This is most of the first chapter. Please offer critics. Right now, this
book (Teaming with Microbes) and "Omnivore's Dilemma" seem to give the
clearest sense of the direction that gardening and farming should be
going to get us off the dependancy on petroleum based pesticides and
fertilizers.
Again, thank to whoever turned me on to this book.

Teaming with Microbes by Jeff Lowenfels and Wayne Lewis

Chapter 1

What Is the Soil Food Web and
Why Should Gardeners Care?

Plants are in control

Most gardeners think of plants as only taking up nutrients through root
systems and feeding the leaves. Few realize that a great deal of the
energy that results from photosynthesis in the leaves is actually used
by plants to produce chemicals they secrete through their roots. These
secretions are known as exudates. A good analogy is perspiration, a
human's exudate. Root exudates are in the form of carbohydrates
(including sugars) and proteins. Amazingly, their presence wakes up,
attracts, and grows specific beneficial bacteria and fungi living in the
soil that subsist on these exudates and the_ cellular material sloughed
off as the plant's root tips grow. All this secretion of_ exudates and
sloughing-off of cells takes place in the rhizosphere, a zone
immediately around the roots, extending out about a tenth of an inch, or
a couple of millimeters (1 millimeter = 1/25 inch). The rhizosphere,
which can look _like a jelly or jam under the electron microscope,
contains a constantly changing mix of soil organisms, including
bacteria, fungi, nematodes, protozoa, and_ even larger organisms. All
this ³life" competes for the exudates in the rhizosphere, or its water
or mineral content.

At the bottom of the soil food web are bacteria and fungi, which are
attracted to and consume plant root exudates. In turn, they attract and
are eaten_ by bigger microbes, specifically nematodes and protozoa
(remember the_ amoebae, paramecia, flagellates, and ciliates you should
have studied in biology?), who eat bacteria and fungi (primarily for
carbon) to fuel their metabolic_ functions. Anything they don't need is
excreted as wastes, which plant roots are readily able to absorb as
nutrients. How convenient that this production of_ plant nutrients takes
place right in the rhizosphere, the site of root-nutrient_ absorption.
At the center of any viable soil food web are plants. Plants control the
food_ web for their own benefit, an amazing fact that is too little
understood and_ surely not appreciated by gardeners who are constantly
interfering with Nature's system. Studies indicate that individual
plants can control the numbers_ and the different kinds of fungi and
bacteria attracted to the rhizosphere by the exudates they produce
during different times of the growing season, populations of the
rhizosphere bacteria and fungi wax and wane, depending on the nutrient
needs of the plant and the exudates it produces.

Soil bacteria and fungi are like small bags of fertilizer, retaining in
their_ bodies nitrogen and other nutrients they gain from root exudates
and other _organic matter (such as those sloughed-off root-tip cells).
Carrying on the _analogy, soil protozoa and nematodes act as ³fertilizer
spreaders" by releasing ,_the nutrients locked up in the bacteria and
fungi ³fertilizer bags." The nematodes and protozoa in the soil come
along and eat the bacteria and fungi in the,_ rhizosphere. They digest
what they need to survive and excrete excess carbon_ and other nutrients
as waste.

Left to their own devices, then, plants produce exudates that attract
fungi_ and bacteria (and, ultimately, nematodes and protozoa); their
survival depends on the interplay between these microbes. It is a
completely natural system, the very same one that has fueled plants
since they evolved. Soil life provides the nutrients needed for plant
life, and plants initiate and fuel the cycle_ by producing exudates.

Soil life creates soil structure

The protozoa and nematodes that feasted on the fungi and bacteria
attracted_ by plant exudates are in turn eaten by arthropods (animals
with segmented_ bodies, jointed appendages, and a hard outer covering
called an exoskeleton). Insects, spiders, even shrimp and lobsters are
arthropods. Soil arthropods eat_ each other and themselves are the food
of snakes, birds, moles, and other animals. Simply put, the soil is one
big fast-food restaurant. In the course of all_ this eating, members of
a soil food web move about in search of prey or protection, and while
they do, they have an impact on the soil.

Bacteria are so small they need to stick to things, or they will wash
away; to_ attach themselves, they produce a slime, the secondary result
of which is that_ individual soil particles are bound together (if the
concept is hard to grasp,_ think of the plaque produced overnight in
your mouth, which enables mouth_ bacteria to stick to your teeth).
Fungal hyphae, too, travel through soil particles, sticking to them and
binding them together, thread-like, into aggregates.

Worms, together with insect larvae and moles and other burrowing
animals, move through the soil in search of food and protection,
creating path-_ways that allow air and water to enter and leave the
soil. Even microscopic_ fungi can help in this regard (see chapter 4).
The soil food web, then, in addition to providing nutrients to roots in
the rhizosphere, also helps create soil_ structu the activities of
its members bind soil particles together even as they_ provide for the
passage of air and water through the soil.

