Category Archives: blog

Dr. Elizabeth Rieke: Selecting for Microbial Life Strategies in Agricultural Soils Under Soil Health Promoting Practices

Soil microbes are largely responsible for degrading organic materials and cycling nutrients in soil, and are highly sensitive to physical and chemical changes in soil. Biological measurements currently used to assess soil health provide an understanding of available resource pools, metabolic byproducts, and overall community sizes of these microbes. While these measurements are sensitive to changes in agricultural management practices, less is known regarding which microbes are responsible for driving the changes due to management. Incorporating 16S rRNA amplicon sequencing in soil health studies allows for examination of bacterial and archaeal taxa at finer resolutions.

The Soil Health Institute, using data from the North American Project to Evaluate Soil Health Measurements, identified inherent soil properties and management practices which significantly affect bacterial and archaeal communities in soil using 16S rRNA amplicon sequencing. Preliminary results show between site variation in bacterial and archaeal community structures is highly dependent on soil pH and climate moisture regimes, while within site variation is dependent on management practices. Reducing tillage intensity from intense management to minimal disruption resulted on average in a 13% shift in bacterial and archaeal community structures. Additionally, relative abundances of three bacterial and archaeal orders directly related to nitrogen cycling were significantly greater in minimum tillage systems.

For more information see our video below:

Dr. Shannon Cappellazzi: Flexible Framework to Quantify the Functions of Soil: Examples with Nitrogen Cycling

The Soil Health Institute is working on building a flexible framework to quantify the functions of soil as a means of interpreting soil health measurements. This framework will be meaningful for farmers and ranchers, those interested in ecosystem services provided by soils, and a host of other stakeholders, according to Dr. Shannon Cappellazzi, Lead Scientist at SHI.

A healthy soil is a vital living ecosystem that functions to its capacity. Soil Health Institute soil scientists are using a suite of tests to develop formulas that assess how well a particular soil is storing carbon, cycling nitrogen and other nutrients, storing water, infiltrating water, purifying water, providing habitat, being a source of biological diversity, suppressing pests and disease, and regulating atmospheric gases such as carbon dioxide (CO2) and nitrous oxide (N2O).

Rather than expensive testing that measures each of these outcomes specifically, we are evaluating more than 31 soil health indicators to draw relationships between simple measurements and these functions. In doing so, we will determine a minimum suite of measurements that provide scientifically rigorous data while maintaining economic feasibility for a wide variety of potential stakeholders, Dr. Cappellazzi said.

Preliminary results show that grouping soils for inherent climate and soil features and then measuring soil organic carbon, microbial respiration through a 24 hour CO2 test, and testing aggregate stability using a smartphone application called SLAKES, can tell us nearly as much about the soil’s ability to function to its potential as a more extensive suite of tests. Additional tests will be analyzed and potentially added to this base suite for quantification of each specific function.

For more information see our video below:

Dr. Daniel Liptzin: Effects of Soil Health Management Practices on Soil Carbon Dynamics

Carbon has long been considered central to soil health because it plays many roles in soil function. Measuring total soil carbon has been possible for decades, but many other soil carbon measurements have been proposed recently to quantify soil health. These alternative indicators measure some type of biological activity or chemical fraction of carbon and are thought to be more sensitive to management decisions. The Soil Health Institute, through the North American Project to Evaluate Soil Health Measurements (NAPESHM), compared soil organic carbon (SOC) measurements with permanganate oxidizable carbon (POx-C), respiration, microbial biomass, water-extractable organic carbon, and beta-glucosidase enzyme activity.

Preliminary results show that correlations of indicators with climate and soil texture were weak. The correlations among the indicators were moderate, except for microbial biomass which was weak. All of the indicators (except microbial biomass) had a similar capability to detect changes in management. While the cost of most of these tests is similar, the POx-C and 24 hour respiration assays have advantages of being widely available at commercial labs and offer the option of a “field” test. These tests are suggested to respond quickly to changes in management.

For more information see our video below:

Dr. Michael Cope: Management Indices that Reflect Foundational Soil Health Practices

Soil health management systems are comprised of many specific management decisions such as crop rotation, tillage and cover cropping practices. Categorical (i.e. text- or label-based) characterizations of soil health management (e.g. “no-till” or “conservation till”) overgeneralize important details about soil health management and can be regionally specific. As a result, the categorical descriptions limit our ability to synthesize soil health data across different sectors of agricultural production.

The Soil Health Institute, through the North American Project to Evaluate Soil Health Measurements (NAPESHM), is developing a numerical indexing system to represent core components of soil health management systems. The management indices, based on the principles of soil health, are being used to evaluate soil health measurements along continuous gradients of soil health management practices within and across different sectors of agricultural production.

