Managing for optimum root health

by | Jul 1, 2023 | Technical, Viticulture research

This article is republished from the proceedings of the Soilborne Plant Disease Symposium 2022, with permission from the author and the organising committee.


Plant health is dependent on root health which is ultimately dependent on soil health.

Roots are the support system of a plant. They anchor the plant and absorb water and nutrients from the soil. They are also the transport system of this water and nutrients throughout the rest of the plant. Without a healthy root system, plant uptake is thus compromised and as such plant health is compromised. It is thus imperative that healthy roots are grown, developed, and maintained.

Within an agricultural system, roots are often grown in soil. It follows that to maintain healthy roots, roots must grow in healthy soil. Soil health is a combination of physical, chemical and biological soil health. Optimum management of each facet of soil health will contribute to optimum root development. To this end, managing for optimum root health will be discussed in the context of optimum management of each facet of soil health, with a focus on biological soil health, the soil food web and the contribution of nematodes to the soil food web.


Physical soil health

The physical soil properties that affect root development are soil texture, depth, structure and temperature, as well as compaction and water availability. Soil texture, depth, structure and temperature (to a degree) are for the most part inherent soil properties and management regimes generally do not directly affect these properties. Compaction and water availability (in irrigated crops), however, can be managed to achieve optimum root development. Soil compaction occurs when soil particles are pressed together. This reduces the pore spaces between the soil particles. As a result, a physical barrier to root development is created in the soil. Roots would rather go around a hard or dense object than go through it. This restricts root growth and distribution within the compacted layer.26 Furthermore, compaction causes anaerobic or anoxic conditions. Root respiration requires oxygen. The anaerobic conditions created as a result of compaction lead to root death and as a result, reduced root growth.3,26 Compaction within the soil should be addressed in order to allow for the optimum development of roots throughout the soil profile. Compaction can be addressed by implementing controlled traffic principles, tillage and the use of appropriate cover crops. The distribution, health and functioning of the root systems are also strongly influenced by the prevailing soil water dynamics.24 Depending on soil type, over-irrigation and poor drainage can result in waterlogged conditions. This much like compaction results in anaerobic or anoxic soil conditions. As discussed earlier, roots require oxygen to respire and as such do not grow optimally in such conditions. The constant availability of water can lead to the development of a shallow root system. Readily available water near the surface results in roots not needing to go searching for water. This causes the majority of the roots to remain near the surface instead of developing throughout the soil profile in search of water.26

A deep-rooted plant is a resilient plant. Plants with deep roots are able to survive periods of water stress as deep roots are able to access water from areas deep within the soil. To develop a deep root system, the water must be managed carefully to allow for periodic water stress which will encourage the roots to go searching for water. This may result in short-term water stress and affect yields, but will result in a deep-rooted plant that will perform better through periods of water stress. Although in irrigated fields, water stress can theoretically be controlled, periods of unplanned water stress may occur due to the erratic electricity supply coupled with the possibility of water shortages in South Africa.26 Land use planning, irrigation scheduling and monitoring irrigation water quality are important irrigation management tools that can be applied to prevent waterlogging and stimulate deep-root development.


Chemical soil health

Soil acidity is considered to be one of the largest crop-limiting soil constraints in rainfed agriculture. The presence of excess aluminium (Al) in the soil and increased iron and manganese solubility create a toxic environment for plants. In addition, it causes a deficiency of base cations, particularly calcium (Ca) and magnesium (Mg). Excess Al can also lead to reduced phosphorus availability. Additionally, the uptake of Ca, Mg, potassium (K) and some micronutrients can also be reduced. Soil acidity in agriculture is caused mainly by the excessive use of nitrogen fertilisers and the loss of Ca, Mg and K when the crop is removed at harvest.21,22,23,27 The effect of soil acidity on plant roots is dependent on the crop grown. In contrast to soil acidity, soil salinity is an excess of freely available Ca and Mg ions in the soil. Soil salinity reduces water uptake by the roots by creating an unfavourable concentration gradient between the soil solution and the root.4 When the salt content in the soil solution is much greater than that of the root cells, the plant is unable to produce sufficient sugars to compensate. As such, the plant has a reduced capacity to absorb water.4,10 Under extremely high salt loadings and high demand for water, plants may exhibit a wilted appearance despite there being enough moisture available in the soil.26 The presence of high levels of sodium (Na) and the resultant high Na exchangeable percentage leads to a sodic soil. Sodic soils have a collapsed soil structure which results in blocked pore spaces and limited movement of water through the soil profile. The resultant anoxic conditions created are similar to those created by compaction and waterlogging. The resultant effect on roots (see physical soil health above) is the same. The key to managing nutritional soil health is soil and crop nutrition monitoring through sampling and testing. Avoid over-fertilising by basing fertiliser regimes on regular soil and crop testing. Acidity can be corrected through the use of lime and or gypsum. Gypsum moves more easily through the soil profile and is usually used to address subsoil acidity. Gypsum can also assist with sodic soils. Soil acidity problems are best addressed at planting and regular monitoring ensures that increasing acidity levels are detected early. Regular water quality monitoring can prevent creating of high salt levels in the soil by detecting and addressing the high salt levels in irrigation water. Much like soil acidity, regular soil monitoring will detect increasing salt levels early. Salt accumulation in soils can be addressed through drainage and flushing of soil with excessive water.26


