Making Microbes: Fungal vs Bacterial Soil Life

Organic gardeners and farmers understand the need to cultivate and protect soil microorganism life. The strategies to do this involve mulching, composting, and avoiding soil disturbance as much as possible. We know that these strategies, in addition to many others, encourage a healthy soil-food-web.

The soil-food-web is the interconnected matrix of invisible (fungi, bacteria, protozoa, nematodes) and visible (earthworms, beetles, arthropods) creatures that have a whole host of functions which create a healthy ecosystem for plant growth. They aerate the soil, decompose organic matter, make nutrients available, prevent nutrient leaching, break down toxins, protect plants from pathogens, fix nitrogen and so forth.

Fungal vs Bacterial Soil Life 01

What we can take away from this bit of knowledge is that we want these organisms operating on our garden or farm. The best way to do this is by creating the habitat and food they need in order to thrive. This seems simple, but it quickly becomes complicated when we explore the details.

Each of these organisms does better with different food sources and each of them change their environment in different ways. In addition each species of plant we are growing thrives in different soil environments; apples and arugula have evolved very differently and the more we can support their evolutionary requirements the healthier the plants will be.

That becomes our starting point; where we ask:

•What type of soil environment do our crops desire?

•How can we then encourage the specific type of microorganisms to create that environment?

Fungal-Bacterial Ratio

Here at the Ranch we are growing tree crops, which as I’ve written in this blog before, thrive in an environment that mimics the forest ecology surrounding our orchards. One measure we can use to understand this ecology is the fungal to bacteria biomass ratio (F/B).

This is a measure of the portions of the microbial biomass, ie. all the living organisms in the soil, that is fungal vs that which is bacterial. The F/B ratio is primarily used to study the impact of human land disturbance on the soil-food-web. It can therefore also be used to determine what individual plants desire. For example annual grains and vegetables like a ratio of 0:3 to 1:1 and orchard trees thrive in 10:1 to 50:1 soils

Depending on the types of crops we are growing, again in our case tree crops, we may want to alter the dominance of fungi or bacteria in our soil. These microorganism, particularly fungi, are quite sensitive to changes in land usage, therefore we need to understand how different techniques affect this ratio and why we want the ratio to be high or low in the first place.

Ecosystem Mimicry

Forest soils have a higher fungi to bacteria ratio. Looking at quantities of each, as measured in a teaspoon of soil, we find that bacteria remain steady in quantities through the spectrum from agricultural soils to prairie soils to forest soils. In one teaspoon of soil there are 100 million to 1 billion individuals. Fungi, measured in yards of hyphae, though increase significantly along this spectrum. In agricultural soils they are measured in several of yards, while in deciduous forest soils hundreds of yards are found, and in coniferous forest this actually increases to miles.

Fungal vs Bacterial Soil Life 02

Fungi love high carbon materials, think cellulose and lignin which are the primary building blocks of tree leaves and wood. Most bacteria struggle to break this down. Bacteria instead thrive with high nitrogen food sources, think manure, incorporated cover crops, etc.

We can gather from this how different gardening and farming techniques affect this ratio. Fox example mulching with wood chips encourages fungi, tillage kills fungi and encourages bacteria, and incorporating organic material into different soil horizons shifts the ratio toward bacteria.

Mineralization/Immoblization Balance

This makes it apparent as well that fungi and bacteria have different roles in the soil-food-web. Fungi are better are taking in and retaining nutrients as part of the mineralization/immobilization process. This is the process where microbes consume nutrients, thereby immobilizing them in their bodies and preventing nutrient leaching.

As they live their lives, producing waste and eventually being consumed further up the food chain, these nutrients re-enter the soil-food-web in a form that is soluble to plants. This is called mineralization. Fungi and bacteria are immensely important to different stages of this process and are each most effective depending on what they are being feed.

Knowledge to Practice

In our orchards we want to cultivate an F/B ratio between 10:1 and 50:1. There are many ways for us to work toward this goal, the simplest being understanding the ecology of fungi and providing the necessary shelter and food source. We do this by consistently mulching our trees with woody materials.

Fungal vs Bacterial Soil Life 03

We can get more specific in the process by cultivating our own indigenous microorganisms from the forest and inoculating them directly into our orchards. This practice is called Mountain Microorganism (MM). We have been applying MM to our orchards consistently over the past year in order to shift our F/B ratio higher and gain the benefits, such as pathogen control, that these microorganisms provide to the native forests.

Next steps for us in this process is to use our microscope to analyze the biological content of our soil. With the proper training and experience we expect to be able to determine rough F/B ratios in both our soils and the MM we are applying as a foliar drench. We will be sure to let you know what we find.

For anyone interested in making their own microbes, below is the recipe we use. If you would like to learn more about this process you should consider joining us for our upcoming Permaculture Design Certification course in April/May of 2017.