For more information see our video below:

Dr. Wayne Honeycutt: Comprehensive Strategy for Advancing Soil Health

Dr. Wayne Honeycutt, President and CEO of the Soil Health Institute, discussed a comprehensive strategy for advancing soil health, a strategy that the Soil Health Institute employs to increase adoption of soil health systems in order to achieve on-farm and environmental benefits at scale.

By 2050, our agricultural systems will need to support another 2 billion people. Yet, in the last century, many agricultural soils have lost 40%-60% of the basic building block that makes them productive (organic matter). The societal and environmental costs of soil loss and degradation in the United States alone are estimated to be as high as $85 billion every single year. Greenhouse gas emissions have reached the highest level ever recorded and are continuing to increase. Drought is expected to increase from impacting 1% of the world’s arable land to over 30% by the end of the century due to climate change. Approximately 80% of our nation’s rivers and streams are currently impaired due to nutrient runoff and other contaminants.

We are at a critical juncture in human history where we must address these challenges by transforming agriculture, and soil health is the framework to do just that, Dr. Honeycutt said.

An abundance of research shows that practices designed to improve soil health also reduce nutrient loss to waterways, reduce greenhouse gas emissions, increase carbon sequestration, increase drought resilience, enhance yield stability, increase biodiversity, enhance pollinator/wildlife habitat, and provide many other benefits. In short, soil health is the foundation for regenerative and sustainable agriculture. However, achieving these benefits at scale requires providing the information our land managers need when deciding whether to adopt new management practices/systems.

For more information see our video below:

Managing for Soil Organic Carbon is fundamental to Regenerative Agriculture

In a recent webinar, the Soil Health Institute’s President and CEO, Dr. Wayne Honeycutt, provided an introduction on how farmers can manage their soils to increase soil organic carbon. He laid out the facts with four essential questions:

    1. What is soil organic carbon?
    2. How does it benefit farming?
    3. How can you increase soil organic carbon?
    4. How long does it take?

Read on to learn more about retaining organic carbon in your soil and the benefits it brings to your farm.

What is soil organic carbon?

Let’s start with soil organic matter, which consists of elements like carbon, nitrogen and phosphorus. It starts as materials from plants and animals that are then further transformed during the decomposition process by microorganisms. Soil organic matter and soil organic carbon are often used interchangeably as organic matter is about half carbon. However, different methods are used to measure them. Put simply, soil organic carbon is the carbon in soil organic matter.

How does it benefit farming? 

Here are the seven most important benefits of soil organic carbon:

    1. Increased water holding capacity in soils. This builds drought resilience.
    1. Lower soil density. As you increase carbon, density decreases because organic compounds are less dense than the soil minerals. When soil is less dense, the roots can travel through the soil and scavenge for nutrients and water more easily. This makes for a healthier plant overall.
    1. Increased water infiltration. Organic carbon helps to form soil aggregates, where organic molecules produced by microorganisms bind mineral particles together. The no-till process helps to preserve these aggregates, increasing carbon in surface soils, which allows more aggregates to form, further stabilizing the soil structure. Tilled fields typically have less carbon and poorer water infiltration – this is evident of ponded water on fields after heavy rainfall.
    1. Increased nutrient availability. When microbes feed on soil organic carbon (in order to get energy), they release nitrogen and phosphorus that were tied to that carbon, thereby providing more nutrients for the plant.
    1. Improved trafficability, meaning that the soil structure is improved and allows farming equipment to traverse the field more days in a given year.
    1. Increased yield stability. Although there is not a lot of experimental data on this, many farmers have found this benefit to be true. When compared to their neighbors, who do not use soil health practices that increase carbon, farmers that do find they have more stable yields from year-to-year. This is often most evident during drought years, likely because of the greater water-holding capacity, reduced density and other benefits that increasing soil organic carbon has for farmers.
    1. Finally, soil organic carbon increases profitability. Soil Health Institute (SHI) scientists recently interviewed 125 farmers about their profitability since they started using soil health systems. While the Institute will be releasing those results in the coming months, Dr. Honeycutt said that almost all of the farmers interviewed reported higher profitability after adopting soil health systems that increase soil organic carbon.

How can you increase soil organic carbon? 

As SHI’s soil scientists have proven, the benefits of soil organic carbon are numerous. However, the question remains for how farmers can increase the amount of carbon in their soil.

One of the first things to think about is the carbon cycle at a fundamental level. It’s important to note that carbon is always coming in and out of the soil. The amount of soil organic carbon is the net balance of how much organic carbon is put into the soil mostly from plants, such as dead leaves, roots, and compounds released by living roots, and how much organic carbon is removed by harvest or returned to the atmosphere as carbon dioxide by microbial processes.

Therefore, the goal is to add more carbon in the soil than you lose to the air or remove through harvest.

