How to Cultivate Indigenous Microorganisms

Aug. 2008
How to Cultivate Indigenous Microorganisms
Hoon Park1 and Michael W. DuPonte2
Ocean Star Hawaii Natural Farms, LLC
CTAHR Department of Human Nutrition, Food and Animal Sciences, Komohana Extension Office
ast trends in conventional western agriculture, including monoculture without crop rotation, overuse
of inorganic fertilizers, and wide-scale applications of
broad-spectrum organophosphate pesticides, have hindered the role of naturally occurring microorganisms in
promoting biological nitrogen fixation and decomposition of organic matter, microbiologically enhanced plant
nutrient uptake, and other natural soil processes that
depend on active soil microbe populations.
The current trend in U.S. agriculture, including
Hawai‘i agriculture, is toward less chemically intensive,
more biologically based practices, in the hope that they
may improve soil health and agricultural production and
be less harmful to the environment than conventional
agricultural production methods. In Asian countries,
including Korea, deliberate collection and culturing of
naturally occurring soil microorganisms has been a common agricultural practice for centuries, and application
of these cultures to crop soils is believed to minimize
the need for applications of inorganic soil amendments.
However, little scientific documentation of the benefits
of these practices exists. This publication outlines the
principal steps in culturing naturally occurring microorganisms in a process similar to one used on farms in
Korea. Those wishing to culture and utilize microorganisms in this way should be aware that the value of
the techniques and applications described has not been
verified in Hawai‘i by controlled experiments. Therefore,
the practices described in this publication should be
considered as suggested, rather than recommended.
Collecting microorganisms from the
When is the best time to collect microorganisms?
Microorganisms (microbes) may be cultured at any time
of the year; however, avoid wet, rainy seasons. Excessive
moisture in the environment promotes growth of fungi
that are less desirable for the intended uses.
How time-consuming is it to collect these
The collection process takes approximately 4–5 days in
cooler weather (about 68°F, 20°C) and 3–4 days under
warmer conditions (> 68°F, 20°C).
Where are the best places to collect
Beneficial microbes are highly concentrated under undisturbed forests or other vegetated areas. Combining
microbes collected from multiple sites will likely result
in a more robust culture.
What collection supplies will I need?
Collection materials are relatively inexpensive and readily obtainable.
• a small wooden box, 12 x 12 x 4 inches deep, preferably made of cedar (photo 1)
• steamed white rice
• white paper towels, enough to cover the wooden box
• two to four large rubber bands
• a sheet of clear plastic, large enough to completely
cover the wooden box
• 1 ⁄4-inch mesh wire screen large enough to completely
cover the wooden box.
Published by the College of Tropical Agriculture and Human Resources (CTAHR) and issued in furtherance of Cooperative Extension work, Acts of May 8 and June 30, 1914, in cooperation with the U.S. Department of Agriculture. Andrew G. Hashimoto, Director/Dean, Cooperative Extension Service/CTAHR, University of Hawai‘i at Mänoa, Honolulu, Hawai‘i 96822.
An equal opportunity/affirmative action institution providing programs and services to the people of Hawai‘i without regard to race, sex, age, religion, color, national origin, ancestry, disability, marital status, arrest and court record, sexual orientation, or status as a covered veteran. CTAHR publications can be found on the Web site <>.
How to Cultivate Indigenous Microorganisms
How are collection supplies assembled?
Fill the wooden box with 3 inches of steamed rice (photo
2). Cover the box with white paper towel, being careful
not to let the towel touch the rice (photo 3). There should
be an inch or so of air space between the rice the paper
towel. Use rubber bands around the top of the box to
secure the paper towel in place.
Cover the top of the box with wire screen (photo 4) to
prevent animals from tampering with the rice. Top the
wire with a sheet of clear plastic to protect the box from
rain, and place it under trees or in another secluded area.
The box should not be in direct sunlight.
Partially bury the box in the soil (photo 5). It should
be buried at least 2 inches deep for best results.
Cover the box with fallen leaves from the harvest location (photo 6). Anchor the plastic sheet on all sides with
small rocks to prevent it from being dislodged by wind.
Leave the box undisturbed for a minimum of 4–5
days. After that time, check to see whether the moist rice
is covered with white mold. If mold growth is sparse,
re-cover the box and wait an additional 2–3 days before
re-checking. If the mold is a color other than white (other
colors indicate growth of less effective fungi) or if rain
has entered the box, the contents should be discarded
and the process repeated.
Culturing the microorganisms
Once the desired microbes have been collected, the next
step is to increase their numbers.
What materials are necessary for culturing?
