While traditional microbiological freshwater tests focus on the detection of specific bacterial indicator species, including pathogens, direct tracing of all aquatic DNA through metagenomics poses a profound alternative. Yet, in situ metagenomic water surveys face substantial challenges in cost and logistics. Here, we present a simple, fast, cost-effective and remotely accessible freshwater diagnostics workflow centred around the portable nanopore sequencing technology. Using defined compositions and spatiotemporal microbiota from surface water of an example river in Cambridge (UK), we provide optimised experimental and bioinformatics guidelines, including a benchmark with twelve taxonomic classification tools for nanopore sequences. We find that nanopore metagenomics can depict the hydrological core microbiome and fine temporal gradients in line with complementary physicochemical measurements. In a public health context, these data feature relevant sewage signals and pathogen maps at species level resolution. We anticipate that this framework will gather momentum for new environmental monitoring initiatives using portable devices.

中文翻译：

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通过纳米孔测序监测淡水


虽然传统的微生物淡水测试侧重于检测特定的细菌指示物种（包括病原体），但通过宏基因组学直接追踪所有水生 DNA 提供了一种意义深远的替代方案。然而，原位宏基因组水调查在成本和物流方面面临着巨大的挑战。在这里，我们提出了一种简单、快速、经济高效且可远程访问的淡水诊断工作流程，以便携式纳米孔测序技术为中心。使用来自剑桥（英国）示例河流地表水的确定成分和时空微生物群，我们提供了优化的实验和生物信息学指南，包括具有十二种纳米孔序列分类工具的基准。我们发现纳米孔宏基因组学可以描述水文核心微生物组和符合互补物理化学测量的精细时间梯度。在公共卫生背景下，这些数据具有物种级别分辨率的相关污水信号和病原体图谱。我们预计该框架将为使用便携式设备的新环境监测举措提供动力。