System-Level Examination of Metabolism in Rhizosphere Grown Burkholderiales

It is well known that rhizosphere (in the vicinity of plant roots) microbes have a significant effect on plant health and growth rate. However, our knowledge of the system-level biochemical interactions between these microbes and their surroundings is incomplete. To gain a better understanding of these interactions, we have sequenced the soil metagenomes and constructed metagenome assembled genomes (MAGs) of active organisms growing in rhizosphere and bulk soil. We have developed a genome-scale model of metabolism for one of these MAGs (a member of the Burkhoderiales family, SM_S39) and used the model to explore time-resolved gene-expression data for samples collected within and outside of the influence of roots.

Our results show that SM_S39 greatly upregulates its import and metabolism of inorganic and complex nitrogen sources such as amino acid dimers, chitosamine when growing in the rhizosphere. In addition, this organism’s rhizosphere CAZyme transcripts were upregulated for enzymes potentially involved in the decomposition of cellulose, hemicellulose, cell membranes, lipids, polysaccharides, proteins, starches, and biopolymers.

We also identified pathways that were significantly upregulated when comparing the bulk soil to the rhizosphere soil environment. We found that pathways related to generation and consumption of fatty metabolites and those involved in biosynthesis and metabolism of amino acids (especially aromatic, branched-chain, as well as some common nitrogen carrying amino acids aspartate and arginine) were strongly upregulated. These results indicate that although it is intuitive to think that exchange of carbon between the root and the microbes is the primary driver of the metabolic interactions between the plant and the soil microbes like SM_S39, microbial nitrogen metabolism might be affected even more significantly by the presence of roots.