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Building the Microbial Bridge for Soil Health

By Gary Zimmer and Leilani Zimmer Durand

The root zone around plants, known as the rhizosphere, is an area of intense activity in the soil. It’s a lot like the snack stand at the state fair on a hot day. Everyone is crowding around trying to get to the cold drinks, funnel cakes and hot dogs. Snacks are being sold as quickly as the workers can make them. In return, the snack stand is bringing in a lot of cash.

While the snack stand exchanges food for money, plant roots feed nearby microbes in exchange for plant nutrients. The roots put sugars down into the soil, creating an area of crowded, busy bacterial feeding in the rhizosphere, and exchange that microbial food for nutrients the plant needs but would otherwise have a hard time accessing.

We tend to think that plants photosynthesize entirely for their own metabolism, but in truth plants spend a good portion of their energy feeding soil life.

corn roots
Corn roots with lots of root exudates and soil sticking to the roots.

Plants fix sugars through photosynthesis, and while 55 to 75 percent of those sugars support plant growth, reproduction and defense from pests, the rest goes into the soil through the roots to feed the soil biology. This isn’t a waste of energy by the plants.

Bruce Tainio: Amending Soil Microbial Life, from the 2005 Eco-Ag Conference & Trade Show. (1 hour, 2 minutes) Listen in as the popular agronomist explains how to feed the microbial life in your soil, and develop optimal microbial biodiversity.

Those organisms living in the rhizosphere, primarily bacteria, not only make nutrients available to the plants — they also provide a protective layer against pests and diseases. It’s a win-win for the plants and the bacteria living in the rhizosphere.

It’s strange to think that plants have a hard time getting enough nutrients when soils are composed of around 45 percent minerals. Many of those minerals are the nutrients plants need to grow, photosynthesize, flower, pollinate and produce fruit or seeds. Although soil is a huge bank of minerals, most of those minerals are not in a form the plant can use.

Nitrogen, sulfur, phosphorus and many trace elements are all either dependent on soil life to make them plant-available, or they greatly benefit from microorganisms changing their form from one that’s hard to utilize to one that’s ideal for the plants.

An analogy I once heard at a farming conference in Australia is that microbes are the bridge between the soil minerals and the plant roots. I really like that analogy, but I would add to it that it’s an active bridge, one where transformations are taking place as things cross the bridge — like a highway bridge that takes semi-trucks full of minerals and converts them as they move across so they end up being small boxes of food at the other side, ready for plants to consume.

How the Microbial Bridge Works

The best example of the role of the microbe bridge in turning unavailable minerals into plant nutrients is how plants take up nitrogen. Just over 78 percent of the Earth’s atmosphere is nitrogen, but in its gaseous form nitrogen doesn’t do the plants much good. It’s like being thirsty while lost at sea. You may be surrounded by water, but you sure can’t drink it!

Plants are surrounded by atmospheric nitrogen, but only microbes are able to turn that nitrogen into a usable form. Microbes also provide nitrogen by transforming soil organic nitrogen (the nitrogen tied up in microbe bodies, mainly in the form of amino acids and proteins) and making it mineral nitrogen in forms of ammonium and nitrate that plants can take up. Without microbial nitrogen fixation and microbial breakdown of organic nitrogen into mineral nitrogen, there would be a great deal fewer plants on our planet. The microbes are the bridge that make the soil/plant system work.


Sulfur follows a similar process, but without the atmospheric fixation component. Most of the sulfur in the soil is organic sulfur, tied up in living and decomposing microbe bodies, and it takes microbes to change organic sulfur into plant-available sulfate.


