The Biology of Soil

The Biology of Soil

Using Ruminant Animals and Foliar Feeding To Build Soil Health and Address Climate Change

by Steven Rockcastle of Panama, NY

The following article was written for a presentation at NOFA-NY Winter Conference 2019. I have become increasingly passionate about building healthy soils and quality nutrient dense forages through my journey to raising 100% grass fed beef and certified organic broiler chickens. This article came about from the lack of farmers and ranchers who understand how healthy soil is created and sustained.

Currently, we are over-wintering 54 purebred Red Devon and Devon cross cows. Of those 54 there are 18 brood cows, yearling heifers and steers and spring born calves. Our demand for butchered steer is greater than our supply so we purchase additional yearling steers to fill the freezer beef demand. We own 300 acres of land and lease an additional 100 acres. The farm is predominantly on leased property consisting of approximately 85 acres of pasture with the remainder being a combination of single cut hay fields and woods. Of the wooded area, maybe 30 acres are silvopasture for the cows in the summer. In addition to our beef herd, we raise 600 broiler chickens on pasture using the Joel Salatin chicken tractors, operate a 2000 log shiitake mushroom operation and collaborate with an Amish 100% grass-fed dairy who raise pastured pork for us. We market our products through a farm store on our property as well as several farmer’s markets both in the summer and the winter.

What exactly do I mean when I talk about soil biology? In my earlier life, soil biology was more in reference to NPK and what inputs I needed to give the plant in order for it to grow. That was pretty much a sequence of constantly feeding the plants low doses of chemically derived nutrients on a consistent basis. There was no talk of “living soil” and how that living soil can maintain all the needs of the plant throughout its growing cycle.

The Biology of Soil

In the last few years I have noticed a lot of buzzwords being used around the grazing industry and in my readings, like sequestration of carbon, living soils, microbes, mycorrhizal fungi, biochar, regenerative agriculture, micro-biome and cover cropping. These all are in reference to techniques and terminology associated with awareness of soil biology. If any of you are like me, I sometimes will not ask a simple question because I don’t want to sound uninformed, so today I will start out with a simple explanation as to what the natural cycle of plant photosynthesis is and how a plant goes about getting the nutrients it needs to grow.

“Imagine there was a process that could remove carbon dioxide (CO2) from the atmosphere, replace it with life-giving oxygen, support a robust soil microbiome, regenerate topsoil, enhance the nutrient density of food, restore water balance to the landscape and increase the profitability of agriculture?

“Fortunately, there is. It’s called photosynthesis.” Dr. Christine Jones, a soil ecologist in Australia has developed a web site,, dedicated to helping others understand the critical role carbon plays in ecosystem function, particularly underground.

The Biology of Soil

When a plant goes through the process of photosynthesis, it combines carbon from the air, water and sunlight and produces what is known as a liquid carbon solution. Liquid carbon is basically dissolved sugars. The sugars are formed in plant chloroplasts during photosynthesis. There is a tool used to check the sugars in the plant leaf called a refractometer. You can use this tool to read the amount of sugars in your forage. If you have never used one, the process is to take a selection of different leaves from your pasture and use a device to squeeze the juices out of the leaves and onto the plate of the refractometer. You take the unit and look through it into the sun. The reading in the viewfinder will tell you your sugar level from the squeezing’s. The plant uses some of these sugars for plant growth and the rest is sent down through the roots and exuded to feed the microbes as they work to acquire nutrients from the soil. This process was originally thought of to be a leaky root syndrome and it was thought to be a problem. Come to find out, this is a natural process and is the plants way of taking the excess carbon it produces and storing it in the soil. This actually is the way new topsoil is formed. This liquid carbon has also been found to have phenolic compounds with allelopathic effects. More simply put, these root exudates seem to have a way of protecting the plant by building the plants own immune response. One of my mentors, Jerry Brunetti, who started the company Agri-Dynamics, first introduced me to this. He spoke of the allelopathic properties in willows and how they help an animal to ward off parasites if you allow the cow to graze the leaves of the tree. I found that when my cows were allowed to graze the willow trees in my pastures, they would completely ignore the free choice mineral PC (parasite control) premix in the mineral box. I will go through some of the work I have done more recently on my farm to show how this works in real life situations later on.

