Herbicide-degrading synthetic microbiome

Soil microbiomes have essential functions in agroecosystems, regulating soil fertility, crop productivity and plant stress tolerance, thereby directly affecting human nutrition and the climate. Soil microbial communities can also be engineered, for example, through strain combinations or by optimizing natural microbiomes, to exert specific functions, such as pollutant degradation, and could thus be applied for environmental remediation. However, the design of such synthetic microbiomes is challenged by the complex metabolic interactions within microbiomes, which remain largely unknown, and the lack of tools for natural microbiome engineering.

The researchers developed a microbiome modelling pipeline, called SuperCC (super community combinations), combining top-down and bottom-up approaches to engineer natural microbiomes for the construction of herbicide-degrading microbiomes. “We started by selecting natural microbiomes, collected from three different soils, for their enhanced herbicide-biodegrading capability through herbicide application and/or herbicide-degrader inoculation,” says Gao. “Potential keystone species were then identified by exploring strain abundance shifts combined with strain isolation.”