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How to Grow Your Soil with Mycorrhizae and Beneficial Bacteria (Video)

By Joshua Burman Thayer, Native Sun Gardens

Tags: healthy soil, beneficial bacteria, fungi, permaculture, food forestry, California, Joshua Burman Thayer,

Soil Beneficial Bacteria Arbuscular

What is the difference between dirt and soil? To me, “dirt” evokes an image of a dead substrate, while “soil” evokes something dynamic and alive. Indeed, millions of under-recognized organisms keep the substrate under our feet alive and evolving. Microbes comprise a world that works in synergy to create soil conducive to healthy organic agriculture. If you find this intriguing, please do read on.

First, a brief history of life on land. Aquatic plants gained a foothold on dry land some time about 450 million to 500 million years ago. Fungi have been on dry land more than 700 million years. How much longer is in debate as some scientist say more than 1,300 million years.  Either way, fungi was on dry land before plants.

Bacteria were present on dry land even before the fungi. As aquatic plants began to try their luck at colonizing the terrestrial earth, from the start they had to associate with these two established orders of bacteria and fungi.

Soil Symbiosis

Symbiosis is a relationship that benefits all parties. These microorganisms have found ways to make their relationship with the rhizosphere, or plant root zone a mutually beneficial arrangement.

Arbuscular” mycorrhizae invade root cells of a plant. They then feed on the plant’s available sugars, benefiting the fungi. In exchange, they increase the root zone by up to 50 percent, and breakdown soil nutrients such as phosphates, mining and converting to make them available for bio-uptake by the plant. (Simon, L.; Bousquet, J.; Lévesque, R. C.; Lalonde, M. (1993). Origin and diversification of endomycorrhizal fungi and coincidence with vascular land plants. Nature, 363 (6424): 67.)

The fact that arbuscular mycorrhizae is found in association with all plant groups and more than 3/4 of all vascular plants leads many to believe that this association has been a key part of plant evolution upon this planet.

As for bacteria, beneficial bacteria can play a huge role in the immune systems of plants. Some cyanobacteria fix nitrogen in the rhizosphere. Others boost the immune system of the plant by preventing disease.

An old-time farmer taught me that chicken manure, high in beneficial bacteria, will help with the disease and bug resistance come fall. I have had luck in side-by-side grows where the plants top dressed in chicken manure staved off infestation far better. How does this apply to my garden?  Please read on.

Mycorrhizae and Beneficial Bacteria in Soils

The soil is alive and as it thrives, microbes are able to convert and store nutrients and minerals.  In this way, a constant remediation is taking place, thereby making nutrients accessible for plants to uptake and benefit from. This process ties up nutrients in the soil where they are less likely to leach out. Bacteria and fungi make all of this happen. They each are generally present in different ratios depending on conditions and soil pH.

From a plant-growing range of acidic soils, 4.5 pH to a high alkaline soil of 7.0 pH, there is a trend of fungal dominance in soils below 5.0 pH and a trend of bacterial dominance in soils above 6.0 pH.

Perennial plant systems trend more toward acidity and fungal dominance and annual plant systems trend toward alkaline and bacterial dominant soils. So, depending on your crops, you can custom tailor your soil pH to reflect your plant audience.

Mulch Feeds Microbes

To foster a healthy microbial system, mulch can play a tremendous role. Mulch protects the soil from the sun’s rays and the evapotranspiration of a portion of the soil’s moisture during hot days.  The mulch helps by retaining water and extending the wet period following each watering.

Mulch also helps to reduce weeds sprouting up through production crops. I recommend putting three to four inches of mulch down around all of your perennial crops.

Nitrogen Fixers Grow Soil

Plants of the family Fabaceae, otherwise known as the bean tribe of plans actually make the soil better by “fixing” nitrogen through root nodules. There is such an amazing range of bean and pea plants to be utilized (see list of Nitrogen-Fixing plants at bottom).

Not only is there a huge diversity of nitrogen-fixing plants, many of the annual varieties grow quickly and can be trained up vertically. Growing upward can be a great strategy for small spaces, such as the rooftop gardens I manage in downtown San Francisco, California.

I have had luck with seeding a blend of several bean, peas and lupines to create a “living mat” of green below my taller production fruit trees, berry bushes and annual veggies. This living mat increases the water-holding capacity of a food system while creating an added harvest in the margins of your main production crops.


To continue to foster the ongoing soil building of your garden, a process of “Chop and Drop” quickens the pace. When this annual bean patch has produced a yield, I chop up the carcasses of the beans and turn them back into the soil of a soon-to-be-planted annual patch.

The term “Chop-N-Drop” refers to chopping up the material pruned and dropping it in production areas to continue to mulch the soil. In the case of annuals, I find digging a one-foot-deep by eighteen-inch-wide trench and lining it with the freshly harvested and chopped up bean and pea (and lupine and vetch) carcasses.

Another reference to Chop-N-Drop is the Permaculture design concept of planting nitrogen fixing trees between each of your production trees (see nitrogen fixing trees list below). These aggressive trees are checked from over-dominance by pruning their growth each season to limit growth and by chopping up the pruned branches to feed the soil below.

When I design permaculture food forest orchards, I like to plant jacaranda or mimosa in between the main orchard fruit trees for this purpose. Annually, before their seed heads are mature, I can coppice prune them back to shoulder height.

In this way, light penetration of the fruit trees is maintained while a significant amount of biomass from these bean tribe trees can be harvested and their soft branch growth chopped up on-site into four- to six-inch pieces and dropped at the base of the production crops, thereby feeding the soil.

Grow your soil through these simple processes and in turn the soil will grow your crops.

Joshua’s List of Nitrogen-Fixing Annual Plants

• bush beans
• ‘Scarlett Runner’ beans
• sugar snap peas
• yard-long beans
• fava beans

Joshua’s List of Nitrogen-Fixing Perennial Plants

• Jacaranda: jacaranda mimosifolia
• Mimosa: albizia julibrissin
• Western Redbud: Cercis occidentalis
• Ceonothus: Ceonothus spp.
• Lupine: lupinus albifrons
• Coffeeberry: rhamnus californica

Joshua Burman Thayer is a landscape designer and permaculture consultant with Native Sun Gardens. He is the Urban Agriculture Supervisor for Tenderloin Neighborhood Development Corporation in San Francisco, Calif. Find him at Native Sun Gardens and read his other MOTHER EARTH NEWS posts here.

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