Phosphorus is another mineral that greatly benefits from microbial transformations. Most farmers are aware of the important role of mycorrhizae in increasing the root surface area and accessing phosphorus that plants would otherwise have a difficult time accessing. It is less well known that up to 50 percent of the phosphorus in soil is organic phosphorus, tied up in living microbes and decomposing roots and microbes.

corn nitrogen comparison
The corn on the left was grown following a worked-down mature vetch crop, while the corn on the right was grown following a worked-down young clover crop. While both cover crops provided ample nitrogen credits, the mature vetch tied up nitrogen as it broke down because it was more lignified, and that nitrogen wasn’t available for the following corn crop. The young clover plants broke down quickly and rapidly released ample nitrogen to support the corn crop.

Organic phosphorus is mineralized to plant-available forms only through microbial activity. Phosphorus converts easily into unavailable forms in both acidic and alkaline soil conditions, so it is a huge advantage to have it in an organic form where it is relatively stable until microbes can mineralize it into a plant-available form.

Many other micronutrients benefit from the microbial bridge to make them plant-available. Microbes can change the form of a nutrient, change its charge, or hold it in a way that makes it less likely to tie up and easier for a plant to take up when it’s needed.

In addition to the role of the microbial bridge in changing the form of nutrients to make them plant-available, microbes are also a highway of nutrient movement and nutrient-holding capacity. While many nutrients require microbes to change their form, all plant nutrients benefit from microbes moving them around, concentrating them in the rhizosphere, and holding them in their bodies so they don’t tie up into forms that are mostly unavailable to plants.

On-Farm Intensive with Zimmer Ag

Learn about soil health in person with Gary Zimmer

The Acres U.S.A. On-Farm Intensive – starting in summer 2021 – is held in partnership with experienced farm consultants Gary Zimmer and Leilani Zimmer-Durand at their famous Otter Creek Farm near Lone Rock, Wisconsin. This two-day educational experience will help farmers, growers and land owners maximize their land’s potential. 

Learn more here!

Building Your Bridge

Knowing how important the microbe bridge is to plant growth and health is a great incentive for building a stronger bridge on your farm. There are a number of different practices that enhance the strength of the microbe bridge, and all involve feeding an abundance of soil biology year-round.

Biology is the key to building a strong microbe bridge, and diversity is what leads to abundant biology. You need diversity because the plants determine the soil life, and different types of plants both feed and benefit from different types of soil life. It’s just like choosing the right inoculant for your legumes — you wouldn’t use the same one on soybeans as you would on clover. The plants are specific to their microbes.

This is true not only for the microbes living around the roots in the rhizosphere, but also for those that digest plants in the soil. The stage of maturity when you feed the plant to the soil microbes is critical if you want to control nutrient availability and biology.

Young succulent plants have a different solubility, or as dairy people call it, “digestibility.” If you want to grow a crop like corn that requires a lot of soluble nutrients and extra nitrogen, you feed the soil microbes a highly digestible crop like young rye plants or alfalfa. Not only will these plants release nutrients quickly as they break down in the soil — they are also high in sugars that feed soil bacteria.

Soil bacteria consume easy-to-digest materials and have a 5:1 carbon-to-nitrogen ratio in their bodies. They live and die quickly and are consumed by other soil organisms like protozoa, which are closer to 10:1. The difference in the C:N ratio of the protozoa compared to the bacteria means there is a lot of extra nitrogen the protozoa don’t need for their own metabolism that gets excreted back into the soil as plant food. By feeding your soil bacteria you are also boosting nitrogen cycling and feeding your plants nitrogen.

If you allow your cover crop plants to get large, they will have more complex carbons and will be mostly fungal food. This gives a very slow release of nutrients and leaves behind more undigested, highly complex carbon. It’s good for building soil organic matter but not so good if you farm organically and need a lot of active nutrient cycling in your soils because you can’t buy commercial soluble fertilizers to make up for the nutrient tie-up as the lignified plant materials slowly break down.

