Seasonal dynamics and pesticide impact on gut microbiome in Amynthas gracilis earthworms: A comparative study across agricultural landscapes assessed by 16S rRNA amplicon-based sequencing

The use of pesticides in agriculture can affect the biodiversity of soil ecosystems and interfere with the ecological services they provide. The gut microbiome of earthworms serves as a bioindicator for changes in diversity within one of the most representative groups of soil macrofauna. In this study, we defined a gradient of soil and pesticide use regimes within a horticultural area, including conventional management, good agricultural practices, organic production and forest. Earthworms (A. gracilis) from these four conditions were sampled, and their microbiomes were assessed by sequencing the V4 region from the 16S rRNA gene. Comparison of ASVs indicated the presence of 142 bacterial genera among all the samples, with Actinobacteriota, Proteobacteria, Firmicutes and Bacteroidota being dominant phyla. Simpson's diversity index revealed diminished biodiversity in the gut microbiomes of earthworms from conventionally managed soil, correlating negatively with the presence of the insecticide chlorpyrifos. Furthermore, a seasonal shift in the dominance of bacterial taxa was observed between dry and rainy seasons. These shifts were evident in the gut microbiome of organisms from organically managed and good practices soils but not in the conventional site. Our results demonstrate that earthworm's gut microbiome serves as a responsive bioindicator for biodiversity changes in agricultural landscapes, suggesting that key features of the microbial community can be altered by pesticide exposure.