Soil life produces soil nutrients

When any member of a soil food web dies, it becomes fodder for other
members of the community. The nutrients in these bodies are passed on to
other_ members of the community. A larger predator may eat them alive,
or they may _be decayed after they die. One way or the other, fungi and
bacteria get involved,_ be it decaying the organism directly or working
on the dung of the successful_ eater. It makes no difference. Nutrients
are preserved and eventually are retained in the bodies of even the
smallest fungi and bacteria. When these are in_the rhizosphere, they
release nutrients in plant-available form when they, in_ turn, are
consumed or die.

Without this system, most important nutrients would drain from soil.
Instead, they are retained in the bodies of soil life. Here is the
gardener's truth: when you apply a chemical fertilizer, a tiny bit hits
the rhizosphere, where it is absorbed, but most of it continues to drain
through soil until it hits the water table._ Not so with the nutrients
locked up inside soil organisms, a state known as immobilization; these
nutrients are eventually released as wastes, or mineralized._ And when
the plants themselves die and are allowed to decay, the nutrients they_
retained are again immobilized in the fungi and bacteria that consume
them.

The nutrient supply in the soil is influenced by soil life in other
ways. For example, worms pull organic matter into the soil, where it is
shredded by_ beetles and the larvae of other insects, opening it up for
fungal and bacterial_ decay. This worm activity provides yet more
nutrients for the soil community.

Healthy soil food webs control disease

A healthy food web is one that is not being destroyed by pathogenic and_
disease-causing organisms. Not all soil organisms are beneficial, after
all. As_ gardeners you know that pathogenic soil bacteria and fungi
cause many plain_ diseases. Healthy soil food webs not only have
tremendous numbers of individual organisms but a great diversity of
organisms. . . . Perhaps 20,000 to 30,000 different species make up
its billion bacteria-a healthy population in numbers and diversity.
A large and diverse community controls troublemakers. . . . they
compete with them for exudates and other nutrients, air, water,_ and
even space. If the soil food web is a healthy one, this competition
keeps the_ pathogens in check; they may even be outcompeted to their
death.

Just as important, every member of the soil food web has its place in
the_ soil community. Each, be it on the surface or subsurface, plays a
specific role._ Elimination of even just one group can drastically alter
a soil community. . . . . A healthy soil_ food web won't allow one set
of members to get so strong as to destroy the web._ If there are too
many nematodes and protozoa, the bacteria and fungi on_ which they prey
are in trouble and, ultimately, so are the plants in the area.

And there are other benefits. The nets or webs fungi form around roots
act_ as physical barriers to invasion and protect plants from pathogenic
fungi and_ bacteria. Bacteria coat surfaces so thoroughly, there is no
room for others to attach themselves. If something impacts these fungi
or bacteria and their numbers drop or they disappear, the plant can
easily be attacked.

Special soil fungi, called mycorrhizal fungi, establish themselves in a
symbiotic relationship with roots, providing them not only with-physical
protection but with nutrient delivery as well. In return for exudates,
these fungi provide water, phosphorus, and other necessary plant
nutrients. Soil food web _populations must be in balance, or these fungi
are eaten and the plant suffers.

Bacteria produce exudates of their own, and the slime they use to attach
to_ surfaces traps pathogens. Sometimes, bacteria work in conjunction
with fungi_ to form protective layers, not only around roots in the
rhizosphere but on an_ equivalent area around leaf surfaces, the
phyllosphere. Leaves produce exudates that attract microorganisms in
exactly the same way roots do; these act_ as a barrier to invasion,
preventing disease-causing organisms from entering_ the plant's system.
Some fungi and bacteria produce inhibitory compounds, things like
vitamins and antibiotics, which help maintain or improve plant health;
penicillin_ and streptomycin, for example, are produced by a soil-borne
fungus and a soil borne bacterium, respectively.

All nitrogen is not the same

Ultimately, from the plant's perspective anyhow, the role of the soil
food web_ is to cycle down nutrients until they become temporarily
immobilized in the bodies of bacteria and fungi and then mineralized.
The most important of _these nutrients is nitrogen-the basic building
block of amino acids and,_ therefore, life. The biomass of fungi and
bacteria (that is, the total amount of_ each in the soil) determines,
for the most part, the amount of nitrogen that is_ readily available for
plant use.

It wasn't until the 1980s that soil scientists could accurately measure
the_ amount of bacteria and fungi in soils. Dr. Elaine Ingham at Oregon
State University along with others started publishing research that
showed the ratio of_ these two organisms in various types of soil. In
general, the least disturbed soils_(those that supported old growth
timber) had far more fungi than bacteria,_ while disturbed soils
(rototilled soil, for example) had far more bacteria than_ fungi. These
and later studies show that agricultural soils have a fungal to
bacterial biomass (F:B ratio) of 1:1 or less, while forest soils have
ten times or more_ fungi than bacteria.