In order to have that carbon flowing to the soil, there needs to be a relationship between the plant roots and the microbes. 85 to 90 percent of the nutrients plants need for healthy growth are received from that carbon exchange. More simply put, the roots supply the energy to the microbes and in exchange the microbes provide the minerals and trace elements that otherwise would not be available. The plant actually has the ability to signal different microbes to go after individual nutrients that it needs. This whole process is known as “the microbial bridge.” Our conventional farming practices have ruined this bridge by supplying high rates of synthetic fertilizers, fungicides and other biocides. These toxic compounds kill the microbes in the soil and break the natural cycle between the microbes that supply the nutrients bound in the soil and the roots, working to dissolve and take up the nutrients.

The Biology of Soil

There are many plants that use the synergy of a helping fungi known as Mycorrhizael fungi to increase its ability to absorb nutrients, increase water uptake and work as an intellectual network between plant systems. There are actually two different mycorrhizael fungi: the ectomycorrhizae and endomycorrhizae, the second one is also known as Arbuscular mycorrhizae. Mycorrhizae is known for its ability to penetrate the root cell walls and form highly branched structures known as arbuscles. The ectomycorrhizael fungi group includes hundreds of species that associate with hardwoods and conifers. Both forms cover the surface of the feeder roots and actually increase the surface area of the plant’s roots by seven hundred to a thousand times. In this discussion, I will be speaking about the Arbuscular Mycorrhiazae. This strain is the one that is associated with grass-fed production.

The basic premise behind the function of mycorrhizae is the effect this fungus has on the root systems of the plants and its ability to increase the plants outreach into the soil and its increased nutrient uptake. Mycorrhizae fungi produce thin hair like threads of cytoplasm (hyphae) with a hyphal tip at each end. One tip enters the root hair; the other explores the surrounding soil. Although the hyphae are small in diameter, the mycelial network can extend across many acres. This network extends well beyond the zone occupied by the roots and root hairs moving deep into the soil matrix. Their ability to absorb nutrients is about 10 times more efficient than the root hairs and about 100 times more efficient than that of the roots. In exchange for soluble carbon from the host plant, mycorrhizal fungi supply nutrients such as phosphorous, zinc, calcium, boron, copper and organic nitrogen. It has a symbiotic relationship with the nutrients. The fungi have the ability to move carbon in one direction while taking up nutrients from the soil in the other direction simultaneously. Mycorrhizae is best known for its relationship with phosphorous and its ability to retrieve that mineral from the soil. Phosphorous is a highly reactive element. As soon as there is any available in the soil, whether it is an element we add as fertilizer or organically available, it becomes fixed. What that means is that it will get bound to another element in the soil like iron or aluminum or calcium, making it unavailable to the plant. There are certain bacteria that produce an enzyme called phosphatase that can break that bond and release the phosphorous. Even though that element has been released, it still needs to be transported back to the plant. This is where the fine hair like filaments of the mycorrhizae come into play, to pick those elements up and bring them back to the plant root system. Plants colonized by mycorrhizae fungi can grow 10-20% times faster than non-colonized plants, even though they are giving away up to 40 – 50% of their photosynthate to support mycorrhizael networks. Photosynthate is the soluble carbon the plant fixed from CO2 and sunlight. One of the reasons for the increased growth is the plants colonized by mycorrhizae exhibit higher leaf chlorophyll content and a higher rate of photosynthesis than non-colonized plants. This enables them to fix greater quantities of carbon for transfer to fungal hyphae in the soil.

