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Chapter 3 - Biological and chemical aspects of soil productivity


Soil biology and the biological micro-environment
Organic matter
Soil organisms associated with the crop
Weeds, crop pests and diseases
Inorganic nutrition
Field indicators of biological and nutritional problems
Management for maintenance of soil biology and nutrition


Observations such as the accumulative beneficial effects of pasture, and the degradative impacts of successive cereal crops on a coarse-textured sandy loam soil in Australia shown in Figure 21, provide a basis for recommending rotations to maintain sustainability. There are many beneficial effects from growing legume crops and pastures in rotation. They improve soil structure, biological activity and crop yields, as well as increasing soil organic matter and nitrogen (Figure 21). This Chapter describes those aspects of soil biology, organic matter and soil nutrition central to the observed benefits of crop rotations.

Soil biology and the biological micro-environment

Organic matter, microscopic and macroscopic organisms (e.g., fungal hyphae and invertebrates), detritus from fungi and animals, and bacteria, and biological exudates, all assist in stabilizing soil structure. The role of each part of the biomass differs according to its size (Figure 22). Broadly, large aggregates greater than 250 m m diameter (macro-aggregates), are stabilized by their inherent physical structure (Chapter 2), wetting and drying cycles, and organic matter. Micro-aggregates (< 250 m m) are stabilized by live or dead roots, fungi, invertebrates and micro-organisms (Figure 22).

The populations of soil organisms of all sizes are linked functionally through their roles in the degradation of various forms of organic material. The latter includes live and dead plant material and other live or dead organisms. A schematic food web is shown in Figure 23. This shows that animals such as nematodes and some fungi feed directly on live plants while other fungi and bacteria feed predominantly on litter.

Earthworms and other large invertebrates create, and inhabit, burrows and pores, and are very mobile. The most notable of these are termites, which are divided into three groups according to the structure of their nests: those that build mounds (a) above ground, (b) on the soil surface, and (c) below ground. Small arthropods, microfauna and fungi live mostly in larger voids and in association with roots. Foster (1988) reviewed the location of the various types of soil-dwelling organisms and found that fungi, which constitute about 80% of the biomass in many soils, tend to be restricted to the rhizosphere of roots, to larger pores between aggregates and to the surface of aggregates. Bacteria, by contrast, are found on roots in the rhizosphere, in small colonies in the larger micropores, within aggregates and on and within cell debris. For more information on location refer to Foster (1988). Smiles (1988) describes the physics of the micro-environment of small soil organisms.

FIGURE 21 - Trends in total soil nitrogen and wheat grain in a long-term rotation experiment at Wongan Hills, Western Australia (adapted from Rowland 1980) - U is uncleared land, F is fallow (cultivated intermittently for one year, before planting pasture) 1 to 7 are successive years of legume-based pasture while 1 to 4 are successive years of wheat cropping which was begun after year 2 or 2 or 5 or 7 of the pasture phase

Organic matter

Both plants and animals provide inputs of organic matter to soils. Once within the soil organic residues can be distinguished on the basis of their chemical structure (e.g., old lignified humic substances that degrade slowly), by their source (plant or animal) or by location.

The standing crop of litter in semi-arid grasslands is usually more than 3 t/ha and in temperate dry steppe may exceed 11 t/ha (e.g., Klemmedson 1989). There has been much debate about the relative contents of organic matter in tropical and temperate soils. Within those wet-and-dry climates that have hot summers assisting rapid decomposition, there is no evidence of inherently lower levels of organic matter in the tropics than in comparable temperate regions (Juo and Payne 1993).

Kowal and Kassam (1978) and Juo and Payne (1993) review the role of organic matter in tropical soils. Here, it is sufficient simply to state that organic matter has various interrelated effects on soil fertility. These are summarized in Table 20. In particular it should be noted that both chemical and physical effects are of relatively great importance in the soils of the semi-arid tropics because these generally have low cation exchange capacity (effective CEC values less than 14 meq/100 g clay, see Chapter 1, section Soils, and this chapter, section Inorganic nutrition).

FIGURE 22 - Model of aggregate organization with major binding agents indicated (Source: Tisdall and Oades 1982) - Major binding agent

FIGURE 22 - Model of aggregate organization with major binding agents indicated (Source: Tisdall and Oades 1982) - Roots and hyphae (medium-term organic)

FIGURE 22 - Model of aggregate organization with major binding agents indicated (Source: Tisdall and Oades 1982) - Plant and fungal debris encrusted with inorganics (persistent organic)

FIGURE 22 - Model of aggregate organization with major binding agents indicated (Source: Tisdall and Oades 1982) - Microbial and fungal debris encrusted with inorganics (persistent organic)

FIGURE 22 - Model of aggregate organization with major binding agents indicated (Source: Tisdall and Oades 1982) - Amorphous aluminopsilicates, oxides and organic polymers sorbed on clay surfaces and electrostatic bonding, flocculation (permanent inorganic)

FIGURE 23 - Representation of detrital food web in shortgrass prairie. Fungal-feeding mites are separated into two groups (I and II) to distinguish the slow-growing cryptostigmatids from faster-growing taxa. Flows omitted from the figure for the sake of clarity include transfers from every organism to the substrate pools (death) and transfers from every animal to the substrate pools (defaecation) and to inorganic N (ammonification). Source: Doran (1987)

The relative importance of litter (crop residue) and manure as inputs of organic matter, varies between cropping systems and spatially within a system. Figure 24 illustrates the flow of litter, manure and by-products (such as dung cake for fuel) in Indian villages practising approximately one-third single cropping and two-thirds double cropping. Here, most of the above-ground crop residue is fed to animals, but an equal amount of below-ground crop material enters the soil organic matter pool. It is noteworthy that in Figure 24 five times as much dung is distributed naturally to grassland and forest than is recycled to the crop.

