Engineered endophytic microbiomes boost crop health and suppress soil-borne diseases

Team of researchers from the Institute of Subtropical Agriculture of the Chinese Academy of Sciences has demonstrated that designed synthetic microbial communities (SynComs) can significantly boost crop growth and curb soil-borne diseases, revealing a promising biocontrol strategy.

Plant endophytes, which live symbiotically within plant tissues, play a critical role in host health, nutrient uptake, and disease resistance. Using these microbes offers a sustainable alternative to chemical pesticides. However, selecting effective strains from complex natural microbiomes and assembling them into stable, functional SynComs remains a major challenge.

By integrating field sampling, microbiome sequencing, and functional assays, the researchers analyzed the endophytic microbiota of edible lilies under long-term monoculture. They found that continuous cropping enriched both the soil-borne pathogen Fusarium oxysporum and beneficial bacteria such as Pseudomonas and Bacillus, forming a network in an "antagonistic equilibrium."

The researchers isolated core antagonistic strains from lily bulbs, including Rhizobium, Methylobacterium, and the fungus Talaromyces, and constructed several SynComs. In tests, multi-strain consortia outperformed single isolates in both promoting plant growth and suppressing pathogens. Importantly, SynComs containing fungi were more effective than those composed solely of bacteria.

Image source: Qin Honglin.