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Colonisation of Roots by AM Fungi


Colonisation of the roots of a plant is crucial for the transfer of minerals and water to the plant and organic carbon to the fungi. The process of colonisation is determined by the specific fungi, host and environment.

Development of Colonisation

Development of colonisation follows a simple model. Initiation of AM typically commences within a few days of the appearance of roots. Over time, the proportion of the root colonised by AM fungi increases sharply and then reaches a plateau. The colonised proportion of the root system of an annual plant declines prior to death of the plant. In perennials, the pattern of colonisation is largely determined by the pattern of root growth. Fresh roots become colonised rapidly. Colonisation declines as carbohydrates are withdrawn from the root prior to death of the root, or secondary development of the root compresses the cortex.

Fungal Factors

Factors influencing colonisation include the quantity of propagules of AM fungi, the species of fungi and the location of propagules in the soil profile relative to the root. LINK


Quantification of AM Fungi

Because AM fungi are obligate biotrophs, traditional methods of quantifying fungi are difficult to use. Further, quantification of a microbe over areas as large as single paddocks seem inherently unreliable. Thus the results of quantification are qualified by the method used to obtain them. Traditionally, three processes have been used; a direct measure of the amount of fungal material in soil, assessment using dilutions of soil, and bioassays.

Direct counts rely on fungal structures or their biochemical markers of one sort or another. In general, the use of DNA and other biochemicals such as fatty acids, sterols etc has not reached the level of accuracy that is necessary to provide useful information. DNA methods commonly require use of PCR which may bias results. Further, DNA of non-viable fungal units may be included. Fatty acids of Glomalean fungi are not particularly specific to AM fungi and in any case do not differentiate different taxa. Thus these results indicate broad quantities.

Spore counts have been used to estimate populations in cropping soils. Use of spores is unreliable because different fungi produce spores at different times of the year and in different quantities. If the aim is to indicate the potential pool from which mycorrhizas arise, then viability of spores of some species declines rapidly in soil, some spores may be dormant, few spores may be viable at any one time and the counts are unreliable. Hyphal length has also been used to quantify the population of AM fungi, though the confounding effect of saprophytic fungi makes most measures difficult to interpret. Indeed, the enormous density of hyphae found in soil (0.5 m in arable soils up to 10m per g in undisturbed soil) may mean that any root is overwhelmed by potential propagules.

Quantification of bacteria commonly uses a dilution series. A dilution is reached at which no viable propagules are detected. The proportions of replicates above this value are then used to indicate the density of propagules. The result indicates quantities of viable propagules, with large inherent variation due to the statistical treatment of the data. Dilution series of soil containing AM fungi have been used to estimate densities of propagules. The measures appear to be of indicative value for cropping soils, and are useful for experimental processes. Because hyphae are shattered by the mixing of soil with diluent, fungi sensitive to disturbance are removed from the calculations. In addition, spores in sporocarps are not separated, and one thosands propagules will be ounted as a single source of colonisation. Thus the measures are useless for soils from undisturbed locations, and an unknown number of AM fungi found in cropping soils.

Bioassays utilise the capacity of AM fungi to initiate colonies and spread through the root system. Trap plants are transferred to cores of undisturbed soil and the trap plants harvested sequentially to provide a colonisation curve (see above for an example). The number of propagules that germinate and initiate colonies before onset of secondary spread (12 days) may indicate quantities of readily germinable propagules. The rate of spread in the root system may indicate the capacity of the root system to be colonised by the fungi present in the specific soil under the specific environmental conditions, and the final level of colonisation may indicate the inherent nature of the interaction, and the environment under which it was developed. These measures indicate the colonising potential of the soil, a factor not necessarily the same as the quantity of propagules.


Relationship Between Colonisation and Quantity of the Fungi

Primary colonisation is the process whereby a single propagule, of any size, initiates a colony and develops a mycorrhiza. Only one unit initiates the colony. Thus a measure of the primary colonisation is an indication of the number of propagules able to initiate colonisation in the root system within that time frame. The measure is constrained by time and space, and thus is highly qualified. However, as secondary colonisation commences about 12 days after initiation of colonisation, the number of colonies (and the proportion of the root colonised) at 12 days indicate density of propagules of AM fungi that respond rapidly to the presence of roots.

