Microorganisms for Fertility

By Doug Kremer

The use of microorganisms for fertility is an exacting process using inexact tools in the production of food, fiber and fuel. Each farmer’s fertility program for plant growth is tied to the desired response of the plants. A simpler way to put it is; how much would you like to produce, at what rate and at what cost to the environment and to the farmer using the inputs? For field crops, newer genetic combinations are race horses in the sense of their yield potential, but also in their need for attention whether fertility or otherwise.

This has been a large part of fostering a reliance on petrochemical industries for growing plants. Our challenge is to grow these plants using different techniques, relying on more natural production strategies — particularly in the use of fertility products.

Microorganisms for Fertility: Fundamentals

Microorganisms are a fundamental part of healthy soils, plants and people. We’re still trying to understand how they contribute to the health of soil and how their omnipresence impacts our environment. This can and will have a direct impact on our ability to provide for plant fertility using microbially mediated processes as we understand and harness this interconnected web of life.

man in field
A field in Hoven, South Dakota, in 2004 using 12.8 ounces per acre MicroAZ-IF Liquid, treated (left), untreated.

Harnessing microorganisms for reliable use has been and will continue to be problematic. The interactions and complexities of the soil microbial community are not well understood.

What is understood is the promise and possibilities they have in providing supplemental, complementary or replacement sources of fertility to plants. Building products that have reliability and performance characteristics similar to more widely accepted sources with better economic and environmental consequences is already happening and getting better.

However, roadblocks exist for using microbes for any application in agriculture. Common ones include reliability, consistent performance in different soils and climates, measurable effect and price to allow a good return on investment. Does a product stay alive and do its intended job after being packaged and delivered? Does the cost give a measurable return? The answers to these questions are just as important as knowing if you have the right seed.

Applied Microorganisms for Fertility

An exciting area in the world of applied microorganisms is the increased understanding and use of specific microbes for specific jobs. Many general microbial mixtures are being used in agriculture, but often their impact is difficult to quantify and replicate.

Often this is because they are targeted at more complicated soil tilth issues and not directly to soil fertility or available plant nutrients. While they may aid plant fertility, it is usually through a series of interactions. The ability to work directly with a known microbe with known functions allows the industry to better target products to specific needs of farmers. Typically, this can be quantified more easily by having microbes that do specific jobs.

The concept and use of disease suppressive soils is not well understood from a “let’s build one and use it” standpoint. It is not difficult to see how these can play a critical role in the control and balancing of plant disease causing organisms. Microbially supported soil health impacts are often directly linked to soil structure. The better tilth a soil has the better it is for growing most plants we produce. The open structure of a soil in good health relates to root growth, drainage and the sustained production of soil aggregates that provide a beneficial environment. These soils provide for better nutrient utilization by the plants whether it is applied fertilizers or naturally occurring deposits of minerals.

Among the many jobs microorganisms do in the soil, their activity providing or mediating fertility to plants is directly linked to very measurable yield goals. Other jobs such as soil structure or tilth and disease moderation are as equally important yet tougher to put a consistent yield picture around.

Microorganisms provide much of the nutritional needs of plants, whether it is nitrogen extracted and converted from the 78 percent nitrogen gas found in the air we breathe or the phosphorus transfer from applied fertilizer sources or naturally existing soil components. There are also hurdles to overcome in this natural system.

A phosphorus deficiency can be seen sometimes in cold, wet soils. This response is generally accepted as the lack of substantial microbial activity, meaning the microorganisms that live there are not yet active enough to release the nutrients that are present. It is in the active growing of the microbes that nutrients are released from soil particles. Unlike nitrogen-fixing microbes, which make usable nitrogen out of “thin air,” phosphorus-mobilizing microbes cannot synthesize the phosphorus out of air components. They need a source, whether applied or in the parent soil material, or through plant residue. Then, through microbial growth and the exudates produced as they grow, the phosphorus is freed.

Biological Nitrogen Fixation

One example of this is biological nitrogen fixation or BNF. While a widely used and longstanding tool for legumes, inoculants for nitrogen fixation have not been so successful with crops other than legumes. The discovery of additional microbes and the advances in formulation technology have moved these types of products out of the lab and into the field. Further work is being done on better understanding the replacement power of these products and how to use them instead of petrochemically derived nitrogen-based fertilizers.

Work is also being done to design these products to provide more nitrogen required for producing yield in a timely fashion to better fit the needs for today’s grain growing operations. Which sets of microorganisms can be packaged together and provide the plant with an increasing supply of nitrogen is a set of questions currently being investigated.

In order to capitalize on BNF capabilities and accomplish desired yield goals, the correct microbes must be used to complete the process of converting atmospheric nitrogen into a plant-usable form. BNF can occur via many different microorganisms; some of these microbes live inside of plants, some form structures within the plant, some attach to the plant, some live in the soil around plant roots and still others live in oceans and lakes. These classes of microorganisms have been characterized and studied for many years, but scientists have struggled to make them into useful and reliable products for plant-growing industries.


Nitrogen is only part of the fertility picture — phosphorus and potassium are also critical. Microorganisms are known and have been used to more efficiently utilize these nutrients whether they come from applied fertilizers and manures or native soil components.

These products are designed to directly mimic nature in their capabilities. The effectiveness of these products will depend on placement in the field, timing of the application and efficacy of the formula. Future designs include microbes that can perform in specific colder, harsher environments.

These products are designed to better utilize nutrients regardless of source. They build a bigger pipeline to the plant than occurs without them. They may do this by having a greater growth rate or by producing compounds that interact directly with the nutrient of interest. For the macronutrients of N, P and K, however these nutrients enter into the soils, more efficient transfer to the plant can have a positive outcome. Often this involves releasing phosphorus from compounds such as calcium appetite — a slow-to-solubilize material that occurs naturally in soils. Breaking the phosphorus free in larger quantities and in a more timely fashion is a function of microbial activity.

There are many other nutrients a plant needs for growth and optimum yield including micronutrients. There are specific microbes that selectively mobilize or convert these nutrients and can make them available to plants. Iron, sulfur and manganese are micronutrients that can be selectively accumulated in bacterial cells or solubilized for addition to the soil solution prior to uptake by the plants. These microbes are similar to the ones that interact with phosphorus in that they

do not synthesize the mineral or nutrient, they provide a conduit for the liberation of the nutrient.

The ability to make products from microorganisms relies on identifying these select microbes, growing them and formulating a product that allows the microbe to be alive and perform its desired specific functions at the time of use. How many of these microbes can be put together and the economics of the products have yet to be determined.

Harnessing of the microbial population for these types of jobs requires the isolation of the microbe. Identification of the microbe and association of its functions, for example, solubilizing iron, are critical to insure you are working with the appropriate microbe. How to economically grow the microbe and formulate it to keep it alive are steps that come after you are sure you have the “right bug for the right job.”

It is safe to say that the use of fertilizers has undergone a transformation in the last decade or so. The materials used, liquid versus dry, timing of applications, placement and need have all been subject to increasing scrutiny and change. The ability to grow food, fiber and fuel is crucial to us. The ability to grow it economically with minimal impact on the environment is also crucial.

Farmers can and should expect returns on their investment in microbial products as they do with fertilizers.

As the microbial products industry matures, the products we produce will be better targeted to specific needs. They will also provide functions that were thought to be superfluous, impossible to control or unnecessary; nitrogen fixation versus applied nitrogen is an example.

Formulations of products for fixing nitrogen are largely due to the improvements in the consistency and repeatability of these applications. Fertility management tools are becoming more reliable and providing the consistent punch of currently used fertilizers.

The economics of using these will be more in line with today’s farmer’s needs and fit into our growing need and appreciation of producing quality yields while minimizing our impact on the ecosystem.

Editor’s Note: This article appeared in the December 2014 issue of Acres U.S.A.

Doug Kremer is founder and CEO of TerraMax. With over 30 years of experience in agriculture and horticulture, including developing patented technology for the formulation of microbial technologies, he is the driving force behind product development at TerraMax.

Do Legumes Really Fix Nitrogen in the Soil?

By Margaret Smith, Ph.D., Forage Agronomist, Sponsored by Albert Lea Seed

Farmers have known for millennia that beans and other food legumes provide benefits when grown with grain species or when grains or vegetables follow beans in rotation. But do legumes really add nitrogen to the soil?

Most of the legumes important in agriculture are known as nitrogen fixers, but the plants themselves don’t really fix nitrogen from the atmosphere. These legumes can form a mutually beneficial association with rhizobia bacteria that “fix” nitrogen from the air and share it with their host plant.

Rhizobia bacteria are free-living soil bacteria that, during a portion of their life cycle, can infect the roots of legumes (in a good way) and form nodules on the plants’ roots. During this portion of the bacteria’s life cycle, their numbers increase. It wasn’t until 1889, when rhizobia bacteria were isolated and identified, that we knew what caused that legume “advantage.”

Nodules on legume roots help fix nitrogen
Root nodules occur on the roots of legumes that associate with symbiotic nitrogen-fixing bacteria (known as rhizobia)

Rhizobia bacterial species co-evolved with their legume hosts, and many of them are specific to individual legume species. In fact, most of our legume oilseed, forage, and cover crops aren’t native to the U.S. and neither are their specific companion rhizobia species. As an example, for alfalfa plants to nodulate and fix nitrogen, a specific rhizobia species (Sinorhizobium meliloti) must be present in the soil or introduced with the seed. This rhizobia can also colonize sweetclover as its host species, but not red clover, which needs a different bacteria (Rhizobia leguminosarum (biovariant) trifolii) to develop its nitrogen-fixing capabilities.

Soybeans require yet another bacteria species (Bradyrhizobium japonicum) to nodulate and fix nitrogen. This bacteria forms round nodules on soybean roots, compared with the knobby or irregularly shaped nodules that form from rhizobia on most other forage legume roots.

Because of this species-specific symbiosis, any legume new to a cropping system should be inoculated to provide the specific rhizobia species needed for nitrogen fixation. Where legume species are repeatedly grown in a crop rotation, you may not need to inoculate each time the legume is planted. Factors that affect rhizobia survival in the soil in years where their host legume isn’t grown include low pH (less that 5.5-6.0) and extremely hot or extremely dry soil conditions.

We recommend inoculating your legume species if:

  • The legume has never been grown before in your cropping system; for example, hairy vetch, dry beans or sunn hemp.
  • The legume was grown in the past, but you aren’t sure that the plants nodulated well. Was performance poor?
  • The legume was grown in the past, but only in a small proportion of the total crop mix, such as lentils in a cover crop mixture.
  • The legume crop has not been grown for several years. In this situation, rhizobia levels in the soil will decline with time. For example, if soybeans have not been grown for three or more years, you should inoculate the next soybean crop.

How to Inoculate Legumes with Beneficial Bacteria

A hundred years ago, farmers were advised to inoculate a “new” field by transferring soil from a field where their preferred legumes had already been grown. Fortunately, inoculation is far easier today.

An inoculant is a formulation of a carrier and the live rhizobia bacteria. Commercial inoculants may be powdered (peat-, clay-, or talc/graphite-based), granular or liquid. They are formulated for either application directly to seeds or to drop in the seed furrow at planting.

Peat-based inoculants contain the most bacteria per unit of carrier, but the bacteria in this formulation is very short lived. After opening a package and applying to seed, the seed should be planted within 24 hours. Granular applications are formulated for ease of application to apply directly in a seed furrow, rather than on the seed. Individual planters and drills may not be equipped for this type of application. Clay-based inoculants are applied to seeds and maintain viable rhizobia for a year or more.

