The arbuscular mycorrhizal symbiosis is formed between arbuscular mycorrhizal fungi (AMF) and plant roots. The fungi provide the plant with inorganic phosphate (P). The symbiosis can result in increased plant growth. Although most global food crops naturally form this symbiosis, very few studies have shown that their practical application can lead to large-scale increases in food production. Application of AMF to crops in the tropics is potentially effective for improving yields. However, a main problem of using AMF on a large-scale is producing cheap inoculum in a clean sterile carrier and sufficiently concentrated to cheaply transport. Recently, mass-produced in vitro inoculum of the model mycorrhizal fungus Rhizophagus irregularis became available, potentially making its use viable in tropical agriculture. One of the most globally important food plants in the tropics is cassava. We evaluated the effect of in vitro mass-produced R. irregularis inoculum on the yield of cassava crops at two locations in Colombia. A significant effect of R. irregularis inoculation on yield occurred at both sites. At one site, yield increases were observed irrespective of P fertilization. At the other site, inoculation with AMF and 50% of the normally applied P gave the highest yield. Despite that AMF inoculation resulted in greater food production, economic analyses revealed that AMF inoculation did not give greater return on investment than with conventional cultivation. However, the amount of AMF inoculum used was double the recommended dose and was calculated with European, not Colombian, inoculum prices. R. irregularis can also be manipulated genetically in vitro, leading to improved plant growth. We conclude that application of in vitro R. irregularis is currently a way of increasing cassava yields, that there is a strong potential for it to be economically profitable and that there is enormous potential to improve this efficiency further in the future.

Tel: +41 79 536 7546 12 13 14 2 The unprecedented challenge to feed the rapidly growing human population can only be 15 achieved with major changes in how we combine technology with agronomy 1 . Despite their 16 potential few beneficial microbes have truly been demonstrated to significantly increase 17 productivity of globally important crops in real farming conditions 2,3 . The way microbes are 18 employed has largely ignored the successes of crop breeding where naturally occurring 19 intraspecific variation of plants has been used to increase yields. Doing this with microbes 20 requires establishing a link between variation in the microbes and quantitative traits of crop 21 growth along with a clear demonstration that intraspecific microbial variation can potentially 22 lead to large differences in crop productivity in real farming conditions. Arbuscular mycorrhizal 23 fungi (AMF), form symbioses with globally important crops and show great potential to improve 24 crop yields 2 . Here we demonstrate the first link between patterns of genome-wide intraspecific 25 AMF variation and productivity of the globally important food crop cassava. Cassava, one of the 26 most important food security crops, feeds approximately 800 million people daily 4 . In 27 subsequent field trials, inoculation with genetically different isolates of the AMF Rhizophagus 28 irregularis altered cassava root productivity by up to 1.46-fold in conventional cultivation in 29 Colombia. In independent field trials in Colombia, Kenya and Tanzania, clonal sibling progeny 30 of homokaryon and dikaryon parental AMF enormously altered cassava root productivity by up 31 to 3 kg per plant and up to a 3.69-fold productivity difference. Siblings were clonal and, thus, 32 qualitatively genetically identical. Heterokaryon siblings can vary quantitatively but monokaryon 33 siblings are identical. Very large among-AMF sibling effects were observed at each location 34 although which sibling AMF was most effective depended strongly on location and cassava 35 variety. We demonstrate the enormous potential of genetic, and possibly epigenetic variation, in 36 AMF to greatly alter productivity of a globally important crop that should not be ignored. A 37 microbial improvement program to accelerate crop yield increases over that possible by plant 38 breeding or GMO technology alone is feasible. However, such a paradigm shift can only be 39 realised if researchers address how plant genetics and local environments affect mycorrhizal 40 responsiveness of crops to predict which fungal variant will be effective in a given location.41 For millennia farmers have improved crops using naturally occurring intraspecific plant genetic variation 42 to improve productivity. However, rates of yield increase attributed to plant breeding and GMO-crop 43 technology are not considered sufficient to feed the projected global human population 1 . Beneficial soil 65 there was a significant phylogenetic signal on spore density and clustering (Supplementary figure 1; 66Supplementary infor...

Water scarcity negatively impacts global crop yields and climate change is expected to greatly increase the severity of future droughts. The use of arbuscular mycorrhizal fungi (AMF) can potentially mitigate the effects of water stress in plants. Cassava is a crop that feeds approximately 800 million people daily. Genetically different isolates of the AMF R. irregularis as well as their clonal progeny have both been shown to greatly alter cassava growth in field conditions. Given that cassava experiences seasonal drought in many of the regions in which it is cultivated, we evaluated whether intraspecific variation in R. irregularis differentially alters physiological responses of cassava to water stress. In a first experiment, conducted in field conditions in Western Kenya, cassava was inoculated with two genetically different R. irregularis isolates and their clonal progeny. All cassava plants exhibited physiological signs of stress during the dry period, but the largest differences occurred among plants inoculated with clonal progeny of each of the two parental fungal isolates. Because drought had not been experimentally manipulated in the field, we conducted a second experiment in the greenhouse where cassava was inoculated with two genetically different R. irregularis isolates and subjected to drought, followed by re-watering, to allow recovery. Physiological stress responses of cassava to drought differed significantly between plants inoculated with the two different fungi. However, plants that experienced higher drought stress also recovered at a faster rate following re-watering. We conclude that intraspecific genetic variability in AMF significantly influences cassava physiological responses during water stress. This highlights the potential of using naturally existing variation in AMF to improve cassava tolerance undergoing water stress. However, the fact that clonal progeny of an AMF isolate can differentially affect how cassava copes with natural drought stress in field conditions, highlights the necessity to understand additional factors, beyond genetic variation, which can account for such large differences in cassava responses to drought.