Ingham and some of her graduate students at OSU also noticed a
correlation between plants and their preference for soils that were
fungally dominated_ versus those that were bacterially dominated or
neutral. Since the path from_ bacterial to fungal domination in soils
follows the general course of plant succession, it became easy to
predict what type of soil particular plants preferred_ by noting where
they came from. In general, perennials, trees, and shrubs prefer
fungally dominated soils, while annuals, grasses, and vegetables prefer
soils_ dominated by bacteria.

One implication of these findings, for the gardener, has to do with the
nitrogen in bacteria and fungi. Remember, this is what the soil food web
means _to a plant: when these organisms are eaten, some of the nitrogen
is retained by_ the eater, but much of it is released as waste in the
form of plant-available ammonium (NH3). Depending on the soil
environment, this can either remain as_ ammonium or be converted into
nitrate (NO3,) by special bacteria. When does_ this conversion occur?
When ammonium is released in soils that are dominated by bacteria. This
is because such soils generally have an alkaline pH_(thanks to bacterial
bioslime), which encourages the nitrogen-fixing bacteria to thrive. The
acids produced by fungi, as they begin to dominate, lower the pH_ and
greatly reduce the amount of these bacteria. In fungally dominated
soils, much of the nitrogen remains in ammonium form.

Ah, here is the rub: chemical fertilizers provide plants with nitrogen,
but_ most do so in the form of nitrates (NO3). An understanding of the
soil food_ web makes it clear, however, that plants that prefer fungally
dominated soils ultimately won't flourish on a diet of nitrates. Knowing
this can make a great deal_ of difference in the way you manage your
gardens and yard. If you can cause_ either fungi or bacteria to
dominate, or provide an equal mix (and you can-_just how is explained in
Part 2), then plants can get the kind of nitrogen they prefer, without
chemicals, and thrive.

Negative impacts on the soil food web

Chemical fertilizers negatively impact the soil food web by killing off
entire_ portions of it. What gardener hasn't seen what table salt does
to a slug? Fertilizers are salts; they suck the water out of the
bacteria, fungi, protozoa, and_ nematodes in the soil. Since these
microbes are at the very foundation of the_ soil food web nutrient
system, you have to keep adding fertilizer once you start_ using it
regularly. The microbiology is missing and not there to do its job,
feeding the plants.

It makes sense that once the bacteria, fungi, nematodes, and protozoa
are_ gone, other members of the food web disappear as well. Earthworms,
for example, lacking food and irritated by the synthetic nitrates in
soluble nitrogen_ fertilizers, move out. Since they are major shredders
of organic material, their_ absence is a great loss. Without the
activity and diversity of a healthy food web, you not only impact the
nutrient system but all the other things a healthy soil_ food web
brings. Soil structure deteriorates, watering can become problematic,"_
pathogens and pests establish themselves and, worst of all, gardening
becomes_ a lot more work than it needs to be.

If the salt-based chemical fertilizers don't kill portions of the soil
food web, rototilling will. This gardening rite of spring breaks up
fungal hyphae, decimates worms, and rips and crushes arthropods. It
destroys soil structure and_ eventually saps soil of necessary air.
Again, this means more work for you in_ the end. Air pollution,
pesticides, fungicides, and herbicides, too, kill off important members
of the food web community or ³chase" them away. Any chain_ is only as
strong as its weakest link: if there is a gap in the soil food web, the
system will break down and stop functioning properly.

Healthy soil food webs benefit you and your plants

Why should a gardener be knowledgeable about how soils and soil food
webs_ work? Because then you can manage them so they work for you and
your_ plants. By using techniques that employ soil food web science as
you garden,_ you can at least reduce and at best eliminate the need for
fertilizers, herbicides,_ fungicides, and pesticides (and a lot of
accompanying work). You can improve_ degraded soils and return them to
usefulness. Soils will retain nutrients in the_ bodies of soil food web
organisms instead of letting them leach out to God_ knows where. Your
plants will be getting nutrients in the form each particular_ plant
wants and needs so they will be less stressed. You will have natural
disease prevention, protection, and suppression. Your soils will hold
more water.

The organisms in the soil food web will do most of the work of
maintaining plant health. Billions of living organisms will be
continuously at work_ throughout the year, doing the heavy chores,
providing nutrients to plants,_ building defense systems against pests
and diseases, loosening soil and increasing drainage, providing
necessary pathways for oxygen and carbon dioxide._ You won't have to do
these things yourself.

Gardening with the soil food web is easy, but you must get the life back
in_ your soils. First, however, you have to know something about the
soil in which_ the soil food web operates; second, you need to know what
each of the key_ members of the food web community does. Both these
concerns are taken up_ in the rest of Part 1.
--
Billy
Coloribus gustibus non disputatum (mostly)