Abstract：
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.
摘要：
农业用水的减少促使人们对使用循环灌溉水进行美国粮食作物生产的兴趣增加。然而,关于这些水源的微生物质量有很大的知识差距。为了弥补这些差距,我们使用16SrRNA基因和宏基因组测序来表征分类学和功能变异(例如，抗菌素抗性）在不同的再生水和地表水灌溉源的细菌群落中。我们在2016年至2018年期间从中大西洋（12个地点）和西南（10个地点）美国收集了1升水样（n=410）。并提取了DNA。然后PCR扩增16SrRNA基因的V3-V4区并测序。还进行了宏基因组测序以表征抗生素，金属,和抗杀菌剂基因。不同类型和季节的细菌α和β多样性差异显著(p<0.001)。病原菌,比如肠道沙门氏菌,金黄色葡萄球菌,不同样本类型观察到嗜水气单胞菌。鉴定出的最常见的抗生素抗性基因编码针对大环内酯类/lincosamides/链脲类，氨基糖苷类,利福平和elfamycins,他们的阅读计数随季节波动。我们还观察到所有类型水的多金属和多杀生物剂抗性。据我们所知,这是迄今为止美国用于灌溉的再生水和地表水的最全面的纵向研究。我们的研究结果提高了对暴露于不同季节和美国地区不同灌溉水源的细菌病原体和抗生素抗性基因的潜在风险差异的理解。