Organic growers have access to many OMRI-approved inoculants specific to each legume species.

At a cost of about $1 to $3.50 per acre, inoculation is a relatively inexpensive “insurance” for your soybean, forage and cover crop legumes.

For more information, visit alseed.com or call 800-352-5247.

What is sponsored content?

This article is sponsored content, also known as native advertising. That means that a sponsoring company wrote the article and paid for placement. However, instead of the information in a traditional ad, the information in a sponsored article is relevant to a specific topic, in which the sponsoring company is an expert. If you’d like to learn more about Acres U.S.A. and native advertising, visit our advertising page here, or call us at 1-800-355-5313.

Fighting Weeds with Microbes

We read many, many studies involving manipulation of DNA with as of yet uncalculated risks. It was quite refreshing to read new research employing DNA-based tools in tandem with common sense for the good of all forms of agriculture and the health of the soil.

Using high-powered DNA-based tools, a recent study at the University of Illinois published in Microbial Biology identified soil microbes that negatively affect ragweed and provided a new understanding of the complex relationships going on beneath the soil surface between plants and microorganisms.


“Plant scientists have been studying plant-soil feedback for decades,” said U of I microbial ecologist Tony Yannarell. “Some microbes are famous for their ability to change the soil, such as the microbes that are associated with legumes — we knew about those bacteria. But now we have the ability to use high-power DNA fingerprinting tools to look at all of the microbes in the soil, beyond just the ones we’ve known about. We were able to look at an entire microbial community and identify those microbes that both preferred ragweed and affected its growth.”

Researchers believe an effective strategy to suppress weeds might be to use plants that are known to attract the microbes that are bad for ragweed, and in so doing, encourage the growth of a microbial community that will kill it.

“We used the same soil continuously so it had a chance to be changed,” Yannarell said. “We let the plants do the manipulation.”

This encapsulation of the research is from the June 2014 issue of Acres U.S.A.

Biological Farming: Customizing Methods for Large-Scale Operations

By David Yarrow

Biological farming is not just limited to small plots. Take the story of one Missouri farmer, who through holistic approaches to farming, managed to improve his yields and the size of corn on the stalk.

At the end of 2015, I talked to Missouri boot-heel farmer David “JR” Bollinger about his experiences growing corn, soybeans and milo using carbon-smart farming principles and practices. In his first year fully committed to biological agriculture, Bollinger cut conventional fertilizers by 50 percent and applied blends of biocarbons, minerals and microbes. Soils, plants and yields are all showing positive results.

Bollinger is the fourth generation to farm on 3,500 acres in the southeast Missouri Delta, with the family’s main crops being corn, soybeans, wheat and milo.

“In 2012, I first dabbled in biological farming on a reclaimed coal mine,” he said. “A gentleman with microbial products first tickled my brain about dead soil. He challenged me to find an earthworm. I went looking, and … none. I noticed there wasn’t much life. The soil looked like moondust, vacant of life.”

Dirt is Inert; Soil is Alive

More than mineral dust, soil is created by living organisms. Soil isn’t only made by microbes; soil is an ecosystem made up of microbes and the living matrix and infrastructure they create to support their invisible communities.

“I sprayed his microbe mix of bacteria, fungi and humate at 1 gallon per acre on 50 acres,” said Bollinger. “That year was the big drought with three rains the whole year; 80 percent loss on the 1,000 acres. But 50 acres where I applied microbes actually had a good crop.”

He questioned why soils are so lifeless.

“Because of the kind of person I am, I started digging in, and wow! I’m fortunate to live in a time when I can dig as far as I want. Why is this? Why is that? So many different layers of life. I tinkered with mixes under grow lights in my basement to see what products do. In test pots, I saw effects and benefits. You can say I went down the wormhole.”

Bollinger now considers earthworms to be very valuable farming partners.

“When you dig into what earthworms do, they’re fascinating. As a kid, I took them for granted as fish bait. Now I see all their benefits — the tunnels they make, their movements in soil, their functions. They’re key to good, healthy soil. If you have worms, you have healthy soil.”

New research reveals earthworms are farmers, too. They pull plant biomass into their tunnels, not to eat, but as a soft lining for the growth of bacteria and fungi. Later, a worm returns to graze this fuzzy film of mycelium and microbes. Worms farm their tunnels to cultivate microbes, and thus spread them underground. One ton of earthworms per acre are a primary workforce to convert biomass into fertility and growth.

Test Biological Farming Plots

Urged by positive results and research, Bollinger advocated changes in the family farm’s operations. Bollinger, Sr. was skeptical of new products and cautious about spending money on them.

“I started talking to Dad about biological farming,” said the younger Bollinger. “We started to use different methods. We started small. We didn’t do it all at once. We did test plots for two years. We applied microbes to 1,000 acres of corn and reduced fertilizer on part. We noticed our plants grew bigger and better, and we didn’t have to water as much.”

Bollinger said after June harvest, they usually burned stubble and planted beans.

“Burning stubble gives away goodies worms and microbes need. So, we did a no-till second crop with microbes and saw more results. We were young at this type of farming. We didn’t know what we were doing, but we were seeing benefits. Every time you see a benefit, human nature is to keep doing that.”

Adding More Acres

In 2015, Bollinger decided to transition more acres to sustainable farming methods.

“I stuck my head in books, read up on bacteria, fungi, mycorrhizae, cover crops, kelp, fish meal, biochar and humates — the whole smorgasbord. I saw benefits from microbes, so what can I do for microbes? … I dug into what makes their lives better, like conservation tillage. I see it as ‘farming microbes’ versus applying a chemical. I dug into new products. When we applied biologicals, all of a sudden plants are thriving. A side result is our soil is improving. Now that I had confidence in biological methods, I wanted to apply this on all our acreage.”

Biochar, Trace Elements and Microbes

On March 28, 2015, I met Bollinger at Missouri University Bradford Research Farm, where I was teaching at a biochar symposium sponsored by Phil Blom of Terra Char. The evening before, Bollinger quizzed me all through dinner. The next day, after I taught two hours, he had a steady stream of questions.

He had made his choice and set his course. Bollinger did his homework to use biologicals in large-scale operations. His first corn planting was 1,000 acres. He had to answer his own questions, follow his own strategy, design his own equipment and use his own resources. He knew that no off-the-shelf solutions exist. His burden was to make this work — and convince his father. In his heart and gut, Bollinger knew a biological path is key to 21st century farming. I visited Bollinger on his farm after Thanksgiving to hear about his progress.

First, Bollinger showed me an impressive assembly of equipment, made to operate as a unit to deposit precise, narrow bands of biological nutrients. With extensive equipment knowledge and savvy mechanical expertise, he built apparatuses to perform a miracle on near-lifeless soil: instantly install the foundation of a healthy soil food web. Bollinger’s genius isn’t just building complicated machinery. Rather, he figured out how to mix nutrients precisely in the root zone with minimum disturbance. Emerging seeds find nutrients and symbiotic fungi all around budding roots.

“These products don’t exist on the market,” said Bollinger.

We know biochar, trace elements and microbes are potent in soil — individually, but much more so when mixed together. Can carbon-smart, microbe-friendly soil stewardship be integrated into commercial farming? Can this be easy, economical and feasible for large-scale farmers?

“At front, hanging on the tractor, two yellow side-saddle tanks hold liquid nutrients and microbes,” said Bollinger. “We inject this as a band 4-inch off-center. We stagger-step fertilizer in bands to chase roots to grow outward. Liquids include anything from fertilizer to fishmeal. We tried different products, all kinds of goodies: humates, humic acid, sea minerals, microbes, fish meal and biochar powder. I wanted to give everything a fair shot in our conventional way and gradually introduce biologicals.”

Most of the microbes that Bollinger applied were in liquid form. One lab brewed blend contains 16 bacteria and nine fungi with support nutrients like humates and trace elements, including free-living nitrogen-cycling bacteria and phosphate-dissolving fungi. The goal is to get them under the surface, in moist, cool soil with nutrients and metabolites, to assure they proliferate.

Feed Soil Microbes, Not Plants

Biochar, however, isn’t a fertilizer or nutrient and doesn’t break down in soil — maybe 3 percent — but greatly boosts fertilizer efficiency. Char is shelter, not food. Microbes don’t eat this superstable biocarbon; they live in it. Burnt biomass is community infrastructure to house microbes with plumbing for water, thin-film wiring for power and nutrient shopping malls. Biochar also curbs nutrient leaching and outgas.

“Montag is our dry fertilizer cart,” said Bollinger. “We get a blend that meets the needs of our soil test. We mix in anything from biochar fines to crab meal, shrimp meal, SEA-90, humates. The Dawn unit does an excellent job mixing fertilizer, char – anything that goes through the hose — and incorporates them into soil.”

Bollinger said that with precise striptill application and biological amendments he had the confidence to cut dry fertilizer use in half.

“We reduced our liquid fertilization as well. We didn’t see any lag. If anything, we saw a boost.”

Dry ingredients are agitated and sucked by vacuum hose to injectors on Dawn cultivators and land in soil. Biochar and biologicals were supplied by Terra Char, a 3-year-old biocarbon business near Columbia, Missouri. Owner Phil Blom delivered a semiload of biochar for Bollinger’s soils, plus minerals, microbes and metabolite. Blom offered guidance and support throughout the growing season.

Dawn Cultivators and Biological Farming

Behind the tractor ride 16 Dawn cultivators, each with injectors for dry, then liquid amendments.

“I use Dawn because we have sandy ground,” said Bollinger. “Its waffle blades are more vertical till, not deep tillage. It moves residue out of the way, so it’s easy to plant through. I don’t deep till, like with shanks, since this makes a trench that fertilizer tends to go into and increases leaching.”

a cultivator
A Dawn cultivator

Bollinger said one side gets dry fertilizer and then, a few inches off center, the liquid band is applied, allowing for precise nutrient placement. Soil between rows isn’t disturbed.

“Dawn keeps soil within the unit. Eventually, dirt hits it, flies up where dry and liquid lines come in. Then it hits the lead edge of a disc blade that fills up, then turns it, like mixing potting soil with your hand. Dawn fluffs soil to make a seedbed. Soil warms quicker in spring to speed up planting dates. It’s a perfect tool to closely place fertilizers. I love how Dawn handles residue and keeps it confined.”

The last part of each Dawn unit are “swirlers” — two rolling wheels with inward-facing fingers that lift and stir soil to mix ingredients and aerate soil in 4-inch slots. The rig’s main benefit is that it can concentrate nutrients and inoculants in soil where seeds will germinate, not broadcast wide, but thin, across the field. Bollinger gently injects his microbes in a dark, moist subsurface world, not exposed to hot sun and dry wind. Precision placement and blending assures close proximity of nutrients for fast-acting effects.

Strip Tilling

Tillage degrades soil, burns out carbon and disrupts microbes. Why burn fuel tilling if worms pull biomass into their tunnels? Let worms do the work.

“I call this ‘strip-till,’ or ‘conservation till’ because we do a percent of tillage,” said Bollinger. “Each year, 20 percent of a field is tilled in 6-inch wide strips, to leave a nice mat of residue on 80 percent to suppress weeds. When we irrigate, or get rain, covered soil stays moist longer under thick residue. Residue was gone by end of July. I was fascinated to see how heavy, thick residue disappeared quickly. I call this ‘carbon-smart’ or ‘biological’ farming. It’s a hybrid — combining both traditional and modern. In my life, traditional became NPK, herbicides, lots of tillage and all.”

