Results were published in the peer-reviewed journal mSystems, signaling rigorous scientific validation.

The article notes the FAO’s perspective on leveraging soil microbiomes for better agriculture and highlights potential practical applications in sustainable farming.

A Penn State study using a BONCAT-based approach finds that microbial activity, not sheer abundance, best predicts which soil microbes colonize plant roots and inhabit internal tissues, with implications for sustainable agriculture.

Active rhizosphere microbes are more likely to enter the plant, whereas abundant but dormant microbes are less likely to colonize, making activity a better predictor of colonization than abundance.

Publication details: The findings appear in mSystems on August 6, 2025, under the title The activity of soil microbial taxa in the rhizosphere predicts the success of root colonization.

Crimson clover (Trifolium incarnatum) was used to map microbial activity and root colonization along the gradient from soil to root interior, within a broader effort to understand plant-microbe interactions in real soils.

Researchers used BONCAT to label and identify only active microbes, coupling BONCAT with flow cytometry and marker-gene sequencing to analyze active sub-populations across soil, rhizosphere, and endosphere.

To identify active members, the team profiled the active subset of the microbial community rather than the dormant majority using BONCAT, flow cytometry, and gene sequencing.

Lead author Jennifer Harris notes that most soil microbes are dormant and must exit dormancy to contribute to plant-beneficial functions, while Estelle Couradeau highlights BONCAT’s novelty in tracing microbes from soil to root interior.

Overall, the study suggests that managing microbial activity could sustainably enhance nutrient uptake and disease resistance in crops.

This BONCAT method, validated with microscopy, is the first to track microbial activity along the soil-to-root interior gradient, as reported by Estelle Couradeau and colleagues.

Active microbes inside the plant, or endosphere, show roughly tenfold higher activity than those in surrounding soil or the rhizosphere.

The study leveraged Penn State core facilities (Flow Cytometry and Genomics) and was supported by USDA-NIFA fellowships and grants, plus Penn State Ecology Institute seed funding.