Microbial activity in the rhizosphere predicts success of root colonization by microbes

Delivering microbes to soil that predictably colonize the rhizosphere and root tissue to enhance nutrient delivery and suppress pests is needed to reduce our dependency on fossil fuel-produced inorganic amendment. However, microbial inoculants are largely ineffective since microbes applied to the soil often cannot colonize the vicinity and tissue of the plant roots. We hypothesized that microbial activity along the soil-root continuum will predict the root colonization success. We used BONCAT-FACS-seq (Bioorthogonal Non-Canonical Amino Acid Tagging) to probe patterns of microbial activity and the structure of the active microbial communities in a spatially resolved manner along the soil-root continuum. We used BONCAT-FACS (Flow Cytometer Activated Cell Sorting) and 16S rRNA amplicon sequencing to compare the active and viable microbial communities across the rhizosphere and endosphere compartments. We found that these two fractions are distinct, and strong ecological filtering in the soil-root continuum applies to both the viable cells and its active subset fraction. Finally, we revealed that microbial activity in the rhizosphere was the most effective predictor of successful microbial plant tissue colonization. This last finding suggests that microbial inoculants' success in colonizing plant roots is linked to their ability to maintain a high level of activity once deployed in the soil.