It’s challenging to properly care for something we cannot see. One of the most complex ecosystems on earth lives beneath our feet and is mostly invisible to the naked eye. There are billions (perhaps trillions) of organisms in a small handful of healthy soil, with millions of different species. 

Less than 10 percent of these organisms have been identified, and only about 1 percent are culturable — meaning the rest are nearly impossible to study in a lab because they only live in complex community with each other in the soil. 

Many publications tout the benefits of systems such as Regenerative Agriculture, No-Till, and Korean Natural Farming. These approaches employ methods such as reduced tillage, cover cropping, microbial inoculants, composting, and the like as ways to improve soil health. 

While these are all important solutions, it’s important to understand the role of soil microorganisms, the driving forces behind these techniques. Understanding a little about soil biology helps farmers take a peek into the mysteries that abound in the soil and hopefully can help shift perspectives on soil management practices. 


Unlearning conventional farming wisdom 
One of the challenges in studying soil today is confronting the reality that many of the concepts soil science is based upon are no longer accurate. Advances in technology, largely through microscopy, have allowed scientists to see firsthand the organisms that are responsible for almost all terrestrial life on our planet. 


soil-living-breathing-ecosystemIt’s amazing how much pressure can be applied to a single soil aggregate. Good soil aggregation helps prevent compaction and is a strong indicator of good soil health


Soil microbiologists estimate that roughly 95 percent of the soil functions we rely on are biologically driven. In other words, it’s the biology in the soil that is fueling the chemistry, not the other way around, as previously believed. 

An example of this outdated thinking is our continued dependence on conventional soil tests developed in the 1960s. The soil tests that most growers rely on are rooted in chemistry, rather than biology. Dr. Christine Jones (PhD, Soil Biochemistry) notes: “A soil test will only tell you what is available to plants by passive uptake. The other 97 percent of minerals — made available by microbes — will not show up on a standard test.” 




Submitting a soil sample that accounts for the biology, such as the Haney Test for Soil Health, in addition to your traditional soil test can help you gain a more complete understanding of how biology in your soil plays a part in your plants’ nutrient uptake. With good biology, fertilizer rates can be greatly reduced (and in some cases eliminated). 


soil-living-breathing-ecosystemAggregated soil at the author’s Blue Raven Farm. It took several years for their soil to look like millions of small pebbles. These aggregates are home to billions of microbes.


Last spring, I submitted soil samples to be evaluated utilizing both the Haney Test and the standard chemical analysis. We have been experimenting with reduced fertilizer application rates at Blue Raven Farm, and it was reassuring to see that the Haney recommendations were much more in line with what I was applying versus the recommendations from the standard test results.

Soil aggregates and their role in soil structure
Simply put, aggregates are like small, sturdy houses for microorganisms. Soil particles are formed into microaggregates and macroaggregates, which give your soil structure. Microaggregates are formed when bacteria adhere to soil particles and organic matter. Macroaggregates are formed when fungi glue microaggregates together using glomalin, a sticky protein substance only they can create. Aggregates are an important indicator of soil health. They help protect microbes, hold organic matter (carbon) in the soil, increase water availability for plants, improve drainage, and decrease soil compaction.  


soil-living-breathing-ecosystemIn this photo taken with a microscope, root exudates can be seen coming out of a living plant root. Root Exudates are a key element to plant-microbe communication. Plant roots excrete a diversity of unique compounds that attract specific microbial species to their root systems. Photo by Phill Lee of Rengenerate Earth.


Soils with good aggregation (especially macroaggregates) resist erosion from tillage, water and wind. A well-structured soil with good aggregation has many small soil crumbs resembling small, brown peas. A soil that has been over tilled resembles a powdered sugar texture, with very little aggregation of the soil particles. 

Communication between plants and microbes 
Soil is a living, breathing ecosystem that would not exist without microbes. Plants convert sunlight and CO2 into energy in the form of proteins and carbohydrates via photosynthesis. However, plants cannot live on these compounds alone, they need many more nutrients to thrive. While the soil theoretically contains everything plants need, most of these compounds are not present in a form the plants can use. This is where the biology in the soil comes into play. 

Bacteria and fungi pull nutrients out of the organic matter, sand, silt, clay and rock materials in the soil matrix. In order for plants to get these nutrients to their root systems, plants and microbes have evolved over millions of years, working out a mutually beneficial communication system that enables them to share resources with each other. 


soil-living-breathing-ecosystemSoil predators like nematodes prey on bacteria and fungi, resulting in the release of nutrients in a plant available form. This nematode is seen using 400x total magnification. All photos courtesy of the author except where noted otherwise.


