Chapter 5

Soils: Foundations of Fertility

Soils are formed from the merger of inorganic material supplied by the disintegration of rocks along with decomposing organic matter. They provide the mineral nutrients plants need to grow. The most basic mineral nutrients are those we apply in fertiliser for our crops or gardens, symbolised ‘NPK’: nitrogen (N), phosphorus (P) and potassium (K). Out in nature these are recycled by decomposition of plant matter. The extent to which these nutrients are retained against leaching by rainwater percolating through soils depends largely on the clay content. This is governed by the bedrock composition and modified by rainfall.

Soils typically exhibit distinct layers (Figure 5.1A). A topsoil layer called the A horizon incorporates decomposing vegetation called humus. Below it a subsoil or B horizon accumulates the downwash of clay particles and other leached products. Deeper still lies the C horizon, constituted by decaying bedrock. A hardpan (or duricrust) may form at the base of the B horizon above the bedrock. However, this ideal profile may not be shown by soils that are rather shallow or very sandy (Figure 5.1B,C). On eroding uplands, the mineral composition largely reflects the underlying bedrock. Lowlands accumulate the products of erosion transported from upslope or elsewhere by water, wind or animals. Specific soil features depend on (1) the underlying bedrock providing the parent material, (2) prevailing climatic conditions affecting weathering (mineral decomposition), (3) local topography determining water movements, (4) vegetation cover controlling organic inputs and, not to be overlooked, (5) time, affecting soil development. Soils may retain features derived from rainfall and temperature conditions back in the distant past. The pertinent outcome for ecology is the soil fertility, determined by the soil texture, in turn governed by the content of fine clay particles able to retain nutrients (Box 5.1).


Figure 5.1

Soil profiles. (A) Idealised soil profile showing distinct A horizon where organic matter (humus) is concentrated, B horizon where clay and nutrients are leached downwards and C horizon where decaying rock becomes incorporated (from Jones et al., 2013), licensed under a Creative Commons Attribution 4.0 International License. (B) Soil on granitic bedrock under grassland in Nyika Plateau of Malawi, showing lack of humus in the surface layer. (C) Soil formed from deep deposit of Kalahari sand in south-eastern Gabon.

Box 5.1Soil Features Affecting Fertility

Soil fertility is governed most fundamentally by the granular texture of the soil particles, in particular the clay content. Clay particles are made up of alternating layers of silica and aluminium oxides, forming a lattice structure.1 One silica sheet coupled with one alumina sheet represents a 1:1 lattice, whereas two silica sheets per alumina sheet form a 2:1 lattice. Negative charges formed on the lattice attract cations, most notably potassium, sodium, calcium and magnesium. Smectite or illite clays with a 2:1 lattice structure have a high cation-holding capacity, in contrast to kaolinite clays with a 1:1 lattice. If cations are leached, they get replaced by hydrogen ions, making soils more acidic. Over time, the mineral component of soils can become weathered into unstructured iron or aluminium sesquioxides with little or no capacity to retain cations, especially in warm tropical regions with high rainfall. Iron oxides contribute to the redness typical of tropical soils. Under wet conditions, prolonged weathering can give rise to duricrusts constituted by iron oxides, variously called ferricrete, plinthite or laterite. Under drier conditions, calcium carbonate precipitates as nodules or larger chunks of calcrete, while sand and gravel can become cemented by dissolved silica to form silcrete. In hot and dry climates, the evaporation of moisture can cause sodium salts to accumulate at the soil surface. This salinisation may lead to the compaction of clay-rich soils, thereby resisting water and air infiltration.

The underlying bedrock contributes to soil fertility by being the source of base cations as well as through its contribution to the phosphorus taken up by plants mainly through the agency of soil fungi. Soils derived from mafic volcanic rocks, like basalt, both retain cations on clay particles and contribute relatively high amounts of phosphorus. Felsic igneous or metamorphic rocks that have high silica contents, like granite or gneiss, yield sandy soils with less capacity to hold mineral nutrients. Very sandy soils derived from sandstone depend almost entirely on organic matter for their cation-holding capacity. Fine-grained sediments formed from wind-blown loess or lacustrine (lake bed) deposits, widely prevalent in Europe, are especially fertile. Limestone and dolomite, derived from marine deposits, produce fine-textured soils that are moderately fertile, as also are soils derived from shale or mudstone.

