Freshwater monitoring by nanopore sequencing

Lara Urban; Andre Holzer; J Jotautas Baronas; Michael Hall; Philipp Braeuninger-Weimer; Michael J Scherm; Daniel J Kunz; Surangi N Perera; Daniel E Martin-Herranz; Edward T Tipper; Susannah J Salter; Maximilian R Stammnitz

The global assurance of safe drinking water and basic sanitation has been recognised as a United Nations Millennium Development Goal 1 , particularly in light of the pressures of rising urbanisation, agricultural intensification and climate change 2,3 . These trends enforce an increasing demand for freshwater monitoring frameworks that combine cost effectiveness, fast technology deployability and data transparency 4 . Environmental metagenomics, the tracing of organisms present in a substrate through high-throughput DNA sequencing, yields informative measures of relative taxonomic species occurrence and functional diversity 5 . Microbial metagenomics studies overcome enrichment biases common to traditional culturing approaches 5 ; however, they usually depend on expensive and stationary equipment, highly specialised operational training and substantial time lags between fieldwork, sample preparation, raw data generation and access.