The Root-Associated Microbiome and Metabolome Spatially Vary Across the Root System of a Mature Maize Plant and Are Inconsistently Altered by Microbial Treatment

Many microbes provide benefits to their plant hosts. Over 100 microbial-based products are available to farmers, but their performance is highly variable. Little is known about the factors that influence the colonization and persistence of microbes across the entire root system architecture, despite the importance of these processes to the efficacy of microbial-based products. We investigated whether large mesocosms could be used to study the 3D spatial patterning of microbes and correlated metabolites across mature corn root systems. The experimental design consisted of 12 mesocosms structures (1 x 1 x 1.3 m), half of which were treated with a synthetic community (SYNCOM) of 18 different bacterial isolates. Although none of the 18 members of the SYNCOM was detected at the end of the experiment, treatment with the SYNCOM caused a long-term shift in the microbiome, specifically at the zones furthest from the original seed. Comparison of replicate samples within and between boxes revealed that most of the highly abundant bacteria were observed by sampling as few as three replicates. However, each box and replicate sample also contained at least a few unique bacteria. The root metabolome was much more consistent across space and unaffected by the SYNCOM treatment; however, several individual metabolites were identified that varied based on depth within the boxes. This work establishes the mesocosm system as a viable experimental platform for tracking microbe-metabolite correlations across a root system and confirms the hypothesis that significant variability exists in the root-associated microbiome across a full-grown root system.Copyright (c) 2025 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.