The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing
Year: 2014
Type: article
Abstract: Microbial ecology is plagued by problems of an abstract nature. Cell sizes are so small and population sizes so large that both are virtually incomprehensible. Niches are so far from our everyday experience as to make their very definition elusive. Organisms that may be abundant and critical to our survival are little understood, seldom described and/or cultured, and sometimes yet to be even seen. One way to confront these problems is to use data of an even more abstract nature: molecular sequence data. Massive environmental nucleic acid sequencing, such as metagenomics or metatranscriptomics, promises functional analysis of microbial communities as a whole, without prior knowledge of which organisms are in the environment or exactly how they are interacting. But sequence-based ecological studies nearly always use a comparative approach, and that requires relevant reference sequences, which are an extremely limited resource when it comes to microbial eukaryotes [1]. In practice, this means sequence databases need to be populated with enormous quantities of data for which we have some certainties about the source. Most important is the taxonomic identity of the organism from which a sequence is derived and as much functional identification of the encoded proteins as possible. In an ideal world, such information would be available as a large set of complete, well-curated, and annotated genomes for all the major organisms from the environment in question. Reality substantially diverges from this ideal, but at least for bacterial molecular ecology, there is a database consisting of thousands of complete genomes from a wide range of taxa, supplemented by a phylogeny-driven approach to diversifying genomics [2]. For eukaryotes, the number of available genomes is far, far fewer, and we have relied much more heavily on random growth of sequence databases [3],[4], raising the question as to whether this is fit for purpose.
Source: PLoS Biology
Authors: Patrick J. Keeling, Fabien Burki, Heather M. Wilcox, Bassem Allam, Eric E. Allen, Linda A. Amaral-Zettler, E. Virginia Armbrust, John M. Archibald, Arvind K. Bharti, Callum J. Bell, Bank Beszteri, Kay D. Bidle, Connor T. Cameron, Lisa Campbell, David A. Caron, Rose Ann Cattolico, Jackie L. Collier, Kathryn Coyne, Simon K. Davy, Phillipe Deschamps, Sonya T. Dyhrman, Bente Edvardsen, Ruth D. Gates, Christopher J. Gobler, Spencer J. Greenwood, Stephanie M. Guida, Jennifer L. Jacobi, Kjetill S. Jakobsen, Erick R. James, Bethany Jenkins, Uwe John, Matthew D. Johnson, Andrew R. Juhl, Anja Kamp, Laura A. Katz, Ronald Kiene, Alexander Kudryavtsev, Brian S. Leander, Senjie Lin, Connie Lovejoy, Denis Lynn, Adrian Marchetti, George McManus, Aurora M. Nedelcu, Susanne Menden-Deuer, Cristina Miceli, Thomas Mock, Marina Montresor, Mary Ann Moran, Shauna Murray, Govind Nadathur, Satoshi Nagai, Peter B. Ngam, Brian Palenik, Jan Pawlowski, Giulio Petroni, Gwenael Piganeau, Matthew C. Posewitz, Karin Rengefors, Giovanna Romano, Mary E. Rumpho, Tatiana Rynearson, Kelly B. Schilling, Declan C. Schroeder, Alastair G. B. Simpson, Claudio H. Slamovits, David R. Smith, G. Jason Smith, Sarah R. Smith, Heidi M. Sosik, Peter Stief, Edward Theriot, Scott N. Twary, Pooja E. Umale, Daniel Vaulot, Boris Wawrik, Glen L. Wheeler, William H. Wilson, Yan Xu, Adriana Zingone, Alexandra Z. Worden
Institutions: Canadian Institute for Advanced Research, University of British Columbia, Monterey Bay Aquarium Research Institute, Stony Brook University, Scripps Institution of Oceanography, University of California San Diego, Marine Biological Laboratory, Brown University, University of Washington, Dalhousie University, National Center for Genome Resources, Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Rutgers, The State University of New Jersey, Texas A&M University, University of Southern California, University of Delaware, Victoria University of Wellington, Université Paris-Sud, Centre National de la Recherche Scientifique, Ecologie, Société, Evolution, Lamont-Doherty Earth Observatory, Columbia University, University of Oslo, University of Hawaiʻi at Mānoa, University of Hawaii System, Hawaii Institute of Marine Biology, University of Prince Edward Island, University of Rhode Island, Woods Hole Oceanographic Institution, Constructor University, Max Planck Institute for Marine Microbiology, Smith College, Dauphin Island Sea Lab, University of South Alabama, University of Geneva, St Petersburg University, University of Connecticut, Université Laval, University of Guelph, University of North Carolina at Chapel Hill, University of New Brunswick, Università di Camerino, University of East Anglia, Stazione Zoologica Anton Dohrn, University of Georgia, University of Technology Sydney, University of Puerto Rico-Mayaguez, University of Pisa, Sorbonne Université, Biologie Intégrative des Organismes Marins, Observatoire Océanologique de Banyuls-sur-Mer, Université Pierre-et-Marie-Curie, Colorado School of Mines, Lund University, Marine Biological Association of the United Kingdom, Western University, Moss Landing Marine Laboratories, The University of Texas at Austin, Los Alamos National Laboratory, Station Biologique de Roscoff, University of Oklahoma, Plymouth Marine Laboratory, Bigelow Laboratory for Ocean Sciences, Princeton University
Language: English
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $5,500
Awards: H+ fluxes in phytoplankton - a mechanistic and modelling study of their physiological roles and impact upon community responses to ocean acidification, Functional adaptation of diatoms to environmental conditions in sea ice of the Southern Ocean, PML Cycling in the Sunlit Ocean (biogeochemical cycling), G3971626879
OpenAlex ID: W2019619926