Many years ago, I conducted numerous chemical analyses of continuously cropped and virgin soils. The cropped soils were consistently superior in mineral constitution. However, the virgin soils were consistently higher in overall microbial population levels, and in the diversity of microbial species. In addition, the virgin soil featured a mellow texture, versus the more compact and difficult to work texture typical of cropped soil. But the most crucial difference, from the perspective of a grower, was that the yields and quality of crops grown in virgin soils were moderately to significantly higher than those of continuously cropped soils.
This is not a new observation. Farmers of the past recognized the merits of amending their soils with animal and green manures. Furthermore, growers in tune with soil conditioning practiced crop rotations—wheat and corn would be rotated with potatoes, and beans and barley would be rotated with broccoli or cauliflower. Those with permanent crops, such as orchards or vineyards, would spread manure and allow groundcover to flourish before incorporating this biomass back into the soil.
But as the trends of agricultural fertilization shifted from organic to defined blends, farmers increasingly focused upon the use of nitrogen, phosphorus, potassium, and the addition of other defined elements. In addition, as profit margins were squeezed, farmers were forced to move away from rotations and other soil-building programs. They instead plant back-to-back high-margin crops, while trying to mitigate the build-up of harmful pathogens with fumigation- and fertilization-based solutions, where disease-free, sterile, and fertilizer-rich soil systems became the norm.
The loss of pesticides and chemical crutches has resulted in a resurgence of interest in conventional soil-building programs.
In the last half century, regulatory restrictions on the use of pesticides and fumigants have reduced the number of such tools available to growers, with once ubiquitous and powerful chemical solutions banned from use.
Consequently, farmers are rediscovering the merits of animal manures, green manures, rotations, the use of various types of compost solids, compost tea, preferred microbial strain inoculations, and the introduction of complex liquid carbon sources for proliferating indigenous species of microbes. Numerous microbial companies and products have emerged in recent decades, each touting broad spectrum and miraculous benefits.
But the agricultural public is getting bombarded with microbial technologies and products. Farmers, PCAs, chemical distributors, and other agriculturists are being asked to evaluate and make decisions without having a necessary understanding of what contributes to the quality and productivity of farmed soils. Indeed, while the great majority of us have been exposed to soil science and soil chemistry, it is rare to find those who have been formally trained in, or even introduced to, the science of soil microbiology.
In this article, I will discuss the basics and key principles of soil microbiology, and how we can apply our knowledge to establish sound agricultural practices to increase the quality of farmed soils and the yields of the crops grown in them.
Healthy soils teem with a variety of microorganisms, which form an ecosystem critical to repelling undesirable pests and infections.
Although oftentimes “out of sight, out of mind,” the soil environment is rich with activity and numerous organisms. Organisms range in size from visible (“macroscopic”) to invisible (“microscopic”), and in complexity from single-celled to complex multicellular organisms. Table 1 gives a hint of the magnitude of diversity that can be found in a piece of soil, and the staggering magnitude of these populations.
Table 1 – Organisms Found in a 3’ x 3’ x 6” Volume of European Grassland
| Organism | Scientific Group | Numbers Found |
| Macroscopic | ||
| Earthworms | Lumbricidae | 30 – 2,000 |
| Potworms | Enchytraeidae | 200 – 20,000 |
| Slugs and Snails | Mollusca | 100 – 8,500 |
| Millipedes and Centipedes | Diplopoda and Chilopoda | 900 – 1,700 |
| Woodlice | Isopoda | 100 – 400 |
| Spiders | Araneida | 180 – 840 |
| Beetles and Larvae | Coleoptera | 500 – 1,000 |
| Fly Maggots | Diptera | 200 – 1,000 |
| Ants | Hymenoptera | 200 – 500 |
| Springtails | Collembola | 10,000 – 40,000 |
| Mites | Acarina | 20,000 – 120,000 |
| Moss | Thallophyta: Bryophyta | 400 – 10,000 |
| Microscopic | ||
| Bacteria | Protista: Schizomycetes | 940 billion – 9.8 trillion |
| Actinomycetes | Protista: Actinomycetes | 1.8 billion – 5.264 trillion |
| Fungi | Mycota | 10 billion – 1 trillion |
| Protozoa | Protista: Protozoa | 583 million – 4.59 billion |
| Algae | Thallophyta | 3.76 billion – 11 billion |
| Nematodes | Nemata | 1.8 million – 9.4 billion |
| Tardigrades | Tardigrada | 1.8 million – 53 million |
As you can see, despite their inconspicuous nature, the microorganism community is diverse and numerous. It is said about nematodes, for example, that if all the soil were removed from the earth, the mass of nematodes would still provide a noticeable outline of the Earth’s sphere.
