[1] | McLusky DS (1993) Marine and estuarine gradients — An overview. Netherlands Journal of Aquatic Ecology 27: 489–493. doi: 10.1007/bf02334809
|
[2] | Pritchard DW (1989) Estuarine classification - a help or a hindrance. In: Neilson BJ, Kuo A, Brubaker J, editors. Estuarine Circulation. Clifton, NJ: Humana Press. pp. 1–38.
|
[3] | Trigueros JM, Orive E (2000) Tidally driven distribution of phytoplankton blooms in a shallow, macrotidal estuary. J Plankton Res 22: 969–986. doi: 10.1093/plankt/22.5.969
|
[4] | Azam F, Fenchel T, Field JG, Gray JS, Meyer-Reil LA, et al. (1983) The ecological role of water-column microbes in the sea. Mar Ecol Prog Ser 10: 257–263. doi: 10.3354/meps010257
|
[5] | Díez B, Pedrós-Alió C, Massana R (2001) Study of genetic diversity of eukaryotic picoplankton in different oceanic regions by small-subunit rRNA gene cloning and sequencing. Appl Environ Microbiol 67: 2932–2941. doi: 10.1128/aem.67.7.2932-2941.2001
|
[6] | Moon-van der Staay SY, De Wachter R, Vaulot D (2001) Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity. Nature 409: 607–610. doi: 10.1038/35054541
|
[7] | Edgcomb VP, Kysela DT, Teske A, De Vera Gomez A, Sogin ML (2002) Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment. Proc Natl Acad Sci U S A 99: 7658–7662. doi: 10.1073/pnas.062186399
|
[8] | Massana R, Balagué V, Guillou L, Pedrós-Alió C (2004) Picoeukaryotic diversity in an oligotrophic coastal site studied by molecular and culturing approaches. FEMS Microbiol Ecol 50: 231–243. doi: 10.1016/j.femsec.2004.07.001
|
[9] | ?lapeta J, Moreira D, López-García P (2005) The extent of protist diversity: insights from molecular ecology of freshwater eukaryotes. Proc Biol Sci/The Royal Society 272: 2073–2081. doi: 10.1098/rspb.2005.3195
|
[10] | Behnke A, Barger KJ, Bunge J, Stoeck T (2010) Spatio-temporal variations in protistan communities along an O2/H2S gradient in the anoxic Framvaren Fjord (Norway). FEMS Microbiol Ecol 72: 89–102. doi: 10.1111/j.1574-6941.2010.00836.x
|
[11] | Moreira D, López-García P (2002) The molecular ecology of microbial eukaryotes unveils a hidden world. Trends Microbiol 10: 31–38. doi: 10.1016/s0966-842x(01)02257-0
|
[12] | Muylaert K, Sabbe K, Vyverman W (2009) Changes in phytoplankton diversity and community composition along the salinity gradient of the Schelde estuary (Belgium/The Netherlands). Estuar Coast Shelf Sci 82: 335–340. doi: 10.1016/j.ecss.2009.01.024
|
[13] | Lionard M, Muylaert K, Hanoutti A, Maris T, Tackx M, et al. (2008) Inter-annual variability in phytoplankton summer blooms in the freshwater tidal reaches of the Schelde estuary (Belgium). Estuar Coast Shelf Sci 79: 694–700. doi: 10.1016/j.ecss.2008.06.013
|
[14] | Vigil P, Countway P, Rose J, Lonsdale D, Gobler C, et al. (2009) Rapid shifts in dominant taxa among microbial eukaryotes in estuarine ecosystems. Aquat Microb Ecol 54: 83–100. doi: 10.3354/ame01252
|
[15] | Herfort L, Peterson TD, McCue L, Zuber P (2011) Protist 18S rRNA gene sequence analysis reveals multiple sources of organic matter contributing to turbidity maxima of the Columbia River estuary. Mar Ecol Prog Ser 438: 19–31. doi: 10.3354/meps09303
|
[16] | Klein C, Claquin P, Bouchart V, Le Roy B, Véron B (2010) Dynamics of Pseudo-nitzschia spp. and domoic acid production in a macrotidal ecosystem of the Eastern English Channel (Normandy, France). Harmful Algae 9: 218–226. doi: 10.1016/j.hal.2009.10.004
|
[17] | Ubertini M, Lefebvre S, Gangnery A, Grangeré K, Le Gendre R, et al. (2012) Spatial variability of benthic-pelagic coupling in an estuary ecosystem: consequences for microphytobenthos resuspension phenomenon. PloS ONE 7(8): e44155 doi:10.1371/journal.pone.0044155.