Strip-till bands are spaced 30 inches apart. Each year, guided by GPS, Bollinger will move his rig over a few inches to inject another band of biochar plus inoculants, minerals and nutrients. In five years, he will deposit this mix all over his field and will need to use very little chemical fertilizer. Meanwhile, Bollinger is assured steady income, larger yields, higher crop quality and improving fertility as soil regenerates.

Seed Starter

Bollinger described another biological application at planting: “We also drench with a seed starter. We apply biological nutrients in furrow, right on top of seeds. As soon as a seed kicks out of its tiny nursery sack, I want it in a happy environment. It’s another stair-step to optimize germination and seed growth. I only use biological products on top of seed. Later, we sidedress 8 inches off the row — another stair-step. At each stage of growth, we key in nutrients before it needs them, to sit there waiting. We use a lubricant such as talc to help seeds flow and not lodge. This year, we used very fine, 40-micron biochar powder and mycorrhyizal inoculant as lubricants. We get beneficial fungi and biocarbon right by the seed, in direct contact. Spores definitely stick to char particles. How much good it did, I don’t know, but it can’t hurt. I know our seed germination was off the charts this year.”

The seed on the farm is non-GMO.

“We’ve grown non-GMO corn about 15 years; never got into GMO corn. Our soybeans are non-GMO. We don’t believe in GMOs, and getting premiums for non-GMO kept us on the train. Now, later in life, I see the effects GMOs have. Farmers who grow GMOs must use herbicide, and weeds are now becoming resistant. So I’m proud we grow non-GMO crops. To feed grain to cattle, I feel non-GMO is better.”

Until nutrients are abundant and soil is fully mature, soil nutrients must be supplemented by seed treatment, foliar feeding, root drenches and sidedressings. The most critical extra feeding is starter food to wake up embryos and stimulate root growth.

Bollinger used a Terra Char formula to blend biochar powder with kelp, humic acid and bacteria. Spores of endo-mycorrhizae initiate symbiosis with infant roots. Fishmeal is amino acid nitrogen for emerging embryo and colonizing microbes. SEA-90 unrefined sea minerals offers complete trace elements with alkaline charge in balanced, fully soluble form. SEA-90 is a fast-acting “igniter” to jumpstart soil biology, which then digests rock into new soil. The same full-spectrum minerals are in other sea products, each packed in different chemistry: kelp (carbon), fishmeal (amino acids), shrimp meal (protein), crab meal (chitin).

Signs of Healthy Corn

“I planted a typical population of 34,000,” said Bollinger. “Years past, I planted 28 to 30,000. In strong or weak parts of a field, my planter can change populations. This corn was 33,500 to 34,000. Typically, seed companies tell you to push population up until you get tip back — corn will grow, but not produce complete ears. My corn had full ears with no tip back. Should I increase population more? I don’t know, but greater population definitely didn’t stress plants.”

The corn came up very uniform with nearly 100 percent germination.

“What was really interesting was the health of plants when they came up. Often corn comes up in its early stage yellow. You see purpling in inclement, wet conditions — phosphorus deficiency. I didn’t see any, and we didn’t apply in-furrow fertilizer other than pre-planting strip-till. Phosphorus was in dry fertilizer. In the past, we put phosphorus right in furrow. This year all we did was add mycorrhizal fungi, which find and move phosphorus in soil. Did it have an effect that quickly? I don’t know, but we didn’t have purple corn.”

In early June, I received a photo of Bollinger in head-high corn. I couldn’t see his face, but I knew he was smiling. His corn was 16 inches taller than his neighbors’, with thicker, longer leaves that were distinctly darker green. His corn had more chlorophyll making more sugar to grow faster. Bollinger knew he made the right choice to go carbon-smart and grow biologically.

“The corn, for its early stage, was taller than it should be,” he said. “You can see in photos, healthy corn has a glossy, waxy look. See how wide the leaves are. And inner veins all consistent color. Not much striping that shows deficiencies. It’s just a healthy plant — as healthy as corn gets.”

Early on, the corn had wider, longer leaves.

“You can go in a field and tell if life is going on, or if it’s hanging onto life. Times of stress, like going without rain, are hard on people. You know it stresses plants. But this year, our plants weren’t stressed the way they should have been. A few fields, some nonirrigated sand, never had a bad day. They held on until it rained.”

Bollinger’s shaded soil needs no herbicide, like conventional no-till. Yet, three growing cycles are needed to mature soil’s full digestive power to rapidly recycle crop biomass.

Biological Farming Inspections

“I was on hands and knees crawling through the crop, looking at soil and plants, at different bugs, different insects, different fungi — lots of life in that soil,” said Bollinger. “You can see earthworms. Microbes, you can’t see. I expected to see mycorrhizae signs in soil after a test I did last winter with seedlings in pots. I overdosed with spores and saw thick white fungal fuzz like snow on the soil. We’re dealing with living organisms, and you’ve got to treat them right, or they won’t treat you right.”

Bollinger has learned to think holistically. He knows there are no single- shot solutions. His concept of soil stewardship now embraces the whole community of living organisms that inhabit healthy, fertile soil. Fighting pathogens is secondary strategy, after encouraging roots, enlisting microbes as allies and a complete menu of minerals.

On July 4th, Bollinger sent me a photo of nearly ripe ears. I’m not familiar with southern Midwest corn growth, yet this seemed early. I was told that it was unprecedented.

“End of June, corn tassel starts here,” said Bollinger. “Sweet corn is earlier. We start to get sweet corn July 4th. Around the 13th, we usually can sweet corn. We planted late, so I didn’t expect such early tassels and ears. I’d say the corn was two weeks early.”

On July 16, Bollinger emailed a photo of three ears.

“Ears were 43 long, majority 16 around, many 18. Typical all over the field. In the past, it might be 12 or 14, a few 16s. But this year, 16 was the norm. Two extra rows on each ear add to overall yield.”

Corn ears by July 4 fed my faith that Bollinger’s 4-inch strips would work, but photos of roots blew a fuse in my imagination. Thick beards of white roots erupted from the base of stalks. I never saw such dense, fine roots. They knew nutrients were there and saturated the zone with roots to suck up the goodies.

In photos, black grains of biochar are visible. Each absorbs eight times its weight in water, adsorps immense amounts of mineral ions, held loosely, ready for H+ exchange with root or microbe. Biochar’s special benefit is to hold anions (nitrogen, phosphorus) as well as cations to keep them near roots.

Bollinger was thrilled by the remarkable roots — and mystified.

“I was scouting for insects the first day I saw roots 6 inches long. Hard to say how long they got, because they twisted and turned, but some grew to 3 feet. This was widespread throughout the field. In fact, the whole 50 acres looked that way — like spaghetti across the field.”

They had a wet spring and timely rains at tassel helped.

“Later, we bridged gaps with irrigation. Foliar sprays to put on nutrients help, but aren’t a full watering. We used a moisture probe this year to monitor water use. We didn’t overwater, but once it got to a certain point, we kept it at that range. Seems like the crop was very efficient with water.”

Weed and insect pressure also decreased.

“Residue in middles suppressed weeds. Corn grew so fast, canopy shaded the middles, and weeds didn’t grow. Not much bug pressure, either. One zone — a high-sand ridge — a bit more.”

Consistently well-nourished plants don’t attract pests. If pests do infest, vigorous plants outgrow bug damage. Once during the year, Bollinger sent me a question about an insect pest. I gave him non-toxic remedies to discourage bugs and strengthen plants. He later reported bugs ate the weeds and hardly touched his crop.

Blending Biochar

Estimating biochar application rates in his biological farming methods was difficult. Field conditions, complex calculations, equipment malfunctions, blending uncertainties, changing recipes and other variables made a precise rate for each field elusive. A minimum of 2 percent biocarbon is needed to sustain strong microbe communities, and Certified Organic requires 4-5 percent carbon. I suggest half as superstable biochar and humus, another 2.5 percent as digestible carbon, like crop stubble, compost, manure, etc. But 2.5 percent biochar tilled in 6 inches is 8 tons per acre — at $0.50 per pound, and $8,000 per acre, and that is too costly for farmers.

Bollinger’s genius is to concentrate biochar and nutrients in narrow bands, thus cutting rates to hundreds of pounds per acre, slashing annual costs and spreading expenses over several years.

Biological Farming: Cheaper, More Effective

“That cornfield produced 235 bushels,” said Bollinger. “The 20-year average for that field is 180 bushels. The crop was easy to grow.”

But Bollinger’s biggest surprise was his grain sorghum crop.

“One sorghum field made 186 bushels in non-irrigated sand. Normal is 100 bushels; most farms were 120, even irrigated. Believe it or not, my field had irrigation on part, but nonirrigated yielded a few extra bushels.”

Yields were good enough to win First Place in Missouri for both irrigated and non-irrigated milo. Continuing to talk numbers, I asked about money saved cutting NPK fertilizer 50 percent versus costs for biochar, biological and metabolites.

David, Sr. replied, “Yeah, we got some figures. I’ll fine-tune fertilizers — exact amounts we cut back. I’d say close to $100 an acre cheaper. Maybe not $100, but way up there.” So, 1,000 acres saved near $100,000 just on fertilizers.

Bollinger said their soybeans show signs of increased health and vitality, and they achieved higher yields.

“Stalk is important in soybeans — usually a little pencil-like stalk,” he said. “This year, stalks were like tree trunks. We noticed more lateral branches. Typically, we have a single stem and nodes stretched farther apart. This year, nodes were more stacked, with three or four lateral branches. Every soybean plant I pulled up, rhizobia were always vibrant, pink, bigger in size and more of them than typical, especially on poorer ground. On average, in this ground after wheat soybeans get 35 bushels. We ended in 50 to 55. Also, we cut our soybean population way back to the 80,000 to 100,000 range. Many farms plant up to 180,000 per acre.”

Bollinger says his journey to more sustainable farming started because a man challenged him to find an earthworm.

“It tickled me yesterday to walk out in a field, stop in a random spot, dig into the soil with two fingers and find an earthworm — then five more. In 2012, I couldn’t find a single earthworm.”

David Yarrow has taught about and organized sustainable food systems in the northeast United States for more than 30 years. He can be reached at dyarrow5@ gmail.com. For more information visit dyarrow.org.

This article appears in the August 2016 issue of Acres U.S.A.

The Soil Food Web: A World Beneath Our Feet

By Mary-Howell R. Martens
From the April 2000 issue of Acres U.S.A. magazine

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 be over 600 million bacterial cells, and if that soil comes from the immediate root zone of a healthy plant, the number can exceed a million bacteria of many different species. These bacterial cells exist in complex predator-prey relationships with countless other diverse organisms.

This topsoil food web forms the foundation for fertile, healthy soil, for healthy plants, and ultimately for a healthy planet. It is an essential but exceedingly delicate foundation that even the brightest scientists know very little about.

Dr. Elaine Ingham has been researching this tiny universe for nearly 20 years. She has sought to understand the importance of these organisms and the relationships that exist between them, and to elucidate the effects that various agricultural practices have on this vast network of life.

For part of her Ph.D. dissertation in 1981 at Colorado State University, Dr. Ingham researched the soil food web structures in Colorado soils that were farmed with and without irrigation. She compared these results to native grassland soils. Not surprisingly, she discovered that the introduction of agricultural systems altered the species of organisms present in soil life, particularly the fungi, which are easily destroyed by agricultural pesticides. For her postdoctoral work, she compared grassland soils to high mountain meadow and pine forest soils, working across a typical successional gradient. Again she found great differences in species present and numbers of the typical organisms in response to other important factors in the soil.

