Complete Guide to

Soil Health in Agriculture

At the heart of our sustenance and the vibrant ecosystem that supports our communities lies the often-overlooked hero: soil health. It’s not just the foundation of farming; it’s the secret sauce for a healthier, more resilient future. More and more farmers and advisors are supporting practices that prioritize soil quality and health, which in turn can improve crop yield, drive long-term resilience, and reduce input costs. Testing the effectiveness of these practices on the soil can help today’s farmers make data-driven business decisions while ensuring an abundant food supply and a healthy planet for generations to come.

Chapter 1:


Since the beginning of the Green Revolution in the 1950s and ’60s, modern agriculture has been primarily focused on two of the three components of soil – namely, its physical and chemical characteristics. These are the abiotic attributes of soil. But we know that soil health depends on the balance and diversity of its biological organisms. 

And this makes sense, since only living things can have health!

Soil health offers myriad benefits to our farmland, food, environment, and communities at large. It can help to reduce surface runoff and erosion, improve water quality and wildlife habitats, and conserve biodiversity. 

Healthy soil can also reduce operational and input costs, increase yields, improve plant resilience and disease resistance, prevent soil compaction, and help sequester carbon from the atmosphere.

So, let’s dive into the fascinating world of soil health. It’s not just about agriculture; it’s the key to a more connected, lively, and resilient future.

Chapter 2:

What is soil health?

According to the USDA and NRCS, soil health is defined by “the continued capacity of soil to function as a vital living ecosystem that sustains plants, animals, and humans.”

Before getting into soil health, it’s essential to understand what soil is and the concept of soil as both a resource and a natural ecosystem. 

Soil is often classified based on its proportional sand, silt, and clay composition. Other components of soil are essential to consider in agronomic practices as well, including the fraction of the soil that is organic matter.


What is organic matter? 

Organic matter is composed mainly of living and decaying microorganisms and plant biomass. It’s often considered one of the main factors to measure when trying to better understand soil health. While not all organic matter is created equal, it often binds and holds moisture and plant nutrients and houses soil microbes that live and feed on decaying plant biomass. Many regenerative agriculture advocates highlight the differences between the terms dirt and soil. And the distinction that is often drawn is that soil is the living component that supports plant growth, whereas dirt is considered inert or sterile. 


What is the function of soil in our ecosystem?

Soil is the lifeblood of our environment, influencing the quality of our food, the vitality of our communities, and our planet’s well-being. Soil degradation is a major threat to the levels of arable land across the world and, thus, a major threat to efforts to feed the planet and support human health.


What is soil degradation?

According to the UN Food and Agriculture Association (FAO), one third of the earth’s soils are already degraded, and by 2050 over 90% could become degraded. There are many causes of soil degradation, from pollution and urban expansion to unsustainable agricultural practices to climate change and wind and water erosion. Rates of soil erosion will vary depending on location and management practices. In the Midwestern US, for example, soil is eroding 10 to 1000 times faster than it forms, According to 2023 data from the National Science Foundation. Fortunately, more and more evidence from soil health studies show with certainty that soil is “renewable” with regenerative agriculture practices. Many of these practices are also shown to enhance crop growth, support long-term resilience, and reduce farm input costs when integrated effectively. 


What key factors affect soil health?

There are a number of factors that can affect soil health. Understanding them can help farmers and crop advisors make informed decisions about how to best care for their soil and improve its health. Some of the key factors include:

Soil Type

Soil type refers to the physical and chemical characteristics of the soil, such as its texture, structure, nutrient content, and pH. Different soil types have different properties that can affect the way that water and nutrients are retained, as well as the types of plants that can be grown. 


Climate is another important factor that can affect soil health. Temperature, humidity, and precipitation all play roles in soil moisture and nutrient levels. Understanding the local climate can help farmers and advisors choose crops that are well-suited to the local conditions and develop appropriate irrigation and fertilization strategies.

Pests and Diseases

Pests and diseases can also have a major impact on soil health. Some pests, such as insects and nematodes, can directly damage plants and soil structure, while others, such as fungi and bacteria, can cause diseases that weaken or kill plants. Understanding the types of pests and diseases that are present in an area, and taking steps to prevent or control them, can help farmers and advisors maintain soil health and protect crops.

Management Practices

Management practices, such as tillage, irrigation, and fertilization, can have a huge effect on soil health. Properly managing these practices can help to improve soil structure, increase nutrient availability, and reduce the risk of soil erosion. Understanding the best management practices for a particular soil type and climate can help farmers and crop advisors to improve soil health and increase crop productivity.

In the following sections, we will discuss different management practices you can incorporate to support the long-term health of your soil. 

