used to formulate most common
agricultural pesticides, only about 75 have been studied to deter mine
their effects on soil organisms. The remaining ingredients have never
been studied for their effects on the whole system or on any non-target
Scientists don’t fully understand the effect of any in individual
ingredient on soil life, much less the synergistic effects of the
ingredients, or combinational effects with inert or soil materials. It
is hardly surprising that a soil treated with numerous agricultural
chemicals lacks a healthy food web. When inorganic ammonium nitrate
fertilizer is applied to agricultural soil, ammonium and nitrate ions
are rapidly released into the soil solution. Nitrate ions are
negatively charged and can be quite mobile. The result is that a large
percentage of these nitrogen-containing ions may move rapidly out of
the plant root zone (rhizosphere) and into the groundwater. This
produces not only reduced plant growth but also environmental
pollution. Plants growing in unhealthy soil require additional
fertilizers and pesticides, furthering the deadly spiral.
PLANT GROWTH REGULATOR COMPOUNDS
In return for the release of nutritional substances from plant
roots, microbes themselves produce chemicals that stimulate plant
growth or protect the plant from attack. These substances include
auxins, enzymes, vitamins, amino acids, indoles and antibiotics. These
complex molecules are able to pass from the soil into plant cells and
be transported to other parts of the plant, with minimal change to
chemical structure, where they can stimulate plant growth and enhance
plant reproduction. They may also play a role in enhancing the
nutritional composition of the plant. The types of molecules released
are specific for a variety of plants grown under certain conditions,
forming in effect a unique chemical signature. As these molecules are
released into the rhizosphere, they serve as food and growth stimulants
for a certain mix of microbes. Dr. Joyce Loper, of the USDA
Agricultural Research Service, and other scientists have shown that for
each plant species, this characteristic chemical soup stimulates the
development of a select, beneficial company of root-dwelling microbes.
This microbial population colonizes the root zone, producing certain
chemicals that inhibit the growth of pathogenic species. These
organisms are also instrumental in supplying the plant’s unique
NUTRIENT CYCLING & RETENTION
Plants require many different mineral ions for optimal growth.
These must be obtained from the soil. Many nutrient ions are
solubilized from the parent rock material in a process known as
mineralization. Bacteria and fungi produce enzymes and acids necessary
to break down inorganic minerals and to convert them into stable
organic forms. Other nutrients are released through the decomposition
of organic matter. In all cases, a healthy, diverse microbial
population will develop with rapid decomposition of organic material
and will facilitate the recycling of nutrients. Organic matter is also
electrically charged and therefore critical to its ability to attract
and hold many different nutrient ions. The higher the organic matter in
the soil, the greater the ion holding capacity, resulting in reduced
leaching of either an ions or cations from the soil.
There is much competition for nitrogen among soil organisms. Those
organisms that have the best enzymes for grabbing nitrogen are usually
the winners. Bacteria possess the most effective nitrogen-grabbing
enzyme system, closely followed by many species of fungi. Plant enzyme
systems do not produce enzymes that operate outside the plant and
cannot compete well when there is strong competition for limited
nitrogen resources. In a healthy soil, this does not mean that the
plant will be deprived of adequate nitrogen. Bacteria require one
nitrogen atom to balance every five carbon atoms, and fungi require 10
carbons for each nitrogen. Therefore, the predator organisms that eat
bacteria and fungi get too much nitrogen for the carbon they require.
Since excess nitrogen is toxic, is excreted as a body waste product
back into the soil in a form that can be absorbed by plant roots.
Nitrogen is not the only nutrient effectively stored and recycled by
soil microbes. Carbon is the major constituent of all cells. When soils
are depleted of organic matter and healthy microbial populations, the
ability of a soil to hold carbon is destroyed and it enters the
atmosphere as carbon dioxide, now recognized as one of the greenhouse
gases that are responsible for breaking down the ozone layer.
There is little scientific evidence that bacteria and fungi simply
die and decompose. If another bacteria or fungus uses the dead cells
for a food source, there is no release of nitrogen. It is only when a
predator consumes excessive amounts of nitrogen in the dead cells that
it is released into the soil solution. It is this system of nitrogen
cycling that has worked brilliantly for the past million years.
HOW IS THIS INFORMATION USEFULL TO YOU AS A GROWER?
Mycorrhizal fungi will colonize the rhizosphere
of any plant, given the right conditions. These fungi are as
diverse as the stars in the sky, and many fungi are plant specific,
some are not. We have had great success with MJ inoculated with SC-27,
developed by Dr. Frank McKenna of Australia. We have also witnessed
mycelium from fungi on MJ roots, visible to the naked eye, develop over
time with no inoculation.
The problem with MJ, and so many plants, is that they are being
grown outside of their native soil environment, much like the southern
pines in Puerto Rico. Some plants adapt more readily to foreign
environments than others and are less dependent on the symbiotic
relationship that exists between plant and fungi. In nature, plants
grow in the same soil season after season, developing a "relationship"
so to speak with soil and its microscopic inhabitants.
It should be noted, that the regeneration of soil is beneficial to
the cultivation of fungi and bacteria. (Composting old soil from pots)
The benefits of organic cultivation simply cannot be measured. Try as
we might, there is no improving on Mother Nature.