A team of Chinese scientists has demonstrated that designed synthetic microbial communities (SynComs) can significantly enhance crop growth and suppress soil-borne diseases. The findings, published in Horticulture Research by researchers from the Institute of Subtropical Agriculture, Chinese Academy of Sciences, reveal a promising biocontrol strategy.

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

By integrating field sampling, microbiome sequencing, and functional assays, the team 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.” Burkholderiaceae and Pseudomonas were identified as key taxa maintaining this microbial balance.

Notably, about 50% of endophytic bacteria originated from the soil, compared to less than 10% of fungi—reflecting strong host selection on fungal members. From lily bulbs, the team isolated core antagonistic strains, 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.

“Our work reveals how monoculture influences the plant microbiome,” said corresponding author Professor Zhu Baoli, “and presents a novel strategy for constructing targeted SynComs to combat Fusarium wilt.” Rationally designed microbial communities not only suppress pathogens but also promote plant growth, offering a sustainable solution to replanting challenges and reducing pesticide overuse. These findings bridge microbial ecology and agricultural practice, with broad implications for green agriculture and soil health management.

Contacted: Baoli Zhu 

EMail: baoli.zhu@isa.ac.cn

Changes in the endophytic microbial community of lily caused by continuous cropping （Imaged by Qin Honglin)

Effectiveness and mechanisms of lily endophytic bacteria and fungi in antagonizing the pathogen Fusarium oxysporum.（Imaged by Qin Honglin)