Biological soil health

Biological soil health, as indicated in the name, refers to the living component of the soil. The concept of biological soil health is based on the presence of a soil food web (Figure 1). The soil food web consists of varying trophic levels at which different organisms play a critical role. The start of the soil food web is the first trophic level which consists of the producers. These are the plants that are present. Within agriculture, this is generally the crop that is grown, as well as any weeds, grasses or cover crops that are being grown. Other organisms within this level include moss, lichens, photosynthetic bacteria and algae. These organisms are identified by their ability to produce their own food by using the sun’s energy and CO2.


Root 1

FIGURE 1. Soil food web.


The next critical component of the soil food web and a requirement for a functioning soil food web is organic matter. Organic matter within the soil is made up of waste, residue and metabolites from plants, animals and microbes. It is usually made up of approximately equal parts of humus and active organic matter. Microorganisms feed on the active fraction of the organic matter. The humus fraction consists of complex organic compounds left behind after decomposition. Not many organisms can decompose this material, so it is referred to as the stable or permanent organic matter fraction.11

The second trophic level consists of bacteria, fungi and root-feeding nematodes. The bacteria and fungi within this trophic level can either be beneficial or parasitic bacteria and fungi. The abundance of either bacteria or fungi is dependent on the type of food source available. Bacteria feed on simpler compounds such as root exudates and fresh easy-to-digest plant tissue. Fungi, on the other hand, feed on more complex plant tissue such as fibrous plant tissue, wood and soil humus. The third trophic level includes arthropods, protozoa, and bacterial and fungal-feeding nematodes. These organisms feed on bacteria, fungi and plant parasitic nematodes. The fourth and fifth trophic levels consist of higher-level predators that feed on the lower levels. These levels include omnivorous and predatory nematodes. All of the organisms within the soil food web recycle nutrients within the soil and make them available to plants, through their feeding and the resultant excretion of excess nutrients.

Management of biological soil health is two-fold. The first is the reduction of soil-borne pests and pathogens, while increasing the levels of beneficial soil insects and microorganisms. In essence, it is about maintaining the balance of the food web such that the percentage of pathogens and pests is at an acceptable level. It is also about creating healthy soil which in turn creates a healthy plant that is able to withstand the effect of pests and pathogens. As indicated above, the soil food web consists of bacteria, fungi, nematodes and numerous other soil organisms. The rest of this paper, however, will focus on nematodes within the soil food web and their role as both contributors to the soil food web, as well as indicators of soil health and ecosystem functioning.

Nematodes are microscopic, worm-like organisms that live in the moisture between the soil particles. A nematode’s main function in the soil food web is organic matter decomposition and nutrient mineralisation. Nematodes, however, do not decompose organic matter or influence the mechanical and physical soil properties directly.16 Their effect is rather through feeding on the microbial population (bacteria and fungi) in the soil. The role of primary decomposition thus lies with bacteria and fungi. The indirect effects of nematode feeding on the microbes include modification of the microbial community, accelerated turnover of microbial cells and inoculation of new substrates through nematode movement.9 Numbers and proportions of bacterial and fungal-feeding nematodes are indicative of the numbers and relative proportions of the relevant food source.

Plant parasitic nematodes are herbivorous nematodes that feed on the roots of plants and in doing so reduce the root systems in plants, in particular fine roots and root hairs. This is the main transport system of the plant and as such can severely affect root and plant health. The most damaging group of plant parasitic nematodes are the sedentary endoparasitic nematodes. The two main types of nematodes belonging to this group are the root-knot and cyst nematodes. These nematodes travel into the root system and alter the morphology of the roots to no longer serve the interest of the plant, but rather the nematode. The semi-endo parasitic group travels within the roots, as well as in and out of the roots, each time wounding the root. This feeding and migration cause necrosis of the root tissue, as well as allow other soil-borne pathogens to enter through the wounds. The last group of nematodes is the ectoparasitic nematodes. These are usually large nematodes, with large stylets able to feed on nutrient-rich areas deep within the roots. Damage due to these nematodes is usually due to large numbers of nematodes feeding on the roots.

