title: Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing.
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.
authors.affiliation: Institut de Ciències del Mar (CSIC), ES-08003, Barcelona, Catalonia, Spain.
authors.forename: Ramon
authors.initials: R
authors.lastname: Massana
authors.affiliation: Ecologie Systematique Evolution, CNRS, FR-29682, Roscoff, France.|UMR7144 - Equipe EPPO: Evolution du Plancton et PaléoOcéans, UPMC Université Paris 06, Roscoff, France.
authors.forename: Angélique
authors.initials: A
authors.lastname: Gobet
authors.affiliation: Ecologie Systematique Evolution, CNRS, FR-29682, Roscoff, France.|UMR7144 - Equipe EPPO: Evolution du Plancton et PaléoOcéans, UPMC Université Paris 06, Roscoff, France.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Audic
authors.affiliation: The Natural History Museum, London, SW7 5BD, UK.|Cefas, Weymouth, Dorset, DT4 8UB, UK.
authors.forename: David
authors.initials: D
authors.lastname: Bass
authors.affiliation: Ecologie Systematique Evolution, CNRS, FR-29682, Roscoff, France.|UMR7144 - Equipe EPPO: Evolution du Plancton et PaléoOcéans, UPMC Université Paris 06, Roscoff, France.|University of Kaiserslautern, D-67663, Kaiserslautern, Germany.
authors.forename: Lucie
authors.initials: L
authors.lastname: Bittner
authors.affiliation: Ecologie Systematique Evolution, CNRS, FR-29682, Roscoff, France.|UMR7144 - Equipe EPPO: Evolution du Plancton et PaléoOcéans, UPMC Université Paris 06, Roscoff, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Boutte
authors.affiliation: Biosciences, University of Exeter, Exeter, EX4 4QD, UK.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Chambouvet
authors.affiliation: CNRS, UMR 7138, Université Nice Sophia Antipolis, FR-06108, Nice, France.
authors.forename: Richard
authors.initials: R
authors.lastname: Christen
authors.affiliation: CNRS, UMR 7256, Aix-Marseille Université, FR-13288, Marseille, France.
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Claverie
authors.affiliation: Ecologie Systematique Evolution, CNRS, FR-29682, Roscoff, France.|UMR7144 - Equipe EPPO: Evolution du Plancton et PaléoOcéans, UPMC Université Paris 06, Roscoff, France.
authors.forename: Johan
authors.initials: J
authors.lastname: Decelle
authors.affiliation: CNRS, UMR 7093, UPMC Université Paris 06, Laboratoire d'Océanographie de Villefranche, FR-06230, Villefranche-sur-Mer, France.
authors.forename: John R
authors.initials: JR
authors.lastname: Dolan
authors.affiliation: University of Kaiserslautern, D-67663, Kaiserslautern, Germany.
authors.forename: Micah
authors.initials: M
authors.lastname: Dunthorn
authors.affiliation: Department Biosciences, University of Oslo, N-0316, Oslo, Norway.
authors.forename: Bente
authors.initials: B
authors.lastname: Edvardsen
authors.affiliation: Institut de Ciències del Mar (CSIC), ES-08003, Barcelona, Catalonia, Spain.
authors.forename: Irene
authors.initials: I
authors.lastname: Forn
authors.affiliation: University of Kaiserslautern, D-67663, Kaiserslautern, Germany.
authors.forename: Dominik
authors.initials: D
authors.lastname: Forster
authors.affiliation: Ecologie Systematique Evolution, CNRS, FR-29682, Roscoff, France.|UMR7144 - Equipe EPPO: Evolution du Plancton et PaléoOcéans, UPMC Université Paris 06, Roscoff, France.
authors.forename: Laure
authors.initials: L
authors.lastname: Guillou
authors.affiliation: CEA, Genoscope, 2 rue Gaston Crémieux, FR-91000, Evry, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Jaillon
authors.affiliation: Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121, Naples, Italy.
authors.forename: Wiebe H C F
authors.initials: WH
authors.lastname: Kooistra
authors.affiliation: Institut de Ciències del Mar (CSIC), ES-08003, Barcelona, Catalonia, Spain.