|
[18] | Jouenne F, Lefebvre S, Véron B, Lagadeuc Y (2007) Phytoplankton community structure and primary production in small intertidal estuarine-bay ecosystem (eastern English Channel, France). Marine Biology 151: 805–825. doi: 10.1007/s00227-006-0440-z
|
[19] | Jouenne F, Lefebvre S, Véron B, Lagadeuc Y (2005) Biological and physicochemical factors controlling short-term variability in phytoplankton primary production and photosynthetic parameters in a macrotidal ecosystem (eastern English Channel). Estuar Coast Shelf Sci 65: 421–439. doi: 10.1016/j.ecss.2005.05.023
|
[20] | Desprez M, Ducrotoy J-P, Sylvand B (1986) Fluctuations naturelles et évolution artificielle des biocenoses macrozoobenthiques intertidales de trois estuaires des c?tes fran?aises de la Manche. Hydrobiologia 142: 249–270. doi: 10.1007/bf00026763
|
[21] | Aminot A, Kérouel R (2007) Dosage automatique des nutriments dans les eaux marines: méthodes en flux continu. Ifremer. Ed Quae. 187 p.
|
[22] | Welschmeyer N (1994) Fluorometric analysis of chlorophyll chlorophyll b and pheopigments. Limnol Oceanogr 39: 1985–1992. doi: 10.4319/lo.1994.39.8.1985
|
[23] | Bazin P, Jouenne F, Deton-Cabanillas AF, Pérez-Ruzafa á, Véron B (2014) Complex patterns in phytoplankton and microeukaryote diversity along the estuarine continuum. Hydrobiologia 726: 155–178. doi: 10.1007/s10750-013-1761-9
|
[24] | Bourrelly P (1981) Les algues d'eau douce - Tome 1,2 et 3. Paris: Ed Boubée. 572, 577 and 606 p.
|
[25] | Tomas CR (1997) Identifying Marine Phytoplankton. San Diego: Academic Press. 858 p.
|
[26] | John DM, Whitton BA, Brook AJ (2002) The Freshwater Algal Flora of the British Isles: An Identification Guide to Freshwater and Terrestrial Algae. Cambridge: Cambridge University Press. 714 p.
|
[27] | Uterm?hl von H (1931) Neue Wege in der quantitativen Erfassung des Planktons. (Mit besondere Beriicksichtigung des Ultrapanktons). Verh Int Verein Theor Angew Limnol 5: 567–595.
|
[28] | EN 15204 (2006) Water quality - Guidance standard on the enumeration of phytoplankton using inverted microscopy (Uterm?hl technique). Brussels, Belgium: European Committee for Standardization. 39 p.
|
[29] | Lund JWG, Kipling C, Le Cren ED (1958) The Inverted Microscope method of estimating algal numbers and the statistical basis of estimations by counting. Hydrobiologia 11: 143–170. doi: 10.1007/bf00007865
|
[30] | Medlin L, Elwood HJ, Stickel S, Sogin ML (1988) The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71: 491–499. doi: 10.1016/0378-1119(88)90066-2
|
[31] | Hepperle D (2004) SeqAssem. A sequence analysis tool, contig assembler and trace data visualization for molecular sequences. Win32-Version. Distributed by the author. Available: http://www.sequentix.de.
|
[32] | Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403–410. doi: 10.1016/s0022-2836(05)80360-2
|
[33] | Huber T, Faulkner G, Hugenholtz P (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20: 2317–2319. doi: 10.1093/bioinformatics/bth226
|
[34] | Viprey M, Guillou L, Ferréol M, Vaulot D (2008) Wide genetic diversity of picoplanktonic green algae (Chloroplastida) in the Mediterranean Sea uncovered by a phylum-biased PCR approach. Environ Microbiol 10: 1804–1822. doi: 10.1111/j.1462-2920.2008.01602.x
|
[35] | Katoh K, Kuma K, Toh H, Miyata T (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33: 511–518. doi: 10.1093/nar/gki198
|
[36] | Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537–7541. doi: 10.1128/aem.01541-09
|
[37] | Romari K, Vaulot D (2004) Composition and temporal variability of picoeukaryote communities at a coastal site of the English Channel from 18S rDNA sequences. Limnol Oceanogr 49: 784–798. doi: 10.4319/lo.2004.49.3.0784
|
[38] | Chao A (1984) Non parametric estimation of the number of classes in a population. Scand J Statist 11: 265–270.
