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3.1 Plant roots and soil biota

What is the rhizosphere?

The rhizosphere is the region of soil that surrounds, and is influenced by, plant roots. A major influence in the rhizosphere is the release of organic molecules into the soil from roots. Although the exudates and mucilaginous materials released by roots diffuse through the soil, they always occur in their highest concentrations adjacent to the root surface. Because soil organisms are attracted to these exudates as a source of food, the abundance of soil organisms also increases close to roots (Newman and Watson 1977). This is a dynamic relationship (Darrah 1991a,b). The rhizospheres of old and young roots provide very different habitats for soil organisms. As roots age, they release different types and quantities of carbon substrates, which in turn affect soil microorganisms.

The rhizosphere also differs from the remainder of the soil in other ways. For example, the amount of inorganic nutrients can be either higher or lower in the vicinity of roots compared with that in the soil some distance away from roots. The concentration or depletion of nutrients around roots depends on physiological processes associated with root function, including nutrient uptake by plants. In addition, roots release hydrogen or bicarbonate ions into the soil, causing the pH in the rhizosphere to decrease or increase (Marschner et al. 1982). Roots also consume or release oxygen. These contrasting effects, in addition to the considerable exudation of carbon compounds from roots into the soil and the compression of soil as roots grow in length and breadth creates a dynamic environment for soil organisms.

Some nutrients move towards roots in soil water by the process of mass flow. Other nutrients are less mobile because they are adsorbed onto soil particles. The availability of adsorbed nutrients such as phosphorus and copper to plants depends on the extent to which roots explore the soil and intercept these ions. This in turn affects the extent of the rhizosphere and the spatial distribution and activity of soil microorganisms.

Water use by plants adds to the dynamic nature of the rhizosphere. Daily cycles of water uptake and loss by roots cause roots to expand and shrink. This adds to physical changes induced by seasonal cycles of wetting and drying or freezing and thawing. These daily and seasonal cycles alter the soil habitat, which influences the growth and activity of soil organisms.

As a root develops, the number of organisms near the root surface increases rapidly. For many plants there is not a clear distinction between the root surface and the soil. Roots are dynamic, growing and casting off cells and navigating soil cavities and rough surfaces. As a consequence, the root surface can be highly irregular (Foster and Bowen 1982).

What is the origin of root exudates?

A variety of organic compounds released from roots provide a source of energy and carbon for soil organisms. In a study of exudation from wheat roots, the plant was labelled with 14C (Liljeroth et al. 1990). This technique allows the carbon released from the plant to be followed precisely. The greater the amount of 14C released into the rhizosphere of the wheat plant, the greater the quantity found in the microbial biomass. The quantity of the compounds released from roots is not the same along the length of a root. Older roots can be more ‘leaky’ than younger roots, although in this experiment there was no difference, at least for one line of wheat. The release of relatively large quantities of organic carbon into soil under normal conditions stimulates microbial activity and provides a source of energy that can accelerate the decomposition of organic matter.

How do roots affect soil organisms?

Roots provide an important habitat for bacteria, fungi and very small soil animals. The number of organisms can be about 500 times more in the rhizosphere than in the bulk soil (Rouatt et al. 1960).

The surface of a root is not completely covered with bacteria and fungi, except in special circumstances, such as where roots are colonised by an ectomycorrhizal fungus. Usually less than 10% of the root surface is colonised. Bacteria accumulate in crevices along the edges of outer root cells (Foster and Bowen 1982) or where the root surface is damaged.

Some organisms form loose associations with roots and simply depend on the plant releasing molecules that they can use. Other organisms have more specific interactions with roots. For example, root nodule bacteria can stimulate the root to form additional cell tissue that proliferates to form a nodule.

Root nodule bacteria live and multiply inside these root cells. When roots begin to disintegrate with age or through disease, there are more chances for opportunistic bacteria and fungi to enter through crevices between the surface cell layers or dead root cells.

