Welcome to your ONFARM resource guide to understanding the complex microscopic network going on beneath your soils. Here you will find four modules, each covering a different topic about the role soil microbiology plays in agriculture.

Module 1 - Soil Microbiology Overview

Module 2 - Cropping Systems & Tillage

Module 3 - Organic Amendments & Biofertilizers

Module 4 - Soil Microbial Health Testing


Module 1: Soil Microbiology as a Component of Soil Health

Your soil is teeming with billions of microscopic organisms. These unseen heroes carry out a suite of functions crucial to the health of your soils and success of your crops. Understanding why these microbes are important and how closely they are tied to soil management practices is a hot topic in the research world. Allowing for a better understanding of soil microbiology outside of the research world is essential for encouraging agriculture practices that promote healthy microbe populations. 

Introduction to Soil Microbiology

New Ideas
Microbial diversity/biodiversity is something that looks at how many types of microorganisms are present – not to be confused by the total amount of microorganisms present. An example is to look at cover crops. A field with a 3-way cover crop mix has less diversity than a field with a 10-way cover crop mix – even if the biomass of each field is the same.  
Key Takeaways
  • Bacteria and fungi are microscopic organisms living in your soils that work together in complex communities to carry out important ecosystem services contributing to soil health.
  • We know it is an extremely important aspect of soil health! But due to research limitations, some of the questions surrounding how the microbial community affects your soil health, and how to improve your soil microbial health, is still unanswered.

Soil Microbes Role in Ecosystem Services

New Ideas 
The rhizosphere: this is the area in soil that surrounds the plant roots. Microbes living here interact closely with the plants. This interaction ensures that the plant is getting access to all the nutrients in the soil, while in turn, the microbes are getting food from the roots so they can thrive!
Soil Resilience: The ability for a soil to adapt and recover from stressors such as drought, flooding, climate change, and intense agriculture is partially due to soil microbial biodiversity (how many DIFFERENT types of microbes are in a community). Having many different microbes that carry out the same functions means that if one species dies because the soil is too dry (stressor would be drought), other species can come in so that specific function isn’t lost.
Key Takeaways 
  • Ecosystem services are the result of the microbial community working together to carry out functions. These include building soil organic matter, nutrient cycling, soil resilience, soil structure and climate regulation.
  • Organic matter in things like crops and organic amendments contains a lot of carbon. Carbon is the fuel that microbes need to grow. Healthy microbial communities start with ensuring they have enough fuel!

What you can do for your soil microbial community

Key Takeaways
  • Focus on the things you can control for bettering your soil microbial community. Ensuring you have a diverse crop rotation, continuous soil cover, and adding organic amendments (these maximize the carbon going into your system), but also reducing disturbances to your system such as tillage. Best Management Practices are a really great place to start!

Thanks for watching Module 1! Please scroll back up to watch Module 2 - Cropping Systems and Tillage 


Module 2: Cropping Systems and Tillage are Important Mediators of Soil Microbial Health

What you plant into your soil is largely influencing soil ecosystem services such as organic matter decomposition, nutrient cycling, soil structure and many more. So there is no surprise knowing that different crop rotations and crop management systems also have a large effect on your soil microbial community. Above ground benefits of diverse crop rotations, crop rotations that use cover crops, and minimizing tillage are well known – but below ground benefits (the microbial community) is not as well understood.

Cropping Systems

New Ideas

Arbuscular mycorrhizal fungi are an important group of microbes living in the rhizosphere. They work in a symbiotic relationship with plant roots, taking sugars that the plant gives off while offering nutrients and water to help the plant grow. Continuous cropping, cover crops and reduced tillage are all strategies to keep this group of fungi healthy.

Key Takeaways
  • Your microbial community uses crops planted in the soil as fuel to grow. Ensuring they have fuel all the time through leaving residue on the soil, or planting cover crops will keep populations high. Having a diverse crop rotation and including cover crops can lead to a healthier microbial community resulting in increased soil organic matter and soil resilience. 


Key Takeaways
  • Tillage alters the structure and function of microbial communities in soil. Namely, it can compromise the integrity of arbuscular mycorrhizal fungi, decrease overall biomass and activity, and sometime changing the amount of biodiversity in a system. This is still a topic that researchers need to look into more as results aren’t always consistent or informative.

Thanks for watching Module 2! Please scroll back up to watch Module 3 - Organic Amendments and Biofertilizers

Module 3: Organic Amendments and Biofertilizers

Applying fertilizer to soil is an important part of growing successful crops. These nutrients are needed in large amounts to sustain intensive agriculture practices needed to feed the global population. Fertilizers affect crop yields, the physico-chemical properties of soil, and overall soil fertility. Knowing the importance of the soil microbial community, it’s easy to see that adding fertilizers will affect these microorganisms over time. 

Adding microorganisms directly to the soil through biofertilizers is another way to enhance ecosystem services provided by the microbial community. Being aware of the benefits and limitations of these products is important when making management decisions.

Organic Amendments vs. Inorganic Fertilizers

Key Takeaways
  • While inorganic fertilizers offer a fast and accurate way to deliver nutrients to crops, organic amendments help feed the soil and rely on the microbial community to transform the nutrients into a form that the plant can easily take up.
  • Organic amendments typically increase microbial biomass and biodiversity resulting in more organic carbon being deposited into the soils, along with more nitrogen and phosphorus availability. These results can be dependent on outside factors.
  • You don’t need to use organic amendments exclusively. You see similar benefits to soil microbial communities when inorganic and organic fertilizers are used in tandem.
What’s the deal with biofertilizers?

Key Takeaways
  • Biofertilizers have limitations and still require more research to understand how they’ll survive and function when applied to the field.
  • If the microorganisms in the biofertilizers can survive and persist it can optimize specific functions carried out by the microbial community, potentially decreasing the need for other inputs on the soil.

Thanks for watching Module 3! Please scroll back up to watch Module 4 - Soil Microbial Health Testing

Module 4: Soil Microbial Health Testing

Monitoring soil quality through soil tests are key to maintaining healthy and sustainable soils. Many of the tests used to monitor soil assess a range of soil chemical, physical, and biological properties, but tests that measure soil microorganisms are much less common. As we’ve learned, microorganisms change alongside management practices and soil conditions so there’s great potential for soil microbial indicators to be used to monitor soil health. Some tests measuring soil microbial biomass and activity are already available, and hopefully with advancements in research these tests will become more accessible to help inform soil management practices.

Soil microbial tests and the future of biological indicators

Key Takeaways 
  • Commercial tests are available to test some microbial indicators such as biomass and activity, but there are certain limitations around these tests. Ensuring that samples are taken in the same weather, field location, and crop in the field is important when tracking changes to these tests over time. With new research becoming more readily available, expect microbial soil health indicators to become a very useful tool in the future.

Thanks for watching Module 4! This is the last of the soil microbial health modules. 

Final Remarks

I encourage everyone interested in this topic to learn more! There are many resources available online and so many other topics to learn about that I wasn’t able to cover. The questions about how soil microbes are playing a role in soil health are still being uncovered, but learning alongside researchers will help get these questions answered. Hopefully from going through these modules you’ve been able to understand a little more about what goes on below your feet out in the field.

Have a question? Please email ONFARM@ontariosoilcrop.org