Study on the Community Characteristics of the Endogenous Microbiome in Earthworm Cocoons in Composting Systems with Different Base Materials

This study investigates earthworm cocoons as key vectors for the vertical transmission of symbiotic bacteria, a process that profoundly shapes the gut microbiota of offspring and influences their environmental adaptability. However, systematic knowledge of the internal microbiome communities within earthworm cocoons remains limited. Here, we characterized the composition and functional potential of bacterial communities within cocoons of earthworms collected from three composting systems (fermented coffee grounds, cow manure, and residual sludge) using high-throughput sequencing, together with diversity analyses, dominant taxa identification, and FAPROTAX-based functional prediction. Our results indicated that the composting system significantly affects bacterial diversity and community structure. The fermented coffee grounds system supported the highest species richness, whereas the cow manure system exhibited the greatest diversity and evenness. At the phylum level, Pseudomonadota, Actinomycetota, and Bacteroidota predominated across all systems, with Pseudomonadota being particularly abundant (62.01–81.41%). At the genus level, Verminephrobacter and Agromyces were consistently dominant, with Verminephrobacter showing particularly high relative abundance, ranging from 22.42% to 51.51%. Although the composition and abundance of dominant phyla and genera varied among systems, the shared OTUs accounted for a substantial proportion of the relative abundance in each sample (54.65–91.84%). Functional predictions revealed chemoorganoheterotrophy as the predominant metabolic function, with relative abundances ranging from 23.87% to 45.42%. Collectively, these findings provide insights into how composting environments shape the bacterial communities within earthworm cocoons, offering a theoretical foundation for understanding the ecological functions of earthworms and their potential applications in ecological restoration and sustainable agriculture.