Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing

Type Article
Date 2015-10
Language English
Author(s) Massana Ramon1, Gobet AngeliqueORCID2, 3, Audic Stephane2, 3, Bass David4, 5, Bittner Lucie2, 3, 6, Boutte Christophe2, 3, Chambouvet Aurelie7, Christen Richard8, Claverie Jean-Michel9, Decelle Johan2, 3, Dolan John R.10, Dunthorn Micah6, Edvardsen Bente11, Forn Irene1, Forster Dominik6, Guillou Laure2, 3, Jaillon Olivier12, Kooistra Wiebe H. C. F.13, Logares Ramiro1, Mahe Frederic6, Not Fabrice2, 3, Ogata Hiroyuki14, Pawlowski Jan15, Pernice Massimo C.1, Probert Ian2, 3, Romac Sarah2, 3, Richards Thomas7, Santini Sebastien9, Shalchian-Tabrizi Kamran11, Siano Raffaele16, Simon Nathalie2, 3, Stoeck Thorsten6, Vaulot Daniel2, 3, Zingone Adriana13, de Vargas Colomban2, 3
Affiliation(s) 1 : CSIC, Inst Ciencias Mar, ES-08003 Barcelona, Catalonia, Spain.
2 : CNRS, Ecol Systemat Evolut, FR-29682 Roscoff, France.
3 : Univ Paris 06, Equipe EPPO Evolut Plancton & PaleoOceans, UMR7144, Roscoff, France.
4 : Nat Hist Museum, London SW7 5BD, England.
5 : Cefas, Weymouth DT4 8UB, Dorset, England.
6 : Univ Kaiserslautern, D-67663 Kaiserslautern, Germany.
7 : Univ Exeter, Biosci, Exeter EX4 4QD, Devon, England.
8 : Univ Nice Sophia Antipolis, CNRS, UMR 7138, FR-06108 Nice, France.
9 : Aix Marseille Univ, CNRS, UMR 7256, FR-13288 Marseille, France.
10 : Univ Paris 06, CNRS, Lab Oceanog Villefranche, UMR 7093, FR-06230 Villefranche Sur Mer, France.
11 : Univ Oslo, Dept Biosci, N-0316 Oslo, Norway.
12 : CEA, Genoscope, FR-91000 Evry, France.
13 : Stn Zool Anton Dohrn, I-80121 Naples, Italy.
14 : Kyoto Univ, Inst Chem Res, Uji, Kyoto 6110011, Japan.
15 : Univ Geneva, CH-1211 Geneva, Switzerland.
16 : Ifremer DYNECO Pelagos, Plouzane, France.
Source Environmental Microbiology (1462-2912) (Wiley-blackwell), 2015-10 , Vol. 17 , N. 10 , P. 4035-4049
DOI 10.1111/1462-2920.12955
WOS© Times Cited 260
Note Special Issue: Marine Microbes
Abstract Although protists are critical components of marine ecosystems, they are still poorly characterized. Here we analysed the taxonomic diversity of planktonic and benthic protist communities collected in six distant European coastal sites. Environmental deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) from three size fractions (pico-, nano- and micro/mesoplankton), as well as from dissolved DNA and surface sediments were used as templates for tag pyrosequencing of the V4 region of the 18S ribosomal DNA. Beta-diversity analyses split the protist community structure into three main clusters: picoplankton-nanoplankton-dissolved DNA, micro/mesoplankton and sediments. Within each cluster, protist communities from the same site and time clustered together, while communities from the same site but different seasons were unrelated. Both DNA and RNA-based surveys provided similar relative abundances for most class-level taxonomic groups. Yet, particular groups were overrepresented in one of the two templates, such as marine alveolates (MALV)-I and MALV-II that were much more abundant in DNA surveys. Overall, the groups displaying the highest relative contribution were Dinophyceae, Diatomea, Ciliophora and Acantharia. Also, well represented were Mamiellophyceae, Cryptomonadales, marine alveolates and marine stramenopiles in the picoplankton, and Monadofilosa and basal Fungi in sediments. Our extensive and systematic sequencing of geographically separated sites provides the most comprehensive molecular description of coastal marine protist diversity to date.
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Massana Ramon, Gobet Angelique, Audic Stephane, Bass David, Bittner Lucie, Boutte Christophe, Chambouvet Aurelie, Christen Richard, Claverie Jean-Michel, Decelle Johan, Dolan John R., Dunthorn Micah, Edvardsen Bente, Forn Irene, Forster Dominik, Guillou Laure, Jaillon Olivier, Kooistra Wiebe H. C. F., Logares Ramiro, Mahe Frederic, Not Fabrice, Ogata Hiroyuki, Pawlowski Jan, Pernice Massimo C., Probert Ian, Romac Sarah, Richards Thomas, Santini Sebastien, Shalchian-Tabrizi Kamran, Siano Raffaele, Simon Nathalie, Stoeck Thorsten, Vaulot Daniel, Zingone Adriana, de Vargas Colomban (2015). Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing. Environmental Microbiology, 17(10), 4035-4049. Publisher's official version : https://doi.org/10.1111/1462-2920.12955 , Open Access version : https://archimer.ifremer.fr/doc/00275/38594/