The pattern of flow of manure and litter to the cropping soil in Figure 24 falls within the wide range of practice common in wet-and-dry climates. Generally, all the root material (say, 40% of total crop growth) and 10-30% of top material may be recycled in an annual cropping system. Where alley cropping and agroforestry are practised, values are more variable, but possible inputs could be very significant where the trees, from which the litter is taken, are grown away from the annual crops. Table 21 gives values for leaf production from trees. If, say, two-thirds of the leaves from leguminous trees are harvested annually, litter values will be substantially higher and the material of better quality than the leaf and stem residue from an annual crop likely to be recycled in the field. Some qualifications, however, should be made. Tree root material is not available for decomposition in the crop field unless it is spatially overlapping (e.g. as an intercrop), in which case the trees will compete with the crop for soil nutrients, water, light and space.

TABLE 20
Effects of organic matter on soil fertility (Source: Young 1989)

Primary effects

Consequences

Physical effects


Binding of particles, root action leading to improved structural stability, balance between fine, medium and large pores

Improved root penetration, erosion resistance and moisture properties; water-holding capacity, permeability, aeration

Chemical effects


Nutrient source, balanced supply, not subject to leaching, with slow, partly controllable, release

Including better response to fertilizers, non-acidifying source of N, mineralization of P in available forms

Complexing and enhanced availability of micronutrients


Increased cation exchange

Better retention of fertilizer nutrients

Improved availability of P through blocking of fixation sites


Biological effects


Provision of a favourable environment for N fixation


Enhanced faunal activity


The proportion of animal and human manure used on cropland is more variable. Some farmers have developed stable systems which strongly emphasize the use of animal manure on crops. For example, Norman et al. (1982) describe how farmers in northern Nigeria managed to apply 4 t/ha of manure to their heavily-cropped crop land though they had only 3 cows each. Many other farmers do not ensure adequate recycling, either because they are more concerned with livestock management or they do not know the importance of maintaining a 'zero nutrient budget' to replace nutrients removed by the crop. For example, Norman et al. (1982) also describe farmers with 10 cows each, who applied only 1.9 t manure/ha to their crops.

Within a cropping system, manuring practice varies with location. There is transference towards the centre of the system. On traditional farms, the area near the household or village is highly fertilized with human and animal manure while more distant fields receive little or no organic matter. Fussell (1992) describes such a traditional 'ring' farming system in semi-arid west Africa. Here, if houses are thatched, the village needs rebuilding or moving every 2 to 4 years. Moving takes advantage of the fertility gradient. Where the huts are not moved, the fertility gradient becomes steeper with time. Rather than trying to even out fertility by labour-intensive transport of manure, farmers vary the cropping of the fields (Figure 25). Continuous cropping of millet is sustainable close to the hut or village where there is plenty of human and animal manure but crop rotations are essential at the periphery.

FIGURE 24 - Energy flow through the agro-ecosystems. Values are means from five villages = 1 SE 106 KJ/yr/ha cultivated land solar radiation = 6.5 x 1010 kJ/yr/ha (Source: Singh and Singh 1992)

TABLE 21
Biomass production of leaves from multipurpose trees (Source: collated in Young 1989)

Country

Land use

Tree

t/ha/year

Malaysia

Plantation

Acacia mangium

3.06

Philippines

Plantation

Albizia falcataria

0.18

Costa Rica

Hedgerow intercropping

Calliandra calothyrsus

2.76

Philippines

Plantation

Gmelina arborea

0.14

Indonesia (Java)

Plantation

L. leucocephala, A. falcataria, Dalbergia latifolia, Acacia auriculiformis

3.00-5.00



Cordia alliodora

2.69


Plantation crop

C. alliodora + cacao,

6.46

Costa Rica

combination

Erythrina poeppigiana,

4.27



E. poeppigiana + cacao

8.18

Nigeria

Hedgerow intercropping

Cajanus cajan

4.10

Nigeria

Hedgerow intercropping

Gliricidia sepium

2.30

Nigeria

Hedgerow intercropping

L. leucocephala

2.47

Nigeria

Hedgerow intercropping

Tephrosia Candida

3.07

India

Plantation

L. leucocephala

2.30

FIGURE 25 - Fields around the residence, Senegal (Source: Fussell 1992)

Closed systems, which rely on maintenance of fertility by recycling organic matter, are not sustainable. Nitrogen levels may be maintained or even enhanced (Figure 21) by using legume crops or pastures in rotation but even then further inputs of nutrients are required to replace those removed by the crop. Fussell (1992) describes the inevitable need to use inorganic nutrients or organic nutrients from off-farm sources such as wastes from cities to complement farm organic matter in the African Sahel:

"Although the importance of organic manure in increasing cereal yields is well recognized, it is unlikely that there is sufficient available, on a regional basis, to sustain yields without the use of additional chemical fertilizers. For example in the Western African savannah 10 t/ha/year of manure are required for sustainable cropping of millet or sorghum.....while in northern Nigeria 2.5 t/ha/year are sufficient to maintain yields in most areas." This four-fold difference largely reflects the integration of livestock with cropping in Nigeria which results in relatively high levels of soil organic matter. Farmers elsewhere, for example in Ghana, give lower priority to crop fertility, which lowers soil organic matter levels and leads to greater nitrogen loss through water erosion when there is little litter cover on the ground. Irrespective of these differences, however "It is doubtful if either of these levels of application can be achieved, as... estimates cattle and sheep manure outputs in the northern savannah zone of Nigeria are estimated to be only 1.4 and 0.25 t dry matter per head per annum respectively."

Off-farm sources of manure, organic matter generally (e.g., industrial by-products) and soil ameliorants will become increasingly important. Some, such as sewage from cities, are being researched. Their use in developing countries seems likely to increase, particularly as labour for transporting these materials is cheap relative to the cost of other nutrients such as manufactured inorganic fertilizers. The treatment and efficacy of various off-farm sources of organic matter are outside the scope of this Bulletin. It suffices to point out that substantial amounts of material are available (Table 22).