The basic supplies for microbe culturing are
• a clean clay pot (hard-fired, glazed, or terra cotta)
• a wooden spoon
• white paper towels
• rubber bands
• a large clear bowl, big enough to hold contents of rice
• a small food scale
• a straw mat
• a shovel
• a composting thermometer
• raw, granulated brown sugar
• wheat mill run* or, if available, mushroom growth
medium waste.
*Wheat mill run (WMR), also called “wheat midds” or
“middlings,” is the materials remaining after flour, or
BIO-9 — Aug. 2008
semolina, is extracted from wheat or durum during milling. WMR generally includes ground screenings from
cleaning; remnant particles of bran, germ, and flour; and
other offal from the milling process. In Hawai‘i, the basic
source of WMR is Hawaiian Flour Mill in Honolulu (808
527-3215), a subsidiary of Pendleton Flour Mills; they
sell it by the truckload or containerload, and in pallets of
various sizes of packaged containers (60-pound bags, and
larger) to the livestock industry (for feed), garden supply
stores (for bokashi compost), and mushroom farms (for
growing medium).
How are the materials assembled to cultivate
1)Weigh and record the weight of the large bowl.
2)Use the wooden spoon to move the molded rice from
the wooden box into the bowl (photos 7, 8). Weigh the
filled bowl and calculate the weight of the rice mass
by subtracting the weight of the empty bowl from the
filled bowl.
3)Gradually add an amount of granulated brown sugar
equal to the weight of the rice mass (photo 9). Handknead the sugar and rice until the material has the
consistency of gooey molasses (photo 10). Protective
gloves are suggested.
4)Fill the clean clay pot two-thirds full with the rice/
sugar mixture (photos 11, 12). Cover it with paper
towel secured in place with rubber bands (photo 13).
5)Store the pot in a cool area away from direct sunlight
for 7 days. This will allow the mixture to ferment.
6)Working in a shaded area (photo 14), add a small
amount of water to the fermented rice mixture in
a 1:500 ratio. Then, slowly blend in wheat mill run
(or used mushroom medium) until mixture is of
semi-moist but not wet consistency (roughly 65–70%
moisture) (photos 15–17).
7)Place a mound of the mixture on a soil surface and
cover it with the straw mat or leaves, protecting it from
sunlight (photo 18). Allow the microbes to propagate
for 7 days. Periodically examine the external surface
of the pile for white mold growth, monitor internal
temperature of the pile with a composting thermometer so as not to exceed 122°F (50°C), and turn the
pile with a shovel (a minimum of three to four times
during the week) to keep fermentation temperatures
from getting too high.
8)When the fermentation process is finished, internal
temperature will stabilize, indicating cultivation is
How to Cultivate Indigenous Microorganisms
BIO-9 — Aug. 2008
How to Cultivate Indigenous Microorganisms
BIO-9 — Aug. 2008
How to Cultivate Indigenous Microorganisms
BIO-9 — Aug. 2008
How to Cultivate Indigenous Microorganisms
finished. Your culture of naturally occurring microorganisms is now ready for use (photos 19, 20).
What do I do with the fermented mixture?
Dilute the final product (1 to 1 by volume) with soil and
incorporate this mixture into the surface soil as a topdressing for crop production, or add it to your compost
pile. This biological soil amendment is expected to enhance soil microorganism activity. For more information,
please contact the author ([email protected]).
The project team thanks the Farm Pilot Project Coordination, Inc (FPPC) and the CTAHR Integrated Pest
Management (IPM) Project for providing funding for
the production of this publication. The team also thanks
Ruth Niino-DuPonte, Glenn Sako, Luisa Castro, and
Piper Selden for their constructive comments and suggestions.
BIO-9 — Aug. 2008
Kyu, Cho Han. Natural farming. 2003. Janong Natural
Farming Institute, Chungbuk, Republic of Korea.
Szmanski, N., and R.A. Patterson. 2003. Effective microorganisms (EM) and waste management systems in
future directions for on-site systems: Best management
practice. Proceedings of the On-site ’03 Conference,
University of New England, Lanfax Laboratories
Armidale. ISBN 0-9579438-1-4 p. 347–354.
Mazzola, M. 2004. Influence of plant genotype on development of interactions with non-symbiotic plant
beneficial soil microorganisms. Research Signpost:
Research Developments in Agricultural and Food
Chemistry. 37:103–122.
Kirk, J.L., L.A. Beaudette, M. Hart, P. Moutoglis, J.N.
Klironomos, H. Lee, and J.T. Trevors. 2004. Methods
of studying soil microbial diversity. Journal of Microbiological Methods 58:169–188.
