Polar oceans belong to the most underexplored ecosystems on Earth, yet they are considered biodiversity hotspots and they disproportionally contribute to global biogeochemical cycles. Furthermore, they are most threatened by global warming. Thus, there is an urgent need to study how environmental change impacts polar organisms that drive biogeochemical cycles such as marine microbes. However, most of these microbes are difficult to study as they need certain temperatures to survive, which limits our ability to transport them to our laboratories for experiments. Long-term maintenance in the laboratory is also challenging as many of them are cold-adapted and require polar-specific environments (e.g. ice and snow). Our project addresses this challenge by bringing the Oxford Nanopore Technologies MinION sequencing technology to polar oceans for real-time studies on the diversity and function of microbial communities from the surface polar ocean and lower atmosphere. This will be a proof-of-concept study to show that probing and analysing polar microbes at the ocean-atmosphere interface can be done while on an expedition in polar oceans. Benefits are manifold: a) real-time assessment of in situ microbial diversity, b) real-time analysis of in situ or on-board experiments in polar oceans and c) genome and transcriptome sequencing of sensitive but ecologically relevant polar microbes.
MinION sequencing has already been used for sequencing in space, on glaciers and on board ships to sequence organisms from tropical oceans. However, there is no report so far of real-time sequencing on board icebreakers or of eukaryotic communities. We are going to adapt the MinION sequencer, which weighs under 100 g, is portable and plugs into a laptop, for sequencing of microbes at the ocean-atmosphere interface, which is critical for global biogeochemical cycles and affected by global warming. There is neither additional computing infrastructure required nor extensive laboratory equipment, which makes MinION very versatile. However, the sequencing protocols and analysis pipelines needs to be tailored to target specific genes and species that are of interest in terms of their function (e.g. trace-gas production) and ecological role (e.g. invasive species), respectively. We want to tackle this challenge through development of new algorithms and experimental approaches. Microbial samples from the surface Southern Ocean will be used to test the MinION and our new algorithms. These data will be validated using published sequence datasets from the same locations. As Prof Mock is involved in the international Arctic Drift Expedition ‘MOSAIC’ (2020), the PhD student will have the opportunity to test our technology under in situ conditions on board the icebreaker ‘Polarstern’.
The NEXUSS CDT provides state-of-the-art, highly experiential training in the application and development of cutting-edge Smart and Autonomous Observing Systems for the environmental sciences, alongside comprehensive personal and professional development. There will be extensive opportunities for students to expand their multi-disciplinary outlook through interactions with a wide network of academic, research and industrial / government / policy partners.
The student will be registered in the School of Environmental Sciences at the University of East Anglia, and hosted at the nearby Earlham Institute. Specific training will include: software development, programming, sequencing, sequence analysis, experiments with polar microbes, molecular biology and field work in the Arctic on drifting sea ice.
This project has been shortlisted for funding by the NexUSS CDT.
Successful candidates who meet RCUK’s eligibility criteria will be awarded a NERC studentship. In most cases, UK and EU nationals who have been resident in the UK for 3 years are eligible for a full award. In 2016/17, the stipend was £14,296.
Castro-Wallace S.L. et al., 2016, Nanopore DNA Sequencing and Genome Assembly on the International Space Station, bioRxiv, doi.org/10.1101/077651
Mock T. et al., 2017, Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus, Nature, doi:10.1038/nature20803
Leggett, RM et al. 2016. NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles, Bioinformatics 32(1):142-4
Applications should be made to the University of East Anglia. The deadline for applications is 23:59 on 26 June 2017.