TABLE 22
Annual production of organic wastes in the USA and their current use on land

Organic wastes

Total production

Current use on land1 (%)

Million metric tons

Percentage of total

Anumal manures

159

21.8

90

Crop residues

391

53.7

68

Sewage sludge and septage

4

0.5

23

Food processing

3

0.4

(13)

Industrial organic

7

1.0

3

Logging and wood manufacturing

32

4.5

(5)

Municipal refuse

132

18.1

(1)

Total

728

100.0

-

1 Values in parentheses are rough estimates because of insufficient data.

TABLE 23
Decomposition constants, k, for tropical legumes. Values were calculated with exponential equation for decomposition using data reported in the literature (Source: Juo and Payne 1993)

Species

Location

Mean annual rainfall

Mean annual temperature °C

k/year

Gliricidia sepium

Ibadan, Nigeria

1250

23-31

8.48

Flemingia congesta

Ibadan, Nigeria

1250

23-31

3.66

Cassia siamea

Ibadan, Nigeria

1250

23-31

2.17

Lonchocarpus cyanescems

Ibadan, Nigeria

1250

23-31

8.87

Inga vera

El Verde, Puerto Rico

4000

22

1.65

Inga sp. And Erythrina (mixed)

Caracas, Venezuela

1200

20

3.01

Erythrina sp. (mixed with non-legumes)

Caracas, Venezuela

1200

20

3.81

Inga edulis

Yurimaguas, Peru

2200

26

0.91

Cajanus cajan

Yurimaguas, Peru

2200

26

1.45

Erythrina sp.

Yurimaguas, Peru

2200

26

3.72

The rate of breakdown of litter and other organic materials both determines and depends on the populations and activities of organisms in the soil. It also determines the extent to which minerals taken up by a crop are released from its organic residues and made available as inorganic ions to the subsequent crop. There are numerous mathematical models of organic matter degradation. Almost all assume that the rate of degradation decreases with time, as the more soluble, digestible and accessible material is selectively and progressively degraded by soil organisms. This selectivity is often arbitrarily described by recognizing several 'pools' of organic matter (Figure 23) and, with time, 'passing' material from labile to less-labile compartments. In practice its physical and chemical composition changes gradually with time, as does its physical binding with soil particles and its relation to the predators that feed on it.

The rate of decomposition of leaf litter depends on its environment, particularly on soil temperature and soil water. Both these affect the physical breakdown of the litter and determine the population and activity of soil animals and fungi that feed on it. Decomposition also varies with plant type and age of litter, being slower for heavily lignified material. The specific properties of litter from different species, and the generally exponential form of litter decay (the rate of decomposition slowing with time) lead to values (Table 23) that suggest half-lives of litter ranging from 1 to about 10 years. Because of the importance of temperature in determining decomposition, rates decline from tropical to temperate locations within wet-and-dry climates.

Plant species, water and temperature are not the only factors affecting the speed of litter decomposition and mineral cycling. Management plays a role. There are four ways for managing crop residues: (a) stubble mulch in which residues are left standing; (b) surface mulch, where above-ground residues are cut and left on the top of the soil after harvest; (c) incorporation by ploughing; and (d) cut-and-carry, in which surface residue is removed and (if not used for livestock or thatching, etc.) returned as a surface mulch about planting time for the subsequent crop; this is usually combined with ploughing of below-ground residues.

Two of the above treatments involve the fragmenting of root residues. All of them affect a range of soil properties (Chapter 2). The degree of contact between the residue and the soil (and its organisms) and other unexplained factors affect the rate of decomposition.

Table 23 suggests that the rates of release of minerals from organic matter, particularly litter, are a significant element in nutrient cycling and crop productivity in semi-arid environments. Such climates have a rainy season in which rainfall exceeds evaporation, so there is a risk of mineral loss through runoff and mineral loss and acidification by leaching. During the dry season there is potential loss of nitrogen as ammonia. This suggests the need to manage litter so most decomposition takes place when the subsequent crop is growing rapidly and is able to take up the nutrients released. It is wise at the same time to maintain ground cover if possible (Chapter 2). Manipulation of litter requires labour, which may already be in maximum demand prior to sowing.

Soil organisms associated with the crop


Bacteria and nitrogen
Fungi, algae and nutrients


Bacteria and nitrogen

Cropping in dryland regions needs nitrogen to be economically successful (e.g., Keating et al. 1991). Two sources of nitrogen are from organic matter (Chapter 2, section Soil pores and water characteristics) and from nitrogen-fixing bacteria associated with plant roots. Bradyrhizobium and Rhizobium species infect plant roots forming galls or nodules, and fix nitrogen from the soil atmosphere directly to the plants. Locally-adapted, heat-tolerant strains survive from crop to crop in wet-and-dry climates and, whether established by natural colonization or by inoculation of the crop seed at sowing, they subsequently fix variable quantities of nitrogen.

Where bacterial infection is effective, the bacteria commonly fix between 70-100% of the nitrogen used by the crop, though the proportion is lower when the crop is given inorganic fertilizers.

TABLE 24
Effect of soil mineral N and N fertilizers on crop N productivity and the proportion (P) and amount of crop N derived from N2 fixation (Source: Peoples and Craswell 1992)

Species

Location

Level

Total crop

N2 fixed

Soil mineral N (kg N/ha)

Fertilizer N (kg N/ha)

N (kg N/ha/crop)

Proportion

Amount (kg N/ha/crop)

Groundnut

India

-

0

196

0.61

120


100

210

0.47

99


200

243

0.42

102

Chickpea

Australia

10 (to 120 cm)


114

0.85

97

326


184

0.17

33


0

109

0.80

87


50

110

0.55

60


100

104

0.29

30

Soybean

Australia

70 (to 120 cm)


230

0.34

78

260


265

0.06

16

India

-

0*

63

0.29

18


100

148

0.26

28

-

0**

89

0.48

43


100

115

0.24

28

Common bean

Kenya

-

10

149

0.39

58


100

158

0.10

16

Cowpea

Kenya

-

20

116

0.53

62


100

137

0.08

11

India

-

0

163

0.77

125


100

138

0.67

92


200

172

0.33

57

* Uninoculated.
** Inoculated.

The extent of the effectiveness of infection of legume crops in the wet-and-dry tropics needs to be surveyed. Temperate research indicates that nitrogen fixed by bacteria ranges from 20 to 120 kg N/ha in a growing season for annual crops (Table 24). In the semi-arid tropics, amounts of nitrogen fixed per hectare range from none, where nodulation is ineffective, to 16 kg N in soybean naturally colonized by rhizobia, to 84 kg N when inoculated. Nitrogen fixation in soybean and groundnut of 50-70 kg N/ha/growing season is reported in Senegal (Gigou et al. 1985). Nitrogen-fixing bacteria associated with tree legumes can fix similar quantities (Table 25).

