Agroecological Practices for Healthy Soil Ecosystems

Module Progress:

As we learned in the beginning of the course, with the rise of modern industrialized agriculture, soil is often treated as if it were mainly a medium holding up plants, and a place to put chemical fertilizers and other compounds. With the over-simplification of agriculture and a reductionist, chemical approach to soil management, the world has seen devastating losses due to soil erosion, nutrient leaching and carbon loss. While soil fertilizers can be added to raise production, it is only by understanding nutrient cycles and soil ecological processes that soil fertility can be maintained and restored. As you’ve learned, the soil is not inert – it is a complex, living ecosystem which has the potential to sequester carbon and boost crop, environment and human health if managed correctly.  In this module, you’ll explore alternative approaches to soil management using an agroecosystems approach. You’ll get some practical, hands-on ideas as well as to how to start managing you soil agroecologically.

Managing agroecosystems for healthy soil

In agroecology, the goal is to maintain and promote soil-forming and soil-protecting processes involving soil organic matter and soil biota. It is also to protect traditional farming practices and related biocultural diversity.

Can you think of some ways that farmers add organic matter back into their systems, and/or protect soil micro-organisms?

Excerpt 1: Soil Management

by Steve Gliessman | Agroecology: The Ecology of Sustainable Food Systems, Third Edition

Once a soil is put under cultivation, the original organic matter levels begin to decline unless specific steps are taken to maintain them. After an initial rapid decline, the decrease slows. Several kinds of changes occur in the soil as a consequence of the loss of organic matter. Crumb structure is lost, bulk density begins to rise, soil porosity suffers, and — because SOM is the basis of the soil food web — biological activity declines. Soil compaction can become a problem as well.

A study comparing soils after 75 years of organic and conventional wheat production in eastern Washington found that organic matter was not only maintained in the organic system, but actually increased over time, while production levels for the organic farmer were near equal to the conventional (Reganold et al. 1987). Since farming tends to deplete SOM, sources of new organic matter must be continually added- at least enough to replace that which is lost through harvest and decomposition… Many agroforestry systems in tropical regions have a large number of plants, many of them non-crop species, whose primary role is biomass production and the return of organic matter to the soil.

Many farmers all over the world still use these systems, however, due to economic and physical constraints, many famers manage systems that are significantly less diverse. These farmers must therefore find ways of adding organic matter to their systems instead of counting on plants in the system to do it themselves.

To follow are some of the agroecological ways to add organic matter into soils.

Reducing Tillage Intensity

Tillage can degrade soil structure, reduce organic matter content, disrupt soil biota, simplify the soil food web, and cause the soil to lose some of the elements of productivity. The main pattern of tillage employed in conventional agriculture is a three-stage process.

  1. Deep plowing that turns the soil
  2. Secondary tilling for preparation of a seed bed
  3. Post-planting cultivations (often combined with herbicide use) for weed control.

Tillage is associated with problems like soil erosion, loss of good soil structure, and nutrient leaching. It often is dependent on fossil fuels and tractors, as well as expensive equipment. Since tillage frequently damages soil structure and soil ecosystems, it isn’t a sustainable soil management method for long-term land management.

At the other extreme, there are many traditional farming systems in which no tillage is used at all. In swidden agriculture, traditional farmers clear land using slash and burn techniques and then poke the soil with a planting stick to sow seeds. Such systems, which have the longest history of sustained management, respect the need for a fallow period to control weedy vegetation and to allow natural soil-building processes to replace removed nutrients.

Crop Residue

Crop residue can be incorporated in a number of ways. Crop residue can be left on the soil surface, or incorprated back into the soil through tillage. However, as you will read below, tillage can damage soil structure. Another way is to leave the crop residue on the soil surface, and plant the next crop directly into it. There is some evidence that the finished crop could harbor pests or disease organisms, which would pass onto the subsequent crop. The final way is to incorporate crop residue into compost, and return it back to the field in the form of finished compost.

Cover Crops
Cover crops serve a multitude of purposes in agroecological systems. Cover crop is usually a crop that is grown in rotation with a crop or during a time of the year that the crop can’t be grown. The resulting biomass of the crop can be incorporated into the soil, or left on the surface as a protective mulch until it decomposes.