To give you an idea of the scale of this on a more comprehensible level: During field experiments in which I activated the soil bacterial populations to unusually high levels, it was calculated that within 3 weeks a bacterial biomass developed which weighed 6 tons per acre furrow slice (1 acre, 6” deep). An additional 2.2 tons of fungal biomass had also developed.
You may ask, “Okay, my soil can support billions of organisms. Why do I care?” The reason that growers should care is that these microorganisms are key in helping plants to take advantage of soil nutrients, while preying upon, repelling, and otherwise keeping in check harmful fungi, nematodes, and other undesirable invaders.
If you want to give your crops the ability to naturally repel infections and infestations that you can no longer easily combat with scorched-earth pesticides and fungicides, you need to encourage the growth and development of these microorganisms.
Growers often disc under crops to introduce fresh plant matter into their fields, but fail to ensure that the plant matter can be decomposed into useful nutrients.
Basic foundational organisms—the microscopic organisms found in the table above—are the first wave of microbial biomass in the ongoing ecology of the soil. If they can’t gain a toehold, let alone flourish, succeeding waves of organisms will move into the scene slowly, or not at all. In other words, without bacteria, fungi, actinomycetes and other microorganisms that growers often never pay much mind to, you will never get the earthworms and other organisms that are the hallmark of healthy soils.
How we can help foundational microorganisms flourish? By feeding them the food and nutrients they need to survive and reproduce, of course. Obviously, most agricultural soils are supplied, either inherently or through fertilizer additions, with inorganic minerals. However, growers often fail to overlook the need for substantial amounts of organic carbon as well.
Where crop rotations and incorporation of cover crops are practices, soils tend to receive greater quantities of organic carbon. However, permanent crops such as vineyards and orchards characteristically institute herbicide stripping and “clean culture.” That is, there is minimal replenishment of the soil with organic carbon. This is a bit like ensuring that your children take their vitamins daily, but not actually feeding them.
In recent years, growers have become more mindful of this, discing under crops to introduce biomatter into the soil in preparation for the next growing season. But this is often done under semi-dry conditions, and no effort is made to ensure that this plant matter can be effectively broken down. In these conditions, it can take years for plant matter to be broken down. The result is that growers face the challenge of trying to grow crops in hard, rocky soils that are cemented together into unmanageable aggregates and cement-like clumps.
Having plant matter slowly decaying over a period of years in your fields will do nothing to set the stage for your crops. The rapidity with which that organic matter is broken down determines whether your efforts will pay off.
For this matter to be broken down in a reasonable amount of time, you need to activate the microorganisms in the soil, accelerating their metabolic activity to the levels necessary to consume biomatter in a reasonable amount of time. Think of this process of activation as being like using kindling to help start a fire.
The ‘kindling’ that we most often recommend are our Fusion 360 Soil and Iota 0-0-1 products. In addition, we often recommend that growers add about 2 to 5 gallons per acre of our Keel 0-0-1 product as part of their microbial activation regime.
In addition, there are two minerals that very commonly deficient in agricultural soils: nitrogen and phosphorus.
Nitrogen and phosphorus supplementation enable the decomposition of plant matter into biomass that can be processed by soil microorganisms.