|
[39] | Hammer ?, Harper DAT, Ryan PD (2001) PAST: Paleontological statistics software package for education and data analysis. Paleontologia Electronica 4: 1–9.
|
[40] | Massana R, Guillou L, Díez B, Pedro C (2002) Unveiling the organisms behind novel eukaryotic ribosomal DNA sequences from the Ocean. Appl Environ Microbiol 68: 4554–4558. doi: 10.1128/aem.68.9.4554-4558.2002
|
[41] | Massana R, Castresana J, Balague V, Guillou L, Romari K, et al. (2004) Phylogenetic and ecological analysis of Novel Marine Stramenopiles. Appl Environ Microbiol 70: 3528–3534. doi: 10.1128/aem.70.6.3528-3534.2004
|
[42] | Charvet S, Vincent WF, Lovejoy C (2011) Chrysophytes and other protists in High Arctic lakes: molecular gene surveys, pigment signatures and microscopy. Polar Biol 35: 733–748. doi: 10.1007/s00300-011-1118-7
|
[43] | Luo W, Bock C, Li HR, Padisák J, Krienitz L (2011) Molecular and microscopic diversity of planktonic eukaryotes in the oligotrophic Lake Stechlin (Germany). Hydrobiologia 661: 133–143. doi: 10.1007/s10750-010-0510-6
|
[44] | Kolodziej K, Stoeck T (2007) Cellular identification of a novel uncultured marine stramenopile (MAST-12 Clade) small-subunit rRNA gene sequence from a norwegian estuary by use of fluorescence in situ hybridization-scanning electron microscopy. Appl Environ Microbiol 73: 2718–2726. doi: 10.1128/aem.02158-06
|
[45] | Massana R, Terrado R, Forn I, Lovejoy C, Pedrós-Alió C (2006) Distribution and abundance of uncultured heterotrophic flagellates in the world oceans. Environ Microbiol 8: 1515–1522. doi: 10.1111/j.1462-2920.2006.01042.x
|
[46] | del Campo J, Massana R (2011) Emerging diversity within chrysophytes, choanoflagellates and bicosoecids based on molecular surveys. Protist 162: 435–448. doi: 10.1016/j.protis.2010.10.003
|
[47] | Andersen RA, Van de Peer Y, Potter D, Sexton JP, Kawachi M, et al. (1999) Phylogenetic analysis of the SSU rRNA from members of the Chrysophyceae. Protist 150: 71–84. doi: 10.1016/s1434-4610(99)70010-6
|
[48] | Boenigk J, Pfandl K, Stadler P, Chatzinotas A (2005) High diversity of the “Spumella-like” flagellates: an investigation based on the SSU rRNA gene sequences of isolates from habitats located in six different geographic regions. Environ Microbiol 7: 685–697. doi: 10.1111/j.1462-2920.2005.00743.x
|
[49] | Shi XL, Marie D, Jardillier L, Scanlan DJ, Vaulot D (2009) Groups without cultured representatives dominate eukaryotic picophytoplankton in the oligotrophic South East Pacific Ocean. PloS ONE 4(10): e7657 doi:10.1371/journal.pone.0007657.
|
[50] | Zuendorf A, Bunge J, Behnke A, Barger KJ, Stoeck T (2006) Diversity estimates of microeukaryotes below the chemocline of the anoxic Mariager Fjord, Denmark. FEMS Microbiol Ecol 58: 476–491. doi: 10.1111/j.1574-6941.2006.00171.x
|
[51] | Bachvaroff TR, Kim S, Guillou L, Delwiche CF, Coats DW (2012) Molecular diversity of the syndinean genus Euduboscquella based on single-cell PCR analysis. Appl Environ Microbiol 78: 334–345. doi: 10.1128/aem.06678-11
|
[52] | Deane JA, Strachan IM, Saunders GW, Hill DRA, Mcfadden GI (2002) Cryptomonad evolution: nuclear 18S rDNA phylogeny versus cell morphology and pigmentation. J Phycol 38 (6): 1236–1244. doi: 10.1046/j.1529-8817.2002.01250.x
|
[53] | Not F, Valentin K, Romari K, Lovejoy C, Massana R, et al. (2007) Picobiliphytes: A marine picoplanktonic algal group with unknown affinities to other eukaryotes. Science 315: 252–254. doi: 10.1126/science.1136264
|
[54] | Seoane S, Laza A, Orive E (2006) Monitoring phytoplankton assemblages in estuarine waters: The application of pigment analysis and microscopy to size-fractionated samples. Estuar Coast Shelf Sci 67: 343–354. doi: 10.1016/j.ecss.2005.10.020
