Exometabolomic profiling of bacterial strains cultivated using Arabidopsis root extract as the sole carbon source

The ability of microorganisms to use root-derived metabolites as growth substrates is a key trait for success in the rhizospheric niche. However, few studies describe which specific metabolites are consumed, or to what degree microbial strains differ in their substrate consumption patterns. Here we present an LC-MS exometabolomic study of three bacterial strains cultivated using either glucose or Arabidopsis thaliana root extract as the sole carbon source in the growth medium. Two of the strains were previously isolated from field-grown Arabidopsis roots, the other is Escherichia coli included as a comparison. When cultivated on root-extract, a set of 62 MS-features were commonly taken up by all three strains, with m/z values matching to components of central metabolism (including amino acids and purine/pyrimidine derivatives). Escherichia coli took up very few MS-features outside of this commonly consumed set, whereas the root-inhabiting strains took up a much larger number of MS-features, many with m/z values matching to plant-specific metabolites. This approach provides new mechanistic insights into microbial community composition in the rhizosphere, by defining the metabolic niche of a given strain. Furthermore, we document a large number of MS-features released by these strains, which could play roles in cross-feeding, antibiosis or signalling.