Difference of microbiome and antibiotic resistome between earthworm gut and soil deciphered by a continental-scale survey

Abstract Background Earthworms are globally distributed and quite capable of redistributing compounds, as well as bacteria and antibiotic resistance genes (ARGs) throughout the soil profile. The spread of medically relevant ARGs in soils has become an emerging environmental and health issue globally. However, our understanding on earthworm gut microbiome and antibiotic resistome is still lacking, especially at the large scale, and little is known about the role of earthworm in the dispersal of ARGs. Methods We conducted a continental-scale survey, including samples (earthworm gut and soil) from 28 provinces across China, from both natural and agricultural ecosystems (arable land: 35 sites and forested land: 16 sites). The 16S rRNA amplicon sequencing and high throughput quantitative PCR were used to characterize the microbiome and antibiotic resistome, respectively. We further explored potential mechanisms behind changes in the abundance and diversity of ARGs in the earthworm gut. Then, the microcosm experiments and long-term field experiments with or without earthworms were employed to test the potential for earthworms to reduce the abundance of ARGs in soils. Results The diversity and structure of bacterial community were observably different between the earthworm gut and soil. Firmicutes (35.7%) and Proteobacteria (34.8%) were the dominant phyla in all earthworm gut samples. A significant correlation between bacterial community dissimilarity and spatial distance was identified in the earthworm gut. The earthworm gut consistently had a lower diversity and abundance of ARGs than in the surrounding soil. We further revealed that the change of ARGs in the earthworm gut was likely a consequence of the reduction in the abundance of mobile genetic elements and dominant bacterial phylotypes that are the likely hosts of ARGs. The microcosm study and long-term field experiments provided the experimental evidence that the presence of earthworms reduced the abundance and diversity of ARGs in soils. Conclusions Our findings highlight that earthworm gut and soil present the distinct microbiome and resistome at the continental scale, and earthworms may play an important role in the continental-scale mitigation of antibiotic resistance.