|
[55] | Harrison PJ, Yin K, Lee JHW, Gan J, Liu H (2008) Physical–biological coupling in the Pearl River Estuary. Cont Shelf Res 28: 1405–1415. doi: 10.1016/j.csr.2007.02.011
|
[56] | Clay BL, Kugrens P (1999) Characterization of Hemiselmis amylosa sp. nov. and phylogenetic placement of the blue-green Cryptomonads H. amylosa and Falcomonas daucoides. Protist 150: 297–310. doi: 10.1016/s1434-4610(99)70031-3
|
[57] | Savin MC, Martin JL, LeGresley M, Giewat M, Rooney-Varga J (2004) Plankton diversity in the Bay of Fundy as measured by morphological and molecular methods. Microb Ecol 48: 51–65. doi: 10.1007/s00248-003-1033-8
|
[58] | Laza-Martínez A (2012) Urgorri complanatus gen. et sp. nov. (Cryptophyceae), a red-tide-forming species in brackish waters. J Phycol 48: 423–435. doi: 10.1111/j.1529-8817.2012.01130.x
|
[59] | Shalchian-Tabrizi K, Br?te J, Logares R, Klaveness D, Berney C, et al. (2008) Diversification of unicellular eukaryotes: cryptomonad colonizations of marine and fresh waters inferred from revised 18S rRNA phylogeny. Environ Microbiol 10: 2635–2644. doi: 10.1111/j.1462-2920.2008.01685.x
|
[60] | Alpine A, Cloern J (1988) Phytoplankton growth rates in a light-limited environment, San Francisco Bay. Mar Ecol Prog Ser 44: 167–173. doi: 10.3354/meps044167
|
[61] | Wylezich C, Jürgens K (2011) Protist diversity in suboxic and sulfidic waters of the Black Sea. Environ Microbiol 13: 2939–2956. doi: 10.1111/j.1462-2920.2011.02569.x
|
[62] | Trigueros JM, Orive E (2000) Tidally driven distribution of phytoplankton blooms in a shallow, macrotidal estuary. J Plankton Res 22: 969–986. doi: 10.1093/plankt/22.5.969
|
[63] | Quinlan EL, Phlips EJ (2007) Phytoplankton assemblages across the marine to low-salinity transition zone in a blackwater dominated estuary. J Plankton Res 29: 401–416. doi: 10.1093/plankt/fbm024
|
[64] | Caron DA, Countway PD, Brown MV (2004) The growing contributions of molecular biology and immunology to protistan ecology: molecular signatures as ecological tools. J Eukaryot Microbiol 51: 38–48. doi: 10.1111/j.1550-7408.2004.tb00159.x
|
[65] | ?lapeta J, López-García P, Moreira D (2006) Global dispersal and ancient cryptic species in the smallest marine eukaryotes. Mol Biol Evol 23: 23–29. doi: 10.1093/molbev/msj001
|
[66] | Liu H, Probert I, Uitz J, Claustre H, Aris-Brosou S, et al. (2009) Extreme diversity in noncalcifying haptophytes explains a major pigment paradox in open oceans. Proc Natl Acad Sci U S A 106: 12803–12808. doi: 10.1073/pnas.0905841106
|
[67] | Stoeck T, Hayward B, Taylor GT, Varela R, Epstein SS (2006) A multiple PCR-primer approach to access the microeukaryotic diversity in environmental samples. Protist 157: 31–43. doi: 10.1016/j.protis.2005.10.004
|
[68] | Zhu F, Massana R, Not F, Marie D, Vaulot D (2005) Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene. FEMS Microbiol Ecol 52: 79–92. doi: 10.1016/j.femsec.2004.10.006
|
[69] | Muylaert K, Van Mieghem R, Sabbe K, Tackx M, Vyverman W (2000) Dynamics and trophic roles of heterotrophic protists in the plankton of a freshwater tidal estuary. Hydrobiologia 432: 25–36. doi: 10.1023/a:1004017018702
|
[70] | Potvin M, Lovejoy C (2009) PCR-based diversity estimates of artificial and environmental 18S rRNA gene libraries. J Eukaryot Microbiol 56: 174–181. doi: 10.1111/j.1550-7408.2008.00386.x
|
[71] | Caron DA, Countway PD, Savai P, Gast RJ, Schnetzer A, et al. (2009) Defining DNA-based operational taxonomic units for microbial eukaryote ecology. Appl Environ Microbiol 75: 5797–5808. doi: 10.1128/aem.00298-09
|