Compost and Vermicompost

Compost and vermicompost (a special kind of compost produced by worms) can add fertility, organic matter, and microorganisms back into your soil, improving soil ecosystem health and soil structure. There are many methods of making and maintaining compost, and many videos on this process. Please read choose at lease one of the following readings on composting and vermicomposting.

Article 1: Assessing Compost Quality for Agriculture

by David M. Crohn | from ANR Publication, August 2016

Article 2: Tipsheet : Compost

by ATTRA Sustainable Agriculture | from National Center for Appropriate Technology

Article 3: Vermicomposting: The Basics

by Richard Myers | from National Center for Appropriate Technology, October 2013

Article 4: A Step-By-Step Guide to Vermicomposting

by Mary Applehof | from Mother Earth News, July/August 1983

Enhancing Beneficial Microorganisms with Compost Teas and Ferments

In addition to increasing the organic matter in soils, there are various ways — beyond composting and vermicomposting described above — to increase the biological activity of soils for greater plant health and nutrition. These practices are based on the theories practiced in Korean Natural Farming. The following descriptions are modified from Planting Justices’s Urban Permaculture Guide.

Lacto Bacilli

Lacto Bacilli is everywhere! It lives in the air, on plants, and in your gut (and the guts of all animals); without it, we would not survive. LB is a major digester in any bio-dynamic system, meaning it breaks down nutrients and makes them available in a form we can use.

How to Collect Lacto Bacilli

Purchase a bag of cheap, highly refined white rice. Pour rice into a bowl and cover with water. Let rice sit in water for a few minutes. Then, strain out the rice and pour the milky colored water into a jar, leaving room for air in the jar so that the rice wash fills no more than half of the jar’s volume. Cover the jar with a cheese cloth, rubberband it, and set it aside in a cool, semi-dark place for 5 days when warm and up to 15 days when cold. A variety of air-born bacteria will colonize this rice wash. When it is ready for the next step, it will have a sweet alcoholic aroma, and a film on top with spores growing on the surface. Skim off this surface skud before the next step.

Now we need to isolate the lacto bacilli by feeding the bacteria food that the LB particularly likes so that it will out-produce the other bacteria living in the rice wash. So, add 10 parts milk (does not need to be raw, can be from a cow, goat, or sheep, even powdered milk will work) to one part rice wash. Cover again with cheese cloth and let sit for 5-7 days. The fats in the milk will separate to the top, and underneath the fats will be a clear yellowish solution which is pure lactose. Carefully skim off the fat without letting it mix back into the lactose (if it does, you’ll have to try again once the fat rises again to the surface). In a refrigerator it will keep for 1 year, or if you add raw sugar such as molasses (1/3 sugar to total volume), you will not need to refrigerate it. It if begins to smell rotten, you know the LB is gone.

Uses of Lacto Bacilli

  1. As foliar spray on leaves of plants, it will totally populate the leaf surface and use up the food supply, thereby starving out any pathogens that might also want to populate the leaf surfaces of plants. Its presence protects the plant, allowing the pores on the plant’s leaves to open up larger and stay open longer so the plant can get more nutrients. To use as foliar spray, dilute it 1:20 with NON-CHLORINATED water (chlorine kills microbes, but if you only have chlorinated water, let it sit for one day and it will evaporate out), and then you can dilute it again 5 tsp/gallon. One batch is enough for a whole year’s usage on a 5 acre farm. It is generally not used alone, but combined with other plant extracts (which I explain below) to feed the plant additional nutrients.
  2. Eat it yourself to aid in digestion and medicinally to stop diarrhea. Used internally, it does not need to be diluted. Feed it to your chickens, goats, cows, dogs, cats, etc by adding it to their water so that they will digest their food more completely, enabling you to reduce feed by 30%.
  3. Add to anything foul smelling, such as your compost toilet or compost pile.

Indigenous Mycorrhizal Fungi

Mycorrhizal fungi are an essential part of healthy organic living soil structure and have an incredible symbiotic relationship with plants. They live in the root zones of plants and feed off of other microbes, called nematodes, and convert them to usable nutrients. They act as a sort of glue, holding soil particles and water in a way that creates plenty of air space.

We will collect mycorrhizal fungi from a healthy ecosystem to use in our garden. By inoculating the root tips of plants we want to propagate or transplant out into the garden, we can stimulate root growth and help the plant’s roots quickly recover from shock we may cause during the transplanting process. In addition, by increasing the amount of m.r. fungi in our soils, we won’t need to water our garden nearly as often, as m.r. fungi fill up like balloons with water to store it for when roots need it most.

