Experimental evolution of mutualistic plant-microbe interactions in the rhizosphere

Abstract

We are living on a hungry planet and securing food supply for the steadily increasing human population is a major challenge for mankind. The productivity of agricultural and horticultural crops is constrained by lack of nutrients, abiotic stressors as well as pests and diseases. Together, all these limitations substantially prevent the accomplishment of the full genetic potential of plants for growth and fitness. The use of pesticides and chemical fertilizers to alleviate restrictions on plant performance causes serious environmental problems. Plant growth and health depend to a large extent on soil microbes that are associated with plant roots. These microbes can supply the plant with nutrients, alleviate effects of abiotic stresses, and protect against pathogens and pests. Thus such beneficial microorganisms may be essential allies to improve crop yields in a sustainable way. However, a major problem for large scale and long term applications in agriculture is that the efficacy of such beneficial microbes is unpredictable, often resulting from insufficient population densities on plant roots. In this study I provide evidence that we can use an evolutionary framework to engineer beneficial microbes to perform better in novel host rhizospheres. I attempted to obtain better colonizers by introducing them on plant roots and allowing the population to grow and evolve over many generations during a period of 8 months. In this simplified experimental evolution setup, we used five independently evolving bacterial populations. We then tracked population densities on plant roots at each cycle, and passed bacteria to a new plant for 8 cycles in total. At the end of each growth cycle bacterial colonies were picked and characterized for a wide range of traits. The results in chapter 2 reveal that plants can domesticate root-associated bacteria. Initially the bacteria had a detrimental effect on plant performance, but within a few generations, mutualists that promote plant growth accumulated in the bacterial population. In chapter 3 changes in the evolving bacterial populations were tracked by sequencing the genomes of bacterial colonies that were randomly picked at the end of different plant growth cycles. Mutations that accumulated in parallel in the independently evolving populations targeted global regulators and bacterial cell surface structures. This suggests that there are different strategies of bacterial adaptation to the plant root environment. Networks of co-varying bacterial traits were the focus of the last experimental chapter. Rather than traits evolving individually, trait co-variation has been linked to the ability to rapidly evolve to adapt to new conditions. In chapter 4 it is shown that whereas the network of traits linked to growth, stress resistance and biotic interactions was modular in the ancestral bacterial population, it rapidly restructured during adaptation to the rhizosphere. The most important knowledge we obtained from this work is that plants have the ability to breed their associated microbiome. This may explain the prevalence of beneficial plant-microbe interactions in nature. This study sets the stage for evolutionary microbiome management by steering the evolution of mutualism out of the existing species pool instead of changing species composition.