Environmental DNA sequencing with Oxford Nanopore: in the lab and in the field

Event overview

Researchers, Lara Urban and David Werner, shared how they are using nanopore sequencing to analyse environmental DNA (eDNA), supporting animal conservation, microbial analysis, and much more.

Non-invasive real-time genomic monitoring of the critically endangered kākāpō

Lara Urban, Principal Investigator, Helmholtz Pioneer Campus, the Helmholtz AI institute, and Technical University of Munich School of Life Sciences, will talk about how her team used non-invasive real-time genomic approaches to monitor one of the last surviving populations of the critically endangered kākāpō (Strigops habroptilus).

This study shows that individual identification is feasible through nanopore sequencing of environmental DNA, with important implications for future efforts in the application of genomics to the conservation of rare species, potentially expanding the application of real-time environmental DNA research from monitoring species distribution to inferring fitness parameters such as genomic diversity and inbreeding.

A suitcase laboratory for molecular microbiology

David Werner, Professor of Environmental Systems Modelling, Newcastle University, will describe the technical feasibility of bacterial community characterisation via analysis of environmental DNA, using only portable equipment items. They assembled a suitcase laboratory which includes the memory stick-sized MinION sequencing device of Oxford Nanopore Technologies, and all the equipment items needed for the biomass concentration, DNA extraction, purification, quantification, gene amplification, and sequencing library preparation. At a sewage treatment plant in the UK, and at the Addis Ababa Water and Sewerage Authority in Ethiopia, the 16S rRNA gene sequencing workflow, including sampling, DNA extraction, PCR amplification, library preparation, and sequencing, was accomplished within one working day. The taxonomic data became available within 24–72 h, depending on internet speed. We also deployed the suitcase laboratory in Tanzania to study impacts of pit latrines on bacterial hazards in shallow and deep groundwater below an informal settlement. In the UK we used the suitcase laboratory for faecal pollution source tracking with a lab in the back of a van. Our field deployable toolbox advances the capability of scientists to comprehensively monitor microbiomes and associated hazards anywhere in the world.