Chapter 3:

The 3 Dimensions of Soil Health

What are the three dimensions of soil health? 

  • Soil Physics
  • Soil Chemistry
  • Soil Biology

Many soil scientists and agronomists divide soil health into three major components: physical, chemical, and biological. Historically speaking, the physical and chemical components have been the main focus of agronomic tools. The biological components have largely been ignored because, until recently, they have been difficult and costly to assess. 

It’s important to note that the three components of soil health do not exist in isolation. They are involved in a wide array of interconnected processes. Soil biology, including bacteria, fungi, protozoa, and nematodes, influence the physical traits of soil, such as its texture and porosity. They do this through bioturbation, the process by which microorganisms physically move soil and create small channels. The physical traits of soil, like water-holding capacity, in turn, influence microbes and potentially select species that can or can’t do well in certain moisture conditions. These are just two examples of the vast range of physical, biological, and/or chemical processes that pertain to soil health and support the life cycles of plants, microorganisms, and animals, including us.


I. Soil Physics

What is soil physics?

Soil physics and the physical aspects of soil health refer to several factors, such as porosity, aeration, texture, and compaction, as well as water infiltration and retention capacity. These combined factors inform on a soil’s ability to absorb and retain nutrients, water, and organic matter. Every soil is unique due to variability in composition and regional variables such as climate and weather patterns. Gathering information on what is typical for your region is the best step in getting started to monitor soil health as it pertains to soil physics. 


What are the different types of soil in agriculture?

We can look more closely at different soil types and what advantages or disadvantages they can have. There are soils with sand, clay, and silt, as well as loam. Oftentimes, they are mixed together and vary within an area. Sand particles are the largest in size and clay particles are the smallest. While we generally separate soil into sand, clay, and silt categories, it is important to note that most soil is a mix of all three, with changes in the relative percentages of each component. This can have advantages and disadvantages regarding moisture and nutrient retention. For example, sandy soils tend to drain easily and need management aid in regard to holding capacity, while clay soils, with their ability to hold onto moisture and nutrients, may fail to drain as easily and struggle with high rainfall. As we experience more extreme weather patterns, knowing how to effectively mitigate and manage for your particular soil type is a tool in your toolbox that we can help add to and strengthen with biological soil analysis.


What are anaerobic soils?

Soil with a proper balance of aeration and moisture is essential to supporting both crops and soil microbial populations. Waterlogged soils become anaerobic, which can kill off beneficial aerobic microbes and favor pathogens. Whereas sandier or coarser soils can struggle to hold moisture and make a challenging environment for seed germination, root growth, and soil microbes which also require moisture to support their metabolism.


What is soil compaction? 

Soil compaction is the process in which soil particles are pressed together, reducing the pore space between them. This reduces the soil’s ability to hold and conduct water, nutrients, and air, which are essential for healthy plant root activity. Compacted soil has a greater density and reduced pore space, resulting in decreased water infiltration and drainage. This can lead to surface runoff, waterlogging, and restricted plant growth. Soil compaction is often caused by heavy machinery or continuous foot traffic, and it can be mitigated by practices such as avoiding working on wet soils, using mechanical methods to break up compacted soil, and introducing conservation tillage practices, like reduced till or no-till.


What is no-till?

No-till farming is an agricultural technique for growing crops or pastures without disturbing the soil through tillage. Some benefits of no-till farming include:

  • Reduced soil erosion, nutrient runoff, and greenhouse gas emissions
  • Increased water infiltration into the soil and soil retention of organic matter
  • Enhanced soil biodiversity and nutrient cycling
  • Decreased fuel and labor costs for farmers

Conventionally, farmers have relied on tillage before seeding each crop to clear the soil and aerate it. Although tillage loosens up soil compaction and does effectively aerate the soil, excessive tilling every year can degrade the soil texture and disturb microbe populations. It has been proven that excessive tillage depletes organic matter and can lead to poorer soil texture over time. 

Growers are increasingly using vertical till, strip till, or other minimal tillage implements that reduce physical soil disturbance in comparison to discs or chisel plows. These implements are less disturbing to the microbiome and serve as an effective solution for soils where compaction cannot be properly managed with cover crops alone. 


What are cover crops?

Cover crops are plants cultivated primarily to enhance soil health, manage water availability, suppress weeds, control pests and diseases, and boost biodiversity on a farm. Unlike cash crops grown for profit, such as corn or soybeans, cover crops are typically planted in fields that would otherwise remain bare between growing seasons, shielding the soil from erosion and nutrient loss. Examples include mustard, alfalfa, rye, clovers, buckwheat, cowpeas, radish, vetch, Sudan grass, and Austrian winter peas. Additionally, beneficial microbes can produce metabolites, such as exopolysaccharides, which improve soil health by promoting soil structure, as well as nutrient cycling, and disease suppression.


