Secrets to sustainable beneficial plant-bacteria associations

Climate change threatens food security, not only by exposing crops to extreme weather, but also by changing patterns of plant disease. The impact of these immense problems can be reduced by using microbes. Certain microbes can improve crop plants’ stress tolerances, protect against pathogens, and promote growth. Because microbes can be quickly grown and applied to plants when needed, they are a quicker intervention than plant breeding. However, how and why beneficial microbes succeed in agricultural field settings, where they face intense competition from other microbes and environmental stresses such as low nutrients, UV light, heat, and drought, is largely unknown. As a result, turning lab findings about microbes into reliable products for use in agriculture often fails.

My research program aims to reveal the genetic and molecular basis of the interactions between plants, microbes, and the environment. This will help to understand the conditions needed to create a beneficial effect of microbial inoculants when applied to plants. One focus in my group deals with plant interactions with bacteria from the genus Sphingomonas. Bacteria from this genus are non-pathogenic, often beneficial, and have an undeniable success in field settings. They often amount to a quarter or more of the leaf-associated bacteria associated with the model plant Arabidopsis thaliana and multiple major crops including maize and poplar, and furthermore widely colonize roots and seeds. Thus, they can reveal robust, stress-tested mechanisms for non-pathogenic colonization and plant growth promotion. We compare bacterial genomes, conduct large genetic screens, and also pursue more specific hypotheses about the role of individual bacterial genes and complex molecules in plant colonization. We also study the phenomenon of biocontrol, in which beneficial bacteria prevent the growth of harmful pathogens, and in particular investigate how bacteria such as Sphingomonas may be effective in protecting Norway spruce trees against fungal root rot.  

Besides a study of bacteria, we investigate the environmental sensitivity of the plant immune response itself. The plant immune system can be regulated very differently in the field vs. in the lab, which can influence how well microbes colonize in each environment. A particular focus of my group is an Arabidopsis thaliana gene called ACCELERATED CELL DEATH 6 (ACD6) that encodes a protein that on the one hand confers resistance to diverse pathogens, but on the other hand can severely reduce growth and seed yield in the absence of pathogens. The strength of ACD6 effects differs among natural versions of the gene, but also greatly depends on the environment. We hypothesize that a gene related to ACD6 in the oilseed crop Brassica napus (canola) may have a large influence on seed yield. 

Our goal in all of our research is to uncover general, widely applicable principles, bridging the gap between fundamental academic research and the applied profit-driven work done in companies, to improve adoption and efficacy of agricultural inoculants and contribute to sustainable agriculture.