Benthic protists: the under-charted majority.
Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists have received relatively little attention. We therefore hypothesize that current diversity surveys have only skimmed the surface of protist diversity in marine sediments, which may harbor greater diversity than planktonic environments. We tested this by analyzing sequences of the hypervariable V4 18S rRNA from benthic and planktonic protist communities sampled in European coastal regions. Despite a similar number of OTUs in both realms, richness estimations indicated that we recovered at least 70% of the diversity in planktonic protist communities, but only 33% in benthic communities. There was also little overlap of OTUs between planktonic and benthic communities, as well as between separate benthic communities. We argue that these patterns reflect the heterogeneity and diversity of benthic habitats. A comparison of all OTUs against the Protist Ribosomal Reference database showed that a higher proportion of benthic than planktonic protist diversity is missing from public databases; similar results were obtained by comparing all OTUs against environmental references from NCBI's Short Read Archive. We suggest that the benthic realm may therefore be the world's largest reservoir of marine protist diversity, with most taxa at present undescribed.
Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger Str. 14, D-67663 Kaiserslautern, Germany.
Dominik
D
Forster
Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger Str. 14, D-67663 Kaiserslautern, Germany.
Micah
M
Dunthorn
Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger Str. 14, D-67663 Kaiserslautern, Germany.
Fréderic
F
Mahé
Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR CNRS UMR 7093 and Laboratoire d'Océanographie de Villefranche-sur-Mer, Université Paris 06, F-06230 Villefranche-sur-Mer, France.
John R
JR
Dolan
Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France.
Stéphane
S
Audic
Department of Life Sciences, the Natural History Museum London, Cromwell Road, London SW7 5BD, UK Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, the Nothe, Weymouth, Dorset DT4 8UB, UK.
David
D
Bass
Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger Str. 14, D-67663 Kaiserslautern, Germany Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France Sorbonne Universités, UPMC, CNRS, Institut de Biologie Paris-Seine (IBPS), Evolution Paris Seine, F-75005 Paris, France.
Lucie
L
Bittner
Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France.
Christophe
C
Boutte
CNRS, UMR 7138 & Université de Nice-Sophia Antipolis, F-06103 Nice cedex 2, France Université de Nice-Sophia Antipolis & CNRS, UMR 7138 F-06103 Nice cedex 2, France.
Richard
R
Christen
CNRS, Aix-Marseille Université, IGS UMR7256, F-13288 Marseille, France.
Jean-Michel
JM
Claverie
Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France.
Johan
J
Decelle
Department of BioSciences, University of Oslo, Blindern, 0316 N-Oslo, Norway.
Bente
B
Edvardsen
Department of BioSciences, University of Oslo, Blindern, 0316 N-Oslo, Norway.
Elianne
E
Egge
Department of BioSciences, University of Oslo, Blindern, 0316 N-Oslo, Norway.
Wenche
W
Eikrem
Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France CNRS, UMR 8227 & UPMC Université Paris 06, Station Biologique de Roscoff, F-29682 Roscoff, France.
Angélique
A
Gobet
Stazione Zoologica Anton Dohrn, Villa Comunale 1, I-80121, Naples, Italy.
Wiebe H C F
WH
Kooistra
Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain.
Ramiro
R
Logares
Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain.
Ramon
R
Massana
Stazione Zoologica Anton Dohrn, Villa Comunale 1, I-80121, Naples, Italy.
Marina
M
Montresor
Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France.
Fabrice
F
Not
Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR CNRS UMR 7093 and Laboratoire d'Océanographie de Villefranche-sur-Mer, Université Paris 06, F-06230 Villefranche-sur-Mer, France Institute for Chemical Research, Kyoto University, Uji, 611-0011, Japan.
Hiroyuki
H
Ogata
Department of Genetics and Evolution, University of Geneva, 4, Boulevard d'Yvoy, CH-1211 Geneva, Switzerland.
Jan
J
Pawlowski
Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain.
Massimo C
MC
Pernice
Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France.
Sarah
S
Romac
Department of BioSciences, University of Oslo, Blindern, 0316 N-Oslo, Norway.
Kamran
K
Shalchian-Tabrizi
Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France.
Nathalie
N
Simon
Biosciences, University of Exeter, Exeter, EX4 4QD, UK.
Thomas A
TA
Richards
CNRS, Aix-Marseille Université, IGS UMR7256, F-13288 Marseille, France.
Sébastien
S
Santini
Stazione Zoologica Anton Dohrn, Villa Comunale 1, I-80121, Naples, Italy.
Diana
D
Sarno
Ifremer, Centre de Brest DYNECO/Pelagos Technopôle Brest Iroise, BP 7029280 Plouzané, France.
Raffaele
R
Siano
Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France.
Daniel
D
Vaulot
CEA, Genoscope, 2 rue Gaston Crémieux, F-91000 Evry, France.
Patrick
P
Wincker
Stazione Zoologica Anton Dohrn, Villa Comunale 1, I-80121, Naples, Italy.
Adriana
A
Zingone
Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France.
Colomban
C
de Vargas
Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger Str. 14, D-67663 Kaiserslautern, Germany stoeck@rhrk.uni-kl.de.
Thorsten
T
Stoeck
D059001:Aquatic Organisms / Q000145:classification* / Q000302:isolation & purification*; D001483:Base Sequence; D044822:Biodiversity; D004247:DNA / Q000235:genetics; D017377:Diatoms / Q000145:classification / Q000302:isolation & purification; D017753:Ecosystem; D056908:Foraminifera / Q000145:classification / Q000302:isolation & purification; D019015:Geologic Sediments / Q000382:microbiology* / Q000469:parasitology*; D060086:Hydrothermal Vents / Q000382:microbiology* / Q000469:parasitology*; D010802:Phylogeny; D010933:Plankton / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D017422:Sequence Analysis, DNA
D012337:RNA, Ribosomal, 18S; D004247:DNA
benthic microbial communities; coastal environments; high-throughput sequencing; protist diversity