In 1996, USDA researcher Sara Wright discovered one of the most important carbon treasures in the soil named Glomalin. It is a glue like substance, which combines soil aggregates creating crumb structure and porosity for air and water movement. This glue like substance, which is actually secreted by the fungi, helps to insulate and hold moisture and nutrients as well as to protect the plants from fungal, bacterial and nematode pathogens. Glomalin is highly stable in the soil and is an important step in holding the organic carbon in place ultimately leading to the formation of Humus. Humus is a high molecular weight gel-like substance that holds four to twenty times its own weight in water. Humic substances significantly improve soil structure, porosity, cation exchange capacity and plant growth. The ability of the aggregated soil to hold water is also very important to the microbes as they move about the soil ingesting nutrients. The importance of a healthy mycorrhizael fungal network in the soil could not be understated when the subject of carbon sequestration is considered. A healthy network of fungi improves soil structure, promotes humus formation increasing the amount of stable carbon in the soil. Later on, I will cover the topic of ways to increase soil carbon in the soil.

The Biology of Soil

Increasing the amount of stable carbon in agricultural soils with the use of mycorrhizae will require different management strategy than what are now being used in American Agriculture. The use of tillage, lack of continuous ground cover, single species crops and pastures (monocultures) and the use of herbicides, pesticides and fungicides are the most limiting factors now facing our soils.

Another factor that limits the growth and vitality of mycorrhizae fungi is the over-use of water soluble phosphorous and the presence of non-mycorrhizal crops such as canola and plants in the brassica family. Soil disturbance can be a detriment to the mycorrhizal fungus but what is even more harmful is the use of chemicals in our agricultural practices. In the conventional farming industry, even those practicing no-till methods rely heavily on herbicides and GMO sourced seed. Farm soils are now becoming devoid of any beneficial microbes and are allowing the harmful predatory fungi to occupy the soil. The types of fungi that tend to survive in conventionally managed agriculture are non-mycorrhizal fungi. They use decaying organic matter such as stubble, dead leaves or dead roots as their energy source rather than being directly connected to living plants. The non-mycorrhizal fungi tend to have small hyphal networks. What is even worse, GMO seeds are now being developed that have no relationship to mycorrhizael fungi at all. These crops are now becoming totally reliant on chemical inputs to obtain their nutrients. We are now developing sterile soils with very little beneficial life to them at all.

Lets go through a review of how we got to where we are today in agriculture and how the soil got into the shape it is now. In an industrial agricultural farm, the way land is prepared to plant corn or other grain crops is to go out onto the field in the spring and spray the ground with an herbicide before planting, or in many cases that field has been in continuous production and has no weed pressure to speak of. The spray application will generally kill any weeds that have emerged in the spring and carry that weed suppression into the growing season. He then takes his huge tractor and goes through and plows the field. He will then fit the field, which means he goes over it again with equipment that will break down the clumps from plowing. If this is your traditional large industrial farm, he will now use a large multi-row planter to plant the GMO corn seed into the field. There is a good chance that there will be an injector on the side of the planter injecting ammonium nitrate into the field to feed the corn as it grows. To harvest this crop, the farmer will take his large and heavy piece of equipment and go through the field chopping the corn. Behind the chopper is a big dump truck receiving the chopped corn and taking it to a bunker for storage to feed his cows throughout the remaining year. If it is the case of a farm raising a grain crop such as wheat, before harvesting the grain, the field will be sprayed with an herbicide to kill the plant. This allows the grain to have a consistent moisture content before it is harvested. Unfortunately, over 98% of farming is done using these conventional practices. Our corn that is used in so many food crops, as well as the wheat, will all be used to produce the food we eat or the food to feed our animals we consume. This grain has a residual trail of herbicides, fungicides and biocides being carried into our food system and into our bodies. This is just one example of how the conventional Industrial Agricultural Farmer is exploiting our land and our bodies.

The Biology of Soil

I will go through a simple scenario and explain how this farming practice is detrimental to our soils and plant life. As the land is tilled year after year, the soil becomes more and more devoid of microbes and organic matter. As the organic matter is reduced, so goes the aggregated soil that holds the air and moisture. Along with that, the use of heavy equipment and continual plowing of the soil compacts the soil, squeezing the air and moisture out of it and creating what is known as hardpan. This hardpan reduces the amount of water able to infiltrate the soil as well as roots. One way the Corn Belt regions are combatting this problem is to install drainage tile to take the excess water away. The big question there is, why do you have excess water? Is it because the soil has lost its porosity and water cannot infiltrate the soil and get down into the aquifer? Could it be that farmers are not planting a diverse cover crop with living roots in the soil for more than a third of the year to take advantage of the moisture? What do you think happens to that water that is being moved off the soil surface and into the watershed? Most likely, that water is carrying large amounts of both nutrients and chemical residues along with precious topsoil into our waterways. As that water compounds down the waterways, the impact on wildlife, fish, water quality and humans can be devastating. Take this whole scenario one step further. Americans are at the top in incidences of chronic diseases such as attention deficit disorder, Alzheimer’s disease, cancer, osteoporosis, autoimmune diseases and the list goes on. As Michael Pollan states in “An Omnivore’s Dilemma,” much of what we eat is not food, it is “edible food-like substances.” There have been case studies showing that our food is becoming deficient in mineral content and nutritional density. Over 1/3 of the global population is chronically deficient in essential minerals. Obesity is growing in epidemic proportions. Our food industry is peddling calorie-dense diets that depend heavily on high fructose corn syrup and fatty soybean oil. Both of those staples are a product of industrial agriculture. We are over fed and undernourished.

The Biology of Soil

I’d like to move on now to steps we can make to improve our soils. We cannot continue to degrade our soils as we have been doing and everyone in agriculture can follow these rules to improve soil health. These principles are known as:

The 5 Principles of Soil Health:

1.) Limit Soil Disturbance: The first principle is to limit mechanical, chemical and physical disturbance of the soil. The philosophy behind this is: Where in nature do you find mechanical disturbance? Nowhere! In his book, “Dirt: The Erosion of Civilizations” by David Montgomery, he states that the demise of civilizations throughout history has been tied to the degradation of their soil resources. The biggest factor in that was tillage. It was believed that if you tilled the soil it would improve soil function. That actually was not true. What happens when you till is, that it destroys soil aggregates, decreases water infiltration rates and increases the breakdown of organic materials. During tillage, oxygen moves into the soil, which stimulates certain types of bacteria that quickly, multiply and consume the highly soluble carbon-based glues. These glues hold the macro and micro aggregates together. When the glues are gone, silt and clay particles fill the void, which reduces porosity. This reduction causes anaerobic soil conditions, altering the soil life, which could lead to a loss in nitrogen or increased bacteria. Carbon dioxide also is released into the atmosphere. A reduction in mycorrizael fungi networks is also a result. This severs the amino acid and organic and inorganic molecule pathways. The reduction in nutrients to the plants also means fewer nutrients for animals and people. This is the main reason for a continued reduction in organic matter in the soil profile. With chronic chemical disturbances the results can be just as devastating. Liberal and continuous use of fertilizers and herbicides can destroy soil structure and the biological community. Glyphosate is registered as a chelator and a biocide. That means not only is it tying up nutrients in the soil but it is also killing the biology in the soil. Just keep in mind that any application of a herbicide, fungicide or pesticide will have a negative effect on the environment.

2.) Armor the Soil Surface: The second principle is to maintain the armor (of plant residue) on the soil surface. Nature is always trying to provide a cover for the soil. If there is not some plant material covering the soil, then it is probably under stress. When the soil is covered, it will generally be cooler in the summer and reduce evaporation and provide a home for earthworms and microorganisms. Water will not roll off soil that has a cover on it. The cover will reduce impact from raindrops and slow down erosion. Consider this. One ton of topsoil spread across a 1-acre field would have the same thickness as a sheet of writing paper. How much soil would be lost in a windstorm on a hot summer day if that field had no plant cover on it?