authors.forename: Ramiro
authors.initials: R
authors.lastname: Logares
authors.affiliation: University of Kaiserslautern, D-67663, Kaiserslautern, Germany.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Mahé
authors.affiliation: Ecologie Systematique Evolution, CNRS, FR-29682, Roscoff, France.|UMR7144 - Equipe EPPO: Evolution du Plancton et PaléoOcéans, UPMC Université Paris 06, Roscoff, France.
authors.forename: Fabrice
authors.initials: F
authors.lastname: Not
authors.affiliation: Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Ogata
authors.affiliation: University of Geneva, CH-1211, Geneva, Switzerland.
authors.forename: Jan
authors.initials: J
authors.lastname: Pawlowski
authors.affiliation: Institut de Ciències del Mar (CSIC), ES-08003, Barcelona, Catalonia, Spain.
authors.forename: Massimo C
authors.initials: MC
authors.lastname: Pernice
authors.affiliation: Ecologie Systematique Evolution, CNRS, FR-29682, Roscoff, France.|UMR7144 - Equipe EPPO: Evolution du Plancton et PaléoOcéans, UPMC Université Paris 06, Roscoff, France.
authors.forename: Ian
authors.initials: I
authors.lastname: Probert
authors.affiliation: Ecologie Systematique Evolution, CNRS, FR-29682, Roscoff, France.|UMR7144 - Equipe EPPO: Evolution du Plancton et PaléoOcéans, UPMC Université Paris 06, Roscoff, France.
authors.forename: Sarah
authors.initials: S
authors.lastname: Romac
authors.affiliation: Biosciences, University of Exeter, Exeter, EX4 4QD, UK.
authors.forename: Thomas
authors.initials: T
authors.lastname: Richards
authors.affiliation: CNRS, UMR 7256, Aix-Marseille Université, FR-13288, Marseille, France.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Santini
authors.affiliation: Department Biosciences, University of Oslo, N-0316, Oslo, Norway.
authors.forename: Kamran
authors.initials: K
authors.lastname: Shalchian-Tabrizi
authors.affiliation: Ifremer DYNECO/Pelagos, BP 7029280, Plouzané, France.
authors.forename: Raffaele
authors.initials: R
authors.lastname: Siano
authors.affiliation: Ecologie Systematique Evolution, CNRS, FR-29682, Roscoff, France.|UMR7144 - Equipe EPPO: Evolution du Plancton et PaléoOcéans, UPMC Université Paris 06, Roscoff, France.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Simon
authors.affiliation: University of Kaiserslautern, D-67663, Kaiserslautern, Germany.
authors.forename: Thorsten
authors.initials: T
authors.lastname: Stoeck
authors.affiliation: Ecologie Systematique Evolution, CNRS, FR-29682, Roscoff, France.|UMR7144 - Equipe EPPO: Evolution du Plancton et PaléoOcéans, UPMC Université Paris 06, Roscoff, France.
authors.forename: Daniel
authors.initials: D
authors.lastname: Vaulot
authors.affiliation: Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121, Naples, Italy.
authors.forename: Adriana
authors.initials: A
authors.lastname: Zingone
authors.affiliation: Ecologie Systematique Evolution, CNRS, FR-29682, Roscoff, France.|UMR7144 - Equipe EPPO: Evolution du Plancton et PaléoOcéans, UPMC Université Paris 06, Roscoff, France.
authors.forename: Colomban
authors.initials: C
authors.lastname: de Vargas
mesh_terms: D056893:Alveolata / Q000235:genetics*; D001483:Base Sequence; D044822:Biodiversity; D017753:Ecosystem; D005060:Europe; D005658:Fungi / Q000235:genetics; D019015:Geologic Sediments / Q000382:microbiology*; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D010933:Plankton / Q000145:classification* / Q000235:genetics*; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D012623:Seawater / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D058009:Stramenopiles / Q000235:genetics*
chemical_list: D012337:RNA, Ribosomal, 18S