Département des Sciences Biologiques, Université de Montréal, Montreal, Canada.
Groupe de Recherche Interuniversitaire en Limnologie et Environnement Aquatique (GRIL), Montreal, Canada.
mSystems. 2022 Apr 26;7(2):e0148221. doi: 10.1128/msystems.01482-21. Epub 2022 Mar 10.
Agrochemicals often contaminate freshwater bodies, affecting microbial communities that underlie aquatic food webs. For example, the herbicide glyphosate has the potential to indirectly select for antibiotic-resistant bacteria. Such cross-selection could occur if the same genes (encoding efflux pumps, for example) confer resistance to both glyphosate and antibiotics. To test for cross-resistance in natural aquatic bacterial communities, we added a glyphosate-based herbicide (GBH) to 1,000-liter 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 in their genomes (17% of variation explained) and, to a lesser extent, by resistance mutations in EPSPS. Together, these results indicate that GBHs can cross-select for antibiotic resistance in natural freshwater bacteria. Glyphosate-based herbicides (GBHs) such as Roundup formulations may have the unintended consequence of selecting for antibiotic resistance genes (ARGs), as demonstrated in previous experiments. However, the effects of GBHs on ARGs remain 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 performed a freshwater mesocosm experiment showing that a GBH strongly selects for ARGs, particularly multidrug efflux pumps. These selective effects were evident after just a few days, and 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. Intensive GBH application may therefore have the unintended consequence of selecting for ARGs in natural freshwater communities.
农药经常污染淡水体，影响水生食物网底层的微生物群落。例如，除草剂草甘膦有可能间接地选择抗生素耐药细菌。如果相同的基因（例如，外排泵基因）同时赋予对草甘膦和抗生素的抗性，则可能发生这种交叉选择。为了在自然水生细菌群落中测试交叉抗性，我们将一种基于草甘膦的除草剂（GBH）添加到装满来自原始湖泊水的 1000 升中观水族箱中。在 57 天的时间里，我们通过 shotgun 宏基因组测序追踪了细菌群落的变化，并对宏基因组组装基因组（MAG）进行了注释，以确定已知抗生素抗性基因（ARGs）、质粒和草甘膦靶酶（烯醇丙酮酸-莽草酸-3-磷酸合酶；EPSPS）的抗性突变。我们发现，高剂量的 GBH 显著增加了 ARG 频率，并特别选择了多药外排泵。GBH 高剂量后 MAG 的相对丰度可以根据其基因组中的 ARG 数量（解释了 17%的变异性），以及 EPSPS 中的抗性突变来预测（解释了较小的变异性）。这些结果表明，GBH 可以在自然淡水中的细菌中交叉选择抗生素抗性。 如 Roundup 制剂等基于草甘膦的除草剂（GBH）可能会产生选择抗生素抗性基因（ARGs）的意外后果，如先前的实验所示。然而，GBH 对自然水生群落中 ARGs 的影响尚不清楚，这些群落经常受到农业径流中农药的污染。此外，与草甘膦靶酶 EPSPS 的经典突变相比，ARGs 提供的抗性尚不清楚。在这里，我们进行了一项淡水中观实验，表明 GBH 强烈选择 ARGs，特别是多药外排泵。这些选择性效应在短短几天内就显现出来，并且细菌在 GBH 胁迫后存活和茁壮成长的能力可以通过其基因组中的 ARG 数量来预测，在较小程度上可以通过 EPSPS 中的突变来预测。因此，密集的 GBH 应用可能会在自然淡水群落中选择 ARGs 产生意想不到的后果。
