Submitted by Rachel Hoffmann on Tue, 19/01/2021 - 13:53
Climate change, rising urbanisation and agricultural intensification lead to global depletions of safe drinking water resources, and consequently reinforce the need for comprehensive monitoring frameworks.
In a case study, published 19 January 19 in the journal eLife, an interdisciplinary research team at the University of Cambridge now exemplifies uses of the world’s smallest, smartphone-sized DNA sequencing device (MinIONTM, Oxford Nanopore Technologies) to monitor hundreds of different bacteria in a river ecosystem.
Since the Victorian era, rowers and swimmers of the studied River Cam have been regularly affected by waterborne infections such as Weil's disease, sometimes leading to public closures of one of England's most iconic waterways. In their article, members of the 2017-born PuntSeq initiative (www.puntseq.co.uk) show how the river’s types of microbes vary across locations, and through the seasons – by extensive sampling and repeated use of their small machine. "This study design has allowed us to provide real transparency on important local questions of public health, with a very exciting new technology" says Lara Urban (@LaraUrban42), co-lead investigator of the work and now an Alexander von Humboldt research fellow at the University of Otago, New Zealand.
The article, which features guidelines for water DNA equipment and analysis software use, details the distinction of closely related pathogenic species from harmless ones. "It's essential to account for the quality of this new type of bacterial DNA sequence information" stresses Andre Holzer (@AndreHolzer), co-first author and PhD student at the Cambridge Department of Plant Sciences, "which is why our team had to test many different algorithms for the data processing". Potentially dangerous bugs like Pseudomonas aeruginosa could thereby be detected downstream of the most urbanised river sections.
While public media reports have repeatedly featured large-scale sewage overflow incidents across rivers in the United Kingdom, results of this study also pinpoint the presence of waste water associated bacterial contamination in the River Cam – by sole means of DNA technology. Upon these early findings, the initiative teamed up with lecturer Edward Tipper and postdoctoral scientist Jotis Baronas at the Department of Earth Sciences. Their chemical follow-up analyses of the same water collection revealed a matching trend of increasing anthropogenic pollution levels along the river's urban axis.
In spirit of this work's multidisciplinary nature – involving members of Cambridge University's Departments of Earth Sciences, Plant Sciences, Physics, Engineering, Physiology, Development & Neuroscience, Biochemistry and Veterinary Medicine, as well as the nearby European Bioinformatics and Sanger Institutes – the team hopes that its results will encourage other independent scientists and initiatives to engage in simplified freshwater management and biodiversity tests around the globe. "This has been a fascinating scientific journey full of learning and public interactions", says Max Stammnitz (@DevilsAdvoMax), founder of PuntSeq, "similar projects in other countries are already on their way."
Improved access to clean freshwater is fundamental to societies, and has been recognised as a United Nations Sustainable Development Goal towards 2030. Yet, traditional microbial freshwater testing requires complex culturing routines for individual bacterial species in well-equipped diagnostics laboratories.
Since the mid 2000s, the direct measurement of all bacterial DNA traces in freshwater has been praised as a valuable alternative. To date, however, such protocols rely on comparably expensive, fridge-sized DNA sequencing machines whose handling demands expert training. While these logistical challenges have so far limited the capacity of field workers to remotely monitor microbes in freshwater systems, this eLife study’s portable DNA analysis framework promises to be significantly more cost-effective, user friendly and deployable.
MinIONTM and the associated nanopore DNA sequencing technology, commercially available since 2015, have already proven invaluable for the tracing of viral transmissions between patients during the EBOLA, ZIKA or SARS-CoV-19 outbreaks.