Ship-seq: Nanopore sequencing of polar microbes on board icebreakers

Lead Research Organisation: University of East Anglia
Department Name: Environmental Sciences

Abstract

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.

Publications

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Studentship Projects

Project Reference Relationship Related To Start End Student Name
NE/N012070/1 01/10/2016 30/09/2023
1942119 Studentship NE/N012070/1 01/10/2017 31/05/2021 Emma Grace Langan
 
Description Earlham Institute Open Day 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Earlham Institute open day - around 150 members of the public and 150 school pupils and teachers attended to hear presentations, tour the lab facilities and participate in activities. Surveys reported increased understanding of the importance of genomics and bioinformatics in a range of areas (health, food, environment, day to day life).
Year(s) Of Engagement Activity 2019
 
Description Local radio interview 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Media (as a channel to the public)
Results and Impact Brief local radio interview discussing fieldwork in Antarctica, climate change, importance of phytoplankton, and DNA sequencing.
Year(s) Of Engagement Activity 2019
 
Description Norwich Science Festival - Presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact A presentation at the Norwich Science Festival for members of the general public, including children. The presentation was followed by questions and discussions and members of the audience reported increased awareness of the importance of phytoplankton, and the oceans generally, in terms of climate change and ecosystems.
Year(s) Of Engagement Activity 2019
 
Description Norwich Science Festival Bee Trail 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Bee Trail event at Norwich Science Festival - helping the general public to build lego DNA sequences based on clues from around the venue. Explaining DNA sequencing and its importance in tracing bee pollination patterns. Members of the public reported increased understanding of the DNA sequencing, and the importance of bee friendly plants and policies.
Year(s) Of Engagement Activity 2019
 
Description Plenary talk and panel discussion at London Calling 2019 (Nanopore conference) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact I gave a plenary talk and participated in a panel discussion at London Calling 2019 on the use of nanopore sequencing in ocean research.
Year(s) Of Engagement Activity 2019
URL https://nanoporetech.com/lc19/speakers#EmmaLangan&modal=EmmaLangan