Reduced availability of agricultural water has spurred increased interest in using recycled irrigation water for U.S. food crop production. However, there are significant knowledge gaps concerning the microbiological quality of these water sources. To address these gaps, we used 16S rRNA gene and metagenomic sequencing to characterize taxonomic and functional variations (e.g., antimicrobial resistance) in bacterial communities across diverse recycled and surface water irrigation sources. We collected 1 L water samples (n = 410) between 2016 and 2018 from the Mid-Atlantic (12 sites) and Southwest (10 sites) U.S. Samples were filtered, and DNA was extracted. The V3–V4 regions of the 16S rRNA gene were then PCR amplified and sequenced. Metagenomic sequencing was also performed to characterize antibiotic, metal, and biocide resistance genes. Bacterial alpha and beta diversities were significantly different (p < 0.001) across water types and seasons. Pathogenic bacteria, such as Salmonella enterica, Staphylococcus aureus, and Aeromonas hydrophilia were observed across sample types. The most common antibiotic resistance genes identified coded against macrolides/lincosamides/streptogramins, aminoglycosides, rifampin and elfamycins, and their read counts fluctuated across seasons. We also observed multi-metal and multi-biocide resistance across all water types. To our knowledge, this is the most comprehensive longitudinal study to date of U.S. recycled water and surface water used for irrigation. Our findings improve understanding of the potential differences in the risk of exposure to bacterial pathogens and antibiotic resistance genes originating from diverse irrigation water sources across seasons and U.S. regions.

中文翻译：

---

大西洋中部和美国西南部不同循环水和地表水灌溉水源中细菌群落和抗生素耐药性基因的变化：为期两年的 CONSERVE 实地研究

农业用水量的减少激发了人们对在美国粮食作物生产中使用循环灌溉水的兴趣增加。然而，关于这些水源的微生物质量存在显着的知识缺口。为了解决这些差距，我们使用 16S rRNA 基因和宏基因组测序来表征不同循环水和地表水灌溉源中细菌群落的分类学和功能变异（例如，抗菌素耐药性）。我们收集了 1 L 水样 ( n= 410) 2016 年至 2018 年间来自美国中大西洋（12 个站点）和西南部（10 个站点）的样本被过滤，并提取了 DNA。然后对 16S rRNA 基因的 V3-V4 区域进行 PCR 扩增和测序。还进行了宏基因组测序以表征抗生素、金属和杀菌剂抗性基因。不同水类型和季节的细菌 alpha 和 beta 多样性显着不同 ( p < 0.001)。致病菌，如肠沙门氏菌、金黄色葡萄球菌和嗜水气单胞菌在样本类型中被观察到。鉴定出的最常见的抗生素抗性基因针对大环内酯类/林可酰胺类/链阳菌素、氨基糖苷类、利福平和 elfamycins 进行编码，它们的读取计数随季节波动。我们还观察了所有水类型的多金属和多杀菌剂抗性。据我们所知，这是迄今为止对美国用于灌溉的再生水和地表水进行的最全面的纵向研究。我们的研究结果提高了对细菌病原体和抗生素抗性基因暴露风险的潜在差异的理解，这些风险来自不同季节和美国地区的不同灌溉水源。