Project description:For shade-intolerant species, shade light indicates the close proximity of neighboring plants and triggers the shade avoidance syndrome (SAS), which causes exaggerated growth and reduced crop yield. We report that microbiotal root commensals(Pseudomonas fluorescens and Root918) alleviate the shade avoidance responses in Arabidopsis. To identify the functions of Pseudomonas fluorescens and Root918 during SAS, we performed RNA-seq to search for differentially expressed genes (DEGs) in different tissues by comparing the transcript levels of shoot and root parts of col0 in germ-free, Pseudomonas fluorescens and Root918 during white light and shade conditions.
Project description:We acquired the largest bacterial proteomic resource, covering 303 species, 119 genera, and five phyla. The proteome coverage is, on average, over 50%. Additionally, we acquired further datasets for bacterial identification algorithm validation: i) 303 species at a 30-minute gradient (38 samples per day throughput), ii) 303 species at a 10-minute gradient (80 samples per day throughput), iii) reproducibility dataset, iv) genus-specific Pseudomonas spp. dataset (94 Pseudomonas spp. strains), v) genus-specific Bacillus spp. dataset (28 Bacillus cereus s.l. strains), vi) food routine dataset (60 dairy product isolates), and vii) clinical routine dataset (570 clinical isolates).
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