Plants send a percentage of the carbohydrates and proteins into their root systems, where they are released as exudates. By doing so, the plants are essentially setting out a buffet table, and these carbon-rich exudates attract bacteria and fungi to the party. This attracts an abundance of microbial life to the plant roots, which happily feast on the buffet and begin to reproduce. 

This microbial rich area around the root system is called the rhizosphere. The exchange of nutrients between microbe and plant is not complete without the help of soil’s microbial predators. Predators, such as amoebas, nematodes and microarthropods are attracted to the abundance of their favorite food, the bacteria and fungi. The microbial predators consume the nutrient dense bacteria and fungi and excrete excess nutrients in a solubilized form which the plants can readily absorb. 


soil-living-breathing-ecosystemHere’s a gorgeous web of mycelium or fungal “roots” running through the soil. Fungi play many key roles in plant health, including nutrient cycling, disease protection, organic matter breakdown, and carbon sequestering.


Scientists have recently discovered that plants have the ability to create unique combinations of exudates that are tailored for the specific microbial community they need at the precise time they need it. Biologists speculate there could be millions of combinations of carbon exudates, which are the plant’s way of communicating what it needs to be healthy and resilient against pathogens and environmental stresses.

The importance of diversity: quorum sensing
The diversity of plants on our farms is directly correlated with the diversity of microbial species in our soils. Growers can encourage more diversity in their soils by growing different plant families in close proximity to each other to encourage root mingling. Plants function best with a diversity of microbes surrounding their root systems, which provide benefits such as nutrient availability, enhanced yield, plant vigor, and protection from disease and environmental stresses, such as cold or drought.

In the last decade, biologists have discovered quorum sensing in soil microbial communities, unlocking a whole new world of understanding how microbes communicate with each other and their host plants. Simply stated, the concept of quorum sensing is that there is a minimum number of microbes needed to make a collective decision. 

When a quorum is reached, microbes can turn on or off specific genes in order to influence functions in each other or in their host. Many microorganisms (bacteria, fungi and viruses) use quorum sensing to communicate, and recent studies show their communication is not limited to within their species. Interspecies communication is in constant flux to ensure the entire community within the soil’s ecosystem is functioning efficiently. 

Fungi: a missing link in agricultural soils  
Like most soil microorganisms, biologists are only scratching the surface in their understanding of the mysterious world of fungi. There are at least 70,000 species of fungi in our soils, which thrive in undisturbed, aerobic (requiring oxygen) conditions. Fungi play many vital roles in the soil such as breaking down organic matter, pulling nutrients out of soil particles, and creating aggregates that are essential for soil structure. 

Fungi also help regulate pests and diseases, mitigate environmental stress, and improve plant growth by forming synergistic relationships with plant roots. It’s impossible to study healthy soil ecosystems without seeing the incredible benefits fungi have on our crops’ health. 

Fungal superstars: mycorrhizae and trichoderma 
Mycorrhiza is a Greek word meaning “fungus root.” Many growers may think of mycorrhiza as a specific fungal species, but technically mycorrhiza refers to the relationship some fungi share with plant roots. About 85 to 90 percent of all plants form mycorrhizal relationships. Brassicaceae and Amaranthaceae are two notable crop families that do not. 


soil-living-breathing-ecosystemRoot mingling of different crop families interplanted within the bed helps diversify microbial species in the soil.


Fungi that form these relationships infiltrate the root tip, where the fungi will benefit from nutrients provided by the plant host. As a result, the fungus grows, expanding its hyphae (microscopic thread like roots) into the soil matrix where it will obtain water and nutrients for the host plant. 

The relationship is beneficial for both organisms. The fungus receives nutrients from the plant roots, and the hyphae on the plant’s root system stretch out well beyond the root system, accessing water and nutrients for the plant. It should be noted that frequent tillage decreases mycorrhizal associations, and fungicides are toxic to mycorrhizae fungi. High levels of nitrogen or phosphorus fertilizer also have been shown to reduce mycorrhizal inoculation of roots. 

There are many groups of fungi that protect plants against disease-causing organisms and environmental stresses. One in particular is Trichoderma (which is not mycorrhizal). This genus includes several beneficial species that have the ability to colonize root systems and influence plants to produce disease-controlling properties. 

These multifunctional fungi can also increase photosynthesis, resistance to cold and drought, root growth and plant yields. It’s worth noting that Trichoderma and mycorrhizal fungi may be antagonistic with each other in some circumstances and with certain strains. In short, it’s complicated. There are studies showing both positive as well as negative effects when these two fungi are paired together.  

Humans, plants, animals are connected through soil  
Without soil, life as we know it would not exist. Plant life and all who consume it could not survive without microbial life. Countless studies confirm that the abundance and diversity of microbes in the soil results in plants that are healthier and more resilient. “By looking after the microbes in the soil we can increase the availability of a huge variety of minerals and trace elements — most of which are not in fertilizers,” Dr. Jones said. 

