Abstract:
With accelerating global environmental changes, plants will more often face hostile environments with increased climate fluctuations, increased biotic pressures from pathogens and herbivores, and accelerated biodiversity decline. As the plant microbiome plays an essential role in plant robustness and environmental tolerance, we must study plant-microbiome interactions in the context of changing environmental conditions, to accurately address the challenges that plants will face in the future. This requires multi-factorial ecological experiments that combine the manipulation of plants, microbes, and their environments, and to test the interactions between these components.
In this thesis, I conducted a series of ecological plant-microbiome experiments. Chapter 2 explains how the genotype-environment interaction (G x E) framework known from experimental ecology can be usefully applied to microbiome research and outlines the two perspectives taken throughout this thesis. These two outlooks are determined by which dependent variable is focused on, i.e. whether plant performance is measured after the manipulation of microbiome and environmental factors, or whether the microbiome is studied after the manipulation of plant and environmental factors. In Chapter 3 I take a plant perspective approach, and in Chapters 4 and 5 a microbiome perspective.
In the third chapter, I used a bacterial isolate collection from Arabidopsis thaliana leaves to create leaf microbiomes of different diversity levels, and test for their effects on plant performance. In a full factorial design, I varied the number of phylogenetic groups (1 or 3), and the total number of strains in the bacterial community (3 or 9), and I tested how this influenced plant growth and Pseudomonas viridiflava pathogen resistance. Using the sequence information of bacterial isolates, I also calculated the phylogenetic and functional diversities of all the bacterial communities used in the experiment. I found that plants inoculated with more diverse microbiomes had higher growth and increased pathogen resistance, and that functional diversity was overall the best predictor of plant performance.
In the fourth chapter, I investigated how temperature fluctuations affected leaf microbiome diversity and composition. I exposed Arabidopsis plants to a series of heat stress and recovery phases, with different frequencies of fluctuations, but with the same total temperature sum for each plant at the end of the experiment. I found that bacterial diversity was significantly lowered after temperature fluctuations, especially in the group of plants exposed to rapid, one day fluctuations, as compared to those exposed to slower fluctuations in temperature. In addition, the composition of the bacterial communities differed significantly depending on the fluctuation frequency, with the group facing rapid fluctuations more significantly affected.
In the fifth chapter, I used reads from whole genome sequencing as metagenomics reads, owing to the methodological overlap. After a common garden experiment with Thlaspi arvense, a relative of A. thaliana, I treated sequencing reads that were not aligned to the genome as microbiome-associated reads. I was then able to extract reads associated with plant herbivores (aphids and aphid-associated bacteria) and pathogens (powdery mildew) present at the time of the experiment. I used this opportunity to conduct an indirect common garden experiment wherein the microbiome reads were used as a proxy for pathogen and herbivore load, and found genomic and epi-genomic mechanisms behind plant pathogen and herbivore resistance.
My thesis demonstrates the power of ecological experiments in studying plant-microbiome interactions within the context of environmental and biodiversity changes. I found that plant microbiome diversity is important to plant performance, and that temperature fluctuations can significantly decrease microbiome bacterial diversity and change community composition. These results demonstrate the importance of incorporating plant-associated microbiomes in genotype-environment interaction research. Future experiments should focus on testing the effects of realistic climate change scenarios on plants and their associated microbiomes, and how these effects may cascade between the intertwined systems of plants and bacterial communities.
microbiome