Secondary colonisation is established when hyphae from primary colonies initiate further colonies along the root, or in an adjacent root. Thus the rate of secondary colonisation indicates the inherent capacity of the fungi to spread in the root system. Spread in the root is dependent on the available energy, environmental conditions, rate of growth of the fungi and the quantity of propagules in the soil. Large energy reserves provide more energy for spread of hyphae. That is, those fungi growing from extensive colonies have larger reserves and will grow through the root system more rapidly than hyphae emerging from soil-borne propagules, which might be energy limited.

Different fungi have different rates of hyphal elongation. This has several consequences. One is that different species will spread at different rates, even from a similar quantity of initial propagules. Thus in the field, several fungi will be competing for entry to the root system, and those that elongate more slowly may have a different set of competitive characteristics that enable them to maintain their populations.

The quantity of propagules may have a direct influence on the rate of secondary spread. Where the soil has severely depleted reserves of AM fungi, initiation of colonisation of plants in the soil will be delayed, and the rate of spread of mycorrhizas in the root system will be slowed.

It comes as no surprise to realise that where cropping soils have been fallowed for long periods, to conserve moisture, the density of propagules of AM fungi at the surface may be seriously depleted. Propagule densities decline down the soil profile, normally. As the density of propagules determines rates of colonisation, plants grown in fallowed soils are often found with low colonisation and an uneven distribution of colonies in the root system. AM can spread up and down the root system. However, spread of hyphae from the root into the soil appears to be dependent on aeration and open structure, factors which are closely related. Thus after long fallow, propagule density at the surface is depleted, and only pockets of propagules may remain in the soil. Subsequent colonisation is a chance event, and uneven. At least in cotton, a single crop restores density and distribution of propagules through the soil profile. However, the soil also modifies the process of recovery (see below).


Host Factors

The host controls colonisation of the root system. The mechanisms are unclear though there is a close relationship between concentration of P in the plant, incident light and genetic factors. Interestingly, the plant appears to recognise the attachment of the fungus. Biochemical responses are complex. Recognition markers produced by plants appear to include flavonols which stimulate hyphae. A trigger to form appressoria is also likely, though is not known at this stage. Interestingly, the genes associated with formation of nodules in legumes are also important in formation of arbuscules in normally mycorrhizal plants. Using mutant plants, the process of colonisation is being elucidated, and appears to involve a range of plant and fungal genes acting at different stages of colonisation. LINK


Environmental Factors

The most important factor determining colonisation is the concentration of available minerals, especially phosphate, in soil. LINK Generally, colonisation declines as available P increases. However, in the field, colonisation is rarely absent even in extremely high P soils which may have consequences for growth of the plant. Light also determines the rate of colonisation. In low PAR, plants slow the rate of colonisation and the consequent loss of carbon to the fungi. LINK Osmotic potential or available water, high or low pH and temperature also influence colonisation, either directly, or indirectly through the plant.

Available oxygen also appears to be important. Hyphae of AM fungi grow from the root into soil. The spread into soil is determined by the texture and structure of the soil, which is linked with the available oxygen. Presumably, roots provide hyphae with oxygen, and thus spread will continue down the root into the anoxic zone. However, AM fungi appear unable to colonise the soil much beyond the root in the anoxic zone. Anoxia can be established readily in clay soils, in poorly structured, blocky soils, under waterlogged conditions and at depth. The energetic resource supplied by the fungi to the soil will be absent under these conditions. Changes in redox may make Mn more available, influencing the plant and the fungus. Aggregation associated with AM fungi will also be absent. LINK The fungi influence the soil, and soils influence AM fungi.



Colonisation of roots by AM fungi is a complex process ultimately governed by genetic factors in both host and fungus. These factors interact with environment. Normally, colonisation is rapid. However a variety of plant, fungal and environmental conditions may modify the process of colonisation.



Smith SE & Read DJ. 2008 Mycorrhizal Symbiosis. Academic Press.


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