The arbuscular mycorrhizal symbiosis formed between arbuscular mycorrhizal fungi (AMF; Glomeromycota) and plant roots is probably the most abundant symbiosis in the world. This symbiosis is formed by the majority of plant species and contributes to improving plant growth and promotes plant diversity (Smith and Read, 2008). Mycorrhizal fungi increase plant growth by improving acquisition of phosphate, an essential nutrient for plant growth. With the rapidly expanding human population, world phosphate reserves are at a critical level, and improved strategies of phosphate use and cycling in agro-ecosytems are essential (Gilbert, 2009; Gross, 2010). Furthermore, producing superphosphate fertilizer is energy intensive and expensive. Clearly, AMF have the potential to improve the sustainable use of phosphate in agro-ecosystems, especially in tropical acidic soils. The fungi can be applied to the soil in the form of spores. The spores are normally applied with a substrate carrier, most often soil, and the fungus with the carrier is known as inoculum. However, for several reasons they have had limited use in agriculture. First, most crops are naturally colonized by AMF in the soil and so adding more AMF may not seem necessary. Second, a given AMF may improve the growth of some plant species but not others. So, there is unlikely to be any universal inoculum that is effective for all crops. Third, and economically the most significant, is that most AMF species have to be grown in unsterile conditions with plants. It is labour intensive, expensive and does not guarantee that the inoculum is free of other soil microorganisms that could be potential pathogens. However, by coupling recent advances in understanding the ecology, natural genetic diversity and genetics of AMF with technological advances in inoculum production, it may be possible in the future to create ‘designer’ mycorrhiza; using inoculum that have been manipulated for a desired growth effect with a given crop and that can be produced in an economically viable way.

For years, researchers working on the mycorrhizal symbiosis have been able to cultivate AMF in vitro in sterile growth conditions on artificial media with plant roots transformed with Agrobacterium rhizogenes (Declerck et al., 2005). This culture system could potentially provide the solution to producing clean inoculum in an economically viable way. The problem is that fungal growth in that culture system is generally quite slow and researchers have had difficulty getting many different AMF species into, or to grow well, in that culture system. One of the few AMF species that seems well adapted to growing in that system is known as Glomus intraradices. It is widely found in agricultural soils. So the question is whether the genetic variation within an AMF species, which is cultivable in vitro, is large and can lead to large variation in how the fungi affect plant growth? Furthermore, is it possible to manipulate this genetic variation within the fungus in an environmentally acceptable way to develop new AMF lines that have improved effects on plant growth with a given crop plant. All these features should be interesting for commercial AMF inoculum producers.

Studies have revealed surprisingly high levels of within-species genetic variability in the AMF G. intraradices. A recent study of G. intradices isolates available worldwide demonstrated very high diversity in rDNA sequences (Stockinger et al., 2009). In that study, two distinct clades were identified, but even within each clade extremely high levels of sequence variation were observed. Amplified fragment length polymorphism and sequence-based markers revealed a very large number of polymorphisms among G. intraradices isolates all originating from one small field in Switzerland (Koch et al., 2004). To obtain very clean DNA, those studies were restricted to a collection of isolates that had been put into the sterile in vitro culture system with transformed carrot roots. Importantly, within that collection, genetic differences were shown to translate into different fungal phenotypes and differential effects on plant growth (Koch et al., 2006; Croll et al., 2008). Thus, natural genetic variation within an AMF species is indeed interesting for development of improved inoculum, both in terms of the growth rate of the fungus in culture and because of its effects on plant growth.

However, an exciting new study reveals even higher levels of genetic diversity within field populations of G. intraradices (Börstler et al., 2010). Börstler et al. revisited the same Swiss field. Instead of restricting themselves to G. intraradices from the in vitro cultivated collection, they looked at the diversity of mitochondrial large-subunit rDNA haplotypes of G. intraradices colonizing roots. Their study predicts much higher levels of diversity in G. intraradices populations than previously thought. Furthermore, the study also included another agricultural field and two grassland sites. This revealed that genetic variability in G. intraradices was also very high among sites, with higher diversity in the agricultural fields than the grasslands. This new level of genetic diversity within one AMF species, which can be cultured in a clean in vitro system, is exciting news for the potential of this fungus for inoculum development. It seems that there is, indeed, a very high level of diversity in this fungus that could be used to select for improved inoculum growth and for its symbiotic effects on plants.

So, how could this genetic variability be used to develop effective new inoculum with a specific growth effect on a given crop? One way is to manipulate the genetics of AMF. Until recently, it was assumed that AMF are completely clonal and that no genetic exchange takes place between genetically different AMF. However, recently genetic exchange has been shown to take place between genetically different G. intraradices and that this gives rise to ‘hybrid’ progeny with phenotypes that are sometimes novel compared with those of the two parents (Croll et al., 2009). AMF are able to harbour genetically different nuclei within a common cytoplasm (Hijri and Sanders, 2005). In a recent study, Angelard et al. (2010) took lines of G. intraradices that actually gave a negative growth effect on rice and manipulated their genetics. These manipulations used naturally existing biological processes in the fungus; namely, genetic exchange and segregation rather than any laboratory-engineered gene insertion. They produced genetically novel G. intraradices lines that could induce up to fivefold growth increases in rice. The manipulations involved taking pairs of genetically distant G. intraradices isolates, allowing them to fuse to produce crossed lines. The crossed lines did not improve rice growth. However, by making single spore lines from crossed lines, genetically different nuclei of the fungus were partitioned in newly forming spores in different proportions; a type of partial segregation. Thus, siblings from one AMF line are genetically different from the parental line and from each other. The genetically different fungal lines induced strong differences in rice growth. Interestingly, some of the segregated AMF lines that did not alter rice growth gave different growth effects on another plant, Plantago lanceolata, showing that genetic changes in the fungus can have specific effects on different plant species. Rice is a globally important food crop. The ability to take an AMF that is not beneficial and produce an AMF line that is highly beneficial on such a plant using ‘environmentally acceptable’ manipulations of the genetics of the fungus is exciting. Perhaps more exciting is that this was carried out with G. intraradices, which, as we now know, is a genetically very diverse AMF. Furthermore, because segregated lines have specific effects on crops, this means that inoculum producers may now be in a position to manipulate natural genetic variation in AMF to make ‘designer’ mycorrhizas, with fungi selected for their symbiotic effects on a particular crop.

Although geneticists have been making advances in understanding genetic variability in AMF and how AMF genetics contributes to the symbiotic effects with plants, biotechnologists have made significant breakthroughs increasing the efficiency of AMF inoculum production in the in vitro system. Some companies are now able to produce AMF in vitro in very large quantities at relatively low cost. As the demand for phosphate fertilizer goes hand –in hand with the growth in the world's population, prices of this important resource will certainly rise. Initial field trials in Colombia with such mass in vitro-produced G. intraradices inoculum show promising results for maintaining food crop yields while greatly reducing phosphate inputs, making the cost of inoculum a minor factor in the production costs (A Rodriguez; personal communication). With the exciting possibly for geneticists and inoculum producers to now manipulate the fungus to produce effective inoculum for a given crop or soil type, the mass-produced ‘designer’ mycorrhiza appears to be a step closer and more of an economic reality.