One way I promote thick armor on the soil in my fields is to allow the forage to grow close to seed head and then use high stock density grazing on it moving the cows several times a day. The cows eat 25 – 35% of the biomass above ground and then trample the rest onto the ground. This creates a mat of protection on the ground and provides an area for the microbes to live. This also helps to break down the mat and promotes new growth. The field I trialed this on last year was a new field for us a couple of years ago and previous to that, it was used as a hay field. The farmer that was leasing the field previously had mined it, not having any concern for the biology of the soil. What I mean by mining the soil is when you take forage off the plant without providing any way for the plant to replenish itself. Every year he came through and applied urea nitrogen to push growth and then took two cuttings of hay from it. The biology in the soil was pretty weak. To re-energize the field, I sprayed the field with an organic liquid fertilizer called Plant Sure, which is an organic plant and soil microbe food containing trace minerals, enzymes, bio-stimulant and crop protection aid in the spring during early growth. In mid July, after the cows had mob grazed the field, I went through and sprayed the trampled foliage with Rhizo-Shield and Regenerex. Rhizo-shield has a mycorrhizal package to support the root zone and also contains bacteria, phosphorous and trace minerals. The Regenerex is an organic carbon source that accelerates the energy and food source for microbes and effectively decomposes crop residue. I was more than pleased with the regrowth of this field and will be doing more of this type of treatment next year.

3.) Build Diversity: A healthy pasture will usually have a diverse mix of plant species in it. It is important to include all four types. Cool season grasses, cool season broadleaves, warm season grasses and warm season broadleaves. Joel Salatin will call this a salad bar mixed pasture. The more diverse your forage mix is in your pasture, the more diverse the field ecosystem will be. This also provides for a broader diet of root exudates for the microbes to live in. When I first started grazing my pastures in 2009, they where sparse and had bare spots between the plants. Because of that, I’ve started a practice of reseeding a new pasture every year. The first year I did frost seeding with some success but I wasn’t that happy with it. I then found out I could rent a no-till seeder and went to using that. It made a big difference. I love to experiment and read about the diversity that a larger number of varieties of species would make. The more diversity, the better it was for the microbes below ground. The last two years I have trialed an 11-way seed mix. This last year my mix consisted of three varieties of clover, forage peas, Hairy Vetch, Sorghum Sudan grass, annual ryegrass, a pasture mix and buckwheat. Before seeding, I will run my cows through the pasture and graze it pretty tight to give the seed a chance to germinate and grow. I then will allow the field to lie fallow most of the summer. I do this to get a good stand of forage and established root systems. When I turn the cows into the pasture, they pretty much go nuts because of the diversity of the mix. Here are some of the things I have noticed from the greater number of species. First off, the density of the forage is intense. I can run the cows in at a greater stock density and still be able to satisfy their feed requirements. Another thing I noticed is that the pasture is ready to re-graze sooner. The third thing I noticed was in the spring, the pasture started to grow much faster than usual and was one of the first fields ready to graze. I am only into this multi-species reseeding project going on three years this spring but I am optimistic with the results I am finding so far. One other thing I might add, when I prepare the seed mix before the seeding, I will inoculate the seed with a mycorrhizae inoculant as well as a microbial package along with the traditional inoculants used for legumes and pea/vetch.

The Biology of Soil

4.) Keep Living Roots in the Soil: I live in an area that is the highest concentration of dairy farmers in all of NY State. It really torments me when I see so much acreage standing idle all winter because it has been used to grow corn, soybean or a grain crop. Most of these fields will not see a lick of green on them all winter or roots in the soil to hold it from erosion. How easy would it be to over seed with a cover crop before that first crop has emerged in the spring or immediately after harvest go in and seed a cover crop to keep roots in the ground all winter? A farmer would not go all winter without feeding his animals but yet he lets his land go all winter without feeding the herd below the soil, the microbes. Another reason for roots in the ground would be to keep the mycorrhizae alive, but we have already gone over the importance of that. Think how much soil runoff can be reduced by living roots available to suck up moisture or slow down movement of excess water in the spring. Too often I see gorges created on hillsides from lack of plants and roots in the ground after a spring rain.

5.) Integrate Animals: One of the biggest tragedies in modern agriculture has been the removal of animals from the landscape. If you look back a century ago, you will find that every farm had animals on them whether it be beef, dairy, poultry, hogs or draft horses. Those animals were on the farm grazing pastures and stimulating the grass to grow. Today you will find all those animals moved inside to feedlots or confinement operations. The difference this makes today is that in years past, animals would graze the land, bite the grass here and there and then move on to avoid predators. The animals moved in mobs stimulating the grass with their bites and trampling the rest leaving their urine and dung to fertilize the land. The land would then rest to re-grow and recover at the same time pumping massive amounts of carbon into the soil, stimulating the microbes to come alive storing organic matter to complete the cycle. Today, with the removal of animals from the landscape, there is much less carbon being sequestered through the system. There are those who will blame the cows for climate change. I say the best way to pump massive amounts of carbon into the soil from the atmosphere is to include animals into this process. Remember, it isn’t the ruminant animals that are the problem; it is the management of the animals and the removal of them from the landscape that has ruined the health of the ecosystem.

