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2023
The Transi琀椀on to
Organic Partnership
Program (TOPP)
Prepared for USDA Organic by Acres U.S.A.
www.acresusa.com | 1
Managing Soil Biology for
Organic Farming
SOIL MICROBES ARE INDISPENSABLE FOR PLANT NUTRITION, AND MANAGING THEM REQUIRES
A FOCUS ON KEEPING THE SOIL COVERED AND ELIMINATING COMPACTION
Bradyrhizobium is a type of nitrogen-昀椀xing bacteria.
oil is alive. This is an idea
that seems to have been
known to our ancestors,
forgo琀琀en for a few genera琀椀ons, and
recently relearned. It’s an important
concept that’s beginning to be
reclaimed.
From bacteria and fungi to archaea,
S
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nematodes and higher-level organisms like worms and beetles, the soil
is teeming with life. And while this
microbial community is extremely
resilient, the ac琀椀ons of farmers have
a profound e昀昀ect on it. Irriga琀椀on,
琀椀llage, fer琀椀liza琀椀on and other interven琀椀ons each either strengthens or
weakens the microbial community.
As soil-biology pioneer Bruce Tainio
said, “Everything in this universe is
connected to everything else. You
cannot isolate one mineral, soil, microbe, plant, animal, or human component and treat that component as
though the others don’t exist.”
PHOTO FROM CANVA
complicated than this, and it’s only
within recent years that we’ve even
had this elementary understanding of
what’s happening in the soil between
microbes and plants.
RHIZOPHAGY
Wheat plants grown from seed without bacteria (le昀琀) and with (right).
HOW SOIL MICROBES INTERACT
WITH PLANTS
There are many di昀昀erent types of
soil microbes, from bacteria and protozoa to fungi, nematodes, and even
worms and beetles. More important
than understanding the physical characteris琀椀cs of these organisms, which
are mostly invisible to the naked eye,
is understanding their func琀椀ons and
how they interact with plants.
The simplest way of explaining
how microbiology helps plants is that
plants, when in need of a certain nutrient, exude sugars, combined with
molecules that communicate their
exact need. They send these compounds out of their roots as signals
to nearby microorganisms (bacteria,
fungi, etc.), telling them what they
need. Those microbes then use the
sugar to feed themselves; in fact, the
plant gives the them not just sugar
but a complete range of primary metabolites — the organic compounds
that are necessary for all life. These
include carbohydrates (sugars), lipids,
proteins and nucleic acids. The exact
metabolites the plant sends out is
probably its way of a琀琀rac琀椀ng the speci昀椀c microorganisms that are able to
give it the nutrients it needs.
If the microbe doesn’t already have
the nutrient the plant needs, it 昀椀nds
it within the soil and transforms the
nutrient from whatever chemical
structure it’s in into a chemical structure that is available to the plant (the
plant can’t use, for example, nitrogen
when it’s in certain molecular combina琀椀ons). The microbe then gives that
newly available nutrient to the plant.
The whole process is much more
Within the past decade, groundbreaking work has been done to help
us further understand how bacteria
provide nutrients to plants. This work,
led by Dr. James White at Rutgers University, discovered what’s called the
rhizophagy cycle. “Rhizo” means root,
and “phagy” means to eat — this is
the process whereby bacteria actually
enter roots (are “eaten” by them).
Insert Bacteria in root (Courtesy of
Dr. James White and Rutgers University): Figure 1: Bacteria inside a plant.
Within the root, the plant bombards
the bacterial cell with reac琀椀ve oxygen
molecules that a琀琀ack the cell wall of
the bacteria. Some bacteria are completely broken apart and become food
for the plant in their en琀椀rety. Serendipitously, it turns out that the bodies
of bacteria are on average 10-2-2 plus
traces — a perfect NPK fer琀椀lizer, along
Bacteria inside a plant.
PHOTOS COURTESY OF DR. JAMES WHITE AND RUTGERS UNIVERSITY
www.acresusa.com | 3
with all the necessary trace minerals.
The bacteria that don’t die inside
the plant are simply damaged, giving
o昀昀 some of the nutrients they had
collected for the plant, but remaining
alive. The plant then pushes these bacteria out of the plant at the 琀椀ps of root
hairs in a process that simultaneously
elongates the root hairs. The bacteria
go back to work mining nutrients for
the plant, comple琀椀ng the cycle.
