Abstract
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.
Highlights
The global assurance of safe drinking water and basic sanitation has been recognised as a United Nations Millennium Development Goal (Bartram et al, 2005), in light of the pressures of rising urbanisation, agricultural intensification, and climate change (Haddeland et al, 2014; Schewe et al, 2014)
The data revealed that the levels of harmful bacteria were highest downstream of urban river sections, near a water treatment plant and river barge moorings. These findings demonstrate that optimising MinION protocols can turn this device into a useful tool to monitor water quality
Nanopore full-length (V1-V9) 16S ribosomal RNA gene sequencing was performed on all location-barcoded freshwater samples at each of the three time points (Figure 1; Supplementary file 1; Materials and methods)
Summary
The global assurance of safe drinking water and basic sanitation has been recognised as a United Nations Millennium Development Goal (Bartram et al, 2005), in light of the pressures of rising urbanisation, agricultural intensification, and climate change (Haddeland et al, 2014; Schewe et al, 2014). Waterborne diseases represent a particular global threat, with zoonotic diseases such as typhoid fever, cholera, or leptospirosis resulting in hundreds of thousands of deaths each year (Pruss et al, 2002; Pruss-Ustun et al, 2019). To control for risks of infection by waterborne diseases, microbial assessments can be conducted. While traditional microbial tests focus on the isolation of specific bacterial indicator organisms through selective media outgrowth in a diagnostic laboratory, this cultivation process is all too often time consuming, infrastructure-dependent and lacks behind in automatisation
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