Growing mixed plant species also results in a more heterogeneous group of microbes and digesters in the soil in which no one population can become dominant. This keeps things in check. The diversity of plant species also builds a stronger microbial bridge that provides a variety of minerals and plant compounds essential for plant health.

healthy soil life and cover crop
Healthy soil life with a newly incorporated mixed-species cover crop. This young cover crop will provide nutrients and carbon to feed the soil biology as it breaks down.

Microbial digestion is also affected by air. Burying residues deep may not be ideal for the type of organisms you want to have in your soil. That’s why I like to shallow incorporate my residues.

By shallow incorporating, some of the residues do still remain on the surface to protect the soil from runoff, but most of them are in the shallow aerobic zone of the soil where they can be broken down by beneficial microbes.

The bigger and denser the crop being worked in, the deeper it can be incorporated without harming soil structure or going down into the anaerobic zone where it won’t break down easily because there is much less microbial activity. Strict no-till with chemicals may be your methods of managing cover crops, but you do give up some benefits of microbial digestion if you don’t incorporate your cover crop. This is still better than not growing cover crops at all, but it’s like putting part of the feed you give your cow on the other side of the fence!

Your soils have a certain ability to dish out minerals, and the microbial bridge is key to making those minerals that are already in the soil available to plants. But that may not be enough. You need to apply fertilizer to feed your crop above and beyond your soil’s ability to provide minerals. That’s how to get high yields on lighter soils.

Be sure to add only quality, low-salt, balanced nutrients. By applying nutrients that are mixed with or bound to carbon, the fertilizer mirrors how things work in the soil. For liquids, molasses-based fertilizers provide sugars that not only buffer out the fertilizers but that provide readily available food for the soil biology to support the microbial bridge.

For dry granulated fertilizers, I like humates and fertilizers made with the digestate from anaerobic digesters on dairy farms. What comes out of the manure digester after the easy energy has been turned into methane is a mix of minerals, fiber and dead bodies of bacteria. We remove the fiber and add other minerals to make fertilizers. Not only are the nutrients in a carbon base, but they also have biological stimulants along with humic acids. This mirrors what happens in active, healthy biological soils to support microbial activity.

Being a biological farmer means switching focus from chemistry to feeding and taking care of soil biology. The emphasis is on the microbial bridge, rather than on soluble fertilizers, to get nutrients to plants. When the soil, plants and microbes are in balance, and a fertilizer that includes trace minerals is applied, you should not need to buy all the plant-protective compounds, technologies and chemistry that many farmers today depend on. Not only are those inputs expensive, but they won’t make your farm any better in the future. Build a strong microbial bridge, focusing on biology and soil health, and you will be well on the road to being a successful biological farmer.

By Leilani Zimmer Durand & Gary Zimmer. This article appeared in the December 2018 issue of Acres U.S.A. magazine.

Gary Zimmer and Leilani Zimmer-Durand are the authors of Advancing Biological Farming, a sequel to Gary’s earlier book, The Biological Farmer — both published by Acres U.S.A. Leilani has written extensively about biological farming and runs training courses for farmers and farming consultants on the principles of biological farming at Midwestern BioAg, where she serves as vice president of education initiatives.

Gary is an organic dairy farmer, an accomplished speaker, a sought-after farm consultant and president of Midwestern BioAg, a biological farming products and services company.

Gary and Leilani also previously presented at the 2018 Acres U.S.A. Conference & Trade Show in Louisville, Kentucky. To download audio and video of their presentations, visit Acres U.S.A.

Learn in the field with Gary Zimmer!

Spend 2 days this summer on Gary Zimmer’s Otter Creek Organic Farm in Lone Rock, Wisconsin. Learn how to use biological farming for better soil health and to improve your farming operation. July 19-20, 2021. Learn more here!

The Acres U.S.A. On-Farm Intensive is held in partnership with experienced farm consultants Gary Zimmer and Leilani Zimmer-Durand at their famous Otter Creek Farm near Lone Rock, Wisconsin. This two-day educational experience will help farmers, growers and land owners maximize their land’s potential. Learn more here!