Metagenomic water quality monitoring with a portable laboratory

Water Research
Kishor AcharyaDavid Werner

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. Sub...Continue Reading

Citations

Jun 3, 2021·International Journal of Environmental Research and Public Health·Tomáš MackuľakAndrea Butor Škulcová
Aug 15, 2021·Environmental Microbiology·Kyle D BrumfieldRita R Colwell

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Methods Mentioned

BETA
amplicon sequencing
PCR
Assay
PCA

Software Mentioned

GUPPY
MinION NGS
ANOSIM
ONT
Matlab
Fathom Toolbox for Matlab
EPI2ME
FASTQ
MinKNOW
Matlab © scripts

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