What is exopolysaccharide production?

Exopolysaccharide production can be referred to as the “glue” of the soil, promoting aggregation and enhancing the ability of soil to maintain water-holding capacity. This is particularly important for roots to both access and retain water and essential nutrients. Exopolysaccharide production not only aids in creating healthy soil textures but it can also influence crop yield. At Biome Makers, we help farmers and advisors decode bacteria and fungi that produce beneficial secondary metabolites like exopolysaccharides.


II. Soil Chemistry

What is soil chemistry?

Soil chemistry refers to the measurement of the naturally occurring chemical composition of soil. Typically, farmers and crop advisors are interested in a range of variables to inform them on what is occurring in the soil, such as pH, cation exchange capacity, the level of organic matter, and macronutrients such as Nitrogen, Phosphorus, and Potassium. It’s also common to seek diagnostic information pertaining to micronutrients, including Fe, Ca, Zn, Mn, Mg, Cu, B, Sulfur, and Chlorine. 

There are several different types of soil chemical analysis to obtain data on these elements. It’s worth doing research on them in order to choose the tests that will provide you with the type of data you’re looking for. With data on soil chemical composition, as land stewards you can make informed decisions on management practices, such as the addition or reduction of compost, tillage, cover cropping, and fertilizer/herbicide use. You will also be better informed on which crops to plant and better able to manage risk of potential heavy metal toxicity. 

Normal levels for different elements will vary based on soil type and region. Collecting historical data is the best place to start, to know if your soil is experiencing deficiencies or overabundance of certain elements, which could be causing stress to your crops. Normal levels of elements will  vary based on pH, soil type, and crop type. Region will also determine management practice choices. Once the plant-available quantities of elements of interest are known, you can start to make informed management decisions. Historically, this is where agricultural management has stopped, considering soil physics and soil chemistry jointly and then treating soils for deficiencies. 

There are several different soil chemical analysis methods you may consider as you gather information about your soil. Two popular tests for macronutrient and fertility analysis are the Mehlich and Haney tests. They differ in their product offerings, and there are advantages and disadvantages to using either test. 


What is the Mehlich Test? 

The Mehlich test is more widely established and was one of the first “universal” extract based tests that can assess the levels of every standard nutrient in a soil using just one set of chemical reagents. Two versions of the Mehlich Test, the Mehlich 1 and Mehlich 3, continue to be widely used as chemical fertility assessments for a wide variety of regions and soil types in the US. One downside of a Mehlich test is its use of strong acid digestion to report on nutrient availability. While this method can show what is chemically available in soil, it doesn’t mimic or necessarily represent what is available to the plant. It also only represents singular forms of nitrogen, phosphorous, and potassium, while we know now that plants rely on multiple forms of N, P, and K. 


What is the Haney Test?

A relatively novel soil test, the Haney Test uses both a water based extraction and the H3A extraction of a suite of organic acids (oxalic, malic, citric). The water extraction assesses the levels of organic C, N, and P (carbon, nitrogen, and phosphorous) that soil microbes can unlock into plant-available forms. The H3A extraction is a reagent designed to mimic the natural root exudates of crops that are composed of various organic acids. It is intended to represent plant-available nutrients for N, P, K, providing data on their availability and a suite of micronutrients as well. The Haney Test also integrates a soil respiration test which provides an indication of microbial activity. This value is used to estimate the extent to which microbes will utilize carbon and unlock N and P. Since this test has been available for a relatively short time, there is less published literature on levels that are typical per region. 

The Haney Test is one of the first types of soil chemistry testing to acknowledge the integral roles that soil microbes play in providing nutrients to crops, providing a C:N ratio and a cover crop mix recommendation.

With updated studies on the soil microbiome, it has become clear how microbial interactions play a key role in painting the full picture of soil health. 

III. Soil Biology: The Microbiome and More

What is the soil microbiome?

The soil microbiome refers to the community of microorganisms, including bacteria, archaea, fungi, viruses, and other microscopic organisms that inhabit the soil. This complex and diverse ecosystem of microorganisms plays a crucial role in various soil functions, such as nutrient cycling, organic matter decomposition, and plant health. The soil microbiome is essential for maintaining soil fertility and supporting plant growth. It has the potential to both positively and negatively impact plant health and crop productivity. 


How does the soil microbiome affect plant health?