Nematodes also play an important role in essential soil processes with their direct contribution to nitrogen mineralisation being the most important one. Studies have shown that the presence of free-living nematodes increases the available nitrogen in the form of ammonia25 and it can increase plant biomass.11 Nematodes contribute directly to nitrogen mineralisation by consuming excess nutrients and excreting the excess in a form that can readily be taken up by plants.2,7,11,15 They have been shown to contribute up to 19% of nitrogen mineralisation.2,15 Omnivorous and predatory nematodes do not contribute to nutrient recycling as much as bacterial and fungal-feeding nematodes. Their role within the soil food web, much like other predators, is population control. In 199913 it was found that predatory nematodes could become important regulators of bacterial-feeding nematodes, while omnivorous nematodes did not have a strong effect on fungal-feeding nematodes. Plant parasitic nematodes can also be regulated through predatory and omnivorous nematodes.18,19 Predatory nematodes, however, do play a central role as indicators within the soil food web. Their presence and abundance may be correlated with predaceous microarthropods.20 By further classifying nematodes according to their c-p values, nematodes can also be indicators of organic enrichment. cp-1 organisms or enrichment opportunists are most responsive to organic enrichment. cp-2 organisms are general opportunists. These organisms may already be present, but are exploiting a new food source.8 Greater dominance of cp-1 organisms indicates enrichment, an increase in cp-2 organisms with a decrease in cp-1 and cp-3-5 indicates stress, while an increase in cp-3-5 represents natural succession mediated by environmental stability.5

Management of biological soil health should aim to minimise the percentage of pests/pathogens in the soil, while increasing the number of beneficial organisms in the soil. Furthermore, it should focus on maintaining healthy plants to minimise the effect of pests and pathogens on plants. The key to a fully functioning effective soil food web is diversity. Different organisms have different life history characteristics, life cycle duration, physiological and behavioural attributes, as well as their adaptation to varying conditions. Their dispersal and exploitation of different areas throughout the soil profile, associated with differing moisture, aeration, texture and chemistry are indicative of the delivery of complementary services within a particular functional guild rather than being in competition with each other. Although these organisms deliver a similar function within the soil food web, their adaptations to differing conditions and niches provide resilience to the soil food web. If environmental conditions affect the growth and development of one type of organism, the entire service within the soil food web is not lost as there are other organisms contributing to the same function.5

Management interventions should be targeted at the lower trophic levels of the soil food web as this is the source of the soil food web.

If the food is available (plants, root exudates, bacteria and fungi) and the environment is conducive (physical and nutritional properties of the soil is well maintained), the higher-level organisms within the soil food web will proliferate.

To promote diversity in below-ground organisms, there must be aboveground diversity. Organisms in the soil respond to root exudates. A variety of root exudates will stimulate a variety of organisms in the soil.28 If these plants are hosts to different pathogens, diversity can also contribute to the reduction of pathogen levels as it decreases the ability of the pathogen to find a host.12 Aboveground diversity can be increased through the use of multi-species cover crops. Multispecies cover crops have the ability to increase microbial diversity, while minimising the increase of soil-borne pathogens and increasing populations of beneficial microbes by increasing plant functional groups richness. The choice of the crop within the mix can also help to suppress plant pathogens through direct effects such as the ability of brassicas to suppress fungal pathogens and promote disease-suppressive bacteria. Native plants may also further promote beneficial soil microbiota.28 Table 1 shows the effects of different groups of cover crops on soil microorganisms. When using cover crops, ensure that the soil pests and pathogens are identified prior to planting so that host crops to those pathogens are avoided or minimised within the mix.


Root 2

Cover crops can either be used as living crops with the aboveground biomass being removed or the organic matter can be incorporated into the soil. The resultant effect on the soil will be different. The composition of the decomposing plant litter has been shown to affect both the activity1 and the community structure of soil microbes.6 Other management interventions include the addition of organic amendments. A meta-analysis was conducted in 201814 of 690 independent organic amendment studies globally. The organic amendment increased the amount of soil organic carbon by 38%, total nitrogen by 20%, microbial biomass carbon by 51% and microbial biomass nitrogen by 24% compared with mineral-only fertilisation. Organic amendments also increased the soil microbiome enzyme activity in terms of soil hydrolytic C acquisition (39%), N acquisition (22%), P acquisition (48%) and oxidative decomposition (58%). There are also many beneficial soil microorganisms specifically targeted toward root health that are commercially available for addition within agricultural systems. Despite the focus on increasing diversity and beneficial organisms within a soil, one must not lose sight of the fact that the objective is to maintain the balance of beneficial and pathogenic organisms within the soil.

Commercial agriculture is an unnatural system and as such the number of pathogens will increase. Numbers of pathogenic organisms within the soil must therefore constantly be monitored and managed such that the numbers remain within acceptable ranges and do not negatively affect root or plant growth.

For optimal root development, all three aspects of soil health must be managed optimally. The key thread that runs throughout all areas is that of monitoring and applying appropriate management interventions, based on data. In order to manage soil and roots effectively, the objectives for all three facets of physical, chemical and biological properties must be set, all three properties must be measured and based on objectives and measurement, appropriate management interventions must be made. This is a continuous process as the soil is a living organism that is constantly evolving in response to change.



The author would like to acknowledge her co-authors of the paper titled: A review of management practices impacting root health in sugarcane.26 The framework of this write-up is largely based on that paper.


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For more information, contact Prabashnie Ramouthar at


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