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Second, the informatics aspects, including processing the raw data into high quality sequences, comparing those sequences to existing databases to generate annotations, and the subsequent data analysis all require high-performance computational resources to generate meaningful biological interpretations ( Meyer et al., 2008 Aziz et al., 2012 Edwards et al., 2012). In addition to the dedicated hardware required to generate the sequences, much of the hardware, and many of the sample preparation steps, require physically separated laboratory space (to reduce cross-contamination between the samples). The principle limitation to taking sequencing into the field is the significant infrastructure and resources required for all steps of the sequencing process. First, the experimental aspects that include sample collection and preparation, DNA extraction, and sequencing, which are routine in the laboratory but challenging in the field. The use of next-generation sequencing for microbial ecology involves two distinct components. In our previous studies of environmental microbial and viral components we identified questions and challenges that could have been answered with additional sample collection but awaited a future return to the field before they could be addressed ( Dinsdale et al., 2008 Bruce et al., 2012). This abstraction of the DNA sequencing from the sampling eliminates the possibility of immediate follow-up studies to explore interesting findings. In a typical environmental exploration, samples are collected at the study site, transported back to the laboratory, and analyzed after the scientific team returns from the field. 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.ДNA sequencing has revolutionized microbial ecology: next-generation sequencing has upended our traditional views of microbial communities, and enabled exploration of the microbial components of many unusual environments. By eliminating the delay between sampling and sequencing, we enhanced the productivity of the research expedition. Sequencing in the field allowed us to propose hypotheses and conduct experiments and further sampling based on the sequences generated. 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.

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.

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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. 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. 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. Genomics and metagenomics have revolutionized our understanding of marine microbial ecology and the importance of microbes in global geochemical cycles. Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition. Cite this article Lim YW, Cuevas DA, Silva GGZ, Aguinaldo K, Dinsdale EA, Haas AF, Hatay M, Sanchez SE, Wegley-Kelly L, Dutilh BE, Harkins TT, Lee CC, Tom W, Sandin SA, Smith JE, Zgliczynski B, Vermeij MJA, Rohwer F, Edwards RA. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

Licence This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed.

PeerJ - General bio (stats, legal, policy, edu)ДЎ1 Division of Mathematics and Computer Science, Argonne National Laboratory, Argonne, IL, USA DOI 10.7717/peerj.520 Published Accepted Received Academic Editor Valeria Souza Subject Areas Bioinformatics, Ecology, Genomics, Marine Biology, Microbiology Keywords Genomics, Sequencing, Expeditions, Metagenomics, Environmental microbiology, Coral reef, Vibrio Copyright В© 2014 Lim et al.

PeerJ - Biology & Life science articles.

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PeerJ (Life, Biological, Environmental and Health Sciences).Biochemistry, Biophysics and Molecular Biology.

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