The humus content can make a further contribution to soil fertility because it forms the basis for nutrient recycling, from the soil via plants, and perhaps also herbivores, back into the soil. Mineral nitrogen originates from the decomposition of organic matter and is taken up by plants in the form of nitrate (NO3–) or ammonia (NH4+). Most of the available phosphorus is also recycled through the organic matter component. Under warm and moist climates, the organic matter content is decomposed rapidly by soil bacteria, reducing the effective soil fertility. Recurrent fires lower the organic matter input, and cause losses particularly of nitrogen. Many legumes have the capacity to alleviate nitrogen shortages by fixing atmospheric nitrogen in root nodules with the aid of symbiotic bacteria.

Plants with the capacity to fix nitrogen may do so only when it is most needed, for example during seedling growth, because of the costs involved. Because phosphate is highly insoluble, its availability for plant growth can depend on how it is rendered to plant roots by soil fungi called mycorrhizae. In heavily weathered soils, phosphorus can become bound to iron and effectively unavailable. Phosphates may be released by volcanic lavas and ash, but high calcium contents (carbonitites) may restrict the effective availability of the phosphorus to herbivores feeding on the vegetation.

The soil texture influences both fertility and water penetration or hydrology. While clay is beneficial for holding cations, soils that are too rich in clay become sticky and difficult to cultivate when wet. The ideal texture for agriculture is loam constituted by a mix of clay and sand. Soil fertility is represented most simply by the cation exchange capacity (CEC), or total exchangeable bases (TEB), taking into account the extent to which this capacity is filled, called the base saturation. The units are expressed either in milli-equivalents per 100 g of soil, or as centimoles of charge per kilogram, which are numerically identical. Soils are rated as relatively fertile if the sum of exchangeable bases exceeds about 20 cmol/kg (Figure 5.2). Soil fertility tends to be greatest where the moisture input from rainfall closely balances potential evaporation, so that there is little leaching of base cations.2 Some of the phosphorus present (in the form of phosphate) also gets removed by weathering due to water passage. However, in warm, tropical climates fertility is actually highest where the water balance is somewhat more negative than is the case for temperate regions; i.e. in situations where evaporative losses somewhat exceed rainfall inputs. Soils in tropical and subtropical latitudes in the southern hemisphere are especially low in organic carbon content compared with those at counterpart latitudes in the northern hemisphere.3 This contributes further to the importance of the bedrock in governing the effective fertility in savanna regions of Africa.


Figure 5.2

Soil fertility map of Africa based on cation exchange capacity of soils. High fertility is shown by dark purple (20-40 cmol/kg) and light purple (10–20 cmol/kg) and low cation exchange capacity by shades of green (<10 cmol/kg). Note the region of high soil fertility extending from Ethiopia through the rift valley region of eastern Africa where volcanic substrates are widespread. The most nutrient-deficient soils occur in the Kalahari Sand region, Congo Basin, the dry northern region of western Africa to the south of the Sahara and in the moist region of south-central Africa with mainly granitic soils (from Jones et al. (2013) Soil Atlas of Africa), licensed under a Creative Commons Attribution 4.0 International License.

Water infiltration is slower in clay soils than in sand, although very heavy clays that swell when wet and crack open when dry allow more water to penetrate. However, clay soils bind whatever moisture remains intensely when they become dry, making this less available to plants. Sandy soils allow water to percolate to greater depths so that it remains available for longer, but in very deep sands, water may sink beyond the reach of all but the most deeply rooted trees. Overall, clay soils retain less water into the dry season than loamy or sandy soils, because more runs off while less of the moisture that penetrates can be extracted.

There is no globally agreed system for naming soil types. In the US taxonomy, savanna soils are typically mollisols, ultisols, oxisols or alfisols. In the World Reference Scheme, they are called luvisols, lixisols or acrisols. In the South African classification, they are described as melanic, plinthic, calcic or duplex. Sticky clays are called vertisols, or vertic in the South African classification. None of these systems clearly exposes the ecologically relevant distinctions for African savanna regions where geology plays such an important role.

Geological Influences on Fertility

I was inducted into the relationships between soil features and the underlying geology during my white rhino study in the Hluhluwe-iMfolozi Park. Sticky clays were associated with Ecca shales of the Karoo Supergroup, interspersed with sandy soils derived from sandstone layers. Dolerite dykes penetrating the Karoo sediments and capping some of the hills formed clay soils that were less sticky and allowed greater water infiltration on account of their more granular texture.