I’d like to cover a little bit of the process that I use in raising our beef herd on pasture. The reason I am so passionate about the soil is without a functioning soil system, it is much harder to raise nutrient dense meats. I use a combination of grazing practices dependent mostly on the time of year rather than any other input. My basic philosophy is centered on rotational grazing strategies with a few alterations along the way. First off, I try to make sure in the spring that there is plenty of top growth on the ground to start grazing and not set the plants back by grazing too soon. There is a fine line there because if you graze too soon, the plant gets stunted because it does not have enough root reserve to bounce back and put on new foliage and start the re-growth process. If you wait too long, by the time you get through your first go around of rotations around your paddocks, the plant growth of the last pastures suffers from being too over-grown and has a loss of nutrition due to too mature growth. My rule of thumb is to count the leaves. Generally, the plant needs to be between the third and fourth leaf stage in order to not harm the regrowth of the plant. I have found that for my animals, the best rotation time period has been to move the animals on a daily basis. If the animals are left on a paddock for three to four days, their performance is hurt by the animals rumen system having to adjust to the different protein/energy ratio from the plant. As a cow grazes, it will go for the “candy” first which is the tastiest and most high-energy part of the plant. That would be the tips of the plant and leaves from the legumes. Depending on how much of an area you give them, it could take them a day or less to get through that part of the plant. If you leave them there for another day, the cow will go back and take another bite from the candy, not quite as yummy but still desirable and then they will go to the next level of plant forage. All this time, the rumen is adjusting to first, high energy, reduced protein, then less energy, more protein. If you leave them in there for a third day, what do you think happens? They consume more of the most desirable plants and more of the lesser plants. Again, the rumen system is adjusting to the different energy/protein mix. Now, say you move them at the end of the third day or the morning of the fourth day. The cows go through and eat the “candy” that they love first. The cows’ rumen system is not adjusted to the high-energy feed and consequently blows most of that day’s feed out the back end because the rumen bugs cannot handle the feed. By the time the animal’s rumen has time to adjust to the grass feed you are on to the second day and then the third. This constant adjustment to different forages takes a toll on the animal. The rate of gain is reduced and the health of the animal is always challenged. I would rather move them daily, giving them enough so that they only consume about a third of the plant, trample about a third and leave a third to restart the growth process. How do I figure the spacing out? “It depends!” It depends on the growing season, whether it is spring, summer or fall, and it depends on the number of animals, how many mother cows are nursing calves, and the weather. I also don’t worry about the fields getting too overgrown by the time I get to the end of the first rotation because there is a grazing practice called mob grazing that I’ve been using and will try to do more of that as fields allow. This process is to take a paddock and put the cows into it in a smaller tighter paddock and move them more often. With this, I am moving the cows twice a day and giving them a two-thirds/one-third section move. I might explain also, I generally will move my cows in the late afternoon because the brix level (sugars) of the forage is the highest then. The cows also will consume two-thirds of their feed in the evening hours so I would much rather have them consume more of the highest energy feed then. I will then get up in the morning and go out and move them to the second section of the paddock for them to consume. With this type of grazing practice, I feel that I am allowing for the animals to have the best nutritional feed possible and also sequestering large quantities of carbon into the soil.

The Biology of Soil

It has been shown that the most carbon sequestration is done when the plant is in active growth and is putting down roots and the leaves are unfolding. If we, as grass farmers, can keep plants in different stages of growth, constantly stimulating the plants as the cows rip the leaves off the plants, supply the roots with proper nutrition and creating nutrient dense feed for our animals, then we are doing our jobs as we should be. Think about how much CO2 can be sequestered into the ground and how much better we are leaving the Earth for our children and those that follow. Farmers can make this a better place.