So, how do you achieve that? According to Dr. Honeycutt, this is done through the management choices that alter the carbon balance.

It is much easier to lose soil organic carbon than it is to gain it. Research shows that continuous no-till builds soil organic carbon in surface soils over time. In the United States, many of our cropland soils have lost 40-50% of their precious soil organic carbon. Much of this has been through tillage. No-tillage results in more organic carbon accumulation in the surface soil and therefore results in the on-farm benefits described above.

The use of cover crops is also a great opportunity for incorporating more carbon to your soil. Cover crops also protect the soil from erosion and help recycle nutrients from deeper in the soil back to the surface. Their residue provides a mulch to keep the soil cool and moist, and as that residue decomposes, some ends up as soil organic carbon.

Other important management decisions also affect carbon in your soil. For example, choice of crop rotation and residue management can dramatically affect the amount carbon that is added to your soil.

Additionally, farmers who integrate livestock in their operation have a wonderful opportunity to increase carbon in their soils through the direct application of animal manure while livestock graze cover crops or crop residue for forage.

How long does it take? 

The golden question: When can you expect to see results? As Dr. Honeycutt says, you’re not going to like his answer.

The answer: It all depends.

It can usually take about three to five years after changing management before you can have a measurable change in your soil due to background variability, including weather and soil type. Of course, this doesn’t mean that you aren’t having change before that. In general, it takes a bit longer to show a measurable increase in soil organic carbon in hot or dry climates and in very sandy soils. Landscape positions can also influence those results. For example, a lower landscape position may retain more water, allowing plants to grow better and therefore return more carbon to the soil. Those same moist conditions can also slow decomposition processes, resulting in greater carbon build-up in those landscape position soils.

Dr. Honeycutt’s best advice is to focus on the management choices that you make and keep a positive outlook.

“If you think you can, you can. If you think you can’t, you're right.”

Final thoughts

Properly managing the soil organic carbon content is fundamental to regenerative agriculture. It can provide many benefits to farmers who are committed to implementing soil health systems. You want to think of yourself as a carbon manager and ask how you can increase the amount of carbon in soil to improve soil health and provide benefits for you and your farm.

Please use the following resources for more information and to answer  questions you may have:

What are the four steps to healthier soils?

The Soil Health Institute (SHI) along with other scientific bodies, advocates four basic soil health principles that apply to all agricultural systems in one way or another.  To maximize benefits through accelerated soil health improvements, they need to be implemented as a system.  This creates a synergistic effect where the sum is greater than the individual parts.

In order to shift the needle, farmers need to look at soils differently.  The definition below of soil health helps producers’ home in on what they need to do to accomplish this:

“Soil Health is the continued capacity of soil to function as a vital living ecosystem that sustains plants, animals, and humans.”

This definition speaks to creating a management system that is sustainable and considers the soil microbes as a key component of the system that drives soil functions necessary for food and fiber production.

Farmers need to understand the role that soils play in agricultural production systems. The functions necessary to be successful are nutrient cycling, regulating water (infiltration and availability), filtering and buffering pollutants, physical stability to support agricultural activities (they must get across the field), and creating habitat for soil organisms beneficial for food and fiber production.  All of these functions are impacted or mediated by soil microbes.  Here at SHI, we like to think of farmers that they are habitat managers for soil microbes.

The four soil health principles are:

    1. Minimize soil disturbance – soil disturbance is any activity that impacts or destroys habitat for soil microbes.  It can be broken into three categories: physical disturbance (tillage destroys the house microbes live in); chemical disturbance that impacts non-targeted organisms disrupting the soil food web, making them less resilient; and biological disturbance which includes the lack of diversity in crop rotations or overgrazing in grazing systems.
    2. Maximizing diversity – helps to create a balanced habitat for soil organisms, breaks pest and disease cycles, and provides diverse biomass both above and below ground that can be converted into soil organic matter. Diversity can be added by lengthening the crop rotation or adding perennials, planting cover crops after harvest, and incorporate livestock grazing through a strategy that ensures even distribution of manure while preventing overgrazing.
    3. Keep continuous living roots growing as much as possible – modern agricultural systems only capture solar energy for a portion of the year (100-120 days), while sunlight hits the earth year-round.  Incorporating cover crops allows for plants to turn sunlight into food for soil microbes in the portions of the year commodity crops are not being grown.  Plants feed soil microbes through exudates, hence the more exudates, the larger the microbial community that can be supported. In some parts of the country this can be done almost year-round, other parts not so much, but they still can provide benefits.
    4. Maintain residue cover as long as possible – residue cover controls erosion while protecting soil aggregates that are so important for water infiltration.  Cover also keeps the soil cool during the heat of the summer.  Bare soil temperatures can exceed 100 °F at a depth of 1” to 2”, which creates a hostile environment for soil microbes, residue cover can keep soil temperatures 15-20 °F cooler.  This reduces evaporation while creating a favorable habitat.

