Immune systems distinguish "self" from "nonself" to maintain homeostasis and must differentially gate access to allow colonization by potentially beneficial, nonpathogenic microbes. Plant roots grow within extremely diverse soil microbial communities but assemble a taxonomically limited root-associated microbiome. We grew isogenic Arabidopsis thaliana mutants with altered immune systems in a wild soil and also in recolonization experiments with a synthetic bacterial community. We established that biosynthesis of, and signaling dependent on, the foliar defense phytohormone salicylic acid is required to assemble a normal root microbiome. Salicylic acid modulates colonization of the root by specific bacterial families. Thus, plant immune signaling drives selection from the available microbial communities to sculpt the root microbiome.

Plants live in biogeochemically diverse soils that harbor extraordinarily diverse microbiota. Plant organs associate intimately with a subset of these microbes; this community’s structure can be altered by soil nutrient content. Plant-associated microbes can compete with the plant and with each other for nutrients; they can also provide traits that increase plant productivity. It is unknown how the plant immune system coordinates microbial recognition with nutritional cues during microbiome assembly. We establish that a genetic network controlling phosphate stress response influences root microbiome community structure, even under non-stress phosphate conditions. We define a molecular mechanism regulating coordination between nutrition and defense in the presence of a synthetic bacterial community. We demonstrate that the master transcriptional regulators of phosphate stress response in Arabidopsis also directly repress defense, consistent with plant prioritization of nutritional stress over defense. Our work will impact efforts to define and deploy useful microbes to enhance plant performance.

Because proteins are the major functional components of cells, knowledge of their cellular localization is crucial to gaining an understanding of the biology of multicellular organisms. We have generated a protein expression map of the Arabidopsis root providing the identity and cell type-specific localization of nearly 2,000 proteins. Grouping proteins into functional categories revealed unique cellular functions and identified cell type-specific biomarkers. Cellular colocalization provided support for numerous protein-protein interactions. With a binary comparison, we found that RNA and protein expression profiles are weakly correlated. We then performed peak integration at cell type-specific resolution and found an improved correlation with transcriptome data using continuous values. We performed GeLC-MS/MS (in-gel tryptic digestion followed by liquid chromatography-tandem mass spectrometry) proteomic experiments on mutants with ectopic and no root hairs, providing complementary proteomic data. Finally, among our root hair-specific proteins we identified two unique regulators of root hair development.plant proteome | cell-type expression | FACS | RNA-protein correlation | root hair mutant M ulticellular organisms use specialized cell types to perform activities that are integral to their function. Cellular tasks are usually achieved by proteins, which act in signaling cascades, provide structural support, and catalyze enzymatic reactions vital to growth and metabolism. Knowledge of protein cellular localization and abundance using proteomic approaches is thus crucial to our understanding of biological systems (1, 2). Proteome data can be visually represented in a map, which highlights the spatial relationships of proteins at the level of cell type, tissue, or organ. Proteome maps are useful representations of the complex "building plan" of a biological system and also serve as valuable tools for the discovery of new cellular functions (2, 3). Proteomic studies of single cell populations isolated from a variety of multicellular organisms have recently been achieved, including the oocytes of worms and mice (4-6); pollen grains (consisting of two sperm and one vegetative cell) and stomatal guard cells of plants (7,8); and sperm cells of mice and flies (9, 10). These cell types were relatively accessible because they either reside on the surface and can be purified in large quantities using biochemical fractionation (e.g., guard cells) or are large and can easily be collected (e.g., Caenorhabditis elegans oocytes). However, similar proteomic studies of internal cell populations have been more difficult and are usually only partially represented in proteomes of whole organs owing to signal dilution (e.g., refs. 11-16).The Arabidopsis thaliana root is an excellent model for investigating cellular functions internal to an organ because it is transparent, radially symmetric, and cell types can be isolated by FACS to allow molecular profiling (17). The goal of this study was to investigate cell-type function by genera...