The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing
Open accessAbstract
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.
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The Marine Microbial Eukaryote Transcriptome Sequencing Project has conducted transcriptome sequencing on almost 700 marine microbial species, including 140 microalgae species.
“The Marine Microbial Eukaryote Transcriptome Sequencing Project has conducted transcriptome sequencing on almost 700 marine microbial species, including 140 microalgae species [229].”
From Microalgae biofuels: illuminating the path to a sustainable future amidst challenges and opportunities (2024) · cites this paper as [229]
The Abstract describes 700 transcriptomes from marine microbial eukaryotes, and “MMETSP—The Right Stuff” says the project is creating over 650 transcriptomes. Neither passage equates that count with species; the paper also notes that multiple strains or conditions can be represented. The passages found do not establish the claimed count of 140 microalgae species (searched: “140” and “140 microalgae species”). (LLM, conf=0.88)
Experimental — accuracy not yet measuredMMETSP transcriptomic samples cover a wide range of primary and complex algae and were recently re-assembled.
“MMETSP transcriptomic samples [9] cover a wide range of primary and complex algae and were recently re-assembled [10].”
From Decontamination, pooling and dereplication of the 678 samples of the Marine Microbial Eukaryote Transcriptome Sequencing Project (2021) · cites this paper as [9]
MMETSP transcriptomes represent a valuable resource for phylogenomic analyses, owing to their broad and rich taxonomic sampling, especially of photosynthetic species.
“MMETSP (Marine Microbial Eukaryote Transcriptome Sequencing Project) transcriptomes represent a valuable resource for phylogenomic analyses, owing to their broad and rich taxonomic sampling, especially of photosynthetic species.”
From Decontamination, pooling and dereplication of the 678 samples of the Marine Microbial Eukaryote Transcriptome Sequencing Project (2021) · cites this paper as [9]
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- Authors
- Keeling, P. J., Burki, F., Wilcox, H. M., Allam, B., Allen, E. E., Amaral-Zettler, L. A., Armbrust, E. V., Archibald, J. M., Bharti, A. K., Bell, C. J., Beszteri, B., Bidle, K. D., Cameron, C. T., Campbell, L., Caron, D. A., Cattolico, R. A., Collier, J. L., Coyne, K., Davy, S. K., Deschamps, P., Dyhrman, S. T., Edvardsen, B., Gates, R. D., Gobler, C. J., Greenwood, S. J., Guida, S. M., Jacobi, J. L., Jakobsen, K. S., James, E. R., Jenkins, B., John, U., Johnson, M. D., Juhl, A. R., Kamp, A., Katz, L. A., Kiene, R., Kudryavtsev, A., Leander, B. S., Lin, S., Lovejoy, C., Lynn, D., Marchetti, A., McManus, G., Nedelcu, A. M., Menden-Deuer, S., Miceli, C., Mock, T., Montresor, M., Moran, M. A., Murray, S., Nadathur, G., Nagai, S., Ngam, P. B., Palenik, B., Pawlowski, J., Petroni, G., Piganeau, G., Posewitz, M. C., Rengefors, K., Romano, G., Rumpho, M. E., Rynearson, T., Schilling, K. B., Schroeder, D. C., Simpson, A. G. B., Slamovits, C. H., Smith, D. R., Smith, G. J., Smith, S. R., Sosik, H. M., Stief, P., Theriot, E., Twary, S. N., Umale, P. E., Vaulot, D., Wawrik, B., Wheeler, G. L., Wilson, W. H., Xu, Y., Zingone, A., & Worden, A. Z.
- Affiliations
- Canadian Institute for Advanced Research (CA)
- University of British Columbia (CA)
- Monterey Bay Aquarium Research Institute (US)
- Stony Brook University (US)
- Scripps Institution of Oceanography (US)
- University of Washington (US)
- National Center for Genome Resources (US)
- Rutgers, The State University of New Jersey (US)
- Texas A&M University (US)
- University of Southern California (US)
- University of Delaware (US)
- Victoria University of Wellington (NZ)
- Université Paris-Sud (FR)
- Lamont-Doherty Earth Observatory (US)
- University of Oslo (NO)
- University of Hawaiʻi at Mānoa (US)
- University of Prince Edward Island (CA)
- University of Rhode Island (US)
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung (DE)
- Woods Hole Oceanographic Institution (US)
- Constructor University (DE)
- Smith College (US)
- Dauphin Island Sea Lab (US)
- University of Geneva (CH)
- University of Connecticut (US)
- University of North Carolina at Chapel Hill (US)
- University of New Brunswick (CA)
- Università di Camerino (IT)
- Stazione Zoologica Anton Dohrn (IT)
- University of Georgia (US)
- University of Technology Sydney (AU)
- University of Pisa (IT)
- Colorado School of Mines (US)
- Lund University (SE)
- Marine Biological Association of the United Kingdom (GB)
- Western University (CA)
- Moss Landing Marine Laboratories (US)
- Max Planck Institute for Marine Microbiology (DE)
- The University of Texas at Austin (US)
- Los Alamos National Laboratory (US)
- Centre National de la Recherche Scientifique (FR)
- University of Oklahoma (US)
- Bigelow Laboratory for Ocean Sciences (US)
- Princeton University (US)
- Corresponding author
- Keeling, Patrick J.
