The Soil Biota in Permaculture

Permaculture Designers Manual



Section 8.12 –

The Soil Biota in Permaculture



On semi-arid and poor pasture, it is difficult to keep sheep at a stocking rate of 3-6 / ha. The very same pasture may support 2-5 t of pasture grubs, or up to 6.5 t of earthworms / ha, so that (like grasses) most of the animal  biomass or yield is underground, out of sight.

Even where wheat cropping is carried on continuously for 140 cycles (Rothhamsted, UK) the plough layer supports 0.5 t of living microbial biomass (New Scientist, 2 Dec ’82).


About 1.2 t/ha of organic carbon is returned annually to the soil as root and stalk material from grain crop.

So large is the soil biomass that its growth must be very slow, sporadic, and based on a turnover of humus/food within the soil rather than a food input from the wheat crop wastes.

Humus in this soil has a mean age of 1,400 years, and probably derives from forests that long preceded the wheat; it yields up its nutrients very slowly, and is resistant to bacterial attack.

However, it is equally clear that there are periods of sudden food supply from root masses at harvest, and from root exudates during the growth of wheat (30% of plant energy may be lost as sugars or compounds released to the soil via roots).

However the soil biota achieve it, they exist on a very meagre food supply for such a biomass, rather like an elephant eating a cabbage once a day!

Of the total biomass at Rothhamsted, 50% is fungi, 20% is bacteria , 20% yeasts, algae, and protozoans, and only 10% the larger fauna such as earthworms, nematodes, arthropods  and mollusc fauna (the micro- and macro-fauna), and their larvae.

Such classes of organisms are found in soils everywhere, in different proportions.

Anderson (New Scientist, 6 Oct.’83) gives some idea of the complexity below ground, where every square metre of forest topsoil can contain a thousand species of animals, and 1-2 km of fungal hyphae!


Very small animals are able to live a basically aquatic life in soil, in the water film attached to soil crumbs, while larger species are confined to pore spaces and the burrows of macrofauna.

A wheat field is not the place most likely to produce high levels of soil biota, and plough cropping has (in Canada) reduced humus levels to 1% of the original levels over much of the wheat country.

Climatically, the balance and proportion of soil biota varies greatly, with the acid soils of coniferous and oak forest yielding few earthworms, and the humic peats even less, so that the soil recycled by worms also varies from  2-150 t / ha  (O.5-25 cm depth of soil/year).

Ecological disturbance or imbalances by predation, aeration, disturbed soils, low oxygen levels, and compaction favour the bacteria over the fungi.

Fungi are certainly more effective in wood or large plant material breakdown, and can transport materials not only from place to place (e.g. move nitrogen into decaying wood) but also move nutrient into higher plants via their intimate contact with the root cells of the host plant.

Usually, such translocations are modest (a few metres), but occasionally a fungal species can send out many metres of hyphae to invade a tree, as a pathogen and decomposer.

Thus, it pays higher plants to give energy to their fungal root associates as sugars, and to gain minerals or nutrients in return.


Over time, the death of these soil organisms returns nutrient to new cycles. Even termite nests die out in 20-30 years, and new colonies start up. Larger animals can have a profound effect on primary litter breakdown (millipedes, woodlice and are typically plentiful in mulch, but rare in compost.

As one can imagine, any accurate account of the relationship between such dynamic mass of species awaits decades of work, but some broad facts are emerging; for example, turnover of nitrogen by earthworms exceeds that of the litter fall of plants.

Few species fall into dear-cut classes of food relationships, and the chain of events of predation, faecal production, and burrowing are further complications.

As it is probably impossible to research at a species-specific level, and as the gross compartmentalization of ecosystem analyses is inappropriate, Anderson (ibid.) suggests a more possible study based on the interactions between the broad functional groups of organisms, or a size-food community.

Here, he laments, we know so little about so much.


Large animals (earthworms to wombats) can create major changes in soils locally, by burrowing, soil turnover, faecal production from vegetation, waste produces, and even alterations to forest successions after fire.

In general, gross disturbances by colonies of larger fauna as in deserts (where rodent biomass can reach 1,000-10,000 kg/ha) shift the balance from soil fungi 10 bacteria.

We can think of the soil biota as a reserve of otherwise easily leached nutrients (nitrogen, sulphur), both of which elements they gather, store, or concentrate. Their cycle of life and death, which in turn depends on soil temperature and season, releases small or large amounts of these essential elements at mullipte mirrosites.

Termites, in addition, may store calcium from subsoils in their mounds, and bacteria store a number of soil minerals. These are held in the mobile living reserves of the soil biota, and are released by their death for slow uptake by plant root associates.

Many plant forms directly eat bacteria (algae in water. fungi) or insects and nematodes, so that plants are either direct predators of the soil fauna, or scavengers of the bodies of the soil organisms.


A useful classification of soil biota based on size is as follows ( New Scientist, 6 Ocl ’83):

MICROFLORA and MICROFAUNA: Size range  1 -100 millimicrons, e. g. bacteria, fungi, nematodes, Protozoa, rotifers.

