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Metagenomic water quality monitoring with a portable laboratory

Lookup NU author(s): Dr Kishor Acharya, Adrian Blackburn, Professor David Werner

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This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).


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.


Publication metadata

Author(s): Acharya K, Blackburn A, Mohammed J, Haile AT, Hiruy AM, Werner D

Publication type: Article

Publication status: Published

Journal: Water Research

Year: 2020

Volume: 184

Print publication date: 01/10/2020

Online publication date: 10/07/2020

Acceptance date: 25/06/2020

Date deposited: 18/07/2020

ISSN (print): 0043-1354

ISSN (electronic): 1879-2448

Publisher: Elsevier

URL: https://doi.org/10.1016/j.watres.2020.116112

DOI: 10.1016/j.watres.2020.116112


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