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Soil Fertility, Biodiversity and the Gut Microbiome

This article was also published in the October 2019 issue of Acres U.S.A.

Georgia farmer Will Harris is known to say that, “nature abhors a monoculture.” I heard him say this on my first visit to White Oak Pastures several years ago. It stuck with me.

Since that time, I have been trying to better understand the connection between pasture health and biodiversity of forages in pastures. The more diverse the pasture, the more resilient that entire plant community is to adverse factors like drought and pestilence. Why is this? Why would a diverse pasture be better suited to adversity and have higher nutrition than a monoculture of alfalfa or orchard grass, for example?

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In complex communities of plants, there is a corresponding greater and more diverse population of soil biology feeding on root exudates and detritus from plant diversity above ground. It is similar to the community of the gut microbiome. Consider the elimination diets that are so popular today. If you go on a 30-day carrot cleanse (an extreme example, of course), the biology in your gut that corresponds with the metabolization of the proteins and carbohydrates in carrots will flourish.

This is very similar to a monoculture planting; we are only supporting the relatively small spectrum of biology in symbiosis with that crop. After 30 days of nothing but carrots, your gut will be simplified to the point that when you eat something new like steak or bread it will upset your stomach and likely ruin your evening.

Now if this was your situation and you were rooted in place, like a plant, and your capacity to metabolize carrots went away, or there was a disease that impacted carrots, you would not be very resilient and you would have a compromised immune system.

Alternatively, if you are used to eating a great variety of fruits, veggies, fats and proteins, then your microbiome would be much more diverse and able to metabolize a greater variety of nutrients. It would allow you to withstand changes in diet without getting an upset stomach or being susceptible to sickness.

Similarly, in a diverse pasture, all of the different plants in that community are feeding different biological communities in the soil. The vast populations in the soil microbiome are fed a feast of diverse proteins, lipids and carbs from all of the plants in the community, resulting in a balanced diet for the soil biome.

This diversity in food sources creates diversity in soil biology. The life in the soil provides large amounts of plant-available nutrients to the rhizosphere. Now all plants in the community can make use of these nutrients and grow more higher-quality vegetation. The plants growing in biodiverse soil have a healthy immune system. Secondary and tertiary metabolites keep the plants resistant to disease and pest pressure.

Spencer Smith on ranch forage
Spencer Smith ponders the diversity of his ranch’s forages.


This process has evolved over the millennia as a way for the ecosystem to function in the face of adversity. Not only do different plants produce different foods for the soil biology; these different plants also correspond with availability of other plant nutrients.

For example, legumes collaborate with certain bacteria to mineralize nitrogen so that the entire plant community can access it. There are similar symbiotic relationships that are responsible for mineralizing other nutrients as well. This gives us an impressive tool in our farming toolbox when we evaluate our soil tests and determine how to make up for nutrient shortcomings in our pastures and crop fields. Intercropping and cover cropping fields increases available calcium, for example. This process occurs through the liquid carbon pathways or the plants’ leaking liquid carbohydrates — which they make via photosynthesis — through root pores to feed soil biology. This happens in predominantly two ways.

Firstly, plants leak low-molecular-weight plant sugars that feed large populations of soil biota. These are called basal exudates, which are the genesis of soils with higher organic matter content. The other way that plants alter the plant community is by emitting exudates for which the plants have specific purposes. These include secondary metabolites that correspond with specific soil biota that can mineralize specific nutrients such as nitrogen, iron, calcium and phosphate. These minerals are common in all soils, but must be “unlocked” by soil life to make them accessible to plants. Many farmers are now cover cropping with the intent of planting crops that will create better nutrient availability for the entire crop.

Many of these secondary metabolites do more than just unlock minerals to the rhizosphere. They are also responsible for creating the plants’ immune system and pest deterrent properties, as well as detoxifying soil pollutants.


Biodiversity in plant communities also impacts the physical properties of soil by creating relationships with arbuscular mycorrhizae. They produce glomalin and create improved aggregate structure. This improved structure is responsible for increased water-infiltration rates, as well as for holding maximum water in the rhizosphere for plant use.

Different plants have different structures that help them break soil compaction, combat erosion and pull mineral nutrients and water from deeper in the soil profile. Tap-rooted plants grow in areas that have challenges with compaction or low gaseous exchange. The tap root will penetrate this compaction zone, allowing air to follow. Greater and more diverse rooting types will follow the tap root, further opening the soil and fostering a greater population of beneficial soil biology.

If you see tap-rooted plants in your pasture and you think that compaction or low gaseous exchange isn’t an issue, I would ask you to carefully dig one up. Most likely you will find that the fine hair at the end of the tap root is penetrating deeper than the rest of the fibrous rooted plants. This is one reason why cover croppers across the country are adding radishes and turnips to their cover crop mixes. These tap-rooted plants deepen the rooting depth, bringing new nutrients up into the rhizosphere.

Figuring out how to increase diversity in our pastures and crop fields will add value and resilience to our operations. This is a deviation from the common teachings of 20 years ago, when farmers were advised to plant monocultures for their ease of management and uniformity. No longer is a plant out place considered a weed on some of the most productive and progressive farms. A plant that shows up in your field could be adding value to your operation by unlocking nutrients and improving soil structure. Next time, before you pull that weed, take a minute to figure out if that plant is trying to tell you something about your soil.

About Spencer Smith

Spencer Smith is a Savory Field Professional. Savory Global Network hubs provide accredited Holistic Management training and support across the world. Abbey and Spencer Smith manage the Savory Global Network hub serving Northern California and Nevada, called the Jefferson Center for Holistic Management. They live in Fort Bidwell, California, on Springs Ranch, where they produce grassfed beef; provide Holistic Management training, consulting and Ecological Outcome Verification enrollment; and manage contract grazing on the ranch pastures. Visit jeffersonhub.com to learn more.

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