Earthworm gut’s potential positive impact on carbon cycle by influencing carbohydrate metabolism and microbial genome size

• Earthworm gut had higher proportion of glycosyl transfer genes than soil. • Earthworm gut had higher proportion of carbon fixation genes in arable systems. • Earthworm gut eukaryome had large genome size to harbor glycosyl transfer genes. • Earthworm gut affected carbon metabolism genes by eukaryotic genome size. The earthworm microbiome significantly impacts global soil ecosystems. This study explores how earthworm gut eukaryome (fungi and protists) and functional genes respond to land use and climatic factors. Over 150 earthworm–soil sample pairs were collected from arable and forest ecosystems across China. High-throughput and shotgun metagenomic sequencing revealed lower fungal, protistan, and CAZyme gene diversities in the earthworm gut than in the soil (0.77-fold, 0.19-fold, and 0.74-fold compared to the soil, respectively), but higher proportions of parasitic protists (3.78-fold compared to the soil) and carbohydrate metabolism genes involved in glycosyl transfer (1.41-fold compared to the soil). Arable systems showed higher abundances of functional genes associated with carbon fixation, nitrification, phosphorus dissolution, and sulfite reduction compared to forest systems. This study highlights the associations between earthworm gut microeukaryotes and functional genes especially glycosyl transferases involved in carbohydrate biosynthesis. Furthermore, larger microbial genomes were found in the earthworm gut compared to the soil, which may harbor more functional genes involved in cellular processes, carbohydrate binding, and glycosyl transfer. These findings suggest that earthworm gut microeukaryotes may have a positive impact on their average genome sizes and carbohydrate metabolism within the carbon cycle. This study contributes to advancing our understanding of the functionality of microeukaryotes in the earthworm gut, especially for the carbon cycle. In this study, we collected earthworm and soil samples from arable and forest ecosystems, and found that earthworm gut had higher proportion of carbon fixation genes in arable systems. Earthworm gut eukaryotes have potential associations with genes involved in carbohydrate metabolism via the regulation of their genome sizes. This study highlights the functionality of earthworm gut eukaryotes in different land use types, especially for the carbon cycle.