Mountain Microorganisms Recipe

Phase 1: MM Solid

Fungal vs Bacterial Soil Life 04


•3 sacks microorganisms (duff layer of primary forest)

•2 sacks semolina, yuca flour, or green banana flour

•1 gallon molasses, cane juice, or fruit juice

•1 gallon water


Spread a layer of duff on a top and cover with a layer of semolina. Mix well with hands. Dilute the molasses with the water and sprinkle on top as you continue to mix. If you grab a fistful of the mixture it should be lightly damp and fall apart easily after you squeeze it.

Next, have someone stand in a 55 gallon plastic drum (never metal), while you shovel the material inside. As you shovel, the person stamps the mixture down with their feet to compress it and remove any air pockets. Seal the barrel and leave at least one month, stored in the shade.

The mixture should be good for three years. When ready, it should have a strong smell of lactic acid.

Phase 2: Liquid MM

Fungal vs Bacterial Soil Life 05


•5 kilos MM Solid

•1 gallon molasses

•55 gallon plastic drum filled with water


Mix the molasses into the water. Put the MM into a screen sack and let hang in the water. Seal the drum and let sit 4 days.

Between day 4 and 15 this can be used as a foliar spray (between 10 and 100% ratio to water). After 15 days use the MM as a soil drench and after three weeks the product should be fully used up.

Once you have used the MM Liquid, you can make one more batch with the same sack of microbes. Just add 1 gallon molasses and refill the drum with water.


Lowenfels, Jeff, and Wayne Lewis. Teaming with Microbes: The Organic Gardener’s Guide to the Soil Food Web. Portland, Or.: Timber, 2010. Print.

“Soil Health.” Soil Health. N.p., n.d. Web. 15 Oct. 2016.

About Rancho Mastatal

Rancho Mastatal Sustainability Education Center is an education center, working permaculture farm, lodge and community rooted in environmental sustainability, meaningful, place-based livelihoods, and caring relationships.

We offer profound, innovative and authentic apprenticeships, residential workshops and guest experiences. We practice, promote and teach about natural building, fermentation, permaculture design, renewable energy, agroforestry and more.

Transition Ethics 03

Our campus encompasses more than 300-acres of picture-perfect waterfalls, crystal-clear rivers, idyllic swimming holes, impressive trees, extraordinary wilderness views, and pristine habitat for the area’s rich flora and fauna. Visitors and participants have access to over 14 km of trails, an extensive library, our working permaculture farm, and the tireless team who make the Ranch such a unique place to learn.

We are located in the rural farming town of Mastatal, situated on the edge of the last remaining virgin rainforest of Costa Rica’s beautiful Puriscal County. It is a wonderful place to take in Costa Rica culture, practice your Spanish, visit other permaculture projects, or catch a pickup game of fútbol.
Originally Published:


  1. I like your article but could you please give another measure for Phase 1 other than 1 sack. Please Kilos or lbs., liters or quart’s. And could the mix in phase 1 be put in a 5 gallon pail if the volume is not to great?

    1. John you can also do it this way as long as the end result is not too damp wet. When mixed squeeze a bit in your hand. Maybe a drop or two of liquid can drop out not too wet not too dry. Then just put it in any container that you can seal tightly. Pack it very tightly.


      •3 gallons microorganisms (duff layer of primary forest)

      •2 gallons semolina, yuca flour, or green banana flour

      •1 gallon molasses, cane juice, or fruit juice

      •1 gallon water

  2. Study the works and life of Raoul H. Francé und Annie Francé-Harrar

    and their fundamental findings on the microorganisms in the soil:

    Raoul H. Francé; Das Edaphon:

    You will then notice the unbalanced concept of the “soil food web” as a subset of the EDAPHON:

    The bacterial/fungal focus leaves out other indispensable types of microorganisms e.g. especially blue and green algae and disregards the importance of the COMMUNITY of ALL the soil microorganisms as a whole to support the fertility of the soil and the production of humus.

    Read: “The ideal Soil”

    and the other 40 types of soil with complete descripton of the microrganism communities they contain:

    Annie Francé-Harrar Handbuch des Bodenlebens / Manual of soil life:


  3. I’m not so sure all that muss and fuss is necessary. Check out what Roger Koide has to say on YouTube especially about ectomycorrhizal fungi.

  4. so many of the examples of supplying the soil with living organisms are set in tropical or at least damp climatic areas where it seems very easy to maintain a salubrious environment. I live in the okanagan valley of british columbia where supplying an adequate amt of moisture and maintaining a supply of organic material is expensive and challenging. most examples of permaculture dont seem helpful to me.

    1. Look into Johnson-Su compost for more degraded soils in temperate to semi arid zones. Dr Johnson’s method of microbe cultivation is more diverse and suited to the climate in which it is collected.
      I too find these subtropical – tropical methods to not suit my environment in Victoria Australia

  5. @Edd Anderson, some names that may help you in your research: The Loess Plateau, Ben Falk in northern Vermont,, Paul Wheaton, Dr. Elaine Ingham, Rocky mountain permaculture institute…….sorry thats all I can think of right now. Hope it helps you. :)

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