MESOFAUNA: Size range 100 mlllimicrons-2 mm, e.g. miles, springtails, small myriapods,  enchytraeid worms, false scorpions, termites.

MACROFAUNA: Size range 2-20 mm , e. g. wood-lice, harvestman, amphipods, centipedes, millipedes, earthworms, beetles, spiders, slugs, snails, ants, large myriapods.

MEGAFAUNA: Size range 20 mm upwards. e. g. crickets, moles, rodents, wombats, rabbits, etc.


In terms of sheer numbers per square metre, nematodes (120 million), mites (100,000), springtails (45,000), enchytraeid worms (20,000), and molluscs (10,000) greatly out-number any other species in temperate grasslands.

Fungi, however, may be 50% of the total living biomass.

While the tradition of soil science has been to treat and analyze soils as mineral matter (the living component being carbonized or burnt off in analyses as “C” or humus content), the preoccupation of sound farmers, biodynamic groups, mulch gardeners, and “no-dig” croppers has been the quantity and quality of soil life both as indicators of soil health and as aerators and conditioners of soil.


Another factor which deserves more treatment in science is the mass, distribution, migration, and function of roots and root associates, and the role of burrowers (not only earthworms, but larger mammals, reptiles, and a host of insects).

The soil (if not sterilized, overworked, or sprayed into lifelessness) is a complex of mineral and active biological materials in process. No soil scientist myself, I rely on soil life and the health of plants to indicate problems.

Diseases and pest irruptions can be the way we are alerted to such problems as over-grazing, erosion, and mineral deficiency.

Removing the pest may not rune the underlying problem of susceptibility. Certainly, strong plants resist most normal levels of insect attack.

Soil analysis, helpful though it is, can help us very little with soil processes. Until very recent years, we have underestimated the contribution of nitrogen by legumes or soil microfauna.


In addition, the measure of soil carbon has rarely been related to the soil biota, whose lives and functions are not fully known. It seems curious that we know so much about sheep, so little about those animals which outweigh them per hectare by factors of ten or a hundred times, and that we do not investigate these matters far more seriously.

Our most sustainable yields may be grubs or caterpillars rather than sheep; we can convert these invertebrates to use by feeding them to poultry or fish.

We can’t go wrong in encouraging a complex of life in soils, from roots and mycorrhiza to moles and earthworms, and in thinking of ways in which soil life assists us to produce crop, it itself becomes a crop.



Worms have played a more important part in the history of the world than most persons would at first suppose.

In almost all humid countries they are extraordinarily numerous, and for their size possess great muscular power.

In many parts of England a weight of more than ten tons (I0.516 kg) of dry earth annually passes through their bodies and is brought to the surface on each acre of land: so that the whole superficial bed of vegetable mould passes through their bodies in the course of every few years…

Thus the particles of earth, forming the superficial mould, are subjected to conditions eminently favorable or their decomposition and disintegration …

“The plough is one of the most ancient and most valuable of man’s Inventions: but long before he existed the land was in fact regularly ploughed, and still continues to be thus ploughed by earthworms.

It may be doubted whether there are many other animals which have played so Important a part in the history of the world, as have these lowly organized creatures.” (Charles  Darwin.  The Formation, of Vegetable Mould Through the Action of Worms, 1881)


From the time of Darwin (and probably long before), copious worm life in soils has been taken as a healthy sign, and indeed more modern reviews have not reversed this belief (Satchell, 1984).

Worms rapidly and efficiently recycle manure and leaves to the soil, keep soil structure open, and (sliding in their tunnels) act as an innumerable army of pistons pumping air in and out of the soils on a 24-hour cycle (more rapidly at night).

Of themselves, they are a form of waste recycling product, with a dry-weight  protein content of from 55-71 % built up from inedible plant wastes.

Only a few peoples eat worms directly, but a host of vertebrates from moles to birds, foxes to fish depend largely on the worm population as a staple or stand-by food.

Cultivated worms are most commonly used as an additive to the diets of livestock (fish, poultry, pigs).


However, as processors of large quantities of plant wastes and soil particles, worms can also accumulate pollutants to extraordinarily high levels; DDT, lead, cadmium, and dioxins may be at levels in worms of from 14 or 20 times higher than the soil levels.

Eaten in quantity by blackbirds or moles, the worms may become lethal. That is, if the “pests” that are moles, blackbirds , and small hawks abound on farms, there is at least some indication of soil health.

Where these are absent, it is an ominous and obvious warning to us to check the soil itself for residual biocides.

As non-scientists, most gardeners deprived of atomic ray spectrometers, a battery of reagents, and a few million research dollars must look to signs of health such as the birds, reptiles, worms, and plants of their garden-farm.

For myself, in a truly natural garden I have come to expect to see, hear, and find evidence of abundant vertebrate life.

This, and this alone, reassures me that invertebrates still thrive there. I know of many farms where neither birds nor worms exist; and I suspect that their products are dangerous to all life forms.

All modem evidence agrees on the value of worms

In fields, as decomposers and manure recyclers. They may be even more valuable as garbage disposal systems, and as fish or poultry food, providing a mass of high-protein food from vegetable wastes.


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