Natural Farming Primer
Written by Jackie Prell
Wednesday, 24 March 2010 14:11
Master Cho mixes it up with research results, philosophy, and humor at the Feb. 26 - March 4,
2010 workshop in Hilo.
What if the best fertilizer was under your feet? What if you could make a product similar to EM
and Bokashi simply and cheaply? Well, you can. It’s been happening in South Korea for
decades and we have been fortunate to learn the basics here in Hawaii. Four years ago we
bought a farm on the Big Island with soil that was flooded for more than seventy years with
herbicides, fungicides, and arsenic: the usual arsenal of chemicals used by ginger, sweet potato
and sugarcane growers. We were excited to be on land with soil, not just lava rock, common on
the Big Island, but were immediately dismayed to see and feel the soil close-up: dry, lifeless
powder, not a worm to be found. Our first crops struggled against weeds and pests. Then, a
year and a half ago we were introduced to Natural Farming with Indigenous Microorganisms
(IMO’s) and we are seeing amazing improvements in our soil structure and plant health.
Wherever we put down our homemade, mycorrhizae-rich, “fertility drug” as my husband calls it,
the soil regains its loaminess, tilth and structure, and the earthworms come in droves.
The basic theories of Natural Farming include:
Use the historic nutrients of seeds
Use the indigenous microorganisms (IMO’s)
Maximize the inborn potential
Do not use chemical fertilizers
Do not till the land
Zero emission of livestock wastewater
Sow less, yield more
Natural Farming with IMO’s is a distinctive approach to organic farming that is practiced
successfully in over 30 countries, in home gardens and on a commercial scale. Mr. Han Kyu
Cho first formulated and fine-tuned these practices for 40 years and has trained over 18,000
Natural Farming Primer
Written by Jackie Prell
Wednesday, 24 March 2010 14:11
people at the Janong Natural Farming Institute ( ). Then Dr. Hoon Park
brought Natural Farming to Hawaii. Dr. Park was in South Korea doing missionary work and
noticed commercial piggeries with virtually no smell that were using Natural Farming methods.
He learned about Natural Farming and realized that this was a practice that could eliminate
hunger and poverty in extremely poor parts of the world. He came back to Hawaii, his home,
and began giving classes for free.
Demonstrations throughout the workshop clearly showed the steps for making potent natural
Natural Farming is unique in that it is not meant to be commercialized, but rather practiced by
farmers, with cheap, easily available ingredients, and microbes or mycorrhizae indigenous to
each locale or farm. These microorganisms are 1) cultured in a simple wooden box of rice, 2)
mixed with brown sugar and stored in a crock, 3) further propagated on rice bran or wheat mill
run, 4) mixed with soil and cultured again. This is then mixed with 5) compost, or added to
potting soil or spread on beds before planting. The entire process takes 3 to 4 weeks. A
complete guide to making this input can be found by following a link on our club’s website, http:
Other inputs and sprays are made from fermented plant juices, made from the tips of growing
plants mixed with brown sugar. There are also recipes for
water soluble calcium
made from eggshells,
fish amino acid
made from fish waste,
lactic acid bacteria
, and
Natural Farming Primer
Written by Jackie Prell
Wednesday, 24 March 2010 14:11
insect attractants
made from rice wine. There is also
water-soluble calcium phosphate
made from animal bones and vinegar and a
seed soak
solution. There are a half dozen more inputs that can be made simply and easily at home,
which are used according to the nutritive/growth cycle of the plants. Many of these inputs are
made from things that would otherwise just be thrown away. We get fish waste from the local
fish market, which the market would have to pay to dispose of otherwise. The fish amino acids
is simply fresh fish waste, de-boned and packed into a container with brown sugar and
fermented for a few months.
Some of the IMO ingredients.
The benefits of using the Natural Farming methods include:
1. Lower cost to the farmer (by as much as 60%)
2. More desirable crops
3. Stronger, healthier and more nutritious plants
4. The inputs are made from natural materials, which are not only safe for the environment,
but actually invigorate and rehabilitate the ecology.
5. Higher yield
6. Better quality
7. Farmer friendly
8. Zero waste emission
Several University of Hawaii at Hilo Community College professors have been learning Natural
Farming and practicing it, as well as going to South Korea to observe it firsthand. David Ikeda, a
professor at HCC teaches basic Natural Farming classes and another professor, Michael
DuPonte, has helped to establish a piggery in Mountain View using Natural Farming methods
and feed. The pigs excrement is so odorless, clean and dry, that you literally don’t even have to
Natural Farming Primer
Written by Jackie Prell
Wednesday, 24 March 2010 14:11
clean it out. Methods for raising chickens are similar, with healthier chickens, less work and no
smell. Their bedding can remain in place for 10-20 years or just be pulled out when it’s needed
for fertilizer.
