Abstract
We describe the technical feasibility of metagenomic water quality analysis using only portable equipment, for example mini-vacuum pumps and filtration units, mini-centrifuges, mini-PCR machines and the memory-stick sized MinION of Oxford Nanopore Technologies, for the library preparation and sequencing of 16S rRNA gene amplicons. Using this portable toolbox on site, we successfully characterized the microbiome of water samples collected from Birtley Sewage Treatment Plant, UK, and its environs. We also demonstrated the applicability of the portable metagenomics toolbox in a low-income country by surveying water samples from the Akaki River around Addis Ababa, Ethiopia. The 16S rRNA gene sequencing workflow, including DNA extraction, PCR amplification, sequencing library preparation, and sequencing was accomplished within one working day. The metagenomic data became available within 24–72 h, depending on internet speed. Metagenomic analysis clearly distinguished the microbiome of pristine samples from sewage influenced water samples. Metagenomic analysis identified the potential role of two bacterial genera not conventionally monitored, Arcobacter and Aeromonas, as predominant faecal pollution indicators/waterborne hazards. Subsequent quantitative PCR analysis validated the high Arcobacter butzleri abundances observed in the urban influenced Akaki River water samples by portable next generation sequencing with the MinION device. Overall, our field deployable metagenomics toolbox advances the capability of scientists to comprehensively monitor microbiomes anywhere in the world, including in the water, food and drinks industries, the health services, agriculture and beyond.
Highlights
Water quality surveying is essential for achieving several United Nation Sustainable Development Goals (Alcamo, 2019), including clean water and sanitation (SDG 6), zero hunger (SDG 2) and good health (SDG 3)
We aimed to demonstrate the technical feasibility of using this toolbox for metagenomic analysis in two case study applications: 1) on site water quality monitoring in a small wastewater treatment plant, as recently envisioned in a Science Policy Forum article on Global Health (Aarestrup and Woolhouse, 2020), and 2) water quality surveying in a low income country with only limited sanitation coverage and laboratory resources
For custom clearance in Ethiopia, we attached an accompanying letter from IWMI
Summary
Water quality surveying is essential for achieving several United Nation Sustainable Development Goals (Alcamo, 2019), including clean water and sanitation (SDG 6), zero hunger (SDG 2) and good health (SDG 3). Peletz et al identified transportation problems as a key factor for inconsistent water testing outcomes in Sub-Saharan Africa, especially where testing samples from rural locations (Peletz et al, 2018). Transportation of water samples from field sites to centralized laboratories adds costs and delays the availability of data for decision making. Portable methods can overcome these limitations and enable near-real time screening of water quality for rapid decision making (Peletz et al, 2018; Aarestrup and Woolhouse, 2020)
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