Reductions in abundances of intracellular and extracellular antibiotic resistance genes by SiO2 nanoparticles during composting driven by mobile genetic elements

Applying exogenous additives during the aerobic composting of livestock manure is effective for slowing down the spread of antibiotic resistance genes (ARGs) in the environment. Nanomaterials have received much attention because only low amounts need to be added and they have a high capacity for adsorbing pollutants. Intracellular ARGs (i-ARGs) and extracellular ARGs (e-ARGs) comprise the resistome in livestock manure but the effects of nanomaterials on the fates of these different fractions during composting are still unclear. Thus, we investigated the effects of adding SiO2 nanoparticles (SiO2NPs) at four levels (0 (CK), 0.5 (L), 1 (M), and 2 g/kg (H)) on i-ARGs, e-ARGs, and the bacterial community during composting. The results showed that i-ARGs represented the main fraction of ARGs during aerobic composting of swine manure, and their abundance was lowest under M. Compared with CK, M increased the removal rates of i-ARGs and e-ARGs by 17.9% and 100%, respectively. SiO2NPs enhanced the competition between ARGs hosts and non-hosts. M optimized the bacterial community by reducing the abundances of co-hosts (Clostridium_sensu_srricto_1, Terrisporobacter, and Turicibacter) of i-ARGs and e-ARGs (by 96.0% and 99.3%, respectively) and killing 49.9% of antibiotic-resistant bacteria. Horizontal gene transfer dominated by mobile genetic elements (MGEs) played a key role in the changes in the abundances of ARGs. i-intI1 and e-Tn916/1545 were key MGEs related closely to ARGs, and the maximum decreases of 52.8% and 100%, respectively, occurred under M, which mainly explained the decreased abundances of i-ARGs and e-ARGs. Our findings provide new insights into the distribution and main drivers of i-ARGs and e-ARGs, as well as demonstrating the possibility of adding 1 g/kg SiO2NPs to reduce the propagation of ARGs.

在畜禽粪便好氧堆肥过程中投加外源添加剂，可有效延缓抗生素抗性基因（antibiotic resistance genes, ARGs）在环境中的传播。纳米材料（nanomaterials）因投加量低且污染物吸附能力强而受到广泛关注。畜禽粪便中的抗性组（resistome）由细胞内抗生素抗性基因（intracellular ARGs, i-ARGs）和细胞外抗生素抗性基因（extracellular ARGs, e-ARGs）共同构成，但目前纳米材料对堆肥过程中这两类抗性组分归趋的影响仍不明确。因此，本研究探究了投加四种梯度（0（对照组CK）、0.5（低剂量L）、1（中剂量M）和2 g/kg（高剂量H））的二氧化硅纳米颗粒（SiO₂ nanoparticles, SiO₂NPs）对堆肥过程中i-ARGs、e-ARGs以及细菌群落的影响。研究结果表明，在猪粪好氧堆肥过程中，i-ARGs是抗生素抗性基因的主要组分，其中中剂量M组的i-ARGs丰度最低。与对照组CK相比，M组的i-ARGs和e-ARGs去除率分别提升了17.9%和100%。二氧化硅纳米颗粒可强化ARGs宿主与非宿主之间的竞争。M组通过降低细胞内和细胞外ARGs的共同宿主（Clostridium_sensu_stricto_1、Terrisporobacter及Turicibacter）的丰度（分别降低96.0%和99.3%），并杀灭49.9%的耐药菌，优化了细菌群落结构。以可移动遗传元件（mobile genetic elements, MGEs）为主导的水平基因转移在ARGs丰度变化中发挥关键作用。细胞内intI1和细胞外Tn916/1545是与ARGs密切相关的关键可移动遗传元件，M组中二者的丰度分别最大降幅达52.8%和100%，这主要解释了i-ARGs和e-ARGs丰度的降低。本研究为细胞内和细胞外ARGs的分布特征及主要驱动因子提供了新的认知，并证实了投加1 g/kg二氧化硅纳米颗粒以降低ARGs传播的可行性。