Over the course of Ingham’s education and subsequent career as a professor at Oregon State University and most recently with Soil Foodweb Inc., a research and consulting firm in Corvallis, Oregon, she has developed methods to quantify and identify the microbial populations of soils. She has learned that most traditional techniques of petri plate counts grossly underestimate both number and diversity of species present in soil, since the artificial conditions are not suitable for the growth of 99.99 percent of bacterial species and of most other organisms. To circumvent this problem, Ingham has developed effective alternative techniques based on direct enumeration methods.

She uses this information to assist farmers and researchers by offering a service that assesses the health and productivity of their soil by measuring the diversity and vitality of the soil food web. Which organisms compose this soil food web? This is not a simple question. The food web has a basic set of expected organism groups, but the numbers of organisms and different species in each group can vary significantly by soil type, climate, plants present and management. Plants and plant structures are a major component in determining the food resources in soil that will be available to bacteria and fungi.

standing in a field of healthy soil
For a healthy soil, unaltered by the application of lethal agricultural chemicals, these “microherds” of microbes colonize the root zone, the rhizosphere, of the plant.

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. The more diverse the initial plant population, the greater the diversity of plant products that will be released, thereby sustaining an increased variety of microbial organisms.

For a healthy soil, unaltered by the application of lethal agricultural chemicals, these “microherds” of microbes colonize the root zone, 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 in more familiar aboveground ecosystems, there are other organisms present that prey on these herbivores. The predators are primarily beneficial nematodes, predatory nematodes, protozoa, mites and other tiny animals which serve to recycle nutrients in the system and to keep other populations in balance. These predators, in turn, are eaten by other animals, primarily those that spend some portion of their life aboveground, such as insects, birds and small animals. It is important to view the soil food web as a complex, whole system. When any group of organisms in the system is eliminated or damaged, the delicate balance of interrelationships can be shifted. Soil ecologists are just beginning to understand how plant production can be affected when this balance is altered. Many species of beneficial bacteria and fungi die as food supplies dwindle. Reduction in natural predators and decreased competition for certain food supplies may allow other species to grow rampantly. Plant nutrient availability often can decline, and populations of pathogens can rise. Much research is currently being done on this subject, attempting to comprehend how such changes occur.

Herbicides, Pesticides and Fertilizers

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 determine their effects on soil organisms. The remaining ingredients have never been studied for their effects on the whole system or on any non-target group.

Scientists don’t fully understand the effect of any 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. Plants growing in unhealthy soil require additional fertilizers and pesticides, furthering the deadly spiral. 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. 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 also are instrumental in supplying the plant’s unique nutritional needs. The residual effects of this unique microbial population in subsequent years may also help explain why certain crop rotations work better than others. It is possible that the microbial population nurtured by one crop species creates a nutritional or microbial environment that is well suited to a particular subsequent crop species but not perhaps for others.

For example, it is likely that crops like broccoli, which inhibit the growth of mycorrhizal fungi, reduce the productivity of a following crop such as corn, which requires mycorrhizal fungi. While this has not been conclusively proven, it could form part of the basis for a better understanding of observable crop rotational effects. Certain soil amendments favor the development of a diverse microbial population. 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 microarthropods, 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 — and even compost teas — 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.

In order to better understand the complex benefits of a healthy soil food web, Ingham has separated the major effects into several primary categories.

Nutrient Cycling and 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 anions 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, this nitrogen is released into the surrounding soil solution, where it can be absorbed by plant roots. It is commonly assumed that when bacteria or fungi decompose, nitrogen in their cells slowly becomes available to plants in a form that is readily assimilated into the roots. However, in a healthy soil, 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. Compare this system to another familiar situation; 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 and into the groundwater. This produces not only reduced plant growth but also environmental pollution.

The least leachable form of nitrogen is that which is incorporated into the bodies of bacteria and fungi, resulting in good plant growth and little loss of nitrogen to groundwater or runoff. Nitrogen is not the only nutrient effectively stored and recycled by soil microbes. Carbon is the major constituent of all cells, and soil-carbon is important. 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. All soil organisms have the ability to sequester carbon, but bacteria are the least efficient in this process. When bacteria consume simple sugars, proteins or complex carbohydrates, they incorporate most of the nutrients, including nitrogen, into their cell structure. However, when they consume more carbon than necessary, the excess is released into the atmosphere as carbon dioxide.

Fungi require more carbon than bacteria and therefore release a much smaller quantity of carbon dioxide. When a soil is dominated by bacterial biomass, as it is in most modern agricultural systems, the ability to hold carbon in the soil is significantly reduced. Fungal cells are responsible in a large part for storing and stabilizing much of the calcium in the soil. Ingham has shown that a soil low in fungi will permit calcium to leach away. Such a soil will require frequent applications of lime to replenish the calcium supply. A healthy fungal population can retain 95 percent of the calcium added to the soil, slowly releasing the calcium for plant use and maintaining a beneficial cation exchange capacity.

The Phosphorus Cycle
The Phosphorus Cycle

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. Virtually all plant species will form beneficial mycorrhizal relationships, given the right conditions. 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. 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 uninoculated 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 stress.

Soil Food Web 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 microaggregates. Threading between these aggregates and binding them together are fine, ribbon-like strands of fungal hyphae which further define and stabilize the soil into macroaggregates. It is this aggregated soil structure, which looks it a bit like spongy chocolate cake, that effectively resists compaction and erosion and promotes optimal plant and microbial growth.

The structural matrix of these aggregates provides adequate pore space for easy air and water movement. Beneficial microbes, like plant roots and most other living organisms, require air and water for survival. Water and air are held in the pores until needed, stimulating a healthy mix of beneficial organisms and facilitating root growth. Larger animals, such as earthworms, move without resistance between the aggregates, further improving soil structure and plant health. When a fragile soil is worked with heavy equipment, aggregates are crushed, killing microbes and forcing out water and air. Plants grow with difficulty in such soil, not only because of physical resistance from the compacted soil particles, but also because the beneficial soil food web has been severely damaged.

If soil is unable to hold sufficient oxygen, harmful anaerobic soil bacteria will proliferate, producing toxins that kill plant roots and other microorganisms. In general, the largest soil organisms are the first damaged by soil compaction. 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.    

Disease Suppression

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, can actually be one of the most common beneficial saprophytes in a healthy soil. He stated that the dividing line between beneficial symbiosis and parasitism can be very narrow. When Fusarium encounters a root that is poorly nourished or is under stress, it can become rapidly pathogenic.

Decomposition of Toxic Materials

Application of chemical salt-based fertilizers tends to change the microbial population in a soil. Many fragile species of microbes are severely damaged by the powerful osmotic effects of the concentrated fertilizers. As with soil compaction, a shift in microbial populations can occur following fertilizer application, resulting in reduced overall plant growth and an increase in plant pathogens. There are species of microbes that are able to withstand the effects of chemical fertilizers. They actually make use of the fertilizer materials for nutrition and in doing so, can change harmful compounds into ones much less damaging to soil life. The presence of ample organic matter in a soil can help to reduce the harmful effects of chemical fertilizers, possibly due its buffering action.

When pesticides and herbicides are applied to soil, they produce an immediate detectable effect, but they can have other subtle residual effects for many years. Removing such contaminants from the soil is quite difficult. A healthy soil food web can help here also, by actually breaking chemicals down into less toxic materials and also by facilitating the absorption of many pesticides in organic material, rendering them less damaging to microbes and plant roots and facilitating their eventual degradation. It is fortunate for the farmer that many types of chemicals can be degraded by certain species of microbes in the soil, if they are present.

Certain bacterial species, such as Bacillus laterosporus, or the fungal species Phanerochete have been noted as degraders of 2,4-D and DDT. There is currently much research being done on bioremediation, using microbes to break down various environmental toxins. In many cases, bioremediation may be preferred over more conventional treatments because it is less expensive and can be more successful in removing a wide variety of contaminants.   

Production of 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.

It is clear, both from studying Dr. Ingham’s work and comparing it to older research, that soil ecology has been largely neglected in the era of chemical fertilizers and pesticides and that the microbial population in soil is the key factor in healthy crop production. Any practice that reduces or shifts normal microbial populations, such as the use of agricultural chemicals and excessive or inappropriate tillage, will effectively reduce crop potential. Conscientiously adopting practices that favor this unseen universe should improve plant health, yield and the nutritional benefits we may obtain from those plants.

Learn about healthy soil with Acres U.S.A. this summer

The second annual Healthy Soil Summit is a virtual event taking place this August 25-26, 2020. It will consist of 2 days of high quality soil education and interaction with experts. Klaas Martens – husband of this article’s author, Mary-Howell Martens – will be giving the keynote presentation. Learn more about the Healthy Soil Summit here.

Healthy Soil Summit 2020

The Biological Nature of Soil

By Jerry Brunetti

Another exciting breakthrough in nitrogen-fixing bacteria originates out of the University of Nottingham’s Center for Crop Nitrogen Fixation. Professor Edward Cocking and colleagues found a specific strain of nitrogen-fixing bacteria in sugar cane that could intracellularly colonize all major crop plants. Remarkably, this development potentially allows all the cells within a plant to x atmospheric nitrogen!

This technology, labeled “N-Fix,” is not a genetic modified/bioengineering technology, either. Rather, it is a seed inoculant, enabling plant cells to become nitrogen fixers, a hopeful boon to annual crop production, which uses wasteful and contaminating amounts of nitrogen.

In the same vein of investigating the “cellular wisdom” that exists among microbes and plants, researchers at the University of Missouri’s Bond Life Sciences Center, under the direction of professor Gary Stacey, discovered that, for reasons yet unclear, non-legumes have not yet made a “pact” with nitrogen-fixing rhizobia bacteria that allow legumes to convert nitrogen gas into plant food that can be used to build proteins.

Rhizobia nodules on bean legume roots.
Rhizobium legominosarum nodules in bean roots (Vicia faba) in a symbiotic relationship.

Legumes recognize these bacteria as their allies, rather than as pathogens, by sensing a signal from the bacteria. The legumes then create nodules where the bacteria gather in order to be fed by the plant in exchange for fixing nitrogen out of the soils’ atmosphere for the plants growth. The rhizobia found ways to produce biochemicals that inhibit the plant’s defense responses, so they can be recognized and accepted as bacterial “friends.”

Non-legumes, like corn and tomatoes, were also found to receive the rhizobia signal, which in turn inhibited their plant defense mechanisms against the friendly rhizobia but for whatever reason did not initiate the next step of forming nodules to allow the rhizobia to become symbiotic partners with those plants.

The scientific challenge is thus to find ways to get non-legumes to activate mechanisms that will produce nodules that the rhizobia bacteria can inoculate. If the research at the University of Nottingham or University of Missouri bears fruit, it could have enormous implications on reducing the $8 billion spent yearly by farmers on nitrogen and the destructive amounts of nitrogen fertilizer leaching into our waterways and aquifers. In the meantime, we are blessed with the miracle of nitrogen fixation by the rhizobia with legumes and nitrogen fixation by the actinomycetes bacteria and the blue-green algae with non-legumes and legumes.

