Growing Healthy Soils

Challenging your Knowledge on Creating Fertile Soils…

Healthy soils are loaded with microorganisms such as bacterias and fungi that consume organic matter and produce readily available nutrients to feed plants. To grow healthy plants it is vital to create a healthy, diverse and alive soil ecosystem.

Soil bacteria and fungi under a microscope. Image: Soil Foodweb Institute

Feed the Fungi

Fungi like woody food (referred to as lignin) which can be dried grass, sugar cane, leaves, wood chips and cardboard.

Old growth forests are fungal dominant, slightly acidic and with very few worms. Leaf matter and woody material found on the forest floor is broken down by fungi, creating ammonium which trees then feed off. Scrubs and trees prefer ammonium as their form of nitrogen due to a lot of fungi in the soil.

Bamboo leaves have high silica content and suppress growth, so they are good to suppress weeds or place on natural looking paths, but not to put into your garden beds. Camphor Laurel trees are allelopathic – they exude an oil substance suppressing other plant growth.

An electron scanning microscope image of calcium on fungi. Image: Soil Foodweb Institute

Nurture the Bacteria

Grasses, vegetables and annuals, prefer nitrates mineralised by bacteria, in turn consumed by protozoa and some other organisms producing the nitrogen for plant uptake in the form required. Grass clippings will provide food for bacteria and break down fairly quickly if conditions are good. A light cover of cut grass just scratched into the soil surface, so bacteria can get access and speed up decomposition will break down quickly.

From Rocks to Forest – Plant Succession in Natural Ecosystems

With the right conditions, succession moves through the following stages – lichens, mosses, grasses, shrubs, understory trees and finally forest. Each stage prepares the way for the next providing the necessary soil conditions and fertility to allow greater diversity to occur.

Beneath the ground, the succession of micro-organisms match the stages – Mosses, visible fungi and lichen grow and bind to rocks, eventually breaking them down, whilst providing a home for micro organisms. Bacteria predominate during the early successional stage where weeds, grasses, vegetables and annuals flourish. When weeds and grasses die back, they return to the soil and provide cellulose, organic matter and easy to digest food for bacteria. As this process continues it paves the way for a more conducive environment with greater diversity of organisms and fertile soils for more complex plant species to inhabit. Perennials, scrubs and old growth forest reflect fungal-dominated soil.

Fungi produce more acidic soils (as in forests) whereas bacteria produce a more alkaline environment.

Applying this Knowledge to your Garden

In the home garden this knowledge can be used to determine what needs to be monitored if plants are not producing well or are showing signs of malnutrition eg pest infestation or leaf discolouration. For example, strawberries prefer a fungal environment and if placed with very leafy vegetables may not do so well. Placing them under a tree and facing a sunny position will provide a fungal habitat, as the tree will have established this environment for its own survival and growth.

Garden veggies that are more bacterially oriented are the brassica’s, onions, root crops and cucurbits. Make a separate bed for these away from vegetables that require more fungal dominant soil such as tomatoes, cereal, legumes, and strawberries. Crop rotation is a good idea, but experiment and rotate vegetables into areas that match their bacterial or fungal preferences. Crop rotation will stimulate the diversity of organisms as each plant species can differ in its needs through its micro organism inhabitants.

Plants that are not adapted to bacterially dominated soils such as trees that have been planted in grass pastures, may take some time to establish. Watch for problems such as yellowing of the leaves and/or insect attack. Check the soil pH, high acidity? Are tap root weeds growing abundantly? It will tell a story as do the weeds in the area. Is the soil compacted? Does the plant require bacteria to dominate, or fungi to dominate for optimum growth?

Caring for your Soil Microorganisms

All micro organisms are sensitive to tillage, but especially fungi which can spread out lengthy distances, so any disturbance to the soil will break and kill these sensitive organisms. For healthy soil, it is important not to kill off important organisms in the food chain. Most soil organisms exist a few millimetres around the roots, called the rhizosphere.

Making Compost

Compost is food for the life in the soil, and the amount needed varies with the crops needs.

Compost under an electron microscope showing a diverse ecosystem of flourishing bacteria and fungi. Image: Soil Foodweb Institute

To create a balanced compost, add more brown matter and leaves for fungi and food scraps and grasses for bacteria. Heat is the by-product of the metabolising organisms multiplying from the rich diversity of food supplied with ample water. When the compost is turned, it provides a fresh lot of food for the organisms and the compost will heat up again. Earthworms search out microorganisms (bacteria) and ingest them; their castings are rich in plant available nutrients but use sparingly. Dark chocolate brown compost which smells sweet indicates a healthy heap.

Compost which has gone bad can be a result of anaerobic conditions; that is in the absence of oxygen. Black compost indicates compost gone bad. If it smells bad, it is of no use.

Composting Non-Organic Vegetation with Traces of Chemicals

If the required temperature (no more than 65 degrees for 3 days before turning) is achieved, chemical binds are broken down into inert substances. Be aware of toxic materials in the compost as too much can overwhelm the micro organisms and the chemicals may remain intact or the appropriate micro organisms may not be present to break down the particular chemical/poison.

Chemical fertilisers are salts disguised as nutrients and when applied are taken up into the plant in soluble form, force feeding the plant rather than its natural process of taking up nutrient through the soil and microorganism activity. The normal cycle of the plant is disrupted and forced to grow. Microorganisms die because fertilisers, through the process of osmosis sucks out moisture from within their cells. The act of inorganically fertilising replaces the many complex functions of the microorganisms, whilst the farmers/growers ongoing responsibility becomes to imitate and replicate those functions of nature.

