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

10/01/2015
Environmental Microbiology
17 (10) pp. 4035-4049

Type

Article dans des revues

Authors

Massana Ramon
Gobet Angélique
Audic Stéphane
Bass David
Bittner Lucie
Boutte Christophe
Chambouvet Aurélie
Christen Richard
Claverie Jean-Michel
Decelle Johan
Dolan John R
Dunthorn Micah
Edvardsen Bente
Forn Irene
Forster Dominik
Guillou Laure
Jaillon Olivier
Kooistra Wiebe
Logares Ramiro
Mahé Frédéric
Not Fabrice
Ogata Hiroyuki
Pawlowski Jan
Pernice Massimo C.
Probert Ian
Romac Sarah
Richards Thomas
Santini Sébastien
Shalchian-Tabrizi Kamran
Siano Raffaele
Simon Nathalie
Stoeck Thorsten
Vaulot Daniel
Zingone Adriana
De Vargas Colomban

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.