Only recently has it been discovered that there are perhaps twice as many archaea species as eubacteria species that are capable of oxidizing nitrogen. Only about 280 species of archaea have been described, yet in upland soils they are estimated to make up 10 percent of the microbial biomass. Like bacteria, archaea are known as prokaryotes, meaning their cells lack a nucleus surrounded by a membrane. Curiously, the genetic construction of archaea is more similar to that of plants and humans than to other bacteria.

Bacteria populations skyrocket in the rhizosphere compared to elsewhere in the soil, to the tune of ten to several hundred times as much. Two types of bacteria inhabit soils.

  • Heterotrophic bacteria utilize organic substances in the soil for their sustenance and transform these organic compounds into plant nutrients.
  • Autotrophic bacteria have the ability to synthesize their own organic compounds from carbon dioxide as well as transform inorganic substances and mineral elements into plant-available nutrients.

Bacteria can also be categorized by their shape—bacillus (rod-shaped), spiral, and coccus (spherical)— and whether they are aerobes, which live in free-oxygen environments, or anaerobes, which live in environments absent of free oxygen. There are also facultative aerobes and facultative anaerobes, meaning that they can inhabit both environments, but the facultative anaerobes prefer oxygen-absent environments, and the facultative aerobes prefer oxygen-rich environments.

Bacteria are primary decomposers, but fungi are more significant in that regard. Bacteria use enzymes to fracture bonds that hold organic complexes together. Some bacteria, for example, are able to decompose the most common carbon raw material on our planet, cellulose, by producing enzymes like cellulase. This is an important relationship in creating soil humus. Since bacteria are able to ingest what they decompose, they create non-leachable plant nutrients that are locked up in their bodies until they either die or are eaten by predators like protozoa and nematodes.

Actinomycetes are bacteria that resemble fungi because they produce spores and grow laments. They are the creators of that great earthy garden soil smell, and actinomycetes have been a lucrative resource to the pharmaceutical industry as a source of antibiotics such as neomycin, tretracycline, actinomycin, and candicidin. One of the more popular antibiotics produced by this organism is streptomycin, the first antibiotic proven to cure tuberculosis, discovered in 1943 by soil scientist Albert Schatz, PhD (1920–2005).

Schatz’s forward thinking about soil formation was associated with the principles of chelation. In fact, he authored a text in 1954 titled Chelation (Sequestration) as a Biological Weathering Factor in Pedogenesis and another on the same subject in 1963, titled The Importance of Metal-Binding Phenomena in the Chemistry and Microbiology of the Soil.

Actinomycetes are also nitrogen-fixers, able to extract nitrogen gas (N2) and convert it to ammonium (NH4) by associating with non-legume plants, invading their root hairs, and forming knobby larger nodules than rhizobia do with legumes. The rhizobia, blue-green algae, and actinomycetes collectively x about 140 million metric tons of nitrogen each year, twice the amount of nitrogen fertilizer manufactured by the plant food industry.

Algae are often thought of as waterborne creatures found in swamps, ponds, streams, and rivers, but they have actually been found to be some of the hardiest terrestrial occupants of any other microbial form. Algae may be plants (e.g., kelp) or protists (e.g., bacteria, like cyanobacteria), and all utilize sunlight to photosynthesize sugars and give o carbon dioxide to form that mild corrosive called carbonic acid that can “eat” rocks. The blue-green algae (cyanobacteria) are also capable of fixing nitrogen.

In the top several inches of soil, where there is sunlight, algae can be found in high numbers—as many as 100 million per gram—and can consequently generate quite a bit of organic matter to soils. According to Nardi, in some Arizona soils, algae annually contribute 6 tons of organic matter to the top 3 inches of each acre.

Algae are also found in extreme climatic conditions, such as deserts, and when they are dormant they can survive temperatures of boiling (212°F/100°C) as well as intense cold (-320°F/-195°C). Algae have evolved to form partnerships with other organisms such as fungi, mosses, and bacteria. In desert environments, these partnerships create what’s known as a microbiotic or cryptobiotic crust, where mutualistic collaborations of algae or cyanobacteria and their fungal/liverwort/moss partners protect these fragile and/or semi-arid lands with a glue-like covering that conserves moisture, supplies nitrogen, adds organic matter, prevents wind and water erosion, and conserves and recycles soil nutrients. These crusts can be irreparably destroyed, however, with off-road vehicles and trampling by hooves and feet.

Many years ago, I read the autobiographical account of the mystic G. I. Gurdjie, called Meetings with Remarkable Men, a report of Gurdjie ’s travels to isolated regions of Central Asia and the Middle East. His expedition found that they could keep their pack animals fed while traveling through a vast span of desert without vegetation by experimenting beforehand with two camels, two yaks, two horses, two mules, two donkeys, ten sheep, ten goats, ten dogs, and ten cats.

The food created and tested with these species was the following recipe: seven and a half parts sand, two parts ground mutton and a half part salt. Not only was this gruel palatable to these animals, they actually were able to gain weight! Of course, Gurdjie and his crew knew that the nutrition in the sand was some form of “organic substance.” It is my belief that this organic substance was the cryptobiotic or microbiotic crust rich in protein, carbohydrates, fats, vitamins, and minerals.

Lichens are another example of symbiosis between fungi and algae, consisting of blue-green algae (cyanobacteria), golden and brown algae, and the ascomycota fungi. These organisms can survive drought, the hardest of rocks, and subfreezing temperatures. They are primary decomposers of lignin and stone, where the algae produce the photosynthetic carbons and nitrogen fixation to nourish the fungi while the fungi harvest the minerals found in the rock or tree bark. Lichens are extremely abundant, occupying 8 percent of the earth’s land surface, and can live hundreds to thousands of years upon their rock host.

Want to learn more? Buy the book, The Farm As Ecosystem, here at the Acres U.S.A. online bookstore.

About Jerry Brunetti

JERRY BRUNETTI, 1950-2014, worked as a soil and crop consultant, primarily for livestock farms and ranches, and improved crop quality and livestock performance and health on certified organic farms. In 1979, he founded Agri-Dynamics Inc., and confounded Earthworks in 1990. He spoke widely on the topics of human, animal and farm health.

Jerry Brunetti
Front cover of the book The Farm as Ecosystem by Jerry Brunetti
The book, The Farm as Ecosystem, written by Jerry Brunetti, features a lifetime of experience and observations woven together into a useful guide and source of information. Through the text, Brunetti seeks to offer the reader a deeper understanding of evaluating your soil, soil fertility management, compost and compost tea, cover cropping systems, the benefits of biodiversity and more!

The Importance of Soil Biology for Biodynamic Pasture Management

By Peter Bacchus

To grow healthy plants and animals and high-quality food products, you need fertile soil. Soil fertility in turn is related to the growth and reproduction of soil organisms and to the plants that grow in the soil. In due process this affects the health, well-being and fertility of the animals and humans who live as a result of the plants that grow in the soil.

We often do not recognize that soil fertility depends on the carbon cycle, which starts with photosynthesis in plant leaves and the absorption of light and carbon and other elements from the air into the plant. The carbon taken in from the air by plants and transformed into sugars is the basis of the carbon cycle, which maintains life in the soil by providing food for soil organisms.

The elements that come from the air in gaseous form can make up to 80 percent of solid plant tissue. And up to 90 percent of a plant is carbon and oxygen, two elements that are not measured in many plant tests. What is below ground helps make it happen.

One of the most often overlooked aspects in our farming is soil biology.

Soil organisms are the facilitators of mineral activity in the soil. They bring about a natural movement of minerals through incorporating them in their bodies. These organisms secrete digestive enzymes into the soil that enable the organisms to absorb the minerals as food. When the organisms die, the minerals are released in a form that plant roots can easily take up.

Tree roots in soil
Soil bacteria need sugars that they get from root exudates.

The payment these organisms exact for doing this work is a requirement for the right living conditions and some nutrition. And we can help achieve these requirements.

The organisms need air and moisture — but not too wet or too dry. They work best in a particular temperature range and, similar to humans, need food to their liking.

Not only do they need organic matter, they need a specific range of mineral nutrients. They can’t hop in the car or bus and go to the supermarket and pharmacy — they depend on us and our animals to deliver the goods.

The bacteria need sugars that they get from root exudates. Some of the sap that carries the sugars created by photosynthesis down to the roots is exuded into the soil.

As sunlight enables the photosynthesis through which sugars are made by plants, the soil organisms are fed indirectly by sunlight.

The mineral balance and health of the plant affects the quality of sugars exuded from plant roots.

For example, the element magnesium is needed by the plant to assist this photosynthesis process, and other elements, such as boron, assist the plant to move the sugars down to the roots and the soil nutrients up into the plant.

Animals and humans should obtain what they need from plants, and these plants should obtain what they need from the soil, air and light, rather than feeding minerals directly to animals and humans.

cows on pasture

When we try to take short cuts to speed things up, trouble may lurk and it often ends up being the long way round as well as the wrong way round. In this circle of life there are no free lunches and everything has to work for its living. Human intervention is part of this cycle and to get our “lunch” we need to do our bit with sensitivity and understanding.

Our first commandment for farmers, as in medicine, should be, “do no harm.”


Energy Cycles & The Soil Food Web

Sunshine begins the energy cycle and enables the plant to form sugars, taking carbon and oxygen from the air and hydrogen from the water.

Carbon, hydrogen and oxygen are the main constituents of sugar. The plant shares some of the sugars with the roots, mycorrhizal fungi and soil bacteria.

Sunlight on corn leaves
Sunshine begins the energy cycle.

Most beneficial soil organisms are aerobic, breathing nitrogen and oxygen from the air that contributes to the protein they build.

Soil organisms feed other organisms of different species in a continuous cycle described by Dr. Elaine Ingham in the Soil Biology Primer as the soil food web.

Some scientists can spend a lifetime studying one or two species of one soil organism group. Dr. Ingham has identified 25,000 different soil organisms, and when she stopped counting it wasn’t that she had run out of organisms, but that she had more important things to do.

Soil microbiologists say that only about 2 percent of all the different soil organisms have been identified and given names.

What is surplus to these organisms in the soil is made available to the plants along with other minerals held in the soil. The energy cycle is long and involved, and where every living thing is fed and watered and contributes to the growth of other organisms.

Bacteria that cluster around the roots help protect plants from other organisms that would attack their roots. Bacteria are the beginning of the food chain in the soil.

Soil Food Web illustration

Many of them use the finely ground rocks that contain essential elements as the raw materials of soil life. They also need sufficient organic material to feed on and eventually they are eaten by other organisms.

Bacteria have the highest protein content of all soil organisms, so when they are eaten by other organisms, such as nematode worms, some nitrogen is given off — as the nematodes don’t need it all. This nitrogen is then available for plant roots to take up.

When a farmer can manage this process well, the nitrogen is released at a rate that plants can take up, rather than having an excess being available that is wasted and may pollute ground water. The plant can then process the nitrates into proteins.

The protein formed in the plant contains nitrogen and sulfur. This added to the elements, carbon, oxygen and hydrogen make up sugar.

Sunlight provides the energy for the development from sugar and nitrate to quality protein. There are a number of sugar forms as well as many forms of protein.

In my opinion the more complex the sugars and proteins that are formed, the better the quality of the fodder or food.

Plants that contain only simple sugars and nitrates are fodder for plant pests, which are usually simple organisms. Plants need to develop complex sugars and proteins to provide fodder suitable for animals and humans to eat.

However, if the plant takes up too much soluble nitrate at once it cannot turn it all into protein, particularly in dreary weather, and the nitrate in the grass becomes a problem for the animal that eats it.