Compost Tea

Biodynamic preps and compost teas work in with soil biology and the ecosystem. Compost tea is a microorganism inoculant that comes from good rich compost, mixed with bacterial and fungal foods such as fish hydrolysate, molasses, and kelp in a brewer. The microorganisms become “unglued” from the compost (organic matter) multiplying in numbers after 24/48hrs of brewing.

Care needs to be taken to protect these organisms so they will not die when brewing or spraying out onto the land. Use clean containers when making and distributing compost tea.

Manures and Soil Amendments

It is not good practice to put fresh manure (cows, horses, pig, and chicken) straight onto gardens or crops. It is high in nitrogen and water soluble, thus forcing the plant to uptake vast quantities of nitrogen in nitrate form and not via microbes. In addition, it will feed bacteria, causing a proliferation of these organisms, leading to bacterially dominant soil when balance may be required between fungi and bacteria.

Plants look great (consumers love this) when bloated with excess nitrates and other nutrients, but it’s like feeding them a Christmas dinner every day, whilst the surrounding habitants are poisoned.

Lime, gypsum and dolomite disturb the soil and kill soil microorganisms. It is because they are chemicals; many acting as salts which have an adverse effect on living biology.

Plants feed in a manner which has been effective for millions of years in an ecosystem that is finely tuned. Spreading fertilisers; both inorganic and organic conflicts with the plants natural cycle and will cause imbalance in the soil ecosystem through killing off diversity of organism and population explosions of certain microorganisms and insects.

Amending Compact Soil

Compact soil will most likely be anaerobic and acidic with a low level of microorganisms present and diversity absent. A possible remedy is to till it once only to break up the soil, and add biodynamic preps and/or compost tea – this is dependent on how badly the soil is needing repair. The biodynamic application and teas will begin the process of fertility, enlivening the soil and inoculating it with microorganisms.

Burning vs Composting

Burning off scars the soil. If it is a clay soil it can then form a hard pan preventing plants from establishing, it will also be very difficult for dead plant matter to break down and breach the surface where microorganisms will be under the surface.

Ask yourself these questions; “what type of soil is present? How fast will the soil regenerate after a fire? Will plants get through that surface easily?”

Foliar Tea

BEFORE: A macadamia leaf under a microscope before spraying with compost tea. Image: Soil Foodweb Institute

AFTER: A macadamia leaf under a microscope after spraying with compost tea. Image: Soil Foodweb Institute

Compost tea sprayed onto the leaves of, for example, tomatoes showing fungal disease provides an inoculant of good microorganisms which stick onto the leaves of the diseased plant thereby out-competing the disease.

But if a plant is sick, always look to the soil for the root of the problem, as the issue will emanate from the soil. The leaves and visible plant will carry the symptom of an imbalanced/unhealthy soil. It is much better to treat the soil with compost tea, rather than the leaves to fix the issue rather than treat the symptom.



Instead of focussing on growing healthy plants, the emphasis should be on growing healthy soils, for a healthy and microorganism rich soil is the foundation to producing healthy plants. Nurture and care for your soil microorganisms and they will in turn grow the plants for you.

This article has been adapted from a talk by Symmone Gordon of the Soil Foodweb Institute to a local Seed Savers group, written by Stephanie Stone and edited by Kat Gawlik.

UPDATE 17 Jan 2012:

Attend the Soil Foodweb Institute workshop “Applying SFI Methodology to Create Compost, Compost Tea and Analysing the Tea Created”
Date: 6-8 March 2012 (10 places still available), 8-10 May and 3-5  July 2012
This is a three day comprehensive hands on course entailing the following plus much more!

Day one will cover Composting: How to make quality compost, ingredients, techniques, and more!

Day two will cover AACT Compost tea: Extracts, building compost and extract brewer, 1000L, 200L, 60L, 20L and more!

Day three will cover Analysing your tea and compost: How to use your microscope, accessing biology, understanding biology, learning how to read and understand your SFI biological analysis and more!

Location: Unit 138 Rifle Range rd, Southern Cross University, East Lismore, NSW 2480
Duration: Three days
Time: 9am to 5pm
Enquiries: Chris Ellery or Merline Olson (02) 6622 5150

5 Responses

  • November 26, 2014 at 9:50 pm

    I have an odd question for you. About to get rid of the electric toilet on our boat and install a composting toilet. Just wondering your thoughts on using this as garden compost? Totally disgusting? Completely unhygienic? Just flat out not good for the plants and soil?

    • November 26, 2014 at 11:31 pm

      Not odd at all I can relate! I live on a sailboat too! Not sure how much the composting toilet actually ‘composts’ the waste as we have an electric toilet, but it definitely can be used on the garden after it has been fully composted, i.e with additional dry material like leaves, twigs, brown/dry plant material like sugar cane etc after further composting or aeration or turning the pile. Your soil and plants will love you for it. I would think twice about using it around vegetables that you eat the leaves of ie lettuce in case it isn’t fully broken down, but fruit trees, yes definitely!

  • Tony C. Saladino-Director ECO-Tours of Wisconsin Inc.
    June 1, 2013 at 12:29 am

    When you say that anaerobic compost is useless, couldn’t you dry it out and put it through pyrolysis to create char?

    • June 2, 2013 at 12:33 pm

      Yes you could but its probably easier to add oxygen through adding dry leaves, twigs, shredded newspaper, straw etc to make it aerobic compost

  • August 29, 2012 at 5:29 pm

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