How to Collect Indigenous Mycorrhizal Fungi

Cook the rice you washed for the lactobacilli. Spread a thin layer of rice onto the bottom of a wide, shallow pan. Put a wire barrier over the pan to keep out rodents and cheese cloth on top of that to keep dirt and bugs off. Then, go find a healthy system, using your eyes and nose to feel out a microbe hot-spot. In this area, you may seek out a particularly old, healthy oak or alder tree to collect m.r. fungi

Collect leaf litter and soil from a foot beneath the ground, and take this litter back to your rice pan, piling the it on top of the wire and cheese cloth. Keep it on the ground in the shade, keeping it moist if it is very hot outside. After 7 days, peek under the cheesecloth, and you should find a colorful array of fungi growing on your rice. Remove and discard the leaf litter, scrape the rice into a 5 gallon bucket, and add raw sugar (1 part sugar to 3 parts rice). Fill bucket with water.

Uses of Indigenous Mycorrhizal Fungi

Use as a root soak. Strain and dilute it 1:20 with non-chlorinated water.

Other Ideas for Indigenous Mycorrhizal Fungi

If you are propagating a specific plant, collect leaf litter from an especially healthy specimen of that same plant species. For example, if you are growing blueberries, colonize your rice with m.r. fungi from a healthy blueberry plant, add molasses, and use as a root soak to inoculate new blueberry transplants.

Here are some other useful plants you may want to collect m.r. fungi from:

Fava Root: Dig up the roots and surrounding soil of healthy favas. Put in a 5 gallon bucket. Add 1/3 molasses to fava volume, and fill with water. Let it sit for 10 days to brew. Then, strain out solids. You can dilute this solution 20:1 with water and add to your indigenous m.r. fungi solution as part of your root soak.

Bamboo: very active microbes. Collect leaf litter and colonize your rice with m.r. fungi from a healthy bamboo plant, and then use their incredible digestion properties in your grey-water system.

Check out the visionary talk, Mushrooms, Mycology of Consciousness, by Paul Stametes at the 2017 EcoFarm Conference that highlights the under-appreciated importance of fungi for animal and ecosystem health.

Film 1: Mushrooms, Mycology of Consciousness

Plant Extracts

Many different plants can be harvested and fermented to extract a variety of beneficial properties which can be delivered directly to your garden easily and for free. These can be all mixed together with the lacto bacilli in one 55 gallon barrel to be used as a bio-dynamic foliar spray. Below are some suggestions of plant extracts to try. Other extracts to try: horsetail, calendula, fruits such as papaya for valuable nutrients.


The only plant I know of that can be fermented without adding any sugar, a nettle extract is a very important part of any tea. All you do is harvest the nettle, chop it up fine, and submerge in water. Cover it and leave for 10 days. It is an amazing stimulant for all plants, and chock full of nutrients. Use as part of a foliar spray or as part of a root soak solution. For all the rest: harvest, chop finely, add 1/3 molasses to volume, add water, and let ferment for 7-10 days


Ferment for high nutrient load.


Ferment for beneficial hormones and nutrients, use as part of foliar spray.

Garlic and Ginger

Use as foliar spray to prevent bugs, or take internally yourself for many health benefits. Fungicidal properties of garlic fight disease and repel bugs.


Use as foliar spray for bug and microbial prevention.


Harvest young shoots, ferment to extract growth hormone, and use as part of foliar spray.

Fava Bean

Harvest tops of plant, ferment to extract growth hormone, use as part of foliar spray.


Explore more! Elaine Ingham, American microbiologist and soil biology researcher and founder of Soil Foodweb Inc, is a great resource for learning more about alternative ways at understanding soil health:

Check out her video resources here.

Here you can watch a free presentation she gave at the Permaculture Voices Conference in Temecula CA in 2014

Her work as well as that of many other great soil stewards is featured in “Symphony of the Soil” available for a small fee here. Its a “documentary by Deborah Koons (The Future of Food), featuring Ignacio Chapela, Dan Barber, Vandana Shiva, Daniel Hillel, Elaine Ingham, and Chuck Benbrook.”


Reflection Questions