Soil microbiome responses to changing environmental conditions are manifested as shifts in community structure and/or by modification of activity. However, molecular-level details underlying functional responses of soil microbiomes to perturbation are largely unknown. Here, we applied a multi-omics approach to assess the impact of nutrient addition and moisture perturbations on the soil microbiome across taxonomic and functional levels. Kansas native prairie soil samples from three field locations were either treated with glycine as a model root exudate, or perturbed by changing moisture conditions. The microbiome response was assessed using a suite of omics measurements: 16S rRNA amplicon sequencing, metagenomics, metatransciptomics, and metabolomics. A community response to glycine was detected at the functional level, but not at the community structure level. In contrast, soil drying resulted in shifts in both the microbiome composition and function. Here by using a multi-omics approach, we elucidate for the first time the functional response of the soil microbiome to nutrient and moisture perturbations across different levels of expression. This approach illustrated key physiological traits expressed by the soil microbiome in response to resource availability. Please note that the Moleculo data has already been published (<http://dx.doi.org/10.1128/mSystems.00045-16>) and is [available on SRA](https://www.ncbi.nlm.nih.gov/sra/?term=Moleculo+long-read+sequencing+facilitates+assembly+and+genomic+binning+from+complex+soil+metagenomes). Authors: Roy Chowdhury, Taniya; Bottos, Eric M; White, Richard A; Bramer, Lisa M; Brown, Joseph M; Zucker, Jeremy D; Kim, Young-Mo; Brislawn, Colin J; Jumpponen, Ari; Rice, Charles W; Fansler, Sarah J; Metz, Thomas O; McCue, Lee Ann; Callister, Stephen J; Jansson, Janet K;