Introducing DNA Sequencing to the Next Generation on a Research Vessel Sailing the Bering Sea Through a Storm

Abstract

Experiential learning in the field is an opportunity for students to enter the heart of a scientific discipline. Through such experience, they can extract conceptual clues and discover motivational stepping stones that will potentially influence the rest of their education and career choice. Unfortunately, in Biology, the inescapable topic of Next-Generation Sequencing represents a challenge when it comes to create an educational curriculum that aims to provide students with hands-on experience on sequencers. It is an even more difficult task to accomplish if one’s purpose was to set such curriculum in a field situation. However, in recent years, educators have seen possibility to bring Next-Generation Sequencing to the reach of students more easily, with the Oxford Nanopore MinION, a low-budget, user-friendly, hand-held sequencer. Academic researchers have illustrated the performances of this device in the field and are inspirational for curricula aiming to take the next generation of scientists in the outdoors. We designed a modular 5-day workshop, with nanopore sequencing to be performed in field conditions. Here we describe the material and methods that lead the students and instructors from sample collection, DNA extraction and preparation for nanopore sequencing with MinION to real-time analysis of the data collected. This curriculum was implemented for the first-time aboard Research Vessel Sikuliaq during a transit organized by the STEMSEAS program at Columbia University in collaboration with the University of Alaska BLaST program. The line of investigation formulated for the workshop was an open-ended question that led the students to establish a proof of concept in terms of technology deployment at sea: what will show metagenomic results from DNA obtained from sea water and sequenced with Oxford Nanopore MinION? The workshop took place in October 2018 while Research Vessel Sikuliaq sailed the Alaskans seas for 7 days. Students successfully used nanopore sequencing for multiple metagenomic seawater samples. Their introductory analysis was consistent with environmental conditions and they were able to present their results by the end of the workshop.

Nanopore sequencing technology, bioinformatics and applications

“…The portability of the MinION system, which consists of the palm-sized MinION, mobile DNA extraction devices (for example, VolTRAX and Bento Lab) and real-time onboard base calling with Guppy and other offline bioinformatics tools, enables field research in scenarios where samples are hard to culture or store or where rapid genomic information is needed 233 . Examples include the International Space Station, future exploration of Mars and the Moon involving microgravity and high levels of ionizing radiation 69,234,235 , ships 236 , Greenland glaciers at subzero temperatures 237 , conservation work in the Madagascar forest 238 and educational outreach 238 .…”

Before you go: a packing list for portable DNA sequencing of microbiomes and metagenomes

“…The principle and utility of portable sequencing has been proven on every continent, e.g [12]. , as well as at sea, e.g [4], inside the Earth [11], and in low-Earth orbit [13]. Lessons learnt from portable sequencing can also be transferred to the laboratory, resulting in more streamlined protocols and equipment with a lighter footprint.…”

“…Relevant factors might include difficulties in transporting preserved samples to the laboratory [3], a need to gain insights to the study system while deployed to direct other field activities, the detection of contamination in high-stakes sampling (e.g. subglacial lake access), emergency response, or to build capacity at the point of need [4]. There is also a line of argument that sequencing on site may have less environmental impact compared with the cold-chain transfer of samples to a laboratory followed by long-term deep-frozen storage of large volumes of samples and reagents.…”

Portable sequencing as a teaching tool in conservation and biodiversity research

“…Short field programs, in which participants travel to natural environments to train, can guide career paths, provide local capacity building, and highlight important environmental problems [14][15][16][17]. Bringing the science to the sample, effectively turning the paradigm on its head, also welcomes local scientists and educators who perform invaluable environmental monitoring without contemporary methodologies or large research funding.…”