Sequencing at Sea: San Diego Scientists are First to Sequence DNA in 'Real Time' in Pacific Ocean

American scientists have managed to sequence DNA in the middle of the sea for the first time, overcoming shark-infested waters and equipment failure.

Researchers at San Diego State University have become the first team to take a genome sequencer out to the Pacific Ocean, to do remote sequencing in real time.

The three-week trip took place in 2013, in which computer scientist Rob Edwards, biologist Forest Rohwer and postdoctoral scholar Andreas Haas and graduate student Yan Wei Lim took equipment worth half-a-million dollars out to the Line Islands, a chain of eleven atolls and low coral islands south of Hawaii.

Researchers have been collecting and analysing data on the coral habitat around the islands for years, to understand the organisms and eco-system that exist there. However, they wanted to find a more immediate way to examine their data and develop new hypotheses.

"If only we had had that data out in the field, we could have asked those questions there and then," Edwards told Phys.org.

To address the problem, the team decided to take the equipment out to location.

"People are a little bit hesitant to take a half-million-dollar piece of equipment into the middle of the Pacific if you're not sure it's going to be coming back," Edwards added.

Samples were collected from the numerous coral reefs around the southern Line Islands.

The team sequenced 26 bacterial genomes along with two metagenomes, which assess the entire DNA present in a given region.

The technology used to carry out the sequencing was provided by the biotech company Life Technologies, based in San Diego.

To facilitate the expedition, the laundry room on board the Hanse Explorer was tranformed into a makeshift, portable laboratory. The upper deck was turned into a microbiology lab.

While calibrating the sequencer normally takes around 15 minutes, the process took as long as five hours on board the vessel. The team encountered various setbacks, including a broken touch screen needed to operate the machine. In order to begin the sequencing, Edwards had to hack into the sequencer's software.

Then there were the sharks. Lim told Nature World News that she counted between 20 and 30 curious sharks milling about, while specimens were being collected in the sea.

"I wasn't afraid," she said. "They would just swim away if you got too close."

The next move for the researchers will be to undertake more complex research and hypotheses out in the field.

"At the end of the day, we were able to come up with the data we needed," Edwards said in a news release. "But when we go back next time, we're going to be better prepared."

The expedition is documented in an article published in the journal PeerJ.