Rhizobia rarely fix all the nitrogen used by the crop and a substantial amount of nitrogen is removed from the field as grain, so the net benefit from symbiosis varies. For example, if rhizobia fix 50% of the crop's requirement and 60% of above-ground nitrogen is in the grain at harvest, soil nitrogen is depleted irrespective of the amount of nitrogen fixed or the grain yield. Peoples and Craswell (1992), studying 21 cases of tropical grain legumes, found positive nitrogen balances in 15 and negative ones in five. Similarly, many experiments with grain legumes in southern, semi-arid Australia show that rhizobial associations give net benefits in more than three-quarters of cases and that the benefit from lupins is substantially greater than that from field peas, largely because a smaller proportion of nitrogen is harvested and removed in lupins.

Fungi, algae and nutrients

Various fungi facilitate uptake of nutrients by plants, particularly phosphorus. Numerous fungi live in close association with plant roots. One group, vesicular arbuscular micorrhizal fungi (VAM), form both vesicles and arbuscules (knot-like structure) on the surface and within the root. They also colonize soil animals including earthworms and woodlice (Table 26).

TABLE 25
Nitrogen fixation by trees and shrubs. Values are per growing season or per year unless the number of months is given in brackets (Various sources, compiled by Young, 1989 and Peoples and Craswell 1992)

Species

N fixation (kg N/ha/year)

Acacia albida

20

Acacia mearnsii

200

Allocasuarina littoralis

220(?)

Casuarina equisetifolia

60-110

Coffee + Inga spp.

35

Coriaria arborea

190

Erythrina poeppigiana

60

Gliricidia septum

13

Inga jinicuil

35-40

Inga jinicuil

50

Inga jinicuil

35

Leucaena leucocephala

100-500

Leucaena leucocephala (in hedgerow intercropping)

75-120

Leucaena leucocephala

100-13 (6)

Prosopis glandulosa

25-30

Prosopis glandulosa

40-50

Prosopis tamarugo

200

Rain forest fallow

400-100

Mature rain forest

16

Alachynomene afrospera

130 (2)

Glyricidia sepium

100 (3)

Sesbania spp.

125-140

119-188 (2)

140-290 (2)

Xalliandra colothyssus

11 (3)

They are most prolific in the topsoil, to about 10 cm depth (Habte 1989). They facilitate uptake of nutrients, particularly phosphorus from soils low in that element. They provide some protection to the host plant, their presence being associated with decreased colonization by pathogens. Ellis et al. (1985) also found that wheat plants inoculated with VAM were more drought-tolerant than plants without VAM. Importantly, comparisons of conventional cropping systems using inorganic fertilizers and herbicides with organic systems not using herbicides have found much higher levels of infection of crop roots by these beneficial fungi in the organic system (Ryan et al. 1994). This suggests that management for desired, associative soil organisms, should become a part of future sustainable cropping.

Other organisms associated with or infecting plants include endophytic fungi which affect plant growth rates and confer resistance to some insects. Cyanobacteria, which belong to the blue-green algae, are believed widespread in the semi-arid tropics and contribute 0.5 to 15 kg N/ha/year. Azospirillum, Klebsiella, Enterobacter and other species are free-living but largely inhabit the root rhizosphere; their distribution and role is still to be defined for cropping systems in wet-and-dry climates. Actinorrhizal associations are known between Casuarina and Frankia sp., but these are not exploited. It is claimed that such associations can fix as much as 60 kg N/ha/year. There are no doubt other symbioses yet to be discovered and exploited.

Weeds, crop pests and diseases

Weeds, pests and diseases all compete with or directly reduce the vigour of crops. Many pests and diseases are soil-borne. Weed life-cycles depend on replenishment of the soil seed bank and survival of the seeds against natural decay, predation by soil animals and depletion by human management, particularly cultivations. Ecological weed control thus aims to minimize recruitment of new seed into the soil as a long-term strategy as well as trying to reduce artificially the size of the weed seed bank in the soil.

TABLE 26
Frequency (%) of VAM fungi in soil-dwelling macro-invertebrates sampled from natural and agricultural ecosystems in Ohio (data are combined from 1986 and 1987 samplings) (Source: Rabatin and Stinner 1989)

Taxa

Ecosystem

Conventional tillage maize

No-tillage maize

Pasture

Old field

Lumbricidae (earthworms)

25.0

83.3

50.0

75.0

Isopoda (woodlice)

100.0

35.7

64.7

36.8

Carabidae (ground beetles)

2.1

19.8

14.5

12.8

FIGURE 26 - A general scheme of seasonal cycle of weed population

FIGURE 27 - Total dynamics of weed plants and seeds over two years. Figure gives average weed populations over two years in potato field during autumn (September-December) and summer (April-July) cropping seasons and intervening Winter (January-March) and summer (August-September) fallow periods. Average number of seeds/plant m2 in 'jhum' (J) and terrace (T) fields are given in boxes. Values in parentheses indicate the percentage of plants arising from vegetative parts. Seedling survival (K), survival of plants, (P), fecundity (F) and growth rate of seed population (seasonal value l 1, annual value l 2) in soil are shown along the lines. S indicates the fall of seeds from the parent plant. Source: Misra et al. (1992)

Weed life cycles and strategic weed control are well understood for temperate wet-and-dry climates. Figure 26 illustrates the life cycle of weed populations and Figure 27 gives informative data for weed populations in north India (2500 mm AAR of which 70-90% falls in 5 months). The weed populations were measured under the contrasting conditions of slash-and-burn and terrace cultivation. Seed recruitment to the soil seed bank was higher under terrace cropping than under slash and burn but fewer survived.

It is generally accepted that there are links between weed populations, their competitiveness, and soil fertility. A good example of this is the various species of witch weed (Striga hermonthica, S. generioides, S. asiatica and approximately 25 other species). These species infect the roots of millet, sorghum, maize and sugar cane. S. generioides also infects legumes and tuberous crops. They are a serious nuisance and are widespread in semi-arid Africa. It is estimated that they currently infect 21 million ha and a further 44 million ha are at risk. Their spread and increased aggressiveness is considered to be due largely to declining fertility and soil carbon contents.