Nitrates can turn into nitrites which inhibit good digestion and the movement of oxygen in animal blood and muscle.

Much of the nitrogen that plant roots take up is in the form of nitrates. Nitrates contain three parts oxygen and one part nitrogen.

Coriander roots in soil
Nitrates carry oxygen into the plant.

Nitrates carry oxygen into the plant and this oxygen may be more important than the nitrogen. The pore spaces in soil created by active biology enable the soil to hold more air that can sustain plant growth into cooler, wetter weather periods.

Air contains oxygen that is vital to all living things as well as being the most active paramagnetic element on the earth. To get good root growth the soil needs a paramagnetic element.

Where there is oxygen, aerobic organisms are encouraged, while the pathogens that are usually anaerobes are greatly diminished.

If air and moisture are not in the correct ratios in soil pores there is insufficient oxygen and moisture for the beneficial bacteria and fungi, so the pathogenic organisms tend to develop. Pathogenic organisms can breed many times faster than those we consider to be beneficial to the crops we wish to grow.

It is therefore most important that we create the right conditions in the soil to achieve our objectives.

Fungi are another primary organism type in the soil. Some varieties are involved in the breakdown of woody material and dry stalks into soil-releasing nutrients.

Another important type is the mycorrhizal fungi which attach themselves to plant roots where they receive sustenance from the plant and in return draw in nutrients from beyond the reach of the plants roots.

mycorrhizal fungi
Healthy mycorrhizal fungi are key to healthy pastures (image from book)

Mycorrhizal fungi play a key role in collecting up phosphorus and calcium for plant roots.

If soil biology is not working properly, these elements remain locked up in the soil. The fungi are able to hold phosphorus and calcium until the plant needs them.

When you think that each of these species has a specific role in nutrient cycling in the soil, it shows how difficult it would be to replace soil biology with soluble fertilizers and get it right.

Nature knows best! In our time of climate change and weather extremes, it is very important to have a large diversity of soil biology that can provide flexibility.

If you have a range of species, each of which functions at a different temperature or water table level, your pasture can keep growing in a much wider range of weather conditions than pasture that is depending on a few species of biology or on soluble fertilizers.

In order for nutrients to be released by soil organisms at the rate that pasture plants can take them up, it is important to have a well-balanced population of the various types and species of soil organisms. Otherwise you can get a lot of release at the wrong time and the nutrient can be leached. Applying compost teas can sometimes lead to this problem, as the organisms introduced may put the whole soil population out of balance.

Soil organisms help to form humus which stores nutrients and holds water in the soil. Humus increases the flexibility of the soil to sustain plant growth into a hot, dry period and creates a much reduced need for irrigation water. Just 2.2 pounds (1 kg) of humus can hold almost 9 pounds (4 kg) of water.

Steps to Improving Soil Fertility – Observing Your Conditions

The first step is to test your soil, pasture and water to understand what you have in the way of minerals in soil and plant material. At the point of collecting these items you should do a thorough physical examination of the soil, plants and animals, noticing how much air space or crumb structure is in the soil and how many worms are active and at what level they reside.

Earthworms in soil
Worms are a clear sign of soil health.

How often do you take a spade, dig out a scoop from your pasture and have a look at what is going on underneath? Are there worms wriggling about, little hoppers, beetles or millipedes, and white fungal strands? Or does the soil look hard and lifeless? This is one of the initial things I do when I visit a farm, right after observing how the livestock and pasture look.

One thing to notice is whether the organic matter in the root zone is being consumed or is it gathering as a thatch layer? This will vary according to the season and moisture conditions.

Also look between the grass stems for worm castings. How many and how big they are should be noted.

In the pasture, take a look at what species of plants are present, what your animals are eating and in what order of preference they are being eaten.

Then look at the drainage. When it is wet, look at where and for how long the water lies on the surface before soaking in.

Knowing what sort of underlying rock your land sits upon and what sort of history it has had is also important information. How long has it been since the last ash shower, if you farm in an active volcanic region, or was the soil upon which you farm washed in or blown in by the wind?

What was on your land before it was farmed and for how long has it been farmed?

When all this information is assembled you can then decide what actions you should take to improve the performance of your land for what you wish to produce.

This might be to apply minerals that are shown to be in deficit on your soil test. You might also consider applying a liquid fish, seaweed or biodynamic spray.

The main point of difference between biodynamic and conventional farming is that all the nutrients should be biologically available, as opposed to being water-soluble with conventional methods.

This means that a plant can choose to take up clean water when it needs to transpire and can draw up nutrients when and as they are needed. The various measures you can take to activate your soil are discussed in upcoming chapters.

Many farms specialize in one or two enterprises which results in specific fertility needs and pasture requirements. For example, the dairy cow requires a different fodder from beef animals, sheep, goats or horses.

Most of us look to minerals for answers to fertility problems, and many farmers take advice from the sales representatives of the various chemical fertilizer companies. From one aspect this is the cheapest advice but for some it can be the most expensive.

How often does a fertilizer sales agent recommend something that his or her firm does not sell? Consequently little attention is paid to soil biology or the dynamics around life and growth.

Organic farmers generally focus on soil biology, but for the biodynamic practitioner, the dynamics and identity of the farm are the first considerations before soil biology, and biology comes before the minerals.

From my perspective, all of those areas should be integrated together. In farming we are working with life and life processes that are interrelated. Focusing on only one thing can throw the rest out of balance.

When I approach a farmer I inquire about which area they understand best and ask them where they want to go. Then I consider their present farm situation and how the dynamics of energy, biology and minerals can be adjusted to help them work toward their goal.

A farmer’s prime objective should be to get the fodder plants growing like weeds.

My definition of a weed is a plant that self-propagates, grows luxuriantly, and for which one has not yet developed a market.

To get our cultivated plants growing like weeds we often need to make some interventions. These interventions could be the addition of finely ground, mineral-rich rockdust, developing and encouraging the soil’s aerobic biological life or managing the energy or dynamics of our farm environment consciously.

To this end we might be working with composts, a manure heap, or an effluent to which special herbs, seaweed or biodynamic preparations might be added.

This is an extremely simplified look at one or two functions that occur in the soil. I have observed that when we have the whole organism of our farm or garden balanced in every respect, plants and animals are much better able to find the nutrition they need.

Want more? Buy the “Biodynamic Pasture Management” book at the Acres U.S.A. bookstore.

About the Author

Peter Bacchus has years of biodynamic farming experience. Raised on a biodynamic dairy farm, he served apprenticeships on other dairy farms while growing up.

Author Peter Bacchus
Peter Bacchus

He studied and worked on biodynamic farms and in a nutritional research laboratory in Switzerland. Later he worked as a medicinal herb grower, developed a large-scale composting business, and converted a commercial glass house to the biodynamic method, which included successful control of whitefly and fungal problems.

Bacchus consults widely and has held leadership positions in biodynamic farming organizations. He lives with his wife Gill near Palmerston North, on the north island of New Zealand.

Soil Health, Quality & Microbial Diversity

By Bob Kremer, Ph.D. 

Soil health and soil quality have evolved as important concepts as we continue to expand our understanding of soil as the vital factor for vigorous plant productivity. These concepts have also stressed our awareness that soil is indeed a limited non-renewable resource that requires deliberate stewardship to avoid or minimize its degradation.

According to John W. Doran, soil health is the capacity of a soil to function and sustain plant and animal productivity, maintain or enhance water and air quality and promote plant and animal health.

Optimal soil health requires a balance between soil functions for productivity, environmental quality and plant and animal health, all of which are greatly affected by management and land-use decisions. Soil health focuses on the living, dynamic nature of soil that incorporates the biological attributes of biodiversity, food web structure, ecosystem functioning and the intimate relationships of soil microorganisms with plants and animals.

Soil quality also refers to the functional capacity of soil, but has a greater emphasis on agricultural productivity and economic benefits. Indeed, the development of the modern soil quality concept by Warkentin and Fletcher in 1977 was within the context of intensive agriculture, where the major concerns were food and fiber production and the capacity of soil to recycle nutrients, presumably from residual fertilizers and crop residues.

The term soil health, with its focus on biological function and protection of environmental quality, is most relevant for eco-agriculture production systems promoting good management practices that foster a balanced focus on all functions of soil health rather than an emphasis on single functions, such as crop yields.

Several articles published in Acres U.S.A. within the past decade illustrate how eco-agriculture embodies soil health, which is an inherent benefit of this production system. In a series of articles from 2012 to 2015, Gary Zimmer focused on the importance of mineral nutrition for both plants and soil microorganisms for improved soil health. He also stated that the capacity of a healthy soil to function could be realized without intervention, suggesting that eco-agricultural systems facilitate functional capacity by minimizing disruptive management of synthetic fertilizer, pesticide inputs and intensive tillage.

John Ikerd, writing in the May 2012 issue of Acres U.S.A., eloquently proposed that declining human health and inadequate nutrition in the United States is related to nutrient-deficient foods produced on soils of poor health resulting from industrial agricultural production practices. A summary of research reported by Reeve et al. in Advances in Agronomy validates Ikerd’s hypothesis and further shows that crops grown in biologically rich soils developed under sustainable farming practices lead to nutrient-dense foods.

Roles & Characterization of Soil Microbial Diversity

In this article we will expand on the role of microbial diversity relative to soil health and demonstrate how this relationship is useful in understanding effects of crop and soil management. Farmers and supporters of eco-agriculture recognize the vital importance of soil microbial diversity as a key resource for maintaining the functional capacity of both agricultural and natural ecosystems.

Previous articles in Acres U.S.A. have discussed the many functions driven by soil microorganisms that are critical for vigorous plant growth including nutrient cycling; decomposition of organic substances leading to soil organic matter (SOM) and aggregate formation; protection from plant pathogens; and synthesis of plant growth-regulating compounds for root growth stimulation and vegetative production. Thriving microbial communities are most abundant on plant roots and within the rhizosphere of plants that exude part of their photosynthetically fixed carbon through roots to feed the microorganisms as they mediate various biological processes (Figure 1).

Bacteria and fungi
Figure 1: Bacteria (small rod-like structures) and fungi (larger spherical shapes) associated with the surface of a root (rhizoplane) readily use organic substances released by the plant as sources of food and energy for mediating many biochemical processes and to maintain dense communities in the rhizosphere. Note the non-random distribution of bacteria showing concentration of cells on the rhizoplane where several processes take place including nutrient transformation, synthesis of plant growth-regulating compounds and antibiotic production for protection from attack by pathogenic microorganisms. Micrograph presented as 5,000X magnification. Source: R.J. Kremer

Although abundance of microorganisms in soils and rhizospheres is readily apparent, we often overlook the importance of microbial biodiversity required for effective performance of most functions. For example, degradation of complex organic substances such as lignin and cellulose in plant residues requires select groups of microorganisms, often termed consortia, wherein each member produces specific enzymes to carry out one or more steps in the degradation pathway.

Bruce Tainio: Amending Soil Microbial Life, from the 2005 Eco-Ag Conference & Trade Show. (1 hour, 2 minutes) Listen in as the popular agronomist explains how to feed the microbial life in your soil, and develop optimal microbial biodiversity.

For example, lignin degradation begins with attack by lignin-decomposing fungi that facilitate initial breakage of the polymer that is sequentially cleaved into simpler compounds by different specialist microorganisms at each step until simple carbon compounds become food and energy for microorganisms or small fragments incorporated in soil organic matter are formed. Thus, practices that disrupt the soil microenvironment and suppress any of the dozen or so microorganisms needed for degradation of lignin or other substances may disrupt overall decomposition and formation of SOM.

