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The Organic Gardening mantra has always been to “Feed the Soil, and the Soil will feed the Plants”, but this oversimplifies the complex web of life that nourishes our plants, and through them, us. A little more knowledge about the microbes in the soil, what they do, what they need, and how that benefits plants, can allow you to fine tune your application of compost, or other organic material, to achieve better results. In this post, I hope to tell you more about the fascinating world of microbes.


When you are told to feed the soil, you’re not actually feeding your plants. I don’t know of any plant that can send a root out to search for some organic matter, and then somehow digest it themselves. In order for nutrients to be available to plants, they need to be already dissolved in the soil water, and immediately adjacent to the plant. Without help, this would not be great for the plant, as the nutrients would wash out as soon as it rains, just like adding an artificial fertiliser. Luckily, the plant has millions of little helpers, which it actively farms, allowing the nutrients to be held in little living sachets, waiting to be opened up. In addition, the soil microbes actually help in the formation of good soil.

In each teaspooon of good garden soil there are about 1 Billion bacteria, several yards of fungal hyphae, several thousand protozoa, and a few dozen nematodes (Lowenfells). These are the primary drivers of soil fertility. The first two, fungi and bacteria, are the primary decomposers of organic material in the soil. The second are the way that this material is recycled. All of them are trying to obtain Carbon, the building block of life. The amount of Nitrogen that is readily available to plants is determined by the total mass of fungi and bacteria.


Fungi are the primary decomposers of organic matter in the soil, and are responsible for breaking down the harder forms of Carbon. For us that is mainly woody material (lignin). It’s not that they cannot use the simpler forms of Carbon, just that the bacteria compete harder for it, and outnumber them. Fungi grow microscopic tubes, called hyphae with a very hard and sharp point. This point can penetrate hard materials like wood, the shells of insect, bone, etc. To feed, powerful enzymes are pushed out of the tip, into the food source, and the pre-digested material is pumped back along the tube, and transported to wherever it is needed. As the hyphae continue to extend, some of these enzymes are left behind, and continue to work, breaking down the material. This creates a source of Carbon that other organisms, like bacteria, can use. It is possible that fungi can ‘sense’ new food sources, and move towards them. Phosphorus is normally locked up in the soil, but fungi are able to free it from it’s chemical bonds, and move it to the rhizosphere (root zone), where it is traded with plants for sugars. More on this later. When hyphae die, they leave microscopic channels in the soil, which allow the movement of air and water through the channels, and a shelter for bacteria, where they can avoid their predators. Fungi also lock up and store calcium.

Mycorrhizal fungi are a type of fungi that establish beneficial relationships with plant roots. They form an extension to the roots of the plant, foraging further and deeper for nutrients and water, that they then exchange with the plant, gaining simple sugars in exchange. There are two types. One type penetrates the roots of the plant in order to exchange nutrients. Called endomycorrhizal fungi, they are preferred by most vegetables, grasses, shrubs, perennials, and softer wooded trees. The other type, called ectomycorrhizal, form a sheath around the roots of hardwood trees, and conifers. Fungi are destroyed when the soil is repeatedly disturbed (rotavating/plouging/digging), or compacted.


Bacteria are the second most important decomposers of organic material in the soil, responsible for recycling the more simple plant materials. As well as carbon, Bacteria help to fix Nitrogen from the air, and change the form of organic nitrogen into forms that plants can use. They help to glue soil particles together by secreting a film, which they use to stick themselves to particles in the soil. As colonies of bacteria buils up, these particles become clumped together, helping to create structure. Generally, bacteria don’t die of old age. Either they are eaten/killed, or if conditions become hostile for them, they become dormant, and wait for favourable conditions.


Protozoa act to control the soil population of bacteria, nematodes, and other protozoa. Their waste provides as much as 80% of the Nitrogen used by plants (Lowenfells). I’ll look at this in more detail shortly. Protozoa need water to move, and can use the thin layer of water around soil particles to do so. If things dry up, they form cysts and wait. Protozoa are a source of food for worms, and other soil dwelling creatures.


The last group of microbes that I’ll be mentioning are the Nematodes. These are very small worm like creatures, difficult to see without a microscope. There are four principle types. Most gardeners will have heard about the root eating nematodes, feeding on plant material. There are also bacterial feeders, fungal feeders, and predatory nematodes, which eat protozoa, other nematodes, and other creatures. Like the protozoa, nematodes help to release nutrients that were locked up in the bodoes of other creatures. Their waste is higher in Nitrogen than that of protozoa, but being larger, require a porous soil through which to travel. Despite having no eyes, they can detect the presence of their food source using methods like temperature, or chemical signature to locate a new source of food.

Plants are Farmers

It’s quite a leap of imagination for most people to think that plants actually grow populations of microbes, to help feed themselves, yet that’s exactly what happens. Up to 25% of the energy produced by plants is secreted out by them, principally through the roots. At first glance, this might seem like a waste, but actually the plant is feeding microbes, from which they will eventually reap significant benefits.

The plant secretes these exudates, primarily sugars, through the roots. These are either used by fungi, in exchange for nutrients and/or water, or by bacteria. The bacteria take these sugars, and multiply rapidly, taking up nitrogen and other nutrients at the same time. So far none of this is helping the plant, but as the bacteria multiply, protozoa and nematodes are attracted to the area and start to feed. Their wastes are high in Nitrogen, and other nutrients, in a form available to plants, and in the immediate vicinity of the root hairs. As more are eaten, numbers of the predators are controlled by them being eaten by their own predators, and by each other. The reduction in numbers of fungi, and bacteria, by predation, makes space, and nutrients available for them to continue to multiply.

If we know what ratio of microbes specific plants need for optimum health, and how to provide the right conditions for those microbes to flourish, we can tailor our use of compost, or mulches, to support the species that we want, and hinder those that we don’t. From a permaculture perspective, creating the right polycultures, including support species, to provide the right forms of carbon for the plants that we are growing, will allow us to create systems which are sustainable without our intervention.

I’ll focus on this in the next post on this subject.

For those who want to find out more about this, I would recommend reading Teaming with Microbes, by Jeff Lowenfels. If you want to delve even deeper into soil life, you can read Soil Microorganisms and higher Plants, by Krasilnikov. It can be read online in the Soil and Health Library.


Take Care