Updated project metadata.
Plant-associated microbial communities play a crucial role in plant health, yet the metabolism and physiology of bacteria in the rhizosphere remain poorly understood. In this study, we used seven bacterial species (Brucella pituitosa AA2, Chryseobacterium indologenes AA5, Curtobacterium pusillum AA3, Enterobacter ludwigii AA4, Herbaspirillum robiniae AA6, Pseudomonas putida AA7, Stenotrophomonas maltophilia AA1) previously isolated by Niu et al. (2018, PNAS 114(12)) to examine microbial gene expression in the maize root environment (Zea mays cv. Sugar Bun). We conducted differential metaproteomic analyses of these species grown in vitro in a minimal medium and individually in planta on sterile maize roots to identify differentially abundant proteins. We had 3 to 5 biological replicates for each species and condition. For the in vitro condition, we collected cells at mid-log phase and froze the resulting pellet at -80°C prior to protein extraction. For the in planta condition, bacterial species were inoculated individually on sterile maize seeds following the protocol described by Salvato et al. (MPMI, 35(11)) and plants were grown for two weeks. The primary roots were then harvested and vortexed with glass beads; the resulting pellet was frozen at -80°C prior to protein extraction. We identified 1,507-2,159 proteins from each bacterial species, with approximately 30-70% of these proteins significantly differentially abundant between the two conditions. Notably, we found that the differentially abundant functions differed between the seven microbial species, suggesting niche specialization within the rhizosphere. Among the proteins found in increased abundance in planta, many were involved in carbon metabolism, secretion systems, adhesion and motility, and transporters. We are including a table with the submission to help identify which files correspond to which species and condition (OverviewFile.txt).