Thus, it’s not a stretch to hypothesize that this will also benefit the animals and humans who consume these healthier plants. We are also learning that human and soil microbiomes are closely connected to each other. In fact, humans share many of the same microbes as are found in soil.

When we are in close relationship with healthy, microbially rich soil, we get the benefit of sharing the soil’s microbiome through eating fruits and veggies, having direct contact with soil, and inhaling soil microbes in the air we breathe. By increasing the diversity of our gut microbiome, studies are beginning to show that we can increase our resilience to stress and disease. 

It’s disheartening that humans are suffering from more chronic disease than ever. Multiple studies show that the nutritional content of our food has declined over the past 50 to 70 years. As a result, we are not getting the same nutrients that our grandparents did, and modern farming practices are largely to blame. 

The Rodale Institute is doing an incredible trial to show the variability in nutrient density between organic and conventionally grown crops. The Vegetable Systems Trial takes place in a field that had been farmed organically for 20 years and was divided into quadrants for the purpose of the trial. 

The conventionally grown quadrants utilize farm techniques that include the use of herbicides or deep tillage. The organically grown quadrants utilize minimal tillage as well as no-till techniques. Within just a few years of production, the data Rodale has gleaned thus far is profound. Protein content, vitamin B6, and vitamin C levels in corn all proved to be substantially higher in the organically managed systems. 

The trial is still in its infancy and some of the data Rodale is hoping to collect in the future will include comparisons of microbial diversity and its subsequent nutritional density. I am excited to have data that is based on a long-term farm trial. This will likely confirm what the early trials are already demonstrating, that soil health is directly connected with our own well-being. 

Getting good biology into the soil
You don’t need a microscope to see the effects of unhealthy soil. If weeds, pests and diseases are affecting your crops negatively, this is a clear indication that something is not quite right with your soil biology. Rather than turning to band-aid solutions such as tillage and increased use of fertilizers, pesticides and herbicides, we need to step back and consider what is really out of balance. As our understanding of soil increases, we can rethink our soil management practices, favoring long-term health over short-sighted solutions. 


soil-living-breathing-ecosystemTipping the scales: Our dedication to soil health has resulted in huge decreases in weeds, pests, diseases and labor in just a few short years.


There are many opinions about the best way to repair soil biology. How farmers repair and maintain their soil is unique to their scale, climate, crops, soil condition, and so on. There isn’t a one-size-fits-all approach to soil repair, and there is still a lot of research and infinite farm trials that need to be done in order to help farmers find solutions that fit their unique set of circumstances. 

That said, biologists from around the world agree on a few points. First, disturb the soil as little as possible. Second, maximize photosynthesis with a diversity of plants growing at all times. Mounting evidence is pointing to the importance of multi-species cover crops to help stimulate a diversity of microbes in the soil. Finally, and perhaps most importantly, eliminating chemical fertilizers, herbicides, pesticides and fungicides plays a key role in increasing and maintaining soil diversity. 

I have been researching and trying to learn more about biological inoculants (such as compost extracts, mycorrhizae, Trichoderma, and other biologically rich soil amendments). Many biologists suggest that inoculating at the time of seeding may help plants form relationships with beneficial microbes early in their development. It’s also a great way to inoculate your entire field at the time of transplanting. 

While studies show varying results depending on soil, climate, moisture level, etc., I am excited to begin a field study here in Oregon. For 2022, I am planning to incorporate a few different inoculants such as Trichoderma and a compost extract to my seeding medium to see if seedlings in spring will better acclimate and have increased resilience to our cold, wet weather. 

Want to stay current about the amazing world of soil? 
If this article left you with more questions than when you started reading, I have done my job well. If you are yearning to learn more, one of my favorite resources is the podcast “In Search of Soil.” Some of my favorite microbiologists and researchers are: Dr. Christine Jones (quorum sensing), Dr. Gary Harman (Trichoderma), James Hoorman, Dr. Elaine Ingham (one of the pioneers in soil microbiology), Peter McCoy (mycology), Rick Haney (Haney Soil Test), and Dr. David Johnson (fungal-dominated compost). 

YouTube is an incredible resource for watching soil health conferences from around the world. It’s a great way to hear from lots of biologists whose research is current. There are so many soil biologists and researchers doing incredible work. I have deep gratitude for what they are doing. 

Stay tuned for part 2: Getting good soil biology back into the soil with compost, multi-species cover crops, and inoculants.


Jen Aron has been a farmer and educator for the past 12 years and currently lives and farms at Blue Raven Farm in Corbett, Oregon. Jen is passionate about soil health and offers classes, consulting, and full-day workshops. You can find her at and on Instagram @blue_raven_farm.