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.
2025-01-01 | GSE285599 | GEO
Project description:Top-down and bottom-up regulation of bacterial community structure in freshwater microcosms
| PRJNA479735 | ENA
Project description:Bacterial diversity in aquaculture enrichment gradient Canada
| PRJNA666128 | ENA
Project description:Bacterial diversity in aquaculture enrichment gradient Scotland
| PRJNA666305 | ENA
Project description:Top-down processes drive taxonomic and phylogenetic diversity in a model aquatic microbial community
Project description:In the present work we developed a sample preparation approach for the combined bottom-up and top-down proteomics analysis of small open reading frame encoded proteins (SEP). Key improvements were made by the application of solid phase extraction (SPE) supported enrichment of LMW proteins, followed by two-dimensional LC-MS top-down analysis encompassing both HCD and EThcD ion activation. Bottom-up experiments were used to support and confirm top-down data interpretation. This strategy allowed for the top-down characterisation 36 proteoforms mapping to 12 SEP of the archaea Methanosarcina mazei, and for the first time the identification of posttranslational modifications in these microproteins.
2021-11-02 | PXD019792 | Pride
Project description:Bacterial diversity in aquaculture enrichment gradient New Zealand
Project description:To explore the bacterial community profile of the gut of the African palm weevil and to identify the abundance and diversity of lignin degradation-associated bacteria in each gut segment.