We are accustomed to looking at soil and quantifying levels of nitrogen and phosphorus like we do levels of high and low cholesterol in our blood stream. However, much like human health, we know today with soil health that there is more to the story. It’s not enough to have high quantities of plant-available nitrogen if we do not have the microbial communities to uptake and deliver it to the plant. The same is true for phosphorus and potassium, and that is where soil biology analytics come into play. Growers often encounter a scenario where chemical nutrient tests look optimal, but they still experience poor yields or nutrient deficiencies in their tissue tests. These scenarios have led us to an expanded focus on soil biology as an agronomic factor. We know that soil microbes can affect soil health in at least five key ways.


5 key ways in which soil microbes affect soil health 

  • Disease Risk: Soil microbes can help to reduce the risk of diseases in plants by competing with pathogenic microbes for nutrients and space. Some soil microbes also produce antibiotics or other compounds that can inhibit the growth of pathogens.
  • Stress Adaptation: Soil microbes can help plants adapt to environmental stresses, such as extreme temperatures or drought. For example, certain bacteria and fungi can produce compounds that help plants tolerate drought conditions, while others can increase plant tolerance to extreme temperatures.
  • Nutrient Cycling: Soil microbes decompose organic matter, releasing nutrients that plants can absorb. They also help to convert inorganic nutrients, such as nitrogen and phosphorous, into forms that plants can use.
  • Hormone Production: Some soil microbes produce hormones or other growth-promoting compounds that can help plants to grow and develop. For example, certain bacteria produce auxins, which are hormones that stimulate root growth and help plants to absorb nutrients.
  • Biocontrol: Soil microbes can also play a role in controlling pests and diseases. For example, some bacteria and fungi produce compounds that can inhibit the growth of pest insects or fungi, while others can stimulate the growth of predatory insects or fungi that feed on pests.

Microbes play an incredibly important role in several elemental cycles, whether they are acting as nitrogen fixers, potassium and phosphorus solubilizers, carbon sequesters, or producing secondary metabolites, such as siderophores that unlock iron and other nutrients from the soil profile. In one teaspoon of soil, on average there exists 10,000 different species of microbes, a biodiverse community responsible for different soil functions.  


What is soil biodiversity?

Biodiversity assesses the community of microbial life that exists in the soil, based on taxonomy. It accounts for all the species of fungi, bacteria, and archaea identified in each sample. It’s based on the number of species present, the evenness (relative abundance) between species, and taxonomic similarity. 


What is soil functionality? 

Functionality is scored based on the quantity of ecological functions performed by soil microbes in a sample. In contrast to biodiversity, which is based on species identity, this metric is based solely on  microbial functions. Resilience is an ecological index based on the ability of communities or populations to remain unchanged when stressed by a disturbance like a drought, flood, tillage, or a pathogen in the soil. 


What is soil quality?

Soil quality refers to the soil’s capacity to function as a living system, sustaining plant, animal, and human life. It encompasses the physical, chemical, and biological properties of the soil, with a growing emphasis on the soil microbiome and its impact on soil health. The soil microbiome (bacteria, archaea, and fungi), plays a vital role in soil biological functions, affecting agriculture, air and water quality, biodiversity, and more.

These all play into overall soil quality, which is also influenced by microbial ecology and synergy. Low values in the Soil Quality index are indicators of intensive practices that can degrade soil health, while high indexes are linked to regenerative practices, such as cover crops, conservation tillage, organic amendments, and biological/biostimulant products.


Chapter 4:

How Plants Interact with the Soil Microbiome

How do plants interact with the soil?

Plants interact with the soil through a complex relationship with various microbes. While conventional agronomy often sees soil microbes as potential issues causing diseases, it’s essential to recognize their beneficial roles in supporting the plant’s natural lifecycle. Microbes, ranging from those in the air and soil to endophytes within plant tissues, play pivotal symbiotic roles in the germination, growth, root establishment, and nutrient uptake processes of plants. This interconnected network of bacteria and fungi contributes to the overall health, yield, and productivity of plants. In fact, plants play a role in microbe selection, including rewarding beneficial microbes in the rhizosphere.


What is the rhizosphere?

The thin layer of soil that surrounds the plant root system is termed the rhizosphere, and this is where the plant is actually a major driver in selecting for microbes that can serve symbiotic functions to support its growth. Plants do this by releasing root exudates, carbon-rich metabolites and compounds which microbes use as fuel and receive as communication signals. Through these microbial food and metabolic signals, plants reward and select for the microbes that can supply what they need, such as nutrients or metabolites that can help the plant deal with environmental stressors. 