The results of the rhizophagy process are that the plant is fed the nutrients it needs and also becomes more
tolerant against oxida琀椀ve stressors.
Addi琀椀onally, because bacteria involved in the cycle are taking some
nutrients not just from the soil but
also from fungi in the soil, those fungi
that are pathogenic become less virulent and are thus less dangerous to
the plant.
This is another major func琀椀on of
soil microbes: protec琀椀ng the plant
from disease. We should keep in mind
that all organisms play important
func琀椀ons; it’s only when they get out
of balance that problems arise. Robust soil microbiology helps keep the
bene昀椀cial and the virulent organisms
in check so that the “pests” can s琀椀ck
to performing the role they’re intended for — decomposing dead organisms so that new ones can thrive.
MANAGING SOIL BIOLOGY
The best farm managers oversee
soil biology in the same way that a
lab technician manages a petri dish:
by a琀琀emp琀椀ng to provide the perfect
environment that will enable the biology to thrive. On the farm, this means
three things:
Providing op琀椀mal temperature.
Microbial enzymes — molecules used
by all organisms as catalysts in the produc琀椀on of other necessary compounds
— are denatured at 105 degrees Fahrenheit. This highlights how cri琀椀cal it is
to keep soil covered. Bare, uncovered
(琀椀lled) soil can reach temperatures of
150 F on the surface and 110 F three
inches deep. In this situa琀椀on — not uncommon in the summer on bare soil in
between crops — there would be zero
microbial ac琀椀vity in the 昀椀rst few inches
of soil (the most important ones) — no
nitrogen 昀椀xa琀椀on, no transferring of nutrients to plants, etc.
Providing good gas exchange. The
common understanding is that plant
roots need to have loose soil in order to be able to breath. Actually, it’s
the microbes in the soil that require
gases from the environment in order
to thrive. Nitrogen and oxygen gases need to be constantly available
to microbes from the air, and the
carbon dioxide the microbes create
needs to be able to escape the soil so
it can be used by the plant above for
photosynthesis.
The problem on many agricultural
昀椀elds is that compac琀椀on layers often prevent this gas exchange from
happening. This is unfortunately
even the case on no-琀椀ll opera琀椀ons.
Reducing 琀椀llage is important — con-
The Rhizophagy Cycle
4 | Copyright Acres U.S.A.
DIAGRAM COURTESY OF DR. JAMES WHITE AND RUTGERS UNIVERSITY
Cover crops are essen琀椀al for covering the soil and protec琀椀ng microbial life.
stantly churning up the soil destroys
biological life, par琀椀cularly fungi, with
their delicate networks that transports nutrients to plants. However,
reduced/no-琀椀ll prac琀椀ces must be
balanced against the unavoidable
impact of compac琀椀on from never 琀椀lling. Although it is true, given a very
long period of 琀椀me, that biology and
cover crops should be able to overcome compac琀椀on (if the 昀椀eld is never driven over), a be琀琀er solu琀椀on is
occasional deep ripping — running a
shank spaced every few feet through
the 昀椀eld once every couple years. This
breaks up the layer that prevents the
penetra琀椀on of both roots and vital
gases — i.e., that prevents life beneath a certain depth.
Providing adequate water. The microbes in the soil essen琀椀ally live in a
sub-aqua琀椀c environment. Abundant
water must be present in the soil aggregates in order for biology to thrive.
The task for the farmer, then, is to
provide both enough irriga琀椀on when
there isn’t rain and — par琀椀cularly in
dryland farming, but really in every
situa琀椀on — to provide good soil aggregate structure, which allows moisture to move within the soil. Like the
PHOTO FROM CANVA
points above, this primarily means
keeping the soil covered and eliminating compac琀椀on as much as possible.
SOIL BIOLOGY TESTING
Growers have successfully nurtured
thriving biological communi琀椀es for
thousands of years without having
any way of measuring the organisms
in their soil. Within the past decade
or two, microbe measurement has
become available to farmers. While
the technology is s琀椀ll in its infancy, it
can be pro昀椀tably used to be琀琀er understand what’s happening in the soil
and how management decisions help
or hurt soil microbes.