The incidence of insect pests and crop diseases depends on the complexity of the cropping system and the types of crops grown. It depends too on management factors, such as the timing and type of tillage and the treatment of the crop residues. These aspects are so complex they warrant a Bulletin to themselves, so they are only touched upon here.

The incidence of pests and diseases is generally believed to be less frequent and/or intense in diverse cropping systems. Data on insects are relatively scarce but Andow (1983) is frequently quoted as showing a positive relationship between insect pest populations and the practice of monoculture. His experience, however, is mainly with cotton, a unique crop, and wheat, though he gives a few examples from maize and rice.

TABLE 27
Viruses for which disease incidence is lower in more diverse cropping systems (Source: various, collated in Power 1990)

Pathogen

Type1

Vector

Alfalfa mosaic virus

N

Aphid

Bean common mosaic virus

N

Aphid

Bean yellow mosaic virus

N

Aphid

Beet yellows virus

P

Aphid

Cauliflower mosaic virus

N

Aphid

Chlorotic mottle virus

N

Aphid

Maize stunt spiroplasma

P

Leafhopper

Cucumber mosaic virus

N

Aphid

Groundnut rosette virus

P

Aphid

Pepper veinbanding mosaic virus

N

Aphid

Tomato yellow leaf curl virus

P

Whitefly

Turnip mosaic virus

N

Aphid

1 Type of pathogen transmission system is given as P (persistent) or N (non-persistent).

Power (1990) shows that the incidence of virus diseases is less in complex cropping systems (Table 27). He suggests that disease transmitted by insects is less common in multiple-cropping than in monocultures because aphids and some other insects settle on plants in response to visual cues that do not enable them to distinguish between host and non-host plants. In this way polyphagous insects can acquire a pathogen from an infected plant and transfer it when feeding on a non-host plant. If the insect is preferentially attracted to the non-host crop, it may be speculated that this crop acts as a 'trap' or 'protection' crop. Power (1990) reviews situations where intercropping or the inclusion of a second, barrier species has led to lower disease levels. In contrast, bacteria and fungi in the root region and rhizosphere are reported to be slightly fewer in a coconut monocrop than in a multi-storied mixed cropping system (Bopaiah and Shetty 1991). Differences in populations, and in their varied (positive or negative) effects on the food crop, are no doubt best understood through analysis of the feeding habits and predation of the organisms themselves, rather than by making superficial generalizations about their numbers. Fick and Power (1992) and Hearn and Fitt (1992) review pest management generally and pests and diseases in cotton crops specifically.

Inorganic nutrition

Inorganic nutrients occur in soil as ions and minerals, e.g., as oxides, silicates and phosphates, both adsorbed onto the surface of clay particles and organic matter, and in solution.

A large proportion of some nutrients, most notably nitrogen, is found in organic matter in all but the most highly degraded soils, so organic matter and the organisms associated with it are given prominence in this chapter.

Clay particles, because of their crystalline structures, carry an inherent electrical charge. This results in attractive forces (mainly van der Waals forces) and repulsive forces (electrostatic forces) which give clay species their particular characteristics. The inherent surface charge also causes a layer of associated ions to align next to the solid particles forming a so-called diffuse double layer because it consists of a relatively inexchangeable layer (the Stem layer) closest to the surface of the particle and an outer, readily exchangeable layer, of varying thickness, called the diffuse layer. Sposito (1984) explains this more fully.

In the present context, it is appropriate to describe briefly four aspects of the physico-electrical structure of soils. These are: the inherent exchange capacity; the linkage between soil particles and soil organic matter, and its effects on soil stability; ions in solution and their solubility; and the ion imbalances (from the perspective of crop growth) associated with acidity and salinity.

TABLE 28
Representative cation exchange capacities (in molC/kg) of surface soils (Source: Sposito 1984)

Soil order

CEC

Alfisols

0.1 2 ± 0.08

Aridisols

0.16 ± 0.05

Entisols

0.13±0.06

Histosols

1.4±0.3

Inceptisols

0.19±0.17

Mollisols

0.22±0.10

Oxisols

0.05±0.03

Spodosols

0.11 ±0.05

Ultisols

0.06 ±0.06

Vertisols

0.37 ± 0.08

Adsorption is the net accumulation of matter at the interface between a solid phase and an aqueous solution. Readily exchangeable ions are those so loosely adsorbed to clay or other particles that they are replaced easily by leaching with an electrolyte solution. The ion exchange capacity of soil is the number of moles of adsorbed ion charge which can be displaced from a unit mass of soil; in most applications, this refers to readily exchangeable ions. Sposito (1984) notes that 'Much controversy exists over the surface chemical significance of ion exchange capacities'. The maximum surface charge measurement indicates a soil's potential to adsorb ions while its actual capacity, which is more relevant agriculturally, has a lesser value. Table 28 gives representative cation exchange capacities (CECs) for selected soil orders. It is notable that though the CEC of each order ranges widely, the predominant soils in wet-and-dry climates have low CECs.

The readily exchangeable proportion of the CEC varies with soil pH: the proportion available to readily-exchangeable bases decreases from about 1 at pH 8 to 0.5 at pH 6 to perhaps 0.2 at pH 4.5. Below pH 6 an increasing proportion is taken up by various aluminium ions and complexes, which are variably toxic to plants.

The electrical conductivity and CEC of a soil are related to its clay content (e.g., Rhoades 1990a). Similarly, because of the electrical charge of the clay particles, a high but variable percentage of the soil organic matter is bound to them. Table 29 shows that it may be as high as 90% and Figure 28 illustrates the two postulated main ways that organic matter is bonded to clay. These are weak anion exchange and strongly-held ligand exchange which is a form of chemical bonding.

It follows from the electrically-charged nature of clay and organic matter and the high likelihood of their association that both contribute to the nutrient-holding capacity and stability of soils. This intimacy led Pieri (1992) to propose that structural stability, at least of the African soils he studied, could be described by a critical value of S greater than 9, where S is the ratio of organic matter to clay plus silt, expressed as a percentage. This is shown in Figure 29.

