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Aug 19, 2014

Next-Generation Sequencing at Sea

Next-Generation Sequencing at Sea

San Diego State University graduate student Yan Wei Lim explores coral reefs in the southern Line Islands. [Rob Edwards, SDSU computer scientist]

  • Like many seafaring scientists of the past, the research crew of the Merchant Yacht Hanse Explorer sailed forth with hopes of collecting novel specimens. Unlike many of their storied predecessors, however, the Explorer’s scientists had no intention of packing their newfound treasures into crates bound for terra firma. No, instead of routing specimens to landlocked laboratories and, eventually, dusty museums of natural history, the scientists would analyze their hauls on the spot, which happened to be in the middle of the Pacific Ocean.

    Scientists from San Diego State University (SDSU) and other institutions as far away as the Netherlands embarked on a three-week, five-island expedition on a 158-foot research vessel. All shared a single goal: be the first research group to bring a DNA sequencer into the field to do remote sequencing in real time.

    While the idea was to study organisms that populate coral habitats—not anything as risky as hunting a white whale—the expedition had its doubters. “People are a little 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,” said crewmember Rob Edwards, an SDSU computer scientist.

    Undeterred, he and his colleagues devised a protocol for how to run a DNA sequencer on a ship. The instrument, provided by Life Technologies, was set up in the laundry room because it was the lowest point in the ship and it would sway the least as the Explorer rocked. The microbiology lab was set up on the upper aft deck. The DNA isolation station found its home in a cabin. And the mess deck hosted the PCR machine used to amplify the DNA samples into analyzable chunks.

    Although working aboard a swaying boat posed special difficulties—for example, instrument calibration took five hours, as opposed to the usual 15 minutes on dry land—managed to sequence the DNA of the samples they collected. As they had hoped, the researchers found that their sequencing results allowed them to develop new research questions on the fly, instead of having to wait until they were back home.

    An account of the Explorer’s voyage, which took place last year, appeared August 19 in the journal PeerJ, in an article entitled, “Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition.”

    “We successfully sequenced twenty six marine microbial genomes, and two marine microbial metagenomes using the Ion Torrent PGM platform,” the authors wrote. “Onboard sequence assembly, annotation, and analysis enabled us to investigate the role of the microbes in the coral reef ecology of these islands and atolls.”

    In all, 26 bacterial genomes were sequenced, along with two metagenomes. In addition, the real-time analyses of these data revealed unique metabolic processes that contribute to the survival of the species that the researchers examined. (In particular, the researchers found that phosphonate is an important phosphorous source for microbes growing in the Line Islands and reinforced the importance of L-serine in marine microbial ecosystems.)

    Despite these successes, all was not smooth sailing. Equipment failures had to be overcome, and procedures that one may take for granted on land—such as centrifugation—had to be rethought on a rocking, wave-riding vessel. Yet another problem, limited access to genomic data stores, may be mitigated only with the rollout of improved computational and communications resources. Internet communications by way of satellite are, at present, pose a serious constraint.

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


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