Pacific Expedition Breaksthrough Real-Time DNA

SDSU Postdoctoral Researcher Andreas Haas at  Vostock island on Hanse Explorer. Photo Rob Edwards

DNA Sequence until now used to be considered tools strictly for clean land closed laboratories. Studies costly, time consuming and available to few. A recent expedition in the Pacific Ocean has had a breakthrough in next generation DNA sequencing by successfully obtaining sequences in mid open waters aboard a small ship. There may come a time when DNA sequencing of marine life forms will be instant, affordable and in hands of everyone but until then this new study proves to be a pathway into Live-Real-DNA sequencing. The value? Priceless for mapping of species, classification of life forms, diverse industries, ecology, conservation and medicine among other sectors.

Science Daily reported on August 19^th on the work “Sequencing at sea: Performing real-time DNA sequencing in the middle of Pacific Ocean”.

Scientists overcame equipment failure, space constraints and shark-infested waters to do real-time DNA sequencing in a remote field location. Despite the setbacks, the researchers successfully collected samples, sequenced DNA and developed new research questions on the fly.

The research expedition included San Diego State University computer scientist Robert Edwards, biologist Forest Rohwer, postdoctoral scholar Andreas Haas and graduate student Yan Wei Lim.  They were accompanied by several other researchers from the San Diego region and around the world.

Single handed they accomplished a breakthrough revealing the Live-Real Time DNA Sequence is possible. In all it took the team just three weeks of their five-island expedition. The conclusions and findings of their expedition were published in the Journal PeerJ.

"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 of San Diego University told media referring to the general doubts which the project set out to prove mistaken.

The crew devised a protocol for how to run a DNA sequencer on a ship -headed first to Tahiti with a sequencer provided by San Diego-based biotech company Life Technologies and met with the vessel Explorer to set final course for the Line Islands.

“Genomics and metagenomics have revolutionized our understanding of marine microbial ecology and the importance of microbes in global geochemical cycles. However, the process of DNA sequencing has always been an abstract extension of the research expedition, completed once the samples were returned to the laboratory,” the paper published by PeerJ stated.

The expedition to the Southern Line Islands was the “first effort to bringing next generation sequencing to some of the most remote locations on the planet“.  Following their ambitious goal the team successfully sequenced twenty six marine microbial genomes, and two marine microbial metagenomes using a Ion Torrent PGM platform on a Merchant Yacht Hanse Explorer.

“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,” the team states.

Sequencing in the field allows for numerous advantages. The group highlights the “elimination of the delay between sampling and sequencing. “By overcoming the hurdles associated with sequencing on a boat in the middle of the Pacific Ocean we proved the flexibility of the sequencing, annotation, and analysis pipelines,” the paper concludes.

In an Interview conducted by PeerJ Edwards revealed details of the expedition which could change DNA Sequence for science. “This has massive implications for ecology, but also for conservation, bioprospecting, and a whole suite of other sequence based technologies.” Edwards assured.

“Most people thought we were completely crazy when we said that we would do this. The protocols for next generation sequencing are designed to be used in clean laboratories, and the data requires high performance computing. Seawater tends not to prolong the life of electronic components, and so everything was really stacked against us. The computational aspects were much more challenging than the biology. That it worked was the biggest surprise – not only to us, but also to the naysayers who said it was impossible!,” the co-author of the paper told PeerJ.

The work of the group proves to have a huge impact on the world’s society “We’re also pushing the boundaries of what is technically feasible and at the same time learning new things about ecology and evolution, areas that we have studied for hundreds of years,” Edwards concluded.