TABLE 29
Proportion of soil organic carbon in the clay-organic complex


Percent organic carbon in soil

Percent soil carbon in clay-organic complex1

Podzol

1.5

18

Solonized brown soil

1.5

77

Grey clay soil

1.1

91

Terra rossa

2.8

82

Groundwater rendzina

5.4

69

Black earth

1.8

82

Krasnozem

4.9

90

Red brown earth

2.5

66

1 Defined as the material sinking when the soil was ultrasonically dispersed in an organic liquid of density 2 g/cm3.

FIGURE 28 - Diagram illustrating anionic bridging: anion exchange. R is a polyanionic humic colloid.

FIGURE 28 - Diagram illustrating anionic bridging: ligand exchange. R is a polyanionic humic colloid.

Plants take up most minerals as inorganic nutrients from the soil solution (except legumes, which may fix dinitrogen gas directly from the soil air). An element is available (to the plant) if it is present as, or can be transformed into, a free ion, and it is within the plant root zone. Most elements move within physical proximity of roots through soil water movement and into the plant through evapotranspiration. Diffusion along concentration gradients is important for less-mobile ions such as phosphorus, particularly where soil solution concentrations are weak and root densities are high (i.e., the transport path is short). Sposito (1984) and others give calculated values for the diffusivity of nutrients. Diffusion times range from 1 day for an ion to move 3 mm (which is comparable with the time it would take to move by convection in the mass flow of water) for nitrate to about 200 days for potassium, magnesium and molybdenum, and to thousands of days for other nutrients.

The concentrations of nutrients in solution fluctuate daily and seasonally. The most dynamic are nitrate and ammonium ions, which are interconverted by bacteria. Fluctuations can be explained by the effects of temperature and soil water on mineralization (breaking down organic matter to release ammonium), immobilization (the reverse) and nitrification (conversion of organic matter to nitrate, which is stable and highly soluble), and by the effects of rainfall leaching nitrate to depth. In seasonally wet-and-dry cropping systems, there is a flush of nitrate following the start of the wet season and nitrate-N may accumulate in the topsoil by capillary rise of water during the dry season. Within the major seasonal patterns driven by soil water, Rochester et al. (1991) found that the soil nitrate cycle lagged three months behind changes in temperature.

FIGURE 29 - Critical organic matter levels for maintenance of physical stability (proposed by Pieri 1992)

Low soil pH affects plant roots directly because of the effects of the hydrogen ion concentration on root membrane integrity and exchange capacity. Acidity also affects roots indirectly in two ways. It alters the availability of ions in the soil solution (possibly making available toxic aluminium species, relatively toxic to plants). It also affects mineralization through the protons competing with cations for dissolved ligands and surface charged groups. Soil pH also affects micro-organisms, and thus the speed of transformations, for example, those between nitrate and ammonium. Poor plant growth on acid soils may thus be caused directly by hydrogen ions, by toxicities of aluminium or manganese, or through deficiencies of calcium, magnesium, potassium, phosphorus, nitrogen or trace elements. Chase et al. (1989) describe these relationships for sandy Sahelian soils. Variation in pH across distances of 15 m can be as much as pH 4.5 to 7.5, with associated decreases in aluminium and hydrogen ions, and increases in crop productivity. The critical pH at which crop growth is affected varies with crop, cultivar and soil type. Critical levels may be as high as pH 5 to 5.5 for less tolerant plants in soils with soluble sources of aluminium but otherwise can be as low as pH 3.9 to 4.

FIGURE 30 - Salt tolerance of grain crops (Source: Rhoades 1990b)

TABLE 30
Relative salt tolerance of various crops at emergence and during growth to maturity (Source: Rhoades 1990b)


Crop

Electrical conductivity of saturated-soil extract

Common name

Botanical name

50% yield (dS/m)

50% emergence (dS/m)

Barley

Hordeum vulgare

18

16-24

Cotton

Gossypium hirsutum

17

15

Sugarbeet

Beta vulgaris

15

6-12

Sorghum

Sorghum bicolor

15

13

Safflower

Carthamus tinctorius

14

12

Wheat

Triticum aestivum

13

14-16

Beet, red

Beta vulgaris

9.6

13.8

Cowpea

Vigna unguiculata

9.1

16

Alfalfa

Medicago sativa

8.9

8-13

Tomato

Lycopersicon lycopersicum

7.6

7.6

Cabbage

Brassica oleracea capitata

7.0

13

Corn (maize)

Zea mays

5.9

21-24

Lettuce

Lactuca sativa

5.2

11

Onion

Allium cepa

4.3

5.6-7.5

Rice

Oryza sativa

3.6

18

Bean

Phaseolus vulgaris

3.6

8.0

TABLE 31
Annual rate of organic matter loss measured in the field in the savannah area (Source: Pieri 1992)

Place and source

Dominant rotation

Clay + silt
(%)
(0-20 cm)

Annual rate of loss

Notes

k (%)

No. of years

Burkina Faso

 

Ploughed

Sorghum monocropping

12

1.4

10

No fertilizer

Sorghum monocropping

12

1.9

10

Low rate manure

Sorghum monocropping

12

2.6

10

High rate manure

Sorghum monocropping

12

2.2

10

m + crop residues

Cotton-cereal

19

6.3

15

Much erosion

Cameroun

Cotton-cereal

17

3.2

5

No fertilizer

Cotton-cereal

17

2.9

5

Fertilizer

Cotton-cereal

17

2.5

5

Fertilizer + kraal

Côte d'Ivoire

Cotton-cereal

-

2.6

5

Low rate manure

Cotton-cereal

-

2.3

3

Low rate manure

Cotton-cereal

-

0.4

3

Improved fallow

Senegal

 

Ploughed

Millet-groundnut

3

7.0

5

No fertilizer

Millet-groundnut

3

4.3

5

Fertilizer

Millet-groundnut

3

6.0

4.5

Fertilizer + straw

Millet monocropping

4

4.6

3

PK fertilizer

Cereal-legume

11

3.8

17

F0T0

Cereal-legume

11

5.2

17

F0T2

Cereal-legume

11

3.2

17

F2T0

Cereal-legume

11

3.9

17

F2T2

Cereal-legume

11

4.7

17

F1T1

Chad

 

