Abstract
We analyzed picoeukaryote assemblages in the German Bight at the Helgoland time series site by sequencing cloned eukaryotic 18S rRNA genes in six genetic libraries plus one library from the Orkney Islands from a cruise of opportunity. The libraries were constructed from environmental samples collected at different periods of the year. The same samples were also analyzed using a fingerprinting technique, single-strand conformational polymorphism (SSCP), and DNA microarrays with class-level oligonucleotide probes. One hundred unique clones were analyzed from each library, thus insuring over 85% coverage of the library. The V4 region of the 18S rRNA gene was sequenced from each of these clones, thus providing the most discrimination among the clones. The nonphotosynthetic picoeukaryotic component dominated over the photosynthetic one and was represented by the ciliates at 45% and group II alveolates at 42%. Prasinophytes dominated the photosynthetic group at 40%, but other picoplankton groups, such as bolidomonads and chrysophytes, were also present. Totally novel groups were found in the cryptomonads and in the dinoflagellates. A new algal group sister to the cryptophyte nuclear gene and the glaucocystophytes was also found. These three groups have been found in other picoeukaryotic planktonic clone libraries. SSCP analyses at closer time intervals suggest that clone libraries should be made at weekly intervals if succession in the picoeukaryotic plankton community is to be monitored accurately. A comparison of annual samples suggests thatthere appears to be an annual cycle with regard to species composition. Microarray analysis supported the clone library data and offered a faster means of community analysis, which can be performed with similar accuracy and with higher throughput for a more in-depth analysis.
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References
RA Andersen, GW Saunders and MP Paskind, Ultrastructure and 18S rRNA gene sequence for Pelagomonas calceolata gen. and sp. nov. and the description of a new algal class, the Pelagophyceae classis nov. J Phycol 29 (1993) 701-715
DA Caron, ER Peele, EL Lim and MR Dennette, Picoplankton and nanoplankton and their trophic coupling in the surface waters of the Sargasso Sea south of Bermuda. Limnol Oceanogr 44 (1999) 259-272
B Diez, C Pedros-Alio and R Massana, Study of genetic diversity of eukaryotic picoplankton in different oceanic regions by small-subunit rRNA gene cloning and sequencing. Appl Environ Microbiol 69 (2001) 2340-2443
G Drebes, On the life history of the marine plankton diatom Stephanopyxis palmeriana. Helgol Wiss Meeresforsch 13 (1966) 101-114
B Edvardsen, W Eikrem and JC Green, Phylogenetic reconstructions of the Haptophyta inferred from rRNA sequences and available morphological data. Phycologia 39 (2000) 19-35
HJ Elwood, GJ Olsen and ML Sogin, The small-subunit ribosomal RNA gene sequences from the hypotrichous ciliates Oxytricha nova and Stylonychia pustulata. Mol Biol and Evol 2 (1985) 399-410
RW Eppley, RW Holmes and JDH Strickland, Sinking rates of the marine phytoplankton measured with a fluorochromometer. J of Exp Mar Biol and Ecol 1 (1967) 191-208
L Guillou, M-J Chrétiennot-Dinet and LK Medlin, Bolidomonas: a new genus with two species belonging to a new algal class, the Bolidophyceae (Heterokonta). J of Phycol 35 (1999) 368-381
JP Huelsenbeck, F Ronquist and R Nielsen, Evolution-Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294 (2001) 2310-2314
M Kawachi, I Inouye and D Honda, The Pinguiophyceae classis nova, a new class of chromophyte algae whose members produce large amounts of omega-3 fatty acids. Phycol Res 50 (2002) 31-47
U John, A Cembella, C Hummert, M Elbrächter, R Groben and LK Meldin, Discrimination of the toxigenic dinoflagellates Alexandrium tamarense and A. ostenfeldii in co-occurring natural populations from Scottish coastal waters. Eur J Phycol 38 (2003) 25-40
M Lange, L Guillou, D Vaulot, N Simon, RI Amann, W Ludwig and LK Medlin, Identification of the class Prymnesiophyceae and the genus Pheocystis with ribosomal RNA-target nucleic acid probes detected by flow cytometry. J Phycol 32 (1996) 858-868
P Lopez-Garcia, F Rodriguez-Valera and C Pedros-Alio, Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton. Nature 409 (2001) 603-607
W Ludwig, O Strunk and R Westram, ARB: a software environment for sequence data. Nucleic Acids Res 25 (2004) 1363-1371
R Massana, L Guillou and B Diez, Unveiling the organisms behind novel eukaryotic ribosomal DNA sequences from the ocean. Appl Environ Microbiol 68 (2002) 4554-4558
R Massana, V Balagué and L Guillou, Picoeukaryotic diversity in an oligotrophic coastal site studied by molecular and culturing approaches. FEMS Microbiol Ecol 50 (2004) 231-243
L Medlin, HJ Elwood and S Stickel, The characterization of enzymatically amplified eukaryotic 16S-like rRNA coding regions. Gene 71 (1988) 491-499
Ø Moestrup, Further studies of presumedly primitive green algae, including the description of Pedinophyceae class. nov. and Resultor gen. nov. J Phycol 27 (1991) 119-133
SY Moon-van der Stay, R Wachter De and D Vaulot, Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity. Nature 409 (2001) 607-610
G Muyzer, EC Waal De and AG Uittrtlinden, Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding of the 16S rRNA. Appl Environ Microbiol 59 (1993) 695-700
F Not, M Latasa and D Marie, Picoplanktonic Prasinophyceae abundance in the western English Channel determined by fluorescent in situ hybridization (F.I.S.H.). Appl Environ Microbiol 70 (2004) 4064-4072
NR Pace, A molecular view of microbial diversity and the biosphere. Science 276 (1997) 734-740
D Posada and KA Crandall, Modeltest: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
M Rappé and S Giovannoni, Culturing the microbial majority. Annu Rev Microbiol 57 (2003) 369-394
K Romari and D Vaulot, Composition and temporal variability of picoeukaryote communities at a coastal site of the English Channel from 18S rDNA sequences. Limnol Oceanogr 49 (2004) 784-798
F Schwieger and CC Tebbe, A new approach to utilize PCR-single-strand-conformation polymorphism for 16s rRNA gene-based microbial community analysis. Appl Environ Microbiol 64 (1998) 4870-4876
N Simon, L Campbell, E Ornolfsdottir, R Groben, L Guillou, M Lange and LK Medlin, Oligonucleotide probes for the identification of three algal groups by dot blot and fluorescent whole-cell hybridization. J Eukaryot Microbiol 47 (2000) 76-84
DL Swofford, PAUP*, Phylogenetic Analysis Using Parsimony, Version 4.0 Beta version 8, program and documentation. Champaign, IL, USA: Illinois Natural History Survey, University of Illinois (2002).
KH Wiltshire and C-D Dürselen, Revision and quality analysis of the Helgoland Reede long-term phytoplankton data archive. Helgol Mar Res 58 (2004) 252-268
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This work was funded by the EU PICODIV project EVK3-CT199-00021.
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Medlin, L.K., Metfies, K., Mehl, H. et al. Picoeukaryotic Plankton Diversity at the Helgoland Time Series Site as Assessed by Three Molecular Methods. Microb Ecol 52, 53–71 (2006). https://doi.org/10.1007/s00248-005-0062-x
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DOI: https://doi.org/10.1007/s00248-005-0062-x