A few months ago we highlighted the work of Dr. Leonid Moroz about the neurological regeneration of the sea comb jellies, the ctenophores, which was subsequently published in Nature in June 2014. In the Behind the Bench post “Taking the Sequencer to Where the Samples Are – the Open Ocean” Dr. Moroz’s work was a proof-of-concept in order to do further ‘field-work’, where the samples were collected and analyzed on-site.
It turns out that Dr. Moroz is not the only one with this idea. Dr. Rob Edwards of San Diego State University studies coral reefs, and outfitted a 158-foot ship called the Merchant Yacht Hanse Explorer for a three week, five island journey to study coral ecology in an environment where there has been minimal human interaction. The Line Islands, a chain of eleven atolls south of the Hawaiian Islands in the Pacific Ocean, stretches for almost 1,500 miles and is sparsely populated, making it an ideal location for their study. A group from San Diego State University has been studying microbial and coral ecology in this region of the world for over a decade.
Dr. Edwards wanted to bring next-generation sequencing to where the samples are since 2008, but due to the expense and fragility of optical systems said, “(p)eople 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”(GenomeWeb Article). The economical Ion PGMTM system with its semiconductor-based sequencing method makes it suitable for this kind of mission.
By the end of their journey they had successfully sequenced twenty six marine microbial genomes and two marine metagenomes using the Ion PGM™ System, and identified phosphonate as an important phosphorus source for microbes in this region, in addition to demonstrating the usefulness of on-board genome assembly, annotation and analysis to reiteratively test hypotheses while out at sea. They were able “to propose hypotheses and conduct experiments and further sampling based on the sequences generated.” (Lim YW, et. al http://dx.doi.org/10.7717/peerj.520)
The paper includes some practical considerations of placement of equipment (their clean pre-PCR room for DNA purification and NGS library preparation also doubled as a bedroom for one of the scientists), and noted that a damaged Ion OneTouch™ 2 System touchscreen was repaired at sea by re-wiring the display onto a laptop. (Without access to technical support in such a remote region, the researchers performed some reverse engineering with an X11 interface and a Linux laptop, to their credit.)
They used 200 base-pair Ion Torrent PGM Sequencing, however the newer 400 base-pair chemistry could also help with the quality of de novo assemblies.
The group’s publication, “Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition”, was recently published in the open-access journal PeerJ.