- Worden, Alexandra Z.
- ORCID
- Keeling, Patrick J.
- Burki, Fabien
- Allam, Bassem
- Allen, Eric E.
- Armbrust, E. Virginia
- Archibald, John M.
- Bharti, Arvind K.
- Bell, Callum J.
- Bidle, Kay D.
- Cameron, Connor T.
- Campbell, Lisa
- Caron, David A.
- Collier, Jackie L.
- Coyne, Kathryn
- Davy, Simon K.
- Dyhrman, Sonya T.
- Edvardsen, Bente
- Gobler, Christopher J.
- Greenwood, Spencer J.
- Jakobsen, Kjetill S.
- James, Erick R.
- Jenkins, Bethany
- John, Uwe
- Johnson, Matthew D.
- Juhl, Andrew R.
- Kamp, Anja
- Katz, Laura A.
- Kiene, Ronald
- Kudryavtsev, Alexander
- Leander, Brian S.
- Lin, Senjie
- Lynn, Denis
- Marchetti, Adrian
- McManus, George
- Nedelcu, Aurora M.
- Miceli, Cristina
- Montresor, Marina
- Moran, Mary Ann
- Murray, Shauna
- Nagai, Satoshi
- Palenik, Brian
- Pawlowski, Jan
- Petroni, Giulio
- Posewitz, Matthew C.
- Rengefors, Karin
- Romano, Giovanna
- Rynearson, Tatiana
- Schilling, Kelly B.
- Schroeder, Declan C.
- Simpson, Alastair G. B.
- Slamovits, Claudio H.
- Smith, David R.
- Smith, G. Jason
- Smith, Sarah R.
- Sosik, Heidi M.
- Stief, Peter
- Theriot, Edward
- Twary, Scott N.
- Vaulot, Daniel
- Wawrik, Boris
- Wheeler, Glen L.
- Wilson, William H.
- Zingone, Adriana
- Worden, Alexandra Z.
- Venue
- PLoS Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2014-06-24
- Volume
- 12
- Issue
- 6
- Pages
- e1001889
- ISSN
- 1544-9173 (ISSN-L)
- 1545-7885
- PMC
- PMC4068987
- OpenAlex
- W2019619926
- Cited by
- 1,042
- References
- 32
- Citations by year
- 2026: 40 · 2025: 71 · 2024: 68 · 2023: 80 · 2022: 110 · 2021: 128 · 2020: 101 · 2019: 108 · 2018: 93 · 2017: 93 · 2016: 75 · 2015: 55 · 2014: 18 · 2013: 1
- FWCI
- 32.92
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS Biology (publishedVersion, public-domain)
- Europe PMC (PubMed Central) (publishedVersion, public-domain)
- PubMed Central (publishedVersion, public-domain)
- PubMed (publishedVersion)
- CentAUR (University of Reading) (acceptedVersion)
- Helmholtz-Zentrum für Polar-und Meeresforschung (Alfred-Wegener-Institut) (acceptedVersion)
- Helmholtz Centre for Ocean Research Kiel (GEOMAR) (acceptedVersion, other-oa)
- Marine Biological Association (acceptedVersion)
- Journal of Media Literacy Education (submittedVersion, public-domain)
- Smith ScholarWorks (Smith College) (submittedVersion, public-domain)
- HAL (submittedVersion, other-oa)
- CINECA IRIS Institutial research information system (University of Pisa) (submittedVersion, cc-by)
- Open Access Server of the Woods Hole Scientific Community (Woods Hole Scientific Community) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- eScholarship (California Digital Library) (submittedVersion)
- Max Planck Digital Library (submittedVersion)
- Lund University Publications (Lund University) (submittedVersion)
- UTS ePRESS (University of Technology Sydney) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- University of Southern Denmark Research Portal (University of Southern Denmark) (submittedVersion)
- UEA Digital Repository (University of East Anglia) (submittedVersion)
- NORA - Norwegian Open Research Archives (submittedVersion, public-domain)
- Columbia Academic Commons (Columbia University)
- Funders
- Gordon and Betty Moore Foundation
- Università di Macerata
- Centre National de la Recherche Scientifique
- Universidade Federal do Rio de Janeiro
- Natural Environment Research Council (NE/J021296/1, NE/I001751/1, pml010002)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protist diversity and phylogeny
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- transcriptome sequencing, reference sequence database, functional diversity, metatranscriptomics, metagenomics, genome annotation, unculturable microorganisms
- MeSH terms
- Environmental Microbiology, Molecular Sequence Data, Oceans and Seas, Databases, Factual, Sequence Analysis, Biodiversity, Eukaryota, Transcriptome
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