A healthy soil rhizosphere consists not only of the common beneficial microbes we talk about a lot in agriculture, such as nitrogen fixers like legumes, but an intricate network of ecological roles that in many ways resemble a food chain. Microbes are constantly absorbing, metabolizing, transforming, and releasing various nutrients in the soil profile. In fact, microbes like mycorrhizal fungi engage in a multi-way symbiotic relationship, collaborating with other microbes to acquire nutrients.


What are mycorrhizal fungi? 

Specifically, mycorrhizal fungi play a crucial role in transferring nutrients from bacteria to plant roots. These fungi, including various others, not only assist in nutrient allocation but also act as a defense mechanism against pathogens and nematodes. Arbuscular mycorrhizal fungi, or endomycorrhizal fungi, colonize the internal structures of plant roots, extending their biomass beyond the roots to access essential nutrients. They typically form mutualistic associations with annual herbaceous crops like corn and soybeans. On the other hand, ectomycorrhizal fungi colonize the external surfaces of plant roots and tend to form symbiotic relationships with woody perennial crops such as trees and shrubs. Both types of mycorrhiza contribute significantly to promoting plant growth, improving drought tolerance, facilitating nutrient accumulation, and enhancing resistance to pests and pathogens.


How do bacteria and fungi work together to improve soil health?

Bacteria and fungi can also support plant growth by releasing organic acids in the soil. These acids help unlock phosphorus, potassium, and other nutrients that are locked up in the soil, by essentially dissolving them out of tight mineral bonds with other compounds, rendering the nutrients available for plant uptake. 


BeCrop® Test can help determine if soil samples contain sufficient levels of these important macronutrient-unlocking microbes. The accompanying BeCrop® soil health report includes metrics that assess the phosphorus and potassium solubilizing potential of the soil microbiome. If P and K pathway metrics are low, then an inoculant that supplies P and K solubilizing microbes may help address the issue. 


What are plant growth promoters?

Aside from providing plants with nutrients by unlocking or fixing them, soil microbes can also produce other metabolites that aid in plant growth. These include plant growth regulator (PGR) hormones, like auxin, cytokinin, and gibberellin. Many of these metabolites are naturally produced by plants themselves and they serve vital roles in regulating plant cell division, growth, and senescence. PGRs are part of a larger group of metabolites referred to as phytohormones, which are responsible for driving a wide range of plant growth and plant stress tolerance related functions. Symbiotic microbes can provide plants with a boost of these metabolites when the plants need them. PGRs or synthetic alternatives to these hormones are shown to increase growth in crops when applied as foliar products. When produced by microbes in the rhizosphere these PGRs can also promote root growth. 


What do hormones do in the soil?

Hormones, like salicylic acid, abscisic acid, and ACC-deaminase, serve as stress-response hormones. Similar to how our immune systems kick in when we get a virus or undergo stress, these hormones help plants manage stress from pathogens, drought, heat, salinity, and other environmental factors, making them more resilient to yield-limiting factors outside our control. Other non-PGR metabolites, like siderophores and exopolysaccharides, can also enhance plant growth and vigor, by making nutrients more bioavailable for plant uptake and improving soil porosity. 

The BeCrop® report includes metrics assessing the levels of microbes that produce all the metabolites and PGRs mentioned above, as well as soil microbes that promote salt tolerance in crops and improve resistance to heavy metal phytotoxicity. In fact, there are microbes that can prevent excess salt and heavy metals from being assimilated by the plant, as well as microbes that can aid in tolerance of present quantities. All this information is included in the section of the BeCrop® Report titled “Stress Adaptation,” which provides insights on how effectively soil biology can mitigate the effects of various stressors.


Chapter 5:

Management Practices and Their Benefits

What are the 5 principles to building soil health

Healthy soil doesn’t occur overnight. The following are principles to follow for promoting soil health.

  1. Minimize soil disturbance 
  2. Protect the soil
  3. Diversify the landscape
  4. Promote biodiversity above and below the soil surface 
  5. Integrate livestock through grazing (optional) 

What are the key management practices and their benefits to soil health?

All farms are different and have different needs. We’ve shared a few management practices, below, so you can explore which ones are the best fit for you. 

Reduce Inversion Tillage and Soil Traffic: Most inversion (e.g., moldboard plow)

and noninversion (e.g., chisel plow) tillage methods compact the subsoil if not managed with a high level of care, creating plow pans that restrict root growth and the crops’ access to water and nutrients in the subsoil. Excessive tilling can also disrupt soil aggregates and expose organic matter, which increases the rate of organic matter decomposition and loss. Inversion tillage methods expose soil to erosion by reducing the coverage provided by crop residues. Additionally, tillage can disrupt the hyphal network of mycorrhizal fungi that supply plant roots with extended reach to nutrients and water. 

