A glyphosate-based herbicide cross-selects for antibiotic resistance genes in bacterioplankton communities

Agrochemicals often contaminate freshwater bodies, affecting microbial communities that underlie aquatic food webs. For example, Roundup, a widely-used glyphosate-based herbicide (GBH), has the potential to indirectly select for antibiotic resistant bacteria. Such cross-selection could occur, for example, if the same genes (e.g. encoding efflux pumps) confer resistance to both glyphosate and antibiotics. To test for cross-resistance in natural aquatic bacterial communities, we added Roundup to 1,000-L mesocosms filled with water from a pristine lake. Over 57 days, we tracked changes in bacterial communities with shotgun metagenomic sequencing, and annotated metagenome-assembled genomes (MAGs) for the presence of known antibiotic resistance genes (ARGs), plasmids, and resistance mutations in the enzyme targeted by glyphosate (enolpyruvyl-shikimate-3-phosphate synthase; EPSPS). We found that high doses of GBH significantly increased ARG frequency and selected for multidrug efflux pumps in particular. The relative abundance of MAGs after a high dose of GBH was predictable based on the number of ARGs encoded in their genomes (17% of variation explained) and, to a lesser extent, by resistance mutations in EPSPS. Together, these results indicate that GBHs have the potential to cross-select for antibiotic resistance in natural freshwater bacteria. IMPORTANCEGlyphosate-based herbicides (GBHs) such as Roundup may have the unintended consequence of selecting for antibiotic resistance genes (ARGs), as demonstrated in previous experiments. However, the effects of GBHs on ARGs remains unknown in natural aquatic communities, which are often contaminated with pesticides from agricultural runoff. Moreover, the resistance provided by ARGs compared to canonical mutations in the glyphosate target enzyme, EPSPS, remains unclear. Here we used freshwater mesocosm experiments to show that GBHs strongly select for ARGs, particularly multidrug efflux pumps. These selective effects are evident after just a few days, and at glyphosate concentrations that are high but still within short-term (1-4 day) regulatory limits. The ability of bacteria to survive and thrive after GBH stress was predictable by the number of ARGs in their genomes, and to a lesser extent by mutations in EPSPS. GBHs are therefore likely to select for higher ARG frequencies in natural streams, lakes, and ponds.