One of the simplest forms of biological tes琀椀ng is microscopy. Take a soil
sample, put it on a slide, and look at it
under a microscope. This method provides undeniable results — you can
see the bacteria and fungi with your
own eyes — but it is not quan琀椀ta琀椀ve,
and it su昀昀ers from needing to have a
decent amount of training to know
what you’re looking at, par琀椀cularly
since the vast majority of microbial
species are uniden琀椀昀椀ed.
A di昀昀erent method is a PLFA
(phospholipid fa琀琀y acid) test. This
test measures chemical signals that
arise from di昀昀erent groups of microbes — fungi (arbuscular vs. saprophy琀椀c), bacteria (gram-posi琀椀ve vs.
gram-nega琀椀ve) and protozoa. It also
provides the fungal:bacterial ra琀椀o,
which can help a grower discern the
state of their soil (perennial crops
and grasslands perform be琀琀er with
fungal-dominated soils; annual crops
prefer bacterial soils).
Another new test on the market
is the Haney test, which, along with
providing other metrics like amount
of available nitrogen, measures microbial respira琀椀on. In other words, it
doesn’t measure microbes directly,
but it does give the farmer a general
benchmark on how much microbial
ac琀椀vity is going on underground.
Finally, the newest type of microbial
measurement is the DNA test. It provides a comprehensive analysis of all
the DNA of the biology that’s in the
soil, iden琀椀fying the millions of di昀昀erent species — both pathogens and
bene昀椀cials (although all living organisms can be either good or bad, depending on the context) — and categorizing them into func琀椀onal groups.
It has the power to tell growers things
like “your nitrogen-昀椀xing bacteria are
low” or “you have plenty of phosphorus-solubilizing bacteria.” This
Labs that offer soil
microbial testing:
Microscopy tes琀椀ng —
Soil Food Web
(h琀琀ps://www.soilfoodweb.com)
PLFA and Haney tes琀椀ng —
Regen Ag Lab
(h琀琀ps://regenaglab.com)
DNA tes琀椀ng — Biome Makers
(h琀琀ps://biomemakers.com)
www.acresusa.com | 5
method of tes琀椀ng holds enormous
promise, although since it’s new, the
benchmarks are only now being established. It’s also expensive — about
$200 per test.
The same equipment that analyzes
the DNA of humans and any other
living thing can be used to determine
the microbial makeup of the soil, providing organic farmers a glimpse into
the bacteria, fungi and other organisms in their soil and giving them an
opportunity to try to grow and/or alter those communi琀椀es.
THE FUTURE OF FARM MICROBIAL
MANAGEMENT
Is it possible to provide 100 percent
of a crop’s nutri琀椀onal requirements
through soil biology? Agronomists
Learn more about soil biology:
Advancing Biological Farming
by Gary Zimmer
The Farm as Ecosystem
by Jerry Brune琀�
The Regenera琀椀ve Agriculture Podcast,
hosted by John Kempf
Teaming with Bacteria, Teaming with Fungi, Teaming with Microbes
and Teaming with Nutrients
by Je昀昀 Lowenfels
disagree, and certainly in very sandy
soils, or soils that for some reason
don’t have even unavailable supplies
of one or more nutrients, this won’t
be achievable. But many growers certainly could supply more of their nutri琀椀onal requirements via biology.
Ecological farming is a process. It
takes 琀椀me, but posi琀椀ve changes build
upon each other — although o昀琀en
more slowly than we’d like!
Improving soil biology is like the old
adage about trees: the best 琀椀me to
start working to improve soil biology
was twenty years ago, but the second-best 琀椀me is right now.
This ar琀椀cle was wri琀琀en by Acres U.S.A., in coordina琀椀on with the Organic Crop Improvement Associa琀椀on
(OCIA) Interna琀椀onal. OCIA is the TOPP administrator for the Plains Region. This ar琀椀cle is supported
through the United States Department of Agriculture
(USDA) Transi琀椀on to Organic Partnership Program
(TOPP). TOPP is a program of the USDA Organic Transi琀椀on Ini琀椀a琀椀ve and is administered by the USDA Agricultural Marke琀椀ng Service (AMS) Na琀椀onal Organic
Program (NOP).
6 | Copyright Acres U.S.A.
PHOTO COURTESY OF BIOME MAKERS