Characterization of transcriptional and metabolic responses to a complex plant growth-promoting soil inoculum

Soil microbes can have large impacts on plant growth and physiology. However, how these impacts manifest at the transcriptional and metabolite level is not well understood, especially responses to complex mixtures of soil microbes. Here we characterize the transcriptional and metabolomic response of Brassica rapa to a complex, naturally occurring soil inoculum that promotes shoot growth. Brassica rapa plants were treated with mock or growth-promoting soil inocula and monitored for growth. Root and shoot tissues were harvested for RNA-seq and metabolite analysis. Gene co-expression analysis and penalized regression were used to test for gene co-expression modules and metabolites that influence growth. We identify gene co-expression modules that both respond to microbial treatment and are associated with leaf growth. Gene ontology and custom category analysis of these modules revealed root modules that are enriched for mineral nutrition (especially nitrogen, phosphorus, and sulfur) and leaf modules enriched for photosynthetic and cellular processes. The metabolite data show an association of leaf length with nucleotide and amino acid levels, consistent with gene ontology terms observed in the leaf and perhaps reflecting the overall impact of growth-promoting microbes on key nitrogen-associated metabolic processes. Overall, this work provides an in-depth characterization of the molecular responses of plants to plant growth-promoting microbes.