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Sustainable agriculture: the role of beneficial soil fungi in promoting crop productivity under drought

Final Report Summary - SOTRES3 (Sustainable agriculture: the role of beneficial soil fungi in promoting crop productivity under drought)

The Intergovernmental Panel on Climate Change (IPCC) projected that the land area affected by drought will increase and water resources in affected areas could decline as much as 30% by mid-century. As a result of global climate change, some of the most severe weather events, including drought, could become more frequent in Europe over the next 50 to 100 years. European agriculture must deal with the effects of drought to provide a sustainable, safe and secure food supply for its citizens. Improving the yield of crops grown under drought conditions has been difficult because of the low heritability of tolerance, varied effects depending on timing of drought, and gaps in understanding of drought physiology. However little attention has been made to the fact that most crops live in symbiosis with soil microbiota. Plants may overcome drought effects by interacting with several beneficial soil microorganisms. Particularly arbuscular mycorrhizal fungi (AMF) are fundamental for plant performance, both in natural and agricultural ecosystems and most land plants are colonised by these fungi thus they can likewise affect critically important ecosystem services. Increasingly, the importance of AMF for agricultural sustainability is being recognised.

The present project defined three main objectives to address how differences in soil AMF biodiversity translate to differences in plant productivity under drought conditions:

1. Test the impact of drought on communities of beneficial root associated microbes, in particular AMF in the field.
2. Test AMF adaptability to drought.
3. Analyse whether AMF provide drought resistance and whether the addition of AMF consortia enhances crop productivity and provides additional drought protection.

For objective one, field sampling was performed both at soil and root level for three common grassland and (temporary) pasture species: Lolium perenne L., Trifolium repens L. and Trifolium pratense L. These plant species were used instead of maize, as described in the proposal. This because Dr. Estrada could take advantage of an ongoing experiment with summer drought simulation in the field which contained the above mentioned species. Also, these plant species are smaller than maize and easier to work with. Plant and soil samples were collected and AMF communities were identified using SMRT sequencing. We identified 62 taxa (operational taxonomic units, OTUs) belonging to 19 AM fungal species plus one undefined species. The species composition of AMF communities was generally not affected by drought. However, drought induced a change in the genetic compositions of the most dominant OTU. One fungal genotype almost completely replaced another genotype under drought conditions. Future work now needs to test whether the genotype with enhanced abundance under drought also provides enhanced plant support under dry conditions.
Subsequently, a greenhouse microcosm grassland experiment was set up to test AMF adaptability and plant performance to drought stress (objective 2). For AMF adaptability, soil was taken from the previous field plots used for objective 1 (randomised non-drought and drought plots). For convenience, both experimental reasons (plant size and workability) and similarity with task 1, the same plant species were planted, L. perenne, T. repens and T. pratense, having a total of 18 plants per pot (6 per species). The hypothesis was to test whether the community of AMF of drought soil could revert to the same previous non-drought community under well watered conditions. The same for non-drought soil, testing whether the AMF community will adapt to drought conditions along the experimental period. Unfortunately due to poor DNA quality, it was impossible to amplify the AMF community in all the samples. As a consequence, the adaptability of AMF to drought could not be assessed. However, at the plant community level we generated a high output of physiological results, including oxidative damage and hormone (particularly ABA) analysis. Plant physiological results showed that plants growing on pre-conditioned drought soils had better physiological status (related to the tested parameters) than plants growing on non-drought pre-conditioned soils under water scarcity conditions.
The model species, Brachypodium distachyon, was selected to tackle objective 3. Nowadays B. distachyon is a commonly used species in crop related experiments due to its similarity to the major cereal grain species, being closely related to the Triticeae (wheat and barley). The benefits of using B. distachyon rather than other cereal grain species, like maize, are: its small genome (diploid ~355 Mbp), small physical size, short life-cycle and few growth requirements. For a greenhouse experiment those are desirable characteristics. On the fungi hand, we tested six AMF species, three isolated from Swiss grasslands (considered as non-drought adapted) and other three isolated from arid zones in the Mediterranean (considered as drought adapted). Single inoculation plus mixed inoculation (both fungi from the same origin and all the fungi together) were performed to test differences in drought tolerance conferred to B. distachyon. For that purpose, phosphorous (P) and nitrogen (N) transporters were studied since in natural ecosystems, plants obtain up to 80% of their requirement for nitrogen and up to 90% of phosphorus from mycorrhizal fungi. Even more, during periods of drought, nitrogen availability is reduced and AMF may have a larger impact on overall plant growth and development in dry relative to well-watered conditions. This experiment showed, for the first time that B. distachyon is a highly mycotropic species and that consortia of AMF inoculation is more successful than single inoculation, independently of origin, improving P relocation to the shoot.
Overall, based on the results, we can conclude that AMF can be used to enhance plant performance both under watered and drought conditions. Interestingly, this research demonstrated, for the first time, that drought altered the genetic structure of AMF populations. Further work now needs to show the impact this has on plant growth and drought resistance.

For more information about the related project, please contact Dr. Beatriz Estrada: