In a three-week expedition to five islands, a team of researchers for the very first time successfully carried out a plan to bring a DNA sequencer onto a ship and out into the sea to perform DNA sequencing right after underwater research.
The researchers—both computer scientists and biologists—from San Diego State University (SDSU) have been on travel for the past decade to the Line Islands to collect and analyze the coral habitat in their efforts to understand the kinds of organisms that live there, the method by which they vie for resources and the effects of their presence on the ecosystem of the reef.
Yet SDSU computer scientist Rob Edwards was always bothered by the fact that they needed to wait till they get back home to examine the data gathered and to create new hypothesis.
“If only we had had that data out in the field, we could have asked those questions there and then,” Edwards said in a statement.
It is for that reason the team dug their hands into an ambitious plan of bringing the expensive DNA sequencing equipment. Much like any first-time experiment, some people were hesitant to bring a half a million dollar equipment into the middle of Pacific Ocean without the assurance of it coming back, said Edwards.
Nevertheless, they pursued their plan and came with a protocol in running a DNA sequencer while onboard a ship. Eventually, biotech firm Life Technologies in San Diego provided a sequencer to them who were then headed to Tahiti.
Carrying out the plan was not without challenges, however. Among these challenges was the touch screen got broken while in transit, which was badly needed to operate the machine. Edward hacked into the software of the sequencer to make it possible for operation with his laptop.
SDSU doctoral student Yan Wei Lim, meanwhile, found it difficult to calibrate the sequencer that usually takes only around 15 minutes in a lab. Out in the sea and the boat on a sway, it took him around five hours to do so.
Besides that, sharks were part of the game, too, while the researchers were underwater for sample collection. Lim narrated seeing between 20 and 30 sharks around, but she wasn’t afraid.
“They would just swim away if you got too close,” said Lim.
The team finally got everything in place regardless of all the setbacks along the way. They collected samples, sequenced its DNA and created new questions for research. Sequenced were 26 bacterial genomes, together with two metagenomes, taking into account all present DNA in the given region.
Edwards brought home not only the idea of a plan successfully carried out, but lessons as well.
“But when we go back next time, we’re going to be better prepared,” he said.
The study, Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition, was published in PeerJ journal.