To encourage the efficient transformation of organic carbon sources to microbial biomass—to break down plant debris into usable sources of nutrition—one must properly balance carbon-nitrogen ratios in the soil. Farmers cognizant of this need will oftentimes spread a nitrogen-based fertilizer before introducing stubble or green manure. But without adding additional nitrogen, there is a dramatic reduction in both the rate and totality of tissue decomposition.
I have personally observed peach orchards where shredded prunings have been incorporated in mid-spring, only to find the emerging foliage turn yellow from lack of nitrogen, literally robbed from the trees by the activated microbes. For carbon to be broken down, the carbon-nitrogen ratio must be around 20:1. Supplying the needed nitrogen is necessary for ensuring effective decomposition and conversion of plant biomass to microbial biomass.
Calculating the necessary amount of nitrogen to apply to your fields is quite easy:
- Estimate the approximate mass of carbon—the plant matter you’re trying to decompose—in the field.
- Take 90% of this estimate and divide it by 25.
- This is the amount of nitrogen that must be introduced into the field
For instance, if you have 2.5 tons of dry biomass, the amount of nitrogen needed to break that biomass down is: (2.5 tons x 0.9) / 25 = 0.09 tons, or 180 pounds of nitrogen.
Phosphorus is the second element that is most frequently deficient in soils, and is also crucial in breaking down plant matter. To calculate how much phosphorus to supplement, take the amount of nitrogen applied to the field and divide it by 2.25. In the example above, we would take our estimate of 180 pounds of nitrogen and divide it by 2.25 to get 80 pounds of phosphorus.
Now, let’s suppose you have supplied the requisite amounts of nitrogen and phosphorus, as well as the aforementioned activation products. How do you determine if the microbes in your soil have been sufficiently activated, without having to wait until the next growing season?
We typically determine this by performing what is called a formazan assay, also known as an MTT assay. This is a test that measures the amount of cellular metabolic activity that is occurring within a soil sample. A desirable formazan measurement falls in the 1,200 to 3,000 range, with a reading of at least 2,000 being desirable.
It’s also important to note that it is necessary to periodically re-supplement the soil with biomass, as well as the nitrogen, phosphorus, and activators needed to fuel the decomposition process. Failing to do so will allow the soil to gradually return to a sterile, dry, unproductive state.
What are the other benefits of a healthy, productive soil with high levels of microbial activity?
Aside from our overall findings that microbially enriched soils produce higher yields and quality crops due to improved decomposition of plant matter, there are numerous additional benefits which contribute to improve crop yields. Some of these benefits include:
Enhanced release of minerals otherwise locked in the soil, due to:
- The microbial production of organic acids, which act to create localized pockets of buffered pH drop, and the chelation or ‘complexing’ of minerals
- Direct solubilization of tied-up minerals through microbial extracts and exudates
- Improved water-holding capacity of soils, assisting in hydration and solubilization of minerals.
Increased root volume, due to:
- Improvements in the timely release of otherwise tied-up minerals
- Antagonism of soil-borne pathogens
- Improved water infiltration rates and aeration factors
Increased rates of water infiltration, due to:
- Copious production of gums, which bind separate clay particles into aggregates
- Greatly enhanced and evenly distributed microbial biomass within the soil (“bulking”)
Reductions in disease levels, due to:
- Substrate or enzymatically advantaged competition for variable food sources
- Byproduct inhibition (e.g. antibiotic production by strains of Bacillus or Penicillium)
- Mycoparasitism (the colonization of pathogens directly by antagonists, such as Trichoderma spp.)
- Siderophore production or education of chelating agents that aid in competition for key minerals
- Competitive displacement of the pathogen by virtue of combined factors, including rapid growth rates
Soil microbiology is a huge missing link in today’s agriculture. If used properly and with pre-characterized specificity for each individual field, the use of microbial activators and nutritional regimes have been shown to provide huge improvements in plant growth and productivity.