Under conservation tillage management, the diversity and abundance of arthropod predators associated with the soil surface can be greater in comparison to conventional inversion tillage, helping to naturally control pest insects. Beneficial soil-dwelling insects are also more likely to survive in fields where noninversion methods are used. Additionally, noninversion tillage causes less soil disturbance and thus less direct mortality of beneficial soil organisms in comparison to inversion tillage practices. 

In certain production systems, some tillage is still necessary, especially in organic systems where herbicides for weed control are not used. In such cases, it’s important to offset the increased rate of organic matter decomposition, by increasing inputs of crop residues, manure, or compost. To reduce tillage intensity over time, one proven method is to integrate several years of a perennial crop into a rotation with annual crops that require tillage. By minimizing tilling, you can secure your healthy topsoil and ensure life for the millions of microorganisms that exist in your soil.

Cover Crops: Cover crops contribute many benefits to soil health. They reduce the risk of erosion by keeping the soil covered between growing seasons. They can enhance organic matter levels if they are returned to the soil. Depending on the type, their roots can create macropores, alleviate compaction, promote aggregation, and stabilize the soil. Species of cover crops that host mycorrhizal fungi or rhizobium bacteria in their roots can promote the growth of populations of these beneficial fungi. Cover crops can also retain nitrates and other nutrients that are susceptible to leaching losses.

Increase Organic Matter Inputs: To maintain or increase soil organic matter levels, inputs of organic matter must meet or exceed the losses due to decomposition. Healthy crops can be a valuable source of organic matter, and crop residues should be returned to the soil as much as possible. Incorporation of cover crops or perennial crops, manure, and compost can also be used to increase or maintain organic matter in the soil.

Prevent Soil Compaction: Soil compaction occurs when soil is exposed to excessive foot and equipment traffic, especially when the soil is wet. When the soil becomes compressed, pore space is reduced, and bulk density increases. This leads to poor water infiltration and drainage, which contributes to increased runoff. Compaction makes it more difficult for plant roots to grow into the soil, and having less pore space also reduces the habitats of many small soil organisms.

Optimize Agricultural Inputs: Beneficial insects that contribute to the biological control of pests can be harmed by the application of broad-spectrum insecticides. The ecological approach to land management maintains biodiversity with the goal of preserving beneficial organisms.

Rotate Crops: Diverse crop rotations facilitate higher biodiversity both above and below ground and disrupt pest and disease lifecycles that feed on specific crops, preventing them from populating farmlands.

Manage Nutrients: The type, quantity, and timing of fertilizer applications can help optimize input costs and minimize nutrient excess, which can actually be harmful to plants. For example, high soluble nitrogen levels in soils can compromise the resistance of plants to pests. When managing nutrients, it’s important to also feed the macro and microorganisms in the soil. Calcium is an important food source for earthworms, and using inputs with verified effects on the soil microbiome will help ensure that long-lasting nutrient cycles are not compromised for the benefit of a one-time application of nutrients. It’s also important to diversify the sources of nutrients to avoid excessive accumulation and maintain balance.

Test and Filter Irrigation Water: Water quality is often overlooked as a source of contamination for crops and soil microbiota. However, irrigation water has been found to be a major driving factor of bacterial diversity in the soil. Chlorine and chloramine are added to almost every municipal water supply in developed countries, and they act as broad-spectrum antibiotics in the soil. Treated wastewater can have similar microbiome-killing effects, potentially fueling the development of antibiotic-resistant bacteria, as well as introducing harmful pathogens to plants and humans. Well water or river water irrigation can pose issues from upstream pollution, though they tend to be much cleaner water sources. The only way to know for sure how your irrigation water is affecting the soil microbiome is to test the water and/or soil. Filtration directly at the irrigation outlet may be the best option to ensure soil microbes are not being killed by soluble contaminants. Carbon filters, and even compost weirs, are affordable forms of filtration.

Employ Agroforestry Practices: Agroforestry is an approach that is integrative, intensive, intentional, and interactive. Each of the land management systems below can have a huge impact on soil quality for agriculture and for the planet at large.