Ploughed, v. fertile

Cotton-cereal

11

2.8

20

Cotton monoculture

 

2.4

20

Cotton-cereal

1.2

20

+ 2-year fallow

0.5

20

+ 4-year fallow

Togo

Cotton-cereal

10

2.4

20

Low rate manure

Cotton-cereal

10

1.1

20

High rate manure

Saline soils and saline-sodic soils have electrical conductivities greater than 4 dS/m. The saturated soil extract of saline soils contains more than 15% exchangeable sodium; that of sodic soil less than 15%. The pH values of both kinds of soils range between 7 and 10.5 directly reflecting the amount of sodium bicarbonate present, this being completely dissolved in moist soil. The sensitivities of crop yields to salt (electrical conductivity of the soil) are shown in Figure 30 and Table 30. Longer lists of plant tolerance to salt are given by Maas (1986) and Rhoades (1990b).

Field indicators of biological and nutritional problems

In this chapter, whilst reviewing relevant recent work on soil organic matter, soil biology and inorganic soil nutrients, a non-traditional perspective has been taken by placing emphasis on soil organic matter and the close chemical and functional relationship between organic matter and soil particles. It is therefore consistent to suggest that the most obvious indicator of biological and nutritional problems is the absence of, or reduction in, organic matter. Rates of loss of organic matter independent of erosion tend to be slow, but important as they are cumulative. Table 31 suggests that under dryland cropping in west Africa, rates of loss are about 2-4% per annum.

TABLE 32
Soil attributes and standard methodologies for their measurement to be included as part of a minimum data set (MDS) for monitoring soil quality (Source: Larson and Pierce 1991)

Soil attribute

Methodology

Total organic carbon

Dry or wet combustion

Labile organic carbon

Digestion with KCI

Nutrient availability

Analytical soil test

pH

Glass electrode-calomel electrode pH meter

Electrolytic conductivity

Conductivity meter

Texture

Pipette or hydrometer method

Plant-available water capacity

Determined in field best or from water desorption curve

Structure

Bulk density from intact soil cores field measured permeability of Ksat

Strength

Bulk density or penetration resistance

Maximum rooting depth

Crop specific - depth of common roots or standard

Larson and Pierce (1991) propose that minimum, analytically-gathered data sets are essential for monitoring soil sustainability. They include two measures of organic matter among the ten attributes that they consider essential (Table 32). Their concept of requiring agreed minimum data sets is consistent with the approach to assessing sustainability outlined here in Figure 4. Once the minimum data set is constructed (Larson and Pierce 1991), each soil attribute is determined for a reference time (T0) and the change in soil conditions can then be measured over time (T1), which they suggest should be one to ten years.

While suggesting that agreed repeated observations or measurements are essential, it is preferable to empower farmers to take responsibility for recording their own observations of surrogate measurements rather than giving responsibility for analytically-based measurements to outsiders.

Policy-makers need to address the need for analytical or surrogate assessments of soil sustainability. A first step would be to ask farmers for their observations of soil characteristics (cf Table 16) and their attitudes and concerns about soil productivity.

In the case of soil organic matter measurements, it is believed that the limited availability of expertise, the costs and the inherent sampling errors make direct measurement of organic carbon neither cost-effective nor informative. As described in Chapter 2, it is more likely that surrogate measures are adequate and, if sufficiently simple and cheap, have some likelihood of being used. Pieri (1992) (Table 33) suggests that a bleached (possibly brittle) soil surface and plant deficiency symptoms are useful surrogates for loss of organic matter, low CEC and soil nutrient imbalances. Given that loss of organic matter is concomitant with soil structural degradation, indicators suggested in Chapter 2, such as turbidity of water in surface catchments, remain useful.

Indicators of plant nutrient deficiencies include: colour (e.g. redness for potassium deficiency); paleness (a more general symptom, but especially obvious in nitrogen deficiency); and small leaves and plants. Other symptoms, such as leaf curling and accelerated dropping of older leaves, may also be helpful but might equally indicate water deficits. There are several publications with photographs of nutrient deficiencies; these, however, might require further tailoring to specific combinations of crops and soils.

Soil acidity is most obviously indicated by stunted plants, by bare ground, and by better relative growth of acid-tolerant weeds in a sensitive crop. Salinity too is indicated by vegetation changes such as trees dying for no apparent reason or an increase in the proportion of salt-tolerant herbs. Other symptoms of salinity include: waterlogged or bare soil; livestock congregating and licking the soil surface for salt; visible salt crystals; the smell of salt; and clear catchment water because salt settles sediment.

TABLE 33
Mineral nutrients and the decline of fertility (Source: Pieri 1992)

General problems

Signs of simple problems

Where they occur

Probable causes

Limitation of nutrient supply to crops

· Nutrient imbalance

Deficiency in organic matter

Bleaching and destruction of soil surface

Senegal, Niger, Burkina Faso, Mali

Insufficient return of crop residues
Accelerated mineralization of dry matter
Too little fertilizer

N (S) deficit

N (S) deficiency in cereals, legumes and cotton

Throughout area

Too little N (S) applied in fertilizers or manures. High C/N ratio
Very little N fixation
Leaching of nitrate

K-Ca-Mg deficit

K deficiency, Al toxicity

Frequent K deficiency in cotton
Al toxicity in groundnut and cotton (Senegal)

Severe leaching of Ca, Mg, K.
Fertilizers low in Ca, Mg, K.

· Low buffer capacity

Progressive drop in CEC

Loss of fine mineral and organic soil particles

Senegal, Mali, Cote d'Ivoire, Burkina Faso, Niger, Chad

Poor erosion control
Rapid mineralization


Acidification

Senegal, N Cote d'Ivoire, Burkina Faso, Chad

NO3/Ca + Mg leaching
Fertilizers too low in Ca, Mg
Too little or no liming

Marginal soils

Nutrient deficiencies

Senegal, N Togo, S Mali, Burkina Faso

Land shortage
Poor cultivation

Inefficient utilization of nutrients




Management for maintenance of soil biology and nutrition

The aim of management should be to create balanced organic matter and mineral budgets. It should ensure that, over several years (a complete crop rotation), soil organic matter is not depleted and that nutrients added equal or exceed those removed by cropping or lost in various ways.

