This study investigates the relationship between bacterial phylogeny and antibiotic resistance (ARG) structures in soil across different habitats. The authors performed functional metagenomic selections for resistance to 18 antibiotics from 18 agricultural and grassland soils, identifying 2895 novel ARGs representing all major resistance mechanisms. They found that distinct soil types harbor distinct resistomes, with nitrogen fertilizer amendments significantly influencing soil ARG content. The resistome composition correlated with microbial phylogenetic and taxonomic structure, both across and within soil types. Mobility elements associated with ARGs were rare in soil compared to sequenced pathogens, suggesting that ARGs in soil may not transfer between bacteria as readily as in clinical settings. The results indicate that bacterial community composition is the primary determinant of soil ARG content, challenging the hypothesis that horizontal gene transfer effectively decouples resistomes from phylogeny. The study also highlights the high diversity of ARGs in soil, which may respond to anthropogenic modulations such as increased antibiotic exposure.This study investigates the relationship between bacterial phylogeny and antibiotic resistance (ARG) structures in soil across different habitats. The authors performed functional metagenomic selections for resistance to 18 antibiotics from 18 agricultural and grassland soils, identifying 2895 novel ARGs representing all major resistance mechanisms. They found that distinct soil types harbor distinct resistomes, with nitrogen fertilizer amendments significantly influencing soil ARG content. The resistome composition correlated with microbial phylogenetic and taxonomic structure, both across and within soil types. Mobility elements associated with ARGs were rare in soil compared to sequenced pathogens, suggesting that ARGs in soil may not transfer between bacteria as readily as in clinical settings. The results indicate that bacterial community composition is the primary determinant of soil ARG content, challenging the hypothesis that horizontal gene transfer effectively decouples resistomes from phylogeny. The study also highlights the high diversity of ARGs in soil, which may respond to anthropogenic modulations such as increased antibiotic exposure.