Increasing the humus content of organic fertilizers and eliminating biological risks such as antibiotic resistance genes (ARGs) are the key challenges faced by the waste treatment in modern agriculture.

A research team led by Prof. LI Dejun from the Institute of Subtropical Agriculture of the Chinese Academy of Sciences used synthetic microbial communities (SynComs) to drive the efficient humification of organic waste and block the transmission of biological hazards. The findings were published in Journal of Environmental Management and Bioresource Technology.

SynCom consists of five bacterial and fungal strains, including Bacillus cereus, Achromobacter sp., Pseudomonas sp., Cladosporium sp., and Trichoderma harzianum. Researchers demonstrated that its inoculation effectively accelerated the co-composting process of cattle manure and mulberry branches while ensuring product safety.

SynCom inoculation significantly increased the pile temperature and shortened the maturation period. The overall degradation rates of lignin, cellulose, and hemicellulose were increased by 19.3%, 7.9%, and 12.0%, respectively, and the humus content was increased by 34.4%. Multi-omics analysis revealed that SynCom reshaped the indigenous microbial networks, enriched key functional genera, and significantly increased the abundance of key carbohydrate-active enzymes.

Besides, researchers found that key humification precursors such as protocatechuic acid and sinapic acid were significantly enriched, providing abundant substrate support for subsequent humus polycondensation reactions.

To enhance biosafety, SynCom drove a metabolic restructuring of the composting microbial community, prompting a shift from a biofilm-dependent defense mode to an active motility metabolic mode. This shift physically restricted opportunities for horizontal gene transfer.

Moreover, the rapid decrease in the carbon-to-nitrogen ratio and the enhanced humification driven by SynCom effectively alleviated the co-selection pressure on metal resistance genes. The structural collapse of high-risk interaction networks effectively severed the connections between ARGs and mobile genetic elements, and synchronously eliminated high-risk pathogens such as Pseudomonas aeruginosa.

The findings of the two studies reveal the multi-level mechanisms of SynCom in improving the resource utilization efficiency of biowaste and ensuring the biosafety of organic fertilizers, providing a foundation and technical support for the application of microbiome engineering in sustainable agriculture.

Mechanisms of synthetic microbial community inoculation in enhancing biosafety (Image by CHEN Shuangshuang)