Various approaches to good management are outlined in Table 34. These complement the aspects listed in Table 33 and the advice on saline water management given by Kandiah (1990) and that on water harvesting offered by Critchley and Siegert (FAO 1991).

When managing organic matter farmers should recognize that the effects of animal and human manure, sewage sludge and plant residues last longer than those of green manure crops. Green manures, though valuable, usually last only one or two seasons because they are incorporated before they are mature and lignified. The longer-term beneficial effects of manures on soil organisms are indicated in Table 35.

TABLE 34
Aspects to consider for maintenance or amelioration of soil biology and nutrition

Maintenance: prevention of degradation

- Crop choice

· Preference for rotations and intercropping with several species, as for Table 19
· Inclusion of legume in rotation

- Cultural practices

· Use of inorganic fertilizers to maintain a neutral nutrient budget
· Plant litter conservation
· Incorporation of human and animal manure
· Incorporation of organic wastes from industry and cities
· Tillage: minimum soil disturbance
· Biological pest and weed management
· Reduce rate of acidification through crop choice, litter and fertilizer management

- Water management

· Water harvesting
· Minimization of salinity, if a problem is likely, through seasonal leaching and other practices

Amelioration to control damage

- Nutrient imbalances and deficiencies

· On basis of visual symptoms, use inorganic fertilizers
· Change cropping pattern to reduce acidity

- Soil surface degradation through loss of organic matter, wind and water erosion

· Increase organic matter through transported wastes, mulches, cover crops, etc. as in Cultural practices above and Table 19

Juo and Payne (1993) advise: 'In spite of the many proven benefits of soil organic matter, its management and recycling in an intensified, modem agro-ecosystem must necessarily revolve around two fundamental characteristics of the system, namely, the availability of organic material at the farm level, and the economic incentive for conserving and recycling organic matter'. To this may be added consideration of the benefits and costs of treating and transporting human wastes from cities (cf Table 22). On-site organic matter, organic material brought in from outside and industrially-produced fertilizers will be used according to their benefit cost ratios and the attitudes of governments and crop managers.

Tillage reduces the frequency of VAM, at least in invertebrates (Table 26). Tillage reduces earthworm populations 10-30-fold, both killing them directly and destroying their burrows (Brust et al. 1986). Haines and Uren (1990) show that differences in earthworm populations between tillage treatments and stubble burning are reflected by 50% differences in numbers of soil pores.

Tillage also effects the location, numbers and activity of micro-organisms within the soil, depending on the type of tillage. For example a mouldboard plough that inverts topsoil has more effect than minimal tillage. Doran (1987) found microbial biomass and potentially-mineralizable nitrogen to be 54% and 37% higher respectively in the top 7.5 cm of no-till than ploughed soil. These would be critical differences if translated to the semi-arid tropics (Keating et al. 1991). Microbial and fungal biomasses may be 20-70% higher after 1 and 2 years no-till (Doran 1980). However, conventional tillage, by burying topsoil, may cause microbial populations and their activities to be higher than under no-till at depths of say 7.5 to 15 cm (Doran 1980). Differences in soil organisms (e.g., microbial biomass) under differing tillage treatments are seasonal, generally being greatest in the period when the weather is most favourable for soil organism activity and plant growth (Carter and Mele 1992). Rasmussen and Collins (1991) summarize many data on the impact of tillage on soil properties and conclude that stubble-mulching with zero tillage conserves up to 2% more organic matter per year than ploughing.

TABLE 35
Micro-arthropod populations in top 10 cm of clay soil 1 and 2 years after adding organic fertilizers in Italy. Additions were made to achieve 4% organic matter and inorganic N and P were to make all treatments equivalent to the manure (Source: Fratello et al. 1989)

Taxon

Control

Fowl manure

Sludge

Green manure

Straw

One year after application

Collembola

13 209

31 635

13 653

17 205

24642

Entomobryidae

2 109

4 329

2 109

222

2 331

Onychiuridae

1 221

333

2 109

222

1 221

Isotomidae

9 990

26 529

9 324

16 650

20 313

C. coecus

8 214

24753

7 659

10 101

18 204

C. thermophilus

0

333

888

0

0

I. Minor

111

111

0

4 995

0

F. Parvulus

0

111

0

0

0

Sminthuridae

0

222

0

111

222

Neelidae

0

111

111

0

555

Acarina

65 046

42 513

35 853

43 068

70263

Pauropoda

3 108

1 221

3 108

2 331

7 104

Microarthropods

83 361

80475

54834

65 157

103 674

Two years after application

Collembola

4773

7 104

8 769

5 328

5 550

Entomobryidae

0

999

444

222

111

Onychiuridae

444

444

111

222

0

Isotomidae

2 886

1 998

6 771

4 107

4 551

C. coecus

1 887

999

2 442

3 108

3 885

C. thermophilus

0

222

3 996

222

111

I. Minor

222

222

0

333

0

F. Parvulus

333

222

0

0

333

Sminthuridae

1 221

3 552

1 221

777

888

Neelidae

222

0

0

0

0

Acarina

12432

28083

24753

27 639

13 764

Pauropoda

999

111

1 554

999

777

Microarthropods

19425

35 964

36 963

35 187

21 090

Cropping patterns and rotations affect soil nutrition. Diversity of cropping increases the number and variety of soil organisms and reduces pests and diseases (e.g., Table 27).

Soil acidification and salination are extreme cases of nutrient imbalance and, unlike other deficiencies, cannot be corrected simply by adding mineral fertilizers. The management techniques to reduce acidification are: (a) to reduce the net proton production of the system by minimizing nitrate leaching (a special problem in seasonally wet-and-dry climates); (b) to avoid using ammonium fertilizers and reduce the accumulation of organic matter; (c) to lime the soil. Liming is a high cost option while adoption of perennial species (to avoid seasonal accumulation of organic matter and nitrate leaching) is less costly. By contrast, salinity is usually managed by strategic leaching. This is done with the sparing use of low-salt water when both soil moisture and the water table are low.


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