Biochar Rewires Root Exudates and the Rhizosphere Microbiome and Its Functionality

ABSTRACT Biochar amendment is beneficial to the soil-plant system; yet the underlying mechanism is not fully understood. Integrating microfluidics and multi-omics and using wheat as a model plant, we found biochar induces differential root exudates, especially complex molecules like secondary metabolites and signaling cues, and rewires the rhizosphere microbiome, evoking a plant-beneficial rhizosphere microbiome centered by diverse plant growth promoting rhizobacteria (PGPR) known to participate in nitrogen cycling, organic matter turnover, nutrient acquisition, phytohormone metabolism, and stress resistance. Network analysis and machine learning identified high co-occurrence between specific root exudates and PGPR. qPCR, 16S rRNA gene sequencing, and untargeted soil metabolomics suggested the restructured rhizosphere microbiome may have shifted nitrogen and methane metabolism leading to reduced potential of N2O and methane emissions, and may participate in the metabolism of signaling cues and redox reactions. This study provides new insights into biochar’s profound impact on the soil-plant system and highlights the potential of engineering the rhizosphere through reshaping root-microbe interactions. Competing Interest Statement The authors have declared no competing interest. Footnotes Title and text (Abstract, Results and Discussion) updated to improve data interpretation; figures updated to improve data presentation; Supplemental file (PDF) updated. DATA AVAILABILITY STATEMENT Raw reads are available at the NCBI Sequence Read Archive under the BioProject accession number PRJNA1394313. Supporting Information tables (Table S1-S13) are also available at https://doi.org/10.5281/zenodo.18930558.