Natural Farming has been embraced by the South Korean government after one county
experimented, with every farmer in the county practicing it for a year. These rice farmers not
only had bigger yields than usual, but saved money on their inputs and sold their rice for a
premium. Where they practiced Natural Farming they had the added benefit of cleaning up the
waterways, rivers and even coastal waters.
Also in South Korea a co-op of 40 strawberry farmers uses Natural Farming methods
exclusively in their 300' long greenhouses producing gorgeous, scrumptious strawberries, which
again sell for a premium. And in another wide scale experiment, an entire county is practicing a
model of totally self-sufficient farming where each farm has 500 chickens, 20 pigs and five beef
Dr. Hoon Park, who brought Natural Farming to Hawaii, interprets for Master Cho at the 2010
Hilo workshop.
Mr. Cho has spread Natural Farming worldwide. He went to the Gobi Desert
in Mongolia and planted trees there. Efforts to plant trees had failed three times earlier, under
the harsh wind and with only a few inches of rainfall a year. With Natural Farming methods the
trees had a 97% survival rate and are now 20' tall. Corn and barnyard grasses have been
planted for livestock feed and wells have been dug. Watermelon farming now provides a stable
income to farmers there also.
When the Chinese were preparing for the Olympics to be held in Beking, China, the Chinese
army came in, bringing with them their pigs, which they raise to feed themselves. The
Natural Farming Primer
Written by Jackie Prell
Wednesday, 24 March 2010 14:11
population of Beking was suddenly assaulted by the smell of pig waste and protested violently.
The head of the Chinese army sent two men to South Korea to study Natural Farming, which he
had heard about. The men came back and the army immediately started practicing the Natural
Farming methods and the smell went away. The University of Peking now offers Masters and
Ph.D programs in Natural Farming.
Mr. Cho’s son has created his own methodology of Natural Farming which is even cheaper. His
basic recipe for introducing indigenous mycorrhizae to the soil and increasing micro-biological
activity on one-quarter acre of land follows. Into 125 gallon container of water, put 5 gallons of
ocean water, 6-7 lbs. of sugar, 2 liters of agricultural mineral water (water which has had an
aquarium pump circulating the water or has been dropped from 10 feet onto mineral stone or
azomite). Now go to a naturally fertile, shaded spot on your land and scoop up a handful of soil
off the top half an inch: soil that has it’s own mycorrhizae already present and thriving. Add to
this, a handful of soil from three different naturally fertile spots. Mix these soils together and take
one handful and drop it into a pint of water. Add to the 125 gallons of water. The last ingredient
you make in a blender with wild grasses. Pack a blender with wild grass and a little water and
blend. Make 2 quarts of this and add it to the 125 gallons of water/mix. Let this mixture sit for 18
to 20 hours. To apply it directly onto the soil, dilute it 10 times. To foliar feed, dilute it 20 times.
Apply it during rain or right before rain or in the evening or early morning. This solution can be
applied 8 to 10 times a year for the best results.
Very simply, Natural Farming is the propagation of mycorrhizae, along with protocols for adding
specific inputs during the nutritive cycle of the plant. Mycorrhizae are “fungus roots” and act as
an interface between plants and soil. They grow into the roots of crops and out into the soil,
increasing the root system many thousands of times over. They act symbiotically, converting
with enzymes the nutrients of the soil into food the plants can use and taking carbohydrates
from the plants and turning it into nutrients the soil can use: “sequestering” carbon in the soil for
later use. Miles of fungal filaments can be present in an ounce of healthy soil. Mycorrhizal
inoculation of soil increases the accumulation of carbon in the soil by depositing glomalin, which
in turn, increases soil structure, by binding organic matter to mineral particles in the soil. It is
glomalin that gives soil its tilth, its texture and rich feel, its buoyancy and ability to hold water.
Can Natural Farming be done with no store-bought fertilizers? It is being done not only in home
gardens but also on a commercial scale. For us, here in Hawai‘i, it is incredibly empowering to
mix our own mycorrhizae-rich soil amendments and to be weaned from the fertilizer store. It is
simple, cheap and easy to try. Follow the steps at the website and make
your own. Plant a tray of seedlings with it, and next to it a tray of seedlings without it. You’ll be
impressed by the difference.
Natural Farming Primer
Written by Jackie Prell
Wednesday, 24 March 2010 14:11