Project description:The microbiota plays a crucial role in protecting plants from pests and pathogens. The protection provided by the microbiota constitutes not just the plant’s first line of defense, but possibly its most potent one, as experimental disruptions to the microbiota cause plants to succumb to otherwise asymptomatic infections. To understand how microbial plant defense is deployed, we applied a complex and tractable plant-soil-microbiome microcosm. This system, consisting of Arabidopsis plants and a 150-member bacterial synthetic community, provides a platform for the discovery of novel bacterial plant-beneficial traits, under a realistically complex microbial community context. To identify which components of the plant microbiota are critical for plant defense, we deconstructed this microcosm top-down, removing different microbial groups from the community to examine their protective effect on the plant when challenged with the leaf pathogen Pseudomonas syringae. This process of community deconstruction revealed a critical role for the genus Bacillus in protecting the plant from infection. Using plant RNA-seq and bacterial co-culturing experiments, we demonstrated that Bacillus-provided plant protection is independent of plant immune system activation. We also show that the level of plant protection is strongly dependent on the diversity of the protective inoculum. We show that deconstructing the microbiome top-down is a powerful tool for identifying and prioritizing microbial taxa with specific functions within it.
Project description:We report the application of a high-throughput technique, RNA-seq, to study the transcriptomic response of Bacillus subtilis growing in the presence of Tse1, a T6SS effector of Pseudomonas chlororaphis
Project description:Multi-species interactions are a major force in the evolution and dynamics of ecosystems. These interactions may occur either when species affect each other directly or when they interact indirectly via an intermediary species. Direct interactions between species are best understood, but indirect interactions may also often be strong enough to alter the evolutionary trajectories of the target species. Little is known about the genetic basis of direct interactions within an ecosystem and even less data is available for indirect interactions. This experiment uses a simple model ecosystem to build a view at the transcriptome level of how interactions between plants (Arabidopsis) and rhizosphere bacteria (Pseudomonas) are altered by biotic stressors (insect herbivores) and abiotic stressors (UV-B). Experiment Overall Design: Arabidopsis plants were established and then split into two cohorts at 15 days. One group were innoculated with Pseudomonas aeruginosa strain 7NR and the other not. 21 days later half of each of these groups were subjected to UV-B treatment for seven days. After this period each of the four groups of plants were further subdivided and infested with aphids, caterpillars or left alone. 24 hours after infestation the plants were harvested, individuals pooled and total RNA extracted giving 12 unique conditions. Five replicates were performed in series, yielding a total of 60 samples.
Project description:Microarray experiments to compare gene expression profiles of ate1 ate2 double-mutant plants and the wild type at different developmental stages and after the infiltration with Pseudomonas syringae strain Pst AvrRpm1.