Metagenomic water quality monitoring with a portable laboratory. (1st October 2020)

• Record Type: Journal Article
• Authors: Acharya, Kishor; Blackburn, Adrian; Mohammed, Jemila; Haile, Alemseged Tamiru; Hiruy, Andualem Mekonnen; Werner, David
• Is Part Of: Water research. Volume 184(2020)
• Publication Date: 2020-10-01
• Subjects: Water quality -- Field kits -- Fecal source tracking -- Waterborne hazards -- Metagenomics -- MinION nanopore sequencing; Water -- Pollution -- Research -- Periodicals; 363.7394
• DOI: 10.1016/j.watres.2020.116112
• Languages: English
• ISSNs: 0043-1354

Abstract

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. Graphical abstract: Image 1 Highlights: A portable toolbox for metagenomic water quality analysis was assembled. Water microbiomes were characterized on site at a sewage treatment plant in the UK. Water microbiomes were characterized in the Akaki River catchment, Ethiopia. Arcobacter and Aeromonas were predominant faecal pollution indicators/hazards. High Arcobacter butzleri abundances observed in Ethiopia were validated by qPCR.