Biological Indicators of Soil and Soil Conditions in Permaculture

Permaculture Designers Manual



Section 8.15 –

Biological Indicators of Soil and Soil Conditions in Permaculture

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In any local area, the composition, shape or size, and distribution of the plants give many clues to soil type, depth, and extrinsic factors.

Some specific factors indicated are:


1 Depth

2 Water reserves

3 pH

4 Mineral status (see preceding Lesson)



5 Fire frequency

6 Frost

7 Drainage

8 Mineral deposits and rock type

9 Overgrazing and compaction of soil

10 Animal (macrofauna) effects



Shallow soils dry out quickly and hold few nutrients.

A very good indication of soil depth is to look at one species of tree (e.g. Acocio, Prosopis, honey locust) over a range of sites; a “height and spread” estimate will reveal areas of deeper soils where the largest specimens grow.

The same species will be dwarfish on shallow soils of the same derivation or rock type.

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Deep-rooted trees which need water – the large nut trees and candlenuts (Aleurites) are good examples which occur naturally only In well-drained but water-conserving sites­ often show water-lines not associated with valleys, and stand over springs or aquifer discharge areas.

In sands, a great variety of deep-rooted shrubs and trees indicate where a clay base lies at 1-2 m down.

This situation is common on desert borders and cliffs in dry lands.

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In brief, large tree stems reveal well-watered sites, small stems drier sites.

Armed with these observations, we can create sites by water diversion and select sites for large trees or shrubs.

3 pH:

Sorrel and oxalis in pastures may indicate compact or acid conditions, whereas several fen and limestone species establish in alkaline areas; large snails and dense snail populations occur only over alkaline soils or in alkaline water.

No snails or minute species occur in acid water (pH < 5.O).

In the garden, our cultivated plants demand acid or alkaline soils, e.g.


Alkaline intolerant (pH 4.5-6.0):  

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  • Blueberry
  • Chicory
  • Chestnut
  • Endive
  • Potato
  • Fennel
  • Tea
  • Coffee
  • Rhubarb
  • Shallot
  • Watermelon

Alkali tolerant:

  • Oats
  • Rye
  • Kale

Acid intolerant (pH 7.Q-8.5):

  • Cauliflower
  • Cabbage
  • Asparagus
  • Green peas, bush beans
  • Celery
  • Leek
  • Beet
  • Onion
  • Chard
  • Parsnip
  • Spinach
  • Lucerne
  • Broccoli

Acid tolerant:

  • Lupin
  • Oats
  • White clover

This will have a profound effect on our home garden planning, but providing garden soils are mulched, and a little lime is added to compost, all plants thrive in high humus soils supplied with some lime at modest levels.

It is the perennial species that may need more care in site selection, or with mulch and compost in alkaline areas.

Almost all our pollutants, and many of our fertilizers, tend to make soils acid, as does continued cropping or over-grazing.



East-west ridges of ten reveal abrupt species changes at the ridge wherever fire occurs.

Fire produces dry, scrabbly, summer­deciduous, thick seeded species; lack of fire develops broad leaf, winter-deciduous, smalled plants with thin seed capsules and a deep litter fail.

Cross-sectional cuts of trees reveal fire scars as gum pockets or charred sections, and these can then be counted to get the “fire frequency” of the site (figure 8.9).

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If tree stem sections are marked for directions before sampling, the direction of fires can also be judged.


6. FROST: 

Many species of tree and plants will indicate frost-lines; it is a matter of observing local fora, or planting frost-susceptible species down a hill profile to measure frost intensity.

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Tomatoes, bananas, and potatoes are all frost-sensitive and will reveal frost-lines on hills in subtropics and deserts.



Mosses, sundews, and fine-leaved heaths indicate poorly-drained soils, as large trees such as chestnuts (which require 2 metres of well-drained soil) indicate good drainage; these indicators assist survey before pits are dug or drainage measured.

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Davidov (Sputnik, 12 Dec. 79) gives data on plant systems over mineral deposits (for Russia). The analysis of plant residues often indicates concentration of ores in the underlying soil or rock. Lead and copper-molybdate are so indicated. Leaves or humus from birch, cherry, honeysuckle, St. John’s Wort, wormwood, juniper, and heather reveal the above lodes plus tungsten and tin concentrates.

All purpose” plants so discovered are:

Rue or violets………….. zinc


Asters……………………. selenium

Milk vetch………………..selenium and uranium

Russian thistle………… boron

Alyssum ………………… nickel

Honeysuckle…………… silver and gold

Horsetail………………….gold and silica


General plant ash analysis may reveal more specific plant-ore associations. This has further implications for the rehabilitation of mine waste areas, and also to select plant sources for the supply of trace minerals in compost.

As plants have the ability to both concentrate and tolerate unusually high levels of specific minerals, there seems to be a field here for the biological concentration (and subsequent removal) of metallic soil pollutants like lead or uranium, and the use of concentrator plants to mine or collect locally rare trace elements. In fact, some patents have apparently been granted for mining gold deposits using banana or citrus plants deprived of some common elements (potash, phosphate); their leaves then concentrate sparse deposits or gold.

Oysters will concentrate zinc (to II%, dry weight, an emetic dose), abalone concentrate cadmium, and several large fish concentrate mercury and biological poisons from corals (to inedible levels).

There are obvious implications for the removal, collection, or use or such species element relationships, and lead, cadmium, or mercury levels in fish or plants need careful monitoring for public health reasons.



Both the levels of grasshopper and pasture grub activity (high on overgrazed landscapes) and the presence or patches of poisonous, inedible, thorny, and unpalatable plants (e.g. Sodom apple, oxalis, capeweed) indicate an over-stocking problem or range mismanagement.

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The effect is a synthesis between changing soil conditions, plant stress, and the heavy selection by livestock or palatable species, so favouring the survival and spread of spiny or inedible species.

Too often, the pastoralist blames the weeds and seeks a chemical rather than a management solution; too seldom do we find an approach combining the sensible utilization or grasshoppers and grubs as a valuable dried-protein supplement for fish or food pellets, and a combination of soil conditioning, slashing, and de-stocking or re-seeding to restore species balance.



The site of a sea­bird rookery, a rabbit warren, the ground nest of a goose or eider clutch, the pellet-pile or an owl, or the decay or a large carcass will cause a sudden and often long-term change in the immediate vegetation, as will termite mounds and harvester-ant colonies.

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Once such sites are recorded, and the plant assembly identified, similar sites can be located and recognized. The data can be used as an aid to conservation, an indication of soil drainage (rabbits choose good drainage), as a result of specific nutrient supply (guano on seabird rookeries).or as a way to establish tree clumps following natural indicators.

A large proportion of wind-blown, nitrogen-loving, and inedible plants, or plants carried by birds as seed, depend on the specific habits or birds or mammals, on their dung, or on soil disturbances.

The role of animals in the distribution or plant seed, and plant root associates, is well-recognized; their role in soil change, less commonly noted.


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