Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition

PeerJ. 2014 Aug 19;2:e520. doi: 10.7717/peerj.520. eCollection 2014.

Abstract

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. During the 2013 Southern Line Islands Research Expedition, we started the first effort to bring next generation sequencing to some of the most remote locations on our planet. We successfully sequenced twenty six marine microbial genomes, and two marine microbial metagenomes using the Ion Torrent PGM platform on the 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. This analysis identified phosphonate as an important phosphorous source for microbes growing in the Line Islands and reinforced the importance of L-serine in marine microbial ecosystems. Sequencing in the field allowed us to propose hypotheses and conduct experiments and further sampling based on the sequences generated. By eliminating the delay between sampling and sequencing, we enhanced the productivity of the research expedition. 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.

Keywords: Coral reef; Environmental microbiology; Expeditions; Genomics; Metagenomics; Sequencing; Vibrio.

Grant support

This work is partially supported by NSF Dimensions Grant (DEB-1046413; Edwards and Rohwer). This project was also funded in part by the Gordon and Betty Moore Foundation through Grant GBMF-3781 to Rohwer. Additional funding for Yan Wei Lim was provided by the Canadian Institute for Advanced Research (CIFAR; IMB-ROHW-141679). Additional funding for Edwards was provided by NSF grants CNS-1305112, and MCB-1330800. Dutilh was supported by an award from CAPES/BRASIL. The SDSU Vice President of Research, Director’s Office of Scripps Institution of Oceanography, Moore Family Foundation, and several private donors provided cruise support. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.