More broadly, felsic granite or gneiss and sandstone produce sandy soils deficient in calcium, magnesium and iron.1 Mafic basalt, dolerite and gabbro, as well as fine-grained sediments, yield clay-rich soils with higher CECs and base saturations and are typically also higher in available phosphorus content (Table 5.1). Schist, syenite and biotite as well as limestone and dolomite generate soils with intermediate properties. Phosphorus appears to be the mineral nutrient most generally restricting soil fertility across Africa.4 This is partly a result of the prolonged erosion to which Africa’s ancient land surfaces have been subjected.

Table 5.1Soil features in relation to bedrock geology


References: 1: de Wit, HA (1978) PhD thesis, Wageningen University, Wageningen. 2: Howison, RA, et al. (2017) In Conserving Africa’s Mega-Diversity in the Anthropocene, ed. Cromsigt et al., pp. 33–55, Cambridge University Press. 3: Thompson, JG and Purves, WD (1978) A Guide to the Soils of Rhodesia. Ministry of Agriculture, Rhodesia. 4: Funakawa, S, et al. (2012) In Soil Health and Land Use Management, ed. MC Hernandez Soriano, Intech. 5: Jager, T (1982) Soils of the Serengeti woodlands, Tanzania. PhD dissertation, Netherlands. 6: Frost, P (1996) The ecology of miombo woodlands. In The Miombo in Transition, ed. Campbell B, Centre for International Forestry Research, Bogor, India, pp. 11–57. 7: Venter, FJ, et al. (2003) In The Kruger Experience, ed. JT du Toit et al., pp. 83–129, Island Press.

Infertile sandy soils predominate through much of southern Tanzania, Zambia and Zimbabwe, which are widely underlain by basement granitic bedrock (Figure 5.2). In central and western Africa where rainfall is high, granitic bedrock has become weathered into red soils containing iron oxide concretions, with low intrinsic fertility. Infertile sandy soils also extend through the Kalahari basin from southern Africa via interior Angola and western Zambia as far as south-eastern Gabon.1,5 They retain a legacy of past weathering in the form of pebbles, clay layers and calcrete or silcrete crusts deep beneath the soil surface. In South Africa’s Highveld region, duricrusts of silcrete or calcrete can be several metres thick.6 Highly weathered profiles with mainly kaolinite (commercially known as white clay or talcum) persist there and elsewhere as a legacy of the more humid conditions that prevailed in the past.

Soils of volcanic origin with high inherent fertility are prevalent in and around the East African Rift System (Figure 5.2). Where rainfall is high enough, they support dense crop production, most notably in Rwanda, situated adjoining the Western Rift only a short distance south of the Equator.1 Soils on the Serengeti Plains in Tanzania have been enriched by volcanic ash deposited by nearby volcanoes, which generated a calcrete crust at shallow depths.7,8 The ash is rich in calcium and sodium, while leaching is blocked by the hardpan of calcrete overlying the granite beneath. Although these soils are too shallow and saline to support crop production, they produce grasses that are especially nutritious for large herbivores. A volcanic influence can detected as far as 200 km west of the volcanoes located in the Crater Highlands.9 In parts of the west-central region of Serengeti NP, ultramafic greenstone and banded ironstone have become exposed, generating soils that are also relatively clay-rich and fertile. In central and northern parts of this park, soils derived from granite with relatively low silicate and high biotite contents are sufficiently fertile to be classified as mollisols. A subtle shift in the substrate in the north-west from granite to gneiss is associated with a vegetation transition from fine-leaved to broad-leaved savanna. South Africa’s Kruger NP presents a striking geological contrast between basaltic soils in the east and granitic soils in the west, intruded locally by dolerite and gabbro sills. A narrow strip of Karoo sediments divides the granite from the basalt.

Hydrological Redistribution

Topography modifies soil features via upland erosion and lowland deposition, especially on Africa’s interior plateau. A topo-sequence or ‘catena’ develops, with shallow eroded soils on crests, while soils on mid or lower slopes and pediments are most leached of cations by water percolating through them. Clay particles and mobile cations get concentrated on foot slopes or bottomlands. Seep zones form where percolating water is forced to the surface by underlying bedrock or ferricrete. Consequently, lowland soils near drainage lines or dambos can be relatively fertile even in landscapes underlain by granitic bedrock.