Understanding the microbial diversity and functional capabilities of soil in agricultural ecosystems can be used to guide and monitor crop and land management. Despite the widely accepted view that microbial structural and functional diversity are critical components for describing soil health, there are few microbiological indicators assessing soil health compared with those for chemical and physical properties.

The lack of microbiological indicators is because the majority of the microbial world cannot be easily cultured to characterize those individuals or groups that mediate the important biological processes in soil and aquatic environments. However, advancements in methods to overcome challenges of measuring the great numbers of microorganisms in soils and the difficulty in culturing provide some alternate approaches based on microbial community structure and function.

Several laboratories in the United States can now characterize microbial communities in soils based on cellular composition of phospholipid fatty acids (PLFA).

The total PLFA content is a measure of the viable microbial biomass present in soil. Identification of individual PLFAs (“biomarkers”) allows classification of specific functional groups of microorganisms (bacteria, actinobacteria, fungi and protists). These biomarker PLFAs yield a pattern of the members of the microbial community for soils of different ecosystems under various land management practices. Depiction of these microbial PLFA groups combined with information from other soil health indicators provides a robust understanding of the functional capacity of soils.

To show how microbial analysis can be applied for soil health assessment, we used PLFA tests to characterize soils under various management practices on a diversified, organic ecologically based farm on a gently sloping landscape predominated by Sharpsburg silt loam in northwest Missouri.

The farm transitioned to organic farming over the past 15 years with restoration of SOM through organic amendments of composts, mulches and biochar and establishment of a reconstructed native prairie ecosystem. An orchard, including a variety of heirloom fruit trees, was established with native prairie plants positioned in the alleys.

Soil microbial biomass represented by total PLFA content is depicted in Figure 2 below as the total height of the bars indicated for each management treatment.

kremer graph
Soil microbial community structure on an organic farm in northwest Missouri. Microbial components are expressed as content of phospholipid fatty acid (PLFA) markers specific for each component. Cnv Orch = conventional orchard and alley (Cnv Alley) with no organic amendments with tall fescue alleys; Org Orch, Org Alley, Org Alley+BC = organically managed orchard, alley and alley supplemented with on-farm produced biochar; Rest Prairie = restored prairie site established in 1995 on sloping landscape with eroded topsoil; Grass = old cool-season grass and forb hayfield with no management; Cultivated = nearby field cropped to corn-soybean rotation with chemical inputs and no cover crop. VAM, vesicular arbuscular mycorrhizae; Actino, actinobacteria; G pos Bac, Gram-positive bacteria; G neg Bac, Gram-negative bacteria.

Microbial biomass is constantly recycled through rapid cell generation to decomposition cycles (“microbial turnover”) and is incorporated into soil organic matter, which contributes to important soil properties. Decomposition of biomass releases available N to both plants and the living microbial community and thereby sustains biological processes in healthy soils.

The high microbial biomass associated with the continuous presence of living roots of prairie plants helps explain the high productivity and soil fertility observed on this farm.

Microbial biomass and all microbial components were highest in the organic orchard that was managed with perennial native vegetation in the alleys plus compost amendments around each tree. Microbial parameters were increased further in portions of the alley where biochar was applied. Mycorrhizae (VAM) were also more abundant in organic treatments indicating better nutrient (P, N, K) mobilization, water availability and protection from root pathogens with these symbiotic fungi. Microbial status of the restored prairie approaches that of the organically managed orchard, but because it was established on the most eroded landscape, reestablishment of the microbial community has been slower.

The results of this long-term study, reported in 2015 eOrganic News, demonstrate how ecologically based management practices enhanced soil biological function, improved overall soil health, promoted the production of horticultural crops without synthetic chemical inputs and improved environmental quality.

Soil Health Assessment

Despite the current interest in the soil health concept and its popular appeal for potential use in developing management decisions, standardized testing for soil health is not yet available. Several public and private laboratories offer soil health analyses based on various physical, chemical, biological and plant nutrient indicators and may include soil health ratings based on different models that incorporate some of the indicator results. This has prompted establishment of interdisciplinary groups such as the Soil Health Institute and the Soil Health Partnership to develop rigorous research protocols, assemble broad soil health databases for representative soils under different management regimes in various agro- and natural ecosystems across geographic regions; and develop a decision support system for farmer use.

Neal Kinsey, Using Soil Analysis to Grow Crops, from the 2005 Eco-Ag Conference & Trade Show. (50 minutes, 12 seconds). Listen in as agronomist Neal Kinsey, the author of Hands-On Agronomy, teaches about how to test your soils, and use that data, to increase crop yield and decrease weed pressures.

Until a standard and accepted system for soil health assessment is in practice, we can consider the principles of assessment, show how a rating can be derived and how this information can be used to assess and adjust your current management system.

Currently, soil health can be directly measured using a suite of selected biological, chemical and physical properties that are highly sensitive to changes in soil function. Soil health indicators should correlate well with ecosystem processes, integrate soil properties and processes, be user-friendly and be sensitive to management and climate. Soil indicators that indirectly measure soil function should represent the diversity of chemical, biological and physical properties and processes of the complex soil system.

Some soil health indicators in wide use include measurements of SOM or soil organic C, microbial biomass C, potentially mineralizable nitrogen (N), aggregate stability, pH, soil nutrient contents including phosphorus (P), potassium (K), and magnesium (Mg); available soil water-holding capacity (AWC), bulk density; topsoil depth; infiltration rate; and soil enzyme activity, specifically beta-glucosidase activity, which is involved in vegetative residue decomposition.

For purposes of this article, the soil management assessment framework (SMAF), developed by USDA-ARS at Ames, Iowa, is used as an example of a model-based program incorporating multiple indicator measurements into an assessment protocol to rate soil health of various ecosystems within landscapes of similar soils in a climatic region. When SMAF was used to evaluate soil health of various sites on claypan soils in northeastern Missouri, pasture and prairie ecosystems comprised of perennial vegetation rated highest relative to agro-ecosystems (Figure 2).

Interestingly, an organically managed pasture of mixed cover crop species (triticale, birdsfoot trefoil, turnip) combined with grazing sheep attained the next to highest rating, showing this management system allowed soil to achieve 97 percent functional capacity; in contrast, a nearby conventional corn-soybean system managed with tillage and chemical inputs functioned at 77 percent.

The survey also showed that crop rotations using no-till or mulch-till that included wheat and a cover crop or manure amendment functioned higher than the simple corn-soybean rotation with tillage. Although we expect prairie ecosystems to rate highest in soil health, we sampled a hardpan prairie with frequently saturated soil and, combined with accumulated decaying organic matter, results in low pH of 4.5-5.0. The rating index is thereby reduced because the model uses an optimum pH indicator value for acceptable plant growth.

This example evaluation validates the ability of well-managed ecosystems such as organic pasture and long crop rotations with cover crops to promote soil health and may serve as examples for farmers looking to develop improved agricultural practices for improving soil function. We can also see that integration of perennial vegetation may improve soil health and environmental quality within agroecosystems by adapting these systems as conservation strips within crop production fields or as field buffers.

Management Implications

More work is needed to improve soil health assessment by expanding measurements for the soil biological diversity and microbial components to be included as critical indicators of soil biological processes. Current models only accommodate values for soil microbial biomass C and one soil enzyme activity despite the view that soil biological processes, along with SOM, are key factors in achieving adequate long-term soil health and environmental quality. Addition of microbiological indicators for the soil health assessment presented in Figure 3 could likely magnify the contrasts among ratings and yield more insight on management system effects.

kremer chart
Soil health index for assessing crop management systems derived using the Soil Management Assessment Framework (SMAF) for soils collected in the Salt River Basin in northeast Missouri. CRP, Conservation Reserve Program acreage; CSG, cool-season grasses; WSG, warm season grasses; NT, no-till; MT, mulch-till (non-inversion tillage such as disk harrowing to partially incorporate residues left on the soil surface); C, corn; Sb, soybean; Wh, wheat; RCl, red clover; Cont., continuous.

Farmers using eco-agriculture practices already know their effectiveness in improving and maintaining soil health; soil health assessment of their systems would validate their management or suggest that it could be adjusted for further improvement. Soil health assessments of eco-agricultural management can be important as models for other management systems that require adjustment to improve the functional capacity of soils.

Soil expert and author William McKibben, The Art of Balancing Soil Nutrients, from the 2009 Eco-Ag Conference & Trade Show. (1 hour, 8 minutes). Listen in as McKibben talks about the steps you can take after you receive your soil test results to help balance your soil.

As soil health working groups assemble datasets for use in developing assessment models and management guidelines, it is imperative that soils from working eco-agricultural farms are tested to assure that the range of indicator values include the potential for optimum performance achieved by these systems.

Farmers wishing to transition from management based on genetically engineered (GE) crops and Roundup (glyphosate) herbicide for weed control will find proven practices from eco-agriculture to rehabilitate their soils for non-GE crop production.

Soils managed under an industrial production mindset have greatly altered microbial diversity as shown by glyphosate released through corn and soybean roots that increase Fusarium and decrease beneficial bacteria (Figure 4), potentially leading to root disease and disruption of nutrient availability to crops. We also know that repeated use of glyphosate reduces mycorrhizal spore germination and root infection or hinders development of the symbiotic association on infected roots; it also suppresses both symbiotic rhizobial and non-symbiotic nitrogen-fixing bacteria; and inhibits some of the microfauna (nematodes and protozoa) involved in nutrient cycling in the soil food web.

Roundup Ready soybean planted into tall fescue killed with Roundup burndown application (upper left) and not treated (upper right); note difference in apparent plant vigor of soybean due to planting into sod two days post-herbicide application. Soybean plants were excavated and roots cultured on a medium selective for the fungi Fusarium spp. (lower photo); left plate shows proliferation of Fusarium spp. (white circular colonies) on soybean roots from plants planted into Roundup-killed sod due to glyphosatemediated stimulation of Fusarium spp. on dead fescue that also colonize soybean roots; right plate shows soybean roots not affected due to no glyphosate treatment. Soybean grown in Jemerson silt loam on author’s family farm in central Missouri.

We are now finding glyphosate residues in soils of up to 1 ppm even one year after last application — the consequences of these residues on soil biology and health are yet to be determined. Practices based on eco-agriculture management can be effective in restoring such degraded soils by establishment of living root systems through cover cropping and/or extended crop rotations; organic amendments and application of effective biological products including inoculants; and integration of livestock (if plausible) can improve soil health necessary during transition to more sustainable agricultural production systems. Therefore, the soil health status achieved in eco-agricultural systems serves as a valuable guide for restoration of soils for farmers seeking balanced sustainability in their management that reflects the vital soil health functions of productivity, environmental quality and plant and animal health rather than focusing on only economic yields.

This article appeared in the December 2016 issue of Acres U.S.A. magazine.

Bob Kremer, Ph.D., retired after 32 years of service as a research microbiologist with the USDA Agricultural Research Service at Columbia, Missouri and currently holds a position as Adjunct Professor of Soil Microbiology in The School of Natural Resources at the University of Missouri. He has published 150 research articles on biological management of weeds; impacts of transgenic crops and glyphosate on soil biology and ecology; plant-microorganism interactions; and soil health.

Acres U.S.A. magazine is the national journal of sustainable agriculture, standing virtually alone with a real track record — over 45 years of continuous publication. Each issue is packed full of information eco-consultants regularly charge top dollar for. You’ll be kept up-to-date on all of the news that affects agriculture — regulations, discoveries, research updates, organic certification issues, and more.

