title: Deep-branching novel lineages and high diversity of haptophytes in the Skagerrak (Norway) uncovered by 454 pyrosequencing.
abstract: Microalgae in the division Haptophyta may be difficult to identify to species by microscopy because they are small and fragile. Here, we used high-throughput sequencing to explore the diversity of haptophytes in outer Oslofjorden, Skagerrak, and supplemented this with electron microscopy. Nano- and picoplanktonic subsurface samples were collected monthly for 2 yr, and the haptophytes were targeted by amplification of RNA/cDNA with Haptophyta-specific 18S ribosomal DNA V4 primers. Pyrosequencing revealed higher species richness of haptophytes than previously observed in the Skagerrak by microscopy. From ca. 400,000 reads we obtained 156 haptophyte operational taxonomic units (OTUs) after rigorous filtering and 99.5% clustering. The majority (84%) of the OTUs matched environmental sequences not linked to a morphological species, most of which were affiliated with the order Prymnesiales. Phylogenetic analyses including Oslofjorden OTUs and available cultured and environmental haptophyte sequences showed that several of the OTUs matched sequences forming deep-branching lineages, potentially representing novel haptophyte classes. Pyrosequencing also retrieved cultured species not previously reported by microscopy in the Skagerrak. Electron microscopy revealed species not yet genetically characterised and some potentially novel taxa. This study contributes to linking genotype to phenotype within this ubiquitous and ecologically important protist group, and reveals great, unknown diversity.
authors.affiliation: Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316, Oslo, Norway.
authors.forename: Elianne S
authors.initials: ES
authors.lastname: Egge
authors.forename: Wenche
authors.initials: W
authors.lastname: Eikrem
authors.forename: Bente
authors.initials: B
authors.lastname: Edvardsen
mesh_terms: D058893:DNA Barcoding, Taxonomic; D017931:DNA Primers / Q000737:chemistry; D048028:DNA, Algal / Q000235:genetics*; D004275:DNA, Ribosomal / Q000235:genetics*; D014644:Genetic Variation; D005838:Genotype; D058087:Haptophyta / Q000145:classification / Q000235:genetics* / Q000648:ultrastructure; D059014:High-Throughput Nucleotide Sequencing; D058086:Microalgae / Q000145:classification / Q000235:genetics* / Q000648:ultrastructure; D008854:Microscopy, Electron; D009664:Norway; D010641:Phenotype; D010802:Phylogeny; D012337:RNA, Ribosomal, 18S / Q000235:genetics*
chemical_list: D017931:DNA Primers; D048028:DNA, Algal; D004275:DNA, Ribosomal; D012337:RNA, Ribosomal, 18S
keywords: 18S rDNA; Haptophyta; Oslofjorden; electron microscopy; environmental sequencing; high-throughput sequencing; phylogeny; protist; richness
references.citation: Science. 2012 Sep 21;337(6101):1546-50
references.pmid: 22997339
references.citation: Proc Natl Acad Sci U S A. 2012 Oct 30;109(44):18000-5
references.pmid: 23071304
references.citation: Appl Environ Microbiol. 2009 Dec;75(23):7537-41
references.pmid: 19801464
references.citation: Bioinformatics. 2012 Dec 1;28(23):3144-6
references.pmid: 23023983
references.citation: Proc Biol Sci. 2006 Dec 22;273(1605):3047-55
references.pmid: 17015309
references.citation: ISME J. 2012 Aug;6(8):1586-601
references.pmid: 22402396
references.citation: BMC Bioinformatics. 2008 Apr 25;9:212
references.pmid: 18439255
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D597-604
references.pmid: 23193267
references.citation: J Cell Biol. 1963 Apr;17:208-12
references.pmid: 13986422
references.citation: PLoS One. 2009 Oct 29;4(10):e7657
references.pmid: 19893617
references.citation: J Eukaryot Microbiol. 2012 Mar-Apr;59(2):185-7
references.pmid: 22236102
references.citation: Proc Natl Acad Sci U S A. 2009 Aug 4;106(31):12803-8
references.pmid: 19622724
references.citation: Mol Ecol. 2010 Mar;19 Suppl 1:21-31
references.pmid: 20331767
references.citation: PLoS One. 2009 Sep 29;4(9):e7143
references.pmid: 19787059
references.citation: ISME J. 2010 Sep;4(9):1180-92
references.pmid: 20393575
references.citation: Environ Microbiol. 2007 May;9(5):1219-32
references.pmid: 17472636
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6
references.pmid: 23193283
references.citation: PLoS One. 2013 Sep 12;8(9):e74371
references.pmid: 24069303
references.citation: BMC Genomics. 2011 May 19;12:245
references.pmid: 21592414
references.citation: J Eukaryot Microbiol. 2011 Jul-Aug;58(4):315-8
references.pmid: 21518078
references.citation: BMC Bioinformatics. 2011 Jan 28;12:38
references.pmid: 21276213
references.citation: Am J Bot. 2004 Oct;91(10):1508-22
references.pmid: 21652306
references.citation: Environ Microbiol. 2009 Feb;11(2):512-25
references.pmid: 19196281
references.citation: Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14679-84
references.pmid: 20668244
references.citation: Microb Ecol. 2014 Jan;67(1):13-23
references.pmid: 24081282
references.citation: Protist. 2011 Nov;162(5):738-61
references.pmid: 21715228
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: Bioinformatics. 2006 Nov 1;22(21):2688-90
references.pmid: 16928733
references.citation: Environ Microbiol. 2011 Feb;13(2):340-9
references.pmid: 21281421
references.citation: Mol Ecol. 2013 Jan;22(1):87-101
references.pmid: 23163508
references.citation: PLoS One. 2013 Dec 04;8(12):e81749
references.pmid: 24324722
references.citation: ISME J. 2014 Jan;8(1):164-76
references.pmid: 23924785
references.citation: ISME J. 2012 Oct;6(10):1823-33
references.pmid: 22534609
references.citation: Environ Microbiol Rep. 2013 Apr;5(2):322-32
references.pmid: 23584973
references.citation: ISME J. 2011 Aug;5(8):1344-56
references.pmid: 21390079
references.citation: Microb Ecol. 2006 Jul;52(1):53-71
references.pmid: 16703447