Soil texture influences how readily rainfall penetrates to deeper depths. The intensity of the rain received during thunderstorms can exceed the infiltration capacity of soils, causing much of this water to run off down slope.8 This threshold capacity lies between 10 and 30 mm/h of rainfall, depending on soil features such as texture, depth and structure.10 Accordingly, on uplands the soil moisture effectively available to support plant growth can be less than half of the total amount of rain received as measured in a rain gauge. Deeper soils in bottomlands gain additional moisture from run on and retain moisture longer into the dry season, especially if their surface texture is sandy. More extensive wetlands develop where drainage is blocked. This redistribution of soil moisture contributes fundamentally to the spatial heterogeneity that is a striking feature of African savannas.

Nutrient Recycling

The recycling of nutrients to support plant growth depends on the mineralisation of organic matter into nitrates and other inorganic compounds that can be taken up by roots. The breakdown of plant detritus ceases when soils become too dry for microbial decomposers to function. This results in a pulsed release of mineral nutrients following the first adequate rains at the start of the wet season.11 Sufficient soil moisture to support decomposer activity may persist quite late into the dry season, extending the period available for nutrient uptake by plants.

The mound-building activities of termites also influence soil features. Through most of the dry tropics and subtropics of Africa, soil has been worked and reworked by termites since these insects evolved in the Triassic period over 200 Ma.12,13 Mound-building species in the subfamily Macrotermitinae convey plant residues into their large mounds where the cellulose content gets degraded by fungi, which in turn are consumed by the termites. Organic breakdown products accumulate within the mounds, along with termite faeces and bodies, and get transported out by animals feeding on the termites. In constructing their mounds, termites raise clay particles towards the surface, generating hotspots of soil fertility within savanna landscapes (see Chapter 13).11 Both CEC and available phosphorus are elevated in the vicinity of Macrotermes mounds. Upward soil movements contribute to the generation of stone-lines in subsoils, which persist long after the mounds have disintegrated.

Human presence has modified soil features in places, especially where dwellings and livestock enclosures were located. Mineral nutrients accumulated where dung from cattle was concentrated can persist for decades or even centuries, most especially phosphorus.14,15,16 These sites stand out as open glades with short grass, attracting concentrations of grazing ungulates. In the Nylsvley Nature Reserve in South Africa, sites of former human habitation exhibited a 10-fold increase in total phosphorus, without much change in the sandy soil texture, several centuries after the inhabitants had moved on.17 Organic matter contributions from human settlements and associated livestock counteract the tendency for phosphorus to become locked in refractory compounds as soils age over time. In eastern Botswana, grass species associated with high soil phosphorus levels indicate sites where Iron Age settlements were located.18


Across much of Africa, soil fertility is dependent largely on the underlying bedrock. This is because most of its eastern and southern regions form an eroding plateau surface exposing bedrock influences. Duricrusts formed by prolonged weathering restrict water infiltration. The relatively low rainfall over the interior plateau contributes additionally. Where rainfall is high, the nature of the underlying geology matters little because leaching overrides it. If rainfall is low, water does not penetrate far and mineral nutrients are retained, especially sodium of high importance for large herbivores. The intermediate range between 500 and 1000 mm in MAR, typical of most of High Africa, is most conducive to bedrock influences on soil fertility. In South American savannas, rainfall is generally double that prevailing in Africa, producing intensely weathered soils with little capacity to retain nutrients. Soils over the southern tropics and subtropics are generally low in organic carbon content compared with those at counterpart latitudes in the northern hemisphere.18 This probably reflects the rapid decomposition that takes place following rainfall events.

Within Africa, volcanic influences on soils are widespread in the rift valley region extending from Ethiopia into northern Tanzania. Sedimentary deposits are less extensive than in other continents, covering the vast Amazon Basin of South America, former lakebeds and intermontane valleys in central Europe, the periglacial region of North America, and temperate China where wind-blown loess formed deep deposits. Soils regarded as adequately fertile cover merely 10 percent of the land surface of South America, restricted mostly to valleys where residual minerals accumulated, or localities where calcareous bedrock or volcanic intrusions occur.19 West African soils are mostly infertile due to high leaching. Within Australia, soils are generally less subject to leaching, but lack much phosphorus, except in the eastern seaboard.20 Fungus-growing termites are absent from Australia and the Americas, so their contribution towards enhancing soil fertility is lacking.

Additional influences on soil functioning beyond the geology and climate come from recurrent fires and through the recycling of vegetation biomass via large herbivores and termites. These will be addressed in Part III of this book.


Jones, A, et al. (2013) Soil Atlas of Africa. European Commission, Publications of the European Union, Luxembourg.


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