  • Windbreaks: Windbreaks consist of trees and shrubs planted in a line. Their purpose is to slow the wind, which creates more beneficial conditions for soils and crops. Windbreak practices control soil erosion and enhance crop production by protecting sensitive crops from intense weather.
  • Alley cropping: Alley cropping combines trees planted in single or multiple rows with crops cultivated in the wide alleys between the tree rows. Specialty crops can be grown in alleys, utilizing the microclimate created by trees to stimulate soil organic matter, protect the soil, and serve as a powerful tool for carbon capture. 
  • Riparian Buffers: Riparian forest buffers are strips of permanent vegetation, such as trees, shrubs, and grasses. These plants are situated between agricultural land and water bodies (rivers, streams, creeks, lakes, and wetlands) to reduce runoff and non-point source pollution.
  • Silvopasture: Silvopasture is the integration of trees and rotational grazing, where livestock operations share space on the same farm as crop production. This practice combines trees with forage (pasture or hay) and livestock. The trees can provide food, fuel, fodder, and fiber for both livestock and human consumption. 

Agroforestry enables you to transform your farm into an ecosystem that improves soil quality and soil health, preserves the air and water, and strengthens biodiversity below and above ground.


Management Practices FAQs

Q: How can I preserve soil structure and health through tillage?
A: Employ alternative techniques like mulching or cover cropping to minimize tillage, preserving soil structure and preventing issues such as erosion and nutrient loss.

Q: What cover crops enhance soil health and how do I use them?
A: Opt for cover crops that contribute to soil structure, reduce erosion, add nutrients, suppress weeds, and attract beneficial insects. Incorporate organic matter like compost or animal manure alongside cover crops.


Q: What are the best irrigation techniques to maintain soil health?
A: Implement efficient irrigation methods, such as drip irrigation or mulching, to preserve soil structure, prevent compaction, and address nutrient stress.


Q: How can I manage fertilization for optimal soil health?
A: Use balanced fertilizers and follow soil test recommendations, adhering to the four R's of fertilizer use: right time, right rate, right place, and right type.


Q: What reduced tillage methods improve soil aeration and moisture retention?
A: Embrace reduced tillage methods, like strip tillage or vertical tillage, to balance aeration and moisture retention, ensuring healthier soil.


Q: How can integrated pest management and intercropping enhance soil health?
A: Adopt proactive pest management practices, including push/pull crops and pest-suppressive cover crops. Explore intercropping to enhance soil health without compromising yield.


Q: Why is diversifying crop rotation important for soil health?
A: Diversify crop rotations beyond common practices like corn-soybean rotations to maximize soil health benefits.


Q: What's the role of biological products in improving the soil microbiome?
A: Biostimulant products, including biological inoculants, can produce biological enhancements in soil microbiome functions based on regional, crop, and soil-specific factors.
Chapter 6:

Soil Health and Climate Change

How does soil health impact climate change?

Extensive scientific research and modeling has connected rising greenhouse gasses in our atmosphere to a changing climate. The primary greenhouse gasses are carbon dioxide, nitrous oxide, and methane. All of these play a huge role in agriculture, both in growing plants and managing livestock. 

Plants absorb carbon dioxide in the metabolic process of photosynthesis. Carbon is a key building block in the formation of plant tissue, and in a healthy relationship with the soil microbiome, the plant will send carbon, in the form of simple sugars, into the soil. Climate change, carbon credits, and sustainability have become such heavily discussed topics in the field of agronomy, because soils have been shown to have potential as carbon sinks. Robust microbial activity in agricultural systems provides a great opportunity to store, or sequester, carbon in the soil. Studies show that the ability of soil to store carbon long term is highly variable depending on the crop, microbial composition, and management practices. For example, fungi generally both live longer and store carbon for longer than bacteria. 

According to the World Economic Forum, “Soils have historically been the most overlooked asset in improving agriculture and mitigating climate change.” Soils can release and sequester carbon depending on the balance of soil microbes and the biochemical and biophysical processes that dictate the building or depletion of soil organic matter, which is largely composed of carbon. Microbes sequester carbon through a few different processes. Some microbes, commonly referred to as autotrophic species, can sequester carbon by directly assimilating it from CO2 in the atmosphere, similarly to plants, via the process of photosynthesis. Other microbes sequester carbon by receiving and taking up carbon from the root exudates of plants. But arguably the most important way in which microbes contribute to carbon sequestration is via the process of decomposition or organic matter release, in which they break down organic materials like crop residues and sequester the available carbon in their biomass. As microbes die-off, their biomass (and the carbon accumulated in it) can become further stabilized in the soil profile. However, microbes also release carbon from the soil, causing net loss. This occurs via metabolic processes that include aerobic respiration, methanogenesis, and fermentation. While these metabolic processes are essential to microbe growth, they can also reduce the potential to sequester carbon in the soil.

Several soil management practices have shown to aid in carbon sequestration, and you might be wondering how to monitor them on your farm. At Biome Makers, we look at microbial functionality data through gain and loss pathways. For the carbon cycle, we look at components such as aerobic respiration, fermentation, and methanogenesis, as well as organic matter release and carbon sequestration potential. 

