Mushroom-based composting can cut farm waste, pathogens and antibiotic resistance genes

Traditional composting often fails due to low lignocellulose degradation efficiency and the persistence of pathogens and antibiotic resistance genes (ARGs). Additionally, the use of antibiotics, like oxytetracycline in livestock, increases the transmission of these ARGs and pathogens in soil-plant systems, threatening agricultural safety and the environment.

To tackle this issue, a research team from the Kunming Institute of Botany of the Chinese Academy of Sciences (CAS) has employed microbial conversion technology to create a closed-loop system that links crop straw, livestock manure, and spent mushroom substrates, promoting the green and efficient use of organic matter to support crop growth.

Taking advantage of Yunnan's abundant agronomic organic matter and fungal resources, the team selected the rare edible mushroom Stropharia rugosoannulata as the core conversion medium to construct a Livestock-Crop-Mushroom (LCM) cross-domain circular system.

Employing multi-omics techniques (metagenomics and endophytic microbial sequencing) alongside functional gene analysis, this study is the first to elucidate the profound influence of LCM biofertilizers on crop-associated microbial communities across spatial compartments (rhizosphere–stem–seed). These insights provide an efficient strategy for sustainable agronomic organic waste utilization and a new approach to mitigating agricultural microbiological risks.

Image source: Liu et al. (2025), Environmental Science & Technology.