Roots indirectly affect soil animals because they respond to changes in the abundance of bacteria and fungi associated with roots. The types of organisms present in the rhizosphere and in the bulk soil change over time (Lussenhop and Fogel 1991). These changes are associated with the intensity of grazing by soil animals and the abundance of other bacteria and fungi. Furthermore, there is a wide range in numbers of different types of animals. Overall, there is great diversity in type and number of organisms in the vicinity of roots.

How are roots affected by soil organisms?

Microorganisms can indirectly increase or decrease root growth. For example, organisms influence the movement of carbon from shoots to roots. This can alter root growth as well as stimulate the release of carbon into the rhizosphere. Some organisms increase root growth by producing compounds that function as root growth hormones. Organisms may decrease root growth by creating a significant drain on carbon reserves in the plant. This reduces the quantity of carbon in the root that would otherwise be used to form more roots.

The effects of soil organisms on roots can be either indirect or direct. For example, earthworms indirectly promote root growth because their burrows provide channels for roots to grow more deeply into the soil profile. In contrast, some rhizosphere bacteria and fungi impede root growth. Roots may grow more extensively if such microorganisms are absent than if they are present (Bowen and Rovira 1969). Ectomycorrhizal fungi also reduce root growth by colonising the surface of roots and stunting their growth. In addition to the thickening of the root, the roots often branch in response to hormones produced by the fungus.

Arbuscular mycorrhizal fungi can reduce root growth. In a study of maize, microorganisms decreased both root hair length and root hair number (Kothari et al. 1990). However, the extent of the decrease depended on whether arbuscular mycorrhizal fungi were present or not. In the presence of these fungi, both root growth and root hair number were considerably impeded in comparison to when these fungi were absent.

Generalisations about the effects of soil organisms on root growth are difficult to make because different species of plant and different types and combinations of soil organisms interact in different ways (Gadagi et al. 2004). Bacteria in the genus Azospirillum are interesting examples of microorganisms that have the potential to influence root growth. Species of Azospirillum commonly live in the rhizosphere of grasses. Some bacteria in the genus Azospirillum increase root growth by contributing nitrogen to the plant and others stimulate root growth by hormone production (Barbieri et al. 1986). Strains of species of Azospirillum vary in their capacities to fix atmospheric nitrogen or produce hormones. Nitrogen fixing strains of Azospirillum are not expected to increase root growth if nitrogen levels in the soil are already adequate for the particular plant species; if root growth is affected, other mechanisms must be involved.

How do roots function in the presence of soil organisms?

Changes in root structure alter the capacity of root systems to absorb nutrients and water. Principally, this is related to the way that roots are distributed in soil. However, close associations between roots and microorganisms enhance nutrient uptake by plants if organisms have access to nutrients to which the plant does not. An example of this is the association between roots and nitrogen-fixing bacteria. Another example is the association between various types of mycorrhizal fungi and roots that allow root systems access to nutrients well beyond the rhizosphere.

Root pathogens commonly interfere with nutrient and water uptake by damaging the root surface and root cortex or by blocking the xylem vessels in the vascular system inside the root. Damage to the cortex or the vascular system will reduce nutrient and water transport between roots and shoots. Soil animals such as nematodes may also damage roots. Parasitic nematodes induce gall formation on some plants and animals such as springtails graze on small roots and damage their surface. Disturbances of this kind create opportunities for a variety of fungi and bacteria to enter roots that would not otherwise be able to do so.

Summary Points (3.1)

• The rhizosphere is the region of soil that is influenced by roots.

• Roots exude many substances into soil, including carbon-rich molecules that are sources of energy and carbon for microorganisms.

• Root exudation stimulates the food-web of organisms around roots. In particular, soil animals increase in abundance in response to an increased activity of bacteria and fungi.

• Organisms in soil can alter the growth of roots. Some greatly change root morphology (e.g. ectomycorrhizal fungi) and others increase or decrease root growth.

• Important root functions such as water and nutrient uptake can be modified by the presence of some bacteria, fungi and soil animals.

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