Whether you are interested in validating the effects on your soil of practices such as rotational grazing, cover cropping, or biological inputs, BeCrop® technology can serve to provide feedback and identify areas to make climate-smart management choices.

Chapter 7:

Unlocking The Secret to Soil Health

How to take a systems approach to healthy soil

Every farm is unique and comes with its own set of challenges. Taking a systems approach to protect your soil will allow the greatest flexibility and versatility. Maybe you will incorporate a new plant that grows well with your current crop system or slowly reduce tillage in one area of the farm and compare the results. And testing is key – because you can’t optimize what you can’t measure.


How do I test the health of my soil?

There are three main tests that can be used to assess soil health: physical, chemical, and biological tests.

  • Physical Soil Tests: Physical tests involve observing and measuring the physical properties of the soil, such as texture, structure, color, and moisture content. These tests are typically quick and easy to perform, and they can provide valuable information about the current state of the soil.
  • Chemical Soil Tests: Chemical tests involve analyzing the soil for the presence of specific nutrients, such as nitrogen, phosphorous, and potassium. They can also provide a soil pH analysis and assess other chemical parameters, such as salinity. These tests are typically more time-consuming and costly than physical tests, but they can provide more detailed information about the nutrient content and chemical makeup of the soil.
  • Biological Soil Tests: Biological tests involve measuring soil health by examining the overall health of the soil ecosystem. These tests can be used to assess the presence, diversity, activity, and abundance of soil microbes, as well as their role in nutrient cycling and other important functions. While biological tests are typically more complex and time-consuming than physical or chemical tests, they can provide valuable insights into the health and functioning of the soil ecosystem.

Check out the Complete Guide to Soil Testing for more information >> 


What is the ultimate secret to rebuilding soil health?

Only in recent years has the paradigm shifted. With state-of-the-art gene sequencing technology and microscopy, along with advancements in data analytics and machine learning, a whole new world has opened up beneath the surface. No one could have predicted that high-tech microscopes and laboratory genomic analyses could become such valuable tools in a farmer’s toolbox. Thanks to these growing technologies, we now know that microorganisms are our allies against plant diseases, pests, erosion, and even gas emissions. 

With these new insights, farmers, crop advisors, and scientists all over the world have discovered the secret to rebuilding soil health: working with the microbes rather than against them. 

BeCrop® Test: The Most Advanced Biological Soil Test

Our soil microbiome analysis tools deliver the most comprehensive assessment of soil health, with reports on biological soil functions for all crops.

Chapter 8:

BeCrop® Test: The Agronomic Decision-Making Tool for Crop Productivity

What is BeCrop® Test? 

The BeCrop® soil health test provides a user-friendly report on soil nutrient cycling, biodiversity, and the overall health of any field. The report provides a data-driven picture of the global functions of the microbial networks. 

  • Analyze Yield Improvements
  • Assess Nutrient Cycling
  • Predict Disease Risks
  • Monitor Farm Practices

The best farming decisions are based on biological soil data.

BeCrop® Test enables farmers and advisors to:

  1. Optimize inputs to improve farm profits and ROI
  2. Identify the root causes of crop underperformance
  3. Predict disease risk in time to act
  4. Troubleshoot soil health problems


Gain a competitive advantage with BeCrop®

Request a sample report

Chapter 9


Healthy soil is like the unsung superhero, quietly working behind the scenes to ensure we have thriving crops, clean water, and a sustainable world. Understanding and harnessing the potential of the soil microbiome is increasingly recognized as a key factor in sustainable agriculture and human health.

By testing and understanding soil health, farmers and advisors will have the actionable tools to improve soil functions and crop yield, predict and prevent soil deficiencies and crop diseases, make better informed input decisions, and improve sustainability.

Get started now.

Check out the Complete Guide to Soil Testing for more information >>



Gus Plamann - Headshot

Gus Plamann



Joy Youwakim


Jamie Nix - Signature Photo

Jamie Nix

Content Writer

Related Articles

From Our Blog

Stay up to date with what is new in our industry, learn more about the upcoming products and events.

Navigating Supply Chain Resilience in Agriculture
Navigating Supply Chain Resilience in Agriculture

Navigating Supply Chain Resilience in Agriculture

10/Jun/24 5 min read
A Retailer's How-To for Using DNA Soil Testing
A Retailer's How-To for Using DNA Soil Testing

A Retailer's How-To for Using DNA Soil Testing

14/Feb/24 7 min read
The Importance of Soil Testing in Preseason Planning in Agriculture

The Importance of Soil Testing in Preseason Planning in Agriculture

18/Jan/24 5 min read