Bacterial phylogeny structures soil resistomes across habitats

Area of Science:

• Environmental microbiology
• Genomics
• Antibiotic resistance

Background:

• Diverse antibiotic resistance genes (ARGs) exist in soil, overlapping with those in human pathogens.
• Factors influencing soil ARG composition and mobility between habitats are largely unknown.
• ARGs are hypothesized to be mobile, potentially decoupling resistomes from phylogeny.

Purpose of the Study:

• To investigate the relationship between bacterial community structure and ARG composition in soil.
• To determine factors influencing ARG content in agricultural and grassland soils.
• To assess the mobility of ARGs in soil environments.

Main Methods:

• Functional metagenomic selections for resistance to 18 antibiotics across 18 soil samples.
• Analysis of ARG content and correlation with microbial phylogeny and taxonomy.
• Investigation of mobility elements associated with ARGs.

Main Results:

• Discovered 2,895 mostly novel ARGs representing major resistance mechanisms.
• Distinct soil types harbor distinct resistomes; nitrogen fertilizer significantly influenced ARG content.
• Resistome composition strongly correlated with microbial phylogenetic and taxonomic structure.
• Mobility elements syntenic with ARGs were rare in soil compared to pathogens.

Conclusions:

• Bacterial community composition is the primary determinant of soil ARG content.
• Horizontal gene transfer may not decouple soil resistomes from phylogeny as readily as previously hypothesized.
• Soil resistomes are more influenced by microbial ecology than by widespread mobile gene transfer.