There are basically five or six conservation practices or activities that farmers can leverage to develop a soil health management system.  These include:

    1. Conservation Tillage – preferably no-till, but some crops require tillage to harvest, limiting the depth and area tillage is done can be useful
    2. Cover Crops – can be used to add diversity to a crop rotation with one or two commodity crops, e.g. corn-soybean, cotton-cotton-peanuts.  They need to be selected with a purpose, a cover crop should benefit the crop that will follow it.  Cover crops should be planted as a mix, multi-species mixes promote more diversity.
    3. Conservation crop rotation – rotation need to move away from monocultures or continuous commodity production, e.g. continuous corn or cotton
    4. Nutrient management – a nutrient management plan should be developed that considers the biological nutrient cycles occurring in the soil
    5. Pest management – pest management strategies need to consider beneficial organisms and how they will be affected

The science has proven that a well-executed soil health management system is key to a more sustainable future for agriculture and the planet.  The benefits are numerous and the on-farm economics in the long-term make it a viable practice to pursue:

    1. Soil health systems build in resiliency against extreme weather events and droughts, reducing soil erosion and nutrient run-off in flooding and maintaining soil water during extended dry spells.
    2. This resiliency smooths out volatility with yields, allowing for more consistent and predictable results.
    3. Input costs such as irrigation, fertilizers, and pesticides are reduced through the adoption of soil health practices that can positively impact margins and therefore profits.
    4. Sequestering more organic carbon in the soil means that crops and the soil biome can thrive. Less CO2 is also released into the atmosphere and helps mitigate climate change.

We can’t over emphasis the importance to develop and implement a soil health management system and the benefits it brings.  While improvements can be made by introducing one activity at a time, to truly see changes requires a synergistic approach.  It may take three to five years for a producer to notice a measurable benefit through adopting soil health management systems, but the proven results should convince a producer to stay with implementing the system.

Soilborne plant pathogen fact sheet

Some soilborne pathogens can have a devastating effect on the economic viability of crops. Thankfully, soil health systems have been shown to help suppress plant pathogens. Below are some facts about soilborne pathogens and how soil conditions affect them.

    • Soilborne pathogens cause seedling, vascular, and root rot diseases. Typical diseases result in visible lesions, rots, and wilts. Plant pathogens include fungi, oomycetes, nematodes, and viruses.
    • Soilborne pathogens are specific to certain crop species and are generally rare in natural, unmanaged systems.
    • Pathogens are not uniformly distributed through the soil profile and exist in microhabitats. This means the existence of a pathogen in soil does not necessarily mean plant disease will occur. However, higher loadings of pathogens in soil increase the likelihood of infected plants.
    • Soilborne plant diseases are most severe when conditions are poor (e.g., inadequate drainage, poor soil structure, low organic matter, high compaction). Their presence is not only influenced by inherent soil properties, but also by climate and agricultural management.
    • Pathogen survival in soil is tied to their ability to form vegetative structures that can survive for long periods. When environmental conditions are suitable, and a pathogen compatible host is present, vegetative structures germinate and penetrate below ground plant organs. After the death of the plant from disease or agronomic termination, “resting” pathogens contained in plant residues are returned to the soil surface.

How Soil Health Management Practices May Help

    • Soil health management practices help alleviate poor conditions, therefore in general are perceived to reduce soilborne plant diseases.
    • Additions of composted materials hold promise for suppressing plant pathogens (~50% success rate); however, mechanisms for successful suppression remain unknown.
    • Conservation tillage leaves residue on the surface which breaks down at a slower rate than if incorporated during tillage events. This can allow pathogens to survive in the residues for extended periods. However, most problems identified with conservation tillage were observed in monoculture systems. Increases in plant disease are generally not found in reduced tillage systems with diverse cropping rotations and/or the use of cover crops.
    • Crop rotations can break up the host-pathogen cycle. Any crop species that is not a host to the same pathogens can be useful in reducing pathogen loading in soils. However, some pathogens can survive for multiple years in the soil prior to infecting a host plant.
    • The use of cover crops can help suppress pathogens. For example, crops in the brassica plant family (broccoli, turnip, radish, canola, rapeseed, and mustards) produce compounds that break down into volatile toxins that can suppress soilborne pathogens.

Take Away

In terms of soil health management studies, disease suppression is commonly measured as disease reduction in the crop based on the implementation of soil health management practices. However, no soil health management practice consistently suppresses disease.

Pathogens are generally contained in low concentrations in soil, making direct quantification difficult. Recent advances in genomics provide finer details of pathogen loading and activity in soil. The incorporation of genomic techniques aims to predict disease rates based on genomic measurements of pathogens in soil.