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

TitleSequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition
Publication TypeJournal Article
Year of Publication2014
AuthorsLim Y.W, Cuevas D.A, Silva G.GZ, Aguinaldo K., Dinsdale E.A, Haas AF, Hatay M., Sanchez S.E, Wegley-Kelly L., Dutilh B.E, Harkins T.T, Lee C.C, Tom W., Sandin SA, Smith JE, Zgliczynski B., Vermeij MJA, Rohwer F, Edwards R.A
JournalPeerj
Volume2
Date Published2014/08
Type of ArticleArticle
ISBN Number2167-8359
Accession NumberWOS:000347617700004
Keywordscoral reef; environmental; Expeditions; generation; genes; genome; genomics; Iron; metagenomics; microbiology; Sequencing; sp-nov.; Vibrio
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.

DOI10.7717/peerj.520
Student Publication: 
Yes
Student: 
sharknado