Building the Microbial Bridge for Soil Health

By Gary Zimmer and Leilani Zimmer Durand

The root zone around plants, known as the rhizosphere, is an area of intense activity in the soil. It’s a lot like the snack stand at the state fair on a hot day. Everyone is crowding around trying to get to the cold drinks, funnel cakes and hot dogs. Snacks are being sold as quickly as the workers can make them. In return, the snack stand is bringing in a lot of cash.

While the snack stand exchanges food for money, plant roots feed nearby microbes in exchange for plant nutrients. The roots put sugars down into the soil, creating an area of crowded, busy bacterial feeding in the rhizosphere, and exchange that microbial food for nutrients the plant needs but would otherwise have a hard time accessing.

We tend to think that plants photosynthesize entirely for their own metabolism, but in truth plants spend a good portion of their energy feeding soil life.

corn roots
Corn roots with lots of root exudates and soil sticking to the roots.

Plants fix sugars through photosynthesis, and while 55 to 75 percent of those sugars support plant growth, reproduction and defense from pests, the rest goes into the soil through the roots to feed the soil biology. This isn’t a waste of energy by the plants.

Bruce Tainio: Amending Soil Microbial Life, from the 2005 Eco-Ag Conference & Trade Show. (1 hour, 2 minutes) Listen in as the popular agronomist explains how to feed the microbial life in your soil, and develop optimal microbial biodiversity.

Those organisms living in the rhizosphere, primarily bacteria, not only make nutrients available to the plants — they also provide a protective layer against pests and diseases. It’s a win-win for the plants and the bacteria living in the rhizosphere.

It’s strange to think that plants have a hard time getting enough nutrients when soils are composed of around 45 percent minerals. Many of those minerals are the nutrients plants need to grow, photosynthesize, flower, pollinate and produce fruit or seeds. Although soil is a huge bank of minerals, most of those minerals are not in a form the plant can use.

Nitrogen, sulfur, phosphorus and many trace elements are all either dependent on soil life to make them plant-available, or they greatly benefit from microorganisms changing their form from one that’s hard to utilize to one that’s ideal for the plants.

An analogy I once heard at a farming conference in Australia is that microbes are the bridge between the soil minerals and the plant roots. I really like that analogy, but I would add to it that it’s an active bridge, one where transformations are taking place as things cross the bridge — like a highway bridge that takes semi-trucks full of minerals and converts them as they move across so they end up being small boxes of food at the other side, ready for plants to consume.

How the Microbial Bridge Works

The best example of the role of the microbe bridge in turning unavailable minerals into plant nutrients is how plants take up nitrogen. Just over 78 percent of the Earth’s atmosphere is nitrogen, but in its gaseous form nitrogen doesn’t do the plants much good. It’s like being thirsty while lost at sea. You may be surrounded by water, but you sure can’t drink it!

Plants are surrounded by atmospheric nitrogen, but only microbes are able to turn that nitrogen into a usable form. Microbes also provide nitrogen by transforming soil organic nitrogen (the nitrogen tied up in microbe bodies, mainly in the form of amino acids and proteins) and making it mineral nitrogen in forms of ammonium and nitrate that plants can take up. Without microbial nitrogen fixation and microbial breakdown of organic nitrogen into mineral nitrogen, there would be a great deal fewer plants on our planet. The microbes are the bridge that make the soil/plant system work.


Sulfur follows a similar process, but without the atmospheric fixation component. Most of the sulfur in the soil is organic sulfur, tied up in living and decomposing microbe bodies, and it takes microbes to change organic sulfur into plant-available sulfate.


Phosphorus is another mineral that greatly benefits from microbial transformations. Most farmers are aware of the important role of mycorrhizae in increasing the root surface area and accessing phosphorus that plants would otherwise have a difficult time accessing. It is less well known that up to 50 percent of the phosphorus in soil is organic phosphorus, tied up in living microbes and decomposing roots and microbes.

corn nitrogen comparison
The corn on the left was grown following a worked-down mature vetch crop, while the corn on the right was grown following a worked-down young clover crop. While both cover crops provided ample nitrogen credits, the mature vetch tied up nitrogen as it broke down because it was more lignified, and that nitrogen wasn’t available for the following corn crop. The young clover plants broke down quickly and rapidly released ample nitrogen to support the corn crop.

Organic phosphorus is mineralized to plant-available forms only through microbial activity. Phosphorus converts easily into unavailable forms in both acidic and alkaline soil conditions, so it is a huge advantage to have it in an organic form where it is relatively stable until microbes can mineralize it into a plant-available form.

Many other micronutrients benefit from the microbial bridge to make them plant-available. Microbes can change the form of a nutrient, change its charge, or hold it in a way that makes it less likely to tie up and easier for a plant to take up when it’s needed.

In addition to the role of the microbial bridge in changing the form of nutrients to make them plant-available, microbes are also a highway of nutrient movement and nutrient-holding capacity. While many nutrients require microbes to change their form, all plant nutrients benefit from microbes moving them around, concentrating them in the rhizosphere, and holding them in their bodies so they don’t tie up into forms that are mostly unavailable to plants.

On-Farm Intensive with Zimmer Ag

Learn about soil health in person with Gary Zimmer

The Acres U.S.A. On-Farm Intensive – starting in summer 2021 – is held in partnership with experienced farm consultants Gary Zimmer and Leilani Zimmer-Durand at their famous Otter Creek Farm near Lone Rock, Wisconsin. This two-day educational experience will help farmers, growers and land owners maximize their land’s potential. 

Learn more here!

Building Your Bridge

Knowing how important the microbe bridge is to plant growth and health is a great incentive for building a stronger bridge on your farm. There are a number of different practices that enhance the strength of the microbe bridge, and all involve feeding an abundance of soil biology year-round.

Biology is the key to building a strong microbe bridge, and diversity is what leads to abundant biology. You need diversity because the plants determine the soil life, and different types of plants both feed and benefit from different types of soil life. It’s just like choosing the right inoculant for your legumes — you wouldn’t use the same one on soybeans as you would on clover. The plants are specific to their microbes.

This is true not only for the microbes living around the roots in the rhizosphere, but also for those that digest plants in the soil. The stage of maturity when you feed the plant to the soil microbes is critical if you want to control nutrient availability and biology.

Young succulent plants have a different solubility, or as dairy people call it, “digestibility.” If you want to grow a crop like corn that requires a lot of soluble nutrients and extra nitrogen, you feed the soil microbes a highly digestible crop like young rye plants or alfalfa. Not only will these plants release nutrients quickly as they break down in the soil — they are also high in sugars that feed soil bacteria.

Soil bacteria consume easy-to-digest materials and have a 5:1 carbon-to-nitrogen ratio in their bodies. They live and die quickly and are consumed by other soil organisms like protozoa, which are closer to 10:1. The difference in the C:N ratio of the protozoa compared to the bacteria means there is a lot of extra nitrogen the protozoa don’t need for their own metabolism that gets excreted back into the soil as plant food. By feeding your soil bacteria you are also boosting nitrogen cycling and feeding your plants nitrogen.

If you allow your cover crop plants to get large, they will have more complex carbons and will be mostly fungal food. This gives a very slow release of nutrients and leaves behind more undigested, highly complex carbon. It’s good for building soil organic matter but not so good if you farm organically and need a lot of active nutrient cycling in your soils because you can’t buy commercial soluble fertilizers to make up for the nutrient tie-up as the lignified plant materials slowly break down.

Growing mixed plant species also results in a more heterogeneous group of microbes and digesters in the soil in which no one population can become dominant. This keeps things in check. The diversity of plant species also builds a stronger microbial bridge that provides a variety of minerals and plant compounds essential for plant health.

healthy soil life and cover crop
Healthy soil life with a newly incorporated mixed-species cover crop. This young cover crop will provide nutrients and carbon to feed the soil biology as it breaks down.

Microbial digestion is also affected by air. Burying residues deep may not be ideal for the type of organisms you want to have in your soil. That’s why I like to shallow incorporate my residues.

By shallow incorporating, some of the residues do still remain on the surface to protect the soil from runoff, but most of them are in the shallow aerobic zone of the soil where they can be broken down by beneficial microbes.

The bigger and denser the crop being worked in, the deeper it can be incorporated without harming soil structure or going down into the anaerobic zone where it won’t break down easily because there is much less microbial activity. Strict no-till with chemicals may be your methods of managing cover crops, but you do give up some benefits of microbial digestion if you don’t incorporate your cover crop. This is still better than not growing cover crops at all, but it’s like putting part of the feed you give your cow on the other side of the fence!

Your soils have a certain ability to dish out minerals, and the microbial bridge is key to making those minerals that are already in the soil available to plants. But that may not be enough. You need to apply fertilizer to feed your crop above and beyond your soil’s ability to provide minerals. That’s how to get high yields on lighter soils.

Be sure to add only quality, low-salt, balanced nutrients. By applying nutrients that are mixed with or bound to carbon, the fertilizer mirrors how things work in the soil. For liquids, molasses-based fertilizers provide sugars that not only buffer out the fertilizers but that provide readily available food for the soil biology to support the microbial bridge.

For dry granulated fertilizers, I like humates and fertilizers made with the digestate from anaerobic digesters on dairy farms. What comes out of the manure digester after the easy energy has been turned into methane is a mix of minerals, fiber and dead bodies of bacteria. We remove the fiber and add other minerals to make fertilizers. Not only are the nutrients in a carbon base, but they also have biological stimulants along with humic acids. This mirrors what happens in active, healthy biological soils to support microbial activity.

Being a biological farmer means switching focus from chemistry to feeding and taking care of soil biology. The emphasis is on the microbial bridge, rather than on soluble fertilizers, to get nutrients to plants. When the soil, plants and microbes are in balance, and a fertilizer that includes trace minerals is applied, you should not need to buy all the plant-protective compounds, technologies and chemistry that many farmers today depend on. Not only are those inputs expensive, but they won’t make your farm any better in the future. Build a strong microbial bridge, focusing on biology and soil health, and you will be well on the road to being a successful biological farmer.

By Leilani Zimmer Durand & Gary Zimmer. This article appeared in the December 2018 issue of Acres U.S.A. magazine.

Gary Zimmer and Leilani Zimmer-Durand are the authors of Advancing Biological Farming, a sequel to Gary’s earlier book, The Biological Farmer — both published by Acres U.S.A. Leilani has written extensively about biological farming and runs training courses for farmers and farming consultants on the principles of biological farming at Midwestern BioAg, where she serves as vice president of education initiatives.

Gary is an organic dairy farmer, an accomplished speaker, a sought-after farm consultant and president of Midwestern BioAg, a biological farming products and services company.

Gary and Leilani also previously presented at the 2018 Acres U.S.A. Conference & Trade Show in Louisville, Kentucky. To download audio and video of their presentations, visit Acres U.S.A.

Learn in the field with Gary Zimmer!

Spend 2 days this summer on Gary Zimmer’s Otter Creek Organic Farm in Lone Rock, Wisconsin. Learn how to use biological farming for better soil health and to improve your farming operation. July 19-20, 2021. Learn more here!

The Acres U.S.A. On-Farm Intensive is held in partnership with experienced farm consultants Gary Zimmer and Leilani Zimmer-Durand at their famous Otter Creek Farm near Lone Rock, Wisconsin. This two-day educational experience will help farmers, growers and land owners maximize their land’s potential. Learn more here!